Marinomonas epiphytica sp. nov., isolated from a marine intertidal macroalga

Genomic insights into novel predatory myxobacteria isolated from human feces

Myxobacteria are Gram-negative, spore-forming predatory bacteria isolated from diverse environmental samples that feed on other microbes for their survival and growth. However, no reports of cultured representatives from the human gut have been published to date, although previous investigations have revealed the presence of myxobacterial operational taxonomic units (OTUs) in skin and fecal samples. In this study, three myxobacterial strains designated as O35, O15, and Y35 were isolated and purified from fecal samples of two inflammatory bowel disease (IBD) patients. The 16S rRNA gene sequence analysis and phylogeny identified the strains as Myxococcus spp. belonging to two different clades. Genome-based phylogeny and overall genome-related indices, i.e., average amino acid identity and percentage of conserved proteins, confirmed the heterogeneity within the genus and placed the three strains within two different clades separated at the level of different genera. Digital DNA-DNA hybridization and average nucleotide identity values indicated that they belonged to two novel Myxococcus spp. The analysis of meta-barcoding data from IBD and control cohorts detected OTU lineages closely affiliated to the three novel strains. Based on evidence from detailed structural and functional genomics, we propose the novel species Myxococcus faecalis sp. nov. O35T and a new genus Pseudomyxococcus gen. nov. to accommodate the novel species Pseudomyxococcus flavus sp. nov. Y35T. Overall, these findings provide new information about the occurrence of myxobacteria in the human gut and lay the foundations for a new classification scheme for myxobacterial taxa.IMPORTANCEMyxobacteria have been described from a variety of niches ranging from terrestrial to marine habitats and are known to harbor a diverse portfolio of bioactive molecules. However, to date, there has been no report of isolating culturable representatives from the human gut. This study describes novel myxobacteria from the human gut based on phylogenomics and phenotypic description. The findings are complemented by sequence-based data, wherein operational taxonomic unit (OTU) lineages closely affiliated with the isolated strains have been identified, thus opening a Pandora's box of opportunities for research into the microbial ecology and functional potential of these taxa in the gut ecosystem. Additionally, the study also seeks to establish a new systematic framework, expanding our understanding of myxobacterial taxonomy.

Marinomonas transparens sp. nov. and Marinomonas sargassi sp. nov., isolated from marine alga

Two Gram-stain-negative, rod-shaped, non-spore-forming, strictly aerobic, motile bacteria with a single polar flagellum, designated strains C1424T and C2222T, were isolated from marine alga collected from the sea shore at Yantai, PR China. Strain C1424T grew at 4-37 °C and in the presence of 1-9 % (w/v) NaCl, while strain C2222T grew at 4-32 °C with 1-6 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences and concatenated amino acid sequences of 120 ubiquitous single-copy proteins showed that both strains C1424T and C2222T belonged to the genus Marinomonas, showing highest 16S rRNA gene sequence similarities to the type strains of Marinomonas primoryensis (98.1 %) and Marinomonas dokdonensis (98.1 %), respectively. The major fatty acids of the two strains were C18 : 1  ω6c and/or C18 : 1  ω7c, C16 : 1  ω6c and/or C16 : 1  ω7c and C16 : 0, their predominant polar lipids were phosphatidylethanolamine and phosphatidylglycerol, and their sole respiratory quinone was Q8. On the basis of polyphasic analyses, strains C1424T and C2222T are considered to represent two novel species within the genus Marinomonas, for which the names Marinomonas transparens sp. nov. and Marinomonas sargassi sp. nov. are proposed. The type strains are C1424T (=KCTC 72119T=MCCC 1K03601T) and C2222T (=KCTC 72120T=MCCC 1K03602T), respectively.

No bacterial-mediated alleviation of thermal stress in a brown seaweed suggests the absence of ecological bacterial rescue effects

While microbiome alterations are increasingly proposed as a rapid mechanism to buffer organisms under changing environmental conditions, studies of these processes in the marine realm are lagging far behind their terrestrial counterparts. Here, we used a controlled laboratory experiment to examine whether the thermal tolerance of the brown seaweed Dictyota dichotoma, a common species in European coastal ecosystems, could be enhanced by the repeated addition of bacteria from its natural environment. Juvenile algae from three genotypes were subjected for two weeks to a temperature gradient, spanning almost the entire thermal range that can be tolerated by the species (11-30 °C). At the start of the experiment and again in the middle of the experiment, the algae were inoculated with bacteria from their natural environment or left untouched as a control. Relative growth rate was measured over the two-week period, and we assessed bacterial community composition prior to and at the end of the experiment. Since the growth of D. dichotoma over the full thermal gradient was not affected by supplementing bacteria, our results indicate no scope for bacterial-mediated stress alleviation. The minimal changes in the bacterial communities linked to bacterial addition, particularly at temperatures above the thermal optimum (22-23 °C), suggest the existence of a barrier to bacterial recruitment. These findings indicate that ecological bacterial rescue is unlikely to play a role in mitigating the effects of ocean warming on this brown seaweed.

Exploring Diversity and Polymer Degrading Potential of Epiphytic Bacteria Isolated from Marine Macroalgae

The macroalgae surface allows specific bacterial communities to colonize, resulting in complex biological interactions. In recent years, several researchers have studied the diversity and function of the epiphytic bacteria associated with algal host, but largely these interactions remain underexplored. In the present study we analysed the cultivable diversity and polymer degradation potential of epiphytic bacteria associated with five different marine macroalgae (Sargassum, Ulva, Padina, Dictyota and Pterocladia sp.) sampled from the central west coast of India. Out of the total 360 strains isolated, purified and preserved, about 238 strains were identified through 16S rRNA gene sequence analysis and processed for polymer (cellulose, pectin, xylan and starch) degrading activities. Phylogeny placed the strains within the classes Actinobacteria, Bacilli, Alpha-proteobacteria, and Gamma-proteobacteria and clustered them into 45 genera, wherein Vibrio, Bacillus, Pseudoalteromonas, Alteromonas, Staphylococcus and Kocuria spp. were the most abundant with 20 strains identified as potentially novel taxa within the genera Bacillus, Cellulosimicrobium, Gordonia, Marinomonas, Vibrio, Luteimonas and Pseudoalteromonas. In terms of polymer hydrolysis potential, 61.3% had xylanase activity, while 59.7%, 58.8%, and 52.2% had amylase, cellulase, and pectinase activity, respectively. Overall, 75.6% of the strains degraded more than one polysaccharide, 24% degraded all polymers, while nine strains (3.8%) degraded raw sugarcane bagasse. This study showed great potential for seaweed-associated bacteria in the bio-remediation of agro-waste based raw materials, which can be employed in the form of green technology.

Marinomonas lutimaris sp. nov., isolated from a tidal flat sediment of the East China Sea

A Gram-stain-negative bacterial strain, designated as E165T, was isolated from a tidal flat sediment of the East China Sea. Strain E165T grew optimally at pH 6, at 32 °C and with 1–2 % (w/v) NaCl. The 16S rRNA gene sequence similarity results revealed that strain E165T was most closely related to Marinomonas rhizomae IVIA-Po-145T, Marinomonas polaris CK13T, Marinomonas foliarum IVIA-Po-155T, Marinomonas hwangdonensis HDW-15T, Marinomonas pontica 46-16T, Marinomonas mangrovi B20-1T and Marinomonas shanghaiensis DSL-35T with values of 97.0–98.5 %. The digital DNA–DNA hybridization and average nucleotide identity values between strain E165T and the reference strains were 21.9–34.3 % and 77.6–87.3 %, respectively. The DNA G+C content of the isolate was 42.9 mol%. Strain E165T contained Q-8 as the sole ubiquinone and C16 : 0, summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) as the major fatty acids. The major polar lipids of strain E165T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, aminolipid and aminophospholipid. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, a novel species, Marinomonas lutimaris sp. nov., is proposed with E165T (=MCCC 1K06241T=KCTC 82809T) as the type strain.

Biodetoxification mercury by using a marine bacterium Marinomonas sp. RS3 and its merA gene expression under mercury stress

Mercury (Hg) pollution in water has been a problem for the ecosystem and human health, thus eco-friendly remediation methods are gaining traction around the world. In this study, a bacterial strain designated as RS3 isolated from the Red Sea (Saudi Arabia) has shown tolerance to more than 250 mg/L of Hg²⁺ on minimum inhibitory studies. The isolate RS3 was identified as Marinomonas sp., (Accession No: OK271312) using 16s rRNA sequencing. Tracing the growth curve for the RS3 showed that maximum growth attained at 72 h and only 10% reduction than the control medium for 50 mg/L HgCl₂ supplemented seawater medium, which continued to reduce as 21% to 60 with the increment of HgCl₂ from 100 to 350 mg/L. The Hg²⁺ removal potential of RS3 is observed to be 78% at 50 mg/L HgCl₂/72 h, which is significantly altered with the addition of carbon source such as glucose (84.5%) > fructose (79.8%) > control (78%) > citrate (73.4%) > acetate (60.2%) > maltose (54.7%). Box-Behnken design (BBD) well proposed a model with R² value of 0.8922, which predict a utmost Hg²⁺ removal of 89.5% by RS2 at favorable conditions (pH-7; NaC 1% and glucose 5%) at 72 h. Mercuric reductase enzyme encoded merA gene expression was found to be high in RS3 isolates cultivated in 100 mg/L of HgCl₂ in comparison with other variables. Thus the seawater isolate Marinomonas sp. RS3 expressed a significant tolerance and removal potential towards the Hg²⁺, which would make it is a noteworthy applicant for effective mercury remediation practices.

Yangia mangrovi sp. nov., a novel member of the Roseobacter clade isolated from mangrove soil and emended description of Yangia pacifica Dai et al. 2006

During a study of the bacterial diversity of mangrove habitats, a novel Gram-stain-negative, rod-shaped bacterium designated as SAOS 153D^T was isolated. Sequence alignment and molecular phylogenetic analyses based on 16S rRNA and core gene sequence of strain SAOS 153D^T with closely related taxa revealed a sequence identity of 99.4 % and clustering with Yangia pacifica DX5-10^T. The fatty acids summed feature 8 (C_18:1 ω7c/C_18:1 ω6c) and the lipids phosphatidylglycerol, phosphatidylethanolamine and an unknown phospholipid were the major components of the cell wall. The only ubiquinone type present was Q-10. The genomic DNA G+C content of the strain calculated from whole genome sequencing was 66.9 mol%. These chemotaxonomic and genomic characteristics supported the molecular phylogenetic analysis and placed the strain well within the radiation of the genus Yangia. The overall genome related indices using digital DNA-DNA hybridization (35.4 %) and ortho-average nucleotide identity (88.1 %) values were much lower than the recommended thresholds for species delineation, which further consolidated the novel species status of strain SAOS 153D^T within the genus Yangia as Yangia mangrovi sp. nov. The type strain is SAOS 153D^T (=JCM 31345^T=KCTC 52280^T=MTCC 12749^T).

Marinomonas vulgaris sp. nov., a marine bacterium isolated from seawater in a coastal intertidal zone of Zhoushan island

A Marinomonas-like, Gram-stain-negative, strictly aerobic and rod to ovoid-shaped bacterium, designated as strain A79^T, was isolated from the seawater mixtures of oyster shells and brown algae in a coastal intertidal zone of Zhoushan, China. The strain was positive for oxidase and catalase. Colonies grown on marine agar for 48 h were round, milky white, smooth and moist with the diameter of 2-3 mm. Growth was observed at 15-30 °C (optimum, 25℃), pH 5.5-9.5 (optimum, pH 8.5) and with 0.5-8% (w/v) NaCl (optimum, 2-2.5%). The G + C content based on the genome sequence was 46.0%. The only respiratory quinone was Q-8. The main polar lipids contained phosphatidylglycerol, phosphatidylethanolamine, unidentified glycolipids, unidentified phospholipid and three unidentified lipids. The major fatty acids (> 10%) were C_16:0, Summed feature 3 (comprising C_16:1 ω6c and/or C_16:1 ω7c) and summed feature 8 (comprising C_18:1 ω6c and/or C_18:1 ω7c). The 16S rRNA gene sequence similarity between strain A79^T and Marinomonas pollencensis IVIA-Po-185^T was 97.4%, the similarities with other type strains of the genus Marinomonas were 93.8-96.7%. Based on the results, Marinomonas vulgaris sp. nov. was proposed as a novel species. The type strain is A79^T (= MCCC 1K05799^T = KCTC 82519^T = JCM 34473^T).

Marinomonas algicola sp. nov. and Marinomonas colpomeniae sp. nov., isolated from marine macroalgae

Two Gram-stain-negative, aerobic, rod-shaped bacteria, polar flagellated, designated strains SM2066^T and SM1966^T, were respectively isolated from the surfaces of Colpomenia sinuosa and Ulva pertusa macroalgae collected off the coastal areas of Rongcheng, PR China. Strain SM2066^T grew at 8-37 °C and with 0.5-7.0 % (w/v) NaCl, while strain SM1966^T grew at 5-30 °C and with 0.5-8.5% (w/v) NaCl. Both of them reduced nitrate to nitrite and required Na⁺ for growth but neither of them hydrolysed starch and DNA. Phylogenetic analysis based on 16S rRNA gene and single-copy orthologous cluster sequences revealed that both strains SM2066^T and SM1966^T were affiliated with the genus Marinomonas but formed distinct phylogenetic branches from known Marinomonas species, respectively sharing the highest 16S rRNA gene sequence similarities with type strains of Marinomonas ushuaiensis (97.9 %) and Marinomonas blandensis (96.7 %). The digital DNA-DNA hybridization and average nucleotide identity values between strains SM2066^T and SM1966^T and type strains of closely related Marinomonas species were all below 22.9 and 79.9 mol%, respectively. The major fatty acids of the two strains were summed feature 3 (C_16 : 1  ω6c/C_16 : 1  ω7c), summed feature 8 (C_18 : 1  ω7c) and C_16 : 0, with their predominant polar lipids being phosphatidylethanolamine and phosphatidylglycerol, and their sole respiratory quinone being Q-8. The genomic DNA G+C contents of strains SM2066^T and SM1966^T determined from genomic sequences were 40.3 and 41.6 mol%, respectively. On the basis of the polyphasic evidence presented in this study, strains SM2066^T and SM1966^T are considered to represent two novel species within the genus Marinomonas, for which the names Marinomonas colpomeniae sp. nov. and Marinomonas algicola sp. nov. are proposed. The type strains are SM2066^T (=MCCC 1K04390^T= KCTC 82372^T) and SM1966^T (=MCCC 1K04387^T= KCTC 72848^T), respectively.

Marinomonas profundi sp. nov., isolated from deep seawater of the Mariana Trench

A Gram-stain-negative, aerobic, polarly flagellated, straight or curved rod-shaped bacterium, designated strain M1K-6^T, was isolated from deep seawater samples collected from the Mariana Trench. The strain grew at -4 to 37 °C (optimum, 25-30 °C), at pH 5.5-10.0 (optimum, pH 7.0) and with 0.5-14.0  % (w/v) NaCl (optimum, 2.0 %). It did not reduce nitrate to nitrite nor hydrolyse gelatin or starch. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M1K-6^T was affiliated with the genus Marinomonas, sharing 93.1-97.0  % sequence similarity with the type strains of recognized Marinomonas species. The major cellular fatty acids were summed feature 3 (C_16 : 1 ω6c/C_16 : 1 ω7c), summed feature 8 (C_18 : 1 ω7c/C_18 : 1 ω6c), C_16 : 0, C_10 : 0 3-OH and C_18 : 0. The predominant respiratory quinone was ubiquinone-8. Polar lipids of strain M1K-6^T included phosphatidylethanolamine, phosphatidylglycerol and two unidentified lipids. The genomic G+C content of strain M1K-6^T was 46.0 mol%. Based on data from the present polyphasic study, strain M1K-6^T was considered to represent a novel species within the genus Marinomonas, for which the name Marinomonas profundi sp. nov. is proposed. The type strain is M1K-6^T (=KCTC 72501^T=MCCC 1K03890^T).

Halocatena pleomorpha gen. nov. sp. nov., an extremely halophilic archaeon of family Halobacteriaceae isolated from saltpan soil

A novel archaeal strain designated as SPP-AMP-1T was isolated from saltpan soil, using the serial dilution method on a halophilic archaeal medium supplemented with ampicillin. Cells were both rod-shaped and pleomorphic in nature, non-motile, unable to produce acid from a variety of sugars or grow anaerobically with different substrates (l-arginine) and electron acceptors (DMSO, nitrate). Optimal growth was observed at 42 °C, 3.4–4.2 M NaCl and pH 7.2. Cells did not lyse in distilled water and grew in the absence of Mg2+ ions. Phylogenetic analysis based on the sequences of 16S rRNA gene, amino acid sequence of β′-subunit of RNA polymerase and 400 conserved proteins retrieved from the whole genome assemblies showed that strain SPP-AMP-1T was distantly related to any existing genera within the family Halobacteriaceae . MK-8 was the only quinone detected. Polar lipid analysis showed a unique combination of diethyl derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, glycosyl-mannosyl-glucosyl diether and sulphated glycosyl-mannosyl-glucosyl diether as the major lipids. The G+C content of genomic DNA is 57.7 mol%. The phenotypic, phylogenetic and genomic data supported the concept of the novel genus status of strain SPP-AMP-1T in the family Halobacteriaceae for which the name Halocatena pleomorpha gen. nov., sp. nov., is proposed; the type strain is SPP-AMP-1T (=JCM 31368T=KCTC 4276T=MTCC 12579T).

Taxonomically Characterized and Validated Bacterial Species Based on 16S rRNA Gene Sequences from India During the Last Decade

Microbial taxonomy dealing with identification and characterization of prokaryotes like bacteria and archaea has always been a major area of research all over the world. Exploring diversity of microbes and description of novel species with different genes and secondary compounds is of utmost importance for better future and sustenance of life. India having an enormous range of ecosystems and diverse species inhabiting these niches is considered to be one of the richest biodiversity regions of the world. During the last decade, with newer methodologies and better technology, the prokaryotic taxonomy from India has extended our inventory of microbial communities in specific niches. However, there still exist some limitations in classifying the microbes from India as compared to that is done world-over. This review enlists the taxonomic description of novel taxa of prokaryotes from India in the past decade. A total of 378 new bacterial species have been classified from different habitats in India in the last ten years and no descriptions of archaeal species is documented till date.