Marinobacter profundi sp. nov., a slightly halophilic bacterium isolated from a deep-sea sediment sample of the New Britain Trench

Cao, Junwei; Liu, Ping; Liu, Renju; Su, Hai-Nan; Wei, Yuli; Liu, Rulong; Fang, Jiasong

doi:10.1007/s10482-018-1176-8

Cited by 15 publications

(3 citation statements)

References 35 publications

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“…Regarding the difference between the original and cultured hadal taxa, we found that members of Marinobacter, Idiomarina, Sulfitobacter, Reyranella, and Erythrobacter were enriched in the cultured microbiota, suggesting that they can proliferate under laboratory conditions. Members of Marinobacter have been isolated from a variety of deep-sea environments, including cold seeps (Sun et al, 2020), hydrothermal vents (Zhou et al, 2020), and trenches (Cao et al, 2019;Ahmad et al, 2020).…”

Section: A L C a N I V O R A X A L I I D O N G I A A L T E R O M O N A S A N A E R O H A L O S P H A E R A B U R K H O L D E R I A C A N mentioning

confidence: 99%

Culture Enrichment Combined With Long-Read Sequencing Facilitates Genomic Understanding of Hadal Sediment Microbes

Wang

Fan

et al. 2021

Front. Mar. Sci.

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Culture enrichment was developed to discover the uncharted microbial species in the environmental microbiota. Yet this strategy has not been widely used to study microbes of deep-sea environments. Here, we report the cultivation and metagenomic analysis of oceanic sediment microbiota collected from 6,477 m deep in the Mariana Trench. The sediment samples were cultured anaerobically in the laboratory for 4 months, before being subjected to full-length 16S rRNA gene sequencing using the PacBio technique and metagenome sequencing using both the Illumina and Oxford Nanopore techniques. The 16S rRNA gene analyses revealed 437 operational taxonomic units specific to the cultured microbes, despite the lower diversity of the cultured microbiota in comparison with the original. Metagenome analyses revealed the prevalence of functions related to respiration, energy production, and stress response in the cultured microbes, suggesting these functions may contribute to microbial proliferation under laboratory conditions. Binning of the assembled metagenome contigs of the cultured microbiota generated four nearly complete genomes affiliated to yet unclassified species under the genera Alcanivorax, Idiomarina, Sulfitobacter, and Erythrobacter. Excepting Alcanivorax, the other three genera were almost undetectable in the original samples and largely enriched in the cultured samples. The four genomes possessed a variety of genes for carbohydrate utilization and nitrite reduction, pointing to an ability to respire diverse carbon sources using nitrite as the final electron acceptor. Taken together, the findings suggest that a combination of culture enrichment and long-read sequencing is an ideal way to mine novel microbial species in the hadal environment, particularly species that are rare in their native environmental niches, and thus expand our understanding of the hadal microbial diversity and function.

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Section: A L C a N I V O R A X A L I I D O N G I A A L T E R O M O N A S A N A E R O H A L O S P H A E R A B U R K H O L D E R I A C A N mentioning

confidence: 99%

Culture Enrichment Combined With Long-Read Sequencing Facilitates Genomic Understanding of Hadal Sediment Microbes

Wang

Fan

et al. 2021

Front. Mar. Sci.

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“…The cls and psd genes play important roles for the bacterial adaptation in deep-sea environment (Yano et al, 1998;Pfeiffer et al, 2003;Kawamoto et al, 2009;Cao et al, 2019).…”

Section: Cell Wall/ Membrane Alterationmentioning

confidence: 99%

Whole genome sequencing of four bacterial strains from South Shetland Trench revealing biosynthetic and environmental adaptation gene clusters

et al. 2020

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Whole genome sequences of four bacterial strains Dietzia maris SST1, Pseudomonas zhaodongensis SST2, Pseudomonas sp. SST3 and Halomonas sulfidaeris SST4, recovered from the South Shetland Trench sediment in Antarctica were analyzed using Ion Torrent sequencing technology. The respective sizes of their genomes (3.88, 4.99, 5.60 and 4.25 Mb) and GC contents (70.0, 60.3, 59.9 and 53.8%) are in agreement with these values of other strains of the species. The bacterial strains displayed promising antimicrobial activity against a number of pathogenic bacterial and fungal species. Whole genomes have been assembled and biosynthetic gene clusters (BGCs) have been identified using the antibiotics and Secondary Metabolite Analysis Shell (antiSMASH) web platform. Comparative analysis of the genome sequences revealed that the strains host abundant BGCs encoding for terpenes, siderophores, arylpolyene, bacteriocins, and lassopeptides. Furthermore, the key stress-related genes were identified and their distribution provided an insight into how these isolates adapt to key marine environmental conditions. This comprehensive study is a contribution to understanding the nature of life on the deepsea environments.

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“…hydrocarbonoclasticus (Gauthier et al, 1992) isolada do mar mediterrâneo próximo a uma refinaria de petróleo, M. profundi isolado do sedimento do mar profundo (Cao et al, 2018), M.…”

Section: Introductionunclassified

Do genoma aos produtos naturais

de França

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pela orientação e por propor novos desafios à minha carreira. Pela paciência, amizade e ensinamentos. À Profª. Drª. Taicia Pacheco Fill do Instituto de Química da UNICAMP pela colaboração nos experimentos químicos, por toda a paciência e por ceder espaço do seu laboratório e o tempo da sua equipe, em especial ao Jonas. À Profa. Drª. Alessandra Eustáquio da University of Illinois at Chicago por me orientar no meu estágio no exterior, pela equipe, em especial à Sylvia Kunakon. À Profª. Drª. Ana Tasca Gois Ruiz e sua equipe pela realização do experimento de atividade antiproliferativa que enriqueceram esse trabalho. Ao Prof. Dr. Marcos José Salvador do Instituto de Biologia pela colaboração, e por toda sua equipe, em especial ao Álvaro. Aos colegas e amigos da Divisão de Recursos Microbianos, por dividir essa experiência e pela ajuda nos experimentos. Ao grupo de pesquisa da Drª. Fabiana, em especial a Nataly, René, Gabriel, Marcela pela colaboração e amizade. E as amigas Milene e Milena pela amizade e momentos de descontração. À querida amiga Rayza, que estará sempre no meu coração. Obrigada pela sua amizade, seu carinho e sua complexidade. Ao CPQBA por ceder espaço e material para os meus experimentos. O presente trabalho foi realizado com apoio da Coordenação de Aperfeiçoamento de Pessoal de Nível Superior -Brasil (CAPES) -Código de Financiamento 001. Ao Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), pela concessão da bolsa de doutorado, Processo 17057612017-5. À UNICAMP, em especial ao Instituto de Biologia, e ao Programa de Pós-Graduação em Genética e Biologia Molecular, pela estrutura cedida, recursos, eficiência e pelo aprendizado. À minha família, meus pais Silvia e Jorge, meus irmãos Bruna e Felipe, e ao meu namorado Raoni, e sua amorosa família, que com paciência me auxiliaram carinhosamente nesse percurso, e me trouxeram confiança. Às minhas amigas, Ângela, Bianca, Mariela, que mesmo longe estavam presentes de alguma forma me acompanhando e dando força. À Deus, minha fortaleza. A todos que, de alguma forma, contribuíram para o desenvolvimento dessa tese e estiveram me apoiando nesse momento da minha vida. RESUMO A pandemia da COVID-19 mostrou a vulnerabilidade da sociedade humana frente às doenças infecciosas. Produtos naturais representam a principal fonte de agentes terapêuticos usados como antivirais, anticâncer e antibióticos. Nesse contexto, o objetivo desse trabalho foi avaliar o potencial biossintético e metabólico de produtos naturais de duas bactérias isoladas da Antártica. Foram sequenciados o genoma completo de duas bactérias, permitindo a análise filogenética das mesmas, concluindo-se que estas são relacionadas à Streptomyces albidoflavus e Marinobacter sp.. A análise de Genome mining identificou 24 clusters gênicos biossintéticos (BGCs) para S. albidoflavus ANT_B131 das classes ectoína, peptídeos não-ribossomais (NRP), policetídeos (PK), peptídeos sintetizados via ribossomos e modificados pós-tradução (RiPPs), sideróforos, entre outros, dos quais 50 % apresentavam baixa...

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Marinobacter profundi sp. nov., a slightly halophilic bacterium isolated from a deep-sea sediment sample of the New Britain Trench

Cited by 15 publications

References 35 publications

Culture Enrichment Combined With Long-Read Sequencing Facilitates Genomic Understanding of Hadal Sediment Microbes

Culture Enrichment Combined With Long-Read Sequencing Facilitates Genomic Understanding of Hadal Sediment Microbes

Whole genome sequencing of four bacterial strains from South Shetland Trench revealing biosynthetic and environmental adaptation gene clusters

Do genoma aos produtos naturais

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