Niche Separation of Methanotrophic Archaea (ANME-1 and -2) in Methane-Seep Sediments of the Eastern Japan Sea Offshore Joetsu

Yanagawa, Katsunori; Sunamura, Michinari; Lever, Mark A.; Morono, Yuki; Hiruta, Akihiro; Ishizaki, O.; Matsumoto, Ryo; Urabe, Tetsuro; Inagaki, Fumio

doi:10.1080/01490451003709334

Cited by 57 publications

(53 citation statements)

References 59 publications

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“…Although ANME-1 archaea have been found most frequently in sulfate-depleted environments (Yanagawa et al, 2011), they are known to be adapted to hypersalinity (Lloyd et al, 2006;Maignien et al, 2013). This suggests salinity is a stronger selective force for this group than sulfate concentration.…”

Section: Methanogenesis and Aommentioning

confidence: 98%

Unveiling microbial activities along the halocline of Thetis, a deep-sea hypersaline anoxic basin

et al. 2014

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Deep-sea hypersaline anoxic basins (DHABs) in the Eastern Mediterranean Sea are considered some of the most hostile environments on Earth. Little is known about the biochemical adaptations of microorganisms living in these habitats. This first metatranscriptome analysis of DHAB samples provides significant insights into shifts in metabolic activities of microorganisms as physicochemical conditions change from deep Mediterranean sea water to brine. The analysis of Thetis DHAB interface indicates that sulfate reduction occurs in both the upper (7.0-16.3% salinity) and lower (21.4-27.6%) halocline, but that expression of dissimilatory sulfate reductase is reduced in the more hypersaline lower halocline. High dark-carbon assimilation rates in the upper interface coincided with high abundance of transcripts for ribulose 1,5-bisphosphate carboxylase affiliated to sulfuroxidizing bacteria. In the lower interface, increased expression of genes associated with methane metabolism and osmoregulation is noted. In addition, in this layer, nitrogenase transcripts affiliated to uncultivated putative methanotrophic archaea were detected, implying nitrogen fixation in this anoxic habitat, and providing evidence of linked carbon, nitrogen and sulfur cycles.

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Section: Methanogenesis and Aommentioning

confidence: 98%

Unveiling microbial activities along the halocline of Thetis, a deep-sea hypersaline anoxic basin

et al. 2014

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“…In contrast, most of the mcrA gene sequences of groups c-d, e and f, hosted by ANME-2a, -2c and -3 , respectively, were found in the shallower depths of sediments (Figure 4). Molecular ecological studies have indicated that the ANME-1 populations occur in deeper, more reductive and more sulfate-depleted habitats than the ANME-2 populations (Knittel et al, 2005;Krüger et al, 2008;Nunoura et al, 2008;Rossel et al, 2011;Yanagawa et al, 2011). Furthermore, the potentially thermophilic ANME-1 group has been recognized as a key component in certain hydrothermal ecosystems, such as Guaymas Basin and Juan de Fuca Ridge (Biddle et al, 2012;Lever et al, 2013;Merkel et al, 2013).…”

Section: Microbial Functions Of Methanogenesis and Aommentioning

confidence: 99%

Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor

et al. 2016

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Subseafloor microbes beneath active hydrothermal vents are thought to live near the upper temperature limit for life on Earth. We drilled and cored the Iheya North hydrothermal field in the MidOkinawa Trough, and examined the phylogenetic compositions and the products of metabolic functions of sub-vent microbial communities. We detected microbial cells, metabolic activities and molecular signatures only in the shallow sediments down to 15.8 m below the seafloor at a moderately distant drilling site from the active hydrothermal vents (450 m). At the drilling site, the profiles of methane and sulfate concentrations and the δ 13 C and δD isotopic compositions of methane suggested the laterally flowing hydrothermal fluids and the in situ microbial anaerobic methane oxidation. In situ measurements during the drilling constrain the current bottom temperature of the microbially habitable zone to~45°C. However, in the past, higher temperatures of 106-198°C were possible at the depth, as estimated from geochemical thermometry on hydrothermally altered clay minerals. The 16S rRNA gene phylotypes found in the deepest habitable zone are related to those of thermophiles, although sequences typical of known hyperthermophilic microbes were absent from the entire core. Overall our results shed new light on the distribution and composition of the boundary microbial community close to the high-temperature limit for habitability in the subseafloor environment of a hydrothermal field.

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“…The potential for ecological niche partitioning within these highly diverse yet seemingly functionally redundant associations is not well understood. Previously, it was demonstrated that temperature (32), methane partial pressure (32), concentrations of sulfate (33,34) and sulfide (34), and the availability of nitrogen (35,36) may influence distribution and activity of AOM consortia. In addition, ANME-community structure can vary dramatically between geographically proximate sites as well as distinct sediment layers (37,38).…”

Section: Significancementioning

confidence: 99%

“…The activity patterns and niche differentiation of these apparently functionally redundant groups are, however, not understood. So far, temperature (32), methane partial pressure (32), concentration of sulfate (33,34) and sulfide (34), and nitrogen availability (35,36) have directly or indirectly been shown to drive the abundance and activity of different ANME lineages. Using BONCAT, we were able to demonstrate that representatives of all major ANME subpopulations (ANME-1 and ANME-2a, -2b, and -2c) cooccurring in a sediment incubation were biosynthetically active under controlled AOM incubation conditions in the laboratory (Table 1).…”

Section: Hpg Amendment Had No Detectable Effect On Microbial Communitymentioning

confidence: 99%

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia

Hatzenpichler

Connon

Goudeau

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

175

209

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To understand the biogeochemical roles of microorganisms in the environment, it is important to determine when and under which conditions they are metabolically active. Bioorthogonal noncanonical amino acid tagging (BONCAT) can reveal active cells by tracking the incorporation of synthetic amino acids into newly synthesized proteins. The phylogenetic identity of translationally active cells can be determined by combining BONCAT with rRNAtargeted fluorescence in situ hybridization (BONCAT-FISH). In theory, BONCAT-labeled cells could be isolated with fluorescenceactivated cell sorting (BONCAT-FACS) for subsequent genetic analyses. Here, in the first application, to our knowledge, of BONCAT-FISH and BONCAT-FACS within an environmental context, we probe the translational activity of microbial consortia catalyzing the anaerobic oxidation of methane (AOM), a dominant sink of methane in the ocean. These consortia, which typically are composed of anaerobic methane-oxidizing archaea (ANME) and sulfatereducing bacteria, have been difficult to study due to their slow in situ growth rates, and fundamental questions remain about their ecology and diversity of interactions occurring between ANME and associated partners. Our activity-correlated analyses of >16,400 microbial aggregates provide the first evidence, to our knowledge, that AOM consortia affiliated with all five major ANME clades are concurrently active under controlled conditions. Surprisingly, sorting of individual BONCAT-labeled consortia followed by whole-genome amplification and 16S rRNA gene sequencing revealed previously unrecognized interactions of ANME with members of the poorly understood phylum Verrucomicrobia. This finding, together with our observation that ANME-associated Verrucomicrobia are found in a variety of geographically distinct methane seep environments, suggests a broader range of symbiotic relationships within AOM consortia than previously thought.activity-based cell sorting | BONCAT | click chemistry | ecophysiology | single-cell microbiology

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Niche Separation of Methanotrophic Archaea (ANME-1 and -2) in Methane-Seep Sediments of the Eastern Japan Sea Offshore Joetsu

Cited by 57 publications

References 59 publications

Unveiling microbial activities along the halocline of Thetis, a deep-sea hypersaline anoxic basin

Unveiling microbial activities along the halocline of Thetis, a deep-sea hypersaline anoxic basin

Defining boundaries for the distribution of microbial communities beneath the sediment-buried, hydrothermally active seafloor

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia

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