Diversity of Five Anaerobic Toluene-Degrading Microbial Communities Investigated Using Stable Isotope Probing

Abstract

Time-series DNA-stable isotope probing (SIP) was used to identify the microbes assimilating carbon from [ 13 C]toluene under nitrate-or sulfate-amended conditions in a range of inoculum sources, including uncontaminated and contaminated soil and wastewater treatment samples. In all, five different phylotypes were found to be responsible for toluene degradation, and these included previously identified toluene degraders as well as novel toluene-degrading microorganisms. In microcosms constructed from granular sludge and amended with nitrate, the putative toluene degraders were classified in the genus Thauera, whereas in nitrate-amended microcosms constructed from a different source (agricultural soil), microorganisms in the family Comamonadaceae (genus unclassified) were the key putative degraders. In one set of sulfate-amended microcosms (agricultural soil), the putative toluene degraders were identified as belonging to the class Clostridia (genus Desulfosporosinus), while in other sulfate-amended microcosms, the putative degraders were in the class Deltaproteobacteria, within the family Syntrophobacteraceae (digester sludge) or Desulfobulbaceae (contaminated soil) (genus unclassified for both). Partial benzylsuccinate synthase gene (bssA, the functional gene for anaerobic toluene degradation) sequences were obtained for some samples, and quantitative PCR targeting this gene, along with SIP, was further used to confirm anaerobic toluene degradation by the identified species. The study illustrates the diversity of toluene degraders across different environments and highlights the utility of ribosomal and functional gene-based SIP for linking function with identity in microbial communities.

Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples

“…The high abundance of Firmicutes in TOLDC and NAPDC is consistent with recent reports of anaerobic monoaromatic hydrocarbon-degrading cultures that implicate Firmicutes (for example, Peptococcaceae) as primary hydrocarbon degraders (Abu Laban et al, 2009;Winderl et al, 2010;Sun and Cupples, 2012;Fowler et al, 2014) or playing key roles alongside Deltaproteobacteria (Ficker et al, 1999;Ulrich and Edwards, 2003;Sakai et al, 2009). In contrast, members of the Deltaproteobacteria, particularly Syntrophus/Smithella sp., have been implicated in methanogenic alkane degradation, particularly of longer-chain alkanes (Zengler et al, 1999;Gray et al, 2011;Cheng et al, 2013).…”

“…Many previous studies have shown that microbial communities in methanogenic hydrocarbonassociated environments (for example, Chang et al, 2005;Kasai et al, 2005;Sun and Cupples, 2012;Wawrik et al, 2012;An et al, 2013) or enrichment cultures (Ficker et al, 1999;Fowler et al, 2012) can be highly diverse. Literature-wide compilations examining such communities (Gray et al, 2011;Strapoc et al, 2011;Kleinsteuber et al, 2012) have revealed that they frequently contain hydrogenotrophic (for example, Methanoculleus, Methanolinea, Candidatus Methanoregula, Methanospirillum), acetotrophic (for example, Methanosaeta), and/or methylotrophic methanogens (for example, Methanolobus; Wuchter et al, 2013).…”

Effects of Seasonal Thermal Stratification on the Functional Diversity and Composition of the Microbial Community in a Drinking Water Reservoir

“…Hence, additional environmental parameters should be considered and measured combined with more sampling times over years. Furthermore, the diversity of the archaeal and eukaryotic community based on the high-throughput and sensitive sequencing technology should be combined with environmental characteristics to establish a more exact relationship between biogeochemistry cycling and microbial communities in drinking water reservoirs [64]. Despite the fact that there may have been some disturbances, the comparison of the communities detected in our study was feasible, since all samples were treated similarly.…”

Global biogeography of microbial nitrogen-cycling traits in soil

“…Other abundant genera were less expected. For example, Azoarcus is an organism studied for its abilities to degrade soil contaminants (33), and Pectobacterium (Gammaproteobacteria) is known primarily as a plant pathogen (34). Indeed, although The models for the individual pathways are based on the residual frequencies of the pathway after correcting for the Total N pathway frequency (see text).…”