scholarly journals Comparative Genomic Analysis of Labrenzia aggregata (Alphaproteobacteria) Strains Isolated From the Mariana Trench: Insights Into the Metabolic Potentials and Biogeochemical Functions

2021 ◽  
Vol 12 ◽  
Author(s):  
Haohui Zhong ◽  
Hao Sun ◽  
Ronghua Liu ◽  
Yuanchao Zhan ◽  
Xinyu Huang ◽  
...  
Keyword(s):  
Deep Sea ◽  
Sea Water ◽  
Extreme Environments ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Surface Seawater ◽  
Bacterial Strains ◽  
The East China Sea ◽  
Mariana Trench ◽  
Secondary Metabolite Biosynthesis

Hadal zones are marine environments deeper than 6,000 m, most of which comprise oceanic trenches. Microbes thriving at such depth experience high hydrostatic pressure and low temperature. The genomic potentials of these microbes to such extreme environments are largely unknown. Here, we compare five complete genomes of bacterial strains belonging to Labrenzia aggregata (Alphaproteobacteria), including four from the Mariana Trench at depths up to 9,600 m and one reference from surface seawater of the East China Sea, to uncover the genomic potentials of this species. Genomic investigation suggests all the five strains of L. aggregata as participants in nitrogen and sulfur cycles, including denitrification, dissimilatory nitrate reduction to ammonium (DNRA), thiosulfate oxidation, and dimethylsulfoniopropionate (DMSP) biosynthesis and degradation. Further comparisons show that, among the five strains, 85% gene functions are similar with 96.7% of them encoded on the chromosomes, whereas the numbers of functional specific genes related to osmoregulation, antibiotic resistance, viral infection, and secondary metabolite biosynthesis are majorly contributed by the differential plasmids. A following analysis suggests the plasmidic gene numbers increase along with isolation depth and most plasmids are dissimilar among the five strains. These findings provide a better understanding of genomic potentials in the same species throughout a deep-sea water column and address the importance of externally originated plasmidic genes putatively shaped by deep-sea environment.

scholarly journals Environmental factors shape the culturable bacterial diversity in deep-sea water and surface sediments from the Mariana Trench

2022 ◽  
Author(s):  
Yuewei MA ◽  
Wenmian DING ◽  
Yuepeng WANG ◽  
Ping CHEN ◽  
Hui ZHOU ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Microbial Diversity ◽  
Bacterial Diversity ◽  
Deep Sea ◽  
Surface Sediments ◽  
Sea Water ◽  
Environmental Parameters ◽  
Bacterial Strains ◽  
Mariana Trench ◽  
Deep Sea Water

Hailed as "The Fourth Pole", the Mariana Trench is the deepest part of the ocean. The microbial diversity in it is extremely complicated, which might be caused by the unique environmental factors such as high salinity, low temperature, high hydrostatic pressure, and limited nutrition. Based on 4 seawater samples and 4 sediment samples obtained from the Mariana Trench, we isolated and fostered the microorganism clones with kinds of culture mediums and high-throughput culturing. By using the molecular identification methods based on PCR of 16S rDNA and ITS gene, 1266 bacterial strains in total were isolated and identified, which affiliated to 7 classes, 16 orders, 25 families and 36 genera in four phyla：Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Strains in genera Halomonas, Pseudoaltermonas were the dominant bacteria isolated from the samples. With Mantel tests on the sample-environmental parameter matrix, the sample-environmental organic matter diversity matrix and the sample-microbial diversity matrix, we concluded that the environmental parameters and the organic matters in the condition can shape the culturable bacterial diversity in deep-sea water and surface sediments from the Mariana Trench.

scholarly journals Genome sequencing of deep-sea hydrothermal vent snails reveals adaptions to extreme environments

GigaScience ◽  
2020 ◽  
Vol 9 (12) ◽  
Author(s):  
Xiang Zeng ◽  
Yaolei Zhang ◽  
Lingfeng Meng ◽  
Guangyi Fan ◽  
Jie Bai ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Deep Sea ◽  
Hydrothermal Vents ◽  
Extreme Environments ◽  
Genomic Analysis ◽  
Gene Families ◽  
Comparative Genomic ◽  
Limited Information ◽  
Long Terminal Repeats ◽  
Family Analysis

Abstract Background The scaly-foot snail (Chrysomallon squamiferum) is highly adapted to deep-sea hydrothermal vents and has drawn much interest since its discovery. However, the limited information on its genome has impeded further related research and understanding of its adaptation to deep-sea hydrothermal vents. Findings Here, we report the whole-genome sequencing and assembly of the scaly-foot snail and another snail (Gigantopelta aegis), which inhabits similar environments. Using Oxford Nanopore Technology, 10X Genomics, and Hi-C technologies, we obtained a chromosome-level genome of C. squamiferum with an N50 size of 20.71 Mb. By constructing a phylogenetic tree, we found that these 2 deep-sea snails evolved independently of other snails. Their divergence from each other occurred ∼66.3 million years ago. Comparative genomic analysis showed that different snails have diverse genome sizes and repeat contents. Deep-sea snails have more DNA transposons and long terminal repeats but fewer long interspersed nuclear elements than other snails. Gene family analysis revealed that deep-sea snails experienced stronger selective pressures than freshwater snails, and gene families related to the nervous system, immune system, metabolism, DNA stability, antioxidation, and biomineralization were significantly expanded in scaly-foot snails. We also found 251 H-2 Class II histocompatibility antigen, A-U α chain-like (H2-Aal) genes, which exist uniquely in the Gigantopelta aegis genome. This finding is important for investigating the evolution of major histocompatibility complex (MHC) genes. Conclusion Our study provides new insights into deep-sea snail genomes and valuable resources for further studies.

Characterization, Pathogenicity, Phylogeny, and Comparative Genomic Analysis of Pseudomonas tolaasii Strains Isolated from Various Mushrooms in China

2021 ◽  
Author(s):  
Zhenghui Liu ◽  
Yitong Zhao ◽  
Frederick Leo Sossah ◽  
Benjamin Azu Okorley ◽  
Daniel G. Amoako ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Genomic Analysis ◽  
Gene Families ◽  
Effective Control ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Bacterial Strains ◽  
Secretion Systems ◽  
Pseudomonas Tolaasii ◽  
Antimicrobial Resistance Genes

Since 2016, devastating bacterial blotch affecting the fruiting bodies of Agaricus bisporus, Cordyceps militaris, Flammulina filiformis, and Pleurotus ostreatus in China has caused severe economic losses. We isolated 102 bacterial strains and characterized them polyphasically. We identified the causal agent as Pseudomonas tolaasii and confirmed the pathogenicity of the strains. A host range test further confirmed the pathogen’s ability to infect multiple hosts. This is the first report in China of bacterial blotch in C. militaris caused by P. tolaasii. Whole-genome sequences were generated for three strains: Pt11 (6.48 Mb), Pt51 (6.63 Mb), and Pt53 (6.80 Mb), and pangenome analysis was performed with 13 other publicly accessible P. tolaasii genomes to determine their genetic diversity, virulence, antibiotic resistance, and mobile genetic elements. The pangenome of P. tolaasii is open, and many more gene families are likely to emerge with further genome sequencing. Multilocus sequence analysis using the sequences of four common housekeeping genes (glns, gyrB, rpoB, and rpoD) showed high genetic variability among the P. tolaasii strains, with 115 strains clustered into a monophyletic group. The P. tolaasii strains possess various genes for secretion systems, virulence factors, carbohydrate-active enzymes, toxins, secondary metabolites, and antimicrobial resistance genes that are associated with pathogenesis and adapted to different environments. The myriad of insertion sequences, integrons, prophages, and genome islands encoded in the strains may contribute to genome plasticity, virulence, and antibiotic resistance. These findings advance understanding of the determinants of virulence, which can be targeted for the effective control of bacterial blotch disease.

scholarly journals Insights into the Metabolism and Evolution of the Genus Acidiphilium, a Typical Acidophile in Acid Mine Drainage

mSystems ◽  
2020 ◽  
Vol 5 (6) ◽  
Author(s):  
Liangzhi Li ◽  
Zhenghua Liu ◽  
Min Zhang ◽  
Delong Meng ◽  
Xueduan Liu ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Evolutionary History ◽  
Mine Drainage ◽  
Extreme Environments ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Metabolic Potential ◽  
Ecological Functions ◽  
History Of

ABSTRACT Here, we report three new Acidiphilium genomes, reclassified existing Acidiphilium species, and performed the first comparative genomic analysis on Acidiphilium in an attempt to address the metabolic potential, ecological functions, and evolutionary history of the genus Acidiphilium. In the genomes of Acidiphilium, we found an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic expansion, including genes conferring photosynthesis (puf, puh), CO2 assimilation (rbc), capacity for methane metabolism (mmo, mdh, frm), nitrogen source utilization (nar, cyn, hmp), sulfur compound utilization (sox, psr, sqr), and multiple metal and osmotic stress resistance capacities (czc, cop, ect). Additionally, the predicted donors of horizontal gene transfer were present in a cooccurrence network of Acidiphilium. Genome-scale positive selection analysis revealed that 15 genes contained adaptive mutations, most of which were multifunctional and played critical roles in the survival of extreme conditions. We proposed that Acidiphilium originated in mild conditions and adapted to extreme environments such as acidic mineral sites after the acquisition of many essential functions. IMPORTANCE Extremophiles, organisms that thrive in extreme environments, are key models for research on biological adaption. They can provide hints for the origin and evolution of life, as well as improve the understanding of biogeochemical cycling of elements. Extremely acidophilic bacteria such as Acidiphilium are widespread in acid mine drainage (AMD) systems, but the metabolic potential, ecological functions, and evolutionary history of this genus are still ambiguous. Here, we sequenced the genomes of three new Acidiphilium strains and performed comparative genomic analysis on this extremely acidophilic bacterial genus. We found in the genomes of Acidiphilium an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic ability expansion, as indicated by phylogenetic reconstruction and gene context comparison. This study has advanced our understanding of microbial evolution and biogeochemical cycling in extreme niches.

scholarly journals Complete Genome Sequencing and Comparative Genomics of Three Potential Probiotic Strains, Lacticaseibacillus casei FBL6, Lacticaseibacillus chiayiensis FBL7, and Lacticaseibacillus zeae FBL8

2022 ◽  
Vol 12 ◽  
Author(s):  
Eiseul Kim ◽  
Seung-Min Yang ◽  
Dayoung Kim ◽  
Hae-Yeong Kim
Keyword(s):  
Complete Genome ◽  
Functional Characterization ◽  
Genomic Analysis ◽  
Raw Milk ◽  
Phenotypic Characterization ◽  
Comparative Genomic ◽  
Probiotic Properties ◽  
Bacterial Strains ◽  
Physiological Control ◽  
Wide Range

Lacticaseibacillus casei, Lacticaseibacillus chiayiensis, and Lacticaseibacillus zeae are very closely related Lacticaseibacillus species. L. casei has long been proposed as a probiotic, whereas studies on functional characterization for L. chiayiensis and L. zeae are some compared to L. casei. In this study, L. casei FBL6, L. chiayiensis FBL7, and L. zeae FBL8 were isolated from raw milk, and their probiotic properties were investigated. Genomic analysis demonstrated the role of L. chiayiensis and L. zeae as probiotic candidates. The three strains were tolerant to acid and bile salt, with inhibitory action against pathogenic bacterial strains and capacity of antioxidants. Complete genome sequences of the three strains were analyzed to highlight the probiotic properties at the genetic level, which results in the discovery of genes corresponding to phenotypic characterization. Moreover, genes known to confer probiotic characteristics were identified, including genes related to biosynthesis, defense machinery, adhesion, and stress adaptation. The comparative genomic analysis with other available genomes revealed 256, 214, and 32 unique genes for FBL6, FBL7, and FBL8, respectively. These genomes contained individual genes encoding proteins that are putatively involved in carbohydrate transport and metabolism, prokaryotic immune system for antiviral defense, and physiological control processes. In particular, L. casei FBL6 had a bacteriocin gene cluster that was not present in other genomes of L. casei, resulting in this strain may exhibit a wide range of antimicrobial activity compared to other L. casei strains. Our data can help us understand the probiotic functionalities of the three strains and suggest that L. chiayiensis and L. zeae species, which are closely related to L. casei, can also be considered as novel potential probiotic candidate strains.

scholarly journals Shift and Metabolic Potentials of Microbial Eukaryotic Communities Across the Full Depths of the Mariana Trench

2021 ◽  
Vol 11 ◽  
Author(s):  
Xiao-Yu Zhu ◽  
Jiwen Liu ◽  
Chun-Xu Xue ◽  
Jiwei Tian ◽  
Xiao-Hua Zhang
Keyword(s):  
Fatty Acid ◽  
Deep Sea ◽  
Fatty Acid Biosynthesis ◽  
Dna Structure ◽  
Surface Seawater ◽  
Acid Biosynthesis ◽  
Mariana Trench ◽  
Microbial Eukaryotes ◽  
Related Distribution ◽  
Hadal Zone

Microbial eukaryotes are widespread and play important roles in marine ecosystems. However, their ecological characteristics in the deep sea (>1,000 m), especially hadal trenches, were largely unknown. Here, we investigated the diversity and metabolic potentials of microbial eukaryotes along the whole water column of the Mariana Trench by metagenomics. Our results showed clear depth-related distribution of microbial eukaryotic community and associated metabolic potentials. Surface seawater was dominated by phototrophic/mixotrophic groups (e.g., Dinoflagellata) and genes involved in biosynthesis (photosynthesis and fatty acid biosynthesis), while deep (bathypelagic and/or hadal) seawaters were enriched with heterotrophic groups (e.g., Bicoecea) and genes related to digestion (lysosomal enzymes and V-type ATPase) and carbohydrate metabolism. Co-occurrence analysis revealed high intra-domain connectivity, indicating that microbial eukaryotic composition was more influenced by microbial eukaryotes themselves than bacteria. Increased abundance of genes associated with unsaturated fatty acid biosynthesis likely plays a role in resisting high hydrostatic pressure. Top1 and hupB genes, responsible for the formation and stabilization of DNA structure, were unique and abundant in the hadal zone and thus may be helpful to stabilize DNA structure in the deep sea. Overall, our results provide insights into the distribution and potential adaptability of microbial eukaryotes in the hadal zone.

scholarly journals Comparative Genomic Analysis of Bacillus thuringiensis Reveals Molecular Adaptations to Copper Tolerance

2018 ◽  
Author(s):  
Low Yi Yik ◽  
Grace Joy Wei Lie Chin ◽  
Collin Glen Joseph ◽  
Kenneth Francis Rodrigues
Keyword(s):  
Bacillus Thuringiensis ◽  
Extreme Environments ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Copper Resistance ◽  
Copper Tolerance ◽  
Contaminated Site ◽  
Comparative Genomic ◽  
Wide Range ◽  
Almost All

ABSTRACTBacillus thuringiensis is a type of Gram positive and rod shaped bacterium that is found in a wide range of habitats. Despite the intensive studies conducted on this bacterium, most of the information available are related to its pathogenic characteristics, with only a limited number of publications mentioning its ability to survive in extreme environments. Recently, a B. thuringiensis MCMY1 strain was successfully isolated from a copper contaminated site in Mamut Copper Mine, Sabah. This study aimed to conduct a comparative genomic analysis by using the genome sequence of MCMY1 strain published in GenBank (PRJNA374601) as a target genome for comparison with other available B. thuringiensis genomes at the GenBank. Whole genome alignment, Fragment all-against-all comparison analysis, phylogenetic reconstruction and specific copper genes comparison were applied to all forty-five B. thuringiensis genomes to reveal the molecular adaptation to copper tolerance. The comparative results indicated that B. thuringiensis MCMY1 strain is closely related to strain Bt407 and strain IS5056. This strain harbors almost all available copper genes annotated from the forty-five B. thuringiensis genomes, except for the gene for Magnesium and cobalt efflux protein (CorC) which plays an indirect role in reducing the oxidative stress that caused by copper and other metal ions. Furthermore, the findings also showed that the Copper resistance gene family, CopABCDZ and its repressor (CsoR) are conserved in almost all sequenced genomes but the presence of the genes for Cytoplasmic copper homeostasis protein (CutC) and CorC across the sample genomes are highly inconsonant. The variation of these genes across the B. thuringiensis genomes suggests that each strain may have adapted to their specific ecological niche. However, further investigations will be need to support this preliminary hypothesis.

scholarly journals Alcanivorax dieselolei sp. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment

2005 ◽  
Vol 55 (3) ◽  
pp. 1181-1186 ◽  
Author(s):  
Chenli Liu ◽  
Zongze Shao
Keyword(s):  
Deep Sea ◽  
Sea Water ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Alkane Hydroxylase ◽  
Biochemical Tests ◽  
Deep Sea Sediment ◽  
Degrading Bacterium ◽  
Internal Transcribed Spacer Sequences

Two bacterial strains, B-5T and NO1A, were isolated from the surface water of the Bohai Sea and deep-sea sediment of the east Pacific Ocean, respectively. Both strains were halophilic, aerobic, Gram-negative, non-spore-forming, catalase- and oxidase-positive motile rods. They grew on a restricted spectrum of organic compounds, including some organic acids and alkanes. On the basis of 16S rRNA gene sequence similarity, strains B-5T and NO1A were shown to belong to the γ-Proteobacteria. Highest similarity values were found with Alcanivorax venustensis (95·2 %), Alcanivorax jadensis (94·6 %) and Alcanivorax borkumensis (94·1 %). Principal fatty acids of both strains were C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. The chemotaxonomically characteristic fatty acid C19 : 0 cyclo ω8c was also detected. On the basis of the above, together with results of physiological and biochemical tests, DNA–DNA hybridization, comparisons of 16S–23S internal transcribed spacer sequences and comparisons of the partial deduced amino acid sequence of alkane hydroxylase, both strains were affiliated to the genus Alcanivorax but were differentiated from recognized Alcanivorax species. Therefore, a novel species, Alcanivorax dieselolei sp. nov., represented by strains B-5T and NO1A is proposed, with the type strain B-5T (=DSM 16502T=CGMCC 1.3690T).

scholarly journals Origins of the current seventh cholera pandemic

2016 ◽  
Vol 113 (48) ◽  
pp. E7730-E7739 ◽  
Author(s):  
Dalong Hu ◽  
Bin Liu ◽  
Lu Feng ◽  
Peng Ding ◽  
Xi Guo ◽  
...  
Keyword(s):  
Middle East ◽  
Driving Forces ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Bacterial Strains ◽  
Pandemic Strain ◽  
Nonpathogenic Strain ◽  
Rapid Diversification ◽  
El Tor ◽  
Key Events

Vibrio choleraehas caused seven cholera pandemics since 1817, imposing terror on much of the world, but bacterial strains are currently only available for the sixth and seventh pandemics. The El Tor biotype seventh pandemic began in 1961 in Indonesia, but did not originate directly from the classical biotype sixth-pandemic strain. Previous studies focused mainly on the spread of the seventh pandemic after 1970. Here, we analyze in unprecedented detail the origin, evolution, and transition to pandemicity of the seventh-pandemic strain. We used high-resolution comparative genomic analysis of strains collected from 1930 to 1964, covering the evolution from the first available El Tor biotype strain to the start of the seventh pandemic. We define six stages leading to the pandemic strain and reveal all key events. The seventh pandemic originated from a nonpathogenic strain in the Middle East, first observed in 1897. It subsequently underwent explosive diversification, including the spawning of the pandemic lineage. This rapid diversification suggests that, when first observed, the strain had only recently arrived in the Middle East, possibly from the Asian homeland of cholera. The lineage migrated to Makassar, Indonesia, where it gained the important virulence-associated elementsVibrioseventh pandemic island I (VSP-I), VSP-II, and El Tor type cholera toxin prophage by 1954, and it then became pandemic in 1961 after only 12 additional mutations. Our data indicate that specific niches in the Middle East and Makassar were important in generating the pandemic strain by providing gene sources and the driving forces for genetic events.

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