Cutting through the smoke: the diversity of microorganisms in deep-sea hydrothermal plumes

There are still notable gaps regarding the detailed distribution of microorganisms between and within insular habitats such as deep-sea hydrothermal vents. This study investigates the community composition of black smoker vent microorganisms in the Southern Hemisphere, and changes thereof along a spatial and chemical gradient ranging from the vent plume to surrounding waters. We sampled two hydrothermal vent fields, one at the South West Indian Ridge (SWIR), the other at the East Scotia Ridge (ESR). Samples were collected across vent fields at varying vertical distances from the origin of the plumes. The microbial data were sequenced on an Illumina MiSeq platform for the 16SrRNA gene. A substantial amount of vent-specific putative chemosynthetic microorganisms were found, particularly in samples from focused hydrothermal venting. Common vent-specific organisms from both vent fields were the genera Arcobacter , Caminibacter and Sulfurimonas from the Epsilonproteobacteria and the SUP05 group from the Gammaproteobacteria. There were no major differences in microbial composition between SWIR and ESR for focused plume samples. However, within the ESR the diffuse flow and focused samples differed significantly in microbial community composition and relative abundance. For Epsilonproteobacteria, we found evidence of niche-specificity to hydrothermal vent environments. This taxon decreased in abundance by three orders of magnitude from the vent orifice to background water. Epsilonproteobacteria distribution followed a distance–decay relationship as vent-effluents mixed with the surrounding seawater. This study demonstrates strong habitat affinity of vent microorganisms on a metre scale with distinct environmental selection.

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Group-Specific Carbon Fixation Activity Measurements Reveal Distinct Responses to Oxygen Among Hydrothermal vent Campylobacteria

10.1101/2020.11.29.402834 ◽

2020 ◽

Author(s):

Jesse McNichol ◽

Stefan Dyksma ◽

Marc Mußmann ◽

Jeffrey S. Seewald ◽

Sean P. Sylva ◽

...

Keyword(s):

Community Composition ◽

Deep Sea ◽

Hydrothermal Vent ◽

Hydrothermal Vents ◽

Carbon Fixation ◽

Genomic Diversity ◽

Sequence Variant ◽

Activity Measurements ◽

Initial Starting

AbstractMolecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that Campylobacteria (prev. Epsilonproteobacteria) often dominate the microbial community and that three subgroups - Arcobacter, Sulfurimonas and Sulfurovum - frequently coexist. In this study, we used replicated radiocarbon incubations of deep-sea hydrothermal fluids to investigate the activities of each group under three distinct incubation conditions. In order to quantify group-specific radiocarbon incorporation, we used newly designed oligonucleotide probes for Arcobacter, Sulfurimonas, and Sulfurovum to quantify their activity using catalyzed-reporter deposition fluorescence in-situ hybridization (CARD-FISH) combined with fluorescence-activated cell sorting. All three groups actively fixed CO2 in short-term (~ 20 h) incubations with either nitrate, oxygen, or no additions (control) at similar per-cell carbon fixation rates. Oxygen additions had the largest effect on community composition and overall cell numbers, and caused a pronounced shift in community composition at the amplicon sequence variant (ASV) level after only 20 h of incubation for all three groups. Interestingly, the effect of oxygen on carbon fixation rates appeared to depend on the initial starting community. Higher carbon fixation rates in oxygen-amended treatments were noted for all three taxa after an unintended disturbance to the sample site that may have selected for more oxygen-tolerant phylotypes. When viewed from a coarse taxonomic level, our data support assertions that these chemoautotrophic groups are functionally redundant in terms of their core metabolic capabilities since they were simultaneously active under all incubation conditions. In contrast, the higher resolution of amplicon sequencing allowed us to reveal finer-scale differences in growth that likely reflect adaptation of physiologically-distinct subtypes to varying oxygen concentrations in situ. Despite this progress, we still know remarkably little about the factors that maintain genomic diversity and allow for stable co-existence among these three campylobacterial groups. Moving forward, we suggest that more subtle biological factors such as enzyme substrate specificity, motility, cell morphology, and tolerance to environmental stress should be more thoroughly investigated to better understand ecological niche differentiation at deep-sea hydrothermal vents.

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Genus-Specific Carbon Fixation Activity Measurements Reveal Distinct Responses to Oxygen Among Hydrothermal Vent Campylobacteria

Applied and Environmental Microbiology ◽

10.1128/aem.02083-21 ◽

2021 ◽

Author(s):

Jesse McNichol ◽

Stefan Dyksma ◽

Marc Mußmann ◽

Jeffrey S. Seewald ◽

Sean P. Sylva ◽

...

Keyword(s):

Community Composition ◽

Deep Sea ◽

Hydrothermal Vent ◽

Hydrothermal Vents ◽

Carbon Fixation ◽

Sequence Variant ◽

Experimental Conditions ◽

Activity Measurements ◽

Initial Starting

Molecular surveys of low temperature deep-sea hydrothermal vent fluids have shown that Campylobacteria (prev. Epsilonproteobacteria ) often dominate the microbial community and that three genera - Arcobacter , Sulfurimonas and Sulfurovum - frequently coexist. In this study, we used replicated radiocarbon incubations of deep-sea hydrothermal fluids to investigate activity of each genus under three experimental conditions. To quantify genus-specific radiocarbon incorporation, we used newly designed oligonucleotide probes for Arcobacter , Sulfurimonas , and Sulfurovum to quantify their activity using catalyzed-reporter deposition fluorescence in-situ hybridization (CARD-FISH) combined with fluorescence-activated cell sorting. All three genera actively fixed CO 2 in short-term (∼ 20 h) incubations, but responded differently to the additions of nitrate and oxygen. Oxygen additions had the largest effect on community composition, and caused a pronounced shift in community composition at the amplicon sequence variant (ASV) level after only 20 h of incubation. The effect of oxygen on carbon fixation rates appeared to depend on the initial starting community. The presented results support the hypothesis that these chemoautotrophic genera possess functionally redundant core metabolic capabilities, but also reveal finer-scale differences in growth likely reflecting adaptation of physiologically-distinct phylotypes to varying oxygen concentrations in situ . Overall, our study provides new insights into how oxygen controls community composition and total chemoautotrophic activity, and underscores how quickly deep-sea vent microbial communities respond to disturbances. Importance: Sulfidic environments worldwide are often dominated by sulfur-oxidizing, carbon-fixing Campylobacteria . Environmental factors associated with this group's dominance are now understood, but far less is known about the ecology and physiology of members of subgroups of chemoautotrophic Campylobacteria . In this study, we used a novel method to differentiate the genus-specific chemoautotrophic activity of three subtypes of Campylobacteria. In combination with evidence from microscopic counts, chemical consumption/production during incubations, and DNA-based measurements, our data show that oxygen concentration affects both community composition and chemoautotrophic function in situ . These results help us better understand factors controlling microbial diversity at deep-sea hydrothermal vents, and provide first-order insights into the ecophysiological differences between these distinct microbial taxa.

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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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Dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis revealed by its hologenome

10.1101/2020.09.23.308304 ◽

2020 ◽

Author(s):

Yi Lan ◽

Jin Sun ◽

Chong Chen ◽

Yanan Sun ◽

Yadong Zhou ◽

...

Keyword(s):

Deep Sea ◽

Hydrothermal Vent ◽

Hydrothermal Vents ◽

Snail Host ◽

Bacterial Symbionts ◽

Mutualistic Relationship ◽

Genomic Studies ◽

Similar Depth ◽

Selection Of ◽

Chromosome Level

AbstractAnimals endemic to deep-sea hydrothermal vents often form obligatory relationships with bacterial symbionts, maintained by intricate host-symbiont interactions. Endosymbiosis with more than one symbiont is uncommon, and most genomic studies focusing on such ‘dual symbiosis’ systems have not investigated the host and the symbionts to a similar depth simultaneously. Here, we report a novel dual symbiosis among the peltospirid snail Gigantopelta aegis and its two Gammaproteobacteria endosymbionts – one being a sulphur oxidiser and the other a methane oxidiser. We assembled high-quality genomes for all three parties of this holobiont, with a chromosome-level assembly for the snail host (1.15 Gb, N50 = 82 Mb, 15 pseudo-chromosomes). In-depth analyses of these genomes reveal an intimate mutualistic relationship with complementarity in nutrition and metabolic codependency, resulting in a system highly versatile in transportation and utilisation of chemical energy. Moreover, G. aegis has an enhanced immune capability that likely facilitates the possession of more than one type of symbiont. Comparisons with Chrysomallon squamiferum, another chemosymbiotic snail in the same family but only with one sulphur-oxidising endosymbiont, show that the two snails’ sulphur-oxidising endosymbionts are phylogenetically distant, agreeing with previous results that the two snails have evolved endosymbiosis independently and convergently. Notably, the same capabilities of biosynthesis of specific nutrition lacking in the host genome are shared by the two sulphur-oxidising endosymbionts of the two snail genera, which may be a key criterion in the selection of symbionts by the hosts.

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Hydrothermal activity lowers trophic diversity in Antarctic sedimented hydrothermal vents

10.5194/bg-2017-288 ◽

2017 ◽

Author(s):

James B. Bell ◽

William D. K. Reid ◽

David A. Pearce ◽

Adrian G. Glover ◽

Christopher J. Sweeting ◽

...

Keyword(s):

Active Site ◽

Deep Sea ◽

Hydrothermal Vents ◽

Hydrothermal Activity ◽

Feeding Strategies ◽

Microbial Composition ◽

Isotopic Signatures ◽

Structure Morphology ◽

Feeding Structure ◽

Niche Area

Abstract. Sedimented hydrothermal vents are those in which hydrothermal fluid is discharged through sediments and are among the least studied deep-sea ecosystems. We present a combination of microbial and biochemical data to assess trophodynamics between and within hydrothermally active and off-vent areas of the Bransfield Strait (1050–1647 m depth). Microbial composition, biomass and fatty acid signatures varied widely between and within vent and non-vent sites and provided evidence of diverse metabolic activity. Several species showed diverse feeding strategies and occupied different trophic positions in vent and nonvent areas. Stable isotope values of consumers were generally not consistent with feeding structure morphology. Niche area and the diversity of microbial fatty acids reflected trends in species diversity and was lowest at the most hydrothermally active site. Faunal utilisation of chemosynthetic activity was relatively limited but was detected at both vent and non-vent sites as evidenced by carbon and sulphur isotopic signatures, suggesting that hydrothermal activity can affect trophodynamics over a much wider area than previously thought.

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262 Voyages Beneath the Sea: a global assessment of macro- and megafaunal biodiversity and research effort at deep-sea hydrothermal vents

PeerJ ◽

10.7717/peerj.7397 ◽

2019 ◽

Vol 7 ◽

pp. e7397 ◽

Cited By ~ 4

Author(s):

Andrew D. Thaler ◽

Diva Amon

Keyword(s):

Deep Sea ◽

Hydrothermal Vent ◽

Hydrothermal Vents ◽

Research Effort ◽

Spreading Center ◽

Biological Research ◽

Northwest Pacific ◽

North East ◽

East Pacific ◽

Biogeographic Provinces

For over 40 years, hydrothermal vents and the communities that thrive on them have been a source of profound discovery for deep-sea ecologists. These ecosystems are found throughout the world on active plate margins as well as other geologically active features. In addition to their ecologic interest, hydrothermal vent fields are comprised of metallic ores, sparking a nascent industry that aims to mine these metal-rich deposits for their mineral wealth. Here, we provide the first systematic assessment of macrofaunal and megafaunal biodiversity at hydrothermal vents normalized against research effort. Cruise reports from scientific expeditions as well as other literature were used to characterize the extent of exploration, determine the relative biodiversity of different biogeographic provinces, identify knowledge gaps related to the distribution of research effort, and prioritize targets for additional sampling to establish biodiversity baselines ahead of potential commercial exploitation. The Northwest Pacific, Southwest Pacific, and Southern Ocean biogeographic provinces were identified as high biodiversity using rarefaction of family-level incidence data, whereas the North East Pacific Rise, Northern East Pacific, Mid-Atlantic Ridge, and Indian Ocean provinces had medium biodiversity, and the Mid-Cayman Spreading Center was identified as a province of relatively low biodiversity. A North/South divide in the extent of biological research and the targets of hydrothermal vent mining prospects was also identified. Finally, we provide an estimate of sampling completeness for each province to inform scientific and stewardship priorities.

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Simple harpacticoid composition observed at deep hydrothermal vent sites on sea knoll calderas in the North-west Pacific

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315421000874 ◽

2022 ◽

pp. 1-10

Author(s):

Futa Nakasugi ◽

Motohiro Shimanaga ◽

Hidetaka Nomaki ◽

Hiromi Kayama Watanabe ◽

Tomo Kitahashi ◽

...

Keyword(s):

Deep Sea ◽

Hydrothermal Vent ◽

Hydrothermal Vents ◽

Environmental Parameters ◽

Sea Floor ◽

North West ◽

Isotopic Signatures ◽

Carbon Isotopic ◽

The North ◽

Spatial Differences

Abstract Dirivultid copepods (Siphonostomatoida), one of the most successful meiobenthic organisms found at deep-sea hydrothermal vents, have been the focus of most previous ecological studies among meiofauna in these habitats. The ecology of Harpacticoida, a major benthic copepod group in typical deep-sea floor, however, is not well understood in terms of variations in community structure and controlling factors at venting sites. The spatial heterogeneities in benthic harpacticoid composition and their association with environmental parameters were investigated at hydrothermal vent chimney structures in the calderas of three neighbouring sea knolls (Bayonnaise Knoll, Myojin Knoll and Myojin-sho Caldera) in the western North Pacific. While a previous study had reported the distribution of dirivultids was strongly associated with spatial differences in stable carbon isotopic signatures (δ13C) of organic matter in the detritus on active chimneys in the field, multivariate analyses detected no significant corelation between the parameter and harpacticoid composition in this study. Instead, high associations of the harpacticoid composition with differences in water depth and total organic carbon (TOC) concentration were detected. Ectinosomatidae dominated at vent sites with lower TOC values in the shallowest Bayonnaise Knoll, while they were less prevalent at deeper vent fields in the other knolls, where Miraciidae was the most abundant family. This study indicated the availability of vent chemoautotrophic carbon is not a primary factor controlling the composition of harpacticoids even in the habitats on the hydrothermal vents, but instead by the food amount, regardless of its resources (including marine snow from the sea surface), in the study area.

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A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota

Briefings in Bioinformatics ◽

10.1093/bib/bbab052 ◽

2021 ◽

Author(s):

Yafei Chang ◽

Qilian Fan ◽

Jialin Hou ◽

Yu Zhang ◽

Jing Li

Keyword(s):

Deep Sea ◽

Hydrothermal Vent ◽

Hydrothermal Vents ◽

Extreme Environments ◽

Reference Database ◽

False Discovery Rate Method ◽

Analysis Strategy ◽

Gene Database ◽

And Function ◽

Functional Profiles

Abstract Microorganisms in deep-sea hydrothermal vents provide valuable insights into life under extreme conditions. Mass spectrometry-based proteomics has been widely used to identify protein expression and function. However, the metaproteomic studies in deep-sea microbiota have been constrained largely by the low identification rates of protein or peptide. To improve the efficiency of metaproteomics for hydrothermal vent microbiota, we firstly constructed a microbial gene database (HVentDB) based on 117 public metagenomic samples from hydrothermal vents and proposed a metaproteomic analysis strategy, which takes the advantages of not only the sample-matched metagenome, but also the metagenomic information released publicly in the community of hydrothermal vents. A two-stage false discovery rate method was followed up to control the risk of false positive. By applying our community-supported strategy to a hydrothermal vent sediment sample, about twice as many peptides were identified when compared with the ways against the sample-matched metagenome or the public reference database. In addition, more enriched and explainable taxonomic and functional profiles were detected by the HVentDB-based approach exclusively, as well as many important proteins involved in methane, amino acid, sugar, glycan metabolism and DNA repair, etc. The new metaproteomic analysis strategy will enhance our understanding of microbiota, including their lifestyles and metabolic capabilities in extreme environments. The database HVentDB is freely accessible from http://lilab.life.sjtu.edu.cn:8080/HventDB/main.html.

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A new squat lobster species of the genus Munida Leach, 1820 (Crustacea: Anomura: Galatheoidea: Munididae) from hydrothermal vents on the Eastern Pacific Rise

Zootaxa ◽

10.11646/zootaxa.4743.1.12 ◽

2020 ◽

Vol 4743 (1) ◽

pp. 131-136 ◽

Cited By ~ 1

Author(s):

XINMING LIU ◽

XINZHENG LI ◽

RONGCHENG LIN

Keyword(s):

New Species ◽

Deep Sea ◽

Hydrothermal Vent ◽

Hydrothermal Vents ◽

Eastern Pacific ◽

Single Specimen ◽

Squat Lobster ◽

The Third ◽

A New Species

A new species of the genus Munida Leach, 1820, is described and illustrated based on a single specimen from the deep-sea hydrothermal vent on the Eastern Pacific Rise. Munida alba sp. nov. closely resembles M. ampliantennulata Komai, 2011, M. watatsumin Komai, 2014. and M. magniantennulata, but differences in the morphologies of the third maxilliped, pollex of the cheliped and the third segment of the antennal peduncle readily distinguish the new species from the three relatives. The new species is the fourth of the genus occurring at the hydrothermal vent areas.

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PSI-10 Establishing a foundation to harvest the potential of the microbiome in poultry production

Journal of Animal Science ◽

10.1093/jas/skz258.594 ◽

2019 ◽

Vol 97 (Supplement_3) ◽

pp. 293-294

Author(s):

Camila S Marcolla ◽

Benjamin Willing

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Community Composition ◽

Relative Abundance ◽

Microbial Community Composition ◽

Alpha Diversity ◽

Poultry Production ◽

Microbiota Composition ◽

Microbial Composition ◽

The Impact

Abstract This study aimed to characterize poultry microbiota composition in commercial farms using 16S rRNA sequencing. Animals raised in sanitized environments have lower survival rates when facing pathogenic challenges compared to animals naturally exposed to commensal organisms. We hypothesized that intensive rearing practices inadvertently impair chicken exposure to microbes and the establishment of a balanced gut microbiota. We compared gut microbiota composition of broilers (n = 78) and layers (n = 20) from different systems, including commercial intensive farms with and without in-feed antibiotics, organic free-range farms, backyard-raised chickens and chickens in an experimental farm. Microbial community composition of conventionally raised broilers was significantly different from antibiotic-free broilers (P = 0.012), from broilers raised outdoors (P = 0.048) and in an experimental farm (P = 0.006) (Fig1). Significant community composition differences were observed between antibiotic-fed and antibiotic-free chickens (Fig2). Antibiotic-free chickens presented higher alpha-diversity, higher relative abundance of Deferribacteres, Fusobacteria, Bacteroidetes and Actinobacteria, and lower relative abundance of Firmicutes, Clostridiales and Enterobacteriales than antibiotic-fed chickens (P < 0.001) (Fig3). Microbial community composition significantly changed as birds aged. In experimental farm, microbial community composition was significant different for 7, 21 and 35 day old broilers (P < 0.001), and alpha diversity increased from 7 to 21d (P < 0.024), but not from 21 to 35d; whereas, in organic systems, increases in alpha-diversity were observed from 7d to 21d, and from 21d to 35d (P < 0.05). Broilers and layers raised together showed no differences in microbiota composition and alpha diversity (P > 0.8). It is concluded that production practices consistently impact microbial composition, and that antibiotics significantly reduces microbial diversity. We are now exploring the impact of differential colonization in a controlled setting, to determine the impact of the microbes associated with extensively raised chickens. This study will support future research and the development of methods to isolate and introduce beneficial microbes to commercial systems.

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