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Ecological and functional capabilities of an uncultured Kordia sp
- Source :
- Digital.CSIC. Repositorio Institucional del CSIC, instname
- Publication Year :
- 2020
- Publisher :
- Urban and Fischer, 2020.
-
Abstract
- This is a Tara Oceans contributed paper number 96.-- 14 pages, 5 figures, 2 tables, supplementary data https://doi.org/10.1016/j.syapm.2019.126045<br />Cultivable bacteria represent only a fraction of the diversity in microbial communities. However, the official procedures for classification and characterization of a novel prokaryotic species still rely on isolates. Nevertheless, due to single cell genomics, it is possible to retrieve genomes from environmental samples by sequencing them individually, and to assign specific genes to a specific taxon, regardless of their ability to grow in culture. In this study, a complete description was performed for uncultured Kordia sp. TARA_039_SRF, a proposed novel species within the genus Kordia, using culture-independent techniques. The type material was a high-quality draft genome (94.97% complete, 4.65% gene redundancy) co-assembled using ten nearly identical single amplified genomes (SAGs) from surface seawater in the North Indian Ocean during the Tara Oceans Expedition. The assembly process was optimized to obtain the best possible assembly metrics and a less fragmented genome. The closest relative of the species was Kordia periserrulae, which shared 97.56% similarity of the 16S rRNA gene, 75% orthologs and 89.13% average nucleotide identity. The functional potential of the proposed novel species included proteorhodopsin, the ability to incorporate nitrate, cytochrome oxidases with high affinity for oxygen, and CAZymes that were unique features within the genus. Its abundance at different depths and size fractions was also evaluated together with its functional annotation, revealing that its putative ecological niche could be particles of phytoplanktonic origin. It could putatively attach to these particles and consume them while sinking to the deeper and oxygen depleted layers of the North Indian Ocean<br />Funding was provided by the Spanish Ministry of Economy and Competitivity grant MAGGY (CTM2017-87736-R) to SGA and CTM2016-80095-C2 to CPA and JMG. PS is funded by MAGGY project and MR-L held a Ph.D. Fellowship FPI (BES-2014-068285) funded by the Spanish Ministry of Economy and Competitivity<br />With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)
- Subjects :
- DNA, Bacterial
Gene redundancy
Genomics
Biology
Applied Microbiology and Biotechnology
Microbiology
Genome
03 medical and health sciences
Bacterial Proteins
Abundance (ecology)
RNA, Ribosomal, 16S
Rhodopsins, Microbial
Seawater
Indian Ocean
Ecosystem
Phylogeny
Ecology, Evolution, Behavior and Systematics
030304 developmental biology
Ecological niche
0303 health sciences
Proteorhodopsin
030306 microbiology
Microbiota
Nucleic Acid Hybridization
Photoheterotrophy
Sequence Analysis, DNA
16S ribosomal RNA
Co-assembly
Kordia
Metagenomics
Evolutionary biology
SAG
biology.protein
Flavobacteriaceae
Genome, Bacterial
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- Digital.CSIC. Repositorio Institucional del CSIC, instname
- Accession number :
- edsair.doi.dedup.....0ec1a80526a288ab8fc765b7c9efaf1a