Changes in Bacterial and Archaeal Community Structure and Functional Diversity along a Geochemically Variable Soil Profile

Abstract

Spatial heterogeneity in physical, chemical, and biological properties of soils allows for the proliferation of diverse microbial communities. Factors influencing the structuring of microbial communities, including availability of nutrients and water, pH, and soil texture, can vary considerably with soil depth and within soil aggregates. Here we investigated changes in the microbial and functional communities within soil aggregates obtained along a soil profile spanning the surface, vadose zone, and saturated soil environments. The composition and diversity of microbial communities and specific functional groups involved in key pathways in the geochemical cycling of nitrogen, Fe, and sulfur were characterized using a coupled approach involving cultivation-independent analysis of both 16S rRNA (bacterial and archaeal) and functional genes (amoA and dsrAB) as well as cultivation-based analysis of Fe(III)-reducing organisms. Here we found that the microbial communities and putative ammonia-oxidizing and Fe(III)-reducing communities varied greatly along the soil profile, likely reflecting differences in carbon availability, water content, and pH. In particular, the Crenarchaeota 16S rRNA sequences are largely unique to each horizon, sharing a distribution and diversity similar to those of the putative (amoA-based) ammonia-oxidizing archaeal community. Anaerobic microenvironments within soil aggregates also appear to allow for both anaerobic-and aerobic-based metabolisms, further highlighting the complexity and spatial heterogeneity impacting microbial community structure and metabolic potential within soils.

Phylogenetic diversity of Acidobacteria in a former agricultural soil

“…Subdivisions 6, 4, 3 and 1 were generally most abundant across the different libraries (Table 1), in agreement with other sequences recovered earlier from soil habitats (Kuske et al, 1997;Barns et al, 1999;Janssen, 2006;Eichorst et al, 2007;Hansel et al, 2008). None of the approaches yielded clones affiliated with subdivisions 8, 9 or 11.…”

Long-term CO2injection and its impact on near-surface soil microbiology

“…The cultivation of Candidatus Nitrososphaera gargensis has proven its ability for aerobic, chemolithoautotrophic nitrification and the potential for a mixotrophic life (Hatzenpichler et al 2008;Pratscher et al 2011;Spang et al 2012) SIMPER analysis at phylum level indicated that Thaumarchaeota contributed most of the differences in the relative abundance between CO 2 -injected and reference sites (78.1%) (Supplementary Table 7). The predominance and importance of thaumarchaeotal I.1b soil group within both CO 2 -injected and reference soil samples agrees with previous studies in different soil ecosystems (Hansel et al 2008;Bates et al 2011;Eilers et al 2012). …”

Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest

“…Throughout the field experiment, acidobacterial communities were more abundant and underwent significant structural changes in girdled, C-limited plots. This may signify their high metabolic versatility to be well-adapted to resource limitation and their ability to decompose complex C substrates deriving from the rather recalcitrant soil organic matter pool (Ward et al, 2009;Hansel et al, 2008;Eichorst et al, 2007;Fierer et al, 2007). Girdling prevents the uptake of available nutrients such as ammonia and nitrate by trees (Högberg et al, 2001), and therefore resulted in relatively higher mineral N concentrations in soils of girdled plots.…”