Deep-sea Sediment Samples Research Articles

Deep-sea sediment metagenome from Bay of Bengal reveals distinct microbial diversity and functional significance

Bay of Bengal (BoB) has immense significance with respect to ecological diversity and natural resources. Studies on microbial profiling and their functional significance at sediment level of BoB remain poorly represented. Herein, we describe the microbial diversity and metabolic potentials of BOB deep-sea sediment samples by subjecting the metagenomes to Nanopore sequencing. Taxonomic diversity ascertained at various levels revealed that bacteria belonging to phylum Proteobacteria predominantly represented in sediment samples NIOT_S7 and NIOT_S9. A comparative study with 16S datasets from similar ecological sites revealed depth as a crucial factor in determining taxonomic diversity. KEGG annotation indicated that bacterial communities possess sequence reads corresponding to carbon dioxide fixation, sulfur, nitrogen metabolism, but at varying levels. Additionally, gene sequences related to bioremediation of dyes, plastics, hydrocarbon, antibiotic resistance, secondary metabolite synthesis and metal resistance from both the samples as studied indicate BoB to represent a highly diverse environmental niche for further exploration.

Sulfurimonas marina sp. nov., an obligately chemolithoautotrophic, sulphur-oxidizing bacterium isolated from a deep-sea sediment sample from the South China Sea.

A novel marine bacterium, designated strain B2T, was isolated from a deep-sea sediment sample collected from the South China Sea. Cells were observed to be Gram-stain negative, motile and rod shaped with a single polar flagellum. B2T could grow at 10-45 °C (optimum, 35 °C), pH 4.5-9.0 (optimum, pH 7.0) and in the presence of 1.0-8.0 % (w/v) NaCl (optimum, 3.0%). The isolate grew chemolithoautotrophically with sulphide, elemental sulphur and thiosulphate as electron donors, carbon dioxide as the sole carbon source, and molecular oxygen as the sole electron acceptor. Molecular hydrogen did not support growth. The predominant fatty acids of B2T were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The results of phylogenetic analysis based on 16S rRNA gene sequence indicated that B2T represented a member of the genus Sulfurimonas, with the highest similarity to the 16S rRNA gene sequences of Sulfurimonas indica NW8NT (95.9 %), Sulfurimonas crateris SN118T (95.7 %), Sulfurimonas xiamenensis 1-1NT (95.6 %) and Sulfurimonas paralvinellae GO25T (95.4 %). Sequence similarities to other members of the genus Sulfurimonas were less than 95.0 %. In addition, the average nucleotide identity (ANI) value and digital DNA-DNA hybridization (dDDH) estimate between B2T and S. indica NW8NT were 73.0 and 23.7 %, respectively. The size of the complete genome of B2T is 22 61 034 bp, with a DNA G+C content of 36.0 mol %. On the basis of the phenotypic, phylogenetic and genomic data presented here, strain B2T represent a novel species of the genus Sulfurimonas, for which the name Sulfurimonas marina sp. nov. is proposed, with the type strain B2T (=MCCC 1A14515T=KCTC 15852T).

Taxonomic revision of the free-living marine nematode genus Deontostoma (Enoplida: Leptosomatidae) and inclusion of a new species from the Southern Ocean

Summary A new species of free-living marine nematode, Deontostoma quadridentatum sp. nov., is described from a deep-sea sediment sample collected off the South Orkney Islands, the Southern Ocean, during a cruise (KH-19-6-Leg 4) conducted on the R/V Hakuho-Maru. Deontostoma quadridentatum sp. nov. differs from its congeners by the possession of: i) a cephalic capsule with a smooth posterior edge and without intralobar lacunae; ii) interlobar fenestrae with two posterior incisions; iii) four odontia on each mandible; iv) three onchia; v) spicules with velum and lateral process; vi) gubernacula with a hollow triangular crus, vii) one ventromedian supplement; viii) two precloacal subventral rows consisting of 8-10 setae and 12-20 papillae; and ix) by the lack of ocelli. Partial 18S rRNA and cytochrome c oxidase subunit I gene sequences were determined for D. quadridentatum sp. nov., and the diagnosis of Deontostoma and the dichotomous keys to the subfamilies of Leptosomatidae, genera of Deontostomatinae, and species of Deontostoma were revised. Two known species, Triceratonema montredonense comb. nov. and Triceratonema papillosum comb. nov., were transferred from Deontostoma. Our molecular phylogenetic analysis did not clarify the position of Deontostoma quadridentatum sp. nov., but we placed this species into Deontostoma based on morphological observations. We also tried to find a relationship between distribution and morphological characteristic because it seems that there are two phylogenetic lineages that exist in Deontostoma based on the distribution of all species. However, no such relationships could be found from our literature survey.

Arsukibacterium indicum sp. nov., isolated from deep-sea sediment, and transfer of Rheinheimera tuosuensis and Rheinheimera perlucida to the genus Arsukibacterium as Arsukibacterium tuosuense comb. nov. and Arsukibacterium perlucidum comb. nov.

A Gram-stain-negative, aerobic, flagellated and rod-shaped bacterium, designated strain SM2107T, was isolated from a deep-sea sediment sample collected from the Southwest Indian Ocean. Strain SM2107T grew at 4-40 °C and with 0-10.0 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed casein, gelatin, chitin and DNA. The phylogenetic trees based on the 16S rRNA genes and single-copy orthologous clusters showed that strain SM2107T, together with Rheinheimera tuosuensis, Rheinheimera perlucida and Arsukibacterium ikkense, formed a separate clade, having the highest similarity to the type strain of Rheinheimera tuosuensis (98.3%). The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol and the major cellular fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0, C17 : 1 ω8с and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The only respiratory quinone was Q-8. The genomic DNA G+C content of strain SM2107T was 48.8 %. The digital DNA-DNA hybridization values between strain SM2107T and type strains of Rheinheimera tuosuensis, Rheinheimera perlucida and Arsukibacterium ikkense were 41.16, 37.70 and 31.80 %, while the average amino acid identity values between them were 87.59, 86.76 and 83.64 %, respectively. Based on the polyphasic evidence presented in this study, strain SM2107T was considered to represent a novel species within the genus Arsukibacterium, for which the name Arsukibacterium indicum was proposed. The type strain is SM2107T (=MCCC M24986T=KCTC 82921T). Moreover, the transfer of Rheinheimera tuosuensis and Rheinheimera perlucida to the genus Arsukibacterium as Arsukibacterium tuosuense comb. nov. (type strain TS-T4T=CGMCC 1.12461T=JCM 19264T) and Arsukibacterium perlucidum comb. nov. (type strain BA131T=LMG 23581T=CIP 109200T) is also proposed.

Alien species invasion of deep-sea bacteria into mouse gut microbiota

IntroductionDeep sea has numerous bacteria which dominate in the biomass of deep-sea sediments. Some deep-sea bacteria may possess the capacity to destroy mammal health by the alteration of gut microbiota, acting as potential pathogens. ObjectivesPathogenic bacteria are great threats to human health. However, the ultimate origin of pathogenic bacteria has not been intensively explored. In this study, therefore, the influence of deep-sea bacteria on the gut microbiota was evaluated on a global scale. MethodsThe bacteria isolated from each of 106 deep-sea sediment samples were transplanted into mice in our study to assess the infectiousness of deep-sea bacteria. ResultsThe results showed that some bacteria from deep sea, an area that has existed since the earth was formed, could proliferate in mouse gut. Based on the infectious evaluation of the bacteria from each of 106 deep-sea sediments, the bacteria isolated from 13 sediments invaded the gut bacterial communities of mice, leading to the significant alteration of mouse gut microbiota. Among the 13 deep-sea sediments, the bacteria isolated from 9 sediments could destroy mouse health by inducing glucose metabolism deterioration, liver damage and inflammatory symptom. As an example, a bacterium was isolated from deep-sea sediment DP040, which was identified to be Bacillus cereus (termed as Bacillus cereus DP040). Bacillus cereus DP040 could invade the gut microbiota of mice to change the gut microbial structure, leading to inflammatory symptom of mice. The deep-sea sediments containing the bacteria destroying the health of mice were distributed in hydrothermal vent, mid-ocean ridge and hadal trench of the Indian Ocean, the Atlantic Ocean and the Pacific Ocean. ConclusionOur findings demonstrate that deep sea is an important origin of potential pathogenic bacteria and provide the first biosecurity insight into the alien species invasion of deep-sea bacteria into mammal gut microbiota.

Microbiomes respond predictably to built habitats on the seafloor.

The seafloor contains complex ecosystems where habitat heterogeneity influences biodiversity. Natural biological and geological features including vents, seeps and reefs create habitats that select for distinct populations of micro- and macrofauna. While largely studied for macrobiological diversity, built habitats may also select distinct microbiomes. Built habitat density on the seafloor is increasing with ocean sprawl expanding in the continental shelf and slope, potentially having widespread effects on benthic communities. This study addresses one type of built habitat, shipwrecks, on microbiomes in surrounding sediment. Using deep-sea sediment samples (762 total) from the Gulf of Mexico, we report elevated diversity and a predictable core microbiome around nine shipwrecks. We show the sphere of influence of built habitats extends up to 300 m onto the seafloor. Supervised learning made predictions of sample proximity to structures based on frequency of taxa. Strongest predictions occurred in sediments nearest and furthest from sites for archaea and mid-transect for bacteria. The response of archaea to built habitats was consistent across sites, while bacteria showed greater between site variability. The archaeal core shipwreck microbiome was enriched in taxa (e.g., Bathyarchaeia, Lokiarchaeia, Thermoplasmata) not present in the surrounding seafloor. Shipwrecks shaped microbiomes in expected ways, providing insight on how built habitats impact microbiome biodiversity in the Anthropocene.

Alteromonas oceanisediminis sp. nov., isolated from deep-sea sediment.

A Gram-stain-negative, aerobic and rod-shaped bacterium, designated strain SM 2104T, was isolated from a deep-sea sediment sample collected from the Southwest Indian Ocean. Strain SM 2104T grew at 10-37°C (optimum at 25°C), and with 1.0-9.0% (w/v, optimum with 2-4%) NaCl. It hydrolyzed starch, tween 80 and gelatin but did not reduced nitrate to nitrite. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM 2104T was affiliated with the genus Alteromonas, sharing the highest 16S rRNA gene sequence similarities with type strains of Alteromonas flava (97.5%) and Alteromonas facilis (97.4%) and forming a distinct clade together with the two Alteromonas species. The digital DNA-DNA hybridization and average nucleotide identity values between strain SM 2104T and type strains of Alteromonas flava and Alteromonas facilis were below 14.5%, and 71.0%, respectively. The major fatty acids of strain SM 2104T were summed feature 3 (C16:1ω6c/C16:1ω7c), C16:0 and summed feature 8 (C18:1ω7c/C18:1ω6c). The major polar lipids of strain SM 2104T were phosphatidylethanolamine and phosphatidylglycerol and the only respiratory quinone of strain SM 2104T was ubiquinone-8. The genomic DNA G + C content of strain SM 2104T was 48.0%. On the basis of the phylogenetic, phenotypic, chemotaxonomic and genomic analyses presented in this study, strain SM 2104T is considered to represent a novel species within the genus Alteromonas, for which the name Alteromonas oceansediminis sp. nov. is proposed. The type strain is SM 2104T (= CCTCC AB 2021121T = KCTC 82867T).

Secondary metabolites from a deep-sea derived fungal strain of Phomopsis lithocarpus FS508

One new isoindolinone lactam lithocarlactam A (1) and one new triterpene lithocarin D (2), along with nine known natural products (3–11) were isolated from the broth extract of marine fungus Phomopsis lithocarpus FS508, which was isolated from a deep-sea sediment sample. Their structures were elucidated by interpretation of spectroscopic analysis and comparison with previously published literatures for the known compounds. Moreover, compounds 1 and 2 were evaluated for cytotoxic activity against SF-268, MCF-7, HepG-2, and A549 cell lines. However, both of them showed no activity against the tumor cell lines.

Microbial diversity and community structure in deep-sea sediments of South Indian Ocean.

Microbial communities composed of bacteria, archaea and fungi play a pivotal role in driving the biogeochemical cycles in the marine ecosystem. Despite the vastness of the South Indian Ocean, only a few studies reported the simultaneous analysis of bacterial, archaeal and fungal diversity therein, particularly archaeal and fungal communities in deep-sea environments received less attention previously. In this study, microbial diversity, community composition and dynamics in microbial community structure in eight deep-sea sediment samples collected from different sites at varying depths of the South Indian Ocean were explored using Next-Generation Sequencing. In total, 21 bacterial phyla representing 541 OTUs were identified from the eight samples, where phylum Proteobacteria was found as the most abundant bacterial phylum in five out of eight samples. Firmicutes and Chloroflexi were the dominant phyla in the rest of the three samples. In the case of archaea, uncultured species belonging to the phyla Thaumarchaeota and Euryarchaeota were the abundant taxa in all the samples. Similarly, Ascomycota and Basidiomycota were the most abundant fungal phyla present therein. In all the eight samples studied here, about 10-58% and 19-26% OTUs in archaeal and fungal communities were mapped to unclassified taxa respectively, suggesting the lack of representation in databases. Co-occurrence network analysis further revealed that bacterial communities tend to be more dynamic than archaeal and fungal communities. This study provides interesting insights into the microbial diversity, community composition and dynamics in microbial community structure in the deep-sea sediments of the South Indian Ocean.

Diversity and Hydrocarbon-Degrading Potential of Deep-Sea Microbial Community from the Mid-Atlantic Ridge, South of the Azores (North Atlantic Ocean).

Deep-sea sediments (DSS) are one of the largest biotopes on Earth and host a surprisingly diverse microbial community. The harsh conditions of this cold environment lower the rate of natural attenuation, allowing the petroleum pollutants to persist for a long time in deep marine sediments raising problematic environmental concerns. The present work aims to contribute to the study of DSS microbial resources as biotechnological tools for bioremediation of petroleum hydrocarbon polluted environments. Four deep-sea sediment samples were collected in the Mid-Atlantic Ridge, south of the Azores (North Atlantic Ocean). Their autochthonous microbial diversity was investigated by 16S rRNA metabarcoding analysis. In addition, a total of 26 deep-sea bacteria strains with the ability to utilize crude oil as their sole carbon and energy source were isolated from the DSS samples. Eight of them were selected for a novel hydrocarbonoclastic-bacterial consortium and their potential to degrade petroleum hydrocarbons was tested in a bioremediation experiment. Bioaugmentation treatments (with inoculum pre-grown either in sodium acetate or petroleum) showed an increase in degradation of the hydrocarbons comparatively to natural attenuation. Our results provide new insights into deep-ocean oil spill bioremediation by applying DSS hydrocarbon-degrading consortium in lab-scale microcosm to simulate an oil spill in natural seawater.

Characterization of two novel psychrophilic and piezotolerant strains, Shewanella psychropiezotolerans sp. nov. and Shewanella eurypsychrophilus sp. nov, adapted to an extreme deep-sea environment

Three marine bacterial strains designated YLB-06T, YLB-08T and YLB-09 were isolated under high hydrostatic pressure from deep-sea sediment samples collected from the Southwest Indian Ocean. They were Gram-stain-negative, oxidase- and catalase-positive, facultative anaerobic and motile. In addition, the strains were capable of growing at 0–20 °C (optimum 4–10 °C) and 0.1–40 MPa (optimum 0.1 MPa), were psychrophiles and piezotolerant, and could use trimethylamine N-oxide (TMAO), DMSO, elemental sulfur and insoluble Fe (III) as terminal electron acceptors during anaerobic growth. Strain YLB-06T could also use nitrate, and strains YLB-08T and YLB-09 could use nitrite as a terminal electron acceptor. Phylogenetic tree analyses based on 16S rRNA gene sequences and 400 optimized universal marker sequences indicated that the strains belonged to the genus Shewanella. The 16S rRNA gene highest similarity, together with the estimated ANI and DDH values for these strains with their related type strains, were below the respective thresholds for species differentiation. The ANI and DDH values between YLB-08T and YLB-09 were 99.9% and 91.8%, respectively, implying that they should belong to the same genospecies. The YLB-06T genome had duplicated genes, and multiple movement modalities, attachment modalities, biofilm synthesis systems, intercellular interactions and a strong antioxidant system, which were all beneficial for survival in an extreme deep-sea environment. The G + C contents of strains YLB-06T, YLB-08T and YLB-09 were 45.1, 43.5 and 43.6 mol%, respectively. Based on polyphasic taxonomic properties, two novel psychropiezotolerant species are proposed, Shewanella psychropiezotolerans sp. nov. with YLB-06T (=MCCC 1A12715T = KCTC 62907T) and S. eurypsychrophilus sp. nov with YLB-08T (=MCCC 1A12718T = KCTC 62909T) as type strains.

Capture by hybridization for full-length barcode-based eukaryotic and prokaryotic biodiversity inventories of deep sea ecosystems.

Biodiversity inventory of marine systems remains limited due to unbalanced access to the three ocean dimensions. The use of environmental DNA (eDNA) for metabarcoding allows fast and effective biodiversity inventory and is forecast as a future biodiversity research and biomonitoring tool. However, in poorly understood ecosystems, eDNA results remain difficult to interpret due to large gaps in reference databases and PCR bias limiting the detection of some major phyla. Here, we aimed to circumvent these limitations by avoiding PCR and recollecting larger DNA fragments to improve assignment of detected taxa through phylogenetic reconstruction. We applied capture by hybridization (CBH) to enrich DNA from deep-sea sediment samples and compared the results with those obtained through an up-to-date metabarcoding PCR-based approach (MTB). Originally developed for bacterial communities and targeting 16S rDNA, the CBH approach was applied to 18S rDNA to improve the detection of species forming benthic communities of eukaryotes, with a particular focus on metazoans. The results confirmed the possibility of extending CBH to metazoans with two major advantages: (i) CBH revealed a broader spectrum of prokaryotic, eukaryotic, and particularly metazoan diversity, and (ii) CBH allowed much more robust phylogenetic reconstructions of full-length barcodes with up to 1900 base pairs. This is particularly important for taxa whose assignment is hampered by gaps in reference databases. This study provides a database and probes to apply 18S CBH to diverse marine systems, confirming this promising new tool to improve biodiversity assessments in data-poor ecosystems such as those in the deep sea.

Pararhodonellum marinum gen. nov., sp. nov., isolated from deep-sea sediment.

A Gram-stain-negative, non-motile bacterial strain, designated SW124T, was isolated from a deep-sea sediment sample collected from the Indian Ocean. SW124T was aerobic and catalase-positive. The strain grew at 4-40 °C (optimum, 30 °C), at pH 5.0-8.6 (optimum, pH 7.0) and in the presence of 0.5-9.5 % (w/v) NaCl (optimum, 3.0%). The results of comparative analyses of the 16S rRNA gene sequence indicated that SW124T was grouped in the vicinity of the genus Rhodonellum in the family Cyclobacteriaceae. The quinone system contained menaquinone MK-7. The predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). SW124T contained phosphatidylethanolamine (PE) as the major polar lipid. The genomic DNA G+C content of SW124T was 41.7 mol%. On the basis of its phenotypic characteristics and phylogenetic data, we propose that strain SW124T (=CGMCC 1.16171T=KCTC 82235T) represents a novel species of a novel genus, with the name Pararhodonellum marinum gen. nov., sp. nov.

Aurantimonas marina sp. nov., isolated from deep-sea sediment

A novel bacterial strain, designated SW136T, was isolated from a deep-sea sediment sample collected from the South China Sea. Cells were Gram-stain-negative, aerobic, catalase-positive and oxidase-positive. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SW136T represented a novel member of the genus Aurantimonas, forming a distinct cluster with 'Aurantimonas litoralis', Aurantimonas coralicida and Aurantimonas manganoxydans (98.2, 98.1 and 97.9% sequence similarity, respectively). The predominant cellular fatty acid of strain SW136T was C18 : 1 ω7c. Strain SW136T contained ubiquinone-10 as the dominant respiratory quinone, and diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genomic DNA G+C content was 64.3 mol%. The average nucleotide identity and digital DNA-DNA hybridization values of strain SW136T with A. coralicida CGMCC 1.12222T and A. manganoxydans CGMCC 1.12225T were 78.8 and 78.6 % and 21.5 and 25.5 %, respectively. On the basis of phylogenetic inference and phenotypic characteristics, we propose that strain SW136T represents a novel species of the genus Aurantimonas, with the name Aurantimonas marina sp. nov. The type strain is SW136T (=CGMCC 1.17725T=KCTC 82366T).

Miltoncostaea marina gen. nov. sp. nov., and Miltoncostaea oceani sp. nov., a novel deep branching phylogenetic lineage within the class Thermoleophilia isolated from marine environments, and proposal of Miltoncostaeaceae fam. nov. and Miltoncostaeales ord. nov

Two novel marine actinobacteria, designated as SCSIO 60955T and SCSIO 61214T, were isolated from deep-sea sediment samples collected from the South China Sea. The cells of these organisms stained Gram-negative and were rod shaped. These strains were aerobic, and catalase- and oxidase-positive. Optimal growth occurred at 28 °C and pH 7 over 14 days of cultivation. Both strains possessed phospholipids and phosphoglycolipids. The main menaquinone was MK-7. The major fatty acid was C16:0. The peptidoglycan structure was type A1γ′ (meso-Dpm). Analysis of genome sequences revealed that the genome size of SCSIO 60955T was 3.37 Mbp with G + C content of 76.1%, while the genome size of SCSIO 61214T was 3.67 Mbp with a G + C content of 74.8%. The ANI and 16S rRNA gene analysis results showed that the pairwise similarities between the two strains were 73.4% and 97.7% and that with other recognized Thermoleophilia species were less than 69.1% and 87.8%, respectively. Phylogenetic analysis of the 16S rRNA gene sequences showed that strains SCSIO 60955T and SCSIO 61214T were separately clustered together and formed a well-separated phylogenetic branch distinct from their most related neighbor Gaiella occulta. Based on the data presented here, these two strains are proposed to represent two novel species of a novel genus, for which the name Miltoncostaea marina gen. nov., sp. nov., with the type strain SCSIO 60955T (=DSM 110281T =CGMCC 1.18757T), and Miltoncostaea oceani sp. nov., with the type strain SCSIO 61214T (=KCTC 49527T =CGMCC 1.18758T) are proposed. We also propose that these organisms represent a novel family named Miltoncostaeaceae fam. nov. of a novel order Miltoncostaeales ord. nov.

Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding.

Environmental DNA metabarcoding is a powerful tool for studying biodiversity. However, bioinformatic approaches need to adjust to the diversity of taxonomic compartments targeted as well as to each barcode gene specificities. We built and tested a pipeline based on read correction with DADA2 allowing analysing metabarcoding data from prokaryotic (16S) and eukaryotic (18S, COI) life compartments. We implemented the option to cluster amplicon sequence variants (ASVs) into operational taxonomic units (OTUs) with swarm, a network-based clustering algorithm, and the option to curate ASVs/OTUs using LULU. Finally, taxonomic assignment was implemented via the Ribosomal Database Project Bayesian classifier (RDP) and BLAST. We validated this pipeline with ribosomal and mitochondrial markers using metazoan mock communities and 42 deep-sea sediment samples. The results show that ASVs and OTUs describe different levels of biotic diversity, the choice of which depends on the research questions. They underline the advantages and complementarity of clustering and LULU-curation for producing metazoan biodiversity inventories at a level approaching the one obtained using morphological criteria. While clustering removes intraspecific variation, LULU effectively removes spurious clusters, originating from errors or intragenomic variability. Swarm clustering affected alpha and beta diversity differently depending on genetic marker. Specifically, d-values > 1 appeared to be less appropriate with 18S for metazoans. Similarly, increasing LULU's minimum ratio level proved essential to avoid losing species in sample-poor data sets. Comparing BLAST and RDP underlined that accurate assignments of deep-sea species can be obtained with RDP, but highlighted the need for a concerted effort to build comprehensive, ecosystem-specific databases.

Croceimicrobium hydrocarbonivorans gen. nov., sp. nov., a novel marine bacterium isolated from a bacterial consortium that degrades polyethylene terephthalate.

A novel Gram-stain-negative, aerobic, gliding, rod-shaped and carotenoid-pigmented bacterium, designated A20-9T, was isolated from a microbial consortium of polyethylene terephthalate enriched from a deep-sea sediment sample from the Western Pacific. Growth was observed at salinities of 1-8 %, at pH 6.5-8 and at temperatures of 10-40 °C. The results of phylogenetic analyses based on the genome indicated that A20-9T formed a monophyletic branch affiliated to the family Schleiferiaceae, and the 16S rRNA gene sequences exhibited the maximum sequence similarity of 93.8 % with Owenweeksia hongkongensis DSM 17368T, followed by similarities of 90.4, 90.1 and 88.8 % with Phaeocystidibacter luteus MCCC 1F01079T, Vicingus serpentipes DSM 103558T and Salibacter halophilus MCCC 1K02288T, respectively. Its complete genome size was 4 035 598 bp, the genomic DNA G+C content was 43.2 mol%. Whole genome comparisons indicated that A20-9T and O. hongkongensis DSM 17368T shared 67.8 % average nucleotide identity, 62.7 % average amino acid identity value, 46.6% of conserved proteins and 17.8 % digital DNA-DNA hybridization identity. A20-9T contained MK-7 as the major respiratory quinone. Its major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospatidylcholine; and the major fatty acids were iso-C15 : 0 (37.5 %), iso-C16 : 0 3-OH (12.4 %), and summed feature 3 (C16 : 1ω7c /C16 : 1ω6c, 11.6 %). Combining the genotypic and phenotypic data, A20-9T could be distinguished from the members of other genera within the family Schleiferiaceae and represents a novel genus, for which the name Croceimicrobium hydrocarbonivorans gen. nov., sp. nov. is proposed. The type strain is A20-9T (=MCCC 1A17358T =KCTC 72878T).

Sulfurimonas sediminis sp. nov., a novel hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a hydrothermal vent at the Longqi system, southwestern Indian ocean.

A novel marine hydrogen- and sulfur-oxidizing bacterium, designated strain S2-6T, was isolated from the deep-sea sediment samples at the Longqi hydrothermal system, southwestern Indian Ocean. Cells were Gram-stain-negative, motile, short rods with a single polar flagellum. Growth was observed at 10-45°C (optimum 33°C), pH 5.0-8.0 (optimum pH 7.0) and 1.5 to 6.0% (w/v) NaCl with an optimum at 3.0% (w/v). The isolate was an obligate chemolithoautotroph capable of growth using thiosulfate, tetrathionate, elemental sulfur or sodium sulfide as the energy source, and oxygen or nitrate as the sole electron acceptor. When hydrogen was used as the energy source, strain S2-6T could respire oxygen, nitrate or element sulfur. The major cellular fatty acids of strain S2-6T were summed feature 3 (C16:1ω7c and/or C16:1ω6c), C16:0 and summed feature 8 (C18:1ω7c and/or C18:1ω6c). The total size of its genome was 2,320,257bp and the genomic DNA G + C content was 37.3mol%. Phylogenetic analysis based on 16S rRNA gene sequences and core genes showed that the novel isolate belonged to the genus Sulfurimonas and was most closely related to Sulfurimonas paralvinellae GO25T (96.8% sequence identity) and Sulfurimonas autotrophica OK10T (95.8% sequence identity). The average nucleotide identity and DNA-DNA hybridization values between strain S2-6T and S. paralvinellae GO25T and S. autotrophica OK10T were 74.6%-81.2% and 19.1%-24.6%, respectively. Based on the polyphase taxonomical data, strain S2-6T represents a novel species of the genus Sulfurimonas, for which the name Sulfurimonas sediminis sp. nov. is proposed, with the type strain S2-6T (= MCCC 1A14513T = KCTC 15854T).

Classification of a Complexly Mixed Magnetic Mineral Assemblage in Pacific Ocean Surface Sediment by Electron Microscopy and Supervised Magnetic Unmixing

Unambiguous magnetic mineral identification in sediments is a prerequisite for reconstructing paleomagnetic and paleoenvironmental information from environmental magnetic parameters. We studied a deep-sea surface sediment sample from the Clarion Fracture Zone region, central Pacific Ocean, by combining magnetic measurements and scanning and transmission electron microscopic analyses. Eight titanomagnetite and magnetite particle types are recognized based on comprehensive documentation of crystal morphology, size, spatial arrangements, and compositions, which are indicative of their corresponding origins. Type-1 particles are detrital titanomagnetites with micron- and submicron sizes and irregular and angular shapes. Type-2 and -3 particles are well-defined octahedral titanomagnetites with submicron and nanometer sizes, respectively, which are likely related to local hydrothermal and volcanic activity. Type-4 particles are nanometer-sized titanomagnetites hosted within silicates, while type-5 particles are typical dendrite-like titanomagnetites that likely resulted from exsolution within host silicates. Type-6 particles are single domain magnetite magnetofossils related to local magnetotactic bacterial activity. Type-7 particles are superparamagnetic magnetite aggregates, while Type-8 particles are defect-rich single crystals composed of many small regions. Electron microscopy and supervised magnetic unmixing reveal that type-1 to -5 titanomagnetite and magnetite particles are the dominant magnetic minerals. In contrast, the magnetic contribution of magnetite magnetofossils appears to be small. Our work demonstrates that incorporating electron microscopic data removes much of the ambiguity associated with magnetic mineralogical interpretations in traditional rock magnetic measurements.

Rubrobacter tropicus sp. nov. and Rubrobacter marinus sp. nov., isolated from deep-sea sediment of the South China Sea.

Two novel Gram-stain-positive bacteria, designated as SCSIO 52909T and SCSIO 52915T, were isolated from a deep-sea sediment sample collected at about 3448 m water depth of the South China Sea. Phenotypic, chemotaxonomic and genomic characteristics were investigated. These strains were aerobic and tested positive for catalase activity, oxidase activity and nitrate reduction. Optimal growth occurred at 28 °C, pH 7 and 3% salinity over 14 days cultivation. Its peptidoglycan structure was type A3α (l-Lys-l-Ala) and the only menaquinone was MK-8. Both strains possessed diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid, an unidentified glycolipid and an unidentified phospholipid. Their major fatty acids differed, but both contained iso-branched components of C16 : 0 12-methyl. Genome sequencing revealed two large genomes of 4.58 Mbp with G+C content of 67.0 mol% in SCSIO 52909T and of 4.42 Mbp with G+C content of 69.1 % in SCSIO 52915T. The two novel strains encoded genes for metabolism that are absent in most other Rubrobacter species, and possessed many more gene copy numbers of alkaline phosphatase and thioredoxin reductase. Results of gANI and 16S rRNA gene analyses suggested that the two strains represent two new species, with 74.9, 95.0 % pairwise similarity between each other, and less than 74.3 and 93.5 % to other recognized Rubrobacter species, respectively. In the phylogenetic analysis, strains SCSIO 52909T and SCSIO 52915T were separately clustered together and formed a well-separated phylogenetic branch distinct from the other known species in the genus Rubrobacter. Based on the data presented here, these two strains should be recognized as two new species in the genus Rubrobacter, for which the names Rubrobacter tropicus sp. nov., with the type strain SCSIO 52909T (=KCTC 49412T=CGMCC 1.13853T), and Rubrobacter marinus sp. nov., with the type strain SCSIO 52915T (=KCTC 49411T=CGMCC 1.13852T), are proposed.