Isotopic Analysis of Sporocarp Protein and Structural Material Improves Resolution of Fungal Carbon Sources

Fungal acquisition of resources is difficult to assess in the field. To determine whether fungi received carbon from recent plant photosynthate, litter or soil-derived organic (C:N bonded) nitrogen, we examined differences in δ13C among bulk tissue, structural carbon, and protein extracts of sporocarps of three fungal types: saprotrophic fungi, fungi with hydrophobic ectomycorrhizae, or fungi with hydrophilic ectomycorrhizae. Sporocarps were collected from experimental plots of the Duke Free-air CO2 enrichment experiment during and after CO2 enrichment. The differential 13C labeling of ecosystem pools in CO2 enrichment experiments was tracked into fungi and provided novel insights into organic nitrogen use. Specifically, sporocarp δ13C as well as δ15N of protein and structural material indicated that fungi with hydrophobic ectomycorrhizae used soil-derived organic nitrogen sources for protein carbon, fungi with hydrophilic ectomycorrhizae used recent plant photosynthates for protein carbon and both fungal groups used photosynthates for structural carbon. Saprotrophic fungi depended on litter produced during fumigation for both protein and structural material

Isotopic Analysis of Sporocarp Protein and Structural Material Improves Resolution of Fungal Carbon Sources

Fungal acquisition of resources is difficult to assess in the field. To determine whether fungi received carbon from recent plant photosynthate, litter or soil-derived organic (C:N bonded) nitrogen, we examined differences in δ13C among bulk tissue, structural carbon, and protein extracts of sporocarps of three fungal types: saprotrophic fungi, fungi with hydrophobic ectomycorrhizae, or fungi with hydrophilic ectomycorrhizae. Sporocarps were collected from experimental plots of the Duke Free-air CO2 enrichment experiment during and after CO2 enrichment. The differential 13C labeling of ecosystem pools in CO2 enrichment experiments was tracked into fungi and provided novel insights into organic nitrogen use. Specifically, sporocarp δ13C as well as δ15N of protein and structural material indicated that fungi with hydrophobic ectomycorrhizae used soil-derived organic nitrogen sources for protein carbon, fungi with hydrophilic ectomycorrhizae used recent plant photosynthates for protein carbon and both fungal groups used photosynthates for structural carbon. Saprotrophic fungi depended on litter produced during fumigation for both protein and structural material

Understanding microbial contributions to soil aggregation and organic matter accumulation

The goal of the project investigators was to characterize soil bacterial and fungal communities and the rates at which they break down specific plant-derived carbon (C) molecules within soil aggregates in three farming systems

Effects of elevated atmospheric carbon dioxide on amino acid and NH 4 + -N cycling in a temperate pine ecosystem

Rising atmospheric carbon dioxide (CO 2 ) is expected to increase forest productivity, resulting in greater carbon (C) storage in forest ecosystems. Because elevated atmospheric CO 2 does not increase nitrogen (N) use efficiency in many forest tree species, additional N inputs will be required to sustain increased net primary productivity (NPP) under elevated atmospheric CO 2 . We investigated the importance of free amino acids (AAs) as a source for forest N uptake at the Duke Forest Free Air CO 2 Enrichment (FACE) site, comparing its importance with that of better-studied inorganic N sources. Potential proteolytic enzyme activity was monitored seasonally, and individual AA concentrations were measured in organic horizon extracts. Potential free AA production in soils ranged from 190 to 690 nmol N g −1  h −1 and was greater than potential rates of soil NH 4 + production. Because of this high potential rate of organic N production, we determined (1) whether intact AA uptake occurs by Pinus taeda L., the dominant tree species at the FACE site, (2) if the rate of cycling of AAs is comparable with that of ammonium (NH 4 + ), and (3) if atmospheric CO 2 concentration alters the aforementioned N cycling processes. A field experiment using universally labeled ammonium ( 15 NH 4 + ) and alanine ( 13 C 3 H 7 15 NO 2 ) demonstrated that 15 N is more readily taken up by plants and heterotrophic microorganisms as NH 4 + . Pine roots and microbes take up on average 2.4 and two times as much NH 4 + 15 N compared with alanine 15 N 1 week after tracer application. N cycling through soil pools was similar for alanine and NH 4 + , with the greatest 15 N tracer recovery in soil organic matter, followed by microbial biomass, dissolved organic N, extractable NH 4 + , and fine roots. Stoichiometric analyses of 13 C and 15 N uptake demonstrated that both plants and soil microorganisms take up alanine directly, with a 13 C :  15 N ratio of 3.3 : 1 in fine roots and 1.5 : 1 in microbial biomass. Our results suggest that intact AA (alanine) uptake contributes substantially to plant N uptake in loblolly pine forests. However, we found no evidence supporting increased recovery of free AAs in fine roots under elevated CO 2 , suggesting plants will need to acquire additional N via other mechanisms, such as increased root exploration or increased N use efficiency.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73167/1/j.1365-2486.2007.01411.x.pd

Spatial Structuring of Cellulase Gene Abundance and Activity in Soil

Microbial mechanisms controlling cellulose degradation in soil habitats remains a critical knowledge gap in understanding and modeling terrestrial carbon-cycling. We investigated land management and soil micro-habitat influences on soil bacterial communities and distribution of cellulose-degrading enzyme genes in three bioenergy cropping systems (corn, prairie, and fertilized prairie). Within the soil, aggregates have been examined as potential micro- habitats with specific characteristics influencing resource partitioning and regulation, thus we also investigated genes associated with cellulose degradation within soil aggregate fractions from the fertilized prairie system. Soil bacterial communities and carbon-cycling gene presence varied across land management and soil microhabitats. Examination of genes specifically involved in cellulose-degradation pathways showed high levels of redundancy across the bioenergy cropping systems, but medium macroaggregates (1,000–2,000 μm) supported greater cellulose-degrading enzyme gene abundance than other aggregate fractions and whole soil. In medium aggregates, the enriched cellulose-degrading genes were most similar to genes previously observed in Actinobacteria. These findings represent gentic potential only, and our previous work on the same samples found elevated cellulase exo-enzyme activity in microaggregates. These contrasting results emphasize the importance of measuring community, functional genes, and metabolic potentials in a coordinated manner. Together, these data indicate that location within the soil matrix matters. Overall, our results indicate that soil aggregate environments are hot-spots that select for organisms with functional attributes like cellulose degradation, and future work should further explore micro-environmental factors that affect realized C-cycling processes

Long-term carbon and nitrogen dynamics at SPRUCE revealed through stable isotopes in peat profiles

Peatlands encode information about past vegetation dynamics, climate, and microbial processes. Here, we used δ15N and δ13C patterns from 16 peat profiles to deduce how the biogeochemistry of the Marcell S1 forested bog in northern Minnesota responded to environmental and vegetation change over the past  ∼ 10000 years. In multiple regression analyses, δ15N and δ13C correlated strongly with depth, plot location, C∕N, %N, and each other. Correlations with %N, %C, C∕N, and the other isotope accounted for 80% of variance for δ15N and 38% of variance for δ13C, reflecting N and C losses. In contrast, correlations with depth and topography (hummock or hollow) reflected peatland successional history and climate. Higher δ15N in plots closer to uplands may reflect upland-derived DON inputs and accompanying shifts in N dynamics in the lagg drainage area surrounding the bog. The Suess effect (declining δ13CO2 since the Industrial Revolution) lowered δ13C in recent surficial samples. High δ15N from −35 to −55cm probably indicated the depth of ectomycorrhizal activity after tree colonization of the peatland over the last 400 years, as confirmed by the occasional presence of wood down to −35cm depth. High δ13C at  ∼ 4000 years BP (−65 to −105cm) could reflect a transition at that time to slower rates of peat accumulation, when 13C discrimination during peat decomposition may increase in importance. Low δ13C and high δ15N at −213 and −225cm ( ∼ 8500 years BP) corresponded to a warm period during a sedge-dominated rich fen stage. The above processes appear to be the primary drivers of the observed isotopic patterns, whereas there was no clear evidence for methane dynamics influencing δ13C patterns

RefSoil: A reference database of soil microbial genomes

A database of curated genomes is needed to better assess soil microbial communities and their processes associated with differing land management and environmental impacts. Interpreting soil metagenomic datasets with existing sequence databases is challenging because these datasets are biased towards medical and biotechnology research and can result in misleading annotations. We have curated a database of 922 genomes of soil-associated organisms (888 bacteria and 34 archaea). Using this database, we evaluated phyla and functions that are enriched in soils as well as those that may be underrepresented in RefSoil. Our comparison of RefSoil to soil amplicon datasets allowed us to identify targets that if cultured or sequenced would significantly increase the biodiversity represented within RefSoil. To demonstrate the opportunities to access these underrepresented targets, we employed single cell genomics in a pilot experiment to sequence 14 genomes. This effort demonstrates the value of RefSoil in the guidance of future research efforts and the capability of single cell genomics as a practical means to fill the existing genomic data gaps

Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes

Soil microorganisms provide key ecological functions that often rely on metabolic interactions between individual populations of the soil microbiome. To better understand these interactions and community processes, we used chitin, a major carbon and nitrogen source in soil, as a test substrate to investigate microbial interactions during its decomposition. Chitin was applied to a model soil consortium that we developed, “model soil consortium-2” (MSC-2), consisting of eight members of diverse phyla and including both chitin degraders and nondegraders. A multiomics approach revealed how MSC-2 community-level processes during chitin decomposition differ from monocultures of the constituent species. Emergent properties of both species and the community were found, including changes in the chitin degradation potential of Streptomyces species and organization of all species into distinct roles in the chitin degradation process. The members of MSC-2 were further evaluated via metatranscriptomics and community metabolomics. Intriguingly, the most abundant members of MSC-2 were not those that were able to metabolize chitin itself, but rather those that were able to take full advantage of interspecies interactions to grow on chitin decomposition products. Using a model soil consortium greatly increased our knowledge of how carbon is decomposed and metabolized in a community setting, showing that niche size, rather than species metabolic capacity, can drive success and that certain species become active carbon degraders only in the context of their surrounding community. These conclusions fill important knowledge gaps that are key to our understanding of community interactions that support carbon and nitrogen cycling in soil

Integrating microbial ecology into ecosystem models: challenges and priorities

Microbial communities can potentially mediate feedbacks between global change and ecosystem function, owing to their sensitivity to environmental change and their control over critical biogeochemical processes. Numerous ecosystem models have been developed to predict global change effects, but most do not consider microbial mechanisms in detail. In this idea paper, we examine the extent to which incorporation of microbial ecology into ecosystem models improves predictions of carbon (C) dynamics under warming, changes in precipitation regime, and anthropogenic nitrogen (N) enrichment. We focus on three cases in which this approach might be especially valuable: temporal dynamics in microbial responses to environmental change, variation in ecological function within microbial communities, and N effects on microbial activity. Four microbially-based models have addressed these scenarios. In each case, predictions of the microbial-based models differ—sometimes substantially—from comparable conventional models. However, validation and parameterization of model performance is challenging. We recommend that the development of microbial-based models must occur in conjunction with the development of theoretical frameworks that predict the temporal responses of microbial communities, the phylogenetic distribution of microbial functions, and the response of microbes to N enrichment