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 1574T (98.29%)and Echinicola shivajiensis AK12T (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 3-6T (= GDMCC 1.2220T = JCM 34403T).

Belnapia mucosa sp. nov. and Belnapia arida sp. nov., isolated from desert biocrust

Two novel Gram-staining-negative, aerobic, cocci-shaped, non-motile, non-spore forming, pink-pigmented bacteria designated strains T6T and T18T, were isolated from a biocrust (biological soil crust) sample from the vicinity of the Tabernas Desert (Spain). Both strains were catalase-positive and oxidase-negative, and grew under mesophilic, neutrophilic and non-halophilic conditions. According to the 16S rRNA gene sequences, strains T6T and T18T showed similarities with Belnapia rosea CGMCC 1.10758T and Belnapia moabensis CP2CT (98.11 and 98.55% gene sequence similarity, respectively). The DNA G+C content was 69.80 and 68.96% for strains T6T and T18T, respectively; the average nucleotide identity by blast (ANIb) and digital DNA–DNA hybridization (dDDH) values confirmed their adscription to two novel species within the genus Belnapia . The predominant fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), C16 : 0, C18 : 1 2-OH and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). According to he results of the polyphasic study, strains T6T and T18T represent two novel species in the genus Belnapia (which currently includes only three species), for which names Belnapia mucosa sp. nov. (type strain T6T = CECT 30228T=DSM 112073T) and Belnapia arida sp. nov. (type strain T18T=CECT 30229T=DSM 112074T) are proposed, respectively.

Ecological and Biotechnological Aspects of Pigmented Microbes: A Way Forward in Development of Food and Pharmaceutical Grade Pigments

Microbial pigments play multiple roles in the ecosystem construction, survival, and fitness of all kinds of organisms. Considerably, microbial (bacteria, fungi, yeast, and microalgae) pigments offer a wide array of food, drug, colorants, dyes, and imaging applications. In contrast to the natural pigments from microbes, synthetic colorants are widely used due to high production, high intensity, and low cost. Nevertheless, natural pigments are gaining more demand over synthetic pigments as synthetic pigments have demonstrated side effects on human health. Therefore, research on microbial pigments needs to be extended, explored, and exploited to find potential industrial applications. In this review, the evolutionary aspects, the spatial significance of important pigments, biomedical applications, research gaps, and future perspectives are detailed briefly. The pathogenic nature of some pigmented bacteria is also detailed for awareness and safe handling. In addition, pigments from macro-organisms are also discussed in some sections for comparison with microbes.

Kaistella gelatinilytica sp. nov., a flavobacterium isolated from Antarctic soil

A Gram-stain-negative, aerobic, non-spore-forming, rod-shaped, non-motile, yellow-pigmented bacteria, designated strain G5-32T, belonging to the genus Kaistella was isolated from soil collected in the Antarctic. The strain was identified using a polyphasic taxonomic approach. The strain grew in the presence of 0–5% (w/v) NaCl (optimum, 1%), at pH 6.0–9.0 (optimum, pH 8.0) and at 4–28 °C (optimum, 20 °C). The predominant menaquinone was MK-6 (99.4%). The major fatty acids were anteiso-C15:0 (28.2%), iso-C15:0 (16.4%), summed feature 9 (comprising iso-C17:1 ω9c and/or 10-methyl C16:0; 10.6%) and iso-C16:0 (5.9%). A phylogenetic tree based on 16S rRNA gene sequences showed that strain G5-32T formed a lineage within the genus Kaistella with the closest phylogenetic neighbours Kaistella yonginensis HMD1043T, Kaistella chaponensis DSM 23145T, Kaistella jeonii DSM 17048T and Kaistella carnis NCTC 13525T (97.9, 97.8, 97.8 and 98.0 % 16S rRNA gene sequence similarity, respectively). The ANI values between strain G5-32T and K. jeonii DSM 17048T, K. chaponensis DSM 23145T, K. carnis NCTC 13525T and K. yonginensis HMD1043T were 90.9, 82.6, 77.1 and 76.3%. Concurrently, digital DNA–DNA hybridization values of strain G5-32T assessed against K. jeonii DSM 17048T, K. chaponensis DSM 23145T, K. carnis NCTC 13525T and K. yonginensis HMD1043T were 42.3, 25.9, 21.7 and 21.3%, respectively. Based on phenotypic, phylogenetic and genotypic data, a novel species, Kaistella gelatinilytica sp. nov., is proposed. The type strain is G5-32T (=CCTCC AA 2019083T=KCTC 72766T).

Glaciochemistry and pigment producing ability of bacteria from roof of the world, the glaciers of Karakoram, Pakistan

The Karakoram Mountain Range (KMR) is one of the largest mountain ranges in the world, with ~ 37% of its area glaciated. Here, we present the geochemistry of ice, sediment and meltwaters sampled from Ghulmet, Ghulkin and Hopar glaciers of the Karakoram Range, Pakistan, in addition to the first information on the diversity of pigmented bacteria evaluated using culture-dependent techniques. Geochemical analyses revealed Ca2+ and SO42− to be the most abundant cation and anion species across all glacial samples, respectively. Total organic carbon (TOC), total nitrogen (TN) and total phosphorus (TP) were found in the sediments of all glaciers studied in current research. Bacterial species were capable of producing a variety of different pigments, including alloxanthin, astaxanthin, bacterioruberin, β-carotene, 19'-hexanoyloxyfucoxanthin, peridinin, violacein and zeaxanthin. Culturable bacterial diversity was studied using two molecular biomarkers, 16S rRNA and rpoB gene, with a total of 82 bacterial strains representing 25 genera identified across all glacial samples. This study provides the first characterization of glacier-associated, pigment-producing bacterial communities from the KMR. Findings are important for considerations of alternative sources of conventional pigment production in industrial fields.

The biological prospective of red-pigmented bacteria cultured from contaminated agar media

Arifiyanto A, Afriani H, Putri MH, Damayanti B, Riyanto CL. 2021. The biological prospective of red-pigmented bacteria cultured from contaminated agar media. Biodiversitas 22: 1152-1159. Contaminated agar media was often depleted due to the growth of microbes, which is undesirable for culture. However, the contaminating microbes usually have a distinctive morphology. This research aimed to identify the potential of red-pigmented bacteria originated from the contamination of Drosophila melanogaster larvae. Fruit fly larvae that grow on contaminated tryptic soy agar were accompanied by the appearance of the red-pigmented bacteria colony. The bacterial colonies were purified by the re-streaking method on tryptic soybean agar. This strain was characterized morphologically, biochemically, and molecularly. Results showed that the MBC1 strain was identified as Serratia marcescens. The various metal susceptibility tests at 25 ppm did not affect the growth of the MBC1 strain. Meanwhile, it was also able to inhibit the growth of certain pathogens such as Aspergillus niger, Candida sp., Fusarium sp., and Rigidoporous sp. Strain MBC1 was able to produce antioxidant compounds. The lipolytic and amylolytic activity can be developed for bioremediate agriculture waste and biosurfactant production.

Characterization of Yellow Pigmented Bacteria Associated with Gracilaria sp.

Research on the kinship analysis of endophytic bacterial isolated from Gracillaria sp has been carried out. The presence of bacteria associated with Gracilaria sp. has enabled the use of these bacteria as a source of new bioactive compounds, such as biopigments. The research aims to isolated bacteria from Gracilaria sp., screened their symbiont bacteria that could potentially produce pigments. Sampling Gracilaria sp. conducted in the waters of the Island of Karimunjawa, Jepara. Furthermore, bacterial isolation was carried out, screening for pigment-producing bacteria and 16S rRNA sequence analysis. Research result showed that the symbiont bacteria isolate TK 373 produced consistent pigments after several regenerations, in several types of growth media incubated at room temperature. The results of 16S rDNA identification showed that the TK 373 isolate had the closest relationship with Pseudoalteromonas sp. with 98.72 % homology.

Resonance Raman spectra for the in-situ identification of bacteria strains and their inactivation mechanism

The resonance Raman spectra of bacterial carotenoids have been employed to identify bacterial strains and their intensity changes as a function of ultraviolet(UV) radiation dose have been used to differentiate between live and dead bacteria. The enhanced resonance Raman spectra of color-pigmented bacteria were recorded after excitation with visible light diode lasers. In addition, the resonance enhanced Raman spectra enabled us to detect bacteria in water at much lower concentrations (~108 cells/mL) than normally detected spectroscopically. A handheld spectrometer capable of recording resonance Raman spectra in-situ was designed, constructed and was used to record the spectra. In addition to bacteria, the method presented in this paper may also be used to identify fungi, viruses and plants, in-situ, and detect infections within a very short period of time.

Kineococcus vitellinus sp. nov., Kineococcus indalonis sp. nov. and Kineococcus siccus sp. nov., Isolated Nearby the Tabernas Desert (Almería, Spain)

Three novel Gram-positive, aerobic, chemoheterotrophic, motile, non-endospore-forming, orange-pigmented bacteria designated strains T13T, T90T and R8T were isolated from the Tabernas Desert biocrust (Almería, Spain). Cells of the three strains were coccus-shaped and occurred singly, in pairs or clusters. The three strains were oxidase-negative and catalase-positive, and showed a mesophilic, neutrophilic and non-halophilic metabolism. Based on the 16S rRNA gene sequences, the closest neighbours of strains T13T, T90T and R8T were Kineococcus aurantiacus IFO 15268T, Kineococcus gypseus YIM 121300T and Kineococcus radiotolerans SRS 30216T (98.5%, 97.1% and 97.9% gene sequence similarity, respectively). The genomes were sequenced, and have been deposited in the GenBank/EMBL/DDBJ databases under the accession numbers JAAALL000000000, JAAALM000000000 and JAAALN000000000, respectively, for strains T13T, T90T and R8T. The average nucleotide identity (ANIb) and digital DNA-DNA hybridization (dDDH) values confirmed their adscription to three new species within the genus Kineococcus. The genomic G + C content of strains T13T, T90T and R8T ranged from 75.1% to 76.3%. The predominant fatty acid of all three strains was anteiso-C15:0. According to a polyphasic study, strains T13T, T90T and R8T are representatives of three new species in the genus Kineococcus, for which names Kineococcus vitellinus sp. nov. (type strain T13T = CECT 9936T = DSM 110024T), Kineococcus indalonis sp. nov. (type strain T90T = CECT 9938T = DSM 110026T) and Kineococcus siccus sp. nov. (type strain R8T = CECT 9937T = DSM 110025T) are proposed.