Comparative genome characterization of Echinicola marina sp. nov., isolated from deep-sea sediment provide insight into carotenoid biosynthetic gene cluster evolution

Echinicola, carotenoid-pigmented bacteria, are isolated from various hypersaline environments. Carotenoid accumulation in response to salt stress can stabilize the cell membrane in order to survive. A pink-colored strain SCS 3-6 was isolated from the deep-sea sediment of the South China Sea. Growth was found to occur at 10-45 °C. The strain could tolerate 10% (w/v) NaCl concentration and grow at pH 5-9. The complete genome of SCS 3-6 comprises 5053 putative genes with a total 5,693,670 bp and an average G + C content of 40.11 mol%. The 16S rRNA gene sequence analysis indicated that strain SCS 3-6 was affiliated with the genus Echinicola, with the closely strains were Echinicola arenosa CAU 1574^T (98.29%)and Echinicola shivajiensis AK12^T (97.98%). For Echinicola species with available genome sequences, pairwise comparisons for average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) revealed ANIb values from 70.77 to 74.71%, ANIm values from 82.72 to 88.88%, and DDH values from 18.00 to 23.40%. To identify their genomic features, we compared their genomes with those of other Echinicola species. Phylogenetic analysis showed that strain SCS 3-6 formed a monophyletic clade. Genomic analysis revealed that strain SCS 3-6 possessed a complete synthetic pathway of carotenoid and speculated that the production was astaxanthin. Based on phenotypic and genotypic analyses in this study, strain SCS 3-6 is considered to represent a novel species of the genus Echinicola for which the name Echinicola marina sp. nov. is proposed. The type strain is SCS 3-6^T (= GDMCC 1.2220^T = JCM 34403^T).

Echinicola arenosa sp. nov., isolated from marine sand

A novel bacterium, designated CAU 1574^T, was isolated from marine sand. Cells were Gram stain negative, aerobic, gliding and rod shaped. Growth was observed at 20-37 °C (optimum, 30 °C), a pH of 5.5-10.0 (optimum, 8.0), and 0-3.0% (w/v) NaCl concentrations (optimum, 1%). Based on the results of 16S rRNA gene sequence analyses, strain CAU 1574^T belonged to the genus Echinicola, and showed the highest similarity to Echinicola shivajiensis JCM 17847^T (97.5%). Phylogenomic analysis based on consisting of 92 core genes extracted from the genome sequences showed that strain CAU 1574^T was affiliated with species in the genus Echinicola. The average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values between strain CAU 1574^T and the closely related species were below the cut-off values of 95-96, 90, and 70%, respectively used for species demarcation. The chemotaxonomic data of CAU 1574^T were as follows: major isoprenoid quinone, MK-7; predominant polar lipids, phosphatidylethanolamine, two unidentified aminophospholipids and two unidentified lipids; major fatty acids, iso-C_15:0, summed feature 3 (C_16:1 ω6c/C_16:1 ω7c). The 5.4 Mb genome included 20 contigs and 4237 protein-coding genes with a 39.8 mol% G + C content. Based on the phylogenetic, phenotypic, and physiological result, strain CAU 1574^T represents a novel species of this genus Echinicola, for which the name Echinicola arenosa sp. nov. is proposed. The type strain is CAU 1574^T (= KCTC 82410^T = MCCC 1K05669^T).

Echinicola salinicaeni sp. nov., a novel bacterium isolated from saltern mud

A novel gram-negative, aerobic, pink, motile, gliding, rod-shaped bacterium, designated P51^T, was isolated from saline silt samples in Yantai, China. It was able to grow at 4-42 °C (optimum 33 °C), pH 4.0-9.0 (optimum 7.0), and in 0-11.0% NaCl (optimum 4.0%, w/v). It grew at 4 °C, which was lower than the minimum temperature for related strains. The genome consisted of 4111 genes with a total length of 5 139 782 bp. The 16S rRNA gene sequence analysis indicated that strain P51^T was a member of the genus Echinicola and most closely related to 'Echinicola shivajiensis'. A genome analysis identified genes encoding proteins associated with carbon source utilisation, and the carotenoid biosynthesis and β-lactam resistance pathways. Strain P51^T shared an average nucleotide identity value below 84.7%, an average amino acid identity value between 70.8 and 89.3%, and a digital DNA-DNA hybridisation identity of between 17.9-28.2% with closely related type strains within the genus Echinicola. The sole menaquinone was MK-7, and the major fatty acids were iso-C_15:0, summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), summed feature 4 (anteiso-C_17:1 B and/or iso-C_17:1 I), and summed feature 9 (iso-C_17:1ω9c and/or 10-methyl C_16:0). The polar lipids included one phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, three unidentified aminolipids, and one unknown lipid. The phenotypic, chemotaxonomic, and phylogenetic analyses suggest that strain P51^T is a novel species of the genus Echinicola, for which the name Echinicola salinicaeni sp. nov. is proposed. The type strain was P51^T (KCTC 82513^T = MCCC 1K04413^T).

Echinicola soli sp. nov., isolated from alkaline saline soil

Strains of Echinicola , thought to play vital roles in the environment for their high enzyme production capacity during decomposition of polysaccharides, are ubiquitous in hypersaline environments. A Gram-negative, non-spore forming, gliding, aerobic bacterial strain, designated LN3S3T, was isolated from alkaline saline soil sampled in Tumd Right Banner, Inner Mongolia, northern PR China. Strain LN3S3T grew at 10–40 °C (optimum, 30 °C), pH 5.0–9.0 (optimum, pH 8.0) and with 0–12.5 % NaCl (optimum, 2.0 %). A phylogenetic tree based on the 16S rRNA gene sequences showed that strain LN3S3T clustered with Echinicola rosea JL3085T and Echinicola strongylocentroti MEBiC08714T, sharing 97.0, 96.7 and <96.50 % of 16S rRNA gene sequence similarities to E. rosea JL3085T, E. strongylocentroti MEBiC08714T and all other type strains. MK-7 was the major respiratory quinone, while phosphatidylethanolamine, two unidentified phospholipids, an unidentified aminophospholipid, an unidentified lipid and two unidentified aminolipids were the major polar lipids. Its major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c). The genome consisted of a circular 5 550 304 bp long chromosome with a DNA G+C content of 44.0 mol%. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA–DNA hybridization (dDDH) values of strain LN3S3T to E. rosea JL3085T and E. strongylocentroti MEBiC08714T were 82.5 and 81.5 %, 87.5 and 86.0 %, and 39.1 and 35.1 %, respectively. Based on physiological, genotypic and phylogenetic analyses, strain LN3S3T could be discriminated from its phylogenetic relatives. Echinicola soli sp. nov. is therefore proposed with strain LN3S3T (=CGMCC 1.17081T=KCTC 72458T) as the type strain.

Isolation and Characterization of a Novel Cold-Active, Halotolerant Endoxylanase from Echinicola rosea sp. Nov. JL3085T

We cloned a xylanase gene (xynT) from marine bacterium Echinicola rosea sp. nov. JL3085^T and recombinantly expressed it in Escherichia coli BL21. This gene encoded a polypeptide with 379 amino acid residues and a molecular weight of ~43 kDa. Its amino acid sequence shared 45.3% similarity with an endoxylanase from Cellvibrio mixtus that belongs to glycoside hydrolases family 10 (GH10). The XynT showed maximum activity at 40 °C and pH 7.0, and a maximum velocity of 62 μmoL min⁻¹ mg⁻¹. The XynT retained its maximum activity by more than 69%, 51%, and 26% at 10 °C, 5 °C, and 0 °C, respectively. It also exhibited the highest activity of 135% in the presence of 4 M NaCl and retained 76% of its activity after 24 h incubation with 4 M NaCl. This novel xylanase, XynT, is a cold-active and halotolerant enzyme that may have promising applications in drug, food, feed, and bioremediation industries.

Complete genome sequence of Echinicola rosea JL3085, a xylan and pectin decomposer

Marine Bacteroidetes are well known for their functional specialization on the decomposition of polysaccharides which results from a great number of carbohydrate-active enzymes. Here we represent the complete genome of a Bacteroitedes member Echinicola rosea JL3085^T that was isolated from surface seawater of the South China Sea. The genome is 6.06 Mbp in size with a GC content of 44.1% and comprises 4613 protein coding genes. A remarkable genomic feature is that the number of glycoside hydrolase genes in the genome of E. rosea JL3085^T is high in comparison with most of the sequenced members of marine Bacteroitedes. E. rosea JL3085^T genome harbored multi-gene polysaccharide utilization loci (PUL) systems involved in the degradation of pectin, xylan and arabinogalactan. The large diversity of hydrolytic enzymes supports the use of E. rosea JL3085^T as a candidate for biotechnological applications in enzymatic conversion of plant polysaccharides.