{"type": "FeatureCollection", "features": [{"id": "10.1128/aem.02264-23", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:19:20Z", "type": "Journal Article", "created": "2024-02-19", "title": "Novel endolithic bacteria of phylum Chloroflexota reveal a myriad of potential survival strategies in the Antarctic desert", "description": "ABSTRACT

The ice-free McMurdo Dry Valleys of Antarctica are dominated by nutrient-poor mineral soil and rocky outcrops. The principal habitat for microorganisms is within rocks (endolithic). In this environment, microorganisms are provided with protection against sub-zero temperatures, rapid thermal fluctuations, extreme dryness, and ultraviolet and solar radiation. Endolithic communities include lichen, algae, fungi, and a diverse array of bacteria. Chloroflexota is among the most abundant bacterial phyla present in these communities. Among the Chloroflexota are four novel classes of bacteria, here named Candidatus Spiritibacteria class. nov. (=UBA5177), Candidatus Martimicrobia class. nov. (=UBA4733), Candidatus Tarhunnaeia class. nov. (=UBA6077), and Candidatus Uliximicrobia class. nov. (=UBA2235). We retrieved 17 high-quality metagenome-assembled genomes (MAGs) that represent these four classes. Based on genome predictions, all these bacteria are inferred to be aerobic heterotrophs that encode enzymes for the catabolism of diverse sugars. These and other organic substrates are likely derived from lichen, algae, and fungi, as metabolites (including photosynthate), cell wall components, and extracellular matrix components. The majority of MAGs encode the capacity for trace gas oxidation using high-affinity uptake hydrogenases, which could provide energy and metabolic water required for survival and persistence. Furthermore, some MAGs encode the capacity to couple the energy generated from H 2 and CO oxidation to support carbon fixation (atmospheric chemosynthesis). All encode mechanisms for the detoxification and efflux of heavy metals. Certain MAGs encode features that indicate possible interactions with other organisms, such as Tc-type toxin complexes, hemolysins, and macroglobulins.

IMPORTANCE

The ice-free McMurdo Dry Valleys of Antarctica are the coldest and most hyperarid desert on Earth. It is, therefore, the closest analog to the surface of the planet Mars. Bacteria and other microorganisms survive by inhabiting airspaces within rocks (endolithic). We identify four novel classes of phylum Chloroflexota , and, based on interrogation of 17 metagenome-assembled genomes, we predict specific metabolic and physiological adaptations that facilitate the survival of these bacteria in this harsh environment\uffe2\uff80\uff94including oxidation of trace gases and the utilization of nutrients (including sugars) derived from lichen, algae, and fungi. We propose that such adaptations allow these endolithic bacteria to eke out an existence in this cold and extremely dry habitat.

", "keywords": ["570", "Bacteria", "Fungi", "Antarctic Regions", "Chloroflexi", "15. Life on land", "Survival strategies", "Cold Temperature", "Extremophiles", "13. Climate action", "Antarctica", "Endolithic communities", "Metagenomics", "14. Life underwater", "Sugars", "Settore BIO/19 - MICROBIOLOGIA GENERALE"]}, "links": [{"href": "https://doi.org/10.1128/aem.02264-23"}, {"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.02264-23", "name": "item", "description": "10.1128/aem.02264-23", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.02264-23"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-19T00:00:00Z"}}, {"id": "10.1002/advs.201901408", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:14:08Z", "type": "Journal Article", "created": "2019-09-19", "title": "Natural Microbial Communities Can Be Manipulated by Artificially Constructed Biofilms", "description": "Abstract

Biofouling proceeds in successive steps where the primary colonizers affect the phylogenetic and functional structure of a future microbial consortium. Using microbiologically influenced corrosion (MIC) as a study case, a novel approach for material surface protection is described, which does not prevent biofouling, but rather shapes the process of natural biofilm development to exclude MIC\uffe2\uff80\uff90related microorganisms. This approach interferes with the early steps of natural biofilm formation affecting how the community is finally developed. It is based on a multilayer artificial biofilm, composed of electrostatically modified bacterial cells, producing antimicrobial compounds, extracellular antimicrobial polyelectrolyte matrix, and a water\uffe2\uff80\uff90proof rubber elastomer barrier. The artificial biofilm is constructed layer\uffe2\uff80\uff90by\uffe2\uff80\uff90layer (LBL) by manipulating the electrostatic interactions between microbial cells and material surfaces. Field testing on standard steel coupons exposed in the sea for more than 30 days followed by laboratory analyses using molecular\uffe2\uff80\uff90biology tools demonstrate that the preapplied artificial biofilm affects the phylogenetic structure of the developing natural biofilm, reducing phylogenetic diversity and excluding MIC\uffe2\uff80\uff90related bacteria. This sustainable solution for material protection showcases the usefulness of artificially guiding microbial evolutionary processes via the electrostatic modification and controlled delivery of bacterial cells and extracellular matrix to the exposed material surfaces.The soil microbiome consists of a vast variety of microorganisms which contribute to essential ecosystem services including nutrient recycling, protecting soil structure, and pathogen suppression. Recalcitrant organic compounds present in soils contaminated with fuel oil can lead to a decrease in functional redundancy within soil microbiomes. Ecopiling is a passive bioremediation technique involving biostimulation of indigenous hydrocarbon degraders, bioaugmentation through inoculation with known petroleum-degrading consortia, and phytoremediation. The current study investigates the assemblage of soil microbial communities and pollutant-degrading potential in soil undergoing the Ecopiling process, through the amplicon marker gene and metagenomics analysis of the contaminated soil. The analysis of key community members including bacteria, fungi, and nematodes revealed a surprisingly diverse microbial community composition within the contaminated soil. The soil bacterial community was found to be dominated by Alphaproteobacteria (60\uffe2\uff80\uff9370%) with the most abundant genera such as Lysobacter, Dietzia, Pseudomonas, and Extensimonas. The fungal community consisted mainly of Ascomycota (50\uffe2\uff80\uff9370% relative abundance). Soil sequencing data allowed the identification of key enzymes involved in the biodegradation of hydrocarbons, providing a novel window into the function of individual bacterial groups in the Ecopile. Although the genus Lysobacter was identified as the most abundant bacterial genus (11\uffe2\uff80\uff9346%) in all of the contaminated soil samples, the metagenomic data were unable to confirm a role for this group in petrochemical degradation. Conversely, genera with relatively low abundance such as Dietzia (0.4\uffe2\uff80\uff939.0%), Pusillimonas (0.7\uffe2\uff80\uff932.3%), and Bradyrhizobium (0.8\uffe2\uff80\uff931.8%) did possess genes involved in aliphatic or aromatic compound degradation. The climate-active gas isoprene (2-methyl-1,3-butadiene) is released to the atmosphere in huge quantities, almost equaling that of methane, yet we know little about the biological cycling of isoprene in the environment. Although bacteria capable of growth on isoprene as the sole source of carbon and energy have previously been isolated from soils and sediments, no microbiological studies have targeted the major source of isoprene and examined the phyllosphere of isoprene-emitting trees for the presence of degraders of this abundant carbon source. Here, we identified isoprene-degrading bacteria in poplar tree-derived microcosms by DNA stable isotope probing. The genomes of isoprene-degrading taxa were reconstructed, putative isoprene metabolic genes were identified, and isoprene-related gene transcription was analyzed by shotgun metagenomics and metatranscriptomics. Gram-positive bacteria of the genus Rhodococcus proved to be the dominant isoprene degraders, as previously found in soil. However, a wider diversity of isoprene utilizers was also revealed, notably Variovorax , a genus not previously associated with this trait. This finding was confirmed by expression of the isoprene monooxygenase from Variovorax in a heterologous host. A Variovorax strain that could grow on isoprene as the sole carbon and energy source was isolated. Analysis of its genome confirmed that it contained isoprene metabolic genes with an identical layout and high similarity to those identified by DNA-stable isotope probing and metagenomics. This study provides evidence of a wide diversity of isoprene-degrading bacteria in the isoprene-emitting tree phyllosphere and greatly enhances our understanding of the biodegradation of this important metabolite and climate-active gas.

", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "570", "0303 health sciences", "QH301 Biology", "Biological Sciences", "15. Life on land", "Mixed Function Oxygenases", "Comamonadaceae", "03 medical and health sciences", "Biodegradation", " Environmental", "Hemiterpenes", "Populus", "13. Climate action", "Butadienes", "Rhodococcus", "Metagenomics", "Genome", " Bacterial", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://ueaeprints.uea.ac.uk/id/eprint/69197/1/Published_manuscript.pdf"}, {"href": "https://pnas.org/doi/pdf/10.1073/pnas.1812668115"}, {"href": "https://repository.essex.ac.uk/23631/1/1812668115.full.pdf"}, {"href": "https://doi.org/10.1073/pnas.1812668115"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Proceedings%20of%20the%20National%20Academy%20of%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1073/pnas.1812668115", "name": "item", "description": "10.1073/pnas.1812668115", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1073/pnas.1812668115"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-11-29T00:00:00Z"}}, {"id": "10.1186/s40793-023-00479-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:19:31Z", "type": "Journal Article", "created": "2023-03-30", "title": "Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis", "description": "Abstract Background

For a sustainable production of food, research on agricultural soil microbial communities is inevitable. Due to its immense complexity, soil is still some kind of black box. Soil study designs for identifying microbiome members of relevance have various scopes and focus on particular environmental factors. To identify common features of soil microbiomes, data from multiple studies should be compiled and processed. Taxonomic compositions and functional capabilities of microbial communities associated with soils and plants have been identified and characterized in the past few decades. From a fertile Loess\uffe2\uff80\uff93Chernozem-type soil located in Germany, metagenomically assembled genomes (MAGs) classified as members of the phylum Thaumarchaeota/Thermoproteota were obtained. These possibly represent keystone agricultural soil community members encoding functions of relevance for soil fertility and plant health. Their importance for the analyzed microbiomes is corroborated by the fact that they were predicted to contribute to the cycling of nitrogen, feature the genetic potential to fix carbon dioxide and possess genes with predicted functions in plant-growth-promotion (PGP). To expand the knowledge on soil community members belonging to the phylum Thaumarchaeota, we conducted a meta-analysis integrating primary studies on European agricultural soil microbiomes.

Results

Taxonomic classification of the selected soil metagenomes revealed the shared agricultural soil core microbiome of European soils from 19 locations. Metadata reporting was heterogeneous between the different studies. According to the available metadata, we separated the data into 68 treatments. The phylum Thaumarchaeota is part of the core microbiome and represents a major constituent of the archaeal subcommunities in all European agricultural soils. At a higher taxonomic resolution, 2074 genera constituted the core microbiome. We observed that viral genera strongly contribute to variation in taxonomic profiles. By binning of metagenomically assembled contigs, Thaumarchaeota MAGs could be recovered from several European soil metagenomes. Notably, many of them were classified as members of the family Nitrososphaeraceae, highlighting the importance of this family for agricultural soils. The specific Loess-Chernozem Thaumarchaeota MAGs were most abundant in their original soil, but also seem to be of importance in other agricultural soil microbial communities. Metabolic reconstruction of Switzerland_1_MAG_2 revealed its genetic potential i.a. regarding carbon dioxide (CO$$_2$$ 2 ) fixation, ammonia oxidation, exopolysaccharide production and a beneficial effect on plant growth. Similar genetic features were also present in other reconstructed MAGs. Three Nitrososphaeraceae MAGs are all most likely members of a so far unknown genus.

Conclusions

On a broad view, European agricultural soil microbiomes are similarly structured. Differences in community structure were observable, although analysis was complicated by heterogeneity in metadata recording. Our study highlights the need for standardized metadata reporting and the benefits of networking open data. Future soil sequencing studies should also consider high sequencing depths in order to enable reconstruction of genome bins. Intriguingly, the family Nitrososphaeraceae commonly seems to be of importance in agricultural microbiomes.

", "keywords": ["2. Zero hunger", "570", "Soil microbial diversity", "Metagenomically assembled genomes", "Research", "European soil", "Open metagenome data analysis", "15. Life on land", "Microbiology", "Thaumarchaeota", "QR1-502", "Environmental sciences", "Agricultural microbiome", "Soil health", "GE1-350"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1186/s40793-023-00479-9.pdf"}, {"href": "https://doi.org/10.1186/s40793-023-00479-9"}, {"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/s40793-023-00479-9", "name": "item", "description": "10.1186/s40793-023-00479-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40793-023-00479-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-03-30T00:00:00Z"}}, {"id": "10.1038/ismej.2017.48", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:17:45Z", "type": "Journal Article", "created": "2017-04-21", "title": "Warming enhances old organic carbon decomposition through altering functional microbial communities", "description": "Abstract

Soil organic matter (SOM) stocks contain nearly three times as much carbon (C) as the atmosphere and changes in soil C stocks may have a major impact on future atmospheric carbon dioxide concentrations and climate. Over the past two decades, much research has been devoted to examining the influence of warming on SOM decomposition in topsoil. Most SOM, however, is old and stored in subsoil. The fate of subsoil SOM under future warming remains highly uncertain. Here, by combining a long-term field warming experiment and a meta-analysis study, we showed that warming significantly increased SOM decomposition in subsoil. We also showed that a decade of warming promoted decomposition of subsoil SOM with turnover times of decades to millennia in a tall grass prairie and this effect was largely associated with shifts in the functional gene structure of microbial communities. By coupling stable isotope probing with metagenomics, we found that microbial communities in warmed soils possessed a higher relative abundance of key functional genes involved in the degradation of organic materials with varying recalcitrance than those in control soils. These findings suggest warming may considerably alter the stability of the vast pool of old SOM in subsoil, contributing to the long-term positive feedback between the C cycle and climate.

", "keywords": ["2. Zero hunger", "0301 basic medicine", "Technology", "0303 health sciences", "Hot Temperature", "Ecology", "Bacteria", "Climate Change", "Biological Sciences", "15. Life on land", "Microbiology", "630", "Carbon", "Climate Action", "Environmental sciences", "Biological sciences", "Soil", "03 medical and health sciences", "13. Climate action", "Original Article", "Metagenomics", "Environmental Sciences", "Soil Microbiology"]}, "links": [{"href": "https://escholarship.org/content/qt8mp28182/qt8mp28182.pdf"}, {"href": "https://doi.org/10.1038/ismej.2017.48"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20ISME%20Journal", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/ismej.2017.48", "name": "item", "description": "10.1038/ismej.2017.48", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2017.48"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-04-21T00:00:00Z"}}, {"id": "10.1038/s41538-021-00087-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:17:49Z", "type": "Journal Article", "created": "2020-09-12", "title": "Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples.", "description": "Abstract

Food processing environments can harbor microorganisms responsible for food spoilage or foodborne disease. Efficient and accurate identification of microorganisms throughout the food chain can allow the identification of sources of contamination and the timely implementation of control measures. Currently, microbial monitoring of the food chain relies heavily on culture-based techniques. These assays are determined on the microbes expected to be present in the environment, and thus do not cater for unexpected contaminants. Many culture-based assays are also unable to distinguish between undesirable taxa and closely related harmless species. Furthermore, even when multiple culture-based approaches are used in parallel, it is still not possible to comprehensively characterize the entire microbiology of a food-chain sample.

High throughput DNA sequencing represents a potential means through which microbial monitoring of the food chain can be enhanced. While sequencing platforms, such as the Illumina MiSeq, NextSeq and NovaSeq, are most typically found in research or commercial sequencing laboratories, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. In this study, having initially assessed the ability of rapid MinION-based sequencing to discriminate between different microbes within a simple mock metagenomic mixture of related food spoilage, spore-forming microorganisms. Subsequently, we proceeded to compare the performance of both ONT and Illumina sequencing for environmental monitoring of an active food processing facility.

Overall, ONT MinION sequencing provided accurate classification to species level, which was comparable to Illumina-derived outputs. However, while the MinION-based approach provided a means of easy library preparations and portability, the high concentrations of DNA needed to run the rapid sequencing protocols was a limiting factor, requiring the random amplification of template DNA in order to generate sufficient material for analysis.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "03 medical and health sciences", "Nutrition. Foods and food supply", "13. Climate action", "0206 medical engineering", "TX341-641", "Metagenomics", "02 engineering and technology", "Food microbiology", "TP368-456", "Food processing and manufacture", "Article"]}, "links": [{"href": "https://www.nature.com/articles/s41538-021-00087-2.pdf"}, {"href": "https://doi.org/10.1038/s41538-021-00087-2"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/npj%20Science%20of%20Food", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41538-021-00087-2", "name": "item", "description": "10.1038/s41538-021-00087-2", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41538-021-00087-2"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-09-11T00:00:00Z"}}, {"id": "10.1038/s41598-023-49194-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:17:53Z", "type": "Journal Article", "created": "2023-12-13", "title": "Unraveling the genome of Bacillus velezensis MEP218, a strain producing fengycin homologs with broad antibacterial activity: comprehensive comparative genome analysis", "description": "Abstract

Bacillus sp. MEP218, a soil bacterium with high potential as a source of bioactive molecules, produces mostly C16\uffe2\uff80\uff93C17 fengycin and other cyclic lipopeptides (CLP) when growing under previously optimized culture conditions. This work addressed the elucidation of the genome sequence of MEP218 and its taxonomic classification. The genome comprises 3,944,892\uffc2\uffa0bp, with a total of 3474 coding sequences and a G\uffe2\uff80\uff89+\uffe2\uff80\uff89C content of 46.59%. Our phylogenetic analysis to determine the taxonomic position demonstrated that the assignment of the MEP218 strain to Bacillus velezensis species provides insights into its evolutionary context and potential functional attributes. The in silico genome analysis revealed eleven gene clusters involved in the synthesis of secondary metabolites, including non-ribosomal CLP (fengycins and surfactin), polyketides, terpenes, and bacteriocins. Furthermore, genes encoding phytase, involved in the release of phytic phosphate for plant and animal nutrition, or other enzymes such as cellulase, xylanase, and alpha 1\uffe2\uff80\uff934 glucanase were detected. In vitro antagonistic assays against Salmonella typhimurium, Acinetobacter baumanii, Escherichia coli, among others, demonstrated a broad spectrum of C16\uffe2\uff80\uff93C17 fengycin produced by MEP218. MEP218 genome sequence analysis expanded our understanding of the diversity and genetic relationships within the Bacillus genus and updated the Bacillus databases with its unique trait to produce antibacterial fengycins and its potential as a resource of biotechnologically useful enzymes.The rhizobiota, particularly nitrogen-fixing bacteria, play a crucial role in plant functioning by providing essential nutrients and defense against pathogens. This study investigated the diversity of nitrogen-fixing bacteria in a relatively understudied habitat: technosoils developed from industrial soda production. To analyze the bacterial diversity in the rhizosphere soils of wheat (Triticum aestivum L.) and aster (Tripolium pannonicum Jacq.), regions of the nifH gene were amplified and sequenced from the resident bacterial communities. A polyvinylidene fluoride (PVDF) membrane was employed for metagenomic DNA extraction, enhancing the detection of nitrogen-fixing bacteria. Prior to standard DNA extraction, an enrichment step was conducted in nitrogen-free JMV medium at 26\uffc2\uffa0\uffc2\uffb0C for 24\uffc2\uffa0h, with a modification that replaced soil with the PVDF membrane. This approach enabled a more comprehensive analysis of the rhizosphere bacterial community, revealing that unique amplicon sequence variants (ASVs) in aster and wheat membrane samples accounted for a notable proportion of all ASVs in the dataset (8.5% and 23%, respectively) that were not captured using the standard method. Additionally, our findings demonstrated higher alpha diversity of nitrogen-fixing bacteria in the wheat rhizosphere compared to the aster rhizosphere. In wheat, the dominant genus was Insolitispirillum (38.80%), followed by unclassified genera within Gammaproteobacteria (9.76%) and Rhodospirillaceae (4.74%). In contrast, the aster rhizosphere was predominantly occupied by Azotobacter (95.69%).Environmental factors relating to soil pH are widely known to be important in structuring soil bacterial communities, yet the relationship between taxonomic community composition and functional diversity remains to be determined. Here, we analyze geographically distributed soils spanning a wide pH gradient and assess the functional gene capacity within those communities using whole genome metagenomics. Low pH soils consistently had fewer taxa (lower alpha and gamma diversity), but only marginal reductions in functional alpha diversity and equivalent functional gamma diversity. However, coherent changes in the relative abundances of annotated genes between pH classes were identified; with functional profiles clustering according to pH independent of geography. Differences in gene abundances were found to reflect survival and nutrient acquisition strategies, with organic-rich acidic soils harboring a greater abundance of cation efflux pumps, C and N direct fixation systems and fermentation pathways indicative of anaerobiosis. Conversely, high pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings show that bacterial functional versatility may not be constrained by taxonomy, and we further identify the range of physiological adaptations required to exist in soils of varying nutrient availability and edaphic conditions.Methane (CH4) exchange in tree stems and canopies and the processes involved are among the least understood components of the global CH4 cycle. Recent studies have focused on quantifying tree stems as sources of CH4 and understanding abiotic CH4 emissions in plant canopies, with the role of microbial in situ CH4 formation receiving less attention. Moreover, despite initial reports revealing CH4 consumption, studies have not adequately evaluated the potential of microbial CH4 oxidation within trees. In this paper, we discuss the current level of understanding on these processes. Further, we demonstrate the potential of novel metagenomic tools in revealing the involvement of microbes in the CH4 exchange of plants, and particularly in boreal trees. We detected CH4\uffe2\uff80\uff90producing methanogens and novel monooxygenases, potentially involved in CH4 consumption, in coniferous plants. In addition, our field flux measurements from Norway spruce (Picea abies) canopies demonstrate both net CH4 emissions and uptake, giving further evidence that both production and consumption are relevant to the net CH4 exchange. Our findings, together with the emerging diversity of novel CH4\uffe2\uff80\uff90producing microbial groups, strongly suggest microbial analyses should be integrated in the studies aiming to reveal the processes and drivers behind plant CH4 exchange.

", "keywords": ["0301 basic medicine", "330", "ta1172", "metaani", "bakteerit", "Trees", "03 medical and health sciences", "boreal forests", "Ymp\u00e4rist\u00f6tiede", "2. Zero hunger", "0303 health sciences", "Norway", "ta1183", "kasvifysiologia", "puut (kasvit)", "genomiikka", "15. Life on land", "ta4112", "methanogenic archaea", "mets\u00e4t", "plant microbiome", "tree", "methane exchange", "boreaalinen vy\u00f6hyke", "mikrobisto", "13. Climate action", "Environmental Science", "aineiden kierto", "Metagenomics", "methanotrophic bacteria", "arkeonit", "Methane", "captured metagenomics"]}, "links": [{"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.17365"}, {"href": "https://doi.org/10.1111/nph.17365"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/nph.17365", "name": "item", "description": "10.1111/nph.17365", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.17365"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-05-02T00:00:00Z"}}, {"id": "10.1128/aem.01081-21", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:19:19Z", "type": "Journal Article", "created": "2021-09-01", "title": "Seasonality and geography have a greater influence than the use of chlorine-based cleaning agents on the microbiota of bulk tank raw milk.", "description": "

The microbiota of raw milk is affected by many factors that can control or promote the introduction of undesirable microorganisms. Chlorine-based cleaning agents have been commonly used due to their effectiveness in controlling undesirable microorganisms, but they have been associated with the formation of chlorine residues that are detrimental to product quality and may impact consumer health.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Geography", "Microbiota", "Dairy", "Dairying", "03 medical and health sciences", "Milk", "Food Microbiology", "Animals", "Equipment Contamination", "DNA sequencing", "Metagenomics", "Seasons", "Chlorine", "Ireland", "Disinfectants"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/AEM.01081-21"}, {"href": "https://doi.org/10.1128/aem.01081-21"}, {"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.01081-21", "name": "item", "description": "10.1128/aem.01081-21", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.01081-21"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-10-28T00:00:00Z"}}, {"id": "10.1128/mBio.00799-17", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:19:20Z", "type": "Journal Article", "created": "2017-03-19", "title": "Bacterial Physiological Adaptations to Contrasting Edaphic Conditions Identified Using Landscape Scale Metagenomics", "description": "Abstract

Environmental factors relating to soil pH are widely known to be important in structuring soil bacterial communities, yet the relationship between taxonomic community composition and functional diversity remains to be determined. Here, we analyze geographically distributed soils spanning a wide pH gradient and assess the functional gene capacity within those communities using whole genome metagenomics. Low pH soils consistently had fewer taxa (lower alpha and gamma diversity), but only marginal reductions in functional alpha diversity and equivalent functional gamma diversity. However, coherent changes in the relative abundances of annotated genes between pH classes were identified; with functional profiles clustering according to pH independent of geography. Differences in gene abundances were found to reflect survival and nutrient acquisition strategies, with organic-rich acidic soils harboring a greater abundance of cation efflux pumps, C and N direct fixation systems and fermentation pathways indicative of anaerobiosis. Conversely, high pH soils possessed more direct transporter-mediated mechanisms for organic C and N substrate acquisition. These findings show that bacterial functional versatility may not be constrained by taxonomy, and we further identify the range of physiological adaptations required to exist in soils of varying nutrient availability and edaphic conditions.

", "keywords": ["Q Science", "0301 basic medicine", "330", "Supplementary Data", "ecophysiology", "Ecophysiology", "NE/E006353/1", "Bacterial Physiological Phenomena", "Microbiology", "Soil", "03 medical and health sciences", "Virology", "European Commission", "Ecosystem", "Phylogeny", "Soil Microbiology", "2. Zero hunger", "655240", "metagenomics", "0303 health sciences", "Bacteria", "Natural Environment Research Council (NERC)", "Q", "NE/M017125/1", "Biodiversity", "Hydrogen-Ion Concentration", "15. Life on land", "Adaptation", " Physiological", "soil microbiology", "QR1-502", "United Kingdom", "3. Good health", "Soil microbiology", "Metagenomics", "Genome", " Bacterial", "Research Article"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/117887v1.full.pdf"}, {"href": "https://journals.asm.org/doi/pdf/10.1128/mBio.00799-17"}, {"href": "https://doi.org/10.1128/mBio.00799-17"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mBio", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/mBio.00799-17", "name": "item", "description": "10.1128/mBio.00799-17", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/mBio.00799-17"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-03-18T00:00:00Z"}}, {"id": "10.1128/msystems.00226-20", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:19:20Z", "type": "Journal Article", "created": "2020-04-06", "title": "Tracking the Dairy Microbiota from Farm Bulk Tank to Skimmed Milk Powder", "description": "

Microorganisms can enter and persist in dairy at several stages of the processing chain. Detection of microorganisms within dairy food processing is currently a time-consuming and often inaccurate process. This study provides evidence that high-throughput sequencing can be used as an effective tool to accurately identify microorganisms along the processing chain. In addition, it demonstrates that the populations of microbes change from raw milk to the end product. Routine implementation of high-throughput sequencing would elucidate the factors that influence population dynamics. This will enable a manufacturer to adopt control measures specific to each stage of processing and respond in an effective manner, which would ultimately lead to increased food safety and quality.

", "keywords": ["2. Zero hunger", "0301 basic medicine", "metagenomics", "0303 health sciences", "whole-milk silo", "collection tanker", "bulk tank milk", "Microbiology", "QR1-502", "3. Good health", "03 medical and health sciences", "skimmed milk silo", "skimmed milk powder", "microbiota", "dairy", "processing", "16S rRNA gene amplicon sequencing", "Research Article"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/mSystems.00226-20"}, {"href": "https://doi.org/10.1128/msystems.00226-20"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/msystems.00226-20", "name": "item", "description": "10.1128/msystems.00226-20", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msystems.00226-20"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-04-28T00:00:00Z"}}, {"id": "10.1128/msystems.00786-20", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:19:20Z", "type": "Journal Article", "created": "2021-01-11", "title": "Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community", "description": "

This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families, and orders, as well as differences in the metabolic potential between the most abundant BSC populations and their cultured relatives, highlighting once more the danger of inferring function on the basis of taxonomy.

", "keywords": ["0301 basic medicine", "BACTERIAL", "dormancy", "Survival", "RUBROBACTER-RADIOTOLERANS", "DIVERSITY", "Biological soil crust", "survival", "Microbiology", "7. Clean energy", "biological soil crust", "03 medical and health sciences", "mixotrophy", "Dormancy", "Mixotrophy", "SPORULATION", "COLORADO PLATEAU", "2. Zero hunger", "106022 Mikrobiologie", "metagenomics", "0303 health sciences", "ARTHROBACTER-RADIOTOLERANS", "15. Life on land", "XYLANOPHILUS", "QR1-502", "SP NOV.", "SURVIVAL", "106022 Microbiology", "RADIATION", "Metagenomics", "MEMBERS", "Research Article"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/mSystems.00786-20"}, {"href": "https://doi.org/10.1128/msystems.00786-20"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/mSystems", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/msystems.00786-20", "name": "item", "description": "10.1128/msystems.00786-20", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/msystems.00786-20"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-02-23T00:00:00Z"}}, {"id": "10.1128/spectrum.01101-23", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:19:21Z", "type": "Journal Article", "created": "2023-09-19", "title": "Bacteriophages limitedly contribute to the antimicrobial resistome of microbial communities in wastewater treatment plants", "description": "ABSTRACT

Bacteriophages are known as players in the transmission of antimicrobial resistance genes (ARGs) by horizontal gene transfer. In this study, we characterized the bacteriophage community and the associated ARGs to estimate the potential for phages to spread ARGs in aquatic ecosystems analyzing the intra- and extracellular DNA isolated from two wastewater treatment plants (WWTPs) by shotgun metagenomics. We compared the phage antimicrobial resistome with the bacterial resistome and investigated the effect of the final disinfection treatment on the phage community and its resistome. Phage community was mainly composed by Siphoviridae and other members of the order Caudovirales . The final disinfection only marginally affected the composition of the phage community, and it was not possible to measure its effect on the antimicrobial resistome. Indeed, only three phage metagenome-assembled genomes (pMAGs) annotated as Siphoviridae , Padoviridae , and Myoviridae were positive for putative ARGs. Among the detected ARGs, i.e., dfr B6, rpo B mutants, and EF-Tu mutants, the first one was not annotated in the bacterial MAGs. Overall, these results demonstrate that bacteriophages limitedly contribute to the whole antimicrobial resistome. However, in order to obtain a comprehensive understanding of the antimicrobial resistome within a microbial community, the role of bacteriophages needs to be investigated.

IMPORTANCE

WWTPs are considered hotspots for the spread of ARGs by horizontal gene transfer. In this study, we evaluated the phage composition and the associated antimicrobial resistome by shotgun metagenomics of samples collected before and after the final disinfection treatment. Only a few bacteriophages carried ARGs. However, since one of the detected genes was not found in the bacterial metagenome-assembled genomes, it is necessary to investigate the phage community in order to gain a comprehensive overview of the antimicrobial resistome. This investigation could help assess the potential threats to human health.

", "keywords": ["metagenomics", "bacteriophages", "11. Sustainability", "Bacteriophages", "metagenomic assembled genomes", "antimicrobial resistance", "antimicrobial resistome", "wastewater treatment plants", "Microbiology", "6. Clean water", "QR1-502", "12. Responsible consumption", "Research Article"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/spectrum.01101-23"}, {"href": "https://doi.org/10.1128/spectrum.01101-23"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiology%20Spectrum", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/spectrum.01101-23", "name": "item", "description": "10.1128/spectrum.01101-23", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/spectrum.01101-23"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-10-17T00:00:00Z"}}, {"id": "10.3390/genes13050850", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:07Z", "type": "Journal Article", "created": "2022-05-11", "title": "Short-Term Responses of Soil Microbial Communities to Changes in Air Temperature, Soil Moisture and UV Radiation", "description": "

We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community\u2019s response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 \u00b0C + 50% water holding capacity (WHC)); increased air temperature (15\u201325 \u00b0C or 20\u201330 \u00b0C + 50% WHC); flood (20 \u00b0C + 75% WHC); drought (20 \u00b0C + 25% WHC); and ultraviolet radiation (UV) (20 \u00b0C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community\u2019s physiological profile and the bacterial community\u2019s structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20\u201330 \u00b0C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome\u2013invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed.

", "keywords": ["0301 basic medicine", "Soil invertebrates", "Ultraviolet Rays", "drought", "microbial activity", "DNA", " Ribosomal", "Flood", "Article", "Quantitative PCR", "Soil", "03 medical and health sciences", "soil microbiome", "2. Zero hunger", "metagenomics", "increased temperature; drought; flood; UV exposure; microbial activity; bacterial diversity; metagenomics; quantitative PCR; soil microbiome; soil invertebrates", "Soil microbiome", "0303 health sciences", "Drought", "Bacteria", "Microbiota", "bacterial diversity", "Temperature", "Water", "flood", "15. Life on land", "soil invertebrates", "6. Clean water", "UV exposure", "Microbial activity", "Bacterial diversity", "13. Climate action", "quantitative PCR", "Metagenomics", "Increased temperature", "increased temperature"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/13/5/850/pdf"}, {"href": "https://doi.org/10.3390/genes13050850"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes13050850", "name": "item", "description": "10.3390/genes13050850", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes13050850"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-10T00:00:00Z"}}, {"id": "10.1186/s13568-024-01764-7", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:19:30Z", "type": "Journal Article", "created": "2024-09-28", "title": "Metagenomic analyses of a consortium for the bioremediation of hydrocarbons polluted soils", "description": "Abstract

A bacterial consortium was isolated from a soil in Noblejas (Toledo, Spain) with a long history of mixed hydrocarbons pollution, by enrichment cultivation. Serial cultures of hydrocarbons polluted soil samples were grown in a minimal medium using diesel (1\uffc2\uffa0mL/L) as the sole carbon and energy source. The bacterial composition of the Noblejas Consortium (NC) was determined by sequencing 16S rRNA gene amplicon libraries. The consortium contained around 50 amplicon sequence variants (ASVs) and the major populations belonged to the genera Pseudomonas, Enterobacter, Delftia, Stenotrophomonas, Achromobacter, Acinetobacter, Novosphingobium, Allorhizobium-Neorhizobium-Rhizobium, Ochrobactrum and Luteibacter. All other genera were below 1%. Metagenomic analysis of NC has shown a high abundance of genes encoding enzymes implicated in aliphatic and (poly) aromatic hydrocarbons degradation, and almost all pathways for hydrocarbon degradation are represented. Metagenomic analysis has also allowed the construction of metagenome assembled genomes (MAGs) for the major players of NC. Metatranscriptomic analysis has shown that several of the ASVs are implicated in hydrocarbon degradation, being Pseudomonas, Acinetobacter and Delftia the most active populations.The microorganisms that inhabit food processing environments (FPE) can strongly influence the associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-resistant microorganisms, and a hotspot for the transmission of antibiotic resistance genes (ARGs) is a concern in meat processing plants. Here, we monitor microbial succession and resistome dynamics relating to FPE through a detailed analysis of a newly opened pork cutting plant over 1.5 years of activity.

Results

We identified a relatively restricted principal microbiota dominated byPseudomonasduring the first 2 months, while a higher taxonomic diversity, an increased representation of other taxa (e.g.,Acinetobacter,Psychrobacter), and a certain degree of microbiome specialization on different surfaces was recorded later on. An increase in total abundance, alpha diversity, and \uffce\uffb2-dispersion of ARGs, which were predominantly assigned toAcinetobacterand associated with resistance to certain antimicrobials frequently used on pig farms of the region, was detected over time. Moreover, a sharp increase in the occurrence of extended-spectrum \uffce\uffb2-lactamase-producingEnterobacteriaceaeand vancomycin-resistantEnterococcaceaewas observed when cutting activities started. ARGs associated with resistance to \uffce\uffb2-lactams, tetracyclines, aminoglycosides, and sulphonamides frequently co-occurred, and mobile genetic elements (i.e., plasmids, integrons) and lateral gene transfer events were mainly detected at the later sampling times in drains.

Conclusions

The observations made suggest that pig carcasses were a source of resistant bacteria that then colonized FPE and that drains, together with some food-contact surfaces, such as equipment and table surfaces, represented a reservoir for the spread of ARGs in the meat processing facility.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Bacteria", "Food Handling", "Swine", "Tecnolog\u00eda de los alimentos", "Research", "QR100-130", "610", "Food processing environments", "Antimicrobial resistance", "Gen\u00e9tica", "630", "Anti-Bacterial Agents", "Microbial ecology", "Red Meat", "03 medical and health sciences", "Genes", " Bacterial", "Pork Meat", "Animals", "Metagenomics"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1186/s40168-021-01131-9.pdf"}, {"href": "https://doi.org/10.1186/s40168-021-01131-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40168-021-01131-9", "name": "item", "description": "10.1186/s40168-021-01131-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-021-01131-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-10-14T00:00:00Z"}}, {"id": "10.3390/genes15010107", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:07Z", "type": "Journal Article", "created": "2024-01-16", "title": "Structural and Functional Shifts in the Microbial Community of a Heavy Metal-Contaminated Soil Exposed to Short-Term Changes in Air Temperature, Soil Moisture and UV Radiation", "description": "

The interplay between metal contamination and climate change may exacerbate the negative impact on the soil microbiome and, consequently, on soil health and ecosystem services. We assessed the response of the microbial community of a heavy metal-contaminated soil when exposed to short-term (48 h) variations in air temperature, soil humidity or ultraviolet (UV) radiation in the absence and presence of Enchytraeus crypticus (soil invertebrate). Each of the climate scenarios simulated significantly altered at least one of the microbial parameters measured. Irrespective of the presence or absence of invertebrates, the effects were particularly marked upon exposure to increased air temperature and alterations in soil moisture levels (drought and flood scenarios). The observed effects can be partly explained by significant alterations in soil properties such as pH, dissolved organic carbon, and water-extractable heavy metals, which were observed for all scenarios in comparison to standard conditions. The occurrence of invertebrates mitigated some of the impacts observed on the soil microbial community, particularly in bacterial abundance, richness, diversity, and metabolic activity. Our findings emphasize the importance of considering the interplay between climate change, anthropogenic pressures, and soil biotic components to assess the impact of climate change on terrestrial ecosystems and to develop and implement effective management strategies.

", "keywords": ["0301 basic medicine", "2. Zero hunger", "Soil invertebrates", "Soil microbiome", "Soil drought", "Ultraviolet Rays", "Soil pollution", "Microbiota", "Temperature", "Enchytraeus crypticus", "15. Life on land", "01 natural sciences", "Article", "6. Clean water", "Soil", "03 medical and health sciences", "13. Climate action", "UVR exposure", "Metals", " Heavy", "Climate change", "Soil flood", "Metagenomics", "Increased temperature", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.3390/genes15010107"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes15010107", "name": "item", "description": "10.3390/genes15010107", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes15010107"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-16T00:00:00Z"}}, {"id": "20.500.14243/459134", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:25:48Z", "type": "Journal Article", "created": "2023-09-19", "title": "Bacteriophages limitedly contribute to the antimicrobial resistome of microbial communities in wastewater treatment plants", "description": "ABSTRACT

Bacteriophages are known as players in the transmission of antimicrobial resistance genes (ARGs) by horizontal gene transfer. In this study, we characterized the bacteriophage community and the associated ARGs to estimate the potential for phages to spread ARGs in aquatic ecosystems analyzing the intra- and extracellular DNA isolated from two wastewater treatment plants (WWTPs) by shotgun metagenomics. We compared the phage antimicrobial resistome with the bacterial resistome and investigated the effect of the final disinfection treatment on the phage community and its resistome. Phage community was mainly composed by Siphoviridae and other members of the order Caudovirales . The final disinfection only marginally affected the composition of the phage community, and it was not possible to measure its effect on the antimicrobial resistome. Indeed, only three phage metagenome-assembled genomes (pMAGs) annotated as Siphoviridae , Padoviridae , and Myoviridae were positive for putative ARGs. Among the detected ARGs, i.e., dfr B6, rpo B mutants, and EF-Tu mutants, the first one was not annotated in the bacterial MAGs. Overall, these results demonstrate that bacteriophages limitedly contribute to the whole antimicrobial resistome. However, in order to obtain a comprehensive understanding of the antimicrobial resistome within a microbial community, the role of bacteriophages needs to be investigated.

IMPORTANCE

WWTPs are considered hotspots for the spread of ARGs by horizontal gene transfer. In this study, we evaluated the phage composition and the associated antimicrobial resistome by shotgun metagenomics of samples collected before and after the final disinfection treatment. Only a few bacteriophages carried ARGs. However, since one of the detected genes was not found in the bacterial metagenome-assembled genomes, it is necessary to investigate the phage community in order to gain a comprehensive overview of the antimicrobial resistome. This investigation could help assess the potential threats to human health.

", "keywords": ["metagenomics", "bacteriophages", "11. Sustainability", "Bacteriophages", "metagenomic assembled genomes", "antimicrobial resistance", "antimicrobial resistome", "wastewater treatment plants", "Microbiology", "6. Clean water", "QR1-502", "12. Responsible consumption", "Research Article"]}, "links": [{"href": "https://journals.asm.org/doi/pdf/10.1128/spectrum.01101-23"}, {"href": "https://doi.org/20.500.14243/459134"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiology%20Spectrum", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "20.500.14243/459134", "name": "item", "description": "20.500.14243/459134", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/20.500.14243/459134"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-10-17T00:00:00Z"}}, {"id": "10.3390/microorganisms8010013", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:11Z", "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": "10.3390/microorganisms11102412", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:11Z", "type": "Journal Article", "created": "2023-09-27", "title": "Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics", "description": "

The current focus on renewable energy in global policy highlights the importance of methane production from biomass through anaerobic digestion (AD). To improve biomass digestion while ensuring overall process stability, microbiome-based management strategies become more important. In this study, metagenomes and metaproteomes were used for metagenomically assembled genome (MAG)-centric analyses to investigate a full-scale biogas plant consisting of three differentially operated digesters. Microbial communities were analyzed regarding their taxonomic composition, functional potential, as well as functions expressed on the proteome level. Different abundances of genes and enzymes related to the biogas process could be mostly attributed to different process parameters. Individual MAGs exhibiting different abundances in the digesters were studied in detail, and their roles in the hydrolysis, acidogenesis and acetogenesis steps of anaerobic digestion could be assigned. Methanoculleus thermohydrogenotrophicum was an active hydrogenotrophic methanogen in all three digesters, whereas Methanothermobacter wolfeii was more prevalent at higher process temperatures. Further analysis focused on MAGs, which were abundant in all digesters, indicating their potential to ensure biogas process stability. The most prevalent MAG belonged to the class Limnochordia; this MAG was ubiquitous in all three digesters and exhibited activity in numerous pathways related to different steps of AD.

", "keywords": ["anaerobic digestion", "biogas process chain", "metagenome analyses", "13. Climate action", "QH301-705.5", "metagenomic binning", "biogas microbiome", "metaproteome analyses", "15. Life on land", "Biology (General)", "7. Clean energy", "Article", "660.6"]}, "links": [{"href": "https://www.mdpi.com/2076-2607/11/10/2412/pdf"}, {"href": "https://doi.org/10.3390/microorganisms11102412"}, {"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/microorganisms11102412", "name": "item", "description": "10.3390/microorganisms11102412", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/microorganisms11102412"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-09-27T00:00:00Z"}}, {"id": "10.3389/fmicb.2019.01347", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:20:54Z", "type": "Journal Article", "created": "2019-06-25", "title": "Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture", "description": "Microbial life usually takes place in a community where individuals interact, by competition for nutrients, cross-feeding, inhibition by end-products, but also by their spatial distribution. Lactic acid bacteria are prominent members of microbial communities responsible for food fermentations. Their niche in a community depends on their own properties as well as those of the other species. Here, we apply a computational approach, which uses only genomic and metagenomic information and functional annotation of genes, to find properties that distinguish a species from others in the community, as well as to follow individual species in a community. We analyzed isolated and sequenced strains from a kefir community, and metagenomes from wine fermentations. We demonstrate how the distinguishing properties of an organism lead to experimentally testable hypotheses concerning the niche and the interactions with other species. We observe, for example, that L. kefiranofaciens, a dominant organism in kefir, stands out among the Lactobacilli because it potentially has more amino acid auxotrophies. Using metagenomic analysis of industrial wine fermentations we investigate the role of an inoculated L. plantarum in malolactic fermentation. We observed that L. plantarum thrives better on white than on red wine fermentations and has the largest number of phosphotransferase system among the bacteria observed in the wine communities. Also, L. plantarum together with Pantoea, Erwinia, Asaia, Gluconobacter, and Komagataeibacter genera had the highest number of genes involved in biosynthesis of amino acids.", "keywords": ["0301 basic medicine", "metagenomics", "0303 health sciences", "microbial communities", "Microbial communities", "Wine", "Microbiology", "QR1-502", "Computational biology", "lactic acid bacteria", "03 medical and health sciences", "Kefir", "computational biology", "Lactic acid bacteria", "Metagenomics", "Genomes", "wine", "genomes"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2019.01347"}, {"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.2019.01347", "name": "item", "description": "10.3389/fmicb.2019.01347", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2019.01347"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-25T00:00:00Z"}}, {"id": "10.3389/fmicb.2019.02700", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:20:54Z", "type": "Journal Article", "created": "2019-12-06", "title": "Novel Isoprene-Degrading Proteobacteria From Soil and Leaves Identified by Cultivation and Metagenomics Analysis of Stable Isotope Probing Experiments", "description": "Isoprene is a climate-active gas and one of the most abundant biogenic volatile organic compounds (BVOC) released into the atmosphere. In the terrestrial environment, plants are the primary producers of isoprene, releasing between 500 and 750 million tons per year to protect themselves from environmental stresses such as direct radiation, heat, and reactive oxygen species. While many studies have explored isoprene production, relatively little is known about consumption of isoprene by microbes and the most well-characterized isoprene degrader is a Rhodococcus strain isolated from freshwater sediment. In order to identify a wider range of bacterial isoprene-degraders in the environment, DNA stable isotope probing (DNA-SIP) with 13C-labeled isoprene was used to identify active isoprene degraders associated with soil in the vicinity of a willow tree. Retrieval by PCR of 16S rRNA genes from the 13C-labeled DNA revealed an active isoprene-degrading bacterial community dominated by Proteobacteria, together with a minor portion of Actinobacteria, mainly of the genus Rhodococcus. Metagenome sequencing of 13C-labeled DNA from SIP experiments enabled analysis of genes encoding key enzymes of isoprene metabolism from novel isoprene degraders. Informed by these DNA-SIP experiments and working with leaves and soil from the vicinity of tree species known to produce high amounts of isoprene, four novel isoprene-degrading strains of the genera Nocardioides, Ramlibacter, Variovorax and Sphingopyxis, along with strains of Rhodococcus and Gordonia, genera that are known to contain isoprene-degrading strains, were isolated. The use of lower concentrations of isoprene during enrichment experiments has revealed active Gram-negative isoprene-degrading bacteria associated with isoprene-emitting trees. Analysis of isoprene-degradation genes from these new isolates provided a more robust phylogenetic framework for analysis of isoA, encoding the \u03b1-subunit of the isoprene monooxygenase, a key molecular marker gene for cultivation-independent studies on isoprene degradation in the terrestrial environment.", "keywords": ["0301 basic medicine", "570", "metagenomics", "0303 health sciences", "isoprene monooxygenase", "DNA-SIP", "isoA", "15. Life on land", "Microbiology", "630", "QR1-502", "03 medical and health sciences", "13. Climate action", "isoprene degradation"]}, "links": [{"href": "https://ueaeprints.uea.ac.uk/id/eprint/73457/2/Published_Version.pdf"}, {"href": "https://repository.essex.ac.uk/26315/1/fmicb-10-02700.pdf"}, {"href": "https://doi.org/10.3389/fmicb.2019.02700"}, {"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.2019.02700", "name": "item", "description": "10.3389/fmicb.2019.02700", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2019.02700"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-06T00:00:00Z"}}, {"id": "10.3390/genes10060424", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:07Z", "type": "Journal Article", "created": "2019-06-03", "title": "Effect of Long-Term Farming Practices on Agricultural Soil Microbiome Members Represented by Metagenomically Assembled Genomes (MAGs) and Their Predicted Plant-Beneficial Genes", "description": "

To follow the hypothesis that agricultural management practices affect structure and function of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) metagenome analyses were performed on Chernozem soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Metagenomic DNA was extracted from soil samples representing the following treatments: (i) plough tillage with standard nitrogen fertilization and use of fungicides and growth regulators, (ii) plough tillage with reduced nitrogen fertilization (50%), (iii) cultivator tillage with standard nitrogen fertilization and use of fungicides and growth regulators, and (iv) cultivator tillage with reduced nitrogen fertilization (50%). Bulk soil (BS), as well as root-affected soil (RS), were considered for all treatments in replicates. HT-sequencing of metagenomic DNA yielded approx. 100 Giga bases (Gb) of sequence information. Taxonomic profiling of soil communities revealed the presence of 70 phyla, whereby Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Thaumarchaeota, Firmicutes, Verrucomicrobia and Chloroflexi feature abundances of more than 1%. Functional microbiome profiling uncovered, i.a., numerous potential plant-beneficial, plant-growth-promoting and biocontrol traits predicted to be involved in nutrient provision, phytohormone synthesis, antagonism against pathogens and signal molecule synthesis relevant in microbe\uffe2\uff80\uff93plant interaction. Neither taxonomic nor functional microbiome profiling based on single-read analyses revealed pronounced differences regarding the farming practices applied. Soil metagenome sequences were assembled and taxonomically binned. The ten most reliable and abundant Metagenomically Assembled Genomes (MAGs) were taxonomically classified and metabolically reconstructed. Importance of the phylum Thaumarchaeota for the analyzed microbiome is corroborated by the fact that the four corresponding MAGs were predicted to oxidize ammonia (nitrification), thus contributing to the cycling of nitrogen, and in addition are most probably able to fix carbon dioxide. Moreover, Thaumarchaeota and several bacterial MAGs also possess genes with predicted functions in plant\uffe2\uff80\uff93growth\uffe2\uff80\uff93promotion. Abundances of certain MAGs (species resolution level) responded to the tillage practice, whereas the factors compartment (BS vs. RS) and nitrogen fertilization only marginally shaped MAG abundance profiles. Hence, soil management regimes promoting plant-beneficial microbiome members are very likely advantageous for the respective agrosystem, its health and carbon sequestration and accordingly may enhance plant productivity. Since Chernozem soils are highly fertile, corresponding microbiome data represent a valuable reference resource for agronomy in general.

", "keywords": ["0301 basic medicine", "570", "plant\u2013growth\u2013promotion (PGP)", "metagenomically-assembled-genomes (MAGs)", "Article", "03 medical and health sciences", "carbon dioxide fixation", "Ammonia", "metagenomic binning", "Germany", "soil microbiome", "Proteobacteria", "Humans", "biocontrol", "secondary metabolite synthesis", "suppressive soil", "Phylogeny", "Soil Microbiology", "soil microbiome; suppressive soil; biocontrol; plant\u2013growth\u2013promotion (PGP); metagenomic binning; metagenomically-assembled-genomes (MAGs); secondary metabolite synthesis; carbon dioxide fixation; carbohydrate-active enzymes; differentially abundant features (DAFs)", "2. Zero hunger", "Bacteria", "Bacteroidetes", "Agriculture", "differentially abundant features (DAFs)", "15. Life on land", "Archaea", "Actinobacteria", "carbohydrate-active enzymes", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/424/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/424/pdf"}, {"href": "https://doi.org/10.3390/genes10060424"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes10060424", "name": "item", "description": "10.3390/genes10060424", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes10060424"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-03T00:00:00Z"}}, {"id": "10.3390/genes10060456", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:07Z", "type": "Journal Article", "created": "2019-06-14", "title": "Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil", "description": "

Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.

", "keywords": ["0301 basic medicine", "TPH", "consortium", "Article", "diesel", "03 medical and health sciences", "PAHs", "rhizoremediation", "Pseudomonas", "RNA", " Ribosomal", " 16S", "11. Sustainability", "Soil Pollutants", "Polycyclic Aromatic Hydrocarbons", "bacteria", "Phylogeny", "Soil Microbiology", "Chryseobacterium", "2. Zero hunger", "metagenomics", "rhizoremediation; diesel; bacteria; consortium; metagenomics; PAHs; TPH", "0303 health sciences", "Microbiota", "Biodiversity", "15. Life on land", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "Rhizoremediation", "Biodegradation", " Environmental", "Petroleum", "13. Climate action", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://doi.org/10.3390/genes10060456"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes10060456", "name": "item", "description": "10.3390/genes10060456", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes10060456"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-14T00:00:00Z"}}, {"id": "10.5061/dryad.h781v", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:21:44Z", "type": "Dataset", "title": "Data from: The microbially-mediated soil organic carbon loss under degenerative succession in an alpine meadow", "description": "unspecifiedMicrobial community and network of meadow alpine soil by Illumina sequencingThe Qinghai-Tibet Plateau is the highest and the largest low-latitude plateau in the world, and also it is an extremely sensitive region to the impact of global warming and environmental changes. The alpine meadow, widely distributed on the Tibetan Plateau, occupies over 40% of the Qinghai-Tibetan Plateau area and plays a critical role in regional sustainable development, biodiversity and water resource conservation. The alpine meadow also was a large soil organic-carbon pool.In recently decades, succession and degradation were gradually occurring between different alpine meadow types, such as alpine meadow might appear in the alpine steppe meadow region according to years of field investigation which could be the consequences of the climate warming and anthropogenic activities. The aims of our study were to determine the effect of degenerated succession from alpine meadow (AM) to alpine steppe meadow (ASM) on soil organic carbon and soil microbial community structure.The archived files included one OTU table generated from the 16S rRNA gene sequencing data, as well as the input and output files for the network analyses.Dryad data deposit.7z", "keywords": ["2. Zero hunger", "soil organic carbon", "16S rDNA sequencing", "ecological function", "13. Climate action", "soil microbes", "Microbial community", "15. Life on land", "Land Cover Change", "6. Clean water", "Metagenomic analysis", "12. Responsible consumption"], "contacts": [{"organization": "Zhang, Yuguang, Liu, Xiao, Cong, Jing, Lu, Hui, Sheng, Yuyu, Wang, Xiulei, Li, Diqiang, Liu, Xueduan, Yin, Huaqun, Zhou, Jizhong, Deng, Ye,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.h781v"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.h781v", "name": "item", "description": "10.5061/dryad.h781v", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.h781v"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-04-19T00:00:00Z"}}, {"id": "PMC7022856", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:28:44Z", "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", "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/PMC7022856"}, {"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": "PMC7022856", "name": "item", "description": "PMC7022856", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PMC7022856"}, {"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.14989604", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:23:01Z", "type": "Software", "title": "Metagenomics-Toolkit: The Flexible and Efficient Cloud-Based Metagenomics Workflow featuring Machine Learning-Enabled Resource Allocation", "description": "The Metagenomics-Toolkit is a scalable, data agnostic workflow that automates the analysis of short and long metagenomic reads obtained from Illumina or Oxford Nanopore Technology devices, respectively. The Toolkit offers not only standard features expected in a metagenome workflow, such as quality control, assembly, binning, and annotation, but also distinctive features, such as plasmid identification based on various tools, the recovery of unassembled microbial community members, and the discovery of microbial interdependencies through a combination of dereplication, co-occurrence, and genome-scale metabolic modeling. Furthermore, the Metagenomics-Toolkit includes a machine learning-optimized assembly step that tailors the peak RAM value requested by a metagenome assembler to match actual requirements, thereby minimizing the dependency on dedicated high-memory hardware. Quickstart and documentation can be found at https://github.com/metagenomics/metagenomics-tk", "keywords": ["Metagenomics/methods", "Cloud Computing", "Workflow"], "contacts": [{"organization": "Belmann, Peter, Osterholz, Benedikt, Kleinb\u00f6lting, Nils, P\u00fchler, Alfred, Schl\u00fcter, Andreas, Sczyrba, Alexander,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.14989604"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.14989604", "name": "item", "description": "10.5281/zenodo.14989604", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.14989604"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-03-07T00:00:00Z"}}, {"id": "10.5281/zenodo.17710964", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:23:25Z", "type": "Dataset", "title": "Dataset for: Metagenomic Insights Into Microbial Controls of Carbon Cycling in Alpine Soils", "description": "Dataset for: Metagenomic Insights Into Microbial Controls of Carbon Cycling in Alpine Soils. Manuscript and Supporting Information published as preprint on biorxiv: https://doi.org/10.1101/2025.09.22.677713", "keywords": ["soil redox dynamics", "microbial metabolism", "Soil organic carbon", "Alpine riparian soils", "microbial community composition", "shotgun metagenomics"], "contacts": [{"organization": "Bright, Kristina, Dienes, Bence, van Dongen, Bart, Strashnov, Ilya, Han, Xingguo, Aeppli, Meret,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5281/zenodo.17710964"}, {"rel": "self", "type": "application/geo+json", "title": "10.5281/zenodo.17710964", "name": "item", "description": "10.5281/zenodo.17710964", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.17710964"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2025-11-25T00:00:00Z"}}, {"id": "10400.14/44005", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:24:57Z", "type": "Journal Article", "created": "2024-01-16", "title": "Structural and Functional Shifts in the Microbial Community of a Heavy Metal-Contaminated Soil Exposed to Short-Term Changes in Air Temperature, Soil Moisture and UV Radiation", "description": "

The interplay between metal contamination and climate change may exacerbate the negative impact on the soil microbiome and, consequently, on soil health and ecosystem services. We assessed the response of the microbial community of a heavy metal-contaminated soil when exposed to short-term (48 h) variations in air temperature, soil humidity or ultraviolet (UV) radiation in the absence and presence of Enchytraeus crypticus (soil invertebrate). Each of the climate scenarios simulated significantly altered at least one of the microbial parameters measured. Irrespective of the presence or absence of invertebrates, the effects were particularly marked upon exposure to increased air temperature and alterations in soil moisture levels (drought and flood scenarios). The observed effects can be partly explained by significant alterations in soil properties such as pH, dissolved organic carbon, and water-extractable heavy metals, which were observed for all scenarios in comparison to standard conditions. The occurrence of invertebrates mitigated some of the impacts observed on the soil microbial community, particularly in bacterial abundance, richness, diversity, and metabolic activity. Our findings emphasize the importance of considering the interplay between climate change, anthropogenic pressures, and soil biotic components to assess the impact of climate change on terrestrial ecosystems and to develop and implement effective management strategies.

", "keywords": ["2. Zero hunger", "0301 basic medicine", "Soil invertebrates", "Soil microbiome", "Soil drought", "Ultraviolet Rays", "Soil pollution", "Microbiota", "Temperature", "Enchytraeus crypticus", "15. Life on land", "01 natural sciences", "Article", "6. Clean water", "Soil", "03 medical and health sciences", "13. Climate action", "UVR exposure", "Metals", " Heavy", "Climate change", "Soil flood", "Metagenomics", "Increased temperature", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10400.14/44005"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10400.14/44005", "name": "item", "description": "10400.14/44005", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10400.14/44005"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-16T00:00:00Z"}}, {"id": "10449/84316", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:24:59Z", "type": "Journal Article", "created": "2024-02-19", "title": "Novel endolithic bacteria of phylum Chloroflexota reveal a myriad of potential survival strategies in the Antarctic desert", "description": "ABSTRACT

The ice-free McMurdo Dry Valleys of Antarctica are dominated by nutrient-poor mineral soil and rocky outcrops. The principal habitat for microorganisms is within rocks (endolithic). In this environment, microorganisms are provided with protection against sub-zero temperatures, rapid thermal fluctuations, extreme dryness, and ultraviolet and solar radiation. Endolithic communities include lichen, algae, fungi, and a diverse array of bacteria. Chloroflexota is among the most abundant bacterial phyla present in these communities. Among the Chloroflexota are four novel classes of bacteria, here named Candidatus Spiritibacteria class. nov. (=UBA5177), Candidatus Martimicrobia class. nov. (=UBA4733), Candidatus Tarhunnaeia class. nov. (=UBA6077), and Candidatus Uliximicrobia class. nov. (=UBA2235). We retrieved 17 high-quality metagenome-assembled genomes (MAGs) that represent these four classes. Based on genome predictions, all these bacteria are inferred to be aerobic heterotrophs that encode enzymes for the catabolism of diverse sugars. These and other organic substrates are likely derived from lichen, algae, and fungi, as metabolites (including photosynthate), cell wall components, and extracellular matrix components. The majority of MAGs encode the capacity for trace gas oxidation using high-affinity uptake hydrogenases, which could provide energy and metabolic water required for survival and persistence. Furthermore, some MAGs encode the capacity to couple the energy generated from H 2 and CO oxidation to support carbon fixation (atmospheric chemosynthesis). All encode mechanisms for the detoxification and efflux of heavy metals. Certain MAGs encode features that indicate possible interactions with other organisms, such as Tc-type toxin complexes, hemolysins, and macroglobulins.

IMPORTANCE

The ice-free McMurdo Dry Valleys of Antarctica are the coldest and most hyperarid desert on Earth. It is, therefore, the closest analog to the surface of the planet Mars. Bacteria and other microorganisms survive by inhabiting airspaces within rocks (endolithic). We identify four novel classes of phylum Chloroflexota , and, based on interrogation of 17 metagenome-assembled genomes, we predict specific metabolic and physiological adaptations that facilitate the survival of these bacteria in this harsh environment\uffe2\uff80\uff94including oxidation of trace gases and the utilization of nutrients (including sugars) derived from lichen, algae, and fungi. We propose that such adaptations allow these endolithic bacteria to eke out an existence in this cold and extremely dry habitat.

", "keywords": ["570", "Bacteria", "Fungi", "Antarctic Regions", "Chloroflexi", "15. Life on land", "Survival strategies", "Cold Temperature", "Extremophiles", "13. Climate action", "Antarctica", "Endolithic communities", "Metagenomics", "14. Life underwater", "Sugars", "Settore BIO/19 - MICROBIOLOGIA GENERALE"]}, "links": [{"href": "https://doi.org/10449/84316"}, {"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": "10449/84316", "name": "item", "description": "10449/84316", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10449/84316"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-02-19T00:00:00Z"}}, {"id": "10486/701388", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:25:01Z", "type": "Journal Article", "created": "2021-03-15", "title": "Soil Microbiome Structure and Function in Ecopiles Used to Remediate Petroleum-Contaminated Soil", "description": "

The soil microbiome consists of a vast variety of microorganisms which contribute to essential ecosystem services including nutrient recycling, protecting soil structure, and pathogen suppression. Recalcitrant organic compounds present in soils contaminated with fuel oil can lead to a decrease in functional redundancy within soil microbiomes. Ecopiling is a passive bioremediation technique involving biostimulation of indigenous hydrocarbon degraders, bioaugmentation through inoculation with known petroleum-degrading consortia, and phytoremediation. The current study investigates the assemblage of soil microbial communities and pollutant-degrading potential in soil undergoing the Ecopiling process, through the amplicon marker gene and metagenomics analysis of the contaminated soil. The analysis of key community members including bacteria, fungi, and nematodes revealed a surprisingly diverse microbial community composition within the contaminated soil. The soil bacterial community was found to be dominated by Alphaproteobacteria (60\uffe2\uff80\uff9370%) with the most abundant genera such as Lysobacter, Dietzia, Pseudomonas, and Extensimonas. The fungal community consisted mainly of Ascomycota (50\uffe2\uff80\uff9370% relative abundance). Soil sequencing data allowed the identification of key enzymes involved in the biodegradation of hydrocarbons, providing a novel window into the function of individual bacterial groups in the Ecopile. Although the genus Lysobacter was identified as the most abundant bacterial genus (11\uffe2\uff80\uff9346%) in all of the contaminated soil samples, the metagenomic data were unable to confirm a role for this group in petrochemical degradation. Conversely, genera with relatively low abundance such as Dietzia (0.4\uffe2\uff80\uff939.0%), Pusillimonas (0.7\uffe2\uff80\uff932.3%), and Bradyrhizobium (0.8\uffe2\uff80\uff931.8%) did possess genes involved in aliphatic or aromatic compound degradation.

Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.

", "keywords": ["0301 basic medicine", "TPH", "consortium", "Article", "diesel", "03 medical and health sciences", "PAHs", "rhizoremediation", "Pseudomonas", "RNA", " Ribosomal", " 16S", "11. Sustainability", "Soil Pollutants", "Polycyclic Aromatic Hydrocarbons", "bacteria", "Phylogeny", "Soil Microbiology", "Chryseobacterium", "2. Zero hunger", "metagenomics", "rhizoremediation; diesel; bacteria; consortium; metagenomics; PAHs; TPH", "0303 health sciences", "Microbiota", "Biodiversity", "15. Life on land", "Biolog\u00eda y Biomedicina / Biolog\u00eda", "Rhizoremediation", "Biodegradation", " Environmental", "Petroleum", "13. Climate action", "Metagenome"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://www.mdpi.com/2073-4425/10/6/456/pdf"}, {"href": "https://doi.org/10486/713957"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10486/713957", "name": "item", "description": "10486/713957", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10486/713957"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-14T00:00:00Z"}}, {"id": "10486/717838", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:25:02Z", "type": "Journal Article", "created": "2024-09-28", "title": "Metagenomic analyses of a consortium for the bioremediation of hydrocarbons polluted soils", "description": "Abstract

A bacterial consortium was isolated from a soil in Noblejas (Toledo, Spain) with a long history of mixed hydrocarbons pollution, by enrichment cultivation. Serial cultures of hydrocarbons polluted soil samples were grown in a minimal medium using diesel (1\uffc2\uffa0mL/L) as the sole carbon and energy source. The bacterial composition of the Noblejas Consortium (NC) was determined by sequencing 16S rRNA gene amplicon libraries. The consortium contained around 50 amplicon sequence variants (ASVs) and the major populations belonged to the genera Pseudomonas, Enterobacter, Delftia, Stenotrophomonas, Achromobacter, Acinetobacter, Novosphingobium, Allorhizobium-Neorhizobium-Rhizobium, Ochrobactrum and Luteibacter. All other genera were below 1%. Metagenomic analysis of NC has shown a high abundance of genes encoding enzymes implicated in aliphatic and (poly) aromatic hydrocarbons degradation, and almost all pathways for hydrocarbon degradation are represented. Metagenomic analysis has also allowed the construction of metagenome assembled genomes (MAGs) for the major players of NC. Metatranscriptomic analysis has shown that several of the ASVs are implicated in hydrocarbon degradation, being Pseudomonas, Acinetobacter and Delftia the most active populations.

We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community\u2019s response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 \u00b0C + 50% water holding capacity (WHC)); increased air temperature (15\u201325 \u00b0C or 20\u201330 \u00b0C + 50% WHC); flood (20 \u00b0C + 75% WHC); drought (20 \u00b0C + 25% WHC); and ultraviolet radiation (UV) (20 \u00b0C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community\u2019s physiological profile and the bacterial community\u2019s structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20\u201330 \u00b0C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome\u2013invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed.

", "keywords": ["0301 basic medicine", "Soil invertebrates", "Ultraviolet Rays", "drought", "microbial activity", "DNA", " Ribosomal", "Flood", "Article", "Quantitative PCR", "Soil", "03 medical and health sciences", "soil microbiome", "2. Zero hunger", "metagenomics", "increased temperature; drought; flood; UV exposure; microbial activity; bacterial diversity; metagenomics; quantitative PCR; soil microbiome; soil invertebrates", "Soil microbiome", "0303 health sciences", "Drought", "Bacteria", "Microbiota", "bacterial diversity", "Temperature", "Water", "flood", "15. Life on land", "soil invertebrates", "6. Clean water", "UV exposure", "Microbial activity", "Bacterial diversity", "13. Climate action", "quantitative PCR", "Metagenomics", "Increased temperature", "increased temperature"]}, "links": [{"href": "http://www.mdpi.com/2073-4425/13/5/850/pdf"}, {"href": "https://doi.org/10400.14/37827"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10400.14/37827", "name": "item", "description": "10400.14/37827", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10400.14/37827"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-05-10T00:00:00Z"}}, {"id": "10449/83878", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-29T16:24:59Z", "type": "Journal Article", "created": "2023-10-27", "title": "Geology and elevation shape bacterial assembly in Antarctic endolithic communities", "description": "Ice free areas of continental Antarctica are among the coldest and driest environments on Earth, and yet, they support surprisingly diverse and highly adapted microbial communities. Endolithic growth is one of the key adaptations to such extreme environments and often represents the dominant life-form. Despite growing scientific interest, little is known of the mechanisms that influence the assembly of endolithic microbiomes across these harsh environments. Here, we used metagenomics to examine the diversity and assembly of endolithic bacterial communities across Antarctica within different rock types and over a large elevation range. While granite supported richer and more heterogeneous communities than sandstone, elevation had no apparent effect on taxonomic richness, regardless of rock type. Conversely, elevation was clearly associated with turnover in community composition, with the deterministic process of variable selection driving microbial assembly along the elevation gradient. The turnover associated with elevation was modulated by geology, whereby for a given elevation difference, turnover was consistently larger between communities inhabiting different rock types. Overall, selection imposed by elevation and geology appeared stronger than turnover related to other spatially-structured environmental drivers. Our findings indicate that at the cold-arid limit of life on Earth, geology and elevation are key determinants of endolithic bacterial heterogeneity. This also suggests that warming temperatures may threaten the persistence of such extreme-adapted organisms.", "keywords": ["570", "Endolithic microbiome", "Shotgun metagenomics", "550", "Community assembly", "Settore BIO/07 - ECOLOGIA", "Altitude", "Granite", "Antarctica", "Sandstone"]}, "links": [{"href": "https://openpub.fmach.it/bitstream/10449/83878/1/2024%20STE%20Larsen.pdf"}, {"href": "https://doi.org/10449/83878"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Science%20of%20The%20Total%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10449/83878", "name": "item", "description": "10449/83878", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10449/83878"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-01-01T00:00:00Z"}}], "links": [{"rel": "self", "type": "application/geo+json", "title": "This document as GeoJSON", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=metagenomic&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=metagenomic&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=metagenomic&", "hreflang": "en-US"}, {"rel": "next", "type": "application/geo+json", "title": "items (next)", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items?keywords=metagenomic&offset=50", "hreflang": "en-US"}], "numberMatched": 70, "numberReturned": 50, "distributedFeatures": [], "timeStamp": "2026-05-30T10:10:24.417553Z"}