Cloning and characterization of a Na+/H+ antiporter gene of the moderately halophilic bacterium Halobacillus aidingensis AD-6T

Salt stimulates sulfide-driven autotrophic denitrification: Microbial network and metagenomics analyses

Sulfur autotrophic denitrification (SADN) is a promising biological wastewater treatment technology for nitrogen removal, and its performance highly relies on the collective activities of the microbial community. However, the effect of salt (a prevailing characteristic of some nitrogen-containing industrial wastewaters) on the microbial community of SADN is still unclear. In this study, the response of the sulfide-SADN process to different salinities (i.e., 1.5 % salinity, 0.5 % salinity, and without salinity) as well as the involved microbial mechanisms were investigated by molecular ecological network and metagenomics analyses. Results showed that the satisfactory nitrogen removal efficiency (>97 %) was achieved in the sulfide-SADN process (S/N molar ratio of 0.88) with 1.5 % salinity. In salinity scenarios, the genus Thiobacillus significantly proliferated and was detected as the dominant sulfur-oxidizing bacteria in the sulfide-SADN system, occupying a relative abundance of 29.4 %. Network analysis further elucidated that 1.5 % salinity had enabled the microbial community to form a more densely clustered network, which intensified the interactions between microorganisms and effectively improved the nitrogen removal performance of the sulfide-SADN. Metagenomics sequencing revealed that the abundance of functional genes encoding for key enzymes involved in SADN, dissimilatory nitrate reduction to ammonium, and nitrification was up-regulated in the 1.5 % salinity scenario compared to that without salinity, stimulating the occurrence of multiple nitrogen transformation pathways. These multi-paths contributed to a robust SADN process (i.e., nitrogen removal efficiency >97 %, effluent nitrogen <2.5 mg N/L). This study deepens our understanding of the effect of salt on the SADN system at the community and functional level, and favors to advance the application of this sustainable bioprocess in saline wastewater treatment.

Efficient flocculation pretreatment of coal gasification wastewater by halophilic bacterium Halovibrio variabilis TG-5

The isolated halophilic bacterial strain Halovibrio variabilis TG-5 showed a good performance in the pretreatment of coal gasification wastewater. With the optimum culture conditions of pH = 7, a temperature of 46 °C, and a salinity of 15%, the chemical oxygen demand and volatile phenol content of pretreated wastewater were decreased to 1721 mg/L and 94 mg/L, respectively. The removal rates of chemical oxygen demand and volatile phenol were over 90% and 70%, respectively. At the optimum salinity conditions of 15%, the total yield of intracellular compatible solutes and the extracellular transient released yield under hypotonic conditions were increased to 6.88 g/L and 3.45 g/L, respectively. The essential compatible solutes such as L-lysine, L-valine, and betaine were important in flocculation mechanism in wastewater pretreatment. This study provided a new method for pretreating coal gasification wastewater by halophilic microorganisms, and revealed the crucial roles of compatible solutes in the flocculation process.

Paracoccus onchidii sp. nov., a moderately halophilic bacterium isolated from a marine invertebrate from the South China Sea

A novel moderately halophilic bacterial strain, designated Z330^T, was isolated from the egg of a marine invertebrate of the genus Onchidium collected in the South China Sea. The 16S rRNA gene sequence of strain Z330^T exhibited the highest similarity value to that of the type strain Paracoccus fistulariae KCTC 22803^T (97.6%), Paracoccus seriniphilus NBRC 100798^T (97.6%) and Paracoccus aestuarii DSM 19484^T (97.6%). Phylogenomic and 16S rRNA phylogenetic analysis showed that strain Z330^T was most closely related to P. seriniphilus NBRC 100798^T and P. fistulariae KCTC 22803^T. Strain Z330^T grew optimally at 28-30 °C, pH 7.0-8.0 with the presence of 5.0-7.0% (w/v) NaCl. In addition, growth of strain Z330^T occurred at 0.5-16% NaCl, indicated strain Z330^T was a moderately halophilic and halotolerant bacterium of genus Paracoccus. The predominant respiratory quinone in strain Z330^T was identified as ubiquinone-10. The major polar lipids of strain Z330^T were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, glycolipid and six unidentified polar lipids. The major fatty acids of strain Z330^T was summed feature 8 (C_18:1 ω6c and/or C_18:1 ω7c). The draft genome sequence of strain Z330^T includes 4,084,570 bp in total (N50 = 174,985 bp) with a medium read coverage of 463.6 × and 83 scaffolds. The DNA G + C content of strain Z330^T was 60.5%. In silico DNA-DNA hybridization with the four type strains showed 20.5, 22.3, 20.1 and 20.1% relatedness to Paracoccus fistulariae KCTC 22803^T, Paracoccus seriniphilus NBRC 100798^T, Paracoccus aestuarii DSM 19484^T and Paracoccus denitrificans 1A10901^T, respectively. And the average nucleotide identity (ANIb) values between strain Z330^T and these four type strains were 76.2, 80.0, 75.8 and 73.8%, respectively, lower than the 95-96% threshold value for dividing prokaryotic species. On the basis of the phenotypic, phylogenetic, phylogenomic and chemotaxonomic properties, a novel species of the genus Paracoccus, Paracoccus onchidii sp. nov. is proposed with the type strain Z330^T (= KCTC 92727^T = MCCC 1K08325^T).

Complete genome sequence of one novel marine Pseudomonas sp. BSw22131 growing with dimethylsulfoniopropionate (DMSP) as the sole carbon source

Members of the genus Pseudomonas have been frequently isolated from the marine environment, indicating their ecological role in native habitats. One bacterial strain, Pseudomonas sp. BSw22131, was isolated from seawater in Kongsfjorden, Svalbard. The bacterium can grow with algae-derived dimethylsulfoniopropionate (DMSP) as the sole carbon source. Here, we sequenced the complete genome of strain BSw22131, which contained a single circular chromosome of 5,739,290 (G + C content of 58.23 mol%) without any plasmids. A total of 5362 protein-coding genes, 65 tRNA genes, and 16 rRNA genes were obtained. Genome sequence analysis revealed that strain BSw22131 was not only a potential novel species of the genus Pseudomonas but also different from Pseudomonas sp. DMSP-1 that was isolated from the same habitat and also utilized DMSP as the sole carbon source for growth. The results can be helpful for understanding the catabolism of the genus Pseudomonas in sulfur cycling in the Arctic fjord ecosystem.

Genomic Analysis of Halotolerant Bacterial Strains Martelella soudanensis NC18T and NC20

Two novel, halotolerant strains of Martelella soudanensis, NC18^T and NC20, were isolated from deep subsurface sediment, deeply sequenced, and comparatively analyzed with related strains. Based on a phylogenetic analysis using 16S rRNA gene sequences, the two strains grouped with members of the genus Martelella. Here, we sequenced the complete genomes of NC18^T and NC20 to understand the mechanisms of their halotolerance. The genome sizes and G+C content of the strains were 6.1 Mb and 61.8 mol%, respectively. Moreover, NC18^T and NC20 were predicted to contain 5,849 and 5,830 genes, and 5,502 and 5,585 protein-coding genes, respectively. Both strains contain the identically predicted 6 rRNAs and 48 tRNAs. The harboring of halotolerant-associated genes revealed that strains NC18^T and NC20 might tolerate high salinity through the accumulation of potassium ions in a "salt-in" strategy induced by K⁺ uptake protein (kup) and the K⁺ transport system (trkAH and kdpFABC). These two strains also use the ectoine transport system (dctPQM), the glycine betaine transport system (proVWX), and glycine betaine uptake protein (opu) to accumulate "compatible solutes," such as ectoine and glycine betaine, to protect cells from salt stress. This study reveals the halotolerance mechanism of strains NC18^T and NC20 in high salt environments and suggests potential applications for these halotolerant and halophilic strains in environmental biotechnology.

Genetic and Comparative Genome Analysis of Exiguobacterium aurantiacum SW-20, a Petroleum-Degrading Bacteria with Salt Tolerance and Heavy Metal-Tolerance Isolated from Produced Water of Changqing Oilfield, China

The genome of Exiguobacterium aurantiacum SW-20 (E. aurantiacum SW-20), a salt-tolerant microorganism with petroleum hydrocarbon-degrading ability isolated from the Changqing Oilfield, was sequenced and analyzed. Genomic data mining even comparative transcriptomics revealed that some genes existed in SW-20 might be related to the salt tolerance. Besides, genes related to petroleum hydrocarbon degradation discovered in genomic clusters were also found in the genome, indicating that these genes have a certain potential in the bioremediation of petroleum pollutants. Multiple natural product biosynthesis gene clusters were detected, which was critical for survival in the extreme conditions. Transcriptomic studies revealed that some genes were significantly up-regulated as salinity increased, implying that these genes might be related to the salt tolerance of SW-20 when living in a high salt environment. In our study, gene clusters including salt tolerance, heavy metal tolerance and alkane degradation were all compared. When the same functional gene clusters from different strains, it was discovered that the gene composition differed. Comparative genomics and in-depth analysis provided insights into the physiological features and adaptation strategies of E. aurantiacum SW-20 in the oilfield environment. Our research increased the understanding of niches adaption of SW-20 at genomic level.

Sulphur-based autotrophic denitrification of wastewater obtained following graphite production: Long-term performance, microbial communities involved, and functional gene analysis

Sulphur-based autotrophic denitrification is an energy-efficient NO3--N removal process; it does not require carbon and may potentially replace traditional denitrification processes. This process was used to treat graphite production-derived wastewater and achieved almost complete removal of NO3--N (concentration in effluent: 5.2 mg/L; concentration in influent: 606 mg/L) at a salinity of 15 g/L with a 30 h hydraulic retention time. A unique microbial community was established, in which the abundance of Thiobacillus increased with the increase of the NO3--N concentration and salinity. Metagenomic analysis revealed that the denitrification metabolic pathway in the bioreactor was active. It also revealed the increased activation of nhaH, a gene encoding Na+/H+ antiporters; proA, proB, and proC, genes encoding proline; and Trk and Kdp systems during the treatment of graphite production-derived wastewater to maintain cell function, providing valuable information about utilizing the sulphur-based autotrophic denitrification process to treat graphite production-derived wastewater.

Genome sequencing of Aspergillus glaucus 'CCHA' provides insights into salt-stress adaptation

Aspergillus, as a genus of filamentous fungi, has members that display a variety of different behavioural strategies, which are affected by various environmental factors. The decoded genomic sequences of many species vary greatly in their evolutionary similarities, encouraging studies on the functions and evolution of the Aspergillus genome in complex natural environments. Here, we present the 26 Mb de novo assembled high-quality reference genome of Aspergillus glaucus 'China Changchun halophilic Aspergillus' (CCHA), which was isolated from the surface of plants growing near a salt mine in Jilin, China, based on data from whole-genome shotgun sequencing using Illumina Solexa technology. The sequence, coupled with data from comprehensive transcriptomic survey analyses, indicated that the redox state and transmembrane transport might be critical molecular mechanisms for the adaptation of A. glaucus 'CCHA' to the high-salt environment of the saltern. The isolation of salt tolerance-related genes, such as CCHA-2114, and their overexpression in Escherichia coli demonstrated that A. glucus 'CCHA' is an excellent organism for the isolation and identification of salt tolerant-related genes. These data expand our understanding of the evolution and functions of fungal and microbial genomes, and offer multiple target genes for crop salt-tolerance improvement through genetic engineering.

Alkaline Response of a Halotolerant Alkaliphilic Halomonas Strain and Functional Diversity of Its Na+(K+)/H+ Antiporters

Halomonas sp. Y2 is a halotolerant alkaliphilic strain from Na⁺-rich pulp mill wastewater with high alkalinity (pH >11.0). Transcriptome analysis of this isolate revealed this strain may use various transport systems for pH homeostasis. In particular, the genes encoding four putative Na⁺/H⁺ antiporters were differentially expressed upon acidic or alkaline conditions. Further evidence, from heterologous expression and mutant studies, suggested that Halomonas sp. Y2 employs its Na⁺/H⁺ antiporters in a labor division way to deal with saline and alkaline environments. Ha-NhaD2 displayed robust Na⁺(Li⁺) resistance and high transport activities in Escherichia coli; a ΔHa-nhaD2 mutant exhibited growth inhibition at high Na⁺(Li⁺) concentrations at pH values of 6.2, 8.0, and 10.0, suggesting its physiological role in osmotic homeostasis. In contrast, Ha-NhaD1 showed much weaker activities in ion exporting and pH homeostasis. Ha-Mrp displayed a combination of properties similar to those of Mrp transporters from some Bacillus alkaliphiles and neutrophiles. This conferred obvious Na⁺(Li⁺, K⁺) resistance in E. coli-deficient strains, as those ion transport spectra of some neutrophil Mrp antiporters. Conversely, similar to the Bacillus alkaliphiles, Ha-Mrp showed central roles in the pH homeostasis of Halomonas sp. Y2. An Ha-mrp-disrupted mutant was seriously inhibited by high concentrations of Na⁺(Li⁺, K⁺) but only under alkaline conditions. Ha-NhaP was determined to be a K⁺/H⁺ antiporter and shown to confer strong K⁺ resistance both at acidic and alkaline stresses.

Progress in decontamination by halophilic microorganisms in saline wastewater and soil

Environments with high-salt concentrations are often populated by dense microbial communities. Halophilic microorganisms can be isolated from different saline environments and different strains even belonging to the same genus have various applications. Wastewater and soil rich in both organic matter and salt are difficult to treat using conventional microorganisms typically found in wastewater treatment and soil bioremediation facilities. Studies on decontaminative capabilities and decontamination pathways of organic contaminants (i.e., aromatic compounds benzoate, cinnamate, 3-phenylpropionate, 4-hydroxybenzoic acid), heavy metals (i.e., tellurium, vanadium), and nutrients in the biological treatment of saline wastewater and soil by halophilic microorganisms are discussed in this review.