Differential Growth Responses of Soil Bacterial Taxa to Carbon Substrates of Varying Chemical Recalcitrance

By Katherine C. Goldfarb, U. Karaoz, China A. Hanson, C. Santee, M. Bradford, K. Treseder, M. Wallenstein, Eoin L. Brodie. Front. Microbio., 2011

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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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/95e8e1950c7a62d9e08bf69a0d3e7a65705f44fb

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Temperatures beyond the community optimum promote the dominance of heat-adapted, fast growing and stress resistant bacteria in alpine soils (2020, background): “This genus grows on simple sugars (Coenye, 2014) and was shown to increase in abundance upon addition of simple sugars (Jenkins et al., 2010; Goldfarb et al., 2011) and under conditions of elevated root exudation (Drigo et al.”
Plant intraspecific variation modulates nutrient cycling through its below ground rhizospheric microbiome (2019, background): “Enrichment in soil organics can lead to the overrepresentation of specific microbial clades with high competitive abilities, influencing the phylogenetic structure of the whole community (Goberna, García, et al., 2014; Goldfarb et al., 2011).”
Dynamics of the bacterial community structure in the rhizosphere of a maize cultivar (2014, background): “Many Betaproteobacteria and Bacteroidetes are copiotrophic soil bacteria, and they become abundant when labile substrates are available (Fierer et al., 2007; Goldfarb et al., 2011).”
Root exudates increase N availability by stimulating microbial turnover of fast-cycling N pools (2017, neutral): “Likewise, exudates can also invoke a functional change in community-level activity or physiology without a compositional change (Van Hees et al., 2005; Goldfarb et al., 2011).”
The effect of resource history on the functioning of soil microbial communities is maintained across time (2011, background): “It is important to note that during the earlier stages of litter decomposition, we would expect to find many more taxa with a shared ability to degrade more labile compounds (Goldfarb et al., 2011), and thus, more likely to find a process which is buffered against environmental perturbations (Schime”
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes (2012, background): “Changes in the types and quantities of organic carbon added to soil can have considerable influences on soil microbial communities (9, 10) and, depending on the gradients being studied or the experimental treatments imposed, other factors such as soil temperature, moisture, and nutrient availability”
Crop rotational diversity increases disease suppressive capacity of soil microbiomes (2018, methodology): “This may indicate carbon resource specialization among bacteria since they are probably the major contributor to C catabolism in these substrate-induced respiration methods (Goldfarb et al. 2011, Allison et al. 2014).”
Digging deeper to find unique microbial communities: The strong effect of depth on the structure of bacterial and archaeal communities in soil (2012, background): “, 2010), as a variety of soil proteobacterial taxa are also considered to be copiotrophic (Eilers et al., 2010; Goldfarb et al., 2011; Nemergut et al., 2010).”
Multiple mechanisms for trait effects on litter decomposition: moving beyond home‐field advantage with a new hypothesis (2012, background): “Indeed, soil bacterial community composition has been recently suggested to change in parallel with both recalcitrant and labile compound contents (Goldfarb et al. 2011).”
Rate-specific responses of prokaryotic diversity and structure to nitrogen deposition in the Leymus chinensis steppe (2014, result): “Our results confirmed the increase in predicted copiotrophic groups (Proteobacteria and Bacteriodetes) (Goldfarb et al., 2011; Ramirez et al., 2012), and a decrease in predicted oligotrophic groups (Acidobacteria and Nitrospirae) (Jones et al., 2009; Bergmann et al., 2011) with N addition.”