Agarwal, V. et al. Enzymatic halogenation and dehalogenation reactions: pervasive and mechanistically diverse. Chem. Rev. 117, 5619–5674 (2017).
Google Scholar
Atashgahi, S., Haggblom, M. M. & Smidt, H. Organohalide respiration in pristine environments: implications for the natural halogen cycle. Environ. Microbiol. 20, 934–948 (2018).
Google Scholar
Gribble G. W. Naturally Occurring Organohalogen Compounds—A Comprehensive Update: (Wien/New York: Springer, 2010).
Stringer, R. & Johnston, P. Chlorine and the environment: an overview of the chlorine industry. Environ. Sci. Pollut. Res. 8, 146–159 (2001).
Google Scholar
Falandysz, J., Rose, M. & Fernandes, A. R. Mixed poly-brominated/chlorinated biphenyls (pxbs): widespread food and environmental contaminants. Environ. Int. 44, 118–127 (2012).
Google Scholar
Zhang, Z. et al. Halogenated organic pollutants in sediments and organisms from mangrove wetlands of the jiulong river estuary, south china. Environ. Res. 171, 145–152 (2019).
Google Scholar
Kunze, C. et al. Cobamide-mediated enzymatic reductive dehalogenation via long-range electron transfer. Nat. Commun. 8, 15858 (2017).
Google Scholar
Wang, S. et al. Electron transport chains in organohalide-respiring bacteria and bioremediation implications. Biotechnol. Adv. 36, 1194–1206 (2018).
Google Scholar
Atashgahi S., Lu Y., Smidt H. Overview of known organohalide-respiring bacteria—phylogenetic diversity and environmental distribution. In Adrian L., Löffler F. E., editors. Organohalide-Respiring Bacteria. (Springer, Berlin, 2016).
Fincker, M. & Spormann, A. M. Biochemistry of catabolic reductive dehalogenation. Annu. Rev. Biochem. 86, 357–386 (2017).
Google Scholar
Rouzeau-Szynalski, K., Maillard, J. & Holliger, C. Frequent concomitant presence of desulfitobacterium spp. and “dehalococcoides” spp. in chloroethene-dechlorinating microbial communities. Appl. Microbiol. Biotechnol. 90, 361–368 (2011).
Google Scholar
Wang, S. & He, J. Dechlorination of commercial pcbs and other multiple halogenated compounds by a sediment-free culture containing dehalococcoides and dehalobacter. Environ. Sci. Technol. 47, 10526–10534 (2013).
Google Scholar
Wang, S. et al. Genomic characterization of three unique dehalococcoides that respire on persistent polychlorinated biphenyls. Proc. Natl. Acad. Sci. U.S.A. 111, 12103–12108 (2014).
Google Scholar
Bachmann, H. et al. Availability of public goods shapes the evolution of competing metabolic strategies. Proc. Natl. Acad. Sci. U.S.A. 110, 14302–14307 (2013).
Google Scholar
Yan, J., Ritalahti, K. M., Wagner, D. D. & Loffler, F. E. Unexpected specificity of interspecies cobamide transfer from geobacter spp. To organohalide-respiring dehalococcoides mccartyi strains. Appl. Environ. Microbiol. 78, 6630–6636 (2012).
Google Scholar
Lawson, C. E. et al. Common principles and best practices for engineering microbiomes. Nat. Rev. Microbiol. 17, 725–741 (2019).
Google Scholar
Wang, S., Chen, C., Zhao, S. & He, J. Microbial synergistic interactions for reductive dechlorination of polychlorinated biphenyls. Sci. Total. Environ. 666, 368–376 (2019).
Google Scholar
Men, Y. et al. Sustainable syntrophic growth of dehalococcoides ethenogenes strain 195 with desulfovibrio vulgaris hildenborough and methanobacterium congolense: Global transcriptomic and proteomic analyses. ISME J. 6, 410–421 (2012).
Google Scholar
Lu, Q. et al. Dehalococcoides as a potential biomarker evidence for uncharacterized organohalides in environmental samples. Front. Microbiol. 8, 1677 (2017).
Google Scholar
Xu, G., Lu, Q., Yu, L. & Wang, S. Tetrachloroethene primes reductive dechlorination of polychlorinated biphenyls in a river sediment microcosm. Water Res. 152, 87–95 (2019).
Google Scholar
Royer, D. L., Osborne, C. P. & Beerling, D. J. Carbon loss by deciduous trees in a co2-rich ancient polar environment. Nature. 424, 60–62 (2003).
Google Scholar
Wang, S. & He, J. Phylogenetically distinct bacteria involve extensive dechlorination of aroclor 1260 in sediment-free cultures. PLoS One 8, e59178 (2013).
Google Scholar
Wang, S. et al. Development of an alkaline/acid pre-treatment and anaerobic digestion (apad) process for methane generation from waste activated sludge. Sci. Total Environ. 708, 134564 (2020).
Google Scholar
Lu, Q. et al. Inhibitory effects of metal ions on reductive dechlorination of polychlorinated biphenyls and perchloroethene in distinct organohalide-respiring bacteria. Environ. Int. 135, 105373 (2020).
Google Scholar
Kumar, S., Stecher, G. & Tamura, K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evolut. 33, 1870–1874 (2016).
Google Scholar
Cummings, D. E. et al. Diversity of geobacteraceae species inhabiting metal-polluted freshwater lake sediments ascertained by 16S rDNA analyses. Microb. Ecol. 46, 257–269 (2003).
Google Scholar
Holmes, V. F., He, J., Lee, P. K. & Alvarez-Cohen, L. Discrimination of multiple dehalococcoides strains in a trichloroethene enrichment by quantification of their reductive dehalogenase genes. Appl. Environ. Microbiol. 72, 5877–5883 (2006).
Google Scholar
Joshi N. A., Fass J. N. Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33) [Software]. https://github.com/najoshi/sickle. (2011).
Bankevich, A. et al. Spades: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).
Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with bowtie 2. Nat. Methods. 9, 357–359 (2012).
Google Scholar
Li, H. et al. The sequence alignment/map format and samtools. Bioinformatics. 25, 2078–2079 (2009).
Google Scholar
Chen, L. X., Anantharaman, K., Shaiber, A., Eren, A. M. & Banfield, J. F. Accurate and complete genomes from metagenomes. Genome Res. 30, 315–333 (2020).
Google Scholar
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. Checkm: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).
Google Scholar
Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30, 2068–2069 (2014).
Google Scholar
Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A. C. & Kanehisa, M. Kaas: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182–W185 (2007).
Google Scholar
Loffler, F. E. et al. Dehalococcoides mccartyi gen. Nov., sp. Nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, dehalococcoidia classis nov., order dehalococcoidales ord. Nov. And family dehalococcoidaceae fam. Nov., within the phylum chloroflexi. Int. J. Syst. Evol. Microbiol. 63, 625–635 (2013).
Google Scholar
Garcia C.A. Subsurface occurrence and potential source areas of chlorinated Ethenes Identified using concentrations and concentration ratios, Air Force Plant 4 and Naval Air Station-Joint Reserve Base Carswell Field, Fort Worth, Texas. U.S. Geological Survey, (2006).
Nichols H. Use of electrical resistive heating for the remediation of CVOC and petroleum impacts in soil and groundwater, NEWMOA Conference. New York City (2012).
Maymó-Gatell, X., Chien, Y., Gossett, J. M. & Zinder, S. H. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science. 276, 1568–1571 (1997).
Google Scholar
Sung, Y. et al. Geobacter lovleyi sp. Nov. Strain sz, a novel metal-reducing and tetrachloroethene-dechlorinating bacterium. Appl. Environ. Microbiol. 72, 2775–2782 (2006).
Google Scholar
Amos, B. K., Suchomel, E. J., Pennell, K. D. & Löffler, F. E. Spatial and temporal distributions of Geobacter lovleyi and Dehalococcoides spp. during bioenhanced PCE-NAPL dissolution. Environ. Sci. Technol. 43, 1977–1985 (2009).
Google Scholar
Lai, Y. & Becker, J. G. Compounded effects of chlorinated ethene inhibition on ecological interactions and population abundance in a Dehalococcoides–Dehalobacter coculture. Environ. Sci. Technol. 47, 1518–1525 (2013).
Google Scholar
Lovley, D. R. et al. Geobacter: the microbe electric’s physiology, ecology, and practical applications. Adv. Microb. Physiol. 59, 1–100 (2011).
Google Scholar
Reguera, G. & Kashefi, K. The electrifying physiology of geobacter bacteria, 30 years on. Adv. Microb. Physiol. 74, 1–96 (2019).
Google Scholar
Kruse, S., Goris, T., Westermann, M., Adrian, L. & Diekert, G. Hydrogen production by sulfurospirillum species enables syntrophic interactions of epsilonproteobacteria. Nat. Commun. 9, 4872 (2018).
Google Scholar
Sanford, R. A., Cole, J. R. & Tiedje, J. M. Characterization and description of anaeromyxobacter dehalogenans gen. Nov., sp. Nov., an aryl-halorespiring facultative anaerobic myxobacterium. Appl. Environ. Microbiol. 68, 893–900 (2002).
Google Scholar
Sung, Y. et al. Characterization of two tetrachloroethene-reducing, acetate-oxidizing anaerobic bacteria and their description as desulfuromonas michiganensis sp. Nov. Appl. Environ. Microbiol. 69, 2964–2974 (2003).
Google Scholar
Peng, P. et al. Organohalide-respiring desulfoluna species isolated from marine environments. ISME J. 14, 815–827 (2020).
Google Scholar
Goris, T. et al. Insights into organohalide respiration and the versatile catabolism of sulfurospirillum multivorans gained from comparative genomics and physiological studies. Environ. Microbiol. 16, 3562–3580 (2014).
Google Scholar
Goris, T. et al. Proteomics of the organohalide-respiring epsilonproteobacterium sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates. Sci. Rep. 5, 13794 (2015).
Google Scholar
Cross, K. L. et al. Targeted isolation and cultivation of uncultivated bacteria by reverse genomics. Nat. Biotechnol. 37, 1314–1321 (2019).
Google Scholar
Lewis, W. H. & Ettema, T. J. G. Culturing the uncultured. Nat. Biotechnol. 37, 1278–1279 (2019).
Google Scholar
Koch, H., van Kessel, M. & Lucker, S. Complete nitrification: insights into the ecophysiology of comammox nitrospira. Appl. Microbiol. Biotechnol. 103, 177–189 (2019).
Google Scholar
Marcy, Y. et al. Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc. Natl. Acad. Sci. U.S.A. 104, 11889–11894 (2007).
Google Scholar
Pfeiffer, T., Schuster, S. & Bonhoeffer, S. Cooperation and competition in the evolution of ATP-producing pathways. Science. 292, 504–507 (2001).
Google Scholar
Roller, B. R. & Schmidt, T. M. The physiology and ecological implications of efficient growth. ISME J. 9, 1481–1487 (2015).
Google Scholar
Lawson, C. E. & Lucker, S. Complete ammonia oxidation: an important control on nitrification in engineered ecosystems? Curr. Opin. Biotechnol. 50, 158–165 (2018).
Google Scholar
Kits, K. D. et al. Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle. Nature. 549, 269–272 (2017).
Google Scholar
Source: Ecology - nature.com
