Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics

Abstract

Microorganisms play a fundamental role in the cycling of nutrients and energy on our planet. A common strategy for many microorganisms mediating biogeochemical cycles in anoxic environments is syntrophy, frequently necessitating close spatial proximity between microbial partners. We are only now beginning to fully appreciate the diversity and pervasiveness of microbial partnerships in nature, the majority of which cannot be replicated in the laboratory. One notable example of such cooperation is the interspecies association between anaerobic methane oxidizing archaea (ANME) and sulfate-reducing bacteria. These consortia are globally distributed in the environment and provide a significant sink for methane by substantially reducing the export of this potent greenhouse gas into the atmosphere. The interdependence of these currently uncultured microbes renders them difficult to study, and our knowledge of their physiological capabilities in nature is limited. Here, we have developed a method to capture select microorganisms directly from the environment, using combined fluorescence in situ hybridization and immunomagnetic cell capture. We used this method to purify syntrophic anaerobic methane oxidizing ANME-2c archaea and physically associated microorganisms directly from deep-sea marine sediment. Metagenomics, PCR, and microscopy of these purified consortia revealed unexpected diversity of associated bacteria, including Betaproteobacteria and a second sulfate-reducing Deltaproteobacterial partner. The detection of nitrogenase genes within the metagenome and subsequent demonstration of 15 N2 incorporation in the biomass of these methane-oxidizing consortia suggest a possible role in new nitrogen inputs by these syntrophic assemblages.betaproteobacteria ͉ methanotrophy ͉ nitrogen fixation ͉ syntrophy

Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria

“…For those cases, where the interaction partners have been studied in more detail, characteristic features such as the loss of essential biosynthetic functions (McInerney et al, 2007) or the formation of physical attachment structures (Ishii et al, 2005;Wanner et al, 2008) have been reported that may have arisen as specific adaptations to the symbiotic lifestyle. Unfortunately, the obligate interdependence of both partners makes it often difficult to study this type of interactions under laboratory conditions (Nauhaus et al, 2002;Pernthaler et al, 2008;McCutcheon and Moran, 2012). As a consequence, many open questions remain regarding the ecological and evolutionary consequences of entering into such an obligate cross-feeding interaction.…”

Ocean currents shape the microbiome of Arctic marine sediments

“…Many studies have characterized the composition and ecological role of microorganisms in methanecontaining marine sediments around the world (Inagaki et al, 2006;Heijs et al, 2007;Parkes et al, 2007;Pernthaler et al, 2008;Wegener et al, 2008;Harrison et al, 2009;Hamdan et al, 2012). These works assist in understanding the biological controls on oceanic methane and may contribute to establishing baselines to monitor change in marine sediments.…”

Thermophilic anaerobic oxidation of methane by marine microbial consortia

“…Another group, ANME-3, occurs for instance at Haakon Mosby Mud Volcano (Niemann et al, 2006; in situ temperature À1.5 1C) and the Eastern Mediterranean seepages (Omoregie et al, 2008;14 1C). Cells of both groups form dense consortia with specific bacterial phylotypes clustering with sulfate-reducing Deltaproteobacteria (most often within Desulfosarcinales, Seep-SRB-1a; Schreiber et al, 2010) or relatives of Desulfobulbus Lösekann et al, 2007;Pernthaler et al, 2008;Schreiber et al, 2010), respectively. A third phylogenetic group, ANME-1, is dominant in the microbial mats covering chimney structures at methane seeps in the Black Sea (Michaelis et al, 2002; in situ temperature of B10 1C), and in several diffusive methane interfaces (Thomsen et al, 2001;Lanoil et al, 2005;Harrison et al, 2009;Aquilina et al, 2010).…”