Three novel marine species of the genus Reichenbachiella exhibiting degradation of complex polysaccharides

Neak Muhammad; Forbes Avila; Olga I Nedashkovskaya; Song-Gun Kim

doi:10.3389/fmicb.2023.1265676

Three novel marine species of the genus Reichenbachiella exhibiting degradation of complex polysaccharides

Front Microbiol. 2023 Dec 14:14:1265676. doi: 10.3389/fmicb.2023.1265676. eCollection 2023.

Authors

Neak Muhammad^{1

2}, Forbes Avila^{1

2}, Olga I Nedashkovskaya³, Song-Gun Kim^{1

2}

Affiliations

¹ Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
² Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea.
³ G.B. Elyakov Pacific Institute of Bioorganic Chemistry of the Far-Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia.

Abstract

Three novel strains designated ABR2-5^T, BKB1-1^T, and WSW4-B4^T belonging to the genus Reichenbachiella of the phylum Bacteroidota were isolated from algae and mud samples collected in the West Sea, Korea. All three strains were enriched for genes encoding up to 216 carbohydrate-active enzymes (CAZymes), which participate in the degradation of agar, alginate, carrageenan, laminarin, and starch. The 16S rRNA sequence similarities among the three novel isolates were 94.0%-94.7%, and against all three existing species in the genus Reichenbachiella they were 93.6%-97.2%. The genome sizes of the strains ABR2-5^T, BKB1-1^T, and WSW4-B4^T were 5.5, 4.4, and 5.0 Mb, respectively, and the GC content ranged from 41.1%-42.0%. The average nucleotide identity and the digital DNA-DNA hybridization values of each novel strain within the isolates and all existing species in the genus Reichenbachiella were in a range of 69.2%-75.5% and 17.7-18.9%, respectively, supporting the creation of three new species. The three novel strains exhibited a distinctive fatty acid profile characterized by elevated levels of iso-C_15:0 (37.7%-47.4%) and C_16:1 ω5c (14.4%-22.9%). Specifically, strain ABR2-5^T displayed an additional higher proportion of C_16:0 (13.0%). The polar lipids were phosphatidylethanolamine, unidentified lipids, aminolipids, and glycolipids. Menaquinone-7 was identified as the respiratory quinone of the isolates. A comparative genome analysis was performed using the KEGG, RAST, antiSMASH, CRISPRCasFinder, dbCAN, and dbCAN-PUL servers and CRISPRcasIdentifier software. The results revealed that the isolates harbored many key genes involved in central metabolism for the synthesis of essential amino acids and vitamins, hydrolytic enzymes, carotenoid pigments, and antimicrobial compounds. The KEGG analysis showed that the three isolates possessed a complete pathway of dissimilatory nitrate reduction to ammonium (DNRA), which is involved in the conservation of bioavailable nitrogen within the ecosystem. Moreover, all the strains possessed genes that participated in the metabolism of heavy metals, including arsenic, copper, cobalt, ferrous, and manganese. All three isolated strains contain the class 2 type II subtype C1 CRISPR-Cas system in their genomes. The distinguished phenotypic, chemotaxonomic, and genomic characteristics led us to propose that the three strains represent three novel species in the genus Reichenbachiella: R. ulvae sp. nov. (ABR2-5^T = KCTC 82990^T = JCM 35839^T), R. agarivorans sp. nov. (BKB1-1^T = KCTC 82964^T = JCM 35840^T), and R. carrageenanivorans sp. nov. (WSW4-B4^T = KCTC 82706^T = JCM 35841^T).

Keywords: Bacteroidota; CRISPRCas; carbohydrate-active enzymes; genome analyses; polysaccharide degradation.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program (KGM5232322) and a National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT; no. NRF-2021M3H9A1030164) supported this research.