Biology subjects

Bartlett, D. H.

Publications and source records attributed to Bartlett, D. H..

8 recordsLinked to original sources

bioRxiv2026

Seafloor topography structures subseafloor microbial communities in the Puerto Rico Trench

The influence of seafloor topography on subseafloor microbial communities is poorly understood. In this study, we systematically sampled subseafloor sedimentary microbial communities and pore-water geochemistry at bathyal, abyssal, and hadal water depths of the Puerto Rico Trench. The Puerto Rico Trench exhibits vertical relief of over 8 km with seafloor topography shaped by active plate tectonics and characterized by a very steep southern wall and active mass wasting. Sampling across these features, we find that subseafloor microbial communities are influenced by topography in the following two ways. First, subseafloor sediment in the deepest part of the trench is anoxic, enriched in organic matter due to mass transport of sediment from shallower water depths, and contains an anaerobic subseafloor community that is quite distinct from the anaerobic subseafloor community in anoxic sediment at bathyal depths. The difference between these bathyal and hadal subseafloor anaerobic communities is consistent with influence of water-depth-related physical properties on subseafloor community composition. Second, subseafloor sediment remains oxygenated for meters below seafloor on steep slopes within the bathyal zone, an abyssal topographic high within the trench, and the abyssal plain seaward of the trench subseafloor, likely due to limited sediment accumulation, which selects for the presence of aerobic microbial communities. The difference between these bathyal and abyssal aerobic subseafloor communities and the anaerobic communities at bathyal and hadal depths reflects the role of seafloor topography in structuring subseafloor availability of redox reactants, which in turn drives the activities and composition of subseafloor microbial communities.

microbiology↗

bioRxiv2026

Piezophilic activity dominates the Puerto Rico Trench deep subseafloor biosphere

Hydrostatic pressure is a defining feature of the deep ocean, yet how it structures microbial activity across the subseafloor biosphere is poorly understood. Here, we assess pressure effects on anabolic activity in seafloor and subseafloor communities across a margin-to-hadal-to-abyssal transect of the Puerto Rico Trench region (493-8,385 m water depth). Community-level responses to pressure reverse with burial, revealing a previously unrecognized shift toward piezophily in resident subseafloor communities down to 20 meters below seafloor (mbsf). In pressure-incubation experiments, atmospheric pressure yielded higher proportions of active cells in surficial sediments, whereas in situ pressure yielded higher proportions in the subseafloor. Pressure also structured active-community composition; in trench-axis sediments extending to 8.35 mbsf, JS1/Atribacterota populations belonging to geographically widespread hadal lineages exhibited a physiological response to in situ pressure, indicative of subseafloor piezophily. These findings suggest that hydrostatic pressure acts as an ecological filter after burial, favoring piezophilic traits that may support microbial persistence in the deep subseafloor biosphere.

microbiology↗

bioRxiv2026

Anaerobic methane oxidation by ANME-2a at two molar chloride in Orca Basin

Anaerobic methane oxidation, typically mediated by consortia of archaea and bacteria, is a key process in the global methane cycle, but little is known about its upper salinity limits. We characterized the microbial methane cycle in the anoxic, hypersaline Orca Basin using metagenomics, metatranscriptomics, fluorescence in situ hybridization, and geochemical measurements at sub-meter resolution. In the brine, we detected transcriptional activity of the halophilic methylotrophic methanogen Methanohalophilus, consistent with a biological source for Orca Basin methane. In the particle-rich halocline ([~]2 M Cl-; [~]2235 meters depth), high mcrA transcription by a novel ANME-2a species was co-located with a positive shift in {delta}13C-CH4 indicative of anaerobic oxidation of methane. ANME-2a also transcribed genes for biosynthesis of the osmolyte N({varepsilon})-acetyl-{beta}-L-lysine, supporting adaptation for hypersaline conditions. At the same depth, consortia of sarcina-like archaea, likely ANME-2a, were observed in association with vibrioid and filamentous bacteria, potentially members of a halotolerant genus in the order Desulfobulbales (family SURF-16, which includes the previously identified ANME partner Seep-DBB) that were active at the same depth. At and above the oxic-anoxic interface, aerobic methane oxidation appears to be mediated by three genera of uncultivated Methylococcales bacteria. Our results double the upper salinity range of ANME-2a to [~]2 M Cl- and reveal the key microbial players in the methane bio-filter between the Orca Basin brine and overlying seawater.

microbiology↗

bioRxiv2025

Effects of increasing hydrostatic pressures on marine microbial enzymatic activities

High hydrostatic pressure is characteristic of the deep ocean and presumed to influence microbial functions and viability. However, marine microbial processes are typically measured only at atmospheric pressure (0.1 MPa), limiting our understanding of pressure effects on the activities of microbes that sink as part of the biological carbon pump as well as those that reside in the deep ocean. To test pressure effects on microbial functions, we measured extracellular enzymatic activities--the first step in organic matter remineralization--of a moderate piezophile (Photobacterium profundum SS9), as well as of microbial communities in waters and sediments from shallow to abyssal (5,500 m) depths and their cell-free enzymes (<0.2 {micro}m). Activities were measured at 0.1-100 MPa to assess the pressure effects across the nearly full range of oceanic depths. P. profundum SS9 enzymes show varying pressure effects, from considerable stimulation at optimal pressure (28 MPa) to near complete inhibition (100 MPa). Pressure effects were measured for diverse protein- and carbohydrate-degrading and phosphorus-acquiring enzymes among pelagic and benthic microbial communities. The most common pressure effect is partial activity reduction, indicating a dampening of the initial step of carbon remineralization at increasing pressures. However, retention of cell-free enzymatic activities at higher pressures was occasionally observed even for enzymes from surface-originating assemblages, indicating functionality down to hadal depths and their potential for piezotolerance. These variable pressure effects must be considered when quantifying degradation rates of sinking and deposited particulate matter at increasing pressures in the deep ocean.

ecology↗

bioRxiv2024

Adaptation to high pressure; insights from the genome of an evolved Escherichia coli strain with increased piezotolerance

Pressure is a key environmental parameter that influences the activity and distribution of microbial life on our planet. Despite its key role there is still not a definitive list of essential genes for microbial adaptation to life under increasing pressure. In this study we used a previously characterized Escherichia coli strain (AN62) evolved to grow at pressure (60 MPa) non-permissive to the parental strain and performed comparative genomics in order to identify the genome-level adaptations that might allowed the observed pressure-adapted phenotype. We identified 18 mutations in total of which 3 mutations were present in both the parental and evolved strain, 3 mutations were only present in the parental strain, and 12 mutations were observed only in the evolved AN62 strain. Among the characterized mutations we observed a point mutation in the acyl carrier protein (acpPV43G). Complementation experiments revealed that the observed V43G mutation in AcpP is responsible for increased levels of cis-vaccenic acid but is not alone responsible for the pressure adapted phenotype. Further molecular dynamics and docking simulations suggested that the V43G mutation promoted stronger binding of the AcpP protein to partner enzymes of the fatty acid biosynthesis pathway involved in fatty acid unsaturation. Data SummaryEscherichia coli reads from the parental and evolved strain have been deposited in the Sequence Read Archive (SRA) under accession number RJNA600359. All software used in the bioinformatic analysis is publicly available. Impact StatementPressure is a key environmental parameter. Two-thirds of our planet is covered by oceans with an average depth of 3800m, which means that the majority of the marine life experiences deep sea conditions. Our results offer a list of gene mutations that could contribute to an improved pressure growth phenotype in Escherichia coli, offering a unique insight on the genome level adaptations that might contribute to high pressure adaptation.

microbiology↗

bioRxiv2022

Low Temperature and High Hydrostatic Pressure Have Compounding Negative Effects on Marine Microbial Motility

Approximately three fourths of all pelagic marine prokaryotes live in the deep-sea, an environment characterized by low temperature and high hydrostatic pressure. Within deep-sea environments labile organic matter is often scarce and motility can serve as a competitive advantage for microorganisms. Experimental work with a handful of species suggests motility is one of the most temperature- and pressure-sensitive cellular processes, however the combined effects of temperature and pressure together have yet to be investigated in detail. Here we employed growth-dependent motility agar assays and growth-independent microscopy assays to assess how changes in these two physical factors impact motility both individually and in combination, using ecologically relevant model organisms from the cosmopolitan genera Halomonas, Alcanivorax, and Marinobacter. At pressures equivalent to bathyal and abyssal depths, changes in temperature from 30{degrees}C to 4{degrees}C (motility assays) or 23{degrees}C to 7{degrees}C (microscopy assays) had a greater influence on motility than pressure. In addition, low-temperature and high-pressure impacts were additive. Exposure to high pressure had varying degrees of effect on flagellar function, depending on the strain and the magnitude of the pressure. These ranged from short-term impacts that were quickly reversible to long-term impacts that were detrimental to the function of the flagellum, leading to complete loss of motility. These findings highlight the sensitivity of deep-sea bacterial motility systems to combined temperature/pressure conditions, phenotypes that will contribute to the modulation of diverse microbial activities at depth. IMPORTANCEMicroorganisms perform critical functions in biogeochemical cycles at depth, as well as likely modulating the carbon sequestration potential of the deep ocean. However, their activities under in situ conditions are poorly constrained. One aspect of microbial activity is motility, generally mediated by the energy-consuming rotation of one or more flagellar filaments that enables swimming behavior. This provides a competitive advantage for microbes in the environment, such as by enhancing nutrient acquisition. Here we report on culture-based and microscopy-based analyses of pressure-temperature (P-T) effects on the motility of three ecologically relevant marine microbes. The results in all cases indicate that high pressure and low temperature exert compounding inhibitory effects. This argues for the need for further investigations into P-T effects on deep-sea microbial processes.

microbiology↗

bioRxiv2022

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. ImportanceHadal trenches, characterized by high hydrostatic pressures and low temperatures, are one of the most extreme environments on our planet. By examining the microbiome of abyssal and hadal fishes, we provide insight into both the physiology of the deepest-living vertebrates and the microbes which colonize them. Our findings show that there are similar microbial populations in fishes geographically separated by thousands of miles, reflecting strong selection for specific microbial lineages. Only a handful of psychropiezophilic taxa, which do not reflect the diversity of microbial life at great depth, have been successfully isolated in the laboratory. Our examination of deep-sea fish microbiomes shows that typical high-pressure culturing methodologies, which have largely remained unchanged since the pioneering work of Claude ZoBell in the 1950s, may simulate the chemical environment found in animal guts and helps explain why the same deep-sea genera are consistently isolated.

microbiology↗

bioRxiv2020

Distinctive Gene and Protein Characteristics of Extremely Piezophilic Colwellia

BackgroundThe 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. ResultsSignificant 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 archaeal 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. ConclusionsWe 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.

microbiology↗