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.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": "10.3389/fmicb.2016.01247", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:21:36Z", "type": "Journal Article", "created": "2016-08-08", "title": "Soil Fungal:Bacterial Ratios Are Linked to Altered Carbon Cycling", "description": "Despite several lines of observational evidence, there is a lack of consensus on whether higher fungal:bacterial (F:B) ratios directly cause higher soil carbon (C) storage. We employed RNA sequencing, protein profiling and isotope tracer techniques to evaluate whether differing F:B ratios are associated with differences in C storage. A mesocosm (13)C labeled foliar litter decomposition experiment was performed in two soils that were similar in their physico-chemical properties but differed in microbial community structure, specifically their F:B ratio (determined by PLFA analyses, RNA sequencing and protein profiling; all three corroborating each other). Following litter addition, we observed a consistent increase in abundance of fungal phyla; and greater increases in the fungal dominated soil; implicating the role of fungi in litter decomposition. Litter derived (13)C in respired CO2 was consistently lower, and residual (13)C in bulk SOM was higher in high F:B soil demonstrating greater C storage potential in the F:B dominated soil. We conclude that in this soil system, the increased abundance of fungi in both soils and the altered C cycling patterns in the F:B dominated soils highlight the significant role of fungi in litter decomposition and indicate that F:B ratios are linked to higher C storage potential.", "keywords": ["Microbiology (medical)", "Proteomics", "0301 basic medicine", "environment/Bioclimatology", "Supplementary Data", "[SDE.MCG]Environmental Sciences/Global Changes", "stable isotopes", "litter decomposition", "Microbiology", "03 medical and health sciences", "proteomics", "[SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry", "[SDV.EE]Life Sciences [q-bio]/Ecology", "[SDU.STU.GC] Sciences of the Universe [physics]/Earth Sciences/Geochemistry", "soil carbon", "European Commission", "bacteria", "Stable isotopes", "2. Zero hunger", "655240", "0303 health sciences", "Bacteria", "Litter decomposition", "Fungi", "RNA sequencing", "QR Microbiology", "15. Life on land", "Soil carbon", "[SDU.ENVI] Sciences of the Universe [physics]/Continental interfaces", " environment", "QR1-502", "6. Clean water", "QR", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "[SDE.MCG] Environmental Sciences/Global Changes", "[SDV.EE] Life Sciences [q-bio]/Ecology", " environment", "[SDV.EE.BIO] Life Sciences [q-bio]/Ecology", " environment/Bioclimatology", "[SDV.EE.BIO]Life Sciences [q-bio]/Ecology", "fungi", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "[SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces", "environment"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2016.01247"}, {"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.2016.01247", "name": "item", "description": "10.3389/fmicb.2016.01247", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2016.01247"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-08-09T00:00:00Z"}}, {"id": "2164/13228", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:26:58Z", "type": "Journal Article", "created": "2016-08-08", "title": "Soil Fungal:Bacterial Ratios Are Linked to Altered Carbon Cycling", "description": "Despite several lines of observational evidence, there is a lack of consensus on whether higher fungal:bacterial (F:B) ratios directly cause higher soil carbon (C) storage. We employed RNA sequencing, protein profiling and isotope tracer techniques to evaluate whether differing F:B ratios are associated with differences in C storage. A mesocosm (13)C labeled foliar litter decomposition experiment was performed in two soils that were similar in their physico-chemical properties but differed in microbial community structure, specifically their F:B ratio (determined by PLFA analyses, RNA sequencing and protein profiling; all three corroborating each other). Following litter addition, we observed a consistent increase in abundance of fungal phyla; and greater increases in the fungal dominated soil; implicating the role of fungi in litter decomposition. Litter derived (13)C in respired CO2 was consistently lower, and residual (13)C in bulk SOM was higher in high F:B soil demonstrating greater C storage potential in the F:B dominated soil. We conclude that in this soil system, the increased abundance of fungi in both soils and the altered C cycling patterns in the F:B dominated soils highlight the significant role of fungi in litter decomposition and indicate that F:B ratios are linked to higher C storage potential.", "keywords": ["Microbiology (medical)", "Proteomics", "0301 basic medicine", "environment/Bioclimatology", "Supplementary Data", "[SDE.MCG]Environmental Sciences/Global Changes", "stable isotopes", "litter decomposition", "Microbiology", "03 medical and health sciences", "proteomics", "[SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry", "[SDV.EE]Life Sciences [q-bio]/Ecology", "[SDU.STU.GC] Sciences of the Universe [physics]/Earth Sciences/Geochemistry", "soil carbon", "European Commission", "bacteria", "Stable isotopes", "2. Zero hunger", "655240", "0303 health sciences", "Bacteria", "Litter decomposition", "Fungi", "RNA sequencing", "QR Microbiology", "15. Life on land", "Soil carbon", "[SDU.ENVI] Sciences of the Universe [physics]/Continental interfaces", " environment", "QR1-502", "6. Clean water", "QR", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "[SDE.MCG] Environmental Sciences/Global Changes", "[SDV.EE] Life Sciences [q-bio]/Ecology", " environment", "[SDV.EE.BIO] Life Sciences [q-bio]/Ecology", " environment/Bioclimatology", "[SDV.EE.BIO]Life Sciences [q-bio]/Ecology", "fungi", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "[SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces", "environment"]}, "links": [{"href": "https://doi.org/2164/13228"}, {"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": "2164/13228", "name": "item", "description": "2164/13228", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2164/13228"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-08-09T00:00:00Z"}}, {"id": "2164/15058", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-27T16:26:58Z", "type": "Journal Article", "created": "2017-03-19", "title": "Bacterial physiological adaptations to contrasting edaphic conditions identified using landscape scale metagenomics", "description": "AbstractEnvironmental 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.