Aliidiomarina minuta sp. nov., a haloalkaliphilic bacterium that forms ultra-small cells under non-optimal conditions

Enrichment of a heterotrophic nitrifying and aerobic denitrifying bacterial consortium: Microbial community succession and nitrogen removal characteristics and mechanisms

This study cultivated a bacterial consortium (S60) from landfill leachate that exhibited effective heterotrophic nitrification and aerobic denitrification (HN-AD) properties. Under aerobic conditions, the removal of NH4+-N reached 100 % when the S60 consortium utilised NH4+-N either as the sole nitrogen source or in combination with NO2--N and NO3--N. Optimal HN-AD performance was achieved with sodium acetate as a carbon source and a pH of 7.0-8.0, dissolved oxygen concentration of 4.0-5.0 mg/L, and a C/N ratio of 10. Furthermore, the presence of functional genes (amoA, hao, napA, nirK, nirS, nosZ), hydroxylamine oxidase, nitrate reductase, and nitrite reductase was confirmed in the S60 consortium. Drawing from these findings, two HN-AD pathways were delineated: NH4+-N → NH2OH → NO2--N → NO3--N → NO2--N → NO → N2O → N2 and NH4+-N → NH2OH → N2O → N2. Metagenomic binning analysis of the S60 consortium uncovered complete pathways for dissimilatory nitrate reduction and denitrification within Halomonas, Zobellella, Stutzerimonas, Marinobacter, and Pannonibacter. These findings offer new insights into the application of HN-AD bacteria and their collaborative nitrogen removal in environments with varying nitrogen sources.

Aliidiomarina quisquiliarum sp. nov., isolated from landfill leachate

Bacterial strain Y-6^T, isolated from a landfill site in Yiwu, PR China, was characterized using a polyphasic taxonomy approach. Cells were Gram-stain-negative, aerobic, rod-shaped, motile by means of a single polar flagellum and formed pale beige colonies. Strain Y-6^T grew at 4-40 °C (optimal at 30-37 °C), pH 6.5-9.5 (optimal at pH 7.2-8.5) and in the presence of 0.5-10.0 % (w/v) NaCl (optimal at 1.0-3.0 %). Phylogenetic analysis revealed that strain Y-6^T was a member of the genus Aliidiomarina and closely related to Aliidiomarina taiwanensis MCCC 1A06493^T with a 16S rRNA sequence similarity of 98.2 %. The major cellular fatty acids of the isolate were iso-C_15 : 0, C_16 : 0, iso-C_17 : 0 and summed feature 9 (iso-C_17 : 1  ω9c and/or 10-methyl-C_16 : 0). Q-8 was the predominant ubiquinone. The major polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminoglycophospholipid, aminophospholipid, phospholipid, three glycolipids and two unknown lipids. The genomic DNA G+C content was 46.6 mol%. The digital DNA-DNA hybridization value between Y-6^T and A. taiwanensis MCCC 1A06493^T was 18.3 %. Strain Y-6^T had an average nucleotide identity value of 74.09 % with A. taiwanensis MCCC 1A06493^T. Results from the polyphasic taxonomy study support the conclusion that strain Y-6^T represents a novel Aliidiomarina species, for which the name Aliidiomarina quisquiliarum sp.nov. is proposed. The type strain is Y-6^T (=MCCC 1K06228^T=KCTC 82676^T).

Aliidiomarina halalkaliphila sp. nov., a haloalkaliphilic bacterium isolated from a soda lake in Inner Mongolia Autonomous Region, China

A haloalkaliphilic strain (IM 1326^T) was isolated from brine sampled at a soda lake in the Inner Mongolia Autonomous Region, China. Cells of the strain were rod-shaped and motile. Strain IM 1326^T was able to grow at 4–42 °C (optimum, 37 °C) with 0–13.0 % (w/v) NaCl concentrations (optimum at 4.0–6.0 %) and at pH 7.5–11.0 (optimum at 9.0–10.0). The 16S rRNA gene phylogenetic analysis revealed that the isolate belongs to the genus Aliidiomarina and is closely related to the type strains of Aliidiomarina sanyensis (95.8 % sequence similarity), Aliidiomarina shirensis (95.7 %), Aliidiomarina iranensis (95.4 %) and Aliidiomarina haloalkalitolerans (95.3 %). The whole genome of strain IM 1326^T was sequenced, and the genomic DNA G+C content was 49.7 mol%. Average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the isolate and the related Aliidiomarina species were 68.1–84.9 %, 76–78 % and 18.4–20.4 %, respectively. The respiratory quinone was ubiquinone-8. The polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified aminophospholipid. The predominant cellular fatty acids were summed feature 9 (10-methyl-C_16 : 0/iso-C_17 : 1 ω9c, 22.2 %), iso-C_15 : 0 (16.1 %) and iso-C_17 : 0 (13.1 %). Based on the results of phylogenetic analysis, genome relatedness, and the physiological and chemotaxonomic properties of the isolate, strain IM 1326^T is considered to represent a novel species of the genus Aliidiomarina, for which the name Aliidiomarina halalkaliphila sp. nov. is proposed (type strain IM 1326^T=CGMCC 1.17056^T=JCM 34227^T).

Draft Genome Sequence of Halomonas sp. Strain KAO, a Halophilic Mn(II)-Oxidizing Bacterium

Halomonas sp. strain KAO is an aerobic, Mn(II)-oxidizing, halophilic bacterium. The draft genome of the isolate contains 47 contigs encompassing 3.7 Mb and a G+C content of 64.22%. This sequence will provide essential information for future studies of Mn(II) oxidation, particularly under halophilic conditions.

Halomonas sp. strain KAO is an aerobic, Mn(II)-oxidizing, halophilic bacterium. The draft genome of the isolate contains 47 contigs encompassing 3.7 Mb and a GC content of 64.22%. This sequence will provide essential information for future studies of Mn(II) oxidation, particularly under halophilic conditions.

Draft Genome Sequence of Halomonas sp. Strain ML-15, a Haloalkaliphilic, Polycyclic Aromatic Hydrocarbon-Degrading Bacterium

Halomonas sp. strain ML-15 is an aerobic, haloalkaliphilic bacterium capable of degrading polycyclic aromatic hydrocarbons (PAHs). The draft genome sequence of the isolate contains 19 contigs encompassing 4.8 Mb and a G+C content of 65.38%. This sequence will provide essential information for future studies of PAH degradation, particularly under haloalkaliphilic conditions.

Halomonas sp. strain ML-15 is an aerobic, haloalkaliphilic bacterium capable of degrading polycyclic aromatic hydrocarbons (PAHs). The draft genome sequence of the isolate contains 19 contigs encompassing 4.8 Mb and a G+C content of 65.38%. This sequence will provide essential information for future studies of PAH degradation, particularly under haloalkaliphilic conditions.

The discovery of antioxidants in marine microorganisms and their protective effects on the hepatic cells from chemical-induced oxidative stress

The marine environment is emerging as a biodiversity resource for the discovery of natural molecules or chemical scaffolds with pharmaceutical activity. Marine microbes have a tremendous ability to sense and respond to their surroundings to survive in a stressful environment by producing different molecules. As oxidative stress is directly or indirectly involved in various pathological conditions in humans, we believe that marine-derived antioxidant molecules will have a great prospect as a novel antioxidant molecule. We, in this work, explored the marine microbial resources from the Gulf of Mannar, Bay of Bengal, India. High-throughput screening of antioxidant molecule producing marine microbes has revealed that extract from Kocuria marina CDMP 10, can effectively reduce the DPPH free radical. Methanolic crude extract obtained by the freeze-thawing was fractionated and purified by using activity guided purification with the help of reverse phase HPLC and analysed through UPLC-MS. Chemical analysis, as well as MS-spectra, indicated that marine bacteria K. marina CDMP 10 derived antioxidant fraction contains the short peptides. The antioxidant activity of the three highly hydrophobic peptides, (Ser-Ser-Gln, Phe-Glu, Asp-Ile and Leu-Glu) was confirmed by in vitro as well as a cell-based assay. These small peptide molecules are noncytotoxic and can prevent the human cells from chemical-induced oxidative stress. Ser-Ser-Gln peptide demonstrated a potent free radical scavenging activity in Hepatocellular carcinoma cell lines. This study suggests that these short peptides from K. marina CDMP 10 may serve as a potential pharmaceutical candidate with antioxidant activity.

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.

Bioreactor performance and microbial community analysis of autotrophic denitrification under micro-aerobic condition

Autotrophic denitrification process is an effective strategy for treating sulfide and nitrate-enriched wastewater with low organic carbon. This study determined the sulfide oxidation and nitrate reduction rates and characterized the dominant bacteria and microbial community structure stimulated by micro-aerobic conditions in autotrophic denitrification system. With gradually increased sulfide concentration, the sulfide removal rate decreased to 37.8% at S^2- = 600 mg/L, while the peak sulfide and nitrate removal rates (100% and 53.8%) were achieved at S^2- = 800 mg/L with the air aeration rate of 20 mL/min. The Illumina sequencing results indicated that Thiobacillus accounted for 63% of total operational taxonomic units at generic level with sulfide concentration of 200 mg/L under anaerobic condition. However, Azoarcus, Thauera and Aliidiomorina became the dominant genera under micro-aerobic condition and their abundance significantly and positively related to the sulfide concentration and aeration rate (p < 0.05). According to the 16S metaproteomics functional composition prediction, one potential mechanism for autotrophic denitrifying under micro-aerobic condition was deduced that the oxidation of sulfide to thiosulfate further to sulfite was reinforced by trace oxygen, while the sulfite reductase activity was restrained. The decreased sulfide concentration weakened the toxicity inhibition on denitrifiers and accordingly the performance of autotrophic denitrification process was enhanced by micro-aerobic condition.

Oxidative Formation and Removal of Complexed Mn(III) by Pseudomonas Species

The observation of significant concentrations of soluble Mn(III) complexes in oxic, suboxic, and some anoxic waters has triggered a re-evaluation of the previous Mn paradigm which focused on the cycling between soluble Mn(II) and insoluble Mn(III,IV) species as operationally defined by filtration. Though Mn(II) oxidation in aquatic environments is primarily bacterially-mediated, little is known about the effect of Mn(III)-binding ligands on Mn(II) oxidation nor on the formation and removal of Mn(III). Pseudomonas putida GB-1 is one of the most extensively investigated of all Mn(II) oxidizing bacteria, encoding genes for three Mn oxidases (McoA, MnxG, and MopA). P. putida GB-1 and associated Mn oxidase mutants were tested alongside environmental isolates Pseudomonas hunanensis GSL-007 and Pseudomonas sp. GSL-010 for their ability to both directly oxidize weakly and strongly bound Mn(III), and to form these complexes through the oxidation of Mn(II). Using Mn(III)-citrate (weak complex) and Mn(III)-DFOB (strong complex), it was observed that P. putida GB-1, P. hunanensis GSL-007 and Pseudomonas sp. GSL-010 and mutants expressing only MnxG and McoA were able to directly oxidize both species at varying levels; however, no oxidation was detected in cultures of a P. putida mutant expressing only MopA. During cultivation in the presence of Mn(II) and citrate or DFOB, P. putida GB-1, P. hunanensis GSL-007 and Pseudomonas sp. GSL-010 formed Mn(III) complexes transiently as an intermediate before forming Mn(III/IV) oxides with the overall rates and extents of Mn(III,IV) oxide formation being greater for Mn(III)-citrate than for Mn(III)-DFOB. These data highlight the role of bacteria in the oxidative portion of the Mn cycle and suggest that the oxidation of strong Mn(III) complexes can occur through enzymatic mechanisms involving multicopper oxidases. The results support the observations from field studies and further emphasize the complexity of the geochemical cycling of manganese.

Aliidiomarina sedimenti sp. nov., a haloalkaliphilic bacterium in the family Idiomarinaceae

A novel Gram-staining-negative straight or curved rod-shaped, moderately halophilic and alkaliphilic bacterium, designated strain GBSy1T, was isolated from a sediment sample from the coastal-marine wetland Gomishan in Iran. GBSy1T was motile, and formed non-pigmented, mucoid colonies. Growth occurred with between 1 and 15 % (w/v) NaCl and the isolate grew optimally with 5 % (w/v) NaCl. The optimum pH and temperature for growth were 8.5 and 34 °C, while the strain was able to grow at pH 7.0-10 and 4-40 °C. On the basis of the results of 16S rRNA gene sequence analysis, GBSy1T was shown to represent a member of the genus Aliidiomarina within the class Gammaproteobacteria, family Idiomarinaceae and showed closest phylogenetic similarity to Aliidiomarina marisCF12-14T (97.7 %). The DNA G+C content of GBSy1T was 51.2 mol%. The cells of GBSy1T contained the isoprenoid ubiquinones Q-8, Q-9 and Q-10 (92, 2 and 2 %, respectively). The major cellular fatty acids of the isolate were iso-C11 : 0 3-OH, iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c and its polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and three unknown phospholipids. The level of DNA-DNA relatedness between GBSy1T and Aliidiomarina marisDSM 22154T was 31 %. All these features confirmed the placement of GBSy1T within the genus Aliidiomarina. On the basis of evidence from this study, a novel species of the genus Aliidiomarina, Aliidiomarina sedimenti sp. nov., is proposed, with GBSy1T (=IBRC-M 10764T=CECT 8340T) as the type strain.

Aliidiomarina soli sp. nov., isolated from saline-alkaline soil

A Gram-stain-negative, motile, non-spore-forming bacterium, designated strain Y4G10-17T, was isolated from the saline-alkali farmland top soil, Inner Mongolia, northern China. Strain Y4G10-17T could grow at 4-45 °C (with 30 °C as the optimal temperature), pH 6.0-12.0 (optimal at pH 9.0) and in the presence of 1.0-12.0 % (w/v) NaCl (optimal at 4.0-6.0 %). Phylogenetic analysis based on the eight different copies of the 16S rRNA gene sequences revealed that strain Y4G10-17T shared the highest sequence similarity with Aliidiomarina maris CF12-14T, 97.93-98.66 %, and lower than 97.0 % sequence similarity with all other type strains. Its major cellular fatty acids contained iso-C15 : 0, iso-C17 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), iso-C15 : 1 F, iso-C11 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). Q-8 was the predominantubiquinone. The major polar lipids of strain Y4G10-17T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unknown lipids and one unknown aminolipid. The genomic DNA G+C content was 49.3 mol%. DNA-DNA hybridization revealed that strain Y4G10-17T showed 20.2±5 % genomic DNA relatedness with its close relative A. maris CF12-14T. Based on the phenotypic, phylogenetic and genotypic characteristics, strain Y4G10-17T represents a novel species within the genus Aliidiomarina, for which the name Aliidiomarina soli sp. nov. is proposed. The type strain is Y4G10-17T (=CGMCC 1.15759T=KCTC 52381T).