{"type": "FeatureCollection", "features": [{"id": "10.1016/j.soilbio.2008.11.003", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:17:28Z", "type": "Journal Article", "created": "2008-12-05", "title": "Functional Shifts Of Grassland Soil Communities In Response To Soil Warming", "description": "In terrestrial ecosystems most carbon (C) occurs below-ground, making the activity of soil decomposer organisms critical to the global carbon cycle. Temperate grassland ecosystems, contain large, diverse and active soil meso- and macrofauna decomposer communities. Understanding the effects of climate change on their ecology offers a first step towards meaningful predictions of changes in soil organic carbon mineralisation. We examined the effects of soil warming on the abundance, diversity and ecology of temperate grassland soil fauna functional groups, ecosystem net CO2 flux and respiration and plant above- and below-ground productivity in a 2-year plant\u2013soil mesocosm experiment. Low voltage heating cable mounted on a framework of stainless steel mesh provided a constant 3.5 \u00b0C difference between control and warmed mesocosm soils. Results showed that this temperature increment had little effect on soil respiration and above-ground plant biomass. There was, however, a significant effect on the soil fauna due to warmer conditions and increased root growth, with significant decreases in the numbers in the large oligochaete groups and Prostigmata mites and the re-distribution of enchytraeids to deeper soil layers. Functional groups exhibited individualistic responses to soil warming, with the total disappearance of epigeic species in the case of the ecosystem engineers and an increased diversity of fungivorous mites that, together, produced significant changes in the composition and trophic structure of the fauna community. The observed switch towards a fungal driven food web has important implications for the fate of soil organic carbon in temperate ecosystems subjected to sustained warming. Accordingly, soil biology needs to be properly incorporated in C models to make better predictions of the fate of SOC under warmer scenarios.", "keywords": ["570", "Soil invertebrates", "13. Climate action", "Trophic food webs", "0401 agriculture", " forestry", " and fisheries", "SOC", "04 agricultural and veterinary sciences", "15. Life on land", "SOM", "Community structure"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2008.11.003"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2008.11.003", "name": "item", "description": "10.1016/j.soilbio.2008.11.003", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2008.11.003"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-02-01T00:00:00Z"}}, {"id": "10.1007/s00248-013-0225-0", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:14:50Z", "type": "Journal Article", "created": "2013-04-15", "title": "Agricultural Management And Labile Carbon Additions Affect Soil Microbial Community Structure And Interact With Carbon And Nitrogen Cycling", "description": "We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose ((13)C) additions at constant soil moisture. We extracted soil genomic DNA before and after incubation for TRFLP community fingerprinting of soil bacteria and fungi. We measured soil C and N pools before and after incubation, and we tracked total C respired and N mineralized at several points during the incubation. Twenty years of organic management altered soil bacterial and fungal community structure compared to continuous conventional management with the bacterial differences caused primarily by a large increase in diversity. Organically managed soils mineralized twice as much NO3 (-) as conventionally managed ones (44 vs. 23 \u03bcg N/g soil, respectively) and increased mineralization when labile C was added. There was no difference in respiration, but organically managed soils had larger pools of C suggesting greater efficiency in terms of respiration per unit soil C. These results indicate that the organic management induced a change in community composition resulting in a more diverse community with enhanced activity towards labile substrates and greater capacity to mineralize N.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Environmental Microbiology and Microbial Ecology", "Bacteria", "Nitrogen", "Fungal Community Structure", "Agriculture", "Nitrogen Cycle", "15. Life on land", "Microbiology", "630", "Carbon", "Carbon Cycle", "Soil", "03 medical and health sciences", "rRNA Gene Copy", "Soil Microbial Community Structure", "fungal community", "Biology", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1007/s00248-013-0225-0"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbial%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00248-013-0225-0", "name": "item", "description": "10.1007/s00248-013-0225-0", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00248-013-0225-0"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-04-16T00:00:00Z"}}, {"id": "10.1016/j.foreco.2022.120637", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:16:50Z", "type": "Journal Article", "created": "2022-11-25", "title": "How does management affect soil C sequestration and greenhouse gas fluxes in boreal and temperate forests? \u2013 A review", "description": "The global forest carbon (C) stock is estimated at 662 Gt of which 45% is in soil organic matter. Thus, comprehensive understanding of the effects of forest management practices on forest soil C stock and greenhouse gas (GHG) fluxes is needed for the development of effective forest-based climate change mitigation strategies. To improve this understanding, we synthesized peer-reviewed literature on forest management practices that canmitigate climate change by increasing soil C stocks and reducing GHG emissions. We further identified soil processes that affect soil GHG balance and discussed how models represent forest management effects on soil in GHG inventories and scenario analyses to address forest climate change mitigation potential.Forest management effects depend strongly on the specific practice and land type. Intensive timber harvesting with removal of harvest residues/stumps results in a reduction in soil C stock, while high stocking density and enhanced productivity by fertilization or dominance of coniferous species increase soil C stock. Nitrogenfertilization increases the soil C stock and N2O emissions while decreasing the CH4 sink. Peatland hydrology management is a major driver of the GHG emissions of the peatland forests, with lower water level corresponding to higher CO2 emissions. Furthermore, the global warming potential of all GHG emissions (CO2, CH4 and N2O) together can be ten-fold higher after clear-cutting than in peatlands with standing trees. The climate change mitigation potential of forest soils, as estimated by modelling approaches, accounts for stand biomass driven effects and climate factors that affect the decomposition rate. A future challenge is to account for the effects of soil preparation and other management that affects soil processes by changing soil temperature, soil moisture, soil nutrient balance, microbial community structure and processes, hydrology and soil oxygen concentration in the models. We recommend that soil monitoring and modelling focus on linkingprocesses of soil C stabilization with the functioning of soil microbiota.", "keywords": ["[SDE] Environmental Sciences", "330", "550", "Peatland hydrology management", "CLIMATE-CHANGE ADAPTATION", "WOOD ASH APPLICATION", "530", "Greenhouse gas", "SITE PREPARATION", "630", "12. Responsible consumption", "BELOW-GROUND CARBON", "11. Sustainability", "SDG 13 - Climate Action", "NITROGEN-FERTILIZATION", "SDG 15 - Life on Land", "2. Zero hunger", "PONDEROSA PINE", "GE", "PLANT LITTER DECOMPOSITION", "NORWAY SPRUCE", "04 agricultural and veterinary sciences", "15. Life on land", "004", "Forest fertilization", "Harvesting practices", "ORGANIC-MATTER", "Forest fire management", "13. Climate action", "[SDE]Environmental Sciences", "Forest soil carbon management", "0401 agriculture", " forestry", " and fisheries", "MICROBIAL COMMUNITY STRUCTURE", "GE Environmental Sciences"]}, "links": [{"href": "https://doi.org/10.1016/j.foreco.2022.120637"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Forest%20Ecology%20and%20Management", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.foreco.2022.120637", "name": "item", "description": "10.1016/j.foreco.2022.120637", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.foreco.2022.120637"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-02-01T00:00:00Z"}}, {"id": "10.1016/j.apsoil.2006.05.001", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:16:06Z", "type": "Journal Article", "created": "2006-06-19", "title": "Influence Of Organic And Mineral Amendments On Microbial Soil Properties And Processes", "description": "Abstract Microbial diversity in soils is considered important for maintaining sustainability of agricultural production systems. However, the links between microbial diversity and ecosystem processes are not well understood. This study was designed to gain better understanding of the effects of short-term management practices on the microbial community and how changes in the microbial community affect key soil processes. The effects of different forms of nitrogen (N) on soil biology and N dynamics was determined in two soils with organic and conventional management histories that varied in soil microbial properties but had the same fertility. The soils were amended with equal amounts of N (100\u00a0kg\u00a0ha\u22121) in organic (lupin, Lupinus angustifolius L.) and mineral form (urea), respectively. Over a 91-day period, microbial biomass C and N, dehydrogenase enzyme activity, community structure of pseudomondas (sensu stricto), actinomycetes and \u03b1 proteobacteria (by denaturing gradient gel electrophoresis (DGGE) following PCR amplification of 16S rDNA fragments) and N mineralisation were measured. Lupin amendment resulted in a two- to five-fold increase in microbial biomass and enzyme activity, while these parameters did not differ significantly between the urea and control treatments. The PCR\u2013DGGE analysis showed that the addition of mineral and organic compounds had an influence on the microbial community composition in the short term (up to 10 days) but the effects were not sustained over the 91-day incubation period. Microbial community structure was strongly influenced by the presence or lack of substrate, while the type of amendment (organic or mineral) had an effect on microbial biomass size and activity. These findings show that the addition of green manures improved soil biology by increasing microbial biomass and activity irrespective of management history, that no direct relationship existed among microbial structure, enzyme activity and N mineralisation, and that microbial community structure (by PCR\u2013DGGE) was more strongly influenced by inherent soil and environmental factors than by short-term management practices.", "keywords": ["2. Zero hunger", "570", "ANZSRC::31 Biological sciences", "nitrogen mineralisation", "urea", "ANZSRC::30 Agricultural", "04 agricultural and veterinary sciences", "15. Life on land", "630", "6. Clean water", "lupin (Lupinus angustifolius L.) green manure", "Marsden::300102 Soil biology", "veterinary and food sciences", "microbial community structure", "13. Climate action", "ANZSRC::41 Environmental sciences", "0401 agriculture", " forestry", " and fisheries", "DGGE", "organic and conventional farming practices"]}, "links": [{"href": "https://doi.org/10.1016/j.apsoil.2006.05.001"}, {"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.2006.05.001", "name": "item", "description": "10.1016/j.apsoil.2006.05.001", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.apsoil.2006.05.001"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-01-01T00:00:00Z"}}, {"id": "10.1007/s00374-011-0539-3", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:14:55Z", "type": "Journal Article", "created": "2011-01-18", "title": "Effects Of Organic And Inorganic Fertilization On Soil Bacterial And Fungal Microbial Diversity In The Kabete Long-Term Trial, Kenya", "description": "The effects of crop manure and inorganic fertilizers on composition of microbial communities of central high land soils of Kenya are poorly known. For this reason, we have carried out a thirty-two-year-old long-term trial in Kabete, Kenya. These soils were treated with organic (maize stover (MS) at 10 t ha\u22121, farmyard manure (FYM) at 10 t ha\u22121) and inorganic fertilizers 120 kg N, 52.8 kg P (N2P2), N2P2 + MS, N2P2 + FYM, a control, and a fallow for over 30 years. We examined 16S rRNA gene and 28S rRNA gene fingerprints of bacterial and fungal diversity by PCR amplification and denaturing gradient gel electrophoresis separation, respectively. The PCR bacterial community structure and diversity were negatively affected by N2P2 and were more closely related to the bacterial structure in the soils without any addition (control) than that of soils with a combination of inorganic and organic or inorganic fertilizers alone. The effect on fungal diversity by N2P2 was different than the effect on bacterial diversity since the fungal diversity was similar to that of the N2P2 + FYM and N2P2 + MS-treated. However, soils treated with organic inputs clustered away from soils amended with inorganic inputs. Organic inputs had a positive effect on both bacterial and fungal diversity with or without chemical fertilizers. Results from this study suggested that total diversity of bacterial and fungal communities was closely related to agro-ecosystem management practices and may partially explain the yield differences observed between the different treatments.", "keywords": ["[SDV.SA]Life Sciences [q-bio]/Agricultural sciences", "Microbial diversity", "soil microorganisms", "engrais organique", "http://aims.fao.org/aos/agrovoc/c_27870", "Organic and inorganic amendments", "F08 - Syst\u00e8mes et modes de culture", "rendement des cultures", "630", "fertilisation", "biodiversit\u00e9", "http://aims.fao.org/aos/agrovoc/c_4592", "http://aims.fao.org/aos/agrovoc/c_36669", "http://aims.fao.org/aos/agrovoc/c_2018", "inorganic fertilizers", "http://aims.fao.org/aos/agrovoc/c_10795", "http://aims.fao.org/aos/agrovoc/c_34326", "fertility", "2. Zero hunger", "[SDV.SA] Life Sciences [q-bio]/Agricultural sciences", "http://aims.fao.org/aos/agrovoc/c_33949", "g\u00e9n\u00e9tique des populations", "04 agricultural and veterinary sciences", "agro\u00e9cosyst\u00e8me", "6. Clean water", "fertilit\u00e9 du sol", "PCR", "http://aims.fao.org/aos/agrovoc/c_34079", "polymerization", "community structure", "abonos inorg\u00e1nicos", "management", "570", "http://aims.fao.org/aos/agrovoc/c_7170", "http://aims.fao.org/aos/agrovoc/c_7172", "flore microbienne", "soil", "http://aims.fao.org/aos/agrovoc/c_36167", "micro-organisme du sol", "http://aims.fao.org/aos/agrovoc/c_10176", "organic fertilizers", "abonos org\u00e1nicos", "pratique culturale", "microorganismos del suelo", "suelo", "flore du sol", "P35 - Fertilit\u00e9 du sol", "P34 - Biologie du sol", "polimerizaci\u00f3n", "15. Life on land", "engrais min\u00e9ral", "http://aims.fao.org/aos/agrovoc/c_16367", "http://aims.fao.org/aos/agrovoc/c_4086", "0401 agriculture", " forestry", " and fisheries", "F04 - Fertilisation"]}, "links": [{"href": "https://doi.org/10.1007/s00374-011-0539-3"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Biology%20and%20Fertility%20of%20Soils", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1007/s00374-011-0539-3", "name": "item", "description": "10.1007/s00374-011-0539-3", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1007/s00374-011-0539-3"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-01-19T00:00:00Z"}}, {"id": "10.1016/j.biortech.2018.09.044", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:16:16Z", "type": "Journal Article", "created": "2018-09-10", "title": "Biokinetics of microbial consortia using biogenic sulfur as a novel electron donor for sustainable denitrification", "description": "In this study, the biokinetics of autotrophic denitrification with biogenic S0 (ADBIOS) for the treatment of nitrogen pollution in wastewaters were investigated. The used biogenic S0, a by-product of gas desulfurization, was an elemental microcrystalline orthorhombic sulfur with a median size of 4.69\u202f\u00b5m and a specific surface area of 3.38\u202fm2/g, which made S0 particularly reactive and bioavailable. During denitritation, the biomass enriched on nitrite (NO2-) was capable of degrading up to 240\u202fmg/l NO2--N with a denitritation activity of 339.5\u202fmg NO2--N/g VSS\u00b7d. The use of biogenic S0 induced a low NO2--N accumulation, hindering the NO2--N negative impact on the denitrifying consortia and resulting in a specific denitrification activity of 223.0\u202fmg NO3--N/g VSS\u00b7d. Besides Thiobacillus being the most abundant genus, Moheibacter and Thermomonas were predominantly selected for denitrification and denitritation, respectively.", "keywords": ["Nitrite accumulation", "Nitrogen", "Microbial Consortia", "Biokinetics", "0211 other engineering and technologies", "Electrons", "02 engineering and technology", "Autotrophic denitrification", "Thiobacillus", "01 natural sciences", "6. Clean water", "Community structure", "12. Responsible consumption", "Kinetics", "Bioreactors", "13. Climate action", "Autotrophic denitrification; Biogenic sulfur; Nitrite accumulation; Biokinetics; Community structure", "Biogenic sulfur", "Denitrification", "Biomass", "Sulfur", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://eprints.gla.ac.uk/168662/1/168662.pdf"}, {"href": "https://www.iris.unina.it/bitstream/11588/722336/1/2018%20-%20Kostrytsia%20et%20al.%20-%20Bioresource%20Technology%20-%20Biokinetics%20of%20microbial%20consortia%20using%20biogenic%20S0.pdf"}, {"href": "https://doi.org/10.1016/j.biortech.2018.09.044"}, {"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.2018.09.044", "name": "item", "description": "10.1016/j.biortech.2018.09.044", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.biortech.2018.09.044"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-12-01T00:00:00Z"}}, {"id": "10.1016/j.jenvman.2018.01.064", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:17:05Z", "type": "Journal Article", "created": "2018-02-05", "title": "Elemental sulfur-based autotrophic denitrification and denitritation: microbially catalyzed sulfur hydrolysis and nitrogen conversions", "description": "The hydrolysis of elemental sulfur (S0) coupled to S0-based denitrification and denitritation was investigated in batch bioassays by microbiological and modeling approaches. In the denitrification experiments, the highest obtained NO3--N removal rate was 20.9\u202fmg/l\u00b7d. In the experiments with the biomass enriched on NO2-, a NO2--N removal rate of 10.7\u202fmg/l\u00b7d was achieved even at a NO2--N concentration as high as 240\u202fmg/l. The Helicobacteraceae family was only observed in the biofilm attached onto the chemically-synthesized S0 particles with a relative abundance up to 37.1%, suggesting it was the hydrolytic biomass capable of S0 solubilization in the novel surface-based model. S0-driven denitrification was modeled as a two-step process in order to explicitly account for the sequential reduction of NO3- to NO2- and then to N2 by denitrifying bacteria.", "keywords": ["Surface-based hydrolysis", "Autotrophic Processes", "Autotrophic denitrification; Autotrophic denitritation; Community structure; Elemental sulfur; Mathematical modeling; Surface-based hydrolysis", "Elemental sulfur", "Nitrates", "Nitrogen", "Hydrolysis", "0211 other engineering and technologies", "02 engineering and technology", "Autotrophic denitrification", "01 natural sciences", "6. Clean water", "Community structure", "Bioreactors", "Autotrophic denitritation", "Denitrification", "Autotrophic denitrification; Autotrophic denitritation; Elemental sulfur; Community structure; Surface-based hydrolysis; Mathematical modeling", "Mathematical modeling", "14. Life underwater", "Sulfur", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/698214/5/anastasiia%20JEMA.pdf"}, {"href": "https://doi.org/10.1016/j.jenvman.2018.01.064"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Environmental%20Management", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.jenvman.2018.01.064", "name": "item", "description": "10.1016/j.jenvman.2018.01.064", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.jenvman.2018.01.064"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-04-01T00:00:00Z"}}, {"id": "10.1186/s40793-020-00354-x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:20:08Z", "type": "Journal Article", "created": "2020-03-02", "title": "Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics", "description": "Abstract Background

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

Results

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

Conclusions

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

", "keywords": ["Integrated -omics", "Bioconversion", "0301 basic medicine", "570", "Polyomics", "Integrated-omics", "Biogas", "Microbiology", "7. Clean energy", "03 medical and health sciences", "Anaerobic digestion", "GE1-350", "2. Zero hunger", "0303 health sciences", "Metagenome assembled genomes", "Microbial community structure", "15. Life on land", "QR1-502", "6. Clean water", "3. Good health", "Environmental sciences", "Metagenome assembled genomes", " Integrated -omics", " Polyomics", " Anaerobic digestion", " Biogas", " Bioconversion", " Microbial community structure", " Methane", " Metabolic activity", "13. Climate action", "Metabolic activity", "Methane", "Research Article"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s40793-020-00354-x.pdf"}, {"href": "https://doi.org/10.1186/s40793-020-00354-x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40793-020-00354-x", "name": "item", "description": "10.1186/s40793-020-00354-x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40793-020-00354-x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-02T00:00:00Z"}}, {"id": "10.1016/j.scitotenv.2013.03.090", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:17:17Z", "type": "Journal Article", "created": "2013-04-24", "title": "Microbial Utilisation Of Biochar-Derived Carbon", "description": "Whilst largely considered an inert material, biochar has been documented to contain a small yet significant fraction of microbially available labile organic carbon (C). Biochar addition to soil has also been reported to alter soil microbial community structure, and to both stimulate and retard the decomposition of native soil organic matter (SOM). We conducted a short-term incubation experiment using two (13)C-labelled biochars produced from wheat or eucalypt shoots, which were incorporated in an aridic arenosol to examine the fate of the labile fraction of biochar-C through the microbial community. This was achieved using compound specific isotopic analysis (CSIA) of phospholipid fatty acids (PLFAs). A proportion of the biologically-available fraction of both biochars was rapidly (within three days) utilised by gram positive bacteria. There was a sharp peak in CO2 evolution shortly after biochar addition, resulting from rapid turnover of labile C components in biochars and through positive priming of native SOM. Our results demonstrate that this CO2 evolution was at least partially microbially mediated, and that biochar application to soil can cause significant and rapid changes in the soil microbial community; likely due to addition of labile C and increases in soil pH.", "keywords": ["Carbon sequestration", "[SDE] Environmental Sciences", "Carbon Sequestration", "Chromatography", " Gas", "Magnetic Resonance Spectroscopy", "550", "short term", "[SDV]Life Sciences [q-bio]", "growth", "black carbon", "Char", "01 natural sciences", "630", "Mass Spectrometry", "c 13 plfa", "Black carbon", "soil organic matter", "Soil Pollutants", "mineralization", "Organic carbon", "Phospholipids", "Soil Microbiology", "char", "0105 earth and related environmental sciences", "2. Zero hunger", "Carbon Isotopes", "decomposition", "wheat straw", "biomass", "organic carbon", "Fatty Acids", "Western Australia", "04 agricultural and veterinary sciences", "Carbon Dioxide", "15. Life on land", "540", "pyrolysis", "forest soil", "carbon sequestration", "Carbon", "[SDV] Life Sciences [q-bio]", "Charcoal", "[SDE]Environmental Sciences", "0401 agriculture", " forestry", " and fisheries", "community structure", "\u00b9\u00b3C-PLFA", "Pyrolysis"]}, "links": [{"href": "https://doi.org/10.1016/j.scitotenv.2013.03.090"}, {"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.2013.03.090", "name": "item", "description": "10.1016/j.scitotenv.2013.03.090", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.scitotenv.2013.03.090"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-11-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2008.05.007", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:17:27Z", "type": "Journal Article", "created": "2008-06-12", "title": "Long-Term Organic Farming Fosters Below And Aboveground Biota: Implications For Soil Quality, Biological Control And Productivity", "description": "Organic farming may contribute substantially to future agricultural production worldwide by improving soil quality and pest control, thereby reducing environmental impacts of conventional farming. We investigated in a comprehensive way soil chemical, as well as below and aboveground biological parameters of two organic and two conventional wheat farming systems that primarily differed in fertilization and weed management strategies. Contrast analyses identified management related differences between \u201cherbicide-free\u201d bioorganic (BIOORG) and biodynamic (BIODYN) systems and conventional systems with (CONFYM) or without manure (CONMIN) and herbicide application within a long-term agricultural experiment (DOK trial, Switzerland). Soil carbon content was significantly higher in systems receiving farmyard manure and concomitantly microbial biomass (fungi and bacteria) was increased. Microbial activity parameters, such as microbial basal respiration and nitrogen mineralization, showed an opposite pattern, suggesting that soil carbon in the conventional system (CONFYM) was more easily accessible to microorganisms than in organic systems. Bacterivorous nematodes and earthworms were most abundant in systems that received farmyard manure, which is in line with the responses of their potential food sources (microbes and organic matter). Mineral fertilizer application detrimentally affected enchytraeids and Diptera larvae, whereas aphids benefited. Spider abundance was favoured by organic management, most likely a response to increased prey availability from the belowground subsystem or increased weed coverage. In contrast to most soil-based, bottom-up controlled interactions, the twofold higher abundance of this generalist predator group in organic systems likely contributed to the significantly lower abundance of aboveground herbivore pests (aphids) in these systems. Long-term organic farming and the application of farmyard manure promoted soil quality, microbial biomass and fostered natural enemies and ecosystem engineers, suggesting enhanced nutrient cycling and pest control. Mineral fertilizers and herbicide application, in contrast, affected the potential for top-down control of aboveground pests negatively and reduced the organic carbon levels. Our study indicates that the use of synthetic fertilizers and herbicide application changes interactions within and between below and aboveground components, ultimately promoting negative environmental impacts of agriculture by reducing internal biological cycles and pest control. On the contrary, organic farming fosters microbial and faunal decomposers and this propagates into the aboveground system via generalist predators thereby increasing conservation biological control. However, grain and straw yields were 23% higher in systems receiving mineral fertilizers and herbicides reflecting the trade-off between productivity and environmental responsibility.", "keywords": ["[SDE] Environmental Sciences", "generalist predators", "respiration microbienne", "[SDV]Life Sciences [q-bio]", "faune du sol", "natural enemies", "alternative prey", "630", "nitrogen", "food-web", "Soil", "agriculture biologique", "cycle biologique", "herbicide", "min\u00e9ralisation de l'azote", "fertilisation organique", "fertilisation min\u00e9rale", "soil quality", "2. Zero hunger", "agriculture biodynamique", "agriculture conventionnelle", "nutrient cycling", "04 agricultural and veterinary sciences", "sustainability", "long terme", "6. Clean water", "[SDV] Life Sciences [q-bio]", "mycorrhizal fungi", "ennemi naturel", "microbial community structure", "ecosystem functioning", "[SDE]Environmental Sciences", "DOK trial;ecosystem functioning;farming system;fertilization;generalist predators;microbial community;nutrient cycling;natural enemies;soil fauna;soil quality;sustainability", "microbial community", "soil fauna", "agricultural systems", "management", "570", "agroecosystems", "Soil quality", "suisse", "productivit\u00e9", "Soil biology", "culture c\u00e9r\u00e9aliere", "triticum aestivum", "biomasse microbienne", "biomass", "DOK trial", "15. Life on land", "qualit\u00e9 biologique du sol", "fertilization", "13. Climate action", "Biodiversity and ecosystem services", "0401 agriculture", " forestry", " and fisheries", "farming system", "Cereals", " pulses and oilseeds"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2008.05.007"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2008.05.007", "name": "item", "description": "10.1016/j.soilbio.2008.05.007", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2008.05.007"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-09-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2007.02.001", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:17:26Z", "type": "Journal Article", "created": "2007-03-13", "title": "Nitrogen Fertilization Reduces Diversity And Alters Community Structure Of Active Fungi In Boreal Ecosystems", "description": "Nitrogen (N) availability is increasing in many ecosystems due to anthropogenic disturbance. We used a nucleotide analog technique and sequencing of ribosomal RNA genes to test whether N fertilization altered active fungal communities in two boreal ecosystems. In decaying litter from a recently burned spruce forest, Shannon diversity decreased significantly with N fertilization, and taxonomic richness declined from 44 to 33 operational taxonomic units (OTUs). In soils from a mature spruce forest, richness also declined with N fertilization, from 67 to 52 OTUs. Fungal community structure in litter differed significantly with N fertilization, primarily because fungi of the order Ceratobasidiales increased in abundance. We observed similar changes in fungal diversity and community structure with starch addition to litter, suggesting that N fertilization may affect fungal communities by altering plant carbon inputs. These changes could have important consequences for ecosystem processes such as decomposition and nutrient mineralization.", "keywords": ["ribosomal genes", "0301 basic medicine", "nucleotide analog", "carbon", "04 agricultural and veterinary sciences", "15. Life on land", "nitrogen", "diversity", "03 medical and health sciences", "fertilization", "litter quality", "0401 agriculture", " forestry", " and fisheries", "fungi", "boreal forest", "community structure"]}, "links": [{"href": "https://escholarship.org/content/qt2rs399mh/qt2rs399mh.pdf"}, {"href": "https://doi.org/10.1016/j.soilbio.2007.02.001"}, {"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.2007.02.001", "name": "item", "description": "10.1016/j.soilbio.2007.02.001", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2007.02.001"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2007-08-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2011.03.005", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:17:30Z", "type": "Journal Article", "created": "2011-04-15", "title": "Experimental Warming Effects On The Microbial Community Of A Temperate Mountain Forest Soil", "description": "Soil microbial communities mediate the decomposition of soil organic matter (SOM). The amount of carbon (C) that is respired leaves the soil as CO(2) (soil respiration) and causes one of the greatest fluxes in the global carbon cycle. How soil microbial communities will respond to global warming, however, is not well understood. To elucidate the effect of warming on the microbial community we analyzed soil from the soil warming experiment Achenkirch, Austria. Soil of a mature spruce forest was warmed by 4\u00a0\u00b0C during snow-free seasons since 2004. Repeated soil sampling from control and warmed plots took place from 2008 until 2010. We monitored microbial biomass C and nitrogen (N). Microbial community composition was assessed by phospholipid fatty acid analysis (PLFA) and by quantitative real time polymerase chain reaction (qPCR) of ribosomal RNA genes. Microbial metabolic activity was estimated by soil respiration to biomass ratios and RNA to DNA ratios. Soil warming did not affect microbial biomass, nor did warming affect the abundances of most microbial groups. Warming significantly enhanced microbial metabolic activity in terms of soil respiration per amount of microbial biomass C. Microbial stress biomarkers were elevated in warmed plots. In summary, the 4\u00a0\u00b0C increase in soil temperature during the snow-free season had no influence on microbial community composition and biomass but strongly increased microbial metabolic activity and hence reduced carbon use efficiency.", "keywords": ["2. Zero hunger", "13. Climate action", "Microbial biomass", "PLFA", "Soil warming", "rRNA genes", "Soil Science", "0401 agriculture", " forestry", " and fisheries", "Microbial community structure", "04 agricultural and veterinary sciences", "15. Life on land", "Microbiology", "Article"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2011.03.005"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2011.03.005", "name": "item", "description": "10.1016/j.soilbio.2011.03.005", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2011.03.005"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2011-07-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2013.07.001", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:17:32Z", "type": "Journal Article", "created": "2013-07-14", "title": "Agricultural Management Affects The Response Of Soil Bacterial Community Structure And Respiration To Water-Stress", "description": "Soil microorganisms are responsible for organic matter decomposition processes that regulate soil carbon storage and mineralisation to CO2. Climate change is predicted to increase the frequency of drought events, with uncertain consequences for soil microbial communities. In this study we tested the hypothesis that agricultural management used to enhance soil carbon stocks would increase the stability of microbial community structure and activity in response to water-stress. Soil was sampled from a long-term field trial with three soil carbon management systems and was used in a laboratory study of the effect of a dry\u2013wet cycle on organic C mineralisation and microbial community structure. After a drying\u2013rewetting event, soil microcosms were maintained wet and microbial community structure and abundance as well as microbial respiration were measured for four weeks. The results showed that the NO-TILL management system, with the highest soil organic matter content and respiration rate, had a distinct bacterial community structure relative to the conventional and the TILL without fertiliser systems. In all management systems, the rewetting event clearly modified microbial community structure and activity. Both returned to their pre-drought state after 28 days. However, the magnitude of variation of C mineralisation was lower (i.e. the resistance to stress was higher) in the NO-TILL system. The genetic structure of the NO-TILL bacterial communities was most modified by water-stress and exhibited a slower recovery rate. This suggests that land use management can increase microbial functional resistance to drought stress via the establishment of bacterial communities with particular metabolic capacities. Nevertheless, the resilience rates of C mineralisation were similar among management regimes, suggesting that similar mechanisms occur, maybe due to a common soil microbial community legacy.", "keywords": ["[SDE] Environmental Sciences", "570", "Agricultural land use", "[SDV]Life Sciences [q-bio]", "630", "Drying-rewetting", "FUNCTIONAL STABILITY", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "Drying\u2013rewetting", "NITROGEN MINERALIZATION", "Global change", "2. Zero hunger", "C mineralisation", "CLIMATE-CHANGE", "MICROBIAL COMMUNITY", "LAND-USE CHANGE", "04 agricultural and veterinary sciences", "RESILIENCE", "15. Life on land", "DRYING-REWETTING FREQUENCY", "6. Clean water", "[SDV] Life Sciences [q-bio]", "ORGANIC-MATTER", "13. Climate action", "[SDE]Environmental Sciences", "Bacterial community structure", "0401 agriculture", " forestry", " and fisheries", "CATABOLIC DIVERSITY", "CARBON STOCKS", "Stability"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2013.07.001"}, {"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.2013.07.001", "name": "item", "description": "10.1016/j.soilbio.2013.07.001", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2013.07.001"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-11-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2014.06.024", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:17:33Z", "type": "Journal Article", "created": "2014-07-03", "title": "Identifying Response Groups Of Soil Nitrifiers And Denitrifiers To Grazing And Associated Soil Environmental Drivers In Tibetan Alpine Meadows", "description": "Defining response groups within N-related microbial communities is needed to predict land management effect on soil N dynamics, but information on such response groups and associated environmental drivers is scarce. We investigated the abundance and major populations of ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nirS- and nirK-harboring denitrifiers under different grazing managements in Tibetan alpine meadow soils. Grazing increased AOB and AOA abundances up to 42 fold and 3.7 fold, respectively, and increased the percentage of AOB within total ammonia oxidizers from 3.1% to 10.8%. The abundance of nirK-like denitrifiers increased with grazing intensity, while the abundance of nirS-like denitrifiers tended to decrease. However, sub-groups within each of these broad groups of (de)nitrifiers responded differently to grazing. Soil nitrate was the main driver of the abundance of denitrifier subgroups (nirK or nirS) positively responding to grazing, while soil moisture and carbon concentration were the main drivers of the abundance of denitrifier sub-groups negatively responding to grazing. AOB and nirK-harboring denitrifiers thus generally responded more positively to grazing than AOA and nirS-harboring denitrifiers, but significant functional diversity existed within each group. Our approach demonstrates the usefulness of the concept of response groups to better characterize and understand (de)nitrifier response to grazing. (C) 2014 Elsevier Ltd. All rights reserved.", "keywords": ["nirS", "2. Zero hunger", "Soil nitrogen cycling", "[SDV]Life Sciences [q-bio]", "04 agricultural and veterinary sciences", "15. Life on land", "630", "AOA", "AOB", "Community structure", "[SDV] Life Sciences [q-bio]", "Abundance", "nirK", "amoA", "0401 agriculture", " forestry", " and fisheries"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2014.06.024"}, {"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.2014.06.024", "name": "item", "description": "10.1016/j.soilbio.2014.06.024", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2014.06.024"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-10-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2016.03.008", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:17:35Z", "type": "Journal Article", "created": "2016-03-26", "title": "Soil microbial carbon use efficiency and biomass turnover in a long-term fertilization experiment in a temperate grassland", "description": "

Soil microbial carbon use efficiency (CUE), defined as the ratio of organic C allocated to growth over organic C taken up, strongly affects soil carbon (C) cycling. Despite the importance of the microbial CUE for the terrestrial C cycle, very little is known about how it is affected by nutrient availability. Therefore, we studied microbial CUE and microbial biomass turnover time in soils of a long-term fertilization experiment in a temperate grassland comprising five treatments (control, PK, NK, NP, NPK). Microbial CUE and the turnover of microbial biomass were determined using a novel substrate-independent method based on incorporation of 18O from labeled water into microbial DNA. Microbial respiration was 28-37% smaller in all three N treatments (NK, NP, and NPK) compared to the control, whereas the PK treatment did not affect microbial respiration. N-fertilization decreased microbial C uptake, while the microbial growth rate was not affected. Microbial CUE ranged between 0.31 and 0.45, and was 1.3- to 1.4-fold higher in the N-fertilized soils than in the control. The turnover time ranged between 80 and 113 days and was not significantly affected by fertilization. Net primary production (NPP) and the abundance of legumes differed strongly across the treatments, and the fungal:bacterial ratio was very low in all treatments. Structural equation modeling revealed that microbial CUE was exclusively controlled by N fertilization and that neither the abundance of legumes (as a proxy for the quality of the organic matter inputs) nor NPP (as a proxy for C inputs) had an effect on microbial CUE. Our results show that N fertilization did not only decrease microbial respiration, but also microbial C uptake, indicating that less C was intracellularly processed in the N fertilized soils. The reason for reduced C uptake and increased CUE in the N-fertilization treatments is likely an inhibition of oxidative enzymes involved in the degradation of aromatic compounds by N in combination with a reduced energy requirement for microbial N acquisition in the fertilized soils. In conclusion, the study shows that N availability can control soil C cycling by affecting microbial CUE, while plant community-mediated changes in organic matter inputs and P and K availability played no important role for C partitioning of the microbial community in this temperate grassland.

", "keywords": ["FUNGAL", "2. Zero hunger", "106022 Mikrobiologie", "Nitrogen addition", "BACTERIAL", "NITROGEN DEPOSITION", "GROWTH EFFICIENCY", "FOREST FLOOR", "Nutrients", "04 agricultural and veterinary sciences", "15. Life on land", "Stoichiometry", "ORGANIC-MATTER", "RESPIRATION", "106026 \u00d6kosystemforschung", "13. Climate action", "Nutrient limitation", "Microbial growth yield", "106022 Microbiology", "0401 agriculture", " forestry", " and fisheries", "Mean residence time", "STOICHIOMETRIC CONTROLS", "ENZYME-ACTIVITY", "106026 Ecosystem research", "COMMUNITY STRUCTURE"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2016.03.008"}, {"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.2016.03.008", "name": "item", "description": "10.1016/j.soilbio.2016.03.008", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2016.03.008"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2015.11.007", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:17:34Z", "type": "Journal Article", "created": "2015-11-25", "title": "Aboveground Litter Quality Is A Better Predictor Than Belowground Microbial Communities When Estimating Carbon Mineralization Along A Land-Use Gradient", "description": "Because of the vegetation cover and anthropogenic disturbances, land-use management strongly influences soil heterotrophic decomposers. Yet, little is known about whether contrasting microbial communities originating from different ecosystems are functionally similar, and only a few studies have disentangled the direct and indirect effects of resource quality on both microbial communities and carbon mineralization rates. To assess the relative importance of aboveground litter quality and belowground microbial communities on litter decomposition, we conducted a reciprocal transplant experiment under controlled conditions using four litters (Triticum aestivum, Fagus sylvatica, Festuca arundinacea and Robinia pseudoacacia) and four soils (culture, plantation, grassland and forest) originating from a land-use gradient. We followed the kinetics of carbon mineralization over 21 dates spanning a 202-day period to assess the variability of responses generated by the plant\u2013soil interactions. Furthermore, at four time points (at 0, 27, 97 and 202 days), the mass loss rates for the main sugars within the cell wall, the microbial biomass (fumigation-extraction), the microbial community structure via phospholipid fatty acid (PLFA), and the activities of four carbon-related hydrolytic enzymes were investigated to assess the functional significance of microbial communities. Our results demonstrated that the importance of soil types and heterotrophic decomposers on carbon mineralization rates was minor (1.2% of the variance explained) compared with the predominant role of litter quality. The structure of the microbial communities responded strongly to both long-term land-use changes and short-term litter additions; specifically, (i) higher proportions of fungi were observed in natural ecosystems compared with agro-systems, and (ii) an opportunistic subset of the bacterial community was stimulated after litter additions. Even if the land-use management and litter quality can shape the microbial community structure in a foreseeable way, we found an important degree of plasticity in the responses of contrasting decomposer communities. In particular, the enzymatic efficiency (defined as the amount of enzyme produced by unit of carbon mineralized) differed among litters but not among soil types, suggesting that the threshold between carbon allocation to growth and acquisition depended more on the \u2018resource-use strategies\u2019 of the soil microorganisms than on the community structure. The recalcitrant litters stimulated \u2018efficient\u2019 communities characterized by low enzymatic activities, microbial biomass and respiration rates at the opposite of labile litters that stimulated \u2018wasteful\u2019 communities characterized by higher activities and metabolic quotient (defined as the amount of carbon respired by unit of biomass). In addition to the direct effects of litter quality, the path analysis reinforced our conclusion that the functional traits of microorganisms via their enzymatic activities are more relevant than their identity for predicting carbon mineralization. Thus, although multiple and coordinated responses of soil microbes can improve our understanding of carbon fluxes, shifts in the plant community composition caused by land-use conversion will have a stronger impact on predictions of carbon mineralization than short-term changes in the microbial community composition.", "keywords": ["2. Zero hunger", "Decomposition", "550", "Functional dissimilarity", "Microbial community structure", "Carbon cycle", "04 agricultural and veterinary sciences", "15. Life on land", "Enzymes", "Litter traits", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "Plant\u2013soil interactions", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology"]}, "links": [{"href": "https://doi.org/10.1016/j.soilbio.2015.11.007"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Soil%20Biology%20and%20Biochemistry", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1016/j.soilbio.2015.11.007", "name": "item", "description": "10.1016/j.soilbio.2015.11.007", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1016/j.soilbio.2015.11.007"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-03-01T00:00:00Z"}}, {"id": "10.1016/j.soilbio.2022.108604", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:17:36Z", "type": "Journal Article", "created": "2022-03-18", "title": "From diversity to complexity: Microbial networks in soils", "description": "ABSTRACT

Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research.Soils 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.

Resource control over abundance, structure and functional diversity of soil microbial communities is a key determinant of soil processes and related ecosystem functioning. Copiotrophic organisms tend to be found in environments which are rich in nutrients, particularly carbon, in contrast to oligotrophs, which survive in much lower carbon concentrations.

We hypothesized that microbial biomass, activity and community structure in nutrient\uffe2\uff80\uff90poor soils of an Amazonian rain forest are limited by multiple elements in interaction. We tested this hypothesis with a fertilization experiment by adding C (as cellulose), N (as urea) and P (as phosphate) in all possible combinations to a total of 40 plots of an undisturbed tropical forest in French Guiana.

After 2\uffc2\uffa0years of fertilization, we measured a 47% higher biomass, a 21% increase in substrate\uffe2\uff80\uff90induced respiration rate and a 5\uffe2\uff80\uff90fold higher rate of decomposition of cellulose paper discs of soil microbial communities that grew in P\uffe2\uff80\uff90fertilized plots compared to plots without P fertilization. These responses were amplified with a simultaneous C fertilization suggesting P and C colimitation of soil micro\uffe2\uff80\uff90organisms at our study site.

Moreover, P fertilization modified microbial community structure (PLFAs) to a more copiotrophic bacterial community indicated by a significant decrease in the Gram\uffe2\uff80\uff90positive\uffc2\uffa0:\uffc2\uffa0Gram\uffe2\uff80\uff90negative ratio. The Fungi\uffc2\uffa0:\uffc2\uffa0Bacteria ratio increased in N fertilized plots, suggesting that fungi are relatively more limited by N than bacteria. Changes in microbial community structure did not affect rates of general processes such as glucose mineralization and cellulose paper decomposition. In contrast, community level physiological profiles under P fertilization combined with either C or N fertilization or both differed strongly from all other treatments, indicating functionally different microbial communities.

While P appears to be the most critical from the three major elements we manipulated, the strongest effects were observed in combination with either supplementary C or N addition in support of multiple element control on soil microbial functioning and community structure.

We conclude that the soil microbial community in the studied tropical rain forest and the processes it drives is finely tuned by the relative availability in C, N and P. Any shifts in the relative abundance of these key elements may affect spatial and temporal heterogeneity in microbial community structure, their associated functions and the dynamics of C and nutrients in tropical ecosystems.

", "keywords": ["tropical forest", "2. Zero hunger", "570", "phospholipid fatty acids (PLFA)", "[SDE.MCG]Environmental Sciences/Global Changes", "functional significance", "[SDV.EE.IEO] Life Sciences [q-bio]/Ecology", " environment/Symbiosis", "04 agricultural and veterinary sciences", "15. Life on land", "16. Peace & justice", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "[SDE.MCG] Environmental Sciences/Global Changes", "13. Climate action", "microbial community structure", "ecosystem functioning", "environment/Symbiosis", "[SDV.EE.ECO]Life Sciences [q-bio]/Ecology", "[SDV.EE.ECO] Life Sciences [q-bio]/Ecology", " environment/Ecosystems", "[SDV.EE.IEO]Life Sciences [q-bio]/Ecology", "0401 agriculture", " forestry", " and fisheries", "multiple resource limitation", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "phosphorus", "environment/Ecosystems", "soil functioning"]}, "links": [{"href": "https://doi.org/10.1111/1365-2435.12329"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Functional%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1365-2435.12329", "name": "item", "description": "10.1111/1365-2435.12329", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1365-2435.12329"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2014-09-29T00:00:00Z"}}, {"id": "10.1111/gcb.16989", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:19:26Z", "type": "Journal Article", "created": "2023-10-27", "title": "Shifts in soil ammonia\u2010oxidizing community maintain the nitrogen stimulation of nitrification across climatic conditions", "description": "Abstract

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.Microorganisms carrying pmoA and nosZ genes are major drivers of methane and nitrous oxide fluxes from soils. However, most studies on these organisms have been conducted in mesic ecosystems; therefore, little is known about the factors driving their distribution in drylands, the largest biome on Earth. We conducted a global survey to evaluate the role of climate\uffe2\uff80\uff90 and soil\uffe2\uff80\uff90related variables as predictors of the richness, abundance and community structure of bacteria carrying pmoA and nosZ genes.

Location

Eighty dryland ecosystems distributed worldwide.

Time period

From February 2006 to December 2011.

Major taxa studied

Methanotrophic (carrying the pmoA gene) and denitrifiying (carrying the nosZ gene) bacteria.

Methods

We used data from a field survey and structural equation modelling to evaluate the direct and indirect effects of climatic (aridity, rainfall seasonality and mean annual temperature) and soil (organic carbon, pH and texture) variables on the total abundance, richness and community structure of microorganisms carrying pmoA and nosZ genes.

Results

Taxa related to Methylococcus capsulatus or Methylocapsa sp., often associated with mesic environments, were common in global drylands. The abundance and richness of methanotrophs were not associated with climate or soil properties. However, mean annual temperature, rainfall seasonality, organic C, pH and sand content were highly correlated with their community structure. Aridity and soil variables, such as sand content and pH, were correlated with the abundance, community structure and richness of the nosZ bacterial community.

Main conclusions

Our study provides new insights into the drivers of the abundance, richness and community structure of soil microorganisms carrying pmoA and nosZ genes in drylands worldwide. We highlight how ongoing climate change will alter the structure of soil microorganisms, which might affect the net CH4 exchange and will probably reduce the capacity of dryland soils to carry out the final step of denitrification, favouring net N2O emissions.Plant community composition is affected by a wide array of soil organisms with diverse feeding modes and functions. Former studies dealt with the high diversity and complexity of soil communities by focusing on particular functional groups in isolation, by grouping soil organisms into body size classes or by using whole communities from different origins. Our approach was to investigate both the individual and the interaction effects of highly abundant soil organisms (microorganisms, nematodes and earthworms) to evaluate their impacts on grassland plant communities. Earthworms increased total plant community biomass by stimulating root growth. Nematodes reduced the biomass of grasses, but this effect was alleviated by the presence of earthworms. Non\uffe2\uff80\uff90leguminous forb biomass increased in the presence of nematodes, probably due to an alleviation of the competitive strength of grasses by nematodes. Microorganisms reduced the diversity and evenness of the plant community, but only in the absence of earthworms. Legume biomass was not affected by soil organisms, butLotus corniculatusflowered earlier in the presence of microorganisms and the number of flowers decreased in the presence of nematodes. The results indicate that earthworms have a profound impact on the structure of grassland plant communities by counterbalancing the negative effects of plant\uffe2\uff80\uff90feeding nematodes on grasses and by conserving the evenness of the plant community. We propose that interacting effects of functionally dissimilar soil organisms on plant community performance have to be taken into account in future studies, since individual effects of soil organism groups may cancel out each other in functionally diverse soil communities.

", "keywords": ["2. Zero hunger", "0106 biological sciences", "0301 basic medicine", "productivity", "microbial biomass", "ground insect herbivory", "early succession", "15. Life on land", "determinant", "01 natural sciences", "03 medical and health sciences", "lumbricidae", "soil food-web", "community structure", "grassland", "performance"]}, "links": [{"href": "https://doi.org/10.1111/j.0030-1299.2008.16333.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Oikos", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.0030-1299.2008.16333.x", "name": "item", "description": "10.1111/j.0030-1299.2008.16333.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.0030-1299.2008.16333.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2008-04-28T00:00:00Z"}}, {"id": "10.1111/j.1365-2745.2008.01472.x", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:19:37Z", "type": "Journal Article", "created": "2009-01-21", "title": "Determinants Of Cryptogam Composition And Diversity In Sphagnum-Dominated Peatlands: The Importance Of Temporal, Spatial And Functional Scales", "description": "Summary

Changing temperature regimes and precipitation patterns in the Subarctic will impact on vegetation composition and diversity including those of bryophyte and lichen communities, which are major drivers of high\uffe2\uff80\uff90latitude carbon and nutrient cycling and hydrology.

We investigated the relative importance of such impacts at different temporal, spatial and plant functional scales in subarctic Sphagnum fuscum\uffe2\uff80\uff90dominated peatlands, comprising both an in situ warming experiment and natural climatic and topographic gradients in northern Sweden and Norway. We applied multivariate analyses to investigate the relationships among cryptogam and vascular plant species composition and abiotic (temperature, moisture) and biotic (Sphagnum growth) regimes at various scales.

At the short\uffe2\uff80\uff90term temporal scale (4\uffe2\uff80\uff90year warming experiment), increased temperature yielded no clear effect on cryptogam or vascular plant species composition. Spatially, direct effects of temperature were decisive for overall species composition across regions (macro\uffe2\uff80\uff90scale) rather than within one region (meso\uffe2\uff80\uff90scale). Moisture and Sphagnum growth were drivers of species composition at all spatial scales, and Sphagnum growth itself depended on its position on the microtopographic gradient and on temperature.

Grouping of bryophytes and lichens at increasing scales of functional aggregation from species, growth form to the major higher taxon level (Sphagnum, other mosses, liverworts, lichens) revealed mostly increasing correlation with climate regimes and Sphagnum growth. Excluding liverworts from the analysis tended to reduce the correlation.

Abundances of lichens, liverworts, non\uffe2\uff80\uff90Sphagnum mosses and (to a lesser degree) vascular plants were negatively related to Sphagnum abundance. Few cryptogam and vascular plant species showed a positive relationship with Sphagnum abundance. Correspondingly, cryptogam species richness and Shannon Index on peatlands strongly declined as Sphagnum abundance increased, while indices for vascular plants showed no significant relationship.

Synthesis. Scale, be it spatial or functional, strongly determined which environmental drivers showed the clearest relationships with vegetation composition and diversity. Our findings will help to optimize predictions about long\uffe2\uff80\uff90term effects of climate on peatland vegetation composition, and subsequently its feedbacks to carbon and water cycles, at the regional scale.

", "keywords": ["0106 biological sciences", "simulated environmental-change", "species composition", "western canada", "alaskan arctic tundra", "response surfaces", "15. Life on land", "01 natural sciences", "hylocomium-splendens", "13. Climate action", "physical gradients", "SDG 13 - Climate Action", "nutrient availability", "community structure", "global change"]}, "links": [{"href": "https://doi.org/10.1111/j.1365-2745.2008.01472.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1365-2745.2008.01472.x", "name": "item", "description": "10.1111/j.1365-2745.2008.01472.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1365-2745.2008.01472.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-02-11T00:00:00Z"}}, {"id": "10.1111/jam.13606", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:19:48Z", "type": "Journal Article", "created": "2017-10-09", "title": "Soil Microbiota Respond To Green Manure In Organic Vineyards", "description": "The aim of this work was to investigate the effects of biodynamic management with and without the addition of green manure, in comparison with organic management, on the microbiota in vineyards soil.High throughput sequencing was used to compare the taxonomic structure of the soil bacterial and fungal communities from vineyards managed with different methods (organic, biodynamic or biodynamic with green manure). Our results showed that microbial communities associated with biodynamic and organic farming systems were very similar, while green manure was the greatest source of soil microbial biodiversity and significantly changed microbial richness and community composition compared with other soils. Green manure also significantly enriched bacterial taxa involved in the soil nitrogen cycle (e.g. Microvirga sp., Pontibacter sp. and Nitrospira sp.).Our results showed that the diversity and composition of the microbial communities associated with biodynamic and organic farming systems were similar, indicating that the use of biodynamic preparations 500 and 501 did not cause any significant detectable changes to the soil microbial community in the short term, while the effects of green manure were significant in soil microbiota.The microbiological richness and structure of soil are used as a sensitive indicator of soil quality. The extension of organic/biodynamic farming, associated with green manure application, could contribute to increase the abundance of functional groups of biological and agronomical relevance and maintaining microbial biodiversity in vineyard soils.", "keywords": ["0301 basic medicine", "2. Zero hunger", "570", "Microbial diversity", "Organic Agriculture", "0303 health sciences", "bacteria; biodynamic vineyard; fungi; green manure; microbial community structure; microbial diversity; organic vineyard; soil microbiology; soil vineyard", "Microbiota", "Green manure", "Microbial community structure", "Biodiversity", "15. Life on land", "630", "Manure", "Soil vineyard", "Soil", "03 medical and health sciences", "Soil microbiology", "13. Climate action", "Settore AGR/16 - MICROBIOLOGIA AGRARIA", "Vitis", "Soil Microbiology"]}, "links": [{"href": "https://iris.unitn.it/bitstream/11572/283669/1/jam.13606.pdf"}, {"href": "https://doi.org/10.1111/jam.13606"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Applied%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/jam.13606", "name": "item", "description": "10.1111/jam.13606", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/jam.13606"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-11-03T00:00:00Z"}}, {"id": "10.1371%2fjournal.pone.0060441", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:20:14Z", "type": "Journal Article", "created": "2013-03-27", "title": "Nitrogen Addition And Warming Independently Influence The Belowground Micro-Food Web In A Temperate Steppe", "description": "Climate warming and atmospheric nitrogen (N) deposition are known to influence ecosystem structure and functioning. However, our understanding of the interactive effect of these global changes on ecosystem functioning is relatively limited, especially when it concerns the responses of soils and soil organisms. We conducted a field experiment to study the interactive effects of warming and N addition on soil food web. The experiment was established in 2006 in a temperate steppe in northern China. After three to four years (2009-2010), we found that N addition positively affected microbial biomass and negatively influenced trophic group and ecological indices of soil nematodes. However, the warming effects were less obvious, only fungal PLFA showed a decreasing trend under warming. Interestingly, the influence of N addition did not depend on warming. Structural equation modeling analysis suggested that the direct pathway between N addition and soil food web components were more important than the indirect connections through alterations in soil abiotic characters or plant growth. Nitrogen enrichment also affected the soil nematode community indirectly through changes in soil pH and PLFA. We conclude that experimental warming influenced soil food web components of the temperate steppe less than N addition, and there was little influence of warming on N addition effects under these experimental conditions.", "keywords": ["China", "Food Chain", "Nematoda", "Nitrogen", "Science", "deposition", "Models", " Biological", "northern china", "Soil", "soil nematodes", "Animals", "Biomass", "organic-matter", "global change", "Phospholipids", "Soil Microbiology", "2. Zero hunger", "elevated co2", "Analysis of Variance", "species composition", "Q", "R", "Temperature", "04 agricultural and veterinary sciences", "Plants", "15. Life on land", "13. Climate action", "international", "climate-change manipulations", "plant-communities", "Medicine", "0401 agriculture", " forestry", " and fisheries", "community structure", "Research Article"]}, "links": [{"href": "https://doi.org/10.1371%2fjournal.pone.0060441"}, {"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%2fjournal.pone.0060441", "name": "item", "description": "10.1371%2fjournal.pone.0060441", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371%2fjournal.pone.0060441"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-03-27T00:00:00Z"}}, {"id": "10.1371/journal.pone.0060441", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:20:16Z", "type": "Journal Article", "created": "2013-03-27", "title": "Nitrogen Addition And Warming Independently Influence The Belowground Micro-Food Web In A Temperate Steppe", "description": "Climate warming and atmospheric nitrogen (N) deposition are known to influence ecosystem structure and functioning. However, our understanding of the interactive effect of these global changes on ecosystem functioning is relatively limited, especially when it concerns the responses of soils and soil organisms. We conducted a field experiment to study the interactive effects of warming and N addition on soil food web. The experiment was established in 2006 in a temperate steppe in northern China. After three to four years (2009-2010), we found that N addition positively affected microbial biomass and negatively influenced trophic group and ecological indices of soil nematodes. However, the warming effects were less obvious, only fungal PLFA showed a decreasing trend under warming. Interestingly, the influence of N addition did not depend on warming. Structural equation modeling analysis suggested that the direct pathway between N addition and soil food web components were more important than the indirect connections through alterations in soil abiotic characters or plant growth. Nitrogen enrichment also affected the soil nematode community indirectly through changes in soil pH and PLFA. We conclude that experimental warming influenced soil food web components of the temperate steppe less than N addition, and there was little influence of warming on N addition effects under these experimental conditions.", "keywords": ["China", "Food Chain", "Nematoda", "Nitrogen", "Science", "deposition", "Models", " Biological", "northern china", "Soil", "soil nematodes", "Animals", "Biomass", "organic-matter", "global change", "Phospholipids", "Soil Microbiology", "2. Zero hunger", "elevated co2", "Analysis of Variance", "species composition", "Q", "R", "Temperature", "04 agricultural and veterinary sciences", "Plants", "15. Life on land", "13. Climate action", "international", "climate-change manipulations", "plant-communities", "Medicine", "0401 agriculture", " forestry", " and fisheries", "community structure", "Research Article"]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0060441"}, {"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.0060441", "name": "item", "description": "10.1371/journal.pone.0060441", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0060441"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2013-03-27T00:00:00Z"}}, {"id": "2309129852", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:26:56Z", "type": "Journal Article", "created": "2016-03-26", "title": "Soil microbial carbon use efficiency and biomass turnover in a long-term fertilization experiment in a temperate grassland", "description": "

Soil microbial carbon use efficiency (CUE), defined as the ratio of organic C allocated to growth over organic C taken up, strongly affects soil carbon (C) cycling. Despite the importance of the microbial CUE for the terrestrial C cycle, very little is known about how it is affected by nutrient availability. Therefore, we studied microbial CUE and microbial biomass turnover time in soils of a long-term fertilization experiment in a temperate grassland comprising five treatments (control, PK, NK, NP, NPK). Microbial CUE and the turnover of microbial biomass were determined using a novel substrate-independent method based on incorporation of 18O from labeled water into microbial DNA. Microbial respiration was 28-37% smaller in all three N treatments (NK, NP, and NPK) compared to the control, whereas the PK treatment did not affect microbial respiration. N-fertilization decreased microbial C uptake, while the microbial growth rate was not affected. Microbial CUE ranged between 0.31 and 0.45, and was 1.3- to 1.4-fold higher in the N-fertilized soils than in the control. The turnover time ranged between 80 and 113 days and was not significantly affected by fertilization. Net primary production (NPP) and the abundance of legumes differed strongly across the treatments, and the fungal:bacterial ratio was very low in all treatments. Structural equation modeling revealed that microbial CUE was exclusively controlled by N fertilization and that neither the abundance of legumes (as a proxy for the quality of the organic matter inputs) nor NPP (as a proxy for C inputs) had an effect on microbial CUE. Our results show that N fertilization did not only decrease microbial respiration, but also microbial C uptake, indicating that less C was intracellularly processed in the N fertilized soils. The reason for reduced C uptake and increased CUE in the N-fertilization treatments is likely an inhibition of oxidative enzymes involved in the degradation of aromatic compounds by N in combination with a reduced energy requirement for microbial N acquisition in the fertilized soils. In conclusion, the study shows that N availability can control soil C cycling by affecting microbial CUE, while plant community-mediated changes in organic matter inputs and P and K availability played no important role for C partitioning of the microbial community in this temperate grassland.

", "keywords": ["FUNGAL", "2. Zero hunger", "106022 Mikrobiologie", "Nitrogen addition", "BACTERIAL", "NITROGEN DEPOSITION", "GROWTH EFFICIENCY", "FOREST FLOOR", "Nutrients", "04 agricultural and veterinary sciences", "15. Life on land", "Stoichiometry", "ORGANIC-MATTER", "RESPIRATION", "106026 \u00d6kosystemforschung", "13. Climate action", "Nutrient limitation", "Microbial growth yield", "106022 Microbiology", "0401 agriculture", " forestry", " and fisheries", "Mean residence time", "STOICHIOMETRIC CONTROLS", "ENZYME-ACTIVITY", "106026 Ecosystem research", "COMMUNITY STRUCTURE"]}, "links": [{"href": "https://doi.org/2309129852"}, {"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": "2309129852", "name": "item", "description": "2309129852", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2309129852"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-06-01T00:00:00Z"}}, {"id": "10.2298/abs0904741f", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:21:20Z", "type": "Journal Article", "created": "2009-12-23", "title": "Patterns And Relationships Of Plant Traits, Community Structural Attributes, And Eco-Hydrological Functions During A Subtropical Secondary Succession In Central Yunnan (Southwest China)", "description": "

Human-induced changes in land use lead to major changes in plant community composition and structure which have strong effects on eco-hydrological processes and functions. We here tested the hypothesis that changes in traits of living plants have resulted in changes in structural attributes of the community that influenced eco-hydrological functions by altering eco-hydrological processes. This was done in the context of a subtropical secondary forest suc?cession following land abandonment in Central Yunnan (Southwest China). During the succession, species with high specific leaf area (SLA), high leaf nitrogen concentration (LNC), high specific root length (SRL), and low leaf dry matter content (LDMC) were progressively replaced by species with the opposite characteristics. The obtained results of correlation analyses were as follows: (1) Correlations were significant between community-aggregated SLA, LNC, and the leaf area index (LAI). Significant correlations were detected between LAI, canopy interception and stemflow, and surface runoff and soil erosion. (2) Significant correlations were also found between community-aggregated SLA, LNC, LDMC, and accumulated litter biomass. High accumulated litter biomass strongly increases the maximum water-retaining capac?ity of litter. However, significant correlations were not found between the maximum water-retaining capacity of litter and surface runoff and soil erosion. (3) Correlations were significant between community-aggregated SLA, LNC, and fine root biomass. Fine root biomass was not significantly related to the maximum water-retaining capacity of the soil, but was significantly related to surface runoff and soil erosion. These results suggest that canopy characteristics play a more important role in control of runoff and soil erosion at the studied site. It follows that plant functional traits are closely linked with canopy characteristics, which should be used as a standard for selecting species in restoration and revegetation for water and soil conservation.

", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "plant functional traits", "forest ecological hydrology", "QH301-705.5", "community structure", "Biology (General)", "15. Life on land", "water and soil conservation"]}, "links": [{"href": "https://doi.org/10.2298/abs0904741f"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Archives%20of%20Biological%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.2298/abs0904741f", "name": "item", "description": "10.2298/abs0904741f", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.2298/abs0904741f"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-01-01T00:00:00Z"}}, {"id": "10.3389/fmicb.2016.01032", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:21:37Z", "type": "Journal Article", "created": "2016-06-30", "title": "Effects Of Short-Term Warming And Altered Precipitation On Soil Microbial Communities In Alpine Grassland Of The Tibetan Plateau", "description": "Open AccessSoil microbial communities are influenced by climate change drivers such as warming and altered precipitation. These changes create abiotic stresses, including desiccation and nutrient limitation, which act on microbes. However, our understanding of the responses of microbial communities to co-occurring climate change drivers is limited. We surveyed soil bacterial and fungal diversity and composition after a 1-year warming and altered precipitation manipulation in the Tibetan plateau alpine grassland. In isolation, warming and decreased precipitation treatments each had no significant effects on soil bacterial community structure; however, in combination of both treatments altered bacterial community structure (p = 0.03). The main effect of altered precipitation specifically impacted the relative abundances of Bacteroidetes and Gammaproteobacteria compared to the control, while the main effect of warming impacted the relative abundance of Betaproteobacteria. In contrast, the fungal community had no significant response to the treatments after 1-year. Using structural equation modeling (SEM), we found bacterial community composition was positively related to soil moisture. Our results indicate that short-term climate change could cause changes in soil bacterial community through taxonomic shifts. Our work provides new insights into immediate soil microbial responses to short-term stressors acting on an ecosystem that is particularly sensitive to global climate change.", "keywords": ["Abiotic component", "Microbial population biology", "Climate Change", "Soil Science", "Precipitation", "soil microbial community structure", "Microbiology", "Mathematical analysis", "Environmental science", "Agricultural and Biological Sciences", "Meteorology", "11. Sustainability", "FOS: Mathematics", "Genetics", "Climate change", "alpine grassland", "Biology", "Ecosystem", "2. Zero hunger", "Plateau (mathematics)", "Ecology", "Geography", "Bacteria", "Global warming", "Marine Microbial Diversity and Biogeography", "Life Sciences", "Microbial Diversity in Antarctic Ecosystems", "15. Life on land", "Grassland", "Community structure", "climate change", "pyrosequencing", "13. Climate action", "FOS: Biological sciences", "Environmental Science", "Physical Sciences", "soil moisture", "Soil Carbon Dynamics and Nutrient Cycling in Ecosystems", "Mathematics"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2016.01032"}, {"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.2016.01032", "name": "item", "description": "10.3389/fmicb.2016.01032", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2016.01032"}, {"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": "10.3389/fmicb.2021.678290", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:21:38Z", "type": "Journal Article", "created": "2021-07-09", "title": "Generalist Taxa Shape Fungal Community Structure in Cropping Ecosystems", "description": "

Fungi regulate nutrient cycling, decomposition, symbiosis, and pathogenicity in cropland soils. However, the relative importance of generalist and specialist taxa in structuring soil fungal community remains largely unresolved. We hypothesized that generalist fungi, which are adaptable to various environmental conditions, could potentially dominate the community and become the basis for fungal coexisting networks in cropping systems. In this study, we identified the generalist and habitat specialist fungi in cropland soils across a 2,200 kms environmental gradient, including three bioclimatic regions (subtropical, warm temperate, and temperate). A few fungal taxa in our database were classified as generalist taxa (~1%). These generalists accounted for >35% of the relative abundance of all fungal populations, and most of them are Ascomycota and potentially pathotrophic. Compared to the specialist taxa (5\u201317% of all phylotypes in three regions), generalists had a higher degree of connectivity and were often identified as hub within the network. Structural equation modeling provided further evidence that after accounting for spatial and climatic/edaphic factors, generalists had larger contributions to the fungal coexistence pattern than habitat specialists. Taken together, our study provided evidence that generalist taxa are crucial components for fungal community structure. The knowledge of generalists can provide important implication for understanding the ecological preference of fungal groups in cropland systems.

", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "500", "15. Life on land", "Microbiology", "333", "QR1-502", "niche differentiation", "3. Good health", "03 medical and health sciences", "coexistence pattern", "XXXXXX - Unknown", "cropland soil", "soil fungi", "functional traits", "community structure", "ecological network"]}, "links": [{"href": "https://doi.org/10.3389/fmicb.2021.678290"}, {"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.2021.678290", "name": "item", "description": "10.3389/fmicb.2021.678290", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2021.678290"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-07-09T00:00:00Z"}}, {"id": "10.3390/agriculture11050445", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:21:42Z", "type": "Journal Article", "created": "2021-05-17", "title": "Changes in Bacterial and Fungal Soil Communities in Long-Term Organic Cropping Systems", "description": "

Long-term organic farming aims to reduce synthetic fertilizer and pesticide use in order to sustainably produce and improve soil quality. To do this, there is a need for more information about the soil microbial community, which plays a key role in a sustainable agriculture. In this paper, we assessed the long-term effects of two organic and one conventional cropping systems on the soil microbial community structure using high-throughput sequencing analysis, as well as the link between these communities and the changes in the soil properties and crop yield. The results showed that the crop yield was similar among the three cropping systems. The microbial community changed according to cropping system. Organic cultivation with manure compost and compost tea (Org_C) showed a change in the bacterial community associated with an improved soil carbon and nutrient content. A linear discriminant analysis effect size showed different bacteria and fungi as key microorganisms for each of the three different cropping systems, for conventional systems (Conv), different microorganisms such as Nesterenkonia, Galbibacter, Gramella, Limnobacter, Pseudoalteromonas, Pantoe, and Sporobolomyces were associated with pesticides, while for Org_C and organic cultivation with manure (Org_M), other types of microorganisms were associated with organic amendments with different functions, which, in some cases, reduce soil borne pathogens. However, further investigations such as functional approaches or network analyses are need to better understand the mechanisms behind this behavior.

", "keywords": ["2. Zero hunger", "compost", "High-throughput sequencing", "Organic farming", "Agriculture (General)", "high-throughput sequencing", "Microbial community structure", "Compost", "04 agricultural and veterinary sciences", "sheep manure", "crop yield", "15. Life on land", "Gen\u00e9tica", "S1-972", "12. Responsible consumption", "agricultural_sciences_agronomy", "3107.01 Producci\u00f3n de Cultivos", "microbial community structure", "organic farming", "soil properties", "5102.01 Agricultura", "0401 agriculture", " forestry", " and fisheries", "Crop yield", "Soil properties", "Sheep manure"]}, "links": [{"href": "http://www.mdpi.com/2077-0472/11/5/445/pdf"}, {"href": "https://www.mdpi.com/2077-0472/11/5/445/pdf"}, {"href": "https://doi.org/10.3390/agriculture11050445"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Agriculture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/agriculture11050445", "name": "item", "description": "10.3390/agriculture11050445", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/agriculture11050445"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-04-14T00:00:00Z"}}, {"id": "10.4067/s0718-58392015000500015", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:22:13Z", "type": "Journal Article", "created": "2015-10-09", "title": "Effect Of Chemical Fertilization And Green Manure On The Abundance And Community Structure Of Ammonia Oxidizers In A Paddy Soil", "description": "Ammonia oxidization is a critical step in the soil N cycle and can be affected by the fertilization regimes. Chinese milk-vetch (Astragalus sinicus L., MV) is a major green manure of rice (Oryza sativa L.) fields in southern China, which is recommended as an important agronomic practice to improve soil fertility. Soil chemical properties, abundance and community structures of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in a MV-rice rotation field under different fertilization regimes were investigated. The field experiment included six treatments: control, without MV and chemical fertilizer (CK); 100% chemical fertilizer (NPK); 18 000 kg MV ha-1 plus 100% chemical fertilizer (NPKM1); 18 000 kg MV ha-1 plus 40% chemical fertilizer (NPKM2); 18 000 kg MV ha-1 alone (MV); and 18 000 kg MV ha-1 plus 40% chemical fertilizer plus straw (NPKMS). Results showed that NPKMS treatment could improve the soil fertility greatly although the application of 60% chemical fertilizer. The abundance of AOB only in the MV treatment had significant difference with the control; AOA were more abundant than AOB in all corresponding treatments. The NPKMS treatment had the highest AOA abundance (1.19 x 108 amoA gene copies g-1) and the lowest abundance was recorded in the CK treatment (3.21 x 107 amoA gene copies g-1). The abundance of AOA was significantly positively related to total N, available N, NH4+-N, and NO3--N. The community structure of AOA exhibited little variation among different fertilization regimes, whereas the community structure of AOB was highly responsive. Phylogenetic analysis showed that all AOB sequences were affiliated with Nitrosospira or Nitrosomonas and all AOA denaturing gradient gel electrophoresis (DGGE) bands belonged to the soil and sediment lineage. These findings could be fundamental to improve our understanding of AOB and AOA in the N cycle in the paddy soil.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "03 medical and health sciences", "Astragalus sinicus", "soil chemical properties", "Abundance", "ammonia-oxidizing bacteria (AOB)", "Chinese milk vetch", "community structure", "15. Life on land", "ammonia-oxidizing archaea (AOA)", "6. Clean water"], "contacts": [{"organization": "Fang, Yu, Yan, Zhi-Lei, Chen, Ji-Chen, Wang, Fei, Wang, Ming-Kuang, Lin, Xin-Jian,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.4067/s0718-58392015000500015"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Chilean%20journal%20of%20agricultural%20research", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.4067/s0718-58392015000500015", "name": "item", "description": "10.4067/s0718-58392015000500015", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.4067/s0718-58392015000500015"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-12-01T00:00:00Z"}}, {"id": "10.5061/dryad.cb7tp6m", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:22:26Z", "type": "Dataset", "title": "Data from: Effects of aridity on soil microbial communities and functions across soil depths on the Mongolian Plateau", "description": "unspecified1. Arid and semi-arid grassland ecosystems cover about 15% of the global land surface and provide vital soil carbon (C) and nitrogen (N) sequestration. Although half of the soil C and N is stored in deep soils (below 30 cm), no regional-scale study of microbial properties and their functions through the soil profile has been conducted in these drylands. 2. To explore the distribution and determinants of microbial properties and C and N mineralization rates through soil profile along aridity gradient at a regional scale, we investigated these variables for four soil layers (0-20, 20-40, 40-60, and 60-100 cm) in 132 plots on the Mongolia Plateau. 3. Soil microbial properties (biomass and bacteria:fungi ratio) and C and N mineralization rates decreased with increasing soil depth and aridity at the regional scale. Aridity-induced declines in soil microbial properties mainly resulted from the negative effects of aridity on ANPP/root biomass and soil organic C (SOC) in the surface soil layers (0-20 and 20-40 cm) but from the direct and indirect (via SOC and soil C/N) negative effects of aridity in the deep soil layers (40-60 and 60-100 cm). 4. Aridity-induced declines in soil C mineralization rates mainly resulted from the negative indirect effect of aridity on SOC and microbial properties in each soil layer, with weaker effects of SOC and stronger effects of soil microbes in the deep soil layers. Aridity-induced declines in soil N mineralization rates mainly resulted from the negative indirect effect of aridity on SOC in the three soil layers above 60 cm and mainly resulted from the negative direct effect of aridity in the 60-100 cm soil layer. 5. Aridity via direct or indirect effects strongly determined the patterns of soil microbial properties and C and N mineralization throughout soil profiles on the Mongolian Plateau. These findings suggest that the increases in aridity are likely to induce changes in soil microorganisms and their associated functions across soil depths of semi-arid grasslands, and future models should consider the dynamic interactions between substrates and microbial properties across soil depths in global drylands.", "keywords": ["2. Zero hunger", "biogeographical patterns", "soil carbon mineralization", "13. Climate action", "microbial community structure", "semi-arid grasslands", "depth profile", "15. Life on land", "soil nitrogen mineralization"], "contacts": [{"organization": "Chen, Dima, Saleem, Muhammad, Cheng, Junhui, Mi, Jia, Chu, Pengfei, Tuvshintogtokh, Indree, Hu, Shuijin, Bai, Yongfei,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.cb7tp6m"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.cb7tp6m", "name": "item", "description": "10.5061/dryad.cb7tp6m", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.cb7tp6m"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-14T00:00:00Z"}}, {"id": "10.5281/zenodo.3572794", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:24:25Z", "type": "Journal Article", "created": "2019-05-14", "title": "Global drivers of methane oxidation and denitrifying gene distribution in drylands", "description": "AbstractAim

Microorganisms carrying pmoA and nosZ genes are major drivers of methane and nitrous oxide fluxes from soils. However, most studies on these organisms have been conducted in mesic ecosystems; therefore, little is known about the factors driving their distribution in drylands, the largest biome on Earth. We conducted a global survey to evaluate the role of climate\uffe2\uff80\uff90 and soil\uffe2\uff80\uff90related variables as predictors of the richness, abundance and community structure of bacteria carrying pmoA and nosZ genes.

Location

Eighty dryland ecosystems distributed worldwide.

Time period

From February 2006 to December 2011.

Major taxa studied

Methanotrophic (carrying the pmoA gene) and denitrifiying (carrying the nosZ gene) bacteria.

Methods

We used data from a field survey and structural equation modelling to evaluate the direct and indirect effects of climatic (aridity, rainfall seasonality and mean annual temperature) and soil (organic carbon, pH and texture) variables on the total abundance, richness and community structure of microorganisms carrying pmoA and nosZ genes.

Results

Taxa related to Methylococcus capsulatus or Methylocapsa sp., often associated with mesic environments, were common in global drylands. The abundance and richness of methanotrophs were not associated with climate or soil properties. However, mean annual temperature, rainfall seasonality, organic C, pH and sand content were highly correlated with their community structure. Aridity and soil variables, such as sand content and pH, were correlated with the abundance, community structure and richness of the nosZ bacterial community.

Main conclusions

Our study provides new insights into the drivers of the abundance, richness and community structure of soil microorganisms carrying pmoA and nosZ genes in drylands worldwide. We highlight how ongoing climate change will alter the structure of soil microorganisms, which might affect the net CH4 exchange and will probably reduce the capacity of dryland soils to carry out the final step of denitrification, favouring net N2O emissions.Anaerobic digestion (AD) of protein-rich grass silage was performed in experimental two-stage two-phase biogas reactor systems at low vs. increased organic loading rates (OLRs) under mesophilic (37\uffe2\uff80\uff89\uffc2\uffb0C) and thermophilic (55\uffe2\uff80\uff89\uffc2\uffb0C) temperatures. To follow the adaptive response of the biomass-attached cellulolytic/hydrolytic biofilms at increasing ammonium/ammonia contents, genome-centered metagenomics and transcriptional profiling based on metagenome assembled genomes (MAGs) were conducted.

Results

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

Conclusions

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

", "keywords": ["Integrated -omics", "Bioconversion", "0301 basic medicine", "2. Zero hunger", "570", "0303 health sciences", "Polyomics", "Integrated-omics", "Metagenome assembled genomes", "Biogas", "Microbial community structure", "15. Life on land", "Microbiology", "7. Clean energy", "QR1-502", "6. Clean water", "3. Good health", "Environmental sciences", "03 medical and health sciences", "13. Climate action", "Anaerobic digestion", "Metabolic activity", "GE1-350", "Methane", "Research Article"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s40793-020-00354-x.pdf"}, {"href": "https://doi.org/10033/622632"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Environmental%20Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10033/622632", "name": "item", "description": "10033/622632", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10033/622632"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-02T00:00:00Z"}}, {"id": "10261/284332", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:25:49Z", "type": "Journal Article", "created": "2022-03-17", "title": "From diversity to complexity: Microbial networks in soils", "description": "ABSTRACT

Network analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research.Anthropogenic nitrogen (N) loading alters soil ammonia\uffe2\uff80\uff90oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize\uffc2\uffa068 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N\uffe2\uff80\uff90stimulation of nitrification, but does so via climate\uffe2\uff80\uff90related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N\uffe2\uff80\uff90availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate\uffe2\uff80\uff90related shifts in soil ammonia\uffe2\uff80\uff90oxidizing community maintain the N\uffe2\uff80\uff90stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.Soils 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.

Fungi regulate nutrient cycling, decomposition, symbiosis, and pathogenicity in cropland soils. However, the relative importance of generalist and specialist taxa in structuring soil fungal community remains largely unresolved. We hypothesized that generalist fungi, which are adaptable to various environmental conditions, could potentially dominate the community and become the basis for fungal coexisting networks in cropping systems. In this study, we identified the generalist and habitat specialist fungi in cropland soils across a 2,200 kms environmental gradient, including three bioclimatic regions (subtropical, warm temperate, and temperate). A few fungal taxa in our database were classified as generalist taxa (~1%). These generalists accounted for >35% of the relative abundance of all fungal populations, and most of them are Ascomycota and potentially pathotrophic. Compared to the specialist taxa (5\u201317% of all phylotypes in three regions), generalists had a higher degree of connectivity and were often identified as hub within the network. Structural equation modeling provided further evidence that after accounting for spatial and climatic/edaphic factors, generalists had larger contributions to the fungal coexistence pattern than habitat specialists. Taken together, our study provided evidence that generalist taxa are crucial components for fungal community structure. The knowledge of generalists can provide important implication for understanding the ecological preference of fungal groups in cropland systems.

", "keywords": ["0301 basic medicine", "570", "0303 health sciences", "500", "15. Life on land", "Microbiology", "333", "QR1-502", "niche differentiation", "3. Good health", "03 medical and health sciences", "coexistence pattern", "XXXXXX - Unknown", "cropland soil", "soil fungi", "functional traits", "community structure", "ecological network"]}, "links": [{"href": "https://doi.org/1959.7/uws:62958"}, {"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": "1959.7/uws:62958", "name": "item", "description": "1959.7/uws:62958", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/1959.7/uws:62958"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-07-09T00:00:00Z"}}, {"id": "2164/19907", "type": "Feature", "geometry": null, "properties": {"updated": "2026-05-30T16:26:52Z", "type": "Journal Article", "created": "2022-11-25", "title": "How does management affect soil C sequestration and greenhouse gas fluxes in boreal and temperate forests? \u2013 A review", "description": "Open AccessThis review has been supported by the grant Holistic management practices, modelling and monitoring for European forest soils \u2013 HoliSoils (EU Horizon 2020 Grant Agreement No 101000289) and the Academy of Finland Fellow project (330136, B. Adamczyk). In addition to the HoliSoils consortium partners, Dr. Abramoff contributed on this study and her work was supported by the United States Department of Energy, Office of Science, Office of Biological and Environmental Research. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the United States Department of Energy under contract DE-AC05- 00OR22725.", "keywords": ["[SDE] Environmental Sciences", "330", "550", "Peatland hydrology management", "CLIMATE-CHANGE ADAPTATION", "WOOD ASH APPLICATION", "530", "Greenhouse gas", "SITE PREPARATION", "630", "12. Responsible consumption", "BELOW-GROUND CARBON", "11. Sustainability", "SDG 13 - Climate Action", "NITROGEN-FERTILIZATION", "SDG 15 - Life on Land", "2. Zero hunger", "PONDEROSA PINE", "GE", "PLANT LITTER DECOMPOSITION", "NORWAY SPRUCE", "04 agricultural and veterinary sciences", "15. Life on land", "004", "Forest fertilization", "Harvesting practices", "ORGANIC-MATTER", "Forest fire management", "13. Climate action", "[SDE]Environmental Sciences", "Forest soil carbon management", "0401 agriculture", " forestry", " and fisheries", "MICROBIAL COMMUNITY STRUCTURE", "GE Environmental Sciences"]}, "links": [{"href": "https://doi.org/2164/19907"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Forest%20Ecology%20and%20Management", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "2164/19907", "name": "item", "description": "2164/19907", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/2164/19907"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-02-01T00:00:00Z"}}, {"id": "2946732851", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-05-30T16:27:11Z", "type": "Journal Article", "created": "2019-05-14", "title": "Global drivers of methane oxidation and denitrifying gene distribution in drylands", "description": "AbstractAim

Microorganisms carrying pmoA and nosZ genes are major drivers of methane and nitrous oxide fluxes from soils. However, most studies on these organisms have been conducted in mesic ecosystems; therefore, little is known about the factors driving their distribution in drylands, the largest biome on Earth. We conducted a global survey to evaluate the role of climate\uffe2\uff80\uff90 and soil\uffe2\uff80\uff90related variables as predictors of the richness, abundance and community structure of bacteria carrying pmoA and nosZ genes.

Location

Eighty dryland ecosystems distributed worldwide.

Time period

From February 2006 to December 2011.

Major taxa studied

Methanotrophic (carrying the pmoA gene) and denitrifiying (carrying the nosZ gene) bacteria.

Methods

We used data from a field survey and structural equation modelling to evaluate the direct and indirect effects of climatic (aridity, rainfall seasonality and mean annual temperature) and soil (organic carbon, pH and texture) variables on the total abundance, richness and community structure of microorganisms carrying pmoA and nosZ genes.

Results

Taxa related to Methylococcus capsulatus or Methylocapsa sp., often associated with mesic environments, were common in global drylands. The abundance and richness of methanotrophs were not associated with climate or soil properties. However, mean annual temperature, rainfall seasonality, organic C, pH and sand content were highly correlated with their community structure. Aridity and soil variables, such as sand content and pH, were correlated with the abundance, community structure and richness of the nosZ bacterial community.

Main conclusions

Our study provides new insights into the drivers of the abundance, richness and community structure of soil microorganisms carrying pmoA and nosZ genes in drylands worldwide. We highlight how ongoing climate change will alter the structure of soil microorganisms, which might affect the net CH4 exchange and will probably reduce the capacity of dryland soils to carry out the final step of denitrification, favouring net N2O emissions.