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

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.

scholarly journals Potential Interactions between Clade SUP05 Sulfur-Oxidizing Bacteria and Phages in Hydrothermal Vent Sponges

2019 ◽  
Vol 85 (22) ◽  
Author(s):  
Kun Zhou ◽  
Rui Zhang ◽  
Jin Sun ◽  
Weipeng Zhang ◽  
Ren-Mao Tian ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Okinawa Trough ◽  
Sulfur Metabolism ◽  
Extreme Environments ◽  
Metagenomic Sequence ◽  
Sulfur Oxidizing ◽  
Biological Entities ◽  
Sulfur Oxidizing Bacteria

ABSTRACT In deep-sea hydrothermal vent environments, sulfur-oxidizing bacteria belonging to the clade SUP05 are crucial symbionts of invertebrate animals. Marine viruses, as the most abundant biological entities in the ocean, play essential roles in regulating the sulfur metabolism of the SUP05 bacteria. To date, vent sponge-associated SUP05 and their phages have not been well documented. The current study analyzed microbiomes of Haplosclerida sponges from hydrothermal vents in the Okinawa Trough and recovered the dominant SUP05 genome, designated VS-SUP05. Phylogenetic analysis showed that VS-SUP05 was closely related to endosymbiotic SUP05 strains from mussels living in deep-sea hydrothermal vent fields. Homology and metabolic pathway comparisons against free-living and symbiotic SUP05 strains revealed that the VS-SUP05 genome shared many features with the deep-sea mussel symbionts. Supporting a potentially symbiotic lifestyle, the VS-SUP05 genome contained genes involved in the synthesis of essential amino acids and cofactors that are desired by the host. Analysis of sponge-associated viral sequences revealed putative VS-SUP05 phages, all of which were double-stranded viruses belonging to the families Myoviridae, Siphoviridae, Podoviridae, and Microviridae. Among the phage sequences, one contig contained metabolic genes (iscR, iscS, and iscU) involved in iron-sulfur cluster formation. Interestingly, genome sequence comparison revealed horizontal transfer of the iscS gene among phages, VS-SUP05, and other symbiotic SUP05 strains, indicating an interaction between marine phages and SUP05 symbionts. Overall, our findings confirm the presence of SUP05 bacteria and their phages in sponges from deep-sea vents and imply a beneficial interaction that allows adaptation of the host sponge to the hydrothermal vent environment. IMPORTANCE Chemosynthetic SUP05 bacteria dominate the microbial communities of deep-sea hydrothermal vents around the world, SUP05 bacteria utilize reduced chemical compounds in vent fluids and commonly form symbioses with invertebrate organisms. This symbiotic relationship could be key to adapting to such unique and extreme environments. Viruses are the most abundant biological entities on the planet and have been identified in hydrothermal vent environments. However, their interactions with the symbiotic microbes of the SUP05 clade, along with their role in the symbiotic system, remain unclear. Here, using metagenomic sequence-based analyses, we determined that bacteriophages may support metabolism in SUP05 bacteria and play a role in the sponge-associated symbiosis system in hydrothermal vent environments.

scholarly journals Microbiome of a Reef-Building Coral Displays Signs of Acclimation to a Stressful Shallow Hydrothermal Vent Habitat

2021 ◽  
Vol 8 ◽  
Author(s):  
Alicia M. Reigel ◽  
David A. Paz-García ◽  
Michael E. Hellberg
Keyword(s):  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Pathogenic Bacteria ◽  
Management Strategies ◽  
Extreme Environments ◽  
Extreme Environment ◽  
Rrna Gene ◽  
Ph Values ◽  
Extreme Habitats ◽  
Functional Profiles

Most tropical reef corals live at temperatures near 27°C and pH values near 8. Conditions outside of these can stress corals and lead to bleaching, disease, and death. However, some corals can survive in marginal or extreme habitats outside of these ranges. To date there is a paucity of knowledge about the role that associated microbes may play in the acclimation of corals to such extreme habitats. Here, we explore differences in the compositional and functional profile of the microbiomes of the scleractinian coral Porites panamensis living both on and off potentially stressful shallow-water hydrothermal vents. The environment near the vents is extreme, with temperatures exceeding 80°C and pH values below 6. Coral microbiomes under stress often exhibit increased diversity, increased abundance of pathogenic bacteria, and functional profiles that shift toward pathways associated with pathogenic taxa. Samples from along a transect that crossed an arc of hydrothermal vents were sequenced for the 16S rRNA gene (V4 region). On-vent coral microbiomes were distinct from those of off-vent corals, but did not have increased alpha or beta diversity. On-vent samples had a higher relative abundance of the beneficial endosymbiont, Endozoicomonas. On- and off-vent microbiomes did not differ in overall abundance of the endolithic green alga Ostreobium, however, a single ASV, close to O. quekettii was more abundant in on-vent corals. Ostreobium can provide many of the same benefits to corals as zooxanthellae and their symbiosis is better maintained under thermal stress. Surprisingly, on-vent coral microbiomes had fewer microbial taxa that are known to be pathogenic or associated with stress than did off-vent corals. The predicted functional profiles of on-vent microbiomes revealed enrichment of pathways related to aerobic respiration, fermentation and amino acid biosynthesis, but not of virulence-related pathways. Our results suggest that P. panamensis microbiomes have acclimated to the extreme environment of the hydrothermal vent habitat rather than showing signs of stress. These results exemplify the need to focus efforts on examining the mechanisms of resilience, including symbioses with microbiota, in corals living in extreme environments in an effort to design better management strategies for reef-building corals under thermal and pH stress.

scholarly journals Primary Production in the Water Column as Major Structuring Element of the Biogeographical Distribution and Function of Archaea in Deep-Sea Sediments of the Central Pacific Ocean

Archaea ◽  
2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Franziska Wemheuer ◽  
Avril Jean Elisabeth von Hoyningen-Huene ◽  
Marion Pohlner ◽  
Julius Degenhardt ◽  
Bert Engelen ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
Primary Production ◽  
Deep Sea ◽  
Archaeal Community ◽  
Central Pacific ◽  
Central Pacific Ocean ◽  
Deep Sea Sediments ◽  
And Function ◽  
Functional Profiles ◽  
Archaeal Communities

Information on environmental conditions shaping archaeal communities thriving at the seafloor of the central Pacific Ocean is limited. The present study was conducted to investigate the diversity, composition, and function of both entire and potentially active archaeal communities within Pacific deep-sea sediments. For this purpose, sediment samples were taken along the 180° meridian of the central Pacific Ocean. Community composition and diversity were assessed by Illumina tag sequencing targeting archaeal 16S rRNA genes and transcripts. Archaeal communities were dominated by CandidatusNitrosopumilus(Thaumarchaeota) and other members of theNitrosopumilaceae(Thaumarchaeota), but higher relative abundances of the Marine Group II (Euryarchaeota) were observed in the active compared to the entire archaeal community. The composition of the entire and the active archaeal communities was strongly linked to primary production (chlorophyll content), explaining more than 40% of the variance. Furthermore, we found a strong correlation of the entire archaeal community composition to latitude and silicic acid content, while the active community was significantly correlated with primary production and ferric oxide content. We predicted functional profiles from 16S rRNA data to assess archaeal community functions. Latitude was significantly correlated with functional profiles of the entire community, whereas those of the active community were significantly correlated with nitrate and chlorophyll content. The results of the present study provide first insights into benthic archaeal communities in the Pacific Ocean and environmental conditions shaping their diversity, distribution, and function. Additionally, they might serve as a template for further studies investigating archaea colonizing deep-sea sediments.

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

2001 ◽  
Vol 67 (10) ◽  
pp. 4566-4572 ◽  
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.

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

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.

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

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7397 ◽  
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.

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

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.

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

Zootaxa ◽  
2020 ◽  
Vol 4743 (1) ◽  
pp. 131-136 ◽  
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. 

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

2017 ◽  
Vol 4 (4) ◽  
pp. 160829 ◽  
Author(s):  
Anni Djurhuus ◽  
Svein-Ole Mikalsen ◽  
Helge-Ansgar Giebel ◽  
Alex D. Rogers
Keyword(s):  
Community Composition ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Microbial Community Composition ◽  
Illumina Miseq ◽  
Black Smoker ◽  
Microbial Composition ◽  
Diffuse Flow ◽  
Environmental Selection

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.

Organic complexation of copper in deep-sea hydrothermal vent systems

2007 ◽  
Vol 4 (2) ◽  
pp. 81 ◽  
Author(s):  
Sylvia G. Sander ◽  
Andrea Koschinsky ◽  
Gary Massoth ◽  
Matthew Stott ◽  
Keith A. Hunter
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Natural Habitat ◽  
Hydrothermal Systems ◽  
Conditional Stability ◽  
Copper Binding ◽  
Medium Temperature ◽  
Ambient Seawater ◽  
Organic Complexation

Environmental context. Deep-sea hydrothermal vents represent a natural habitat for many extremophile organisms able to cope with extreme physical and chemical conditions, including high loads of heavy metals and reduced gases. To date, no information is available on the level and role of organic complexation of metals in these systems, which will have consequences on the bioavailability and precipitation or mineralisation of metals. In this work, we give evidence for the presence of organic molecules, including thiols, capable of forming complexes with copper strong enough to compete against sulfide present at high levels in hydrothermal systems. Abstract. Here we report, for the first time, that strong organic complexation plays an important role in the chemical speciation of copper in hydrothermal vent systems including medium temperature outlets, diffuse vents with an adjacent hydrothermal biocommunity, and local mixing zone with seawater. Samples from three deep-sea hydrothermal vent areas show a wide concentration range of organic copper-binding ligands, up to 4000 nM, with very high conditional stability constants (log K′Cu′L = 12.48 to 13.46). Measurements were usually made using voltammetric methods after removal of sulfide species under ambient seawater conditions (pH 7.8), but binding still occurs at pH 4.5 and 2.1. The voltammetric behaviour of our hydrothermal samples is compared with that of glutathione (GSH) a known strong Cu-binding ligand, as a representative of an organic thiol. Our results provide compelling evidence for the presence of organic ligands, including thiols, which form complexes strong enough to play an important role in controlling the bioavailability and geochemical behaviour of metal ions around hydrothermal vents.

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