Novel Barite Chimneys at the Loki's Castle Vent Field Shed Light on Key Factors Shaping Microbial Communities and Functions in Hydrothermal Systems

Microbes as marine habitat formers and ecosystem engineers

Despite their small individual size, marine prokaryotic and eukaryotic microbes can form large 3D structures and complex habitats. These habitats contribute to seafloor heterogeneity, facilitating colonization by animals and protists. They also provide food and refuge for a variety of species and promote novel ecological interactions. Here we illustrate the role of microbes as ecosystem engineers and propose a classification based on five types of habitat: microbial mats, microbial forests, microbial-mineralized habitats, microbial outcrops and microbial nodules. We also describe the metabolic processes of microbial habitat formers and their ecological roles, highlighting current gaps in knowledge. Their biogeography indicates that these habitats are widespread in all oceans and are continuously being discovered across latitudes and depths. These habitats are also expected to expand under future global change owing to their ability to exploit extreme environmental conditions. Given their high ecological relevance and their role in supporting endemic species and high biodiversity levels, microbial habitats should be included in future spatial planning, conservation and management measures.

Diversity, habitat endemicity and trophic ecology of the fauna of Loki's Castle vent field on the Arctic Mid-Ocean Ridge

Loki's Castle Vent Field (LCVF, 2300 m) was discovered in 2008 and represents the first black-smoker vent field discovered on the Arctic Mid-Ocean Ridge (AMOR). However, a comprehensive faunal inventory of the LCVF has not yet been published, hindering the inclusion of the Arctic in biogeographic analyses of vent fauna. There is an urgent need to understand the diversity, spatial distribution and ecosystem function of the biological communities along the AMOR, which will inform environmental impact assesments of future deep-sea mining activities in the region. Therefore, our aim with this paper is to provide a comprehensive inventory of the fauna at LCVF and present a first insight into the food web of the vent community. The fauna of LCVF has a high degree of novelty, with five new species previously described and another ten new species awaiting formal description. Most of the new species from LCVF are either hydrothermal vent specialists or have been reported from other chemosynthesis-based ecosystems. The highest taxon richness is found in the diffuse venting areas and may be promoted by the biogenic habitat generated by the foundation species Sclerolinum contortum. The isotopic signatures of the vent community of LCVF show a clear influence of chemosynthetic primary production on the foodweb. Considering the novel and specialised fauna documented in this paper, hydrothermal vents on the AMOR should be regarded as vulnerable marine ecosystems and protective measures must therefore be implemented, especially considering the potential threat from resource exploration and exploitation activities in the near future.

Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field

IMPORTANCE

Knowledge on microbial iron oxidation is important for understanding the cycling of iron, carbon, nitrogen, nutrients, and metals. The current study yields important insights into the niche sharing, diversification, and Fe(III) oxyhydroxide morphology of Ghiorsea, an iron- and hydrogen-oxidizing Zetaproteobacteria representative belonging to Zetaproteobacteria operational taxonomic unit 9. The study proposes that Ghiorsea exhibits a more extensive morphology of Fe(III) oxyhydroxide than previously observed. Overall, the results increase our knowledge on potential drivers of Zetaproteobacteria diversity in iron microbial mats and can eventually be used to develop strategies for the cultivation of sheath-forming Zetaproteobacteria.

Phylogenetic and functional diverse ANME-1 thrive in Arctic hydrothermal vents

The methane-rich areas, the Loki's Castle vent field and the Jan Mayen vent field at the Arctic Mid Ocean Ridge (AMOR), host abundant niches for anaerobic methane-oxidizers, which are predominantly filled by members of the ANME-1. In this study, we used a metagenomic-based approach that revealed the presence of phylogenetic and functional different ANME-1 subgroups at AMOR, with heterogeneous distribution. Based on a common analysis of ANME-1 genomes from AMOR and other geographic locations, we observed that AMOR subgroups clustered with a vent-specific ANME-1 group that occurs solely at vents, and with a generalist ANME-1 group, with a mixed environmental origin. Generalist ANME-1 are enriched in genes coding for stress response and defense strategies, suggesting functional diversity among AMOR subgroups. ANME-1 encode a conserved energy metabolism, indicating strong adaptation to sulfate-methane-rich sediments in marine systems, which does not however prevent global dispersion. A deep branching family named Ca. Veteromethanophagaceae was identified. The basal position of vent-related ANME-1 in phylogenomic trees suggests that ANME-1 originated at hydrothermal vents. The heterogeneous and variable physicochemical conditions present in diffuse venting areas of hydrothermal fields could have favored the diversification of ANME-1 into lineages that can tolerate geochemical and environmental variations.

Exploring Codon Adjustment Strategies towards Escherichia coli-Based Production of Viral Proteins Encoded by HTH1, a Novel Prophage of the Marine Bacterium Hypnocyclicus thermotrophus

Marine viral sequence space is immense and presents a promising resource for the discovery of new enzymes interesting for research and biotechnology. However, bottlenecks in the functional annotation of viral genes and soluble heterologous production of proteins hinder access to downstream characterization, subsequently impeding the discovery process. While commonly utilized for the heterologous expression of prokaryotic genes, codon adjustment approaches have not been fully explored for viral genes. Herein, the sequence-based identification of a putative prophage is reported from within the genome of Hypnocyclicus thermotrophus, a Gram-negative, moderately thermophilic bacterium isolated from the Seven Sisters hydrothermal vent field. A prophage-associated gene cluster, consisting of 46 protein coding genes, was identified and given the proposed name Hypnocyclicus thermotrophus phage H1 (HTH1). HTH1 was taxonomically assigned to the viral family Siphoviridae, by lowest common ancestor analysis of its genome and phylogeny analyses based on proteins predicted as holin and DNA polymerase. The gene neighbourhood around the HTH1 lytic cassette was found most similar to viruses infecting Gram-positive bacteria. In the HTH1 lytic cassette, an N-acetylmuramoyl-L-alanine amidase (Amidase_2) with a peptidoglycan binding motif (LysM) was identified. A total of nine genes coding for enzymes putatively related to lysis, nucleic acid modification and of unknown function were subjected to heterologous expression in Escherichia coli. Codon optimization and codon harmonization approaches were applied in parallel to compare their effects on produced proteins. Comparison of protein yields and thermostability demonstrated that codon optimization yielded higher levels of soluble protein, but codon harmonization led to proteins with higher thermostability, implying a higher folding quality. Altogether, our study suggests that both codon optimization and codon harmonization are valuable approaches for successful heterologous expression of viral genes in E. coli, but codon harmonization may be preferable in obtaining recombinant viral proteins of higher folding quality.

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys

BACKGROUND

Deep-sea hydrothermal vents are highly productive biodiversity hotspots in the deep ocean supported by chemosynthetic microorganisms. Prominent features of these systems are sulfide chimneys emanating high-temperature hydrothermal fluids. While several studies have investigated the microbial diversity in both active and inactive sulfide chimneys that have been extinct for up to thousands of years, little is known about chimneys that have ceased activity more recently, as well as the microbial succession occurring during the transition from active to inactive chimneys.

RESULTS

Genome-resolved metagenomics was applied to an active and a recently extinct (~ 7 years) sulfide chimney from the 9-10° N hydrothermal vent field on the East Pacific Rise. Full-length 16S rRNA gene and a total of 173 high-quality metagenome assembled genomes (MAGs) were retrieved for comparative analysis. In the active chimney (L-vent), sulfide- and/or hydrogen-oxidizing Campylobacteria and Aquificae with the potential for denitrification were identified as the dominant community members and primary producers, fixing carbon through the reductive tricarboxylic acid (rTCA) cycle. In contrast, the microbiome of the recently extinct chimney (M-vent) was largely composed of heterotrophs from various bacterial phyla, including Delta-/Beta-/Alphaproteobacteria and Bacteroidetes. Gammaproteobacteria were identified as the main primary producers, using the oxidation of metal sulfides and/or iron oxidation coupled to nitrate reduction to fix carbon through the Calvin-Benson-Bassham (CBB) cycle. Further analysis revealed a phylogenetically distinct Nitrospirae cluster that has the potential to oxidize sulfide minerals coupled to oxygen and/or nitrite reduction, as well as for sulfate reduction, and that might serve as an indicator for the early stages of chimneys after venting has ceased.

CONCLUSIONS

This study sheds light on the composition, metabolic functions, and succession of microbial communities inhabiting deep-sea hydrothermal vent sulfide chimneys. Collectively, microbial succession during the life span of a chimney could be described to proceed from a "fluid-shaped" microbial community in newly formed and actively venting chimneys supported by the oxidation of reductants in the hydrothermal fluid to a "mineral-shaped" community supported by the oxidation of minerals after hydrothermal activity has ceased. Remarkably, the transition appears to occur within the first few years, after which the communities stay stable for thousands of years. Video Abstract.

"Candidatus Ethanoperedens," a Thermophilic Genus of Archaea Mediating the Anaerobic Oxidation of Ethane

Cold seeps and hydrothermal vents deliver large amounts of methane and other gaseous alkanes into marine surface sediments. Consortia of archaea and partner bacteria thrive on the oxidation of these alkanes and its coupling to sulfate reduction. The inherently slow growth of the involved organisms and the lack of pure cultures have impeded the understanding of the molecular mechanisms of archaeal alkane degradation. Here, using hydrothermal sediments of the Guaymas Basin (Gulf of California) and ethane as the substrate, we cultured microbial consortia of a novel anaerobic ethane oxidizer, "Candidatus Ethanoperedens thermophilum" (GoM-Arc1 clade), and its partner bacterium "Candidatus Desulfofervidus auxilii," previously known from methane-oxidizing consortia. The sulfate reduction activity of the culture doubled within one week, indicating a much faster growth than in any other alkane-oxidizing archaea described before. The dominance of a single archaeal phylotype in this culture allowed retrieval of a closed genome of "Ca. Ethanoperedens," a sister genus of the recently reported ethane oxidizer "Candidatus Argoarchaeum." The metagenome-assembled genome of "Ca. Ethanoperedens" encoded a complete methanogenesis pathway including a methyl-coenzyme M reductase (MCR) that is highly divergent from those of methanogens and methanotrophs. Combined substrate and metabolite analysis showed ethane as the sole growth substrate and production of ethyl-coenzyme M as the activation product. Stable isotope probing demonstrated that the enzymatic mechanism of ethane oxidation in "Ca. Ethanoperedens" is fully reversible; thus, its enzymatic machinery has potential for the biotechnological development of microbial ethane production from carbon dioxide.IMPORTANCE In the seabed, gaseous alkanes are oxidized by syntrophic microbial consortia that thereby reduce fluxes of these compounds into the water column. Because of the immense quantities of seabed alkane fluxes, these consortia are key catalysts of the global carbon cycle. Due to their obligate syntrophic lifestyle, the physiology of alkane-degrading archaea remains poorly understood. We have now cultivated a thermophilic, relatively fast-growing ethane oxidizer in partnership with a sulfate-reducing bacterium known to aid in methane oxidation and have retrieved the first complete genome of a short-chain alkane-degrading archaeon. This will greatly enhance the understanding of nonmethane alkane activation by noncanonical methyl-coenzyme M reductase enzymes and provide insights into additional metabolic steps and the mechanisms underlying syntrophic partnerships. Ultimately, this knowledge could lead to the biotechnological development of alkanogenic microorganisms to support the carbon neutrality of industrial processes.

Tailoring Hydrothermal Vent Biodiversity Toward Improved Biodiscovery Using a Novel in situ Enrichment Strategy

Deep-sea hydrothermal vents are amongst the most extreme environments on Earth and represent interesting targets for marine bioprospecting and biodiscovery. The microbial communities in hydrothermal vents are often dominated by chemolithoautotrophs utilizing simple chemical compounds, though the full extent of their heterotrophic abilities is still being explored. In the bioprocessing industry, where degradation of complex organic materials often is a major challenge, new microbial solutions are heavily needed. To meet these needs, we have developed novel in situ incubators and tested if deployment of recalcitrant materials from fish farming and wood-pulping industries introduced changes in the microbial community structure in hot marine hydrothermal sediments. The incubation chambers were deployed in sediments at the Bruse vent site located within the Jan Mayen vent field for 1 year, after which the microbial populations in the chambers were profiled by 16S rRNA Ion Torrent amplicon sequencing. A total of 921 operational taxonomic units (OTUs) were assigned into 74 different phyla where differences in community structure were observed depending on the incubated material, chamber depth below the sea floor and/or temperature. A high fraction of putative heterotrophic microbial lineages related to cultivated members within the Thermotogales were observed. However, considerable fractions of previously uncultivated and novel Thermotogales and Bacteroidetes were also identified. Moreover, several novel lineages (e.g., members within the DPANN superphylum, unidentified archaeal lineages, unclassified Thermoplasmatales and Candidatus division BRC-1 bacterium) of as-yet uncultivated thermophilic archaea and bacteria were identified. Overall, our data illustrate that amendment of hydrothermal vent communities by in situ incubation of biomass induces shifts in community structure toward increased fractions of heterotrophic microorganisms. The technologies utilized here could aid in subsequent metagenomics-based enzyme discovery for diverse industries.

Hydrothermal chimneys host habitat-specific microbial communities: analogues for studying the possible impact of mining seafloor massive sulfide deposits

To assess the risk that mining of seafloor massive sulfides (SMS) from extinct hydrothermal vent environments has for changing the ecosystem irreversibly, we sampled SMS analogous habitats from the Kairei and the Pelagia vent fields along the Indian Ridge. In total 19.8 million 16S rRNA tags from 14 different sites were analyzed and the microbial communities were compared with each other and with publicly available data sets from other marine environments. The chimneys appear to provide habitats for microorganisms that are not found or only detectable in very low numbers in other marine habitats. The chimneys also host rare organisms and may function as a vital part of the ocean’s seed bank. Many of the reads from active and inactive chimney samples were clustered into OTUs, with low or no resemblance to known species. Since we are unaware of the chemical reactions catalyzed by these unknown organisms, the impact of this diversity loss and bio-geo-coupling is hard to predict. Given that chimney structures can be considered SMS analogues, removal of sulfide deposits from the seafloor in the Kairei and Pelagia fields will most likely alter microbial compositions and affect element cycling in the benthic regions and probably beyond.

Genetic connectivity from the Arctic to the Antarctic: Sclerolinum contortum and Nicomache lokii (Annelida) are both widespread in reducing environments

The paradigm of large geographic ranges in the deep sea has been challenged by genetic studies, which often reveal putatively widespread species to be several taxa with more restricted ranges. Recently, a phylogeographic study revealed that the tubeworm Sclerolinum contortum (Siboglinidae) inhabits vents and seeps from the Arctic to the Antarctic. Here, we further test the conspecificity of the same populations of S. contortum with additional mitochondrial and nuclear markers. We also investigate the genetic connectivity of another species with putatively the same wide geographic range - Nicomache lokii (Maldanidae). Our results support the present range of S. contortum, and the range of N. lokii is extended from vents and seeps in the Nordic Seas to mud volcanoes in the Barbados Trench and Antarctic vents. Sclerolinum contortum shows more pronounced geographic structure than N. lokii, but whether this is due to different dispersal capacities or reflects the geographic isolation of the sampled localities is unclear. Two distinct mitochondrial lineages of N. lokii are present in the Antarctic, which may result from two independent colonization events. The environmental conditions inhabited by the two species and implications for their distinct habitat preference is discussed.

Do ampharetids take sedimented steps between vents and seeps? Phylogeny and habitat-use of Ampharetidae (Annelida, Terebelliformia) in chemosynthesis-based ecosystems

BACKGROUND

A range of higher animal taxa are shared across various chemosynthesis-based ecosystems (CBEs), which demonstrates the evolutionary link between these habitats, but on a global scale the number of species inhabiting multiple CBEs is low. The factors shaping the distributions and habitat specificity of animals within CBEs are poorly understood, but geographic proximity of habitats, depth and substratum have been suggested as important. Biogeographic studies have indicated that intermediate habitats such as sedimented vents play an important part in the diversification of taxa within CBEs, but this has not been assessed in a phylogenetic framework. Ampharetid annelids are one of the most commonly encountered animal groups in CBEs, making them a good model taxon to study the evolution of habitat use in heterotrophic animals. Here we present a review of the habitat use of ampharetid species in CBEs, and a multi-gene phylogeny of Ampharetidae, with increased taxon sampling compared to previous studies.

RESULTS

The review of microhabitats showed that many ampharetid species have a wide niche in terms of temperature and substratum. Depth may be limiting some species to a certain habitat, and trophic ecology and/or competition are identified as other potentially relevant factors. The phylogeny revealed that ampharetids have adapted into CBEs at least four times independently, with subsequent diversification, and shifts between ecosystems have happened in each of these clades. Evolutionary transitions are found to occur both from seep to vent and vent to seep, and the results indicate a role of sedimented vents in the transition between bare-rock vents and seeps.

CONCLUSION

The high number of ampharetid species recently described from CBEs, and the putative new species included in the present phylogeny, indicates that there is considerable diversity still to be discovered. This study provides a molecular framework for future studies to build upon and identifies some ecological and evolutionary hypotheses to be tested as new data is produced.

Capturing the genetic makeup of the active microbiome in situ

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.