Archaea in Organic-Lean and Organic-Rich Marine Subsurface Sediments: An Environmental Gradient Reflected in Distinct Phylogenetic Lineages

Durbin, Alan M.; Teske, Andreas

doi:10.3389/fmicb.2012.00168

Cited by 87 publications

(111 citation statements)

References 135 publications

(281 reference statements)

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“…This supports recent metagenomic studies, which showed that besides gut and rumen environments (6,13,14), Methanomassiliicoccales also occur ubiquitously in marine and terrestrial anaerobic environments (10,15,82,83). Similarly to the case for WOR, 16S rRNA gene sequences of Methanomassiliicoccales were not reported for the investigated sites, likely due to a mismatch of commonly used primers against hitherto-undetected clades (22), while other uncultured Thermoplasmata were detected (84). In some samples, for instance in the equatorial Pacific, BDGTs were not detected, which is probably related to low total organic carbon (TOC) concentrations (29) and sulfate-reducing conditions (85) at this site.…”

Section: Lipid Inventory Of M Luminyensis Compared To Other Archaeasupporting

confidence: 57%

Unusual Butane- and Pentanetriol-Based Tetraether Lipids in Methanomassiliicoccus luminyensis, a Representative of the Seventh Order of Methanogens

Becker

Elling

Yoshinaga

et al. 2016

Appl Environ Microbiol

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A new clade of archaea has recently been proposed to constitute the seventh methanogenic order, the Methanomassiliicoccales, which is related to the Thermoplasmatales and the uncultivated archaeal clades deep-sea hydrothermal vent Euryarchaeota group 2 and marine group II Euryarchaeota but only distantly related to other methanogens. In this study, we investigated the membrane lipid composition of Methanomassiliicoccus luminyensis, the sole cultured representative of this seventh order. The lipid inventory of M. luminyensis comprises a unique assemblage of novel lipids as well as lipids otherwise typical for thermophilic, methanogenic, or halophilic archaea. For instance, glycerol sesterpanyl-phytanyl diether core lipids found mainly in halophilic archaea were detected, and so were compounds bearing either heptose or methoxylated glycosidic head groups, neither of which have been reported so far for other archaea. The absence of quinones or methanophenazines is consistent with a biochemistry of methanogenesis different from that of the methanophenazine-containing methylotrophic methanogens. The most distinctive characteristic of the membrane lipid composition of M. luminyensis, however, is the presence of tetraether lipids in which one glycerol backbone is replaced by either butane-or pentanetriol, i.e., lipids recently discovered in marine sediments. Butanetriol dibiphytanyl glycerol tetraether (BDGT) constitutes the most abundant core lipid type (>50% relative abundance) in M. luminyensis. We have thus identified a source for these unusual orphan lipids. The complementary analysis of diverse marine sediment samples showed that BDGTs are widespread in anoxic layers, suggesting an environmental significance of Methanomassiliicoccales and/or related BDGT producers beyond gastrointestinal tracts. IMPORTANCECellular membranes of members of all three domains of life, Archaea, Bacteria, and Eukarya, are largely formed by lipids in which glycerol serves as backbone for the hydrophobic alkyl chains. Recently, however, archaeal tetraether lipids with either butanetriol or pentanetriol as a backbone were identified in marine sediments and attributed to uncultured sediment-dwelling archaea. Here we show that the butanetriol-based dibiphytanyl tetraethers constitute the major lipids in Methanomassiliicoccus luminyensis, currently the only isolate of the novel seventh order of methanogens. Given the absence of these lipids in a large set of archaeal isolates, these compounds may be diagnostic for the Methanomassiliicoccales and/or closely related archaea. Methane is a potent greenhouse gas and an important intermediate in the global carbon cycle (1-3). Biogenic methane is produced predominantly by archaea inhabiting diverse anoxic environments such as sediments, soils, wetlands, and the digestive tracts of termites and ruminants (2, 4). All cultured methanogens to date belong to the phylum Euryarchaeota, while metagenomic sequencing revealed a putative methanogenic metabolism for members of the uncultivated Bathyarc...

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Section: Lipid Inventory Of M Luminyensis Compared To Other Archaeasupporting

confidence: 57%

Unusual Butane- and Pentanetriol-Based Tetraether Lipids in Methanomassiliicoccus luminyensis, a Representative of the Seventh Order of Methanogens

Becker

Elling

Yoshinaga

et al. 2016

Appl Environ Microbiol

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“…Analyses of the factors underlying these distribution patterns have proposed varying theories. One hypothesis is that geochemical zonation, or electron acceptor availability, may influence the vertical organization of subsurface prokaryotic populations (Durbin & Teske 2012. The community patterns that can be correlated to geochemical zonation are likely exhibited by functional groups of terminal oxidizers, which perform remineralization processes associated with specific zones (Loy et al 2004, Leloup et al 2007, Lever 2013).…”

Section: Microbial Diversity In Sedimentsmentioning

confidence: 99%

Microbial community assembly in marine sediments

Petro¹,

Starnawski²,

Schramm³

et al. 2017

Aquat. Microb. Ecol.

114

112

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Marine sediments are densely populated by diverse communities of archaea and bacteria, with intact cells detected kilometers below the seafloor. Analyses of microbial diversity in these unique environments have identified several dominant taxa that comprise a significant portion of the community in geographically and environmentally disparate locations. While the distributions of these populations are well documented, there is significantly less information describing the means by which such specialized communities assemble within the sediment column. Here, we review known patterns of subsurface microbial community composition and perform a meta-analysis of publicly available 16S rRNA gene datasets collected from 9 locations at depths from 1 cm to > 2 km below the surface. All data are discussed in relation to the 4 major processes of microbial community assembly: diversification, dispersal, selection, and drift. Microbial diversity in the subsurface decreases with depth on a global scale. The transition from the seafloor to the deep subsurface biosphere is marked by a filtering of populations from the surface that leaves only a subset of taxa to populate the deeper sediment zones, indicating that selection is a main mechanism of community assembly. The physiological underpinnings for the success of these persisting taxa are largely unknown, as the majority of them lack cultured representatives. Ecological explanations for the observed trends are presented, including the possible influence of energy depletion and the physiological basis of major taxonomic shifts.

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“…Furthermore, a few specific microbial groups, such as anaerobic methane oxidizers (ANME) (32,33) and anaerobic ammonium oxidizers (anammox) (34) have been associated consistently with specific redox zones. In addition, samples obtained from markedly different sedimentary settings (e.g., high or low temperature, presence or absence of methane, high or low carbon load) have been found to show distinct microbial community compositions (7,35,36). Nonetheless, an explicit, quantitative correlation between stratigraphic variability in geochemical properties and concomitant changes in the structure of the total microbial community or the relative abundance of individual taxa has remained elusive.…”

Section: -10mentioning

confidence: 99%

Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge

Jørgensen¹,

Hannisdal

Lanzén

et al. 2012

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

259

232

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Microbial communities and their associated metabolic activity in marine sediments have a profound impact on global biogeochemical cycles. Their composition and structure are attributed to geochemical and physical factors, but finding direct correlations has remained a challenge. Here we show a significant statistical relationship between variation in geochemical composition and prokaryotic community structure within deep-sea sediments. We obtained comprehensive geochemical data from two gravity cores near the hydrothermal vent field Loki's Castle at the Arctic Mid-Ocean Ridge, in the Norwegian-Greenland Sea. Geochemical properties in the rift valley sediments exhibited strong centimeter-scale stratigraphic variability. Microbial populations were profiled by pyrosequencing from 15 sediment horizons (59,364 16S rRNA gene tags), quantitatively assessed by qPCR, and phylogenetically analyzed. Although the same taxa were generally present in all samples, their relative abundances varied substantially among horizons and fluctuated between Bacteria-and Archaea-dominated communities. By independently summarizing covariance structures of the relative abundance data and geochemical data, using principal components analysis, we found a significant correlation between changes in geochemical composition and changes in community structure. Differences in organic carbon and mineralogy shaped the relative abundance of microbial taxa. We used correlations to build hypotheses about energy metabolisms, particularly of the Deep Sea Archaeal Group, specific Deltaproteobacteria, and sediment lineages of potentially anaerobic Marine Group I Archaea. We demonstrate that total prokaryotic community structure can be directly correlated to geochemistry within these sediments, thus enhancing our understanding of biogeochemical cycling and our ability to predict metabolisms of uncultured microbes in deep-sea sediments.taxonomic profiling | ultraslow-spreading ridge | amplicon sequencing

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Archaea in Organic-Lean and Organic-Rich Marine Subsurface Sediments: An Environmental Gradient Reflected in Distinct Phylogenetic Lineages

Cited by 87 publications

References 135 publications

Unusual Butane- and Pentanetriol-Based Tetraether Lipids in Methanomassiliicoccus luminyensis, a Representative of the Seventh Order of Methanogens

Unusual Butane- and Pentanetriol-Based Tetraether Lipids in Methanomassiliicoccus luminyensis, a Representative of the Seventh Order of Methanogens

Microbial community assembly in marine sediments

Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge

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