MINI REVIEW article

Front. Microbiol., 20 September 2011

Sec. Physiology and Metabolism of Microorganisms

volume 2 - 2011 | https://doi.org/10.3389/fmicb.2011.00192

Sulfur Metabolisms in Epsilon- and Gamma-Proteobacteria in Deep-Sea Hydrothermal Fields

  • MY

    Masahiro Yamamoto 1,2*

  • KT

    Ken Takai 1,2

  • 1. Subsurface Geobiology Advanced Research Project, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan

  • 2. Precambrian Ecosystem Laboratory, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan

Abstract

In deep-sea hydrothermal systems, super hot and reduced vent fluids from the subseafloor blend with cold and oxidized seawater. Very unique and dense ecosystems are formed within these environments. Many molecular ecological studies showed that chemoautotrophic epsilon- and gamma-Proteobacteria are predominant primary producers in both free-living and symbiotic microbial communities in global deep-sea hydrothermal fields. Inorganic sulfur compounds are important substrates for the energy conservative metabolic pathways in these microorganisms. Recent genomic and metagenomic analyses and biochemical studies have contributed to the understanding of potential sulfur metabolic pathways for these chemoautotrophs. Epsilon-Proteobacteria use sulfur compounds for both electron-donors and -acceptors. On the other hand, gamma-Proteobacteria utilize two different sulfur-oxidizing pathways. It is hypothesized that differences between the metabolic pathways used by these two predominant proteobacterial phyla are associated with different ecophysiological strategies; extending the energetically feasible habitats with versatile energy metabolisms in the epsilon-Proteobacteria and optimizing energy production rate and yield for relatively narrow habitable zones in the gamma-Proteobacteria.

Introduction

The deep-sea hydrothermal system is one of the most extreme environments on Earth. It is characterized by darkness, high pressures, and steep physical and chemical gradients formed in mixing zones between hot hydrothermal vent fluid and cold deep-sea water. Very unique and dense communities of invertebrates are sustained in absence of a photosynthetic energy source (Dubilier et al., ). Almost all vent-endemic animals are strongly associated with the primary production of the endo- and/or epi-symbiotic chemoautotrophic microorganisms (Jeanthon, ). With the discovery of deep-sea hydrothermal ecosystem in 1977, it had been proposed that hydrogen sulfide-oxidizing and oxygen-reducing chemoautotrophs potentially sustain the primary production in these unique ecosystems (Kvenvolden et al., ). However, anoxic hydrothermal fluids contain several reduced compounds such as H2, CH4, and reduced metal ions in addition to H2S (Jannasch and Mottl, ). Recent cultivation studies have demonstrated that these chemicals are all used as energy sources for chemoautotrophs (Jannasch and Mottl, ; Nakagawa et al., ; Campbell et al., ; Emerson et al., ), indicating the great diversity of chemoautotrophic energy metabolic processes in the ecosystems. Hydrogen gas (H2) is one of the most important energy sources, and the hydrogen-dependent ecosystems may represent analogs for the earliest biological communities on Earth (Takai et al., , ; Nealson et al., ).

Hydrogen sulfide or sulfide is primarily supplied via high temperatures of seawater–rock interactions in the subseafloor hydrothermal reaction zones (Jannasch and Mottl, ). Thermodynamic modeling indicated that the hydrogen sulfide or sulfide abundantly contained in the hydrothermal fluids represented the dominating energy source in the mesophilic deep-sea vent chemoautotrophic ecosystems (McCollom and Shock, ). In addition, partially oxidized inorganic sulfur compounds such as polysulfide, elemental sulfur, and thiosulfate are generated in the in situ mixing zones, and serve as both electron donor and acceptor in a variety of energy metabolisms. The chemical and microbial oxidation and reduction reactions of sulfur compounds probably establish the overall complex sulfur metabolism network in the ecosystem. This article reviews the representative microbial components capable of utilizing the inorganic sulfur compounds as the energy sources in the deep-sea hydrothermal environments and highlights the biochemical and genetic components of their metabolisms. In addition, the possible segregation of different sulfur metabolic pathways and their host chemoautotrophic Proteobacteria associated with the physical and chemical transition in the mixing zones of the deep-sea hydrothermal environments is discussed.

Microbial Communities in Deep-Sea Hydrothermal Fields

Recent culture-independent analyses of the both symbiotic and free-living microbial communities in the various deep-sea hydrothermal environments have revealed a great phylogenetic diversity of Archaea and Bacteria (Takai et al., ); these analyses have also indicated a predominance in biomass of members within the gamma-Proteobacteria and epsilon-Proteobacteria (Stewart et al., ; Suzuki et al., ; Urakawa et al., ; Campbell et al., ; Nakagawa and Takai, ; Table 1). Based on the culture-dependent characterization and genetic components analyses, these Proteobacteria are found to be chemoautotrophs strongly associated with utilization of inorganic sulfur compounds (Durand et al., ; Inagaki et al., , ; Takai et al., , ,). Therefore, the sulfur-related energy metabolisms in these Proteobacteria are important traits for understanding ecology and biogeochemistry in deep-sea hydrothermal vent ecosystems.

Table 1

Organism, isolation, or observation siteGenome accession number*1Growth tem- perature (°C)Electron donorElectron acceptorGenesLocus tagPathways
EPSILON-PROTEOBACTERIA
Sulfurovum sp. NBC37-1 Sediment, Mid-Okinawa TroughAP00917930–37H2, S0, S0, , O2psrACBSUN0510-0508Sulfur respirationNakagawa et al. (, )
soxXYZABSUN0497-0501Sox systemYamamoto et al. ()
soxCDYZSUN0049-0052Sox system
soxJSUN0058, 1338Sox system (?)
sqrSUN0047, 0073, 0192Sulfide oxidation
sorABSUN1104-1103, 1476-1477Sulfite oxidation
Nitratiruptor sp. SB155-2 Sediment, Mid-Okinawa TroughAP00917855H2, S0, S0, , O2psrACBNIS0573-0571Sulfur respirationNakagawa et al. (, )
soxXYZABNIS1832-1828Sox system
soxYZNIS0034-0035Sox system
soxJNIS0032Sox system (?)
sqrNIS0146, 0158, 0326Sulfide oxidation
Nautilia profundicola AmH Alvinella tube, East Pacific RiseCP00127945H2, formateS0psrABCNAMH1518-1520Sulfur respirationCampbell et al. (, )
Sulfurimonas autotrophica DSM16294 Sediment, Mid-Okinawa TroughCP00220525H2S, S0, O2psrACBSaut1622-1644Sulfur respirationInagaki et al. ()
soxXYZABSaut0991-0995Sox system
soxCDYZSaut2096-2099Sox system
soxJSaut1356Sox system (?)
sqrSaut0503, 1543Sulfide oxidation
sorABSaut1022-1023Sulfite oxidation
Sulfurimonas denitrificans DSM1251 Tidal flat mud, Dutch Wadden Sea*2CP00015325psrACBSuden0500-0498Sulfur respirationSievert et al. ()
soxXYZABSuden0260-0264Sox system
soxCDYZSuden2060-2057Sox system
soxJSuden2049Sox system (?)
sqrSuden0619Sulfide oxidation
Alvinella episymbiont East Pacific RiseAAUQ10-65NDNDpsrABNDSulfur respirationGrzymski et al. ()
01000000*3soxXYZABCDNDSox system
DNDSox system (?)
soxJ
GAMMA-PROTEOBACTERIA
Thiomicrospira crunogena XCL-2 Galapagos Rift ventCP00010933H2, H2S, S0, O2soxXYZATcr0604-0601Sox systemScott et al. ()
soxBTcr1549Sox system
soxCDTcr0156-0157Sox system
sqrTcr0619Sulfide oxidation
CoSym Vesicomyosocious symbiontAP009247NDNDNDsoxXYZACOSY0733-0730Sox systemKuwahara et al. ()
soxBCOSY 0161Sox system
soxJCOSY0750Sox system (?)
sqrCOSY0953Sulfide oxidation
dsrABCOSY0795-0794Reverse sulfate reduction
aprABCOSY0092-0091Reverse sulfate reduction
satCOSY0089Reverse sulfate reduction
Ruthia magnifica Calyptogena symbiontCP000488NDNDNDsoxXYZARmag0808-0805Sox systemNewton et al. ()
soxBRmag0156Sox system
soxJRmag0824Sox system (?)
sqrRmag1053Sulfide oxidation
dsrABRmag0870-0869Reverse sulfate reduction
aprABRmag0088-0087Reverse sulfate reduction
satRmag0085Reverse sulfate reduction
Endoriftia persephone Riftia symbiontAASFNDNDNDsoxXAB*4NDSox systemRobidart et al. ()
00000001*3dsrABNDReverse sulfate reduction
aprABNDReverse sulfate reduction
satNDReverse sulfate reduction
Beggiatoa spp. Sediment, Baltic SeaABBYNDNDNDsoxXYZABNDSox systemMußmann et al. ()
00000000,fccABNDSulfide oxidation
ABBBZsqrNDSulfide oxidation
00000000*5dsrABNDReverse sulfate reduction
aprABNDReverse sulfate reduction
satNDReverse sulfate reduction
dmsABCNDDMSO respiration
phsABCNDThiosulfate respiration

Sulfur metabolic genes in epsilon- and gamma-Proteobacteria isolated or identified from deep-sea hydrothermal fields.

ND no data, psr, polysulfide reductase; sox, Sox multi enzyme system; sqr, sulfide:quinone oxidoreductase; fcc, flavocytochrome c; dsr, dissimilatory sulfite reductase; apr, adenosine 5′-phosphosulfate reductase; sat, sulfate adenylyltransferase; dms, dimethyl sulfoxide reductase; phs, thiosulfate reductase.

*1Deposited in DDBJ/EMBL/GenBank databases.

*2It is not a hydrothermal field.

*3For which the metagenome sequence is published.

*4SoxXAB were detected, but not SoxYZ.

*5Sequence assembles were incomplete.

Microbial Sulfur Metabolic Pathways for Energy Conservation

Inorganic sulfur compounds are used as both electron donor and acceptor by microorganisms. Sulfur-oxidation pathways have been well studied biochemically in anaerobic phototrophs (e.g., Chlorobium and Allochromatium), facultatively chemoautotrophic Proteobacteria (e.g., Acidithiobacillus and Paracoccus) and Sulfolobales (e.g., Sulfolobus and Acidianus; Friedrich, ; Kletzin et al., ; Friedrich et al., ; Frigaard and Dahl, ). Bacterial sulfur-oxidation pathways under the neutral pH are generally classified into two different types: (1) reverse sulfate reduction, and (2) Sox multienzyme system. Reverse sulfate reduction is reversal of sulfate reduction pathway, in which sulfide is oxidized to sulfate via sulfite. This pathway uses the same families of enzymes as of the sulfate reduction pathway, such as dissimilatory sulfite reductase (Dsr), adenylphosphosulfate reductase (Apr), and sulfate adenylyltransferase (Sat; Kappler and Dahl, ). Sox multienzyme complex catalyzes oxidation of inorganic sulfur compounds. Four protein components, SoxYZ, SoxXA, SoxB, and SoxCD are required for complete oxidation of sulfide and thiosulfate to sulfate (Complete Sox pathway; Friedrich et al., ). However, the sulfur oxidizers that possess the soxYZXAB genes but not soxCD have often been reported (Friedrich et al., ). It is considered that SoxCD acts as sulfur dehydrogenase. Sox system without SoxCD is able to oxidize sulfite and sulfone group () in thiosulfate, but not sulfide, elemental sulfur, and sulfane sulfur (-S−) in thiosulfate (Friedrich et al., ). In addition to these two sulfur-oxidation pathways, several enzymes have been proposed to oxidize inorganic sulfur compounds, including sulfide:quinone oxidoreductase (Sqr), flavocytochrome c (Fcc), and sulfite oxidase (SO), though the exact physiological functions are still debated. Sqr is a single-subunit flavoprotein that catalyzes oxidation of sulfide to elemental sulfur (Shahak and Hauska, ; Frigaard and Dahl, ). Recent protein structural study divided Sqr family into six groups (Marcia et al., ). These different types of Sqr probably have different mechanisms and physiological roles (Chan et al., ; Gregersen et al., ; Holkenbrink et al., ). Fcc also catalyzes oxidation of sulfide to elemental sulfur, but electrons are transferred to the level of cytochrome c (Oh-oka and Blankenship, ). Fcc consists of a flavoprotein subunit, FccB, and a c-type cytochrome subunit, FccA (Kusai and Yamanaka, ; Reinartz et al., ). The soxEF genes conserved in the sox gene clusters are homologous genes of the fccAB genes (Friedrich et al., ). The soxJ gene is a homologous gene of fccB/soxF, that does not cluster with a homolog of fccA/soxE (Gregersen et al., ). SO is a molybdenum enzyme and catalyzes the direct oxidation of sulfite to sulfate (Kappler and Dahl, ). Acidophilic sulfur-oxidizing bacteria and archaea use different sulfur-oxidation pathways that will not be further described here (see Ghosh and Dam, ).

Sulfur-reduction pathways can be classified into two types based on the substrates: (1) sulfur-reduction (sulfur respiration), and (2) sulfate reduction (sulfate respiration). Sulfur-reduction pathways have been intensively studied in gastrointestinal epsilon-Proteobacterium, Wolinella succinogenes (Wolin et al., ; Hedderich et al., ). Sulfur-reduction is catalyzed by polysulfide reductase (Psr), in which the actual substrate of the reaction is polysulfide but not elemental sulfur (Pfennig and Biebel, ). Sulfate reducing bacteria are found in several different phylogenetic lines (e.g., delta-Proteobacteria, Clostridia, Thermodesulfobacteria, and Nitrospirae; Muyzer and Stams, ). Sat, Apr, and Dsr catalyze the reduction of sulfate to sulfide.

Sulfur Metabolism in Epsilon-Proteobacteria in Deep-Sea Hydrothermal Fields

The most well known epsilon-Proteobacteria are gastrointestinal pathogens such as Helicobacter and Campylobacter. They are heterotrophic and do not have inorganic sulfur metabolic pathways. The genus Wolinella isolated from cattle rumen can reduce elemental sulfur to hydrogen sulfide (Wolin et al., ).

There are many reports that chemoautotrophic epsilon-Proteobacteria are predominant in sulfidic environments such as deep-sea hydrothermal and subsurface environments (Takai et al., ; Campbell et al., ; Nakagawa and Takai, ). Recently, whole genome sequences of five strains of marine epsilon-Proteobacteria, i.e., Sulfurovum sp. NBC37-1, Nitratiruptor sp. SB155-2, Nautilia profundicola AmH, Sulfurimonas autotrophica DSM16294 isolated from deep-sea hydrothermal fields, and S. denitrificans DSM1251 isolated from a coastal wetland, have been determined (Nakagawa et al., ; Sievert et al., ; Campbell et al., ; Table 1). Moreover, the metabolism of episymbiontic epsilon-Proteobacterium in a polychaete worm was analyzed by metagenomic analysis (Grzymski et al., ). In addition, several biochemical studies on sulfur metabolic pathways in deep-sea epsilon-Proteobacteria have also been reported (Takai et al., ; Yamamoto et al., ).

Genetic and enzymatic components characterized by the genomic and biochemical analyses of deep-sea epsilon-Proteobacteria have facilitated considerable progress in determining the possible sulfur metabolism pathways of the deep-sea chemoautotrophic epsilon-Proteobacteria (Table 1). The deep-sea epsilon-Proteobacteria characterized so far possess (1) a hydrogen-oxidizing sulfur respiration pathway using hydrogenase and polysulfide reductase (Psr). And the epsilon-Proteobacteria except for N. profundicola AmH, possess (2) a sulfur compounds-oxidizing oxygen/nitrate-respiration pathway using the Sox multienzyme system. Both of the Sox systems coupled with and without SoxCD have been found. The sox genes are not organized in a single region, but at least in two separated regions of the soxXYZAB and sox(CD)YX genes. One or more soxF gene was conserved in each sox gene cluster. Sulfurovum sp., Nitratiruptor sp., and S. autotrophica have several sqr genes. Two sets and one set of the sorAB genes coding SO were observed in Sulfurovum sp. and S. autotrophica, respectively. No gene for sulfur-oxidation pathways was found in N. profundicola. In addition to the sulfur metabolic pathways, many deep-sea epsilon-Proteobacteria are capable of chemoautotrophic growth without sulfur compounds using a third metabolic pathway: (3) a hydrogen-oxidizing oxygen/nitrate-reduction pathway (Figure 1). The bacterial members that can use sulfur compounds as both electron acceptors and donors are identified only in the phyla of epsilon-Proteobacteria and Aquificae, both of which predominantly inhabit in deep-sea hydrothermal environments. This may provide an important clue into how the versatile energy metabolic pathways are associated with the energetic advantages adapted to the dynamic and transient environmental conditions in the mixing zones of the hydrothermal vent environments.

Figure 1

Sulfur Metabolism in Gamma-Proteobacteria in Deep-Sea Hydrothermal Fields

Gamma-proteobacterial symbionts with invertebrates have never been isolated from deep-sea hydrothermal vents. Furthermore only a couple of free-living sulfur-oxidizing gamma-Proteobacteria have been isolated from deep-sea hydrothermal fields (Kuever et al., ; Takai et al., , ). Unculturable gamma-proteobacterial sulfur-oxidizing endosymbionts are classified into three groups based on their host invertebrates: symbionts of (1) Bathymodiolus mussels and Calyptogena clams, (2) Alviniconcha gastropods, and (3) gastropods (e.g., Ifremeria) and tubeworms (Nakagawa and Takai, ). In recent years, two genome sequences of sulfur-oxidizing symbionts in Calyptogena have been published (Kuwahara et al., ; Newton et al., ; Table 1). Moreover, the metabolisms of symbiont in tubeworm were analyzed by metagenomic analysis (Robidart et al., ). In addition, a whole genome sequence of free-living sulfur-oxidizing gamma-Proteobacterium, Thiomicrospira crunogena XCL-2 was also published (Scott et al., ). Putative metabolic pathways in Beggiatoa sp. from marine sediments had also analyzed by using incomplete genome sequence (Mußmann et al., ). From these genome-based genetic characteristics, we can develop a preliminary outline of representative sulfur-related energy metabolisms in the deep-sea hydrothermal gamma-Proteobacteria, which possess two different sulfur-oxidization pathways: (1) the reverse sulfate reduction using Dsr, Apr, and Sat, and (2) the Sox multienzyme system without SoxCD (Figure 1). T. crunogena XCL-2, however, is an exception, in which no gene for the reverse sulfate reduction pathway was found. Moreover, this organism has the soxCD genes separated from other sox genes. In contrast, functional genes amplification studies suggested that hydrothermal gamma-Proteobacteria use the reverse sulfate reduction pathway, but not the Sox pathway (Hügler et al., ). These results indicate that either of the two distinct sulfur-oxidization pathways is dispensable. Both of these pathways require O2 as a terminal electron acceptor in most cases. This fact indicates that the relatively reductive environment (O2-depleted condition) is inhibitory for the growth of deep-sea chemoautotrophic gamma-Proteobacteria due to the limitation of primary electron acceptor despite an increasing abundance of electron-donors (reduced sulfur compounds). Thus, it is predicted that the metabolically habitable spaces of deep-sea chemoautotrophic gamma-Proteobacteria strictly requiring co-existence of reduced sulfur compounds and O2 are much more limited than those of deep-sea epsilon-Proteobacteria in the mixing zones of hydrothermal environments. Conversely, however, it seems likely that the genomic installation and the biochemical operation of two different sulfur-oxidizing pathways in the deep-sea chemoautotrophic gamma-Proteobacteria are kinetically advantageous if both the reduced sulfur compounds and O2 are steadily supplied into the habitats. Particularly for the gamma-proteobacterial sulfur-oxidizing symbionts, the host invertebrates would prepare the metabolically suitable habitats in and around the bodies in the mixing zones of deep-sea hydrothermal environments (Arp and Childress, ; Zal et al., ; Numoto et al., ). This may be one of the possible rationales for the domination of deep-sea gamma-proteobacterial sulfur-oxidizing chemoautotrophs in symbiotic communities in deep-sea hydrothermal environments. All deep-sea sulfur-oxidizing gamma-Proteobacteria possess one sqr gene in the genome, except for the metagenome of Riftia symbiont. Therefore, Sqr probably has an important role for the sulfur-oxidation in the organisms. It is interesting that genes for sulfur compound (thiosulfate and dimethyl sulfoxide) respiration were found in genome of Beggiatoa sp. (Mußmann et al., ). This is in accordance with previous results in Beggiatoa alba that can reduce stored elemental sulfur to overcome short-term anoxic conditions (Nelson and Castenholz, ; Schmidt et al., ).

Concluding Remarks

In this review, we described the sulfur-related energy metabolisms of epsilon- and gamma-Proteobacteria dominating the microbial communities in the global deep-sea hydrothermal environments. Most of the metabolic characteristics summarized in this article are based on the reconstruction of genetic components in the genomes determined for only a few representative species. Further genetic and biochemical variability associated with the sulfur-related energy metabolisms will be clarified in many species of deep-sea hydrothermal vent epsilon- and gamma-Proteobacteria in the future. Surely, the investigation of other inorganic sulfur metabolizing groups of microbial components such as sulfate-reducers (delta-Proteobacteria, Thermodesulfobacteria, and Deferribacteres) and sulfur-reducing thermophiles (Aquificae, Thermococcaceae, and Desulfurococcaceae) will be important for understanding the biogeochemical processes and energy- and elemental fluxes of sulfur compounds in the deep-sea hydrothermal environments (Reysenbach et al., , ; Teske et al., ; Takai et al., ). Recently, genetic information has been rapidly accumulating and has been providing the important genetic potential for understanding the complex sulfur-related metabolic networks in deep-sea hydrothermal vent ecosystems. In contrast, enzymatic and biochemical data are highly insufficient to clarify the in vivo and in situ kinetics, operation and control of metabolic pathways. These will be an important focus for future studies.

Statements

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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Summary

Keywords

deep-sea hydrothermal vents, energy metabolism, chemoautotroph

Citation

Yamamoto M and Takai K (2011) Sulfur Metabolisms in Epsilon- and Gamma-Proteobacteria in Deep-Sea Hydrothermal Fields. Front. Microbio. 2:192. doi: 10.3389/fmicb.2011.00192

Received

03 March 2011

Accepted

30 August 2011

Published

20 September 2011

Volume

2 - 2011

Edited by

Niels-Ulrik Frigaard, University of Copenhagen, Denmark

Reviewed by

Masaharu Ishii, University of Tokyo, Japan; Biswarup Mukhopadhyay, Virginia Bioinformatics Institute, USA

Copyright

© 2011 Yamamoto and Takai.

This is an open-access article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and other Frontiers conditions are complied with.

*Correspondence: Masahiro Yamamoto, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, 237-0061 Yokosuka, Japan. e-mail:

This article was submitted to Frontiers in Microbial Physiology and Metabolism, a specialty of Frontiers in Microbiology.

Disclaimer

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

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