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Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients. Nat Commun 2017; 8:1507. [PMID: 29142241 PMCID: PMC5688066 DOI: 10.1038/s41467-017-01376-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 09/11/2017] [Indexed: 12/22/2022] Open
Abstract
Microbial communities drive biogeochemical cycles through networks of metabolite exchange that are structured along energetic gradients. As energy yields become limiting, these networks favor co-metabolic interactions to maximize energy disequilibria. Here we apply single-cell genomics, metagenomics, and metatranscriptomics to study bacterial populations of the abundant "microbial dark matter" phylum Marinimicrobia along defined energy gradients. We show that evolutionary diversification of major Marinimicrobia clades appears to be closely related to energy yields, with increased co-metabolic interactions in more deeply branching clades. Several of these clades appear to participate in the biogeochemical cycling of sulfur and nitrogen, filling previously unassigned niches in the ocean. Notably, two Marinimicrobia clades, occupying different energetic niches, express nitrous oxide reductase, potentially acting as a global sink for the greenhouse gas nitrous oxide.
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152
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Bertagnolli AD, Padilla CC, Glass JB, Thamdrup B, Stewart FJ. Metabolic potential and
in situ
activity of marine Marinimicrobia bacteria in an anoxic water column. Environ Microbiol 2017; 19:4392-4416. [DOI: 10.1111/1462-2920.13879] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 07/17/2017] [Accepted: 07/26/2017] [Indexed: 11/29/2022]
Affiliation(s)
| | - Cory C. Padilla
- School of Biological SciencesGeorgia Institute of TechnologyAtlanta GA USA
| | - Jennifer B. Glass
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlanta GA USA
| | - Bo Thamdrup
- Department of Biology and Nordic Center for Earth Evolution (NordCEE)University of Southern DenmarkOdense Denmark
| | - Frank J. Stewart
- School of Biological SciencesGeorgia Institute of TechnologyAtlanta GA USA
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153
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Matys ED, Sepúlveda J, Pantoja S, Lange CB, Caniupán M, Lamy F, Summons RE. Bacteriohopanepolyols along redox gradients in the Humboldt Current System off northern Chile. GEOBIOLOGY 2017; 15:844-857. [PMID: 28771908 DOI: 10.1111/gbi.12250] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 06/21/2017] [Indexed: 06/07/2023]
Abstract
Marine oxygen minimum zones (OMZs) are characterized by the presence of subsurface suboxic or anoxic waters where diverse microbial processes are responsible for the removal of fixed nitrogen. OMZs have expanded over past decades and are expected to continue expanding in response to the changing climate. The implications for marine biogeochemistry, particularly nitrogen cycling, are uncertain. Cell membrane lipids (biomarkers), such as bacterial bacteriohopanepolyols (BHPs) and their degradation products (hopanoids), have distinctive structural attributes that convey information about their biological sources. Since the discovery of fossil hopanoids in ancient sediments, the study of BHPs has been of great biogeochemical interest due to their potential to serve as proxies for bacteria in the geological record. A stereoisomer of bacteriohopanetetrol (BHT), BHT II, has been previously identified in OMZ waters and has as been unequivocally identified in culture enrichments of anammox bacteria, a key group contributing to nitrogen loss in marine OMZs. We tested BHT II as a proxy for suboxia/anoxia and anammox bacteria in suspended organic matter across OMZ waters of the Humboldt Current System off northern Chile, as well as in surface and deeply buried sediments (125-150 ky). The BHT II ratio (BHT II/total BHT) increases as oxygen content decreases through the water column, consistent with previous results from Perú, the Cariaco Basin and the Arabian Sea, and in line with microbiological evidence indicating intense anammox activity in the Chilean OMZ. Notably, BHT II is transported from the water column to surface sediments, and preserved in deeply buried sediments, where the BHT II ratio correlates with changes in δ15 N sediment values during glacial-interglacial transitions. This study suggests that BHT II offers a proxy for past changes in the relative importance of anammox, and fluctuations in nitrogen cycling in response to ocean redox changes through the geological record.
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Affiliation(s)
- E D Matys
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - J Sepúlveda
- Department of Geological Sciences, Institute of Arctic and Alpine Research (INSTAAR), University of Colorado Boulder, Boulder, CO, USA
| | - S Pantoja
- Department of Oceanography and COPAS Sur-Austral, University of Concepción, Concepción, Chile
| | - C B Lange
- Department of Oceanography and COPAS Sur-Austral, University of Concepción, Concepción, Chile
| | - M Caniupán
- Department of Oceanography and COPAS Sur-Austral, University of Concepción, Concepción, Chile
| | - F Lamy
- Alfred Wegener Institute for Polar and Marine Research (AWI), Bremerhaven, Germany
| | - R E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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154
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Hallam SJ, Torres-Beltrán M, Hawley AK. Monitoring microbial responses to ocean deoxygenation in a model oxygen minimum zone. Sci Data 2017; 4:170158. [PMID: 29087370 PMCID: PMC5663219 DOI: 10.1038/sdata.2017.158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/19/2017] [Indexed: 11/09/2022] Open
Abstract
Today in Scientific Data, two compendia of geochemical and
multi-omic sequence information (DNA, RNA, protein) generated over almost a
decade of time series monitoring in a seasonally anoxic coastal marine setting
are presented to the scientific community. These data descriptors introduce a
model ecosystem for the study of microbial responses to ocean deoxygenation, a
phenotype that is currently expanding due to climate change. Public access to
this time series information is intended to promote scientific collaborations
and the generation of new hypotheses relevant to microbial ecology,
biogeochemistry and global change issues.
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Affiliation(s)
- Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.,Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z2.,Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Mónica Torres-Beltrán
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Alyse K Hawley
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
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155
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Hawley AK, Torres-Beltrán M, Zaikova E, Walsh DA, Mueller A, Scofield M, Kheirandish S, Payne C, Pakhomova L, Bhatia M, Shevchuk O, Gies EA, Fairley D, Malfatti SA, Norbeck AD, Brewer HM, Pasa-Tolic L, del Rio TG, Suttle CA, Tringe S, Hallam SJ. A compendium of multi-omic sequence information from the Saanich Inlet water column. Sci Data 2017; 4:170160. [PMID: 29087368 PMCID: PMC5663217 DOI: 10.1038/sdata.2017.160] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 08/02/2017] [Indexed: 01/08/2023] Open
Abstract
Marine oxygen minimum zones (OMZs) are widespread regions of the ocean that are currently expanding due to global warming. While inhospitable to most metazoans, OMZs are hotspots for microbial mediated biogeochemical cycling of carbon, nitrogen and sulphur, contributing disproportionately to marine nitrogen loss and climate active trace gas production. Our current understanding of microbial community responses to OMZ expansion is limited by a lack of time-resolved data sets linking multi-omic sequence information (DNA, RNA, protein) to geochemical parameters and process rates. Here, we present six years of time-resolved multi-omic observations in Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia, Canada that undergoes recurring changes in water column oxygenation status. This compendium provides a unique multi-omic framework for studying microbial community responses to ocean deoxygenation along defined geochemical gradients in OMZ waters.
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Affiliation(s)
- Alyse K. Hawley
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Mónica Torres-Beltrán
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Elena Zaikova
- Department of Biology, Georgetown University,
Washington, District Of Columbia 20057,
USA
| | - David A. Walsh
- Department of Biology, Concordia University,
Montreal, Quebec, Canada H4B 1R6
| | - Andreas Mueller
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Melanie Scofield
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Sam Kheirandish
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Chris Payne
- Earth, Ocean and Atmospheric Sciences, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Larysa Pakhomova
- Earth, Ocean and Atmospheric Sciences, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Maya Bhatia
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Olena Shevchuk
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | - Esther A. Gies
- Department of Civil Engineering, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Diane Fairley
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
| | | | - Angela D. Norbeck
- Biological and Computational Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington
99352, USA
| | - Heather M. Brewer
- Biological and Computational Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington
99352, USA
| | - Ljiljana Pasa-Tolic
- Biological and Computational Sciences Division, Pacific
Northwest National Laboratory, Richland, Washington
99352, USA
| | | | - Curtis A. Suttle
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
- Earth, Ocean and Atmospheric Sciences, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
- Department of Botany, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z4
| | - Susannah Tringe
- Department of Energy Joint Genome Institute,
Walnut Creek, California 94598, USA
| | - Steven J. Hallam
- Department of Microbiology and Immunology, University of
British Columbia, Vancouver, British
Columbia, Canada V63 1Z3
- Peter Wall Institute for Advanced Studies, University of
British Columbia, Canada V6T 1Z2
- Genome Science and Technology Program, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z3
- Graduate Program in Bioinformatics, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z3
- ECOSCOPE Training Program, University of British
Columbia, Vancouver,
British Columbia, Canada
V6T 1Z3
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156
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Torres-Beltrán M, Hawley AK, Capelle D, Zaikova E, Walsh DA, Mueller A, Scofield M, Payne C, Pakhomova L, Kheirandish S, Finke J, Bhatia M, Shevchuk O, Gies EA, Fairley D, Michiels C, Suttle CA, Whitney F, Crowe SA, Tortell PD, Hallam SJ. A compendium of geochemical information from the Saanich Inlet water column. Sci Data 2017; 4:170159. [PMID: 29087371 PMCID: PMC5663218 DOI: 10.1038/sdata.2017.159] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/21/2017] [Indexed: 11/13/2022] Open
Abstract
Extensive and expanding oxygen minimum zones (OMZs) exist at variable depths in
coastal and open ocean waters. As oxygen levels decline, nutrients and energy
are increasingly diverted away from higher trophic levels into microbial
community metabolism, resulting in fixed nitrogen loss and production of climate
active trace gases including nitrous oxide and methane. While ocean
deoxygenation has been reported on a global scale, our understanding of OMZ
biology and geochemistry is limited by a lack of time-resolved data sets. Here,
we present a historical dataset of oxygen concentrations spanning fifty years
and nine years of monthly geochemical time series observations in Saanich Inlet,
a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia,
Canada that undergoes recurring changes in water column oxygenation status. This
compendium provides a unique geochemical framework for evaluating long-term
trends in biogeochemical cycling in OMZ waters.
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Affiliation(s)
- Mónica Torres-Beltrán
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Alyse K Hawley
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - David Capelle
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Elena Zaikova
- Department of Biology, Georgetown University, Washington, DC 20007, USA
| | - David A Walsh
- Department of Biology, Concordia University, Montreal, Quebec, Canada H4B 1R6
| | - Andreas Mueller
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Melanie Scofield
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Chris Payne
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Larysa Pakhomova
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Sam Kheirandish
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Jan Finke
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Maya Bhatia
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Olena Shevchuk
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Esther A Gies
- Department of Civil Engineering, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Diane Fairley
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Céline Michiels
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Curtis A Suttle
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.,Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Frank Whitney
- Department of Fisheries and Oceans Canada, Sidney, British Columbia, Canada V9L 6V9
| | - Sean A Crowe
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.,Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Philippe D Tortell
- Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,Peter Wall Institute for Advanced Studies, University of British Columbia, Canada V6T 1Z2
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.,Peter Wall Institute for Advanced Studies, University of British Columbia, Canada V6T 1Z2.,Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
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157
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Brewer PG, Peltzer ET. Depth perception: the need to report ocean biogeochemical rates as functions of temperature, not depth. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2016.0319. [PMID: 28784710 PMCID: PMC5559415 DOI: 10.1098/rsta.2016.0319] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/21/2017] [Indexed: 05/13/2023]
Abstract
For over 50 years, ocean scientists have oddly represented ocean oxygen consumption rates as a function of depth but not temperature in most biogeochemical models. This unique tradition or tactic inhibits useful discussion of climate change impacts, where specific and fundamental temperature-dependent terms are required. Tracer-based determinations of oxygen consumption rates in the deep sea are nearly universally reported as a function of depth in spite of their well-known microbial basis. In recent work, we have shown that a carefully determined profile of oxygen consumption rates in the Sargasso Sea can be well represented by a classical Arrhenius function with an activation energy of 86.5 kJ mol-1, leading to a Q10 of 3.63. This indicates that for 2°C warming, we will have a 29% increase in ocean oxygen consumption rates, and for 3°C warming, a 47% increase, potentially leading to large-scale ocean hypoxia should a sufficient amount of organic matter be available to microbes. Here, we show that the same principles apply to a worldwide collation of tracer-based oxygen consumption rate data and that some 95% of ocean oxygen consumption is driven by temperature, not depth, and thus will have a strong climate dependence. The Arrhenius/Eyring equations are no simple panacea and they require a non-equilibrium steady state to exist. Where transient events are in progress, this stricture is not obeyed and we show one such possible example.This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'.
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Affiliation(s)
- Peter G Brewer
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Edward T Peltzer
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
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158
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Brewer PG, Peltzer ET. Depth perception: the need to report ocean biogeochemical rates as functions of temperature, not depth. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017. [PMID: 28784710 DOI: 10.1098/rsta.2017.0319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
For over 50 years, ocean scientists have oddly represented ocean oxygen consumption rates as a function of depth but not temperature in most biogeochemical models. This unique tradition or tactic inhibits useful discussion of climate change impacts, where specific and fundamental temperature-dependent terms are required. Tracer-based determinations of oxygen consumption rates in the deep sea are nearly universally reported as a function of depth in spite of their well-known microbial basis. In recent work, we have shown that a carefully determined profile of oxygen consumption rates in the Sargasso Sea can be well represented by a classical Arrhenius function with an activation energy of 86.5 kJ mol-1, leading to a Q10 of 3.63. This indicates that for 2°C warming, we will have a 29% increase in ocean oxygen consumption rates, and for 3°C warming, a 47% increase, potentially leading to large-scale ocean hypoxia should a sufficient amount of organic matter be available to microbes. Here, we show that the same principles apply to a worldwide collation of tracer-based oxygen consumption rate data and that some 95% of ocean oxygen consumption is driven by temperature, not depth, and thus will have a strong climate dependence. The Arrhenius/Eyring equations are no simple panacea and they require a non-equilibrium steady state to exist. Where transient events are in progress, this stricture is not obeyed and we show one such possible example.This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'.
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Affiliation(s)
- Peter G Brewer
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Edward T Peltzer
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
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159
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Abstract
Marine regions that have seasonal to long-term low dissolved oxygen (DO) concentrations, sometimes called “dead zones,” are increasing in number and severity around the globe with deleterious effects on ecology and economics. One of the largest of these coastal dead zones occurs on the continental shelf of the northern Gulf of Mexico (nGOM), which results from eutrophication-enhanced bacterioplankton respiration and strong seasonal stratification. Previous research in this dead zone revealed the presence of multiple cosmopolitan bacterioplankton lineages that have eluded cultivation, and thus their metabolic roles in this ecosystem remain unknown. We used a coupled shotgun metagenomic and metatranscriptomic approach to determine the metabolic potential of Marine Group II Euryarchaeota, SAR406, and SAR202. We recovered multiple high-quality, nearly complete genomes from all three groups as well as candidate phyla usually associated with anoxic environments—Parcubacteria (OD1) and Peregrinibacteria. Two additional groups with putative assignments to ACD39 and PAUC34f supplement the metabolic contributions by uncultivated taxa. Our results indicate active metabolism in all groups, including prevalent aerobic respiration, with concurrent expression of genes for nitrate reduction in SAR406 and SAR202, and dissimilatory nitrite reduction to ammonia and sulfur reduction by SAR406. We also report a variety of active heterotrophic carbon processing mechanisms, including degradation of complex carbohydrate compounds by SAR406, SAR202, ACD39, and PAUC34f. Together, these data help constrain the metabolic contributions from uncultivated groups in the nGOM during periods of low DO and suggest roles for these organisms in the breakdown of complex organic matter. Dead zones receive their name primarily from the reduction of eukaryotic macrobiota (demersal fish, shrimp, etc.) that are also key coastal fisheries. Excess nutrients contributed from anthropogenic activity such as fertilizer runoff result in algal blooms and therefore ample new carbon for aerobic microbial metabolism. Combined with strong stratification, microbial respiration reduces oxygen in shelf bottom waters to levels unfit for many animals (termed hypoxia). The nGOM shelf remains one of the largest eutrophication-driven hypoxic zones in the world, yet despite its potential as a model study system, the microbial metabolisms underlying and resulting from this phenomenon—many of which occur in bacterioplankton from poorly understood lineages—have received only preliminary study. Our work details the metabolic potential and gene expression activity for uncultivated lineages across several low DO sites in the nGOM, improving our understanding of the active biogeochemical cycling mediated by these “microbial dark matter” taxa during hypoxia.
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160
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Broman E, Sjöstedt J, Pinhassi J, Dopson M. Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism. MICROBIOME 2017; 5:96. [PMID: 28793929 PMCID: PMC5549381 DOI: 10.1186/s40168-017-0311-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 07/18/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface. RESULTS Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation. CONCLUSIONS These novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses upon oxygenation of dead zones. Moreover, these results highlight that microbial responses, and therefore ultimately remediation efforts, depend largely on the oxygenation history of sites. Furthermore, it was shown that re-oxygenation efforts to remediate dead zones could ultimately be facilitated by in situ microbial molecular mechanisms involved in removal of toxic H2S and the potent greenhouse gas methane.
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Affiliation(s)
- Elias Broman
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Johanna Sjöstedt
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- Present address: Department of Biology/Aquatic ecology, Lund University, Sölvesgatan 37, 223 62 Lund, Sweden
- Present address: Centre for Ocean Life, Institute for Aquatic Resources, Technical University of Denmark, 2900 Charlottenlund, Denmark
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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161
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Taylor GT, Suter EA, Li ZQ, Chow S, Stinton D, Zaliznyak T, Beaupré SR. Single-Cell Growth Rates in Photoautotrophic Populations Measured by Stable Isotope Probing and Resonance Raman Microspectrometry. Front Microbiol 2017; 8:1449. [PMID: 28824580 PMCID: PMC5541042 DOI: 10.3389/fmicb.2017.01449] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 07/17/2017] [Indexed: 12/17/2022] Open
Abstract
A new method to measure growth rates of individual photoautotrophic cells by combining stable isotope probing (SIP) and single-cell resonance Raman microspectrometry is introduced. This report explores optimal experimental design and the theoretical underpinnings for quantitative responses of Raman spectra to cellular isotopic composition. Resonance Raman spectra of isogenic cultures of the cyanobacterium, Synechococcus sp., grown in 13C-bicarbonate revealed linear covariance between wavenumber (cm−1) shifts in dominant carotenoid Raman peaks and a broad range of cellular 13C fractional isotopic abundance. Single-cell growth rates were calculated from spectra-derived isotopic content and empirical relationships. Growth rates among any 25 cells in a sample varied considerably; mean coefficient of variation, CV, was 29 ± 3% (σ/x¯), of which only ~2% was propagated analytical error. Instantaneous population growth rates measured independently by in vivo fluorescence also varied daily (CV ≈ 53%) and were statistically indistinguishable from single-cell growth rates at all but the lowest levels of cell labeling. SCRR censuses of mixtures prepared from Synechococcus sp. and T. pseudonana (a diatom) populations with varying 13C-content and growth rates closely approximated predicted spectral responses and fractional labeling of cells added to the sample. This approach enables direct microspectrometric interrogation of isotopically- and phylogenetically-labeled cells and detects as little as 3% changes in cellular fractional labeling. This is the first description of a non-destructive technique to measure single-cell photoautotrophic growth rates based on Raman spectroscopy and well-constrained assumptions, while requiring few ancillary measurements.
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Affiliation(s)
- Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook UniversityStony Brook, NY, United States
| | - Elizabeth A Suter
- School of Marine and Atmospheric Sciences, Stony Brook UniversityStony Brook, NY, United States
| | - Zhuo Q Li
- School of Marine and Atmospheric Sciences, Stony Brook UniversityStony Brook, NY, United States
| | - Stephanie Chow
- School of Marine and Atmospheric Sciences, Stony Brook UniversityStony Brook, NY, United States
| | - Dallyce Stinton
- School of Marine and Atmospheric Sciences, Stony Brook UniversityStony Brook, NY, United States
| | - Tatiana Zaliznyak
- School of Marine and Atmospheric Sciences, Stony Brook UniversityStony Brook, NY, United States
| | - Steven R Beaupré
- School of Marine and Atmospheric Sciences, Stony Brook UniversityStony Brook, NY, United States
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Garcia-Robledo E, Padilla CC, Aldunate M, Stewart FJ, Ulloa O, Paulmier A, Gregori G, Revsbech NP. Cryptic oxygen cycling in anoxic marine zones. Proc Natl Acad Sci U S A 2017; 114:8319-8324. [PMID: 28716941 PMCID: PMC5547588 DOI: 10.1073/pnas.1619844114] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oxygen availability drives changes in microbial diversity and biogeochemical cycling between the aerobic surface layer and the anaerobic core in nitrite-rich anoxic marine zones (AMZs), which constitute huge oxygen-depleted regions in the tropical oceans. The current paradigm is that primary production and nitrification within the oxic surface layer fuel anaerobic processes in the anoxic core of AMZs, where 30-50% of global marine nitrogen loss takes place. Here we demonstrate that oxygenic photosynthesis in the secondary chlorophyll maximum (SCM) releases significant amounts of O2 to the otherwise anoxic environment. The SCM, commonly found within AMZs, was dominated by the picocyanobacteria Prochlorococcus spp. Free O2 levels in this layer were, however, undetectable by conventional techniques, reflecting a tight coupling between O2 production and consumption by aerobic processes under apparent anoxic conditions. Transcriptomic analysis of the microbial community in the seemingly anoxic SCM revealed the enhanced expression of genes for aerobic processes, such as nitrite oxidation. The rates of gross O2 production and carbon fixation in the SCM were found to be similar to those reported for nitrite oxidation, as well as for anaerobic dissimilatory nitrate reduction and sulfate reduction, suggesting a significant effect of local oxygenic photosynthesis on Pacific AMZ biogeochemical cycling.
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Affiliation(s)
- Emilio Garcia-Robledo
- Microbiology Section, Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark;
| | - Cory C Padilla
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-0230
| | - Montserrat Aldunate
- Graduate Program in Oceanography, Department of Oceanography, University of Concepción, 4070386 Concepcion, Chile
- Departamento de Oceanografía, Instituto Milenio de Oceanografía, Universidad de Concepción, 4070386 Concepción, Chile
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-0230
| | - Osvaldo Ulloa
- Departamento de Oceanografía, Instituto Milenio de Oceanografía, Universidad de Concepción, 4070386 Concepción, Chile
| | - Aurélien Paulmier
- Laboratoire d'Etudes en Géophysique et Océanographie Spatiales, Institut de Recherche pour le Développement, CNRS, Centre National d'Etudes Spatiales, University of Toulouse, 31400 Toulouse, France
| | - Gerald Gregori
- Aix Marseille Université, Université de Toulon, CNRS, Institut pour la Recherche et le Développement, Mediterranean Institute of Oceanography UM 110, 13288 Marseille, France
| | - Niels Peter Revsbech
- Microbiology Section, Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark
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163
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Wasmund K, Mußmann M, Loy A. The life sulfuric: microbial ecology of sulfur cycling in marine sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:323-344. [PMID: 28419734 PMCID: PMC5573963 DOI: 10.1111/1758-2229.12538] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle.
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Affiliation(s)
- Kenneth Wasmund
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Austrian Polar Research InstituteViennaAustria
| | - Marc Mußmann
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | - Alexander Loy
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Austrian Polar Research InstituteViennaAustria
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164
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Sulfide-Induced Dissimilatory Nitrate Reduction to Ammonium Supports Anaerobic Ammonium Oxidation (Anammox) in an Open-Water Unit Process Wetland. Appl Environ Microbiol 2017; 83:AEM.00782-17. [PMID: 28526796 DOI: 10.1128/aem.00782-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/14/2017] [Indexed: 02/01/2023] Open
Abstract
Open-water unit process wetlands host a benthic diatomaceous and bacterial assemblage capable of nitrate removal from treated municipal wastewater with unexpected contributions from anammox processes. In exploring mechanistic drivers of anammox, 16S rRNA gene sequencing profiles of the biomat revealed significant microbial community shifts along the flow path and with depth. Notably, there was an increasing abundance of sulfate reducers (Desulfococcus and other Deltaproteobacteria) and anammox microorganisms (Brocadiaceae) with depth. Pore water profiles demonstrated that nitrate and sulfate concentrations exhibited a commensurate decrease with biomat depth accompanied by the accumulation of ammonium. Quantitative PCR targeting the anammox hydrazine synthase gene, hzsA, revealed a 3-fold increase in abundance with biomat depth as well as a 2-fold increase in the sulfate reductase gene, dsrA These microbial and geochemical trends were most pronounced in proximity to the influent region of the wetland where the biomat was thickest and influent nitrate concentrations were highest. While direct genetic queries for dissimilatory nitrate reduction to ammonium (DNRA) microorganisms proved unsuccessful, an increasing depth-dependent dominance of Gammaproteobacteria and diatoms that have previously been functionally linked to DNRA was observed. To further explore this potential, a series of microcosms containing field-derived biomat material confirmed the ability of the community to produce sulfide and reduce nitrate; however, significant ammonium production was observed only in the presence of hydrogen sulfide. Collectively, these results suggest that biogenic sulfide induces DNRA, which in turn can explain the requisite coproduction of ammonium and nitrite from nitrified effluent necessary to sustain the anammox community.IMPORTANCE This study aims to increase understanding of why and how anammox is occurring in an engineered wetland with limited exogenous contributions of ammonium and nitrite. In doing so, the study has implications for how geochemical parameters could potentially be leveraged to impact nutrient cycling and attenuation during the operation of treatment wetlands. The work also contributes to ongoing discussions about biogeochemical signatures surrounding anammox processes and enhances our understanding of the contributions of anammox processes in freshwater environments.
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165
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Dang H, Chen CTA. Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment. Front Microbiol 2017; 8:1246. [PMID: 28769878 PMCID: PMC5509916 DOI: 10.3389/fmicb.2017.01246] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/20/2017] [Indexed: 11/15/2022] Open
Abstract
Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field.
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Affiliation(s)
- Hongyue Dang
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
| | - Chen-Tung A Chen
- Department of Oceanography, National Sun Yat-sen UniversityKaohsiung, Taiwan
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166
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Marine Bacterioplankton Seasonal Succession Dynamics. Trends Microbiol 2017; 25:494-505. [DOI: 10.1016/j.tim.2016.12.013] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 01/08/2023]
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167
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Edwardson CF, Hollibaugh JT. Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA. ISME JOURNAL 2017; 11:2195-2208. [PMID: 28548659 PMCID: PMC5607362 DOI: 10.1038/ismej.2017.80] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 04/04/2017] [Accepted: 04/18/2017] [Indexed: 11/09/2022]
Abstract
This study evaluates the transcriptionally active, dissimilatory sulfur- and arsenic-cycling components of the microbial community in alkaline, hypersaline Mono Lake, CA, USA. We sampled five depths spanning the redox gradient (10, 15, 18, 25 and 31 m) during maximum thermal stratification. We used custom databases to identify transcripts of genes encoding complex iron-sulfur molybdoenzyme (CISM) proteins, with a focus on arsenic (arrA, aioA and arxA) and sulfur cycling (dsrA, aprA and soxB), and assigned them to taxonomic bins. We also report on the distribution of transcripts related to the ars arsenic detoxification pathway. Transcripts from detoxification pathways were not abundant in oxic surface waters (10 m). Arsenic cycling in the suboxic and microaerophilic zones of the water column (15 and 18 m) was dominated by arsenite-oxidizing members of the Gammaproteobacteria most closely affiliated with Thioalkalivibrio and Halomonas, transcribing arxA. We observed a transition to arsenate-reducing bacteria belonging to the Deltaproteobacteria and Firmicutes transcribing arsenate reductase (arrA) in anoxic bottom waters of the lake (25 and 31 m). Sulfur cycling at 15 and 18 m was dominated by Gammaproteobacteria (Thioalkalivibrio and Thioalkalimicrobium) oxidizing reduced S species, with a transition to sulfate-reducing Deltaproteobacteria at 25 and 31 m. Genes related to arsenic and sulfur oxidation from Thioalkalivibrio were more highly transcribed at 15 m relative to other depths. Our data highlight the importance of Thioalkalivibrio to arsenic and sulfur biogeochemistry in Mono Lake and identify new taxa that appear capable of transforming arsenic.
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Affiliation(s)
- Christian F Edwardson
- Department of Marine Sciences, University of Georgia, Athens, GA, USA.,Department of Microbiology, University of Georgia, Athens, GA, USA
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168
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Rogge A, Vogts A, Voss M, Jürgens K, Jost G, Labrenz M. Success of chemolithoautotrophic SUP05 and Sulfurimonas GD17 cells in pelagic Baltic Sea redox zones is facilitated by their lifestyles as K- and r-strategists. Environ Microbiol 2017; 19:2495-2506. [PMID: 28464419 DOI: 10.1111/1462-2920.13783] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 04/25/2017] [Accepted: 04/25/2017] [Indexed: 11/27/2022]
Abstract
Chemolithoautotrophic sulfur-oxidizing and denitrifying Gamma- (particularly the SUP05 cluster) and Epsilonproteobacteria (predominantly Sulfurimonas subgroup GD17) are assumed to compete for substrates (electron donors and acceptors) in marine pelagic redox gradients. To elucidate their ecological niche separation we performed 34 S0 , 15 NO3- and H13 CO3- stable-isotope incubations with water samples from Baltic Sea suboxic, chemocline and sulfidic zones followed by combined phylogenetic staining and high-resolution secondary ion mass spectrometry of single cells. SUP05 cells were small-sized (0.06-0.09 µm3 ) and most abundant in low-sulfidic to suboxic zones, whereas Sulfurimonas GD17 cells were significantly larger (0.26-0.61 µm3 ) and most abundant at the chemocline and below. Together, SUP05 and GD17 cells accumulated up to 48% of the labelled substrates but calculation of cell volume-specific rates revealed that GD17 cells incorporated labelled substrates significantly faster throughout the redox zone, thereby potentially outcompeting SUP05 especially at high substrate concentrations. Thus, in synopsis with earlier described features of SUP05/GD17 we conclude that their spatially overlapping association in stratified sulfidic zones is facilitated by their different lifestyles: whereas SUP05 cells are streamlined, non-motile K-strategists adapted to low substrate concentrations, GD17 cells are motile r-strategists well adapted to fluctuating substrate and redox conditions.
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Affiliation(s)
- Andreas Rogge
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Angela Vogts
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Maren Voss
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Günter Jost
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
| | - Matthias Labrenz
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Rostock-Warnemünde, Germany
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169
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Smith DA, Sessions AL, Dawson KS, Dalleska N, Orphan VJ. Rapid quantification and isotopic analysis of dissolved sulfur species. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:791-803. [PMID: 28249106 DOI: 10.1002/rcm.7846] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 01/06/2017] [Accepted: 02/23/2017] [Indexed: 06/06/2023]
Abstract
RATIONALE Dissolved sulfur species are of significant interest, both as important substrates for microbial activities and as key intermediaries in biogeochemical cycles. Species of intermediate oxidation state such as sulfite, thiosulfate, and thiols are of particular interest but are notoriously difficult to analyze, because of low concentrations and rapid oxidation during storage and analysis. METHODS Dissolved sulfur species are reacted with monobromobimane which yields a fluorescent bimane derivative that is stable to oxidation. Separation by Ultra-Performance Liquid Chromatography (UPLC) on a C18 column yields baseline resolution of analytes in under 5 min. Fluorescence detection (380 nm excitation, 480 nm emission) provides highly selective and sensitive quantitation, and Time-of-Flight Mass Spectrometry (TOF-MS) is used to quantify isotopic abundance, providing the ability to detect stable isotope tracers (either 33 S or 34 S). RESULTS Sulfite, thiosulfate, methanethiol, and bisulfide were quantified with on-column detection limits of picomoles (μM concentrations). Other sulfur species with unshared electrons are also amenable to analysis. TOF-MS detection of 34 S enrichment was accurate and precise to within 0.6% (relative) when sample and standard had similar isotope ratios, and was able to detect enrichments as small as 0.01 atom%. Accuracy was validated by comparison to isotope-ratio mass spectrometry. Four example applications are provided to demonstrate the utility of this method. CONCLUSIONS Derivatization of aqueous sulfur species with bromobimane is easily accomplished in the field, and protects analytes from oxidation during storage. UPLC separation with fluorescence detection provides low-μM detection limits. Using high-resolution TOF-MS, accurate detection of as little as 0.01% 34 S label incorporation into multiple species is feasible. This provides a useful new analytical window into microbial sulfur cycling. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Derek A Smith
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | - Alex L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | - Katherine S Dawson
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | - Nathan Dalleska
- Environmental Science and Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA
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170
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Ludington WB, Seher TD, Applegate O, Li X, Kliegman JI, Langelier C, Atwill ER, Harter T, DeRisi JL. Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater. PLoS One 2017; 12:e0174930. [PMID: 28384184 PMCID: PMC5383146 DOI: 10.1371/journal.pone.0174930] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/18/2017] [Indexed: 12/12/2022] Open
Abstract
Background Climate change produces extremes in both temperature and precipitation causing increased drought severity and increased reliance on groundwater resources. Agricultural practices, which rely on groundwater, are sensitive to but also sources of contaminants, including nitrate. How agricultural contamination drives groundwater geochemistry through microbial metabolism is poorly understood. Methods On an active cow dairy in the Central Valley of California, we sampled groundwater from three wells at depths of 4.3 m (two wells) and 100 m (one well) below ground surface (bgs) as well as an effluent surface water lagoon that fertilizes surrounding corn fields. We analyzed the samples for concentrations of solutes, heavy metals, and USDA pathogenic bacteria of the Escherichia coli and Enterococcus groups as part of a long term groundwater monitoring study. Whole metagenome shotgun sequencing and assembly revealed taxonomic composition and metabolic potential of the community. Results Elevated nitrate and dissolved organic carbon occurred at 4.3m but not at 100m bgs. Metagenomics confirmed chemical observations and revealed several Planctomycete genomes, including a new Brocadiaceae lineage and a likely Planctomycetes OM190, as well novel diversity and high abundance of nano-prokaryotes from the Candidate Phyla Radiation (CPR), the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea (DPANN) and the Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota (TACK) superphyla. Pathway analysis suggests community interactions based on complimentary primary metabolic pathways and abundant secondary metabolite operons encoding antimicrobials and quorum sensing systems. Conclusions The metagenomes show strong resemblance to activated sludge communities from a nitrogen removal reactor at a wastewater treatment plant, suggesting that natural bioremediation occurs through microbial metabolism. Elevated nitrate and rich secondary metabolite biosynthetic capacity suggest incomplete remediation and the potential for novel pharmacologically active compounds.
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Affiliation(s)
- William B. Ludington
- Molecular Cell Biology Department, University of California, Berkeley, United States of America
- * E-mail:
| | - Thaddeus D. Seher
- Molecular Cell Biology Department, University of California, Berkeley, United States of America
| | - Olin Applegate
- Department of Land, Air and Water Resources, University of California, Davis, Davis, United States of America
| | - Xunde Li
- Department of Population Health and Reproduction, University of California, Davis, Davis, United States of America
- Western Institute for Food Safety and Security, University of California, Davis, Davis, United States of America
| | - Joseph I. Kliegman
- Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco, United States of America
| | - Charles Langelier
- Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco, United States of America
| | - Edward R. Atwill
- Department of Population Health and Reproduction, University of California, Davis, Davis, United States of America
- Western Institute for Food Safety and Security, University of California, Davis, Davis, United States of America
| | - Thomas Harter
- Department of Land, Air and Water Resources, University of California, Davis, Davis, United States of America
| | - Joseph L. DeRisi
- Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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171
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Kappler A, Bryce C. Cryptic biogeochemical cycles: unravelling hidden redox reactions. Environ Microbiol 2017; 19:842-846. [DOI: 10.1111/1462-2920.13687] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andreas Kappler
- Geomicrobiology; Center for Applied Geosciences, University of Tuebingen; Germany
| | - Casey Bryce
- Geomicrobiology; Center for Applied Geosciences, University of Tuebingen; Germany
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172
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Dick GJ. Embracing the mantra of modellers and synthesizing omics, experiments and models. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:18-20. [PMID: 27775862 DOI: 10.1111/1758-2229.12491] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
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173
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Jessen GL, Lichtschlag A, Ramette A, Pantoja S, Rossel PE, Schubert CJ, Struck U, Boetius A. Hypoxia causes preservation of labile organic matter and changes seafloor microbial community composition (Black Sea). SCIENCE ADVANCES 2017; 3:e1601897. [PMID: 28246637 PMCID: PMC5302875 DOI: 10.1126/sciadv.1601897] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/04/2017] [Indexed: 05/13/2023]
Abstract
Bottom-water oxygen supply is a key factor governing the biogeochemistry and community composition of marine sediments. Whether it also determines carbon burial rates remains controversial. We investigated the effect of varying oxygen concentrations (170 to 0 μM O2) on microbial remineralization of organic matter in seafloor sediments and on community diversity of the northwestern Crimean shelf break. This study shows that 50% more organic matter is preserved in surface sediments exposed to hypoxia compared to oxic bottom waters. Hypoxic conditions inhibit bioturbation and decreased remineralization rates even within short periods of a few days. These conditions led to the accumulation of threefold more phytodetritus pigments within 40 years compared to the oxic zone. Bacterial community structure also differed between oxic, hypoxic, and anoxic zones. Functional groups relevant in the degradation of particulate organic matter, such as Flavobacteriia, Gammaproteobacteria, and Deltaproteobacteria, changed with decreasing oxygenation, and the microbial community of the hypoxic zone took longer to degrade similar amounts of deposited reactive matter. We conclude that hypoxic bottom-water conditions-even on short time scales-substantially increase the preservation potential of organic matter because of the negative effects on benthic fauna and particle mixing and by favoring anaerobic processes, including sulfurization of matter.
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Affiliation(s)
- Gerdhard L Jessen
- Max Planck Institute for Marine Microbiology, Bremen, Germany.; HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Sciences, Bremerhaven, Germany
| | - Anna Lichtschlag
- Max Planck Institute for Marine Microbiology, Bremen, Germany.; HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Sciences, Bremerhaven, Germany
| | - Alban Ramette
- Max Planck Institute for Marine Microbiology, Bremen, Germany.; HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Sciences, Bremerhaven, Germany
| | - Silvio Pantoja
- Department of Oceanography and COPAS Sur-Austral, University of Concepción, Concepción, Chile
| | - Pamela E Rossel
- Max Planck Institute for Marine Microbiology, Bremen, Germany.; HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Sciences, Bremerhaven, Germany.; Research Group for Marine Geochemistry (ICBM-MPI Bridging Group), Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Carsten J Schubert
- Department of Surface Waters-Research and Management, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Ulrich Struck
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology, Bremen, Germany.; HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Sciences, Bremerhaven, Germany
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174
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Hansel C. Small but mighty: how minor components drive major biogeochemical cycles. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:8-10. [PMID: 27701847 DOI: 10.1111/1758-2229.12481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Affiliation(s)
- Colleen Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
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175
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Impacts of chemical gradients on microbial community structure. ISME JOURNAL 2017; 11:920-931. [PMID: 28094795 PMCID: PMC5363838 DOI: 10.1038/ismej.2016.175] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 10/25/2016] [Accepted: 11/08/2016] [Indexed: 12/05/2022]
Abstract
Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.
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176
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Singh RP, Manchanda G, Li ZF, Rai AR. Insight of Proteomics and Genomics in Environmental Bioremediation. ACTA ACUST UNITED AC 2017. [DOI: 10.4018/978-1-5225-2325-3.ch003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Bioremediation of hazardous substances from environment is a major human and environmental health concern but can be managed by the microorganism due to their variety of properties that can effectively change the complexity. Microorganisms convey endogenous genetic, biochemical and physiological assets that make them superlative proxies for pollutant remediation in habitat. But, the crucial step is to degrade the complex ring structured pollutants. Interestingly, the integration of genomics and proteomics technologies that allow us to use or alter the genes and proteins of interest in a given microorganism towards a cell-free bioremediation approach. Resultantly, efforts have been finished by developing the genetically modified (Gm) microbes for the remediation of ecological contaminants. Gm microorganisms mediated bioremediation can affect the solubility, bioavailability and mobility of complex hazardous.
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177
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Colin Y, Goñi-Urriza M, Gassie C, Carlier E, Monperrus M, Guyoneaud R. Distribution of Sulfate-Reducing Communities from Estuarine to Marine Bay Waters. MICROBIAL ECOLOGY 2017; 73:39-49. [PMID: 27581035 DOI: 10.1007/s00248-016-0842-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/17/2016] [Indexed: 06/06/2023]
Abstract
Estuaries are highly dynamic ecosystems in which freshwater and seawater mix together. Depending on tide and river inflows, particles originating from rivers or from the remobilization of sediments accumulate in the water column. Due to the salinity gradient and the high heterotrophic activity in the estuarine plume, hypoxic and anoxic microniches may form in oxygenated waters, sustaining favorable conditions for resuspended anaerobic microorganisms. In this context, we tested the hypothesis that anaerobic sulfate-reducing prokaryotes may occur in the water column of the Adour River. Using 16S ribosomal RNA (rRNA) and dsrAB-based terminal restriction fragment length polymorphism (T-RFLP) techniques, we characterized total prokaryotic and sulfate-reducing communities along a gradient from estuarine to marine bay waters. Sulfate-reducing prokaryotes were further characterized by the description of dsrB genes and the cultivation of sulfidogenic anaerobic microorganisms. As a result, physical-chemical parameters had a significant effect on water bacterial diversity and community structure along the studied gradient. The concentration of cultured sulfidogenic microorganisms ranged from 1 to 60 × 103 cells l-1 in the water column. Sulfate-reducing prokaryotes occurring in estuarine waters were closely related to microorganisms previously detected in freshwater sediments, suggesting an estuarine origin, mainly by the remobilization of the sediments. In the marine bay station, sediment-derived sulfate-reducing prokaryotes were not cultured anymore, probably due to freshwater dilution, increasing salinity and extended oxic stress. Nevertheless, isolates related to the type strain Desulfovibrio oceani were cultured from the diluted plume and deep marine waters, indicating the occurrence of autochthonous sulfate-reducing bacteria offshore.
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Affiliation(s)
- Yannick Colin
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France.
- INRA, UMR 1136 INRA/Université de Lorraine, Interactions Arbres Micro-organismes, Centre de Nancy, 54280, Champenoux, France.
| | - Marisol Goñi-Urriza
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
| | - Claire Gassie
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
| | - Elisabeth Carlier
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
| | - Mathilde Monperrus
- Laboratoire de Chimie Analytique Bio-Inorganique et Environnement (LCABIE), IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, Pau, France
| | - Rémy Guyoneaud
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
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178
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Bosak T, Schubotz F, de Santiago-Torio A, Kuehl JV, Carlson HK, Watson N, Daye M, Summons RE, Arkin AP, Deutschbauer AM. System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions. PLoS One 2016; 11:e0168719. [PMID: 28030630 PMCID: PMC5193443 DOI: 10.1371/journal.pone.0168719] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/04/2016] [Indexed: 12/13/2022] Open
Abstract
The prevalence of lipids devoid of phosphorus suggests that the availability of phosphorus limits microbial growth and activity in many anoxic, stratified environments. To better understand the response of anaerobic bacteria to phosphate limitation and starvation, this study combines microscopic and lipid analyses with the measurements of fitness of pooled barcoded transposon mutants of the model sulfate reducing bacterium Desulfovibrio alaskensis G20. Phosphate-limited G20 has lower growth rates and replaces more than 90% of its membrane phospholipids by a mixture of monoglycosyl diacylglycerol (MGDG), glycuronic acid diacylglycerol (GADG) and ornithine lipids, lacks polyphosphate granules, and synthesizes other cellular inclusions. Analyses of pooled and individual mutants reveal the importance of the high-affinity phosphate transport system (the Pst system), PhoR, and glycolipid and ornithine lipid synthases during phosphate limitation. The phosphate-dependent synthesis of MGDG in G20 and the widespread occurrence of the MGDG/GADG synthase among sulfate reducing ∂-Proteobacteria implicate these microbes in the production of abundant MGDG in anaerobic environments where the concentrations of phosphate are lower than 10 μM. Numerous predicted changes in the composition of the cell envelope and systems involved in transport, maintenance of cytoplasmic redox potential, central metabolism and regulatory pathways also suggest an impact of phosphate limitation on the susceptibility of sulfate reducing bacteria to other anthropogenic or environmental stresses.
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Affiliation(s)
- Tanja Bosak
- Department of Earth and Planetary Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | | | - Ana de Santiago-Torio
- Department of Earth and Planetary Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jennifer V Kuehl
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Nicki Watson
- W.M. Keck Microscopy Facility, The Whitehead Institute, Cambridge, Massachusetts, United States of America
| | - Mirna Daye
- Department of Earth and Planetary Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Roger E Summons
- Department of Earth and Planetary Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.,Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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179
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Anas A, Nilayangod C, Jasmin C, Vinothkumar S, Parameswaran PS, Nair S. Diversity and bioactive potentials of culturable heterotrophic bacteria from the surficial sediments of the Arabian Sea. 3 Biotech 2016; 6:238. [PMID: 28330310 PMCID: PMC5106401 DOI: 10.1007/s13205-016-0556-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/19/2016] [Indexed: 11/28/2022] Open
Abstract
Marine sediments accommodate plethora of diverse microorganisms with varying ecological functions. In the present study, we isolated bacteria from surficial sediments of south east Arabian Sea (AS) and evaluated their bioactive potentials. A total of 131 isolates belonging to the phylum: γ-Proteobacteria (63%), Bacillales (34%) and Micrococcaceae (3%) were isolated. Among these, about 40% of the isolates showed the presence of secondary metabolite biosynthetic genes such as PKS or NRPS or both. Organic extracts of nearly 50% of these organisms were cytotoxic to human breast cancer MCF-7 cells and were bactericidal to human pathogens, Escherichia coli and Pseudomonas sp., while 20–30% of them were bactericidal to Vibrio sp. and Staphylococcus sp. too. In all, 8 isolates, belonging to Pseudomonas spp., Bacillus sp. and/or Lysinibacillus sp. displayed high level of bactericidal/cytotoxic properties. The study proposes AS sediment as a rich source for microorganisms with prospective bioactive molecules.
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Affiliation(s)
- Abdulaziz Anas
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India.
| | - Charulatha Nilayangod
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India
| | - C Jasmin
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India
| | - Saradavey Vinothkumar
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India
| | - P S Parameswaran
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India
| | - Shanta Nair
- CSIR-National Institute of Oceanography, Regional Centre, Kochi, Kerala, 682 018, India
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180
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Baltar F, Lundin D, Palovaara J, Lekunberri I, Reinthaler T, Herndl GJ, Pinhassi J. Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO 2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic. Front Microbiol 2016; 7:1670. [PMID: 27818655 PMCID: PMC5073097 DOI: 10.3389/fmicb.2016.01670] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/06/2016] [Indexed: 02/05/2023] Open
Abstract
To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryotic abundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, community composition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments with water from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organic matter (i.e., pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organic matter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DIC fixation rates-assumed to be related to autotrophic metabolisms-were equally stimulated as all the other heterotrophic-related parameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation via anaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be related to cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balance during catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into the mesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic and autotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudied microbial processes of potential importance in mesopelagic waters that require future attention.
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Affiliation(s)
- Federico Baltar
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus UniversityKalmar, Sweden
- Department of Marine Sciences, University of OtagoDunedin, New Zealand
- National Institute of Water and Atmospheric Research (NIWA)/University of Otago Research Centre for OceanographyDunedin, New Zealand
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus UniversityKalmar, Sweden
| | - Joakim Palovaara
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus UniversityKalmar, Sweden
| | - Itziar Lekunberri
- Division of Bio-Oceanography, Department of Limnology and Oceanography, University of ViennaVienna, Austria
- Institut Català de Recerca de l'AiguaGirona, Spain
| | - Thomas Reinthaler
- Division of Bio-Oceanography, Department of Limnology and Oceanography, University of ViennaVienna, Austria
| | - Gerhard J. Herndl
- Division of Bio-Oceanography, Department of Limnology and Oceanography, University of ViennaVienna, Austria
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems, EEMiS, Linnaeus UniversityKalmar, Sweden
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181
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Leavitt WD, Venceslau SS, Pereira IAC, Johnston DT, Bradley AS. Fractionation of sulfur and hydrogen isotopes in Desulfovibrio vulgaris with perturbed DsrC expression. FEMS Microbiol Lett 2016; 363:fnw226. [PMID: 27702753 DOI: 10.1093/femsle/fnw226] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2016] [Indexed: 12/11/2022] Open
Abstract
Dissimilatory sulfate reduction is the central microbial metabolism in global sulfur cycling. Understanding the importance of sulfate reduction to Earth's biogeochemical S cycle requires aggregating single-cell processes with geochemical signals. For sulfate reduction, these signals include the ratio of stable sulfur isotopes preserved in minerals, as well as the hydrogen isotope ratios and structures of microbial membrane lipids preserved in organic matter. In this study, we cultivated the model sulfate reducer, Desulfovibrio vulgaris DSM 644T, to investigate how these parameters were perturbed by changes in expression of the protein DsrC. DsrC is critical to the final metabolic step in sulfate reduction to sulfide. S and H isotopic fractionation imposed by the wild type was compared to three mutants. Discrimination against 34S in sulfate, as calculated from the residual reactant, did not discernibly differ among all strains. However, a closed-system sulfur isotope distillation model, based on accumulated sulfide, produced inconsistent results in one mutant strain IPFG09. Lipids produced by IPFG09 were also slightly enriched in 2H. These results suggest that DsrC alone does not have a major impact on sulfate-S, though may influence sulfide-S and lipid-H isotopic compositions. While intriguing, a mechanistic explanation requires further study under continuous culture conditions.
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Affiliation(s)
- William D Leavitt
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA .,Department of Earth Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - David T Johnston
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Alexander S Bradley
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA .,Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA
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182
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Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters. Proc Natl Acad Sci U S A 2016; 113:10601-6. [PMID: 27601665 DOI: 10.1073/pnas.1600359113] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A major percentage of fixed nitrogen (N) loss in the oceans occurs within nitrite-rich oxygen minimum zones (OMZs) via denitrification and anammox. It remains unclear to what extent ammonium and nitrite oxidation co-occur, either supplying or competing for substrates involved in nitrogen loss in the OMZ core. Assessment of the oxygen (O2) sensitivity of these processes down to the O2 concentrations present in the OMZ core (<10 nmol⋅L(-1)) is therefore essential for understanding and modeling nitrogen loss in OMZs. We determined rates of ammonium and nitrite oxidation in the seasonal OMZ off Concepcion, Chile at manipulated O2 levels between 5 nmol⋅L(-1) and 20 μmol⋅L(-1) Rates of both processes were detectable in the low nanomolar range (5-33 nmol⋅L(-1) O2), but demonstrated a strong dependence on O2 concentrations with apparent half-saturation constants (Kms) of 333 ± 130 nmol⋅L(-1) O2 for ammonium oxidation and 778 ± 168 nmol⋅L(-1) O2 for nitrite oxidation assuming one-component Michaelis-Menten kinetics. Nitrite oxidation rates, however, were better described with a two-component Michaelis-Menten model, indicating a high-affinity component with a Km of just a few nanomolar. As the communities of ammonium and nitrite oxidizers were similar to other OMZs, these kinetics should apply across OMZ systems. The high O2 affinities imply that ammonium and nitrite oxidation can occur within the OMZ core whenever O2 is supplied, for example, by episodic intrusions. These processes therefore compete with anammox and denitrification for ammonium and nitrite, thereby exerting an important control over nitrogen loss.
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183
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Rodriguez-Mora MJ, Edgcomb VP, Taylor C, Scranton MI, Taylor GT, Chistoserdov AY. The Diversity of Sulfide Oxidation and Sulfate Reduction Genes Expressed by the Bacterial Communities of the Cariaco Basin, Venezuela. Open Microbiol J 2016; 10:140-9. [PMID: 27651847 PMCID: PMC5012083 DOI: 10.2174/1874285801610010140] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 12/15/2015] [Accepted: 01/29/2016] [Indexed: 11/22/2022] Open
Abstract
Qualitative expression of dissimilative sulfite reductase (dsrA), a key gene in sulfate reduction, and sulfide:quinone oxidoreductase (sqr), a key gene in sulfide oxidation was investigated. Neither of the two could be amplified from mRNA retrieved with Niskin bottles but were amplified from mRNA retrieved by the Deep SID. The sqr and sqr-like genes retrieved from the Cariaco Basin were related to the sqr genes from a Bradyrhizobium sp., Methylomicrobium alcaliphilum, Sulfurovum sp. NBC37-1, Sulfurimonas autotrophica, Thiorhodospira sibirica and Chlorobium tepidum. The dsrA gene sequences obtained from the redoxcline of the Cariaco Basin belonged to chemoorganotrophic and chemoautotrophic sulfate and sulfur reducers belonging to the class Deltaproteobacteria (phylum Proteobacteria) and the order Clostridiales (phylum Firmicutes).
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Affiliation(s)
- Maria J Rodriguez-Mora
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, 70504, USA
| | - Virginia P Edgcomb
- Geology and Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA
| | - Craig Taylor
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, 02543, USA
| | - Mary I Scranton
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, 11794, USA
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, 11794, USA
| | - Andrei Y Chistoserdov
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, 70504, USA
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184
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Orsi WD, Barker Jørgensen B, Biddle JF. Transcriptional analysis of sulfate reducing and chemolithoautotrophic sulfur oxidizing bacteria in the deep subseafloor. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:452-460. [PMID: 26991974 DOI: 10.1111/1758-2229.12387] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Sulfate reducing bacteria (SRB) oxidize a significant proportion of subseafloor organic carbon, but their metabolic activities and subsistence mechanisms are poorly understood. Here, we report in depth phylogenetic and metabolic analyses of SRB transcripts in the Peru Margin subseafloor and interpret these results in the context of sulfate reduction activity in the sediment. Relative abundance of overall SRB gene transcripts declines strongly whereas relative abundance of ribosomal protein transcripts from sulfate reducing δ-Proteobacteria peak at 90 m below seafloor (mbsf) within a deep sulfate methane transition zone. This coincides with isotopically heavy δ(34) S values of pore water sulfate (70‰), indicating active subseafloor microbial sulfate reduction. Within the shallow sulfate reduction zone (0-5 mbsf), a transcript encoding the beta subunit of dissimilatory sulfite reductase (dsrB) was related to Desulfitobacterium dehalogenans and environmental sequences from Aarhus Bay (Denmark). At 159 mbsf we discovered a transcript encoding the reversely operating dissimilatory sulfite reductase α-subunit (rdsrA), with basal phylogenetic relation to the chemolithoautotrophic SUP05 Group II clade. A diversity of SRB transcripts involved in cellular maintenance point toward potential subsistence mechanisms under low-energy over long time periods, and provide a detailed new picture of SRB activities underlying sulfur cycling in the deep subseafloor.
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Affiliation(s)
- William D Orsi
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Germany
| | - Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, 8000, Aarhus, Denmark
| | - Jennifer F Biddle
- College of Earth, Ocean and Environment, University of Delaware, Lewes, DE, 19958, USA
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185
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Cultivation of a chemoautotroph from the SUP05 clade of marine bacteria that produces nitrite and consumes ammonium. ISME JOURNAL 2016; 11:263-271. [PMID: 27434424 PMCID: PMC5315479 DOI: 10.1038/ismej.2016.87] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 03/02/2016] [Accepted: 05/20/2016] [Indexed: 11/10/2022]
Abstract
Marine oxygen minimum zones (OMZs) are expanding regions of intense nitrogen cycling. Up to half of the nitrogen available for marine organisms is removed from the ocean in these regions. Metagenomic studies have identified an abundant group of sulfur-oxidizing bacteria (SUP05) with the genetic potential for nitrogen cycling and loss in OMZs. However, SUP05 have defied cultivation and their physiology remains untested. We cultured, sequenced and tested the physiology of an isolate from the SUP05 clade. We describe a facultatively anaerobic sulfur-oxidizing chemolithoautotroph that produces nitrite and consumes ammonium under anaerobic conditions. Genetic evidence that closely related strains are abundant at nitrite maxima in OMZs suggests that sulfur-oxidizing chemoautotrophs from the SUP05 clade are a potential source of nitrite, fueling competing nitrogen removal processes in the ocean.
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186
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Seston SL, Beinart RA, Sarode N, Shockey AC, Ranjan P, Ganesh S, Girguis PR, Stewart FJ. Metatranscriptional Response of Chemoautotrophic Ifremeria nautilei Endosymbionts to Differing Sulfur Regimes. Front Microbiol 2016; 7:1074. [PMID: 27486438 PMCID: PMC4949241 DOI: 10.3389/fmicb.2016.01074] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/27/2016] [Indexed: 12/26/2022] Open
Abstract
Endosymbioses between animals and chemoautotrophic bacteria are ubiquitous at hydrothermal vents. These environments are distinguished by high physico-chemical variability, yet we know little about how these symbioses respond to environmental fluctuations. We therefore examined how the γ-proteobacterial symbionts of the vent snail Ifremeria nautilei respond to changes in sulfur geochemistry. Via shipboard high-pressure incubations, we subjected snails to 105 μM hydrogen sulfide (LS), 350 μM hydrogen sulfide (HS), 300 μM thiosulfate (TS) and seawater without any added inorganic electron donor (ND). While transcript levels of sulfur oxidation genes were largely consistent across treatments, HS and TS treatments stimulated genes for denitrification, nitrogen assimilation, and CO2 fixation, coincident with previously reported enhanced rates of inorganic carbon incorporation and sulfur oxidation in these treatments. Transcripts for genes mediating oxidative damage were enriched in the ND and LS treatments, potentially due to a reduction in O2 scavenging when electron donors were scarce. Oxidative TCA cycle gene transcripts were also more abundant in ND and LS treatments, suggesting that I. nautilei symbionts may be mixotrophic when inorganic electron donors are limiting. These data reveal the extent to which I. nautilei symbionts respond to changes in sulfur concentration and species, and, interpreted alongside coupled biochemical metabolic rates, identify gene targets whose expression patterns may be predictive of holobiont physiology in environmental samples.
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Affiliation(s)
| | - Roxanne A Beinart
- Department of Organismic and Evolutionary Biology, Harvard University Cambridge, MA, USA
| | - Neha Sarode
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Abigail C Shockey
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Madison, WI, USA
| | - Piyush Ranjan
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Sangita Ganesh
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University Cambridge, MA, USA
| | - Frank J Stewart
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
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187
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Meyerhof MS, Wilson JM, Dawson MN, Michael Beman J. Microbial community diversity, structure and assembly across oxygen gradients in meromictic marine lakes, Palau. Environ Microbiol 2016; 18:4907-4919. [PMID: 27312889 DOI: 10.1111/1462-2920.13416] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 06/13/2016] [Indexed: 11/29/2022]
Abstract
Microbial communities consume oxygen, alter biogeochemistry and compress habitat in aquatic ecosystems, yet our understanding of these microbial-biogeochemical-ecological interactions is limited by a lack of systematic analyses of low-oxygen ecosystems. Marine lakes provide an ideal comparative system, as they range from well-mixed holomictic lakes to stratified, anoxic, meromictic lakes that vary in their vertical extent of anoxia. We examined microbial communities inhabiting six marine lakes and one ocean site using pyrosequencing of 16S rRNA genes. Microbial richness and evenness was typically highest in the anoxic monimolimnion of meromictic lakes, with common marine bacteria present in mixolimnion communities replaced by anoxygenic phototrophs, sulfate-reducing bacteria and SAR406 in the monimolimnion. These sharp changes in community structure were linked to environmental gradients (constrained variation in redundancy analysis = 68%-76%) - particularly oxygen and pH. However, in those lakes with the steepest oxygen gradients, salinity and dissolved nutrients were important secondary constraining variables, indicating that subtle but substantive differences in microbial communities occur within similar low-oxygen habitats. Deterministic processes were a dominant influence on whole community assembly (all nearest taxon index values >4), demonstrating that the strong environmental gradients present in meromictic marine lakes drive microbial community assembly.
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Affiliation(s)
- Matthew S Meyerhof
- Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
| | - Jesse M Wilson
- Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
| | - Michael N Dawson
- Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
| | - J Michael Beman
- Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
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188
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Lüke C, Speth DR, Kox MAR, Villanueva L, Jetten MSM. Metagenomic analysis of nitrogen and methane cycling in the Arabian Sea oxygen minimum zone. PeerJ 2016; 4:e1924. [PMID: 27077014 PMCID: PMC4830246 DOI: 10.7717/peerj.1924] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 03/21/2016] [Indexed: 01/24/2023] Open
Abstract
Oxygen minimum zones (OMZ) are areas in the global ocean where oxygen concentrations drop to below one percent. Low oxygen concentrations allow alternative respiration with nitrate and nitrite as electron acceptor to become prevalent in these areas, making them main contributors to oceanic nitrogen loss. The contribution of anammox and denitrification to nitrogen loss seems to vary in different OMZs. In the Arabian Sea, both processes were reported. Here, we performed a metagenomics study of the upper and core zone of the Arabian Sea OMZ, to provide a comprehensive overview of the genetic potential for nitrogen and methane cycling. We propose that aerobic ammonium oxidation is carried out by a diverse community of Thaumarchaeota in the upper zone of the OMZ, whereas a low diversity of Scalindua-like anammox bacteria contribute significantly to nitrogen loss in the core zone. Aerobic nitrite oxidation in the OMZ seems to be performed by Nitrospina spp. and a novel lineage of nitrite oxidizing organisms that is present in roughly equal abundance as Nitrospina. Dissimilatory nitrate reduction to ammonia (DNRA) can be carried out by yet unknown microorganisms harbouring a divergent nrfA gene. The metagenomes do not provide conclusive evidence for active methane cycling; however, a low abundance of novel alkane monooxygenase diversity was detected. Taken together, our approach confirmed the genomic potential for an active nitrogen cycle in the Arabian Sea and allowed detection of hitherto overlooked lineages of carbon and nitrogen cycle bacteria.
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Affiliation(s)
- Claudia Lüke
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Daan R Speth
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Martine A R Kox
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Laura Villanueva
- Department of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), 't Horntje (Texel), Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, Netherlands.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands.,Soehngen Institute of Anaerobic Microbiology, Nijmegen, Netherlands
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189
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Moura RL, Amado-Filho GM, Moraes FC, Brasileiro PS, Salomon PS, Mahiques MM, Bastos AC, Almeida MG, Silva JM, Araujo BF, Brito FP, Rangel TP, Oliveira BCV, Bahia RG, Paranhos RP, Dias RJS, Siegle E, Figueiredo AG, Pereira RC, Leal CV, Hajdu E, Asp NE, Gregoracci GB, Neumann-Leitão S, Yager PL, Francini-Filho RB, Fróes A, Campeão M, Silva BS, Moreira APB, Oliveira L, Soares AC, Araujo L, Oliveira NL, Teixeira JB, Valle RAB, Thompson CC, Rezende CE, Thompson FL. An extensive reef system at the Amazon River mouth. SCIENCE ADVANCES 2016; 2:e1501252. [PMID: 27152336 PMCID: PMC4846441 DOI: 10.1126/sciadv.1501252] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 03/25/2016] [Indexed: 05/15/2023]
Abstract
Large rivers create major gaps in reef distribution along tropical shelves. The Amazon River represents 20% of the global riverine discharge to the ocean, generating up to a 1.3 × 10(6)-km(2) plume, and extensive muddy bottoms in the equatorial margin of South America. As a result, a wide area of the tropical North Atlantic is heavily affected in terms of salinity, pH, light penetration, and sedimentation. Such unfavorable conditions were thought to imprint a major gap in Western Atlantic reefs. We present an extensive carbonate system off the Amazon mouth, underneath the river plume. Significant carbonate sedimentation occurred during lowstand sea level, and still occurs in the outer shelf, resulting in complex hard-bottom topography. A permanent near-bottom wedge of ocean water, together with the seasonal nature of the plume's eastward retroflection, conditions the existence of this extensive (~9500 km(2)) hard-bottom mosaic. The Amazon reefs transition from accretive to erosional structures and encompass extensive rhodolith beds. Carbonate structures function as a connectivity corridor for wide depth-ranging reef-associated species, being heavily colonized by large sponges and other structure-forming filter feeders that dwell under low light and high levels of particulates. The oxycline between the plume and subplume is associated with chemoautotrophic and anaerobic microbial metabolisms. The system described here provides several insights about the responses of tropical reefs to suboptimal and marginal reef-building conditions, which are accelerating worldwide due to global changes.
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Affiliation(s)
- Rodrigo L. Moura
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro RJ CEP 21941-599, Brazil
- Laboratório de Sistemas Avançados de Gestão da Produção, Instituto Alberto Luiz Coimbra de Pós-Graduação e Pesquisa de Engenharia, COPPE, UFRJ, Rio de Janeiro RJ CEP 21941-972, Brazil
| | - Gilberto M. Amado-Filho
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro RJ CEP 22460-030, Brazil
| | - Fernando C. Moraes
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro RJ CEP 22460-030, Brazil
- Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ 20940-040, Brazil
| | - Poliana S. Brasileiro
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro RJ CEP 22460-030, Brazil
| | - Paulo S. Salomon
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro RJ CEP 21941-599, Brazil
- Laboratório de Sistemas Avançados de Gestão da Produção, Instituto Alberto Luiz Coimbra de Pós-Graduação e Pesquisa de Engenharia, COPPE, UFRJ, Rio de Janeiro RJ CEP 21941-972, Brazil
| | - Michel M. Mahiques
- Instituto Oceanográfico, Universidade de São Paulo, São Paulo SP CEP 05508-120, Brazil
| | - Alex C. Bastos
- Departamento de Oceanografia, Universidade Federal do Espírito Santo, Vitória ES CEP 29199-970, Brazil
| | - Marcelo G. Almeida
- Laboratório de Ciências Ambientais, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes RJ CEP 28013-602, Brazil
| | - Jomar M. Silva
- Laboratório de Ciências Ambientais, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes RJ CEP 28013-602, Brazil
| | - Beatriz F. Araujo
- Laboratório de Ciências Ambientais, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes RJ CEP 28013-602, Brazil
| | - Frederico P. Brito
- Laboratório de Ciências Ambientais, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes RJ CEP 28013-602, Brazil
| | - Thiago P. Rangel
- Laboratório de Ciências Ambientais, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes RJ CEP 28013-602, Brazil
| | - Braulio C. V. Oliveira
- Laboratório de Ciências Ambientais, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes RJ CEP 28013-602, Brazil
| | - Ricardo G. Bahia
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro RJ CEP 22460-030, Brazil
| | - Rodolfo P. Paranhos
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro RJ CEP 21941-599, Brazil
| | - Rodolfo J. S. Dias
- Instituto Oceanográfico, Universidade de São Paulo, São Paulo SP CEP 05508-120, Brazil
| | - Eduardo Siegle
- Instituto Oceanográfico, Universidade de São Paulo, São Paulo SP CEP 05508-120, Brazil
| | - Alberto G. Figueiredo
- Instituto de Geociências, Universidade Federal Fluminense, Niterói RJ CEP 24210-346, Brazil
| | - Renato C. Pereira
- Instituto de Biologia, Universidade Federal Fluminense, Niterói RJ CEP 24210-130, Brazil
| | - Camille V. Leal
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro RJ CEP 21941-599, Brazil
- Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ 20940-040, Brazil
| | - Eduardo Hajdu
- Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro RJ 20940-040, Brazil
| | - Nils E. Asp
- Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança PA CEP 68600-000, Brazil
| | - Gustavo B. Gregoracci
- Departmento de Ciências do Mar, Universidade Federal de São Paulo, Santos SP CEP 11070-100, Brazil
| | - Sigrid Neumann-Leitão
- Departamento de Oceanografia, Universidade Federal de Pernambuco, Recife PE CEP 50670-901, Brazil
| | - Patricia L. Yager
- Department of Marine Sciences, University of Georgia, Athens, GA 30602–2626, USA
| | | | - Adriana Fróes
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro RJ CEP 21941-599, Brazil
| | - Mariana Campeão
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro RJ CEP 21941-599, Brazil
| | - Bruno S. Silva
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro RJ CEP 21941-599, Brazil
| | - Ana P. B. Moreira
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro RJ CEP 21941-599, Brazil
| | - Louisi Oliveira
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro RJ CEP 21941-599, Brazil
| | - Ana C. Soares
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro RJ CEP 21941-599, Brazil
| | - Lais Araujo
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro RJ CEP 21941-599, Brazil
| | - Nara L. Oliveira
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA CEP 45650-000, Brazil
| | - João B. Teixeira
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA CEP 45650-000, Brazil
| | - Rogerio A. B. Valle
- Laboratório de Sistemas Avançados de Gestão da Produção, Instituto Alberto Luiz Coimbra de Pós-Graduação e Pesquisa de Engenharia, COPPE, UFRJ, Rio de Janeiro RJ CEP 21941-972, Brazil
| | - Cristiane C. Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro RJ CEP 21941-599, Brazil
| | - Carlos E. Rezende
- Laboratório de Ciências Ambientais, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes RJ CEP 28013-602, Brazil
- Corresponding author: E-mail: (F.L.T.); (C.E.R.)
| | - Fabiano L. Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro RJ CEP 21941-599, Brazil
- Laboratório de Sistemas Avançados de Gestão da Produção, Instituto Alberto Luiz Coimbra de Pós-Graduação e Pesquisa de Engenharia, COPPE, UFRJ, Rio de Janeiro RJ CEP 21941-972, Brazil
- Corresponding author: E-mail: (F.L.T.); (C.E.R.)
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190
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Houghton JL, Foustoukos DI, Flynn TM, Vetriani C, Bradley AS, Fike DA. Thiosulfate oxidation by Thiomicrospira thermophila: metabolic flexibility in response to ambient geochemistry. Environ Microbiol 2016; 18:3057-72. [PMID: 26914243 DOI: 10.1111/1462-2920.13232] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 01/17/2016] [Indexed: 11/29/2022]
Abstract
Previous studies of the stoichiometry of thiosulfate oxidation by colorless sulfur bacteria have failed to demonstrate mass balance of sulfur, indicating that unidentified oxidized products must be present. Here the reaction stoichiometry and kinetics under variable pH conditions during the growth of Thiomicrospira thermophila strain EPR85, isolated from diffuse hydrothermal fluids at the East Pacific Rise, is presented. At pH 8.0, thiosulfate was stoichiometrically converted to sulfate. At lower pH, the products of thiosulfate oxidation were extracellular elemental sulfur and sulfate. We were able to replicate previous experiments and identify the missing sulfur as tetrathionate, consistent with previous reports of the activity of thiosulfate dehydrogenase. Tetrathionate was formed under slightly acidic conditions. Genomic DNA from T. thermophila strain EPR85 contains genes homologous to those in the Sox pathway (soxAXYZBCDL), as well as rhodanese and thiosulfate dehydrogenase. No other sulfur oxidizing bacteria containing sox(CD)2 genes have been reported to produce extracellular elemental sulfur. If the apparent modified Sox pathway we observed in T. thermophila is present in marine Thiobacillus and Thiomicrospira species, production of extracellular elemental sulfur may be biogeochemically important in marine sulfur cycling.
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Affiliation(s)
- J L Houghton
- Department of Earth and Planetary Sciences, Washington University, St. Louis, MO, 63130, USA.
| | - D I Foustoukos
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, DC, 20015, USA
| | - T M Flynn
- Biosciences Division, Argonne National Laboratory, Lemont, IL, 60439, USA.,Computation Institution, The University of Chicago, Chicago, IL, 60637, USA
| | - C Vetriani
- Department of Biochemistry and Microbiology and Institute of Earth, Ocean and Atmospheric Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Alexander S Bradley
- Department of Earth and Planetary Sciences, Washington University, St. Louis, MO, 63130, USA
| | - D A Fike
- Department of Earth and Planetary Sciences, Washington University, St. Louis, MO, 63130, USA
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191
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Dreux Chappell P, Vedmati J, Selph KE, Cyr HA, Jenkins BD, Landry MR, Moffett JW. Preferential depletion of zinc within Costa Rica upwelling dome creates conditions for zinc co-limitation of primary production. JOURNAL OF PLANKTON RESEARCH 2016; 38:244-255. [PMID: 27275028 PMCID: PMC4889994 DOI: 10.1093/plankt/fbw018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 02/04/2016] [Indexed: 05/25/2023]
Abstract
The Costa Rica Dome (CRD) is a wind-driven feature characterized by high primary production and an unusual cyanobacterial bloom in surface waters. It is not clear whether this bloom arises from top-down or bottom-up processes. Several studies have argued that trace metal geochemistry within the CRD contributes to the composition of the phytoplankton assemblages, since cyanobacteria and eukaryotic phytoplankton have different transition metal requirements. Here, we report that total dissolved zinc (Zn) is significantly depleted relative to phosphate (P) and silicate (Si) within the upper water column of the CRD compared with other oceanic systems, and this may create conditions favorable for cyanobacteria, which have lower Zn requirements than their eukaryotic competitors. Shipboard grow-out experiments revealed that while Si was a limiting factor under our experimental conditions, additions of Si and either iron (Fe) or Zn led to higher biomass than Si additions alone. The addition of Fe and Zn alone did not lead to significant enhancements. Our results suggest that the depletion of Zn relative to P in upwelled waters may create conditions in the near-surface waters that favor phytoplankton with low Zn requirements, including cyanobacteria.
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Affiliation(s)
- P. Dreux Chappell
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
- Department of Ocean, Earth, and Atmospheric Sciences, Old Dominion University, Norfolk, VA 23529, USA
| | - Jagruti Vedmati
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Karen E. Selph
- Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Heather A. Cyr
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Bethany D. Jenkins
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Michael R. Landry
- Scripps Institution of Oceanography, University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0227, USA
| | - James W. Moffett
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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192
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Cheung S, Xia X, Guo C, Liu H. Diazotroph community structure in the deep oxygen minimum zone of the Costa Rica Dome. JOURNAL OF PLANKTON RESEARCH 2016; 38:380-391. [PMID: 27275037 PMCID: PMC4889993 DOI: 10.1093/plankt/fbw003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 01/11/2016] [Indexed: 05/10/2023]
Abstract
Oxygen minimum zones (OMZs), characterized by depleted dissolved oxygen concentration in the intermediate depth of the water column, are predicted to expand under the influence of global warming. Recent studies in the Eastern Tropical South Pacific Ocean and Arabian Sea have reported that heterotrophic nitrogen fixation is active in the OMZs. In this study, we investigated the community structure of diazotrophs in the OMZ of the Costa Rica Dome (CRD) upwelling region in the Eastern Tropical North Pacific Ocean, using 454-pyrosequencing of nifH gene amplicons. Comparing diazotroph assemblages in different depth strata of the OMZ (200-1000 m in depth), we found a unique diazotroph community in the OMZ core, which was mainly dominated by methanotroph-like diazotrophs, suggesting a potential coupling of nitrogen cycle and methane assimilation. In addition, some OTUs revealed in this study, especially those belonging to the large sub-cluster Vibrio diazotrophicus, were reported to be abundant and expressing the nifH gene in other OMZs. Our results suggest that the unique hydrographic conditions in OMZs may support similar assemblages of diazotrophs, and heterotrophic nitrogen fixation could also be occurring in our studied region. Our study provides the first insight into the composition and distribution of putative diazotrophs in the CRD OMZ.
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193
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Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments. ISME JOURNAL 2016; 10:1939-53. [PMID: 26872043 DOI: 10.1038/ismej.2015.257] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/27/2015] [Accepted: 12/01/2015] [Indexed: 01/10/2023]
Abstract
Marine sediments are the largest carbon sink on earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70-86% of dark carbon fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with (14)C-bicarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark carbon fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and carbon fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine carbon and sulfur cycles.
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194
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Mikucki JA, Lee PA, Ghosh D, Purcell AM, Mitchell AC, Mankoff KD, Fisher AT, Tulaczyk S, Carter S, Siegfried MR, Fricker HA, Hodson T, Coenen J, Powell R, Scherer R, Vick-Majors T, Achberger AA, Christner BC, Tranter M. Subglacial Lake Whillans microbial biogeochemistry: a synthesis of current knowledge. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2014.0290. [PMID: 26667908 DOI: 10.1098/rsta.2014.0290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Liquid water occurs below glaciers and ice sheets globally, enabling the existence of an array of aquatic microbial ecosystems. In Antarctica, large subglacial lakes are present beneath hundreds to thousands of metres of ice, and scientific interest in exploring these environments has escalated over the past decade. After years of planning, the first team of scientists and engineers cleanly accessed and retrieved pristine samples from a West Antarctic subglacial lake ecosystem in January 2013. This paper reviews the findings to date on Subglacial Lake Whillans and presents new supporting data on the carbon and energy metabolism of resident microbes. The analysis of water and sediments from the lake revealed a diverse microbial community composed of bacteria and archaea that are close relatives of species known to use reduced N, S or Fe and CH4 as energy sources. The water chemistry of Subglacial Lake Whillans was dominated by weathering products from silicate minerals with a minor influence from seawater. Contributions to water chemistry from microbial sulfide oxidation and carbonation reactions were supported by genomic data. Collectively, these results provide unequivocal evidence that subglacial environments in this region of West Antarctica host active microbial ecosystems that participate in subglacial biogeochemical cycling.
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Affiliation(s)
- J A Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - P A Lee
- Hollings Marine Lab, College of Charleston, Charleston, SC 29412, USA
| | - D Ghosh
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - A M Purcell
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - A C Mitchell
- Department of Geography and Earth Sciences, Aberystwyth University, Aberystwyth, UK
| | - K D Mankoff
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - A T Fisher
- Earth and Planetary Sciences, University of California, Santa Cruz, CA, USA
| | - S Tulaczyk
- Earth and Planetary Sciences, University of California, Santa Cruz, CA, USA
| | - S Carter
- Institute for Geophysics and Planetary Physics, Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA
| | - M R Siegfried
- Institute for Geophysics and Planetary Physics, Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA
| | - H A Fricker
- Institute for Geophysics and Planetary Physics, Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA
| | - T Hodson
- Department of Geology and Environmental Geosciences Northern, Illinois University, DeKalb, IL 60115, USA
| | - J Coenen
- Department of Geology and Environmental Geosciences Northern, Illinois University, DeKalb, IL 60115, USA
| | - R Powell
- Department of Geology and Environmental Geosciences Northern, Illinois University, DeKalb, IL 60115, USA
| | - R Scherer
- Department of Geology and Environmental Geosciences Northern, Illinois University, DeKalb, IL 60115, USA
| | - T Vick-Majors
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT 59717, USA
| | - A A Achberger
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - B C Christner
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - M Tranter
- Bristol Glaciology Centre, Geographical Sciences, University of Bristol, Bristol BS8 1SS, UK
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195
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Santos AA, Venceslau SS, Grein F, Leavitt WD, Dahl C, Johnston DT, Pereira IAC. A protein trisulfide couples dissimilatory sulfate reduction to energy conservation. Science 2016; 350:1541-5. [PMID: 26680199 DOI: 10.1126/science.aad3558] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Microbial sulfate reduction has governed Earth's biogeochemical sulfur cycle for at least 2.5 billion years. However, the enzymatic mechanisms behind this pathway are incompletely understood, particularly for the reduction of sulfite-a key intermediate in the pathway. This critical reaction is performed by DsrAB, a widespread enzyme also involved in other dissimilatory sulfur metabolisms. Using in vitro assays with an archaeal DsrAB, supported with genetic experiments in a bacterial system, we show that the product of sulfite reduction by DsrAB is a protein-based trisulfide, in which a sulfite-derived sulfur is bridging two conserved cysteines of DsrC. Physiological studies also reveal that sulfate reduction rates are determined by cellular levels of DsrC. Dissimilatory sulfate reduction couples the four-electron reduction of the DsrC trisulfide to energy conservation.
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Affiliation(s)
- André A Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Fabian Grein
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - William D Leavitt
- Department of Earth and Planetary Science, Harvard University, Cambridge, MA, USA
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany
| | - David T Johnston
- Department of Earth and Planetary Science, Harvard University, Cambridge, MA, USA
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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196
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Frank KL, Rogers KL, Rogers DR, Johnston DT, Girguis PR. Key Factors Influencing Rates of Heterotrophic Sulfate Reduction in Active Seafloor Hydrothermal Massive Sulfide Deposits. Front Microbiol 2015; 6:1449. [PMID: 26733984 PMCID: PMC4686611 DOI: 10.3389/fmicb.2015.01449] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/04/2015] [Indexed: 11/14/2022] Open
Abstract
Hydrothermal vents are thermally and geochemically dynamic habitats, and the organisms therein are subject to steep gradients in temperature and chemistry. To date, the influence of these environmental dynamics on microbial sulfate reduction has not been well constrained. Here, via multivariate experiments, we evaluate the effects of key environmental variables (temperature, pH, H2S, SO42−, DOC) on sulfate reduction rates and metabolic energy yields in material recovered from a hydrothermal flange from the Grotto edifice in the Main Endeavor Field, Juan de Fuca Ridge. Sulfate reduction was measured in batch reactions across a range of physico-chemical conditions. Temperature and pH were the strongest stimuli, and maximum sulfate reduction rates were observed at 50°C and pH 6, suggesting that the in situ community of sulfate-reducing organisms in Grotto flanges may be most active in a slightly acidic and moderate thermal/chemical regime. At pH 4, sulfate reduction rates increased with sulfide concentrations most likely due to the mitigation of metal toxicity. While substrate concentrations also influenced sulfate reduction rates, energy-rich conditions muted the effect of metabolic energetics on sulfate reduction rates. We posit that variability in sulfate reduction rates reflect the response of the active microbial consortia to environmental constraints on in situ microbial physiology, toxicity, and the type and extent of energy limitation. These experiments help to constrain models of the spatial contribution of heterotrophic sulfate reduction within the complex gradients inherent to seafloor hydrothermal deposits.
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Affiliation(s)
- Kiana L Frank
- Department of Molecular Biology, Harvard UniversityCambridge, MA, USA; Department of Oceanography, University of HawaiiHonolulu, HI, USA
| | - Karyn L Rogers
- Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute Troy, NY, USA
| | - Daniel R Rogers
- Department of Chemistry, Stonehill CollegeEaston, MA, USA; Department of Earth and Planetary Sciences, Harvard UniversityCambridge, MA, USA
| | - David T Johnston
- Department of Earth and Planetary Sciences, Harvard University Cambridge, MA, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University Cambridge, MA, USA
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197
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Schobben M, Stebbins A, Ghaderi A, Strauss H, Korn D, Korte C. Eutrophication, microbial-sulfate reduction and mass extinctions. Commun Integr Biol 2015; 9:e1115162. [PMID: 27066181 PMCID: PMC4802792 DOI: 10.1080/19420889.2015.1115162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/26/2015] [Accepted: 10/26/2015] [Indexed: 10/27/2022] Open
Abstract
In post-Cambrian time, life on Earth experienced 5 major extinction events, likely instigated by adverse environmental conditions. Biodiversity loss among marine taxa, for at least 3 of these mass extinction events (Late Devonian, end-Permian and end-Triassic), has been connected with widespread oxygen-depleted and sulfide-bearing marine water. Furthermore, geochemical and sedimentary evidence suggest that these events correlate with rather abrupt climate warming and possibly increased terrestrial weathering. This suggests that biodiversity loss may be triggered by mechanisms intrinsic to the Earth system, notably, the biogeochemical sulfur and carbon cycle. This climate warming feedback produces large-scale eutrophication on the continental shelf, which, in turn, expands oxygen minimum zones by increased respiration, which can turn to a sulfidic state by increased microbial-sulfate reduction due to increased availability of organic matter. A plankton community turnover from a high-diversity eukaryote to high-biomass bacterial dominated food web is the catalyst proposed in this anoxia-extinction scenario and stands in stark contrast to the postulated productivity collapse suggested for the end-Cretaceous mass extinction. This cascade of events is relevant for the future ocean under predicted greenhouse driven climate change. The exacerbation of anoxic "dead" zones is already progressing in modern oceanic environments, and this is likely to increase due to climate induced continental weathering and resulting eutrophication of the oceans.
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Affiliation(s)
- Martin Schobben
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung , Berlin, Germany
| | - Alan Stebbins
- School for the Environment, University of Massachusetts Boston , Boston, MA, USA
| | - Abbas Ghaderi
- Department of Geology, Ferdowsi University of Mashhad , Mashhad, Iran
| | - Harald Strauss
- Institut für Geologie und Paläontologie, Westfälische Wilhelms-Universität Münster , Münster, Germany
| | - Dieter Korn
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung , Berlin, Germany
| | - Christoph Korte
- Department of Geosciences and Natural Resource Management, University of Copenhagen , Copenhagen, Denmark
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198
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Genome Sequence of "Candidatus Thioglobus autotrophica" Strain EF1, a Chemoautotroph from the SUP05 Clade of Marine Gammaproteobacteria. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01156-15. [PMID: 26494660 PMCID: PMC4616170 DOI: 10.1128/genomea.01156-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Chemoautotrophic marine bacteria from the SUP05 clade of marine gammaproteobacteria often dominate low-oxygen waters in upwelling regions, fjords, and hydrothermal systems. Here, we announce the complete genome sequence of "Candidatus Thioglobus autotrophica" strain EF1, the first cultured chemoautotrophic representative from the SUP05 clade.
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199
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Colatriano D, Ramachandran A, Yergeau E, Maranger R, Gélinas Y, Walsh DA. Metaproteomics of aquatic microbial communities in a deep and stratified estuary. Proteomics 2015. [PMID: 26223443 DOI: 10.1002/pmic.201500079] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Here we harnessed the power of metaproteomics to assess the metabolic diversity and function of stratified aquatic microbial communities in the deep and expansive Lower St. Lawrence Estuary, located in eastern Canada. Vertical profiling of the microbial communities through the stratified water column revealed differences in metabolic lifestyles and in carbon and nitrogen processing pathways. In productive surface waters, we identified heterotrophic populations involved in the processing of high and low molecular weight organic matter from both terrestrial (e.g. cellulose and xylose) and marine (e.g. organic compatible osmolytes) sources. In the less productive deep waters, chemosynthetic production coupled to nitrification by MG-I Thaumarchaeota and Nitrospina appeared to be a dominant metabolic strategy. Similar to other studies of the coastal ocean, we identified methanol oxidation proteins originating from the common OM43 marine clade. However, we also identified a novel lineage of methanol-oxidizers specifically in the particle-rich bottom (i.e. nepheloid) layer. Membrane transport proteins assigned to the uncultivated MG-II Euryarchaeota were also specifically detected in the nepheloid layer. In total, these results revealed strong vertical structure of microbial taxa and metabolic activities, as well as the presence of specific "nepheloid" taxa that may contribute significantly to coastal ocean nutrient cycling.
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Affiliation(s)
- David Colatriano
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | | | - Etienne Yergeau
- National Research Council Canada, Energy, Mining and Environment, Montreal, Quebec, Canada
| | - Roxane Maranger
- Département des Sciences Biologiques, Université de Montréal, Montréal, Quebec, Canada.,Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Montreal, Quebec, Canada
| | - Yves Gélinas
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, Canada.,Geochemistry and Geodynamics Research Center (GEOTOP), Montreal, Quebec, Canada
| | - David A Walsh
- Department of Biology, Concordia University, Montreal, Quebec, Canada.,Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Montreal, Quebec, Canada.,Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Toronto ON, Canada
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200
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Light-dependent sulfide oxidation in the anoxic zone of the Chesapeake Bay can be explained by small populations of phototrophic bacteria. Appl Environ Microbiol 2015; 81:7560-9. [PMID: 26296727 DOI: 10.1128/aem.02062-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 08/17/2015] [Indexed: 11/20/2022] Open
Abstract
Microbial sulfide oxidation in aquatic environments is an important ecosystem process, as sulfide is potently toxic to aerobic organisms. Sulfide oxidation in anoxic waters can prevent the efflux of sulfide to aerobic water masses, thus mitigating toxicity. The contribution of phototrophic sulfide-oxidizing bacteria to anaerobic sulfide oxidation in the Chesapeake Bay and the redox chemistry of the stratified water column were investigated in the summers of 2011 to 2014. In 2011 and 2013, phototrophic sulfide-oxidizing bacteria closely related to Prosthecochloris species of the phylum Chlorobi were cultivated from waters sampled at and below the oxic-anoxic interface, where measured light penetration was sufficient to support populations of low-light-adapted photosynthetic bacteria. In 2012, 2013, and 2014, light-dependent sulfide loss was observed in freshly collected water column samples. In these samples, extremely low light levels caused 2- to 10-fold increases in the sulfide uptake rate over the sulfide uptake rate under dark conditions. An enrichment, CB11, dominated by Prosthecochloris species, oxidized sulfide with a Ks value of 11 μM and a Vmax value of 51 μM min(-1) (mg protein(-1)). Using these kinetic values with in situ sulfide concentrations and light fluxes, we calculated that a small population of Chlorobi similar to those in enrichment CB11 can account for the observed anaerobic light-dependent sulfide consumption activity in natural water samples. We conclude that Chlorobi play a far larger role in the Chesapeake Bay than currently appreciated. This result has potential implications for coastal anoxic waters and expanding oxygen-minimum zones as they begin to impinge on the photic zone.
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