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Litchman E, Villéger S, Zinger L, Auguet JC, Thuiller W, Munoz F, Kraft NJB, Philippot L, Violle C. Refocusing the microbial rare biosphere concept through a functional lens. Trends Ecol Evol 2024:S0169-5347(24)00143-5. [PMID: 38987022 DOI: 10.1016/j.tree.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 06/04/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024]
Abstract
The influential concept of the rare biosphere in microbial ecology has underscored the importance of taxa occurring at low abundances yet potentially playing key roles in communities and ecosystems. Here, we refocus the concept of rare biosphere through a functional trait-based lens and provide a framework to characterize microbial functional rarity, a combination of numerical scarcity across space or time and trait distinctiveness. We demonstrate how this novel interpretation of the rare biosphere, rooted in microbial functions, can enhance our mechanistic understanding of microbial community structure. It also sheds light on functionally distinct microbes, directing conservation efforts towards taxa harboring rare yet ecologically crucial functions.
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Affiliation(s)
- Elena Litchman
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA; Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA.
| | | | - Lucie Zinger
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, Paris, France; Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300, CNRS, Institut de Recherche pour le Développement (IRD), Toulouse INP, Université Toulouse 3 Paul Sabatier, Toulouse, France
| | | | - Wilfried Thuiller
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - François Munoz
- Université Grenoble Alpes, CNRS, LIPhy, F-38000 Grenoble, France
| | - Nathan J B Kraft
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRAE, Institut Agro Dijon, Agroecology, Dijon, France
| | - Cyrille Violle
- CEFE, Université Montpellier, CNRS, IRD, EPHE, Montpellier, France
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2
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Scilipoti S, Molari M. High-quality draft genome of Gammaproteobacterial SUP05 cluster from non-buoyant hydrothermal plumes of ultraslow spreading Gakkel Ridge (Central Arctic Ocean). Microbiol Resour Announc 2024; 13:e0012124. [PMID: 38456699 PMCID: PMC11008202 DOI: 10.1128/mra.00121-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/09/2024] Open
Abstract
Hydrothermal plumes are an important yet understudied component of deep-sea microbial ecosystems. We report metagenome-assembled genomes (MAGs) of three Bacteria belonging to the Gammaproteobacterial SUP05 cluster (family Thioglobaceae), assembled from the metagenomes of two non-buoyant hydrothermal plumes in the ultraslow spreading Gakkel Ridge.
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Affiliation(s)
- Stefano Scilipoti
- HGF MPG Joint Research Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Massimiliano Molari
- HGF MPG Joint Research Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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3
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Fullerton H, Smith L, Enriquez A, Butterfield D, Wheat CG, Moyer CL. Seafloor incubation experiments at deep-sea hydrothermal vents reveal distinct biogeographic signatures of autotrophic communities. FEMS Microbiol Ecol 2024; 100:fiae001. [PMID: 38200713 PMCID: PMC10808952 DOI: 10.1093/femsec/fiae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/20/2023] [Accepted: 01/09/2024] [Indexed: 01/12/2024] Open
Abstract
The discharge of hydrothermal vents on the seafloor provides energy sources for dynamic and productive ecosystems, which are supported by chemosynthetic microbial populations. These populations use the energy gained by oxidizing the reduced chemicals contained within the vent fluids to fix carbon and support multiple trophic levels. Hydrothermal discharge is ephemeral and chemical composition of such fluids varies over space and time, which can result in geographically distinct microbial communities. To investigate the foundational members of the community, microbial growth chambers were placed within the hydrothermal discharge at Axial Seamount (Juan de Fuca Ridge), Magic Mountain Seamount (Explorer Ridge), and Kama'ehuakanaloa Seamount (Hawai'i hotspot). Campylobacteria were identified within the nascent communities, but different amplicon sequence variants were present at Axial and Kama'ehuakanaloa Seamounts, indicating that geography in addition to the composition of the vent effluent influences microbial community development. Across these vent locations, dissolved iron concentration was the strongest driver of community structure. These results provide insights into nascent microbial community structure and shed light on the development of diverse lithotrophic communities at hydrothermal vents.
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Affiliation(s)
- Heather Fullerton
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC 29424, United States
| | - Lindsey Smith
- Department of Biology, Western Washington University, 516 High St, Bellingham, WA 98225, United States
| | - Alejandra Enriquez
- Department of Biology, College of Charleston, 66 George Street, Charleston, SC 29424, United States
| | - David Butterfield
- Cooperative Institute for Climate, Ocean, and Ecosystem Studies, University of Washington and NOAA/PMEL, John M. Wallace Hall, 3737 Brooklyn Ave NE, Seattle, WA 98105, United States
| | - C Geoffrey Wheat
- Institute of Marine Studies, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 2150 Koyukuk Drive, 245 O’Neill Building, PO Box 757220, Fairbanks, Alaska 99775-7220, United States
| | - Craig L Moyer
- Department of Biology, Western Washington University, 516 High St, Bellingham, WA 98225, United States
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4
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Hart R, Cardace D. Mineral Indicators of Geologically Recent Past Habitability on Mars. Life (Basel) 2023; 13:2349. [PMID: 38137950 PMCID: PMC10744562 DOI: 10.3390/life13122349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/25/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
We provide new support for habitable microenvironments in the near-subsurface of Mars, hosted in Fe- and Mg-rich rock units, and present a list of minerals that can serve as indicators of specific water-rock reactions in recent geologic paleohabitats for follow-on study. We modeled, using a thermodynamic basis without selective phase suppression, the reactions of published Martian meteorites and Jezero Crater igneous rock compositions and reasonable planetary waters (saline, alkaline waters) using Geochemist's Workbench Ver. 12.0. Solid-phase inputs were meteorite compositions for ALH 77005, Nakhla, and Chassigny, and two rock units from the Mars 2020 Perseverance rover sites, Máaz and Séítah. Six plausible Martian groundwater types [NaClO4, Mg(ClO4)2, Ca(ClO4)2, Mg-Na2(ClO4)2, Ca-Na2(ClO4)2, Mg-Ca(ClO4)2] and a unique Mars soil-water analog solution (dilute saline solution) named "Rosy Red", related to the Phoenix Lander mission, were the aqueous-phase inputs. Geophysical conditions were tuned to near-subsurface Mars (100 °C or 373.15 K, associated with residual heat from a magmatic system, impact event, or a concentration of radionuclides, and 101.3 kPa, similar to <10 m depth). Mineral products were dominated by phyllosilicates such as serpentine-group minerals in most reaction paths, but differed in some important indicator minerals. Modeled products varied in physicochemical properties (pH, Eh, conductivity), major ion activities, and related gas fugacities, with different ecological implications. The microbial habitability of pore spaces in subsurface groundwater percolation systems was interrogated at equilibrium in a thermodynamic framework, based on Gibbs Free Energy Minimization. Models run with the Chassigny meteorite produced the overall highest H2 fugacity. Models reliant on the Rosy Red soil-water analog produced the highest sustained CH4 fugacity (maximum values observed for reactant ALH 77005). In general, Chassigny meteorite protoliths produced the best yield regarding Gibbs Free Energy, from an astrobiological perspective. Occurrences of serpentine and saponite across models are key: these minerals have been observed using CRISM spectral data, and their formation via serpentinization would be consistent with geologically recent-past H2 and CH4 production and sustained energy sources for microbial life. We list index minerals to be used as diagnostic for paleo water-rock models that could have supported geologically recent-past microbial activity, and suggest their application as criteria for future astrobiology study-site selections.
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Affiliation(s)
- Roger Hart
- Department of Physics and Engineering, Community College of Rhode Island, Lincoln, RI 02865, USA
- Department of Geosciences, University of Rhode Island, Kingston, RI 02881, USA;
| | - Dawn Cardace
- Department of Geosciences, University of Rhode Island, Kingston, RI 02881, USA;
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5
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Adam-Beyer N, Laufer-Meiser K, Fuchs S, Schippers A, Indenbirken D, Garbe-Schönberg D, Petersen S, Perner M. Microbial ecosystem assessment and hydrogen oxidation potential of newly discovered vent systems from the Central and South-East Indian Ridge. Front Microbiol 2023; 14:1173613. [PMID: 37886064 PMCID: PMC10598711 DOI: 10.3389/fmicb.2023.1173613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
In order to expand the knowledge of microbial ecosystems from deep-sea hydrothermal vent systems located on the Central and South-East Indian Ridge, we sampled hydrothermal fluids, massive sulfides, ambient water and sediments of six distinct vent fields. Most of these vent sites were only recently discovered in the course of the German exploration program for massive sulfide deposits and no previous studies of the respective microbial communities exist. Apart from typically vent-associated chemosynthetic members of the orders Campylobacterales, Mariprofundales, and Thiomicrospirales, high numbers of uncultured and unspecified Bacteria were identified via 16S rRNA gene analyses in hydrothermal fluid and massive sulfide samples. The sampled sediments however, were characterized by an overall lack of chemosynthetic Bacteria and the presence of high proportions of low abundant bacterial groups. The archaeal communities were generally less diverse and mostly dominated by members of Nitrosopumilales and Woesearchaeales, partly exhibiting high proportions of unassigned Archaea. Correlations with environmental parameters were primarily observed for sediment communities and for microbial species (associated with the nitrogen cycle) in samples from a recently identified vent field, which was geochemically distinct from all other sampled sites. Enrichment cultures of diffuse fluids demonstrated a great potential for hydrogen oxidation coupled to the reduction of various electron-acceptors with high abundances of Hydrogenovibrio and Sulfurimonas species. Overall, given the large number of currently uncultured and unspecified microorganisms identified in the vent communities, their respective metabolic traits, ecosystem functions and mediated biogeochemical processes have still to be resolved for estimating consequences of potential environmental disturbances by future mining activities.
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Affiliation(s)
- Nicole Adam-Beyer
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Katja Laufer-Meiser
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Sebastian Fuchs
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Axel Schippers
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | | | | | - Sven Petersen
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Mirjam Perner
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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6
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Barosa B, Ferrillo A, Selci M, Giardina M, Bastianoni A, Correggia M, di Iorio L, Bernardi G, Cascone M, Capuozzo R, Intoccia M, Price R, Vetriani C, Cordone A, Giovannelli D. Mapping the microbial diversity associated with different geochemical regimes in the shallow-water hydrothermal vents of the Aeolian archipelago, Italy. Front Microbiol 2023; 14:1134114. [PMID: 37637107 PMCID: PMC10452888 DOI: 10.3389/fmicb.2023.1134114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Shallow-water hydrothermal vents are unique marine environments ubiquitous along the coast of volcanically active regions of the planet. In contrast to their deep-sea counterparts, primary production at shallow-water vents relies on both photoautotrophy and chemoautotrophy. Such processes are supported by a range of geochemical regimes driven by different geological settings. The Aeolian archipelago, located in the southern Tyrrhenian sea, is characterized by intense hydrothermal activity and harbors some of the best sampled shallow-water vents of the Mediterranean Sea. Despite this, the correlation between microbial diversity, geochemical regimes and geological settings of the different volcanic islands of the archipelago is largely unknown. Here, we report the microbial diversity associated with six distinct shallow-water hydrothermal vents of the Aeolian Islands using a combination of 16S rRNA amplicon sequencing along with physicochemical and geochemical measurements. Samples were collected from biofilms, fluids and sediments from shallow vents on the islands of Lipari, Panarea, Salina, and Vulcano. Two new shallow vent locations are described here for the first time. Our results show the presence of diverse microbial communities consistent in their composition with the local geochemical regimes. The shallow water vents of the Aeolian Islands harbor highly diverse microbial community and should be included in future conservation efforts.
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Affiliation(s)
- Bernardo Barosa
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | | | - Matteo Selci
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Marco Giardina
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Alessia Bastianoni
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Monica Correggia
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Luciano di Iorio
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | | | - Martina Cascone
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Rosaria Capuozzo
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Michele Intoccia
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Roy Price
- School of Marine and Atmospheric Sciences, Stony Brook, NY, United States
| | - Costantino Vetriani
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States
| | - Angelina Cordone
- Department of Biology, University of Naples “Federico II”, Naples, Italy
| | - Donato Giovannelli
- Department of Biology, University of Naples “Federico II”, Naples, Italy
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, United States
- Istituto per le Risorse Biologiche e Biotecnologiche Marine, Consiglio Nazionale Delle Ricerche, CNR-IRBIM, Ancona, Italy
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Tokyo, Japan
- Marine Chemistry and Geochemistry Department–Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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7
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Kuppa Baskaran DK, Umale S, Zhou Z, Raman K, Anantharaman K. Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes. ISME COMMUNICATIONS 2023; 3:42. [PMID: 37120693 PMCID: PMC10148797 DOI: 10.1038/s43705-023-00242-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/20/2023] [Accepted: 04/12/2023] [Indexed: 05/01/2023]
Abstract
Deep-sea hydrothermal vents are abundant on the ocean floor and play important roles in ocean biogeochemistry. In vent ecosystems such as hydrothermal plumes, microorganisms rely on reduced chemicals and gases in hydrothermal fluids to fuel primary production and form diverse and complex microbial communities. However, microbial interactions that drive these complex microbiomes remain poorly understood. Here, we use microbiomes from the Guaymas Basin hydrothermal system in the Pacific Ocean to shed more light on the key species in these communities and their interactions. We built metabolic models from metagenomically assembled genomes (MAGs) and infer possible metabolic exchanges and horizontal gene transfer (HGT) events within the community. We highlight possible archaea-archaea and archaea-bacteria interactions and their contributions to the robustness of the community. Cellobiose, D-Mannose 1-phosphate, O2, CO2, and H2S were among the most exchanged metabolites. These interactions enhanced the metabolic capabilities of the community by exchange of metabolites that cannot be produced by any other community member. Archaea from the DPANN group stood out as key microbes, benefiting significantly as acceptors in the community. Overall, our study provides key insights into the microbial interactions that drive community structure and organisation in complex hydrothermal plume microbiomes.
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Affiliation(s)
- Dinesh Kumar Kuppa Baskaran
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India
| | - Shreyansh Umale
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, India
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai, India.
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, India.
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India.
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8
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Molari M, Hassenrueck C, Laso-Pérez R, Wegener G, Offre P, Scilipoti S, Boetius A. A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes. Nat Microbiol 2023; 8:651-665. [PMID: 36894632 PMCID: PMC10066037 DOI: 10.1038/s41564-023-01342-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 02/10/2023] [Indexed: 03/11/2023]
Abstract
Members of the bacterial genus Sulfurimonas (phylum Campylobacterota) dominate microbial communities in marine redoxclines and are important for sulfur and nitrogen cycling. Here we used metagenomics and metabolic analyses to characterize a Sulfurimonas from the Gakkel Ridge in the Central Arctic Ocean and Southwest Indian Ridge, showing that this species is ubiquitous in non-buoyant hydrothermal plumes at Mid Ocean Ridges across the global ocean. One Sulfurimonas species, USulfurimonas pluma, was found to be globally abundant and active in cold (<0-4 °C), oxygen-saturated and hydrogen-rich hydrothermal plumes. Compared with other Sulfurimonas species, US. pluma has a reduced genome (>17%) and genomic signatures of an aerobic chemolithotrophic metabolism using hydrogen as an energy source, including acquisition of A2-type oxidase and loss of nitrate and nitrite reductases. The dominance and unique niche of US. pluma in hydrothermal plumes suggest an unappreciated biogeochemical role for Sulfurimonas in the deep ocean.
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Affiliation(s)
- Massimiliano Molari
- Max Planck Institute for Marine Microbiology, Bremen, Germany. .,Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
| | | | - Rafael Laso-Pérez
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Pierre Offre
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
| | - Stefano Scilipoti
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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9
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Disproportionation of Inorganic Sulfur Compounds by Mesophilic Chemolithoautotrophic Campylobacterota. mSystems 2023; 8:e0095422. [PMID: 36541763 PMCID: PMC9948710 DOI: 10.1128/msystems.00954-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The disproportionation of inorganic sulfur compounds could be widespread in natural habitats, and microorganisms could produce energy to support primary productivity through this catabolism. However, the microorganisms that carry this process out and the catabolic pathways at work remain relatively unstudied. Here, we investigated the bacterial diversity involved in sulfur disproportionation in hydrothermal plumes from Carlsberg Ridge in the northwestern Indian Ocean by enrichment cultures. A bacterial community analysis revealed that bacteria of the genera Sulfurimonas and Sulfurovum, belonging to the phylum Campylobacterota and previously having been characterized as chemolithoautotrophic sulfur oxidizers, were the most dominant members in six enrichment cultures. Subsequent bacterial isolation and physiological studies confirmed that five Sulfurimonas and Sulfurovum isolates could disproportionate thiosulfate and elemental sulfur. The ability to disproportionate sulfur was also demonstrated in several strains of Sulfurimonas and Sulfurovum that were isolated from hydrothermal vents or other natural environments. Dialysis membrane experiments showed that S0 disproportionation did not require the direct contact of cells with bulk sulfur. A comparative genomic analysis showed that Campylobacterota strains did not contain some genes of the Dsr and rDSR pathways (aprAB, dsrAB, dsrC, dsrMKJOP, and qmoABC) that are involved in sulfur disproportionation in some other taxa, suggesting the existence of an unrevealed catabolic pathway for sulfur disproportionation. These findings provide evidence for the catabolic versatility of these Campylobacterota genera, which are widely distributed in chemosynthetic environments, and expand our knowledge of the microbial taxa involved in this reaction of the biogeochemical sulfur cycle in hydrothermal vent environments. IMPORTANCE The phylum Campylobacterota, notably represented by the genera Sulfurimonas and Sulfurovum, is ubiquitous and predominant in deep-sea hydrothermal systems. It is well-known to be the major chemolithoautotrophic sulfur-oxidizing group in these habitats. Herein, we show that the mesophilic predominant chemolithoautotrophs of the genera Sulfurimonas and Sulfurovum could grow via sulfur disproportionation to gain energy. This is the first report of the chemolithoautotrophic disproportionation of thiosulfate and elemental sulfur within the genera Sulfurimonas and Sulfurovum, and this comes in addition to their already known role in the chemolithoautotrophic oxidation of sulfur compounds. Sulfur disproportionation via chemolithoautotrophic Campylobacterota may represent a previously unrecognized primary production process in hydrothermal vent ecosystems.
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10
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DePoy AN, King GM. Distribution and diversity of anaerobic thermophiles and putative anaerobic nickel-dependent carbon monoxide-oxidizing thermophiles in mesothermal soils and sediments. Front Microbiol 2023; 13:1096186. [PMID: 36699584 PMCID: PMC9868602 DOI: 10.3389/fmicb.2022.1096186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Even though thermophiles are best known from geothermal and other heated systems, numerous studies have demonstrated that they occur ubiquitously in mesothermal and permanently cold soils and sediments. Cultivation based studies of the latter have revealed that the thermophiles within them are mostly spore-forming members of the Firmicutes. Since the geographic distribution of spores is presumably unconstrained by transport through the atmosphere, similar communities (composition and diversity) of thermophiles might be expected to emerge in mesothermal habitats after they are heated. Alternatively, thermophiles might experience environmental selection before or after heating leading to divergent communities. After demonstrating the ubiquity of anaerobic thermophiles and CO uptake in a variety of mesothermal habitats and two hot springs, we used high throughput sequencing of 16S rRNA genes to assess the composition and diversity of populations that emerged after incubation at 60°C with or without headspace CO concentrations of 25%. Anaerobic Firmicutes dominated relative abundances at most sites but anaerobic thermophilic members of the Acidobacteria and Proteobacteria were also common. Nonetheless, compositions at the amplicon sequence variant (ASV) level varied among the sites with no convergence resulting from heating or CO addition as indicated by beta diversity analyses. The distinctions among thermophilic communities paralleled patterns observed for unheated "time zero" mesothermal soils and sediments. Occupancy analyses showed that the number of ASVs occupying each of n sites decreased unimodally with increasing n; no ASV occupied all 14 sites and only one each occupied 11 and 12 sites, while 69.3% of 1873 ASVs occupied just one site. Nonetheless, considerations of distances among the sites occupied by individual ASVs along with details of their distributions indicated that taxa were not dispersal limited but rather were constrained by environmental selection. This conclusion was supported by βMNTD and βNTI analyses, which showed dispersal limitation was only a minor contributor to taxon distributions.
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11
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Cheng R, Li X, Jiang L, Gong L, Geslin C, Shao Z. Virus diversity and interactions with hosts in deep-sea hydrothermal vents. MICROBIOME 2022; 10:235. [PMID: 36566239 PMCID: PMC9789665 DOI: 10.1186/s40168-022-01441-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The deep sea harbors many viruses, yet their diversity and interactions with hosts in hydrothermal ecosystems are largely unknown. Here, we analyzed the viral composition, distribution, host preference, and metabolic potential in different habitats of global hydrothermal vents, including vent plumes, background seawater, diffuse fluids, and sediments. RESULTS From 34 samples collected at eight vent sites, a total of 4662 viral populations (vOTUs) were recovered from the metagenome assemblies, encompassing diverse phylogenetic groups and defining many novel lineages. Apart from the abundant unclassified viruses, tailed phages are most predominant across the global hydrothermal vents, while single-stranded DNA viruses, including Microviridae and small eukaryotic viruses, also constitute a significant part of the viromes. As revealed by protein-sharing network analysis, hydrothermal vent viruses formed many novel genus-level viral clusters and are highly endemic to specific vent sites and habitat types. Only 11% of the vOTUs can be linked to hosts, which are the key microbial taxa of hydrothermal habitats, such as Gammaproteobacteria and Campylobacterota. Intriguingly, vent viromes share some common metabolic features in that they encode auxiliary genes that are extensively involved in the metabolism of carbohydrates, amino acids, cofactors, and vitamins. Specifically, in plume viruses, various auxiliary genes related to methane, nitrogen, and sulfur metabolism were observed, indicating their contribution to host energy conservation. Moreover, the prevalence of sulfur-relay pathway genes indicated the significant role of vent viruses in stabilizing the tRNA structure, which promotes host adaptation to steep environmental gradients. CONCLUSIONS The deep-sea hydrothermal systems hold untapped viral diversity with novelty. They may affect both vent prokaryotic and eukaryotic communities and modulate host metabolism related to vent adaptability. More explorations are needed to depict global vent virus diversity and its roles in this unique ecosystem. Video Abstract.
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Affiliation(s)
- Ruolin Cheng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resource, Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Xiaofeng Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Linfeng Gong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Claire Geslin
- Univ Brest, CNRS, IFREMER, IRP 1211 MicrobSea, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, IUEM, Rue Dumont d'Urville, F-29280, Plouzané, France
- Sino-French Laboratory of Deep-Sea Microbiology (MICROBSEA-LIA), Plouzané, France
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
- Sino-French Laboratory of Deep-Sea Microbiology (MICROBSEA-LIA), Plouzané, France.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China.
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12
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Targeted next generation sequencing of Cyclospora cayetanensis mitochondrial genomes from seeded fresh produce and other seeded food samples. Heliyon 2022; 8:e11575. [DOI: 10.1016/j.heliyon.2022.e11575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 08/17/2022] [Accepted: 11/08/2022] [Indexed: 11/14/2022] Open
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13
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Djebaili R, Mignini A, Vaccarelli I, Pellegrini M, Spera DM, Del Gallo M, D’Alessandro AM. Polyhydroxybutyrate-producing cyanobacteria from lampenflora: The case study of the “Stiffe” caves in Italy. Front Microbiol 2022; 13:933398. [PMID: 35966678 PMCID: PMC9366245 DOI: 10.3389/fmicb.2022.933398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/27/2022] [Indexed: 11/23/2022] Open
Abstract
This study aimed to estimate the green formation lampenflora of “Stiffe” caves in order to evaluate their suitability as an isolation source of cyanobacteria useful for the production of polyhydroxyalkanoates (PHAs). The cave system was chosen as the sampling site due to its touristic use and the presence of high-impact illuminations. The biofilms and the mats of the illuminated walls were sampled. Samples were investigated by 16S rRNA gene analysis and culturable cyanobacteria isolation. The isolated strains were then screened for the production of PHAs under typical culturing and nutritional starvation. Cultures were checked for PHA accumulation, poly-β-hydroxybutyrate (PHB) presence (infrared spectroscopy), and pigment production. The 16S rRNA gene metabarcoding. Highlighted a considerable extent of the pressure exerted by anthropogenic activities. However, the isolation yielded eleven cyanobacteria isolates with good PHA (mainly PHB)-producing abilities and interesting pigment production rates (chlorophyll a and carotenoids). Under normal conditions (BG110), the accumulation abilities ranged from 266 to 1,152 ng mg dry biomass–1. The optimization of bioprocesses through nutritional starvation resulted in a 2.5-fold increase. Fourier transform infrared (FTIR) studies established the occurrence of PHB within PHAs extracted by cyanobacteria isolates. The comparison of results with standard strains underlined good production rates. For C2 and C8 strains, PHA accumulation rates under starvation were higher than Azospirillum brasilense and similar to Synechocystis cf. salina 192. This study broadened the knowledge of the microbial communities of mats and biofilms on the lightened walls of the caves. These findings suggested that these structures, which are common in tourist caves, could be used to isolate valuable strains before remediation measures are adopted.
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Affiliation(s)
- Rihab Djebaili
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Amedeo Mignini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Ilaria Vaccarelli
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Marika Pellegrini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
- *Correspondence: Marika Pellegrini,
| | | | - Maddalena Del Gallo
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Anna Maria D’Alessandro
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
- Anna Maria D’Alessandro,
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14
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Wang Y, Bi HY, Chen HG, Zheng PF, Zhou YL, Li JT. Metagenomics Reveals Dominant Unusual Sulfur Oxidizers Inhabiting Active Hydrothermal Chimneys From the Southwest Indian Ridge. Front Microbiol 2022; 13:861795. [PMID: 35694283 PMCID: PMC9174799 DOI: 10.3389/fmicb.2022.861795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/12/2022] [Indexed: 11/25/2022] Open
Abstract
The deep-sea hydrothermal vents (DSHVs) in the Southwest Indian Ridge (SWIR) are formed by specific geological settings. However, the community structure and ecological function of the microbial inhabitants on the sulfide chimneys of active hydrothermal vents remain largely unknown. In this study, our analyses of 16S rRNA gene amplicons and 16S rRNA metagenomic reads showed the dominance of sulfur-oxidizing Ectothiorhodospiraceae, Thiomicrorhabdus, Sulfurimonas, and Sulfurovum on the wall of two active hydrothermal chimneys. Compared with the inactive hydrothermal sediments of SWIR, the active hydrothermal chimneys lacked sulfur-reducing bacteria. The metabolic potentials of the retrieved 82 metagenome-assembled genomes (MAGs) suggest that sulfur oxidation might be conducted by Thiohalomonadales (classified as Ectothiorhodospiraceae based on 16S rRNA gene amplicons), Sulfurovaceae, Hyphomicrobiaceae, Thiotrichaceae, Thiomicrospiraceae, and Rhodobacteraceae. For CO2 fixation, the Calvin-Benson-Bassham and reductive TCA pathways were employed by these bacteria. In Thiohalomonadales MAGs, we revealed putative phytochrome, carotenoid precursor, and squalene synthesis pathways, indicating a possible capacity of Thiohalomonadales in adaptation to dynamics redox conditions and the utilization of red light from the hot hydrothermal chimneys for photolithotrophic growth. This study, therefore, reveals unique microbiomes and their genomic features in the active hydrothermal chimneys of SWIR, which casts light on ecosystem establishment and development in hydrothermal fields and the deep biosphere.
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Affiliation(s)
- Yong Wang
- Institute for Marine Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- *Correspondence: Yong Wang,
| | - Hong-Yu Bi
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Hua-Guan Chen
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- College of Marine Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peng-Fei Zheng
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Ying-Li Zhou
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- College of Marine Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiang-Tao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
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15
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Breusing C, Genetti M, Russell SL, Corbett-Detig RB, Beinart RA. Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses. Proc Natl Acad Sci U S A 2022; 119:e2115608119. [PMID: 35349333 PMCID: PMC9168483 DOI: 10.1073/pnas.2115608119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 03/02/2022] [Indexed: 12/11/2022] Open
Abstract
SignificanceIn marine ecosystems, transmission of microbial symbionts between host generations occurs predominantly through the environment. Yet, it remains largely unknown how host genetics, symbiont competition, environmental conditions, and geography shape the composition of symbionts acquired by individual hosts. To address this question, we applied population genomic approaches to four species of deep-sea hydrothermal vent snails that live in association with chemosynthetic bacteria. Our analyses show that environment is more important to strain-level symbiont composition than host genetics and that symbiont strains show genetic variation indicative of adaptation to the distinct geochemical conditions at each vent site. This corroborates a long-standing hypothesis that hydrothermal vent invertebrates affiliate with locally adapted symbiont strains to cope with the variable conditions characterizing their habitats.
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Affiliation(s)
- Corinna Breusing
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882
| | - Maximilian Genetti
- Jack Baskin School of Engineering, University of California, Santa Cruz, CA 95064
| | - Shelbi L. Russell
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064
| | | | - Roxanne A. Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882
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16
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Gorlas A, Mariotte T, Morey L, Truong C, Bernard S, Guigner JM, Oberto J, Baudin F, Landrot G, Baya C, Le Pape P, Morin G, Forterre P, Guyot F. Precipitation of greigite and pyrite induced by Thermococcales: an advantage to live in Fe- and S-rich environments? Environ Microbiol 2022; 24:626-642. [PMID: 35102700 PMCID: PMC9306673 DOI: 10.1111/1462-2920.15915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/05/2022] [Accepted: 01/17/2022] [Indexed: 11/29/2022]
Abstract
Thermococcales, a major order of archaea inhabiting the iron- and sulfur-rich anaerobic parts of hydrothermal deep-sea vents, have been shown to rapidly produce abundant quantities of pyrite FeS2 in iron-sulfur-rich fluids at 85°C, suggesting that they may contribute to the formation of 'low temperature' FeS2 in their ecosystem. We show that this process operates in Thermococcus kodakarensis only when zero-valent sulfur is directly available as intracellular sulfur vesicles. Whether in the presence or absence of zero-valent sulfur, significant amounts of Fe3 S4 greigite nanocrystals are formed extracellularly. We also show that mineralization of iron sulfides induces massive cell mortality but that concomitantly with the formation of greigite and/or pyrite, a new generation of cells can grow. This phenomenon is observed for Fe concentrations of 5 mM but not higher suggesting that above a threshold in the iron pulse all cells are lysed. We hypothesize that iron sulfides precipitation on former cell materials might induce the release of nutrients in the mineralization medium further used by a fraction of surviving non-mineralized cells allowing production of new alive cells. This suggests that biologically induced mineralization of iron-sulfides could be part of a survival strategy employed by Thermococcales to cope with mineralizing high-temperature hydrothermal environments.
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Affiliation(s)
- A Gorlas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - T Mariotte
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - L Morey
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - C Truong
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 - CNRS, Sorbonne Université, Museum National d'Histoire Naturelle, Paris Cedex 05, 75252, France
| | - S Bernard
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 - CNRS, Sorbonne Université, Museum National d'Histoire Naturelle, Paris Cedex 05, 75252, France
| | - J-M Guigner
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 - CNRS, Sorbonne Université, Museum National d'Histoire Naturelle, Paris Cedex 05, 75252, France
| | - J Oberto
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - F Baudin
- Institut des Sciences de la Terre de Paris, UMR 7193 - Sorbonne Université - CNRS, Paris, 75005, France
| | - G Landrot
- Synchrotron SOLEIL - SAMBA beamline, Saint-Aubin, 91190, France
| | - C Baya
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 - CNRS, Sorbonne Université, Museum National d'Histoire Naturelle, Paris Cedex 05, 75252, France
| | - P Le Pape
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 - CNRS, Sorbonne Université, Museum National d'Histoire Naturelle, Paris Cedex 05, 75252, France
| | - G Morin
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 - CNRS, Sorbonne Université, Museum National d'Histoire Naturelle, Paris Cedex 05, 75252, France
| | - P Forterre
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - F Guyot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 - CNRS, Sorbonne Université, Museum National d'Histoire Naturelle, Paris Cedex 05, 75252, France.,Institut Universitaire de France (IUF), Paris, France
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17
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Pan J, Xu W, Zhou Z, Shao Z, Dong C, Liu L, Luo Z, Li M. Genome-resolved evidence for functionally redundant communities and novel nitrogen fixers in the deyin-1 hydrothermal field, Mid-Atlantic Ridge. MICROBIOME 2022; 10:8. [PMID: 35045876 PMCID: PMC8767757 DOI: 10.1186/s40168-021-01202-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/24/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Deep-sea hydrothermal vents represent unique ecosystems that redefine our understanding of the limits of life. They are widely distributed in deep oceans and typically form along mid-ocean ridges. To date, the hydrothermal systems in the Mid-Atlantic Ridge south of 14°S remain barely explored, limiting our understanding of the microbial community in this distinct ecosystem. The Deyin-1 is a newly discovered hydrothermal field in this area. By applying the metagenomic analysis, we aim at gaining much knowledge of the biodiversity and functional capability of microbial community inhabiting this field. RESULTS In the current study, 219 metagenomic assembled genomes (MAGs) were reconstructed, unveiling a diverse and variable community dominated by Bacteroidetes, Nitrospirae, Alpha-, Delta-, and Gammaproteobacteria in the active and inactive chimney samples as well as hydrothermal oxide samples. Most of these major taxa were potentially capable of using reduced sulfur and hydrogen as primary energy sources. Many members within the major taxa exhibited potentials of metabolic plasticity by possessing multiple energy metabolic pathways. Among these samples, different bacteria were found to be the major players of the same metabolic pathways, further supporting the variable and functionally redundant community in situ. In addition, a high proportion of MAGs harbored the genes of carbon fixation and extracellular carbohydrate-active enzymes, suggesting that both heterotrophic and autotrophic strategies could be essential for their survival. Notably, for the first time, the genus Candidatus Magnetobacterium was shown to potentially fix nitrogen, indicating its important role in the nitrogen cycle of inactive chimneys. Moreover, the metabolic plasticity of microbes, diverse and variable community composition, and functional redundancy of microbial communities may represent the adaptation strategies to the geochemically complex and fluctuating environmental conditions in deep-sea hydrothermal fields. CONCLUSIONS This represents the first assembled-genome-based investigation into the microbial community and metabolism of a hydrothermal field in the Mid-Atlantic Ridge south of 14°S. The findings revealed that a high proportion of microbes could benefit from simultaneous use of heterotrophic and autotrophic strategies in situ. It also presented novel members of potential diazotrophs and highlighted the metabolic plasticity and functional redundancy across deep-sea hydrothermal systems. Video abstract.
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Affiliation(s)
- Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Zhichao Zhou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Chunming Dong
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
| | - Lirui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Fujian Xiamen, People’s Republic of China
- School of Marine Sciences, Nanjing University of Information Science & Technology, 210044 Nanjing, People’s Republic of China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong People’s Republic of China
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18
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Cathalot C, Roussel EG, Perhirin A, Creff V, Donval JP, Guyader V, Roullet G, Gula J, Tamburini C, Garel M, Godfroy A, Sarradin PM. Hydrothermal plumes as hotspots for deep-ocean heterotrophic microbial biomass production. Nat Commun 2021; 12:6861. [PMID: 34824206 PMCID: PMC8617075 DOI: 10.1038/s41467-021-26877-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/19/2021] [Indexed: 11/09/2022] Open
Abstract
Carbon budgets of hydrothermal plumes result from the balance between carbon sinks through plume chemoautotrophic processes and carbon release via microbial respiration. However, the lack of comprehensive analysis of the metabolic processes and biomass production rates hinders an accurate estimate of their contribution to the deep ocean carbon cycle. Here, we use a biogeochemical model to estimate the autotrophic and heterotrophic production rates of microbial communities in hydrothermal plumes and validate it with in situ data. We show how substrate limitation might prevent net chemolithoautotrophic production in hydrothermal plumes. Elevated prokaryotic heterotrophic production rates (up to 0.9 gCm-2y-1) compared to the surrounding seawater could lead to 0.05 GtCy-1 of C-biomass produced through chemoorganotrophy within hydrothermal plumes, similar to the Particulate Organic Carbon (POC) export fluxes reported in the deep ocean. We conclude that hydrothermal plumes must be accounted for as significant deep sources of POC in ocean carbon budgets.
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Affiliation(s)
- Cécile Cathalot
- Laboratoire Cycles Géochimiques et ressources - LCG/GM/REM, Ifremer, Plouzané, France.
| | - Erwan G. Roussel
- grid.4825.b0000 0004 0641 9240Laboratoire de Microbiologie des Environnements Extrêmes – LMEE/EEP/REM, Ifremer, Plouzané, France
| | - Antoine Perhirin
- grid.4825.b0000 0004 0641 9240Laboratoire Environnement Profond – LEP/EEP/REM, IFREMER, Plouzané, France
| | - Vanessa Creff
- grid.4825.b0000 0004 0641 9240Laboratoire de Microbiologie des Environnements Extrêmes – LMEE/EEP/REM, Ifremer, Plouzané, France
| | - Jean-Pierre Donval
- grid.4825.b0000 0004 0641 9240Laboratoire Cycles Géochimiques et ressources – LCG/GM/REM, Ifremer, Plouzané, France
| | - Vivien Guyader
- grid.4825.b0000 0004 0641 9240Laboratoire Cycles Géochimiques et ressources – LCG/GM/REM, Ifremer, Plouzané, France
| | - Guillaume Roullet
- Univ Brest, CNRS, IRD, Ifremer, Laboratoire d’Océanographie Physique et Spatiale (LOPS), IUEM, Plouzané, France
| | - Jonathan Gula
- Univ Brest, CNRS, IRD, Ifremer, Laboratoire d’Océanographie Physique et Spatiale (LOPS), IUEM, Plouzané, France ,grid.440891.00000 0001 1931 4817Institut Universitaire de France (IUF), Paris, France
| | - Christian Tamburini
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110 Marseille, France
| | - Marc Garel
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM110 Marseille, France
| | - Anne Godfroy
- grid.4825.b0000 0004 0641 9240Laboratoire de Microbiologie des Environnements Extrêmes – LMEE/EEP/REM, Ifremer, Plouzané, France
| | - Pierre-Marie Sarradin
- grid.4825.b0000 0004 0641 9240Laboratoire Environnement Profond – LEP/EEP/REM, IFREMER, Plouzané, France
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19
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Yücel M, Sevgen S, Le Bris N. Soluble, Colloidal, and Particulate Iron Across the Hydrothermal Vent Mixing Zones in Broken Spur and Rainbow, Mid-Atlantic Ridge. Front Microbiol 2021; 12:631885. [PMID: 34777267 PMCID: PMC8586216 DOI: 10.3389/fmicb.2021.631885] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 09/30/2021] [Indexed: 11/23/2022] Open
Abstract
The slow-spreading Mid-Atlantic Ridge (MAR) forms geological heterogeneity throughout the ridge system by deep crustal faults and their resultant tectonic valleys, which results in the existence of different types of hydrothermal vent fields. Therefore, investigating MAR hydrothermal systems opens a gate to understanding the concentration ranges of ecosystem-limiting metals emanating from compositionally distinct fluids for both near-field chemosynthetic ecosystems and far-field transport into the ocean interiors. Here, we present novel data regarding onboard measured, size-fractionated soluble, colloidal, and particulate iron concentrations from the 2018 R/V L’Atalante – ROV Victor research expedition, during which samples were taken from the mixing zone of black smokers using a ROV-assisted plume sampling. Iron size fractionation (<20, 20–200, and >200nm) data were obtained from onboard sequential filtering, followed by measurement via ferrozine assay and spectrophotometric detection at 562nm. Our results showed the persistent presence of a nanoparticulate/colloidal phase (retained within 20–200nm filtrates) even in high-temperature samples. A significant fraction of this phase was retrievable only under treatment with HNO3 – a strong acid known to attack and dissolve pyrite nanocrystals. Upon mixing with colder bottom waters and removal of iron in the higher parts of the buoyant plume, the larger size fractions became dominant as the total iron levels decreased, but it was still possible to detect significant (micromolar) levels of nanoparticulate Fe even in samples collected 5m above the orifice in the rising plume. The coolest sample (<10°C) still contained more than 1μM of only nitric acid-leachable nanoparticle/colloidal, at least 200 times higher than a typical Fe concentration in the non-buoyant plume. Our results support previous reports of dissolved Fe in MAR vent plumes, and we propose that this recalcitrant Fe pool – surviving immediate precipitation – contributes to maintaining high hydrothermal iron fluxes to the deep ocean.
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Affiliation(s)
- Mustafa Yücel
- Institute of Marine Sciences, Middle East Technical University, Mersin, Turkey
| | - Serhat Sevgen
- Institute of Marine Sciences, Middle East Technical University, Mersin, Turkey
| | - Nadine Le Bris
- LECOB, SU-CNRS, Sorbonne Université, Banyuls-sur-Mer, France
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20
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Understanding the Impacts of Blue Economy Growth on Deep-Sea Ecosystem Services. SUSTAINABILITY 2021. [DOI: 10.3390/su132212478] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The deep sea is the vastest environment on Earth and provides many services and goods. Understanding the services and goods of deep-sea ecosystems would enable better resource governance and decision-making. In the present study, we reviewed and assessed deep-sea ecosystems services using the Ma conceptual framework, which incorporates ecosystems services and goods with human welfare. We also analyzed and measured the scientific production between 2012 and 2021 using the Dimension dataset. The bibliometric analysis showed a lack of studies related to deep-sea ecosystem services, which suggest the urgent need to overcome the existing knowledge gap regarding deep-sea components. However, the current knowledge revealed the crucial role that these ecosystems provide to the planet. Furthermore, we highlighted that there are common services and goods, and every ecosystem service feeds into another one. Developing actions and policies based on approaches that combine all deep-sea ecosystems services and goods are needed for the sustainable growth of the deep-sea economy in accordance with the United Nations Development Goal 14: Life Below Water.
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21
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Boeuf D, Eppley JM, Mende DR, Malmstrom RR, Woyke T, DeLong EF. Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage. MICROBIOME 2021; 9:172. [PMID: 34389059 PMCID: PMC8364033 DOI: 10.1186/s40168-021-01119-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/22/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Oceanic microbiomes play a pivotal role in the global carbon cycle and are central to the transformation and recycling of carbon and energy in the ocean's interior. SAR324 is a ubiquitous but poorly understood uncultivated clade of Deltaproteobacteria that inhabits the entire water column, from ocean surface waters to its deep interior. Although some progress has been made in elucidating potential metabolic traits of SAR324 in the dark ocean, very little is known about the ecology and the metabolic capabilities of this group in the euphotic and twilight zones. To investigate the comparative genomics, ecology, and physiological potential of the SAR324 clade, we examined the distribution and variability of key genomic features and metabolic pathways in this group from surface waters to the abyss in the North Pacific Subtropical Gyre, one of the largest biomes on Earth. RESULTS We leveraged a pangenomic ecological approach, combining spatio-temporally resolved single-amplified genome, metagenomic, and metatranscriptomic datasets. The data revealed substantial genomic diversity throughout the SAR324 clade, with distinct depth and temporal distributions that clearly differentiated ecotypes. Phylogenomic subclade delineation, environmental distributions, genomic feature similarities, and metabolic capacities revealed strong congruence. The four SAR324 ecotypes delineated in this study revealed striking divergence from one another with respect to their habitat-specific metabolic potentials. The ecotypes living in the dark or twilight oceans shared genomic features and metabolic capabilities consistent with a sulfur-based chemolithoautotrophic lifestyle. In contrast, those inhabiting the sunlit ocean displayed higher plasticity energy-related metabolic pathways, supporting a presumptive photoheterotrophic lifestyle. In epipelagic SAR324 ecotypes, we observed the presence of two types of proton-pumping rhodopsins, as well as genomic, transcriptomic, and ecological evidence for active photoheterotrophy, based on xanthorhodopsin-like light-harvesting proteins. CONCLUSIONS Combining pangenomic and both metagenomic and metatranscriptomic profiling revealed a striking divergence in the vertical distribution, genomic composition, metabolic potential, and predicted lifestyle strategies of geographically co-located members of the SAR324 bacterial clade. The results highlight the utility of metapangenomic approaches employed across environmental gradients, to decipher the properties and variation in function and ecological traits of specific phylogenetic clades within complex microbiomes. Video abstract.
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Affiliation(s)
- Dominique Boeuf
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI 96822 USA
| | - John M. Eppley
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI 96822 USA
| | - Daniel R. Mende
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI 96822 USA
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA 94720 USA
| | - Edward F. DeLong
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI 96822 USA
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22
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Ma L, Wang WX. Subcellular metal distribution in two deep-sea mollusks: Insight of metal adaptation and detoxification near hydrothermal vents. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 266:115303. [PMID: 32836047 DOI: 10.1016/j.envpol.2020.115303] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/03/2020] [Accepted: 07/25/2020] [Indexed: 06/11/2023]
Abstract
In this study, we determined the concentrations of Cu, Zn, Ni, Cd, Pb and As and their subcellular distributions within the tissues of mussels (Bathymodiolus marisindicus) and snails (Gigantopelta aegis) from two hydrothermal vent regions, i.e., Tiancheng and Longqi, at Southwest Indian Ridge. Mussels collected from the two venting regions showed comparable concentrations for Ni and Pb, but Cu, Zn, Cd and As concentrations were significantly different in mussel gills between the two vent regions. Similar ranges of metal concentrations were found in the snails as those in the mussels, but most of the metals were mainly accumulated in the viscera, except for Ni. Similar subcellular partitioning of Cu, Zn and Cd was documented in different mussel tissues, with cellular debris (50%) being the predominant fraction, followed by equivalent values in other fractions. Lead was distributed in both cellular debris and metal-rich granules (MRG) fraction, whereas Ni was predominantly distributed in MRG (90%). Arsenic was mainly partitioned in cellular debris and metallothionein-like protein. However, deep-sea snails displayed elevated subcellular partitioning of Cu in the organelles (up to 60%) and may be more susceptible to Cu stress than the mussels. Our results demonstrated the metal-specificity of detoxification strategies in these deep-sea hydrothermal vent mollusks, and the mussels may be more adaptable to high metal exposures than the snails at hydrothermal vent.
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Affiliation(s)
- Lan Ma
- School of Energy and Environment, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), City University of Hong Kong, Kowloon, Hong Kong; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China
| | - Wen-Xiong Wang
- School of Energy and Environment, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), City University of Hong Kong, Kowloon, Hong Kong; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China.
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23
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Zambare NM, Naser NY, Gerlach R, Chang CB. Mineralogy of microbially induced calcium carbonate precipitates formed using single cell drop-based microfluidics. Sci Rep 2020; 10:17535. [PMID: 33067478 PMCID: PMC7568533 DOI: 10.1038/s41598-020-73870-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/21/2020] [Indexed: 11/28/2022] Open
Abstract
Microbe-mineral interactions are ubiquitous and can facilitate major biogeochemical reactions that drive dynamic Earth processes such as rock formation. One example is microbially induced calcium carbonate precipitation (MICP) in which microbial activity leads to the formation of calcium carbonate precipitates. A majority of MICP studies have been conducted at the mesoscale but fundamental questions persist regarding the mechanisms of cell encapsulation and mineral polymorphism. Here, we are the first to investigate and characterize precipitates on the microscale formed by MICP starting from single ureolytic E. coli MJK2 cells in 25 µm diameter drops. Mineral precipitation was observed over time and cells surrounded by calcium carbonate precipitates were observed under hydrated conditions. Using Raman microspectroscopy, amorphous calcium carbonate (ACC) was observed first in the drops, followed by vaterite formation. ACC and vaterite remained stable for up to 4 days, possibly due to the presence of organics. The vaterite precipitates exhibited a dense interior structure with a grainy exterior when examined using electron microscopy. Autofluorescence of these precipitates was observed possibly indicating the development of a calcite phase. The developed approach provides an avenue for future investigations surrounding fundamental processes such as precipitate nucleation on bacteria, microbe-mineral interactions, and polymorph transitions.
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Affiliation(s)
- Neerja M Zambare
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
| | - Nada Y Naser
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Robin Gerlach
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
| | - Connie B Chang
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
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24
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Zhou Z, Liu Y, Pan J, Cron BR, Toner BM, Anantharaman K, Breier JA, Dick GJ, Li M. Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes. ISME JOURNAL 2020; 14:3136-3148. [PMID: 32820229 DOI: 10.1038/s41396-020-00745-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 08/03/2020] [Accepted: 08/10/2020] [Indexed: 11/09/2022]
Abstract
Deep-sea hydrothermal plumes are considered natural laboratories for understanding ecological and biogeochemical interactions. Previous studies focused on interactions between microorganisms and inorganic, reduced hydrothermal inputs including sulfur, hydrogen, iron, and manganese. However, little is known about transformations of organic compounds, especially methylated, sulfur-containing compounds, and petroleum hydrocarbons. Here, we reconstructed nine gammaproteobacterial metagenome-assembled genomes, affiliated with Methylococcales, Methylophaga, and Cycloclasticus, from three hydrothermal ecosystems. We present evidence that these three groups have high transcriptional activities of genes encoding cycling of C1-compounds, petroleum hydrocarbons, and organic sulfur in hydrothermal plumes. This includes oxidation of methanethiol, the simplest thermochemically-derived organic sulfur, for energy metabolism in Methylococcales and Cycloclasticus. Together with active transcription of genes for thiosulfate and methane oxidation in Methylococcales, these results suggest an adaptive strategy of versatile and simultaneous use of multiple available electron donors. Meanwhile, the first near-complete MAG of hydrothermal Methylophaga aminisulfidivorans and its transcriptional profile point to active chemotaxis targeting small organic compounds. Petroleum hydrocarbon-degrading Cycloclasticus are abundant and active in plumes of oil spills as well as deep-sea vents, suggesting that they are indigenous and effectively respond to stimulus of hydrocarbons in the deep sea. These findings suggest that these three groups of Gammaproteobacteria transform organic carbon and sulfur compounds via versatile and opportunistic metabolism and modulate biogeochemistry in plumes of hydrothermal systems as well as oil spills, thus contributing broad ecological impact to the deep ocean globally.
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Affiliation(s)
- Zhichao Zhou
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yang Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Brandi R Cron
- Department of Earth and Environmental Sciences, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA
| | - Brandy M Toner
- Department of Earth and Environmental Sciences, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA.,Department of Soil, Water, and Climate, University of Minnesota Twin Cities, St. Paul, MN, 55108, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John A Breier
- School of Earth, Environmental, and Marine Sciences, The University of Texas Rio Grande Valley, Edinburg, TX, 78539, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
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25
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Zhou Z, Tran PQ, Kieft K, Anantharaman K. Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation. ISME JOURNAL 2020; 14:2060-2077. [PMID: 32393808 PMCID: PMC7367891 DOI: 10.1038/s41396-020-0669-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/15/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022]
Abstract
Proteobacteria constitute one of the most diverse and abundant groups of microbes on Earth. In productive marine environments like deep-sea hydrothermal systems, Proteobacteria are implicated in autotrophy coupled to sulfur, methane, and hydrogen oxidation, sulfate reduction, and denitrification. Beyond chemoautotrophy, little is known about the ecological significance of poorly studied Proteobacteria lineages that are globally distributed and active in hydrothermal systems. Here we apply multi-omics to characterize 51 metagenome-assembled genomes from three hydrothermal vent plumes in the Pacific and Atlantic Oceans that are affiliated with nine Proteobacteria lineages. Metabolic analyses revealed these organisms to contain a diverse functional repertoire including chemolithotrophic ability to utilize sulfur and C1 compounds, and chemoorganotrophic ability to utilize environment-derived fatty acids, aromatics, carbohydrates, and peptides. Comparative genomics with marine and terrestrial microbiomes suggests that lineage-associated functional traits could explain niche specificity. Our results shed light on the ecological functions and metabolic strategies of novel Proteobacteria in hydrothermal systems and beyond, and highlight the relationship between genome diversification and environmental adaptation.
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Affiliation(s)
- Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Patricia Q Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Kristopher Kieft
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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26
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The oxidation of hydrocarbons by diverse heterotrophic and mixotrophic bacteria that inhabit deep-sea hydrothermal ecosystems. ISME JOURNAL 2020; 14:1994-2006. [PMID: 32355200 PMCID: PMC7368058 DOI: 10.1038/s41396-020-0662-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/24/2020] [Accepted: 04/15/2020] [Indexed: 11/08/2022]
Abstract
Hydrothermal activity can generate numerous and diverse hydrocarbon compounds. However, little is known about the influence of such hydrocarbons on deep-sea hydrothermal microbial ecology. We hypothesize that certain bacteria live on these hydrocarbons. Therefore, in this study, the distribution of hydrocarbons and their associated hydrocarbon-degrading bacteria were investigated at deep-sea hydrothermal vents at the Southern Mid-Atlantic Ridge, the Southwest Indian Ridge, and the East Pacific Rise. A variety of hydrocarbon-degrading consortia were obtained from hydrothermal samples collected at the aforementioned sites after low-temperature enrichment under high hydrostatic pressures, and the bacteria responsible for the degradation of hydrocarbons were investigated by DNA-based stable-isotope probing with uniformly 13C-labeled hydrocarbons. Unusually, we identified several previously recognized sulfur-oxidizing chemoautotrophs as hydrocarbon-degrading bacteria, e.g., the SAR324 group, the SUP05 clade, and Sulfurimonas, and for the first time confirmed their ability to degrade hydrocarbons. In addition, Erythrobacter, Pusillimonas, and SAR202 clade were shown to degrade polycyclic aromatic hydrocarbons for the first time. These results together with relatively high abundance in situ of most of the above-described bacteria highlight the potential influence of hydrocarbons in configuring the vent microbial community, and have made the importance of mixotrophs in hydrothermal vent ecosystems evident.
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27
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Dick GJ. The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally. Nat Rev Microbiol 2020; 17:271-283. [PMID: 30867583 DOI: 10.1038/s41579-019-0160-2] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The discovery of chemosynthetic ecosystems at deep-sea hydrothermal vents in 1977 changed our view of biology. Chemosynthetic bacteria and archaea form the foundation of vent ecosystems by exploiting the chemical disequilibrium between reducing hydrothermal fluids and oxidizing seawater, harnessing this energy to fix inorganic carbon into biomass. Recent research has uncovered fundamental aspects of these microbial communities, including their relationships with underlying geology and hydrothermal geochemistry, interactions with animals via symbiosis and distribution both locally in various habitats within vent fields and globally across hydrothermal systems in diverse settings. Although 'black smokers' and symbioses between microorganisms and macrofauna attract much attention owing to their novelty and the insights they provide into life under extreme conditions, habitats such as regions of diffuse flow, subseafloor aquifers and hydrothermal plumes have important roles in the global cycling of elements through hydrothermal systems. Owing to sharp contrasts in physical and chemical conditions between these various habitats and their dynamic, extreme and geographically isolated nature, hydrothermal vents provide a valuable window into the environmental and ecological forces that shape microbial communities and insights into the limits, origins and evolution of microbial life.
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Affiliation(s)
- Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA.
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28
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Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment. mSystems 2020; 5:5/1/e00795-19. [PMID: 31911466 PMCID: PMC6946796 DOI: 10.1128/msystems.00795-19] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Hydrothermal vents release reduced compounds and small organic carbon compounds into the surrounding seawater, providing essential substrates for microbial growth and bioenergy transformations. Despite the wide distribution of the marine benthic group E archaea (referred to as Hydrothermarchaeota) in the hydrothermal environment, little is known about their genomic repertoires and biogeochemical significance. Here, we studied four highly complete (>80%) metagenome-assembled genomes (MAGs) from a black smoker chimney and the surrounding sulfur-rich sediments on the South Atlantic Mid-Ocean Ridge and publicly available data sets (the Integrated Microbial Genomes system of the U.S. Department of Energy-Joint Genome Institute and NCBI SRA data sets). Genomic analysis suggested a wide carbon metabolic diversity of Hydrothermarchaeota members, including the utilization of proteins, lactate, and acetate; the anaerobic degradation of aromatics; the oxidation of C1 compounds (CO, formate, and formaldehyde); the utilization of methyl compounds; CO2 incorporation by the tetrahydromethanopterin-based Wood-Ljungdahl pathway; and participation in the type III ribulose-1,5-bisphosphate carboxylase/oxygenase-based Calvin-Benson-Bassham cycle. These microbes also potentially oxidize sulfur, arsenic, and hydrogen and engage in anaerobic respiration based on sulfate reduction and denitrification. Among the 140 MAGs reconstructed from the black smoker chimney microbial community (including Hydrothermarchaeota MAGs), community-level metabolic predictions suggested a redundancy of carbon utilization and element cycling functions and interactive syntrophic and sequential utilization of substrates. These processes might make various carbon and energy sources widely accessible to the microorganisms. Further, the analysis suggested that Hydrothermarchaeota members contained important functional components obtained from the community via lateral gene transfer, becoming a distinctive clade. This might serve as a niche-adaptive strategy for metabolizing heavy metals, C1 compounds, and reduced sulfur compounds. Collectively, the analysis provides comprehensive metabolic insights into the Hydrothermarchaeota IMPORTANCE This study provides comprehensive metabolic insights into the Hydrothermarchaeota from comparative genomics, evolution, and community-level perspectives. Members of the Hydrothermarchaeota synergistically participate in a wide range of carbon-utilizing and element cycling processes with other microorganisms in the community. We expand the current understanding of community interactions within the hydrothermal sediment and chimney, suggesting that microbial interactions based on sequential substrate metabolism are essential to nutrient and element cycling.
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29
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Pillot G, Davidson S, Auria R, Combet-Blanc Y, Godfroy A, Liebgott PP. Production of Current by Syntrophy Between Exoelectrogenic and Fermentative Hyperthermophilic Microorganisms in Heterotrophic Biofilm from a Deep-Sea Hydrothermal Chimney. MICROBIAL ECOLOGY 2020; 79:38-49. [PMID: 31079197 DOI: 10.1007/s00248-019-01381-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
To study the role of exoelectrogens within the trophic network of deep-sea hydrothermal vents, we performed successive subcultures of a hyperthermophilic community from a hydrothermal chimney sample on a mix of electron donors in a microbial fuel cell system. Electrode (the electron acceptor) was swapped every week to enable fresh development from spent media as inoculum. The MFC at 80 °C yielded maximum current production increasing from 159 to 247 mA m-2 over the subcultures. The experiments demonstrated direct production of electric current from acetate, pyruvate, and H2 and indirect production from yeast extract and peptone through the production of H2 and acetate from fermentation. The microorganisms found in on-electrode communities were mainly affiliated to exoelectrogenic Archaeoglobales and Thermococcales species, whereas in liquid media, the communities were mainly affiliated to fermentative Bacillales and Thermococcales species. The work shows interactions between fermentative microorganisms degrading complex organic matter into fermentation products that are then used by exoelectrogenic microorganisms oxidizing these reduced compounds while respiring on a conductive support. The results confirmed that with carbon cycling, the syntrophic relations between fermentative microorganisms and exoelectrogens could enable some microbes to survive as biofilm in extremely unstable conditions. Graphical Abstract Schematic representation of cross-feeding between fermentative and exoelectrogenic microbes on the surface of the conductive support. B, Bacillus/Geobacillus spp.; Tc, Thermococcales; Gg, Geoglobus spp.; Py, pyruvate; Ac, acetate.
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Affiliation(s)
- Guillaume Pillot
- Aix-Marseille Université, IRD, CNRS, MIO, UM110, Marseille, France
- Université du Sud Toulon-Var, IRD, CNRS, MIO, UM 110, La Garde, France
| | - Sylvain Davidson
- Aix-Marseille Université, IRD, CNRS, MIO, UM110, Marseille, France
- Université du Sud Toulon-Var, IRD, CNRS, MIO, UM 110, La Garde, France
| | - Richard Auria
- Aix-Marseille Université, IRD, CNRS, MIO, UM110, Marseille, France
- Université du Sud Toulon-Var, IRD, CNRS, MIO, UM 110, La Garde, France
| | - Yannick Combet-Blanc
- Aix-Marseille Université, IRD, CNRS, MIO, UM110, Marseille, France
- Université du Sud Toulon-Var, IRD, CNRS, MIO, UM 110, La Garde, France
| | - Anne Godfroy
- IFREMER, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes - UMR6197, Ifremer, Université de Bretagne Occidentale, Centre de Brest, CS10070, Plouzané, France
| | - Pierre-Pol Liebgott
- Aix-Marseille Université, IRD, CNRS, MIO, UM110, Marseille, France.
- Université du Sud Toulon-Var, IRD, CNRS, MIO, UM 110, La Garde, France.
- Campus de Luminy, Bâtiment OCEANOMED, Mediterranean Institute of Oceanography, 13288, Marseille Cedex 09, France.
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30
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Zhao Y, Chen C, Gu HJ, Zhang J, Sun L. Characterization of the Genome Feature and Toxic Capacity of a Bacillus wiedmannii Isolate From the Hydrothermal Field in Okinawa Trough. Front Cell Infect Microbiol 2019; 9:370. [PMID: 31750261 PMCID: PMC6842932 DOI: 10.3389/fcimb.2019.00370] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 10/10/2019] [Indexed: 11/13/2022] Open
Abstract
The Bacillus cereus group is frequently isolated from soil, plants, food, and other environments. In this study, we report the first isolation and characterization of a B. cereus group member, Bacillus wiedmannii SR52, from the hydrothermal field in the Iheya Ridge of Okinawa Trough. SR52 was isolated from the gills of shrimp Alvinocaris longirostris, an invertebrate species found abundantly in the ecosystems of the hydrothermal vents, and is most closely related to B. wiedmannii FSL W8-0169. SR52 is aerobic, motile, and able to form endospores. SR52 can grow in NaCl concentrations up to 9%. SR52 has a circular chromosome of 5,448,361 bp and a plasmid of 137,592 bp, encoding 5,709 and 189 genes, respectively. The chromosome contains 297 putative virulence genes, including those encoding enterotoxins and hemolysins. Fourteen rRNA operons, 107 tRNAs, and 5 sRNAs are present in the chromosome, and 7 tRNAs are present in the plasmid. SR52 possesses 13 genomic islands (GIs), all on the chromosome. Comparing to FSL W8-0169, SR52 exhibits several streaking features in its genome, notably an exceedingly large number of non-coding RNAs and GIs. In vivo studies showed that following intramuscular injection into fish, SR52 was able to disseminate in tissues and cause mortality; when inoculated into mice, SR52 induced acute mortality and disseminated transiently in tissues. In vitro studies showed that SR52 possessed hemolytic activity, and the extracellular product of SR52 exhibited a strong cytotoxic effect. These results provided the first insight into the cytotoxicity and genomic feature of B. wiedmannii from the deep-sea hydrothermal environment.
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Affiliation(s)
- Yan Zhao
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chen Chen
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Han-Jie Gu
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Zhang
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.,Deep Sea Research Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
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31
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Orellana-Saez M, Pacheco N, Costa JI, Mendez KN, Miossec MJ, Meneses C, Castro-Nallar E, Marcoleta AE, Poblete-Castro I. In-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological Potential. Front Microbiol 2019; 10:1154. [PMID: 31178851 PMCID: PMC6543543 DOI: 10.3389/fmicb.2019.01154] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/07/2019] [Indexed: 12/12/2022] Open
Abstract
We obtained the complete genome sequence of the psychrotolerant extremophile Pseudomonas sp. MPC6, a natural Polyhydroxyalkanoates (PHAs) producing bacterium able to rapidly grow at low temperatures. Genomic and phenotypic analyses allowed us to situate this isolate inside the Pseudomonas fluorescens phylogroup of pseudomonads as well as to reveal its metabolic versatility and plasticity. The isolate possesses the gene machinery for metabolizing a variety of toxic aromatic compounds such as toluene, phenol, chloroaromatics, and TNT. In addition, it can use both C6- and C5-carbon sugars like xylose and arabinose as carbon substrates, an uncommon feature for bacteria of this genus. Furthermore, Pseudomonas sp. MPC6 exhibits a high-copy number of genes encoding for enzymes involved in oxidative and cold-stress response that allows it to cope with high concentrations of heavy metals (As, Cd, Cu) and low temperatures, a finding that was further validated experimentally. We then assessed the growth performance of MPC6 on glycerol using a temperature range from 0 to 45°C, the latter temperature corresponding to the limit at which this Antarctic isolate was no longer able to propagate. On the other hand, the MPC6 genome comprised considerably less virulence and drug resistance factors as compared to pathogenic Pseudomonas strains, thus supporting its safety. Unexpectedly, we found five PHA synthases within the genome of MPC6, one of which clustered separately from the other four. This PHA synthase shared only 40% sequence identity at the amino acid level against the only PHA polymerase described for Pseudomonas (63-1 strain) able to produce copolymers of short- and medium-chain length PHAs. Batch cultures for PHA synthesis in Pseudomonas sp. MPC6 using sugars, decanoate, ethylene glycol, and organic acids as carbon substrates result in biopolymers with different monomer compositions. This indicates that the PHA synthases play a critical role in defining not only the final chemical structure of the biosynthesized PHA, but also the employed biosynthetic pathways. Based on the results obtained, we conclude that Pseudomonas sp. MPC6 can be exploited as a bioremediator and biopolymer factory, as well as a model strain to unveil molecular mechanisms behind adaptation to cold and extreme environments.
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Affiliation(s)
- Matias Orellana-Saez
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Nicolas Pacheco
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - José I Costa
- Integrative Microbiology Group, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Katterinne N Mendez
- Center for Bioinformatics and Integrative Biology, Faculty of Life Science, Universidad Andres Bello, Santiago, Chile
| | - Matthieu J Miossec
- Computational Genomics Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Science, Universidad Andres Bello, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,FONDAP Center for Genome Regulation, Santiago, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Faculty of Life Science, Universidad Andres Bello, Santiago, Chile
| | - Andrés E Marcoleta
- Integrative Microbiology Group, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ignacio Poblete-Castro
- Biosystems Engineering Laboratory, Center for Bioinformatics and Integrative Biology, Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
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32
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Dutta A, Peoples LM, Gupta A, Bartlett DH, Sar P. Exploring the piezotolerant/piezophilic microbial community and genomic basis of piezotolerance within the deep subsurface Deccan traps. Extremophiles 2019; 23:421-433. [PMID: 31049708 DOI: 10.1007/s00792-019-01094-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/23/2019] [Indexed: 01/22/2023]
Abstract
The deep biosphere is often characterized by multiple extreme physical-chemical conditions, of which pressure is an important parameter that influences life but remains less studied. This geomicrobiology study was designed to understand the response of a subterranean microbial community of the Deccan traps to high-pressure conditions and to elucidate their genomic properties. Groundwater from a deep basaltic aquifer of the Deccan traps was used to ascertain the community response to 25 MPa and 50 MPa pressure following enrichment in high-salt and low-salt organic media. Quantitative PCR data indicated a decrease in bacterial and archaeal cell numbers with increasing pressure. 16S rRNA gene sequencing displayed substantial changes in the microbial community in which Acidovorax appeared to be the most dominant genus in the low-salt medium and Microbacteriaceae emerged as the major family in the high-salt medium under both pressure conditions. Genes present in metagenome-associated genomes which have previously been associated with piezotolerance include those related to nutrient uptake and extracytoplasmic stress (omp, rseC), protein folding and unfolding (dnaK, groEL and others), and DNA repair mechanisms (mutT, uvr and others). We hypothesize that these genes facilitate tolerance to high pressure by certain groups of microbes residing in subsurface Deccan traps.
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Affiliation(s)
- Avishek Dutta
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.,School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Logan M Peoples
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, San Diego, CA, 92093, USA
| | - Abhishek Gupta
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, San Diego, CA, 92093, USA
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
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Castelán-Sánchez HG, Lopéz-Rosas I, García-Suastegui WA, Peralta R, Dobson ADW, Batista-García RA, Dávila-Ramos S. Extremophile deep-sea viral communities from hydrothermal vents: Structural and functional analysis. Mar Genomics 2019; 46:16-28. [PMID: 30857856 DOI: 10.1016/j.margen.2019.03.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/25/2019] [Accepted: 03/01/2019] [Indexed: 12/29/2022]
Abstract
Ten publicly available metagenomic data sets from hydrothermal vents were analyzed to determine the taxonomic structure of the viral communities present, as well as their potential metabolic functions. The type of natural selection on two auxiliary metabolic genes was also analyzed. The structure of the virome in the hydrothermal vents was quite different in comparison with the viruses present in sediments, with specific populations being present in greater abundance in the plume samples when compared with the sediment samples. ssDNA genomes such as Circoviridae and Microviridae were predominantly present in the sediment samples, with Caudovirales which are dsDNA being present in the vent samples. Genes potentially encoding enzymes that participate in carbon, nitrogen and sulfur metabolic pathways were found in greater abundance, than those involved in the oxygen cycle, in the hydrothermal vents. Functional profiling of the viromes, resulted in the discovery of genes encoding proteins involved in bacteriophage capsids, DNA synthesis, nucleotide synthesis, DNA repair, as well as viral auxiliary metabolic genes such as cytitidyltransferase and ribonucleotide reductase. These auxiliary metabolic genes participate in the synthesis of phospholipids and nucleotides respectively and are likely to contribute to enhancing the fitness of their bacterial hosts within the hydrothermal vent communities. Finally, evolutionary analysis suggested that these auxiliary metabolic genes are highly conserved and evolve under purifying selection, and are thus maintained in their genome.
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Affiliation(s)
- Hugo G Castelán-Sánchez
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa. Cuernavca, Morelos. C.P, Cuernavaca 62209, Mexico
| | - Itzel Lopéz-Rosas
- CONACyT Research fellow-Colegio de Postgraduados Campus Campeche, Carretera Haltunchén - Edzná Km 17.5. Colonia Sihochac. Champotón, Campeche 24450, Mexico
| | - Wendy A García-Suastegui
- Laboratorio de Toxicología Molecular, Departamento de Biología y Toxicología de la Reproducción, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla C.P., 72570, Mexico
| | - Raúl Peralta
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa. Cuernavca, Morelos. C.P, Cuernavaca 62209, Mexico
| | - Alan D W Dobson
- School of Microbiology, University College Cork. Cork, Ireland; Environmental Research Institute, University College, Cork, Ireland
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa. Cuernavca, Morelos. C.P, Cuernavaca 62209, Mexico
| | - Sonia Dávila-Ramos
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa. Cuernavca, Morelos. C.P, Cuernavaca 62209, Mexico.
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Abstract
Gaseous oxygen is essential for all aerobic animals, without which mitochondrial respiration and oxidative phosphorylation cannot take place. It is not, however, regarded as a "nutrient" by nutritionists and does not feature as such within the discipline of nutritional science. This is primarily a consequence of the route by which O2 enters the body, which is via the nose and lungs in terrestrial animals as opposed to the mouth and gastrointestinal tract for what are customarily considered as nutrients. It is argued that the route of entry should not be the critical factor in defining whether a substance is, or is not, a nutrient. Indeed, O2 unambiguously meets the standard dictionary definitions of a nutrient, such as "a substance that provides nourishment for the maintenance of life and for growth" (Oxford English Dictionary). O2 is generally available in abundance, but deficiency occurs at high altitude and during deep sea dives, as well as in lung diseases. These impact on the provision at a whole-body level, but a low pO2 is characteristic of specific tissues includings the retina and brain, while deficiency, or overt hypoxia, is evident in certain conditions such as ischaemic disease and in tumours - and in white adipose tissue in obesity. Hypoxia results in a switch from oxidative metabolism to increased glucose utilisation through anaerobic glycolysis, and there are extensive changes in the expression of multiple genes in O2-deficient cells. These changes are driven by hypoxia-sensitive transcription factors, particularly hypoxia-inducible factor-1 (HIF-1). O2 deficiency at a whole-body level can be treated by therapy or supplementation, but O2 is also toxic through the generation of reactive oxygen species. It is concluded that O2 is a critical, but overlooked, nutrient which should be considered as part of the landscape of nutritional science.
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Affiliation(s)
- Paul Trayhurn
- Clore Laboratory, University of Buckingham, Buckingham, United Kingdom.,Obesity Biology Unit, University of Liverpool, Liverpool, United Kingdom
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Dang H, Klotz MG, Lovell CR, Sievert SM. Editorial: The Responses of Marine Microorganisms, Communities and Ecofunctions to Environmental Gradients. Front Microbiol 2019; 10:115. [PMID: 30800101 PMCID: PMC6375845 DOI: 10.3389/fmicb.2019.00115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 01/18/2019] [Indexed: 12/16/2022] Open
Affiliation(s)
- Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Martin G Klotz
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, and College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,School of Molecular Biosciences, Washington State University, Richland, WA, United States
| | - Charles R Lovell
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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36
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Nesbø CL, Charchuk R, Pollo SMJ, Budwill K, Kublanov IV, Haverkamp THA, Foght J. Genomic analysis of the mesophilic Thermotogae genusMesotogareveals phylogeographic structure and genomic determinants of its distinct metabolism. Environ Microbiol 2018; 21:456-470. [DOI: 10.1111/1462-2920.14477] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/15/2018] [Accepted: 11/06/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Camilla L. Nesbø
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
- BioZone, Department of Chemical Engineering and Applied Chemistry; Wallberg Building, University of Toronto; Toronto ON Canada
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences; University of Oslo; Blindern, Oslo Norway
| | - Rhianna Charchuk
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
| | - Stephen M. J. Pollo
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
| | | | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology; Russian Academy of Sciences; Moscow Russia
| | - Thomas H. A. Haverkamp
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences; University of Oslo; Blindern, Oslo Norway
- Norwegian Veterinary Institute; Oslo Norway
| | - Julia Foght
- Department of Biological Sciences; University of Alberta; Edmonton AB Canada
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Cerqueira T, Barroso C, Froufe H, Egas C, Bettencourt R. Metagenomic Signatures of Microbial Communities in Deep-Sea Hydrothermal Sediments of Azores Vent Fields. MICROBIAL ECOLOGY 2018; 76:387-403. [PMID: 29354879 DOI: 10.1007/s00248-018-1144-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/02/2018] [Indexed: 05/25/2023]
Abstract
The organisms inhabiting the deep-seafloor are known to play a crucial role in global biogeochemical cycles. Chemolithoautotrophic prokaryotes, which produce biomass from single carbon molecules, constitute the primary source of nutrition for the higher organisms, being critical for the sustainability of food webs and overall life in the deep-sea hydrothermal ecosystems. The present study investigates the metabolic profiles of chemolithoautotrophs inhabiting the sediments of Menez Gwen and Rainbow deep-sea vent fields, in the Mid-Atlantic Ridge. Differences in the microbial community structure might be reflecting the distinct depth, geology, and distance from vent of the studied sediments. A metagenomic sequencing approach was conducted to characterize the microbiome of the deep-sea hydrothermal sediments and the relevant metabolic pathways used by microbes. Both Menez Gwen and Rainbow metagenomes contained a significant number of genes involved in carbon fixation, revealing the largely autotrophic communities thriving in both sites. Carbon fixation at Menez Gwen site was predicted to occur mainly via the reductive tricarboxylic acid cycle, likely reflecting the dominance of sulfur-oxidizing Epsilonproteobacteria at this site, while different autotrophic pathways were identified at Rainbow site, in particular the Calvin-Benson-Bassham cycle. Chemolithotrophy appeared to be primarily driven by the oxidation of reduced sulfur compounds, whether through the SOX-dependent pathway at Menez Gwen site or through reverse sulfate reduction at Rainbow site. Other energy-yielding processes, such as methane, nitrite, or ammonia oxidation, were also detected but presumably contributing less to chemolithoautotrophy. This work furthers our knowledge of the microbial ecology of deep-sea hydrothermal sediments and represents an important repository of novel genes with potential biotechnological interest.
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Affiliation(s)
- Teresa Cerqueira
- Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, 9901-862, Horta, Portugal.
- MARE - Marine and Environmental Sciences Centre, 9901-862, Horta, Portugal.
- OKEANOS Research Unit, Faculty of Science and Technology, University of the Azores, 9901-862, Horta, Portugal.
| | - Cristina Barroso
- Next Generation Sequencing Unit - UC-Biotech, Center for Neuroscience and Cell Biology, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
- Biocant, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| | - Hugo Froufe
- Biocant, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| | - Conceição Egas
- Next Generation Sequencing Unit - UC-Biotech, Center for Neuroscience and Cell Biology, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
- Biocant, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| | - Raul Bettencourt
- MARE - Marine and Environmental Sciences Centre, 9901-862, Horta, Portugal
- OKEANOS Research Unit, Faculty of Science and Technology, University of the Azores, 9901-862, Horta, Portugal
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38
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Jones RM, Goordial JM, Orcutt BN. Low Energy Subsurface Environments as Extraterrestrial Analogs. Front Microbiol 2018; 9:1605. [PMID: 30072971 PMCID: PMC6058055 DOI: 10.3389/fmicb.2018.01605] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/27/2018] [Indexed: 11/13/2022] Open
Abstract
Earth's subsurface is often isolated from phototrophic energy sources and characterized by chemotrophic modes of life. These environments are often oligotrophic and limited in electron donors or electron acceptors, and include continental crust, subseafloor oceanic crust, and marine sediment as well as subglacial lakes and the subsurface of polar desert soils. These low energy subsurface environments are therefore uniquely positioned for examining minimum energetic requirements and adaptations for chemotrophic life. Current targets for astrobiology investigations of extant life are planetary bodies with largely inhospitable surfaces, such as Mars, Europa, and Enceladus. Subsurface environments on Earth thus serve as analogs to explore possibilities of subsurface life on extraterrestrial bodies. The purpose of this review is to provide an overview of subsurface environments as potential analogs, and the features of microbial communities existing in these low energy environments, with particular emphasis on how they inform the study of energetic limits required for life. The thermodynamic energetic calculations presented here suggest that free energy yields of reactions and energy density of some metabolic redox reactions on Mars, Europa, Enceladus, and Titan could be comparable to analog environments in Earth's low energy subsurface habitats.
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Affiliation(s)
| | | | - Beth N. Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
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39
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Pillot G, Frouin E, Pasero E, Godfroy A, Combet-Blanc Y, Davidson S, Liebgott PP. Specific enrichment of hyperthermophilic electroactive Archaea from deep-sea hydrothermal vent on electrically conductive support. BIORESOURCE TECHNOLOGY 2018; 259:304-311. [PMID: 29573609 DOI: 10.1016/j.biortech.2018.03.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/09/2018] [Accepted: 03/10/2018] [Indexed: 06/08/2023]
Abstract
While more and more investigations are done to study hyperthermophilic exoelectrogenic communities from environments, none have been performed yet on deep-sea hydrothermal vent. Samples of black smoker chimney from Rainbow site on the Atlantic mid-oceanic ridge have been harvested for enriching exoelectrogens in microbial electrolysis cells under hyperthermophilic (80 °C) condition. Two enrichments were performed in a BioElectrochemical System specially designed: one from direct inoculation of crushed chimney and the other one from inoculation of a pre-cultivation on iron (III) oxide. In both experiments, a current production was observed from 2.4 A/m2 to 5.8 A/m2 with a set anode potential of -0.110 V vs Ag/AgCl. Taxonomic affiliation of the exoelectrogen communities obtained on the electrode exhibited a specific enrichment of Archaea belonging to Thermococcales and Archeoglobales orders, even when both inocula were dominated by Bacteria.
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Affiliation(s)
- Guillaume Pillot
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, Marseille, France
| | - Eléonore Frouin
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, Marseille, France
| | - Emilie Pasero
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, Marseille, France
| | - Anne Godfroy
- IFREMER, CNRS, Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes - UMR6197, Ifremer, Centre de Brest CS10070, Plouzané, France
| | - Yannick Combet-Blanc
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, Marseille, France
| | - Sylvain Davidson
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, Marseille, France
| | - Pierre-Pol Liebgott
- Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, Marseille, France.
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40
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Le Moine Bauer S, Stensland A, Daae FL, Sandaa RA, Thorseth IH, Steen IH, Dahle H. Water Masses and Depth Structure Prokaryotic and T4-Like Viral Communities Around Hydrothermal Systems of the Nordic Seas. Front Microbiol 2018; 9:1002. [PMID: 29904373 PMCID: PMC5990851 DOI: 10.3389/fmicb.2018.01002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/30/2018] [Indexed: 12/04/2022] Open
Abstract
The oceanographic features of the Nordic Seas, situated between Iceland and Svalbard, have been extensively studied over the last decades. As well, the Nordic Seas hydrothermal systems situated on the Arctic Mid-Ocean Ridge System have received an increasing interest. However, there is very little knowledge on the microbial communities inhabiting the water column of the Nordic Seas, and nothing is known about the influence of the different water masses and hydrothermal plumes on the microbial community structures. In this study, we aimed at characterizing the impact of hydrothermal plumes on prokaryotic and T4-like viral communities around the island of Jan Mayen. To this end, we used 16S rRNA-gene and g23-gene profiling as well as flow cytometry counts to examine prokaryotic and viral communities in 27 samples obtained from different water masses in this area. While Thaumarchaeota and Marine group II Archaea dominated the waters deeper than 500 m, members of Flavobacteria generally dominated the shallower waters. Furthermore, extensive chemical and physical characteristics of all samples were obtained, including temperature measurements and concentrations of major ions and gases. The effect of these physiochemical variables on the communities was measured by using constrained and unconstrained multivariate analyzes, Mantel tests, network analyzes, phylogenetic analyzes, taxonomic analyzes and temperature-salinity (Θ-S) plots. Our results suggest that hydrothermal activity has little effect on pelagic microbial communities in hydrothermal plumes of the Nordic Seas. However, we provide evidences that observed differences in prokaryotic community structure can largely be attributed to which water mass each sample was taken from. In contrast, depth was the major factor structuring the T4-like viral communities. Our results also show that it is crucial to include water masses when studying the influence of hydrothermal plumes on microbial communities, as it could prevent to falsely associate a change in community structure with the presence of a plume.
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Affiliation(s)
- Sven Le Moine Bauer
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Anne Stensland
- Department of Earth Science and K.G. Jebsen Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Frida L Daae
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ingunn H Thorseth
- Department of Earth Science and K.G. Jebsen Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Ida H Steen
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, Bergen, Norway
| | - Håkon Dahle
- Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, University of Bergen, Bergen, Norway
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41
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Møller MH, Glombitza C, Lever MA, Deng L, Morono Y, Inagaki F, Doll M, Su CC, Lomstein BA. D:L-Amino Acid Modeling Reveals Fast Microbial Turnover of Days to Months in the Subsurface Hydrothermal Sediment of Guaymas Basin. Front Microbiol 2018; 9:967. [PMID: 29867871 PMCID: PMC5963217 DOI: 10.3389/fmicb.2018.00967] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/25/2018] [Indexed: 11/13/2022] Open
Abstract
We investigated the impact of temperature on the microbial turnover of organic matter (OM) in a hydrothermal vent system in Guaymas Basin, by calculating microbial bio- and necromass turnover times based on the culture-independent D:L-amino acid model. Sediments were recovered from two stations near hydrothermal mounds (<74°C) and from one cold station (<9°C). Cell abundance at the two hydrothermal stations dropped from 108 to 106 cells cm-3 within ∼5 m of sediment depth resulting in a 100-fold lower cell number at this depth than at the cold site where numbers remained constant at 108 cells cm-3 throughout the recovered sediment. There were strong indications that the drop in cell abundance was controlled by decreasing OM quality. The quality of the sedimentary OM was determined by the diagenetic indicators %TAAC (percentage of total organic carbon present as amino acid carbon), %TAAN (percentage of total nitrogen present as amino acid nitrogen), aspartic acid:β-alanine ratios, and glutamic acid:γ-amino butyric acid ratios. All parameters indicated that the OM became progressively degraded with increasing sediment depth, and the OM in the hydrothermal sediment was more degraded than in the uniformly cold sediment. Nonetheless, the small community of microorganisms in the hydrothermal sediment demonstrated short turnover times. The modeled turnover times of microbial bio- and necromass in the hydrothermal sediments were notably faster (biomass: days to months; necromass: up to a few hundred years) than in the cold sediments (biomass: tens of years; necromass: thousands of years), suggesting that temperature has a significant influence on the microbial turnover rates. We suggest that short biomass turnover times are necessary for maintance of essential cell funtions and to overcome potential damage caused by the increased temperature.The reduced OM quality at the hyrothemal sites might thus only allow for a small population size of microorganisms.
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Affiliation(s)
- Mikkel H Møller
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.,Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Clemens Glombitza
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.,National Aeronautics and Space Administration-Ames Research Center, Moffett Field, CA, United States
| | - Mark A Lever
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - Longhui Deng
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Fumio Inagaki
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Mechthild Doll
- Faculty of Geosciences (FB 05), University of Bremen, Bremen, Germany
| | - Chin-Chia Su
- Department of Mechanical Engineering, National Taiwan University, Taipei, Taiwan
| | - Bente A Lomstein
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.,Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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42
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Wirth R, Luckner M, Wanner G. Validation of a Hypothesis: Colonization of Black Smokers by Hyperthermophilic Microorganisms. Front Microbiol 2018; 9:524. [PMID: 29619021 PMCID: PMC5871681 DOI: 10.3389/fmicb.2018.00524] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/08/2018] [Indexed: 11/22/2022] Open
Abstract
Newly erupted black smokers (hydrothermal vent chimneys) are sterile during their formation, but house hyperthermophilic microorganisms in substantial amounts in later stages. No direct experimental data exist by which mechanisms hyperthermophiles colonize newly erupted black smokers, but a scenario was proposed recently how this might happen. Here we combine high temperature light microscopy with electron microscopy to show that two hyperthermophilic Archaea, namely Pyrococcus furiosus and Methanocaldococcus villosus are able to adhere onto authentic black smoker material (BSM). We especially are able to directly observe the adhesion process via video recordings taken at high temperatures. These data validate the hypothesis that hyperthermophiles are transferred by serendipitous water currents to the outside of newly formed black smokers and react within seconds to the there prevailing high temperatures by very fast movements. They scan the surface of the hydrothermal chimneys via a much slower zigzag seek-movement and adhere via their flagella at a suitable place, building up biofilms.
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Affiliation(s)
- Reinhard Wirth
- Faculty of Biology, Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Manja Luckner
- Department of Biology I, Ludwig-Maximilians-University, Munich, Germany
| | - Gerhard Wanner
- Department of Biology I, Ludwig-Maximilians-University, Munich, Germany
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43
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Fortunato CS, Larson B, Butterfield DA, Huber JA. Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent fluids. Environ Microbiol 2017; 20:769-784. [DOI: 10.1111/1462-2920.14011] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 10/20/2017] [Accepted: 11/22/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Caroline S. Fortunato
- Marine Biological Laboratory; Josephine Bay Paul Center; Woods Hole MA USA
- Department of Biology; Wilkes University; Wilkes-Barre PA USA
| | - Benjamin Larson
- Joint Institute for the Study of the Atmosphere and Ocean; University of Washington and NOAA Pacific Marine Environmental Lab; Seattle WA USA
| | - David A. Butterfield
- Joint Institute for the Study of the Atmosphere and Ocean; University of Washington and NOAA Pacific Marine Environmental Lab; Seattle WA USA
| | - Julie A. Huber
- Marine Biological Laboratory; Josephine Bay Paul Center; Woods Hole MA USA
- Marine Chemistry and Geochemistry Department; Woods Hole Oceanographic Institution; Woods Hole MA USA
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Muto H, Takaki Y, Hirai M, Mino S, Sawayama S, Takai K, Nakagawa S. A Simple and Efficient RNA Extraction Method from Deep-Sea Hydrothermal Vent Chimney Structures. Microbes Environ 2017; 32:330-335. [PMID: 29187693 PMCID: PMC5745017 DOI: 10.1264/jsme2.me17048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RNA-based microbiological analyses, e.g., transcriptome and reverse transcription-quantitative PCR, require a relatively large amount of high quality RNA. RNA-based analyses on microbial communities in deep-sea hydrothermal environments often encounter methodological difficulties with RNA extraction due to the presence of unique minerals in and the low biomass of samples. In the present study, we assessed RNA extraction methods for deep-sea vent chimneys that had complex mineral compositions. Mineral-RNA adsorption experiments were conducted using mock chimney minerals and Escherichia coli total RNA solution, and showed that detectable RNA significantly decreased possibly due to adsorption onto minerals. This decrease in RNA was prevented by the addition of sodium tripolyphosphate (STPP), deoxynucleotide triphosphates (dNTPs), salmon sperm DNA, and NaOH. The addition of STPP was also effective for RNA extraction from the mixture of E. coli cells and mock chimney minerals when TRIzol reagent and the RNeasy column were used, but not when the RNeasy PowerSoil total RNA kit was used. A combination of STPP, TRIzol reagent, the RNeasy column, and sonication resulted in the highest RNA yield from a natural chimney. This indirect extraction procedure is simple, rapid, inexpensive, and may be used for large-scale RNA extraction.
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Affiliation(s)
- Hisashi Muto
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Miho Hirai
- Research and Development (R&D) Center for Marine Biosciences, Marine Functional Biology Group (MFbio), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University.,Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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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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Olins HC, Rogers DR, Preston C, Ussler W, Pargett D, Jensen S, Roman B, Birch JM, Scholin CA, Haroon MF, Girguis PR. Co-registered Geochemistry and Metatranscriptomics Reveal Unexpected Distributions of Microbial Activity within a Hydrothermal Vent Field. Front Microbiol 2017; 8:1042. [PMID: 28659879 PMCID: PMC5468400 DOI: 10.3389/fmicb.2017.01042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 05/24/2017] [Indexed: 12/11/2022] Open
Abstract
Despite years of research into microbial activity at diffuse flow hydrothermal vents, the extent of microbial niche diversity in these settings is not known. To better understand the relationship between microbial activity and the associated physical and geochemical conditions, we obtained co-registered metatranscriptomic and geochemical data from a variety of different fluid regimes within the ASHES vent field on the Juan de Fuca Ridge. Microbial activity in the majority of the cool and warm fluids sampled was dominated by a population of Gammaproteobacteria (likely sulfur oxidizers) that appear to thrive in a variety of chemically distinct fluids. Only the warmest, most hydrothermally-influenced flows were dominated by active populations of canonically vent-endemic Epsilonproteobacteria. These data suggest that the Gammaproteobacteria collected during this study may be generalists, capable of thriving over a broader range of geochemical conditions than the Epsilonproteobacteria. Notably, the apparent metabolic activity of the Gammaproteobacteria—particularly carbon fixation—in the seawater found between discrete fluid flows (the intra-field water) suggests that this area within the Axial caldera is a highly productive, and previously overlooked, habitat. By extension, our findings suggest that analogous, diffuse flow fields may be similarly productive and thus constitute a very important and underappreciated aspect of deep-sea biogeochemical cycling that is occurring at the global scale.
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Affiliation(s)
- Heather C Olins
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridge, MA, United States
| | - Daniel R Rogers
- Department of Chemistry, Stonehill CollegeEaston, MA, United States
| | - Christina Preston
- Research and Development, Monterey Bay Aquarium Research InstituteMoss Landing, CA, United States
| | - William Ussler
- Research and Development, Monterey Bay Aquarium Research InstituteMoss Landing, CA, United States
| | - Douglas Pargett
- Research and Development, Monterey Bay Aquarium Research InstituteMoss Landing, CA, United States
| | - Scott Jensen
- Research and Development, Monterey Bay Aquarium Research InstituteMoss Landing, CA, United States
| | - Brent Roman
- Research and Development, Monterey Bay Aquarium Research InstituteMoss Landing, CA, United States
| | - James M Birch
- Research and Development, Monterey Bay Aquarium Research InstituteMoss Landing, CA, United States
| | - Christopher A Scholin
- Research and Development, Monterey Bay Aquarium Research InstituteMoss Landing, CA, United States
| | - M Fauzi Haroon
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridge, MA, United States
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridge, MA, United States
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Djurhuus A, Mikalsen SO, Giebel HA, Rogers AD. Cutting through the smoke: the diversity of microorganisms in deep-sea hydrothermal plumes. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160829. [PMID: 28484604 PMCID: PMC5414241 DOI: 10.1098/rsos.160829] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 03/10/2017] [Indexed: 05/19/2023]
Abstract
There are still notable gaps regarding the detailed distribution of microorganisms between and within insular habitats such as deep-sea hydrothermal vents. This study investigates the community composition of black smoker vent microorganisms in the Southern Hemisphere, and changes thereof along a spatial and chemical gradient ranging from the vent plume to surrounding waters. We sampled two hydrothermal vent fields, one at the South West Indian Ridge (SWIR), the other at the East Scotia Ridge (ESR). Samples were collected across vent fields at varying vertical distances from the origin of the plumes. The microbial data were sequenced on an Illumina MiSeq platform for the 16SrRNA gene. A substantial amount of vent-specific putative chemosynthetic microorganisms were found, particularly in samples from focused hydrothermal venting. Common vent-specific organisms from both vent fields were the genera Arcobacter, Caminibacter and Sulfurimonas from the Epsilonproteobacteria and the SUP05 group from the Gammaproteobacteria. There were no major differences in microbial composition between SWIR and ESR for focused plume samples. However, within the ESR the diffuse flow and focused samples differed significantly in microbial community composition and relative abundance. For Epsilonproteobacteria, we found evidence of niche-specificity to hydrothermal vent environments. This taxon decreased in abundance by three orders of magnitude from the vent orifice to background water. Epsilonproteobacteria distribution followed a distance-decay relationship as vent-effluents mixed with the surrounding seawater. This study demonstrates strong habitat affinity of vent microorganisms on a metre scale with distinct environmental selection.
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Affiliation(s)
- Anni Djurhuus
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS UK
- e-mail:
| | - Svein-Ole Mikalsen
- Department of Science and Technology, University of the Faroe Islands, Noatun 3, Torshavn, Faroe Islands
| | - Helge-Ansgar Giebel
- Institute of Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky University Oldenburg, , Germany
| | - Alex D. Rogers
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS UK
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Abstract
Microbial life has been detected well into the igneous crust of the seafloor (i.e., the oceanic basement), but there have been no reports confirming the presence of viruses in this habitat. To detect and characterize an ocean basement virome, geothermally heated fluid samples (ca. 60 to 65°C) were collected from 117 to 292 m deep into the ocean basement using seafloor observatories installed in two boreholes (Integrated Ocean Drilling Program [IODP] U1362A and U1362B) drilled in the eastern sediment-covered flank of the Juan de Fuca Ridge. Concentrations of virus-like particles in the fluid samples were on the order of 0.2 × 105 to 2 × 105 ml−1 (n = 8), higher than prokaryote-like cells in the same samples by a factor of 9 on average (range, 1.5 to 27). Electron microscopy revealed diverse viral morphotypes similar to those of viruses known to infect bacteria and thermophilic archaea. An analysis of virus-like sequences in basement microbial metagenomes suggests that those from archaeon-infecting viruses were the most common (63 to 80%). Complete genomes of a putative archaeon-infecting virus and a prophage within an archaeal scaffold were identified among the assembled sequences, and sequence analysis suggests that they represent lineages divergent from known thermophilic viruses. Of the clustered regularly interspaced short palindromic repeat (CRISPR)-containing scaffolds in the metagenomes for which a taxonomy could be inferred (163 out of 737), 51 to 55% appeared to be archaeal and 45 to 49% appeared to be bacterial. These results imply that the warmed, highly altered fluids in deeply buried ocean basement harbor a distinct assemblage of novel viruses, including many that infect archaea, and that these viruses are active participants in the ecology of the basement microbiome. The hydrothermally active ocean basement is voluminous and likely provided conditions critical to the origins of life, but the microbiology of this vast habitat is not well understood. Viruses in particular, although integral to the origins, evolution, and ecology of all life on earth, have never been documented in basement fluids. This report provides the first estimate of free virus particles (virions) within fluids circulating through the extrusive basalt of the seafloor and describes the morphological and genetic signatures of basement viruses. These data push the known geographical limits of the virosphere deep into the ocean basement and point to a wealth of novel viral diversity, exploration of which could shed light on the early evolution of viruses.
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Colonization of Black Smokers by Hyperthermophilic Microorganisms. Trends Microbiol 2017; 25:92-99. [DOI: 10.1016/j.tim.2016.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/10/2016] [Accepted: 11/02/2016] [Indexed: 11/19/2022]
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Zhang L, Xi L, Ruan J, Huang Y. Kocuria oceani sp. nov., isolated from a deep-sea hydrothermal plume. Int J Syst Evol Microbiol 2017; 67:164-169. [DOI: 10.1099/ijsem.0.001599] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Limin Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Lijun Xi
- Present address: State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering & Biotechnology, China University of Petroleum, Qingdao 266580, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jisheng Ruan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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