Soil characteristics more strongly influence soil bacterial communities than land-use type

Abstract

To gain insight into the factors driving the structure of bacterial communities in soil, we applied real-time PCR, PCR-denaturing gradient gel electrophoreses, and phylogenetic microarray approaches targeting the 16S rRNA gene across a range of different land usages in the Netherlands. We observed that the main differences in the bacterial communities were not related to land-use type, but rather to soil factors. An exception was the bacterial community of pine forest soils (PFS), which was clearly different from all other sites. PFS had lowest bacterial abundance, lowest numbers of operational taxonomic units (OTUs), lowest soil pH, and highest C : N ratios. C : N ratio strongly influenced bacterial community structure and was the main factor separating PFS from other fields. For the sites other than PFS, phosphate was the most important factor explaining the differences in bacterial communities across fields. Firmicutes were the most dominant group in almost all fields, except in PFS and deciduous forest soils (DFS). In PFS, Alphaproteobacteria was most represented, while in DFS, Firmicutes and Gammaproteobacteria were both highly represented. Interestingly, Bacillii and Clostridium OTUs correlated with pH and phosphate, which might explain their high abundance across many of the Dutch soils. Numerous bacterial groups were highly correlated with specific soil factors, suggesting that they might be useful as indicators of soil status.

Bacteria as Emerging Indicators of Soil Condition

“…The results highlighted that this trend not only occurs in a wide range of geographic settings but also remains consistent even when collecting samples across larger spatial scales than normally considered (14) or indeed when using a DNA sequencing approach instead of DNA-fingerprinting approaches, which have dominated investigations of microbial biogeography for many years (4,5). Another previously reported trend that we observed for our samples was the relationship between bacterial communities and the ratio of carbon to nitrogen in the soil (5,26,27).…”

Microbial minorities modulate methane consumption through niche partitioning

“…The active methane-oxidizing species (types Ia and Ib) in the studied wetland constitute a numerically subordinate group within the functional guild of methanotrophs, which is already a minority on itself. When assuming the total amount of bacteria to be approximately 1.10 9 cells per gram of dry soil (Wessen et al, 2010;Ho et al, 2011;Daniell et al, 2012;Kuramae et al, 2012), which is even the lower limit of the range typically observed, then type Ia and Ib MOB constitute 0.001-0.05% and 0.08-0.5% of the total community, respectively. The individual species carrying out the observed activity that are collectively targeted by the qPCR assays constitute an even lower percentage of the community.…”

C:N:P stoichiometry and nutrient limitation of the soil microbial biomass in a grazed grassland site under experimental P limitation or excess

“…Liu et al (2012) similarly showed an altered PLFA pattern in the P-limited old-growth forest with added P, but in their case an increased fungal-to-bacterial ratio. Phosphate has recently been shown to be an important driver of microbial community structure in a range of soils (Kuramae et al 2012). Figure 3 Regression analysis of biomass C (C mic (μg C g −1 soil dry weight)) and biomass P (P mic (μg P g −1 soil dry weight)) in different soil P-fertilisation treatments.…”