Inferring community dynamics of organohalide-respiring bacteria in chemostats by covariance ofrdhAgene abundance

Abstract

We have developed a novel approach to identifying and quantifying closely related organohalide-respiring bacteria. Our approach made use of the unique genomic associations of specific reductive dehalogenase subunit A encoding genes (rdhA) that exist in known strains of Dehalococcoides mccartyi and Desulfitobacterium and the distinguishing covariance pattern of observed rdhA genes to assign genes to unknown strains. To test this approach, we operated five anaerobic reductively dechlorinating chemostats for 3-4 years with tetrachloroethene and trichloroethene as terminal electron acceptors and lactate/formate as electron donors. The presence and abundance of rdhA genes were determined comprehensively at the community level using a custom-developed Reductive Dehalogenase Chip (RDH Chip) DNA microarray and used to define putative strains of Dehalococcoides mccartyi and Desulfitobacterium sp. This monitoring revealed that stable chemical performance of chemostats was reflected by a stable community of reductively dechlorinating bacteria. However, perturbations introduced by, for example, electron donor limitation or addition of the competing electron acceptor sulfate led to overall changes in the chemostat performance, including incomplete reduction in the chloroethene substrates, and in the population composition of reductively dehalogenating bacteria. Interestingly, there was a high diversity of operationally defined D. mccartyi strains between the chemostats with almost all strains unique to their specific chemostats in spite of similar selective pressure and similar inocula shared between chemostats.

1,2-Dichloroethane Exposure Alters the Population Structure, Metabolism, and Kinetics of a Trichloroethene-Dechlorinating Dehalococcoides mccartyi Consortium

“…To investigate the ecological effects of 1,2-DCA exposure on Dehalococcoides populations within a chloroethene-dehalogenating consortium, we used a TCE-fed reactor (EV-5), maintained for the 8 years prior, to seed a set of experimental reactors: EV-3, EV-TCE, EV-P (Table ). A previous study indicated that the parent reactor EV-5 was comprised of multiple populations of organohalide-respiring bacteria, and our recent metagenomic analysis revealed that it contained distinct tceA -containing and vcrA -containing populations. Reactor EV-3 was exposed to a changing mixture of TCE and 1,2-DCA over the course of a year and then fed 1,2-DCA only.…”

Inferring Gene Networks for Strains of Dehalococcoides Highlights Conserved Relationships between Genes Encoding Core Catabolic and Cell-Wall Structural Proteins

“…Therefore, strain specific nodes are more likely to connect with other nodes from the same cluster; the consensus network therefore represented at least two populations of Dhc . Overall, the slight genomic variations between strains of Dhc [41] lead to different survival patterns, metabolic capabilities, and environmental responses as experimentally displayed in the suitability of various strains to differing culturing conditions in Marshall et al [42]. …”

Simultaneous anaerobic transformation of tetrachloroethene and carbon tetrachloride in a continuous flow column

“…The study was conducted in a continuous flow column packed with quartz Ottawa sand. The column was bioaugmented with Evanite culture (EV) that contains strains of Dehalococcoides mccartyi (Dhc) (Behrens et al, 2008;Marshall et al, 2013) that is capable of transforming PCE to ethene (ETH) (Yu et al, 2005). The reductive dehalogenase (rdh) genes in the Evenite culture were identified as being closely related to the population of Dhc previously found under chemostat growth conditions (Marshall et al, 2013;Mayer-Blackwell et al, 2014),…”

“…The column was bioaugmented with the EV mixed dehalogenating culture that contained at least two strains of Dehalococcoides mccartyi (Marshall et al, 2013). Molecular characterization of the EV culture in a previous column study where the EV was bioagumented showed 73% of bacteria in the EV culture were strains of Dhc (Azizian et al, 2008).…”