Marinobacter sediminicola sp. nov. and Marinobacter xiaoshiensis sp. nov., Isolated from Coastal Sediment

Two Gram-stain-negative, facultative anaerobic, rod-shaped, motile bacterial strains, designated F26243T and F60267T were isolated from coastal sediment in Weihai, China. Strains F26243T and F60267T were grown at 4-40 °C (optimum 33 °C), pH 7.0-9.5 and pH 6.5-9.5 (optimum at pH 7.0), in the presence of 1.0-7.0% (w/v) NaCl (optimum 2.5%) and 1.0-12.0% (w/v) NaCl (optimum 2.0%), respectively. The 16S rRNA gene sequences phylogenetic analysis showed that strains F26243T and F60267T are closely related to the genus Marinobacter and exhibited the highest sequence similarities to Marinobacter salexigens HJR7T (97.7% and 98.0%, respectively), the similarity between two isolates was 96.7%. Strains F26243T and F60267T displayed genomic DNA G + C content of 53.6% and 53.8%, respectively. When compared to the M. salexigens HJR7T, the average nucleotide identity (ANI) values were 83.7% and 84.1%, and the percentage of conserved proteins (POCP) values were 79.9% and 84.6%, respectively. Ubiquinone 9 (Q-9) was the only respiratory quinone detected in both isolates. The major cellular fatty acids (> 10.0%) were summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c), C16:0 and C18:1ω9c. The polar lipid profiles of strains F26243T and F60267T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylglycerol, aminophospholipid and one unidentified phospholipid. Based on genomic characteristics, phenotypic and chemotaxonomic, strains F26243T and F60267T represent two novel species of the genus Marinobacter, for which the names Marinobacter sediminicola sp. nov. and Marinobacter xiaoshiensis sp. nov. are proposed, the type strains are F26243T (= KCTC 92640T = MCCC 1H01345T) and F60267T (= KCTC 92638T = MCCC 1H01346T).

Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics

Marinobacter spp. are cosmopolitan in saline environments, displaying a diverse set of metabolisms that allow them to competitively occupy these environments, some of which can be extreme in both salinity and temperature. Here, we introduce a distinct cluster of Marinobacter genomes, composed of novel isolates and in silico assembled genomes obtained from subzero, hypersaline cryopeg brines, relic seawater-derived liquid habitats within permafrost sampled near Utqiaġvik, Alaska. Using these new genomes and 45 representative publicly available genomes of Marinobacter spp. from other settings, we assembled a pangenome to examine how the new extremophile members fit evolutionarily and ecologically, based on genetic potential and environmental source. This first genus-wide genomic analysis revealed that Marinobacter spp. in general encode metabolic pathways that are thermodynamically favored at low temperature, cover a broad range of organic compounds, and optimize protein usage, e.g., the Entner–Doudoroff pathway, the glyoxylate shunt, and amino acid metabolism. The new isolates contributed to a distinct clade of subzero brine-dwelling Marinobacter spp. that diverged genotypically and phylogenetically from all other Marinobacter members. The subzero brine clade displays genomic characteristics that may explain competitive adaptations to the extreme environments they inhabit, including more abundant membrane transport systems (e.g., for organic substrates, compatible solutes, and ions) and stress-induced transcriptional regulatory mechanisms (e.g., for cold and salt stress) than in the other Marinobacter clades. We also identified more abundant signatures of potential horizontal transfer of genes involved in transcription, the mobilome, and a variety of metabolite exchange systems, which led to considering the importance of this evolutionary mechanism in an extreme environment where adaptation via vertical evolution is physiologically rate limited. Assessing these new extremophile genomes in a pangenomic context has provided a unique view into the ecological and evolutionary history of the genus Marinobacter, particularly with regard to its remarkable diversity and its opportunism in extremely cold and saline environments.

Draft Genome Sequence of Marinobacter sp. Strain AL4B, a Marine Bacterium Isolated from Quintero Bay, Chile

Quintero Bay, located along the central coast of Chile, has suffered different oil spills during the past 10 years, impacting its marine ecosystems. Here, we report the genome sequence of Marinobacter sp. strain AL4B, a marine bacterium isolated from Quintero Bay, Chile.

Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines

Subzero hypersaline brines are liquid microbial habitats within otherwise frozen environments, where concentrated dissolved salts prevent freezing. Such extreme conditions presumably require unique microbial adaptations, and possibly altered ecologies, but specific strategies remain largely unknown. Here we examined prokaryotic taxonomic and functional diversity in two seawater-derived subzero hypersaline brines: first-year sea ice, subject to seasonally fluctuating conditions; and ancient cryopeg, under relatively stable conditions geophysically isolated in permafrost. Overall, both taxonomic composition and functional potential were starkly different. Taxonomically, sea-ice brine communities (∼10⁵ cells mL^–1) had greater richness, more diversity and were dominated by bacterial genera, including Polaribacter, Paraglaciecola, Colwellia, and Glaciecola, whereas the more densely inhabited cryopeg brines (∼10⁸ cells mL^–1) lacked these genera and instead were dominated by Marinobacter. Functionally, however, sea ice encoded fewer accessory traits and lower average genomic copy numbers for shared traits, though DNA replication and repair were elevated; in contrast, microbes in cryopeg brines had greater genetic versatility with elevated abundances of accessory traits involved in sensing, responding to environmental cues, transport, mobile elements (transposases and plasmids), toxin-antitoxin systems, and type VI secretion systems. Together these genomic features suggest adaptations and capabilities of sea-ice communities manifesting at the community level through seasonal ecological succession, whereas the denser cryopeg communities appear adapted to intense bacterial competition, leaving fewer genera to dominate with brine-specific adaptations and social interactions that sacrifice some members for the benefit of others. Such cryopeg genomic traits provide insight into how long-term environmental stability may enable life to survive extreme conditions.

Marinobacter orientalis sp. nov., a thiosulfate-oxidizing bacterium isolated from a marine solar saltern

A facultatively anaerobic bacterium, strain W62^T, was isolated from the marine solar saltern in Weihai, China. Cells of the novel strain were Gram-stain negative, non-flagellated, non-gliding, rod-shaped and around 0.3-0.5 × 2.5-3.9 µm in size. Optimum growth occurred at 33-37 °C, with 3-5% (w/v) NaCl and at pH 7.0-7.5. On the basis of phylogenetic analysis of the 16S rRNA gene sequence, strain W62^T had close relationship with Marinobacter vulgaris F01^T (98.6%), Marinobacter confluentis KCTC 42705^T (98.4%) and Marinobacter halotolerans NBRC 110910^T (97.7%). Genome sequencing revealed a genome size of 4,050,555 bp, a G+C content of 57.3% and a complete sox system related to thiosulfate oxidization. Strain W62^T had ubiquinone-9 as the sole respiratory quinone and possessed Summed Features 3 (C_16:1 ω7c/C_16:1 ω6c), C_16:0 and C_18:1 ω9c as the major fatty acids. The major polar lipids of strain W62^T were identified as aminophospholipid, phosphatidylglycerol and phosphatidylethanolamine. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic properties and genome analysis, strain W62^T should represent a novel specie of the genus Marinobacter, for which the name Marinobacter orientalis sp. nov. is proposed. The type strain is W62^T (= MCCC 1H00317^T = KCTC 62593^T).

Marinobacter caseinilyticus sp. nov., Isolated from Saline Soil

A Gram-stain-negative, motile, aerobic, rod-shaped bacterium with flagella, designated M3-13^T, was isolated from a saline soil in Zhoushan, China. According to phylogenetic analysis based on 16S rRNA gene sequences, strain M3-13^T was assigned to the genus Marinobacter with highest 16S rRNA gene sequence similarity of 97.7% to Marinobacter maroccanus LMG 30466^T, followed by Marinobacter sediminum R65 ^T (97.5%) and M. salsuginis SD-14B^T (97.2%). Digital DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) were determined to evaluate the genomic relationship between strain M3-13^T and M. maroccanus LMG 30466^T. Digital DDH estimation (19.8%) as well as ANI (72.98%) proved the dissimilarity of strain M3-13^T. Optimal growth of the strain M3-13^T was at 28-30 °C and at pH 8.0-8.5, in the presence of 3-6% (w/v) NaCl. The major fatty acids detected in strain M3-13^T were C_16:1 ω7c/C_16:1 ω6c, C_16:0, C_18:1ω7c/C_18:1 ω6c and C_12:03-OH, and the predominant respiratory quinone was ubiquinone-9. The major polar lipids included diphosphatidyglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminophosphoglycolipid and one unidentified phosphoglycolipid. The DNA G+C content was 56.6%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain M3-13^T belongs to the genus Marinobacter. Based on the polyphasic taxonomic characterization, strain M3-13^T is considered to represent a novel species of the genus Marinobacter, for which the name Marinobacter caseinlyticus sp. nov. is proposed (type strain M3-13^T = MCCC 1K04560^T = KCTC 72043^T).

Marinobacter changyiensis, sp. nov., isolated from offshore sediment

An aerobic, Gram-stain-negative bacterium, designated CLL7-20^T, was isolated from a marine sediment sample from offshore of Changyi, Shandong Province, China. Cells of strain CLL7-20^T were rod-shaped, motile with one or more polar flagella, and grew optimally at pH 7.0, at 28 °C and with 3 % (w/v) NaCl. The principal fatty acids of strain CLL7-20^T were C_16 : 0 and summed feature 3 (C_16 : 1 ω7c/C_16 : 1 ω6c). The main polar lipids of strain CLL7-20^T were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG) and an unidentified aminolipid (AL). Strain CLL7-20^T contained Q-9 as the major respiratory quinone. The G+C content of its genomic DNA was 56.2 mol%. Phylogenetically, strain CLL7-20^T branched within the genus Marinobacter, with M. daqiaonensis YCSA40^T being its closest phylogenetic relative (96.7 % 16S rRNA gene sequence similarity), followed by M. sediminum R65^T (96.6 %). Average nucleotide identity and in silico DNA-DNA hybridization values between strain CLL7-20^T and the closest related reference strains were 73.2% and 19.8 %, respectively. On the basis of its phenotypic, phylogenetic and chemotaxonomic characteristics, we suggest that strain CLL7-20^T (=MCCC 1A14855^T=KCTC 72664^T) is the type strain of a novel species in the genus Marinobacter, for which the name Marinobacter changyiensis sp. nov. is proposed. Based on the genomic analysis, siderophore genes were found from strain CLL7-20^T, which indicate its potential as a promising alternative to chemical fertilizers in iron-limitated environments such as saline soils.

Marinobacter denitrificans sp. nov., isolated from marine sediment of southern Scott Coast, Antarctica

A novel bacterium, designated JB02H27^T, was isolated from marine sediment collected from the southern Scott Coast, Antarctica. Cells were Gram-stain-negative, facultatively anaerobic, polar-flagellated and motile rods. Growth occurred at 4-45 °C, at pH 7.0-9.0 and with 3-25 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain JB02H27^T consistently fell within the genus Marinobacter and formed a clade together with Marinobacter algicola DG893^T (98.8 % similarity), Marinobacter confluentis KCTC 42705^T (98.4 %), Marinobacter salarius R9SW1^T (98.4%) and Marinobacter halotolerans CP12^T (97.9 %), which were subsequently used as reference strains for comparisons of phenotypic and chemotaxonomic characteristics. Average nucleotide identity values between strain JB02H27^T and the four related type strains were 80.9, 76.6, 81.9 and 76.3 %, respectively. The major fatty acids were summed feature 3, C_16 : 0, C_18 : 1 ω9c and C_16 : 0 N alcohol. The polar lipids included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unidentified phospholipid, aminolipid, aminophospholipid and glycolipids. The sole respiratory quinone was ubiquinone-9. The DNA G+C content was 56.9 mol%. Based on the genomic, phylogenetic, phenotypic and chemotaxonomic analysis, we propose that strain JB02H27^T represents a novel species of the genus Marinobacter, for which the name Marinobacter denitrificans sp. nov. is proposed. The type strain is JB02H27^T (=GDMCC 1.1528^T=KCTC 62941^T).

Marinobacter vulgaris sp. nov., a moderately halophilic bacterium isolated from a marine solar saltern

A facultatively anaerobic, Gram-stain-negative and non-gliding bacterium, designated F01^T, was isolated from marine solar saltern in Weihai, PR China. Cells of F01^T were 0.2-0.4 µm wide and 1.4-4.1 µm long, weakly catalase-positive and oxidase-negative. Growth of F01^T was determined to occur at 4-40 °C (optimum, 33-37 °C), pH 6.5-8.5 (optimum, 7.0-8.0), and with 0.5-18.0 % (w/v) NaCl (optimum, 3.0-6.0 %). The 16S rRNA gene sequence analysis indicated that F01^T represented a member of the genus Marinobacter within the family Alteromonadaceae. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was most closely related to Marinobacter algicola DSM 16394^T, with a sequence similarity of 97.5 %. The DNA G+C content of the isolate was 57.6 mol%. The major respiratory quinone of F01^T was ubiquinone-9 (Q-9) and the major fatty acids were anteiso-C_15 : 0, C_16 : 0 and C_18 : 1ω9c. The major polar lipids were phosphoaminolipid, phosphatidylglycerol and phosphatidylethanolamine. On the basis of the results of the phylogenetic analysis and phenotypic properties, it is concluded that F01^T can be considered to represent a novel species in the genus Marinobacter, for which the name Marinobacter vulgaris sp. nov. is proposed. The type strain is F01^T (=MCCC 1H00290^T=KCTC 52700^T).

Salino-alkaline lime of anthropogenic origin a reservoir of diverse microbial communities

This paper presents study on the microbiome of a unique extreme environment - saline and alkaline lime, a by-product of soda ash and table salt production in Janikowo, central Poland. High-throughput 16S rDNA amplicon sequencing was used to reveal the structure of bacterial and archaeal communities in the lime samples, taken from repository ponds differing in salinity (2.3-25.5% NaCl). Surprisingly abundant and diverse bacterial communities were discovered in this extreme environment. The most important geochemical drivers of the observed microbial diversity were salinity, calcium ions, nutrients, and water content. The bacterial and archaeal communities in saline, alkaline lime were similar to those found in natural haloalkaline environments. Although the archaeal contribution to the whole microbial community was lower than 4%, the four archaeal genera Natronomonas, Halorubrum, Halobellus, and Halapricum constituted the core microbiome of saline, alkaline lime - a set of OTUs (> 0.1% of total archaeal relative abundance) present in all samples under study. The high proportion of novel, unclassified archaeal and bacterial sequences (not identified at 97% similarity level) in the 16S rRNA gene libraries indicated that potentially new genera, especially within the class of Thermoplasmata inhabit this unique environment.

Marinobacter bohaiensis sp. nov., a moderate halophile isolated from benthic sediment of the Bohai Sea

A Gram-stain-negative, motile, aerobic and rod-shaped bacterial strain, designated T17^T, was isolated from benthic sediment sampled at Jiaozhou Bay, Bohai Sea, China, and its taxonomic position was investigated. The 16S rRNA gene sequence of strain T17^T exhibited the highest similarity values to those of the type strain Marinobacter lacisalsi FP2.5 (96.2 %) and Marinobacter koreensis DD-M3^T (96.2 %). Strain T17^T grew optimally at 35 °C, pH 7.0-8.0 and in the presence of 6.0-10.0 % (w/v) NaCl. The predominant ubiquinone in strain T17^T was identified as Q-9. The major fatty acids of strain T17^T were C12 : 0, C16 : 0 and C16 : 0 10-CH3. The major polar lipids of strain T17^T were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidglycerol, an unidentified aminolipid and an unidentified phospholipid. The DNA G+C content of strain T17^T was 63.0 mol%. The draft genome sequence of strain T17^T includes 4 755 891 bp in total (N50=2 856 325 bp) with a medium read coverage of 100.0x and 11 scaffolds. In silico DNA-DNA hybridization with the three type strains showed 20.3, 19.7 and 19.9 % relatedness to Marinobacter santoriniensis NKSG1^T, Marinobacter segnicrescens SS11B1-4^T and Marinobacter daqiaonensis CGMCC 1.9167^T, respectively. On the basis of the phenotypic, phylogenetic, genomic and chemotaxonomic properties, strain T17^T is considered to represent a novel species within the genus Marinobacter, for which the name Marinobacterbohaiensis sp. nov. is proposed. The type strain is T17^T (=KCTC 52710^T=MCCC 1K03282^T).

Marinobacter salexigens sp. nov., isolated from marine sediment

A novel bacterium, designated as strain HJR7^T, was isolated from a marine sediment sample collected from the coastal area of Weihai, China (121° 57' E, 37° 29' N). Cells were Gram-stain-negative, facultative anaerobic, non-motile and rod-shaped. The temperature, pH and NaCl ranges for growth were determined as 4-40 °C, pH 6.5-9.5 and 0.5-15.0 % (w/v), respectively. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain HJR7^T belongs to the genus Marinobacter in the family Alteromonadaceae. The most closely related species were Marinobacter aromaticivorans (97.6 % 16S rRNA gene sequence similarity) and Marinobacter maritimus (97.3 % similarity). Ubiquinone 9 (Q-9) was the only respiratory quinone detected in strain HJR7^T. The major fatty acids of strain HJR7^T were C12 : 0, C16 : 0, C16 : 0 N alcohol, C18 : 1ω9c and C18 : 3ω6, 9, 12c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid. The DNA G+C content of strain HJR7^T was 53.7 mol%. On the basis of phylogenetic, genotypic, phenotypic, and chemotaxonomic analyses, strain HJR7^T represents a novel species within the genus Marinobacter, for which the name Marinobacter salexigens sp. nov. is proposed. The type strain is HJR7^T (=KCTC 52545^T=MCCC 1H00176^T).

Marinobacter lipolyticus from Red Sea for lipase production and modulation of silver nanomaterials for anti-candidal activities

In this study, the bacterial strain CEES 33 was isolated from the coastal area of the Red Sea, Jeddah, Kingdom of Saudi Arabia. The bacterium isolate was identified and characterized by using biochemical and molecular methods. The isolate CEES 33 has been identified as Gram-negative rod shaped and cream pigmented spherical colonies. It also demonstrated a positive result for nitrate reduction, oxidase, catalase, citrate utilization, lipase and exopolysaccharide production. Strain CEES 33 was characterized at the molecular level by partial 16S rRNA sequencing and it has been identified as Marinobacter lipolyticus (EMBL|LN835275.1). The lipolytic activity of the isolate was also observed 2.105 nkatml-1. Furthermore, the bacterial aqueous extract was used for green synthesis of silver nanoparticles (AgNPs), which was further confirmed by UV-visible spectra (430 nm), XRD and SEM analysis. Moreover, the biological functional group that involved in AgNPs synthesis was confirmed by FTIR spectra. The biological activities of AgNPs were also investigated, which showed a significant growth inhibition of Candida albicans with 16 ± 2 mm zone of inhibition at 10 μg dose/wells. Therefore, bacterium Marinobacter lipolyticus might be used in future for lipase production and nanoparticles fabrication for biomedical application, to control fungal diseases caused by C. albicans.