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ISSN 1664-8714 ISBN 978-2-88919-682-1 DOI 10.3389/978-2-88919-682-1 About Frontiers Frontiers is more than just an open-access publisher of scholarly articles: it is a pioneering approach to the world of academia, radically improving the way scholarly research is managed. The grand vision of Frontiers is a world where all people have an equal opportunity to seek, share and generate knowledge. Frontiers provides immediate and permanent online open access to all its publications, but this alone is not enough to realize our grand goals. Frontiers Journal Series The Frontiers Journal Series is a multi-tier and interdisciplinary set of open-access, online journals, promising a paradigm shift from the current review, selection and dissemination processes in academic publishing. All Frontiers journals are driven by researchers for researchers; therefore, they constitute a service to the scholarly community. 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What are Frontiers Research Topics? Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: researchtopics@frontiersin.org 2 November 2015 | Hydrothermal Microbial Ecosystems Frontiers in Microbiology The papers in the “Hydrothermal Vent” e-book cover a range of microbiological research in deep and shallow hydrothermal environments, from high temperature “black smokers,” to diffuse flow habitats and episodically discharging subsurface fluids, to the hydrothermal plumes. Together they provide a snapshot of current research interests in a field that has evolved rapidly since the discovery of hydrothermal vents in 1977. Hydrothermally influenced microbial habitats and communities represent a wide spectrum of geological setting, chemical in-situ regimes, and biotic communities; the classical examples of basalt-hosted black smoker chimneys at active mid-ocean spreading centers have been augmented by hydrothermally heated and chemically altered sedi- ments, microbiota fueled by serpentinization reactions, and low-temperature vents with unusual menus of electron donors. Environmental gradients and niches provide habitats for unusual or unprecedented microorganisms and microbial ecosystems. The discovery of novel extremophiles underscores untapped microbial diversity in hydrothermal vent microbial communities. Different stages of hydrothermal activity, from early onset to peak activity, gradual decline, and persistence HYDROTHERMAL MICROBIAL ECOSYSTEMS Hydrothermal Chimneys with Microbial Mats in Guaymas Basin, a sedimented spreading center in the Gulf of California. The yellow and orange-colored bacterial mats overgrowing the chimneys are sulfur- oxidizing, filamentous Beggiatoaceae, which form luxuriant microbial mats on hydrothermal hot spots. Image by: Woods Hole Oceanographic Institution, Woods Hole, MA, USA, used with permission. Topic Editors: Andreas Teske, University of North Carolina at Chapel Hill, USA Anna-Louise Reysenbach, Portland State University, USA 3 November 2015 | Hydrothermal Microbial Ecosystems Frontiers in Microbiology of cold and fossil vent sites, correspond to different colonization waves by microorganisms as well as megafauna. Perhaps no other field in microbiology is so intertwined with the geological and geochemical evolution of the oceans, and promises so many biochemical and physiological discoveries still to be made within the unexhausted richness of extreme microbial life. Citation: Teske, A., Reysenbach, A-L., eds. (2015). Hydrothermal Microbial Ecosystems. Lausanne: Frontiers Media. doi: 10.3389/978-2-88919-682-1 4 November 2015 | Hydrothermal Microbial Ecosystems Frontiers in Microbiology Table of Contents 06 Editorial: Hydrothermal microbial ecosystems Andreas Teske and Anna-Louise Reysenbach 09 Anaerobic oxidation of short-chain alkanes in hydrothermal sediments: potential influences on sulfur cycling and microbial diversity Melissa M. Adams, Adrienne L. Hoarfrost, Arpita Bose, Samantha B. Joye and Peter R. Girguis 20 Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal vent fluids Nancy H. Akerman, David A. Butterfield and Julie A. Huber 34 The pH and pCO2 dependence of sulfate reduction in shallow-sea hydrothermal CO2 – venting sediments (Milos Island, Greece) Elisa Bayraktarov, Roy E. Price, Timothy G. Ferdelman and Kai Finster 44 Microbial colonization of basaltic glasses in hydrothermal organic-rich sediments at Guaymas Basin Nolwenn Callac, Céline Rommevaux-Jestin, Olivier Rouxel, Françoise Lesongeur, Céline Liorzou, Claire Bollinger, Antony Ferrant and Anne Godfroy 64 Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities Barbara J. Campbell, Shawn W. Polson, Lisa Zeigler Allen, Shannon J. Williamson, Charles K. Lee, K. Eric Wommack and S. Craig Cary 79 The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats Gregory J. Dick, Karthik Anantharaman, Brett J. Baker, Meng Li, Daniel C. Reed and Cody S. Sheik 95 Diversity and phylogenetic analyses of bacteria from a shallow-water hydrothermal vent in Milos island (Greece) Donato Giovannelli, Giuseppe d’Errico, Elena Manini, Michail Yakimov and Costantino Vetriani 108 Biogeochemical implications of the ubiquitous colonization of marine habitats and redox gradients by Marinobacter species Kim M. Handley and Jonathan R. Lloyd 118 Metagenome reveals potential microbial degradation of hydrocarbon coupled with sulfate reduction in an oil-immersed chimney from Guaymas Basin Ying He, Xiang Xiao and Fengping Wang 131 A comparative study of microbial diversity and community structure in marine sediments using poly(A) tailing and reverse transcription-PCR Tatsuhiko Hoshino and Fumio Inagaki 5 November 2015 | Hydrothermal Microbial Ecosystems Frontiers in Microbiology 139 Characteristics of microbial communities in crustal fluids in a deep-sea hydrothermal field of the Suiyo Seamount Shingo Kato, Michiyuki Nakawake, Junko Kita, Toshiro Yamanaka, Motoo Utsumi, Kei Okamura, Jun-ichiro Ishibashi, Moriya Ohkuma and Akihiko Yamagishi 150 Microbiological characterization of post-eruption “snowblower” vents at Axial Seamount, Juan de Fuca Ridge Julie L. Meyer, Nancy H. Akerman, Giora Proskurowski and Julie A. Huber 163 Microbial habitat connectivity across spatial scales and hydrothermal temperature gradients at Guaymas Basin Stefanie Meyer, Gunter Wegener, Karen G. Lloyd, Andreas Teske, Antje Boetius and Alban Ramette, 174 Biogeography of Persephonella in deep-sea hydrothermal vents of the Western Pacific Sayaka Mino, Hiroko Makita, Tomohiro Toki, Junichi Miyazaki, Shingo Kato, Hiromi Watanabe, Hiroyuki Imachi, Tomo-o Watsuji, Takuro Nunoura, Shigeaki Kojima, Tomoo Sawabe, Ken Takai and Satoshi Nakagawa 186 Archaeal and bacterial diversity in an arsenic-rich shallow-sea hydrothermal system undergoing phase separation Roy E. Price, Ryan Lesniewski, Katja S. Nitzsche, Anke Meyerdierks, Chad Saltikov, Thomas Pichler and Jan P . Amend 205 Microbial diversity in the deep-subsurface hydrothermal aquifer feeding the giant gypsum crystal-bearing Naica Mine, Mexico Marie Ragon, Alexander E. S. Van Driessche, Juan M. García-Ruíz, David Moreira and Purificación López-García 217 Presence and diversity of anammox bacteria in cold hydrocarbon-rich seeps and hydrothermal vent sediments of the Guaymas Basin Lina Russ, Boran Kartal, Huub J. M. op den Camp, Martina Sollai, Julie Le Bruchec, Jean-Claude Caprais, Anne Godfroy, Jaap S. Sinninghe Damsté and Mike S. M. Jetten 227 Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at L ō ́ihi, Hawai ́l Esther Singer, John F . Heidelberg, Ashita Dhillon and Katrina J. Edwards 236 Low temperature geomicrobiology follows host rock composition along a geochemical gradient in Lau Basin Jason B. Sylvan, Tiffany Y . Sia, Amanda G. Haddad, Lindsey J. Briscoe, Brandy M. Toner, Peter R. Girguis and Katrina J. Edwards, 254 Widespread occurrence of two carbon fixation pathways in tubeworm endosymbionts: lessons from hydrothermal vent associated tubeworms from the Mediterranean Sea Vera Thiel, Michael Hügler, Martina Blümel, Heike I. Baumann, Andrea Gärtner, Rolf Schmaljohann, Harald Strauss, Dieter Garbe-Schönberg, Sven Petersen, Dominique A. Cowart, Charles R. Fisher and Johannes F . Imhoff 274 Multilocus sequence analysis of Thermoanaerobacter isolates reveals recombining, but differentiated, populations from geothermal springs of the Uzon Caldera, Kamchatka, Russia Isaac D. Wagner, Litty B. Varghese, Christopher L. Hemme and Juergen Wiegel EDITORIAL published: 01 September 2015 doi: 10.3389/fmicb.2015.00884 Frontiers in Microbiology | www.frontiersin.org September 2015 | Volume 6 | Article 884 Edited by: Virginia P. Edgcomb, Woods Hole Oceanographic Institution, USA Reviewed by: Maria Pachiadaki, Woods Hole Oceanographic Institution, USA *Correspondence: Andreas Teske, teske@email.unc.edu Specialty section: This article was submitted to Extreme Microbiology, a section of the journal Frontiers in Microbiology Received: 12 June 2015 Accepted: 12 August 2015 Published: 01 September 2015 Citation: Teske A and Reysenbach A-L (2015) Editorial: Hydrothermal microbial ecosystems. Front. Microbiol. 6:884. doi: 10.3389/fmicb.2015.00884 Editorial: Hydrothermal microbial ecosystems Andreas Teske 1 * and Anna-Louise Reysenbach 2 1 Department of Marine Sciences, University of North Carolina, Chapel Hill, NC, USA, 2 Biology Department, Portland State University, Portland, OR, USA Keywords: hydrothermal vent, extremophiles, biogeography, chemosynthesis, archaea, bacteria, Guaymas basin The papers in the “Hydrothermal Vent” research topic cover a range of microbiological research in deep and shallow hydrothermal environments, from high temperature “black smokers,” to diffuse flow habitats and episodically discharging subsurface fluids, to the hydrothermal plumes. Together they provide a snapshot of current research interests in a field that has evolved rapidly since the discovery of hydrothermal vents in 1977. The topic opens with a review by Dick et al. (2013) on hydrothermal plumes and their microbial communities in the deep sea. The review synthesizes recent advances in the microbial ecology, physiology, and genomics of the mostly chemosynthetic bacteria that have adapted to the supply of carbon and energy sources in the turbulently mixed vent plume. These pelagic communities are distinct from those in hydrothermal chimneys, sediments and the subsurface, yet they show some taxonomic and physiological linkages. This review is followed by four papers that shed new light on microbial ecosystems in mixed vent fluids. The high-flow example is represented by sulfide- rich subsurface vent fluids discharging in “snow blower” bursts dominated by sulfur-oxidizing, microaerobic, and often moderately thermophilic Epsilonproteobacteria (Meyer et al., 2013a). Similar epsilonproteobacterial communities, dominated by the chemosynthetic, sulfur-oxidizing genera Sulfurimonas and Sulfurovum , were also found in cool, diffusive flow at the same location, Axial Seamount on the Juan de Fuca Ridge (Akerman et al., 2013). The authors proposed that both diffuse flow and episodic high-flow events tap into the same subsurface community of microaerobic sulfur oxidizers. Epsilonproteobacteria accounted again for most of the microbial taxa found in diffuse flow samples from the basalt-hosted vent sites of 9 ◦ N East Pacific Rise, but not in similar habitats in the organic-rich hydrothermal sediments of Guaymas Basin in the Gulf of California, where other bacterial groups and hyperthermophilic archaea predominated (Campbell et al., 2013). Changing flow paths and reservoirs for subseafloor mixed fluids and their microbiota can also change the composition of venting microbial communities over time as reported by Kato and colleagues. At Suiyo Seamount in the Izu-Bonin Arc within the Western Pacific, a hot and reducing subsurface reservoir accessed by drilling underwent increasing seawater in-mixing over several years. Consequently, the crustal fluid community of sulfur-oxidizing chemolithotrophs changed to a mixed assemblage harboring abundant marine heterotrophic bacteria (Kato et al., 2013). While deep-sea hydrothermal vent sites are difficult to access and to sample, shallow water hydrothermal vents that can be reached by scuba divers provide an accessible alternative environment to study. Perhaps the best-investigated of these shallow-water vents are found on the coast of the Greek island Milos in the Aegean Sea, where hot, briny, reducing, CO 2 -rich vent fluids permeate the sandy seafloor sediments of Paleochori Bay. Giovannelli et al. (2013) show that in the surficial sediments the microbial community is dominated by Epsilonproteo-bacteria (genus Sulfurovum ) similar to those seen in deep-sea vents; however proteobacterial lineages that are distinct from those of deep-sea vents were also detected. In contrast, in the deeper sediment layers of this sample vent field, Price et al. (2013) find Epsilonproteobacteria, but also Firmicutes, Planctomycetes, and Bacteroidetes coexisting with thermophilic archaea. In addition, arsenite-oxidizing bacteria were identified by 6 | Teske and Reysenbach Editorial: Hydrothermal microbial ecosystems functional gene analysis in these arsenite-rich sediments. Site- specific adaptations of vent communities are also the focus of Bayraktarov et al. (2013), as they examine the pH preferences of sulfate-reducing microbial communities in the Milos vent sediments. In the proximity of CO 2 -rich, low-pH fluids, the sulfate-reducing microbial communities show maximal activities at a distinctly lower pH range than at less acidic control sites not impacted by CO 2 -rich vent fluids. Among deep-sea vent sites, the sediment-covered Guaymas Basin hydrothermal vents in the central Gulf of California is unusual; the buried organic matter in these sediments are hydrothermally processed to petroleum compounds, low- molecular weight organic acids, short-chain alkanes, methane and ammonia. These substrates sustain a unique microbial ecosystem that combines the characteristics of communities from hydrocarbon seeps and mid-ocean ridge hydrothermal vents. Meyer and colleagues demonstrate that the microbial populations in Guaymas sediments show a high degree of microbial connectivity and population overlap within an area of a few 100 m—a consequence of vigorous venting, rapid dispersal via bottom currents, and closely spaced hydrothermal features (Meyer et al., 2013b). Abundant aromatic and aliphatic hydrocarbons in Guaymas Basin sediments and chimneys enrich for microbial specialists—especially sulfate-reducing bacteria— that utilize hydrocarbons, remineralize them to CO 2 , or assimilate them into microbial biomass; these communities feature prominently in metagenomic analyses of hydrocarbon- rich Guaymas chimneys (He et al., 2013). The ammonia-rich and methane-rich hydrothermal fluids at Guaymas sustain ammonia- oxidizing bacteria (anammox) and methane- oxidizing archaea (ANME) in the surficial sediments. The anammox bacteria combine ammonia and nitrite to N2, and are usually better known from marine oxygen minimum zones and stratified water columns (Russ et al., 2013). A recently identified, high- temperature tolerant clade of the cosmopolitan seep methane- oxidizing archaeal lineage ANME-1 is widespread at Guaymas Basin. The “ANME_1Guaymas” have been enriched using in- situ colonization chambers that were placed into surficial hydrothermal sediments on the seafloor (Callac et al., 2013). One of the relatively few analogous environments to Guaymas Basin, the alkane-rich hydrothermal sediments of the Middle Valley vent field on the northern Juan de Fuca ridge, provide the opportunity to study similar microbial communities and processes. In anaerobic batch reaction incubations, short alkanes (ethane, propane, butane) were consumed within a mesophilic to thermophilic temperature range, probably by sulfate-reducing bacteria (Adams et al., 2013). Hydrothermal vents are suitable model systems to explore microbial biogeography because they are island habitats in the deep sea; their thermophilic, chemosynthetic or special substrate-adapted microbial inhabitants likely cannot survive, and certainly cannot thrive in the cold, oxidized sediments and bottom waters of the deep sea that separate hydrothermal hot spots. In this volume several papers evaluate the controls of microbial community structure, geographic distance vs. environmental selection pressures in different habitats such as tubeworm trophosomes, sulfides, and ferric iron hydroxides. Sulfur-oxidizing endosymbionts of vestimentiferan tubeworms, which thrive in seep and vent habitats, showed a clear separation into different Gulf of Mexico and Mediterranean genotypes by 16S rRNA gene, mitochondrial cytochrome C oxidase, and functional genes of the two coexisting CO 2 assimilation pathways that coexist in the endosymbiont, the Calvin-Benson- Bassham and the reverse TCA cycle (Thiel et al., 2012). Mino et al. (2013) use multi-locus sequence analysis to show that isolates of the chemosynthetic thermophilic genus Persephonella from different vent sites in the Okinawa Trough and in the distant Southern Mariana Trench in the western Pacific undergo sympatric speciation. Similarly, Wagner et al. (2013) use multi- locus sequence analysis to demonstrate genetic differentiation among strains of the thermophilic fermenting Firmicute, Thermoanaerobacter uzonensis , from different terrestrial hot spring locations within the Uzon Caldera in Kamtchatka. In this case, genetic divergence did not correlate with geographic separation on these short distances of mostly a few 100 m. Sylvan et al. (2013) describe how the biogeographical boundary of the north-south transition from basalt-hosted to andesite-hosted vents on the Eastern Lau spreading Center and Valu Fa ridge, appears to select for distinct bacterial taxa on silicate rocks, whereas inactive sulfides show major differences in bacterial community structure between the surface and the interior sulfide mineral matrix. Members of the Zetaproteobacteria, including the microaerobic and chemolithotrophic iron oxidizer Mariprofundus ferrooxidans , fall into different 16S rRNA phylotypes of Zetaproteobacteria from the Southern Mariana Arc, the Hawaiian hot spot, and from the Vai’lulu/Tonga Arc/East Lau Spreading Center/Kermadec Arc. This study shows that the Zetaproteobacteria from these sites form mutually intertwined microclusters on the 16S rRNA gene level, suggesting more detailed genomic analyses to explore their biogeography in fine resolution (Singer et al., 2013). This research topic includes methodological assessments. Molecular surveys of biogeographic patterns and dominant microbial populations depend critically on the molecular tools used. To document inherent methodological biases, Hoshino and Inagaki (2013) perform a comparative molecular analysis of bacterial populations in hydrothermal sediments of Yonaguni Knoll in the Southern Okinawa Trough. By comparing the phylotypes recovered by conventional reverse-transcription PCR with domain-specific primers and by previous poly-A tailing of the extracted rRNA, they find different clades of Deltaproteobacteria and detect unusual archaea in the poly-A tailing assay that may escape detection by conventional PCR or RT-PCR using domain-specific primers. The last two contributions to this research topic discuss microbial groups that are not commonly considered as components of hydrothermal microbiota, marine heterotrophic bacteria and pelagic marine archaea. When cosmopolitan, heterotrophic marine bacteria appear in molecular diversity surveys of hydrothermal vents or other extreme habitats, they are regarded as “hitchhikers” or potentially contaminants from entrainment of seawater. Handley and Lloyd (2013) examine the cosmopolitan marine genus Marinobacter and find that these versatile bacteria—commonly regarded as aerobes or fermenters—include nitrate-reducing and metal-reducing representatives from low-temperature vents, marine sediments Frontiers in Microbiology | www.frontiersin.org September 2015 | Volume 6 | Article 884 7 | Teske and Reysenbach Editorial: Hydrothermal microbial ecosystems and mid-ocean ridge basalts. This genus is therefore well- suited to colonize aerobic- to-anoxic gradients in most marine environments, including hydrothermal vents. Likewise, the Thaumarchaeota—marine archaea that are ubiquitous in the cold and oxic marine water column—have been found in surficial marine sediments, hydrothermal plumes, and hot spring sediments. Ragon et al. (2013) report a new phylotype within the terrestrial hot spring branch of the Thaumarchaeota, detected in deep hot (60 ◦ C) spring waters in Naica Mine, Chihuahua, Mexico. Thus, the Thaumarchaeota emerge as one of the most adaptable archaeal lineages that inhabit marine and terrestrial, oxic and anoxic, cold, and hydrothermal habitats. These papers represent a sampler of ongoing microbiological research in hydrothermal environments, and demonstrate the wide multidisciplinary context of this field. Hydrothermal vents are not disconnected in time and space from the wider deep-sea ecosystem, without geological and biogeographical context. The research papers assembled here integrate geology, biogeochemistry, microbial physiology, microbial genomics and systematics across spatial scales that zoom in and out depending on the research question at hand. Perhaps no other field is so intertwined with the geological and geochemical evolution of the oceans, and promises so many biochemical and physiological discoveries still to be made within the unexhausted richness of extreme microbial life. Acknowledgments The editors’ hydrothermal vent research and their efforts to develop this research topic were supported by NSF grants OCE- 0647633 and 1334371 (AT) and OCE-1235432 (AR). References Adams, M. M., Hoarfrost, A. L., Bose, A., Joye, S. B., and Girguis, P. R. (2013). Anaerobic oxidation of short-chain alkanes in hydrothermal sediments: potential influences on sulfur cycling and microbial diversity. Front. Microbiol 4:110. doi: 10.3389/ fmicb.2013.00110 Akerman, N. H., Butterfield, D. A., and Huber, J. A. (2013). Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal fluids. Front. Microbiol . 4:185. doi: 10.3389/fmicb.2013.00185 Bayraktarov, E., Price, R. E., Ferdelman, T. G., and Finster, K. (2013). The pH and pCO 2 dependence of sulfate reduction in shallow-sea hydrothermal CO 2 - venting sediments (Milos Island, Greece). Front. Microbiol . 4:111. doi: 10.3389/ fmicb.2013.00111 Callac, N., Rommevaux-Jestin, C., Rouxel, O., Lesongeur, F., Liorzou, C., Bollinger, C., et al. (2013). Microbial colonization of basaltic glasses in hydrothermal organic-rich sediments at Guaymas Basin. Front. Microbiol . 4:250. doi: 10.3389/ fmicb.2013.00250 Campbell, B. J., Polson, S. W., Allen, L. Z., Williamson, S. J., Lee, C. K., Wommack, K. E., et al. (2013). Diffuse flow environments within basalt- and sediment-hosted hydrothermal vent ecosystems harbor specialized microbial communities. Front. Microbiol . 4:182. doi: 10.3389/fmicb.2013.00182 Dick, G. J., Anantharaman, K., Baker, B. J., Li, M., Reed, D. C., and Sheik, C. S. (2013). The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographical linkages to seafloor and water column habitats. Front. Microbiol . 4:124. doi: 10.3389/fmicb.2013.00124 Giovannelli, D., d’Errico, G., Manini, E., Yakimov, M., and Vetriani, C. (2013). Diversity and phylogenetic analyses of bacteria from a shallow-water hydrothermal vent in Milos Island (Greece). Front. Microbiol . 4:184. doi: 10.3389/fmicb.2013.00184 Handley, K. M., and Lloyd, J. R. (2013). Biogeochemical implications of the ubiquitous colonization of marine habitat and redox gradients by Marinobacter species. Front. Microbiol . 4:136. doi: 10.3389/fmicb.2013.00136 He, Y., Xiao, X., and Wang, F. (2013). Metagenome reveals potential microbial degradation of hydrocarbon coupled with sulfate reduction in an oil- immersed chimney from Guaymas Basin. Front. Microbiol . 4:148. doi: 10.3389/ fmicb.2013.00148 Hoshino, T., and Inagaki, F. (2013). A comparative study of microbial diversity and community structure in marine sediments using poly(A) tailing and reverse transcription PCR. Front. Microbiol . 4:160. doi: 10.3389/ fmicb.2013.00160 Kato, S., Nakawake, M., Kita, J., Yamanaka, T., Utsumi, M., Okamura, K., et al. (2013). Characteristics of microbial communities in crustal fluids in a deep- sea hydrothermal field of the Suiyo Seamount. Front. Microbiol . 4:85. doi: 10.3389/fmicb.2013.00085 Meyer, J. L., Akerman, N. H., Proskurowski, G., and Huber, J. A. (2013a). Microbiological characterization of post-eruption “snowblower” vents at Axial Seamount, Juan de Fuca Ridge. Front. Microbiol 4:153. doi: 10.3389/fmicb.2013.00153 Meyer, S., Wegener, G., Lloyd, K. G., Teske, A., Boetius, A., and Ramette, A. (2013b). Microbial habitat connectivity across spatial scales and hydrothermal temperature gradients at Guaymas Basin. Front. Microbiol . 4:207. doi: 10.3389/ fmicb.2013.00207 Mino, S., Makita, H., Toki, T., Miyazaki, J., Kato, S., Watanabe, H., et al. (2013). Biogeography of Persephonella in deep-sea hydrothermal vents of the Western Pacific. Front. Microbiol . 4:107. doi: 10.3389/ fmicb.2013.00107 Price, R. E., Lesniewski, R., Nitzsche, K. S., Meyerdierks, A., Saltikov, C., Pichler, T., et al. (2013). Archaeal and bacterial diversity in an arsenic-rich shallow-sea hydrothermal system undergoing phase separation. Front. Microbiol . 4:158. doi: 10.3389/fmicb.2013.00158 Ragon, M., Van Driessche, A. E. S., García-Ruíz, J. M., Moreira, D., and López- García, P. (2013). Microbial diversity in the deep-subsurface hydrothermal aquifer feeding the giant gypsum crystal-bearing Naica Mine, Mexico. Front. Microbiol . 4:37. doi: 10.3389/fmicb.2013.00037 Russ, L., Kartal, B., op den Camp, H. J., Sollai, M., Le Bruchec, J., Caprais, C. J., et al. (2013). Presence and diversity of anammox bacteria in cold hydrocarbon-rich seeps and hydrothermal vent sediments of the Guaymas Basin. Front. Microbiol 4:219. doi: 10.3389/ fmicb.2013.00219 Singer, E., Heidelberg, J. F., Dhillon, A., and Edwards, K. J. (2013). Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lo’ihi, Hawai’i. Front. Microbiol . 4:52. doi: 10.3389/ fmicb.2013. 00052 Sylvan, J. B., Sia, T. Y., Haddad, A. G., Briscoe, L. J., Toner, B. M., Girguis, P. R., et al. (2013). Low temperature geomicrobiology follows host rock composition along a geochemical gradient in Lau Basin. Front. Microbiol. 4:61. doi: 10.3389/fmicb.2013.00061 Thiel, V., Hügler, M., Blümel, M., Baumann, H. I., Gärtner, A., Schmaljohann, R., et al. (2012). Widespread occurrence of two carbon fixation pathways in tubeworm endosymbionts: lessons from hydrothermal vent associated tubeworms from the Mediterranean Sea. Front. Microbiol . 3:423. doi: 10.3389/ fmicb.2012.00423 Wagner, I. D., Varghese, J. B., Hemme, C. L., and Wiegel, J. (2013). Multilocus sequence analysis of Thermoanaerobacter isolates reveals recombining, but differentiated, populations from geothermal springs of the Uzon Chaldera, Kamtchtka, Russia. Front. Microbiol 4:169. doi: 10.3389/ fmicb.2012. 00169 Conflict of Interest Statement: 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. Copyright © 2015 Teske and Reysenbach. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Frontiers in Microbiology | www.frontiersin.org September 2015 | Volume 6 | Article 884 8 | ORIGINAL RESEARCH ARTICLE published: 14 May 2013 doi: 10.3389/fmicb.2013.00110 Anaerobic oxidation of short-chain alkanes in hydrothermal sediments: potential influences on sulfur cycling and microbial diversity Melissa M. Adams 1 , Adrienne L. Hoarfrost 2 , Arpita Bose 1 , Samantha B. Joye 3 and Peter R. Girguis 1 * 1 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA 2 Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA 3 Department of Marine Sciences, University of Georgia, Athens, GA, USA Edited by: Andreas Teske, University of North Carolina at Chapel Hill, USA Reviewed by: Julie A. Huber, Marine Biological Laboratory, USA Elizaveta Bonch-Osmolovskyaya, Winogradsky Institute of Microbiology Russian Academy of Sciences, Russia *Correspondence: Peter R. Girguis, Department of Organismic and Evolutionary Biology, Harvard University, Biological Laboratories, Room 3085, 16 Divinity Avenue, Cambridge, MA 02138, USA. e-mail: pgirguis@oeb.harvard.edu Short-chain alkanes play a substantial role in carbon and sulfur cycling at hydrocarbon- rich environments globally, yet few studies have examined the metabolism of ethane (C 2 ), propane (C 3 ), and butane (C 4 ) in anoxic sediments in contrast to methane (C 1 ). In hydrothermal vent systems, short-chain alkanes are formed over relatively short geological time scales via thermogenic processes and often exist at high concentrations. The sediment-covered hydrothermal vent systems at Middle Valley (MV, Juan de Fuca Ridge) are an ideal site for investigating the anaerobic oxidation of C 1 –C 4 alkanes, given the elevated temperatures and dissolved hydrocarbon species characteristic of these metalliferous sediments. We examined whether MV microbial communities oxidized C 1 –C 4 alkanes under mesophilic to thermophilic sulfate-reducing conditions. Here we present data from discrete temperature (25, 55, and 75 ◦ C) anaerobic batch reactor incubations of MV sediments supplemented with individual alkanes. Co-registered alkane consumption and sulfate reduction (SR) measurements provide clear evidence for C 1 –C 4 alkane oxidation linked to SR over time and across temperatures. In these anaerobic batch reactor sediments, 16S ribosomal RNA pyrosequencing revealed that Deltaproteobacteria , particularly a novel sulfate-reducing lineage, were the likely phylotypes mediating the oxidation of C 2 –C 4 alkanes. Maximum C 1 –C 4 alkane oxidation rates occurred at 55 ◦ C, which reflects the mid-core sediment temperature profile and corroborates previous studies of rate maxima for the anaerobic oxidation of methane (AOM). Of the alkanes investigated, C 3 was oxidized at the highest rate over time, then C 4 , C 2 , and C 1 , respectively. The implications of these results are discussed with respect to the potential competition between the anaerobic oxidation of C 2 –C 4 alkanes with AOM for available oxidants and the influence on the fate of C 1 derived from these hydrothermal systems. Keywords: hydrothermal vent, metalliferous sediments, Juan de Fuca Ridge, short-chain alkanes, sulfate reduction INTRODUCTION Hydrocarbon gases, including methane (C 1 ), ethane (C 2 ), propane (C 3 ), and n -butane (C 4 ), are produced via thermogenic and biogenic processes in the deep subsurface and are substantial com- ponents of the organic carbon pool across marine and terrestrial ecosystems (Joye et al., 2004; Milkov, 2005; Cruse and Seewald, 2006; Hinrichs et al., 2006; Savage et al., 2010). Over the past decade, studies focused on the anaerobic oxidation of methane (AOM) revealed the functional potential, ecological physiology, and diversity of microorganisms mediating this process and the global distribution of AOM as an effective benthic filter that reduces methane emissions into the oceans and atmosphere (for reviews, see Conrad, 2009; Knittel and Boetius, 2009; Valentine, 2011). In contrast, the anaerobic oxidation of long-chain alkanes ( > C 6 ) and aromatics has also been studied extensively resulting in the isolation of several bacteria, such as sulfate-reducing bacte- ria (SRB) that oxidize crude oil anaerobically (Van Hamme et al., 2003). There is a gap in our understanding of the metabolism and fate of non-methane, short-chain (C 2 –C 4 ) alkanes in deep sea sediments. Furthermore, there is growing interest in determin- ing the extent to which microorganisms mediate the anaerobic oxidation of C 2 –C 4 alkanes, as many studies have indicated that the degradation of these aliphatic hydrocarbons may be linked to global biogeochemical cycles (Lorenson et al., 2002; Formolo et al., 2004; Sassen et al., 2004; Milkov, 2005; Bowles et al., 2011; Quistad and Valentine, 2011). Recently, SRB from hydrocarbon seep sediments of the Gulf of Mexico and Guaymas Basin – both of which are environments rich in short-chain alkanes – were documented to oxidize short-chain alkanes to CO 2 anaerobically (Kniemeyer et al., 2007). Different temperature regimens (12, 28, and 60 ◦ C) along with multiple sub- strates were tested and a pure culture (deemed BuS5) was isolated from mesophilic enrichments with C 3 or C 4 as the sole exogenous carbon source. Through comparative sequence analysis, strain BuS5 was determined to cluster with the metabolically diverse Desulfosarcina/Desulfococcus (DSS) cluster, which also contains the www.frontiersin.org May 2013 | Volume 4 | Article 110 | 9 Adams et al. Anaerobic oxidation of alkanes in hydrothermal vents SRB found in consortia with anaerobic methanotrophs (ANME) in seep sediments. Enrichments from a terrestrial, low tempera- ture sulfidic hydrocarbon seep corroborated the biodegradation mechanism of complete C 3 oxidation to CO 2 with most bac- terial phylotypes surveyed belonging to the Deltaproteobacteria , particularly within the family Desulfobacteraceae (Savage et al., 2010). Cold adapted C 3 and C 4 , sulfate-reducing cultures have also been obtained from Gulf of Mexico and Hydrate Ridge sed- iments with maximum rates of SR between 16 and 20 ◦ C and dominant phylotypes allied to the DSS cluster including BuS5 (Jaekel et al., 2012). In the study by Kniemeyer et al. (2007) C 4 alkane degradation linked to sulfate reduction (SR) was not quan- tified at thermophilic temperatures, buta Guaymas Basin sediment enrichment with C 3 at 60 ◦ C was dominated by Gram positive bac- teria most closely allied to the Desulfotomaculum . Moreover, there was no evidence for C 2 degradation in mesophilic (28 ◦ C) or ther- mophilic (60 ◦ C) enrichments or C 2 -linked SR (albeit, there was very slow C 2 -dependent SR in Gulf of Mexico enrichments at 12 ◦ C after > 200 days). The Middle Valley (MV) hydrothermal vent field – located on the northern Juan de Fuca Ridge – is an ideal environment for investigating mesophilic to thermophilic anaerobic oxidation of C 2 –C 4 alkanes, given the elevated temperatures and dissolved hydrocarbon species characteristic of these sediments (Goodfel- low and Blaise, 1988; Davis and Fisher, 1994; Cruse and Seewald, 2006). Deep sea hydrothermal vents are complex and dynamic habitats characterized by steep thermal and chemical gradients, a diverse array of carbon and energy sources, and high con- centrations of dissolved volatiles (Butterfield et al., 1990, 1994; Von Damm et al., 1995). In the MV system, hydrothermal vent fluids interact with overlying sediments and the thermal alter- ation of sedimentary organic matter results in the production and/or release of a number of carbon sources, including short- chain alkanes (Cruse and Seewald, 2006; Cruse et al., 2008; Cruse and Seewald, 2010). These hydrothermally influenced sediments also contain high concentrations of reduced compounds, such as H 2 and hydrogen sulfide (H 2 S; Ames et al., 1993; Rushdl and Simonelt, 2002), and metals and metal sulfides at various reduced and oxidized states (Goodfellow and Blaise, 1988; Ames et al., 1993; Wankel et al., 2012). In contrast to the extremely organic-rich sediments of other sedimented hydrothermal systems, e.g., the Guaymas Basin hydrothermal vent fields in the Gulf of California (% OC = 2–4), MV