A full-ocean-depth rated modular lander and pressure-retaining sampler capable of collecting hadal-endemic microbes under in situ conditions

Peoples, Logan M.; Norenberg, Matthew; Price, David H.; McGoldrick, Madeline; Novotny, M. A.; Bochdansky, Alexander B.; Bartlett, Douglas H.

doi:10.1016/j.dsr.2018.11.010

Cited by 48 publications

(27 citation statements)

References 66 publications

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“…3c and S4c), which may be explained by lower nutrient availability in abyssal than hadal sites. Overall, these trends were consistent with previous studies [4,52,55,56], supporting more vigorous microbial activity in hadal trench bottom sediments, especially in the subsurface under 5 cmbsf.…”

Section: Microbial Abundancessupporting

confidence: 92%

“…The Flavobacterial OTUs abundant in station JC showed low similarity (88.0-91.4%) against Flavobacteriaceae sp. PRS1, whose genome was reconstructed from the Maria Trench water sample via single cell technique [56]. Because members of Flavobacteriia were reported to be abundant in eutrophic oceans [70], our results likely reflect eutrophic productivity in the Japan Trench.…”

Section: Taxonomic Composition Of Microbial Communities In Sediment Smentioning

confidence: 89%

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Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments

Hiraoka

Hirai

Matsui

et al. 2019

ISME J

115

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Hadal trench bottom (>6000 m below sea level) sediments harbor higher microbial cell abundance compared with adjacent abyssal plain sediments. This is supported by the accumulation of sedimentary organic matter (OM), facilitated by trench topography. However, the distribution of benthic microbes in different trench systems has not been well explored yet. Here, we carried out small subunit ribosomal RNA gene tag sequencing for 92 sediment subsamples of seven abyssal and seven hadal sediment cores collected from three trench regions in the northwest Pacific Ocean: the Japan, Izu-Ogasawara, and Mariana Trenches. Tag-sequencing analyses showed specific distribution patterns of several phyla associated with oxygen and nitrate. The community structure was distinct between abyssal and hadal sediments, following geographic locations and factors represented by sediment depth. Co-occurrence network revealed six potential prokaryotic consortia that covaried across regions. Our results further support that the OM cycle is driven by hadal currents and/or rapid burial shapes microbial community structures at trench bottom sites, in addition to vertical deposition from the surface ocean. Our trans-trench analysis highlights intra-and inter-trench distributions of microbial assemblages and geochemistry in surface seafloor sediments, providing novel insights into ultradeep-sea microbial ecology, one of the last frontiers on our planet.

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Section: Microbial Abundancessupporting

confidence: 92%

Section: Taxonomic Composition Of Microbial Communities In Sediment Smentioning

confidence: 89%

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments

Hiraoka

Hirai

Matsui

et al. 2019

ISME J

115

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“…Horizontal gene transfer (HGT) can provide genetic material that enhances fitness in new environments. An experimental demonstration of this impact is the introduction of a DNA photolyase gene, missing in piezophilic Colwellia and other deep-sea species [31,61,67,110], into the piezophile Photobacterium profundum SS9 to generate a UV resistant phenotype [70]. It is striking that many of the Colwellia genes most similar to those in other piezophiles appear in clusters within variable regions that include genomic islands, putative phage genes, transposases, and toxin-antitoxin systems.…”

Section: Discussionmentioning

confidence: 99%

Distinctive gene and protein characteristics of extremely piezophilic Colwellia

et al. 2020

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Background The deep ocean is characterized by low temperatures, high hydrostatic pressures, and low concentrations of organic matter. While these conditions likely select for distinct genomic characteristics within prokaryotes, the attributes facilitating adaptation to the deep ocean are relatively unexplored. In this study, we compared the genomes of seven strains within the genus Colwellia, including some of the most piezophilic microbes known, to identify genomic features that enable life in the deep sea. Results Significant differences were found to exist between piezophilic and non-piezophilic strains of Colwellia. Piezophilic Colwellia have a more basic and hydrophobic proteome. The piezophilic abyssal and hadal isolates have more genes involved in replication/recombination/repair, cell wall/membrane biogenesis, and cell motility. The characteristics of respiration, pilus generation, and membrane fluidity adjustment vary between the strains, with operons for a nuo dehydrogenase and a tad pilus only present in the piezophiles. In contrast, the piezosensitive members are unique in having the capacity for dissimilatory nitrite and TMAO reduction. A number of genes exist only within deep-sea adapted species, such as those encoding d-alanine-d-alanine ligase for peptidoglycan formation, alanine dehydrogenase for NADH/NAD+ homeostasis, and a SAM methyltransferase for tRNA modification. Many of these piezophile-specific genes are in variable regions of the genome near genomic islands, transposases, and toxin-antitoxin systems. Conclusions We identified a number of adaptations that may facilitate deep-sea radiation in members of the genus Colwellia, as well as in other piezophilic bacteria. An enrichment in more basic and hydrophobic amino acids could help piezophiles stabilize and limit water intrusion into proteins as a result of high pressure. Variations in genes associated with the membrane, including those involved in unsaturated fatty acid production and respiration, indicate that membrane-based adaptations are critical for coping with high pressure. The presence of many piezophile-specific genes near genomic islands highlights that adaptation to the deep ocean may be facilitated by horizontal gene transfer through transposases or other mobile elements. Some of these genes are amenable to further study in genetically tractable piezophilic and piezotolerant deep-sea microorganisms.

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“…In the deepest parts of the ocean, pressures can reach 110 MPa, and access to these environments is limited to only a few ROVs and landers. Recently, Bartlett and colleagues developed a modular lander capable of sampling these hadal trenches at depths greater than 6000 m (Peoples et al, 2019). While spatially limited, these regions nonetheless represent 45% of the depth range of the ocean (Jamieson, 2015).…”

Section: What Are the Limits?mentioning

confidence: 99%

Exploring the Deep Marine Biosphere: Challenges, Innovations, and Opportunities

2019

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The deep marine biosphere is one of the largest, and yet least explored, microbial habitats on the planet. Quantifying the extent, diversity, and activity of subsurface microbial communities is a crucial part of understanding their role in global biogeochemical cycles. Even though deep biosphere habitats can vary widely in chemistry, temperature, turnover rates, and energy sources, all subsurface microbes inherently experience high pressures. While not all subsurface microbes require elevated pressures, for many high pressures are essential to their cellular function and metabolism. Thus, when targeting this elusive portion of the biosphere, it is critical to maintain in situ pressure while sampling and cultivating subsurface microorganisms. In this perspective paper we highlight the sampling and cultivation technologies available to study these communities under in situ conditions. Maintaining elevated pressures throughout sampling, transfer, cultivation, and isolation is challenging, and more often than not samples are decompressed at some point during sample handling, potentially leading to biases in both community diversity and isolate physiology. The development of devices that maintain in situ pressures during sampling and allow for sample transfer without decompression have begun to address this challenge (like the PUSH-Pressurized Underwater Sample Handler). Such vessels can be used for both retrieval and enrichment of deep subsurface samples, as well as high-pressure growth and physiology experiments, thus expanding possibilities for deep biosphere exploration. Finally, we discuss the significant need to develop and share high-pressure facilities across the deep biosphere community, in order to expand the opportunities to discover novel piezophiles from the deep subsurface.

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A full-ocean-depth rated modular lander and pressure-retaining sampler capable of collecting hadal-endemic microbes under in situ conditions

Cited by 48 publications

References 66 publications

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments

Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments

Distinctive gene and protein characteristics of extremely piezophilic Colwellia

Exploring the Deep Marine Biosphere: Challenges, Innovations, and Opportunities

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