1
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Astorch-Cardona A, Bertaux L, Denis Y, Dolla A, Rommevaux C. Diversity and dynamics of bacteria from iron-rich microbial mats and colonizers in the Mediterranean Sea (EMSO-Western Ligurian Sea Observatory): Focus on Zetaproteobacteria. PLoS One 2024; 19:e0305626. [PMID: 39008445 PMCID: PMC11249232 DOI: 10.1371/journal.pone.0305626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 06/03/2024] [Indexed: 07/17/2024] Open
Abstract
Autotrophic microaerophilic iron-oxidizing Zetaproteobacteria seem to play an important role in mineral weathering and metal corrosion in different environments. Here, we compare the bacterial and zetaproteobacterial communities of a mature iron-rich mat together with in situ incubations of different Fe-bearing materials at the EMSO-Ligure West seafloor observatory, which is located on the abyssal plain in the NW Mediterranean Sea. Our results on bacterial communities enable us to make a clear distinction between those growing on mild steel anthropic substrata and those developing on basaltic substrata. Moreover, on anthropic substrata we highlight an influence of mat age on the bacterial communities. Regarding zetaproteobacterial communities, our results point to an increase in ZetaOTUs abundance and diversification with the age of the mat. We corroborate the key role of the ZetaOTU 2 in mat construction, whatever the environment, the substrata on which they develop or the age of the mat. We also show that ZetaOTU 28 is specific to anthropogenic substrata. Finally, we demonstrate the advantage of using dPCR to precisely quantify very low abundant targets, as Zetaproteobacteria on our colonizers. Our study, also, allows to enrich our knowledge on the biogeography of Zetaproteobacteria, by adding new information on this class and their role in the Mediterranean Sea.
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Affiliation(s)
| | | | - Yann Denis
- Institut de Microbiologie de la Méditerranée, CNRS - Aix Marseille Université, Marseille, France
| | - Alain Dolla
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Céline Rommevaux
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, Marseille, France
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2
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Tom M, Lubinevsky H, Kanari M. Integrative data system for monitoring biota and natural habitats in the Israeli Eastern Mediterranean marine environment. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:1068. [PMID: 37598114 DOI: 10.1007/s10661-023-11693-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/07/2023] [Indexed: 08/21/2023]
Abstract
An integrative data system for monitoring the biota of the Mediterranean waters of Israel as well as selected records from adjacent Levantine basin regions is presented here, aimed at providing data and research tools for long-term bio-geographic and ecological studies and more important, providing background data for assisting governmental regulators to establish educated habitat-oriented environmental policy. The system relies on the geographic information system (GIS) online map-based platform and contains at present the following components: biotic database of ~ 170,000 recorded sampling events; uniform habitat maps of 63 benthic habitats and 2 pelagic ones, constructed using relevant bathymetric features and biotic community compositions; bathymetric hill-shade map; depth contours; raster depth grid and human interference map. Other informative auxiliary maps are planned to be added (e.g., map of potential pockmark sites, detailed maps of tiny carbonate crust nolls and more). A number of 883 cited documents were listed by us for potential extraction of sampling efforts, most of them are available to us as PDFs and are available also to the users, excluding copyright-protected ones. Forty-three major projects were depicted in addition to a variety of small studies (e.g., university theses). Thirty-five sampling devices were documented and described, and 3187 species-level identifications were already recorded. In addition, the system provides access to description of sampling devices and pictures of species and seascapes. New data is continuously deposited to the system and the system is flexible, allowing future addition of new types of information. The system site is accessible through the link: https://experience.arcgis.com/experience/40e86605ff4d4e5096ed2c901fec2a2f .
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Affiliation(s)
- Moshe Tom
- Department of Marine Biology and Biotechnology, Israel Oceanographic and Limnological Research, P.O.B 2336, 3102201, Haifa, Israel.
| | - Hadas Lubinevsky
- Department of Marine Biology and Biotechnology, Israel Oceanographic and Limnological Research, P.O.B 2336, 3102201, Haifa, Israel
| | - Mor Kanari
- Department of Marine Geology and Geophysics, Israel Oceanographic and Limnological Research, P.O.B. 2336, 3102201, Haifa, Israel
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3
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Levy EJ, Thomas C, Antler G, Gavrieli I, Turchyn A, Grossi V, Ariztegui D, Sivan O. Intensified microbial sulfate reduction in the deep Dead Sea during the early Holocene Mediterranean sapropel 1 deposition. GEOBIOLOGY 2022; 20:518-532. [PMID: 35384246 PMCID: PMC9325388 DOI: 10.1111/gbi.12493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 01/25/2022] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
The hypersaline Dead Sea and its sediments are natural laboratories for studying extremophile microorganism habitat response to environmental change. In modern times, increased freshwater runoff to the lake surface waters resulted in stratification and dilution of the upper water column followed by microbial blooms. However, whether these events facilitated a microbial response in the deep lake and sediments is obscure. Here we investigate archived evidence of microbial processes and changing regional hydroclimate conditions by reconstructing deep Dead Sea chemical compositions from pore fluid major ion concentration and stable S, O, and C isotopes, together with lipid biomarkers preserved in the hypersaline deep Dead Sea ICDP-drilled core sediments dating to the early Holocene (ca. 10,000 years BP). Following a significant negative lake water balance resulting in salt layer deposits at the start of the Holocene, there was a general period of positive net water balance at 9500-8300 years BP. The pore fluid isotopic composition of sulfate exhibit evidence of intensified microbial sulfate reduction, where both δ34S and δ18O of sulfate show a sharp increase from estimated base values of 15.0‰ and 13.9‰ to 40.2‰ and 20.4‰, respectively, and a δ34S vs. δ18O slope of 0.26. The presence of the n-C17 alkane biomarker in the sediments suggests an increase of cyanobacteria or phytoplankton contribution to the bulk organic matter that reached the deepest parts of the Dead Sea. Although hydrologically disconnected, both the Mediterranean Sea and the Dead Sea microbial ecosystems responded to increased freshwater runoff during the early Holocene, with the former depositing the organic-rich sapropel 1 layer due to anoxic water column conditions. In the Dead Sea prolonged positive net water balance facilitated primary production and algal blooms in the upper waters and intensified microbial sulfate reduction in the hypolimnion and/or at the sediment-brine interface.
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Affiliation(s)
- Elan J. Levy
- Department of Earth and Environmental SciencesBen‐Gurion University of the NegevBeer ShevaIsrael
- Geological Survey of IsraelJerusalemIsrael
- Department of Climate GeochemistryMax Planck Institute for ChemistryMainzGermany
| | - Camille Thomas
- Department of Earth SciencesUniversity of GenevaGenevaSwitzerland
| | - Gilad Antler
- Department of Earth and Environmental SciencesBen‐Gurion University of the NegevBeer ShevaIsrael
- The Interuniversity Institute for Marine Sciences in EilatEilatIsrael
| | | | | | - Vincent Grossi
- Laboratoire de Géologie de LyonUniv. Lyon 1CNRSENSLVilleurbanneFrance
| | - Daniel Ariztegui
- Department of Earth SciencesUniversity of GenevaGenevaSwitzerland
| | - Orit Sivan
- Department of Earth and Environmental SciencesBen‐Gurion University of the NegevBeer ShevaIsrael
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4
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Koeksoy E, Bezuidt OM, Bayer T, Chan CS, Emerson D. Zetaproteobacteria Pan-Genome Reveals Candidate Gene Cluster for Twisted Stalk Biosynthesis and Export. Front Microbiol 2021; 12:679409. [PMID: 34220764 PMCID: PMC8250860 DOI: 10.3389/fmicb.2021.679409] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/06/2021] [Indexed: 12/15/2022] Open
Abstract
Twisted stalks are morphologically unique bacterial extracellular organo-metallic structures containing Fe(III) oxyhydroxides that are produced by microaerophilic Fe(II)-oxidizers belonging to the Betaproteobacteria and Zetaproteobacteria. Understanding the underlying genetic and physiological mechanisms of stalk formation is of great interest based on their potential as novel biogenic nanomaterials and their relevance as putative biomarkers for microbial Fe(II) oxidation on ancient Earth. Despite the recognition of these special biominerals for over 150 years, the genetic foundation for the stalk phenotype has remained unresolved. Here we present a candidate gene cluster for the biosynthesis and secretion of the stalk organic matrix that we identified with a trait-based analyses of a pan-genome comprising 16 Zetaproteobacteria isolate genomes. The “stalk formation in Zetaproteobacteria” (sfz) cluster comprises six genes (sfz1-sfz6), of which sfz1 and sfz2 were predicted with functions in exopolysaccharide synthesis, regulation, and export, sfz4 and sfz6 with functions in cell wall synthesis manipulation and carbohydrate hydrolysis, and sfz3 and sfz5 with unknown functions. The stalk-forming Betaproteobacteria Ferriphaselus R-1 and OYT-1, as well as dread-forming Zetaproteobacteria Mariprofundus aestuarium CP-5 and Mariprofundus ferrinatatus CP-8 contain distant sfz gene homologs, whereas stalk-less Zetaproteobacteria and Betaproteobacteria lack the entire gene cluster. Our pan-genome analysis further revealed a significant enrichment of clusters of orthologous groups (COGs) across all Zetaproteobacteria isolate genomes that are associated with the regulation of a switch between sessile and motile growth controlled by the intracellular signaling molecule c-di-GMP. Potential interactions between stalk-former unique transcription factor genes, sfz genes, and c-di-GMP point toward a c-di-GMP regulated surface attachment function of stalks during sessile growth.
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Affiliation(s)
- Elif Koeksoy
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.,Leibniz Institute DSMZ (German Collection of Microorganisms and Cell Cultures), Braunschweig, Germany
| | - Oliver M Bezuidt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Timm Bayer
- Geomicrobiology Group, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Clara S Chan
- Department of Earth Sciences, University of Delaware, Newark, DE, United States.,School of Marine Sciences and Policy, University of Delaware, Newark, DE, United States
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
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5
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McAllister SM, Moore RM, Gartman A, Luther GW, Emerson D, Chan CS. The Fe(II)-oxidizing Zetaproteobacteria: historical, ecological and genomic perspectives. FEMS Microbiol Ecol 2019; 95:fiz015. [PMID: 30715272 PMCID: PMC6443915 DOI: 10.1093/femsec/fiz015] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/29/2019] [Indexed: 01/22/2023] Open
Abstract
The Zetaproteobacteria are a class of bacteria typically associated with marine Fe(II)-oxidizing environments. First discovered in the hydrothermal vents at Loihi Seamount, Hawaii, they have become model organisms for marine microbial Fe(II) oxidation. In addition to deep sea and shallow hydrothermal vents, Zetaproteobacteria are found in coastal sediments, other marine subsurface environments, steel corrosion biofilms and saline terrestrial springs. Isolates from a range of environments all grow by autotrophic Fe(II) oxidation. Their success lies partly in their microaerophily, which enables them to compete with abiotic Fe(II) oxidation at Fe(II)-rich oxic/anoxic transition zones. To determine the known diversity of the Zetaproteobacteria, we have used 16S rRNA gene sequences to define 59 operational taxonomic units (OTUs), at 97% similarity. While some Zetaproteobacteria taxa appear to be cosmopolitan, others are enriched by specific habitats. OTU networks show that certain Zetaproteobacteria co-exist, sharing compatible niches. These niches may correspond with adaptations to O2, H2 and nitrate availability, based on genomic analyses of metabolic potential. Also, a putative Fe(II) oxidation gene has been found in diverse Zetaproteobacteria taxa, suggesting that the Zetaproteobacteria evolved as Fe(II) oxidation specialists. In all, studies suggest that Zetaproteobacteria are widespread, and therefore may have a broad influence on marine and saline terrestrial Fe cycling.
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Affiliation(s)
- Sean M McAllister
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Road, 204 Cannon Lab, Lewes, Delaware, USA 19958
| | - Ryan M Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, 205 Delaware Biotechnology Institute, Newark, Delaware, USA 19711
| | - Amy Gartman
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Road, 204 Cannon Lab, Lewes, Delaware, USA 19958
| | - George W Luther
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Road, 204 Cannon Lab, Lewes, Delaware, USA 19958
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, Maine, USA 04544
| | - Clara S Chan
- School of Marine Science and Policy, University of Delaware, 700 Pilottown Road, 204 Cannon Lab, Lewes, Delaware, USA 19958
- Department of Geological Sciences, University of Delaware, 101 Penny Hall, Newark, Delaware, USA 19716
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6
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Vander Roost J, Daae FL, Steen IH, Thorseth IH, Dahle H. Distribution Patterns of Iron-Oxidizing Zeta- and Beta-Proteobacteria From Different Environmental Settings at the Jan Mayen Vent Fields. Front Microbiol 2018; 9:3008. [PMID: 30574135 PMCID: PMC6292416 DOI: 10.3389/fmicb.2018.03008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/20/2018] [Indexed: 12/26/2022] Open
Abstract
Iron oxidizers are widespread in marine environments and play an important role in marine iron cycling. However, little is known about the overall distribution of iron oxidizers within hydrothermal systems, including settings with little hydrothermal activity. Moreover, the extent to which different phylogenetic groups of iron oxidizers exhibit niche specialization toward different environmental settings, remains largely unknown. Obtaining such knowledge is critical to unraveling the impact of the activity of iron oxidizers and how they are adapted. Here, we used 16S rRNA sequencing to characterize the distribution of iron oxidizers in different environmental settings within the Jan Mayen hydrothermal vent fields (JMVFs). Putative iron oxidizers affiliated to Zetaproteobacteria and Betaproteobacteria were detected within iron mounds, bottom seawater, basalt surfaces, and surface layers of sediments. The detected iron oxidizers were compared to sequence types previously observed in patchily distributed iron mats associated with diffuse venting at the JMVFs. Most OTUs of iron oxidizers reoccurred under different environmental settings, suggesting a limited degree of niche specialization. Consequently, most of the detected iron oxidizers seem to be generalists with a large habitat range. Our study highlights the importance of gathering information about the overall distribution of iron oxidizers in hydrothermal systems to fully understand the role of this metabolic group regarding cycling of iron. Furthermore, our results provide further evidence of the presence of iron-oxidizing members of Betaproteobacteria in marine environments.
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Affiliation(s)
- Jan Vander Roost
- Centre for Geobiology, University of Bergen, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
| | - Frida Lise Daae
- Centre for Geobiology, University of Bergen, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
| | - Ida Helene Steen
- Centre for Geobiology, University of Bergen, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
| | - Ingunn Hindeness Thorseth
- Centre for Geobiology, University of Bergen, Bergen, Norway.,Department of Earth Science, University of Bergen, Bergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of Bergen, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
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7
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Iron-oxidizing bacteria in marine environments: recent progresses and future directions. World J Microbiol Biotechnol 2018; 34:110. [PMID: 29974320 DOI: 10.1007/s11274-018-2491-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/26/2018] [Indexed: 10/28/2022]
Abstract
Iron-oxidizing bacteria (FeOB) refers to a group of bacteria with the ability to exchange and accumulate divalent iron dissolved in water as trivalent iron inside and outside the bacterial cell. Most FeOB belong the largest bacterial phylum, Proteobacteria. Within this phylum, FeOB with varying physiology with regards to their response to oxygen (obligate aerobes, facultative and obligate anaerobes) and pH optimum for proliferation (neutrophiles, moderate and extreme acidophiles) can be found. Although FeOB have been reported from a wide variety of environments, most of them have not been isolated and their biochemical characteristics remain largely unknown. This is especially true for those living in the marine realm, where the properties of FeOB was not known until the isolation of the Zetaproteobacteria Mariprofundus ferrooxydans, first reported in 2007. Since the proposal of Zetaproteobacteria by Emerson et al., the detection and isolation of those microorganisms from the marine environment has greatly escalated. Furthermore, FeOB have also recently been reported from works on ocean drilling and metal corrosion. This review aims to summarize the current state of phylogenetic and physiological diversity in marine FeOB, the significance of their roles in their environments (on both global and local scales), as well as their growing importance and applications in the industry.
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8
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Beam JP, Scott JJ, McAllister SM, Chan CS, McManus J, Meysman FJR, Emerson D. Biological rejuvenation of iron oxides in bioturbated marine sediments. ISME JOURNAL 2018; 12:1389-1394. [PMID: 29343830 DOI: 10.1038/s41396-017-0032-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 11/22/2017] [Accepted: 11/29/2017] [Indexed: 02/04/2023]
Abstract
The biogeochemical cycle of iron is intricately linked to numerous element cycles. Although biological processes that catalyze the reductive side of the iron cycle are established, little is known about microbial oxidative processes on iron cycling in sedimentary environments-resulting in the formation of iron oxides. Here we show that a potential source of sedimentary iron oxides originates from the metabolic activity of iron-oxidizing bacteria from the class Zetaproteobacteria, presumably enhanced by burrowing animals in coastal sediments. Zetaproteobacteria were estimated to be a global total of 1026 cells in coastal, bioturbated sediments, and predicted to annually produce 8 × 1015 g of Fe in sedimentary iron oxides-55 times larger than the annual flux of iron oxides deposited by rivers. These data suggest that iron-oxidizing Zetaproteobacteria are keystone organisms in marine sedimentary environments-despite their low numerical abundance-yet exert a disproportionate impact via the rejuvenation of iron oxides.
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Affiliation(s)
- Jacob P Beam
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA.
| | - Jarrod J Scott
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA.,Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Panamá, Republic of Panama
| | - Sean M McAllister
- Department of Geological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Clara S Chan
- Department of Geological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - James McManus
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Filip J R Meysman
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium.,Department of Biotechnology, Technical University of Delft, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
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9
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Vander Roost J, Thorseth IH, Dahle H. Microbial analysis of Zetaproteobacteria and co-colonizers of iron mats in the Troll Wall Vent Field, Arctic Mid-Ocean Ridge. PLoS One 2017; 12:e0185008. [PMID: 28931087 PMCID: PMC5607188 DOI: 10.1371/journal.pone.0185008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 09/05/2017] [Indexed: 11/30/2022] Open
Abstract
Over the last decade it has become increasingly clear that Zetaproteobacteria are widespread in hydrothermal systems and that they contribute to the biogeochemical cycling of iron in these environments. However, how chemical factors control the distribution of Zetaproteobacteria and their co-occurring taxa remains elusive. Here we analysed iron mats from the Troll Wall Vent Field (TWVF) located at the Arctic Mid-Ocean Ridge (AMOR) in the Norwegian-Greenland Sea. The samples were taken at increasing distances from high-temperature venting chimneys towards areas with ultraslow low-temperature venting, encompassing a large variety in geochemical settings. Electron microscopy revealed the presence of biogenic iron stalks in all samples. Using 16S rRNA gene sequence profiling we found that relative abundances of Zetaproteobacteria in the iron mats varied from 0.2 to 37.9%. Biogeographic analyses of Zetaproteobacteria, using the ZetaHunter software, revealed the presence of ZetaOtus 1, 2 and 9, supporting the view that they are cosmopolitan. Relative abundances of co-occurring taxa, including Thaumarchaeota, Euryarchaeota and Proteobacteria, also varied substantially. From our results, combined with results from previous microbiological and geochemical analyses of the TWVF, we infer that the distribution of Zetaproteobacteria is connected to fluid-flow patterns and, ultimately, variations in chemical energy landscapes. Moreover, we provide evidence for iron-oxidizing members of Gallionellaceae being widespread in TWVF iron mats, albeit at low relative abundances.
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Affiliation(s)
- Jan Vander Roost
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Ingunn Hindenes Thorseth
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
- * E-mail:
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10
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Hager KW, Fullerton H, Butterfield DA, Moyer CL. Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc. Front Microbiol 2017; 8:1578. [PMID: 28970817 PMCID: PMC5609546 DOI: 10.3389/fmicb.2017.01578] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/03/2017] [Indexed: 01/08/2023] Open
Abstract
The Mariana region exhibits a rich array of hydrothermal venting conditions in a complex geological setting, which provides a natural laboratory to study the influence of local environmental conditions on microbial community structure as well as large-scale patterns in microbial biogeography. We used high-throughput amplicon sequencing of the bacterial small subunit (SSU) rRNA gene from 22 microbial mats collected from four hydrothermally active locations along the Mariana Arc and back-arc to explore the structure of lithotrophically-based microbial mat communities. The vent effluent was classified as iron- or sulfur-rich corresponding with two distinct community types, dominated by either Zetaproteobacteria or Epsilonproteobacteria, respectively. The Zetaproteobacterial-based communities had the highest richness and diversity, which supports the hypothesis that Zetaproteobacteria function as ecosystem engineers creating a physical habitat within a chemical environment promoting enhanced microbial diversity. Gammaproteobacteria were also high in abundance within the iron-dominated mats and some likely contribute to primary production. In addition, we also compare sampling scale, showing that bulk sampling of microbial mats yields higher diversity than micro-scale sampling. We present a comprehensive analysis and offer new insights into the community structure and diversity of lithotrophically-driven microbial mats from a hydrothermal region associated with high microbial biodiversity. Our study indicates an important functional role of for the Zetaproteobacteria altering the mat habitat and enhancing community interactions and complexity.
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Affiliation(s)
- Kevin W Hager
- Department of Biology, Western Washington UniversityBellingham, WA, United States
| | - Heather Fullerton
- Department of Biology, Western Washington UniversityBellingham, WA, United States
| | - David A Butterfield
- National Oceanic and Atmospheric Administration Pacific Marine Environmental Lab, Joint Institute for the Study of the Atmosphere and Ocean, University of WashingtonSeattle, WA, United States
| | - Craig L Moyer
- Department of Biology, Western Washington UniversityBellingham, WA, United States
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11
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Microaerophilic Fe(II)-Oxidizing Zetaproteobacteria Isolated from Low-Fe Marine Coastal Sediments: Physiology and Composition of Their Twisted Stalks. Appl Environ Microbiol 2017; 83:AEM.03118-16. [PMID: 28159791 DOI: 10.1128/aem.03118-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/28/2017] [Indexed: 11/20/2022] Open
Abstract
Microaerophilic Fe(II) oxidizers are commonly found in habitats containing elevated Fe(II) and low O2 concentrations and often produce characteristic Fe mineral structures, so-called twisted stalks or tubular sheaths. Isolates originating from freshwater habitats are all members of the Betaproteobacteria, while isolates from marine habitats belong almost exclusively to the Zetaproteobacteria So far, only a few isolates of marine microaerophilic Fe(II) oxidizers have been described, all of which are obligate microaerophilic Fe(II) oxidizers and have been thought to be restricted to Fe-rich systems. Here, we present two new isolates of marine microaerophilic Fe(II)-oxidizing Zetaproteobacteria that originate from typical coastal marine sediments containing only low Fe concentrations (2 to 11 mg of total Fe/g of sediment [dry weight]; 70 to 100 μM dissolved Fe2+ in the porewater). The two novel Zetaproteobacteria share characteristic physiological properties of the Zetaproteobacteria group, even though they come from low-Fe environments: the isolates are obligate microaerophilic Fe(II) oxidizers and, like most isolated Zetaproteobacteria, they produce twisted stalks. We found a low organic carbon content in the stalks (∼0.3 wt%), with mostly polysaccharides and saturated aliphatic chains (most likely lipids). The Fe minerals in the stalks were identified as lepidocrocite and possibly ferrihydrite. Immobilization experiments with Ni2+ showed that the stalks can function as a sink for trace metals. Our findings show that obligate microaerophilic Fe(II) oxidizers belonging to the Zetaproteobacteria group are not restricted to Fe-rich environments but can also be found in low-Fe marine environments, which increases their overall importance for the global biogeochemical Fe cycle.IMPORTANCE So far, only a few isolates of benthic marine microaerophilic Fe(II) oxidizers belonging to the Zetaproteobacteria exist, and most isolates were obtained from habitats containing elevated Fe concentrations. Consequently, it was thought that these microorganisms are important mainly in habitats with high Fe concentrations. The two novel isolates of Zetaproteobacteria that are presented in the present study were isolated from typical coastal marine sediments that do not contain elevated Fe concentrations. This increases the knowledge about possible habitats in which Zetaproteobacteria can exist. Furthermore, we show that the physiology and the typical organo-mineral structures (twisted stalks) that are produced by the isolates do not notably differ from the physiology and the cell-mineral structures of isolates from environments with high Fe concentrations. We also showed that the organo-mineral structures can function as a sink for trace metals.
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12
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Scott JJ, Glazer BT, Emerson D. Bringing microbial diversity into focus: high-resolution analysis of iron mats from the Lō'ihi Seamount. Environ Microbiol 2016; 19:301-316. [PMID: 27871143 DOI: 10.1111/1462-2920.13607] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 10/27/2016] [Accepted: 11/16/2016] [Indexed: 01/22/2023]
Abstract
Thirty kilometers south of the island of Hawai'i lies the Lō'ihi Seamount, an active submarine volcano that hosts a network of low-temperature hydrothermal vents enriched in ferrous iron that supports extensive microbial mats. These mats, which can be a half a meter deep, are composed of ferric iron bound to organic polymers - the metabolic byproduct of iron-oxidizing Zetaproteobacteria. Though the role of Zetaproteobacteria in mat formation is well established, we have a limited understanding of how differences in diversity are related to mat morphology. We used Minimum Entropy Decomposition and ZetaOtu classification to demonstrate cryptic diversity between closely related Zetaproteobacteria while showing habitat and geographic specificity. Veiled mats, common structures at Lō'ihi, exhibit distinct community composition and contain diversity not detected in other mat types, including specific Zetaproteobacteria and an unclassified Gammaproteobacteria. Our analyses also indicate that diversity can change dramatically across small spatial transects from points of active venting, yet we found comparatively few differences between major sampling sites. This study provides a better picture of the microbiome responsible for iron mat production at Lō'ihi and has broad implications for our understanding of these globally distributed communities.
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Affiliation(s)
- Jarrod J Scott
- Ocean Microbiome & Blue Biotechnology Center, Bigelow Laboratory for Ocean Sciences, PO Box 380, East Boothbay, ME, 04544, USA
| | - Brian T Glazer
- Department of Oceanography, University of Hawai'i at Mānoa, 1000 Pope Rd. Honolulu, HI, 96822, USA
| | - David Emerson
- Ocean Microbiome & Blue Biotechnology Center, Bigelow Laboratory for Ocean Sciences, PO Box 380, East Boothbay, ME, 04544, USA
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Henri PA, Rommevaux-Jestin C, Lesongeur F, Mumford A, Emerson D, Godfroy A, Ménez B. Structural Iron (II) of Basaltic Glass as an Energy Source for Zetaproteobacteria in an Abyssal Plain Environment, Off the Mid Atlantic Ridge. Front Microbiol 2016; 6:1518. [PMID: 26834704 PMCID: PMC4720738 DOI: 10.3389/fmicb.2015.01518] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/17/2015] [Indexed: 12/27/2022] Open
Abstract
To explore the capability of basaltic glass to support the growth of chemosynthetic microorganisms, complementary in situ and in vitro colonization experiments were performed. Microbial colonizers containing synthetic tholeitic basaltic glasses, either enriched in reduced or oxidized iron, were deployed off-axis from the Mid Atlantic Ridge on surface sediments of the abyssal plain (35°N; 29°W). In situ microbial colonization was assessed by sequencing of the 16S rRNA gene and basaltic glass alteration was characterized using Scanning Electron Microscopy, micro-X-ray Absorption Near Edge Structure at the Fe-K-edge and Raman microspectroscopy. The colonized surface of the reduced basaltic glass was covered by a rind of alteration made of iron-oxides trapped in a palagonite-like structure with thicknesses up to 150 μm. The relative abundance of the associated microbial community was dominated (39% of all reads) by a single operational taxonomic unit (OTU) that shared 92% identity with the iron-oxidizer Mariprofundus ferrooxydans PV-1. Conversely, the oxidized basaltic glass showed the absence of iron-oxides enriched surface deposits and correspondingly there was a lack of known iron-oxidizing bacteria in the inventoried diversity. In vitro, a similar reduced basaltic glass was incubated in artificial seawater with a pure culture of the iron-oxidizing M. ferrooxydans DIS-1 for 2 weeks, without any additional nutrients or minerals. Confocal Laser Scanning Microscopy revealed that the glass surface was covered by twisted stalks characteristic of this iron-oxidizing Zetaproteobacteria. This result supported findings of the in situ experiments indicating that the Fe(II) present in the basalt was the energy source for the growth of representatives of Zetaproteobacteria in both the abyssal plain and the in vitro experiment. In accordance, the surface alteration rind observed on the reduced basaltic glass incubated in situ could at least partly result from their activity.
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Affiliation(s)
- Pauline A Henri
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Univ Paris Diderot, Centre National de la Recherche Scientifique Paris, France
| | - Céline Rommevaux-Jestin
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Univ Paris Diderot, Centre National de la Recherche Scientifique Paris, France
| | - Françoise Lesongeur
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS/UMR 6197 Plouzané, France
| | - Adam Mumford
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
| | - Anne Godfroy
- Laboratoire de Microbiologie des Environnements Extrêmes, Ifremer, CNRS/UMR 6197 Plouzané, France
| | - Bénédicte Ménez
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Univ Paris Diderot, Centre National de la Recherche Scientifique Paris, France
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Emerson D. The Irony of Iron - Biogenic Iron Oxides as an Iron Source to the Ocean. Front Microbiol 2016; 6:1502. [PMID: 26779157 PMCID: PMC4701967 DOI: 10.3389/fmicb.2015.01502] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/14/2015] [Indexed: 11/16/2022] Open
Abstract
Primary productivity in at least a third of the sunlit open ocean is thought to be iron-limited. Primary sources of dissolved iron (dFe) to the ocean are hydrothermal venting, flux from the sediments along continental margins, and airborne dust. This article provides a general review of sources of hydrothermal and sedimentary iron to the ocean, and speculates upon the role that iron-cycling microbes play in controlling iron dynamics from these sources. Special attention is paid to iron-oxidizing bacteria (FeOB) that live by oxidizing iron and producing biogenic iron oxides as waste products. The presence and ubiquity of FeOB both at hydrothermal systems and in sediments is only beginning to be appreciated. The biogenic oxides they produce have unique properties that could contribute significantly to the dynamics of dFe in the ocean. Changes in the physical and chemical characteristics of the ocean due to climate change and ocean acidification will undoubtedly impact the microbial iron cycle. A better understanding of the contemporary role of microbes in the iron cycle will help in predicting how these changes could ultimately influence marine primary productivity.
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Affiliation(s)
- David Emerson
- Bigelow Laboratory for Ocean Sciences East Boothbay, ME, USA
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15
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Laufer K, Nordhoff M, Røy H, Schmidt C, Behrens S, Jørgensen BB, Kappler A. Coexistence of Microaerophilic, Nitrate-Reducing, and Phototrophic Fe(II) Oxidizers and Fe(III) Reducers in Coastal Marine Sediment. Appl Environ Microbiol 2015; 82:1433-1447. [PMID: 26682861 PMCID: PMC4771319 DOI: 10.1128/aem.03527-15] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 12/14/2015] [Indexed: 02/04/2023] Open
Abstract
Iron is abundant in sediments, where it can be biogeochemically cycled between its divalent and trivalent redox states. The neutrophilic microbiological Fe cycle involves Fe(III)-reducing and three different physiological groups of Fe(II)-oxidizing microorganisms, i.e., microaerophilic, anoxygenic phototrophic, and nitrate-reducing Fe(II) oxidizers. However, it is unknown whether all three groups coexist in one habitat and how they are spatially distributed in relation to gradients of O2, light, nitrate, and Fe(II). We examined two coastal marine sediments in Aarhus Bay, Denmark, by cultivation and most probable number (MPN) studies for Fe(II) oxidizers and Fe(III) reducers and by quantitative-PCR (qPCR) assays for microaerophilic Fe(II) oxidizers. Our results demonstrate the coexistence of all three metabolic types of Fe(II) oxidizers and Fe(III) reducers. In qPCR, microaerophilic Fe(II) oxidizers (Zetaproteobacteria) were present with up to 3.2 × 10(6) cells g dry sediment(-1). In MPNs, nitrate-reducing Fe(II) oxidizers, anoxygenic phototrophic Fe(II) oxidizers, and Fe(III) reducers reached cell numbers of up to 3.5 × 10(4), 3.1 × 10(2), and 4.4 × 10(4) g dry sediment(-1), respectively. O2 and light penetrated only a few millimeters, but the depth distribution of the different iron metabolizers did not correlate with the profile of O2, Fe(II), or light. Instead, abundances were homogeneous within the upper 3 cm of the sediment, probably due to wave-induced sediment reworking and bioturbation. In microaerophilic Fe(II)-oxidizing enrichment cultures, strains belonging to the Zetaproteobacteria were identified. Photoferrotrophic enrichments contained strains related to Chlorobium and Rhodobacter; the nitrate-reducing Fe(II) enrichments contained strains related to Hoeflea and Denitromonas. This study shows the coexistence of all three types of Fe(II) oxidizers in two near-shore marine environments and the potential for competition and interrelationships between them.
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Affiliation(s)
- Katja Laufer
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Mark Nordhoff
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Hans Røy
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Caroline Schmidt
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
| | - Sebastian Behrens
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen, Germany
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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Polymenakou PN, Christakis CA, Mandalakis M, Oulas A. Pyrosequencing analysis of microbial communities reveals dominant cosmopolitan phylotypes in deep-sea sediments of the eastern Mediterranean Sea. Res Microbiol 2015; 166:448-457. [PMID: 25908548 DOI: 10.1016/j.resmic.2015.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/22/2015] [Accepted: 03/23/2015] [Indexed: 10/23/2022]
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Microbial iron mats at the Mid-Atlantic Ridge and evidence that Zetaproteobacteria may be restricted to iron-oxidizing marine systems. PLoS One 2015; 10:e0119284. [PMID: 25760332 PMCID: PMC4356598 DOI: 10.1371/journal.pone.0119284] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 01/26/2015] [Indexed: 12/02/2022] Open
Abstract
Chemolithoautotrophic iron-oxidizing bacteria play an essential role in the global iron cycle. Thus far, the majority of marine iron-oxidizing bacteria have been identified as Zetaproteobacteria, a novel class within the phylum Proteobacteria. Marine iron-oxidizing microbial communities have been found associated with volcanically active seamounts, crustal spreading centers, and coastal waters. However, little is known about the presence and diversity of iron-oxidizing communities at hydrothermal systems along the slow crustal spreading center of the Mid-Atlantic Ridge. From October to November 2012, samples were collected from rust-colored mats at three well-known hydrothermal vent systems on the Mid-Atlantic Ridge (Rainbow, Trans-Atlantic Geotraverse, and Snake Pit) using the ROV Jason II. The goal of these efforts was to determine if iron-oxidizing Zetaproteobacteria were present at sites proximal to black smoker vent fields. Small, diffuse flow venting areas with high iron(II) concentrations and rust-colored microbial mats were observed at all three sites proximal to black smoker chimneys. A novel, syringe-based precision sampler was used to collect discrete microbial iron mat samples at the three sites. The presence of Zetaproteobacteria was confirmed using a combination of 16S rRNA pyrosequencing and single-cell sorting, while light micros-copy revealed a variety of iron-oxyhydroxide structures, indicating that active iron-oxidizing communities exist along the Mid-Atlantic Ridge. Sequencing analysis suggests that these iron mats contain cosmopolitan representatives of Zetaproteobacteria, but also exhibit diversity that may be uncommon at other iron-rich marine sites studied to date. A meta-analysis of publically available data encompassing a variety of aquatic habitats indicates that Zetaproteobacteria are rare if an iron source is not readily available. This work adds to the growing understanding of Zetaproteobacteria ecology and suggests that this organism is likely locally restricted to iron-rich marine environments but may exhibit wide-scale geographic distribution, further underscoring the importance of Zetaproteobacteria in global iron cycling.
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