Toward an Ecological Classification of Soil Bacteria

Abstract

Although researchers have begun cataloging the incredible diversity of bacteria found in soil, we are largely unable to interpret this information in an ecological context, including which groups of bacteria are most abundant in different soils and why. With this study, we examined how the abundances of major soil bacterial phyla correspond to the biotic and abiotic characteristics of the soil environment to determine if they can be divided into ecologically meaningful categories. To do this, we collected 71 unique soil samples from a wide range of ecosystems across North America and looked for relationships between soil properties and the relative abundances of six dominant bacterial phyla (Acidobacteria, Bacteroidetes, Firmicutes, Actinobacteria, alpha-Proteobacteria, and the beta-Proteobacteria). Of the soil properties measured, net carbon (C) mineralization rate (an index of C availability) was the best predictor of phylum-level abundances. There was a negative correlation between Acidobacteria abundance and C mineralization rates (r2 = 0.26, P < 0.001), while the abundances of beta-Proteobacteria and Bacteroidetes were positively correlated with C mineralization rates (r2 = 0.35, P < 0.001 and r2 = 0.34, P < 0.001, respectively). These patterns were explored further using both experimental and meta-analytical approaches. We amended soil cores from a specific site with varying levels of sucrose over a 12-month period to maintain a gradient of elevated C availabilities. This experiment confirmed our survey results: there was a negative relationship between C amendment level and the abundance of Acidobacteria (r2 = 0.42, P < 0.01) and a positive relationship for both Bacteroidetes and beta-Proteobacteria (r2 = 0.38 and 0.70, respectively; P < 0.01 for each). Further support for a relationship between the relative abundances of these bacterial phyla and C availability was garnered from an analysis of published bacterial clone libraries from bulk and rhizosphere soils. Together our survey, experimental, and meta-analytical results suggest that certain bacterial phyla can be differentiated into copiotrophic and oligotrophic categories that correspond to the r- and K-selected categories used to describe the ecological attributes of plants and animals. By applying the copiotroph-oligotroph concept to soil microorganisms we can make specific predictions about the ecological attributes of various bacterial taxa and better understand the structure and function of soil bacterial communities.

Plant community and soil conditions individually affect soil microbial community assembly in experimental mesocosms

“…We might have expected Acidobacteria, a largely oligotrophic phylum, to decrease with increasing N content (i.e., increasing topsoil content; Leff et al., 2015; Ramirez et al., 2010) and Bacteroidetes, a copiotrophic phylum (Fierer et al., 2007), to increase, but we found the opposite. Acidobacteria were negatively correlated with nitrate levels and positively correlated with ammonia, while Bacteroidetes abundance was negatively correlated with ammonia.…”

Isothermal Microcalorimetry Provides New Insight into Terrestrial Carbon Cycling

“…Microbial metabolism in soils consists of a plethora of processes 278 including reactions that do not produce CO 2 as an end-product. 11 Isothermal microcalorimetry 279 quantifies all metabolic processes and therefore accounts for the different processes that occur 280 within different microbial communities, regardless of the different life strategies of soil 281 organisms 14 . This is not always the case with respiration measurements.…”

“…From an energy point of 44 view, soil ecosystems can be characterized as open systems of non-equilibrium thermodynamics 45 with the decomposition of soil organic matter to carbon dioxide (CO 2 ) as a dissipative process 46 that increases entropy 3,4 . Microbial metabolism is divided into two categories: catabolic reactions 47 allochtonous r-versus zymogenous K-selection concept 17 has been criticized as being an 76 oversimplified view of the processes of natural selection in ecology 18 , it is still consistent with 77 modern interpretation of community type and soil microbial functioning 14 . In general, 78 allochtonous r-strategists are adapted to rapidly acquiring resources when abundant and 79 maximizing their growth rate.…”

Links between soil microbial communities and plant traits in a species‐rich grassland under long‐term climate change

“…We found evidence of links between plant traits and soil microbial communities despite the breadth of microbial functional groups included in our community fingerprints; the seemingly small effect sizes in our study are unsurprising, given the high microbial diversity and the potential influence of numerous soil physical and chemical properties. Soil pH in particular has an overriding effect on soil bacteria (Fierer, Bradford, & Jackson, 2007; Griffiths et al., 2011), and it is conceivable that some of the observed differences in bacterial community structure are a result of lower soil pH in the drought plots and deep microsites (Fridley et al., 2011) or a direct effect of differences in soil depth. Nevertheless, plant C:N ratios explained a greater proportion of the variation in soil bacteria compared to microsite characteristics (soil depth and pH) and the carbon construction costs of plant material explained an equivalent amount of variation in both bacterial and fungal community structures.…”