The phylogeny and metabolic potentials of an n-alkane-degrading Venatorbacter bacterium isolated from deep-sea sediment of the Mariana Trench

Abstract

Recently, several reports showed that n-alkanes were abundant in the hadal zone, suggesting that n-alkanes could be an important source of nutrients for microorganisms in hadal ecosystems. To date, most of the published studies on the microbial capacity to degrade hydrocarbons were conducted only at atmospheric temperature and pressure (0.1 MPa), and little is known about whether and which microbes could utilize n-alkanes at in situ environmental conditions in the hadal zone, including low temperature and high hydrostatic pressure (especially >30 MPa). In this study, a piezotolerant bacterium, strain C2-1, was isolated from a Mariana Trench sediment at depth of 5,800 m. Strain C2-1 was able to grow at in situ temperature (4°C) and pressure (58 MPa) with n-alkanes as the sole carbon source. Phylogenetically, strain C2-1 and related strains (TMPB967, ST750PaO-4, IMCC1826, and TTBP476) should be classified into the genus Venatorbacter. Metagenomic analysis using ~5,000 publicly available datasets showed that Venatorbacter has a wide environmental distribution in seawater (38), marine sediments (3), hydrothermal vent plumes (2), Antarctic ice (1), groundwater (13), and marine sponge ecosystems (1). Most Venatorbacter species are non-obligate n-alkane degraders that could utilize, at a minimal, C16−C18n-alkanes, as well as other different types of carbon substrates, including carbohydrates, amino acids, peptides, and phospholipids. The type II secretion system, extracellular proteases, phospholipase, and endonuclease of Venatorbacter species were robustly expressed in the metatranscriptomes of deep-sea hydrothermal vents, suggesting their important contribution to secondary productivity by degrading extracellular macromolecules. The identification of denitrifying genes suggested a genus-specific ecological potential that allowed Venatorbacter species to be active in anoxic environments, e.g., the oxygen-minimal zone (OMZ) and the deeply buried marine sediments. Our results show that Venatorbacter species are responsible for the degradation of hydrocarbon and extracellular macromolecules, suggesting that they may play an important role in the biogeochemistry process in the Trench ecosystems.

The Phylogeny, Metabolic Potentials, and Environmental Adaptation of an Anaerobe, Abyssisolibacter sp. M8S5, Isolated from Cold Seep Sediments of the South China Sea

“…Compatible solutes, commonly referred to as osmoprotectants, are low molecular weight, highly soluble organic compounds that mainly protect microorganisms from a variety of environmental stresses, such as drought, high salt, low or high temperature, HHP, and heavy metals [ 87 , 88 , 89 , 90 , 91 , 92 , 93 ]. In this study, we found that strain M8S5 possesses 21 genes to transport diverse kinds of compatible solutes, including glycine betaine/carnitine/choline, proline, sarcosine, and trehalose ( Figure 4 and Supplementary Table S14 ).…”

“…Moreover, a total of five genes encoding molecular chaperones, including dnaJK , grpE , htpG , and hslO , were predicted in strain M8S5 ( Supplementary Table S14 ). These molecular chaperones may be induced by high-pressure and low-temperature stresses, help proteins to fold correctly, and maintain protein function [ 87 , 92 , 95 ]. Also, two genes related to cold shock proteins ( cspA ) were detected in the genome of strain M8S5 ( Supplementary Table S14 ), which may serve as cryoprotectants in low-temperature adaptation [ 96 ].…”

“…Moreover, a total of five genes encoding molecular chaperones, including dnaJK, grpE, htpG, and hslO, were predicted in strain M8S5 (Supplementary Table S14). These molecular chaperones may be induced by high-pressure and low-temperature stresses, help proteins to fold correctly, and maintain protein function [87,92,95]. Also, two genes related to cold shock proteins (cspA) were detected in the genome of strain M8S5 (Supplementary Table S14), which may serve as cryoprotectants in low-temperature adaptation Compatible solutes, commonly referred to as osmoprotectants, are low molecular weight, highly soluble organic compounds that mainly protect microorganisms from a variety of environmental stresses, such as drought, high salt, low or high temperature, HHP, and heavy metals [87][88][89][90][91][92][93].…”

Unravelling Diatoms’ Potential for the Bioremediation of Oil Hydrocarbons in Marine Environments

“…Among the biodegradable structural group, n-alkanes are the most susceptible to biodegradation, except for C20-C40, which are hydrophobic solids and are not easily degraded [46]. Another major group of petroleum hydrocarbons are polycyclic aromatic hydrocarbons (PAHs), which are partially recalcitrant to biodegradation.…”

“…Short-chain alkanes are aliphatic hydrocarbons and are the most easily degraded, followed by alkanes with side chains or branched alkanes and then aromatic hydrocarbons with stable ring structures. Although alkanes have been reported in groundwater, rivers, lakes, oceans, and soil [46], they may also occur in aquatic organisms and sediments (estuarine, marine, and riverine). Alkanes with chains of up to 44 carbon atoms are susceptible to microbial degradation; however, only a limited number of species can use Cl-C4 and C5-C9 alkanes because of their toxicity [93,94].…”