ORIGINAL RESEARCH published: 03 August 2015 doi: 10.3389/fmars.2015.00053 Microbial communities associated with benthic faunal assemblages at cold seep sediments of the Sonora Margin, Guaymas Basin Perrine Cruaud 1, 2, 3*, Adrien Vigneron 1, 2, 3, Patricia Pignet 1, Jean-Claude Caprais 4, Françoise Lesongeur 1, 2, 3, Laurent Toffin 1, 2, 3, Anne Godfroy 1, 2, 3 and Marie-Anne Cambon-Bonavita 1, 2, 3 Edited by: Hongyue Dang, 1 UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, IFREMER, Technopôle Brest Iroise, Plouzané, Xiamen University, China France, 2 UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Université de Bretagne Occidentale, Plouzané, France, 3 UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Centre National de la Recherche Reviewed by: Scientifique, Technopôle Brest Iroise, Plouzané, France, 4 Laboratoire ≪ Environnements Profonds ≫, IFREMER, EEP-LEP, J. Michael Beman, Technopôle Brest Iroise, Plouzané, France University of California, Merced, USA Olivia U. Mason, Florida State University, USA The Sonora Margin cold seeps present a seafloor mosaic pattern consisting of different *Correspondence: faunal assemblages and microbial mats. To better understand if sedimentary microbial Perrine Cruaud, EEP/LM2E, UMR6197, Laboratoire de communities reflect this patchy distribution, all major habitats were investigated using Microbiologie des Environnements four complementary approaches: 16S rRNA gene sequence 454 pyrosequencing, Extremes, IFREMER, Technopole Brest Iroise, BP70, Plouzane 29280, quantitative polymerase chain reaction, fluorescence in situ hybridization and France geochemistry analyses. This study reveals that sediments populated by different surface [email protected] assemblages show distinct porewater geochemistry features and are associated with Specialty section: distinct microbial communities. In the sediments underlying the microbial mat and This article was submitted to the surrounding macrofauna, microbial communities were dominated by anaerobic Aquatic Microbiology, methane oxidizers (archaeal anaerobic methanotroph ANME) and sulfate-reducing a section of the journal Frontiers in Marine Science Deltaproteobacteria. In contrast, sediment-associated microbial communities underlying Received: 04 May 2015 the megafauna habitats (vesicomyids and siboglinids) were characterized by a lower Accepted: 15 July 2015 biomass and important proportions of the Marine Benthic Group D (MBG-D), Chloroflexi Published: 03 August 2015 as well as filamentous Gammaproteobacteria and Deltaproteobacteria. Together, Citation: geochemical and microbial surveys indicate that porewater methane concentrations Cruaud P, Vigneron A, Pignet P, Caprais J-C, Lesongeur F, Toffin L, play an important role in the microbial community structure and subsequently in the Godfroy A and Cambon-Bonavita M-A establishment of the surface colonizers. Furthermore, presence and activity of the (2015) Microbial communities associated with benthic faunal surface colonizers influence the underlying microbial communities probably because of assemblages at cold seep sediments modification of energy source availabilities. of the Sonora Margin, Guaymas Basin. Front. Mar. Sci. 2:53. Keywords: microbial communities, pyrosequencing, MBG-D, ANME, faunal assemblages, Vesicomyidae, doi: 10.3389/fmars.2015.00053 Siboglinidae, microbial mat Frontiers in Marine Science | www.frontiersin.org 1 August 2015 | Volume 2 | Article 53 Cruaud et al. Microbial communities of the Sonora Margin seeps Introduction a complex ecosystem showing various surface assemblages (Lonsdale, 1985; Simoneit et al., 1990; Paull et al., 2007; Vigneron Seafloor emissions of hydrocarbon low-temperature fluids are a et al., 2013). Microbial communities, especially those involved characteristic feature of cold seep ecosystems. These fluids are in AOM, occurring in sediments underlying microbial mats and derived mainly from sedimented organic matter and support the surrounding macrofauna habitats have been recently studied complex food webs based on microbial chemoautotrophic (Vigneron et al., 2013, 2014a). These works highlighted that primary production (Van Dover et al., 2002). Diffusive and ANMEs were metabolically active and AOM might represent advective transports of potential substrates in sediment establish a major microbial process at the Sonora Margin cold seeps. a succession of different redox zones from aerobic to anaerobic However, the microbial diversity and distribution in sediments processes, based on the availability of electron donors (e.g., underlying other dominant benthic cold seep assemblages and sulfide and methane) and acceptors (e.g., oxygen, nitrate, sulfate) an overview of the microbial communities of the Sonora Margin (Jørgensen, 1977; Froelich et al., 1979; Engelen and Cypionka, sediments are still missing. 2009; Orcutt et al., 2011). For example, the sulfate-dependent In this study, we investigated four cold seep sites in the Anaerobic Oxidation of Methane (AOM) occurs in anoxic zones Guaymas Basin, which exhibited contrasted surface assemblages of sediments, where upward diffusing methane meets sulfate (Figure 1, Table S1). Two sites (Ayala and Vasconcelos BIG13) from the seawater (Devol et al., 1984; Iversen and Jørgensen, were populated by chemosynthetic vesicomyid bivalves, one site 1985; Orcutt et al., 2011). This process appears to be mainly (Juarez) was colonized by chemosynthetic siboglinid tubeworms mediated by anaerobic methanotrophic Archaea (ANMEs), while the fourth site (Vasconcelos BIG18) hosted a white which are frequently observed in structured aggregates with microbial mat surrounded by a macrofaunal assemblage sulfate-reducing bacteria mostly affiliated to Deltaproteobacteria. composed of ampharetid polychaetes and gastropods. This process, as well as the activity of abundant sulfate-reducing Additionally, one site without observable seepage activity bacteria, generates high concentrations of sulfide produced in or microbial/faunal presence was analyzed as a “reference” porewater sediments which provides high fluxes of sulfide to sample. the seafloor (Boetius et al., 2000; Orphan et al., 2001; Hinrichs At each site, we analyzed the diversity and distribution of and Boetius, 2002; Jørgensen and Boetius, 2007). These uprising microbial communities from the seawater/sediment interface sulfide-enriched fluids fuelled various surface assemblages such down to 15 cm below the seafloor (cmbsf), using ARISA as mat-forming giant bacteria (Lloyd et al., 2010; Grünke et al., fingerprinting, 454-pyrosequencing, quantification of dominant 2011; Mckay et al., 2012) or symbiont-bearing invertebrates microbial groups and microscopy, completed by porewater (Sibuet and Olu, 1998; Dubilier et al., 2008; Cambon-Bonavita geochemistry. Our main objectives were (i) to characterize and et al., 2009). These different types of communities are associated compare microbial communities inhabiting these sediments, with specific seeps (characterized by different rates of fluid flow and (ii) to evaluate how biogeochemical factors shaped the velocity and composition) depending on their ability to grow on microbial community structures. Doing so we tried to better available energy sources and to tolerate oxygen limitations and understand (i) how the sedimentary microbial communities toxic sulfide concentrations (Barry et al., 1997; Sibuet and Olu, and their potential metabolisms may impact the surface 1998; Sahling et al., 2002; Niemann et al., 2006; Lichtschlag et al., colonizer distribution and therefore influence diversity patterns 2010; Pop Ristova et al., 2012; Ruff et al., 2013). of chemosynthetic organisms at cold seeps and in return, (ii) Sulfide-consuming bacterial mats live at the interface between how the surface chemosynthetic organisms may influence the opposed gradients of oxygen from the water column and sulfide sedimentary microbial communities. from the sediments (Nelson et al., 1989; Schulz and Jorgensen, 2001; Lloyd et al., 2010; Grünke et al., 2011; Mckay et al., 2012). Some mobile organisms, such as gastropods, might feed Materials and Methods on these mat-forming bacteria (Waren and Bouchet, 2009). At cold seeps with moderate fluid flow rates (Dubilier et al., Sampling Sites and Methods 2008), benthic assemblages are dominated by chemosynthetic Four cold seep sites situated at the Sonora Margin were tubeworms (e.g., Siboglinidae) and bivalves (e.g., Vesicomyidae) investigated. Sediment samples were collected using push cores harboring intracellular bacterial symbionts that consume sulfide operated by the manned submersible Nautile during the “BIG” and/or methane (Felbeck et al., 1981; Cavanaugh, 1983; Fisher, cruise (June 2010). Sampling sites were selected according to 1990). While vesicomyids live partially buried in sediments, visual observations of the seafloor and methane plumes in the capturing sulfide from sediments with their foot and pumping water column (H. Ondreas, pers. com.). The Ayala site, located oxygen from seawater with their siphons (Cavanaugh, 1983; Arp at a water depth of 1560m and spotted with the marker BIG14, et al., 1984; Fisher, 1990), siboglinids mainly use the posterior was covered by abundant and scattered vesicomyid aggregates extension of their body (the “root”), to acquire sulfide from distributed on an estimated area of 15 by 20 meters (Figure 1, sediments and extend their branchial plumes in ambient seawater Table S1). The Vasconcelos BIG13 site, 1 km away from the for oxygen uptake (Julian et al., 1999; Freytag