Soil microbial communities are so vastly diverse that complex interactions, which alter ecosystem functions, may occur among microbial species and functional groups. In this review, we explore the empirical evidence for situations when shifts in the community structure of microbes would elicit a change in ecosystem process rates, specifically decomposition, even when microbial biomass remains constant. In particular, we are interested in a subset of these scenarios in which knowledge of microbial community structure would improve model predictions for ecosystem functions. Results from microcosm and field studies indicate that microbial species diversity, functional group diversity, and community composition can all influence ecosystem process rates. The underlying mechanisms that may elicit changes in ecosystem functions from shifts in microbial community structure include evolutionary constraints on microbial trait adaptation, trait correlations, dispersal limitation, and species interactions. The extent of microbial diversity in soils is not known, so it is presently not possible to model all scenarios of microbial community structure shifts. However, by incorporating documented patterns in functional groups that are relevant for a particular ecosystem process and potential relationships between microbial phylogeny and function, the predictive power of process models will be significantly improved. The inclusion of this information into process models is critical for predicting and understanding how ecosystem functions may shift in response to global change.

Boreal forests store a large fraction of global terrestrial carbon and are susceptible to environmental change, particularly rising temperatures and increased fire frequency. These changes have the potential to drive positive feedbacks between climate warming and the boreal carbon cycle. Because few studies have examined the warming response of boreal ecosystems recovering from fire, we established a greenhouse warming experiment near Delta Junction, Alaska, seven years after a 1999 wildfire. We hypothesized that experimental warming would increase soil CO2 efflux, stimulate nutrient mineralization, and alter the composition and function of soil fungal communities. Although our treatment resulted in 1.20 °C soil warming, we found little support for our hypothesis. Only the activities of cellulose- and chitin-degrading enzymes increased significantly by 15% and 35%, respectively, and there were no changes in soil fungal communities. Warming resulted in drier soils, but the corresponding change in soil water potential was probably not sufficient to limit microbial activity. Rather, the warming response of this soil may be constrained by depletion of labile carbon substrates resulting from combustion and elevated soil temperatures in the years after the 1999 fire. We conclude that positive feedbacks between warming and the microbial release of soil carbon are weak in boreal ecosystems lacking permafrost. Since permafrost-free soils underlie 45–60% of the boreal zone, our results should be useful for modeling the warming response during recovery from fire in a large fraction of the boreal forest.

Plant diversity is considered one factor structuring soil fungal communities because the diversity of compounds in leaf litter might determine the extent of resource heterogeneity for decomposer communities. Lowland tropical rain forests have the highest plant diversity per area of any biome. Since fungi are responsible for much of the decomposition occurring in forest soils, understanding the factors that structure fungi in tropical forests may provide valuable insight for predicting changes in global carbon and nitrogen fluxes. To test the role of plant diversity in shaping fungal community structure and function, soil (0-20 cm) and leaf litter (O horizons) were collected from six established 1-ha forest census plots across a natural plant diversity gradient on the Isthmus of Panama. We used 454 pyrosequencing and phospholipid fatty acid analysis to evaluate correlations between microbial community composition, precipitation, soil nutrients, and plant richness. In soil, the number of fungal taxa increased significantly with increasing mean annual precipitation, but not with plant richness. There were no correlations between fungal communities in leaf litter and plant diversity or precipitation, and fungal communities were found to be compositionally distinct between soil and leaf litter. To directly test for effects of plant species richness on fungal diversity and function, we experimentally re-created litter diversity gradients in litter bags with 1, 25, and 50 species of litter. After 6 months, we found a significant effect of litter diversity on decomposition rate between one and 25 species of leaf litter. However, fungal richness did not track plant species richness. Although studies in a broader range of sites is required, these results suggest that precipitation may be a more important factor than plant diversity or soil nutrient status in structuring tropical forest soil fungal communities.

Habitat fragmentation is widespread across ecosystems, detrimentally affecting biodiversity. Although most habitat fragmentation studies have been conducted on macroscopic organisms, microbial communities and fungal processes may also be threatened by fragmentation. This study investigated whether fragmentation, and the effects of fragmentation on plants, altered fungal diversity and function within a fragmented shrubland in southern California. Using fluorimetric techniques, we assayed enzymes from plant litter collected from fragments of varying sizes to investigate enzymatic responses to fragmentation. To isolate the effects of plant richness from those of fragment size on fungi, we deployed litter bags containing different levels of plant litter diversity into the largest fragment and incubated in the field for one year. Following field incubation, we determined litter mass loss and conducted molecular analyses of fungal communities. We found that leaf-litter enzyme activity declined in smaller habitat fragments with less diverse vegetation. Moreover, we detected greater litter mass loss in litter bags containing more diverse plant litter. Additionally, bags with greater plant litter diversity harbored greater numbers of fungal taxa. These findings suggest that both plant litter resources and fungal function may be affected by habitat fragmentation's constraints on plants, possibly because plant species differ chemically, and may thus decompose at different rates. Diverse plant assemblages may produce a greater variety of litter resources and provide more ecological niche space, which may support greater numbers of fungal taxa. Thus, reduced plant diversity may constrain both fungal taxa richness and decomposition in fragmented coastal shrublands. Altogether, our findings provide evidence that even fungi may be affected by human-driven habitat fragmentation via direct effects of fragmentation on plants. Our findings underscore the importance of restoring diverse vegetation communities within larger coastal sage scrub fragments and suggest that this may be an effective way to improve the functional capacity of degraded sites.

Fungi influence nutrient cycling in terrestrial ecosystems, as they are major regulators of decomposition and soil respiration. However, little is known about the substrate preferences of individual fungal species outside of laboratory culture studies. If active fungi differ in their substrate preferences in situ, then changes in fungal diversity due to global change may dramatically influence nutrient cycling in ecosystems. To test the responses of individual fungal taxa to specific substrates, we used a nucleotide-analogue procedure in the boreal forest of Alaska (USA). Specifically, we added four organic N compounds commonly found in plant litter (arginine, glutamate, lignocellulose, and tannin-protein) to litterbags filled with decomposed leaf litter (black spruce and aspen) and assessed the responses of active fungal species using qPCR (quantitative polymerase chain reaction), oligonucleotide fingerprinting of rRNA genes, and sequencing. We also compared the sequences from our experiment with a concurrent warming experiment to see if active fungi that targeted more recalcitrant compounds would respond more positively to soil warming. We found that individual fungal taxa responded differently to substrate additions and that active fungal communities were different across litter types (spruce vs. aspen). Active fungi that targeted lignocellulose also responded positively to experimental warming. Additionally, resource-use patterns in different fungal taxa were genetically correlated, suggesting that it may be possible to predict the ecological function of active fungal communities based on genetic information. Together, these results imply that fungi are functionally diverse and that reductions in fungal diversity may have consequences for ecosystem functioning.

Although fungal communities are known to vary along latitudinal gradients, mechanisms underlying this pattern are not well-understood. We used high-throughput sequencing to examine the large-scale distributions of soil fungi and their relation to evolutionary history. We tested the Tropical Conservatism Hypothesis, which predicts that ancestral fungal groups should be more restricted to tropical latitudes and conditions than would more recently derived groups. We found support for this hypothesis in that older phyla preferred significantly lower latitudes and warmer, wetter conditions than did younger phyla. Moreover, preferences for higher latitudes and lower precipitation levels were significantly phylogenetically conserved among the six younger phyla, possibly because the older phyla possess a zoospore stage that is vulnerable to drought, whereas the younger phyla retain protective cell walls throughout their life cycle. Our study provides novel evidence that the Tropical Conservatism Hypothesis applies to microbes as well as plants and animals.

Fertilization may impact ecosystem processes that sustain agriculture, such as nutrient cycling, by altering the composition of soil microbial communities that regulate such processes. These processes are crucial to low‐input, smallholder tropical agriculture, which supports 900 million of the world's poorest people. Yet little is known about how efforts to increase crop yield on such farms will affect the capacity of soil microbial communities to carry out ecosystem processes. We studied the diversity and functional capacity of microbial communities on smallholder farms in western Kenya. We measured functional capacity as the abundance of functional genes involved in several components of nutrient cycling as well as catabolism of multiple carbon substrates; taxonomic diversity was measured using metagenomic sequencing. Diversity and functional capacity were measured on short‐term, experimental mineral fertilizer addition plots and on actively managed farms that have maintained for at least seven years a management strategy of low mineral fertilization, high mineral fertilization, or high fertilization combined with legume rotations. Soil bacterial diversity decreased with mineral fertilizer addition, with a community shift towards taxa that thrive in high‐resource conditions. This taxonomic response did not correspond with decreased microbial functional capacity. Instead, functional capacity was increased, along with yields, when fertilizers were combined with legume rotations that add organic matter to soil. Policy implications. Mineral fertilizer use is associated with lower soil microbial diversity on smallholder farms, but not associated with changes in microbial functional capacity. Functional capacity is highest, along with yields, when mineral fertilizers are paired with legume rotations. Our findings suggest that this type of agroforestry can be an important strategy for maintaining the long‐term functional capacity of soil microbes as well as increasing crop yields on smallholder farms. These observations support proposals to achieve long‐term food production targets in sub‐Saharan Africa by combining mineral fertilizers with organic inputs.

The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.