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

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.

Dynamics of the bacterial community structure in the rhizosphere of a maize cultivar

“…This is considered to be a carbon-rich environment, and ecological theory suggests that copiotrophic behavior or r-selected populations should be well adapted to such nutrient-rich conditions. 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). Our results confirmed that these organisms predominate in the rhizosphere, presumably because labile organic substrates are more available than in bulk soil.…”

“…SI_2). Members of Burkholderiales were enriched in the rhizosphere, possibly due to their versatile abilities to utilize root metabolites, degrade aromatic compounds (Goldfarb et al, 2011;Vandenkoornhuyse et al, 2007) and produce anti-microbial substances (Coenye and Vandamme, 2003). In this order, genera Massilia predominated at the early stages of succession, while Burkholderia and Variovorax increased at later growth stages (Fig.…”

The effect of resource history on the functioning of soil microbial communities is maintained across time

“…Indeed, microbial communities are highly complex entities, making identification of mechanisms underlying the effects of history on ecosystem processes difficult to unravel (Allison and Martiny, 2008;Bradford et al, 2008;Green et al, 2008). Differences might arise from physiological adjustments of individuals, capacity for colonization, evolutionary adaptation, epigenetics, and/or shifts in the abundance of different taxa (Goddard and Bradford, 2003;Bossdorf et al, 2008;Fukami et al, 2010). What is clear from our results is the potential for initial microbial functional dissimilarity to be maintained despite a recent history of the same environment.…”

Quantitative Microbial Ecology through Stable Isotope Probing

“…Bromodeoxyuridine (BrdU) uptake has been proposed as a universal technique for identifying growing organisms (52) and their responses to environmental perturbations (53). However, there is up to 10-fold variation among taxa in the conversion between BrdU uptake and growth that is unrelated to taxonomic affiliation, a bias calling into question the quantitative universality of this technique (54).…”