scholarly journals Interaction between Microbes, Minerals, and Fluids in Deep-Sea Hydrothermal Systems

Minerals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1324
Author(s):  
Shamik Dasgupta ◽  
Xiaotong Peng ◽  
Kaiwen Ta
Keyword(s):  
Microbial Communities ◽  
Deep Sea ◽  
Hydrothermal Vents ◽  
Extreme Environments ◽  
Past Research ◽  
Hydrothermal Systems ◽  
Chemical Gradients ◽  
Basement Rocks ◽  
The Rich ◽  
Metabolic Activities

The discovery of deep-sea hydrothermal vents in the late 1970s widened the limits of life and habitability. The mixing of oxidizing seawater and reduction of hydrothermal fluids create a chemical disequilibrium that is exploited by chemosynthetic bacteria and archaea to harness energy by converting inorganic carbon into organic biomass. Due to the rich variety of chemical sources and steep physico-chemical gradients, a large array of microorganisms thrive in these extreme environments, which includes but are not restricted to chemolithoautotrophs, heterotrophs, and mixotrophs. Past research has revealed the underlying relationship of these microbial communities with the subsurface geology and hydrothermal geochemistry. Endolithic microbial communities at the ocean floor catalyze a number of redox reactions through various metabolic activities. Hydrothermal chimneys harbor Fe-reducers, sulfur-reducers, sulfide and H2-oxidizers, methanogens, and heterotrophs that continuously interact with the basaltic, carbonate, or ultramafic basement rocks for energy-yielding reactions. Here, we briefly review the global deep-sea hydrothermal systems, microbial diversity, and microbe–mineral interactions therein to obtain in-depth knowledge of the biogeochemistry in such a unique and geologically critical subseafloor environment.

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.

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.

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

mSystems ◽  
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.

scholarly journals Microbial Eukaryotes Associated With Sediments in Deep-Sea Cold Seeps

2021 ◽  
Vol 12 ◽  
Author(s):  
Yue Zhang ◽  
Ning Huang ◽  
Minxiao Wang ◽  
Hongbin Liu ◽  
Hongmei Jing
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vents ◽  
High Throughput Sequencing ◽  
Northern South China Sea ◽  
Extreme Environments ◽  
Operational Taxonomic Unit ◽  
Trophic Relationships ◽  
Rrna Gene ◽  
Cold Seeps ◽  
Microbial Eukaryotes

Microbial eukaryotes are key components of the marine food web, but their distribution in deep-sea chemosynthetic ecosystems has not been well studied. Here, high-throughput sequencing of the 18S rRNA gene and network analysis were applied to investigate the diversity, distribution and potential relationships between microbial eukaryotes in samples collected from two cold seeps and one trough in the northern South China Sea. SAR (i.e., Stramenopiles, Alveolata, and Rhizaria) was the predominant group in all the samples, and it was highly affiliated to genotypes with potential symbiotic and parasitic strategies identified from other deep-sea extreme environments (e.g., oxygen deficient zones, bathypelagic waters, and hydrothermal vents). Our findings indicated that specialized lineages of deep-sea microbial eukaryotes exist in chemosynthetic cold seeps, where microbial eukaryotes affiliated with parasitic/symbiotic taxa were prevalent in the community. The biogeographic pattern of the total community was best represented by the intermediate operational taxonomic unit (OTU) category, whose relative abundance ranged 0.01–1% within a sample, and the communities of the two cold seeps were distinct from the trough, which suggests that geographical proximity has no critical impact on the distribution of deep-sea microbial eukaryotes. Overall, this study has laid the foundations for future investigations regarding the ecological function and in situ trophic relationships of microbial eukaryotes in deep-sea ecosystems.

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.

Review Lecture - The chemosynthetic support of life and the microbial diversity at deep-sea hydrothermal vents

1985 ◽  
Vol 225 (1240) ◽  
pp. 277-297 ◽  
Keyword(s):  
Primary Production ◽  
Deep Sea ◽  
Hydrothermal Vents ◽  
Sea Floor ◽  
Animal Populations ◽  
Inorganic Species ◽  
Chemolithotrophic Bacteria ◽  
New Type ◽  
The Rich ◽  
Aerobic And Anaerobic

Circulation of seawater through the upper few kilometres of oceanic crust at tectonic spreading zones results in a transformation of geothermal into chemical energy. Reduced inorganic species are emitted from warm (under 25 °C) and hot (under 400 °C) vents on the sea floor at depths of 1600 and 3000 m and are used by chemolithotrophic bacteria as terrestrial sources of energy for the primary production of organic carbon from carbon dioxide. Thus, the rich and unique animal populations found in the immediate vicinity of the vents represent ecosystems that are largely or totally independent of solar energy. They subsist by means of a food chain that is based on various microbial processes. In addition to aerobic and anaerobic bacterial chemosynthesis, a new type of symbiosis between yet undescribed chemolithotrophic prokaryotes and certain invertebrates appears to account for the major part of the total primary production at the deep-sea vent sites.

Distribution and behaviour of the spider crab Macroregonia macrochira Sakai (Brachyura) around the hydrothermal vents of the northeast Pacific

1987 ◽  
Vol 65 (10) ◽  
pp. 2443-2449 ◽  
Author(s):  
Verena Tunnicliffe ◽  
R. Gordon Jensen
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vents ◽  
Food Source ◽  
Hydrothermal Activity ◽  
Spider Crab ◽  
Northeast Pacific ◽  
Juan De Fuca ◽  
The Rich ◽  
Planktotrophic Larvae ◽  
Hard Substrata

Over 200 individuals of the majid crab Macroregonia macrochira Sakai, 1978 were examined on submersible and towed camera photographs from the Juan de Fuca and Explorer ridges. The crab is found at bathyal depths and shows a preference for hard substrata. Its attraction to the food source at hydrothermal vents is reflected in the high population concentrations around vent sites of the northeast Pacific. Mature males, distinguished by their large chelipeds, tend to be widely dispersed while the female–juvenile group clusters in and around vents. Stomachs of captured specimens contain remains of vent animals, confirming, along with submersible observations, that this crab is a major predator of animals at these vents. Other aspects of M. macrochira biology suggest that the sexes are separable on the basis of carapace aspect ratio, that polygamy is not apparent, and that planktotrophic larvae are released. The crab's ability to range both in and away from vents makes it an excellent indicator of the proximity of hydrothermal activity. In addition, it represents a mechanism for transferring the rich production of chemosynthetic activity to the oligotrophic deep-sea environment.

scholarly journals Diverse viruses have restricted biogeography in deep-sea hydrothermal vent fluids

2020 ◽  
Author(s):  
Elaina Thomas ◽  
Rika Anderson ◽  
Viola Li ◽  
Jenni Rogan ◽  
Julie A. Huber
Keyword(s):  
Host Range ◽  
Deep Sea ◽  
Hydrothermal Vents ◽  
Hydrothermal Systems ◽  
Viral Diversity ◽  
Metabolic Potential ◽  
Host Interactions ◽  
The Pacific ◽  
Wide Range ◽  
Axial Seamount

AbstractIn the ocean, viruses impact microbial mortality, regulate biogeochemical cycling, and alter the metabolic potential of microbial lineages. At deep-sea hydrothermal vents, abundant viruses infect a wide range of hosts among the archaea and bacteria that inhabit these dynamic habitats. However, little is known about viral diversity, host range, and biogeography across different vent ecosystems, which has important implications for how viruses manipulate microbial function and evolution. Here, we examined viral diversity, viral and host distribution, and viral-host interactions in venting fluids from two geographically distant hydrothermal systems, the Mid-Cayman Rise in the Caribbean Sea and Axial Seamount in the Pacific Ocean. Analysis of viral sequences and CRISPR spacers revealed highly diverse viral assemblages and abundant lysogenic viruses, with 40% of metagenome-assembled genomes encoding a putative prophage. Network analysis revealed that viral host range was relatively narrow, with very few viruses infecting multiple microbial lineages. Viruses were largely endemic to individual vent sites, indicating restricted dispersal, and in some cases viral assemblages persisted over time. Thus, while the viruses at deep-sea hydrothermal systems play an important role in driving the evolution and ecology of resident vent microbial communities, their influence is highly localized to specific regions and taxa.

scholarly journals The Geoglobus acetivorans Genome: Fe(III) Reduction, Acetate Utilization, Autotrophic Growth, and Degradation of Aromatic Compounds in a Hyperthermophilic Archaeon

2014 ◽  
Vol 81 (3) ◽  
pp. 1003-1012 ◽  
Author(s):  
Andrey V. Mardanov ◽  
Galina B. Slododkina ◽  
Alexander I. Slobodkin ◽  
Alexey V. Beletsky ◽  
Sergey N. Gavrilov ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Aromatic Compounds ◽  
Deep Sea ◽  
Hydrothermal Vents ◽  
Anaerobic Respiration ◽  
Hydrothermal Systems ◽  
Content Type ◽  
Acetate Utilization ◽  
Oxide Particles ◽  
Modified Embden Meyerhof Pathway

ABSTRACTGeoglobus acetivoransis a hyperthermophilic anaerobic euryarchaeon of the orderArchaeoglobalesisolated from deep-sea hydrothermal vents. A unique physiological feature of the members of the genusGeoglobusis their obligate dependence on Fe(III) reduction, which plays an important role in the geochemistry of hydrothermal systems. The features of this organism and its complete 1,860,815-bp genome sequence are described in this report. Genome analysis revealed pathways enabling oxidation of molecular hydrogen, proteinaceous substrates, fatty acids, aromatic compounds,n-alkanes, and organic acids, including acetate, through anaerobic respiration linked to Fe(III) reduction. Consistent with the inability ofG. acetivoransto grow on carbohydrates, the modified Embden-Meyerhof pathway encoded by the genome is incomplete. Autotrophic CO2fixation is enabled by the Wood-Ljungdahl pathway. Reduction of insoluble poorly crystalline Fe(III) oxide depends on the transfer of electrons from the quinone pool to multihemec-type cytochromes exposed on the cell surface. Direct contact of the cells and Fe(III) oxide particles could be facilitated by pilus-like appendages. Genome analysis indicated the presence of metabolic pathways for anaerobic degradation of aromatic compounds andn-alkanes, although an ability ofG. acetivoransto grow on these substrates was not observed in laboratory experiments. Overall, our results suggest thatGeoglobusspecies could play an important role in microbial communities of deep-sea hydrothermal vents as lithoautotrophic producers. An additional role as decomposers would close the biogeochemical cycle of carbon through complete mineralization of various organic compounds via Fe(III) respiration.

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