1
|
Bremer K, Yasuo H, Debes PV, Jacobs HT. The alternative oxidase (AOX) increases sulphide tolerance in the highly invasive marine invertebrate Ciona intestinalis. J Exp Biol 2021; 224:271920. [PMID: 34423818 PMCID: PMC8407659 DOI: 10.1242/jeb.242985] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/26/2021] [Indexed: 12/29/2022]
Abstract
Ecological communities and biodiversity are shaped by both abiotic and biotic factors. This is well illustrated by extreme environments and invasive species. Besides naturally occurring sulphide-rich environments, global change can lead to an increase in hydrogen sulphide episodes that threaten many multicellular organisms. With the increase in the formation, size and abundance of oxygen minimum zones and hypoxic environments, bacterial-associated sulphide production is favoured and, as such, hydrogen-sulphide-rich environments are likely to also increase in size and abundance. Many species are challenged by the inhibiting effect of sulphide on aerobic energy production via cytochrome c oxidase, ultimately causing the death of the organism. Interestingly, many protist, yeast, plant and also animal species possess a sulphide-resistant alternative oxidase (AOX). In this study, we investigated whether AOX is functionally involved in the sulphide stress response of the highly invasive marine tunicate Ciona intestinalis. At the LC50, the sulphide-induced reduction of developmental success was three times stronger in AOX knock-down embryos than in control embryos. Further, AOX mRNA levels were higher under sulphide than under control conditions, and this effect increased during embryonic development. Together, we found that AOX is indeed functionally involved in the sulphide tolerance of C. intestinalis embryos, hence, very likely contributing to its invasive potential; and that the response of AOX to sulphide seems to be controlled at the transcriptional level. We suggest that AOX-possessing species play an important role in shaping marine ecological communities, and this importance may increase under ongoing global change. Summary: A functional study on the role of the mitochondrial alternative oxidase (AOX) in an animal species indicates that AOX increases the sulphide tolerance of the marine chordate Ciona intestinalis.
Collapse
Affiliation(s)
- Katharina Bremer
- Tampere University, Faculty of Medicine and Health Technology, 33014 Tampere, Finland
| | - Hitoyoshi Yasuo
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, 06230 Villefranche-sur-mer, France
| | - Paul Vincent Debes
- Hólar University College, Department of Aquaculture and Fish Biology, 551 Sauðárkrókur, Iceland
| | - Howard Trevor Jacobs
- Tampere University, Faculty of Medicine and Health Technology, 33014 Tampere, Finland
| |
Collapse
|
2
|
Zoss R, Medina Ferrer F, Flood BE, Jones DS, Louw DC, Bailey J. Microbial communities associated with phosphogenic sediments and phosphoclast-associated DNA of the Benguela upwelling system. GEOBIOLOGY 2019; 17:76-90. [PMID: 30369004 DOI: 10.1111/gbi.12318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 07/20/2018] [Accepted: 08/21/2018] [Indexed: 06/08/2023]
Abstract
The processes that lead to the precipitation of authigenic calcium phosphate minerals in certain marine pore waters remain poorly understood. Phosphogenesis occurs in sediments beneath some oceanic upwelling zones that harbor polyphosphate-accumulating bacteria. These bacteria are believed to concentrate phosphate in sediment pore waters, creating supersaturated conditions with respect to apatite precursors. However, the relationship between microbes and phosphorite formation is not fully resolved. To further study this association, we examined microbial community data generated from two sources: sediment cores recovered from the shelf of the Benguela upwelling region where phosphorites are currently forming, and DNA preserved within phosphoclasts recovered from a phosphorite deposit along the Benguela shelf. iTag and clone library sequencing of the 16S rRNA gene showed that many of our sediment-hosted communities shared large numbers of phylotypes with one another, and that the same metabolic guilds were represented at localities across the shelf. Sulfate-reducing bacteria and sulfur-oxidizing bacteria were particularly abundant in our datasets, as were phylotypes that are known to carry out nitrification and the anaerobic oxidation of ammonium. The DNA extracted from phosphoclasts contained the signature of a distinct microbial community from those observed in the modern sediments. While some aspects of the modern and phosphoclast communities were similar, we observed both an enrichment of certain common microbial classes found in the modern phosphogenic sediments and a relative depletion of others. The phosphoclast-associated DNA could represent a relict signature of one or more microbial assemblages that were present when the apatite or its precursors precipitated. While these taxa may or may not have contributed to the precipitation of the apatite that now hosts their genetic remains, several groups represented in the phosphoclast extract dataset have the genetic potential to metabolize polyphosphate, and perhaps modulate phosphate concentrations in pore waters where carbonate fluorapatite (or its precursors) are known to be precipitating.
Collapse
Affiliation(s)
- Roman Zoss
- Department of Earth Sciences, University of Minnesota, Minnesota, Minneapolis
| | | | - Beverly E Flood
- Department of Earth Sciences, University of Minnesota, Minnesota, Minneapolis
| | - Daniel S Jones
- Department of Earth Sciences, University of Minnesota, Minnesota, Minneapolis
- BioTechnology Institute, University of Minnesota, St. Paul, Minneapolis
| | - Deon C Louw
- Ministry of Fisheries and Marine Resources, National Marine Information and Research Centre, Swakopmund, Namibia
| | - Jake Bailey
- Department of Earth Sciences, University of Minnesota, Minnesota, Minneapolis
| |
Collapse
|
3
|
Vuillemin A, Horn F, Friese A, Winkel M, Alawi M, Wagner D, Henny C, Orsi WD, Crowe SA, Kallmeyer J. Metabolic potential of microbial communities from ferruginous sediments. Environ Microbiol 2018; 20:4297-4313. [PMID: 29968357 DOI: 10.1111/1462-2920.14343] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/22/2018] [Accepted: 06/25/2018] [Indexed: 01/22/2023]
Abstract
Ferruginous (Fe-rich, SO4 -poor) conditions are generally restricted to freshwater sediments on Earth today, but were likely widespread during the Archean and Proterozoic Eons. Lake Towuti, Indonesia, is a large ferruginous lake that likely hosts geochemical processes analogous to those that operated in the ferruginous Archean ocean. The metabolic potential of microbial communities and related biogeochemical cycling under such conditions remain largely unknown. We combined geochemical measurements (pore water chemistry, sulfate reduction rates) with metagenomics to link metabolic potential with geochemical processes in the upper 50 cm of sediment. Microbial diversity and quantities of genes for dissimilatory sulfate reduction (dsrAB) and methanogenesis (mcrA) decrease with increasing depth, as do rates of potential sulfate reduction. The presence of taxa affiliated with known iron- and sulfate-reducers implies potential use of ferric iron and sulfate as electron acceptors. Pore-water concentrations of acetate imply active production through fermentation. Fermentation likely provides substrates for respiration with iron and sulfate as electron donors and for methanogens that were detected throughout the core. The presence of ANME-1 16S and mcrA genes suggests potential for anaerobic methane oxidation. Overall our data suggest that microbial community metabolism in anoxic ferruginous sediments support coupled Fe, S and C biogeochemical cycling.
Collapse
Affiliation(s)
- Aurèle Vuillemin
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany.,Department of Earth & Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| | - André Friese
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| | - Matthias Winkel
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| | - Mashal Alawi
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany.,University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute of Earth and Environmental Sciences, Potsdam, Germany
| | - Cynthia Henny
- Research Center for Limnology (LIPI), Indonesian Institute of Sciences, Division of Inland Waterways Dynamics, Cibinong-Bogor, Indonesia
| | - William D Orsi
- Department of Earth & Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,Geobio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada.,Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, Canada
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3: Geomicrobiology, Potsdam, Germany
| |
Collapse
|
4
|
Kanao T, Onishi M, Kajitani Y, Hashimoto Y, Toge T, Kikukawa H, Kamimura K. Characterization of tetrathionate hydrolase from the marine acidophilic sulfur-oxidizing bacterium, Acidithiobacillus thiooxidans strain SH. Biosci Biotechnol Biochem 2018; 82:152-160. [PMID: 29303046 DOI: 10.1080/09168451.2017.1415128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Tetrathionate hydrolase (4THase), a key enzyme of the S4-intermediate (S4I) pathway, was partially purified from marine acidophilic bacterium, Acidithiobacillus thiooxidans strain SH, and the gene encoding this enzyme (SH-tth) was identified. SH-Tth is a homodimer with a molecular mass of 97 ± 3 kDa, and contains a subunit 52 kDa in size. Enzyme activity was stimulated in the presence of 1 M NaCl, and showed the maximum at pH 3.0. Although 4THases from A. thiooxidans and the closely related Acidithiobacillus caldus strain have been reported to be periplasmic enzymes, SH-Tth seems to be localized on the outer membrane of the cell, and acts as a peripheral protein. Furthermore, both 4THase activity and SH-Tth proteins were detected in sulfur-grown cells of strain SH. These results suggested that SH-Tth is involved in elemental sulfur-oxidation, which is distinct from sulfur-oxidation in other sulfur-oxidizing strains such as A. thiooxidans and A. caldus.
Collapse
Affiliation(s)
- Tadayoshi Kanao
- a Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science , Okayama University , Okayama , Japan
| | - Moe Onishi
- b Faculty of Agriculture , Okayama University , Okayama , Japan
| | | | - Yuki Hashimoto
- b Faculty of Agriculture , Okayama University , Okayama , Japan
| | - Tatsuya Toge
- b Faculty of Agriculture , Okayama University , Okayama , Japan
| | | | - Kazuo Kamimura
- a Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life Science , Okayama University , Okayama , Japan
| |
Collapse
|
5
|
Rogge A, Vogts A, Voss M, Jürgens K, Jost G, Labrenz M. Success of chemolithoautotrophic SUP05 and Sulfurimonas GD17 cells in pelagic Baltic Sea redox zones is facilitated by their lifestyles as K- and r-strategists. Environ Microbiol 2017; 19:2495-2506. [PMID: 28464419 DOI: 10.1111/1462-2920.13783] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 04/25/2017] [Accepted: 04/25/2017] [Indexed: 11/27/2022]
Abstract
Chemolithoautotrophic sulfur-oxidizing and denitrifying Gamma- (particularly the SUP05 cluster) and Epsilonproteobacteria (predominantly Sulfurimonas subgroup GD17) are assumed to compete for substrates (electron donors and acceptors) in marine pelagic redox gradients. To elucidate their ecological niche separation we performed 34 S0 , 15 NO3- and H13 CO3- stable-isotope incubations with water samples from Baltic Sea suboxic, chemocline and sulfidic zones followed by combined phylogenetic staining and high-resolution secondary ion mass spectrometry of single cells. SUP05 cells were small-sized (0.06-0.09 µm3 ) and most abundant in low-sulfidic to suboxic zones, whereas Sulfurimonas GD17 cells were significantly larger (0.26-0.61 µm3 ) and most abundant at the chemocline and below. Together, SUP05 and GD17 cells accumulated up to 48% of the labelled substrates but calculation of cell volume-specific rates revealed that GD17 cells incorporated labelled substrates significantly faster throughout the redox zone, thereby potentially outcompeting SUP05 especially at high substrate concentrations. Thus, in synopsis with earlier described features of SUP05/GD17 we conclude that their spatially overlapping association in stratified sulfidic zones is facilitated by their different lifestyles: whereas SUP05 cells are streamlined, non-motile K-strategists adapted to low substrate concentrations, GD17 cells are motile r-strategists well adapted to fluctuating substrate and redox conditions.
Collapse
Affiliation(s)
- Andreas Rogge
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Angela Vogts
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Maren Voss
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Günter Jost
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Matthias Labrenz
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| |
Collapse
|
6
|
Bosak T, Schubotz F, de Santiago-Torio A, Kuehl JV, Carlson HK, Watson N, Daye M, Summons RE, Arkin AP, Deutschbauer AM. System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions. PLoS One 2016; 11:e0168719. [PMID: 28030630 PMCID: PMC5193443 DOI: 10.1371/journal.pone.0168719] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/04/2016] [Indexed: 12/13/2022] Open
Abstract
The prevalence of lipids devoid of phosphorus suggests that the availability of phosphorus limits microbial growth and activity in many anoxic, stratified environments. To better understand the response of anaerobic bacteria to phosphate limitation and starvation, this study combines microscopic and lipid analyses with the measurements of fitness of pooled barcoded transposon mutants of the model sulfate reducing bacterium Desulfovibrio alaskensis G20. Phosphate-limited G20 has lower growth rates and replaces more than 90% of its membrane phospholipids by a mixture of monoglycosyl diacylglycerol (MGDG), glycuronic acid diacylglycerol (GADG) and ornithine lipids, lacks polyphosphate granules, and synthesizes other cellular inclusions. Analyses of pooled and individual mutants reveal the importance of the high-affinity phosphate transport system (the Pst system), PhoR, and glycolipid and ornithine lipid synthases during phosphate limitation. The phosphate-dependent synthesis of MGDG in G20 and the widespread occurrence of the MGDG/GADG synthase among sulfate reducing ∂-Proteobacteria implicate these microbes in the production of abundant MGDG in anaerobic environments where the concentrations of phosphate are lower than 10 μM. Numerous predicted changes in the composition of the cell envelope and systems involved in transport, maintenance of cytoplasmic redox potential, central metabolism and regulatory pathways also suggest an impact of phosphate limitation on the susceptibility of sulfate reducing bacteria to other anthropogenic or environmental stresses.
Collapse
Affiliation(s)
- Tanja Bosak
- Department of Earth and Planetary Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | | | - Ana de Santiago-Torio
- Department of Earth and Planetary Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jennifer V Kuehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Nicki Watson
- W.M. Keck Microscopy Facility, The Whitehead Institute, Cambridge, Massachusetts, United States of America
| | - Mirna Daye
- Department of Earth and Planetary Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Roger E Summons
- Department of Earth and Planetary Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.,Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| |
Collapse
|
7
|
Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 462] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
Collapse
|
8
|
Dalsgaard T, Stewart FJ, Thamdrup B, De Brabandere L, Revsbech NP, Ulloa O, Canfield DE, DeLong EF. Oxygen at nanomolar levels reversibly suppresses process rates and gene expression in anammox and denitrification in the oxygen minimum zone off northern Chile. mBio 2014; 5:e01966. [PMID: 25352619 PMCID: PMC4217175 DOI: 10.1128/mbio.01966-14] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
UNLABELLED A major percentage (20 to 40%) of global marine fixed-nitrogen loss occurs in oxygen minimum zones (OMZs). Concentrations of O2 and the sensitivity of the anaerobic N2-producing processes of anammox and denitrification determine where this loss occurs. We studied experimentally how O2 at nanomolar levels affects anammox and denitrification rates and the transcription of nitrogen cycle genes in the anoxic OMZ off Chile. Rates of anammox and denitrification were reversibly suppressed, most likely at the enzyme level. Fifty percent inhibition of N2 and N2O production by denitrification was achieved at 205 and 297 nM O2, respectively, whereas anammox was 50% inhibited at 886 nM O2. Coupled metatranscriptomic analysis revealed that transcripts encoding nitrous oxide reductase (nosZ), nitrite reductase (nirS), and nitric oxide reductase (norB) decreased in relative abundance above 200 nM O2. This O2 concentration did not suppress the transcription of other dissimilatory nitrogen cycle genes, including nitrate reductase (narG), hydrazine oxidoreductase (hzo), and nitrite reductase (nirK). However, taxonomic characterization of transcripts suggested inhibition of narG transcription in gammaproteobacteria, whereas the transcription of anammox narG, whose gene product is likely used to oxidatively replenish electrons for carbon fixation, was not inhibited. The taxonomic composition of transcripts differed among denitrification enzymes, suggesting that distinct groups of microorganisms mediate different steps of denitrification. Sulfide addition (1 µM) did not affect anammox or O2 inhibition kinetics but strongly stimulated N2O production by denitrification. These results identify new O2 thresholds for delimiting marine nitrogen loss and highlight the utility of integrating biogeochemical and metatranscriptomic analyses. IMPORTANCE The removal of fixed nitrogen via anammox and denitrification associated with low O2 concentrations in oceanic oxygen minimum zones (OMZ) is a major sink in oceanic N budgets, yet the sensitivity and dynamics of these processes with respect to O2 are poorly known. The present study elucidated how nanomolar O2 concentrations affected nitrogen removal rates and expression of key nitrogen cycle genes in water from the eastern South Pacific OMZ, applying state-of-the-art (15)N techniques and metatranscriptomics. Rates of both denitrification and anammox responded rapidly and reversibly to changes in O2, but denitrification was more O2 sensitive than anammox. The transcription of key nitrogen cycle genes did not respond as clearly to O2, although expression of some of these genes decreased. Quantifying O2 sensitivity of these processes is essential for predicting through which pathways and in which environments, from wastewater treatment to the open oceans, nitrogen removal may occur.
Collapse
Affiliation(s)
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
| | - Loreto De Brabandere
- Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
| | | | - Osvaldo Ulloa
- Departamento de Oceanografía & Instituto Mileno de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - Don E Canfield
- Department of Biology and Nordic Center for Earth Evolution (NordCEE), University of Southern Denmark, Odense, Denmark
| | | |
Collapse
|
9
|
Hanke A, Hamann E, Sharma R, Geelhoed JS, Hargesheimer T, Kraft B, Meyer V, Lenk S, Osmers H, Wu R, Makinwa K, Hettich RL, Banfield JF, Tegetmeyer HE, Strous M. Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat. Front Microbiol 2014; 5:231. [PMID: 24904545 PMCID: PMC4032931 DOI: 10.3389/fmicb.2014.00231] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 04/30/2014] [Indexed: 11/13/2022] Open
Abstract
Sandy coastal sediments are global hotspots for microbial mineralization of organic matter and denitrification. These sediments are characterized by advective porewater flow, tidal cycling and an active and complex microbial community. Metagenomic sequencing of microbial communities sampled from such sediments showed that potential sulfur oxidizing Gammaproteobacteria and members of the enigmatic BD1-5/SN-2 candidate phylum were abundant in situ (>10% and ~2% respectively). By mimicking the dynamic oxic/anoxic environmental conditions of the sediment in a laboratory chemostat, a simplified microbial community was selected from the more complex inoculum. Metagenomics, proteomics and fluorescence in situ hybridization showed that this simplified community contained both a potential sulfur oxidizing Gammaproteobacteria (at 24 ± 2% abundance) and a member of the BD1-5/SN-2 candidate phylum (at 7 ± 6% abundance). Despite the abundant supply of organic substrates to the chemostat, proteomic analysis suggested that the selected gammaproteobacterium grew partially autotrophically and performed hydrogen/formate oxidation. The enrichment of a member of the BD1-5/SN-2 candidate phylum enabled, for the first time, direct microscopic observation by fluorescent in situ hybridization and the experimental validation of the previously predicted translation of the stop codon UGA into glycine.
Collapse
Affiliation(s)
- Anna Hanke
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Emmo Hamann
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Ritin Sharma
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee Knoxville, TN, USA ; Chemical Science Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Jeanine S Geelhoed
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Theresa Hargesheimer
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Beate Kraft
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Volker Meyer
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Sabine Lenk
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Harald Osmers
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Rong Wu
- Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology Delft, Netherlands
| | - Kofi Makinwa
- Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology Delft, Netherlands
| | - Robert L Hettich
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee Knoxville, TN, USA ; Chemical Science Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, Department of Environmental Science, Policy, and Management, University of California Berkeley, CA, USA
| | - Halina E Tegetmeyer
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany ; Center for Biotechnology, University of Bielefeld Bielefeld, Germany
| | - Marc Strous
- Microbial Fitness Group, Max Planck Institute for Marine Microbiology Bremen, Germany ; Center for Biotechnology, University of Bielefeld Bielefeld, Germany ; Department of Geoscience, University of Calgary Calgary, AB, Canada
| |
Collapse
|
10
|
Schunck H, Lavik G, Desai DK, Großkopf T, Kalvelage T, Löscher CR, Paulmier A, Contreras S, Siegel H, Holtappels M, Rosenstiel P, Schilhabel MB, Graco M, Schmitz RA, Kuypers MMM, LaRoche J. Giant hydrogen sulfide plume in the oxygen minimum zone off Peru supports chemolithoautotrophy. PLoS One 2013; 8:e68661. [PMID: 23990875 PMCID: PMC3749208 DOI: 10.1371/journal.pone.0068661] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 06/01/2013] [Indexed: 11/30/2022] Open
Abstract
In Eastern Boundary Upwelling Systems nutrient-rich waters are transported to the ocean surface, fuelling high photoautotrophic primary production. Subsequent heterotrophic decomposition of the produced biomass increases the oxygen-depletion at intermediate water depths, which can result in the formation of oxygen minimum zones (OMZ). OMZs can sporadically accumulate hydrogen sulfide (H2S), which is toxic to most multicellular organisms and has been implicated in massive fish kills. During a cruise to the OMZ off Peru in January 2009 we found a sulfidic plume in continental shelf waters, covering an area >5500 km2, which contained ∼2.2×104 tons of H2S. This was the first time that H2S was measured in the Peruvian OMZ and with ∼440 km3 the largest plume ever reported for oceanic waters. We assessed the phylogenetic and functional diversity of the inhabiting microbial community by high-throughput sequencing of DNA and RNA, while its metabolic activity was determined with rate measurements of carbon fixation and nitrogen transformation processes. The waters were dominated by several distinct γ-, δ- and ε-proteobacterial taxa associated with either sulfur oxidation or sulfate reduction. Our results suggest that these chemolithoautotrophic bacteria utilized several oxidants (oxygen, nitrate, nitrite, nitric oxide and nitrous oxide) to detoxify the sulfidic waters well below the oxic surface. The chemolithoautotrophic activity at our sampling site led to high rates of dark carbon fixation. Assuming that these chemolithoautotrophic rates were maintained throughout the sulfidic waters, they could be representing as much as ∼30% of the photoautotrophic carbon fixation. Postulated changes such as eutrophication and global warming, which lead to an expansion and intensification of OMZs, might also increase the frequency of sulfidic waters. We suggest that the chemolithoautotrophically fixed carbon may be involved in a negative feedback loop that could fuel further sulfate reduction and potentially stabilize the sulfidic OMZ waters.
Collapse
Affiliation(s)
- Harald Schunck
- Research Division Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
| | - Gaute Lavik
- Department of Biogeochemistry, Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Dhwani K. Desai
- Research Division Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Tobias Großkopf
- Research Division Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, United Kingdom
| | - Tim Kalvelage
- Department of Biogeochemistry, Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Carolin R. Löscher
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
| | - Aurélien Paulmier
- Department of Biogeochemistry, Max-Planck-Institute for Marine Microbiology, Bremen, Germany
- Laboratory for Studies in Geophysics and Spatial Oceanography, Institute of Research for Development, Toulouse, France
- Dirección de Investigaciones Oceanográficas, Instituto del Mar del Perú, Callao, Peru
| | - Sergio Contreras
- Department of Biogeochemistry, Max-Planck-Institute for Marine Microbiology, Bremen, Germany
- Large Lakes Observatory, University of Minnesota Duluth, Duluth, Minnesota, United States of America
| | - Herbert Siegel
- Physical Oceanography and Instrumentation, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Moritz Holtappels
- Department of Biogeochemistry, Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Markus B. Schilhabel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Michelle Graco
- Dirección de Investigaciones Oceanográficas, Instituto del Mar del Perú, Callao, Peru
| | - Ruth A. Schmitz
- Institute for General Microbiology, Christian-Albrechts-University, Kiel, Germany
| | - Marcel M. M. Kuypers
- Department of Biogeochemistry, Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Julie LaRoche
- Research Division Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail:
| |
Collapse
|
11
|
Distinctive microbial community structure in highly stratified deep-sea brine water columns. Appl Environ Microbiol 2013; 79:3425-37. [PMID: 23542623 DOI: 10.1128/aem.00254-13] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Atlantis II and Discovery are two hydrothermal and hypersaline deep-sea pools in the Red Sea rift that are characterized by strong thermohalo-stratification and temperatures steadily peaking near the bottom. We conducted comprehensive vertical profiling of the microbial populations in both pools and highlighted the influential environmental factors. Pyrosequencing of the 16S rRNA genes revealed shifts in community structures vis-à-vis depth. High diversity and low abundance were features of the deepest convective layers despite the low cell density. Surprisingly, the brine interfaces had significantly higher cell counts than the overlying deep-sea water, yet they were lowest in diversity. Vertical stratification of the bacterial populations was apparent as we moved from the Alphaproteobacteria-dominated deep sea to the Planctomycetaceae- or Deferribacteres-dominated interfaces to the Gammaproteobacteria-dominated brine layers. Archaeal marine group I was dominant in the deep-sea water and interfaces, while several euryarchaeotic groups increased in the brine. Across sites, microbial phylotypes and abundances varied substantially in the brine interface of Discovery compared with Atlantis II, despite the near-identical populations in the overlying deep-sea waters. The lowest convective layers harbored interestingly similar microbial communities, even though temperature and heavy metal concentrations were very different. Multivariate analysis indicated that temperature and salinity were the major influences shaping the communities. The harsh conditions and the low-abundance phylotypes could explain the observed correlation in the brine pools.
Collapse
|
12
|
SUP05 dominates the Gammaproteobacterial sulfur oxidizer assemblages in pelagic redoxclines of the central Baltic and Black Seas. Appl Environ Microbiol 2013; 79:2767-76. [PMID: 23417000 DOI: 10.1128/aem.03777-12] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Gammaproteobacterial sulfur oxidizers (GSOs), particularly SUP05-related sequences, have been found worldwide in numerous oxygen-deficient marine environments. However, knowledge regarding their abundance, distribution, and ecological role is scarce. In this study, on the basis of phylogenetic analyses of 16S rRNA gene sequences originating from a Baltic Sea pelagic redoxcline, the in situ abundances of different GSO subgroups were quantified by CARD-FISH (catalyzed reporter fluorescence in situ hybridization) with oligonucleotide probes developed specifically for this purpose. Additionally, ribulose bisphosphate carboxylase/oxygenase form II (cbbM) gene transcript clone libraries were used to detect potential active chemolithoautotrophic GSOs in the Baltic Sea. Taken together, the results obtained by these two approaches demonstrated the existence of two major phylogenetic subclusters embedded within the GSO, one of them affiliated with sequences of the previously described SUP05 subgroup. CARD-FISH analyses revealed that only SUP05 occurred in relatively high numbers, reaching 10 to 30% of the total prokaryotes around the oxic-anoxic interface, where oxygen and sulfide concentrations are minimal. The applicability of the oligonucleotide probes was confirmed with samples from the Black Sea redoxcline, in which the SUP05 subgroup accounted for 10 to 13% of the total prokaryotic abundance. The cbbM transcripts presumably originating from SUP05 cells support previous evidence for the chemolithoautotrophic activity of this phylogenetic group. Our findings on the vertical distribution and high abundance of SUP05 suggest that this group plays an important role in marine redoxcline biogeochemistry, probably as anaerobic or aerobic sulfur oxidizers.
Collapse
|