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.
ResultsIn 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.
ConclusionsAn 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": "10.1016/j.soilbio.2008.05.007", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-31T06:57:42Z", "type": "Journal Article", "created": "2008-06-12", "title": "Long-Term Organic Farming Fosters Below And Aboveground Biota: Implications For Soil Quality, Biological Control And Productivity", "description": "Organic farming may contribute substantially to future agricultural production worldwide by improving soil quality and pest control, thereby reducing environmental impacts of conventional farming. We investigated in a comprehensive way soil chemical, as well as below and aboveground biological parameters of two organic and two conventional wheat farming systems that primarily differed in fertilization and weed management strategies. Contrast analyses identified management related differences between \u201cherbicide-free\u201d bioorganic (BIOORG) and biodynamic (BIODYN) systems and conventional systems with (CONFYM) or without manure (CONMIN) and herbicide application within a long-term agricultural experiment (DOK trial, Switzerland). Soil carbon content was significantly higher in systems receiving farmyard manure and concomitantly microbial biomass (fungi and bacteria) was increased. Microbial activity parameters, such as microbial basal respiration and nitrogen mineralization, showed an opposite pattern, suggesting that soil carbon in the conventional system (CONFYM) was more easily accessible to microorganisms than in organic systems. Bacterivorous nematodes and earthworms were most abundant in systems that received farmyard manure, which is in line with the responses of their potential food sources (microbes and organic matter). Mineral fertilizer application detrimentally affected enchytraeids and Diptera larvae, whereas aphids benefited. Spider abundance was favoured by organic management, most likely a response to increased prey availability from the belowground subsystem or increased weed coverage. In contrast to most soil-based, bottom-up controlled interactions, the twofold higher abundance of this generalist predator group in organic systems likely contributed to the significantly lower abundance of aboveground herbivore pests (aphids) in these systems. Long-term organic farming and the application of farmyard manure promoted soil quality, microbial biomass and fostered natural enemies and ecosystem engineers, suggesting enhanced nutrient cycling and pest control. Mineral fertilizers and herbicide application, in contrast, affected the potential for top-down control of aboveground pests negatively and reduced the organic carbon levels. Our study indicates that the use of synthetic fertilizers and herbicide application changes interactions within and between below and aboveground components, ultimately promoting negative environmental impacts of agriculture by reducing internal biological cycles and pest control. On the contrary, organic farming fosters microbial and faunal decomposers and this propagates into the aboveground system via generalist predators thereby increasing conservation biological control. However, grain and straw yields were 23% higher in systems receiving mineral fertilizers and herbicides reflecting the trade-off between productivity and environmental responsibility.", "keywords": ["[SDE] Environmental Sciences", "generalist predators", "respiration microbienne", "[SDV]Life Sciences [q-bio]", "faune du sol", "natural enemies", "alternative prey", "630", "nitrogen", "food-web", "Soil", "agriculture biologique", "cycle biologique", "herbicide", "min\u00e9ralisation de l'azote", "fertilisation organique", "fertilisation min\u00e9rale", "soil quality", "2. Zero hunger", "agriculture biodynamique", "agriculture conventionnelle", "nutrient cycling", "04 agricultural and veterinary sciences", "sustainability", "long terme", "6. Clean water", "[SDV] Life Sciences [q-bio]", "mycorrhizal fungi", "ennemi naturel", "microbial community structure", "ecosystem functioning", "[SDE]Environmental Sciences", "DOK trial;ecosystem functioning;farming system;fertilization;generalist predators;microbial community;nutrient cycling;natural enemies;soil fauna;soil quality;sustainability", "microbial community", "soil fauna", "agricultural systems", "management", "570", "agroecosystems", "Soil quality", "suisse", "productivit\u00e9", "Soil biology", "culture c\u00e9r\u00e9aliere", "triticum aestivum", "biomasse microbienne", "biomass", "DOK trial", "15. Life on land", "qualit\u00e9 biologique du sol", "fertilization", "13. Climate action", "Biodiversity and ecosystem services", "0401 agriculture", " forestry", " and fisheries", "farming system", "Cereals", " pulses and oilseeds"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2008.05.007"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2008.05.007", "name": "item", "description": "10.1016/j.soilbio.2008.05.007", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2008.05.007"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-09-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2011.03.005", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-31T06:57:44Z", "type": "Journal Article", "created": "2011-04-15", "title": "Experimental Warming Effects On The Microbial Community Of A Temperate Mountain Forest Soil", "description": "Soil microbial communities mediate the decomposition of soil organic matter (SOM). The amount of carbon (C) that is respired leaves the soil as CO(2) (soil respiration) and causes one of the greatest fluxes in the global carbon cycle. How soil microbial communities will respond to global warming, however, is not well understood. To elucidate the effect of warming on the microbial community we analyzed soil from the soil warming experiment Achenkirch, Austria. Soil of a mature spruce forest was warmed by 4\u00a0\u00b0C during snow-free seasons since 2004. Repeated soil sampling from control and warmed plots took place from 2008 until 2010. We monitored microbial biomass C and nitrogen (N). Microbial community composition was assessed by phospholipid fatty acid analysis (PLFA) and by quantitative real time polymerase chain reaction (qPCR) of ribosomal RNA genes. Microbial metabolic activity was estimated by soil respiration to biomass ratios and RNA to DNA ratios. Soil warming did not affect microbial biomass, nor did warming affect the abundances of most microbial groups. Warming significantly enhanced microbial metabolic activity in terms of soil respiration per amount of microbial biomass C. Microbial stress biomarkers were elevated in warmed plots. In summary, the 4\u00a0\u00b0C increase in soil temperature during the snow-free season had no influence on microbial community composition and biomass but strongly increased microbial metabolic activity and hence reduced carbon use efficiency.", "keywords": ["2. Zero hunger", "13. Climate action", "Microbial biomass", "PLFA", "Soil warming", "rRNA genes", "Soil Science", "0401 agriculture", " forestry", " and fisheries", "Microbial community structure", "04 agricultural and veterinary sciences", "15. Life on land", "Microbiology", "Article"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2011.03.005"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2011.03.005", "name": "item", "description": "10.1016/j.soilbio.2011.03.005", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2011.03.005"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-07-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2015.11.007", "type": "Feature", "geometry": null, "properties": {"license": "Closed Access", "updated": "2026-05-31T06:57:49Z", "type": "Journal Article", "created": "2015-11-25", "title": "Aboveground Litter Quality Is A Better Predictor Than Belowground Microbial Communities When Estimating Carbon Mineralization Along A Land-Use Gradient", "description": "Because of the vegetation cover and anthropogenic disturbances, land-use management strongly influences soil heterotrophic decomposers. Yet, little is known about whether contrasting microbial communities originating from different ecosystems are functionally similar, and only a few studies have disentangled the direct and indirect effects of resource quality on both microbial communities and carbon mineralization rates. To assess the relative importance of aboveground litter quality and belowground microbial communities on litter decomposition, we conducted a reciprocal transplant experiment under controlled conditions using four litters (Triticum aestivum, Fagus sylvatica, Festuca arundinacea and Robinia pseudoacacia) and four soils (culture, plantation, grassland and forest) originating from a land-use gradient. We followed the kinetics of carbon mineralization over 21 dates spanning a 202-day period to assess the variability of responses generated by the plant\u2013soil interactions. Furthermore, at four time points (at 0, 27, 97 and 202 days), the mass loss rates for the main sugars within the cell wall, the microbial biomass (fumigation-extraction), the microbial community structure via phospholipid fatty acid (PLFA), and the activities of four carbon-related hydrolytic enzymes were investigated to assess the functional significance of microbial communities. Our results demonstrated that the importance of soil types and heterotrophic decomposers on carbon mineralization rates was minor (1.2% of the variance explained) compared with the predominant role of litter quality. The structure of the microbial communities responded strongly to both long-term land-use changes and short-term litter additions; specifically, (i) higher proportions of fungi were observed in natural ecosystems compared with agro-systems, and (ii) an opportunistic subset of the bacterial community was stimulated after litter additions. Even if the land-use management and litter quality can shape the microbial community structure in a foreseeable way, we found an important degree of plasticity in the responses of contrasting decomposer communities. In particular, the enzymatic efficiency (defined as the amount of enzyme produced by unit of carbon mineralized) differed among litters but not among soil types, suggesting that the threshold between carbon allocation to growth and acquisition depended more on the \u2018resource-use strategies\u2019 of the soil microorganisms than on the community structure. The recalcitrant litters stimulated \u2018efficient\u2019 communities characterized by low enzymatic activities, microbial biomass and respiration rates at the opposite of labile litters that stimulated \u2018wasteful\u2019 communities characterized by higher activities and metabolic quotient (defined as the amount of carbon respired by unit of biomass). In addition to the direct effects of litter quality, the path analysis reinforced our conclusion that the functional traits of microorganisms via their enzymatic activities are more relevant than their identity for predicting carbon mineralization. Thus, although multiple and coordinated responses of soil microbes can improve our understanding of carbon fluxes, shifts in the plant community composition caused by land-use conversion will have a stronger impact on predictions of carbon mineralization than short-term changes in the microbial community composition.", "keywords": ["2. Zero hunger", "Decomposition", "550", "Functional dissimilarity", "Microbial community structure", "Carbon cycle", "04 agricultural and veterinary sciences", "15. Life on land", "Enzymes", "Litter traits", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Plant\u2013soil interactions", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2015.11.007"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2015.11.007", "name": "item", "description": "10.1016/j.soilbio.2015.11.007", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2015.11.007"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-03-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2022.108604", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-31T06:57:50Z", "type": "Journal Article", "created": "2022-03-18", "title": "From diversity to complexity: Microbial networks in soils", "description": "ABSTRACTNetwork analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research.
Resource control over abundance, structure and functional diversity of soil microbial communities is a key determinant of soil processes and related ecosystem functioning. Copiotrophic organisms tend to be found in environments which are rich in nutrients, particularly carbon, in contrast to oligotrophs, which survive in much lower carbon concentrations.
We hypothesized that microbial biomass, activity and community structure in nutrient\uffe2\uff80\uff90poor soils of an Amazonian rain forest are limited by multiple elements in interaction. We tested this hypothesis with a fertilization experiment by adding C (as cellulose), N (as urea) and P (as phosphate) in all possible combinations to a total of 40 plots of an undisturbed tropical forest in French Guiana.
After 2\uffc2\uffa0years of fertilization, we measured a 47% higher biomass, a 21% increase in substrate\uffe2\uff80\uff90induced respiration rate and a 5\uffe2\uff80\uff90fold higher rate of decomposition of cellulose paper discs of soil microbial communities that grew in P\uffe2\uff80\uff90fertilized plots compared to plots without P fertilization. These responses were amplified with a simultaneous C fertilization suggesting P and C colimitation of soil micro\uffe2\uff80\uff90organisms at our study site.
Moreover, P fertilization modified microbial community structure (PLFAs) to a more copiotrophic bacterial community indicated by a significant decrease in the Gram\uffe2\uff80\uff90positive\uffc2\uffa0:\uffc2\uffa0Gram\uffe2\uff80\uff90negative ratio. The Fungi\uffc2\uffa0:\uffc2\uffa0Bacteria ratio increased in N fertilized plots, suggesting that fungi are relatively more limited by N than bacteria. Changes in microbial community structure did not affect rates of general processes such as glucose mineralization and cellulose paper decomposition. In contrast, community level physiological profiles under P fertilization combined with either C or N fertilization or both differed strongly from all other treatments, indicating functionally different microbial communities.
While P appears to be the most critical from the three major elements we manipulated, the strongest effects were observed in combination with either supplementary C or N addition in support of multiple element control on soil microbial functioning and community structure.
We conclude that the soil microbial community in the studied tropical rain forest and the processes it drives is finely tuned by the relative availability in C, N and P. Any shifts in the relative abundance of these key elements may affect spatial and temporal heterogeneity in microbial community structure, their associated functions and the dynamics of C and nutrients in tropical ecosystems.
", "keywords": ["tropical forest", "2. Zero hunger", "570", "phospholipid fatty acids (PLFA)", "[SDE.MCG]Environmental Sciences/Global Changes", "functional significance", "[SDV.EE.IEO] Life Sciences [q-bio]/Ecology", " environment/Symbiosis", "04 agricultural and veterinary sciences", "15. Life on land", "16. Peace & justice", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "[SDE.MCG] Environmental Sciences/Global Changes", "13. Climate action", "microbial community structure", "ecosystem functioning", "environment/Symbiosis", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", "[SDV.EE.ECO] Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "[SDV.EE.IEO]Life Sciences [q-bio]/Ecology", "0401 agriculture", " forestry", " and fisheries", "multiple resource limitation", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "phosphorus", "environment/Ecosystems", "soil functioning"]}, "links": [{"href": "https://doi.org/10.1111/1365-2435.12329"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Functional%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1365-2435.12329", "name": "item", "description": "10.1111/1365-2435.12329", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1365-2435.12329"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-09-29T00:00:00Z"}}, {"id": "10.1111/gcb.16989", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-31T06:59:30Z", "type": "Journal Article", "created": "2023-10-27", "title": "Shifts in soil ammonia\u2010oxidizing community maintain the nitrogen stimulation of nitrification across climatic conditions", "description": "AbstractAnthropogenic nitrogen (N) loading alters soil ammonia\uffe2\uff80\uff90oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize\uffc2\uffa068 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N\uffe2\uff80\uff90stimulation of nitrification, but does so via climate\uffe2\uff80\uff90related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N\uffe2\uff80\uff90availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate\uffe2\uff80\uff90related shifts in soil ammonia\uffe2\uff80\uff90oxidizing community maintain the N\uffe2\uff80\uff90stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.Long-term organic farming aims to reduce synthetic fertilizer and pesticide use in order to sustainably produce and improve soil quality. To do this, there is a need for more information about the soil microbial community, which plays a key role in a sustainable agriculture. In this paper, we assessed the long-term effects of two organic and one conventional cropping systems on the soil microbial community structure using high-throughput sequencing analysis, as well as the link between these communities and the changes in the soil properties and crop yield. The results showed that the crop yield was similar among the three cropping systems. The microbial community changed according to cropping system. Organic cultivation with manure compost and compost tea (Org_C) showed a change in the bacterial community associated with an improved soil carbon and nutrient content. A linear discriminant analysis effect size showed different bacteria and fungi as key microorganisms for each of the three different cropping systems, for conventional systems (Conv), different microorganisms such as Nesterenkonia, Galbibacter, Gramella, Limnobacter, Pseudoalteromonas, Pantoe, and Sporobolomyces were associated with pesticides, while for Org_C and organic cultivation with manure (Org_M), other types of microorganisms were associated with organic amendments with different functions, which, in some cases, reduce soil borne pathogens. However, further investigations such as functional approaches or network analyses are need to better understand the mechanisms behind this behavior.
", "keywords": ["2. Zero hunger", "compost", "High-throughput sequencing", "Organic farming", "Agriculture (General)", "high-throughput sequencing", "Microbial community structure", "Compost", "04 agricultural and veterinary sciences", "sheep manure", "crop yield", "15. Life on land", "Gen\u00e9tica", "S1-972", "12. Responsible consumption", "agricultural_sciences_agronomy", "3107.01 Producci\u00f3n de Cultivos", "microbial community structure", "organic farming", "soil properties", "5102.01 Agricultura", "0401 agriculture", " forestry", " and fisheries", "Crop yield", "Soil properties", "Sheep manure"]}, "links": [{"href": "http://www.mdpi.com/2077-0472/11/5/445/pdf"}, {"href": "https://www.mdpi.com/2077-0472/11/5/445/pdf"}, {"href": "https://doi.org/10.3390/agriculture11050445"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/agriculture11050445", "name": "item", "description": "10.3390/agriculture11050445", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/agriculture11050445"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-04-14T00:00:00Z"}}, {"id": "10.5061/dryad.cb7tp6m", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-05-31T07:02:15Z", "type": "Dataset", "title": "Data from: Effects of aridity on soil microbial communities and functions across soil depths on the Mongolian Plateau", "description": "unspecified1. Arid and semi-arid grassland ecosystems cover about 15% of the global land surface and provide vital soil carbon (C) and nitrogen (N) sequestration. Although half of the soil C and N is stored in deep soils (below 30 cm), no regional-scale study of microbial properties and their functions through the soil profile has been conducted in these drylands. 2. To explore the distribution and determinants of microbial properties and C and N mineralization rates through soil profile along aridity gradient at a regional scale, we investigated these variables for four soil layers (0-20, 20-40, 40-60, and 60-100 cm) in 132 plots on the Mongolia Plateau. 3. Soil microbial properties (biomass and bacteria:fungi ratio) and C and N mineralization rates decreased with increasing soil depth and aridity at the regional scale. Aridity-induced declines in soil microbial properties mainly resulted from the negative effects of aridity on ANPP/root biomass and soil organic C (SOC) in the surface soil layers (0-20 and 20-40 cm) but from the direct and indirect (via SOC and soil C/N) negative effects of aridity in the deep soil layers (40-60 and 60-100 cm). 4. Aridity-induced declines in soil C mineralization rates mainly resulted from the negative indirect effect of aridity on SOC and microbial properties in each soil layer, with weaker effects of SOC and stronger effects of soil microbes in the deep soil layers. Aridity-induced declines in soil N mineralization rates mainly resulted from the negative indirect effect of aridity on SOC in the three soil layers above 60 cm and mainly resulted from the negative direct effect of aridity in the 60-100 cm soil layer. 5. Aridity via direct or indirect effects strongly determined the patterns of soil microbial properties and C and N mineralization throughout soil profiles on the Mongolian Plateau. These findings suggest that the increases in aridity are likely to induce changes in soil microorganisms and their associated functions across soil depths of semi-arid grasslands, and future models should consider the dynamic interactions between substrates and microbial properties across soil depths in global drylands.", "keywords": ["2. Zero hunger", "biogeographical patterns", "soil carbon mineralization", "13. Climate action", "microbial community structure", "semi-arid grasslands", "depth profile", "15. Life on land", "soil nitrogen mineralization"], "contacts": [{"organization": "Chen, Dima, Saleem, Muhammad, Cheng, Junhui, Mi, Jia, Chu, Pengfei, Tuvshintogtokh, Indree, Hu, Shuijin, Bai, Yongfei,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.cb7tp6m"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.cb7tp6m", "name": "item", "description": "10.5061/dryad.cb7tp6m", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.cb7tp6m"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-14T00:00:00Z"}}, {"id": "10033/622632", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-31T07:05:04Z", "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 BackgroundAnaerobic 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.
ResultsIn 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.
ConclusionsAn 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": "10261/284332", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-31T07:05:12Z", "type": "Journal Article", "created": "2022-03-17", "title": "From diversity to complexity: Microbial networks in soils", "description": "ABSTRACTNetwork analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research.Anthropogenic nitrogen (N) loading alters soil ammonia\uffe2\uff80\uff90oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize\uffc2\uffa068 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N\uffe2\uff80\uff90stimulation of nitrification, but does so via climate\uffe2\uff80\uff90related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N\uffe2\uff80\uff90availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate\uffe2\uff80\uff90related shifts in soil ammonia\uffe2\uff80\uff90oxidizing community maintain the N\uffe2\uff80\uff90stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.