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Salvaging high-quality genomes of microbial species from a meromictic lake using a hybrid sequencing approach / Y. H. Chen, P. W. Chiang, D. Y. Rogozin [et al.] // Commun. Biol. - 2021. - Vol. 4, Is. 1. - Ст. 996, DOI 10.1038/s42003-021-02510-6. - Cited References:99. - Y This work was supported by the Ministry of Science and Technology in Taiwan through the Taiwan-Russia Joint Project Grant NSC 102-2923-B-001-004-MY3 and Russian Foundation for Basic Research Grant 21-54-52001 and MOST 105-2923-B-001-001-MY3. Y.H.C. would like to acknowledge the Taiwan International Graduate Program (TIGP) for its fellowship towards his graduate studies. We would like to thank Noah Last of Third Draft Editing for his English language editing. . - ISSN 2399-3642

РУБ Biology + Multidisciplinary Sciences
Рубрики:
DIMETHYL SULFIDE
   SULFUR BACTERIUM
   SP-NOV.
   CHLAMYDIALES
   METAGENOME
Аннотация: Most of Earth's bacteria have yet to be cultivated. The metabolic and functional potentials of these uncultivated microorganisms thus remain mysterious, and the metagenome-assembled genome (MAG) approach is the most robust method for uncovering these potentials. However, MAGs discovered by conventional metagenomic assembly and binning are usually highly fragmented genomes with heterogeneous sequence contamination. In this study, we combined Illumina and Nanopore data to develop a new workflow to reconstruct 233 MAGs-six novel bacterial orders, 20 families, 66 genera, and 154 species-from Lake Shunet, a secluded meromictic lake in Siberia. With our workflow, the average N50 of reconstructed MAGs greatly increased 10-40-fold compared to when the conventional Illumina assembly and binning method were used. More importantly, six complete MAGs were recovered from our datasets. The recovery of 154 novel species MAGs from a rarely explored lake greatly expands the current bacterial genome encyclopedia. Chen and colleagues develop a workflow for assembling high quality metagenome-associated genomes for microbial species using long and short reads, in this case from a meromictic lake. A full, detailed workflow is provided in for use by the community.

WOS
Держатели документа:
Natl Taiwan Univ, Taiwan Int Grad Program, Bioinformat Program, Taipei, Taiwan.
Acad Sinica, Taiwan Int Grad Program, Bioinformat Program, Inst Informat Sci, Taipei, Taiwan.
Acad Sinica, Biodivers Res Ctr, Taipei, Taiwan.
Russian Acad Sci, Siberian Branch, Inst Biophys, Krasnoyarsk, Russia.
Siberian Fed Univ, Krasnoyarsk, Russia.

Доп.точки доступа:
Chen, Yu-Hsiang; Chiang, Pei-Wen; Rogozin, Denis Yu; Degermendzhy, Andrey G.; Chiu, Hsiu-Hui; Tang, Sen-Lin; Ministry of Science and Technology in Taiwan through the Taiwan-Russia Joint Project [NSC 102-2923-B-001-004-MY3]; Russian Foundation for Basic Research GrantRussian Foundation for Basic Research (RFBR) [21-54-52001, MOST 105-2923-B-001-001-MY3]; Taiwan International Graduate Program (TIGP)

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Bacteria of Lake Pyasino and Adjacent Rivers after an Accidental Diesel Spill in 2020 / O. V. Kolmakova, M. Y. Trusova, O. A. Baturina, M. R. Kabilov // Contemp. Probl. Ecol. - 2021. - Vol. 14, Is. 4. - P356-367, DOI 10.1134/S1995425521040053. - Cited References:22. - This work was supported by economic agreement no. 223-EP-2020/07 with the Siberian Branch of the Russian Academy of Sciences and the Project Office for the Development of the Arctic (PORA), and State Task of the Fundamental Research Program of the Russian Federation, topic no. 51.1.1. Bioinformatics analysis was supported by basic budget funding from the ICBFM SB RAS (AAAAA17-117020210021-7). . - ISSN 1995-4255. - ISSN 1995-4263

РУБ Ecology
Рубрики:
SP-NOV.
   GEN. NOV.
   OIL
   BACTERIOPLANKTON
   SEQUENCES
Кл.слова (ненормированные):
bacterioplankton -- sediments -- high-throughput sequencing -- oil spill -- Lake -- Pyasino -- 16S rRNA
Аннотация: The bacterial composition of water and sediments in Lake Pyasino and adjacent rivers has been studied by high-throughput sequencing for the first time. No hydrocarbon-degrading bacteria are found in the river sections exposed to the diesel spillage in May 2020. The Daldykan and Ambarnaya rivers, located downstream of the spill site, are dominated by bacteria that oxidize sulfur and heavy metals. At the same time, these bacteria are not found in Lake Pyasino, which is dominated by small cyanobacteria. Thus, the composition of bacteria in the water and sediments of the Norilsk-Pyasino lake-river system corresponds to the technogenic impact to which it is exposed and also demonstrates the buffer properties of Lake Pyasino as water flows into the Kara Sea.

WOS
Держатели документа:
Russian Acad Sci, Siberian Branch, Krasnoyarsk Sci Ctr, Inst Biophys, Krasnoyarsk 660036, Akademgorodok, Russia.
Siberian Fed Univ, Krasnoyarsk 660041, Russia.
Russian Acad Sci, Siberian Branch, Inst Chem Biol & Fundamental Med, Genom Core Facil, Novosibirsk 630090, Russia.

Доп.точки доступа:
Kolmakova, O. V.; Trusova, M. Yu.; Baturina, O. A.; Kabilov, M. R.; Siberian Branch of the Russian Academy of SciencesRussian Academy of Sciences [223-EP-2020/07]; Project Office for the Development of the Arctic (PORA); State Task of the Fundamental Research Program of the Russian Federation [51.1.1]; ICBFM SB RAS [AAAAA17-117020210021-7]

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