{"type": "FeatureCollection", "features": [{"id": "10.5061/dryad.cz8w9gj78", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:21:13Z", "type": "Dataset", "title": "Soil microbial relative resource limitation exhibited contrasting seasonal patterns along an elevational gradient in Yulong snow mountain", "description": "unspecified", "keywords": ["2. Zero hunger", "mountain ecosystems", "13. Climate action", "microbial metabolic mechanisms", "microbial relative C limitation", "microbial relative P limitation", "C use efficiency", "FOS: Earth and related environmental sciences", "15. Life on land", "elevations"], "contacts": [{"organization": "Zhang, Dandan, Wu, Baoyun, Li, Jinsheng, Cheng, Xiaoli,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.cz8w9gj78"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.cz8w9gj78", "name": "item", "description": "10.5061/dryad.cz8w9gj78", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.cz8w9gj78"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-02-02T00:00:00Z"}}, {"id": "10.1016/j.agee.2018.05.008", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:15:26Z", "type": "Journal Article", "created": "2018-05-16", "title": "Response Of Soil Microbial Communities To Agroecological Versus Conventional Systems Of Extensive Agriculture", "description": "Abstract World population growth has led to a rise in resource demands imposed on agricultural systems, generating an increased global use of natural resources. However, agroecology proposes self-regulation in order to achieve a sustainable agricultural balance. Therefore, considering the rapid responses of microbial communities to small changes in soil use, the objective of this study was to assess the response of soil microbial communities to agroecological vs. conventional systems of extensive agriculture. Soil sampling was carried out in 2016 and 2017 with three different treatments using the sequence soybean/maize (Glycine max L./Zea mays L.) as the main crop: Agroecological (AE), conventional with cover crops (CC) and conventional without cover crops (control). Species used as cover crops were wheat (Triticum aestivum), vetch (Vicia sativa L.), oat (Avena sativa L.) and radish (Raphanus sativus L.). Agroecological treatment showed the lowest total nitrogen (0.18\u202fmg\u202fN\u202fg\u22121) and organic carbon (1.99\u202fmg\u202fC\u202fg\u22121) content of soil, and CC treatment showed the highest value of fluorescein diacetate hydrolysis, with values 63.2% and 12.1% higher than AE and the control, respectively. However, AE treatment also produced the highest F:B ratio (44.8) and the lowest metabolic quotient (1.14), which indicates an improvement in metabolic efficiency and soil quality. No significant differences were recorded in the abundance of fungal and bacterial communities between treatments. Our results suggest that agroecological management is characterised by fungal dominance in soil microbial communities and a higher microbial metabolic efficiency compared to conventional management. These results demonstrate more efficient use of carbon substrates in agroecological systems, which could counteract the negative effect of the lack of synthetic fertilisation and reduced-tillage in the long term. The findings demonstrate that sustainable agricultural tools with adequate management can be effectively used to preserve soil quality.", "keywords": ["2. Zero hunger", "SUSTAINABILITY", "AGROECOLOGY", "https://purl.org/becyt/ford/1.5", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "METABOLIC EFFICIENCY", "MICROBIAL ABUNDANCE", "04 agricultural and veterinary sciences", "15. Life on land", "https://purl.org/becyt/ford/1", "6. Clean water", "12. Responsible consumption"]}, "links": [{"href": "https://doi.org/10.1016/j.agee.2018.05.008"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agriculture%2C%20Ecosystems%20%26amp%3B%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.agee.2018.05.008", "name": "item", "description": "10.1016/j.agee.2018.05.008", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.agee.2018.05.008"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-09-01T00:00:00Z"}}, {"id": "10.1002/biot.202000165", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:14:00Z", "type": "Journal Article", "created": "2020-10-21", "title": "Engineering Native and Synthetic Pathways in Pseudomonas putida for the Production of Tailored Polyhydroxyalkanoates", "description": "Abstract

Growing environmental concern sparks renewed interest in the sustainable production of (bio)materials that can replace oil\uffe2\uff80\uff90derived goods. Polyhydroxyalkanoates (PHAs) are isotactic polymers that play a critical role in the central metabolism of producer bacteria, as they act as dynamic reservoirs of carbon and reducing equivalents. PHAs continue to attract industrial attention as a starting point toward renewable, biodegradable, biocompatible, and versatile thermoplastic and elastomeric materials. Pseudomonas species have been known for long as efficient biopolymer producers, especially for medium\uffe2\uff80\uff90chain\uffe2\uff80\uff90length PHAs. The surge of synthetic biology and metabolic engineering approaches in recent years offers the possibility of exploiting the untapped potential of Pseudomonas cell factories for the production of tailored PHAs. In this article, an overview of the metabolic and regulatory circuits that rule PHA accumulation in Pseudomonas putida is provided, and approaches leading to the biosynthesis of novel polymers (e.g., PHAs including nonbiological chemical elements in their structures) are discussed. The potential of novel PHAs to disrupt existing and future market segments is closer to realization than ever before. The review is concluded by pinpointing challenges that currently hinder the wide adoption of bio\uffe2\uff80\uff90based PHAs, and strategies toward programmable polymer biosynthesis from alternative substrates in engineered P. putida strains are proposed.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Biopolymer", "PHA", "Pseudomonas putida", "Polyhydroxyalkanoates", "Carbon", "12. Responsible consumption", "03 medical and health sciences", "/dk/atira/pure/sustainabledevelopmentgoals/affordable_and_clean_energy; name=SDG 7 - Affordable and Clean Energy", "Metabolic Engineering", "Pseudomonas", "Pathway engineering", "Metabolic engineering", "Synthetic biology"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1002/biot.202000165"}, {"href": "https://doi.org/10.1002/biot.202000165"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biotechnology%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1002/biot.202000165", "name": "item", "description": "10.1002/biot.202000165", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1002/biot.202000165"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-09T00:00:00Z"}}, {"id": "10.1007/s00253-020-10811-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:14:22Z", "type": "Journal Article", "created": "2020-08-13", "title": "Industrial biotechnology of Pseudomonas putida: advances and prospects", "description": "Abstract

Pseudomonas putidais a Gram-negative, rod-shaped bacterium that can be encountered in diverse ecological habitats. This ubiquity is traced to its remarkably versatile metabolism, adapted to withstand physicochemical stress, and the capacity to thrive in harsh environments. Owing to these characteristics, there is a growing interest in this microbe for industrial use, and the corresponding research has made rapid progress in recent years. Hereby, strong drivers are the exploitation of cheap renewable feedstocks and waste streams to produce value-added chemicals and the steady progress in genetic strain engineering and systems biology understanding of this bacterium. Here, we summarize the recent advances and prospects in genetic engineering, systems and synthetic biology, and applications ofP. putidaas a cell factory.

Key points

\uffe2\uff80\uffa2 Pseudomonas putida advances to a global industrial cell factory.

\uffe2\uff80\uffa2 Novel tools enable system-wide understanding and streamlined genomic engineering.

\uffe2\uff80\uffa2 Applications of P. putida range from bioeconomy chemicals to biosynthetic drugs.

", "keywords": ["0301 basic medicine", "ddc:500", "0303 health sciences", "Pseudomonas putida", "EDEMP cycle", "PHA", "Systems Biology", "500", "Genomics", "Mini-Review", "Bioeconomy", "Bacterial chassis", "Lignin", "03 medical and health sciences", "/dk/atira/pure/sustainabledevelopmentgoals/affordable_and_clean_energy; name=SDG 7 - Affordable and Clean Energy", "Microbial cell factory", "13. Climate action", "Biocatalysis", "Synthetic Biology", "KT2440", "Metabolic engineering", "Biotransformation", "Synthetic biology", "Biotechnology"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s00253-020-10811-9.pdf"}, {"href": "https://doi.org/10.1007/s00253-020-10811-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Microbiology%20and%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00253-020-10811-9", "name": "item", "description": "10.1007/s00253-020-10811-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00253-020-10811-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-13T00:00:00Z"}}, {"id": "10.1007/s00374-003-0612-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:14:24Z", "type": "Journal Article", "created": "2003-10-27", "title": "Effect Of Eisenia Foetida Earthworms On Mineralization Kinetics, Microbial Biomass, Enzyme Activities, Respiration And Labile C Fractions Of Three Soils Treated With A Composted Organic Residue", "description": "Open AccessPeer reviewed", "keywords": ["Microbial metabolic quotient", "2. Zero hunger", "Biomass C", "Clay soils", "C mineralization", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "Sandy soil"]}, "links": [{"href": "https://doi.org/10.1007/s00374-003-0612-7"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biology%20and%20Fertility%20of%20Soils", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00374-003-0612-7", "name": "item", "description": "10.1007/s00374-003-0612-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00374-003-0612-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2003-06-01T00:00:00Z"}}, {"id": "10.1007/s11104-022-05382-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:15:01Z", "type": "Journal Article", "created": "2022-01-11", "title": "On maintenance and metabolisms in soil microbial communities", "description": "Abstract

Biochemistry is an essential yet often undervalued aspect of soil ecology, especially in soil C cycling. We assume based on tradition, intuition or hope that the complexity of biochemistry is confined to the microscopic world, and can be ignored when dealing with whole soil systems. This opinion paper draws attention to patterns caused by basic biochemical processes that permeate the world of ecosystem processes. From these patterns, we can estimate activities of the biochemical reactions of the central C metabolic network and gain insights into the ecophysiology of microbial biosynthesis and growth and maintenance energy requirements; important components of Carbon Use Efficiency (CUE).The biochemical pathways used to metabolize glucose vary from soil to soil, with mostly glycolysis in some soils, and pentose phosphate or Entner-Doudoroff pathways in others. However, notwithstanding this metabolic diversity, glucose use efficiency is high and thus substrate use for maintenance energy and overflow respiration is low in these three soils. These results contradict current dogma based on four decades of research in soil ecology. We identify three main shortcomings in our current understanding of substrate use efficiency: 1) in numeric and conceptual models, we lack appreciation of the strategies that microbes employ to quickly reduce energy needs in response to starvation; 2) production of exudates and microbial turnover affect whole-soil CUE more than variation in maintenance energy demand; and 3) whether tracer experiments can be used to measure the long-term substrate use efficiency of soil microbial communities depends critically on the ability of non-growing cells to take up tracer substrates, how biosynthesis responds to these substrates, as well as on how cellular activities scale to the community level.To move the field of soil ecology forward, future research must consider the details of microbial ecophysiology and develop new tools that enable direct measurement of microbial functioning in intact soils. We submit that 13C metabolic flux analysis is one of those new tools.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Embden-Meyerhof-Parnass glycolysis", "Biochemical efficiency", "Maintenance", "Entner-Doudoroff pathway", "Carbon use efficiency", "Metabolic flux analysis", "15. Life on land", "Turnover", "Grassland", "03 medical and health sciences", "Marsh", "13. Climate action", "Exudation", "Forest", "Pentose phosphate pathway"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1007/s11104-022-05382-9.pdf"}, {"href": "https://doi.org/10.1007/s11104-022-05382-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20and%20Soil", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s11104-022-05382-9", "name": "item", "description": "10.1007/s11104-022-05382-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s11104-022-05382-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-11T00:00:00Z"}}, {"id": "10.1016/j.catena.2016.02.013", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:15:44Z", "type": "Journal Article", "created": "2016-02-27", "title": "Land Use Affects Soil Biochemical Properties In Mt. Kilimanjaro Region", "description": "\u00a9 2016 Elsevier B.V.Microbial parameters have been used to monitor changes in soil quality. Soils from four land use systems common in East Africa and present in the Mt. Kilimanjaro region: (1) montane forest, (2) savannah (3) maize fields and (4) Chagga homegardens were used in laboratory incubations to assess the effects of landuse changes on soil quality. Soil organic matter mineralization and the following microbial parameters: microbial biomass C, mineralization quotient, metabolic quotient and activities of four enzymes: \u03b2-glucosidase, cellobiohydrolase, phosphatase and chitinase were determined. Microbial biomass C content, \u03b2-glucosidase, cellobiohydrolase and chitinase activities were higher in natural systems compared to agricultural soils. High phosphatase activity observed in all land use types reflected strong phosphorus limitation in andic soils of the Mt. Kilimanjaro region. Chitinase activity in montane forest soils was 3 times higher than in Chagga homegardens. Mineralization quotient and cellobiohydrolase activity best exhibited the effect of land-use changes on soil quality in the Mt. Kilimanjaro region. Cellobiohydrolase activity was up to 3 times higher under natural ecosystems compared to agroecosystems. A high percentage of microbial biomass C content in total organic C and low metabolic quotient were observed in Chagga homegarden soils. Soil enzymes (especially cellobiohydrolase) best distinguished between natural and agricultural ecosystems, and are therefore useful for monitoring changes in soil quality. In conclusion, the measured microbial parameters clearly show that the microbial organisms in traditional Chagga homegardens system have high substrate use efficiency. This demonstrates that traditional agroforestry systems promotes soil fertility and are more suitable for agricultural production in the tropics compared to monocropping systems like maize plantations.", "keywords": ["Mineralization quotient", "2. Zero hunger", "Metabolic quotient", "Microbial biomass content", "13. Climate action", "Enzyme activity", "Agroforestry", "Chagga homegardens", "15. Life on land", "630"]}, "links": [{"href": "https://doi.org/10.1016/j.catena.2016.02.013"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/CATENA", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.catena.2016.02.013", "name": "item", "description": "10.1016/j.catena.2016.02.013", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.catena.2016.02.013"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-01T00:00:00Z"}}, {"id": "10.1016/j.jhazmat.2020.122027", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:16:28Z", "type": "Journal Article", "created": "2020-01-07", "title": "Bioaccumulation, physiological distribution, and biotransformation of tetrabromobisphenol A (TBBPA) in the geophagous earthworm Metaphire guillelmi \u2013 Hint for detoxification strategy", "description": "The mechanisms underlying the bioaccumulation and detoxification of tetrabromobisphenol A (TBBPA) by terrestrial invertebrates are poorly understood. We used uniformly ring-14C-labelled TBBPA to investigate the bioaccumulation kinetics, metabolites distribution, and subsequent detoxification strategy of TBBPA in the geophagous earthworm Metaphire guillelmi in soil. The modeling of bioaccumulation kinetics showed a higher biota-soil-accumulation-factor of total 14C than that of the parent compound TBBPA, indicating that most of the ingested TBBPA was transformed into metabolites or sequestered as bound residues in the earthworms. Bound-residue formation in the digestive tract may hinder the accumulation of TBBPA in other parts of the body. Nonetheless, via the circulatory system, TBBPA was transferred to other tissues, especially the clitellum region, where sensitive organs are located. In the clitellum region, TBBPA was quickly transformed to less toxic dimethyl TBBPA ether and rapidly depurated through feces. We conclude that the detoxification of TBBPA in M. guillelmi occurred via bound-residue formation in the digestive tract as well as the generation and depuration of O-methylation metabolites. Our results provided direct evidence of TBBPA detoxification in earthworms. Further researches are needed to confirm whether O-methylation coupled with depuration is a common detoxification strategy for phenolic xenobiotics in other soil organisms needs to be determined.", "keywords": ["Gastrointestinal Tract", "Kinetics", "Inactivation", " Metabolic", "Polybrominated Biphenyls", "0211 other engineering and technologies", "Animals", "Soil Pollutants", "02 engineering and technology", "Oligochaeta", "Bioaccumulation", "01 natural sciences", "Biotransformation", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.jhazmat.2020.122027"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jhazmat.2020.122027", "name": "item", "description": "10.1016/j.jhazmat.2020.122027", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jhazmat.2020.122027"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-01T00:00:00Z"}}, {"id": "10.1016/j.mec.2020.e00126", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:16:31Z", "type": "Journal Article", "created": "2020-03-19", "title": "Synthetic control of plasmid replication enables target- and self-curing of vectors and expedites genome engineering of Pseudomonas putida", "description": "Genome engineering of non-conventional microorganisms calls for the development of dedicated synthetic biology tools. Pseudomonas putida is a Gram-negative, non-pathogenic soil bacterium widely used for metabolic engineering owing to its versatile metabolism and high levels of tolerance to different types of stress. Genome editing of P. putida largely relies on homologous recombination events, assisted by helper plasmid-based expression of genes encoding DNA modifying enzymes. Plasmid curing from selected isolates is the most tedious and time-consuming step of this procedure, and implementing commonly used methods to this end in P. putida (e.g. temperature-sensitive replicons) is often impractical. To tackle this issue, we have developed a toolbox for both target- and self-curing of plasmid DNA in Pseudomonas species. Our method enables plasmid-curing in a simple cultivation step by combining in vivo digestion of vectors by the I-SceI homing nuclease with synthetic control of plasmid replication, triggered by the addition of a cheap chemical inducer (3-methylbenzoate) to the medium. The system displays an efficiency of vector curing >90% and the screening of plasmid-free clones is greatly facilitated by the use of fluorescent markers that can be selected according to the application intended. Furthermore, quick genome engineering of P. putida using self-curing plasmids is demonstrated through genome reduction of the platform strain EM42 by eliminating all genes encoding \u03b2-lactamases, the catabolic ben gene cluster, and the pyoverdine synthesis machinery. Physiological characterization of the resulting streamlined strain, P. putida SEM10, revealed advantageous features that could be exploited for metabolic engineering.", "keywords": ["Genome engineering", "0301 basic medicine", "0303 health sciences", "Pseudomonas putida", "QH301-705.5", "Plasmid curing", "3. Good health", "03 medical and health sciences", "Special issue on Non-conventional microbes edited by Ian Wheeldon and Aindrila Mukhopadhyay", "Biology (General)", "Metabolic engineering", "Synthetic biology", "TP248.13-248.65", "Biotechnology"]}, "links": [{"href": "https://doi.org/10.1016/j.mec.2020.e00126"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Metabolic%20Engineering%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.mec.2020.e00126", "name": "item", "description": "10.1016/j.mec.2020.e00126", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.mec.2020.e00126"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-06-01T00:00:00Z"}}, {"id": "10.1016/j.tim.2020.02.015", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:08Z", "type": "Journal Article", "created": "2020-03-31", "title": "Pseudomonas putida", "description": "Pseudomonas putida is a ubiquitous rhizosphere saprophytic bacterium and soil colonizer that belongs to the wide group of fluorescent Pseudomonas species. P. putida strain KT2440, the best-characterized member of the group, became a model laboratory species that attracted considerable attention as a cell host for synthetic biology and metabolic engineering due to its remarkable and versatile metabolism, which has evolved to withstand harsh environmental conditions and physicochemical stress. This species has also retained the ability to survive and thrive in natural soil environments. P. putida mt-2 and other isolates have been recognized and used as agents for bioremediation due to their ability to grow on complex substrates, including aromatic compounds (e.g., toluene and xylenes). The absence of pathogenic determinants is another key feature of strain KT2440 that facilitated its adoption for both fundamental and applied research in microbiology.", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Metabolic Engineering", "Pseudomonas putida", "Synthetic Biology"]}, "links": [{"href": "https://doi.org/10.1016/j.tim.2020.02.015"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Trends%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.tim.2020.02.015", "name": "item", "description": "10.1016/j.tim.2020.02.015", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.tim.2020.02.015"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-06-01T00:00:00Z"}}, {"id": "10.1016/j.tree.2017.12.007", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:08Z", "type": "Journal Article", "created": "2018-01-08", "title": "Energy Flux: The Link between Multitrophic Biodiversity and Ecosystem Functioning", "description": "Relating biodiversity to ecosystem functioning in natural communities has become a paramount challenge as links between trophic complexity and multiple ecosystem functions become increasingly apparent. Yet, there is still no generalised approach to address such complexity in biodiversity-ecosystem functioning (BEF) studies. Energy flux dynamics in ecological networks provide the theoretical underpinning of multitrophic BEF relationships. Accordingly, we propose the quantification of energy fluxes in food webs as a powerful, universal tool for understanding ecosystem functioning in multitrophic systems spanning different ecological scales. Although the concept of energy flux in food webs is not novel, its application to BEF research remains virtually untapped, providing a framework to foster new discoveries into the determinants of ecosystem functioning in complex systems.", "keywords": ["0106 biological sciences", "0301 basic medicine", "ecological stoichiometry", "Food Chain", "food web", "interaction network", "Biodiversity", "15. Life on land", "metabolic theory", "Models", " Biological", "01 natural sciences", "630", "004", "trophic cascade", "03 medical and health sciences", "13. Climate action", "ecosystem multifunctionality", "Ecosystem"]}, "links": [{"href": "https://doi.org/10.1016/j.tree.2017.12.007"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Trends%20in%20Ecology%20%26amp%3B%20Evolution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.tree.2017.12.007", "name": "item", "description": "10.1016/j.tree.2017.12.007", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.tree.2017.12.007"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-03-01T00:00:00Z"}}, {"id": "10.1021/acs.est.1c05289", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:14Z", "type": "Journal Article", "created": "2021-12-03", "title": "Identification of Extracellular Key Enzyme and Intracellular Metabolic Pathway in Alginate-Degrading Consortia via an Integrated Metaproteomic/Metagenomic Analysis", "description": "Uronic acid in extracellular polymeric substances is a primary but often ignored factor related to the difficult hydrolysis of waste-activated sludge (WAS), with alginate as a typical polymer. Previously, we enriched alginate-degrading consortia (ADC) in batch reactors that can enhance methane production from WAS, but the enzymes and metabolic pathway are not well documented. In this work, two chemostats in series were operated to enrich ADC, in which 10 g/L alginate was wholly consumed. Based on it, the extracellular alginate lyase (\u223c130 kD, EC 4.2.2.3) in the cultures was identified by metaproteomic analysis. This enzyme offers a high specificity to convert alginate to disaccharides over other mentioned hydrolases. Genus Bacteroides (>60%) was revealed as the key bacterium for alginate conversion. A new Entner\u2212Doudoroff pathway
of alginate via 5-dehydro-4-deoxy-D-glucuronate (DDG) and 3-deoxy-D-glycerol-2,5-hexdiulosonate (DGH) as the intermediates to 2-keto-3-deoxy-gluconate (KDG) was constructed based on the metagenomic and metaproteomic analysis. In summary, this work documented the core enzymes and metabolic pathway for alginate degradation, which provides a good paradigm when analyzing the degrading mechanism of unacquainted substrates. The outcome will further contribute to the application of Bacteroides-dominated ADC on WAS methanogenesis in the future.", "keywords": ["DDG and DGH", "alginate-degrading consortia", "Bacteria", "Sewage", "Alginates", "two chemostats in series", "0211 other engineering and technologies", "02 engineering and technology", "01 natural sciences", "6. Clean water", "Glucuronic Acid", "extracellular alginate lyase (EC 4.2.2.3)", "Bacteroides", "new Entner\u2212Doudoroff pathway", "Metabolic Networks and Pathways", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1021/acs.est.1c05289"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1021/acs.est.1c05289", "name": "item", "description": "10.1021/acs.est.1c05289", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1021/acs.est.1c05289"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-12-03T00:00:00Z"}}, {"id": "10.1038/s41467-021-25665-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:34Z", "type": "Journal Article", "created": "2021-09-06", "title": "Growth-coupled selection of synthetic modules to accelerate cell factory development.", "description": "Synthetic biology has brought about a conceptual shift in our ability to redesign microbial metabolic networks. Combining metabolic pathway-modularization with growth-coupled selection schemes is a powerful tool that enables deep rewiring of the cell factories\u2019 biochemistry for rational bioproduction.", "keywords": ["0301 basic medicine", "0303 health sciences", "Science", "Q", "Comment", "Recombinant Proteins", "Biological Factors", "03 medical and health sciences", "Metabolic Engineering", "Saccharomycetales", "Escherichia coli", "Life Science", "Humans", "Synthetic Biology", "Metabolic Networks and Pathways"]}, "links": [{"href": "https://www.nature.com/articles/s41467-021-25665-6.pdf"}, {"href": "https://doi.org/10.1038/s41467-021-25665-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41467-021-25665-6", "name": "item", "description": "10.1038/s41467-021-25665-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41467-021-25665-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-09-06T00:00:00Z"}}, {"id": "10.1079/bjn20051517", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:55Z", "type": "Journal Article", "created": "2005-11-03", "title": "Effect Of Ruminal Administration Of Escherichia Coli Wild Type Or A Genetically Modified Strain With Enhanced High Nitrite Reductase Activity On Methane Emission And Nitrate Toxicity In Nitrate-Infused Sheep", "description": "

The effects of two kinds ofEscherichia coli(E. coli) strain, wild-typeE. coliW3110 andE. colinir-Ptac, which has enhanced NO2reduction activity, on oral CH4emission and NO3toxicity in NO3-treated sheep were assessed in a respiratory hood system in a 4\uffc3\uff976 Youden square design. NO3(1\uffc2\uffb73g NaNO3/kg0\uffc2\uffb775body weight) and/orE. colistrains were delivered into the rumen through a fistula as a single dose 30min after the morning meal.Escherichia colicells were inoculated for sheep to provide an initialE. colicell density of optical density at 660nm of 2, which corresponded to 2\uffc3\uff971010cells/ml. The six treatments consisted of saline,E. coliW3110,E. colinir-Ptac, NO3, NO3plusE. coliW3110, and NO3plusE. colinir-Ptac. CH4emission from sheep was reduced by the inoculation ofE. coliW3110 orE. colinir-Ptac by 6% and 12%, respectively. NO3markedly inhibited CH4emission from sheep. Compared with sheep given NO3alone, the inoculation ofE. coliW3110 to NO3-infused sheep lessened ruminal and plasma toxic NO2accumulation and blood methaemoglobin production, while keeping ruminal methanogenesis low. Ruminal and plasma toxic NO2accumulation and blood methaemoglobin production in sheep were unaffected by the inoculation ofE. colinir-Ptac. These results suggest that ruminal methanogenesis may be reduced by the inoculation ofE. coliW3110 orE. colinir-Ptac. The inoculation ofE. coliW3110 may abate NO3toxicity when NO3is used to inhibit CH4emission from ruminants.

", "keywords": ["Male", "2. Zero hunger", "Nitrates", "Rumen", "Sheep", "Metabolic Clearance Rate", "0402 animal and dairy science", "04 agricultural and veterinary sciences", "Carbon Dioxide", "Nitrate Reductase", "3. Good health", "Oxygen Consumption", "Fermentation", "Escherichia coli", "Animals", "Infusions", " Parenteral", "Methane", "Methemoglobin", "Nitrites"], "contacts": [{"organization": "Junichi Takahashi, I. Shinzato, Y. Asakura, C. Sar, B. Pen, R. Morikawa, B. Mwenya, A. Tsujimoto, K. Kuwaki, K. Takaura, N. Isogai, Yasuhiko Toride,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1079/bjn20051517"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/British%20Journal%20of%20Nutrition", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1079/bjn20051517", "name": "item", "description": "10.1079/bjn20051517", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1079/bjn20051517"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2005-11-01T00:00:00Z"}}, {"id": "10.1099/mic.0.000931", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:18:17Z", "type": "Journal Article", "created": "2020-05-22", "title": "Microbial metabolism of isoprene: a much-neglected climate-active gas", "description": "

The climate-active gas isoprene is the major volatile produced by a variety of trees and is released into the atmosphere in enormous quantities, on a par with global emissions of methane. While isoprene production in plants and its effect on atmospheric chemistry have received considerable attention, research into the biological isoprene sink has been neglected until recently. Here, we review current knowledge on the sources and sinks of isoprene and outline its environmental effects. Focusing on degradation by microbes, many of which are able to use isoprene as the sole source of carbon and energy, we review recent studies characterizing novel isoprene degraders isolated from soils, marine sediments and in association with plants. We describe the development and use of molecular methods to identify, quantify and genetically characterize isoprene-degrading strains in environmental samples. Finally, this review identifies research imperatives for the further study of the environmental impact, ecology, regulation and biochemistry of this interesting group of microbes.

", "keywords": ["0301 basic medicine", "0303 health sciences", "550", "Bacteria", "Review", "Plants", "15. Life on land", "03 medical and health sciences", "Biodegradation", " Environmental", "Hemiterpenes", "Genes", " Bacterial", "13. Climate action", "8. Economic growth", "Butadienes", "Seawater", "Metabolic Networks and Pathways", "Soil Microbiology"]}, "links": [{"href": "https://ueaeprints.uea.ac.uk/id/eprint/75324/1/Published_Version.pdf"}, {"href": "https://repository.essex.ac.uk/29368/1/Microbial%20metabolism%20of%20isoprene%20a%20much-neglected%20climate-active%20gas.pdf"}, {"href": "https://doi.org/10.1099/mic.0.000931"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1099/mic.0.000931", "name": "item", "description": "10.1099/mic.0.000931", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1099/mic.0.000931"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-07-01T00:00:00Z"}}, {"id": "10.3389/fmicb.2022.813480", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:20:31Z", "type": "Journal Article", "created": "2022-03-01", "title": "Metatranscriptomic analyses unravel dynamic changes in the microbial and metabolic transcriptional profiles in artisanal Austrian hard-cheeses during ripening", "description": "

Vorarlberger Bergk\uffc3\uffa4se (VB) is an artisanal Austrian washed-rind hard cheese produced from alpine cows\uffe2\uff80\uff99 raw milk without the addition of ripening cultures. Ripening time is a key factor in VB, as it strongly influences the microbial communities present in the cheeses and the organoleptic properties of the product. In this study, the microbial and metabolic transcriptional profiles in VB rinds at different ripening times were investigated. VB products before (30\uffe2\uff80\uff89days of ripening) and after (90\uffe2\uff80\uff89days of ripening) selling were selected, RNA was extracted and subjected to shotgun metatranscriptomic sequencing. The analysis revealed some of the previously described abundant bacterial taxa of Brevibacterium, Corynebacterium, Halomonas, Psychrobacter, and Staphylococcus to be highly active in VB rinds. Additionally, the investigation of most important metabolic pathways in cheese ripening clearly showed differences in the gene transcription profiles and the active microbiota between the two ripening points investigated. At 30\uffe2\uff80\uff89days of ripening, metabolic events related with the degradation of residual lactose, lactate, citrate, proteolysis, and lipolysis were significantly more transcribed and mainly associated with Staphylococcus. On the other hand, genes involved in the degradation of smaller compounds derived from previous metabolism (i.e., metabolism of free amino acids and fatty acids) were significantly more expressed in VB rinds with 90 of ripening, and mainly associated with Brevibacterium and Corynebacterium. These latter metabolic activities are responsible of the generation of compounds, such as methanethiol and 2,3-butanediol, that are very important for the flavor and aroma characteristics of cheeses. This study shows the dynamic changes in the gene transcriptional profiles associated with energy substrates metabolism and the generation of organoleptic compounds during VB ripening and uncovers bacterial taxa as key drivers of the ripening process. These taxa might be the target for future studies toward an accelerated cheese ripening and the enhancement of its organoleptic properties.

", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "791", "metatranscriptomics", "organoleptic compounds", "cheese ripening", "DegreeDisciplines::Life Sciences::Animal Sciences", "microbial dynamics", "Microbiology", "QR1-502", "differential gene transcription", "03 medical and health sciences", "metabolic pathways", "Bacteria; Identification; Quality; Communities; Microflora; Alignment; Pathways; Products; Genes; Acid", "DegreeDisciplines::Life Sciences::Food Science::Food Microbiology"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2022.813480"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fmicb.2022.813480", "name": "item", "description": "10.3389/fmicb.2022.813480", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2022.813480"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-03-01T00:00:00Z"}}, {"id": "10.1093/bioinformatics/btz584", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:18:09Z", "type": "Journal Article", "created": "2019-08-19", "title": "MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network", "description": "Abstract Motivation

Analysis of differential expression of genes is often performed to understand how the metabolic activity of an organism is impacted by a perturbation. However, because the system of metabolic regulation is complex and all changes are not directly reflected in the expression levels, interpreting these data can be difficult.

Results

In this work, we present a new algorithm and computational tool that uses a genome-scale metabolic reconstruction to infer metabolic changes from differential expression data. Using the framework of constraint-based analysis, our method produces a qualitative hypothesis of a change in metabolic activity. In other words, each reaction of the network is inferred to have increased, decreased, or remained unchanged in flux. In contrast to similar previous approaches, our method does not require a biological objective function and does not assign on/off activity states to genes. An implementation is provided and it is available online. We apply the method to three published datasets to show that it successfully accomplishes its two main goals: confirming or rejecting metabolic changes suggested by differentially expressed genes based on how well they fit in as parts of a coordinated metabolic change, as well as inferring changes in reactions whose genes did not undergo differential expression.

Availability and implementation

github.com/htpusa/moomin.

Supplementary information

Supplementary data are available at Bioinformatics online.

", "keywords": ["0301 basic medicine", "570", "[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]", "Metabolic networks; omics data", "Genome", "[INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS]", "0206 medical engineering", "610", "Computational Biology", "[INFO.INFO-DS] Computer Science [cs]/Data Structures and Algorithms [cs.DS]", "02 engineering and technology", "[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]", "Original Papers", "Models", " Biological", "03 medical and health sciences", "[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]", "Algorithms", "Metabolic Networks and Pathways", "[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]"]}, "links": [{"href": "https://iris.uniroma1.it/bitstream/11573/1321358/5/Pusa_MOOMIN_2020.pdf"}, {"href": "https://academic.oup.com/bioinformatics/article-pdf/36/2/514/48991611/btz584.pdf"}, {"href": "https://doi.org/10.1093/bioinformatics/btz584"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioinformatics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1093/bioinformatics/btz584", "name": "item", "description": "10.1093/bioinformatics/btz584", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1093/bioinformatics/btz584"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-22T00:00:00Z"}}, {"id": "10.1111/1751-7915.13372", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:18:24Z", "type": "Journal Article", "created": "2019-02-01", "title": "Breaking the state-of-the-art in the chemical industry with new-to-Nature products via synthetic microbiology", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Editorial: Synthetic Microbiology as a Source of New Enterprises and Job Creation", "Metabolic Engineering", "Synthetic Biology", "Organic Chemicals", "Biotechnology"]}, "links": [{"href": "http://onlinelibrary.wiley.com/wol1/doi/10.1111/1751-7915.13372/fullpdf"}, {"href": "https://doi.org/10.1111/1751-7915.13372"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Biotechnology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1751-7915.13372", "name": "item", "description": "10.1111/1751-7915.13372", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1751-7915.13372"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-01-31T00:00:00Z"}}, {"id": "10.1111/gcb.16982", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:18:32Z", "type": "Journal Article", "created": "2023-10-30", "title": "New ways for (in)validating the forest carbon neutrality hypothesis", "description": "Abstract

Over 50\uffe2\uff80\uff89years ago, Eugene Odum postulated that mature or climax forests reside in carbon neutrality. As climate change rose to prominence in the international environmental agenda, the neutrality hypothesis transformed from an ecological principle to a justification for using forest management in combating climate change. Despite persistent efforts, Odum's neutrality hypothesis has resisted both confirmation and refutation. In this opinion we show the limitations of past efforts to (in)validate Odum's neutrality hypothesis and propose new research directions for the community to permit a more general confirmation or refutation with current and near\uffe2\uff80\uff90future observations. We then demonstrate such an approach by using metabolic theory to formulate testable predictions for the total sink strength considering soil, litter, and biomass of mature or climax forests based on observations of tree biomass and individual density. In doing so, we show that ecological theory can create additional relevant, testable hypotheses to provide timely support to decision\uffe2\uff80\uff90makers seeking to address one of the world's most pressing environmental challenges.

A large fraction of plant litter comprises recalcitrant aromatic compounds (lignin and other phenolics). Quantifying the fate of aromatic compounds is difficult, because oxidative degradation of aromatic carbon (C) is a costly but necessary endeavor for microorganisms, and we do not know when gains from the decomposition of aromatic C outweigh energetic costs.

To evaluate these tradeoffs, we developed a litter decomposition model in which the aromatic C decomposition rate is optimized dynamically to maximize microbial growth for the given costs of maintaining ligninolytic activity. We tested model performance against >\uffe2\uff80\uff89200 litter decomposition datasets collected from published literature and assessed the effects of climate and litter chemistry on litter decomposition.

The model predicted a time\uffe2\uff80\uff90varying ligninolytic oxidation rate, which was used to calculate the lag time before the decomposition of aromatic C is initiated. Warmer conditions increased decomposition rates, shortened the lag time of aromatic C oxidation, and improved microbial C\uffe2\uff80\uff90use efficiency by decreasing the costs of oxidation. Moreover, a higher initial content of aromatic C promoted an earlier start of aromatic C decomposition under any climate.

With this contribution, we highlight the application of eco\uffe2\uff80\uff90evolutionary approaches based on optimized microbial life strategies as an alternative parametrization scheme for litter decomposition models.

The main change in soil use in Amazonia is, after slash and burn deforestation followed by annual crops, the establishment of pastures. This conversion of forest to pasture induces changes in the carbon cycle, modifies soil organic matter content and quality and affects biological activity responsible for numerous biochemical and biological processes essential to ecosystem functioning. The aim of this study was to assess changes in microbial biomass and activity in fallow and pasture soils after forest clearing. The study was performed in smallholder settlements of eastern Brazilian Amazonia. Soil samples from depths of 0\uffe2\uff80\uff932, 2\uffe2\uff80\uff935 and 5\uffe2\uff80\uff9310\uffc2\uffa0cm were gathered in native forest, fallow land 8\uffe2\uff80\uff9310\uffc2\uffa0yr old and pastures with ages of 1\uffe2\uff80\uff932, 5\uffe2\uff80\uff937 and 10\uffe2\uff80\uff9312\uffc2\uffa0yr. Once fallow began, soil microbial biomass and its activity showed little change. In contrast, conversion to pasture modified soil microbial functioning significantly. Microbial biomass and its basal respiration decreased markedly after pasture establishment and continued to decrease with pasture age. The increase in metabolic quotient in the first years of pasture indicated a disturbance in soil functioning. Our study confirms that microbial biomass is a sensitive indicator of soil disturbance caused by land\uffe2\uff80\uff90use change.

", "keywords": ["2. Zero hunger", "570", "Soil microbial carbon", "land use", "04 agricultural and veterinary sciences", "15. Life on land", "630", "13. Climate action", "microbial basal respiration", "tropical soil", "deforestation", "0401 agriculture", " forestry", " and fisheries", "metabolic quotient"], "contacts": [{"organization": "Melo, V. S., /Desjardins, Thierry, Silva, M. L., Santos, E. R., /Sarrazin, Max, Santos, M. M. L. S.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1111/sum.12003"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Use%20and%20Management", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/sum.12003", "name": "item", "description": "10.1111/sum.12003", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/sum.12003"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-11-01T00:00:00Z"}}, {"id": "10.1128/aem.03393-12", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:00Z", "type": "Journal Article", "created": "2012-12-16", "title": "Functional Gene Differences In Soil Microbial Communities From Conventional, Low-Input, And Organic Farmlands", "description": "ABSTRACT

Various agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO 3 \uffe2\uff88\uff92 , NH 4 + , available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO 3 \uffe2\uff88\uff92 concentration and denitrification genes, NH 4 + concentration and ammonification genes, and N 2 O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes.

", "keywords": ["2. Zero hunger", "Michigan", "Nitrogen", "Agriculture", "Phosphorus", "04 agricultural and veterinary sciences", "15. Life on land", "Microarray Analysis", "Biota", "Carbon", "Soil", "Genes", " Bacterial", "Metagenome", "0401 agriculture", " forestry", " and fisheries", "Metabolic Networks and Pathways", "Soil Microbiology", "Sulfur"]}, "links": [{"href": "https://doi.org/10.1128/aem.03393-12"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.03393-12", "name": "item", "description": "10.1128/aem.03393-12", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.03393-12"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-02-15T00:00:00Z"}}, {"id": "10.1186/s40793-020-00354-x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:11Z", "type": "Journal Article", "created": "2020-03-02", "title": "Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics", "description": "Abstract Background

Anaerobic digestion (AD) of protein-rich grass silage was performed in experimental two-stage two-phase biogas reactor systems at low vs. increased organic loading rates (OLRs) under mesophilic (37\uffe2\uff80\uff89\uffc2\uffb0C) and thermophilic (55\uffe2\uff80\uff89\uffc2\uffb0C) temperatures. To follow the adaptive response of the biomass-attached cellulolytic/hydrolytic biofilms at increasing ammonium/ammonia contents, genome-centered metagenomics and transcriptional profiling based on metagenome assembled genomes (MAGs) were conducted.

Results

In total, 78 bacterial and archaeal MAGs representing the most abundant members of the communities, and featuring defined quality criteria were selected and characterized in detail. Determination of MAG abundances under the tested conditions by mapping of the obtained metagenome sequence reads to the MAGs revealed that MAG abundance profiles were mainly shaped by the temperature but also by the OLR. However, the OLR effect was more pronounced for the mesophilic systems as compared to the thermophilic ones. In contrast, metatranscriptome mapping to MAGs subsequently normalized to MAG abundances showed that under thermophilic conditions, MAGs respond to increased OLRs by shifting their transcriptional activities mainly without adjusting their proliferation rates. This is a clear difference compared to the behavior of the microbiome under mesophilic conditions. Here, the response to increased OLRs involved adjusting of proliferation rates and corresponding transcriptional activities. The analysis led to the identification of MAGs positively responding to increased OLRs. The most outstanding MAGs in this regard, obviously well adapted to higher OLRs and/or associated conditions, were assigned to the order Clostridiales (Acetivibrio sp.) for the mesophilic biofilm and the orders Bacteroidales (Prevotella sp. and an unknown species), Lachnospirales (Herbinix sp. and Kineothrix sp.) and Clostridiales (Clostridium sp.) for the thermophilic biofilm. Genome-based metabolic reconstruction and transcriptional profiling revealed that positively responding MAGs mainly are involved in hydrolysis of grass silage, acidogenesis and / or\uffc2\uffa0acetogenesis.

Conclusions

An integrated -omics approach enabled the identification of new AD biofilm keystone species featuring outstanding performance under stress conditions such as increased OLRs. Genome-based knowledge on the metabolic potential and transcriptional activity of responsive microbiome members will contribute to the development of improved microbiological AD management strategies for biomethanation of renewable biomass.

", "keywords": ["Integrated -omics", "Bioconversion", "0301 basic medicine", "570", "Polyomics", "Integrated-omics", "Biogas", "Microbiology", "7. Clean energy", "03 medical and health sciences", "Anaerobic digestion", "GE1-350", "2. Zero hunger", "0303 health sciences", "Metagenome assembled genomes", "Microbial community structure", "15. Life on land", "QR1-502", "6. Clean water", "3. Good health", "Environmental sciences", "Metagenome assembled genomes", " Integrated -omics", " Polyomics", " Anaerobic digestion", " Biogas", " Bioconversion", " Microbial community structure", " Methane", " Metabolic activity", "13. Climate action", "Metabolic activity", "Methane", "Research Article"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s40793-020-00354-x.pdf"}, {"href": "https://doi.org/10.1186/s40793-020-00354-x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40793-020-00354-x", "name": "item", "description": "10.1186/s40793-020-00354-x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40793-020-00354-x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-02T00:00:00Z"}}, {"id": "10.3390/microorganisms8122024", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:20:45Z", "type": "Journal Article", "created": "2020-12-17", "title": "The Role of Petrimonas mucosa ING2-E5AT in Mesophilic Biogas Reactor Systems as Deduced from Multiomics Analyses", "description": "

Members of the genera Proteiniphilum and Petrimonas were speculated to represent indicators reflecting process instability within anaerobic digestion (AD) microbiomes. Therefore, Petrimonas mucosa ING2-E5AT was isolated from a biogas reactor sample and sequenced on the PacBio RSII and Illumina MiSeq sequencers. Phylogenetic classification positioned the strain ING2-E5AT in close proximity to Fermentimonas and Proteiniphilum species (family Dysgonomonadaceae). ING2-E5AT encodes a number of genes for glycosyl-hydrolyses (GH) which are organized in Polysaccharide Utilization Loci (PUL) comprising tandem susCD-like genes for a TonB-dependent outer-membrane transporter and a cell surface glycan-binding protein. Different GHs encoded in PUL are involved in pectin degradation, reflecting a pronounced specialization of the ING2-E5AT PUL systems regarding the decomposition of this polysaccharide. Genes encoding enzymes participating in amino acids fermentation were also identified. Fragment recruitments with the ING2-E5AT genome as a template and publicly available metagenomes of AD microbiomes revealed that Petrimonas species are present in 146 out of 257 datasets supporting their importance in AD microbiomes. Metatranscriptome analyses of AD microbiomes uncovered active sugar and amino acid fermentation pathways for Petrimonas species. Likewise, screening of metaproteome datasets demonstrated expression of the Petrimonas PUL-specific component SusC providing further evidence that PUL play a central role for the lifestyle of Petrimonas species.

", "keywords": ["Bioconversion", "anaerobic digestion", "0301 basic medicine", "2. Zero hunger", "bioconversion", "Biomethanation", "QH301-705.5", "570 Biologie", "polysaccharide utilization loci", "metabolic pathway reconstruction", "16. Peace & justice", "7. Clean energy", "Article", "660.6", "biomethanation", "03 medical and health sciences", "Metabolic pathway reconstruction", "Polysaccharide utilization loci", "carbohydrate-active enzymes; polysaccharide utilization loci; anaerobic digestion; biomethanation; metabolic pathway reconstruction; bioconversion", "Anaerobic digestion", "carbohydrate-active enzymes", "Carbohydrate-active enzymes", "ddc:570", "Biology (General)"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/8/12/2024/pdf"}, {"href": "https://www.mdpi.com/2076-2607/8/12/2024/pdf"}, {"href": "https://doi.org/10.3390/microorganisms8122024"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/microorganisms8122024", "name": "item", "description": "10.3390/microorganisms8122024", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms8122024"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-12-17T00:00:00Z"}}, {"id": "10.1590/s0044-59672010000100003", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:32Z", "type": "Journal Article", "created": "2010-05-05", "title": "Carbono Org\u00e2nico E Biomassa Microbiana Do Solo Em Plantios De Acacia Mangium No Cerrado De Roraima", "description": "

O objetivo do estudo foi avaliar os efeitos de plantios de Acacia mangium, localizados no cerrado em Roraima, sobre o carbono org\uffc3\uffa2nico e biomassa microbiana do solo. Foram realizadas amostragens de solo nas profundidades de 0-20 cm e 20-40 cm em dois plantios de A. mangium com cerca de cinco anos de idade, e em duas \uffc3\uffa1reas de Cerrado nativo consideradas refer\uffc3\uffaancia. Um dos plantios de A. mangium (localizado na Fazenda Cigolina) correspondeu a um plantio homog\uffc3\uffaaneo (espa\uffc3\uffa7amento de 3,6 m entre linhas e 2,0 m entre plantas) enquanto que o outro (localizado no Campo Experimental \uffc3\uff81gua Boa - CEAB) correspondeu a um plantio em faixas com duas linhas de plantio (espa\uffc3\uffa7amento de 6 m entre linhas, 2,5 m entre plantas e cerca de 30 m entre faixas). As amostras de solo foram analisadas quanto ao carbono org\uffc3\uffa2nico, carbono da biomassa microbiana, respira\uffc3\uffa7\uffc3\uffa3o basal do solo e quociente metab\uffc3\uffb3lico, al\uffc3\uffa9m de atributos qu\uffc3\uffadmicos de fertilidade. Foi verificado que os plantios de A. mangium n\uffc3\uffa3o proporcionaram aumentos significativos do carbono org\uffc3\uffa2nico do solo em compara\uffc3\uffa7\uffc3\uffa3o \uffc3\uffa0s \uffc3\uffa1reas de refer\uffc3\uffaancia. Entretanto, na m\uffc3\uffa9dia geral, esses plantios proporcionaram aumento do carbono da biomassa microbiana do solo e redu\uffc3\uffa7\uffc3\uffa3o do quociente metab\uffc3\uffb3lico, indicando a possibilidade de ac\uffc3\uffbamulo de carbono org\uffc3\uffa2nico no solo em longo prazo. Tamb\uffc3\uffa9m foi observado que, em compara\uffc3\uffa7\uffc3\uffa3o ao plantio da fazenda Cigolina e \uffc3\uffa0s \uffc3\uffa1reas de refer\uffc3\uffaancia, o carbono microbiano do solo foi maior e acompanhado de menor quociente metab\uffc3\uffb3lico no plantio de A. mangium no CEAB, mostrando que a estrutura de plantio exerceu influ\uffc3\uffaancia sobre a biomassa microbiana do solo.

", "keywords": ["0106 biological sciences", "plantios florestais", "Amazonian", "forest plantation", "04 agricultural and veterinary sciences", "quociente metab\u00f3lico", "01 natural sciences", "Amaz\u00f4nia", "Respira\u00e7\u00e3o basal do solo", "0401 agriculture", " forestry", " and fisheries", "Soil basal respiration", "qualidade do solo", "soil quality", "metabolic quotient"]}, "links": [{"href": "https://doi.org/10.1590/s0044-59672010000100003"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Acta%20Amazonica", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1590/s0044-59672010000100003", "name": "item", "description": "10.1590/s0044-59672010000100003", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1590/s0044-59672010000100003"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-03-01T00:00:00Z"}}, {"id": "10.1590/s0100-06832005000500007", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:32Z", "type": "Journal Article", "created": "2006-04-19", "title": "Efeito Do Monocultivo De Pinus E Da Queima Do Campo Nativo Em Atributos Biol\u00f3gicos Do Solo No Planalto Sul Catarinense", "description": "

O presente estudo objetivou avaliar o impacto da queima tradicional de campo nativo e do monocultivo de Pinus sp. em Lages (SC), no CO total do solo (COT), carbono da biomassa microbiana (CBM), respira\uffc3\uffa7\uffc3\uffa3o basal (C-CO2), quociente metab\uffc3\uffb3lico microbiano (qCO2) e rela\uffc3\uffa7\uffc3\uffa3o CBM:COT. Foram selecionadas quatro \uffc3\uffa1reas representativas da regi\uffc3\uffa3o, de 0,5 ha cada, sendo: (a) Campo nativo, sem queima nos \uffc3\uffbaltimos 50 anos (CN); (b) Campo nativo submetido \uffc3\uffa0 queima tradicional (CNQ), ambas, pastagens naturais; (c) Mata natural com predomin\uffc3\uffa2ncia de Araucaria angustifolia (MATA); e (d) Reflorestamento de Pinus taeda com oito anos (PINUS). Para tanto, coletaram-se seis amostras, compostas de nove subamostras de solo em cada \uffc3\uffa1rea, na profundidade de 0-5 cm, em dezembro de 2002. Para avaliar o CBM, foi utilizado o m\uffc3\uffa9todo da fumiga\uffc3\uffa7\uffc3\uffa3o-extra\uffc3\uffa7\uffc3\uffa3o. O C-CO2 foi determinado em laborat\uffc3\uffb3rio. Os maiores valores de libera\uffc3\uffa7\uffc3\uffa3o de C-CO2 foram encontrados na MATA e no PINUS, seguidos de CNQ e CN, respectivamente. Os maiores valores de CBM, COT e rela\uffc3\uffa7\uffc3\uffa3o CBM:COT foram encontrados na MATA, n\uffc3\uffa3o tendo as demais \uffc3\uffa1reas estudadas apresentado diferen\uffc3\uffa7as entre si. O qCO2 foi maior no PINUS, seguido de CNQ, em compara\uffc3\uffa7\uffc3\uffa3o com MATA e CN. A an\uffc3\uffa1lise multivariada mostrou ser uma ferramenta auxiliar importante ao discriminar o CBM como sendo o atributo que mais contribuiu na separa\uffc3\uffa7\uffc3\uffa3o entre as \uffc3\uffa1reas estudadas.

", "keywords": ["CO total", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "total organic carbon", "soil microbial biomass carbon", "bioindicador de qualidade", "C-biomassa", "quociente metab\u00f3lico", "soil quality bioindicator", "metabolic quotient"], "contacts": [{"organization": "Baretta, Dilmar, Santos, Julio Cesar Pires, Figueiredo, Samuel Ribeiro, Klauberg-Filho, Osmar,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1590/s0100-06832005000500007"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Revista%20Brasileira%20de%20Ci%C3%AAncia%20do%20Solo", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1590/s0100-06832005000500007", "name": "item", "description": "10.1590/s0100-06832005000500007", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1590/s0100-06832005000500007"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2005-10-01T00:00:00Z"}}, {"id": "10.1590/s0100-06832011000200028", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:33Z", "type": "Journal Article", "created": "2011-06-21", "title": "Sistemas De Preparo Do Solo E Culturas De Cobertura Na Produ\u00e7\u00e3o Org\u00e2nica De Feij\u00e3o E Milho: I - Atributos F\u00edsicos Do Solo", "description": "

H\uffc3\uffa1 necessidade de se avaliar a contribui\uffc3\uffa7\uffc3\uffa3o de culturas de cobertura e do seu manejo na manuten\uffc3\uffa7\uffc3\uffa3o da qualidade biol\uffc3\uffb3gica do solo em \uffc3\uffa1reas sob produ\uffc3\uffa7\uffc3\uffa3o org\uffc3\uffa2nica. Este trabalho objetivou determinar a influ\uffc3\uffaancia das plantas de cobertura crotal\uffc3\uffa1ria (Crotalaria juncea), guandu (Cajanus cajan (L.) Millsp), mucuna-preta (Mucuna aterrima), sorgo-vassoura (Sorghum technicum) e pousio nos atributos biol\uffc3\uffb3gicos de solo cultivado com feij\uffc3\uffa3o e milho org\uffc3\uffa2nicos, sob semeadura direta (SD) e preparo convencional (PC). O trabalho foi conduzido em Santo Ant\uffc3\uffb4nio de Goi\uffc3\uffa1s-GO, em Latossolo Vermelho distr\uffc3\uffb3fico, no delineamento de blocos ao acaso, com quatro repeti\uffc3\uffa7\uffc3\uffb5es. Em novembro de 2003 foram instalados quatro experimentos, dois em SD e dois em PC, sendo um com feij\uffc3\uffa3o e outro com milho em cada sistema. Amostragens de solo das parcelas e de uma mata pr\uffc3\uffb3xima aos experimentos foram realizadas em novembro de 2007, nas camadas de 0,00-0,10 e 0,10-0,20 m, para determina\uffc3\uffa7\uffc3\uffa3o do teor de C org\uffc3\uffa2nico total (COT), carbono da biomassa microbiana (CBM), respira\uffc3\uffa7\uffc3\uffa3o basal do solo (RBS), quociente metab\uffc3\uffb3lico (qCO2) e quociente microbiano (qMIC). As principais altera\uffc3\uffa7\uffc3\uffb5es nos atributos biol\uffc3\uffb3gicos com o uso agr\uffc3\uffadcola ocorreram na camada superficial, onde, de maneira geral, os valores de CBM foram menores que no solo sob mata, sendo esse fato mais pronunciado nas \uffc3\uffa1reas sob PC. O qCO2 mostrou-se sens\uffc3\uffadvel \uffc3\uffa0s altera\uffc3\uffa7\uffc3\uffb5es decorrentes do preparo do solo, apresentando valores mais favor\uffc3\uffa1veis na camada superficial do solo sob SD.

", "keywords": ["microbial quotient", "respira\u00e7\u00e3o basal do solo", "bulk density", "Agriculture (General)", "soil porosity", "quociente metab\u00f3lico", "Zea mays", "S1-972", "S index", "soil basal respiration", "Phaseolus vulgaris L", "densidade do solo", "2. Zero hunger", "04 agricultural and veterinary sciences", "\u00edndice S", "15. Life on land", "porosidade do solo", "6. Clean water", "soil organic carbon", "C org\u00e2nico do solo", "microbial biomass carbon", "carbono da biomassa microbiana", "0401 agriculture", " forestry", " and fisheries", "metabolic quotient", "quociente microbiano"]}, "links": [{"href": "https://doi.org/10.1590/s0100-06832011000200028"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Revista%20Brasileira%20de%20Ci%C3%AAncia%20do%20Solo", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1590/s0100-06832011000200028", "name": "item", "description": "10.1590/s0100-06832011000200028", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1590/s0100-06832011000200028"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-04-01T00:00:00Z"}}, {"id": "10.1590/s0100-06832012000400013", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:33Z", "type": "Journal Article", "created": "2012-10-24", "title": "Chemical And Biochemical Properties Of Araucaria Angustifolia (Bert.) Ktze. Forest Soils In The State Of S\u00e3o Paulo", "description": "

Araucaria angustifolia, commonly named Araucaria, is a Brazilian native species that is intensively exploited due to its timber quality. Therefore, Araucaria is on the list of species threatened by extinction. Despite the importance of soil for forest production, little is known about the soil properties of the highly fragmented Araucaria forests. This study was designed to investigate the use of chemical and biological properties as indicators of conservation and anthropogenic disturbance of Araucaria forests in different sampling periods. The research was carried out in two State parks of S\uffc3\uffa3o Paulo: Parque Estadual Tur\uffc3\uffadstico do Alto do Ribeira and Parque Estadual de Campos de Jord\uffc3\uffa3o. The biochemical properties carbon and nitrogen in microbial biomass (MB-C and MB-N), basal respiration (BR), the metabolic quotient (qCO2) and the following enzyme activities: \uffce\uffb2-glucosidase, urease, and fluorescein diacetate hydrolysis (FDA) were evaluated. The sampling period (dry or rainy season) influenced the results of mainly MB-C, MB-N, BR, and qCO2. The chemical and biochemical properties, except K content, were sensitive indicators of differences in the conservation and anthropogenic disturbance stages of Araucaria forests. Although these forests differ in biochemical and chemical properties, they are efficient in energy use and conservation, which is shown by their low qCO2, suggesting an advanced stage of succession.

", "keywords": ["microbial metabolic quotient", "microbial biomass", "(qCO2)", "Agriculture (General)", "04 agricultural and veterinary sciences", "quociente metab\u00f3lico", "soil respiration", "S1-972", "biomassa microbiana", "respira\u00e7\u00e3o do solo", "enzimas do solo", "qCO2", "0401 agriculture", " forestry", " and fisheries", "qualidade do solo", "soil quality", "soil enzymes"]}, "links": [{"href": "https://doi.org/10.1590/s0100-06832012000400013"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Revista%20Brasileira%20de%20Ci%C3%AAncia%20do%20Solo", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1590/s0100-06832012000400013", "name": "item", "description": "10.1590/s0100-06832012000400013", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1590/s0100-06832012000400013"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-08-01T00:00:00Z"}}, {"id": "10.1590/s0100-204x2004001100008", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:34Z", "type": "Journal Article", "created": "2005-04-26", "title": "Din\u00e2mica Da Mat\u00e9ria Org\u00e2nica E Da Biomassa Microbiana Em Solo Submetido A Diferentes Sistemas De Manejo Na Amaz\u00f4nia Ocidental", "description": "

O objetivo deste trabalho foi avaliar as altera\uffc3\uffa7\uffc3\uffb5es na atividade da biomassa microbiana como um indicador da din\uffc3\uffa2mica de C e N em solo submetido \uffc3\uffa0 sucess\uffc3\uffa3o de cobertura vegetal e de manejo na Amaz\uffc3\uffb4nia Ocidental. Os trabalhos foram realizados em duas cronosseq\uffc3\uffbc\uffc3\uffaancias: CA - sucess\uffc3\uffa3o floresta prim\uffc3\uffa1ria e cupua\uffc3\uffa7uzal (Theobroma grandiflorum) de tr\uffc3\uffaas anos - e CB - sucess\uffc3\uffa3o floresta prim\uffc3\uffa1ria, pastagem de Brachiaria humidicola de oito anos e cupua\uffc3\uffa7uzal de tr\uffc3\uffaas anos. A sucess\uffc3\uffa3o floresta prim\uffc3\uffa1ria-pastagem-cupua\uffc3\uffa7uzal afeta negativamente o estoque de C do solo, com diminui\uffc3\uffa7\uffc3\uffa3o significativa da mat\uffc3\uffa9ria org\uffc3\uffa2nica e do C da biomassa microbiana do solo, ao passo que na sucess\uffc3\uffa3o floresta prim\uffc3\uffa1ria-cupua\uffc3\uffa7uzal ocorre diminui\uffc3\uffa7\uffc3\uffa3o apenas do C da biomassa microbiana. A floresta prim\uffc3\uffa1ria apresenta menor quociente metab\uffc3\uffb3lico e maior rela\uffc3\uffa7\uffc3\uffa3o C/N da biomassa, o que resulta em menor perda de carbono. O N da biomassa microbiana na camada de 0-10 cm, independentemente do manejo adotado, aumenta significativamente na \uffc3\uffa1rea de cupua\uffc3\uffa7uzal, ao passo que o N total diminui. A concentra\uffc3\uffa7\uffc3\uffa3o de am\uffc3\uffb4nio no solo diminui com a profundidade, de modo oposto ao verificado com o nitrato.

", "keywords": ["carbon", "04 agricultural and veterinary sciences", "15. Life on land", "floresta prim\u00e1ria", "carbono", "quociente metab\u00f3lico", "01 natural sciences", "nitrogen", "nitrog\u00eanio", "forest", "13. Climate action", "basal respiration", "respira\u00e7\u00e3o basal", "0401 agriculture", " forestry", " and fisheries", "metabolic quotient", "Theobroma grandiflorum", "0105 earth and related environmental sciences"], "contacts": [{"organization": "Moreira, Ad\u00f4nis, Malavolta, Eur\u00edpedes,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1590/s0100-204x2004001100008"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Pesquisa%20Agropecu%C3%A1ria%20Brasileira", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1590/s0100-204x2004001100008", "name": "item", "description": "10.1590/s0100-204x2004001100008", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1590/s0100-204x2004001100008"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2004-11-01T00:00:00Z"}}, {"id": "10.1590/s0100-204x2007001200013", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:34Z", "type": "Journal Article", "created": "2008-02-28", "title": "Atributos Biol\u00f3gicos Do Solo Sob Influ\u00eancia Da Cobertura Vegetal E Do Sistema De Manejo", "description": "

O objetivo deste trabalho foi avaliar os efeitos de culturas de cobertura e dos sistemas plantio direto (PD) e convencional (PC) sobre indicadores biol\uffc3\uffb3gicos do solo, cultivado com feijoeiro-comum, no inverno, sob irriga\uffc3\uffa7\uffc3\uffa3o. O experimento foi conduzido em Santo Ant\uffc3\uffb4nio de Goi\uffc3\uffa1s, GO, em Latossolo Vermelho distr\uffc3\uffb3fico textura argilosa. Culturas de cobertura foram implantadas anualmente no ver\uffc3\uffa3o, desde 2001, sendo utilizadas a braqui\uffc3\uffa1ria, guandu, milheto, capim-momba\uffc3\uffa7a, sorgo, estilosantes, braqui\uffc3\uffa1ria consorciada com milho, e mata nativa, como tratamento refer\uffc3\uffaancia. Em 2005, 60 dias ap\uffc3\uffb3s o corte das culturas de cobertura foi implantada a cultura do feijoeiro, cultivar BRS Valente, sob irriga\uffc3\uffa7\uffc3\uffa3o, com semeadura realizada em 16/6/2005 e colheita efetuada em 19/9/2005. Coletaram-se amostras de solo, na profundidade de 0-10 cm, em tr\uffc3\uffaas \uffc3\uffa9pocas: novembro de 2004 (pr\uffc3\uffa9-plantio das culturas de coberturas), junho (pr\uffc3\uffa9-plantio do feijoeiro) e julho (florescimento do feijoeiro) de 2005. Avaliaram-se a respira\uffc3\uffa7\uffc3\uffa3o basal, o carbono e o nitrog\uffc3\uffaanio da biomassa microbiana, a raz\uffc3\uffa3o carbono da biomassa microbiana/carbono org\uffc3\uffa2nico, a raz\uffc3\uffa3o nitrog\uffc3\uffaanio da biomassa microbiana/nitrog\uffc3\uffaanio total e o quociente metab\uffc3\uffb3lico do solo. Esses atributos biol\uffc3\uffb3gicos do solo s\uffc3\uffa3o influenciados pelas culturas de cobertura, manejo do solo e \uffc3\uffa9pocas de amostragem.

", "keywords": ["microbial quotient", "04 agricultural and veterinary sciences", "quociente metab\u00f3lico", "plantas de cobertura", "microbial biomass carbon", "basal respiration", "respira\u00e7\u00e3o basal", "carbono da biomassa microbiana", "0401 agriculture", " forestry", " and fisheries", "cover crops", "nitrog\u00eanio da biomassa microbiana", "microbial biomass nitrogen", "metabolic quotient", "quociente microbiano"], "contacts": [{"organization": "Silva, Mozaniel Batista da, Kliemann, Huberto Jos\u00e9, Silveira, Pedro Marques da, Lanna, Anna Cristina,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1590/s0100-204x2007001200013"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Pesquisa%20Agropecu%C3%A1ria%20Brasileira", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1590/s0100-204x2007001200013", "name": "item", "description": "10.1590/s0100-204x2007001200013", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1590/s0100-204x2007001200013"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-12-01T00:00:00Z"}}, {"id": "10.1590/s0100-204x2009000600012", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:34Z", "type": "Journal Article", "created": "2009-08-13", "title": "Biological Indicator Attributes Of Soil Quality Under Cultivated And Natural Pasture In The Pantanal Wetlands", "description": "

O objetivo deste trabalho foi avaliar as altera\uffc3\uffa7\uffc3\uffb5es nos atributos biol\uffc3\uffb3gicos do solo, em raz\uffc3\uffa3o da convers\uffc3\uffa3o floresta nativa pastagem cultivada e submiss\uffc3\uffa3o de pastagens nativas a sistema pastejo cont\uffc3\uffadnuo, um Neossolo Quartzar\uffc3\uffaanico, no Pantanal sul-mato-grossense. O trabalho consistiu avalia\uffc3\uffa7\uffc3\uffa3o tr\uffc3\uffaas florestas nativas; Brachiaria decumbens com diferentes idades de forma\uffc3\uffa7\uffc3\uffa3o, implantadas em substitui\uffc3\uffa7\uffc3\uffa3o \uffc3\uffa0s florestas nativas; e tr\uffc3\uffaas pastagens nativas (uma sob sistema de pastejo cont\uffc3\uffadnuo e duas sem pastejo por 3 e 19 anos). Foram coletadas amostras de solo nas profundidades 0-10 e 10-20 cm, em tr\uffc3\uffaas transectos de 100 m estabelecidos em cada ambiente de estudo, cada um dos quais constituiu uma repeti\uffc3\uffa7\uffc3\uffa3o. Os atributos avaliados foram: carbono org\uffc3\uffa2nico total (COT), carbono microbiano (Cmic), quociente microbiano (qMIC), respira\uffc3\uffa7\uffc3\uffa3o basal (RB) e quociente metab\uffc3\uffb3lico (qCO2). A substitui\uffc3\uffa7\uffc3\uffa3o da floresta nativa por pastagem cultivada promoveu redu\uffc3\uffa7\uffc3\uffa3o nos teores de COT, Cmic e qMIC e eleva\uffc3\uffa7\uffc3\uffa3o da RB; o sistema de pastejo cont\uffc3\uffadnuo em pastagem nativa promoveu redu\uffc3\uffa7\uffc3\uffa3o nos teores de COT e no Cmic. O Cmic \uffc3\uffa9 o atributo mais sens\uffc3\uffadvel \uffc3\uffa0s altera\uffc3\uffa7\uffc3\uffb5es impostas ao solo, pelos sistemas de pastagens cultivada e nativa, pois foi marcado por redu\uffc3\uffa7\uffc3\uffb5es mais expressivas.

", "keywords": ["microbial quotient", "carbono microbiano", "04 agricultural and veterinary sciences", "quociente metab\u00f3lico", "microbial activity", "01 natural sciences", "atividade microbiana", "microbial biomass carbon", "basal respiration", "respira\u00e7\u00e3o basal", "0401 agriculture", " forestry", " and fisheries", "metabolic quotient", "quociente microbiano", "0105 earth and related environmental sciences"], "contacts": [{"organization": "Cardoso, Evaldo Luis, Silva, Marx Leandro Naves, Moreira, F\u00e1tima Maria de Souza, Curi, Nilton,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1590/s0100-204x2009000600012"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Pesquisa%20Agropecu%C3%A1ria%20Brasileira", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1590/s0100-204x2009000600012", "name": "item", "description": "10.1590/s0100-204x2009000600012", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1590/s0100-204x2009000600012"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-06-01T00:00:00Z"}}, {"id": "10.1590/s1413-70542009000400010", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:34Z", "type": "Journal Article", "created": "2010-01-08", "title": "Indicadores Biol\u00f3gicos De Qualidade Do Solo Em Diferentes Sistemas De Uso No Brejo Paraibano", "description": "

A avalia\uffc3\uffa7\uffc3\uffa3o da qualidade do solo \uffc3\uffa9 uma ferramenta importante para monitorar a sua degrada\uffc3\uffa7\uffc3\uffa3o, bem como planejar a implanta\uffc3\uffa7\uffc3\uffa3o de pr\uffc3\uffa1ticas sustent\uffc3\uffa1veis de manejo. Neste trabalho, objetivou-se avaliar indicadores biol\uffc3\uffb3gicos de qualidade do solo em um Latossolo Amarelo distr\uffc3\uffb3fico, submetido a diferentes sistemas de uso em Areia-PB. Foram utilizadas amostras de solo coletadas na camada ar\uffc3\uffa1vel (0-20 cm) em \uffc3\uffa1reas de mata nativa, fruticultura, cana-de-a\uffc3\uffa7\uffc3\uffbacar, sucess\uffc3\uffa3o de cultivos, pastagem e cons\uffc3\uffb3rcio de culturas. Foram avaliados o carbono org\uffc3\uffa2nico total (COT), carbono da biomassa microbiana (CBM), quociente microbiano (qMic), respira\uffc3\uffa7\uffc3\uffa3o basal (RB) e quociente metab\uffc3\uffb3lico (qCO2). Os resultados obtidos indicaram que as \uffc3\uffa1reas sob gram\uffc3\uffadneas apresentaram uma tend\uffc3\uffaancia de manuten\uffc3\uffa7\uffc3\uffa3o do COT e menores redu\uffc3\uffa7\uffc3\uffb5es no CBM, entretanto, apresentaram elevados valores de qCO2, indicando a ocorr\uffc3\uffaancia de um processo degradativo. A \uffc3\uffa1rea sob fruticultura apresentou leves redu\uffc3\uffa7\uffc3\uffb5es no COT e CBM e baixos valores de qCO2, indicando que esse sistema pode estar se ajustando a um novo estado de equil\uffc3\uffadbrio. As \uffc3\uffa1reas sob sucess\uffc3\uffa3o de cultivos e cons\uffc3\uffb3rcio de culturas apresentaram as maiores redu\uffc3\uffa7\uffc3\uffb5es no COT e CBM e elevados valores de qCO2, demonstrando um elevado est\uffc3\uffa1gio de degrada\uffc3\uffa7\uffc3\uffa3o desses sistemas. Pode-se concluir que todos os sistemas agr\uffc3\uffadcolas estudados promoveram perda de qualidade do solo, sendo esse fato mais pronunciado nas \uffc3\uffa1reas sob manejo mais intensivo. O CBM e qCO2 mostraram-se bastantes sens\uffc3\uffadveis \uffc3\uffa0s altera\uffc3\uffa7\uffc3\uffb5es decorrentes do uso agr\uffc3\uffadcola do solo, apresentando grande potencial para estudos de sua qualidade.

", "keywords": ["2. Zero hunger", "microbial quotient", "microbial biomass", "Agroecosystem", "04 agricultural and veterinary sciences", "15. Life on land", "quociente metab\u00f3lico", "microbial activity", "Agroecossistema", "6. Clean water", "atividade microbiana", "biomassa microbiana", "0401 agriculture", " forestry", " and fisheries", "metabolic quotient", "quociente microbiano"]}, "links": [{"href": "https://doi.org/10.1590/s1413-70542009000400010"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ci%C3%AAncia%20e%20Agrotecnologia", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1590/s1413-70542009000400010", "name": "item", "description": "10.1590/s1413-70542009000400010", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1590/s1413-70542009000400010"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-08-01T00:00:00Z"}}, {"id": "10.17221/446/2013-pse", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:38Z", "type": "Journal Article", "created": "2018-02-10", "title": "Soil Microbial Metabolism And Invertase Activity Under Crop Rotation And No-Tillage In North China", "description": "Soil samples were collected at both jointing and maturing stages of maize and wheat to compare the effects of 4-year no-tillage (NT) and conventional tillage (CT) on seasonal variations of microbial biomass carbon (C), metabolic quotient, and invertase activity in a sandy loam soil in North China. Soil invertase activity significantly increased (P < 0.05) from summer to spring of the next year and then significantly decreased (P < 0.05) from spring to summer. With a delay of about 3 months, soil microbial biomass C and basal respiration altered in a similar pattern, while microbial metabolic quotient changed on the contrary. Compared with CT, the NT practice significantly increased (P < 0.05) soil organic C content, and tended to result in higher soil microbial biomass C and invertase activity, as well as lower soil microbial metabolic quotient, especially at the jointing stage of maize. Our results indicated that NT might play an important role in the improvement of soil microbial efficiency, especially at the maize seedling season.", "keywords": ["soil organic carbon", "2. Zero hunger", "seasonal variation", "microbial biomass", "basal respiration", "Plant culture", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "metabolic quotient", "SB1-1110"]}, "links": [{"href": "https://doi.org/10.17221/446/2013-pse"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%2C%20Soil%20and%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.17221/446/2013-pse", "name": "item", "description": "10.17221/446/2013-pse", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.17221/446/2013-pse"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-11-30T00:00:00Z"}}, {"id": "10.21203/rs.3.rs-1193625/v1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:48Z", "type": "Journal Article", "created": "2022-01-11", "title": "On Maintenance and Metabolisms in Soil Microbial Communities", "description": "Abstract

Biochemistry is an essential yet often undervalued aspect of soil ecology, especially in soil C cycling. We assume based on tradition, intuition or hope that the complexity of biochemistry is confined to the microscopic world, and can be ignored when dealing with whole soil systems. This opinion paper draws attention to patterns caused by basic biochemical processes that permeate the world of ecosystem processes. From these patterns, we can estimate activities of the biochemical reactions of the central C metabolic network and gain insights into the ecophysiology of microbial biosynthesis and growth and maintenance energy requirements; important components of Carbon Use Efficiency (CUE).The biochemical pathways used to metabolize glucose vary from soil to soil, with mostly glycolysis in some soils, and pentose phosphate or Entner-Doudoroff pathways in others. However, notwithstanding this metabolic diversity, glucose use efficiency is high and thus substrate use for maintenance energy and overflow respiration is low in these three soils. These results contradict current dogma based on four decades of research in soil ecology. We identify three main shortcomings in our current understanding of substrate use efficiency: 1) in numeric and conceptual models, we lack appreciation of the strategies that microbes employ to quickly reduce energy needs in response to starvation; 2) production of exudates and microbial turnover affect whole-soil CUE more than variation in maintenance energy demand; and 3) whether tracer experiments can be used to measure the long-term substrate use efficiency of soil microbial communities depends critically on the ability of non-growing cells to take up tracer substrates, how biosynthesis responds to these substrates, as well as on how cellular activities scale to the community level.To move the field of soil ecology forward, future research must consider the details of microbial ecophysiology and develop new tools that enable direct measurement of microbial functioning in intact soils. We submit that 13C metabolic flux analysis is one of those new tools.Abstract

enviPath is a widely used database and prediction system for microbial biotransformation pathways of primarily xenobiotic compounds. Data and prediction system are freely available both via a web interface and a public REST API. Since its initial release in 2016, we extended the data available in enviPath and improved the performance of the prediction system and usability of the overall system. We now provide three diverse data sets, covering microbial biotransformation in different environments and under different experimental conditions. This also enabled developing a pathway prediction model that is applicable to a more diverse set of chemicals. In the prediction engine, we implemented a new evaluation tailored towards pathway prediction, which returns a more honest and holistic view on the performance. We also implemented a novel applicability domain algorithm, which allows the user to estimate how well the model will perform on their data. Finally, we improved the implementation to speed up the overall system and provide new functionality via a plugin system. Overall, enviPath has developed into a reliable database and prediction system with a unique use case in research in microbial biotransformations.

", "keywords": ["10120 Department of Chemistry", "0301 basic medicine", "0303 health sciences", "Biodegradation database", "Information technology", "T58.5-58.64", "1704 Computer Graphics and Computer-Aided Design", "3. Good health", "Database", "Chemistry", "03 medical and health sciences", "Metabolic pathways", "540 Chemistry", "Machine learning", "1706 Computer Science Applications", "Biodegradation pathway prediction", "3309 Library and Information Sciences", "1606 Physical and Theoretical Chemistry", "QD1-999"]}, "links": [{"href": "https://doi.org/10.21203/rs.3.rs-3607847/v1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Cheminformatics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.21203/rs.3.rs-3607847/v1", "name": "item", "description": "10.21203/rs.3.rs-3607847/v1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.21203/rs.3.rs-3607847/v1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-11-15T00:00:00Z"}}, {"id": "10.20944/preprints202106.0434.v1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:47Z", "type": "Journal Article", "created": "2021-06-16", "title": "Going beyond Soil Conservation with the Use of Cover Crops in Mediterranean Sloping Olive Orchards", "description": "

Among the agricultural practices promoted by the Common Agricultural Policy to increase soil functions, the use of cover crops is a recommended tool to improve the sustainability of Mediter-ranean woody crops such as olive orchards. However, there is a broad range of cover crop ty-pologies in relation to its implementation, control and species composition. In that sense, the in-fluence of different plant species on soil quality indicators in olive orchards remains unknown yet. This study describes the effects of four treatments based on the implementation of different ground covers (CC-NAT, CC-GRA and CC-MIX) and conventional tillage (TILL) on soil erosion, soil physicochemical and biological properties, and soil microbial communities after 8 years of cover crop establishment. Our results have demonstrated that the presence of a temporary cover crop (CC), compared to a soil under tillage (TILL), can reduce soil losses and maintain good soil physicochemical properties and modify greatly the structure and diversity of soil bacterial com-munities and its functioning. The presence of a homogeneous CC of gramineous (Lolium rigidum or Lolilum multiflorum) (CC-GR) for 8 years significantly increased the functional properties of the soil as compared to TILL; although the most significant change was a modification on the bacte-rial community composition that was clearly different from the rest of treatments. On the other hand, the use of a mixture of plant species (CC-MIX) as a CC for only two years although did not modify greatly the structure and diversity of soil bacterial communities compared to the TILL soil, induced significant changes on the functional properties of the soil, and reverted those properties to a level similar to that of an undisturbed soil that had maintained a natural cover of spontaneous vegetation for decades (CC-NAT).

", "keywords": ["0301 basic medicine", "2. Zero hunger", "Microbial diversity", "soil erosion", "S", "Agriculture", "04 agricultural and veterinary sciences", "metabolic activity", "15. Life on land", "Soil quality", "6. Clean water", "bacterial community composition", "03 medical and health sciences", "13. Climate action", "microbial diversity", "Bacterial community composition", "Metabolic activity", "11. Sustainability", "Soil erosion", "biochemistry", "0401 agriculture", " forestry", " and fisheries", "soil quality"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/11/7/1387/pdf"}, {"href": "https://www.mdpi.com/2073-4395/11/7/1387/pdf"}, {"href": "https://doi.org/10.20944/preprints202106.0434.v1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.20944/preprints202106.0434.v1", "name": "item", "description": "10.20944/preprints202106.0434.v1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.20944/preprints202106.0434.v1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-06-16T00:00:00Z"}}, {"id": "10.3389/fams.2019.00018", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:20:28Z", "type": "Journal Article", "created": "2019-04-12", "title": "Metabolic Games", "description": "Metabolic networks have been used to successfully predict phenotypes based on optimization principles. However, a general framework that would extend to situations not governed by simple optimization, such as multispecies communities, is still lacking. Concepts from evolutionary game theory have been proposed to amend the situation. Alternative metabolic states can be seen as strategies in a \u201cmetabolic game,\u201d and phenotypes can be predicted based on the equilibria of this game. In this survey, we review the literature on applying game theory to the study of metabolism, present the general idea of a metabolic game, and discuss open questions and future challenges.", "keywords": ["T57-57.97", "[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]", "Applied mathematics. Quantitative methods", "flux balance analysis", "microbial interactions", "01 natural sciences", "QA273-280", "metabolic modeling", "0103 physical sciences", "metabolic networks", "[INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation", "evolutionary game theory", "Probabilities. Mathematical statistics", "[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]"]}, "links": [{"href": "https://doi.org/10.3389/fams.2019.00018"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Applied%20Mathematics%20and%20Statistics", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fams.2019.00018", "name": "item", "description": "10.3389/fams.2019.00018", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fams.2019.00018"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-04-12T00:00:00Z"}}, {"id": "10.3390/agronomy11071387", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:20:36Z", "type": "Journal Article", "created": "2021-06-16", "title": "Going beyond Soil Conservation with the Use of Cover Crops in Mediterranean Sloping Olive Orchards", "description": "

Among the agricultural practices promoted by the Common Agricultural Policy to increase soil functions, the use of cover crops is a recommended tool to improve the sustainability of Mediter-ranean woody crops such as olive orchards. However, there is a broad range of cover crop ty-pologies in relation to its implementation, control and species composition. In that sense, the in-fluence of different plant species on soil quality indicators in olive orchards remains unknown yet. This study describes the effects of four treatments based on the implementation of different ground covers (CC-NAT, CC-GRA and CC-MIX) and conventional tillage (TILL) on soil erosion, soil physicochemical and biological properties, and soil microbial communities after 8 years of cover crop establishment. Our results have demonstrated that the presence of a temporary cover crop (CC), compared to a soil under tillage (TILL), can reduce soil losses and maintain good soil physicochemical properties and modify greatly the structure and diversity of soil bacterial com-munities and its functioning. The presence of a homogeneous CC of gramineous (Lolium rigidum or Lolilum multiflorum) (CC-GR) for 8 years significantly increased the functional properties of the soil as compared to TILL; although the most significant change was a modification on the bacte-rial community composition that was clearly different from the rest of treatments. On the other hand, the use of a mixture of plant species (CC-MIX) as a CC for only two years although did not modify greatly the structure and diversity of soil bacterial communities compared to the TILL soil, induced significant changes on the functional properties of the soil, and reverted those properties to a level similar to that of an undisturbed soil that had maintained a natural cover of spontaneous vegetation for decades (CC-NAT).

", "keywords": ["2. Zero hunger", "0301 basic medicine", "Microbial diversity", "soil erosion", "S", "Agriculture", "04 agricultural and veterinary sciences", "metabolic activity", "15. Life on land", "Soil quality", "6. Clean water", "bacterial community composition", "03 medical and health sciences", "13. Climate action", "microbial diversity", "Bacterial community composition", "Metabolic activity", "11. Sustainability", "Soil erosion", "biochemistry", "0401 agriculture", " forestry", " and fisheries", "soil quality"]}, "links": [{"href": "http://www.mdpi.com/2073-4395/11/7/1387/pdf"}, {"href": "https://www.mdpi.com/2073-4395/11/7/1387/pdf"}, {"href": "https://doi.org/10.3390/agronomy11071387"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agronomy", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/agronomy11071387", "name": "item", "description": "10.3390/agronomy11071387", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/agronomy11071387"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-06-16T00:00:00Z"}}, {"id": "10.3390/microorganisms8010013", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:20:45Z", "type": "Journal Article", "created": "2019-12-20", "title": "Genome Analyses and Genome-Centered Metatranscriptomics of Methanothermobacter wolfeii Strain SIV6, Isolated from a Thermophilic Production-Scale Biogas Fermenter", "description": "

In the thermophilic biogas-producing microbial community, the genus Methanothermobacter was previously described to be frequently abundant. The aim of this study was to establish and analyze the genome sequence of the archaeal strain Methanothermobacter wolfeii SIV6 originating from a thermophilic industrial-scale biogas fermenter and compare it to related reference genomes. The circular chromosome has a size of 1,686,891 bases, featuring a GC content of 48.89%. Comparative analyses considering three completely sequenced Methanothermobacter strains revealed a core genome of 1494 coding sequences and 16 strain specific genes for M. wolfeii SIV6, which include glycosyltransferases and CRISPR/cas associated genes. Moreover, M. wolfeii SIV6 harbors all genes for the hydrogenotrophic methanogenesis pathway and genome-centered metatranscriptomics indicates the high metabolic activity of this strain, with 25.18% of all transcripts per million (TPM) belong to the hydrogenotrophic methanogenesis pathway and 18.02% of these TPM exclusively belonging to the mcr operon. This operon encodes the different subunits of the enzyme methyl-coenzyme M reductase (EC: 2.8.4.1), which catalyzes the final and rate-limiting step during methanogenesis. Finally, fragment recruitment of metagenomic reads from the thermophilic biogas fermenter on the SIV6 genome showed that the strain is abundant (1.2%) within the indigenous microbial community. Detailed analysis of the archaeal isolate M. wolfeii SIV6 indicates its role and function within the microbial community of the thermophilic biogas fermenter, towards a better understanding of the biogas production process and a microbial-based management of this complex process.

", "keywords": ["2. Zero hunger", "0301 basic medicine", "570", "Methanothermobacter wolfeii", "metagenomics", "0303 health sciences", "metatranscriptomics", "thermophilic biogas fermenter", "comparative analyses", "Methanothermobacter wolfeii; thermophilic biogas fermenter; genome mining; comparative analyses; CRISPR/cas; metabolic pathway reconstruction; metagenomics; fragment recruitment; metatranscriptomics", "CRISPR/cas", "metabolic pathway reconstruction", "7. Clean energy", "Article", "03 medical and health sciences", "CRISPR/cas", "genome mining", "8. Economic growth", "Methanothermobacter wolfeii", "fragment recruitment"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/8/1/13/pdf"}, {"href": "https://www.mdpi.com/2076-2607/8/1/13/pdf"}, {"href": "https://doi.org/10.3390/microorganisms8010013"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/microorganisms8010013", "name": "item", "description": "10.3390/microorganisms8010013", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms8010013"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-20T00:00:00Z"}}, {"id": "10.5281/zenodo.14626839", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:22:21Z", "type": "Dataset", "title": "Data set of soil microbial components in response to extreme spring events at variable temperatures", "description": "The soil microbial response to prolonged soil drought (20% field capacity FC), wetness (above FC) and moderate drought (common at 50% FC) was simulated in pots at two spring temperatures - 2\u00b0C and +2.5\u00b0C colder and warmer, respectively, compared to the average in the central-eastern Po Valley, Italy (decade 2014-2024).\u00a0 Two soils (a ploughed soil and an adjacent renatured soil) were subjected to two 60-day cycles (cold and warm spring) at three levels of soil water content. The climate simulation started after the wheat seedlings had reached the two-leaf stage in all pots. Soil samples were taken from the wheat rhizome at the end of each experiment. The response of microbial biomass was evaluated in terms of double-stranded DNA (dsDNA), total bacteria quantified as 16S gene copy number using Real Time PCR and total fungi quantified as 18S gene copy number using Digital PCR. Three major bacterial groups, Pseudomonas, Actinomycetes and Bacillus, were quantified by real-time PCR using specific primers of the 16S region (F968/Ps-r; F243/518r; BacF/518). Twenty-two enzyme activities were also quantified in soil samples. The data set contains a total of twenty-eight variables.", "keywords": ["climate change", "microbial biomass", "soil bacteria", "Pseudomonas", "actinomycetes", "estreme events", "soil fungi", "microrganisms", "Bacillus", "metabolic activity", "soil"], "contacts": [{"organization": "Manici, Luisa M.", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.14626839"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.14626839", "name": "item", "description": "10.5281/zenodo.14626839", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.14626839"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2026-01-10T00:00:00Z"}}, {"id": "1887/73460", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:24:51Z", "type": "Journal Article", "created": "2018-01-31", "title": "Optimization of the metabolic stability of a fluorinated cannabinoid receptor subtype 2 (CB2) ligand designed for PET studies", "description": "The central CB2 receptor represents a promising target for the treatment of neuroinflammatory diseases as CB2 activation mediates anti-inflammatory effects. Recently, the F-18 labeled PET radiotracer [18F]7a was reported, which shows high CB2 affinity and high selectivity over the CB1 subtype but low metabolic stability due to hydrolysis of the amide group. Based on these findings twelve bioisosteres of 7a were synthesized containing a non-hydrolysable functional group instead of the amide group. The secondary amine 23a (Ki\u202f=\u202f7.9\u202fnM) and the ketone 26a (Ki\u202f=\u202f8.6\u202fnM) displayed high CB2 affinity and CB2:CB1 selectivity in in\u00a0vitro radioligand binding studies. Incubation of 7a, 23a and 26a with mouse liver microsomes and LC-quadrupole-MS analysis revealed a slightly higher metabolic stability of secondary amine 23a, but a remarkably higher stability of ketone 26a in comparison to amide 7a. Furthermore, a logD7.4 value of 5.56\u202f\u00b1\u202f0.08 was determined for ketone 26a by micro shake-flask method and LC-MS quantification.", "keywords": ["0301 basic medicine", "Amide bioisosteres", "Halogenation", "CB(2) receptor ligands", "Ligands", "Receptor", " Cannabinoid", " CB2", "Mice", "Structure-Activity Relationship", "03 medical and health sciences", "Animals", "Humans", "Identification of metabolites", "Amines", "2. Zero hunger", "0303 health sciences", "Dose-Response Relationship", " Drug", "Molecular Structure", "Fluorinated carbazole derivatives", "Ketones", "Amides", "3. Good health", "Metabolic stabilization", "PET", "Drug Design", "Positron-Emission Tomography", "Microsomes", " Liver", "Structure affinity relationships"]}, "links": [{"href": "https://doi.org/1887/73460"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/European%20Journal%20of%20Medicinal%20Chemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "1887/73460", "name": "item", "description": "1887/73460", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1887/73460"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-01T00:00:00Z"}}, {"id": "34860015", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:25:57Z", "type": "Journal Article", "created": "2021-12-03", "title": "Identification of Extracellular Key Enzyme and Intracellular Metabolic Pathway in Alginate-Degrading Consortia via an Integrated Metaproteomic/Metagenomic Analysis", "description": "Uronic acid in extracellular polymeric substances is a primary but often ignored factor related to the difficult hydrolysis of waste-activated sludge (WAS), with alginate as a typical polymer. Previously, we enriched alginate-degrading consortia (ADC) in batch reactors that can enhance methane production from WAS, but the enzymes and metabolic pathway are not well documented. In this work, two chemostats in series were operated to enrich ADC, in which 10 g/L alginate was wholly consumed. Based on it, the extracellular alginate lyase (\u223c130 kD, EC 4.2.2.3) in the cultures was identified by metaproteomic analysis. This enzyme offers a high specificity to convert alginate to disaccharides over other mentioned hydrolases. Genus Bacteroides (>60%) was revealed as the key bacterium for alginate conversion. A new Entner\u2212Doudoroff pathway
of alginate via 5-dehydro-4-deoxy-D-glucuronate (DDG) and 3-deoxy-D-glycerol-2,5-hexdiulosonate (DGH) as the intermediates to 2-keto-3-deoxy-gluconate (KDG) was constructed based on the metagenomic and metaproteomic analysis. In summary, this work documented the core enzymes and metabolic pathway for alginate degradation, which provides a good paradigm when analyzing the degrading mechanism of unacquainted substrates. The outcome will further contribute to the application of Bacteroides-dominated ADC on WAS methanogenesis in the future.", "keywords": ["DDG and DGH", "alginate-degrading consortia", "Bacteria", "Sewage", "Alginates", "two chemostats in series", "0211 other engineering and technologies", "02 engineering and technology", "01 natural sciences", "6. Clean water", "Glucuronic Acid", "extracellular alginate lyase (EC 4.2.2.3)", "Bacteroides", "new Entner\u2212Doudoroff pathway", "Metabolic Networks and Pathways", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/34860015"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "34860015", "name": "item", "description": "34860015", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/34860015"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-12-03T00:00:00Z"}}, {"id": "10.5281/zenodo.6934168", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:23:12Z", "type": "Dataset", "title": "In Situ Diversity of Metabolism and Carbon Use Efficiency among Soil Bacteria", "description": "Dataset for the MS", "keywords": ["Soil microbiology", " metabolic flux analysis", " phospholipid fatty acids"], "contacts": [{"organization": "Wu, Weichao, Dijkstra, Paul, Hungate, Bruce A., Lingling Shi, Dippold, Michaela,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.6934168"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.6934168", "name": "item", "description": "10.5281/zenodo.6934168", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.6934168"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-07-29T00:00:00Z"}}, {"id": "10.5281/zenodo.6934169", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:23:12Z", "type": "Dataset", "title": "In Situ Diversity of Metabolism and Carbon Use Efficiency among Soil Bacteria", "description": "Dataset for the MS", "keywords": ["Soil microbiology", " metabolic flux analysis", " phospholipid fatty acids"], "contacts": [{"organization": "Wu, Weichao, Dijkstra, Paul, Hungate, Bruce A., Lingling Shi, Dippold, Michaela,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.6934169"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.6934169", "name": "item", "description": "10.5281/zenodo.6934169", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.6934169"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-07-29T00:00:00Z"}}, {"id": "10.5424/fs/20112003-11458", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:23:28Z", "type": "Journal Article", "created": "2011-12-21", "description": "

Mixed stands with nitrogen fixing secondary species can improve the vigour and the stand environment of the targeted species. The aim of this study was to better understand the effect of the consociation of a N-fixing species (black locust) with a broadleaf quality timber production (wild cherry). The study was conducted in 11 year old plantations located in the Northeast of Portugal. The treatments considered were: pure black locust, pure wild cherry and mixture of wild cherry and black locust. Each plot had six lines with 12 trees and a buffer strip line. The samplings were collected on the plantation line within a radius of 50 to 100 cm from the tree. In each plot we measured soil N mineralization dynamic, soil microbial biomass carbon (MBC) and nitrogen (MBN), microbial quotient (MBC/Corg), metabolic quotient (qCO2), microbial respiration and dehydrogenase activity. Results showed a positive impact of the black locust species on the supply of nitrogen to the soil. The net N-mineralization rates were, at the end of this study, about three times greater in the pure black locust than in the pure wild cherry and about two times greater in the mixture than in the pure wild cherry. MBC and cumulative soil respiration were higher in the mixture than in the pure cherry plantation soil which may reflect positive changes in the soil environment.

", "keywords": ["Accessory trees", "2. Zero hunger", "0106 biological sciences", "dehydrogenase activity", "Metabolic quotient", "actividad deshidrogenasa", "Soil respiration", "04 agricultural and veterinary sciences", "Prunus avium", "15. Life on land", "soil respiration", "01 natural sciences", "Prunus avium; Robinia pseudoacacia; accessory trees; soil respiration; dehydrogenase activity; metabolic", "Robinia pseudoacacia", "\u00e1rboles accesorios", "metabolic", "accessory trees", "Dehydrogenase activity", "0401 agriculture", " forestry", " and fisheries", "Prunus avium; Robinia pseudoacacia; \u00e1rboles accesorios; respiraci\u00f3n del suelo; actividad deshidrogenasa;", "respiraci\u00f3n del suelo"]}, "links": [{"href": "https://doi.org/10.5424/fs/20112003-11458"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Forest%20Systems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.5424/fs/20112003-11458", "name": "item", "description": "10.5424/fs/20112003-11458", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5424/fs/20112003-11458"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-12-04T00:00:00Z"}}, {"id": "10033/622632", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:24:11Z", "type": "Journal Article", "created": "2020-03-02", "title": "Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics", "description": "Abstract Background

Anaerobic digestion (AD) of protein-rich grass silage was performed in experimental two-stage two-phase biogas reactor systems at low vs. increased organic loading rates (OLRs) under mesophilic (37\uffe2\uff80\uff89\uffc2\uffb0C) and thermophilic (55\uffe2\uff80\uff89\uffc2\uffb0C) temperatures. To follow the adaptive response of the biomass-attached cellulolytic/hydrolytic biofilms at increasing ammonium/ammonia contents, genome-centered metagenomics and transcriptional profiling based on metagenome assembled genomes (MAGs) were conducted.

Results

In total, 78 bacterial and archaeal MAGs representing the most abundant members of the communities, and featuring defined quality criteria were selected and characterized in detail. Determination of MAG abundances under the tested conditions by mapping of the obtained metagenome sequence reads to the MAGs revealed that MAG abundance profiles were mainly shaped by the temperature but also by the OLR. However, the OLR effect was more pronounced for the mesophilic systems as compared to the thermophilic ones. In contrast, metatranscriptome mapping to MAGs subsequently normalized to MAG abundances showed that under thermophilic conditions, MAGs respond to increased OLRs by shifting their transcriptional activities mainly without adjusting their proliferation rates. This is a clear difference compared to the behavior of the microbiome under mesophilic conditions. Here, the response to increased OLRs involved adjusting of proliferation rates and corresponding transcriptional activities. The analysis led to the identification of MAGs positively responding to increased OLRs. The most outstanding MAGs in this regard, obviously well adapted to higher OLRs and/or associated conditions, were assigned to the order Clostridiales (Acetivibrio sp.) for the mesophilic biofilm and the orders Bacteroidales (Prevotella sp. and an unknown species), Lachnospirales (Herbinix sp. and Kineothrix sp.) and Clostridiales (Clostridium sp.) for the thermophilic biofilm. Genome-based metabolic reconstruction and transcriptional profiling revealed that positively responding MAGs mainly are involved in hydrolysis of grass silage, acidogenesis and / or\uffc2\uffa0acetogenesis.

Conclusions

An integrated -omics approach enabled the identification of new AD biofilm keystone species featuring outstanding performance under stress conditions such as increased OLRs. Genome-based knowledge on the metabolic potential and transcriptional activity of responsive microbiome members will contribute to the development of improved microbiological AD management strategies for biomethanation of renewable biomass.

", "keywords": ["Integrated -omics", "Bioconversion", "0301 basic medicine", "2. Zero hunger", "570", "0303 health sciences", "Polyomics", "Integrated-omics", "Metagenome assembled genomes", "Biogas", "Microbial community structure", "15. Life on land", "Microbiology", "7. Clean energy", "QR1-502", "6. Clean water", "3. Good health", "Environmental sciences", "03 medical and health sciences", "13. Climate action", "Anaerobic digestion", "Metabolic activity", "GE1-350", "Methane", "Research Article"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s40793-020-00354-x.pdf"}, {"href": "https://doi.org/10033/622632"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10033/622632", "name": "item", "description": "10033/622632", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10033/622632"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-02T00:00:00Z"}}, {"id": "1871.1/c3b579db-d9ee-49cc-91ce-d3afcf0ae422", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:24:50Z", "type": "Journal Article", "created": "2023-10-30", "title": "New ways for (in)validating the forest carbon neutrality hypothesis", "description": "Abstract

Over 50\uffe2\uff80\uff89years ago, Eugene Odum postulated that mature or climax forests reside in carbon neutrality. As climate change rose to prominence in the international environmental agenda, the neutrality hypothesis transformed from an ecological principle to a justification for using forest management in combating climate change. Despite persistent efforts, Odum's neutrality hypothesis has resisted both confirmation and refutation. In this opinion we show the limitations of past efforts to (in)validate Odum's neutrality hypothesis and propose new research directions for the community to permit a more general confirmation or refutation with current and near\uffe2\uff80\uff90future observations. We then demonstrate such an approach by using metabolic theory to formulate testable predictions for the total sink strength considering soil, litter, and biomass of mature or climax forests based on observations of tree biomass and individual density. In doing so, we show that ecological theory can create additional relevant, testable hypotheses to provide timely support to decision\uffe2\uff80\uff90makers seeking to address one of the world's most pressing environmental challenges.

Members of the genera Proteiniphilum and Petrimonas were speculated to represent indicators reflecting process instability within anaerobic digestion (AD) microbiomes. Therefore, Petrimonas mucosa ING2-E5AT was isolated from a biogas reactor sample and sequenced on the PacBio RSII and Illumina MiSeq sequencers. Phylogenetic classification positioned the strain ING2-E5AT in close proximity to Fermentimonas and Proteiniphilum species (family Dysgonomonadaceae). ING2-E5AT encodes a number of genes for glycosyl-hydrolyses (GH) which are organized in Polysaccharide Utilization Loci (PUL) comprising tandem susCD-like genes for a TonB-dependent outer-membrane transporter and a cell surface glycan-binding protein. Different GHs encoded in PUL are involved in pectin degradation, reflecting a pronounced specialization of the ING2-E5AT PUL systems regarding the decomposition of this polysaccharide. Genes encoding enzymes participating in amino acids fermentation were also identified. Fragment recruitments with the ING2-E5AT genome as a template and publicly available metagenomes of AD microbiomes revealed that Petrimonas species are present in 146 out of 257 datasets supporting their importance in AD microbiomes. Metatranscriptome analyses of AD microbiomes uncovered active sugar and amino acid fermentation pathways for Petrimonas species. Likewise, screening of metaproteome datasets demonstrated expression of the Petrimonas PUL-specific component SusC providing further evidence that PUL play a central role for the lifestyle of Petrimonas species.

", "keywords": ["Bioconversion", "anaerobic digestion", "0301 basic medicine", "2. Zero hunger", "bioconversion", "Biomethanation", "QH301-705.5", "570 Biologie", "polysaccharide utilization loci", "metabolic pathway reconstruction", "16. Peace & justice", "7. Clean energy", "Article", "660.6", "biomethanation", "03 medical and health sciences", "Metabolic pathway reconstruction", "Polysaccharide utilization loci", "Anaerobic digestion", "carbohydrate-active enzymes", "Carbohydrate-active enzymes", "ddc:570", "Biology (General)"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/8/12/2024/pdf"}, {"href": "https://www.mdpi.com/2076-2607/8/12/2024/pdf"}, {"href": "https://doi.org/21.11116/0000-0007-B312-A"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "21.11116/0000-0007-B312-A", "name": "item", "description": "21.11116/0000-0007-B312-A", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/21.11116/0000-0007-B312-A"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-12-17T00:00:00Z"}}, {"id": "2995045825", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:25:32Z", "type": "Journal Article", "created": "2019-12-20", "title": "Genome Analyses and Genome-Centered Metatranscriptomics of Methanothermobacter wolfeii Strain SIV6, Isolated from a Thermophilic Production-Scale Biogas Fermenter", "description": "

In the thermophilic biogas-producing microbial community, the genus Methanothermobacter was previously described to be frequently abundant. The aim of this study was to establish and analyze the genome sequence of the archaeal strain Methanothermobacter wolfeii SIV6 originating from a thermophilic industrial-scale biogas fermenter and compare it to related reference genomes. The circular chromosome has a size of 1,686,891 bases, featuring a GC content of 48.89%. Comparative analyses considering three completely sequenced Methanothermobacter strains revealed a core genome of 1494 coding sequences and 16 strain specific genes for M. wolfeii SIV6, which include glycosyltransferases and CRISPR/cas associated genes. Moreover, M. wolfeii SIV6 harbors all genes for the hydrogenotrophic methanogenesis pathway and genome-centered metatranscriptomics indicates the high metabolic activity of this strain, with 25.18% of all transcripts per million (TPM) belong to the hydrogenotrophic methanogenesis pathway and 18.02% of these TPM exclusively belonging to the mcr operon. This operon encodes the different subunits of the enzyme methyl-coenzyme M reductase (EC: 2.8.4.1), which catalyzes the final and rate-limiting step during methanogenesis. Finally, fragment recruitment of metagenomic reads from the thermophilic biogas fermenter on the SIV6 genome showed that the strain is abundant (1.2%) within the indigenous microbial community. Detailed analysis of the archaeal isolate M. wolfeii SIV6 indicates its role and function within the microbial community of the thermophilic biogas fermenter, towards a better understanding of the biogas production process and a microbial-based management of this complex process.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "570", "Methanothermobacter wolfeii", "metagenomics", "0303 health sciences", "metatranscriptomics", "thermophilic biogas fermenter", "comparative analyses", "Methanothermobacter wolfeii; thermophilic biogas fermenter; genome mining; comparative analyses; CRISPR/cas; metabolic pathway reconstruction; metagenomics; fragment recruitment; metatranscriptomics", "CRISPR/cas", "metabolic pathway reconstruction", "7. Clean energy", "Article", "03 medical and health sciences", "CRISPR/cas", "genome mining", "8. Economic growth", "Methanothermobacter wolfeii", "fragment recruitment"]}, "links": [{"href": "http://www.mdpi.com/2076-2607/8/1/13/pdf"}, {"href": "https://www.mdpi.com/2076-2607/8/1/13/pdf"}, {"href": "https://doi.org/2995045825"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microorganisms", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2995045825", "name": "item", "description": "2995045825", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2995045825"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-20T00:00:00Z"}}, {"id": "3216494747", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:25:19Z", "type": "Journal Article", "created": "2021-12-03", "title": "Identification of Extracellular Key Enzyme and Intracellular Metabolic Pathway in Alginate-Degrading Consortia via an Integrated Metaproteomic/Metagenomic Analysis", "description": "Uronic acid in extracellular polymeric substances is a primary but often ignored factor related to the difficult hydrolysis of waste-activated sludge (WAS), with alginate as a typical polymer. Previously, we enriched alginate-degrading consortia (ADC) in batch reactors that can enhance methane production from WAS, but the enzymes and metabolic pathway are not well documented. In this work, two chemostats in series were operated to enrich ADC, in which 10 g/L alginate was wholly consumed. Based on it, the extracellular alginate lyase (\u223c130 kD, EC 4.2.2.3) in the cultures was identified by metaproteomic analysis. This enzyme offers a high specificity to convert alginate to disaccharides over other mentioned hydrolases. Genus Bacteroides (>60%) was revealed as the key bacterium for alginate conversion. A new Entner\u2212Doudoroff pathway
of alginate via 5-dehydro-4-deoxy-D-glucuronate (DDG) and 3-deoxy-D-glycerol-2,5-hexdiulosonate (DGH) as the intermediates to 2-keto-3-deoxy-gluconate (KDG) was constructed based on the metagenomic and metaproteomic analysis. In summary, this work documented the core enzymes and metabolic pathway for alginate degradation, which provides a good paradigm when analyzing the degrading mechanism of unacquainted substrates. The outcome will further contribute to the application of Bacteroides-dominated ADC on WAS methanogenesis in the future.", "keywords": ["DDG and DGH", "alginate-degrading consortia", "Bacteria", "Sewage", "Alginates", "two chemostats in series", "0211 other engineering and technologies", "02 engineering and technology", "01 natural sciences", "6. Clean water", "Glucuronic Acid", "extracellular alginate lyase (EC 4.2.2.3)", "Bacteroides", "new Entner\u2212Doudoroff pathway", "Metabolic Networks and Pathways", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/3216494747"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Science%20%26amp%3B%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "3216494747", "name": "item", "description": "3216494747", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/3216494747"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-12-03T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=metabolic&f=json", "hreflang": "en-US"}, {"rel": "alternate", "type": "text/html", "title": "This document as HTML", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=metabolic&f=html", "hreflang": "en-US"}, {"rel": "collection", "type": "application/json", "title": "Collection URL", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main", "hreflang": "en-US"}, {"type": "application/geo+json", "rel": "first", "title": "items (first)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=metabolic&", "hreflang": "en-US"}, {"rel": "next", "type": "application/geo+json", "title": "items (next)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=metabolic&offset=50", "hreflang": "en-US"}], "numberMatched": 54, "numberReturned": 50, "distributedFeatures": [], "timeStamp": "2026-05-25T12:09:13.125445Z"}