Soil Microbe Active Community Composition and Capability of Responding to Litter Addition after 12 Years of No Inputs

Abstract

bOne explanation given for the high microbial diversity found in soils is that they contain a large inactive biomass that is able to persist in soils for long periods of time. This persistent microbial fraction may help to buffer the functionality of the soil community during times of low nutrients by providing a reservoir of specialized functions that can be reactivated when conditions improve. A study was designed to test the hypothesis: in soils lacking fresh root or detrital inputs, microbial community composition may persist relatively unchanged. Upon addition of new inputs, this community will be stimulated to grow and break down litter similarly to control soils. Soils from two of the Detrital Input and Removal Treatments (DIRT) at the H. J. Andrews Experimental Forest, the no-input and control treatment plots, were used in a microcosm experiment where Douglas-fir needles were added to soils. After 3 and 151 days of incubation, soil microbial DNA and RNA was extracted and characterized using quantitative PCR (qPCR) and 454 pyrosequencing. The abundance of 16S and 28S gene copies and RNA copies did not vary with soil type or amendment; however, treatment differences were observed in the abundance of archaeal ammonia-oxidizing amoA gene abundance. Analysis of ϳ110,000 bacterial sequences showed a significant change in the active (RNA-based) community between day 3 and day 151, but microbial composition was similar between soil types. These results show that even after 12 years of plant litter exclusion, the legacy of community composition was well buffered against a dramatic disturbance.

Abundance and Activity of 16S rRNA,AmoAandNifHBacterial Genes During Assisted Phytostabilization of Mine Tailings

“…For example, in a study of forest soils, Yarwood et al . (2012) could not detect amoA bacterial activity despite the presence of amoA gene copy numbers at levels comparable to those detected in the QB rhizosphere (Yarwood et al . 2012).…”

Controls on soil microbial community stability under climate change

“…Recent advances in sequence-based metagenomics allow for identification of functional genes in a microbial community (Thomas et al, 2012). However, although the presence and expression of specific functional genes in soil microbial communities has been shown to respond to global change and climate change disturbances (e.g., Baldrian et al, 2012; Yergeau et al, 2012; Yarwood et al, 2013), the relative abundance of functional genes has never been used to infer a community's ability to withstand and recover from disturbances. This approach still has many caveats; newly discovered gene sequences often lack homology to known genes in current databases and remain unknown until biochemical characterization and annotation of their functional abilities, and microorganisms may carry the genetic capacity to exhibit a certain functional trait, but, ultimately, not express the gene or produce an active gene product in nature.…”

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

“…Historically, rRNA analyses have been used to quantify populations' growth rates in mixed microbial communities (for example, Poulsen et al, 1993;Muttray et al, 2001), but recent application has shifted toward the more qualitative approach using rRNA to identify currently active microbial populations in a mixed community (for example, Jones and Lennon, 2010;Kamke et al, 2010;Campbell et al, 2011;DeAngelis et al, 2011;Gaidos et al, 2011;Reid et al, 2011;Baldrian et al, 2012;Mannisto et al, 2012;Mattila et al, 2012;Simister et al, 2012;Campbell and Kirchman, 2013;Hunt et al, 2013;Yarwood et al, 2013). Two principal lines of evidence used to support rRNA as an indicator of current activity originate from earlier studies testing how rRNA scales with growth rate.…”