Microbiomes of hadal fishes contain similar taxa, obligate symbionts, and known piezophiles across trench habitats

Hadal snailfishes are the deepest-living fishes in the ocean, inhabiting trenches from depths of ~6,000 to 8,000 m. While the microbial communities in trench environments have begun to be characterized, the microbes associated with hadal megafauna remain relatively unknown. Here, we describe the gut microbiomes of two hadal snailfishes, Pseudoliparis swirei (Mariana Trench) and Notoliparis kermadecensis (Kermadec Trench) using 16S rRNA gene amplicon sequencing. We contextualize these microbiomes with comparisons to the abyssal macrourid Coryphaenoides yaquinae and the continental shelf-dwelling snailfish Careproctus melanurus. The microbial communities of the hadal snailfishes were distinct from their shallower counterparts and were dominated by the same sequences related to the Mycoplasmataceae and Desulfovibrionaceae. These shared taxa indicate that symbiont lineages may have remained similar to the ancestral symbiont since their geographic separation or that they are dispersed between geographically distant trenches and subsequently colonize specific hosts. The abyssal and hadal fishes contained sequences related to known, cultured piezophiles, microbes that grow optimally under high hydrostatic pressure, including Psychromonas, Moritella, and Shewanella. These taxa are adept at colonizing nutrient-rich environments present in the deep ocean, such as on particles and in the guts of hosts, and we hypothesize they could make a dietary contribution to deep-sea fishes by degrading chitin and producing fatty acids. We characterize the gut microbiota within some of the deepest fishes to provide new insight into the diversity and distribution of host-associated microbial taxa and the potential of these animals, and the microbes they harbor, for understanding adaptation to deep-sea habitats.

Environmental factors shape the culturable bacterial diversity in deep-sea water and surface sediments from the Mariana Trench

Hailed as "The Fourth Pole", the Mariana Trench is the deepest part of the ocean. The microbial diversity in it is extremely complicated, which might be caused by the unique environmental factors such as high salinity, low temperature, high hydrostatic pressure, and limited nutrition. Based on 4 seawater samples and 4 sediment samples obtained from the Mariana Trench, we isolated and fostered the microorganism clones with kinds of culture mediums and high-throughput culturing. By using the molecular identification methods based on PCR of 16S rDNA and ITS gene, 1266 bacterial strains in total were isolated and identified, which affiliated to 7 classes, 16 orders, 25 families and 36 genera in four phyla：Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Strains in genera Halomonas, Pseudoaltermonas were the dominant bacteria isolated from the samples. With Mantel tests on the sample-environmental parameter matrix, the sample-environmental organic matter diversity matrix and the sample-microbial diversity matrix, we concluded that the environmental parameters and the organic matters in the condition can shape the culturable bacterial diversity in deep-sea water and surface sediments from the Mariana Trench.

Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench

The Mariana Trench harbors a substantial number of infective viral particles. However, very little is known about the identity, survival strategy, and potential functions of viruses in the trench sediments.

The Capability of Utilizing Abiotic Enantiomers of Amino Acids by Halomonas sp. LMO_D1 Derived From the Mariana Trench

D-amino acids (D-AAs) have been produced both in organisms and in environments via biotic or abiotic processes. However, the existence of these organic materials and associated microbial degradation activity has not been previously investigated in subduction zones where tectonic activities result in the release of hydrothermal organic matter. Here, we isolated the bacterium Halomonas sp. LMO_D1 from a sample obtained from the Mariana trench, and we determined that this isolate utilized 13 different D-AAs (D-Ala, D-Glu, D-Asp, D-Ser, D-Leu, D-Val, D-Tyr, D-Gln, D-Asn, D-Pro, D-Arg, D-Phe, and D-Ile) in the laboratory and could grow on D-AAs under high hydrostatic pressure (HHP). Moreover, the metabolism of L-AAs was more severely impaired under HHP conditions compared with that of their enantiomers. The essential function gene (Chr_2344) required for D-AA catabolism in strain LMO_D1 was identified and confirmed according to the fosmid library method used on the D-AAs plate. The encoded enzyme of this gene (DAADH_2344) was identified as D-amino acid dehydrogenase (DAADH), and this gene product supports the catabolism of a broad range of D-AAs. The ubiquitous distribution of DAADHs within the Mariana Trench sediments suggests that microorganisms that utilize D-AAs are common within these sediments. Our findings provide novel insights into the microbial potential for utilizing abiotic enantiomers of amino acids within the subduction zone of the Mariana trench under HHP, and our results provide an instructive significance for understanding these abiotic enantiomers and allow for insights regarding how organisms within extraterrestrial HHP environments can potentially cope with toxic D-AAs.

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.

Development of a Hadal Microbial In Situ Multi-Stage Filtering and Preserving Device

The unique environment of the hadal zone has created material circulation patterns and biological gene characteristics. Microbes play an irreplaceable role in the ocean ecological environment and material circulation due to their pervasiveness, abundance, and metabolic diversity. In this paper, we designed and developed a microbial sampling device that can be used in a depth of 10,000 m, with its working parts suitable for the full-sea depth. The multi-stage membrane realized the in situ multi-stage filtrations. The samples were in situ fixedly preserved by RNAlater storage solution. At the same time, we modeled and calculated the multi-stage membrane separation and filtration process, simulated the interception phenomenon of particles with different sizes passing through the multi-stage membrane area, and explored the influence of varying inlet velocities. A multi-stage membrane separation and filtration test system was built. The operational characteristics of different filters were compared and analyzed, and the appropriate filter material was selected according to the flow capacity and physical properties. A 100 MPa high-pressure test was carried out to check the device’s performance under a high-pressure environment. The sampler prototype was constructed and tested in the Mariana Trench. The results indicated that the device could work at the deepest point of the Mariana trench.

Complete Genome Sequence of a Halophilic Bacterium, Halomonas sp. Strain NyZ770, from Mariana Trench Sediment

Halomonas sp. strain NyZ770 is a bacterium that was isolated from Mariana Trench sediment. Here, the complete genome sequence of this strain is reported. The genome was sequenced with the Illumina NovaSeq and Pacific Biosciences Sequel sequencing platforms and consists of a single chromosome of 4,024,853 bp, with a G+C content of 60.21%.

Effects of Mismanagement of Medical and Plastic Waste in Pre and During COVID-19 Outbreak

Many countries already have problems with waste management, but when the COVID-19 outbreak happens, the existing problems are worsened. This review aims to examine how mismanagement of medical and plastic waste affects the environment and people, especially those who work in healthcare facilities. Prior to the COVID-19 pandemic, it was clear that the majority of issues stemmed from mismanagement of plastic waste. For example, plastic waste can be seen in various places, such as the deepest oceanic floor, The Mariana trench, which is proved by microplastics found in amphipods’ digestive tract living down there. Apart from environmental effects, the economy is also affected by plastic pollution as the tourism business has decreased in Korea and USA due to the increasing amount of plastic waste. While normal plastic waste can largely affect society, medical wastes seem to pose more severe consequences as medical wastes might be contaminated, pathologic, and radioactive. However, during the pandemic, the usage of both medical and plastic waste has increased in general. Mismanaged waste also carries COVID-19 like other pathogens, and the virus can survive on it for a long period of time, making any mismanaged waste a risk factor. Incinerated ashes from medical waste used for fighting the virus can also cause pollution as they contain heavy metals. In conclusion, mismanaged plastic waste mostly affects the environment, while mismanaged medical waste might carry harmful pathogens, including the COVID-19, putting people at risk. More actions need to be done to improve the effectiveness of waste management procedures.