scholarly journals Wide distribution of phage that infect freshwater SAR11 bacteria

2019 ◽  
Author(s):  
Lin-Xing Chen ◽  
Yan-Lin Zhao ◽  
Katherine D. McMahon ◽  
Jiro F. Mori ◽  
Gerdhard L. Jessen ◽  
...  
Keyword(s):  
Draft Genome ◽  
Wide Distribution ◽  
Freshwater Ecosystems ◽  
Metagenomic Data ◽  
Genomic Features ◽  
Related Phage ◽  
Lake Mendota ◽  
Worldwide Distribution ◽  
Marine Habitats ◽  
Occurrence Patterns

AbstractFonsibacter (LD12 subclade) are among the most abundant bacterioplankton in freshwater ecosystems. These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11) that dominate many marine habitats. Although a handful of Pelagibacter phage (Pelagiphage) have been described, no phage that infect Fonsibacter have been reported. In this study, a complete Fonsibacter genome containing a prophage was reconstructed from metagenomic data. A circularized and complete genome related to the prophage, referred to as uv-Fonsiphage-EPL, shows high similarity to marine Pelagiphage HTVC025P. Additionally, we reconstructed three complete and one draft genome of phage related to marine Pelagiphage HTVC010P, and predicted a lytic strategy. The similarity in codon usage and co-occurrence patterns of HTVC010P-related phage and Fonsibacter suggested that these phage infect Fonsibacter. Similar phage were detected in Lake Mendota, Wisconsin, where Fonsibacter is also present. A search of related phage revealed the worldwide distribution of some genotypes in freshwater ecosystems, suggesting their substantial role in shaping indigenous microbial assemblages and influence on biogeochemical cycling. However, the uv-Fonsiphage-EPL and one lineage of HTVC010P-related phage have a more limited distribution in freshwater ecosystems. Based on this, and their close phylogenetic relatedness with Pelagiphage, we predict that they transitioned from saline into freshwater ecosystems comparatively recently. Overall, the findings provide insights into the genomic features of phage that infect Fonsibacter, and expand understanding of the ecology and evolution of these important bacteria.

scholarly journals Wide Distribution of Phage That Infect Freshwater SAR11 Bacteria

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Lin-Xing Chen ◽  
Yanlin Zhao ◽  
Katherine D. McMahon ◽  
Jiro F. Mori ◽  
Gerdhard L. Jessen ◽  
...  
Keyword(s):  
Draft Genome ◽  
Wide Distribution ◽  
Freshwater Ecosystems ◽  
Metagenomic Data ◽  
Related Phage ◽  
Lake Mendota ◽  
Worldwide Distribution ◽  
Marine Habitats ◽  
Complete Genomes ◽  
Freshwater Habitats

ABSTRACT Fonsibacter (LD12 subclade) is among the most abundant bacterioplankton in freshwater ecosystems. These bacteria belong to the order Pelagibacterales (SAR11) and are related to Pelagibacter (marine SAR11), which dominates many marine habitats. Although a few Pelagibacter phage (Pelagiphage) have been described, no phage that infect Fonsibacter have been reported. In this study, we describe two groups of Podoviridae phage that infect Fonsibacter. A complete Fonsibacter genome containing a prophage was reconstructed from metagenomic data. A circularized and complete genome related to the prophage, referred to as uv-Fonsiphage-EPL (lysogenic strategy), shows high similarity to marine Pelagiphage HTVC025P. Additionally, we reconstructed three complete genomes and one draft genome of phage related to marine Pelagiphage HTVC010P and predicted a lytic strategy. The similarity in codon usage and cooccurrence patterns of HTVC010P-related phage and Fonsibacter suggested that these phage infect Fonsibacter. Similar phage were detected in Lake Mendota, Wisconsin, where Fonsibacter is also present. A search of related phage revealed the worldwide distribution of some genotypes in freshwater ecosystems, suggesting their substantial role in shaping indigenous microbial assemblages and influence on biogeochemical cycling. However, the uv-Fonsiphage-EPL and one group of HTVC010P-related phage have a more limited distribution in freshwater ecosystems. Overall, the findings provide insights into the genomic features of phage that infect Fonsibacter and expand understanding of the ecology and evolution of these important bacteria. IMPORTANCE Fonsibacter represents a significant microbial group of freshwater ecosystems. Although the genomic and metabolic features of these bacteria have been well studied, no phage infecting them has been reported. In this study, we reconstructed complete genomes of Fonsibacter and infecting phage and revealed their close relatedness to the phage infecting marine SAR11 members. Also, we illustrated that phage that infect Fonsibacter are widely distributed in freshwater habitats. In summary, the results contribute new insights into the ecology and evolution of Fonsibacter and phage.

scholarly journals Draft Genome Sequence of Plant Growth-Promoting Drought-Tolerant Bacillus sp. Strain CMAA 1363 Isolated from the Brazilian Caatinga Biome

2017 ◽  
Vol 5 (5) ◽  
Author(s):  
Vanessa Nessner Kavamura ◽  
Suikinai Nobre Santos ◽  
Rodrigo Gouvêa Taketani ◽  
Rafael Leandro Figueiredo Vasconcellos ◽  
Itamar Soares Melo
Keyword(s):  
Plant Growth ◽  
Growth Promotion ◽  
Draft Genome ◽  
Negative Effects ◽  
Genomic Features ◽  
Drought Tolerant ◽  
Caatinga Biome ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Plant Growth Promoting Traits

ABSTRACT The strain of Bacillus sp. CMAA 1363 was isolated from the Brazilian Caatinga biome and showed plant growth-promoting traits and ability to promote maize growth under drought stress. Sequencing revealed genes involved in stress response and plant growth promotion. These genomic features might aid in the protection of plants against the negative effects imposed by drought.

Prediction and analysis of Metagenomic operons via MetaRon: a Pipeline for Prediction of Metagenomic OpeRons

2020 ◽  
Author(s):  
Syed Shujaat Ali Zaidi ◽  
Masood Ur Rehman Kayani ◽  
Xuegong Zhang ◽  
Imran Haider Shamsi
Keyword(s):  
Draft Genome ◽  
Gene Clusters ◽  
Transcriptional Unit ◽  
Metagenomic Data ◽  
Functional Information ◽  
Data Set ◽  
E Coli ◽  
Operon Prediction ◽  
K 12 ◽  
Gut Metagenome

Abstract Background: Efficient regulation of bacterial genes against the environmental stimulus results in unique operonic organizations. Lack of complete reference and functional information makes metagenomic operon prediction challenging and therefore opens new perspectives on the interpretation of the host-microbe interactions. Methods: Here we present MetaRon (pipeline for the prediction of Metagenomic operons), an open-source pipeline explicitly designed for the metagenomic shotgun sequencing data. It recreates the operonic structure without functional information. MetaRon identifies closely packed co-directional gene clusters with a promoter upstream and downstream of the first and last gene, respectively. Promoter prediction marks the transcriptional unit boundary (TUB) of closely packed co-directional gene clusters.Results: Escherichia coli (E. coli) K-12 MG1655 presents a gold standard for operon prediction. Therefore, MetaRon was initially implemented on two simulated illumina datasets: (1) E. coli MG1655 genome (2) a mixture of E. coli MG1655, Mycobacterium tuberculosis H37Rv and Bacillus subtilis str. 168 genomes. Operons were predicted in the single genome and mixture of genomes with a sensitivity of 97.8% and 93.7%, respectively. In the next phase, operons predicted from E. coli c20 draft genome isolated from chicken gut metagenome achieved a sensitivity of 94.1%. Lastly, the application of MetaRon on 145 paired-end gut metagenome samples identified 1,232,407 unique operons. Conclusion: MetaRon removes two notable limitations of existing methods: (1) dependency on functional information, and (2) liberates the users from enormous metagenomic data management. Current study showed the idea of using operons as subset to represent the whole-metagenome in terms of secondary metabolites and demonstrated its effectiveness in explaining the occurrence of a disease condition. This will significantly reduce the hefty whole-metagenome data to a small more precise data set. Furthermore, metabolic pathways from the operonic sequences were identified in association with the occurrence of type 2 diabetes (T2D). Presumably, this is the first organized effort to predict metagenomic operons and perform a detailed analysis in association with a disease, in this case T2D. The application of MetaRon to metagenome data at diverse scale will be beneficial to understand the gene regulation and therapeutic metagenomics.

scholarly journals Worldwide distribution and abundance of microplastic: How dire is the situation?

2018 ◽  
Vol 36 (10) ◽  
pp. 873-897 ◽  
Author(s):  
Fauziah Shahul Hamid ◽  
Mehran Sanam Bhatti ◽  
Norkhairiyah Anuar ◽  
Norkhairah Anuar ◽  
Priya Mohan ◽  
...  
Keyword(s):  
Aquatic Environment ◽  
Freshwater Ecosystems ◽  
Hydrodynamic Conditions ◽  
Widespread Occurrence ◽  
Environmental Pressure ◽  
Worldwide Distribution ◽  
Abundance And Distribution

The widespread occurrence of microplastic has invaded the environment to an extent that it appears to be present throughout the globe. This review investigated the global abundance and distribution of microplastics in marine and freshwater ecosystems. Furthermore, the issues and challenges have been addressed for better findings in microplastics studies. Findings revealed that the accumulation of microplastics varies geographically, with locations, hydrodynamic conditions, environmental pressure, and time. From this review, it is crucial that proper regulations are proposed and implemented in order to reduce the occurrence of microplastics in the aquatic environment. Without appropriate law and regulations, microplastic pollution will eventually threaten human livelihood.

scholarly journals Draft Genome Sequence of the Marine Bacterium Pseudomonas aestusnigri VGXO14T

2017 ◽  
Vol 5 (32) ◽  
Author(s):  
Margarita Gomila ◽  
Magdalena Mulet ◽  
Jorge Lalucat ◽  
Elena García-Valdés
Keyword(s):  
Crude Oil ◽  
Genome Sequence ◽  
Type Strain ◽  
Marine Bacterium ◽  
Draft Genome ◽  
Phylogenetic Group ◽  
Sand Sample ◽  
Content Type ◽  
Marine Habitats ◽  
Marine Sand

ABSTRACT The type strain of Pseudomonas aestusnigri (VGXO14), isolated from a crude oil-polluted marine sand sample, is a member of the P. pertucinogena phylogenetic group. Here, we report the genome sequence (3.83 Mb) of P. aestusnigri to gain insights into the biology and taxonomy of marine Pseudomonas spp. adapted to polluted marine habitats.

scholarly journals Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0250092
Author(s):  
Bruce Parrello ◽  
Rory Butler ◽  
Philippe Chlenski ◽  
Gordon D. Pusch ◽  
Ross Overbeek
Keyword(s):  
Draft Genome ◽  
Single Copy ◽  
Metagenomic Data ◽  
Use Case ◽  
High Quality ◽  
Complete Genomes ◽  
Downstream Analysis ◽  
Low Coverage ◽  
Derived Data ◽  
Reference Genomes

Large amounts of metagenomically-derived data are submitted to PATRIC for analysis. In the future, we expect even more jobs submitted to PATRIC will use metagenomic data. One in-demand use case is the extraction of near-complete draft genomes from assembled contigs of metagenomic origin. The PATRIC metagenome binning service utilizes the PATRIC database to furnish a large, diverse set of reference genomes. We provide a new service for supervised extraction and annotation of high-quality, near-complete genomes from metagenomically-derived contigs. Reference genomes are assigned to putative draft genome bins based on the presence of single-copy universal marker roles in the sample, and contigs are sorted into these bins by their similarity to reference genomes in PATRIC. Each set of binned contigs represents a draft genome that will be annotated by RASTtk in PATRIC. A structured-language binning report is provided containing quality measurements and taxonomic information about the contig bins. The PATRIC metagenome binning service emphasizes extraction of high-quality genomes for downstream analysis using other PATRIC tools and services. Due to its supervised nature, the binning service is not appropriate for mining novel or extremely low-coverage genomes from metagenomic samples.

Checklist of the marine and estuarine fishes of New Ireland Province, Papua New Guinea, western Pacific Ocean, with 810 new records

Zootaxa ◽  
2019 ◽  
Vol 4588 (1) ◽  
pp. 1
Author(s):  
RONALD FRICKE ◽  
GERALD R. ALLEN ◽  
DIETMAR AMON ◽  
SERGE ANDRÉFOUËT ◽  
WEI-JEN CHEN ◽  
...  
Keyword(s):  
New Records ◽  
Fish Fauna ◽  
Wide Distribution ◽  
Estuarine Fish ◽  
Western Pacific Ocean ◽  
Transitional Waters ◽  
Estuarine Fishes ◽  
Marine Habitats ◽  
Freshwater Habitats ◽  
Wide Distribution Range

A checklist of the marine and estuarine fishes of New Ireland Province is presented, with special emphasis on Kavieng District, combining both previous and new records. After the recent KAVIENG 2014 expedition, a total of 1325 species in 153 families were recorded from the region. The largest families are the Gobiidae, Pomacentridae, Labridae, Serranidae, Apogonidae, Lutjanidae, Chaetodontidae, Blenniidae, Carangidae, Acanthuridae, Scaridae, Holocentridae, Syn-gnathidae, Lethrinidae and Scorpaenidae. A total of 810 fish species (61.1 % of the total marine and estuarine fish fauna) are recorded from New Ireland for the first time.The fish fauna of New Ireland includes 142 species in transitional waters and 1264 species in marine habitats, and 54 species species in freshwater habitats. Zoogeographically, 1179 species have a wide distribution range, most frequently a broad Indo-West Pacific distribution. Among the remaining species, just 12 are endemic to New Ireland. 

scholarly journals Draft Genome Sequences of Nine Cultivable Heterotrophic Proteobacteria Isolated from Phycosphere Microbiota of Toxic Alexandrium catenella LZT09

2020 ◽  
Vol 9 (22) ◽  
Author(s):  
Xiao-Ling Zhang ◽  
Xi Yang ◽  
Shu-Jun Wang ◽  
Zhi-Wei Jiang ◽  
Zhang-Xian Xie ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Aquatic Ecosystems ◽  
Draft Genome ◽  
Toxic Dinoflagellate ◽  
Genome Sequences ◽  
Alexandrium Catenella ◽  
Genomic Features ◽  
Content Type ◽  
Microscopic Interactions

ABSTRACT Microscopic interactions between phycosphere microbiota and host algae play crucial roles in aquatic ecosystems. Despite their significance, there is a scarcity of available genome sequences derived from the phycosphere microbiome. Here, we report the draft genome sequences of nine heterotrophic proteobacterial strains isolated from the toxic dinoflagellate Alexandrium catenella LZT09 during execution of our Phycosphere Microbiome Project. Further exploration of the genomic features of the alga-associated bacterial community will profoundly help in deeply deciphering the processes and mechanisms governing the host-microbe interactome within algal holobionts in the ocean.

scholarly journals Draft Genome Sequence of a Harveyi Clade Bacterium Isolated from Lolliguncula brevis Squid

2020 ◽  
Vol 9 (8) ◽  
Author(s):  
Alecia N. Septer ◽  
Lauren Speare ◽  
Collin K. Coleman ◽  
Stephanie Smith ◽  
Coby Dorsey ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Free Living ◽  
Content Type ◽  
Marine Habitats ◽  
Lolliguncula Brevis

Vibrio species of the Harveyi clade are commonly found in free-living and host-associated marine habitats. Here, we report the draft genome sequence for a Harveyi clade bacterium, Vibrio sp. strain LB10LO1, which was isolated from the Atlantic brief squid Lolliguncula brevis.

scholarly journals Draft Genome Sequence of Salinispora sp. Strain H7-4, Isolated from Deep-Sea Sediments of the Shikoku Basin

2020 ◽  
Vol 9 (45) ◽  
Author(s):  
Dana Ulanova ◽  
Yuka Uenaka ◽  
Masazumi Sakama ◽  
Tetsuya Sakurai
Keyword(s):  
16S Rdna ◽  
Genome Sequence ◽  
Deep Sea ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Marine Actinomycetes ◽  
Marine Habitats ◽  
Shikoku Basin ◽  
Deep Sea Sediments

ABSTRACT Salinispora spp. are obligate marine actinomycetes reported mainly from shallow tropical and subtropical marine habitats. In this announcement, we present the isolation and draft genome sequence of Salinispora sp. strain H7-4 of a new 16S rDNA phylotype from deep-sea sediments of the Shikoku Basin.

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