Comparative genomic analysis of obligately piezophilic Moritella yayanosii DB21MT-5 reveals bacterial adaptation to the Challenger Deep, Mariana Trench

Albibacterium profundi sp. nov., isolated from sediment of the Challenger Deep of Mariana Trench, and reclassification of Pedobacter indicus as Albibacterium indicum comb. nov

A rod-shaped, white-pigmented, non-motile, Gram-stain-negative bacterium, designated RHL897T, was isolated from sediments collected at the Mariana Trench Challenger Deep (10,816 m). Strain RHL897T was strictly aerobic and grew at 4-37 °C, pH 6.0-10.0 and in the presence of 0-11.0 % (w/v) NaCl. Its genomic DNA G+C content was 41.2%. Metabolic analysis revealed mechanisms for salt tolerance, abundant metal ion transport proteins and stronger resistance to heavy metals such as arsenic and mercury compared to the closest reference strains, likely linked to adaptation to the hadal sediment environment. The predominant menaquinone was MK-7, and the major polar lipids were phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified glycolipid. The main fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and iso-C17 : 0 3OH. Strain RHL897T exhibited the highest 16S rRNA gene sequence similarity to the type strain of Pedobacter indicus (97.9%) and Albibacterium bauzanense (96.1%). Phylogenetic trees constructed based on 16S rRNA gene sequences and a 549 core gene set indicated that strain RHL897T was closely related to P. indicus and A. bauzanense, with all three species clustering within a distinct clade. Combined with the analyses of average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization, strain RHL897T represented a novel species of the genus Albibacterium, for which the name Albibacterium profundi sp. nov. is proposed. The type strain is RHL897T (=MCCC 1K09221T=KCTC 102276T). Furthermore, the revised phylogeny with the inclusion of RHL897T suggested that P. indicus should be reclassified under the genus Albibacterium and renamed Albibacterium indicum.

Biological functions at high pressure: transcriptome response of Shewanella oneidensis MR-1 to hydrostatic pressure relevant to Titan and other icy ocean worlds

High hydrostatic pressure (HHP) is a key driver of life's evolution and diversification on Earth. Icy moons such as Titan, Europa, and Enceladus harbor potentially habitable high-pressure environments within their subsurface oceans. Titan, in particular, is modeled to have subsurface ocean pressures ≥ 150 MPa, which are above the highest pressures known to support life on Earth in natural ecosystems. Piezophiles are organisms that grow optimally at pressures higher than atmospheric (0.1 MPa) pressure and have specialized adaptations to the physical constraints of high-pressure environments - up to ~110 MPa at Challenger Deep, the highest pressure deep-sea habitat explored. While non-piezophilic microorganisms have been shown to survive short exposures at Titan relevant pressures, the mechanisms of their survival under such conditions remain largely unelucidated. To better understand these mechanisms, we have conducted a study of gene expression for Shewanella oneidensis MR-1 using a high-pressure experimental culturing system. MR-1 was subjected to short-term (15 min) and long-term (2 h) HHP of 158 MPa, a value consistent with pressures expected near the top of Titan's subsurface ocean. We show that MR-1 is metabolically active in situ at HHP and is capable of viable growth following 2 h exposure to 158 MPa, with minimal pressure training beforehand. We further find that MR-1 regulates 264 genes in response to short-term HHP, the majority of which are upregulated. Adaptations include upregulation of the genes argA, argB, argC, and argF involved in arginine biosynthesis and regulation of genes involved in membrane reconfiguration. MR-1 also utilizes stress response adaptations common to other environmental extremes such as genes encoding for the cold-shock protein CspG and antioxidant defense related genes. This study suggests Titan's ocean pressures may not limit life, as microorganisms could employ adaptations akin to those demonstrated by terrestrial organisms.

Characterization and bioactive component analysis of filamentous bacterium XJ-16

Actinomycetes, which can produce a variety of bioactive compounds in the metabolic process, is one of the important sources of novel drugs, enzymes, anti-tumor drugs and enzyme inhibitors. It has been the focus of researchers to find and develop Actinomycetes with special characters. Strain XJ-16 is a blue alkali-resistant filamentous bacterium with high antimicrobial activity isolated from saline-alkali land of Xinjiang. Based on the classification, the enzyme production, metabolite antibacterial activity, and antibacterial substance isolation of XJ-16 were explored. which showed that XJ-16 belongs to the blue group of Streptomyces sp, and it can secrete cellulase, lipase, urease, protease, catalase and oxidase during metabolism. In addition, the bacteriostatic substance secreted by the strain XJ-16 showed inhibitory effects against both Gram-positive and Gram-negative bacteria, as well as the yeast Candida albicans. Then it was found that the bacteriostasis produced by XJ-16 has strong tolerance to acid, weak tolerance to alkali, and easy to be inactivated. After tested by HPLC, the retention time of antimicrobial substance was 13.261 min. This study provides new research ideas and theoretical support for searching for new antibacterial compounds and further developing the blue alkaline Actinomycete XJ-16.

Spatial Variability of Bacterial Community Compositions in the Mariana Trench

Hadal microorganisms play an important role in the biogeochemical processes in marine ecosystems and act as a valuable resource for industrial applications. This paper presents the bacterial community analysis of samples taken from the Challenger Deep within the Mariana Trench, which is the deepest site in the ocean. High-throughput 16S rRNA gene amplicon sequencing was used to reveal that the vertically sampled bacterial populations at eight stations varied at the surface to 10 km depth. The surface water samples harbored a distinct bacterial assemblage, while the mesopelagic and bathyal samples manifested different bacterial community composition, which was not consistent with previous studies. Gammaproteobacteria was the most abundant bacteria in the bathyal and hadal water. The hadal bacterial community consisted mostly of Alteromonadales and Oceanospirillales. The former was widely spread in the water column, which might suggest habitat partitioning at the genus and OTU levels, while the latter might represent hadal-enriched hydrocarbon degraders. The present work complements the current knowledge and understanding of the bathyal and hadal bacterial communities of the Mariana Trench.