Microbiota associated with tubes of Escarpia sp. from cold seeps in the southwestern Atlantic Ocean constitutes a community distinct from that of surrounding marine sediment and water

Microbial communities in the deep-sea sediments of the South São Paulo Plateau, Southwestern Atlantic Ocean

Microbial communities play a key role in the ocean, acting as primary producers, nutrient recyclers, and energy providers. The São Paulo Plateau is a region located on the southeastern coast of Brazil within economic importance, due to its oil and gas reservoirs. With this focus, this study examined the diversity and composition of microbial communities in marine sediments located at three oceanographic stations in the southern region of São Paulo Plateau using the HOV Shinkai 6500 in 2013. The 16S rRNA gene was sequenced using the universal primers (515F and 926R) by the Illumina Miseq platform. The taxonomic compositions of samples recovered from SP3 station were markedly distinct from those obtained from SP1 and SP2. Although all three stations exhibited a high abundance of Gammaproteobacteria (> 15%), this taxon dominated more than 90% of composition of the A and C sediment layers at SP3. The highest abundance of the archaeal class Nitrososphaeria was presented at SP1, mainly at layer C (~ 21%), being absent at SP3 station. The prediction of chemoheterotrophy and fermentation as important microbial functions was supported by the data. Additionally, other metabolic pathways related to the cycles of nitrogen, carbon and sulfur were also predicted. The core microbiome analysis comprised only two ASVs. Our study contributes to a better understanding of microbial communities in an economically important little-explored region. This is the third microbiological survey in plateau sediments and the first focused on the southern region.

A tale of two tubeworms: taxonomy of vestimentiferans (Annelida: Siboglinidae) from the Mid-Cayman Spreading Centre

The vestimentiferan tubeworm genera Lamellibrachia and Escarpia inhabit deep-sea chemosynthesis-based ecosystems, such as seeps, hydrothermal vents and organic falls, and have wide distributions across the Pacific, Atlantic and Indian Oceans. In 2010–2012 during initial explorations of hydrothermal vents of the Mid-Cayman Spreading Centre (MCSC), both genera were found to co-occur at the Von Damm Vent Field (VDVF), a site characterised by diffuse flow, therefore resembling a ‘hydrothermal seep’. Here, we erect two new vestimentiferan tubeworm species from the VDVF, Lamellibrachia judigobini sp. nov. and Escarpia tritentaculata sp. nov. Lamellibrachia judigobini sp. nov. differs genetically and morphologically from other Lamellibrachia species, and has a range that extends across the Gulf of Mexico, MCSC, off Trinidad and Tobago, and Barbados, and also across both vents and seeps and 964–3304-m water depth. Escarpia tritentaculata sp. nov. is distinguished from other Escarpia species primarily based on morphology and is known only from vents of the MCSC at 2300-m depth. This study highlights the incredible habitat flexibility of a single Lamellibrachia species and the genus Escarpia, and historic biogeographic connections to the eastern Pacific for L. judigobini sp. nov. and the eastern Atlantic for E. tritentaculata sp. nov. ZooBank: urn:lsid:zoobank.org:pub:D9F72BD4-FDE1-4C0A-B84B-A08D06F2A981

Bacteria Associated with Benthic Invertebrates from Extreme Marine Environments: Promising but Underexplored Sources of Biotechnologically Relevant Molecules

Microbe–invertebrate associations, commonly occurring in nature, play a fundamental role in the life of symbionts, even in hostile habitats, assuming a key importance for both ecological and evolutionary studies and relevance in biotechnology. Extreme environments have emerged as a new frontier in natural product chemistry in the search for novel chemotypes of microbial origin with significant biological activities. However, to date, the main focus has been microbes from sediment and seawater, whereas those associated with biota have received significantly less attention. This review has been therefore conceived to summarize the main information on invertebrate–bacteria associations that are established in extreme marine environments. After a brief overview of currently known extreme marine environments and their main characteristics, a report on the associations between extremophilic microorganisms and macrobenthic organisms in such hostile habitats is provided. The second part of the review deals with biotechnologically relevant bioactive molecules involved in establishing and maintaining symbiotic associations.

Genomic, biochemical, and phylogenetic evaluation of bacteria isolated from deep-sea sediment harboring methane hydrates

Over half of the organic carbon on Earth's surface is trapped in marine sediment as methane hydrates. Ocean warming causes hydrate dissociation and methane leakage to the water column, rendering the characterization of microbes from hydrate depositions a pressing matter. Through genomic, phylogenetic, and biochemical assays, we characterize the first microorganisms isolated from the Rio Grande Cone (Brazil), reservoir responsible for massive methane releases to the water column. From sediment harboring rich benthic communities, we obtained 43 strains of Brevibacillus sp., Paenibacillus sp. and groups of Bacillus sp. Methane-enriched samples yielded strains of the Pseudomonas fluorescens complex, exhibiting fluorescent siderophore production and broad multi-carbon catabolism. Genomic characterization of a novel Pseudomonas sp. strain indicated 32 genes not identified in the closest related type-species, including proteins involved with mercury resistance. Our results provide phylogenetic and genomic insights on the first bacterial isolates retrieved from a poorly explored region of the South Atlantic Ocean.

High-Throughput Sequencing Reveals a Potentially Novel Sulfurovum Species Dominating the Microbial Communities of the Seawater-Sediment Interface of a Deep-Sea Cold Seep in South China Sea

In the Formosa cold seep of the South China Sea (SCS), large amounts of methane and sulfide hydrogen are released from the subseafloor. In this study, we systematically investigated the microbial communities in the seawater–sediment interface of Formosa cold seep using high-throughput sequencing techniques including amplicon sequencing based on next-generation sequencing and Pacbio amplicon sequencing platforms, and metagenomics. We found that Sulfurovum dominated the microbial communities in the sediment–seawater interface, including the seawater close to the seepage, the surface sediments, and the gills of the dominant animal inhabitant (Shinkaia crosnieri). A nearly complete 16S rRNA gene sequence of the dominant operational taxonomic units (OTUs) was obtained from the Pacbio sequencing platforms and classified as OTU-L1, which belonged to Sulfurovum. This OTU was potentially novel as it shared relatively low similarity percentages (<97%) of the gene sequence with its close phylogenetic species. Further, a draft genome of Sulfurovum was assembled using the binning technique based on metagenomic data. Genome analysis suggested that Sulfurovum sp. in this region may fix carbon by the reductive tricarboxylic acid (rTCA) pathway, obtain energy by oxidizing reduced sulfur through sulfur oxidizing (Sox) pathway, and utilize nitrate as electron acceptors. These results demonstrated that Sulfurovum probably plays an important role in the carbon, sulfur, and nitrogen cycles of the Formosa cold seep of the SCS. This study improves our understanding of the diversity, distribution, and function of sulfur-oxidizing bacteria in deep-sea cold seep.

Siboglinidae Tubes as an Additional Niche for Microbial Communities in the Gulf of Cádiz-A Microscopical Appraisal

Siboglinids were sampled from four mud volcanoes in the Gulf of Cádiz (El Cid MV, Bonjardim MV, Al Gacel MV, and Anastasya MV). These invertebrates are characteristic to cold seeps and are known to host chemosynthetic endosymbionts in a dedicated trophosome organ. However, little is known about their tube as a potential niche for other microorganisms. Analyses by scanning and transmission electron microscopy showed dense biofilms on the tube in Al Gacel MV and Anastasya MV specimens by prokaryotic cells. Methanotrophic bacteria were the most abundant forming these biofilms as further supported by 16S rRNA sequence analysis. Furthermore, elemental analyses with electron microscopy and energy-dispersive X-ray spectroscopy point to the mineralization and silicification of the tube, most likely induced by the microbial metabolisms. Bacterial and archaeal 16S rRNA sequence libraries revealed abundant microorganisms related to these siboglinid specimens and certain variations in microbial communities among samples. Thus, the tube remarkably increases the microbial biomass related to the worms and provides an additional microbial niche in deep-sea ecosystems.

Characterization of the Gut Microbiota of the Antarctic Heart Urchin (Spatangoida) Abatus agassizii

Abatus agassizii is an irregular sea urchin species that inhabits shallow waters of South Georgia and South Shetlands Islands. As a deposit-feeder, A. agassizii nutrition relies on the ingestion of the surrounding sediment in which it lives barely burrowed. Despite the low complexity of its feeding habit, it harbors a long and twice-looped digestive tract suggesting that it may host a complex bacterial community. Here, we characterized the gut microbiota of specimens from two A. agassizii populations at the south of the King George Island in the West Antarctic Peninsula. Using a metabarcoding approach targeting the 16S rRNA gene, we characterized the Abatus microbiota composition and putative functional capacity, evaluating its differentiation among the gut content and the gut tissue in comparison with the external sediment. Additionally, we aimed to define a core gut microbiota between A. agassizii populations to identify potential keystone bacterial taxa. Our results show that the diversity and the composition of the microbiota, at both genetic and predicted functional levels, were mostly driven by the sample type, and to a lesser extent by the population location. Specific bacterial taxa, belonging mostly to Planctomycetacia and Spirochaetia, were differently enriched in the gut content and the gut tissue, respectively. Predictive functional profiles revealed higher abundance of specific pathways, as the sulfur cycle in the gut content and the amino acid metabolism, in the gut tissue. Further, the definition of a core microbiota allowed to obtain evidence of specific localization of bacterial taxa and the identification of potential keystone taxa assigned to the Desulfobacula and Spirochaeta genera as potentially host selected. The ecological relevance of these keystone taxa in the host metabolism is discussed.

Planctopirus ephydatiae, a novel Planctomycete isolated from a freshwater sponge

The microbiome of freshwater sponges is rarely studied, and not a single novel bacterial species has been isolated and subsequently characterized from a freshwater sponge to date. A previous study showed that 14.4% of the microbiome from Ephydatia fluviatilis belong to the phylum Planctomycetes. Therefore, we sampled an Ephydatia sponge from a freshwater lake and employed enrichment techniques targeting bacteria from the phylum Planctomycetes. The obtained strain spb1^T was subject to genomic and phenomic characterization and found to represent a novel planctomycetal species proposed as Planctopirus ephydatiae sp. nov. (DSM 106606 = CECT 9866). In the process of differentiating spb1^T from its next relative Planctopirus limnophila DSM 3776^T, we identified and characterized the first phage - Planctopirus phage vB_PlimS_J1 - infecting planctomycetes that was only mentioned anecdotally before. Interestingly, classical chemotaxonomic methods would have failed to distinguish Planctopirus ephydatiae strain spb1^T from Planctopirus limnophila DSM 3776^T. Our findings demonstrate and underpin the need for whole genome-based taxonomy to detect and differentiate planctomycetal species.

Gas Seeps at the Edge of the Gas Hydrate Stability Zone on Brazil’s Continental Margin

Gas hydrate provinces occur in two sedimentary basins along Brazil’s continental margin: (1) The Rio Grande Cone in the southeast, and (2) the Amazon deep-sea fan in the equatorial region. The occurrence of gas hydrates in these depocenters was first detected geophysically and has recently been proven by seafloor sampling of gas vents, detected as water column acoustic anomalies rising from seafloor depressions (pockmarks) and/or mounds, many associated with seafloor faults formed by the gravitational collapse of both depocenters. The gas vents include typical features of cold seep systems, including shallow sulphate reduction depths (<4 m), authigenic carbonate pavements, and chemosynthetic ecosystems. In both areas, gas sampled in hydrate and in sediments is dominantly formed by biogenic methane. Calculation of the methane hydrate stability zone for water temperatures in the two areas shows that gas vents occur along its feather edge (water depths between 510 and 760 m in the Rio Grande Cone and between 500 and 670 m in the Amazon deep-sea fan), but also in deeper waters within the stability zone. Gas venting along the feather edge of the stability zone could reflect gas hydrate dissociation and release to the oceans, as inferred on other continental margins, or upward fluid flow through the stability zone facilitated by tectonic structures recording the gravitational collapse of both depocenters. The potential quantity of venting gas on the Brazilian margin under different scenarios of natural or anthropogenic change requires further investigation. The studied areas provide natural laboratories where these critical processes can be analyzed and quantified.

Molecular and Isotopic Composition of Hydrate-Bound, Dissolved and Free Gases in the Amazon Deep-Sea Fan and Slope Sediments, Brazil

In this work, we investigated the molecular stable isotope compositions of hydrate-bound and dissolved gases in sediments of the Amazon deep-sea fan and adjacent continental slope, Foz do Amazonas Basin, Brazil. Some cores were obtained in places with active gas venting on the seafloor and, in one of the locations, the venting gas is probably associated with the dissociation of hydrates near the edge of their stability zone. Results of the methane stable isotopes (δ13C and δD) of hydrate-bound and dissolved gases in sediments for the Amazon fan indicated the dominant microbial origin of methane via carbon dioxide reduction, in which 13C and deuterium isotopes were highly depleted (δ13C and δD of −102.2% to −74.2% V-PDB and −190 to −150% V-SMOW, respectively). The combination of C1/(C2+C3) versus δ13C plot also suggested a biogenic origin for methane in all analysed samples (commonly >1000). However, a mixture of thermogenic and microbial gases was suggested for the hydrate-bound and dissolved gases in the continental slope adjacent to the Amazon fan, in which the combination of chemical and isotopic gas compositions in the C1/(C2+C3) versus δ13C plot were <100 in one of the recovered cores. Moreover, the δ13C-ethane of −30.0% indicates a thermogenic origin.