Abstract
Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeled DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin–protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition.
Highlights
With over a billion individual cells and estimates of 104–105 distinct genomes per gram of soil (Gans et al, 2005; Tringe et al, 2005; Fierer et al, 2007b), bacteria in soil are the reservoirs for much of Earth’s genetic biodiversity
BrdU was incorporated into the genomes of a broad diversity of soil bacteria Across all BrdU-labeled incubations, we detected 2,233 bacterial taxa (1,938 taxa with sequence lengths >600 bp are displayed in the phylogenetic tree; Figure 1)
The active bacterial community is impacted to a greater degree by labile organic C Non-metric Multidimensional Scaling of inter-sample Bray– Curtis distances, based on PhyloChip probe set intensities, demonstrated that more labile substrates such as glycine and sucrose resulted in a greater divergence of the active bacterial population from the BrdU-only controls than did more chemically recalcitrant substrates (Figure 2)
Summary
With over a billion individual cells and estimates of 104–105 distinct genomes per gram of soil (Gans et al, 2005; Tringe et al, 2005; Fierer et al, 2007b), bacteria in soil are the reservoirs for much of Earth’s genetic biodiversity. This vast phylogenetic and functional diversity can be attributed in part to the dynamic physical and chemical heterogeneity of soil, which results in spatial and temporal separation of microorganisms (Papke and Ward, 2004). Improving our understanding of the metabolic plasticity/rigidity of soil bacteria and determining their ability to utilize different types www.frontiersin.org
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
