Meiofauna (all invertebrates smaller than 1\uffe2\uff80\uff89mm) are not only sensitive to environmental changes but also contribute significantly to nutrient cycling and energy transfer to higher trophic levels. Despite their importance, meiofauna distribution and ecology in the Siberian seas remain understudied. Here, we employ sediment environmental DNA metabarcoding to characterize meiofauna diversity across the unexplored Siberian seas. We show that meiofauna community structure is primarily driven by river discharge and coastal erosion, which are heavily influenced by climate change, rather than geographical distinctions between the seas. We observed higher meiofauna diversity in nearshore areas where river plumes promoted colonizer nematode communities that are resilient to disturbances. Yet, their dominance may lead to decreased ecosystem stability in the future. This study provides a valuable baseline for meiofauna diversity in remote Siberian seas undergoing rapid environmental change, which will be useful for assessing the future direction and pace of benthic ecological trajectories.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.Little is known about the role of ant colonies in regulating the distribution and diversity of soil microbial communities across large spatial scales. Here, we conducted a survey across >1000\uffe2\uff80\uff89km in eastern Australia and found that, compared with surrounding bare soils, ant colonies promoted the richness (number of phylotypes) and relative abundance of rare taxa of fungi and bacteria. Ant nests were also an important reservoir for plant pathogens. Our study also provides a portfolio of microbial phylotypes only found in ant nests, and which are associated with high nutrient availability. Together, our work highlights the fact that ant nests are an important refugia for microbial diversity.Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.The relationship between biodiversity and biomass has been a long standing debate in ecology. Soil biodiversity and biomass are essential drivers of ecosystem functions. However, unlike plant communities, little is known about how the diversity and biomass of soil microbial communities are interlinked across globally distributed biomes, and how variations in this relationship influence ecosystem function. To fill this knowledge gap, we conducted a field survey across global biomes, with contrasting vegetation and climate types. We show that soil carbon (C) content is associated to the microbial diversity\uffe2\uff80\uff93biomass relationship and ratio in soils across global biomes. This ratio provides an integrative index to identify those locations on Earth wherein diversity is much higher compared with biomass and vice versa. The soil microbial diversity-to-biomass ratio peaks in arid environments with low C content, and is very low in C-rich cold environments. Our study further advances that the reductions in soil C content associated with land use intensification and climate change could cause dramatic shifts in the microbial diversity-biomass ratio, with potential consequences for broad soil processes.Soil microorganisms act as gatekeepers for soil\uffe2\uff80\uff93atmosphere carbon exchange by balancing the accumulation and release of soil organic matter. However, poor understanding of the mechanisms responsible hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically test the link between microbial ecophysiological traits and topsoil carbon content across geographically distributed soils and land use contrasts. We discovered distinct pH controls on microbial mechanisms of carbon accumulation. Land use intensification in low-pH soils that increased the pH above a threshold (~6.2) leads to carbon loss through increased decomposition, following alleviation of acid retardation of microbial growth. However, loss of carbon with intensification in near-neutral pH soils was linked to decreased microbial biomass and reduced growth efficiency that was, in turn, related to trade-offs with stress alleviation and resource acquisition. Thus, less-intensive management practices in near-neutral pH soils have more potential for carbon storage through increased microbial growth efficiency, whereas in acidic soils, microbial growth is a bigger constraint on decomposition rates.Microbial activity in drylands tends to be confined to rare and short periods of rain. Rapid growth should be key to the maintenance of ecosystem processes in such narrow activity windows, if desiccation and rehydration cause widespread cell death due to osmotic stress. Here, simulating rain with 2H2O followed by single-cell NanoSIMS, we show that biocrust microbial communities in the Negev Desert are characterized by limited productivity, with median replication times of 6 to 19 days and restricted number of days allowing growth. Genome-resolved metatranscriptomics reveals that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy, and invest their activity into repair and energy generation. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. We conclude that desert biocrust communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity.Drought severely restricts plant production and global warming is further increasing drought stress for crops. Much information reveals the ability of individual microbes affecting plant stress tolerance. However, the effects of emergent bacterial community properties on plant drought tolerance remain largely unexplored. Here, we inoculated Arabidopsis plants in vivo with a four-species bacterial consortium (Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans, and Paenibacillus amylolyticus, termed as SPMX), which is able to synergistically produce more biofilm biomass together than the sum of the four single-strain cultures, to investigate its effects on plant performance and rhizo-microbiota during drought. We found that SPMX remarkably improved Arabidopsis survival post 21-day drought whereas no drought-tolerant effect was observed when subjected to the individual strains, revealing emergent properties of the SPMX consortium as the underlying cause of the induced drought tolerance. The enhanced drought tolerance was associated with sustained chlorophyll content and endogenous abscisic acid (ABA) signaling. Furthermore, our data showed that the addition of SPMX helped to stabilize the diversity and structure of root-associated microbiomes, which potentially benefits plant health under drought. These SPMX-induced changes jointly confer an increased drought tolerance to plants. Our work may inform future efforts to engineer the emergent bacterial community properties to improve plant tolerance to drought.Climate change can trigger shifts in community structure and may therefore pose a severe threat to soil microbial communities, especially in high northern latitudes such as the Arctic. Arctic soils are covered by snow and ice throughout most of the year. This insulation shields them from high temperature variability and low surface temperatures. If this protective layer thaws, these soils are predicted to warm up at 1.5x to 4x the rate of other terrestrial biomes. In this study, we sampled arctic soils from sites with different elevations in Alaska, incubated them for 5 months with a simulated, gradual or abrupt temperature increase of +5\uffe2\uff80\uff89\uffc2\uffb0C, and compared bacterial and fungal community compositions after the incubation. We hypothesized that the microbial communities would not significantly change with a gradual temperature treatment, whereas an abrupt temperature increase would decrease microbial diversity and shift community composition. The only differences in community composition that we observed were, however, related to the two elevations. The abrupt and gradual temperature increase treatments did not change the microbial community composition as compared to the control indicating resistance of the microbial community to changes in temperature. This points to the potential importance of microbial dormancy and resting stages in the formation of a \uffe2\uff80\uff9cbuffer\uffe2\uff80\uff9d against elevated temperatures. Microbial resting stages might heavily contribute to microbial biomass and thus drive the responsiveness of arctic ecosystems to climate change.
", "keywords": ["Microbial ecology", "0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Soil microbiology", "500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::579 Mikroorganismen", " Pilze", " Algen", "13. Climate action", "11. Sustainability", "579", "15. Life on land", "Article"]}, "links": [{"href": "https://www.nature.com/articles/s41598-020-65329-x.pdf"}, {"href": "https://doi.org/10.1038/s41598-020-65329-x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41598-020-65329-x", "name": "item", "description": "10.1038/s41598-020-65329-x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-020-65329-x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-05-22T00:00:00Z"}}, {"id": "10.1038/s41598-020-68099-8", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:18:27Z", "type": "Journal Article", "created": "2020-07-03", "title": "Growth rate trades off with enzymatic investment in soil filamentous fungi", "description": "AbstractSaprobic soil fungi drive many important ecosystem processes, including decomposition, and many of their effects are related to growth rate and enzymatic ability. In mycology, there has long been the implicit assumption of a trade-off between growth and enzymatic investment, which we test here using a set of filamentous fungi from the same soil. For these fungi we measured growth rate (as colony radial extension) and enzymatic repertoire (activities of four enzymes: laccase, cellobiohydrolase, leucine aminopeptidase and acid phosphatase), and explored the interaction between the traits based on phylogenetically corrected methods. Our results support the existence of a trade-off, however only for the enzymes presumably representing a larger metabolic cost (laccase and cellobiohydrolase). Our study offers new insights into potential functional complementarity within the soil fungal community in ecosystem processes, and experimentally supports an enzymatic investment/growth rate trade-off underpinning phenomena including substrate succession.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::579 Mikroorganismen", " Pilze", " Algen", "Acid Phosphatase", "Laccase", "Fungi", "579", "15. Life on land", "Article", "Fungal Proteins", "Microbial ecology", "Leucyl Aminopeptidase", "03 medical and health sciences", "Cellulose 1", "4-beta-Cellobiosidase", "Fungal ecology", "Ecosystem", "Phylogeny", "Soil Microbiology"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/360511v1.full.pdf"}, {"href": "https://www.nature.com/articles/s41598-020-68099-8.pdf"}, {"href": "https://doi.org/10.1038/s41598-020-68099-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s41598-020-68099-8", "name": "item", "description": "10.1038/s41598-020-68099-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s41598-020-68099-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-07-02T00:00:00Z"}}, {"id": "10.1038/s42003-022-04178-y", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:18:29Z", "type": "Journal Article", "created": "2022-11-17", "title": "Both abundant and rare fungi colonizing Fagus sylvatica ectomycorrhizal root-tips shape associated bacterial communities", "description": "AbstractEctomycorrhizal fungi live in close association with their host plants and form complex interactions with bacterial/archaeal communities in soil. We investigated whether abundant or rare ectomycorrhizal fungi on root-tips of young beech trees (Fagus sylvatica) shape bacterial/archaeal communities. We sequenced 16S rRNA genes and fungal internal transcribed spacer regions of individual root-tips and used ecological networks to detect the tendency of certain assemblies of fungal and bacterial/archaeal taxa to inhabit the same root-tip (i.e. modularity). Individual ectomycorrhizal root-tips hosted distinct fungal communities associated with unique bacterial/archaeal communities. The structure of the fungal-bacterial/archaeal association was determined by both, dominant and rare fungi. Integrating our data in a conceptual framework suggests that the effect of rare fungi on the bacterial/archaeal communities of ectomycorrhizal root-tips contributes to assemblages of bacteria/archaea on root-tips. This highlights the potential impact of complex fine-scale interactions between root-tip associated fungi and other soil microorganisms for the ectomycorrhizal symbiosis.Colonization of terrestrial environments by filamentous fungi relies on their ability to form networks that can forage for and connect resource patches. Despite the importance of these networks, ecologists rarely consider network features as functional traits because their measurement and interpretation are conceptually and methodologically difficult. To address these challenges, we have developed a pipeline to translate images of fungal mycelia, from both micro- and macro-scales, to weighted network graphs that capture ecologically relevant fungal behaviour. We focus on four properties that we hypothesize determine how fungi forage for resources, specifically: connectivity; relative construction cost; transport efficiency; and robustness against attack by fungivores. Constrained ordination and Pareto front analysis of these traits revealed that foraging strategies can be distinguished predominantly along a gradient of connectivity for micro- and macro-scale mycelial networks that is reminiscent of the qualitative \uffe2\uff80\uff98phalanx\uffe2\uff80\uff99 and \uffe2\uff80\uff98guerilla\uffe2\uff80\uff99 descriptors previously proposed in the literature. At one extreme are species with many inter-connections that increase the paths for multidirectional transport and robustness to damage, but with a high construction cost; at the other extreme are species with an opposite phenotype. Thus, we propose this approach represents a significant advance in quantifying ecological strategies for fungi using network information.
", "keywords": ["Microbial ecology", "0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "500 Naturwissenschaften und Mathematik::570 Biowissenschaften; Biologie::579 Mikroorganismen", " Pilze", " Algen", "579", "15. Life on land", "Fungal ecology", "ecological strategies", "Article"]}, "links": [{"href": "https://orca.cardiff.ac.uk/id/eprint/146532/1/Aguilar-Trigueros_et_al-2022-ISME_Communications.pdf"}, {"href": "https://www.nature.com/articles/s43705-021-00085-1.pdf"}, {"href": "https://doi.org/10.1038/s43705-021-00085-1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/ISME%20Communications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/s43705-021-00085-1", "name": "item", "description": "10.1038/s43705-021-00085-1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/s43705-021-00085-1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-05T00:00:00Z"}}, {"id": "10.1038/srep19536", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:18:30Z", "type": "Journal Article", "created": "2016-01-14", "title": "Soil Microbial Responses To Forest Floor Litter Manipulation And Nitrogen Addition In A Mixed-Wood Forest Of Northern China", "description": "AbstractChanges in litterfall dynamics and soil properties due to anthropogenic or natural perturbations have important implications to soil carbon (C) and nutrient cycling via microbial pathway. Here we determine soil microbial responses to contrasting types of litter inputs (leaf vs. fine woody litter) and nitrogen (N) deposition by conducting a multi-year litter manipulation and N addition experiment in a mixed-wood forest. We found significantly higher soil organic C, total N, microbial biomass C (MBC) and N (MBN), microbial activity (MR) and activities of four soil extracellular enzymes, including \uffce\uffb2-glucosidase (BG), N-acetyl-\uffce\uffb2-glucosaminidase (NAG), phenol oxidase (PO) and peroxidase (PER), as well as greater total bacteria biomass and relative abundance of gram-negative bacteria (G-) community, in top soils of plots with presence of leaf litter than of those without litter or with presence of only fine woody litter. No apparent additive or interactive effects of N addition were observed in this study. The occurrence of more labile leaf litter stimulated G-, which may facilitate microbial community growth and soil C stabilization as inferred by findings in literature. A continued treatment with contrasting types of litter inputs is likely to result in divergence in soil microbial community structure and function.
", "keywords": ["Biomass (ecology)", "China", "Biogeochemical Cycling of Nutrients in Aquatic Ecosystems", "Microbial population biology", "Nitrogen", "Soil Science", "Organic chemistry", "Forests", "Nitrogen cycle", "Article", "Plant litter", "Nutrient cycle", "Environmental science", "Microbial Ecology", "Agricultural and Biological Sciences", "Soil", "Soil biology", "Litter", "Soil water", "Genetics", "Environmental Chemistry", "Biomass", "Forest floor", "Biology", "Soil Microbiology", "Ecosystem", "2. Zero hunger", "Ecology", "Bacteria", "Marine Microbial Diversity and Biogeography", "Life Sciences", "04 agricultural and veterinary sciences", "15. Life on land", "Wood", "Soil carbon", "Carbon", "Agronomy", "6. Clean water", "3. Good health", "Chemistry", "FOS: Biological sciences", "Environmental Science", "Physical Sciences", "0401 agriculture", " forestry", " and fisheries", "Soil Carbon Dynamics and Nutrient Cycling in Ecosystems", "Nutrient"]}, "links": [{"href": "https://doi.org/10.1038/srep19536"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1038/srep19536", "name": "item", "description": "10.1038/srep19536", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1038/srep19536"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-01-14T00:00:00Z"}}, {"id": "10.3389/fmicb.2016.00525", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-23T16:21:31Z", "type": "Journal Article", "created": "2016-04-20", "title": "Belowground Response To Drought In A Tropical Forest Soil. I. Changes In Microbial Functional Potential And Metabolism", "description": "Global climate models predict a future of increased severity of drought in many tropical forests. Soil microbes are central to the balance of these systems as sources or sinks of atmospheric carbon (C), yet how they respond metabolically to drought is not well-understood. We simulated drought in the typically aseasonal Luquillo Experimental Forest, Puerto Rico, by intercepting precipitation falling through the forest canopy. This approach reduced soil moisture by 13% and water potential by 0.14 MPa (from -0.2 to -0.34). Previous results from this experiment have demonstrated that the diversity and composition of these soil microbial communities are sensitive to even small changes in soil water. Here, we show prolonged drought significantly alters the functional potential of the community and provokes a clear osmotic stress response, including the production of compatible solutes that increase intracellular C demand. Subsequently, a microbial population emerges with a greater capacity for extracellular enzyme production targeting macromolecular carbon. Significantly, some of these drought-induced functional shifts in the soil microbiota are attenuated by prior exposure to a short-term drought suggesting that acclimation may occur despite a lack of longer-term drought history.", "keywords": ["tropical forests", "0301 basic medicine", "2. Zero hunger", "570", "0303 health sciences", "Ecology", "Environmental Science and Management", "osmolytes", "drought", "Biological Sciences", "Medical microbiology", "15. Life on land", "551", "microbial ecology", "Microbiology", "QR1-502", "6. Clean water", "03 medical and health sciences", "13. Climate action", "Soil Sciences", "functional gene microarray"]}, "links": [{"href": "https://escholarship.org/content/qt5ts293tg/qt5ts293tg.pdf"}, {"href": "https://doi.org/10.3389/fmicb.2016.00525"}, {"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.2016.00525", "name": "item", "description": "10.3389/fmicb.2016.00525", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fmicb.2016.00525"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2016-04-20T00:00:00Z"}}, {"id": "10.1101/2022.12.02.518905", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-23T16:19:12Z", "type": "Journal Article", "created": "2022-12-04", "title": "Highly diverse and unknown viruses may enhance Antarctic endoliths\u2019 adaptability", "description": "AbstractRock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology. Here, we performed metagenomic analyses on rocks from across Antarctica comprising >75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities potentially influencing bacterial adaptation and biogeochemistry. This catalog lays the foundation for expanding knowledge of the virosphere in extreme environments.
Soil microbes provide multiple ecosystem functions such as nutrient cycling, decomposition and climate regulation. However, we lack a quantitative understanding of the relative importance of microbial richness and composition in controlling multifunctionality. This knowledge gap limits our capacity to understand the influence of biotic attributes in the provision of services and functions on which humans depend.
We used two independent approaches (i.e. experimental and observational), and applied statistical modelling to identify the role and relative importance of bacterial richness and composition in driving multifunctionality (here defined as seven measures of respiration and enzyme activities). In the observational study, we measured soil microbial communities and functions in both tree\uffe2\uff80\uff90 and bare soil\uffe2\uff80\uff90dominated microsites at 22 locations across a 1,200\uffc2\uffa0km transect in southeastern Australia. In the experimental study we used soils from two of those locations and developed gradients of bacterial diversity and composition through inoculation of sterilized soils.
Microbial richness and the relative abundance of Gammaproteobacteria, Actinobacteria, and Bacteroidetes were positively related to multifunctionality in both the observational and experimental approaches; however, only Bacteroidetes was consistently selected as a key predictor of multifunctionality across all experimental approaches and statistical models used here. Moreover, our results, from two different approaches, provide evidence that microbial richness and composition are both important, yet independent, drivers of multiple ecosystem functions.
Overall, our findings advance our understanding of the mechanisms underpinning relationships between microbial diversity and ecosystem functionality in terrestrial ecosystems, and further suggest that information on microbial richness and composition needs to be considered when formulating sustainable management and conservation policies, and when predicting the effects of global change on ecosystem functions.
A plain language summary is available for this article.
We lack strong empirical evidence for links between plant attributes (plant community attributes and functional traits) and the distribution of soil microbial communities at large spatial scales.
Using datasets from two contrasting regions and ecosystem types in Australia and England, we report that aboveground plant community attributes, such as diversity (species richness) and cover, and functional traits can predict a unique portion of the variation in the diversity (number of phylotypes) and community composition of soil bacteria and fungi that cannot be explained by soil abiotic properties and climate. We further identify the relative importance and evaluate the potential direct and indirect effects of climate, soil properties and plant attributes in regulating the diversity and community composition of soil microbial communities.
Finally, we deliver a list of examples of common taxa from Australia and England that are strongly related to specific plant traits, such as specific leaf area index, leaf nitrogen and nitrogen fixation.
Together, our work provides new evidence that plant attributes, especially plant functional traits, can predict the distribution of soil microbial communities at the regional scale and across two hemispheres.
Soil bacteria play key roles in regulating terrestrial carbon dynamics, nutrient cycles, and plant productivity. However, the natural histories and distributions of these organisms remain largely undocumented. Delgado-Baquerizo et al. provide a survey of the dominant bacterial taxa found around the world. In soil collections from six continents, they found that only 2% of bacterial taxa account for nearly half of the soil bacterial communities across the globe. These dominant taxa could be clustered into ecological groups of co-occurring bacteria that share habitat preferences. The findings will allow for a more predictive understanding of soil bacterial diversity and distribution.Science , this issue p. 320 Soil microbes are highly diverse and control most soil biogeochemical reactions. We examined how microbial functional genes and biogeochemical pools responded to the altered chemical inputs accompanying land use change. We examined paired native grasslands and adjacentEucalyptusplantations (previously grassland) in Uruguay, a region that lacked forests before European settlement. Along with measurements of soil carbon, nitrogen, and bacterial diversity, we analyzed functional genes using the GeoChip 2.0 microarray, which simultaneously quantified several thousand genes involved in soil carbon and nitrogen cycling. Plantations and grassland differed significantly in functional gene profiles, bacterial diversity, and biogeochemical pool sizes. Most grassland profiles were similar, but plantation profiles generally differed from those of grasslands due to differences in functional gene abundance across diverse taxa. Eucalypts decreased ammonification and N fixation functional genes by 11% and 7.9% (P< 0.01), which correlated with decreased microbial biomass N and more NH4+in plantation soils. Chitinase abundance decreased 7.8% in plantations compared to levels in grassland (P= 0.017), and C polymer-degrading genes decreased by 1.5% overall (P< 0.05), which likely contributed to 54% (P< 0.05) more C in undecomposed extractable soil pools and 27% less microbial C (P< 0.01) in plantation soils. In general, afforestation altered the abundance of many microbial functional genes, corresponding with changes in soil biogeochemistry, in part through altered abundance of overall functional gene types rather than simply through changes in specific taxa. Such changes in microbial functional genes correspond with altered C and N storage and have implications for long-term productivity in these soils.
", "keywords": ["Nitrogen", "Argentina", "Sequence Homology", "soil science", "Microbiology", "333", "Trees", "Soil", "afforestation", "Cluster Analysis", "Biology", "Soil Microbiology", "Oligonucleotide Array Sequence Analysis", "2. Zero hunger", "Environmental Microbiology and Microbial Ecology", "Bacteria", "Chitinases", "Biodiversity", "DNA", "Gene Pool", "04 agricultural and veterinary sciences", "South America", "15. Life on land", "Microarray Analysis", "Carbon", "Uruguay", "0401 agriculture", " forestry", " and fisheries", "Eucalyptus plantation"]}, "links": [{"href": "https://doi.org/10.1128/aem.01126-09"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Applied%20and%20Environmental%20Microbiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1128/aem.01126-09", "name": "item", "description": "10.1128/aem.01126-09", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1128/aem.01126-09"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-10-01T00:00:00Z"}}, {"id": "10.1371/journal.pone.0038858", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:20:14Z", "type": "Journal Article", "created": "2012-06-11", "title": "Decline In Topsoil Microbial Quotient, Fungal Abundance And C Utilization Efficiency Of Rice Paddies Under Heavy Metal Pollution Across South China", "description": "Open AccessLos suelos agr\u00edcolas han estado cada vez m\u00e1s sujetos a la contaminaci\u00f3n por metales pesados en todo el mundo. Sin embargo, los impactos en la estructura y actividad de la comunidad microbiana del suelo de los suelos de campo a\u00fan no se han caracterizado bien. En 2009 se recolectaron muestras de tierra vegetal de campos de arroz contaminados con metales pesados (PS) y sus campos de fondo (BGS) en cuatro sitios del sur de China. Los cambios con la contaminaci\u00f3n met\u00e1lica en relaci\u00f3n con el BGS en el tama\u00f1o y la estructura de la comunidad de los microorganismos del suelo se examinaron con m\u00faltiples ensayos microbiol\u00f3gicos de medici\u00f3n de carbono de biomasa (MBC) y nitr\u00f3geno (MBN), recuento en placa de colonias cultivables y an\u00e1lisis de \u00e1cidos grasos fosfol\u00edpidos (PLFA) junto con el perfil de electroforesis en gel de gradiente desnaturalizante (DGGE) del gen de ARNr 16S y ARNr 18S y ensayo de PCR en tiempo real. Adem\u00e1s, se llev\u00f3 a cabo una incubaci\u00f3n de laboratorio de 7 d\u00edas a una temperatura constante de 25 \u00b0C para realizar un seguimiento adicional de los cambios en la actividad metab\u00f3lica. Si bien la disminuci\u00f3n de la contaminaci\u00f3n por metales en MBC y MBN, as\u00ed como en el tama\u00f1o de la poblaci\u00f3n cultivable, el contenido total de PLFA y el n\u00famero de bandas DGGE de bacterias no se observaron de manera significativa y consistente, de hecho se observ\u00f3 una reducci\u00f3n significativa de la contaminaci\u00f3n por metales en el cociente microbiano, en el tama\u00f1o de la poblaci\u00f3n f\u00fangica cultivable y en la proporci\u00f3n de PLFA f\u00fangicos a bacterianos de manera consistente en todos los sitios en una medida que var\u00eda de 6% a 74%. Adem\u00e1s, se observ\u00f3 un aumento consistentemente significativo en el cociente metab\u00f3lico de hasta un 68% bajo contaminaci\u00f3n en todos los sitios. Estas observaciones apoyaron un cambio de la comunidad microbiana con disminuci\u00f3n en su abundancia, disminuci\u00f3n en la proporci\u00f3n de hongos y, por lo tanto, en la eficiencia de utilizaci\u00f3n de C bajo contaminaci\u00f3n en los suelos. Adem\u00e1s, las proporciones de cociente microbiano, de hongos a bacterias y qCO2 son mejores indicativas de los impactos de los metales pesados en la estructura y actividad de la comunidad microbiana. Los efectos potenciales de estos cambios en el ciclo del carbono y la producci\u00f3n de CO2 en los arrozales contaminados merecen m\u00e1s estudios de campo.", "keywords": ["Microbial population biology", "Colony Count", " Microbial", "Agricultural and Biological Sciences", "Sociology", "Soil water", "Soil Pollutants", "Soil Microbiology", "2. Zero hunger", "Principal Component Analysis", "Temperature gradient gel electrophoresis", "Ecology", "Q", "Fatty Acids", "R", "Life Sciences", "Agriculture", "04 agricultural and veterinary sciences", "Biota", "Pollution", "6. Clean water", "FOS: Sociology", "Chemistry", "Physical Sciences", "Environmental chemistry", "Medicine", "Research Article", "Environmental Monitoring", "16S ribosomal RNA", "China", "Microorganism", "Environmental Impact of Heavy Metal Contamination", "Nitrogen", "Science", "Population", "Soil Science", "Real-Time Polymerase Chain Reaction", "Environmental science", "Microbial Ecology", "12. Responsible consumption", "Metals", " Heavy", "Genetics", "Biology", "Demography", "Bacteria", "Denaturing Gradient Gel Electrophoresis", "Marine Microbial Diversity and Biogeography", "Oryza", "15. Life on land", "Topsoil", "Carbon", "Agronomy", "RNA", " Ribosomal", "13. Climate action", "FOS: Biological sciences", "Environmental Science", "0401 agriculture", " forestry", " and fisheries", "Soil Carbon Dynamics and Nutrient Cycling in Ecosystems"]}, "links": [{"href": "https://doi.org/10.1371/journal.pone.0038858"}, {"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.0038858", "name": "item", "description": "10.1371/journal.pone.0038858", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1371/journal.pone.0038858"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-06-11T00:00:00Z"}}, {"id": "10.1186/s40168-019-0757-8", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-23T16:20:06Z", "type": "Journal Article", "created": "2019-10-31", "title": "Suppressed N fixation and diazotrophs after four decades of fertilization", "description": "Abstract BackgroundN fixation is one of the most important microbially driven ecosystem processes on Earth, allowing N to enter the soil from the atmosphere, and regulating plant productivity. A question that remains to be answered is whether such a fundamental process would still be that important in an over-fertilized world, as the long-term effects of fertilization on N fixation and associated diazotrophic communities remain to be tested. Here, we used a 35-year fertilization experiment, and investigated the changes in N fixation rates and the diazotrophic community in response to long-term inorganic and organic fertilization.
ResultsIt was found that N fixation was drastically reduced (dropped by 50%) after almost four decades of fertilization. Our results further indicated that functionality losses were associated with reductions in the relative abundance of keystone and phylogenetically clustered N fixers such as Geobacter spp.
ConclusionsOur work suggests that long-term fertilization might have selected against N fixation and specific groups of N fixers. Our study provides solid evidence that N fixation and certain groups of diazotrophic taxa will be largely suppressed in a more and more fertilized world, with implications for soil biodiversity and ecosystem functions.
", "keywords": ["2. Zero hunger", "0301 basic medicine", "Diazotrophs", "0303 health sciences", "Nitrogen", "Research", "QR100-130", "Agriculture", "Biodiversity", "15. Life on land", "Microbial ecology", "03 medical and health sciences", "13. Climate action", "Nitrogen Fixation", "XXXXXX - Unknown", "Long-term fertilization", "Ecological clusters", "Fertilizers", "Ecosystem", "Phylogeny", "Soil Microbiology", "Nitrogen fixation rates"]}, "links": [{"href": "https://doi.org/10.1186/s40168-019-0757-8"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40168-019-0757-8", "name": "item", "description": "10.1186/s40168-019-0757-8", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-019-0757-8"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-10-31T00:00:00Z"}}, {"id": "10.1186/s40168-020-00941-7", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-23T16:20:06Z", "type": "Journal Article", "created": "2020-11-19", "title": "Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms", "description": "Abstract BackgroundThe global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment. Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from 38 farms.
ResultsOur results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome across sample types, with a higher richness and dispersion of ARGs within environmental samples than on those from feces or slurry. Indeed, a deeper analysis revealed that differences among the three sample types were defined by taxa-ARGs associations. Interestingly, mobilome analyses revealed that the observed AMR differences between intensive and extensive farms could be linked to differences in the abundance of mobile genetic elements (MGEs). Thus, while there were no differences in the abundance of chromosomal-associated ARGs between intensive and extensive herds, a significantly higher abundance of integrons in the environment and plasmids, regardless of the sample type, was detected on intensive farms.
ConclusionsOverall, this study shows how AMU, production system, and sample type influence, mainly through MGEs, the profile and dispersion of ARGs in pig production.
", "keywords": ["0301 basic medicine", "Farms", "Sanidad animal", "Swine", "Antimicrobial resistance", "Microbial ecology", "Sustainable farming", "Cerdos", "Feces", "03 medical and health sciences", "Anti-Infective Agents", "Environmental Microbiology", "Animals", "Mobilome", "Antiinfecciosos", "One health", "2. Zero hunger", "Excrementos", "0303 health sciences", "Research", "QR100-130", "Drug Resistance", " Microbial", "15. Life on land", "Farm environment", "6. Clean water", "Genes", " Bacterial", "Animals", " Domestic", "2401.05 desarrollo Animal", "Metagenome", "Veterinaria"]}, "links": [{"href": "http://link.springer.com/content/pdf/10.1186/s40168-020-00941-7.pdf"}, {"href": "https://doi.org/10.1186/s40168-020-00941-7"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40168-020-00941-7", "name": "item", "description": "10.1186/s40168-020-00941-7", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-020-00941-7"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-11-19T00:00:00Z"}}, {"id": "10.1186/s40168-021-01131-9", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:20:06Z", "type": "Journal Article", "created": "2021-10-14", "title": "Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity", "description": "AbstractBackgroundThe microorganisms that inhabit food processing environments (FPE) can strongly influence the associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-resistant microorganisms, and a hotspot for the transmission of antibiotic resistance genes (ARGs) is a concern in meat processing plants. Here, we monitor microbial succession and resistome dynamics relating to FPE through a detailed analysis of a newly opened pork cutting plant over 1.5 years of activity.
ResultsWe identified a relatively restricted principal microbiota dominated byPseudomonasduring the first 2 months, while a higher taxonomic diversity, an increased representation of other taxa (e.g.,Acinetobacter,Psychrobacter), and a certain degree of microbiome specialization on different surfaces was recorded later on. An increase in total abundance, alpha diversity, and \uffce\uffb2-dispersion of ARGs, which were predominantly assigned toAcinetobacterand associated with resistance to certain antimicrobials frequently used on pig farms of the region, was detected over time. Moreover, a sharp increase in the occurrence of extended-spectrum \uffce\uffb2-lactamase-producingEnterobacteriaceaeand vancomycin-resistantEnterococcaceaewas observed when cutting activities started. ARGs associated with resistance to \uffce\uffb2-lactams, tetracyclines, aminoglycosides, and sulphonamides frequently co-occurred, and mobile genetic elements (i.e., plasmids, integrons) and lateral gene transfer events were mainly detected at the later sampling times in drains.
ConclusionsThe observations made suggest that pig carcasses were a source of resistant bacteria that then colonized FPE and that drains, together with some food-contact surfaces, such as equipment and table surfaces, represented a reservoir for the spread of ARGs in the meat processing facility.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Bacteria", "Food Handling", "Swine", "Tecnolog\u00eda de los alimentos", "Research", "QR100-130", "610", "Food processing environments", "Antimicrobial resistance", "Gen\u00e9tica", "630", "Anti-Bacterial Agents", "Microbial ecology", "Red Meat", "03 medical and health sciences", "Genes", " Bacterial", "Pork Meat", "Animals", "Metagenomics"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1186/s40168-021-01131-9.pdf"}, {"href": "https://doi.org/10.1186/s40168-021-01131-9"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40168-021-01131-9", "name": "item", "description": "10.1186/s40168-021-01131-9", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-021-01131-9"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-10-14T00:00:00Z"}}, {"id": "10.1186/s40168-021-01144-4", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:20:06Z", "type": "Journal Article", "created": "2021-09-20", "title": "Trophic level drives the host microbiome of soil invertebrates at a continental scale", "description": "Abstract BackgroundIncreasing our knowledge of soil biodiversity is fundamental to forecast changes in ecosystem functions under global change scenarios. All multicellular organisms are now known to be holobionts, containing large assemblages of microbial species. Soil fauna is now known to have thousands of species living within them. However, we know very little about the identity and function of host microbiome in contrasting soil faunal groups, across different terrestrial biomes, or at a large spatial scale. Here, we examined the microbiomes of multiple functionally important soil fauna in contrasting terrestrial ecosystems across China.
ResultsDifferent soil fauna had diverse and unique microbiomes, which were also distinct from those in surrounding soils. These unique microbiomes were maintained within taxa across diverse sampling sites and in contrasting terrestrial ecosystems. The microbiomes of nematodes, potworms, and earthworms were more difficult to predict using environmental data, compared to those of collembolans, oribatid mites, and predatory mites. Although stochastic processes were important, deterministic processes, such as host selection, also contributed to the assembly of unique microbiota in each taxon of soil fauna. Microbial biodiversity, unique microbial taxa, and microbial dark matter (defined as unidentified microbial taxa) all increased with trophic levels within the soil food web.
ConclusionsOur findings demonstrate that soil animals are important as repositories of microbial biodiversity, and those at the top of the food web harbor more diverse and unique microbiomes. This hidden source of biodiversity is rarely considered in biodiversity and conservation debates and stresses the importance of preserving key soil invertebrates.
", "keywords": ["0301 basic medicine", "0303 health sciences", "Microbial dark matter", "Trophic dynamics", "Research", "Microbiota", "QR100-130", "Biodiversity", "15. Life on land", "Microbiology", "Invertebrates", "Microbial ecology", "Soil", "03 medical and health sciences", "Soil food web", "13. Climate action", "XXXXXX - Unknown", "Host microbiome", "Animals", "Network analysis", "Continental-scale survey", "Deterministic process", "Unique microbial taxa", "Ecosystem", "Soil Microbiology"]}, "links": [{"href": "https://doi.org/10.1186/s40168-021-01144-4"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40168-021-01144-4", "name": "item", "description": "10.1186/s40168-021-01144-4", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-021-01144-4"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-09-20T00:00:00Z"}}, {"id": "10.1186/s40168-022-01405-w", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:20:06Z", "type": "Journal Article", "created": "2022-12-12", "title": "The global distribution and environmental drivers of the soil antibiotic resistome", "description": "Abstract BackgroundLittle is known about the global distribution and environmental drivers of key microbial functional traits such as antibiotic resistance genes (ARGs). Soils are one of Earth\uffe2\uff80\uff99s largest reservoirs of ARGs, which are integral for soil microbial competition, and have potential implications for plant and human health. Yet, their diversity and global patterns remain poorly described. Here, we analyzed 285 ARGs in soils from 1012 sites across all continents and created the first global atlas with the distributions of topsoil ARGs.
ResultsWe show that ARGs peaked in high latitude cold and boreal forests. Climatic seasonality and mobile genetic elements, associated with the transmission of antibiotic resistance, were also key drivers of their global distribution. Dominant ARGs were mainly related to multidrug resistance genes and efflux pump machineries. We further pinpointed the global hotspots of the diversity and proportions of soil ARGs.
ConclusionsTogether, our work provides the foundation for a better understanding of the ecology and global distribution of the environmental soil antibiotic resistome.
", "keywords": ["Ecolog\u00eda (Biolog\u00eda)", "0301 basic medicine", "SDG-03: Good health and well-being", "550", "Antibiotic resistance", "Edafolog\u00eda (Biolog\u00eda)", "Antibiotic resistance genes (ARGs)", "910", "http://metadata.un.org/sdg/3", "631.4", "Microbial ecology", "2417.14 Gen\u00e9tica Vegetal", "Soil", "03 medical and health sciences", "XXXXXX - Unknown", "Global scale", "Humans", "Global change", "SCALE", "Ensure healthy lives and promote well-being for all at all ages", "2. Zero hunger", "0303 health sciences", "Ecology", "Research", "QR100-130", "Human health", "15. Life on land", "Gen\u00e9tica", "Anti-Bacterial Agents", "3. Good health", "Phenotype", "Mobile genetic elements", "13. Climate action", "BACTERIA", "2511.02 Biolog\u00eda de Suelos", "RESISTANCE GENES"]}, "links": [{"href": "https://doi.org/10.1186/s40168-022-01405-w"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Microbiome", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s40168-022-01405-w", "name": "item", "description": "10.1186/s40168-022-01405-w", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s40168-022-01405-w"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-07-11T00:00:00Z"}}, {"id": "10.1890/08-1730.1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:20:43Z", "type": "Journal Article", "created": "2009-11-18", "title": "A global meta-analysis of soil exchangeable cations, pH, carbon, and nitrogen with afforestation", "description": "Afforestation, the conversion of non\uffe2\uff80\uff90forested lands to forest plantations, can sequester atmospheric carbon dioxide, but the rapid growth and harvesting of biomass may deplete nutrients and degrade soils if managed improperly. The goal of this study is to evaluate how afforestation affects mineral soil quality, including pH, sodium, exchangeable cations, organic carbon, and nitrogen, and to examine the magnitude of these changes regionally where afforestation rates are high. We also examine potential mechanisms to reduce the impacts of afforestation on soils and to maintain long\uffe2\uff80\uff90term productivity.
Across diverse plantation types (153 sites) to a depth of 30 cm of mineral soil, we observed significant decreases in nutrient cations (Ca, K, Mg), increases in sodium (Na), or both with afforestation. Across the data set, afforestation reduced soil concentrations of the macronutrient Ca by 29% on average (P< 0.05). Afforestation byPinusalone decreased soil K by 23% (P< 0.05). Overall, plantations of all genera also led to a mean 71% increase of soil Na (P< 0.05). Mean pH decreased 0.3 units (P< 0.05) with afforestation.
Afforestation caused a 6.7% and 15% (P< 0.05) decrease in soil C and N content respectively, though the effect was driven principally byPinusplantations (15% and 20% decrease,P< 0.05). Carbon to nitrogen ratios in soils under plantations were 5.7\uffe2\uff80\uff9311.6% higher (P< 0.05). In several regions with high rates of afforestation, cumulative losses of N, Ca, and Mg are likely in the range of tens of millions of metric tons. The decreases indicate that trees take up considerable amounts of nutrients from soils; harvesting this biomass repeatedly could impair long\uffe2\uff80\uff90term soil fertility and productivity in some locations. Based on this study and a review of other literature, we suggest that proper site preparation and sustainable harvest practices, such as avoiding the removal or burning of harvest residue, could minimize the impact of afforestation on soils. These sustainable practices would in turn slow soil compaction, erosion, and organic matter loss, maintaining soil fertility to the greatest extent possible.
", "keywords": ["0106 biological sciences", "Nitrogen", "Microbiology", "01 natural sciences", "333", "salinity", "Trees", "12. Responsible consumption", "acidification", "Soil", "SOIL NUTRIENTS", "afforestation", "SALINITY", "https://purl.org/becyt/ford/4.1", "https://purl.org/becyt/ford/4", "soil carbon", "Biology", "BASE CATIONS", "Ecosystem", "2. Zero hunger", "Environmental Microbiology and Microbial Ecology", "Forestry", "04 agricultural and veterinary sciences", "Hydrogen-Ion Concentration", "15. Life on land", "Carbon", "sustainable harvest", "13. Climate action", "SUSTAINABLE HARVEST", "AFFORESTATION", "0401 agriculture", " forestry", " and fisheries", "soil nutrients", "base cations", "SOIL CARBON", "ACIDIFICATION"]}, "links": [{"href": "https://doi.org/10.1890/08-1730.1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecological%20Applications", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1890/08-1730.1", "name": "item", "description": "10.1890/08-1730.1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1890/08-1730.1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2009-12-01T00:00:00Z"}}, {"id": "10.1890/14-0088.1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:20:44Z", "type": "Journal Article", "created": "2014-07-18", "title": "Plant Diversity Effects On Soil Microbial Functions And Enzymes Are Stronger Than Warming In A Grassland Experiment", "description": "Anthropogenic changes in biodiversity and atmospheric temperature significantly influence ecosystem processes. However, little is known about potential interactive effects of plant diversity and warming on essential ecosystem properties, such as soil microbial functions and element cycling. We studied the effects of orthogonal manipulations of plant diversity (one, four, and 16 species) and warming (ambient, +1.5\uffc2\uffb0C, and +3\uffc2\uffb0C) on soil microbial biomass, respiration, growth after nutrient additions, and activities of extracellular enzymes in 2011 and 2012 in the BAC (biodiversity and climate) perennial grassland experiment site at Cedar Creek, Minnesota, USA. Focal enzymes are involved in essential biogeochemical processes of the carbon, nitrogen, and phosphorus cycles. Soil microbial biomass and some enzyme activities involved in the C and N cycle increased significantly with increasing plant diversity in both years. In addition, 16\uffe2\uff80\uff90species mixtures buffered warming induced reductions in topsoil water content. We found no interactive effects of plant diversity and warming on soil microbial biomass and growth rates. However, the activity of several enzymes (1,4\uffe2\uff80\uff90\uffce\uffb2\uffe2\uff80\uff90glucosidase, 1,4\uffe2\uff80\uff90\uffce\uffb2\uffe2\uff80\uff90N\uffe2\uff80\uff90acetylglucosaminidase, phosphatase, peroxidase) depended on interactions between plant diversity and warming with elevated activities of enzymes involved in the C, N, and P cycles at both high plant diversity and high warming levels. Increasing plant diversity consistently decreased microbial biomass\uffe2\uff80\uff90specific enzyme activities and altered soil microbial growth responses to nutrient additions, indicating that plant diversity changed nutrient limitations and/or microbial community composition. In contrast to our expectations, higher plant diversity only buffered temperature effects on soil water content, but not on microbial functions. Temperature effects on some soil enzymes were greatest at high plant diversity. In total, our results suggest that the fundamental temperature ranges of soil microbial communities may be sufficiently broad to buffer their functioning against changes in temperature and that plant diversity may be a dominant control of soil microbial processes in a changing world.
", "keywords": ["aboveground-belowground interactions", "Hot Temperature", "warming", "Climate Change", "biodiversity-ecosystem functioning", "global warming", "soil microbial ecology", "Soil", "XXXXXX - Unknown", "Biomass", "global change", "Soil Microbiology", "2. Zero hunger", "microbial biomass", "grasslands", "extracellular enzymes", "Biodiversity", "04 agricultural and veterinary sciences", "Plants", "15. Life on land", "plant diversity", "Enzymes", "grassland ecosystem", "13. Climate action", "0401 agriculture", " forestry", " and fisheries", "ecosystems"]}, "links": [{"href": "https://doi.org/10.1890/14-0088.1"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1890/14-0088.1", "name": "item", "description": "10.1890/14-0088.1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1890/14-0088.1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2015-01-01T00:00:00Z"}}, {"id": "10.3389/fpls.2019.00910", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:21:33Z", "type": "Journal Article", "created": "2019-07-12", "title": "Characterization of the Wood Mycobiome of Vitis vinifera in a Vineyard Affected by Esca. Spatial Distribution of Fungal Communities and Their Putative Relation With Leaf Symptoms", "description": "Esca is a disease complex belonging to the grapevine trunk diseases cluster. It comprises five syndromes, three main fungal pathogenic agents and several symptoms, both internal (i.e., affecting woody tissue) and external (e.g., affecting leaves and bunches). The etiology and epidemiology of this disease complex remain, in part, unclear. Some of the points that are still under discussion concern the sudden rise in disease incidence, the simultaneous presence of multiple wood pathogens in affected grapevines, the causal agents and the discontinuity in time of leaf symptoms manifestation. The standard approach to the study of esca has been mostly through culture-dependent studies, yet, leaving many questions unanswered. In this study, we used Illumina\u00ae next-generation amplicon sequencing to investigate the mycobiome of grapevines wood in a vineyard with history of esca. We characterized the wood mycobiome composition, investigated the spatial dynamics of the fungal communities in different areas of the stem and in canes, and assessed the putative link between mycobiome and leaf symptoms. An unprecedented diversity of fungi is presented (289 taxa), including five genera reported for the first time in association with grapevines wood (Debaryomyces, Trematosphaeria, Biatriospora, Lopadostoma, and Malassezia) and numerous hitherto unreported species. Esca-associated fungi Phaeomoniella chlamydospora and Fomitiporia sp. dominate the fungal community, and numerous other fungi associated with wood syndromes are also encountered (e.g., Eutypa spp., Inonotus hispidus). The spatial analysis revealed differences in diversity, evenness and taxa abundances, the unique presence of certain fungi in specific areas of the plants, and tissue specificity. Lastly, the mycobiome composition of the woody tissue in proximity to leaves manifesting 'tiger stripes' symptoms of esca, as well as in leaf-symptomatic canes, was highly similar to that of plants not exhibiting any leaf symptomatology. This observation supports the current understanding that leaf symptoms are not directly linked with the fungal communities in the wood. This work builds to the understanding of the microbial ecology of the grapevines wood, offering insights and a critical view on the current knowledge of the etiology of esca.", "keywords": ["2. Zero hunger", "0301 basic medicine", "matabarcoding", "0303 health sciences", "Plant culture", "Plant Science", "15. Life on land", "Grapevine trunk diseases", "microbial ecology", "esca disease", "SB1-1110", "Microbial ecology", "mycobiome", "03 medical and health sciences", "Vitis vinifera", "metabarcoding", "Metabarcoding", "Vitis", "grapevine trunk diseases", "Esca disease", "Mycobiome"]}, "links": [{"href": "https://doi.org/10.3389/fpls.2019.00910"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fpls.2019.00910", "name": "item", "description": "10.3389/fpls.2019.00910", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fpls.2019.00910"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-07-12T00:00:00Z"}}, {"id": "10.5061/dryad.66t1g1k7n", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-06-23T16:22:13Z", "type": "Dataset", "created": "2023-12-05", "title": "Biotic and abiotic properties of biocrus", "description": "unspecifiedEukaryotic algae, as the primary group of photosynthetic autotrophs, exert a significant influence on the development and functions of biological crusts in dryland ecosystems. Despite their importance, there are substantial knowledge gaps on the composition of eukaryotic algal communities and their effects on the distributions of bacteria and fungi in dryland soils. This study examined the eukaryotic algal community along a successional sequence of biocrusts in the Gurbantunggut desert, while also investigating their patterns of co-occurrence with bacteria and fungi through high-throughput sequencing and bioinformatic analyses. The results showed that nitrogen and phosphorus levels played a crucial role in the regulation of changes in the abundance and composition of the algal community. In particular, changes in the structure of the algal community arise primarily from fluctuations in the main species, rather than from loss and appearance of species during the biocrust succession. The accumulation of nitrogen and phosphorus in the biocrust led to increases in the relative abundance of algal species in the Chlorophyta. The results also indicated that eukaryotic algae played an important role in affecting bacterial and fungal communities and significantly improved the stability of the microbial community, reflected by the robustness of co-occurrence networks. The network analysis further indicated that eukaryotic algae affected the stability of microbial co-occurrence networks either by acting as keystone taxa or associating with the keystone bacterial and fungal taxa. These findings reveal a clear mechanism by which soil nitrogen and phosphorus levels affected the composition of eukaryotic algae communities and further regulated bacterial and fungal communities during biocrust development, providing valuable information on the development and functional execution of biocrusts in dryland ecosystems.", "keywords": ["2. Zero hunger", "Microbial ecology", "Succession of biocrusts", "13. Climate action", "Physicochemical properties", "15. Life on land", "FOS: Natural sciences"], "contacts": [{"organization": "Zhao, Kang", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.5061/dryad.66t1g1k7n"}, {"rel": "self", "type": "application/geo+json", "title": "10.5061/dryad.66t1g1k7n", "name": "item", "description": "10.5061/dryad.66t1g1k7n", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5061/dryad.66t1g1k7n"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-12-12T00:00:00Z"}}, {"id": "10.5281/zenodo.1323927", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:23:11Z", "type": "Journal Article", "created": "2017-12-09", "title": "New insights into the role of microbial community composition in driving soil respiration rates", "description": "New insights into the role of microbial community composition in driving soil respiration rates. Published in Soil Biology and Biochemistry", "keywords": ["Carbon cycling", "2. Zero hunger", "Bacteria", "550", "carbon", "Fungi", "Ecosystem processes", "04 agricultural and veterinary sciences", "15. Life on land", "soil microbial ecology", "13. Climate action", "Microbial community", "XXXXXX - Unknown", "Bacteria", " fungi", " carbon cycling", " ecosystem processes", " microbial community", " global change", "0401 agriculture", " forestry", " and fisheries", "fungi", "bacteria", "Global change"]}, "links": [{"href": "https://doi.org/10.5281/zenodo.1323927"}, {"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": "10.5281/zenodo.1323927", "name": "item", "description": "10.5281/zenodo.1323927", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.5281/zenodo.1323927"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-03-01T00:00:00Z"}}, {"id": "10.6084/m9.figshare.21276675.v1", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-06-23T16:25:19Z", "type": "Dataset", "created": "2024-06-07", "title": "OTU tables, Metadata, Taxonomy files", "description": "OTU tables, Taxonomy and Metadata files for nifH gene and 16S rRNA gene that were used in the analysis are uploaded.", "keywords": ["60504 Microbial Ecology", "FOS: Biological sciences"], "contacts": [{"organization": "Dietrich, Marlies", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.6084/m9.figshare.21276675.v1"}, {"rel": "self", "type": "application/geo+json", "title": "10.6084/m9.figshare.21276675.v1", "name": "item", "description": "10.6084/m9.figshare.21276675.v1", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.6084/m9.figshare.21276675.v1"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-01T00:00:00Z"}}, {"id": "10261/284332", "type": "Feature", "geometry": null, "properties": {"updated": "2026-06-23T16:25:40Z", "type": "Journal Article", "created": "2022-03-17", "title": "From diversity to complexity: Microbial networks in soils", "description": "ABSTRACTNetwork analysis has been used for many years in ecological research to analyze organismal associations, for example in food webs, plant-plant or plant-animal interactions. Although network analysis is widely applied in microbial ecology, only recently has it entered the realms of soil microbial ecology, shown by a rapid rise in studies applying co-occurrence analysis to soil microbial communities. While this application offers great potential for deeper insights into the ecological structure of soil microbial ecosystems, it also brings new challenges related to the specific characteristics of soil datasets and the type of ecological questions that can be addressed. In this Perspectives Paper we assess the challenges of applying network analysis to soil microbial ecology due to the small-scale heterogeneity of the soil environment and the nature of soil microbial datasets. We review the different approaches of network construction that are commonly applied to soil microbial datasets and discuss their features and limitations. Using a test dataset of microbial communities from two depths of a forest soil, we demonstrate how different experimental designs and network constructing algorithms affect the structure of the resulting networks, and how this in turn may influence ecological conclusions. We will also reveal how assumptions of the construction method, methods of preparing the dataset, and definitions of thresholds affect the network structure. Finally, we discuss the particular questions in soil microbial ecology that can be approached by analyzing and interpreting specific network properties. Targeting these network properties in a meaningful way will allow applying this technique not in merely descriptive, but in hypothesis-driven research.Under controlled laboratory conditions, high and low ammonium availability are known to favor soil ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities, respectively. However, whether this niche segregation is maintained under field conditions in terrestrial ecosystems remains unresolved, particularly at the global scale. We hypothesized that perennial vegetation might favor AOB vs. AOA communities compared with adjacent open areas devoid of perennial vegetation (i.e., bare soil) via several mechanisms, including increasing the amount of ammonium in soil. To test this niche-differentiation hypothesis, we conducted a global field survey including 80 drylands from 6 continents. Data supported our hypothesis, as soils collected under plant canopies had higher levels of ammonium, as well as higher richness (number of terminal restriction fragments; T-RFs) and abundance (qPCR amoA genes) of AOB, and lower richness and abundance of AOA, than those collected in open areas located between plant canopies. Some of the reported associations between plant canopies and AOA and AOB communities can be a consequence of the higher organic matter and available N contents found under plant canopies. Other aspects of soils associated with vegetation including shading and microclimatic conditions might also help explain our results. Our findings provide strong evidence for niche differentiation between AOA and AOB communities in drylands worldwide, advancing our understanding of their ecology and biogeography at the global scale.