Deep-sea Water Column Research Articles

Vertical distribution of microplastic along the main gate of Indonesian Throughflow pathways

Even though Pacific – Indian Ocean exchange [Indonesian Throughflow (ITF)] has been measured for the last three decades, the measurements of microplastic in the region is very limited. This study was the initial investigation of the vertical distribution of microplastic in the deep-sea areas across the ITF Pathway. Niskin water samples were utilized to obtain the samples from a water column in a range of 5 to 2450 m. A total of 924 microplastic particles with an average abundance of 1.062 ± 0.646. n/L were found in the water column. Our findings indicate that water temperature and water density are the most significant factors correlated to the microplastic concentration. This study will be the first report discussing the distribution of microplastics in the deep-sea water column that could be highly significant in determining the fate and transport of microplastic within Indonesian waters that exits into the Indian Ocean.

Comparative Genomic Analysis of Labrenzia aggregata (Alphaproteobacteria) Strains Isolated From the Mariana Trench: Insights Into the Metabolic Potentials and Biogeochemical Functions.

Hadal zones are marine environments deeper than 6,000 m, most of which comprise oceanic trenches. Microbes thriving at such depth experience high hydrostatic pressure and low temperature. The genomic potentials of these microbes to such extreme environments are largely unknown. Here, we compare five complete genomes of bacterial strains belonging to Labrenzia aggregata (Alphaproteobacteria), including four from the Mariana Trench at depths up to 9,600 m and one reference from surface seawater of the East China Sea, to uncover the genomic potentials of this species. Genomic investigation suggests all the five strains of L. aggregata as participants in nitrogen and sulfur cycles, including denitrification, dissimilatory nitrate reduction to ammonium (DNRA), thiosulfate oxidation, and dimethylsulfoniopropionate (DMSP) biosynthesis and degradation. Further comparisons show that, among the five strains, 85% gene functions are similar with 96.7% of them encoded on the chromosomes, whereas the numbers of functional specific genes related to osmoregulation, antibiotic resistance, viral infection, and secondary metabolite biosynthesis are majorly contributed by the differential plasmids. A following analysis suggests the plasmidic gene numbers increase along with isolation depth and most plasmids are dissimilar among the five strains. These findings provide a better understanding of genomic potentials in the same species throughout a deep-sea water column and address the importance of externally originated plasmidic genes putatively shaped by deep-sea environment.

Bacterial and archaeal communities in deep sea waters near the Ninetyeast Ridge in Indian Ocean

Depth-dependent distribution patterns of bacterial and archaeal communities in deep sea water column around the Ninetyeast Ridge in the Indian Ocean were investigated using 16S rRNA gene profiling. Sampling was conducted at the northern Ninetyeast Ridge (1°59.89′N–9°59.70′S, 87°58.90′E–88°00.03′E) from September to November 2016 where samples were collected from the bathyal (1 000 m) to bathypelagic depths (>4 000 m) in four different stations. A total of 1 565 405 clean data falling into 6 712 bacterial OTUs and 1 452 727 clean data falling into 806 archaeal OTUs based on 97% similarity level were analyzed. Most of the bacterial 16S rRNA gene sequences were affiliated with Gammaproteobacteria, followed by Alphaproteobacteria and Bacteroidia. The archaeal 16S rRNA gene sequences mostly affiliated to Nitrososphaeria (Thaumarchaeota) dominated with relative abundances ranging from 52.68% to 97.2%, followed by Thermoplasmata (Euryarchaeota). Vertical partitioning of bacterial and archaeal communities among different water layers was observed. Canonical correspondence analysis (CCA) and Spearman’s correlations revealed that depth (P=0.003), dissolved oxygen (P=0.019), and nitrite (P=0.033) were the main environmental factors affecting bacterial community structure at genus level in the Ninetyeast Ridge. On the other hand, the first two CCA axes accounted for 74.4% of the explained total variance, it seems that the archaeal communities at genus level were heavily influenced by the environmental variables including depth, dissolved oxygen (DO), nitrite, salinity, phosphate, ammonia, nitrate, and silicate, but none of them exhibited any significant correlation on the structuring (P>0.1).

Genomic, physiologic, and proteomic insights into metabolic versatility in Roseobacter clade bacteria isolated from deep-sea water.

Roseobacter clade bacteria are ubiquitous in marine environments and now thought to be significant contributors to carbon and sulfur cycling. However, only a few strains of roseobacters have been isolated from the deep-sea water column and have not been thoroughly investigated. Here, we present the complete genomes of phylogentically closed related Thiobacimonas profunda JLT2016 and Pelagibaca abyssi JLT2014 isolated from deep-sea water of the Southeastern Pacific. The genome sequences showed that the two deep-sea roseobacters carry genes for versatile metabolisms with functional capabilities such as ribulose bisphosphate carboxylase-mediated carbon fixation and inorganic sulfur oxidation. Physiological and biochemical analysis showed that T. profunda JLT2016 was capable of autotrophy, heterotrophy, and mixotrophy accompanied by the production of exopolysaccharide. Heterotrophic carbon fixation via anaplerotic reactions contributed minimally to bacterial biomass. Comparative proteomics experiments showed a significantly up-regulated carbon fixation and inorganic sulfur oxidation associated proteins under chemolithotrophic conditions compared to heterotrophic conditions. Collectively, rosebacters show a high metabolic flexibility, suggesting a considerable capacity for adaptation to the marine environment.

Beyond the vent: New perspectives on hydrothermal plumes and pelagic biology

Submarine hydrothermal vent fields introduce buoyant plumes of chemically altered seawater to the deep-sea water column. Chemoautotrophic microbes exploit this energy source, facilitating seafloor-based primary production that evidence suggests may transfer to pelagic consumers. While most hydrothermal plumes have relatively small volumes, there are recent examples of large-scale plume events associated with periods of eruptive activity, which have had a pronounced effect on water-column biology. This correlation suggests that hydrothermal plumes may have influenced basin-scale ocean chemistry during periods of increased submarine volcanism during the Phanerozoic eon. This paper synthesizes a growing body of scientific evidence supporting the hypothesis that hydrothermal plumes are the energetic basis of unique deep-sea pelagic food webs. While many important questions remain concerning the biology of hydrothermal plumes, this discussion is not present in ongoing management efforts related to seafloor massive sulfide (SMS) mining. Increased research efforts, focused on high-resolution surveys of midwater biology relative to plume structures, are recommended to establish baseline conditions and monitor the impact of future mining-based disturbances to the pelagic biosphere.

The diversity of PAH-degrading bacteria in a deep-sea water column above the Southwest Indian Ridge.

The bacteria involved in organic pollutant degradation in pelagic deep-sea environments are largely unknown. In this report, the diversity of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria was analyzed in deep-sea water on the Southwest Indian Ridge (SWIR). After enrichment with a PAH mixture (phenanthrene, anthracene, fluoranthene, and pyrene), nine bacterial consortia were obtained from depths of 3946–4746 m. While the consortia degraded all four PAHs when supplied in a mixture, when PAHs were tested individually, only phenanthrene supported growth. Thus, degradation of the PAH mixture reflected a cometabolism of anthracene, fluoranthene, and pyrene with phenanthrene. Further, both culture-dependent and independent methods revealed many new bacteria involved in PAH degradation. Specifically, the alpha and gamma subclasses of Proteobacteria were confirmed as the major groups within the communities. Additionally, Actinobacteria, the CFB group and Firmicutes were detected. Denaturing Gradient Gel Electrophoresis (DGGE) analysis showed that bacteria closely affiliated with Alcanivorax, Novosphingobium, and Rhodovulum occurred most frequently in different PAH-degrading consortia. By using general heterotrophic media, 51 bacteria were isolated from the consortia and of these 34 grew with the PAH mixture as a sole carbon source. Of these, isolates most closely related to Alterierythrobacter, Citricella, Erythrobacter, Idiomarina, Lutibacterium, Maricaulis, Marinobacter, Martelella, Pseudidiomarina, Rhodobacter, Roseovarius, Salipiger, Sphingopyxis, and Stappia were found to be PAH degraders. To the best of our knowledge, this is the first time these bacteria have been identified in this context. In summary, this report revealed significant diversity among the PAH-degrading bacteria in the deep-sea water column. These bacteria may play a role in PAH removal in deep-sea environments.

Induction of apoptosis and cell cycle arrest by Bis (2-ethylhexyl) phthalate produced by marine Bacillus pumilus MB 40

Marine microorganisms represent a potential source for the production of biomedically useful compounds active against inflammation, cancer, diabetes, etc. Marine Bacillus pumilus MB 40 (GenBank accession no. HQ705771) isolated from deep sea water column (1000m depth) near Andaman and Nicobar islands produced a bioactive lead, Bis (2-ethylhexyl) phthalate (BEHP) with a molecular formula of C6H4(CO2C8H17)2 and a molecular ion at m/z 391 (M+). Anti proliferative effect of the isolated compound was examined by MTT assay in human erythroleukemic K562 cells and the IC50 of BEHP was found to be 21μM. BEHP was able to induce apoptosis involving caspases pathway, besides regulating mitochondrial enzymes. Further, western blot analysis revealed the activation of caspases family proteins viz., caspase 8, caspase-9 and caspase-3. An increase in the expression of Bax mRNA concomitant with a decrease in mRNA of Bcl-2 in BEHP treated K562 cells was also observed. AO/EB staining of BEHP treated K562 cells further confirmed the progression of apoptosis as evidenced by morphological changes including nuclear condensation, cell shrinkage, and formation of apoptotic bodies. Treatment of K562 cells with BEHP induced the progressive accumulation of fragmented DNA in a time dependent manner. This pattern appeared as a typical laddering distribution of DNA fragmentation due to intranucleosomal cleavage associated with apoptosis. Based on flow cytometric analysis it has become evident that the compound was also effective in arresting the cell cycle at a sub G0/G1 phase.

Microbial ammonia oxidation and enhanced nitrogen cycling in the Endeavour hydrothermal plume

Ammonium was injected from the subseafloor hydrothermal system at the Endeavour Segment, Juan de Fuca Ridge, into the deep-sea water column resulting in an NH 4 + -rich (⩽177 nM) neutrally buoyant hydrothermal plume. This NH 4 + was quickly removed by both autotrophic ammonia oxidation and assimilation. The former accounted for at least 93% of total net NH 4 + removal, with its maximum rate in the neutrally buoyant plume (⩽53 nM d −1) up to 10-fold that in background deep water. Ammonia oxidation in this plume potentially added 26–130 mg NO 3 - m - 2 d - 1 into the deep-sea water column. This oxidation process was heavily influenced by the presence of organic-rich particles, with which ammonia-oxidizing bacteria (AOB) were often associated (40–68%). AOB contributed up to 10.8% of the total microbial communities within the plume, and might constitute a novel lineage of β-proteobacterial AOB based on 16S rRNA and amoA phylogenetic analyses. Meanwhile, NH 4 + assimilation rates were also substantially enhanced within the neutrally buoyant plume (⩽26.4 nM d −1) and accounted for at least 47% of total net NH 4 + removal rates. The combined NH 4 + oxidation and assimilation rates always exceeded total net removal rates, suggesting active in situ NH 4 + regeneration rates of at least an order of magnitude greater than the particulate nitrogen flux from the euphotic zone. Ammonia oxidation is responsible for NH 4 + turnover of 0.7–13 days and is probably the predominant in situ organic carbon production process (0.6–13 mg C m −2 d −1) at early stages of Endeavour neutrally buoyant plumes.

Autotrophic ammonia oxidation in a deep-sea hydrothermal plume

Direct evidence for autotrophic ammonia oxidation is documented for the first time in a deep-sea hydrothermal plume. Elevated NH 4 + concentrations of up to 341±136 nM were recorded in the plume core at Main Endeavour Field, Juan de Fuca Ridge. This fueled autotrophic ammonia oxidation rates as high as 91 nM day −1, or 92% of the total net NH 4 + removal. High abundance of ammonia-oxidizing bacteria was detected using fluorescence in situ hybridization. Ammonia-oxidizing bacteria within the plume core (1.0–1.4×10 4 cells ml −1) accounted for 7.0–7.5% of the total microbial community, and were at least as abundant as methanotrophs. Ammonia-oxidizing bacteria were a substantial component of the particle-associated communities (up to 51%), with a predominance of the r-strategist Nitrosomonas-like cells. In situ chemolithoautotrophic organic carbon production via ammonia oxidation may yield 3.9–18 mg C m −2 day −1 within the plume directly over Main Endeavour Field. This rate was comparable to that determined for methane oxidation in a previous study, or at least four-fold greater than the flux of photosynthetic carbon reaching plume depths measured in another study. Hence, autotrophic ammonia oxidation in the neutrally buoyant hydrothermal plume is significant to both carbon and nitrogen cycling in the deep-sea water column at Endeavour, and represents another important link between seafloor hydrothermal systems and deep-sea biogeochemistry.

Nature of organic matter in rivers with deep sea connections: The Ganges-Brahmaputra and Indus

Tropical seas receive the bulk of the annual water and sediment discharged from the land to the sea via rivers. A significant part of it comes from the major Asian rivers with direct connections to the deep sea. Within the framework of the ongoing SCOPE/UNEP World River Programme we have examined the detailed nature and seasonal variability of organic matter in the Ganges, Brahmaputra and Indus rivers. Our results show that tropical seas, such as the Bay of Bengal and the Arabian Sea, receive large quantities of land-derived organic matter, both in the dissolved and the particulate phases, which has already undergone significant biogeochemical alteration on land. The relative stability and low nutritive value of this material enable its accumulation in the deep sea water column and sediments.