scholarly journals Tripartite holobiont system in a vent snail broadens the concept of chemosymbiosis

2020 ◽  
Author(s):  
Yi Yang ◽  
Jin Sun ◽  
Chong Chen ◽  
Yadong Zhou ◽  
Yi Lan ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Deep Sea ◽  
Extreme Environments ◽  
Host Immunity ◽  
Energy Sources ◽  
High Quality ◽  
Genomic Plasticity ◽  
Changing Environments ◽  
Metabolic Heterogeneity ◽  
Genomic Basis

AbstractMany animals inhabiting deep-sea vents are energetically dependent on chemosynthetic endosymbionts, but how such symbiont community interacts with host, and whether other nutritional sources are available to such animals remain unclear. To reveal the genomic basis of symbiosis in the vent snail Alviniconcha marisindica, we sequenced high-quality genomes of the host and gill campylobacterial endosymbionts, as well as metagenome of the gut microbiome. The gill endosymbiont has a streamlined genome for efficient chemoautotrophy, but also shows metabolic heterogeneity among populations. Inter- and intra-host variabilities among endosymbiont populations indicate the host poses low selection on gill endosymbionts. Virulence factors and genomic plasticity of the endosymbiont provide advantages for cooperating with host immunity to maintain mutualism and thriving in changing environments. In addition to endosymbiosis, the gut and its microbiome expand the holobiont’s utilisation of energy sources. Host-microbiota mutualism contributes to a highly flexible holobiont that can excel in various extreme environments.

Genomic plasticity and antibody response of Bordetella bronchiseptica strain HT200, a natural variant from a thermal spring

2021 ◽  
Vol 368 (6) ◽  
Author(s):  
Jhasketan Badhai ◽  
Subrata K Das
Keyword(s):  
Antibody Response ◽  
Virulence Factors ◽  
Thermal Spring ◽  
Asymptomatic Infection ◽  
Bordetella Bronchiseptica ◽  
Divergent Evolution ◽  
Environmental Niche ◽  
Genomic Plasticity ◽  
Genes Encoding ◽  
Natural Variant

ABSTRACT Classical Bordetella species are primarily isolated from animals and humans causing asymptomatic infection to lethal pneumonia. However, isolation of these bacteria from any extra-host environmental niche has not been reported so far. Here, we have characterized the genomic plasticity and antibody response of Bordetella bronchiseptica strain HT200, isolated from a thermal spring. Genomic ANI value and SNPs-based phylogenetic tree suggest a divergent evolution of strain HT200 from a human-adapted lineage of B. bronchiseptica. Growth and survivability assay showed strain HT200 retained viability for more than 5 weeks in the filter-sterilized spring water. In addition, genes or loci encoding the Bordetella virulence factors such as DNT, ACT and LPS O-antigen were absent in strain HT200, while genes encoding other virulence factors were highly divergent. Phenotypically, strain HT200 was non-hemolytic and showed weak hemagglutination activity, but was able to colonize in the respiratory organs of mice. Further, both infection and vaccination with strain HT200 induced protective antibody response in mouse against challenge infection with virulent B. bronchiseptica strain RB50. In addition, genome of strain HT200 (DSM 26023) showed presence of accessory genes and operons encoding predicted metabolic functions pertinent to the ecological conditions of the thermal spring.

scholarly journals High-Quality Draft Genome Sequence of the Multidrug-Resistant Clinical Isolate Enterococcus faecium VRE16

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Suelen Scarpa de Mello ◽  
Daria Van Tyne ◽  
Andrei Nicoli Gebieluca Dabul ◽  
Michael S. Gilmore ◽  
Ilana L. B. C. Camargo
Keyword(s):  
Antibiotic Resistance ◽  
Virulence Factors ◽  
Genome Sequence ◽  
Enterococcus Faecium ◽  
Draft Genome ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Draft Genome Sequence ◽  
Commensal Bacterium ◽  
High Quality

Specific lineages of the commensal bacterium Enterococcus faecium belonging to CC17, especially ST412, have been isolated from patients in several hospitals worldwide and harbor antibiotic resistance genes and virulence factors. Here, we report a high-quality draft genome sequence and highlight features of E. faecium VRE16, a representative of this ST.

A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota

2021 ◽  
Author(s):  
Yafei Chang ◽  
Qilian Fan ◽  
Jialin Hou ◽  
Yu Zhang ◽  
Jing Li
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Extreme Environments ◽  
Reference Database ◽  
False Discovery Rate Method ◽  
Analysis Strategy ◽  
Gene Database ◽  
And Function ◽  
Functional Profiles

Abstract Microorganisms in deep-sea hydrothermal vents provide valuable insights into life under extreme conditions. Mass spectrometry-based proteomics has been widely used to identify protein expression and function. However, the metaproteomic studies in deep-sea microbiota have been constrained largely by the low identification rates of protein or peptide. To improve the efficiency of metaproteomics for hydrothermal vent microbiota, we firstly constructed a microbial gene database (HVentDB) based on 117 public metagenomic samples from hydrothermal vents and proposed a metaproteomic analysis strategy, which takes the advantages of not only the sample-matched metagenome, but also the metagenomic information released publicly in the community of hydrothermal vents. A two-stage false discovery rate method was followed up to control the risk of false positive. By applying our community-supported strategy to a hydrothermal vent sediment sample, about twice as many peptides were identified when compared with the ways against the sample-matched metagenome or the public reference database. In addition, more enriched and explainable taxonomic and functional profiles were detected by the HVentDB-based approach exclusively, as well as many important proteins involved in methane, amino acid, sugar, glycan metabolism and DNA repair, etc. The new metaproteomic analysis strategy will enhance our understanding of microbiota, including their lifestyles and metabolic capabilities in extreme environments. The database HVentDB is freely accessible from http://lilab.life.sjtu.edu.cn:8080/HventDB/main.html.

scholarly journals De novo assembly of a Tibetan genome and identification of novel structural variants associated with high-altitude adaptation

2019 ◽  
Vol 7 (2) ◽  
pp. 391-402 ◽  
Author(s):  
Yaoxi He ◽  
Haiyi Lou ◽  
Chaoying Cui ◽  
Lian Deng ◽  
Yang Gao ◽  
...  
Keyword(s):  
High Altitude ◽  
De Novo Assembly ◽  
De Novo ◽  
Population Analysis ◽  
Extreme Environments ◽  
Structural Variants ◽  
Base Pairs ◽  
High Quality ◽  
Long Read ◽  
Altitude Adaptation

Abstract Structural variants (SVs) may play important roles in human adaptation to extreme environments such as high altitude but have been under-investigated. Here, combining long-read sequencing with multiple scaffolding techniques, we assembled a high-quality Tibetan genome (ZF1), with a contig N50 length of 24.57 mega-base pairs (Mb) and a scaffold N50 length of 58.80 Mb. The ZF1 assembly filled 80 remaining N-gaps (0.25 Mb in total length) in the reference human genome (GRCh38). Markedly, we detected 17 900 SVs, among which the ZF1-specific SVs are enriched in GTPase activity that is required for activation of the hypoxic pathway. Further population analysis uncovered a 163-bp intronic deletion in the MKL1 gene showing large divergence between highland Tibetans and lowland Han Chinese. This deletion is significantly associated with lower systolic pulmonary arterial pressure, one of the key adaptive physiological traits in Tibetans. Moreover, with the use of the high-quality de novo assembly, we observed a much higher rate of genome-wide archaic hominid (Altai Neanderthal and Denisovan) shared non-reference sequences in ZF1 (1.32%–1.53%) compared to other East Asian genomes (0.70%–0.98%), reflecting a unique genomic composition of Tibetans. One such archaic hominid shared sequence—a 662-bp intronic insertion in the SCUBE2 gene—is enriched and associated with better lung function (the FEV1/FVC ratio) in Tibetans. Collectively, we generated the first high-resolution Tibetan reference genome, and the identified SVs may serve as valuable resources for future evolutionary and medical studies.

scholarly journals Black sea cucumber (Holothuria atra Jaeger, 1833) rescues Pseudomonas aeruginosa-infected Caenorhabditis elegans via reduction of pathogen virulence factors and enhancement of host immunity

2019 ◽  
Vol 10 (9) ◽  
pp. 5759-5767
Author(s):  
Wan-Ting Lee ◽  
Boon-Khai Tan ◽  
Su-Anne Eng ◽  
Gan Chee Yuen ◽  
Kit Lam Chan ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Virulence Factors ◽  
Black Sea ◽  
Sea Cucumber ◽  
Multidrug Resistant ◽  
Host Immunity ◽  
Bacterial Virulence ◽  
Pathogen Virulence ◽  
Multidrug Resistant Pathogens ◽  
Holothuria Atra

A strategy to circumvent the problem of multidrug resistant pathogens is the discovery of anti-infectives targeting bacterial virulence or host immunity.

scholarly journals RETRACTED ARTICLE: Novel life history strategy in a deep sea fish challenges assumptions about reproduction in extreme environments

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Randal A. Singer ◽  
Jon A. Moore ◽  
Edward L. Stanley
Keyword(s):  
Life History ◽  
Deep Sea ◽  
Extreme Environments ◽  
Life History Strategy ◽  
Deep Ocean ◽  
Homogeneous System ◽  
Life History Strategies ◽  
Life History Trait ◽  
Retracted Article ◽  
Sea Fish

Abstract The deep ocean is frequently assumed to be a homogeneous system lacking the same diverse life history strategies found in shallower waters. However, as our methods for exploring the deep ocean improve, common assumptions about dispersal, reproduction and behavior are constantly being challenged. Fishes exhibit the most diverse reproductive strategies among vertebrates. Understanding life history strategies in deep-sea environments is lacking for many species of fishes. Here, we report a novel reproductive strategy where a fish (Parazen pacificus) provides parental care via mouth brooding. This behavior is observed from a specimen collected with eggs present in the buccal cavity, along with other specimens exhibiting pre-brooding morphologies. This is the first description of this unique life history trait in a deep-sea fish and fills in a gap in the larval literature for this family of fishes and prompts further investigation into other novel reproductive modes of deep-sea fauna.

The Latest Innovation in Pressure Compensated Deep-Sea Wet Mateable High Voltage Connectors

2006 ◽  
Author(s):  
Tobias Frerck
Keyword(s):  
Research And Development ◽  
Market Share ◽  
High Voltage ◽  
Deep Sea ◽  
World Wide ◽  
High Quality ◽  
Marine Technology ◽  
Offshore Industry

GISMA GmbH was founded in 1983 and is today a medium-sized company with 42 employees. With a real net output of 90%, GISMA in Neumu¨nster develops, designs and produces 3,500 different connectors. The high-quality electrical and fibre-optical connectors are used world-wide in the offshore industry, marine technologies and in submarine technologies. With a market share of approx. 30% GISMA is nowadays one of the leading connector manufacturers in European marine technology. 350,000 Euro is invested annually in research and development.

scholarly journals The Mycobiota of the Deep Sea: What Omics Can Offer

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 292
Author(s):  
Lluvia Vargas-Gastélum ◽  
Meritxell Riquelme
Keyword(s):  
Deep Sea ◽  
Fungal Diversity ◽  
High Salinity ◽  
Extreme Environments ◽  
Abiotic Conditions ◽  
Culture Independent ◽  
Sequencing Platforms ◽  
Generation Sequencing ◽  
Culture Dependent

The deep sea (>1000 m below sea level) represents one of the most extreme environments of the ocean. Despite exhibiting harsh abiotic conditions such as low temperatures, high hydrostatic pressure, high salinity concentrations, a low input of organic matter, and absence of light, the deep sea encompasses a great fungal diversity. For decades, most knowledge on the fungal diversity of the deep sea was obtained through culture-dependent techniques. More recently, with the latest advances of high-throughput next generation sequencing platforms, there has been a rapid increment in the number of studies using culture-independent techniques. This review brings into the spotlight the progress of the techniques used to assess the diversity and ecological role of the deep-sea mycobiota and provides an overview on how the omics technologies have contributed to gaining knowledge about fungi and their activity in poorly explored marine environments. Finally, current challenges and suggested coordinated efforts to overcome them are discussed.

Crucial role of reactive pulse-gas on a sputtered Zn3N2 thin film formation

RSC Advances ◽  
2016 ◽  
Vol 6 (97) ◽  
pp. 94905-94910 ◽  
Author(s):  
Narathon Khemasiri ◽  
Chanunthorn Chananonnawathorn ◽  
Annop Klamchuen ◽  
Sukittaya Jessadaluk ◽  
Apirak Pankiew ◽  
...  
Keyword(s):  
Room Temperature ◽  
Film Formation ◽  
Rf Magnetron Sputtering ◽  
Energy Sources ◽  
High Quality ◽  
Additional Energy ◽  
Thin Film Formation ◽  
Reactive Pulse ◽  
Reactive Gas

Herein, we demonstrate a powerful technique, known as reactive gas-timing (RGT) rf magnetron sputtering, to fabricate high quality Zn3N2 thin films at room temperature without applying any additional energy sources.

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