Insights in the ecology and evolutionary history of the <i>Miscellaneous Crenarchaeotic Group</i> lineage

Fillol, Mireia; Auguet, Jean‐Christophe; Casamayor, Emilio O.; Borrego, Carles M.

doi:10.1038/ismej.2015.143

Cited by 97 publications

(103 citation statements)

References 79 publications

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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).…”

Section: Lipid Inventory Of M Luminyensis Compared To Other Archaeasupporting

confidence: 87%

“…Indeed, we evaluated commonly used primers against Methanomassiliicoccales, including the one used to sequence archaea from WOR sediments (22,80), using TestPrime 1.0 and the SILVA SSU r126 RefNR database (81), and the coverage was only between 0.5% and 56% for zero mismatches. Accordingly, the positive correlation of MCG with BDGTs in the WOR sediments (35) may instead result from the cooccurrence of MCG and Methanomassiliicoccales and/or uncultivated Thermoplasmata, such as TMEG and MBG-D, which was observed by operational taxonomic unit network analysis in various marine sediments (82). However, in samples where MBG-D dominate 16S rRNA clone libraries, both BDGTs and PDGTs were not detected, while GDGTs were the most abundant lipids (26).…”

Section: Lipid Inventory Of M Luminyensis Compared To Other Archaeamentioning

confidence: 99%

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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: 87%

Section: Lipid Inventory Of M Luminyensis Compared To Other Archaeamentioning

confidence: 99%

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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“…Among the archaeal groups, there is a dominance of Lokiarchaeota (MBG-B/ DSAG), MG-I, Bathyarchaeota (MCG), and Methanomicrobia. The Bathyarchaeota are arguably the most widespread and abundant members of sediment communities, with relative abundances anywhere between 1 and 100% and a very large phylogenetic diversity (Kubo et al 2012, Lloyd et al 2013, Fillol et al 2016. Stable isotopic analyses of subsurface sediments off Peru have indicated that Bathyarchaeota may have a heterotrophic metabolism, growing by assimilation of fossil organic matter (Biddle et al 2006).…”

Section: Traits For Selective Persistencementioning

confidence: 99%

Microbial community assembly in marine sediments

Petro¹,

Starnawski²,

Schramm³

et al. 2017

Aquat. Microb. Ecol.

113

111

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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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“…(between 30.5 and 48.4 % of total archaeal 16S rRNA gene reads detected in those samples), we performed phylogenetic analyses to determine the diversity of subgroups of the MCG within these sediments. A total of 57 representative 16S rRNA gene reads assigned to MCG were extracted from the dataset and incorporated into a MCG phylogenetic tree of Fillol et al (2015) (Fig. 2).…”

Section: Archaeal Diversity In the Surface And Subsurface Sedimentmentioning

confidence: 99%

Benthic archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone

et al. 2018

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Abstract. Benthic archaea comprise a significant part of the total prokaryotic biomass in marine sediments. Recent genomic surveys suggest they are largely involved in anaerobic processing of organic matter, but the distribution and abundance of these archaeal groups are still largely unknown. Archaeal membrane lipids composed of isoprenoid diethers or tetraethers (glycerol dibiphytanyl glycerol tetraether, GDGT) are often used as archaeal biomarkers. Here, we compare the archaeal diversity and intact polar lipid (IPL) composition in both surface (0-0.5 cm) and subsurface (10-12 cm) sediments recovered within, just below, and well below the oxygen minimum zone (OMZ) of the Arabian Sea. Archaeal 16S rRNA gene amplicon sequencing revealed a predominance of Thaumarchaeota (Marine Group I, MG-I) in oxygenated sediments. Quantification of archaeal 16S rRNA and ammonia monoxygenase (amoA) of Thaumarchaeota genes and their transcripts indicated the presence of an active in situ benthic population, which coincided with a high relative abundance of hexose phosphohexose crenarchaeol, a specific biomarker for living Thaumarchaeota. On the other hand, anoxic surface sediments within the OMZ and all subsurface sediments were dominated by archaea belonging to the Miscellaneous Crenarchaeota Group (MCG), the Thermoplasmatales and archaea of the DPANN (superphylum grouping Micrarchaeota, Diapherotrites, Aenigmarchaeota, Nanohaloarchaeota, Parvarchaeota, Nanoarchaeota, Pacearchaeota and Woesearchaeota). Members of the MCG were diverse, with a dominance of subgroup MCG-12 in anoxic surface sediments. This coincided with a high relative abundance of IPL GDGT-0 with an unknown polar head group. Subsurface anoxic sediments were characterized by higher relative abundance of GDGT-0, -2 and -3 with dihexose IPL types, GDGT-0 with a cyclopentanetetraol molecule and hexose, as well as the presence of specific MCG subgroups, suggesting that these groups could be the biological sources of these archaeal lipids.

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Insights in the ecology and evolutionary history of the Miscellaneous Crenarchaeotic Group lineage

Cited by 97 publications

References 79 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

Benthic archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone

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