Organohalide Respiration

Microbial reductive dehalogenation mediated by organohalide-respiring bacteria plays a critical role in the natural halogen cycle, representing a promising solution for removal of organohalide pollutants. This Research Topic presents many of the more recent advances that have been made in this area. Authors from leading research groups contributed to this eBook, and provided mechanistic insights into organohalide respiration, as well as their bioremediation implications, at molecular, cellular, community and system levels.

Vinyl chloride (VC) is a widespread groundwater pollutant and Group 1 carcinogen. Microbial respiration of VC is both critical for complete remediation of chloroethenes in situ, and a unique physiology only observed by certain strains of Dehalococcoides. Two different genes independently encoding VC respiration in Dehalococcoides, vcrA and bvcA, were identified previously, each a member of the diverse family of reductive dehalogenase homologous genes, or rdhA. In this thesis I report that vcrA and bvcA are among a subset of putative 'foreign' rdhA with a low GC3 codon usage that favors the nucleotide T, even though tRNAs recognizing T-ending codons are categorically absent in Dehalococcoides genomes. Comparative genomics of the first two complete genome sequences of microorganisms able to respire VC, Dehalococcoides strains VS and BAV1, reveals that vcrA and bvcA are both located within recently integrated, but different, genomic islands (GIs). These islands have different predicted integration sites and different relative positions in the genome, suggesting that bvcA and vcrA were acquired independently and through different mechanisms. In particular, the vcrA-containing GI appears to have integrated at the single-copy tmRNA encoding gene, ssrA, along with many other homologous elements that site-specifically integrate/excise at ssrA -- some of which contain other rdhA. A detailed analysis of these 'ssrA-GIs' in Dehalococcoides identifies the precise position of insertion as well as a conserved module of syntenic integration-associated genes that includes the likely ssrA-specific integrase. Further analysis of (meta)genomic data, as well as targeted sequencing from 4 additional VC-respiring cultures, provided a total of 8 syntenic vcr-GIs from independently derived cultures. Evolutionary estimates for the age of divergence of these 8 vcrA sequences is not confidently distinguishable from the first industrial synthesis of chlorinated ethenes approximately 100 years ago. By contrast, the estimated age of divergence of Dehalococcoides strains far precedes industrial civilization. Overall, ssrA-GIs appear to be a major contributor to the second of two high plasticity regions, genetically dynamic regions that interrupt an otherwise stable, syntenic, and streamlined Dehalococcoides genome -- among the smallest of any free living microorganism. The apparent compartmentalization of Dehalococcoides genome dynamics within specialized regions may enhance opportunistic adaptation to (new) organohalide respiratory niches while protecting a core genome that is highly adapted to life in the anoxic subsurface, exemplified here by the recent site-specific acquisition of VC reductase genes.

This book summarizes the current state of knowledge concerning bacteria that use halogenated organic compounds as respiratory electron acceptors. The discovery of organohalide-respiring bacteria has expanded the range of electron acceptors used for energy conservation, and serves as a prime example of how scientific discoveries are enabling innovative engineering solutions that have transformed remediation practice. Individual chapters provide in-depth background information on the discovery, isolation, phylogeny, biochemistry, genomic features, and ecology of individual organohalide-respiring genera, including Dehalococcoides, Dehalogenimonas, Dehalobacter, Desulfitobacterium and Sulfurospirillum, as well as organohalide-respiring members of the Deltaproteobacteria. The book introduces readers to the fascinating biology of organohalide-respiring bacteria, offering a valuable resource for students, engineers and practitioners alike.

Advances in Microbial Physiology, Volume 74, the latest release in this ongoing series, continues the long tradition of topical, important, cutting-edge reviews in microbiology. The book contains updates in the field, with comprehensive chapters covering The electrifying physiology of Geobacter bacteria 30 years on, Adaptive morphogenesis in bacteria, Bacterial energetics and respiratory metabolism, Bacteria respiration during infection, Regulation of Organohalide Respiration, Bioenergetics of Campylobacter jejuni, Formate Hydrogenlyases, Bioenergetical Aspects of the Bacterial and Archaeal Hydrogen Metabolism, and more. Contains contributions from leading authorities in microbial physiology Informs and updates on all the latest developments in the field of microbial physiology

This important new book covers recent advancements, innovations, and technologies in industrial biotechnology, specifically addressing the application of various biomolecules in industrial production and in cleaning and environmental remediation sectors. The goal of industrial biotechnology is to develop new techniques and technologies to transform renewable raw materials into chemicals, materials, and fuels by the substitution of fossil fuels. With the increase in the world’s population and the resultant growing energy demand, the need for more energy can be successfully met with the advancements in industrial biotechnology. Currently across the globe significant research has been undertaken in the production of cleaner fuels, materials, and semi-synthetic chemicals, with environmental benefits. Developing countries have huge agricultural resources that could be utilized for production of value-added byproducts for the sustainable development of bio-based economy. The book opens with the chapter on the production of exopolysaccharides from halophilic microorganisms, a polymer that is normally very useful in various production sectors of the food, pharmaceutical, and petroleum industries. The book goes on to cover: The production of antimicrobial compounds from alkaliphilic bacteria Thermophilic actinomycetes Food, agro, and pharmaceutical potential and biotechnological applications of biosurfactants, halophiles, cyclodextrin glycosyl transferease, fungal chitinase, proteases, yeasts and yeast products Also covered in the book are the environmental aspects of industrial biotechnology such as the genetic enhancement for biofuel production, the production of biodegradable thermoplastics, advancements in the synthesis of bio-oil, ecofriendly treatment of agro-based lignocelluloses, and anaerobic bio reactors for hydrocarbon remediation. The international roster of chapter authors have been chosen for their renowned expertise and contribution to the various fields of industrial biotechnology. This book is suitable to chemists, biotechnologists from research institutes, academia, and students as well as for industry professionals