Actinobacterial community dynamics in long term managed grasslands

Abstract

Palace Leas, a long-term experiment at Cockle Park Farm, Northumberland, UK was established in winter 1896-1897 since when the 13 plots have received regular and virtually unchanged mineral fertiliser and farm yard manure inputs. Fertilisers have had a profound impact on soil pH with the organically fertilised plots showing a significantly higher pH than those receiving mineral fertiliser where ammonium sulphate has led to soil acidification. Here, we investigate the impact of organic and mineral fertilisers on the actinobacterial community structure of these soils using terminal restriction fragment length polymorphism (T-RFLP) and 16S rRNA gene analysis. To differentiate fertiliser effects from seasonal variation, soils were sampled three times over one growing season between May and September 2004 and January 2005. Community profiles obtained using T-RFLP were analysed using multivariate statistics to investigate the relationship between community structure, seasonality and fertiliser management. Soil pH was shown to be the most significant edaphic factor influencing actinobacterial communities. Canonical correspondence analysis, used to investigate the relationship between the 16S rRNA gene community profiles and the environmental parameters, showed that actinobacterial communities also responded to soil water content with major changes evident over the summer months between May and September. Quantitative PCR of the actinobacterial and fungal 16S and 18S rRNA genes, respectively suggested that fungal rRNA gene copy numbers were negatively correlated (P = 0.0131) with increasing actinobacterial signals. A similar relationship (P = 0.000365) was also evident when fatty acid methyl esters indicative of actinobacterial biomass (10-methyloctadecanoic acid) were compared with the amounts of fungal octadecadienoic acid (18:2omega9,12). These results show clearly that soil pH is a major driver of change in actinobacterial communities and that genera such as Arthrobacter and Micrococcus are particularly abundant in soils receiving organic inputs whilst others such as Streptomyces, Acidimicrobium and Actinospica are more prevalent in acid soils. The importance of these findings in terms of fungal abundance and potential disease suppression are discussed.

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

“…Recently, this has also been reported in the pH gradient studied here (Aciego Pietri and Brookes, 2009;Rousk et al, 2010a). In addition, characterizations of soil bacterial communities across a wide range of sample sets have consistently indicated the same powerful correlation between soil pH and bacterial community composition, regardless of the technique used, including DNA fingerprinting-based techniques (Fierer and Jackson, 2006;Männistö et al, 2007;Jenkins et al, 2009), clone library-based techniques Jesus et al, 2009) and pyrosequencing-based techniques ). The results from previous studies are thus corroborated by our results, and the strong connection between pH and the bacterial community composition is consequently consistent both across Figure 5 The relationships between relative abundances of three abundant fungal sequences and soil pH.…”

“…This pattern holds both for overall bacterial community composition (Fierer and Jackson, 2006;Baker et al, 2009;Lauber et al, 2009) and for the composition of individual bacterial groups (Nicol et al, 2008;Davis et al, 2009;Jenkins et al, 2009;Jones et al, 2009). It also seems to hold across a variety of spatial scales, including continental scales (Fierer and Jackson, 2006;Lauber et al, 2009), across land-use types at a given location Jenkins et al, 2009), and across small, submeter scales (Baker et al, 2009;Philippot et al, 2009). However, one limitation of these observational studies is that it is impossible to determine whether the communities are structured directly or indirectly by pH.…”

“…Recent study has demonstrated that changes in soil microbial communities across space are often strongly correlated with differences in soil chemistry (Frey et al, 2004;Nilsson et al, 2007;Lauber et al, 2008;Jenkins et al, 2009). In particular, it has been shown that the composition, and in some cases diversity, of soil bacterial communities is often strongly correlated with soil pH (Fierer and Jackson, 2006;Hartman et al, 2008;Jenkins et al, 2009;Lauber et al, 2009).…”

“…In particular, it has been shown that the composition, and in some cases diversity, of soil bacterial communities is often strongly correlated with soil pH (Fierer and Jackson, 2006;Hartman et al, 2008;Jenkins et al, 2009;Lauber et al, 2009). This pattern holds both for overall bacterial community composition (Fierer and Jackson, 2006;Baker et al, 2009;Lauber et al, 2009) and for the composition of individual bacterial groups (Nicol et al, 2008;Davis et al, 2009;Jenkins et al, 2009;Jones et al, 2009).…”

“…In particular, it has been shown that the composition, and in some cases diversity, of soil bacterial communities is often strongly correlated with soil pH (Fierer and Jackson, 2006;Hartman et al, 2008;Jenkins et al, 2009;Lauber et al, 2009). This pattern holds both for overall bacterial community composition (Fierer and Jackson, 2006;Baker et al, 2009;Lauber et al, 2009) and for the composition of individual bacterial groups (Nicol et al, 2008;Davis et al, 2009;Jenkins et al, 2009;Jones et al, 2009). It also seems to hold across a variety of spatial scales, including continental scales (Fierer and Jackson, 2006;Lauber et al, 2009), across land-use types at a given location Jenkins et al, 2009), and across small, submeter scales (Baker et al, 2009;Philippot et al, 2009).…”