Spatial Stratification of Soil Bacterial Populations in Aggregates of Diverse Soils

Abstract

Most soil microbial community studies to date have focused on homogenized bulk soil samples. However, it is likely that many important microbial processes occur in spatially segregated microenvironments in the soil leading to a microscale biogeography. This study attempts to localize specific microbial populations to different fractions or compartments within the soil matrix. Microbial populations associated with macroaggregates and inner- versus total-microaggregates of three diverse soils were characterized using culture-independent, molecular methods. Despite their relative paucity in most surveys of soil diversity, representatives of Gemmatimonadetes and Actinobacteria subdivision Rubrobacteridae were found to be highly abundant in inner-microaggregates of most soils analyzed. By contrast, clones affiliated with Acidobacteria were found to be relatively enriched in libraries derived from macroaggregate fractions of nearly all soils, but poorly represented in inner-microaggregate fractions. Based upon analysis of 16S rRNA, active community members within microaggregates of a Georgian Ultisol were comprised largely of Gemmatimonadetes and Rubrobacteridae, while within microaggregates of a Nebraska Mollisol, Rubrobacteridae and Alphaproteobacteria were the predominant active bacterial lineages. This work suggests that microaggregates represent a unique microenvironment that selects for specific microbial lineages across disparate soils.

Response and resilience of soil biocrust bacterial communities to chronic physical disturbance in arid shrublands

“…The majority (74%) of Actinobacteria sequences identified in this study belong to the deepest branch of the phylum, the Rubrobacteridae, which are common in arid soils and on rock surfaces worldwide and are extremely resistant to desiccation and UV stress (Holmes et al, 2000;Rainey et al, 2005). The involvement of Rubrobacteridae in soil aggregate formation and calcite precipitation suggests that they may also be involved in engineering the soil surface structure during biocrust formation (Mummey and Stahl, 2004;Rainey et al, 2005;Mummey et al, 2006;Pellerin et al, 2009). Filamentous Chloroflexi bacteria have been visualized within sheaths of Microcoleus chthonoplastes in hypersaline microbial mats and co-located with M. vaginatus in biocrusts of a high elevation site in Colorado, but whether the relationship between the two species is symbiotic or antagonistic is not known (Ley et al, 2006;Freeman et al, 2009).…”

Global Biogeography and Quantitative Seasonal Dynamics of Gemmatimonadetes in Soil

“…In combination, this evidence suggests either an adaptation to drier soils or, alternatively, that Gemmatimonadetes may be outcompeted when moisture is available. In microbial communities associated with soil microaggregates, a much higher percentage of Gemmatimonadetes (10 to 32% of the community) was found in the inner microaggregates than in the whole aggregates (36). This may be indicative of an adaptation to low-moisture (or lowoxygen) conditions typical of inner aggregates.…”

Trade-offs between the short- and long-term effects of residue quality on soil C and N dynamics

“…Therefore, SOM may not be stabilized in the long-term if it is not protected by physical mechanisms against micro-bial utilization (Marschner et al 2008). Soil aggregates physically protect soil organic matter (Tisdall and Oades 1982) and influence microbial community composition (Mummey et al 2006), thus their dynamics may play an important role in SOM stabilization. Since high quality residues and N fertilizer are postulated to increase aggregate turnover (Harris et al 1963;Six et al 2001), interactions between residue and fertilizer inputs may influence physical SOM stabilization.…”