Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions

Comparative genome analysis of the genus Marivirga and proposal of two novel marine species: Marivirga arenosa sp. nov., and Marivirga salinae sp. nov

BACKGROUND

The phylum Bacteroidota represents a significant proportion of heterotrophic bacteria found in marine ecosystems. Members of the phylum Bacteroidota are actively involved in the degradation of biopolymers such as polysaccharides and proteins. Bacteroidota genomes exhibit a significant enrichment of various enzymes, including carbohydrate-active enzymes (CAZymes), carboxypeptidases, esterases, isomerases, peptidases, phosphatases, and sulfatases. The genus Marivirga, a member of the family Marivirgaceae within the phylum Bacteroidota, comprises six documented species. During a microbial diversity study, three novel Marivirga strains (BKB1-2 T, ABR2-2, and BDSF4-3 T) were isolated from the West Sea, Republic of Korea.

RESULTS

To explore the taxonomic status and genomic characteristics of the novel isolates, we employed a polyphasic taxonomic approach, which included phylogenetic, chemotaxonomic and comprehensive genome analysis. The three isolates were Gram-stain-negative, aerobic, rod-shaped, moderately halophilic, and had a gliding motility. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the two isolates, BKB1-2 T and BDSF4-3 T, and the six reference strains were 70.5-76.5% for ANI and 18.1-25.7% for dDDH. Interestingly, the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the strains harbor genes for a comprehensive pathway for dissimilatory nitrate reduction to ammonium (DNRA), as well as other nitrogen pathways for the reduction of nitrite, nitric oxide, and nitrous oxide. Additionally, the antiSMASH analysis indicated that the strains contained three to eight biosynthetic gene clusters (BGCs) associated with the synthesis of secondary metabolites. Furthermore, the strains carried a high number of CAZyme ranging from 53 to 152, which was also demonstrated by an in vitro analysis of degradation of the polysaccharide cellulose, chitin, laminarin, starch, and xylan. Additionally, all the strains carried genes for the metabolism of heavy metals, and exhibited tolerance to heavy metals, with minimum inhibitory concentrations (MICs) in millimoles (mM) in ranges of Co2+ (3-6), Cu2+ (0.2-0.4), Ni2+ (3-5), Zn2+ (2-4), Mn2+ (20-50), and Hg2+ (0.3).

CONCLUSIONS

Based on polyphasic taxonomic approach, the three isolated strains represent two novel species names Marivirga arenosa sp. nov. (BKB1-2 T = KCTC 82989 T = InaCC B1618T), and Marivirga salinae sp. nov. (BDSF4-3 T = KCTC 82973 T = InaCC B1619T).

High-throughput nanopore DNA sequencing of large insert fosmid clones directly from bacterial colonies

Fosmids and cosmids are vectors frequently used in functional metagenomic studies. With a large insert capacity (around 30 kb) they can encode dozens of cloned genes or in some cases, entire biochemical pathways. Fosmids with cloned inserts can be transferred to heterologous hosts and propagated to enable screening for new enzymes and metabolites. After screening, fosmids from clones with an activity of interest must be de novo sequenced, a critical step toward the identification of the gene(s) of interest. In this work, we present a new approach for rapid and high-throughput fosmid sequencing directly from Escherichia coli colonies without liquid culturing or fosmid purification. Our sample preparation involves fosmid amplification with phi29 polymerase and then direct nanopore sequencing using the Oxford Nanopore Technologies system. We also present a bioinformatics pipeline termed "phiXXer" that facilitates both de novo read assembly and vector trimming to generate a linear sequence of the fosmid insert. Finally, we demonstrate the accurate sequencing of 96 fosmids in a single run and validate the method using two fosmid libraries that contain cloned large insert (~30-40 kb) genomic or metagenomic DNA.IMPORTANCELarge-insert clone (fosmids or cosmids) sequencing is challenging and arguably the most limiting step of functional metagenomic screening workflows. Our study establishes a new method for high-throughput nanopore sequencing of fosmid clones directly from lysed Escherichia coli cells. It also describes a companion bioinformatic pipeline that enables de novo assembly of fosmid DNA insert sequences. The devised method widens the potential of functional metagenomic screening by providing a simple, high-throughput approach to fosmid clone sequencing that dramatically speeds the pace of discovery.

Maribellus comscasis sp. nov., a novel deep-sea Bacteroidetes bacterium, possessing a prominent capability of degrading cellulose

Bacteroidetes are thought to be specialized for the degradation of algae-derived ocean polysaccharides. Here, we show that Bacteroidetes are the predominant phylum in deep-sea sediments and possess more genes associated with polysaccharides degradation than other bacteria. We have isolated a novel Bacteroidetes species from the deep-sea sediments by using a special polysaccharide containing medium, Maribellus comscasis WC007, which possesses 82 putative polysaccharide utilization loci (PULs) containing 374 glycoside hydrolases and 82 SusC/D pairs (Sus indicates starch utilization system; SusC represents the actual TonB-dependent transporter, and SusD is an associated substrate-binding outer membrane lipoprotein) together with 58 sigma/antisigma factors. Through an in-depth analysis of these PULs, strain WC007 can efficiently degrade numerous different polysaccharides including cellulose, pectin, fucoidan, mannan, xylan and starch, which are verified by growth assays. Notably, we find that cellulose has the most significant growth-promoting effect on M. comscasis WC007. And based on scanning electron microscope observation, transcriptomics and metabolomics, we further report on the underlying mechanisms of cellulose degradation and utilization, as well as potential contributions to the carbon cycle. Overall, our results suggest that Bacteroidetes may play key roles in the carbon cycle, likely due to their high abundance and prominent polysaccharide degradation capabilities.

Artificial construction of the biocoenosis of deep-sea ecosystem via seeping methane

Deep-sea ecosystems, such as cold seeps and hydrothermal vents, have high biomass, even though they are located in the benthic zone, where no sunlight is present to provide energy for organism proliferation. Based on the coexistence of the reduced gases and chemoautotrophic microbes, it is inferred that the energy from the reduced gases supports the biocoenosis of deep-sea ecosystems. However, there is no direct evidence to support this deduction. Here, we developed and placed a biocoenosis generator, a device that continuously seeped methane, on the 1000-m deep-sea floor of the South China Sea to artificially construct a deep-sea ecosystem biocoenosis. The results showed that microorganisms, including bacteria and archaea, appeared in the biocoenosis generator first, followed by jellyfish and Gammaridea arthropods, indicating that a biocoenosis had been successfully constructed in the deep sea. Anaerobic methane-oxidizing archaea, which shared characteristics with the archaea of natural deep-sea cold seeps, acted as the first electron acceptors of the emitted methane; then, the energy in the electrons was transferred to downstream symbiotic archaea and bacteria and finally to animals. Nitrate-reducing bacteria served as partners to complete anaerobic oxidation of methane process. Further analysis revealed that viruses coexisted with these organisms during the origin of the deep-sea biocoenosis. Therefore, our study mimics a natural deep-sea ecosystem and provides the direct evidence to show that the chemical energy of reduced organic molecules, such as methane, supports the biocoenosis of deep-sea ecosystems.

Corpse decomposition increases nitrogen pollution and alters the succession of nirK-type denitrifying communities in different water types

Cadaver decomposition as high-quality nutrient inputs may exert strong perturbation on the aquatic environments, such as high nitrogen or nitrate pollution. Denitrifying bacteria may reduce nitrate to nitrogen gas, thereby decreasing the nitrogen pollution and improving self-purification ability of aquatic ecosystem. However, how nirK denitrifying communities in water respond to cadaver decomposition remains unknown. Thus, we employed high-throughput sequencing and chemical analysis to investigate the succession of nirK-type denitrifying communities in tap water and Yellow river water (experimental groups) as well as their corresponding control groups during two important stages of fish corpse decomposition called advanced floating decay and sunken remains. Our data showed that the concentration of NH₄⁺-N in the experimental groups increased approximately 3-4 times compared with the control groups. Proteobacteria was the predominant phylum for nirK denitrifying communities. Several potential pathogenic genera, such as Brucella and Achromobacter, were enriched in the corpse groups. Notably, nirK-type community structures were significantly impacted by cadaver decomposition. Community structures in the corpse groups become more similar with succession, indicating community convergence at the final stage. Water pH, oxidation-reduction potential (ORP) and treatment were three important factors affecting the community structures. However, water type was not a main driving factor determining carcass-associated nirK-type bacterial communities. Four phylogenetic clusters were detected in the denitrifying communities, but showed significantly different distribution between the corpse and control groups. These results provide an in-depth understanding for nirK denitrifying functional bacteria and potential pathogenic bacteria during carrion decomposition process, which offer valuable reference to environmental evaluation and management.

Influence of suspended mariculture on vertical distribution profiles of bacteria in sediment from Daya Bay, Southern China

Mariculture is known to contribute to oxygen depletion, pH decline and accumulation of nutrients and organic matter in sediments. However, studies on the bacterial vertical distribution of mariculture area are very limited. The bacterial abundance in the non-culture site (3.8 ± 0.8 × 10⁹ copies g^-1) was significantly higher than that in the three mariculture sites (1.2 ± 0.2 × 10⁹ copies g^-1), and bacterial diversity in the non-culture site was significantly higher than that in fish cage-TF (p < 0.05). The vertical distribution profiles of bacteria in non-culture and oyster culture sites were similar but very different from that of fish cage-TF. In addition, significant downward trends in bacterial abundance and diversity were observed as sediment depth increased (p < 0.05), and the most relevant environmental factors were moisture content, total nitrogen, total organic carbon and carbon/nitrogen. The dominant bacterial phyla in sediment were Proteobacteria, Chloroflexi and Bacteroidetes.

The homeostasis-maintaining metabolites from bacterial stress response to bacteriophage infection suppress tumor metastasis

The antiviral metabolites from bacterial stress response to bacteriophage infection can maintain homeostasis of host cells, while metabolism disorder is a remarkable characteristic of tumorigenesis. In the aspect of metabolic homeostasis, therefore, the antiviral homeostasis-maintaining metabolites of bacteria may possess anti-tumor activity. However, this issue has not been addressed. Here we show that the homeostasis-challenged maintaining metabolites from deep-sea bacteriophage-challenged thermophile can suppress tumor metastasis. The results indicated that the metabolic profiles of the bacteriophage GVE2-infected and virus-free thermophile Geobacillus sp. E263 from a deep-sea hydrothermal vent were remarkably different. Thirteen metabolites were significantly elevated and two metabolites were downregulated in thermophile stress response to GVE2 infection. As an example, the upregulated L-norleucine was characterized. The data showed that L-norleucine had antiviral activity in thermophile. Furthermore, the in vitro and in vivo assays revealed that L-norleucine, as well as its derivative, significantly suppressed metastasis of gastric and breast cancer cells. L-norleucine interacted with hnRNPA2/B1 protein to inhibit the expressions of Twist1 and Snail, two inhibitors of E-cadherin, and promote the E-cadherin expression, leading to the inhibition of tumor metastasis. Therefore, our study presented that antiviral homeostasis-maintaining metabolites of microbes might be a promising source for anti-tumor drugs.

Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions

Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation. The metagenomic analysis of viromes without exogenous DNA contamination and microbiomes of vent samples indicated that viruses had compensation effects on the metabolisms of their host microorganisms. Viral genes not only participated in most of the microbial metabolic pathways but also formed branched pathways in microbial metabolisms, including pyrimidine metabolism; alanine, aspartate, and glutamate metabolism; nitrogen metabolism and assimilation pathways of the two-component system; selenocompound metabolism; aminoacyl-tRNA biosynthesis; and amino sugar and nucleotide sugar metabolism. As is well known, deep-sea hydrothermal vent ecosystems exist in relatively isolated environments which are barely influenced by other ecosystems. The metabolic compensation of hosts mediated by viruses might represent a very important aspect of virus-host interactions.

Viruses are the most abundant biological entities in the oceans and have very important roles in regulating microbial community structure and biogeochemical cycles. The relationship between virus and host microbes is broadly thought to be that of predator and prey. Viruses can lyse host cells to control microbial population sizes and affect community structures of hosts by killing specific microbes. However, viruses also influence their hosts through manipulation of bacterial metabolism. We found that viral genes not only participated in most microbial metabolic pathways but also formed branched pathways in microbial metabolisms. The metabolic compensation of hosts mediated by viruses may help hosts to adapt to extreme environments and may be essential for host survival.

Complete genome sequence of Serinicoccus sp. JLT9, an actinomycete isolated from the shallow-sea hydrothermal system

Serinicoccus sp. JLT9 was a novel rare actinomycete, isolated from the shallow-sea hydrothermal system. Here, we present the complete genome sequence of Serinicoccus sp. JLT9, which consists of 3,610,932bp with a GC content of 72.43%. The genome data provides insight into microbial adaption to the shallow-sea hydrothermal system and facilitates the discovery of natural compounds in the future.

First Comparative Analysis of the Community Structures and Carbon Metabolic Pathways of the Bacteria Associated with Alvinocaris longirostris in a Hydrothermal Vent of Okinawa Trough

Alvinocaris longirostris is a species of shrimp existing in the hydrothermal fields of Okinawa Trough. To date the structure and function of the microbial community associated with A. longirostris are essentially unknown. In this study, by employment of the techniques of high through-put sequencing and clone library construction and analysis, we compared for the first time the community structures and metabolic profiles of microbes associated with the gill and gut of A. longirostris in a hydrothermal field of Okinawa Trough. Fourteen phyla were detected in the gill and gut communities, of which 11 phyla were shared by both tissues. Proteobacteria made up a substantial proportion in both tissues, while Firmicutes was abundant only in gut. Although gill and gut communities were similar in bacterial diversities, the bacterial community structures in these two tissues were significantly different. Further, we discovered for the first time the existence in the gill and gut communities of A. longirostris the genes (cbbM and aclB) encoding the key enzymes of Calvin-Benson-Bassham (CBB) cycle and the reductive tricarboxylic acid (rTCA) cycle, and that both cbbM and aclB were significantly more abundant in gill than in gut. Taken together, these results provide the first evidence that at least two carbon fixation pathways are present in both the gill and the gut communities of A. longirostris, and that the communities in different tissues likely differ in autotrophic productivity.