Serpentinite-hosted systems are amongst the most challenging environments for life on Earth. Serpentinization, a geochemical alteration of exposed ultramafic rock, produces hydrothermal fluids ...enriched in abiotically derived hydrogen (H
), methane (CH
), and small organic molecules. The hyperalkaline pH of these fluids poses a great challenge for metabolic energy and nutrient acquisition, curbing the cellular membrane potential and limiting electron acceptor, carbon, and phosphorous availability. Nevertheless, serpentinization supports the growth of diverse microbial communities whose metabolic make-up might shed light on the beginning of life on Earth and potentially elsewhere. Here, we outline current hypotheses on metabolic energy production, carbon fixation, and nutrient acquisition in serpentinizing environments. A taxonomic survey is performed for each important metabolic function, highlighting potential key players such as H
and CH
cycling
,
,
,
, and novel candidate phyla. Methodological biases of the available data and future approaches are discussed.
The southeastern part of New Caledonia main island (Grande Terre) is the location of a large ophiolitic formation that hosts several hyperalkaline springs discharging high pH (∼11) and warm (<40°C) ...fluids enriched in methane (CH
) and hydrogen (H
). These waters are produced by the serpentinization of the ultrabasic rock formations. Molecular surveys had previously revealed the prokaryotic diversity of some of these New Caledonian springs, especially from the submarine chimneys of Prony Bay hydrothermal field. Here we investigate the microbial community of hyperalkaline waters from on-land springs and their relationships with elevated concentrations of dissolved H
(21.1-721.3 μmol/L) and CH
(153.0-376.6 μmol/L). 16S rRNA gene analyses (metabarcoding and qPCR) provided evidence of abundant and diverse prokaryotic communities inhabiting hyperalkaline fluids at all the collected springs. The abundance of prokaryotes was positively correlated to the H
/CH
ratio. Prokaryotes consisted mainly of bacteria that use H
as an energy source, such as microaerophilic
/
(detected in all sources on land) or anaerobic sulfate-reducing
, which were exclusively found in the most reducing (E
ref H
∼ -700 mV) and the most H
-enriched waters discharging at the intertidal spring of the Bain des Japonais. The relative abundance of a specific group of uncultured Methanosarcinales that thrive in serpentinization-driven ecosystems emitting H
, considered potential H
-consuming methanogens, was positively correlated with CH
concentrations, and negatively correlated to the relative abundance of methylotrophic Gammaproteobacteria. Firmicutes were also numerous in hyperalkaline waters, and their relative abundance (e.g.,
or
) was proportional to the dissolved H
concentrations, but their role in the H
budget remains to be assessed. The prokaryotic communities thriving in New Caledonia hyperalkaline waters are similar to those found in other serpentinite-hosted high-pH waters worldwide, such as Lost City (North Atlantic) and The Cedars (California).
Two novel anaerobic alkaliphilic strains, designated as LacTT and LacVT, were isolated from the Prony Bay Hydrothermal Field (PBHF, New Caledonia). Cells were motile, Gram-positive, terminal ...endospore-forming rods, displaying a straight to curved morphology during the exponential phase. Strains LacTT and LacVT were mesophilic (optimum 30°C), moderately alkaliphilic (optimum pH 8.2 and 8.7, respectively) and halotolerant (optimum 2% and 2.5% NaCl, respectively). Both strains were able to ferment yeast extract, peptone and casamino acids, but only strain LacTT could use sugars (glucose, maltose and sucrose). Both strains disproportionated crotonate into acetate and butyrate. Phylogenetic analysis revealed that strains LacTT and LacVT shared 96.4% 16S rRNA gene sequence identity and were most closely related to A. peptidifermentans Z-7036, A. namsaraevii X-07-2 and A. hydrothermalis FatMR1 (95.7%–96.3%). Their genome size was of 3.29Mb for strain LacTT and 3.06Mb for strain LacVT with a G+C content of 36.0 and 33.9mol%, respectively. The ANI value between both strains was 73.2 %. Finally, strains LacTT (=DSM 100337=JCM 30643) and LacVT (=DSM 100017=JCM 30644) are proposed as two novel species of the genus Alkaliphilus, order Clostridiales, phylum Firmicutes, Alkaliphilus serpentinus sp. nov. and Alkaliphilus pronyensis sp. nov., respectively. The genomes of the three Alkaliphilus species isolated from PBHF were consistently detected in the PBHF chimney metagenomes, although at very low abundance, but not significantly in the metagenomes of other serpentinizing systems (marine or terrestrial) worldwide, suggesting they represent indigenous members of the PBHF microbial ecosystem.
A novel thermophilic, anaerobic bacterium, strain F1F22
, was isolated from hot spring water collected in northern Tunisia. The cells were non-motile, Gram-negative and helical with hooked ends, ...0.5×10-32 µm in size. Growth of the strain was observed at 45-70 °C (optimum, 55 °C), in 0.0-1.0 % (w/v) NaCl (optimum without NaCl) and at pH 6.5-8.5 (optimum, pH 7.5). Yeast extract was required for growth, and the strain grew on glucose, sucrose and maltose. The major fatty acids were C
(40.2 %), iso-C
(30.2 %) and C
DMA (14.5 %). The genome consisted of a circular chromosome (2.5 Mb) containing 2672 predicted protein-encoding genes with a G+C content of 43.15 mol %. Based on a comparative 16S rRNA gene sequence analysis, strain F1F22
formed a deeply branching lineage within the phylum
, class
, order
, and had only low sequence similarity to other species of the phylum (lower than 83 %). Genome-based analysis of average nucleotide identity and digital DNA-DNA hybridization of strain F1F22
with
DSM 7334
,
ATCC 43811
and
DSM 6578
showed values between 63.26 and 63.52 %, and between 20 and 25 %. Hence, we propose strain F1F22
as a representative of a novel family (
fam. nov.), genus and species of
:
gen. nov., sp. nov. (type strain F1F22
=JCM 31314
=DSM 101182
).
Mobilome of hyperthermophilic archaea dwelling in deep-sea hydrothermal vents is poorly characterized. To gain insight into genetic diversity and dynamics of mobile genetic elements in these ...environments we have sequenced five new plasmids from different Thermococcus strains that have been isolated from geographically remote hydrothermal vents. The plasmids were ascribed to two subfamilies, pTN2-like and pEXT9a-like. Gene content and phylogenetic analyses illuminated a robust connection between pTN2-like plasmids and Pyrococcus abyssi virus 1 (PAV1), with roughly half of the viral genome being composed of genes that have homologues in plasmids. Unexpectedly, pEXT9a-like plasmids were found to be closely related to the previously sequenced plasmid pMETVU01 from Methanocaldococcus vulcanius M7. Our data suggests that the latter observation is most compatible with an unprecedented horizontal transfer of a pEXT9a-like plasmid from Thermococcales to Methanococcales. Gene content analysis revealed that thermococcal plasmids encode Hfq-like proteins and toxin-antitoxin (TA) systems of two different families, VapBC and RelBE. Notably, although abundant in archaeal genomes, to our knowledge, TA and hfq-like genes have not been previously found in archaeal plasmids or viruses. Finally, the plasmids described here might prove to be useful in developing new genetic tools for hyperthermophiles.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
A novel anaerobic, alkaliphilic, mesophilic, Gram-stain-positive, endospore-forming bacterium was isolated from an alkaline thermal spring (42 °C, pH 9.0) in New Caledonia. This bacterium, designated ...strain LB2
, grew at 25-50 °C (optimum, 37 °C) and pH 8.2-10.8 (optimum, pH 9.5). Added NaCl was not required for growth (optimum, 0-1 %) but was tolerated up to 7 %. Strain LB2
utilized a limited range of substrates, such as peptone, pyruvate, yeast extract and xylose. End products detected from pyruvate fermentation were acetate and formate. Both ferric citrate and thiosulfate were used as electron acceptors. Elemental sulphur, nitrate, nitrite, fumarate, sulphate, sulfite and DMSO were not used as terminal electron acceptors. The two major cellular fatty acids were iso-C
and C
. The genome consists of a circular chromosome (3.7 Mb) containing 3626 predicted protein-encoding genes with a G+C content of 36.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate is a member of the family
, order
within the phylum
. Strain LB2
was most closely related to the thermophilic
LBS3
(93.2 % 16S rRNA gene sequence identity). Genome-based analysis of average nucleotide identity and digital DNA-DNA hybridization of strain LB2
with
LBS3
showed respective values of 70.8 and 13.4 %. Based on phylogenetic, genomic, chemotaxonomic and physiological properties, strain LB2
is proposed to represent the first species of a novel genus, for which the name
gen. nov., sp. nov. is proposed (type strain LB2
=DSM 100588
=JCM 30958
).
A novel thermophilic strain, designated BP5-C20A
T
, was isolated from the shallow hydrothermal field of the Panarea island in the Aeolian archipelago close to Sicily, Italy. Cells are motile rods ...surrounded with a ‘toga’, Gram-stain-negative and display a straight to curved morphology during the exponential phase. Strain BP5-C20A
T
is thermophilic (optimum 55 °C), moderately acidophilic (optimum pH 5.6) and halotolerant (optimum 25 g l
−1
NaCl). It can use yeast extract, peptone and tryptone. It uses the following carbohydrates: cellobiose, fructose, glucose, maltose, starch, sucrose and xylan. Elemental sulphur is used as an electron acceptor and reduced to hydrogen sulphide. The predominant cellular fatty acid is C
16 : 0
. Phylogenetic analysis showed that strain BP5-C20A
T
shared 97.3 % 16S rRNA gene sequence identity with the closest related species
Marinitoga lauensis
LG1
T
. The complete genome of strain BP5-C20A
T
is 2.44 Mb in size with a G+C content of 27.3 mol%. The dDDH and ANI values between the genomes of strains BP5-C20A
T
and
M. lauensis
LG1
T
are 31.0 and 85.70% respectively. Finally, from its physiological, metabolic and genomic characteristics, strain BP5-C20A
T
(=DSM 112332
T
=JCM 39183
T
) is proposed as representative of a novel species of the genus
Marinitoga
named
Marinitoga aeolica
sp. nov. and belonging to the order
Petrotogales
, in the phylum
Thermotogota
.
The Voltri Massif is an ophiolitic complex located in the Ligurian Alps close to the city of Genova (Northern Italy) where several springs discharge high pH (up to 11.7), low salinity waters produced ...by the active serpentinization of the ultramafic basement. Mixing of these hyperalkaline waters with the river waters along with the uptake of atmospheric carbon dioxide forms brownish carbonate precipitates covering the bedrock at the springs. Diverse archaeal and bacterial communities were detected in these carbonate precipitates using 454 pyrosequencing analyses of 16S ribosomal RNA (rRNA) genes. Archaeal communities were dominated by members of potential methane-producing and/or methane-oxidizing
Methanobacteriales
and
Methanosarcinale
s (
Euryarchaeota
) together with ammonia-oxidizing
Nitrososphaerales
(
Thaumarchaeota
) similar to those found in other serpentinization-driven submarine and terrestrial ecosystems. Bacterial communities consisted of members of the
Proteobacteria
,
Actinobacteria
,
Planctomycetes
,
Bacteroidetes
,
Chloroflexi
, and
Verrucomicrobia
phyla, altogether accounting for 92.2 % of total retrieved bacterial 16S rRNA gene sequences. Amongst
Bacteria
, potential chemolithotrophy was mainly associated with
Alpha-
and
Betaproteobacteria
classes, including nitrogen-fixing, methane-oxidizing or hydrogen-oxidizing representatives of the genera
Azospirillum
,
Methylosinus
, and
Hydrogenophaga/
‘
Serpentinomonas
’, respectively. Besides, potential chemoorganotrophy was attributed mainly to representatives of
Actinobacteria
and
Planctomycetales
phyla. The reported 16S rRNA gene data strongly suggested that hydrogen, methane, and nitrogen-based chemolithotrophy can sustain growth of the microbial communities inhabiting the carbonate precipitates in the hyperalkaline springs of the Voltri Massif, similarly to what was previously observed in other serpentinite-hosted ecosystems.
Rock-hosted subseafloor habitats are very challenging for life, and current knowledge about microorganisms inhabiting such lithic environments is still limited. This study explored the cultivable ...microbial diversity in anaerobic enrichment cultures from cores recovered during the International Ocean Discovery Program (IODP) Expedition 357 from the Atlantis Massif (Mid-Atlantic Ridge, 30°N). 16S rRNA gene survey of enrichment cultures grown at 10-25°C and pH 8.5 showed that
and
were generally dominant. However, cultivable microbial diversity significantly differed depending on incubation at atmospheric pressure (0.1 MPa), or hydrostatic pressures (HP) mimicking the
pressure conditions (8.2 or 14.0 MPa). An original, strictly anaerobic bacterium designated 70B-A
was isolated from core M0070C-3R1 (1150 meter below sea level; 3.5 m below seafloor) only from cultures performed at 14.0 MPa. This strain named
is a novel species of a new genus within the newly described family
(order
, phylum
). It is a mesophilic, moderately halotolerant and piezophilic chemoorganotroph, able to grow by fermentation of carbohydrates and proteinaceous compounds. Its 3.5 Mb genome contains numerous genes for ABC transporters of sugars and amino acids, and pathways for fermentation of mono- and di-saccharides and amino acids were identified. Genes encoding multimeric FeFe hydrogenases and a Rnf complex form the basis to explain hydrogen and energy production in strain 70B-A
. This study outlines the importance of using hydrostatic pressure in culture experiments for isolation and characterization of autochthonous piezophilic microorganisms from subseafloor rocks.
Serpentinizing hydrothermal systems result from water circulating into the subsurface and interacting with mantle-derived rocks notably near mid-ocean ridges or continental ophiolites. ...Serpentinization and associated reactions produce alkaline fluids enriched in molecular hydrogen, methane, and small organic molecules that are assumed to feed microbial inhabitants. In this study, we explored the relationships linking serpentinization to associated microbial communities by comparative metagenomics of serpentinite-hosted systems, basalt-hosted vents, and hot springs. The shallow Prony bay hydrothermal field (PBHF) microbiome appeared to be more related to those of ophiolitic sites than to the Lost City hydrothermal field (LCHF) microbiome, probably because of the meteoric origin of its fluid, like terrestrial alkaline springs. This study emphasized the ubiquitous importance of a set of genes involved in the catabolism of phosphonates and highly enriched in all serpentinizing sites compared to other ecosystems. Because most of the serpentinizing systems are depleted in inorganic phosphate, the abundance of genes involved in the carbon-phosphorus lyase pathway suggests that the phosphonates constitute a source of phosphorus in these ecosystems. Additionally, hydrocarbons such as methane, released upon phosphonate catabolism, may contribute to the overall budget of organic molecules in serpentinizing systems.
This first comparative metagenomic study of serpentinite-hosted environments provides an objective framework to understand the functioning of these peculiar ecosystems. We showed a taxonomic similarity between the PBHF and other terrestrial serpentinite-hosted ecosystems. At the same time, the LCHF microbial community was closer to deep basalt-hosted hydrothermal fields than continental ophiolites, despite the influence of serpentinization. This study revealed shared functional capabilities among serpentinite-hosted ecosystems in response to environmental stress, the metabolism of abundant dihydrogen, and the metabolism of phosphorus. Our results are consistent with the generalized view of serpentinite environments but provide deeper insight into the array of factors that may control microbial activities in these ecosystems. Moreover, we show that metabolism of phosphonate is widespread among alkaline serpentinizing systems and could play a crucial role in phosphorus and methane biogeochemical cycles. This study opens a new line of investigation of the metabolism of reduced phosphorus compounds in serpentinizing environments.
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