8
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Roles of Organohalide-Respiring Dehalococcoidia in Carbon Cycling

      discussion

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The class Dehalococcoidia within the Chloroflexi phylum comprises the obligate organohalide-respiring genera Dehalococcoides, Dehalogenimonas, and “ Candidatus Dehalobium.” Knowledge of the unique ecophysiology and biochemistry of Dehalococcoidia has been largely derived from studies with enrichment cultures and isolates from sites impacted with chlorinated pollutants; however, culture-independent surveys found Dehalococcoidia sequences in marine, freshwater, and terrestrial biomes considered to be pristine (i.

          ABSTRACT

          The class Dehalococcoidia within the Chloroflexi phylum comprises the obligate organohalide-respiring genera Dehalococcoides, Dehalogenimonas, and “ Candidatus Dehalobium.” Knowledge of the unique ecophysiology and biochemistry of Dehalococcoidia has been largely derived from studies with enrichment cultures and isolates from sites impacted with chlorinated pollutants; however, culture-independent surveys found Dehalococcoidia sequences in marine, freshwater, and terrestrial biomes considered to be pristine (i.e., not impacted with organohalogens of anthropogenic origin). The broad environmental distribution of Dehalococcoidia, as well as other organohalide-respiring bacteria, supports the concept of active halogen cycling and the natural formation of organohalogens in various ecosystems. Dechlorination reduces recalcitrance and renders organics susceptible to metabolic oxidation by diverse microbial taxa. During reductive dechlorination, hydrogenotrophic organohalide-respiring bacteria, in particular Dehalococcoidia, can consume hydrogen to low consumption threshold concentrations (<0.3 nM) and enable syntrophic oxidation processes. These functional attributes and the broad distribution imply that Dehalococcoidia play relevant roles in carbon cycling in anoxic ecosystems.

          Related collections

          Most cited references63

          • Record: found
          • Abstract: found
          • Article: not found

          Microbiological effects of sublethal levels of antibiotics.

          The widespread use of antibiotics results in the generation of antibiotic concentration gradients in humans, livestock and the environment. Thus, bacteria are frequently exposed to non-lethal (that is, subinhibitory) concentrations of drugs, and recent evidence suggests that this is likely to have an important role in the evolution of antibiotic resistance. In this Review, we discuss the ecology of antibiotics and the ability of subinhibitory concentrations to select for bacterial resistance. We also consider the effects of low-level drug exposure on bacterial physiology, including the generation of genetic and phenotypic variability, as well as the ability of antibiotics to function as signalling molecules. Together, these effects accelerate the emergence and spread of antibiotic-resistant bacteria among humans and animals.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage.

            Anaerobic oxidation of methane (AOM) is critical for controlling the flux of methane from anoxic environments. AOM coupled to iron, manganese and sulphate reduction have been demonstrated in consortia containing anaerobic methanotrophic (ANME) archaea. More recently it has been shown that the bacterium Candidatus 'Methylomirabilis oxyfera' can couple AOM to nitrite reduction through an intra-aerobic methane oxidation pathway. Bioreactors capable of AOM coupled to denitrification have resulted in the enrichment of 'M. oxyfera' and a novel ANME lineage, ANME-2d. However, as 'M. oxyfera' can independently couple AOM to denitrification, the role of ANME-2d in the process is unresolved. Here, a bioreactor fed with nitrate, ammonium and methane was dominated by a single ANME-2d population performing nitrate-driven AOM. Metagenomic, single-cell genomic and metatranscriptomic analyses combined with bioreactor performance and (13)C- and (15)N-labelling experiments show that ANME-2d is capable of independent AOM through reverse methanogenesis using nitrate as the terminal electron acceptor. Comparative analyses reveal that the genes for nitrate reduction were transferred laterally from a bacterial donor, suggesting selection for this novel process within ANME-2d. Nitrite produced by ANME-2d is reduced to dinitrogen gas through a syntrophic relationship with an anaerobic ammonium-oxidizing bacterium, effectively outcompeting 'M. oxyfera' in the system. We propose the name Candidatus 'Methanoperedens nitroreducens' for the ANME-2d population and the family Candidatus 'Methanoperedenaceae' for the ANME-2d lineage. We predict that 'M. nitroreducens' and other members of the 'Methanoperedenaceae' have an important role in linking the global carbon and nitrogen cycles in anoxic environments.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin.

              The deep subseafloor biosphere is among the least-understood habitats on Earth, even though the huge microbial biomass therein plays an important role for potential long-term controls on global biogeochemical cycles. We report here the vertical and geographical distribution of microbes and their phylogenetic diversities in deeply buried marine sediments of the Pacific Ocean Margins. During the Ocean Drilling Program Legs 201 and 204, we obtained sediment cores from the Peru and Cascadia Margins that varied with respect to the presence of dissolved methane and methane hydrate. To examine differences in prokaryotic distribution patterns in sediments with or without methane hydrates, we studied >2,800 clones possessing partial sequences (400-500 bp) of the 16S rRNA gene and 348 representative clone sequences (approximately 1 kbp) from the two geographically separated subseafloor environments. Archaea of the uncultivated Deep-Sea Archaeal Group were consistently the dominant phylotype in sediments associated with methane hydrate. Sediment cores lacking methane hydrates displayed few or no Deep-Sea Archaeal Group phylotypes. Bacterial communities in the methane hydrate-bearing sediments were dominated by members of the JS1 group, Planctomycetes, and Chloroflexi. Results from cluster and principal component analyses, which include previously reported data from the West and East Pacific Margins, suggest that, for these locations in the Pacific Ocean, prokaryotic communities from methane hydrate-bearing sediment cores are distinct from those in hydrate-free cores. The recognition of which microbial groups prevail under distinctive subseafloor environments is a significant step toward determining the role these communities play in Earth's essential biogeochemical processes.
                Bookmark

                Author and article information

                Contributors
                Role: Editor
                Journal
                mSystems
                mSystems
                msys
                msys
                mSystems
                mSystems
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2379-5077
                9 June 2020
                May-Jun 2020
                : 5
                : 3
                : e00757-19
                Affiliations
                [a ]Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning, China
                [b ]Department of Geology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
                [c ]Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
                [d ]Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
                [e ]Department of Civil Engineering, Environmental Engineering Program, Auburn University, Auburn, Alabama, USA
                [f ]Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
                [g ]Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, USA
                [h ]Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, Tennessee, USA
                [i ]Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
                Lawrence Berkeley National Laboratory
                Author notes
                Address correspondence to Yi Yang, yangyi@ 123456iae.ac.cn , or Frank E. Löffler, frank.loeffler@ 123456utk.edu .

                Citation Yang Y, Sanford R, Yan J, Chen G, Cápiro NL, Li X, Löffler FE. 2020. Roles of organohalide-respiring Dehalococcoidia in carbon cycling. mSystems 5:e00757-19. https://doi.org/10.1128/mSystems.00757-19.

                Author information
                https://orcid.org/0000-0002-3519-5472
                https://orcid.org/0000-0002-9607-9897
                https://orcid.org/0000-0002-8125-1658
                https://orcid.org/0000-0002-9797-4279
                Article
                mSystems00757-19
                10.1128/mSystems.00757-19
                7289593
                32518199
                09a11bf0-f56a-4b57-8fca-c13586a1e488
                Copyright © 2020 Yang et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Page count
                supplementary-material: 1, Figures: 2, Tables: 3, Equations: 6, References: 82, Pages: 12, Words: 8018
                Categories
                Perspective
                Applied and Environmental Science
                Custom metadata
                May/June 2020

                dehalococcoidia,carbon cycling,hydrogen thresholds,organohalide respiration,syntrophy,thermodynamics

                Comments

                Comment on this article