Soil bacterial and fungal communities across a pH gradient in an arable soil

Abstract

Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth.

Effects of temperature, soil substrate, and microbial community on carbon mineralization across three climatically contrasting forest sites

“…For example, the cool temperate forest soils with rich SOM and better development were closely associated with the total bacteria and gram‐negative bacteria group, similar to the findings of other studies (Balser & Firestone, 2005; Kramer & Gleixner, 2008; You et al., 2014). The subtropical soils, being more acidic, were strongly associated with actino‐bacteria—a metabolically versatile group of microorganisms that degrade lignin and cellulose (Rousk et al., 2010). Our previous studies well established that biotic and environmental factors control soil C transformation and turnover by shaping the soil microbial structure (Sun et al., 2016; You et al., 2014, 2016).…”

Wastewater reuse in irrigation: A microbiological perspective on implications in soil fertility and human and environmental health

“…In opposition, the decrease of soil pH was reported in agricultural soils dedicated to lettuce, livestock fodder and orange production irrigated with wastewater for more than 15, 20 and 40 years, respectively (Table 4). Although the effects on soil microbiota due to the abovementioned pH variations were not explored in those studies, this parameter seems to be an important determinant of the richness (number of different species) and diversity (variety of organ-isms) of soil bacterial communities (Fierer and Jackson, 2006;Lauber et al, 2009;Rousk et al, 2010). In a comprehensive study comparing soil bacterial communities from distinct ecosystems it was observed that communities of sites with identical pH values share similar indices of bacterial diversity and richness, irrespective of other factors such as climate conditions or edaphic properties (Fierer and Jackson, 2006).…”

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter

“…PyOM produced from different materials under different conditions can result in a wide range of pH values (Enders et al, 2012), and in this study, PyOM additions significantly increased soil pH (Supplementary Figure 17), albeit by less than a full pH unit. Soil pH is strongly correlated with community composition (Lauber et al, 2009;Rousk et al, 2010). In particular, the aptly named phylum Acidobacteria has been shown to be especially sensitive to pH shifts, although its subgroups show variable responses to acidity: subgroups 1, 2 and 3 have been shown to increase at lower pHs, whereas subgroups 4, 5, 6, 7 and 17 have been shown to increase at higher pHs (Rousk et al, 2010;Bartram et al, 2013).…”

“…Soil pH is strongly correlated with community composition (Lauber et al, 2009;Rousk et al, 2010). In particular, the aptly named phylum Acidobacteria has been shown to be especially sensitive to pH shifts, although its subgroups show variable responses to acidity: subgroups 1, 2 and 3 have been shown to increase at lower pHs, whereas subgroups 4, 5, 6, 7 and 17 have been shown to increase at higher pHs (Rousk et al, 2010;Bartram et al, 2013). Both Bartram et al (2013) and Rousk et al (2010) characterized soils from long-term (50+ and 100+ years, respectively) liming trials, so it is not possible to predict from those studies the expected timescale of a soil bacterial community response to pH changes.…”