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Litter decay rates often correlate with the initial ratios of lignin : nitrogen (N) or lignin : cellulose in litter. However, the chemical and microbial mechanisms that give rise to these patterns are still unclear. To identify these mechanisms, we studied the decomposition of a model plant system, Arabidopsis thaliana , in which plants were manipulated to have low levels of lignin, cellulose, or litter N. Nitrogen fertilizer often increases the loss of cellulose, but it suppresses the breakdown of lignin in plant litter. To understand the mechanisms driving these patterns, we decomposed plants in litterbags for one year in control and N-fertilized plots in an Alaskan boreal forest. We found that litter N had a positive effect on total mass loss because it increased the loss of lignin, N, and soluble C. Lignin had a negative effect on rates of total litter mass loss due to decreases in the loss of cellulose and hemicellulose. Cellulose had a positive effect on lignin loss, supporting the concept of a \"priming effect\" for lignin breakdown. However, the low-cellulose plants also lost more of their original cellulose compared to the other plant types, indicating that decomposers mined the litter for cellulose despite the presence of lignin. Low-lignin litter had higher fungal biomass and N-acetyl glucosaminidase (NAG, a chitinase) activity, suggesting that lignin restricted fungal growth and may have influenced competitive interactions between decomposers. Nitrogen fertilization increased NAG activity in the early stages of decay. In the later stages, N fertilization led to increased cellulase activity on the litters and tended to reduce lignin losses. The transition over time from competition among decomposers to high cellulase activity and suppressed lignin loss under N fertilization suggests that, in N-limited systems, N fertilization may alter decomposer community structure by favoring a shift toward cellulose- and mineral-N users.

Identifying the ecological processes that structure communities and the consequences for ecosystem function is a central goal of ecology. The recognition that fungi, bacteria, and viruses control key ecosystem functions has made microbial communities a major focus of this field. Because many ecological processes are apparent only at particular spatial or temporal scales, a complete understanding of the linkages between microbial community, environment, and function requires analysis across a wide range of scales. Here, we map the biological and functional geography of soil fungi from local to continental scales and show that the principal ecological processes controlling community structure and function operate at different scales. Similar to plants or animals, most soil fungi are endemic to particular bioregions, suggesting that factors operating at large spatial scales, like dispersal limitation or climate, are the first-order determinants of fungal community structure in nature. By contrast, soil extracellular enzyme activity is highly convergent across bioregions and widely differing fungal communities. Instead, soil enzyme activity is correlated with local soil environment and distribution of fungal traits within the community. The lack of structure–function relationships for soil fungal communities at continental scales indicates a high degree of functional redundancy among fungal communities in global biogeochemical cycles.

Ecologists have long acknowledged the importance of seed banks; yet, despite the fact that many plants rely on mycorrhizal fungi for survival and growth, the structure of ectomycorrhizal (ECM) fungal spore banks remains poorly understood. The primary goal of this study was to assess the geographic structure in pine‐associated ECM fungal spore banks across the North American continent. Soils were collected from 19 plots in forests across North America. Fresh soils were pyrosequenced for fungal internal transcribed spacer (ITS) amplicons. Adjacent soil cores were dried and bioassayed with pine seedlings, and colonized roots were pyrosequenced to detect resistant propagules of ECM fungi. The results showed that ECM spore banks correlated strongly with biogeographic location, but not with the identity of congeneric plant hosts. Minimal community overlap was found between resident ECM fungi vs those in spore banks, and spore bank assemblages were relatively simple and dominated by Rhizopogon, Wilcoxina, Cenococcum, Thelephora, Tuber, Laccaria and Suillus. Similar to plant seed banks, ECM fungal spore banks are, in general, depauperate, and represent a small and rare subset of the mature forest soil fungal community. Yet, they may be extremely important in fungal colonization after large‐scale disturbances such as clear cuts and forest fires.

Key Points Fungi have crucial ecological roles — as microbial saprotrophs, pathogens and mutualists — in both terrestrial and aquatic ecosystems. Advances in DNA sequencing have facilitated the ecological exploration of the 'mycobiome' and begun to change our view of fungal taxonomic and functional diversity. Molecular-based work has shown that fungal communities are more diverse than previously known across a range of spatial scales, from the diversity of local communities to biogeographical differences across continents. In contrast with earlier ideas, mycobiome studies have suggested that dispersal has an important role in both local community assembly and in generating large-scale biogeographical diversity patterns. The identification of key functional traits is helping to make predictions about the newly discovered diversity of the mycobiome and decode its role in the health of plants, animals and ecosystems. Molecular-based studies of fungal biodiversity have revealed fundamental differences from the biodiversity of bacteria, plants and animals. In this Review, Peay and colleagues consider the roles of ecology and fungal biology in determining fungal biodiversity at different spatial scales. Fungi represent a large proportion of the genetic diversity on Earth and fungal activity influences the structure of plant and animal communities, as well as rates of ecosystem processes. Large-scale DNA-sequencing datasets are beginning to reveal the dimensions of fungal biodiversity, which seem to be fundamentally different to bacteria, plants and animals. In this Review, we describe the patterns of fungal biodiversity that have been revealed by molecular-based studies. Furthermore, we consider the evidence that supports the roles of different candidate drivers of fungal diversity at a range of spatial scales, as well as the role of dispersal limitation in maintaining regional endemism and influencing local community assembly. Finally, we discuss the ecological mechanisms that are likely to be responsible for the high heterogeneity that is observed in fungal communities at local scales.

The carbon use efficiency (CUE) of microbial communities partitions the flow of C from primary producers to the atmosphere, decomposer food webs, and soil C stores. CUE, usually defined as the ratio of growth to assimilation, is a critical parameter in ecosystem models, but is seldom measured directly in soils because of the methodological difficulty of measuring in situ rates of microbial growth and respiration. Alternatively, CUE can be estimated indirectly from the elemental stoichiometry of organic matter and microbial biomass, and the ratios of C to nutrient-acquiring ecoenzymatic activities. We used this approach to estimate and compare microbial CUE in >2000 soils from a broad range of ecosystems. Mean CUE based on C:N stoichiometry was 0.269 ± 0.110 (mean ± SD). A parallel calculation based on C:P stoichiometry yielded a mean CUE estimate of 0.252 ± 0.125. The mean values and frequency distributions were similar to those from aquatic ecosystems, also calculated from stoichiometric models, and to those calculated from direct measurements of bacterial and fungal growth and respiration. CUE was directly related to microbial biomass C with a scaling exponent of 0.304 (95% CI 0.237–0.371) and inversely related to microbial biomass P with a scaling exponent of –0.234 (95% CI –0.289 to –0.179). Relative to CUE, biomass specific turnover time increased with a scaling exponent of 0.509 (95% CI 0.467–0.551). CUE increased weakly with mean annual temperature. CUE declined with increasing soil pH reaching a minimum at pH 7.0, then increased again as soil pH approached 9.0, a pattern consistent with pH trends in the ratio of fungal:bacteria abundance and growth. Structural equation models that related geographic variables to CUE component variables showed the strongest connections for paths linking latitude and pH to β-glucosidase activity and soil C:N:P ratios. The integration of stoichiometric and metabolic models provides a quantitative description of the functional organization of soil microbial communities that can improve the representation of CUE in microbial process and ecosystem simulation models.

Tannins are abundant secondary chemicals in leaf litter that are hypothesized to slow the rate of soil-N cycling by binding protein into recalcitrant polyphenol-protein complexes (PPCs). We studied the effects of tannins purified from sugar maple, red oak, and eastern hemlock leaf litter on microbial activity and N cycling in soils from northern hardwood-conifer forests of the northeastern US. To create ecologically relevant conditions, we applied tannins to soil at a concentration (up to 2 mg g⁻¹ soil) typical of mineral soil horizons. Sugar maple tannins increased microbial respiration significantly more than red oak or hemlock tannins. The addition of sugar maple tannins also decreased gross N mineralization by 130% and, depending upon the rate of application, decreased net rates of N mineralization by 50-290%. At low concentrations, the decrease in mineralization appeared to be driven by greater microbial-N immobilization, while at higher concentrations the decrease in mineralization was consistent with the formation of recalcitrant PPCs. Low concentrations of red oak and hemlock tannins stimulated microbial respiration only slightly, and did not significantly affect fluxes of inorganic N in the soil. When applied to soils containing elevated levels of protein, red oak and hemlock tannins decreased N mineralization without affecting rates of microbial respiration, suggesting that PPC formation decreased substrate availability for microbial immobilization. Our results indicate that tannins from all three species form recalcitrant PPCs, but that the degree of PPC formation and its attendant effect on soil-N cycling depends on tannin concentration and the pool size of available protein in the soil.

Litter decay rates are often correlated with the initial lignin:N or lignin:cellulose content of litter, suggesting that interactions between lignin and more labile compounds are important controls over litter decomposition. The chemical composition of lignin may influence these interactions, if lignin physically or chemically protects labile components from microbial attack. We tested the effect of lignin chemical composition on litter decay in the field during a year-long litterbag study using the model system Arabidopsis thaliana. Three Arabidopsis plant types were used, including one with high amounts of guaiacyl-type lignin, one with high aldehyde-and p hydroxyphenyl-type lignin, and a wild type control with high syringyl-type lignin. The high aldehyde litter lost significantly more mass than the other plant types, due to greater losses of cellulose, hemicellulose, and N. Aldehyde-rich lignins and p-hydroxyphenyl-type lignins have low levels of cross-linking between lignins and polysaccharides, supporting the hypothesis that chemical protection of labile polysaccharides and N is a mechanism by which lignin controls total litter decay rates. 2D NMR of litters showed that lignin losses were associated with the ratio of guaiacyl-to-p-hydroxyphenyl units in lignin, because these units polymerize to form different amounts of labile- and recalcitrant-linkages within the lignin polymer. Different controls over lignin decay and polysaccharide and N decay may explain why lignin:N and lignin:cellulose ratios can be better predictors of decay rates than lignin content alone.

Empirical and modeling studies of the N cycle in temperate forests of eastern North America have focused on the mechanisms regulating the production of inorganic N, and assumed that only inorganic forms of N are available for plant growth. Recent isotope studies in field conditions suggest that amino acid capture is a widespread ecological phenomenon, although northern temperate forests have yet to be studied. We quantified fine root biomass and applied tracer-level quantities of U-¹³C₂-¹⁵N-glycine, ¹⁵NH₄ ⁺ and ¹⁵NO₃ ⁻ in two stands, one dominated by sugar maple and white ash, the other dominated by red oak, beech, and hemlock, to assess the importance of amino acids to the N nutrition of northeastern US forests. Significant enrichment of ¹³C in fine roots 2 and 5 h following tracer application indicated intact glycine uptake in both stands. Glycine accounted for up to 77% of total N uptake in the oak-beech-hemlock stand, a stand that produces recalcitrant litter, cycles N slowly and has a thick, amino acid-rich organic horizon. By contrast, glycine accounted for only 20% of total N uptake in the sugar maple and white ash stand, a stand characterized by labile litter and rapid rates of amino acid production and turnover resulting in high rates of mineralization and nitrification. This study shows that amino acid uptake is an important process occurring in two widespread, northeastern US temperate forest types with widely differing rates of N cycling.

Accurate prediction of future atmospheric CO2 concentrations is essential for evaluating climate change impacts on ecosystems and human societies. One major source of uncertainty in model predictions is the extent to which global warming will increase atmospheric CO2 concentrations through enhanced microbial decomposition of soil organic carbon. Recent advances in microbial ecology could help reduce this uncertainty, but current global models do not represent direct microbial control over decomposition. Instead, all of the coupled climate models reviewed in the most recent Intergovernmental Panel on Climate Change (IPCC) report assume that decomposition is a first-order decay process, proportional to the size of the soil carbon pool. Here we argue for the development of a new generation of models that link decomposition directly to the size and activity of microbial communities in coupled global models. This process begins with the formulation and validation of fine-scale models that capture fundamental microbial mechanisms without excessive mathematical complexity. These mechanistic models must then be scaled up through an aggregation process and validated at ecosystem to global scales prior to incorporation into global climate models (GCMs). Parameterizing microbial models at the global scale is challenging because some microbial properties such as in situ extracellular enzyme activities are very difficult to measure directly. New parameter fitting procedures may therefore be needed to infer the values of important microbial variables. Validating decomposition models at the global scale is also a challenge, and has not yet been accomplished with the land carbon models embedded in current GCMs. Fortunately new global datasets on soil carbon stocks and fluxes offer promising opportunities to validate both existing land carbon models and new microbial models. If challenges in scaling, parameterization, and validation can be overcome, a new generation of microbially-based decomposition models could substantially improve predictions of carbon–climate feedbacks in the Earth system. Development of new models structures would also reduce any bias due to the assumption of first-order decomposition across all of the models currently referenced in reports of the IPCC.

The corticioid fungi are commonly encountered, highly diverse, ecologically important, and understudied. We collected specimens in 60 pine and spruce forests across North America to survey corticioid fungal frequency and distribution and to compile an internal transcribed spacer (ITS) database for the group. Sanger sequences from the ITS region of vouchered specimens were compared with sequences on GenBank and UNITE, and with high-throughput sequence data from soil and roots taken at the same sites. Out of 425 high-quality Sanger sequences from vouchered specimens, we recovered 223 distinct operational taxonomic units (OTUs), the majority of which could not be assigned to species by matching to the BLAST database. Corticioid fungi were found to be hyperdiverse, as supported by the observations that nearly two-thirds of our OTUs were represented by single collections and species estimator curves showed steep slopes with no plateaus. We estimate that 14.8-24.7% of our voucher-based OTUs are likely to be ectomycorrhizal (EM). Corticioid fungi recovered from the soil formed a different community assemblage, with EM taxa accounting for 40.5-58.6% of OTUs. We compared basidioma sequences with EM root tips from our data, GenBank, or UNITE, and with this approach, we reiterate existing speculations that Trechispora stellulata is EM. We found that corticioid fungi have a significant distance-decay pattern, adding to the literature supporting fungi as having geographically structured communities. This study provides a first view of the diversity of this important group across North American pine forests, but much of the biology and taxonomy of these diverse, important, and widespread fungi remains unknown.