Development of an Environmental Functional Gene Microarray for Soil Microbial Communities

Abstract

Functional attributes of microbial communities are difficult to study, and most current techniques rely on DNA-and rRNA-based profiling of taxa and genes, including microarrays containing sequences of known microorganisms. To quantify gene expression in environmental samples in a culture-independent manner, we constructed an environmental functional gene microarray (E-FGA) consisting of 13,056 mRNA-enriched anonymous microbial clones from diverse microbial communities to profile microbial gene transcripts. A new normalization method using internal spot standards was devised to overcome spotting and hybridization bias, enabling direct comparisons of microarrays. To evaluate potential applications of this metatranscriptomic approach for studying microbes in environmental samples, we tested the E-FGA by profiling the microbial activity of agricultural soils with a low or high flux of N 2 O. A total of 109 genes displayed expression that differed significantly between soils with low and high N 2 O emissions. We conclude that mRNA-based approaches such as the one presented here may complement existing techniques for assessing functional attributes of microbial communities.

Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning

“…Due to the importance of microbial communities in mediating soil biogeochemical processes ( van Bruggen and Semenov, 2000 ; Jackson et al, 2003 ; Xue et al, 2011 ), influences of warming on microbial community activities may potentially affect the biogeochemical cycling and ecosystem functioning. However, DNA-based technologies are hard to directly reflect the actual activity of active microbial populations ( McGrath et al, 2010 ; Simon and Daniel, 2011 ; Franzosa et al, 2015 ). In contrast, RNA-based approaches can provide better insights into functional attributes of active populations in microbial community ( McGrath et al, 2010 ; Simon and Daniel, 2011 ; Takasaki et al, 2013 ).…”

Analysis of the microbial gene landscape and transcriptome for aromatic pollutants and alkane degradation using a novel internally calibrated microarray system

“…Despite its crucial importance, the reliability of microarray results has not been carefully assessed yet. We reasoned that the proper approach to determine the reliability of microarray results requires the use of internal positive controls (IPCs) for setting the correct threshold according to the desired precision of the experiment, rather than artificial signal to noise ratios (Rhee et al ., 2004; McGrath et al ., 2010).…”

Linking microbial community structure to β-glucosidic function in soil aggregates

“…Efforts to study the in situ activities in the soil by directly analyzing mRNAs have proven difficult, given the ephemeral nature of mRNA and the abundance of nucleases in soil (Cai et al, 2006;Pietramellara et al, 2009). Additionally, both enzyme assays and the mRNA analyses are limited; most enzyme assays will probably be reflective of multiple genes and organisms, and mRNA analyses are dependent on a priori sequence knowledge (Bailey et al, 2010;McGrath et al, 2010;Wang et al, 2011). Finally, both analyses have traditionally been conducted on relatively large sample sizes, compared with the scale at which microorganisms interact as a community, the latter of which would better able researchers to draw correlations (that is, (Kumaresan et al, 2011)) between the community structure and function.…”