We studied the dominant protists found in soils across the globe and their contributions to belowground food webs.
The ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co\uffe2\uff80\uff90occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co\uffe2\uff80\uff90occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator. Temperature was the major environmental driver of the relative abundance of ecological clusters when Australia and Antarctica are analyzed together. Temperature, aridity, soil properties and vegetation types were the major drivers of the relative abundance of different ecological clusters within Australia. Our data supports significant reductions in the diversity of bacteria, archaea and eukaryotes in Antarctica vs. Australia linked to strong reductions in temperature. However, we only detected small latitudinal variations in soil biodiversity within Australia. Different environmental drivers regulate the diversity of soil archaea (temperature and soil carbon), bacteria (aridity, vegetation attributes and pH) and eukaryotes (vegetation type and soil carbon) across Australia. Together, our findings provide new insights into the mechanisms driving soil biodiversity in the Southern Hemisphere.Natural products present an environmentally attractive alternative to synthetic pesticides which have been implicated in the off\uffe2\uff80\uff90target effect. Currently, the assessment of pesticide toxicity on soil microorganisms relies on the OECD 216 N transformation assay (OECD stands for the Organisation Economic Co\uffe2\uff80\uff90operation and Development, which is a key international standard\uffe2\uff80\uff90setting organisation). We tested the hypotheses that (i) the OECD 216 assay fails to identify unacceptable effects of pesticides on soil microbiota compared to more advanced molecular and standardized tests, and (ii) the natural products tested (dihydrochalcone, isoflavone, aliphatic phenol, and spinosad) are less toxic to soil microbiota compared to a synthetic pesticide compound (3,5\uffe2\uff80\uff90dichloraniline). We determined the following in three different soils: (i) ammonium (NH4+) and nitrate (NO3\uffe2\uff88\uff92) soil concentrations, as dictated by the OECD 216 test, and (ii) the abundance of phylogenetically (bacteria and fungi) and functionally distinct microbial groups [ammonia\uffe2\uff80\uff90oxidizing archaea (AOA) and bacteria (AOB)] using quantitative polymerase chain reaction (q\uffe2\uff80\uff90PCR).
RESULTSAll pesticides tested exhibited limited persistence, with spinosad demonstrating the highest persistence. None of the pesticides tested showed clear dose\uffe2\uff80\uff90dependent effects on NH4+ and NO3\uffe2\uff88\uff92 levels and the observed effects were <25% of the control, suggesting no unacceptable impacts on soil microorganisms. In contrast, q\uffe2\uff80\uff90PCR measurements revealed (i) distinct negative effects on the abundance of total bacteria and fungi, which were though limited to one of the studied soils, and (ii) a significant reduction in the abundance of both AOA and AOB across soils. This reduction was attributed to both natural products and 3,5\uffe2\uff80\uff90dichloraniline.
CONCLUSIONOur findings strongly advocate for a revision of the current regulatory framework regarding the toxicity of pesticides to soil microbiota, which should integrate advanced and well\uffe2\uff80\uff90standardized tools. \uffc2\uffa9 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two\uffe2\uff80\uff90year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biological soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.
", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Colorado", "Nitrogen", "Fungi", "15. Life on land", "Plants", "Archaea", "Grassland", "Soil", "03 medical and health sciences", "13. Climate action", "Rhizosphere", "Biomass", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/1462-2920.13678"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1462-2920.13678", "name": "item", "description": "10.1111/1462-2920.13678", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.13678"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-03-13T00:00:00Z"}}, {"id": "10.1007/s12275-012-2409-6", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:15:10Z", "type": "Journal Article", "created": "2012-11-03", "title": "Characterization Of The Bacterial And Archaeal Communities In Rice Field Soils Subjected To Long-Term Fertilization Practices", "description": "The bacterial and archaeal communities in rice field soils subjected to different fertilization regimes for 57 years were investigated in two different seasons, a non-planted, drained season (April) and a rice-growing, flooded season (August), by performing soil dehydrogenase assay, real-time PCR assay and pyrosequencing analysis. All fertilization regimes increased the soil dehydrogenase activity while the abundances of bacteria and archaea increased in the plots receiving inorganic fertilizers plus compost and not in those receiving inorganic fertilizers only. Rice-growing and flooding decreased the soil dehydrogenase activity while they increased the bacterial diversity in rice field soils. The bacterial communities were dominated by Chloroflexi, Proteobacteria, and Actinobacteria and the archaeal communities by Crenarchaeota at the phylum level. In principal coordinates analysis based on the weighted Fast UniFrac metric, the bacterial and archaeal communities were separated primarily by season, and generally distributed along with soil pH, the variation of which had been caused by long-term fertilization. Variations in the relative abundance according to the season or soil pH were observed for many bacterial and archaeal groups. In conclusion, the microbial activity, prokaryotic abundance and diversity, and prokaryotic community structure in the rice field soils were changed by season and long-term fertilization.", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Bacteria", "Molecular Sequence Data", "Agriculture", "Oryza", "15. Life on land", "Archaea", "6. Clean water", "Soil", "03 medical and health sciences", "RNA", " Ribosomal", " 16S", "Seasons", "Fertilizers", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s12275-012-2409-6"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s12275-012-2409-6", "name": "item", "description": "10.1007/s12275-012-2409-6", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s12275-012-2409-6"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-10-01T00:00:00Z"}}, {"id": "10.1016/j.apsoil.2017.09.041", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:15:37Z", "type": "Journal Article", "created": "2017-11-20", "title": "Ammonia-Oxidizing Archaea Are More Sensitive Than Ammonia-Oxidizing Bacteria To Long-Term Application Of Green Manure In Red Paddy Soil", "description": "Abstract Growing winter green manure is an effective method for improving nitrogen (N) management in paddy fields to enhance rice production. Ammonia oxidization is a key process in N cycling in these soils, but effects of green manuring on ammonia oxidizers have not been fully addressed for red paddy soils. The objective of this study was to investigate long-term impacts of winter green manure on abundance and diversity of ammonia oxidizers in rice paddy soils of Southern China. The field experiment established in 1982 included four treatments: rice-rice-winter fallow (RRF), rice-rice-ryegrass (RRG), rice\u2013rice\u2013rape (RRP) and rice\u2013rice\u2013milk vetch (RRV). The abundance and diversity of amoA genes from ammonia-oxidizing archaea (AOA) and bacteria (AOB) were quantified using quantitative PCR and 454 pyrosequencing, respectively. The AOA were more abundant than AOB in red paddy soils, with ratios of AOA to AOB from 36 to 1686. Long-term application of milk vetch increased the abundance of both AOA and AOB after green manures were incorporated. Some of the relative abundances of most abundant operational taxonomic units (OTUs) of AOA increased and others decreased after application of green manures, while most abundant OTUs of AOB remained unaffected. Redundancy analysis (RDA) found a clear separation between milk vetch and winter fallow, indicating that the community structure of AOA was influenced by application of milk vetch. Phylogenetic analysis showed that the most dominant OTUs of AOA and AOB were affiliated with Nitrososphaera and Nitrosospira, respectively. In conclusion, in red paddy soil, long-term application of milk vetch increased the abundances of AOA and AOB after incorporated. Moreover, long-term application of green manures had more profound influences on AOA community than on AOB in red paddy soils.", "keywords": ["Ammonia-oxidizing bacteria", "0301 basic medicine", "2. Zero hunger", "03 medical and health sciences", "Paddy soil", "Green manure", "0401 agriculture", " forestry", " and fisheries", "04 agricultural and veterinary sciences", "15. Life on land", "6. Clean water", "Ammonia-oxidizing archaea"], "contacts": [{"organization": "Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture/Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China ( host institution ), Gao, Songjuan ( author ), Cao, Weidong ( author ), Zou, Chunqin ( author ), Gao, Jusheng ( author ), Huang, Jing ( author ), Bai, Jinshun ( author ), Zeng, Naohua ( author ), Shimizu, Katsu-yoshi ( author ), Wright, Alan ( UF author ), Dou, Fugen ( author ),", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1016/j.apsoil.2017.09.041"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20Soil%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.apsoil.2017.09.041", "name": "item", "description": "10.1016/j.apsoil.2017.09.041", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.apsoil.2017.09.041"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-03-01T00:00:00Z"}}, {"id": "10.1016/j.biortech.2019.122033", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:15:42Z", "type": "Journal Article", "created": "2019-08-18", "title": "High rate continuous biohydrogen production by hyperthermophilic Thermotoga neapolitana", "description": "This study focused on continuous-flow hydrogen production by Thermotoga neapolitana at a hydraulic retention time (HRT) decreasing from 24 to 5\u202fh. At each HRT reduction, the hydrogen yield (HY) immediately dropped, but recovered during prolonged cultivation at constant HRT. The final HY in each operating period decreased from 3.4 (\u00b10.1) to 2.0 (\u00b10.0) mol H2/mol glucose when reducing the HRT from 24 to 7\u202fh. Simultaneously, the hydrogen production rate (HPR) and the liquid phase hydrogen concentration (H2aq) increased from 82 (\u00b11) to 192 (\u00b14) mL/L/h and from 9.1 (\u00b10.3) to 15.6 (\u00b10.7) mL/L, respectively. Additionally, the effluent glucose concentration increased from 2.1 (\u00b10.1) to above 10\u202fmM. Recirculating H2-rich biogas prevented the supersaturation of H2aq reaching a value of 9.3 (\u00b10.7) mL/L, resulting in complete glucose consumption and the highest HPR of 277\u202fmL/L/h at an HRT of 5\u202fh.", "keywords": ["0211 other engineering and technologies", "02 engineering and technology", "Acetic acid", "Archaea", "01 natural sciences", "7. Clean energy", "Continuous-flow dark fermentation", "Thermotoga neapolitana", "Acetic acid; Continuous-flow dark fermentation; Gas recirculation; Hydraulic retention time; Hydrogen; Thermotoga neapolitana", "Bioreactors", "Glucose", "Fermentation", "Gas recirculation", "Hydraulic retention time", "Hydrogen", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/758593/1/Post-print%20for%20IRIS.pdf"}, {"href": "https://doi.org/10.1016/j.biortech.2019.122033"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bioresource%20Technology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.biortech.2019.122033", "name": "item", "description": "10.1016/j.biortech.2019.122033", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.biortech.2019.122033"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-12-01T00:00:00Z"}}, {"id": "10.1016/j.chemosphere.2019.02.158", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:15:47Z", "type": "Journal Article", "created": "2019-02-25", "title": "Bioreduction of selenate in an anaerobic biotrickling filter using methanol as electron donor", "description": "The anaerobic bioreduction of selenate, fed in step (up to 60\u202fmg.L-1) or continuous (\u223c7\u202fmg.L-1) trickling mode, in the presence of gas-phase methanol (4.3-50\u202fg\u202fm-3.h-1) was evaluated in a biotrickling filter (BTF). During the 48\u202fd of step-feed and 41\u202fd of continuous-feed operations, average selenate removal efficiencies (RE)\u202f>\u202f90% and \u223c68% was achieved, corresponding to a selenate reduction rate of, respectively, 7.3 and 4.5\u202fmg.L-1.d-1. During the entire period of BTF operation, 65.6% of the total Se fed as SeO42- was recovered. Concerning gas-phase methanol, the maximum elimination capacity (ECmax) was 46.4\u202fg\u202fm-3.h-1, with a RE\u202f>\u202f80%. Methanol was mainly utilized for acetogenesis and converted to volatile fatty acids (VFA) in the liquid-phase. Up to 5000\u202fmg.L-1 of methanol and 800\u202fmg.L-1 of acetate accumulated in the trickling liquid of the BTF.", "keywords": ["Bacteria", "Sewage", "Methanol", "0211 other engineering and technologies", "02 engineering and technology", "Selenic Acid", "Fatty Acids", " Volatile", "Archaea", "01 natural sciences", "6. Clean water", "Biodegradation", " Environmental", "Bioreactors", "Oxidation-Reduction", "Filtration", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.chemosphere.2019.02.158"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Chemosphere", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.chemosphere.2019.02.158", "name": "item", "description": "10.1016/j.chemosphere.2019.02.158", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.chemosphere.2019.02.158"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-01T00:00:00Z"}}, {"id": "10.1016/j.ejsobi.2018.05.008", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:15:56Z", "type": "Journal Article", "created": "2018-06-11", "title": "Archaea Are The Predominant And Responsive Ammonia Oxidizing Prokaryotes In A Red Paddy Soil Receiving Green Manures", "description": "Abstract Application of green manures is an effective approach to optimizing N management in paddy soils. Nitrification is a key process in the N cycle and ammonia oxidization is the first and typically limiting step in nitrification. In this study, we investigated the changes of ammonium oxidizing prokaryotes after the application of green manure in a red paddy soil using pot experiments. The experiment included four treatments; milk vetch-rice, radish-rice, ryegrass-rice and winter fallow-rice. The nitrification potential was measured, and the abundance and community of amoA genes from ammonia-oxidizing archaea (AOA) and bacteria (AOB) were quantified. The results showed that the AOA to AOB ratios ranged from 7 to 80, and that the milk vetch treatment increased the abundances of AOA and AOB. The abundance of AOA showed negative correlations with nitrification potential and NH4+-N, and positive correlation with soil pH in the acidic red paddy soil. DNA sequence analyses revealed that the Nitrososphaera and Nitrosospira were the dominant clusters of AOA and AOB, respectively. The dominant clusters of AOA were significantly changed by utilization of green manures, especially radish. Partial least squares path modeling analysis showed that green manures exerted larger effects on the abundances of AOA than on AOB, and the community structure of AOA had the strongest effect on nitrification potential. The high abundance of AOA found in this study and their responsiveness to green manuring suggests that AOA are critically important for soil ammonia oxidation in these soils and more sensitive to green manuring than AOB.", "keywords": ["2. Zero hunger", "Driving factors", "Green manure", "0401 agriculture", " forestry", " and fisheries", "Nitrification potential", "04 agricultural and veterinary sciences", "15. Life on land", "6. Clean water", "Ammonia-oxidizing archaea", "Red paddy soil"]}, "links": [{"href": "https://doi.org/10.1016/j.ejsobi.2018.05.008"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/European%20Journal%20of%20Soil%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.ejsobi.2018.05.008", "name": "item", "description": "10.1016/j.ejsobi.2018.05.008", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.ejsobi.2018.05.008"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-07-01T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2013.10.011", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:16:37Z", "type": "Journal Article", "created": "2013-10-26", "title": "Shifts In The Abundance And Community Structure Of Soil Ammonia Oxidizers In A Wet Sclerophyll Forest Under Long-Term Prescribed Burning", "description": "Fire shapes global biome distribution and promotes the terrestrial biogeochemical cycles. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) play a vital role in the biogeochemical cycling of nitrogen (N). However, behaviors of AOB and AOA under long-term prescribed burning remain unclear. This study was to examine how fire affected the abundances and communities of soil AOB and AOA. A long-term repeated forest fire experiment with three burning treatments (never burnt, B0; biennially burnt, B2; and quadrennially burnt, B4) was used in this study. The abundances and community structure of soil AOB and AOA were determined using quantitative PCR, restriction fragment length polymorphism and clone library. More frequent fires (B2) increased the abundance of bacterium amoA gene, but tended to decrease archaeal amoA genes. Fire also modified the composition of AOA and AOB communities. Canonical correspondence analysis showed soil pH and dissolved organic C (DOC) strongly affected AOB genotypes, while nitrate-N and DOC shaped the AOA distribution. The increased abundance of bacterium amoA gene by fires may imply an important role of AOB in nitrification in fire-affected soils. The fire-induced shift in the community composition of AOB and AOA demonstrates that fire can disturb nutrient cycles.", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "Bacteria", "Nitrogen", "Forestry", "Biodiversity", "15. Life on land", "Archaea", "Nitrification", "Fires", "Trees", "Soil", "03 medical and health sciences", "Biodegradation", " Environmental", "Soil biology", "Ammonia", "13. Climate action", "Oxidation-Reduction", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2013.10.011"}, {"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": "10.1016/j.scitotenv.2013.10.011", "name": "item", "description": "10.1016/j.scitotenv.2013.10.011", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2013.10.011"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-02-01T00:00:00Z"}}, {"id": "10.1111/1462-2920.13954", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:18:24Z", "type": "Journal Article", "created": "2022-10-18", "title": "Application of stable-isotope labelling techniques for the detection of active diazotrophs", "description": "SummaryInvestigating active participants in the fixation of dinitrogen gas is vital as N is often a limiting factor for primary production. Biological nitrogen fixation is performed by a diverse guild of bacteria and archaea (diazotrophs), which can be free\uffe2\uff80\uff90living or symbionts. Free\uffe2\uff80\uff90living diazotrophs are widely distributed in the environment, yet our knowledge about their identity and ecophysiology is still limited. A major challenge in investigating this guild is inferring activity from genetic data as this process is highly regulated. To address this challenge, we evaluated and improved several 15N\uffe2\uff80\uff90based methods for detecting N2 fixation activity (with a focus on soil samples) and studying active diazotrophs. We compared the acetylene reduction assay and the 15N2 tracer method and demonstrated that the latter is more sensitive in samples with low activity. Additionally, tracing 15N into microbial RNA provides much higher sensitivity compared to bulk soil analysis. Active soil diazotrophs were identified with a 15N\uffe2\uff80\uff90RNA\uffe2\uff80\uff90SIP approach optimized for environmental samples and benchmarked to 15N\uffe2\uff80\uff90DNA\uffe2\uff80\uff90SIP. Lastly, we investigated the feasibility of using SIP\uffe2\uff80\uff90Raman microspectroscopy for detecting 15N\uffe2\uff80\uff90labelled cells. Taken together, these tools allow identifying and investigating active free\uffe2\uff80\uff90living diazotrophs in a highly sensitive manner in diverse environments, from bulk to the single\uffe2\uff80\uff90cell level.
", "keywords": ["Spectrum Analysis", " Raman", "BIOLOGICAL SOIL CRUSTS", "106005 Bioinformatik", "106023 Molekularbiologie", "Nitrogen Fixation", "REVEALS", "FLUORESCENCE", "Research Articles", "Soil Microbiology", "106022 Mikrobiologie", "SPECTROSCOPY", "Bacteria", "Nitrogen Isotopes", "106003 Biodiversity research", "106023 Molecular biology", "GENETIC-REGULATION", "Archaea", "6. Clean water", "SURFACE-ENHANCED RAMAN", "COMMUNITY", "106003 Biodiversit\u00e4tsforschung", "13. Climate action", "Isotope Labeling", "106022 Microbiology", "NITROGEN-FIXATION", "106005 Bioinformatics", "RIBOSOMAL-RNA", "N-2 FIXATION"]}, "links": [{"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.13954"}, {"href": "https://doi.org/10.1111/1462-2920.13954"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1462-2920.13954", "name": "item", "description": "10.1111/1462-2920.13954", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1462-2920.13954"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-12-15T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2017.10.005", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:16:54Z", "type": "Journal Article", "created": "2017-10-16", "title": "Recovery of methane turnover and the associated microbial communities in restored cutover peatlands is strongly linked with increasing Sphagnum abundance", "description": "Abstract Vegetation succession is known to affect carbon-cycling patterns of recovering cutover peatlands, displayed as shifts in emissions of the greenhouse gases CO2 and CH4. However, the related plant-microbe interactions are still poorly understood. We aimed to link the recovery of the organisms responsible for CH4 turnover, the methanogens and the methanotrophs, to the re-vegetation related compositional changes of three functional plant types (Sphagna, sedges and shrubs). In peat layers, the Sphagnum coverage was the most influential factor for the activity, abundance and community structures of both these microbial groups, demonstrating a succession pattern towards a pristine stage. Analysis of mcrA and pmoA genes revealed Methanoregulaceae and Methylocystis as the most dominant methanogens and methanotrophs, respectively. The relatively fast recovery of both CH4 production and oxidation in the peat layers supports earlier flux based results from these same fen-type peatland sites. In contrast to peat, CH4 oxidation in living Sphagnum mosses appeared to be independent of vegetation succession as CH4 oxidation potential was similar throughout the succession stages. This indicated that Sphagnum may be a valuable CH4 biofilter especially in the early re-vegetation stages when the oxidation in the peat has not yet recovered. Therefore, we recommend Sphagnum transplantation as a tool for climate friendly peatland restoration with faster recovery of the carbon sink function and altered CH4 emissions.", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "Aitoneva", "peat extraction", "ta1172", "ta1183", "Methanogenic archaea", "plant functional types", "15. Life on land", "Methanotrophic bacteria", "ecosystem restoration", "ekosysteemit", "Kihni\u00f6", "03 medical and health sciences", "13. Climate action", "616", "ta1181", "ennallistaminen", "turvemaat", "Finland"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2017.10.005"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2017.10.005", "name": "item", "description": "10.1016/j.soilbio.2017.10.005", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2017.10.005"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-01-01T00:00:00Z"}}, {"id": "10.1038/s41396-019-0465-1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:32Z", "type": "Journal Article", "created": "2019-06-27", "title": "Plant-driven niche differentiation of ammonia-oxidizing bacteria and archaea in global drylands", "description": "AbstractUnder controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.Ammonia oxidising archaea are among the most abundant living organisms on Earth and key microbial players in the global nitrogen cycle. They carry out oxidation of ammonia to nitrite, and their activity is relevant for both food security and climate change. Since their discovery nearly 20 years ago, major insights have been gained into their nitrogen and carbon metabolism, growth preferences and their mechanisms of adaptation to the environment, as well as their diversity, abundance and activity in the environment. Despite significant strides forward through the cultivation of novel organisms and omics-based approaches, there are still many knowledge gaps on their metabolism and the mechanisms which enable them to adapt to the environment. Ammonia oxidising microorganisms are typically considered metabolically streamlined and highly specialised. Here we review the physiology of ammonia oxidising archaea, with focus on aspects of metabolic versatility and regulation, and discuss these traits in the context of nitrifier ecology.For centuries, biodiversity has spellbound biologists focusing mainly on macroorganism's diversity and almost neglecting the geographic mediated dynamics of microbial communities. We surveyed the diversity of soil bacteria and archaea along a steep precipitation gradient ranging from the Negev Desert in the south of Israel (<100\uffe2\uff80\uff89mm annual rain) to the Mediterranean forests in the north (>900\uffe2\uff80\uff89mm annual rain). Soil samples were retrieved from triplicate plots at five long-term ecological research stations, collected from two types of patches: plant interspaces and underneath the predominant perennial at each site. The molecular fingerprint of each soil sample was taken using terminal restriction length polymorphism of the 16S rRNA gene to evaluate the bacterial and archaeal community composition and diversity within and across sites. The difference in community compositions was not statistically significant within sites (P=0.33 and 0.77 for bacteria and archaea, respectively), but it differed profoundly by ecosystem type. These differences could largely be explained by the precipitation gradient combined with the vegetation cover: the archaeal and bacterial operational taxonomic units were unique to each climatic region, that is, arid, semiarid and Mediterranean (P=0.0001, for both domains), as well as patch type (P=0.009 and 0.02 for bacteria and archaea, respectively). Our results suggest that unlike macroorganisms that are more diverse in the Mediterranean ecosystems compared with the desert sites, archaeal and bacterial diversities are not constrained by precipitation. However, the community composition is unique to the climate and vegetation cover that delineates each ecosystem.
", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Bacteria", "Geography", "Biodiversity", "15. Life on land", "Archaea", "DNA Fingerprinting", "DNA", " Ribosomal", "03 medical and health sciences", "DNA", " Archaeal", "13. Climate action", "RNA", " Ribosomal", " 16S", "Cluster Analysis", "Israel", "Polymorphism", " Restriction Fragment Length", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/ismej.2009.136"}, {"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.2009.136", "name": "item", "description": "10.1038/ismej.2009.136", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2009.136"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-12-24T00:00:00Z"}}, {"id": "10.1038/ismej.2010.3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:31Z", "type": "Journal Article", "created": "2010-02-04", "title": "Shifts In Microbial Community Structure Along An Ecological Gradient Of Hypersaline Soils And Sediments", "description": "AbstractStudies of hypersaline ecosystems often yield novel organisms and contribute to our understanding of extreme environments. Soils and sediments from La Sal del Rey, a previously uncharacterized, hypersaline lake located in southern Texas, USA, were surveyed to characterize the structure and diversity of their microbial communities. Samples were collected along a transect that spanned vegetated uplands, exposed lakebed sediments, and water-logged locations, capturing a wide range of environments and physical and chemical gradients. Community quantitative PCR (qPCR) was used in combination with tag-encoded pyrosequencing, 16S rRNA gene cloning, and Sanger sequencing to characterize the lake's soil and sediment microbial communities. Further, we used multivariate statistics to identify the relationships shared between sequence diversity and heterogeneity in the soil environment. The overall microbial communities were surprisingly diverse, harboring a wide variety of taxa, and sharing significant correlations with site water content, phosphorus and total organic carbon concentrations, and pH. Some individual populations, especially of Archaea, also correlated with sodium concentration and electrical conductivity salinity. Across the transect, Bacteria were numerically dominant relative to Archaea, and among them, three phyla\uffe2\uff80\uff94the Proteobacteria, Bacteroidetes, and Firmicutes\uffe2\uff80\uff94accounted for the majority of taxa detected. Although these taxa were detected with similar abundances to those described in other hypersaline ecosystems, the greater depth of sequencing achieved here resulted in the detection of taxa not described previously in hypersaline sediments. The results of this study provide new information regarding a previously uncharacterized ecosystem and show the value of high-throughput sequencing in the study of complex ecosystems.
", "keywords": ["DNA", " Bacterial", "0301 basic medicine", "Geologic Sediments", "Salinity", "0303 health sciences", "Bacteria", "Genes", " rRNA", "Sequence Analysis", " DNA", "15. Life on land", "Archaea", "Polymerase Chain Reaction", "Texas", "6. Clean water", "Soil", "03 medical and health sciences", "DNA", " Archaeal", "13. Climate action", "RNA", " Ribosomal", " 16S", "Water Microbiology", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/ismej.2010.3"}, {"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.2010.3", "name": "item", "description": "10.1038/ismej.2010.3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/ismej.2010.3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2010-02-04T00:00:00Z"}}, {"id": "10.1038/s41396-021-01064-z", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:33Z", "type": "Journal Article", "created": "2021-07-27", "title": "Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities", "description": "AbstractNitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that\uffe2\uff80\uff94like for AOB\uffe2\uff80\uff94ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.Ectomycorrhizal fungi live in close association with their host plants and form complex interactions with bacterial/archaeal communities in soil. We investigated whether abundant or rare ectomycorrhizal fungi on root-tips of young beech trees (Fagus sylvatica) shape bacterial/archaeal communities. We sequenced 16S rRNA genes and fungal internal transcribed spacer regions of individual root-tips and used ecological networks to detect the tendency of certain assemblies of fungal and bacterial/archaeal taxa to inhabit the same root-tip (i.e. modularity). Individual ectomycorrhizal root-tips hosted distinct fungal communities associated with unique bacterial/archaeal communities. The structure of the fungal-bacterial/archaeal association was determined by both, dominant and rare fungi. Integrating our data in a conceptual framework suggests that the effect of rare fungi on the bacterial/archaeal communities of ectomycorrhizal root-tips contributes to assemblages of bacteria/archaea on root-tips. This highlights the potential impact of complex fine-scale interactions between root-tip associated fungi and other soil microorganisms for the ectomycorrhizal symbiosis.Archaeal (AOA) and bacterial (AOB) ammonia-oxidizer responses to long-term field fertilization in a Mollisol soil were assessed through pyrosequencing of amoA genes. Long-term fertilization treatments including chemical fertilizer (NPK), NPK plus manure (NPKM) and no fertilization over 23 years altered soil properties resulting in significant shifts in AOA and AOB community composition and abundance. NPK exhibited a strong influence on AOA and AOB composition while the addition of manure neutralized the community change induced by NPK. NPK also led to significant soil acidification and enrichment of Nitrosotalea. Nitrosospira cluster 9 and 3c were the most abundant AOB populations with opposing responses to fertilization treatments. NPKM had the largest abundance of ammonia-oxidizers and highest potential nitrification activity (PNA), suggesting high N loss potential due to a doubling of nutrient input compared to NPK. PNA was strongly correlated to AOA and AOB community composition indicating that both were important in ammonium oxidization in this Mollisol soil. Total N and organic C were the most important factors driving shifts in AOA and AOB community composition. The AOA community was strongly correlated to the activities of all sugar hydrolysis associated soil enzymes and was more responsive to C and N input than AOB.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "Bacteria", "Agriculture", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "15. Life on land", "Archaea", "Biota", "Article", "6. Clean water", "Genes", " Archaeal", "03 medical and health sciences", "Ammonia", "Genes", " Bacterial", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Oxidation-Reduction", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/srep28981"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/srep28981", "name": "item", "description": "10.1038/srep28981", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep28981"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-30T00:00:00Z"}}, {"id": "10.1038/srep32791", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:17:40Z", "type": "Journal Article", "created": "2016-09-06", "title": "Responses Of Soil Hydrolytic Enzymes, Ammonia-Oxidizing Bacteria And Archaea To Nitrogen Applications In A Temperate Grassland In Inner Mongolia", "description": "AbstractWe used a seven-year urea gradient applied field experiment to investigate the effects of nitrogen (N) applications on soil N hydrolytic enzyme activity and ammonia-oxidizing microbial abundance in a typical steppe ecosystem in Inner Mongolia. The results showed that N additions inhibited the soil N-related hydrolytic enzyme activities, especially in 392\uffe2\uff80\uff89kg N ha\uffe2\uff88\uff921\uffe2\uff80\uff89yr\uffe2\uff88\uff921 treatment. As N additions increased, the amoA gene copy ratios of ammonia-oxidizing archaea (AOA) to ammonia-oxidizing bacteria (AOB) decreased from 1.13 to 0.65. Pearson correlation analysis showed that the AOA gene copies were negatively related with NH4+-N content. However, the AOB gene copies were positively correlated with NO3\uffe2\uff88\uff92-N content. Moderate N application rates (56\uffe2\uff80\uff93224\uffe2\uff80\uff89kg N ha\uffe2\uff88\uff921\uffe2\uff80\uff89yr\uffe2\uff88\uff921) accompanied by P additions are beneficial to maintaining the abundance of AOB, as opposed to the inhibition of highest N application rate (392\uffe2\uff80\uff89kg N ha\uffe2\uff88\uff921\uffe2\uff80\uff89yr\uffe2\uff88\uff921) on the abundance of AOB. This study suggests that the abundance of AOB and AOA would not decrease unless N applications exceed 224\uffe2\uff80\uff89kg N ha\uffe2\uff88\uff921\uffe2\uff80\uff89yr\uffe2\uff88\uff921 in temperate grasslands in Inner Mongolia.
", "keywords": ["2. Zero hunger", "China", "Bacteria", "Nitrogen", "Hydrolysis", "04 agricultural and veterinary sciences", "15. Life on land", "Archaea", "Grassland", "Nitrification", "Article", "Soil", "Ammonia", "0401 agriculture", " forestry", " and fisheries", "Fertilizers", "Oxidation-Reduction", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1038/srep32791"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/srep32791", "name": "item", "description": "10.1038/srep32791", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep32791"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-09-06T00:00:00Z"}}, {"id": "10.1093/ismejo/wrae156", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:18:11Z", "type": "Journal Article", "created": "2024-08-06", "title": "Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates", "description": "AbstractSoils provide essential ecosystem services and represent the most diverse habitat on Earth. It has been suggested that the presence of various physico-chemically heterogeneous microhabitats supports the enormous diversity of microbial communities in soil. However, little is known about the relationship between microbial communities and their immediate environment at the micro- to millimetre scale. In this study, we examined whether bacteria, archaea, and fungi organize into distinct communities in individual 2-mm-sized soil aggregates and compared them to communities of homogenized bulk soil samples. Furthermore, we investigated their relationship to their local environment by concomitantly determining microbial community structure and physico-chemical properties from the same individual aggregates. Aggregate communities displayed exceptionally high beta-diversity, with 3\uffe2\uff80\uff934 aggregates collectively capturing more diversity than their homogenized parent soil core. Up to 20%\uffe2\uff80\uff9330% of ASVs (particularly rare ones) were unique to individual aggregates selected within a few centimetres. Aggregates and bulk soil samples showed partly different dominant phyla, indicating that taxa that are potentially driving biogeochemical processes at the small scale may not be recognized when analysing larger soil volumes. Microbial community composition and richness of individual aggregates were closely related to aggregate-specific carbon and nitrogen content, carbon stable-isotope composition, and soil moisture, indicating that aggregates provide a stable environment for sufficient time to allow co-development of communities and their environment. We conclude that the soil microbiome is a metacommunity of variable subcommunities. Our study highlights the necessity to study small, spatially coherent soil samples to better understand controls of community structure and community-mediated processes in soils.Ammonia-oxidising archaea (AOA) are environmentally important microorganisms involved in the biogeochemical cycling of nitrogen. Routine cultivation of AOA is exclusively performed in liquid cultures and reports on their growth on solid medium are scarce. The ability to grow AOA on solid medium would be beneficial for not only the purification of enrichment cultures but also for developing genetic tools. The aim of this study was to develop a reliable method for growing individual colonies from AOA cultures on solid medium. Three phylogenetically distinct AOA strains were tested: \uffe2\uff80\uff98Candidatus Nitrosocosmicus franklandus C13\uffe2\uff80\uff99, Nitrososphaera viennensis EN76 and \uffe2\uff80\uff98Candidatus Nitrosotalea sinensis Nd2\uffe2\uff80\uff99. Of the gelling agents tested, agar and Bacto-agar severely inhibited growth of all three strains. In contrast, both \uffe2\uff80\uff98Ca. N. franklandus C13\uffe2\uff80\uff99 and N. viennensis EN76 tolerated Phytagel\uffe2\uff84\uffa2 while the acidophilic \uffe2\uff80\uff98Ca. N. sinensis Nd2\uffe2\uff80\uff99 was completely inhibited. Based on these observations, we developed a Liquid-Solid (LS) method that involves immobilising cells in Phytagel\uffe2\uff84\uffa2 and overlaying with liquid medium. This approach resulted in the development of visible distinct colonies from \uffe2\uff80\uff98Ca. N. franklandus C13\uffe2\uff80\uff99 and N. viennensis EN76 cultures and lays the groundwork for the genetic manipulation of this group of microorganisms.Ammonia oxidizers are key players in the global nitrogen cycle and are responsible for the oxidation of ammonia to nitrite, which is further oxidized to nitrate by other microorganisms. Their activity can lead to adverse effects on some human-impacted environments, including water pollution through leaching of nitrate and emissions of the greenhouse gas nitrous oxide (N2O). Ammonia monooxygenase (AMO) is the key enzyme in microbial ammonia oxidation and shared by all groups of aerobic ammonia oxidizers. The AMO has not been purified in an active form, and much of what is known about its potential structure and function comes from studies on its interactions with inhibitors. The archaeal AMO is less well studied as ammonia oxidizing archaea were discovered much more recently than their bacterial counterparts. The inhibition of ammonia oxidation by aliphatic alcohols (C1-C8) using the model terrestrial ammonia oxidizing archaeon \uffe2\uff80\uff98Candidatus Nitrosocosmicus franklandus\uffe2\uff80\uff99 C13 and the ammonia oxidizing bacterium Nitrosomonas europaea was examined in order to expand knowledge about the range of inhibitors of ammonia oxidizers. Methanol was the most potent specific inhibitor of the AMO in both ammonia oxidizers, with half-maximal inhibitory concentrations (IC50) of 0.19 and 0.31\uffe2\uff80\uff89mM, respectively. The inhibition was AMO-specific in \uffe2\uff80\uff98Ca. N. franklandus\uffe2\uff80\uff99 C13 in the presence of C1-C2 alcohols, and in N. europaea in the presence of C1-C3 alcohols. Higher chain-length alcohols caused non-specific inhibition and also inhibited hydroxylamine oxidation. Ethanol was tolerated by \uffe2\uff80\uff98Ca. N. franklandus\uffe2\uff80\uff99 C13 at a higher threshold concentration than other chain-length alcohols, with 80\uffe2\uff80\uff89mM ethanol being required for complete inhibition of ammonia oxidation.Investigating active participants in the fixation of dinitrogen gas is vital as N is often a limiting factor for primary production. Biological nitrogen fixation is performed by a diverse guild of bacteria and archaea (diazotrophs), which can be free\uffe2\uff80\uff90living or symbionts. Free\uffe2\uff80\uff90living diazotrophs are widely distributed in the environment, yet our knowledge about their identity and ecophysiology is still limited. A major challenge in investigating this guild is inferring activity from genetic data as this process is highly regulated. To address this challenge, we evaluated and improved several 15N\uffe2\uff80\uff90based methods for detecting N2 fixation activity (with a focus on soil samples) and studying active diazotrophs. We compared the acetylene reduction assay and the 15N2 tracer method and demonstrated that the latter is more sensitive in samples with low activity. Additionally, tracing 15N into microbial RNA provides much higher sensitivity compared to bulk soil analysis. Active soil diazotrophs were identified with a 15N\uffe2\uff80\uff90RNA\uffe2\uff80\uff90SIP approach optimized for environmental samples and benchmarked to 15N\uffe2\uff80\uff90DNA\uffe2\uff80\uff90SIP. Lastly, we investigated the feasibility of using SIP\uffe2\uff80\uff90Raman microspectroscopy for detecting 15N\uffe2\uff80\uff90labelled cells. Taken together, these tools allow identifying and investigating active free\uffe2\uff80\uff90living diazotrophs in a highly sensitive manner in diverse environments, from bulk to the single\uffe2\uff80\uff90cell level.The ammonia monooxygenase (AMO) is a key enzyme in ammonia\uffe2\uff80\uff90oxidizing archaea, which are abundant and ubiquitous in soil environments. The AMO belongs to the copper\uffe2\uff80\uff90containing membrane monooxygenase (CuMMO) enzyme superfamily, which also contains particulate methane monooxygenase (pMMO). Enzymes in the CuMMO superfamily are promiscuous, which results in co\uffe2\uff80\uff90oxidation of alternative substrates. The phylogenetic and structural similarity between the pMMO and the archaeal AMO is well\uffe2\uff80\uff90established, but there is surprisingly little information on the influence of methane and methanol on the archaeal AMO and terrestrial nitrification. The aim of this study was to examine the effects of methane and methanol on the soil ammonia\uffe2\uff80\uff90oxidizing archaeon \uffe2\uff80\uff98Candidatus Nitrosocosmicus franklandus C13\uffe2\uff80\uff99. We demonstrate that both methane and methanol are competitive inhibitors of the archaeal AMO. The inhibition constants (Ki) for methane and methanol were 2.2 and 20\uffe2\uff80\uff89\uffce\uffbcM, respectively, concentrations which are environmentally relevant and orders of magnitude lower than those previously reported for ammonia\uffe2\uff80\uff90oxidizing bacteria. Furthermore, we demonstrate that a specific suite of proteins is upregulated and downregulated in \uffe2\uff80\uff98Ca. Nitrosocosmicus franklandus C13\uffe2\uff80\uff99 in the presence of methane or methanol, which provides a foundation for future studies into metabolism of one\uffe2\uff80\uff90carbon (C1) compounds in ammonia\uffe2\uff80\uff90oxidizing archaea.Ammonia\uffe2\uff80\uff90oxidising archaea (AOA) are important microorganisms contributing towards the nitrogen flux in the environment. Unlike archaea from other major phyla, genetic tools are yet to be developed for the AOA, and identification of antibiotic resistance markers for selecting mutants is required for a genetic system. The aim of this study was to test the effects of selected antibiotics (hygromycin B, neomycin, apramycin, puromycin, novobiocin) on pure cultures of three well studied AOA strains, \uffe2\uff80\uff98Candidatus Nitrosocosmicus franklandianus C13\uffe2\uff80\uff99, Nitrososphaera viennensis EN76 and Nitrosopumilus maritimus SCM1. Puromycin, hygromycin B and neomycin inhibited some but not all tested archaeal strains. All strains were resistant to apramycin and inhibited by novobiocin to various degrees. As N. viennensis EN76 was relatively more resistant to the tested antibiotics, a wider range of concentrations and compounds (chloramphenicol, trimethoprim, statins) was tested against this strain. N. viennensis EN76 was inhibited by trimethoprim, but not by chloramphenicol, and growth recovered within days in the presence of simvastatin, suggesting either degradation of, or spontaneous resistance against, this compound. This study highlights the physiological differences between different genera of AOA and has identified new candidate antibiotics for selective enrichment and the development of selectable markers for genetic systems in AOA. We investigate the potential for the globally distributed marine ammonia oxidising archaeon (AOA) Nitrosopumilus maritimus to oxidise iodide (I \uffe2\uff88\uff92 ), with the aim of identifying a key driver of seawater iodate (IO 3 \uffe2\uff88\uff92 ) renewal. Batch cultures of N. maritimus grew well in concentrations of 0.1 to 1\uffe2\uff80\uff89mM NH 4 + and from 0.0001 to 1\uffe2\uff80\uff89mM I \uffe2\uff88\uff92 . There was near 100% conversion of ammonium to nitrite over an 8\uffe2\uff80\uff90day growth period. No loss of I \uffe2\uff88\uff92 or production of IO 3 \uffe2\uff88\uff92 was detected in cultures where I \uffe2\uff88\uff92 was added, indicating that N. maritimus is unable to drive I \uffe2\uff88\uff92 oxidation under the tested conditions. This contrasts with previous observations of I \uffe2\uff88\uff92 oxidation by ammonium oxidising bacteria (AOB). We explore whether differences between the metabolism of AOA and AOB could explain their differing actions on I \uffe2\uff88\uff92 . N. maritimus cultures grown with the equivalent IO 3 \uffe2\uff88\uff92 concentrations also showed no reduction in [IO 3 \uffe2\uff88\uff92 ]. In addition, the growth of the N. maritimus culture was unaffected by inorganic iodine concentrations over 1000 times higher than in ambient seawater, suggesting a resilience to high iodine. These results suggest that AOA might have very little role in inorganic iodine turnover in the global ocean. Anthropogenic nitrogen (N) loading alters soil ammonia\uffe2\uff80\uff90oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize\uffc2\uffa068 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N\uffe2\uff80\uff90stimulation of nitrification, but does so via climate\uffe2\uff80\uff90related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N\uffe2\uff80\uff90availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate\uffe2\uff80\uff90related shifts in soil ammonia\uffe2\uff80\uff90oxidizing community maintain the N\uffe2\uff80\uff90stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.Many studies have shown that changes in nitrogen (N) availability affect primary productivity in a variety of terrestrial systems, but less is known about the effects of the changing N cycle on soil organic matter (SOM) decomposition. We used a variety of techniques to examine the effects of chronic N amendments on SOM chemistry and microbial community structure and function in an alpine tundra soil. We collected surface soil (0\uffe2\uff80\uff935\uffe2\uff80\uff83cm) samples from five control and five long\uffe2\uff80\uff90term N\uffe2\uff80\uff90amended plots established and maintained at the Niwot Ridge Long\uffe2\uff80\uff90term Ecological Research (LTER) site. Samples were bulked by treatment and all analyses were conducted on composite samples. The fungal community shifted in response to N amendments, with a decrease in the relative abundance of basidiomycetes. Bacterial community composition also shifted in the fertilized soil, with increases in the relative abundance of sequences related to the Bacteroidetes and Gemmatimonadetes, and decreases in the relative abundance of the Verrucomicrobia. We did not uncover any bacterial sequences that were closely related to known nitrifiers in either soil, but sequences related to archaeal nitrifiers were found in control soils. The ratio of fungi to bacteria did not change in the N\uffe2\uff80\uff90amended soils, but the ratio of archaea to bacteria dropped from 20% to less than 1% in the N\uffe2\uff80\uff90amended plots. Comparisons of aliphatic and aromatic carbon compounds, two broad categories of soil carbon compounds, revealed no between treatment differences. However, G\uffe2\uff80\uff90lignins were found in higher relative abundance in the fertilized soils, while proteins were detected in lower relative abundance. Finally, the activities of two soil enzymes involved in N cycling changed in response to chronic N amendments. These results suggest that chronic N fertilization induces significant shifts in soil carbon dynamics that correspond to shifts in microbial community structure and function.
", "keywords": ["2. Zero hunger", "Bacteria", "Nitrogen", "Molecular Sequence Data", "Fungi", "Biodiversity", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "15. Life on land", "Archaea", "Carbon", "6. Clean water", "Soil", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Organic Chemicals", "Fertilizers", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1111/j.1462-2920.2008.01735.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1462-2920.2008.01735.x", "name": "item", "description": "10.1111/j.1462-2920.2008.01735.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1462-2920.2008.01735.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-09-30T00:00:00Z"}}, {"id": "10.3390/genes10060424", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:20:41Z", "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": "10.1371/journal.pone.0076500", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:18Z", "type": "Journal Article", "created": "2013-10-04", "title": "Response Of The Abundance Of Key Soil Microbial Nitrogen-Cycling Genes To Multi-Factorial Global Changes", "description": "Multiple co-occurring environmental changes are affecting soil nitrogen cycling processes, which are mainly mediated by microbes. While it is likely that various nitrogen-cycling functional groups will respond differently to such environmental changes, very little is known about their relative responsiveness. Here we conducted four long-term experiments in a steppe ecosystem by removing plant functional groups, mowing, adding nitrogen, adding phosphorus, watering, warming, and manipulating some of their combinations. We quantified the abundance of seven nitrogen-cycling genes, including those for fixation (nifH), mineralization (chiA), nitrification (amoA of ammonia-oxidizing bacteria (AOB) or archaea (AOA)), and denitrification (nirS, nirK and nosZ). First, for each gene, we compared its sensitivities to different environmental changes and found that the abundances of various genes were sensitive to distinct and different factors. Overall, the abundances of nearly all genes were sensitive to nitrogen enrichment. In addition, the abundances of the chiA and nosZ genes were sensitive to plant functional group removal, the AOB-amoA gene abundance to phosphorus enrichment when nitrogen was added simultaneously, and the nirS and nirK gene abundances responded to watering. Second, for each single- or multi-factorial environmental change, we compared the sensitivities of the abundances of different genes and found that different environmental changes primarily affected different gene abundances. Overall, AOB-amoA gene abundance was most responsive, followed by the two denitrifying genes nosZ and nirS, while the other genes were less sensitive. These results provide, for the first time, systematic insights into how the abundance of each type of nitrogen-cycling gene and the equilibrium state of all these nitrogen-cycling gene abundances would shift under each single- or multi-factorial global change.", "keywords": ["2. Zero hunger", "Bacteria", "Science", "Microbiota", "Q", "R", "04 agricultural and veterinary sciences", "Environment", "Nitrogen Cycle", "15. Life on land", "Archaea", "Soil", "13. Climate action", "Medicine", "0401 agriculture", " forestry", " and fisheries", "Gene-Environment Interaction", "Ecosystem", "Soil Microbiology", "Research Article"]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0076500"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/PLoS%20ONE", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1371/journal.pone.0076500", "name": "item", "description": "10.1371/journal.pone.0076500", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0076500"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-10-04T00:00:00Z"}}, {"id": "10.1111/j.1574-6941.2007.00394.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:18:50Z", "type": "Journal Article", "created": "2007-10-19", "title": "Quantitation And Diversity Analysis Of Ruminal Methanogenic Populations In Response To The Antimethanogenic Compound Bromochloromethane", "description": "Methyl coenzyme-M reductase A (mcrA) clone libraries were generated from microbial DNA extracted from the rumen of cattle fed a roughage diet with and without supplementation of the antimethanogenic compound bromochloromethane. Bromochloromethane reduced total methane emissions by c. 30%, with a resultant increase in propionate and branched chain fatty acids. The mcrA clone libraries revealed that Methanobrevibacter spp. were the dominant species identified. A decrease in the incidence of Methanobrevibacter spp. from the clone library generated from bromochloromethane treatment was observed. In addition, a more diverse methanogenic population with representatives from Methanococcales, Methanomicrobiales and Methanosacinales orders was observed for the bromochloromethane library. Sequence data generated from these libraries aided in the design of an mcrA-targeted quantitative PCR (qPCR) assay. The reduction in methane production by bromochloromethane was associated with an average decrease of 34% in the number of methanogenic Archaea when monitored with this qPCR assay. Dissociation curve analysis of mcrA amplicons showed a clear difference in melting temperatures for Methanobrevibacter spp. (80-82 degrees C) and all other methanongens (84-86 degrees C). A decrease in the intensity of the Methanobrevibacter spp. specific peak and an increase for the other peak in the bromochloromethane-treated animals corresponded with the changes within the clone libraries.", "keywords": ["Male", "0301 basic medicine", "Rumen", "Bromochloromethane", "Methanogens", "Molecular Sequence Data", "Euryarchaeota", "Methanobrevibacter", "Polymerase Chain Reaction", "630", "03 medical and health sciences", "2402 Applied Microbiology and Biotechnology", "Animals", "Methyl coenzyme-M reductase", "Phylogeny", "Gene Library", "2. Zero hunger", "0303 health sciences", "Hydrocarbons", " Halogenated", "2404 Microbiology", "Sequence Analysis", " DNA", "mcrA", "qPCR", "DNA", " Archaeal", "Cattle", "Oxidoreductases", "2303 Ecology", "Methane"]}, "links": [{"href": "https://doi.org/10.1111/j.1574-6941.2007.00394.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/FEMS%20Microbiology%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1574-6941.2007.00394.x", "name": "item", "description": "10.1111/j.1574-6941.2007.00394.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1574-6941.2007.00394.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-12-01T00:00:00Z"}}, {"id": "10.1111/nph.17365", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:18:55Z", "type": "Journal Article", "created": "2021-03-29", "title": "New insight to the role of microbes in the methane exchange in trees: evidence from metagenomic sequencing", "description": "SummaryMethane (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": "10.1126/sciadv.aax8787", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:18:59Z", "type": "Journal Article", "created": "2020-01-25", "title": "The global-scale distributions of soil protists and their contributions to belowground systems", "description": "We studied the dominant protists found in soils across the globe and their contributions to belowground food webs.
Ammonia-oxidizing archaea (AOA) are among the most numerous living organisms on Earth, and they play a pivotal role in the global biogeochemical nitrogen cycle. Despite this, little is known about the physiology and metabolism of AOA.
Due to their abilities to survive intense radiation and low water availability, hypersaline microbial mats are often suggested to be analogs of potential extraterrestrial life. However, even on Earth, the limitations imposed on microbial processes by saturation-level salinity have rarely been studied in situ . Archaeal and bacterial ammonia oxidizers (AOA and AOB, respectively) initiate nitrification by oxidizing ammonia to hydroxylamine, a reaction catalyzed by ammonia monooxygenase (AMO). AMO enzyme is difficult to purify in its active form, and its structure and biochemistry remain largely unexplored. The bacterial AMO and the closely related particulate methane monooxygenase (pMMO) have a broad range of hydrocarbon cooxidation substrates. This study provides insights into the AMO of previously unstudied archaeal genera, by comparing the response of the archaeal AMO, a bacterial AMO, and pMMO to inhibition by linear 1-alkynes and the aromatic alkyne, phenylacetylene. Reduced sensitivity to inhibition by larger alkynes suggests that the archaeal AMO has a narrower hydrocarbon substrate range than the bacterial AMO, as previously reported for other genera of AOA. Phenylacetylene inhibited the archaeal and bacterial AMOs at different thresholds and by different mechanisms of inhibition, highlighting structural differences between the two forms of monooxygenase.
The objectives of this study were to formulate a vaccine based upon the different species/strains of methanogens present in sheep intended to be immunized and to determine if a targeted vaccine could be used to decrease the methane output of the sheep. Two 16S rRNA gene libraries were used to survey the methanogenic archaea in sheep prior to vaccination, and methanogens representing five phylotypes were found to account for >52% of the different species/strains of methanogens detected. A vaccine based on a mixture of these five methanogens was then formulated, and 32 sheep were vaccinated on days 0, 28, and 103 with either a control or the anti-methanogen vaccine. Enzyme-linked immunosorbent assay analysis revealed that each vaccination with the anti-methanogen formulation resulted in higher specific immunoglobulin G titers in plasma, saliva, and rumen fluid. Methane output levels corrected for dry-matter intake for the control and treatment groups were not significantly different, and real-time PCR data also indicated that methanogen numbers were not significantly different for the two groups after the second vaccination. However, clone library data indicated that methanogen diversity was significantly greater in sheep receiving the anti-methanogen vaccine and that the vaccine may have altered the composition of the methanogen population. A correlation between 16S rRNA gene sequence relatedness and cross-reactivity for the methanogens ( R 2 = 0.90) also exists, which suggests that a highly specific vaccine can be made to target specific strains of methanogens and that a more broad-spectrum approach is needed for success in the rumen. Our data also suggest that methanogens take longer than 4 weeks to adapt to dietary changes and call into question the validity of experimental results based upon a 2- to 4-week acclimatization period normally observed for bacteria.
", "keywords": ["Rumen", "Molecular Sequence Data", "DNA", " Ribosomal", "630", "Antibodies", "Plasma", "RNA", " Ribosomal", " 16S", "2402 Applied Microbiology and Biotechnology", "Animals", "Saliva", "1106 Food Science", "2. Zero hunger", "Vaccines", "Gastric Juice", "Sheep", "0402 animal and dairy science", "Biodiversity", "Sequence Analysis", " DNA", "04 agricultural and veterinary sciences", "Archaea", "3. Good health", "DNA", " Archaeal", "Immunoglobulin G", "1305 Biotechnology", "2303 Ecology", "Methane"]}, "links": [{"href": "https://doi.org/10.1128/aem.02453-08"}, {"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.02453-08", "name": "item", "description": "10.1128/aem.02453-08", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.02453-08"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-04-01T00:00:00Z"}}, {"id": "10.13145/bacdive11415.20170425.1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-23T16:19:15Z", "type": "Dataset", "title": "Brevibacillus parabrevis (Takagi et al. 1993) Shida et al. 1996", "description": "The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.", "keywords": ["Strain-linked information about bacterial and archaeal biodiversity", "15. Life on land"], "contacts": [{"organization": "Reimer, L.C., Vetcininova, A., Soehngen, C., Podstawka, A., Gleim, D., Overmann, J.,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.13145/bacdive11415.20170425.1"}, {"rel": "self", "type": "application/geo+json", "title": "10.13145/bacdive11415.20170425.1", "name": "item", "description": "10.13145/bacdive11415.20170425.1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.13145/bacdive11415.20170425.1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-04-25T00:00:00Z"}}, {"id": "10.13145/bacdive109630.20190402.4", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-24T16:19:05Z", "type": "Dataset", "title": "Streptomyces sp.", "description": "The range of data encompasses taxonomy, morphology, 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