Preliminary assessment of methanogenic microbial communities in marine caves of Zakynthos Island (Ionian Sea, Greece)

Mediterranean marine caves remain largely unexplored, while particularly limited information is available about the microbial life existing in these unique environments. The present study is a preliminary assessment of the composition of the active anaerobic microbial community colonizing the walls of newly explored systems of underwater caves and small cavities in Zakynthos Island. The interior of these caves is densely coated with egg-shaped, foam-shaped and filamentous biological structures that are characterised by a strong odor of hydrogen sulfide gas. A total of twelve structures scrapped from cave rocks were subjected to anaerobic cultivation for up to 208 days. Strong to moderate methanogenesis was observed in two different types of egg-shaped structures and one foam-like structure. Interestingly, this was observed in experiments that were performed at room temperature (i.e. 25oC) which is substantially lower than those typically considered optimum for methane production (e.g. 35oC). Analysis of the 16S rRNA genes revealed a clear dominance of archaea and bacteria closely related to known methane producers and sulfate reducers, including members of the families Methanomicrobiaceae, Desulfobulbaceae, Desulfobacteraceae, Desulfuromonaceae, Campylobacteraceae, Marinifilaceae, Clostridiaceae, Incertae Sedis – Family I & II. These results show that Mediterranean marine caves can host members of archaea and bacteria with potential biotechnological interest that deserve further investigation

Metagenomics : tools and insights for analyzing next-generation sequencing data derived from biodiversity studies

Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of “metagenomics”, often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards

Biodiversity, Anti-Trypanosomal Activity Screening, and Metabolomic Profiling of Actinomycetes Isolated from Mediterranean Sponges

Marine sponge–associated actinomycetes are considered as promising sources for the discovery of novel biologically active compounds. In the present study, a total of 64 actinomycetes were isolated from 12 different marine sponge species that had been collected offshore the islands of Milos and Crete, Greece, eastern Mediterranean. The isolates were affiliated to 23 genera representing 8 different suborders based on nearly full length 16S rRNA gene sequencing. Four putatively novel species belonging to genera Geodermatophilus, Microlunatus, Rhodococcus and Actinomycetospora were identified based on a 16S rRNA gene sequence similarity of < 98.5% to currently described strains. Eight actinomycete isolates showed bioactivities against Trypanosma brucei brucei TC221 with half maximal inhibitory concentration (IC50) values <20 μg/mL. Thirty four isolates from the Milos collection and 12 isolates from the Crete collection were subjected to metabolomic analysis using high resolution LC-MS and NMR for dereplication purposes. Two isolates belonging to the genera Streptomyces (SBT348) and Micromonospora (SBT687) were prioritized based on their distinct chemistry profiles as well as their anti-trypanosomal activities. These findings demonstrated the feasibility and efficacy of utilizing metabolomics tools to prioritize chemically unique strains from microorganism collections and further highlight sponges as rich source for novel and bioactive actinomycetes

Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology

Hydrothermal vents represent a deep, hot, aphotic biosphere where chemosynthetic primary producers, fuelled by chemicals from Earth\u27s subsurface, form the basis of life. In this study, we examined microbial mats from two distinct volcanic sites within the Hellenic Volcanic Arc (HVA). The HVA is geologically and ecologically unique, with reported emissions of CO2‐saturated fluids at temperatures up to 220°C and a notable absence of macrofauna. Metagenomic data reveals highly complex prokaryotic communities composed of chemolithoautotrophs, some methanotrophs, and to our surprise, heterotrophs capable of anaerobic degradation of aromatic hydrocarbons. Our data suggest that aromatic hydrocarbons may indeed be a significant source of carbon in these sites, and instigate additional research into the nature and origin of these compounds in the HVA. Novel physiology was assigned to several uncultured prokaryotic lineages; most notably, a SAR406 representative is attributed with a role in anaerobic hydrocarbon degradation. This dataset, the largest to date from submarine volcanic ecosystems, constitutes a significant resource of novel genes and pathways with potential biotechnological applications

Geochemistry of CO2-Rich Gases Venting From Submarine Volcanism: The Case of Kolumbo (Hellenic Volcanic Arc, Greece)

Studies of submarine hydrothermal systems in Mediterranean Sea are limited to the southern Italian volcanism, while are totally missing in the Aegean. Here, we report on the geochemistry of high-temperature fluids (up to 220°C) venting at 500 m b.s.l. from the floor of Kolumbo submarine volcano (Hellenic Volcanic Arc, Greece), which is located 7 km northeast of Santorini Island. Despite the recent unrest at Santorini, Kolumbo submarine volcano is considered more active due to a higher seismicity. Rizzo et al. (2016) investigated the He-isotope composition of gases collected from seven chimneys and showed that are dominated by CO2 (&gt;97%), with only a small air contamination. Here we provide more-complete chemical data and isotopic compositions of CO2 and CH4, and Hg(0) concentration. We show that the gases emitted from different vents are fractionated by the partial dissolution of CO2 in water. Fractionation is also evident in the C-isotope composition (δ13CCO2), which varies between -0.04 and 1.15‰. We modeled this process to reconstruct the chemistry and δ13CCO2 of intact magmatic gases before fractionation. We argue that the CO2 prior to CO2 dissolution in water had δ13C ∼-0.4‰ and CO2/3He ∼1 × 1010. This model reveals that the gases emitted from Kolumbo originate from a homogeneous mantle contaminated with CO2, probably due to decarbonation of subducting limestone, which is similar to other Mediterranean arc volcanoes (e.g., Stromboli, Italy). The isotopic signature of CH4 (δ13C ∼-18‰ and δD ∼-117‰) is within a range of values typically observed for hydrothermal gases (e.g., Panarea and Campi Flegrei, Italy), which is suggestive of mixing between thermogenic and abiotic CH4. We report that the concentrations of Hg(0) in Kolumbo fluids are particularly high (∼61 to 1300 ng m-3) when compared to land-based fumaroles located on Santorini and worldwide aerial volcanic emissions. This finding may represent further evidence for the high level of magmatic activity at Kolumbo. Based on the geo-indicators of temperature and pressure, we calculate that the magmatic gases equilibrate within the Kolumbo hydrothermal system at about 270°C and at a depth of ∼1 km b.s.l

New insights into hydrothermal vent processes in the unique shallow-submarine arc-volcano, Kolumbo (Santorini), Greece

We report on integrated geomorphological, mineralogical, geochemical and biological investigations of the hydrothermal vent field located on the floor of the density-stratified acidic (pH , 5) crater of the Kolumbo shallow-submarine arc-volcano, near Santorini. Kolumbo features rare geodynamic setting at convergent boundaries, where arc-volcanism and seafloor hydrothermal activity are occurring in thinned continental crust. Special focus is given to unique enrichments of polymetallic spires in Sb and Tl (6Hg, As, Au, Ag, Zn) indicating a new hybrid seafloor analogue of epithermal-to-volcanic-hosted-massive-sulphide deposits. Iron microbial-mat analyses reveal dominating ferrihydrite-type phases, and high-proportion of microbial sequences akin to &quot;Nitrosopumilus maritimus&quot;, a mesophilic Thaumarchaeota strain capable of chemoautotrophic growth on hydrothermal ammonia and CO2. Our findings highlight that acidic shallow-submarine hydrothermal vents nourish marine ecosystems in which nitrifying Archaea are important and suggest ferrihydrite-type Fe31-(hydrated)-oxyhydroxides in associated low-temperature iron mats are formed by anaerobic Fe21-oxidation, dependent on microbially produced nitrate

Structure and metabolic potential of the prokaryotic communities from the hydrothermal system of Paleochori Bay, Milos, Greece

IntroductionShallow hydrothermal systems share many characteristics with their deep-sea counterparts, but their accessibility facilitates their study. One of the most studied shallow hydrothermal vent fields lies at Paleochori Bay off the coast of Milos in the Aegean Sea (Greece). It has been studied through extensive mapping and its physical and chemical processes have been characterized over the past decades. However, a thorough description of the microbial communities inhabiting the bay is still missing.MethodsWe present the first in-depth characterization of the prokaryotic communities of Paleochori Bay by sampling eight different seafloor types that are distributed along the entire gradient of hydrothermal influence. We used deep sequencing of the 16S rRNA marker gene and complemented the analysis with qPCR quantification of the 16S rRNA gene and several functional genes to gain insights into the metabolic potential of the communities.ResultsWe found that the microbiome of the bay is strongly influenced by the hydrothermal venting, with a succession of various groups dominating the sediments from the coldest to the warmest zones. Prokaryotic diversity and abundance decrease with increasing temperature, and thermophilic archaea overtake the community.DiscussionRelevant geochemical cycles of the Bay are discussed. This study expands our limited understanding of subsurface microbial communities in acidic shallow-sea hydrothermal systems and the contribution of their microbial activity to biogeochemical cycling

Deep-Sea Biodiversity in the Mediterranean Sea: The Known, the Unknown, and the Unknowable

Deep-sea ecosystems represent the largest biome of the global biosphere, but knowledge of their biodiversity is still scant. The Mediterranean basin has been proposed as a hot spot of terrestrial and coastal marine biodiversity but has been supposed to be impoverished of deep-sea species richness. We summarized all available information on benthic biodiversity (Prokaryotes, Foraminifera, Meiofauna, Macrofauna, and Megafauna) in different deep-sea ecosystems of the Mediterranean Sea (200 to more than 4,000 m depth), including open slopes, deep basins, canyons, cold seeps, seamounts, deep-water corals and deep-hypersaline anoxic basins and analyzed overall longitudinal and bathymetric patterns. We show that in contrast to what was expected from the sharp decrease in organic carbon fluxes and reduced faunal abundance, the deep-sea biodiversity of both the eastern and the western basins of the Mediterranean Sea is similarly high. All of the biodiversity components, except Bacteria and Archaea, displayed a decreasing pattern with increasing water depth, but to a different extent for each component. Unlike patterns observed for faunal abundance, highest negative values of the slopes of the biodiversity patterns were observed for Meiofauna, followed by Macrofauna and Megafauna. Comparison of the biodiversity associated with open slopes, deep basins, canyons, and deep-water corals showed that the deep basins were the least diverse. Rarefaction curves allowed us to estimate the expected number of species for each benthic component in different bathymetric ranges. A large fraction of exclusive species was associated with each specific habitat or ecosystem. Thus, each deep-sea ecosystem contributes significantly to overall biodiversity. From theoretical extrapolations we estimate that the overall deep-sea Mediterranean biodiversity (excluding prokaryotes) reaches approximately 2805 species of which about 66% is still undiscovered. Among the biotic components investigated (Prokaryotes excluded), most of the unknown species are within the phylum Nematoda, followed by Foraminifera, but an important fraction of macrofaunal and megafaunal species also remains unknown. Data reported here provide new insights into the patterns of biodiversity in the deep-sea Mediterranean and new clues for future investigations aimed at identifying the factors controlling and threatening deep-sea biodiversity