Benthic C fixation and cycling in diffuse hydrothermal and background sediments in the Bransfield Strait, Antarctica

Abstract. Sedimented hydrothermal vents are likely to be widespread compared to hard substrate hot vents. They host chemosynthetic microbial communities which fix inorganic C at the seafloor, as well as a wide range of macroinfauna, including vent-obligate and background non-vent taxa. There are no previous direct observations of Carbon cycling at a sedimented hydrothermal vent. We conducted 13C isotope tracing experiments at 3 sedimented sites in the Bransfield Strait, Antarctica, which showed different degrees of hydrothermalism. Two experimental treatments were applied, with 13C added as either algal detritus (photosynthetic C), or as bicarbonate (substrate for benthic C fixation). Algal 13C was taken up by both bacteria and metazoan macrofaunal, but its dominant fate was respiration, as observed at deeper and more food limited sites elsewhere. Rates of 13C uptake and respiration suggested that the diffuse hydrothermal site was not the hotspot of benthic C-cycling that we hypothesised it would be. Fixation of inorganic C into bacterial biomass was observed at all, and was measurable at 2 out of 3 sites. At all sites, newly fixed C was transferred to metazoan macrofauna. Fixation rates were relatively low compared to similar experiments elsewhere, thus C fixed at the seafloor was a minor C source for the benthic ecosystem. However, as the greatest amount of benthic C fixation occurred at the off vent (non-hydrothermal) site (0.077 ± 0.034 mg C m−2 fixed during 60 h), we suggest that benthic fixation of inorganic C is more widespread than previously thought, and warrants further study.

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Benthic carbon fixation and cycling in diffuse hydrothermal and background sediments in the Bransfield Strait, Antarctica

Biogeosciences ◽

10.5194/bg-17-1-2020 ◽

2020 ◽

Vol 17 (1) ◽

pp. 1-12

Author(s):

Clare Woulds ◽

James B. Bell ◽

Adrian G. Glover ◽

Steven Bouillon ◽

Louise S. Brown

Keyword(s):

Hydrothermal Vents ◽

Carbon Fixation ◽

Hot Spot ◽

Bacterial Biomass ◽

Bransfield Strait ◽

Direct Observations ◽

13C Isotope ◽

Wide Range ◽

Experimental Treatments ◽

A Minor

Abstract. Sedimented hydrothermal vents are likely to be widespread compared to hard substrate hot vents. They host chemosynthetic microbial communities which fix inorganic carbon (C) at the seafloor, as well as a wide range of macroinfauna, including vent-obligate and background non-vent taxa. There are no previous direct observations of carbon cycling at a sedimented hydrothermal vent. We conducted 13C isotope tracing experiments at three sedimented sites in the Bransfield Strait, Antarctica, which showed different degrees of hydrothermalism. Two experimental treatments were applied, with 13C added as either algal detritus (photosynthetic C), or as bicarbonate (substrate for benthic C fixation). Algal 13C was taken up by both bacteria and metazoan macrofaunal, but its dominant fate was respiration, as observed at deeper and more food-limited sites elsewhere. Rates of 13C uptake and respiration suggested that the diffuse hydrothermal site was not the hot spot of benthic C cycling that we hypothesised it would be. Fixation of inorganic C into bacterial biomass was observed at all sites, and was measurable at two out of three sites. At all sites, newly fixed C was transferred to metazoan macrofauna. Fixation rates were relatively low compared with similar experiments elsewhere; thus, C fixed at the seafloor was a minor C source for the benthic ecosystem. However, as the greatest amount of benthic C fixation occurred at the “Off Vent” (non-hydrothermal) site (0.077±0.034 mg C m−2 fixed during 60 h), we suggest that benthic fixation of inorganic C is more widespread than previously thought, and warrants further study.

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Diverse Viruses in Deep-Sea Hydrothermal Vent Fluids Have Restricted Dispersal across Ocean Basins

mSystems ◽

10.1128/msystems.00068-21 ◽

2021 ◽

Author(s):

Elaina Thomas ◽

Rika E. Anderson ◽

Viola Li ◽

L. Jenni Rogan ◽

Julie A. Huber

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Microbial Communities ◽

Deep Sea ◽

Hydrothermal Vent ◽

Hydrothermal Vents ◽

Viral Ecology ◽

Unique Nature

Viruses play important roles in manipulating microbial communities and their evolution in the ocean, yet not much is known about viruses in deep-sea hydrothermal vents. However, viral ecology and evolution are of particular interest in hydrothermal vent habitats because of their unique nature: previous studies have indicated that most viruses in hydrothermal vents are temperate rather than lytic, and it has been established that rates of horizontal gene transfer (HGT) are particularly high among thermophilic vent microbes, and viruses are common vectors for HGT.

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Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome

Microbiome ◽

10.1186/s40168-020-00981-z ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Hannes Petruschke ◽

Christian Schori ◽

Sebastian Canzler ◽

Sarah Riesbeck ◽

Anja Poehlein ◽

...

Keyword(s):

Microbial Communities ◽

Intestinal Microbiota ◽

De Novo ◽

Bacterial Species ◽

Intestinal Microbiome ◽

Single Strain ◽

Small Proteins ◽

Human Intestinal Microbiota ◽

Wide Range

Abstract Background The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. Results We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. Conclusions We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract.

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Macrofaunal Ecology of Sedimented Hydrothermal Vents in the Bransfield Strait, Antarctica

Frontiers in Marine Science ◽

10.3389/fmars.2016.00032 ◽

2016 ◽

Vol 3 ◽

Cited By ~ 7

Author(s):

James B. Bell ◽

Clare Woulds ◽

Lee E. Brown ◽

Christopher J. Sweeting ◽

William D. K. Reid ◽

...

Keyword(s):

Hydrothermal Vents ◽

Bransfield Strait

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Lipid composition of the hydrothermal vent clam Calyptogena pacifica (Mollusca: Bivalvia) as a trophic indicator

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315401004647 ◽

2001 ◽

Vol 81 (5) ◽

pp. 817-821 ◽

Cited By ~ 15

Author(s):

Catherine E. Allen ◽

Paul A. Tyler ◽

Cindy L. Van Dover

Keyword(s):

Fatty Acids ◽

Gas Chromatography ◽

Hydrothermal Vent ◽

Hydrothermal Vents ◽

Unsaturated Fatty Acids ◽

Monounsaturated Fatty Acids ◽

Eicosatrienoic Acid ◽

Symbiotic Bacteria ◽

Large Contribution ◽

Flame Ionization

Specimens of the chemoautotrophic symbiont-bearing hydrothermal vent clam Calyptogena pacifica were collected from hydrothermal vents at the Endeavour segment of the Juan de Fuca Ridge. Total lipid was extracted from gill, foot and mantle tissues, and lipid class and fatty acid composition determined by thin layer chromatography with flame ionization detection (TLC–FID), gas chromatography (GC) and gas chromatography with mass spectrometry (GC–MS). An abundance of n–7 monounsaturated fatty acids (MUFA), especially in the gill, reflected the large contribution of chemoautotrophic symbiotic bacteria to the nutrition of this clam. The absence of n–8 MUFA suggests that C. pacifica does not contain methanotrophic symbiotic bacteria. Low levels of highly unsaturated fatty acids (HUFA) such as 20:5 n–3 and 22:6 n–3 were detected in C. pacifica and their presence is attributed to a source other than chemoautotrophic symbiotic bacteria. Significant levels of non-methylene interrupted dienoic fatty acids and eicosatrienoic acid (20:3) were also detected in C. pacifica and it is suggested that these fatty acids are synthesized from n–7 MUFA as alternatives to HUFA. In contrast to shallow water bivalves, elevated levels of triglyceride were detected in the gills compared to the mantle.

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Growth and Phylogenetic Properties of Novel Bacteria Belonging to the Epsilon Subdivision of the Proteobacteria Enriched fromAlvinella pompejana and Deep-Sea Hydrothermal Vents

Applied and Environmental Microbiology ◽

10.1128/aem.67.10.4566-4572.2001 ◽

2001 ◽

Vol 67 (10) ◽

pp. 4566-4572 ◽

Cited By ~ 102

Author(s):

Barbara J. Campbell ◽

Christian Jeanthon ◽

Joel E. Kostka ◽

George W. Luther ◽

S. Craig Cary

Keyword(s):

Deep Sea ◽

Hydrothermal Vent ◽

Hydrothermal Vents ◽

Heterotrophic Bacteria ◽

Geographic Location ◽

Optimal Growth ◽

Small Subunit ◽

Ribosomal Gene ◽

Moderately Thermophilic ◽

Novel Bacteria

ABSTRACT Recent molecular characterizations of microbial communities from deep-sea hydrothermal sites indicate the predominance of bacteria belonging to the epsilon subdivision of Proteobacteria(epsilon Proteobacteria). Here, we report the first enrichments and characterizations of four epsilonProteobacteria that are directly associated withAlvinella pompejana, a deep sea hydrothermal vent polychete, or with hydrothermal vent chimney samples. These novel bacteria were moderately thermophilic sulfur-reducing heterotrophs growing on formate as the energy and carbon source. In addition, two of them (Am-H and Ex-18.2) could grow on sulfur lithoautrotrophically using hydrogen as the electron donor. Optimal growth temperatures of the bacteria ranged from 41 to 45°C. Phylogenetic analysis of the small-subunit ribosomal gene of the two heterotrophic bacteria demonstrated 95% similarity to Sulfurospirillum arcachonense, an epsilon Proteobacteria isolated from an oxidized marine surface sediment. The autotrophic bacteria grouped within a deeply branching clade of the epsilonProteobacteria, to date composed only of uncultured bacteria detected in a sample from a hydrothermal vent along the mid-Atlantic ridge. A molecular survey of various hydrothermal vent environments demonstrated the presence of two of these bacteria (Am-N and Am-H) in more than one geographic location and habitat. These results suggest that certain epsilonProteobacteria likely fill important niches in the environmental habitats of deep-sea hydrothermal vents, where they contribute to overall carbon and sulfur cycling at moderate thermophilic temperatures.

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Denaturing gradient gel electrophoresis as a fingerprinting method for the analysis of soil microbial communities

Plant Soil and Environment ◽

10.17221/132/2009-pse ◽

2009 ◽

Vol 55 (No. 10) ◽

pp. 413-423 ◽

Cited By ~ 23

Author(s):

V. Valášková ◽

P. Baldrian

Keyword(s):

Microbial Communities ◽

Gel Electrophoresis ◽

Denaturing Gradient Gel Electrophoresis ◽

Soil Microbial Communities ◽

Soil Microbial ◽

Genes Encoding ◽

Gradient Gel Electrophoresis ◽

Temperature Gradient Gel Electrophoresis ◽

Experimental Treatments ◽

Multiple Samples

In soil microbial ecology, the effects of environmental factors and their gradients, temporal changes or the response to specific experimental treatments of microbial communities can only be effectively analyzed using methods that address the structural differences among whole communities. Fingerprinting methods are the most appropriate technique for this task when multiple samples must be analyzed. Among the methods currently used to compare microbial communities based on nucleic acid sequences, the techniques based on differences in the melting properties of double-stranded molecules, denaturing gradient gel electrophoresis (DGGE) or temperature gradient gel electrophoresis (TGGE), are the most widely used. Their main advantage is that they provide the possibility to further analyze whole sequences contained in fingerprints using molecular methods. In addition to the analysis of microbial communities based on DNA extracted from soils, DGGE/TGGE can also be used for the assessment of the active part of the community based on the analysis of RNA-derived sequences or for the analysis of sequences of functional genes encoding for proteins involved in important soil processes.

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Sediment community responses to marine vs. terrigenous organic matter in a submarine canyon

Biogeosciences ◽

10.5194/bg-10-67-2013 ◽

2013 ◽

Vol 10 (1) ◽

pp. 67-80 ◽

Cited By ~ 29

Author(s):

W. R. Hunter ◽

A. Jamieson ◽

V. A. I. Huvenne ◽

U. Witte

Keyword(s):

Organic Matter ◽

Feeding Activity ◽

N Uptake ◽

Bacterial Biomass ◽

Submarine Canyon ◽

Stable Isotope Labelling ◽

C And N ◽

13C Label ◽

Experimental Treatments

Abstract. The Whittard Canyon is a branching submarine canyon on the Celtic continental margin, which may act as a conduit for sediment and organic matter (OM) transport from the European continental slope to the abyssal sea floor. In situ stable-isotope labelling experiments were conducted in the eastern and western branches of the Whittard Canyon, testing short-term (3–7 days) responses of sediment communities to deposition of nitrogen-rich marine (Thalassiosira weissflogii) and nitrogen-poor terrigenous (Triticum aestivum) phytodetritus. 13C and 15N labels were traced into faunal biomass and bulk sediments, and the 13C label traced into bacterial polar lipid fatty acids (PLFAs). Isotopic labels penetrated to 5 cm sediment depth, with no differences between stations or experimental treatments (substrate or time). Macrofaunal assemblage structure differed between the eastern and western canyon branches. Following deposition of marine phytodetritus, no changes in macrofaunal feeding activity were observed between the eastern and western branches, with little change between 3 and 7 days. Macrofaunal C and N uptake was substantially lower following deposition of terrigenous phytodetritus with feeding activity governed by a strong N demand. Bacterial C uptake was greatest in the western branch of the Whittard Canyon, but feeding activity decreased between 3 and 7 days. Bacterial processing of marine and terrigenous OM were similar to the macrofauna in surficial (0–1 cm) sediments. However, in deeper sediments bacteria utilised greater proportions of terrigenous OM. Bacterial biomass decreased following phytodetritus deposition and was negatively correlated to macrofaunal feeding activity. Consequently, this study suggests that macrofaunal–bacterial interactions influence benthic C cycling in the Whittard Canyon, resulting in differential fates for marine and terrigenous OM.

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Coupling of Bacterial Endosymbiont and Host Mitochondrial Genomes in the Hydrothermal Vent Clam Calyptogena magnifica

Applied and Environmental Microbiology ◽

10.1128/aem.69.4.2058-2064.2003 ◽

2003 ◽

Vol 69 (4) ◽

pp. 2058-2064 ◽

Cited By ~ 48

Author(s):

Luis A. Hurtado ◽

Mariana Mateos ◽

Richard A. Lutz ◽

Robert C. Vrijenhoek

Keyword(s):

Dna Sequences ◽

Hydrothermal Vent ◽

Hydrothermal Vents ◽

Nuclear Gene ◽

Sexual Population ◽

Origin And Evolution ◽

Bacterial Endosymbionts ◽

Sulfur Oxidizing ◽

Tight Association ◽

Clam Population

ABSTRACT The hydrothermal vent clam Calyptogena magnifica (Bivalvia: Vesicomyidae) depends for its nutrition on sulfur-oxidizing symbiotic bacteria housed in its gill tissues. This symbiont is transmitted vertically between generations via the clam's eggs; however, it remains uncertain whether occasionally symbionts are horizontally transmitted or acquired from the environment. If symbionts are transmitted strictly vertically through the egg cytoplasm, inheritance of symbiont lineages should behave as if coupled to the host's maternally inherited mitochondrial DNA. This coupling would be obscured, however, with low rates of horizontal or environmental transfers, the equivalent of recombination between host lineages. Population genetic analyses of C. magnifica clams and associated symbionts from eastern Pacific hydrothermal vents clearly supported the hypothesis of strictly maternal cotransmission. Host mitochondrial and symbiont DNA sequences were coupled in a clam population that was polymorphic for both genetic markers. These markers were not similarly coupled with sequence variation at a nuclear gene locus, as expected for a randomly mating sexual population. Phylogenetic analysis of the two cytoplasmic genes also revealed no evidence for recombination. The tight association between vesicomyid clams and their vertically transmitted bacterial endosymbionts is phylogenetically very young (<50 million years) and may serve as a model for the origin and evolution of eukaryotic organelles.

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