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.
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 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": "10.5281/zenodo.1323927", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:23:17Z", "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": "29046544", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:27:16Z", "type": "Journal Article", "created": "2017-08-06", "title": "Palaeoclimate explains a unique proportion of the global variation in soil bacterial communities", "description": "The legacy impacts of past climates on the current distribution of soil microbial communities are largely unknown. Here, we use data from more than 1,000 sites from five separate global and regional datasets to identify the importance of palaeoclimatic conditions (Last Glacial Maximum and mid-Holocene) in shaping the current structure of soil bacterial communities in natural and agricultural soils. We show that palaeoclimate explains more of the variation in the richness and composition of bacterial communities than current climate. Moreover, palaeoclimate accounts for a unique fraction of this variation that cannot be predicted from geographical location, current climate, soil properties or plant diversity. Climatic legacies (temperature and precipitation anomalies from the present to ~20\u2009kyr ago) probably shape soil bacterial communities both directly and indirectly through shifts in soil properties and plant communities. The ability to predict the distribution of soil bacteria from either palaeoclimate or current climate declines greatly in agricultural soils, highlighting the fact that anthropogenic activities have a strong influence on soil bacterial diversity. We illustrate how climatic legacies can help to explain the current distribution of soil bacteria in natural ecosystems and advocate that climatic legacies should be considered when predicting microbial responses to climate change.", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "Bacteria", "Climate Change", "Microbiota", "Agriculture", "910", "15. Life on land", "soil microbial ecology", "climatic changes", "03 medical and health sciences", "13. Climate action", "XXXXXX - Unknown", "soils", "Soil Microbiology", "palaeoclimatology"]}, "links": [{"href": "https://www.nature.com/articles/s41559-017-0259-7.pdf"}, {"href": "https://doi.org/29046544"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Nature%20Ecology%20%26amp%3B%20Evolution", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "29046544", "name": "item", "description": "29046544", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/29046544"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2017-08-07T00:00:00Z"}}, {"id": "29348236", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-27T16:27:18Z", "type": "Journal Article", "created": "2018-01-18", "title": "A global atlas of the dominant bacteria found in soil", "description": "A global map of soil bacteriaSoil 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 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. 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
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 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.