Bacillus marisflavi sp. nov. and Bacillus aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea

Bioprospecting of extremophilic perchlorate-reducing bacteria: report of promising Bacillus spp. isolated from sediments of the bay of Cartagena, Colombia

Three extremophile bacterial strains (BBCOL-009, BBCOL-014 and BBCOL-015), capable of degrading high concentrations of perchlorate at a range of pH (6.5 to 10.0), were isolated from Colombian Caribbean Coast sediments. Morphological features included Gram negative strain bacilli with sizes averaged of 1.75 × 0.95, 2.32 × 0.65 and 3.08 × 0.70 μm, respectively. The reported strains tolerate a wide range of pH (6.5 to 10.0); concentrations of NaCl (3.5 to 7.5% w/v) and KClO4- (250 to 10000 mg/L), reduction of KClO4- from 10 to 25%. LB broth with NaCl (3.5-30% w/v) and KClO4- (250-10000 mg/L) were used in independent trials to evaluate susceptibility to salinity and perchlorate, respectively. Isolates increased their biomass at 7.5 % (w/v) NaCl with optimal development at 3.5 % NaCl. Subsequently, ClO4- reduction was assessed using LB medium with 3.5% NaCl and 10000 mg/L ClO4-. BBCOL-009, BBCOL-014 and BBCOL-015 achieved 10%, 17%, and 25% reduction of ClO4-, respectively. The 16 S rRNA gene sequence grouped them as Bacillus flexus T6186-2, Bacillus marisflavi TF-11 (T), and Bacillus vietnamensis 15 - 1 (T) respectively, with < 97.5% homology. In addition, antimicrobial resistance to ertapenem, vancomycine, amoxicillin clavulanate, penicillin, and erythromycin was present in all the isolates, indicating their high adaptability to stressful environments. The isolated strains from marine sediments in Cartagena Bay, Colombia are suitable candidates to reduce perchlorate contamination in different environments. Although the primary focus of the study of perchlorate-reducing and resistant bacteria is in the ecological and agricultural realms, from an astrobiological perspective, perchlorate-resistant bacteria serve as models for astrobiological investigations.

Innovative Microbial Immobilization Strategy for Di-n-Butyl Phthalate Biodegradation Using Biochar-Calcium Alginate-Waterborne Polyurethane Composites

Di-n-butyl phthalate (DBP) is a prevalent phthalate ester widely used as a plasticizer, leading to its widespread presence in various environmental matrices. This study presents an innovative microbial immobilization strategy utilizing biochar, calcium alginate (alginate-Ca, (C12H14CaO12)n), and waterborne polyurethane (WPU) composites to enhance the biodegradation efficiency of DBP. The results revealed that rice husk biochar, pyrolyzed at 300 °C, exhibits relatively safer and more stable physical and chemical properties, making it an effective immobilization matrix. Additionally, the optimal cultural conditions for Bacillus aquimaris in DBP biodegradation were identified as incubation at 30 °C and pH 7, with the supplementation of 0.15 g of yeast extract, 0.0625 g of glucose, and 1 CMC of Triton X-100. Algal biotoxicity results indicated a significant decrease in biotoxicity, as evidenced by an increase in chlorophyll a content in Chlorella vulgaris following DBP removal from the culture medium. Finally, microbial community analysis demonstrated that encapsulating B. aquimaris within alginate-Ca and WPU layers not only enhanced DBP degradation, but also prevented ecological competition from indigenous microorganisms. This novel approach showcases the potential of agricultural waste utilization and microbial immobilization techniques for the remediation of DBP-contaminated environments.

Genome analysis of Rossellomorea sp. y25, a deep sea bacterium isolated from the sediments of South China Sea

Rossellomorea sp. y25, a putative new species of yellow pigment-producing, aerobic and chemoheterotrophic bacterium belonging to the family Bacillaceae, was isolated from the sediments at the depth of 1829 m in the South China Sea. In this study, we present the complete genome sequences of strain y25, which consisted of only one circular chromosome with 4,633,006 bp and the content of G + C was 41.76%. A total of 4466 CDSs, 106 tRNA, 33 rRNA, and 101 sRNA genes were obtained. Genomic analysis of strain y25 showed that it has the ability to produce antioxidant carotenoids and a large number of heavy metal resistance genes, such as arsenic, cadmium and zinc. In addition, strain y25 contains a prophage that may contribute to host protection against lysis by related Bacillus-like phages. This is the first report of genome-wide information on a bacterium of the genus Rossellomorea isolated from the deep sea, providing insights into how microorganisms of this genus adapt to deep-sea environments.

Genomic insights into symbiosis and host adaptation of sponge-associated novel bacterium, Rossellomorea orangium sp. nov

Sponge-associated microorganisms play vital roles in marine sponge ecology. This study presents a genomic investigation of Rossellomorea sp. MCCB 382, isolated from Stelletta sp., reveals insights into its adaptations and symbiotic roles. Phylogenomic study and Overall Genomic Relatedness Index (OGRI) classify MCCB 382 as a novel species, Rossellomorea orangium sp. nov. The genome encodes numerous carbohydrate metabolism enzymes (CAZymes), likely aiding nutrient cycling in the sponge host. Unique eukaryotic-like protein domains hint at potential mechanisms of symbiosis. Defence mechanisms include CRISPR, restriction-modification systems, DNA phosphorothioation, toxin-antitoxin systems, and heavy metal and multidrug resistance genes, indicating adaptation to challenging marine environments. Unlike obligate mutualists, MCCB 382 shows no genome reduction. Furthermore, the presence of mobile genetic elements, horizontal gene transfer, and prophages suggest genetic versatility, implying flexible metabolic potential and capacity for rapid adaptation and symbiosis shifts. MCCB 382 possesses six biosynthetic gene clusters for secondary metabolites, including both type II and III polyketide synthases (PKS), terpenes, (NRPS), NRPS-independent-siderophore, and lassopeptide. Further genome mining using BiGScape revealed four distinct gene cluster families, T2PKS, NRPS-independent-siderophore, lasso peptide, and terpene, presenting opportunities for novel compound elucidation. Our study reveals a symbiotic lifestyle of MCCB 382 with the host sponge, highlighting symbiont factors that aid in establishing and sustaining this relationship. This is the pioneering genomic characterization of a novel Rossellomorea sp. within the sponge Stelletta sp. holobiont.

Complete genome of Rossellomorea sp. DA94, an agarolytic and orange-pigmented bacterium isolated from mangrove sediment of the South China Sea

Rossellomorea sp. DA94, isolated from mangrove sediment in the South China Sea (Beihai, Guangxi province), is an agarolytic and orange-pigmented bacterium. Here, we present the complete genome sequence of strain DA94, which comprises 4.63 Mb sequences with 43.5% GC content. In total, 4589 CDSs, 33 rRNA genes and 110 tRNA genes were obtained. Genomic analysis of strain DA94 revealed that 108 CAZymes were organized in 4578 PULs involved in polysaccharides degradation, transport, and regulation. Further, we performed the diversity of CAZymes and PULs comparison among Rossellomorea strains. Less CAZymes were organized more PULs, indicating highly efficiently polysaccharides utilization in Rossellomorea. Meanwhile, PUL0459, PUL0460 and PUL0316 related to agar degradation, and exolytic beta-agarase GH50, endo-type beta-agarase GH86 and arylsulfatase were identified in the genome of strain DA94. We verified that strain DA94 can degrade agar to form a bright clear zone around the bacterial colonies in the laboratory. Moreover, the carotenoid biosynthetic pathways were proposed, which may be responsible for orange-pigment of Rossellomorea sp. DA94. This study represents a thorough genomic characterization of CAZymes repertoire and carotenoid biosynthetic pathways of Rossellomorea, provides insight into diversity of related enzymes and their potential biotechnological applications.

Antibiotic and Heavy Metal Co-Resistant Strain Isolated from Enrichment Culture of Marine Sediments, with Potential for Environmental Bioremediation Applications

Antibiotics and heavy metals have caused serious contamination of the environment and even resulted in public health concerns. It has therefore become even more urgent to adopt a sustainable approach to combating these polluted environments. In this paper, we investigated the microbial community of marine sediment samples after 255 days of enrichment culture under Cu (II) and lincomycin stress and ZC255 was the most resistant strain obtained. The 16S rRNA gene sequence confirmed that it belonged to the genus Rossellomorea. Strain ZC255 was resistant to 12 kinds of antibiotics, and had a superior tolerance to Cu (II), Pb (II), Ni (II), Zn (II), Cr (III), and Cd (II). Moreover, it exhibits strong bioremoval ability of Cu and lincomycin. The removal efficiency of Cu (II) and lincomycin can achieve 651 mg/g biomass and 32.5 mg/g biomass, respectively. Strain ZC255 was a promising isolate for pollution bioremediation applications.

An Update on Novel Taxa and Revised Taxonomic Status of Bacteria (Including Members of the Phylum Planctomycetota) Isolated from Aquatic Host Species Described in 2018 to 2021

Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness and recognition of novel microbial species and revisions to bacterial taxonomy. Because this need has largely been unmet, through a 4-year literature review, we present lists of novel and revised bacterial species (including members of the phylum Planctomycetota) derived from aquatic hosts that can serve as a baseline for future biennial summaries of taxonomic revisions in this field. Most new and revised taxa were noted within oxidase-positive and/or nonglucose fermentative Gram-negative bacilli, including members of the Tenacibaculum, Flavobacterium, and Vibrio genera. Valid and effectively published novel members of the Streptococcus, Erysipelothrix, and Photobacterium genera are additionally described from disease pathogenesis perspectives.

Microbial Diversity and Adaptation under Salt-Affected Soils: A Review

The salinization of soil is responsible for the reduction in the growth and development of plants. As the global population increases day by day, there is a decrease in the cultivation of farmland due to the salinization of soil, which threatens food security. Salt-affected soils occur all over the world, especially in arid and semi-arid regions. The total area of global salt-affected soil is 1 billion ha, and in India, an area of nearly 6.74 million ha−1 is salt-stressed, out of which 2.95 million ha−1 are saline soil (including coastal) and 3.78 million ha−1 are alkali soil. The rectification and management of salt-stressed soils require specific approaches for sustainable crop production. Remediating salt-affected soil by chemical, physical and biological methods with available resources is recommended for agricultural purposes. Bioremediation is an eco-friendly approach compared to chemical and physical methods. The role of microorganisms has been documented by many workers for the bioremediation of such problematic soils. Halophilic Bacteria, Arbuscular mycorrhizal fungi, Cyanobacteria, plant growth-promoting rhizobacteria and microbial inoculation have been found to be effective for plant growth promotion under salt-stress conditions. The microbial mediated approaches can be adopted for the mitigation of salt-affected soil and help increase crop productivity. A microbial product consisting of beneficial halophiles maintains and enhances the soil health and the yield of the crop in salt-affected soil. This review will focus on the remediation of salt-affected soil by using microorganisms and their mechanisms in the soil and interaction with the plants.

Chromogenicity of aerobic spore-forming bacteria of the Bacillaceae family isolated from different ecological niches and physiographic zones

To determine the distribution patterns of pigmented bacteria of the Bacilaceae family in different physiographic zones and ecological niches, we recovered 787 isolates from 185 environmental samples (including the areas with radiation pollution). Among the strains obtained, 149 pigmented representatives were detected, which synthesized intracellular and extracellular pigments of yellow, red, pink, and dark colors. In compliance with physiological, biochemical, and chemotaxonomic features, the isolates were identified as 7 species of the Bacilaceae family. We demonstrated that the ability to synthesize pigments significantly depended on the culture medium composition. According to the color of the colonies, the absorption spectra of pigment extracts, their physicochemical properties, and the implementation of several qualitative tests, the pigmented isolates were divided into ten groups. The relative number of pigmented strains in the physiographic zone was consistent with the total level of solar radiation for the year. Most pigmented members of the Bacillaceae family were recovered from deserts and semi-deserts, and fewest of them originated from mixed forests. We show that among the studied ecological niches, pigmented strains were most often isolated from the phyllosphere and aquatic environment and least often from soils. However, the isolates from soils and aquatic environments exhibited a greater diversity of pigmentation, and a lesser variety of colored strains was obtained from the phyllosphere and the gastrointestinal tract of animals. We established that the quantitative and qualitative composition of pigmented isolates from the areas with radiation contamination differed significantly from those coming from the natural radiation background.

Evidence of Genomic Diversification in a Natural Symbiotic Population Within Its Host

Planktonic cells of the luminous marine bacterium Vibrio fischeri establish themselves in the light-emitting organ of each generation of newly hatched Euprymna scolopes bobtail squid. A symbiont population is maintained within the 6 separated crypts of the organ for the ∼9-month life of the host. In the wild, the initial colonization step is typically accomplished by a handful of planktonic V. fischeri cells, leading to a species-specific, but often multi-strain, symbiont population. Within a few hours, the inoculating cells proliferate within the organ’s individual crypts, after which there is evidently no supernumerary colonization. Nevertheless, every day at dawn, the majority of the symbionts is expelled, and the regrowth of the remaining ∼5% of cells provides a daily opportunity for the population to evolve and diverge, thereby increasing its genomic diversity. To begin to understand the extent of this diversification, we characterized the light-organ population of an adult animal. First, we used 16S sequencing to determine that species in the V. fischeri clade were essentially the only ones detectable within a field-caught E. scolopes. Efforts to colonize the host with a minor species that appeared to be identified, V. litoralis, revealed that, although some cells could be imaged within the organ, they were <0.1% of the typical V. fischeri population, and did not persist. Next, we determined the genome sequences of seventy-two isolates from one side of the organ. While all these isolates were associated with one of three clusters of V. fischeri strains, there was considerable genomic diversity within this natural symbiotic population. Comparative analyses revealed a significant difference in both the number and the presence/absence of genes within each cluster; in contrast, there was little accumulation of single-nucleotide polymorphisms. These data suggest that, in nature, the light organ is colonized by a small number of V. fischeri strains that can undergo significant genetic diversification, including by horizontal-gene transfer, over the course of ∼1500 generations of growth in the organ. When the resulting population of symbionts is expelled into seawater, its genomic mix provides the genetic basis for selection during the subsequent environmental dispersal, and transmission to the next host.

Rossellomorea arthrocnemi sp. nov., a novel plant growth-promoting bacterium used in heavy metal polluted soils as a phytoremediation tool

Strain EAR8^T is a root endophyte isolated from Arthrocnemum macrostachyum plants collected from the Odiel marshes, Huelva (Spain). It presented in vitro plant growth-promoting properties and improved the plant growth and heavy metal accumulation in polluted soils playing an important role in phytoremediation strategies. Phenotypically, strain EAR8^T cells were Gram-positive, aerobic and non-motile rods with terminal oval endospores and non-swollen sporangia which form beige, opaque, butyrous, raised and irregular colonies with undulate margins. The strain was able to grow between 15–45 °C, at pH 6.0–9.0 and tolerated 0–25 % NaCl (w/v) showing optimal growth conditions on trypticase soy agar plates supplemented with 2.5 % NaCl (w/v) at pH 7.0 and 37 °C for 24 h. Chemotaxonomic analyses showed that the isolate has meso-diaminopimelic acid as the peptidoglycan in the cell wall and MK-7 as the major respiratory quinone. The predominant fatty acids were anteiso-C_15 : 0 and iso-C_15 : 0 and the polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phylogenetic analyses based on the whole proteomes of closest sequenced relatives confirmed that strain EAR8^T is affiliated to the genus Rossellomorea and forms a clade with Rossellomorea vietnamensis 15-1^T with maximum support. Genome analyses showed that EAR8^T has indole-3-acetic acid and siderophore biosynthesis and transporters genes and genes related to resistance against heavy metals. Phenotypic and phylogenomic comparative studies suggested that strain EAR8^T is a new representative of the genus Rossellomorea and the name Rossellomorea arthrocnemi sp. nov. is proposed. Type strain is EAR8^T (=CECT 9072^T=DSM 103900^T).

Stimulation of Nicotiana tabacum L. In Vitro Shoot Growth by Endophytic Bacillus cereus Group Bacteria

In vitro plant tissue cultures face various unfavorable conditions, such as mechanical damage, osmotic shock, and phytohormone imbalance, which can be detrimental to culture viability, growth efficiency, and genetic stability. Recent studies have revealed a presence of diverse endophytic bacteria, suggesting that engineering of the endophytic microbiome of in vitro plant tissues has the potential to improve their acclimatization and growth. Therefore, the aim of this study was to identify cultivated tobacco (Nicotiana tabacum L.) endophytic bacteria isolates that are capable of promoting the biomass accumulation of in vitro tobacco shoots. Forty-five endophytic bacteria isolates were obtained from greenhouse-grown tobacco plant leaves and were assigned to seven Bacillus spp. and one Pseudomonas sp. based on 16S rRNA or genome sequence data. To evaluate the bacterial effect on in vitro plant growth, tobacco shoots were inoculated with 22 isolates selected from distinct taxonomic groups. Four isolates of Bacillus cereus group species B. toyonensis, B. wiedmannii and B. mycoides promoted shoot growth by 11-21%. Furthermore, a contrasting effect on shoot growth was found among several isolates of the same species, suggesting the presence of strain-specific interaction with the plant host. Comparative analysis of genome assemblies was performed on the two closely related B. toyonensis isolates with contrasting plant growth-modulating properties. This revealed distinct structures of the genomic regions, including a putative enzyme cluster involved in the biosynthesis of linear azol(in)e-containing peptides and polysaccharides. However, the function of these clusters and their significance in plant-promoting activity remains elusive, and the observed contrasting effects on shoot growth are more likely to result from genomic sequence variations leading to differences in metabolic or gene expression activity. The Bacillus spp. isolates with shoot-growth-promoting properties have a potential application in improving the growth of plant tissue cultures in vitro.

Priestia veravalensis sp. nov., isolated from coastal sample

The taxonomic position of two isolates, SGD-V-76^T and SGD-M-37, isolated from sediment sample of Veraval coast, India, was examined using the polyphasic taxonomic approach. The morphological and chemotaxonomic characteristics of these two organisms are typical of the genus Priestia. The phylogenetic analyses performed using almost complete 16S rRNA gene sequences demonstrated that the isolate belongs to the Bacillaceae family, and forms a clade within the cluster containing Priestia flexus MTCC 2909^T, Priestia aryabhattai B8W22^T and Priestia megaterium KCTC 3007^T and both strains showed highest similarity of > 98% with 3-29 nucleotide differences. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant isoprenoid quinone was MK-7 and the G + C content of strains was 37.5-37.7 mol%. However, the DNA-DNA hybridization and the phenotypic characteristics revealed that, the strain SGD-V-76^T and strain SGD-M-37 are similar species but different from any known Priestia species with ANI values of 79.2, 79.3 and 79.2 and the dDDH values of 17.7, 17.8 and 18.0% respectively. On the basis of phenotypic characteristics, phylogenetic analysis and the results of biochemical and physiological tests, and genomic data strain SGD-V-76^T was clearly distinguished from closely related members of the Priestia genus. Based on the above data analysis strain SGD-V-76^T (= DSM28242^T = KCTC33802^T = CIP111056^T = NCIM5510^T) represents a novel species of the genus Priestia, and we propose the name Priestia veravalensis sp. nov.

Biodegradation of endocrine disrupting chemicals benzyl butyl phthalate and dimethyl phthalate by Bacillus marisflavi RR014

AIM

The objectives of the present study were to explore the benzyl butyl phthalate (BBP) and dimethyl phthalate (DMP) degradation potential of Bacillus marisflavi RR014 isolated from the tap water of public toilet and also to optimize the phthalates degradation process using response surface methodology.

METHODS AND RESULTS

The minimal salt medium was used for the biodegradation analysis of phthalates. The quantification of phthalates and their intermediate metabolites identification were done by using UHPLC and LC-MS/MS respectively. The results revealed that B. marisflavi RR014 is capable of degrading both the phthalates under varying pH, temperature and salinity conditions. The formation of phthalic acid from the breakdown of BBP and DMP (500 mg l^-1 ) in the medium was observed after 24 h. After 72 h, 61% of BBP and 98·9% of DMP in the medium was degraded as monitored by UHPLC. The identification of intermediate metabolites by LC-MS/MS revealed that hydrolysis of BBP and DMP produces phthalic acid.

CONCLUSIONS

The degradation rate of both the phthalates was increased as the parameters increased up to an optimum level. The three environmental factors (pH, temperature and salt concentration) strongly affect the rate of degradation of both the phthalates. The maximum degradation rate for both the phthalates was achieved at pH 7, temperature 35°C and salt concentration of 1% as observed from the central composite experimental design.

SIGNIFICANCE AND IMPACT OF THE STUDY

It is the first report on the phthalates biodegradation potential of B. marisflavi RR014 isolated from the tap water of public toilet. The bacterium is capable of degrading BBP and DMP under varying pH, temperature and salinity, therefore, ideal to treat the phthalate contaminated environments.

Community Structure of Protease-Producing Bacteria Cultivated From Aquaculture Systems: Potential Impact of a Tropical Environment

Protease-producing bacteria play vital roles in degrading organic matter of aquaculture system, while the knowledge of diversity and bacterial community structure of protease-producing bacteria is limited in this system, especially in the tropical region. Herein, 1,179 cultivable protease-producing bacterial strains that belonged to Actinobacteria, Firmicutes, and Proteobacteria were isolated from tropical aquaculture systems, of which the most abundant genus was Bacillus, followed by Vibrio. The diversity and relative abundance of protease-producing bacteria in sediment were generally higher than those in water. Twenty-one genera from sediment and 16 genera from water were identified, of which Bacillus dominated by Bacillus hwajinpoensis in both and Vibrio dominated by Vibrio owensii in water were the dominant genera. The unique genera in sediment or water accounted for tiny percentage may play important roles in the stability of community structure. Eighty V. owensii isolates were clustered into four clusters (ET-1-ET-4) at 58% of similarity by ERIC-PCR (enterobacterial repetitive intergenic consensus-polymerase chain reaction), which was identified as a novel branch of V. owensii. Additionally, V. owensii strains belonged to ET-3 and ET-4 were detected in most aquaculture ponds without outbreak of epidemics, indicating that these protease-producing bacteria may be used as potential beneficial bacteria for wastewater purification. Environmental variables played important roles in shaping protease-producing bacterial diversity and community structure in aquaculture systems. In sediment, dissolved oxygen (DO), chemical oxygen demand (COD), and salinity as the main factors positively affected the distributions of dominant genus (Vibrio) and unique genera (Planococcus and Psychrobacter), whereas temperature negatively affected that of Bacillus (except B. hwajinpoensis). In water, Alteromonas as unique genus and Photobacterium were negatively affected by NO₃ ^--N and NO₂ ^--N, respectively, whereas pH as the main factor positively affected the distribution of Photobacterium. These findings will lay a foundation for the development of protease-producing bacterial agents for wastewater purification and the construction of an environment-friendly tropical aquaculture model.

Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species

To clarify the evolutionary relationships and classification of Bacillus species, comprehensive phylogenomic and comparative analyses were performed on >300 Bacillus/Bacillaceae genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of Bacillus species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the Bacillus species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some Bacillus species reliably grouped with the genera Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium and Salisediminibacterium. The distinctness of identified Bacillus species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 Bacillus species clades should be recognized as novel genera, with the names Alteribacter gen. nov., Ectobacillus gen. nov., Evansella gen. nov., Ferdinandcohnia gen. nov., Gottfriedia gen. nov., Heyndrickxia gen. nov., Lederbergia gen. nov., Litchfieldia gen. nov., Margalitia gen. nov., Niallia gen. nov., Priestia gen. nov., Robertmurraya gen. nov., Rossellomorea gen. nov., Schinkia gen. nov., Siminovitchia gen. nov., Sutcliffiella gen. nov. and Weizmannia gen. nov. We also propose to transfer 'Bacillus kyonggiensis' to Robertmurraya kyonggiensis sp. nov. (type strain: NB22=JCM 17569^T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species B. subtilis) or the Cereus clade (containing B. anthracis and B. cereus). As most Bacillus species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus Bacillus to restrict it to only the members of the Subtilis and Cereus clades.

Bacillus rugosus sp. nov. producer of a diketopiperazine antimicrobial, isolated from marine sponge Spongia officinalis L

A novel Gram-positive and endospore-forming bacterium assigned as strain SPB7^T which is also a new source of a cyclic diketopiperazine (3S,6S)-3,6-diisobutylpiperazine-2,5-dione is described. A polyphasic (biochemical, phenotypic and genotypic) approach was used to clarify the taxonomic affiliation of this strain. The partial and complete 16S rRNA gene sequences revealed that strain SPB7^T is a member of the Bacillus genus [showing high similarity (> 98.70%) with Bacillus spizizenii NRRL B-23049^T, Bacillus tequilensis KCTC 13622^T, Bacillus inaquosorum KCTC 13429^T and Bacillus cabrialesii TE3^T]. The maximum values for average nucleotide identity (ANI) and in silico DNA-DNA hybridization (GGDC, Formula 2) of strain SPB7^T was obtained for twenty-five strains of Bacillus spizizenii (ANI 95.01-95.48% and GGDC 62.70-60.00%). The whole-genome phylogenetic relationship showed that SPB7^T formed an individual and separated clade with the Bacillus spizizenii group. Principal cellular fatty acids identified in strain SPB7^T were anteiso C_15:0, anteiso C_17:0, iso C_15:0, iso C_17:0, C_16:0, C_10:0 3OH and iso C_{17:1 ϖ10c}. Polar lipid profile showed presence of diphosphotidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unknown phospholipids and five unknown lipids. Cells were rod shaped, catalase, oxidase-positive and motile. Growth occurred at 20-45 °C (optimal 35 °C), at pH 6.0-10.0 (optimal pH 8) and 0-10% (w/v) NaCl (optimal 2%). The phenotypic, biochemical, and genotypic traits of strain SPB7^T strongly supported its taxonomic affiliation as a novel species of the Bacillus genus, for which the name Bacillus rugosus sp. nov. is proposed. The type strain is SPB7^T (= NRRL B-65559^T, = CICC 24827^T, = MCC 4185^T).

Molecular Identification and Characterization of Bacillus sp. NIGAB-1 for Phenol Degradation Under Saline Conditions

Background

Phenol is an aromatic pollutant in industrial wastes that in combination with salts is highly toxic for all forms of life. Phenol elimination is the foremost challenge to meet the goal of pollutant-free environment.

Objective

The present study was carried out to isolate phenol degrading bacteria which can degrade phenol under saline conditions and to identify the isolated strains using 16S rRNA gene sequence analysis.

Material and Methods

Sediment samples were collected from Rawal Lake, Islamabad, Pakistan and enriched in mineral salt medium (MSM) containing phenol (150 mg.L^-1). Isolated strains were identified on the basis of 16S rRNA gene sequence analysis. Growth of strains were tested at different pH, NaCl concentrations and temperature using Tryptic Soy Agar (TSA). Tolerance to phenol (0-750 mg.L^-1) was checked at 5% NaCl and phenol degrading experiment was performed at 4% NaCl, pH 7 and 30 oC. In both, phenol tolerance and degradation study, phenol was used a sole source of carbon and energy.

Results

Thirteen bacterial strains were isolated after enrichment among which, NIGAB-1 was found capable of degrading phenol in saline conditions. This strain was identified as Bacillus sp. NIGAB-1 on the basis of 16S rRNA gene sequence analysis and the closest match was Bacillus marisflavi with 99.71% sequence identity. The Bacillus sp. NIGAB-1 exhibited best growth at 30 oC at pH 7 with 10% NaCl. The optimum phenol concentration for growth was recorded as 300 mg.L^-1. This strain degraded 300 mg.L-1 of phenol at 4% NaCl in 120 hours with the average degradation rate of 2.63 mg.L^-1.h.

Conclusion

These findings suggest that this strain could be efficient in phenol degradation at adverse environmental conditions and helpful in remediation of phenol where the salt concentration is high.

Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs)

Recent advancements in the use of microbial cells for scalable production of industrial enzymes encourage exploring new environments for efficient microbial cell factories (MCFs). Here, through a comparison study, ten newly sequenced Bacillus species, isolated from the Rabigh Harbor Lagoon on the Red Sea shoreline, were evaluated for their potential use as MCFs. Phylogenetic analysis of 40 representative genomes with phylogenetic relevance, including the ten Red Sea species, showed that the Red Sea species come from several colonization events and are not the result of a single colonization followed by speciation. Moreover, clustering reactions in reconstruct metabolic networks of these Bacillus species revealed that three metabolic clades do not fit the phylogenetic tree, a sign of convergent evolution of the metabolism of these species in response to special environmental adaptation. We further showed Red Sea strains Bacillus paralicheniformis (Bac48) and B. halosaccharovorans (Bac94) had twice as much secreted proteins than the model strain B. subtilis 168. Also, Bac94 was enriched with genes associated with the Tat and Sec protein secretion system and Bac48 has a hybrid PKS/NRPS cluster that is part of a horizontally transferred genomic region. These properties collectively hint towards the potential use of Red Sea Bacillus as efficient protein secreting microbial hosts, and that this characteristic of these strains may be a consequence of the unique ecological features of the isolation environment.

Culturable hydrocarbonoclastic marine bacterial isolates from Indonesian seawater in the Lombok Strait and Indian Ocean

Purpose

The study aims to isolate the culturable marine bacteria and to assess their potential as the bioremediation agent for petroleum hydrocarbons contamination in marine environment.

Methods

Bacteria isolates were obtained by repetitive streaks to obtain purified bacteria on Zobell marine agar plates before further analysis and culture through direct visualization on agar plates. Identification were conducted using 16S rDNA sequence which are compared using NCBI BLAST and, combined with phenotypic and phylogenetic data. The potential use of the selected bacteria was tested by culturing them with two carbon sources i.e., glucose and crude oil.

Result

Fifty-one culturable marine hydrocarbonoclastic bacteria were isolated from the Lombok Strait (LS-3, LS-13, LS-14, LS-15, LS-16 and LS-20) and Indian Ocean (IO-1, IO-6, IO-8, IO-19, IO-24 and IO-25). Twelve isolates were found to degrade crude oil efficiently at a >2% concentration and to grow with crude oil as their sole carbon and energy source. These 12 strains belong to the genus Bacillus, which is well known to produce surface active agents, and the oil displacement assay indicated the production of these agents by these strains. Within the genera Bacillus, five species (Bacillus flexus, B. methylotrophicus, B. aquimaris, B. horikoshii, and B. thioparans) were represented by the 12 identified strains.

Conclusion

Selected strains from the Lombok Strait and Indian Ocean were capable of degrading crude oil (2% v/v) by 43.9-71.9% over 14 days. These results are important for marine bioremediation in Indonesia, which often faces risks of oil spill contamination and disaster.

Utilization of Grape Seed Flour for Antimicrobial Lipopeptide Production by Bacillus amyloliquefaciens C5 Strain

An endophytic Bacillus amyloliquefaciens strain called C5, able to produce biosurfactant lipopeptides with a broad antibacterial activity spectrum, has been isolated from the roots of olive tree. Optimization of antibacterial activity was undertaken using grape seed flour (GSF) substrate at 0.02, 0.2, and 2% (w/v) in M9 medium. Strain C5 exhibited optimal growth and antimicrobial activity (MIC value of 60 μg/ml) when incubated in the presence of 0.2% GSF while lipopeptide production culminated at 2% GSF. Thin layer chromatography analysis of lipopeptide extract revealed the presence of at least three active spots at Rf 0.35, 0.59, and 0.72 at 0.2% GSF. Data were similar to those obtained in LB-rich medium. MALDI-TOF/MS analysis of lipopeptide extract obtained from 0.2% GSF substrate revealed the presence of surfactin and bacillomycin D. These results show that GSF could be used as a low-cost culture medium supplement for optimizing the production of biosurfactants by strain C5.

Bacillus salacetis sp. nov., a slightly halophilic bacterium from Thai shrimp paste (Ka-pi)

A Gram-stain-positive, slightly halophilic, endospore-forming, strictly aerobic, rod-shaped bacterium, designated SKP7-4^T, was isolated from shrimp paste collected from Samut Sakhon province, Thailand. Strain SKP7-4^T grew at pH 6.0-9.0 (optimum, 7.5), at 20-40 °C (37 °C) and in 0-15 % (w/v) NaCl (1-3 %). The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Menaquinone with seven isoprene units was the major isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unidentified phospholipids were detected as polar lipids. It contained iso-C15 : 0 and anteiso-C15 : 0 as major cellular fatty acids. On the basis of 16S rRNA gene sequence analysis, strain SKP7-4^T belonged to the genus Bacillus and was closely related to Bacillus vietnamensis JCM 11124^T, Bacillus marisflavi JCM 11544^T, Bacillus aquimaris JCM 11545^T and Bacillusoryzaecorticis JCM 19602^T, with 98.7, 97.9, 97.8 and 97.8 % similarity, respectively. The draft genome of SKP7-4^T was 4.68 Mb with 5208 coding sequences with an average G+C content of 43.2 mol%. The ANIb and ANIm values of strain SKP7-4^T were 70.0 and 84.3 %, respectively, and the digital DNA-DNA hybridization value was 20 % in comparison with the draft genome of B. vietnamensis JCM 11124^T. On the basis of the results of phenotypic, chemotaxonomic and phylogenetic analyses, the strain should represent a novel species of the genus Bacillus and the name Bacillus salacetis sp. nov. is proposed. The type strain is SKP7-4^T (=JCM 33205^T=KCTC 43014^T=TISTR 2596^T).

Characterization of halotolerant, pigmented, plant growth promoting bacteria of groundnut rhizosphere and its in-vitro evaluation of plant-microbe protocooperation to withstand salinity and metal stress

The use of plant associated, indigenous beneficial microbes for sustainable agriculture is getting worldwide acceptance as they successfully colonize at different plant niche under stress conditions to enhance the crop productivity. They also generate several plant growth regulators and protect plants from adversity like presence of salts and metals. In the present study, indigenous, halotolerant, plant growth promoting (PGP) bacterial isolates were isolated from the saline rhizospheric soil of groundnut plants aiming to investigate its in-vitro metal remediation capabilities under saline stress condition. Two pigmented bacteria were selected based on their phenotypic, biochemical, physiological and PGP characters and identified as members of family Bacillaceae (Bacillus and Halobacillus) based on 16S rRNA gene sequence similarity. The pigments were extracted, tested for different antioxidant properties and identified by GC-MS and FT-IR spectra. Simultaneously, both strains exhibited a wide range of salinity (NaCl≥25%), metal resistance (Zinc≈1700mgkg^-1, Aluminium≈1800mgkg^-1, Lead≈1800mgkg^-1), pH (6-10), PGP attributes (indole - 1.05-3.15μgml^-1, ammonia - 0.13-19.95mmolml^-1, nitrite - 0.07-0.26mmolml^-1) and antibiotics sensitivity revealing their wide range of metabolic diversity. In-vitro inoculation of groundnut seedlings with selected isolates under salinity (1% NaCl) and metal (Zn, Al and Pb) stress had a positive impact on different plant physiological parameters (lesser lignification, intact proto xylem and cortical parenchyma) which was correlated with PGP attributes. Microwave plasma atomic emission spectroscopy analysis of seedling samples also detected less amount of metals in plants treated with bacteria indicating, an establishment of plant-microbe protocooperation to withstand salinity and metal stress. This strategy can be implemented to improve crop production in saline metal polluted agriculture fields.

Microbial culturomics to isolate halophilic bacteria from table salt: genome sequence and description of the moderately halophilic bacterium Bacillus salis sp. nov

Bacillus salis strain ES3^T (= CSUR P1478 = DSM 100598) is the type strain of B. salis sp. nov. It is an aerobic, Gram-positive, moderately halophilic, motile and spore-forming bacterium. It was isolated from commercial table salt as part of a broad culturomics study aiming to maximize the culture conditions for the in-depth exploration of halophilic bacteria in salty food. Here we describe the phenotypic characteristics of this isolate, its complete genome sequence and annotation, together with a comparison with closely related bacteria. Phylogenetic analysis based on 16S rRNA gene sequences indicated 97.5% similarity with Bacillus aquimaris, the closest species. The 8 329 771 bp long genome (one chromosome, no plasmids) exhibits a G+C content of 39.19%. It is composed of 18 scaffolds with 29 contigs. Of the 8303 predicted genes, 8109 were protein-coding genes and 194 were RNAs. A total of 5778 genes (71.25%) were assigned a putative function.

Bacillus kwashiorkori sp. nov., a new bacterial species isolated from a malnourished child using culturomics

Strain SIT6^T was isolated from the fecal flora of a severely malnourished child as part of a broad “culturomics” study aiming to maximize the culture conditions for the in‐depth exploration of the human microbiota. An analysis of the 16S rRNA gene sequence showed that strain SIT6^T shared 94.1% 16S rRNA gene sequence similarity with Bacillus thermoamylovorans DKP^T (NR_029151), the phylogenetically closest type species. Colonies are creamy white, circular, 4–5 mm in diameter after cultivation at 37°C for 24 hr on 5% sheep blood‐enriched Colombia agar. Growth occurs at temperatures in the range of 25–56°C (optimally at 37°C). Strain SIT6^T is a gram‐positive, facultative anaerobic rod and motile by means of peritrichous flagella and sporulating; it is catalase and oxidase positive. The 2,784,637‐bp‐long genome, composed of 16 contigs, has a G+C content of 35.19%. Of the 2,646 predicted genes, 2,572 were protein‐coding genes and 74 were RNAs. The major fatty acids are saturated species (15:0 iso, 16:0 and 17:0 anteiso). Of the 14 detected fatty acids, 11 are saturated, either linear or branched (iso and anteiso). Digital DNA–DNA hybridization (dDDH) estimation and average genomic identity of orthologous gene sequences (AGIOS) of the strain SIT6^T against genomes of the type strains of related species ranged between 18.6% and 38.3% and between 54.77% and 65.50%, respectively. According to our taxonogenomics results, we propose the creation of Bacillus kwashiorkori sp. nov. that contains the type strain SIT6^T (=CSUR P2452^T, =DSM 29059^T).

Lindane Bioremediation Capability of Bacteria Associated with the Demosponge Hymeniacidon perlevis

Lindane is an organochlorine pesticide belonging to persistent organic pollutants (POPs) that has been widely used to treat agricultural pests. It is of particular concern because of its toxicity, persistence and tendency to bioaccumulate in terrestrial and aquatic ecosystems. In this context, we assessed the role of bacteria associated with the sponge Hymeniacidon perlevis in lindane degradation. Seven bacteria isolates were characterized and identified. These isolates showed a remarkable capacity to utilize lindane as a sole carbon source leading to a percentage of residual lindane ranging from 3% to 13% after 12 days of incubation with the pesticide. The lindane metabolite, 1,3–6-pentachloro-cyclohexene, was identified as result of lindane degradation and determined by gas chromatography–mass spectrometry (GC–MS). The bacteria capable of lindane degradation were identified on the basis of the phenotypic characterization by morphological, biochemical and cultural tests, completed with 16S rDNA sequence analysis, and assigned to Mameliella phaeodactyli, Pseudovibrioascidiaceicola, Oceanicaulis stylophorae, Ruegeria atlantica and to three new uncharacterized species. The results obtained are a prelude to the development of future strategies for the in situ bioremediation of lindane.

Antibacterial Activities of Bacteria Isolated from the Marine Sponges Isodictya compressa and Higginsia bidentifera Collected from Algoa Bay, South Africa

Due to the rise in multi-drug resistant pathogens and other diseases, there is renewed interest in marine sponge endosymbionts as a rich source of natural products (NPs). The South African marine environment is rich in marine biota that remains largely unexplored and may represent an important source for the discovery of novel NPs. We first investigated the bacterial diversity associated with five South African marine sponges, whose microbial populations had not previously been investigated, and select the two sponges (Isodictya compressa and Higginsia bidentifera) with highest species richness to culture bacteria. By employing 33 different growth conditions 415 sponge-associated bacterial isolates were cultured and screened for antibacterial activity. Thirty-five isolates showed antibacterial activity, twelve of which exhibited activity against the multi-drug resistant Escherichia coli 1699, implying that some of the bioactive compounds could be novel. Genome sequencing of two of these isolates confirmed that they harbour uncharacterized biosynthetic pathways that may encode novel chemical structures.

Chelatococcus composti sp. nov., isolated from penicillin fermentation fungi residue with pig manure co-compost

A novel Gram-stain-negative bacterium, designated strain PC-2^T, was isolated from penicillin fermentation fungi residue with pig manure co-compost in China. Phylogenetic analysis, based on 16S rRNA gene sequence comparisons, revealed that strain PC-2^T should be assigned to the genus Chelatococcus and that it had 98.9 % similarity with Chelatococcus daeguensis, 98.8 % with Chelatococcus sambhunathii, 98.4 %, with Chelatococcus caeni and 96.0 % with Chelatococcus asaccharovorans. The G+C content of genomic DNA was 70.9 mol%. On the basis of the phylogenetic analysis, DNA-DNA relatedness values, phenotypic characteristics and chemotaxonomic data, strain PC-2 ^T represents a novel species of the genus Chelatococcus, for which the name Chelatococcus composti sp. nov. is proposed. The type strain is PC-2^T (=DSM 101465^T=CGMCC 1.15283^T).

Screening of pigmented Bacillus aquimaris SH6 from the intestinal tracts of shrimp to develop a novel feed supplement for shrimp

AIMS

To develop a novel feed supplement for shrimp using pigmented spore-forming bacterial strains isolated from their gastrointestinal tracts.

METHODS AND RESULTS

Eight pigmented Bacillus strains were selected from the isolates based on high production of heat-stable spores, typical UV-Vis spectra of produced carotenoids (400-550 nm), and free radical scavenging activity of their extracts. Of the eight strains, the red-orange pigmented Bacillus aquimaris SH6 was selected because it showed the highest abundance in shrimp guts (70% population). Whiteleg shrimp (n = 30 per group) fed with SH6 spores, at >3 × 10⁶  CFU g^-1  pellet for 4 weeks had redder colour (score of 21-23 vs 20-22), 2·7-fold higher astaxanthin level (0·69 vs 0·25 μg g^-1 shrimp), 34% higher weight gain (7·18 vs 5·32 g shrimp^-1 ), and 85% higher phenoloxidase activity (OD490  = 0·265 vs 0·143) than shrimp in the control group.

CONCLUSIONS

The result supports the potential use of B. aquimaris SH6 as a feed supplement for promoting the colourization and weight gain, and for enhancing innate immunity of whiteleg shrimp.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates that carotenoids produced by B. aquimaris SH6 can be successfully absorbed and converted to astaxanthin in whiteleg shrimp.

Alkaline bioleaching of municipal solid waste incineration fly ash by autochthonous extremophiles

The increasing demand for energy and the generation of solid waste have caused an alarming rise in fly ash production globally. Since heavy metals continue to be in demand for the production of materials, resource recovery from the recycling of these wastes has the potential to delay the depletion of natural ores. The use of microorganisms for the leaching of metals, in a process called bioleaching, is an eco-friendly and economical way to treat the metal-laden wastes. Bioleaching of fly ash is challenging due largely to the alkaline nature and toxic levels of heavy metals which are detrimental to microbial growth and bioleaching activity. The present work reports the isolation of indigenous bacteria from a local landfill site and their bioleaching performance [corrected]. 38 autochthonous strains of bacteria were isolated from eight samples collected and plated on five different media. 18 of the isolates showed bioleaching potential, with significant alkaline pH or fly ash tolerance. Genetic characterization of the strains revealed a dominance of Firmicutes, with Alkalibacterium sp. TRTYP6 showing highest fly ash tolerance of up to 20% w/v fly ash, and growth over a pH range 8-12.5. The organism selectively recovered about 52% Cu from the waste. To the best of our knowledge, this is the first time a study on bioleaching with extreme alkaliphiles is reported.

Draft Whole-Genome Sequence of the Type Strain Bacillus aquimaris TF12T

Bacillus aquimaris TF12 is a Gram-positive bacteria isolated from a tidal flat of the Yellow Sea in South Korea. We report the draft whole-genome sequence of Bacillus aquimaris TF12, the type strain of a set of bacteria typically associated with marine habitats and with a potentially high biotechnology value.

Draft Genome Sequence of Bacillus marisflavi TF-11T (JCM 11544), a Carotenoid-Producing Bacterium Isolated from Seawater from a Tidal Flat in the Yellow Sea

Bacillus marisflavi TF-11^T (JCM 11544) is a Gram-positive, spore-forming, and carotenoid-producing bacterium isolated from seawater from a tidal flat in the Yellow Sea. Here, we report the first draft genome sequence of B. marisflavi TF-11^T, which comprises 4.31 Mb in 11 scaffolds with a G+C content of 48.57%.

Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert

The Atacama Desert, one of the driest deserts in the world, represents a unique extreme environmental ecosystem to explore the bacterial diversity as it is considered to be at the dry limit for life. A 16S rRNA gene (spanning the hyper variable V3 region) library was constructed from an alkaline sample of unvegetated soil at the hyperarid margin in the Atacama Desert. A total of 244 clone sequences were used for MOTHUR analysis, which revealed 20 unique phylotypes or operational taxonomic units (OTUs). V3 region amplicons of the 16S rRNA were suitable for distinguishing the bacterial community to the genus and specie level. We found that all OTUs were affiliated with taxa representative of the Firmicutes phylum. The extremely high abundance of Firmicutes indicated that most bacteria in the soil were spore-forming survivors. In this study we detected a narrower diversity as compared to other ecological studies performed in other areas of the Atacama Desert. The reported genera were Oceanobacillus (representing the 69.5 % of the clones sequenced), Bacillus, Thalassobacillus and Virgibacillus. The present work shows physical and chemical parameters have a prominent impact on the microbial community structure. It constitutes an example of the communities adapted to live in extreme conditions caused by dryness and metal concentrations .

Draft Genome Sequence of Bacillus vietnamensis Strain UCD-SED5 (Phylum Firmicutes)

Here, we present the draft genome sequence of Bacillus vietnamensis UCD-SED5 (phylum Firmicutes). This strain was isolated from sediment surrounding Zostera marina roots near the UC Davis Bodega Marine Laboratory (Bodega, Bay, California) and represents the second genome of this species. The assembly consists of 4,325,707 bp, in 108 contigs.

Bacillus encimensis sp. nov. isolated from marine sediment

A Gram-stain-positive, rod-shaped, endospore-forming, aerobic bacterium designated SGD-V-25(T) was isolated from Veraval sediment sample, India. Strain SGD-V-25(T) was capable of growing at 25-50 °C (optimum 37 °C), pH 6-12 (optimum pH 7.0) and with 0-5% (w/v) NaCl. The taxonomic position of this strain was deduced using a polyphasic approach and the 16S rRNA gene sequence analysis showed that the isolate belongs to the phylum Firmicutes , forming the cluster with Bacillus badius MTCC 1548(T), with which it shares highest similarity of 99.1% with 13 nt differences. Other type strains of the genus Bacillus showed less than 96% similarity. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. The polar lipid profile of strain SGD-V-25(T) showed the presence of diphosphatidylglycerol, phosphatidylglycerol, phsophoglycolipid and two aminophospholipids. The predominant isoprenoid quinone was MK-7. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0, C16 : 1ω11c and C16 : 0. The genomic DNA G+C content of strain SGD-V-25(T) was 37.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA-DNA hybridization, strain SGD-V-25(T) could be clearly distinguished from closely related members of the genus Bacillus , and the name Bacillus encimensis sp. nov., is proposed to accommodate this strain. The type strain is SGD-V-25(T) ( =NCIM 5513(T) =DSM 28241(T)).

Evolution in the Bacillaceae

The family Bacillaceae constitutes a phenotypically diverse and globally ubiquitous assemblage of bacteria. Investigation into how evolution has shaped, and continues to shape, this family has relied on several widely ranging approaches from classical taxonomy, ecological field studies, and evolution in soil microcosms to genomic-scale phylogenetics, laboratory, and directed evolution experiments. One unifying characteristic of the Bacillaceae , the endospore, poses unique challenges to answering questions regarding both the calculation of evolutionary rates and claims of extreme longevity in ancient environmental samples.

Bacillus haikouensis sp. nov., a facultatively anaerobic halotolerant bacterium isolated from a paddy soil

A Gram-stain positive, rod-shaped, endospore-forming and facultatively anaerobic halotolerant bacterium, designated as C-89(T), was isolated from a paddy field soil in Haikou, Hainan Province, People's Republic of China. Optimal growth was observed at 37 °C and pH 7.0 in the presence of 4% NaCl (w/v). The predominant menaquinone was identified as MK-7, the major cellular fatty acids were identified as anteiso-C(15:0) and iso-C(15:0), and the major cellular polar lipids were identified as phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and two unknown phospholipids. The peptidoglycan type was determined to be based on meso-DAP. Based on 16S rRNA gene sequence similarity, the closest phylogenetic relatives were identified as Bacillus vietnamensis JCM 11124(T) (98.8% sequence similarity), Bacillus aquimaris JCM 11545(T) (98.6%) and Bacillus marisflavi JCM 11544(T) (98.5%). The DNA G+C content of strain C-89(T) was determined to be 45.4 mol%. The DNA-DNA relatedness values of strain C-89(T) with its closest relatives were below 18%. Therefore, on the basis of phylogenetic, chemotaxonomic, and phenotypic results, strain C-89(T) can be considered to represent a novel species within the genus Bacillus, for which the name Bacillus haikouensis sp. nov., is proposed. The type strain is C-89(T) (=KCTC 33545(T) = CCTCC AB 2014076(T)).

Bacillus oryzaecorticis sp. nov., a moderately halophilic bacterium isolated from rice husks

A Gram-stain-positive, aerobic, endospore-forming, moderately halophilic rod, designated strain R1T, was isolated from rice husks and subjected to a taxonomic study using a polyphasic approach. Strain R1T produced spherical or ellipsoidal endospores at a subterminal position in swollen sporangia, and was catalase- and oxidase-positive. The isolate grew optimally at 37 °C and pH 6.0–7.0, and could grow in the presence of up to 9 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R1T belongs to the genus Bacillus . The closest relatives of strain R1T were Bacillus subtilis subsp. subtilis NCIB 3610T, Bacillus aquimaris TF-12T, and Bacillus marisflavi TF-11T, with 16S rRNA gene sequence similarities of 96.0 %, 98.4 %, and 98.7 %, respectively. DNA–DNA relatedness values between the isolate and the reference strains were ≤42±3 %. The predominant menaquinones were MK-5 (50 %) and MK-7 (50 %). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethanolamine. The major cellular fatty acids were iso-C15 : 0 (48.6 %) and anteiso-C15 : 0 (20.6 %), and the cell-wall diamino acid was meso-diaminopimelic acid. On the basis of 16S rRNA gene sequence analyses and chemotaxonomic and phenotypic characteristics, it is concluded that strain R1T represents a novel species of the genus Bacillus , for which we propose the name Bacillus oryzaecorticis sp. nov. The type strain is R1T ( = KACC 17217T = KCCM 90231T = JCM 19602T).

Bacillus pakistanensis sp. nov., a halotolerant bacterium isolated from salt mines of the Karak Area in Pakistan

A rod shaped, non-motile, endospore forming, Gram-stain positive and moderately halotolerant strain, designated as NCCP-168(T), was isolated from salt mines sampled in the Karak district of Khyber Pakhtunkhwa Province in Pakistan. To delineate its taxonomic position, the strain was subjected to polyphasic characterization. Cells of strain NCCP-168(T) can grow at 10-40 (○)C (optimum at 30-35 (○)C), in a pH range of 5.0-9.0 (optimum at pH 8.0) and in 0-17 % (w/v) NaCl on agar medium. The phylogenetic analysis based on the 16S rRNA gene sequence showed that strain NCCP-168(T) belongs to the genus Bacillus with the highest similarity to Bacillus seohaeanensis BH724(T) (97.1 %), and less than 97 % similarity with other closely related taxa (95.6 % with B. subtilis subsp. subtilis NCIB3610(T)). DNA-DNA relatedness between strain NCCP-168(T) and the type strains of closely related species was lower than 30 %. Chemotaxonomic data (major menaquinone, MK-7; cell wall peptidoglycan type, A1γ [meso-diaminopimelic acid]; major fatty acids, iso-C15:0 29.9 %, anteiso-C15:0 29.3 %, iso-C16:0 11.4 %, iso-C14:0 8.9 % and anteiso-C17:0 7.0 %; major polar lipids, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine) support the affiliation of strain NCCP-168(T) with genus Bacillus. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain NCCP-168(T) can be distinguished from the closely related taxa and thus represents a novel species in the genus Bacillus, for which the name Bacillus pakistanensis sp. nov. is proposed, with the type strain NCCP-168(T) (= KCTC 13786(T) = DSM 24834(T) = JCM 18975(T)).

Biodegradation of the allelopathic chemical m-tyrosine by Bacillus aquimaris SSC5 involves the homogentisate central pathway

m-Tyrosine is an amino acid analogue, exuded from the roots of fescue grasses, which acts as a potent allelopathic and a broad spectrum herbicidal chemical. Although the production and toxic effects of m-tyrosine are known, its microbial degradation has not been documented yet. A soil microcosm study showed efficient degradation of m-tyrosine by the inhabitant microorganisms. A bacterial strain designated SSC5, that was able to utilize m-tyrosine as the sole source of carbon, nitrogen, and energy, was isolated from the soil microcosm and was characterized as Bacillus aquimaris. Analytical methods such as HPLC, GC-MS, and ¹H-NMR performed on the resting cell samples identified the formation of 3-hydroxyphenylpyruvate (3-OH-PPA), 3-hydroxyphenylacetate (3-OH-PhAc), and homogentisate (HMG) as major intermediates in the m-tyrosine degradation pathway. Enzymatic assays carried out on cell-free lysates of m-tyrosine-induced cells confirmed transamination reaction as the first step of m-tyrosine degradation. The intermediate 3-OH-PhAc thus obtained was further funneled into the HMG central pathway as revealed by a hydroxylase enzyme assay. Subsequent degradation of HMG occurred by ring cleavage catalyzed by the enzyme homogentisate 1, 2-dioxygenase. This study has significant implications in terms of understanding the environmental fate of m-tyrosine as well as regulation of its phytotoxic effect by soil microorganisms.

Bacillus songklensis sp. nov., isolated from soil

A Gram-stain-positive, spore-forming, rod-shaped, motile, strictly aerobic bacterial strain, designated CAU 1033(T), was isolated from soil and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1033(T) formed a distinct lineage within the genus Bacillus and was most closely related to Bacillus drentensis KCTC 13025(T) (similarity 95.9 %). CAU 1033(T) contained MK-7 as the only isoprenoid quinone and iso-C15 : 0 and anteiso-C15 : 0 as the major fatty acids. The cell wall peptidoglycan of strain CAU 1033(T) contained meso-diaminopimelic acid and the major whole-cell sugars were arabinose, sucrose and ribose. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, four unidentified aminophospholipids, an unidentified aminolipid, two unidentified glycolipids and another unidentified polar lipid. The DNA G+C content was 41.4 mol%. On the basis of phenotypic data and phylogenetic inference, strain CAU 1033(T) was classified as a representative of a novel species in the genus Bacillus for which the name Bacillus songklensis sp. nov. is proposed. The type strain is CAU 1033(T) ( = KCTC 13881(T) = CCUG 61889(T)).

Seasonal variation in the antifouling defence of the temperate brown alga Fucus vesiculosus

The important role of marine epibiotic biofilms in the interactions of the host with its environment has been acknowledged recently. Previous studies with the temperate brown macroalga Fucus vesiculosus have identified polar and non-polar compounds recovered from the algal surface that have the potential to control such biofilms. Furthermore, both the fouling pressure and the composition of the epibiotic bacterial communities on this macroalga varied seasonally. The extent to which this reflects a seasonal fluctuation of the fouling control mechanisms of the host is, however, unexplored in an ecological context. The present study investigated seasonal variation in the anti-settlement activity of surface extracts of F. vesiculosus against eight biofilm-forming bacteria isolated from rockweed-dominated habitats, including replication of two populations from two geographically distant sites. The anti-settlement activity at both sites was found to vary temporally, reaching a peak in summer/autumn. Anti-settlement activity also showed a consistent and strong difference between sites throughout the year. This study is the first to report temporal variation of antifouling defence originating from ecologically relevant surface-associated compounds.