Bacillus hunanensis sp. nov., a slightly halophilic bacterium isolated from non-saline forest soil

Shouchella tritolerans sp. nov., a facultative anaerobic bacterium isolated from marine sediments

An alkali, salt, and thermo-tolerant strain designated FJAT-45399^T was isolated from marine sediment in Fujian Province, China. Strain FJAT-45399^T was Gram-stain-positive, rod-shaped, and facultatively aerobic. It shared high 16S rRNA gene sequence similarities with the members of the genus Shouchella. Further, the phylogenetic and phylogenomic analysis also suggested strain FJAT-45399^T clustered with the members of the genus Shouchella. Growth of strain FJAT-45399^T was observed at 15-55 °C (optimum 45-50 °C), pH 7.0-13.0 (optimum 9.0) and 0-15% (w/v) NaCl (optimum 2%). It contained MK-7 as the menaquinone. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and an unidentified glycolipid (UGL) and lipid (UL). The major fatty acids (> 10%) were C_16:0 (22.8%), iso-C_15:0 (21.3%), and anteiso-C_15:0 (14.0%). The genomic DNA G + C content was 44.5%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain FJAT-45399^T and the most closely related type strain Shouchella clausii DSM 8716^T (ANI 94.1% and dDDH 55.4%) were both below the cut-off level for species delineation. Based on the above results, strain FJAT-45399^T represents a novel species of the genus Shouchella, for which the name Shouchella tritolerans sp. nov., is proposed. The type strain is FJAT-45399^T (= GDMCC 1.3098^T = JCM 35613^T).

A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov

The genus Bacillus, harbouring 293 species/subspecies, constitutes a phylogenetically incoherent group. In the absence of reliable means for grouping known Bacillus species into distinct clades, restricting the placement of new species into this genus has proven difficult. To clarify the evolutionary relationships among Bacillus species, 352 available genome sequences from the family Bacillaceae were used to perform comprehensive phylogenomic and comparative genomic analyses. Four phylogenetic trees were reconstructed based on multiple datasets of proteins including 1172 core Bacillaceae proteins, 87 proteins conserved within the phylum Firmicutes, GyrA-GyrB-RpoB-RpoC proteins, and UvrD-PolA proteins. All trees exhibited nearly identical branching of Bacillus species and consistently displayed six novel monophyletic clades encompassing 5-23 Bacillus species (denoted as the Simplex, Firmus, Jeotgali, Niacini, Fastidiosus and Alcalophilus clades), interspersed with other Bacillaceae species. Species from these clades also generally grouped together in 16S rRNA gene trees. In parallel, our comparative genomic analyses of Bacillus species led to the identification of 36 molecular markers comprising conserved signature indels in protein sequences that are specifically shared by the species from these six observed clades, thus reliably demarcating these clades based on multiple molecular synapomorphies. Based on the strong evidence from multiple lines of investigations supporting the existence of these six distinct 'Bacillus' clades, we propose the transfer of species from these clades into six novel Bacillaceae genera viz. Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. These results represent an important step towards clarifying the phylogeny/taxonomy of the genus Bacillus.

Sediminibacillus terrae sp. nov., a moderate halophile isolated from non-saline farm soil

A Gram-stain-positive, moderately halophilic, strictly aerobic, endospore-forming, rod-shaped bacterium, strain JSM 102062^T, was isolated from a non-saline farm soil sample collected from Dehang Canyon in Hunan, PR China. Growth occurred with 0.5-20 % (w/v) NaCl (optimum 4-7 %) at pH 5.5-11.0 (optimum pH 8.0) and at 20-50 °C (optimum 30-35 °C). Contained cell-wall peptidoglycan based on meso-diaminopimelic acid and possessed menaquinone-7 (MK-7) as the major respiratory isoprenoid quinone. The major cellular fatty acids were anteiso-C_15 : 0, anteiso-C_17 : 0 and iso-C_16 : 0. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, five unidentified phospholipids and an unidentified glycolipid. The DNA G+C content was 44.1 mol%. Phylogeny based on 16S rRNA gene sequences indicated that strain JSM 102062^T belonged to the genus Sediminibacillus, sharing high 16S rRNA gene sequence similarities to Sediminibacillus halophilus EN8d^T (99.4 %) and Sediminibacillus albus NHBX5^T (98.3 %). The whole genomic analysis showed that strain JSM 102062^T constituted a different taxon separated from the recognized Sediminibacillus species. Combined data from phenotypic and genotypic studies demonstrated that strain JSM 102062^T represents a noval species of the genus Sediminibacillus, for which the name Sediminibacillus terrae sp. nov. is proposed; the type strain is JSM 102062^T (=CCTCC AB 2014166^T = CGMCC 1.12957^T=DSM 28949^T=KCTC 33541^T).

Prevalence of sucretolerant bacteria in common soils and their isolation and characterization

Sucretolerant microbes grow in the presence of sugar concentrations high enough to substantially lower water activities. Natural habitats high in sugars are mainly limited to dried fruit, floral nectar, honey, sugarcane, and associated soils. Organisms that tolerate extremes of solute concentration, high enough to lower water activities, might not be expected in common oligoosmotic soils. We report on the isolation of sucretolerant bacteria from common soils using media supplemented with 50% sucrose (a w 0.91) and their physiological characterization and identification by 16S rRNA gene phylogeny. Fifteen of these sucretolerant isolates from common soils were related to four Bacillus spp. A Lysinibacillus and a Microbacterium (actinomycete) also were collected. All grew at 50% sucrose and 13 grew at 60% sucrose. Most probable number counts were used to determine the abundance of sucretolerant microbes in several common soil types, including agricultural, managed turf, and native prairie. Microbial abundance (with fungicides) was about 105 and 103 cells g-1 soil in media containing 50 or 70% sucrose, respectively. The abundances of sucretolerant bacteria in common soils mirror those of halotolerant bacteria that grow at 10 and 20% NaCl. However, there is not a correlation between halotolerance and sucretolerance in our isolates, nor can predictions be made based on taxonomy. Specific solute effects may be at work, rather than biological responses to a single physicochemical parameter such as a w. The occurrence of spore-forming sucretolerant bacteria in common soils has relevance to forward planetary protection and astrobiology. Extraterrestrial habitable regions are defined in part by tolerance to high solute concentrations and osmotolerant soil microbes may contaminate spacecraft.

Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments

The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation. This review highlights the various strategies adopted by halophiles to compensate for their saline surroundings and includes descriptions of recent studies that have used these microorganisms for bioremediation of environments contaminated by petroleum hydrocarbons. The known halotolerant dehalogenase-producing microbes, their dehalogenation mechanisms, and how their proteins are stabilized is also reviewed. In view of their robustness in saline environments, efforts to document their full potential regarding remediation of contaminated hypersaline ecosystems merits further exploration.

Halotolerant bacteria in the São Paulo Zoo composting process and their hydrolases and bioproducts

Halophilic microorganisms are able to grow in the presence of salt and are also excellent source of enzymes and biotechnological products, such as exopolysaccharides (EPSs) and polyhydroxyalkanoates (PHAs). Salt-tolerant bacteria were screened in the Organic Composting Production Unit (OCPU) of São Paulo Zoological Park Foundation, which processes 4 ton/day of organic residues including plant matter from the Atlantic Rain Forest, animal manure and carcasses and mud from water treatment. Among the screened microorganisms, eight halotolerant bacteria grew at NaCl concentrations up to 4 M. These cultures were classified based on phylogenetic characteristics and comparative partial 16S rRNA gene sequence analysis as belonging to the genera Staphylococcus, Bacillus and Brevibacterium. The results of this study describe the ability of these halotolerant bacteria to produce some classes of hydrolases, namely, lipases, proteases, amylases and cellulases, and biopolymers. The strain characterized as of Brevibacterium avium presented cellulase and amylase activities up to 4 M NaCl and also produced EPSs and PHAs. These results indicate the biotechnological potential of certain microorganisms recovered from the composting process, including halotolerant species, which have the ability to produce enzymes and biopolymers, offering new perspectives for environmental and industrial applications.

Genome sequence of the aerobic bacterium Bacillus sp. strain FJAT-13831

Bacillus sp. strain FJAT-13831 was isolated from the no. 1 pit soil of Emperor Qin's Terracotta Warriors in Xi'an City, People's Republic of China. The isolate showed a close relationship to the Bacillus cereus group. The draft genome sequence of Bacillus sp. FJAT-13831 was 4,425,198 bp in size and consisted of 5,567 genes (protein-coding sequences [CDS]) with an average length of 782 bp and a G+C value of 36.36%.