Search bioRxivSearch

Biology subjects

Noah Fierer

Publications and source records attributed to Noah Fierer.

3 recordsLinked to original sources

Temperature drives plant and soil microbial diversity patterns across an elevation gradient from the Andes to the Amazon

More than 200 years ago, von Humboldt reported decreases in tropical plant species richness with increasing elevation and decreasing temperature. Surprisingly, co-ordinated patterns in plant, bacterial and fungal diversity on tropical mountains are yet to be observed, despite the central role of soil microorganisms in terrestrial biogeochemistry. We studied an Andean transect traversing 3.5 km in elevation to test whether the species diversity and composition of tropical forest plants, soil bacteria and fungi can follow similar biogeographical patterns with shared environmental drivers. We found co-ordinated changes with elevation in all three groups: species richness declined as elevation increased, and the compositional-dissimilarity of communities increased with increased separation in elevation, although changes in plant diversity were larger than in bacteria and fungi. Temperature was the dominant driver of these diversity gradients, with weak influences of edaphic properties, including soil pH. The gradients in microbial diversity were strongly correlated with the activities of enzymes involved in organic matter cycling, and were accompanied by a transition in microbial traits towards slower-growing, oligotrophic taxa at higher elevations. We provide the first evidence of co-ordinated temperature-driven patterns in the diversity and distribution of three major biotic groups in tropical ecosystems: soil bacteria, fungi and plants. These findings suggest that, across landscape scales of relatively constant soil pH, inter-related patterns of plant and microbial communities with shared environmental drivers can occur, with large implications for tropical forest communities under future climate change.

Ecology

Genome reduction in an abundant and ubiquitous soil bacterial lineage

Although bacteria within the Verrucomicrobia phylum are pervasive in soils around the world, they are underrepresented in both isolate collections and genomic databases. Here we describe a single verrucomicrobial phylotype within the class Spartobacteria that is not closely related to any previously described taxa. We examined >1000 soils and found this spartobacterial phylotype to be ubiquitous and consistently one of the most abundant soil bacterial phylotypes, particularly in grasslands, where it was typically the most abundant phylotype. We reconstructed a nearly complete genome of this phylotype from a soil metagenome for which we propose the provisional name Candidatus Udaeobacter copiosus. The Ca. U. copiosus genome is unusually small for soil bacteria, estimated to be only 2.81 Mbp compared to the predicted effective mean genome size of 4.74 Mbp for soil bacteria. Metabolic reconstruction suggests that Ca. U. copiosus is an aerobic chemoorganoheterotroph with numerous amino acid and vitamin auxotrophies. The large population size, relatively small genome and multiple putative auxotrophies characteristic of Ca. U. copiosus suggests that it may be undergoing streamlining selection to minimize cellular architecture, a phenomenon previously thought to be restricted to aquatic bacteria. Although many soil bacteria need relatively large, complex genomes to be successful in soil, Ca. U. copiosus appears to have identified an alternate strategy, sacrificing metabolic versatility for efficiency to become dominant in the soil environment.

Microbiology

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

It is implicitly assumed that the microbial DNA recovered from soil originates from living cells. However, because relic DNA (DNA from dead cells) can persist in soil for weeks to years, it could impact DNA-based analyses of microbial diversity. We examined a wide range of soils and found that, on average, 40% of prokaryotic and fungal DNA was derived from the relic DNA pool. Relic DNA inflated the observed prokaryotic and fungal diversity by as much as 55%, and caused misestimation of taxon abundances, including taxa integral to key ecosystem processes. These findings imply that relic DNA can obscure treatment effects, spatiotemporal patterns, and relationships between taxa and environmental conditions. Moreover, relic DNA may represent a historical record of microbes formerly living in soil.\n\nOne Sentence SummarySoils can harbor substantial amounts of DNA from dead microbial cells; this relic DNA inflates estimates of microbial diversity and obscures assessments of community structure.

Ecology