Ureibacillus aquaedulcis sp. nov., isolated from freshwater well and reclassification of Lysinibacillus yapensis and Lysinibacillus antri as Ureibacillus yapensis comb. nov. and Ureibacillus antri comb. Nov

A Gram-stain-positive aerobic, rod-shaped, spore-producing bacterium forming colonies with convex elevation and a smooth, intact margin was isolated from a freshwater sample collected from a well situated in an agricultural field. The 16S rRNA gene sequence of the isolated strain BA0131T showed the highest sequence similarity to Lysinibacillus yapensis ylb-03T (99.25%) followed by Ureibacillus chungkukjangi 2RL3-2T (98.91%) and U. sinduriensis BLB-1T (98.65%). The strain BA0131T was oxidase and catalase positive and urease negative. It also tested positive for esculin hydrolysis and reduction of potassium nitrate, unlike its phylogenetically closest relatives. The predominant fatty acids in strain BA0131T included were anteiso-C15:0, iso-C16:0, iso-C15:0, iso-C14:0 and the major polar lipids comprised were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The respiratory quinones identified in strain BA0131T were MK8 (H2) (major) and MK8 (minor). The strain BA0131T shared the lowest dDDH values with L. yapensis ylb-03T (21%) followed by U. chungkukjangi 2RL3-2T (24.2%) and U. sinduriensis BLB-1T (26.4%) suggesting a closer genetic relationship U. sinduriensis BLB-1T. The ANI percentage supported the close relatedness with U. sinduriensis BLB-1T (83.61%) followed by U. chungkukjangi 2RL3-2T (82.03%) and U. yapensis ylb-03T (79.57%). The core genome-based phylogeny constructed using over 13,704 amino acid positions and 92 core genes revealed the distinct phylogenetic position of strain BA0131T among the genus Ureibacillus. The distinct physiological, biochemical characteristics and genotypic relatedness data indicate the strain BA0131T represents a novel species of the genus Ureibacillus for which the name Ureibacillus aquaedulcis sp. nov. (Type strain, BA0131T = MCC 5284 = JCM 36475) is proposed. Additionally, based on extensive genomic and phylogenetic analyses, we propose reclassification of two species, L. yapensis and L. antri, as U. yapensis comb. nov. (Type strain, ylb-03T = JCM 32871T = MCCC 1A12698T) and U. antri (Type strain, SYSU K30002T = CGMCC 1.13504T = KCTC 33955T).

Parageobacillus thermoglucosidasius as an emerging thermophilic cell factory

Parageobacillus thermoglucosidasius is a thermophilic and facultatively anaerobic microbe, which is emerging as one of the most promising thermophilic model organisms for metabolic engineering. The use of thermophilic microorganisms for industrial bioprocesses provides the advantages of increased reaction rates and reduced cooling costs for bioreactors compared to their mesophilic counterparts. Moreover, it enables starch or lignocellulose degradation and fermentation to occur at the same temperature in a Simultaneous Saccharification and Fermentation (SSF) or Consolidated Bioprocessing (CBP) approach. Its natural hemicellulolytic capabilities and its ability to convert CO to metabolic energy make P. thermoglucosidasius a potentially attractive host for bio-based processes. It can effectively degrade hemicellulose due to a number of hydrolytic enzymes, carbohydrate transporters, and regulatory elements coded from a genomic cluster named Hemicellulose Utilization (HUS) locus. The growing availability of effective genetic engineering tools in P. thermoglucosidasius further starts to open up its potential as a versatile thermophilic cell factory. A number of strain engineering examples showcasing the potential of P. thermoglucosidasius as a microbial chassis for the production of bulk and fine chemicals are presented along with current research bottlenecks. Ultimately, this review provides a holistic overview of the distinct metabolic characteristics of P. thermoglucosidasius and discusses research focused on expanding the native metabolic boundaries for the development of industrially relevant strains.

Structure of the Lysinibacillus sphaericus Tpp49Aa1 pesticidal protein elucidated from natural crystals using MHz-SFX

The Lysinibacillus sphaericus proteins Tpp49Aa1 and Cry48Aa1 can together act as a toxin toward the mosquito Culex quinquefasciatus and have potential use in biocontrol. Given that proteins with sequence homology to the individual proteins can have activity alone against other insect species, the structure of Tpp49Aa1 was solved in order to understand this protein more fully and inform the design of improved biopesticides. Tpp49Aa1 is naturally expressed as a crystalline inclusion within the host bacterium, and MHz serial femtosecond crystallography using the novel nanofocus option at an X-ray free electron laser allowed rapid and high-quality data collection to determine the structure of Tpp49Aa1 at 1.62 Å resolution. This revealed the packing of Tpp49Aa1 within these natural nanocrystals as a homodimer with a large intermolecular interface. Complementary experiments conducted at varied pH also enabled investigation of the early structural events leading up to the dissolution of natural Tpp49Aa1 crystals-a crucial step in its mechanism of action. To better understand the cooperation between the two proteins, assays were performed on a range of different mosquito cell lines using both individual proteins and mixtures of the two. Finally, bioassays demonstrated Tpp49Aa1/Cry48Aa1 susceptibility of Anopheles stephensi, Aedes albopictus, and Culex tarsalis larvae-substantially increasing the potential use of this binary toxin in mosquito control.

Identification and characterization of a novel bacteriocin gene cluster in Lysinibacillus boronitolerans

Although the antibiotics inhibit or kill pathogens, the abuse leads to the resistance formation and even "Super Bacteria." Therefore, it is urgent to explore the natural and safe alternatives such as bacteriocin. In this study, an uncharacterized bacteriocin gene cluster for Lysinibacillus boronitolerans was first predicted by genome sequencing and bioinformatics analysis, of which including two biosynthetic genes, a regulatory gene, a transport-related gene, and six other genes. Subsequently, the 10.24-kb gene cluster was expressed in Escherichia coli BL21, and the lysate effectively inhibited the growths of pathogenic bacteria containing Bacillus pumilus, Bacillus velezensis, Pseudomonas syringae pv. tomato DC3000, and Xanthomonas axonopodis pv. manihotis. The antibacterial substance was purified by 70% ammonium sulfate precipitation and further identified by liquid chromatography-tandem mass spectrometry. The results showed that the antibacterial substance consisted of 44 amino acids and had 24.1% sequence identity with the cyanobacterin Piricyclamide 7005 E4 PirE4, a bacteriocin analogue. The minimal set of genes required for the biosynthesis of the antibacterial substance was determined by site-directed mutagenesis, suggesting both a transcriptional repressor and a phosphohydroxythreonine transaminase were essential. Subsequently, the evolution and conservation of the two proteins were analyzed among 22 Lysinibacillus species. Among them, the residues responsible for functions were identified. Collectively, our results set a solid foundation for investigation of the biosynthesis and application of bacteriocin.

Cr(VI) reduction by Agrobacterium sp. Cr-1 and Lysinibacillus sp. Cr-2, novel Cr(VI)-reducing strains isolated from chromium plant soil

The bioremediation of Cr(VI)-contaminated soil is a promising strategy; however, the performance of Cr(VI)-reducing bacteria is limited by the toxicity of Cr(VI). In this study, two novel Cr(VI)-reducing bacteria were isolated from a Cr salt plant and identified as Agrobacterium sp. and Lysinibacillus sp. The Cr(VI) reduction conditions of the two strains were optimized. At a Cr(VI) concentration of 500 mg/L, Agrobacterium sp. Cr-1 reduced Cr(VI) with a removal rate of 96.91%, while that for Lysinibacillus sp. Cr-2 was 92.82%. First-order reaction kinetic equations simulated the positive relationship between time and Cr(VI) concentration during Cr(VI) reduction in these two strains. Agrobacterium sp. Cr-1 was further studied, and the effects of different cell components on Cr(VI) reduction were detected. The extracellular extracts of Agrobacterium sp. Cr-1 played a major role in Cr(VI) reduction, followed by intracellular extracts and cell membranes. The scanning electron microscope-energy dispersive spectrometer (SEM-EDS) images show that the precipitation was Cr. The high Cr(VI) reducing ability of Agrobacterium sp. Cr-1 suggests that this strain is promising for the remediation of Cr(VI)-contaminated sites.

Structural and Biochemical Insights into Bis(2-hydroxyethyl) Terephthalate Degrading Carboxylesterase Isolated from Psychrotrophic Bacterium Exiguobacterium antarcticum

This study aimed to elucidate the crystal structure and biochemically characterize the carboxylesterase EaEst2, a thermotolerant biocatalyst derived from Exiguobacterium antarcticum, a psychrotrophic bacterium. Sequence and phylogenetic analyses showed that EaEst2 belongs to the Family XIII group of carboxylesterases. EaEst2 has a broad range of substrate specificities for short-chain p-nitrophenyl (pNP) esters, 1-naphthyl acetate (1-NA), and 1-naphthyl butyrate (1-NB). Its optimal pH is 7.0, losing its enzymatic activity at temperatures above 50 °C. EaEst2 showed degradation activity toward bis(2-hydroxyethyl) terephthalate (BHET), a polyethylene terephthalate degradation intermediate. We determined the crystal structure of EaEst2 at a 1.74 Å resolution in the ligand-free form to investigate BHET degradation at a molecular level. Finally, the biochemical stability and immobilization of a crosslinked enzyme aggregate (CLEA) were assessed to examine its potential for industrial application. Overall, the structural and biochemical characterization of EaEst2 demonstrates its industrial potency as a biocatalyst.

Removal of an Aminopeptidase N From Midgut Brush Border Does Not Affect Susceptibility of Spodoptera litura (Lepidoptera: Noctuidae) Larvae to Four Insecticidal Proteins of Bacillus thuringiensis (Bacillales: Bacillaceae)

Spodoptera litura is one of the most destructive lepidopteran insects of cabbages and cauliflowers in the world. Cry1 and Vip3 toxins from Bacillus thuringiensis have been reported to show toxicity in multiple lepidopteran insects. Binding of toxic molecules to specific receptors on the midgut epithelial cells is known to be a key step in the action mode of Bt toxins. Aminopeptidase N (APN) -like proteins have been reported to be binding sites of multiple Cry toxins in the midgut of Cry susceptible insects. In the present study, we identified six midgut APNs by analysis of the genome and midgut transcriptome of S. litura. CRISPR/Cas9 mediated gene-knockout system was utilized to mutate the GPI-anchor signal peptide at the C terminus of SlAPN1. SlAPN1 was verified to be removed from the midgut brush border membrane vesicles of a homozygous knockout strain of S. litura (SlAPN1-KO). Bioassay results indicated that susceptibility of the SlAPN1-KO strain to Cry1Aa, Cry1Ac, Cry1Ca, and Vip3Aa toxins was close to that of the wild-type strain of S. litura. RT-qPCR results showed that the transcriptional level of SlAPN2-6 was not up-regulated after knockout of the SlAPN1. Results in this study indicated that the SlAPN1 did not play a critical role in the pathway of toxicity of Cry1Aa, Cry1Ac, Cry1Ca, and Vip3Aa toxins in S. litura.

Simultaneous bioremediation of phenol and tellurite by Lysinibacillus sp. EBL303 and characterization of biosynthesized Te nanoparticles

Aromatic compounds and metalloid oxyanions are abundant in the environment due to natural resources and industrial wastes. The high toxicity of phenol and tellurite poses a significant threat to all forms of life. A halotolerant bacterium was isolated and identified as Lysinibacillus sp. EBL303. The remediation analysis shows that 500 mg/L phenol and 0.5 mM tellurite can be remediated entirely in separate cultures within 74 and 56 h, respectively. In addition, co-remediation of pollutants resulted in the same phenol degradation and 27% less tellurite reduction within 98 h. Since phenol and tellurite exhibited inhibitory behavior, their removal kinetics fitted well with the first-order model. In the characterization of biosynthesized tellurium nanoparticles (TeNPs), transmission electron microscopy, dynamic light scattering, FE-SEM, and dispersive X-ray (EDX) showed that the separated intracellular TeNPs were spherical and consisted of only tellurium with 22-148 nm in size. Additionally, investigations using X-ray diffraction and Fourier-transform infrared spectroscopy revealed proteins and lipids covering the surface of these amorphous TeNPs. Remarkably, this study is the first report to demonstrate the simultaneous bioremediation of phenol and tellurite and the biosynthesis of TeNPs, indicating the potential of Lysinibacillus sp. EBL303 in this matter, which can be applied to environmental remediation and the nanotechnology industry.

Biotransformation of d-Xylose-Rich Rice Husk Hydrolysate by a Rice Paddy Soil Bacterium, Priestia sp. Strain JY310, to Low Molecular Weight Poly(3-hydroxybutyrate)

Poly(3-hydroxybutyrate) (PHB) is a versatile thermoplastic with superior biodegradability and biocompatibility that is intracellularly accumulated by numerous bacterial and archaeal species. Priestia sp. strain JY310 that was able to efficiently biotransform reducing sugars in d-xylose-rich rice husk hydrolysate (reducing sugar_RHH) to PHB was isolated from the soil of a rice paddy. Reducing sugar_RHH including 12.5% d-glucose, 75.3% d-xylose, and 12.2% d-arabinose was simply prepared using thermochemical hydrolysis of 3% H₂SO₄-treated rice husk for 15 min at 121 °C. When cultured with 20 g/L reducing sugar_RHH under optimized culture conditions in a batch bioreactor, Priestia sp. strain JY310 could produce PHB homopolymer up to 50.4% of cell dry weight (6.2 g/L). The melting temperature, heat of fusion, and thermal decomposition temperature of PHB were determined to be 167.9 °C, 92.1 J/g, and 268.1 °C, respectively. The number average and weight average molecular weights of PHB with a broad polydispersity index value (4.73) were estimated to be approximately 16.2 and 76.8 kg/mol, respectively. The findings of the present study suggest that Priestia sp. strain JY310 can be exploited as a good candidate for the low-cost production of low molecular weight PHB with improved biodegradability and reduced brittleness from inexpensive agricultural waste hydrolysates.

The Bacillaceae-1 RNA motif comprises two distinct classes

Non-coding RNAs are key regulatory players in bacteria. Many computationally predicted non-coding RNAs, however, lack functional associations. An example is the Bacillaceae-1 RNA motif, whose Rfam model consists of two hairpin loops. We find the motif conserved in nine of 13 non-pathogenic strains of the genus Bacillus but only in one pathogenic strain. To elucidate functional characteristics, we studied 118 hits of the Rfam model in 11 Bacillus spp. and found two distinct classes based on the ensemble diversity of their RNA secondary structure and the genomic context concerning the ribosomal RNA (rRNA) cluster. Forty hits are associated with the rRNA cluster, of which all 19 hits upstream flanking of 16S rRNA have a reverse complementary structure of low structural diversity. Fifty-two hits have large ensemble diversity, of which 38 are located between two coding genes. For eight hits in Bacillus subtilis, we investigated public expression data under various conditions and observed either the forward or the reverse complementary motif expressed. Five hits are associated with the rRNA cluster. Four of them are located upstream of the 16S rRNA and are not transcriptionally active, but instead, their reverse complements with low structural diversity are expressed together with the rRNA cluster. The three other hits are located between two coding genes in non-conserved genomic loci. Two of them are independently expressed from their surrounding genes and are structurally diverse. In summary, we found that Bacillaceae-1 RNA motifs upstream flanking of ribosomal RNA clusters tend to have one stable structure with the reverse complementary motif expressed in B. subtilis. In contrast, a subgroup of intergenic motifs has the thermodynamic potential for structural switches.

High-expression and characterization of a novel serine protease from Ornithinibacillus caprae L9T with eco-friendly applications

In the current work, a novel thermophilic serine protease gene (P3862) from Ornithinibacillus caprae L9^T was functionally expressed in Bacillus subtilis SCK6. The monomeric enzyme of about 29 kDa was purified to homogeneity with 43.91% of recovery and 2.81-folds of purification. Characterization of the purified protease revealed the optimum activity at pH 7 and 65 °C. The protease exhibited excellent activity and stability in the presence of Na⁺, Mg²⁺, Ca²⁺, ethanediol, n-hexane, Tween-20, Tween-80 and Triton X-100. P3862 displayed favorable caseinolytic activity, moderate keratinolytic activity but no collagenolytic activity. Besides, the homology model of P3862 possessed a globular configuration and characteristic of α/β hydrolase fold, and displayed stable interactions with casein, glycoprotein and keratin rather than collagen. Moreover, the crude enzyme could completely dehair goatskin within 6 h, resulting in decrease in BOD₅, COD and TSS loads by 72.86, 74.07, and 73.79%, respectively, as compared with Na₂S treatment. Biocatalytic applications revealed that it could effectively remove egg-stains from fabrics at 37 °C for 30 min with low supplementation (300 U/mL), and was able to degrade the feathers of duck and chicken. Overall, these outstanding properties make P3862 valuable in the development of environmentally friendly biotechnologies .

Lysinibacillus Isolate MK212927: A Natural Producer of Allylamine Antifungal ‘Terbinafine’

Resistance to antifungal agents represents a major clinical challenge, leading to high morbidity and mortality rates, especially in immunocompromised patients. In this study, we screened soil bacterial isolates for the capability of producing metabolites with antifungal activities via the cross-streak and agar cup-plate methods. One isolate, coded S6, showed observable antifungal activity against Candida (C.) albicans ATCC 10231 and Aspergillus (A.) niger clinical isolate. This strain was identified using a combined approach of phenotypic and molecular techniques as Lysinibacillus sp. MK212927. The purified metabolite displayed fungicidal activity, reserved its activity in a relatively wide range of temperatures (up to 60 °C) and pH values (6–7.8) and was stable in the presence of various enzymes and detergents. As compared to fluconazole, miconazole and Lamisil, the minimum inhibitory concentration of the metabolite that showed 90% inhibition of the growth (MIC₉₀) was equivalent to that of Lamisil, half of miconazole and one fourth of fluconazole. Using different spectroscopic techniques such as FTIR, UV spectroscopy, 1D NMR and 2D NMR techniques, the purified metabolite was identified as terbinafine, an allylamine antifungal agent. It is deemed necessary to note that this is the first report of terbinafine production by Lysinibacillus sp. MK212927, a fast-growing microbial source, with relatively high yield and that is subject to potential optimization for industrial production capabilities.

Reduction of Hexavalent Chromium [Cr(VI)] by Heavy Metal Tolerant Bacterium Alkalihalobacillus clausii CRA1 and Its Toxicity Assessment Through Flow Cytometry

A chromate-resistant bacterial strain was isolated from tannery effluent; based on morphological, biochemical, and 16S rRNA gene sequencing, it was identified as Alkalihalobacillus clausii and designated A. clausii CRA1. It was found to be halophilic, alkaliphilic, and resistant to multiple heavy metals like Cr(VI), Cd(II), As(II), Pb(II), Ni(II), Hg(II), Cu(II), Zn(II), and Fe(II). The strain was found to reduce 72% of chromate in 6 days in Cr(VI) spiked Luria Bertani medium with unaffected bacterial growth at an initial C(VI) concentration of 50 mg L^-1. Chromate reductase activity of culture supernatant (cultivated in LB broth) and cell lysate of the bacterium was found to be 23 and 43U, where 1U is µmol of Cr(VI) reduced/min/mg protein. Flow cytometry studies revealed that no significant effect of Cr(VI) on cell viability was observed till 12 h of exposure at 100, 200, 400 mg L^-1 concentrations, indicated by non-significant cell death (propidium iodide positive cells). However, at 800 and 1000 mg L^-1 Cr(VI) concentration, toxicity (cell death) was observed after 12 h of exposure. FACs studies also indicated that exposure to Cr(VI) increases cell size and cell granularity, which was also confirmed in SEM and TEM images of Cr(VI) treated cells. The presence of Cr(III) species in EDX spectra of Cr(VI) treated cells confirms that reduction of Cr(VI) to Cr(III) is the primary mechanism of Cr(VI) removal by the bacterium. Therefore, the bacterium A. clausii has potential for application in chromate removal from industrial waste effluents.

Cytotoxic Effects and Intracellular Localization of Bin Toxin from Lysinibacillus sphaericus in Human Liver Cancer Cell Line

Binary toxin (Bin toxin), BinA and BinB, produced by Lysinibacillus sphaericus has been used as a mosquito-control agent due to its high toxicity against the mosquito larvae. The crystal structures of Bin toxin and non-insecticidal but cytotoxic parasporin-2 toxin share some common structural features with those of the aerolysin-like toxin family, thus suggesting a common mechanism of pore formation of these toxins. Here we explored the possible cytotoxicity of Bin proteins (BinA, BinB and BinA + BinB) against Hs68 and HepG2 cell lines. The cytotoxicity of Bin proteins was evaluated using the trypan blue exclusion assay, MTT assay, morphological analysis and LDH efflux assay. The intracellular localization of Bin toxin in HepG2 cells was assessed by confocal laser scanning microscope. HepG2 cells treated with BinA and BinB (50 µg/mL) showed modified cell morphological features and reduced cell viability. Bin toxin showed no toxicity against Hs68 cells. The EC₅₀ values against HepG2 at 24 h were 24 ng/mL for PS2 and 46.56 and 39.72 µg/mL for BinA and BinB, respectively. The induction of apoptosis in treated HepG2 cells was confirmed by upregulation of caspase levels. The results indicated that BinB mediates the translocation of BinA in HepG2 cells and subsequently associates with mitochondria. The study supports the possible development of Bin toxin as either an anticancer agent or a selective delivery vehicle of anticancer agents to target mitochondria of human cancer cells in the future.

Green Synthesis of Silver Nanoparticles by Cytobacillus firmus Isolated from the Stem Bark of Terminalia arjuna and Their Antimicrobial Activity

This work reports an eco-friendly synthesis of silver nanoparticles (AgNPs) using endophytic bacteria, Cytobacillus firmus isolated from the stem bark of Terminalia arjuna. The synthesis of AgNPs was confirmed by visual observation as a change in color of the bacterial solution impregnated with silver. Further, the morphology of the AgNPs, average size, and presence of elemental silver were characterized by UV-Visible spectroscopy, scanning electron microscopy, and dynamic light scattering spectroscopy. The roles of endophytic secondary metabolites in the metal reduction, stabilization, and capping of silver nanoparticles were studied by qualitative FTIR spectral peaks. The antimicrobial ability of AgNPs was evaluated against Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria and pearl millet blast disease-causing fungi (Magnoporthe grisea). The biosynthesized AgNPs showed good antibacterial and antifungal activities. AgNPs effectively inhibited the bacterial growth in a dose-dependent manner and presented as good antifungal agents towards the growth of Magnoporthe grisea.

Bacterial synthesis of PbS nanocrystallites in one-step with L-cysteine serving as both sulfur source and capping ligand

The green bacterial biosynthesis of lead sulfide nanocrystallites by L-cysteine-desulfurizing bacterium Lysinibacillus sphaericus SH72 was demonstrated in this work. Nanocrystals formed by this bacterial method were characterized using the mineralogical and morphological approaches. The results revealed that the microbially synthesized PbS nanocrystals assume a cubic structure, and are often aggregated as spheroids of about 105 nm in size. These spheroids are composed of numerous nanoparticles with diameter 5-10 nm. Surface characterization of the bacterial nanoparticles with FTIR spectroscopy shows that the L-cysteine coats the surface of PbS nanoparticle as a stabilizing ligand. The optical features of the PbS nanocrystallites were assessed by UV-Vis spectroscopy and PL spectroscopy. The maximum absorption wavelength of the bacterial PbS particles occurs at 240 nm, and the photoluminescence emission band ranges from 375 to 550 nm. The band gap energy is calculated to be 4.36 eV, compared to 0.41 eV for the naturally occurring bulk PbS, with this clear blue shift attributable to the quantum size effect.

Genomic analysis of Caldalkalibacillus thermarum TA2.A1 reveals aerobic alkaliphilic metabolism and evolutionary hallmarks linking alkaliphilic bacteria and plant life

The aerobic thermoalkaliphile Caldalkalibacillus thermarum strain TA2.A1 is a member of a separate order of alkaliphilic bacteria closely related to the Bacillales order. Efforts to relate the genomic information of this evolutionary ancient organism to environmental adaptation have been thwarted by the inability to construct a complete genome. The existing draft genome is highly fragmented due to repetitive regions, and gaps between and over repetitive regions were unbridgeable. To address this, Oxford Nanopore Technology's MinION allowed us to span these repeats through long reads, with over 6000-fold coverage. This resulted in a single 3.34 Mb circular chromosome. The profile of transporters and central metabolism gives insight into why the organism prefers glutamate over sucrose as carbon source. We propose that the deamination of glutamate allows alkalization of the immediate environment, an excellent example of how an extremophile modulates environmental conditions to suit its own requirements. Curiously, plant-like hallmark electron transfer enzymes and transporters are found throughout the genome, such as a cytochrome b6c1 complex and a CO2-concentrating transporter. In addition, multiple self-splicing group II intron-encoded proteins closely aligning to those of a telomerase reverse transcriptase in Arabidopsis thaliana were revealed. Collectively, these features suggest an evolutionary relationship to plant life.

Occurrence and Analysis of Thermophilic Poly(butylene adipate-co-terephthalate)-Degrading Microorganisms in Temperate Zone Soils

The ubiquity and character of thermophilic poly(butylene adipate-co-terephthalate) (PBAT)-degrading microorganisms in soils were investigated and compared to the process in an industrial composting plant. PBAT degraders were sought in 41 temperate zone soils. No mesophilic degraders were found by the employed method, but roughly 10² colony-forming units (CFUs) of thermophilic degraders per gram of soil were found in nine soils, and after an enrichment procedure, the PBAT-degrading consortia were isolated from 30 out of 41 soils. Thermophilic actinomycetes, Thermobispora bispora in particular, together with bacilli proved to be the key constituents of the isolated and characterized PBAT-degrading consortia, with bacilli comprising from about 30% to over 90% of the retrieved sequences. It was also shown that only consortia containing both constituents were able to decompose PBAT. For comparison, a PBAT film together with two types of PBAT/starch films were subjected to biodegradation in compost and the degrading microorganisms were analyzed. Bacilli and actinobacteria were again the most common species identified on pure PBAT film, especially at the beginning of biodegradation. Later, the composition of the consortia on all three tested materials became very similar and more diverse. Since waste containing PBAT-based materials is often intended to end up in composting plants, this study increases our confidence that thermophilic PBAT degraders are rather broadly present in the environment and the degradation of the material during the composting process should not be limited by the absence of specific microorganisms.

The effect of bioaugmentation with Exiguobacterium sp. AO-11 on crude oil removal and the bacterial community in sediment microcosms, and the development of a liquid ready-to-use inoculum

This study demonstrates the feasibility of using Exiguobacterium sp. AO-11 to remediate oil-contaminated environments. Bioaugmentation using AO-11 showed the best removal percentage, 75%, of 4% (w/w) crude oil in sediment microcosms in 100 days. In terms of the bacterial community structure during crude oil degradation, the addition of AO-11 did not change the indigenous bacterial community, while the addition of urea fertilizer induced structural shift of indigenous bacterial community. Exiguobacterium sp. AO-11 was developed as a bioremediation product, and a liquid formulation of AO-11 was developed. Coconut milk residue and soybean oil mill sludge were used for bacterial cultivation to reduce the production cost, and they could enhance bacterial cell growth. The liquid formulation of AO-11 prepared in phosphate buffer could be stored at 4 °C for at least 2 months, and it maintained efficacy in the treatment of crude oil-contaminated seawater. Overall, bioaugmentation with strain AO-11 could be an effective solution for the bioremediation of crude oil-contaminated environments.

Transcriptome profiling reveals the molecular processes for survival of Lysinibacillus fusiformis strain 15-4 in petroleum environments

A bacterial strain designated Lysinibacillus fusiformis 15-4 was isolated from oil-free soil on the Qinghai-Tibet Plateau, which can grow well utilizing petroleum hydrocarbons as a carbon source at a lower temperature. To deeply characterize the molecular adaptations and metabolic processes of this strain when grown in a petroleum-containing environment, transcriptome analysis was performed. A total of 4664 genes and the expression of 3969 genes were observed in strain 15-4. When the strain was grown in petroleum-containing medium, 2192 genes were significantly regulated, of which 1312 (60%) were upregulated and 880 (40%) were downregulated. This strain degraded and adapted to petroleum via modulation of diverse molecular processes, including improvements in transporter activity, oxidoreductase/dehydrogenase activity, two-component system/signal transduction, transcriptional regulation, fatty acid catabolism, amino acid metabolism, and environmental stress responses. Many strain-specific genes were involved in the oxidation of hydrocarbon compounds, such as several luciferase family alkane monooxygenase genes, flavin-utilizing monooxygenase family genes, and flavoprotein-like family alkanesulfonate monooxygenase genes. Several cold shock protein genes were also induced suggesting adaptation to cold environments and the potential for petroleum degradation at low temperatures. The results obtained in this study may broaden our understanding of molecular adaptation of bacteria to hydrocarbon-containing environments and may provide valuable data for further study of L. fusiformis.

Metabolic engineering of Parageobacillus thermoglucosidasius for the efficient production of (2R, 3R)-butanediol

High-temperature fermentation using thermophilic microorganisms may provide cost-effective processes for the industrial production of fuels and chemicals, due to decreased hygiene and cooling costs. In the present study, the genetically trackable thermophile Parageobacillus thermoglucosidasius DSM2542^T was engineered to produce (2R, 3R)-butanediol (R-BDO), a valuable chemical with broad industrial applications. The R-BDO biosynthetic pathway was optimized by testing different combinations of pathway enzymes, with acetolactate synthase (AlsS) from Bacillus subtilis and acetolactate decarboxylase (AlsD) from Streptococcus thermophilus yielding the highest production in P. thermoglucosidasius DSM2542^T. Following fermentation condition optimization, shake flask fermentation at 55 °C resulted in the production of 7.2 g/L R-BDO with ~ 72% theoretical yield. This study details the microbial production of R-BDO at the highest fermentation temperature reported to date and demonstrates that P. thermoglucosidasius DSM2542^T is a promising cell factory for the production of fuels and chemicals using high-temperature fermentation.

Biodegradation of aliphatic and polycyclic aromatic hydrocarbons by the thermophilic bioemulsifier-producing Aeribacillus pallidus strain SL-1

The utilization of thermophilic hydrocarbon-degrading microorganisms is a suitable strategy for improving biodegradation of petroleum hydrocarbons and PAHs, as well as enhancing oil recovery from high-temperature reservoirs. In this study, the thermophilic strain Aeribacillus pallidus SL-1 was evaluated for the biodegradation of crude oil and PAHs at 60 °C. Strain SL-1 was found to preferentially degrade short-chain n-alkanes (<C17) and aromatic hydrocarbons from crude oil. The highest degradation rate of 84% was obtained with 1000 mg/l naphthalene as sole carbon source. Additionally, the strain was able to degrade 80% of phenanthrene (200 mg/l) and 50% of pyrene (50 mg/l) within 5 days at 60 °C. The SL-bioemulsifier produced by strain SL-1 was identified as a glycoprotein with stable emulsifying activity over a wide range of environmental conditions. Chemical composition studies exhibited that the SL-bioemulsifier consisted of polysaccharides (65.6%) and proteins (13.1%), among them, proteins were the major emulsifying functional substrates. Furthermore, the SL-bioemulsifier was able to enhance the solubility of PAHs. Thus, the bioemulsifier-producing strain SL-1 has great potential for applications in high-temperature bioremediation.

Production, characterization and antimicrobial activities of bio-pigments by Aquisalibacillus elongatus MB592, Salinicoccus sesuvii MB597, and Halomonas aquamarina MB598 isolated from Khewra Salt Range, Pakistan

Hypersaline ecosystems offer unique habitats to microbial populations capable of withstanding extreme stress conditions and producing novel metabolites of commercial importance. Herein, we have characterized for the first time the production of bioactive pigments from newly isolated halophilic bacterial species. Halophilic bacteria were isolated from Khewra Salt Range of Pakistan. Three distinctly colored isolates were selected for pigment production. Selected colonies were identified as Aquisalibacillus elongatus MB592, Salinicoccus sesuvii MB597, and Halomonas aquamarina MB598 based on morphological, biochemical, and physiological evidences as well as 16S rRNA analysis. The optimum pigment production observed at mesophilic condition, nearly neutral pH, and moderate salinity was validated using response surface methodology. Different analytical techniques (UV spectroscopy, infrared spectroscopy, and HPLC) characterized these purified pigments as derivatives of bacterioruberin carotenoids. Antioxidant activity of pigments revealed up to 85% free-radical scavenging activity at the concentration of 30 µg ml^-1. Pigments also showed significant antimicrobial activity against Bacillus subtilis, Bacillus pumilus, Enterococcus faecalis, Bacillus cereus, Klebsiella pneumoniae, Alcaligenes faecalis, Pseudomonas geniculata, Enterococcus faecium, Aspergillus fumigatus, Aspergillus flavus, Fusarium solani, and Mucor spp., suggesting potential biomedical applications.

Cell envelop is the key site for Cr(Ⅵ) reduction by Oceanobacillus oncorhynchi W4, a newly isolated Cr(Ⅵ) reducing bacterium

The Cr(Ⅵ) removal way and Cr(Ⅵ) reducing site of Oceanobacillus oncorhynchi W4, a novel Cr(Ⅵ) reducing bacterium, were investigated in this study. Results showed that about 74.2% of Cr(Ⅵ) was removed from solution by growing cells within 72 h. Moreover, heating-killed resting cells had little Cr(Ⅵ) removal capacity, which was significantly lower than that of resting cells, which reached nearly 80% removal rate, suggesting that the way of Cr(Ⅵ) removal mainly relied on biological reduction rather than biosorption. And the Cr(Ⅵ) reduction was found to be significantly enhanced by some electron donors, especially glycerin, which further verified enzyme-mediated biological reduction as the way for Cr(Ⅵ) removal. Experiments of Cr(Ⅵ) removal by permeable cells indicated that there was no significant difference in chromium reduction between the impermeable cells and the permeable cells. The cell envelop fraction had a Cr(Ⅵ) removal rate of 82.9%, apparently higher than cytoplasmic fraction (11.1%), indicating that the cell envelop was the main location for Cr(Ⅵ) reduction, which were further demonstrated by Scanning Electron Microscope and Transmission electron microscopy plus EDS analysis. Furthermore, analysis of X-ray photoelectron spectroscopy manifested that CO, C-OH and C-OC groups on the surfaces played major roles in correlation with chromium species.

Effective degradation of polychlorinated biphenyls by a facultative anaerobic bacterial consortium using alternating anaerobic aerobic treatments

Polychlorinated biphenyls (PCBs) are synthetic mixtures of chlorinated hydrocarbon compounds that were widely used in the past and still found in the environment due to their highly recalcitrant nature. A combination of anaerobic dechlorination and aerobic oxidation is essential to degrade these PCB mixtures into less toxic products. It was hypothesized that due to the complexity of PCB mixtures, a consortium of carefully selected suitable microbial species will perform better than the application of individual microbes. In the present study, biodegradation of the commercial PCB mixture, Aroclor 1260, was studied under two different combined anaerobic-aerobic conditions, namely, alternating (AN) and two stage (TS). The facultative anaerobic bacterial consortium consisted of naturally occurring Achromobacter sp. NP03, Ochrobactrum sp. NP04 and Lysinibacillus sp. NP05. These bacteria were found capable as individuals of solubilizing and degrading PCBs under both anaerobic and aerobic conditions. 49.2 ± 2.5% total reduction of the original 50 mg/L Aroclor 1260 mixture was achieved after 2 weeks in AN treatment whereas the reduction was only 24.44 ± 2.46% in TS treatment. At the end of week 6, a yield of 17.63 ± 0.91 mg/L chloride released was measured under AN condition compared to 11.79 ± 1.28 mg/L measured under TS condition. The overall results suggested that the microbial consortia capable of degrading and utilizing PCBs under both, anaerobic and aerobic conditions achieved better PCB degradation by repeated exposure to short periods of anaerobic and aerobic conditions alternatingly rather than the conventional two stage anaerobic-aerobic conditions.

Two selenium tolerant Lysinibacillus sp. strains are capable of reducing selenite to elemental Se efficiently under aerobic conditions

Microbes play important roles in the transport and transformation of selenium (Se) in the environment, thereby influencing plant resistance to Se and Se accumulation in plant. The objectives are to characterize the bacteria with high Se tolerance and reduction capacity and explore the significance of microbial origins on their Se tolerance, reduction rate and efficiency. Two bacterial strains were isolated from a naturally occurred Se-rich soil at tea orchard in southern Anhui Province, China. The reduction kinetics of selenite was investigated and the reducing product was characterized using scanning electron microscopy and transmission electron microscopy-energy dispersive spectroscopy. The bacteria were identified as Lysinibacillus xylanilyticus and Lysinibacillus macrolides, respectively, using morphological, physiological and molecular methods. The results showed that the minimal inhibitory concentrations (MICs) of selenite for L. xylanilyticus and L. macrolides were 120 and 220 mmol/L, respectively, while MICs of selenate for L. xylanilyticus and L. macrolides were 800 and 700 mmol/L, respectively. Both strains aerobically reduced selenite with an initial concentration of 1.0 mmol/L to elemental Se nanoparticles (SeNPs) completely within 36 hr. Biogenic SeNPs were observed both inside and outside the cells suggesting either an intra- or extracellular reduction process. Our study implied that the microbes from Se-rich environments were more tolerant to Se and generally quicker and more efficient than those from Se-free habitats in the reduction of Se oxyanions. The bacterial strains with high Se reduction capacity and the biological synthesized SeNPs would have potential applications in agriculture, food, environment and medicine.

Salipaludibacillus keqinensis sp. nov., a moderately halophilic bacterium isolated from a saline-alkaline lake

A novel Gram-stain positive, short rod, forming sub-terminal endospores of ellipsoidal shape, halophilic, alkaliphilic and aerobic bacterium, designated strain KQ-12^T, was isolated from a saline-alkaline lake in China, and characterised by a polyphasic taxonomic approach. The isolate grew at 4-40 °C (optimum, 25 °C), at pH 8.0-10.0 (pH 9.0) and in the presence of 0-16% (w/v) NaCl (8%). 16S rRNA gene sequence similarity of KQ-12^T to species in the genera Salipaludibacillus ranged from 96.6 to 98.1%. Phylogenetic trees indicated that the strain should be assigned to the genus Salipaludibacillus. The polar lipids of KQ-12^T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified phospholipid and its major cellular fatty acids were anteiso-C_15:0, anteiso-C_17:0, iso-C_15:0, and C_16:0. The isoprenoid quinone was MK-7. These key chemotaxonomic properties also confirmed the affiliation of the strain to the genus Salipaludibacillus. However, some physiological, biochemical properties, low average nucleotide identity and low digital DNA-DNA hybridization relatedness values enabled the strain to be differentiated from closely related species of the genus Salipaludibacillus. Thus, KQ-12^T can be classified as a novel species in the genus Salipaludibacillus, for which the name Salipaludibacillus keqinensis sp. nov. is proposed. The type strain is KQ-12^T ( =  ACCC 60430^T   =  KCTC 33935^T).

The whole genome insight on condition-specific redox activity and arsenopyrite interaction promoting As-mobilization by strain Lysinibacillus sp. B2A1

A gram-positive spore former, Lysinibacillus sp. B2A1 was isolated from a high arsenic containing groundwater of Beimen2A well, Chianan Plain area, Southwestern Taiwan. Noteworthy, in the subsurface-mimicking anoxic incubation with a Na-lactate amendment system, this isolate could interact with arsenic-source mineral arsenopyrite and enhance arsenic mobilization. Further, the isolate showed elevated levels of arsenic resistance, 200 mM and 7.5 mM for arsenate and arsenite, respectively. Lysinibacillus sp. B2A1 demonstrated condition-specific redox activities including salient oxic oxidation of arsenite and anoxic reduction of arsenate. The elevated rate of As(III) oxidation (V_max = 0.13 μM min^-1 per 10⁶ cells, K_m = 15.3 μM) under oxic conditions was potent. Correlating with stout persistence in an arsenic-rich niche, remarkably, the lesser toxic effects of arsenic ions on bacterial sporulation frequency and germination highlight this strain's ability to thrive under catastrophic conditions. Moreover, the whole genome analysis elucidated diverse metal redox/resistance genes that included a potential arsenite S-adenosylmethyltransferase capable of mitigating arsenite toxicity. Owing to its arsenic resistance, conditional redox activities and ability to interact with arsenic minerals leading to arsenic mobilization, the presence of such spore-forming strains could be a decisive indication towards arsenic mobilization in subsurface aquifers having a high concentration of soluble arsenic or its source minerals.

Metal(loid)-resistant bacteria reduce wheat Cd and As uptake in metal(loid)-contaminated soil

This study characterized the effect of the metal(loid)-resistant bacteria Ralstonia eutropha Q2-8 and Exiguobacterium aurantiacum Q3-11 on Cd and As accumulation in wheat grown in Cd- and As-polluted soils (1 mg kg^-1 of Cd + 40 mg kg^-1 of As and 2 mg kg^-1 of Cd + 60 mg kg^-1 of As). The influence of strains Q2-8 and Q3-11 on water-soluble Cd and As and NH₄⁺concentration and pH in the soil filtrate were also analyzed. Inoculation with these strains significantly reduced wheat plant Cd (12-32%) and As (9-29%) uptake and available Cd (15-28%) and As (22-38%) contents in rhizosphere soils compared to the controls. Furthermore, these strains significantly increased the relative abundances of the arsM bacterial As metabolism gene and of Fe- and Mn-oxidizing Leptothrix species in rhizosphere soils. Notably, these strains significantly reduced water-soluble Cd and As concentrations and increased pH and NH₄⁺ concentration in the soil filtrate. These results suggest that these strains increased soil pH and the abundance of genes possibly involved in metal(loid) unavailability, resulting in reduced wheat Cd and As accumulation and highlight the possibility of using bacteria for in situ remediation and safe production of wheat or other food crops in metal(loid)-polluted soils.

In-situ 2D bacterial crystal growth as a function of protein concentration: An atomic force microscopy study

The interplay between protein concentration and (observation) time has been investigated for the adsorption and crystal growth of the bacterial SbpA proteins on hydrophobic fluoride-functionalized SiO2 surfaces. For this purpose, atomic force microscopy (AFM) has been performed in real-time for monitoring protein crystal growth at different protein concentrations. Results reveal that (1) crystal formation occurs at concentrations above 0.08 µM and (2) the compliance of the formed crystal decreases by increasing protein concentration. All the crystal domains observed presented similar lattice parameters (being the mean value for the unit cell: a = 14.8 ± 0.5 nm, b = 14.7 ± 0.5 nm, γ = 90 ° ± 2). Protein film formation is shown to take place from initial nucleation points which originate a gradual and fast extension of the crystalline domains. The Avrami equation describes well the experimental results. Overall, the results suggest that protein-substrate interactions prevail over protein-protein interactions. RESEARCH HIGHLIGHTS: AFM enables to monitor protein crystallization in real-time. AFM high-resolution determines lattice parameters and viscoelastic properties. S-layer crystal growth rate increases with protein concentration. Avrami equation models protein crystal growth.

Potential of Lentibacillus sp. NS12IITR for production of lipids with enriched branched-chain fatty acids for improving biodiesel properties along with hydrocarbon co-production

Hypersaline environment is inhabited by array of microbes which have the potential to produce industrially important products. This study explored biomass and lipid production potential of the halophilic bacterium, strain NS12IITR which was isolated from Sambhar Lake, Rajasthan. Sequencing and phylogenetic analysis revealed that the bacterium belonged to genus Lentibacillus. The salient feature of the isolate is its ability to accumulate total cellular lipid up to 18.9 ± 0.45% of dry cell weight. In addition, trans-esterification of extracted lipid yielded 77.6 ± 5.56% of total esters as methyl ester of branched-chain fatty acids (BCFAs). To assess the nature of extracted lipid, lipid sample was fractionated on the silicic acid column, which demonstrated that 49.03 ± 1.35% of the total lipids was neutral in nature. Trans-esterification of the neutral lipid fraction yielded 60.62 ± 4.88% of total esters as methyl ester of BCFAs. Methyl esters of BCFAs were present in trans-esterified products of neutral as well as polar lipid fractions. Furthermore, the isolate produced hydrocarbons both extracellularly (C₁₀-C₃₀) and intra-cellularly (C₁₅-C₂₈). The concentration of extracellular hydrocarbon (21.11 ± 0.78 mg/L) synthesized by strain NS12IITR is in close agreement with the yield reported from other hydrocarbon producing bacteria. This is hereby a first report on the co-production of lipids and hydrocarbon from a halophilic bacterium. The production of neutral lipid with high percentage of BCFAs and co-production of hydrocarbons makes the isolate NS12IITR a potential claimant for biofuel production.

Morphology-tunable tellurium nanomaterials produced by the tellurite-reducing bacterium Lysinibacillus sp. ZYM-1

Although tellurite is highly toxic to organisms, elemental tellurium nanomaterials (TeNMs) have many uses. The microbe-mediated reduction of tellurite to Te(0) has been shown to be a green and cost-effective approach for turning waste into wealth. However, it is difficult to tune the morphology of biogenic nanomaterials. In this study, a series of experiments was conducted to investigate the factors influencing tellurite reduction by the tellurite-reducing bacterium Lysinibacillus sp. ZYM-1, including pH, tellurite concentration, temperature, and heavy metal ions. The optimal removal efficiency of tellurite was respectively achieved at pH 8, 0.5 mM tellurite, and 40 °C. All of the tested metal ions retarded the reduction of tellurite, especially Cd²⁺ and Co²⁺, which completely inhibited its reduction. Further characterization of the biogenic TeNMs indicated that their morphology could be tuned by the tellurite concentration, pH, temperature, and organic solvents used. Regular Te nanosheets were produced using 5 mM tellurite. The TeNMs were primarily synthesized in the cell membrane. Hexagonal Te nanoplates, nanorods, nanoflowers, and nanobranches were synthesized when combining membrane fractions with tellurite and NADH. The diverse morphologies are assumed to be induced by the synergy between the reduction kinetics and the protein structure. Therefore, this study confirmed that the bacterium can tune the morphology of TeNMs, broadening the potential application of biogenic TeNMs.

Isolation of levoglucosan-utilizing thermophilic bacteria

We previously developed an industrial production process for novel water-soluble indigestible polysaccharides (resistant glucan mixture, RGM). During the process, an anhydrosugar-levoglucosan -is formed as a by-product and needs to be removed to manufacture a complete non-calorie product. Here, we attempted to isolate thermophilic bacteria that utilize levoglucosan as a sole carbon source, to establish a removing process for levoglucosan at higher temperature. Approximately 800 natural samples were used to isolate levoglucosan-utilizing microorganisms. Interestingly, levoglucosan-utilizing microorganisms-most of which were filamentous fungi or yeasts-could be isolated from almost all samples at 25°C. We isolated three thermophilic bacteria that grew well on levoglucosan medium at 60°C. Two of them and the other were identified as Bacillus smithii and Parageobacillus thermoglucosidasius, respectively, by 16S rDNA sequence analysis. Using B. smithii S-2701M, which showed best growth on levoglucosan, glucose and levoglucosan in 5% (wt/vol) RGM were completely diminished at 50°C for 144 h. These bacteria are known to have a biotechnological potential, given that they can ferment a range of carbon sources. This is the first report in the utilization of levoglucosan by these thermophiles, suggesting that our results expand their biotechnological potential for the unutilized carbon resources.

Biodegradation of Ethyl Carbamate and Urea with Lysinibacillus sphaericus MT33 in Chinese Liquor Fermentation

It is important to reduce the concentration of ethyl carbamate (EC) in fermented foods. However, controlling the formation of EC and its precursor urea is difficult in spontaneous food fermentation because urea is a natural product of nitrogen metabolism. Biodegradation is a better solution to reduce the concentration of EC. This study aimed to reduce the concentration of EC in Chinese liquor via an indigenous strain Lysinibacillus sphaericus MT33. This strain produced urethanase (940 U/L) and urease (1580 U/L) and degraded 76.52% of EC and 56.48% of urea. After inoculation in liquor fermentation, the maximal relative abundance of Lysinibacillus increased from 0.02% to 8.46%, the final EC and urea contents decreased by 41.77% and 28.15%. Moreover, the concentration of EC decreased by 63.32% in liquor. The negative correlation between abundance of Lysinibacillus and contents of EC and urea indicated the effect of L. sphaericus on EC and urea degradation.

Draft genome sequence of Exiguobacterium aurantiacum strain PN47 isolate from saline ponds, known as "Salar del Huasco", located in the Altiplano in the North of Chile

In this report, we present a draft genome of 2,886,173bp of an Exiguobacterium aurantiacum strain PN47 isolate from the sediment of a saline pond named "Salar del Huasco" in the Altiplano in the North of Chile. Strain PN47 encodes adaptive characteristics enabling survival in extreme environmental conditions of high heavy metal and salt concentrations and high alkalinity.

Effect of Microbial Interaction on Urea Metabolism in Chinese Liquor Fermentation

Urea is the primary precursor of the carcinogen ethyl carbamate in fermented foods. Understanding urea metabolism is important for controlling ethyl carbamate production. Using Chinese liquor as a model system, we used metatranscriptome analysis to investigate urea metabolism in spontaneous food fermentation processes. Saccharomyces cerevisiae was dominant in gene transcription for urea biosynthesis and degradation. Lysinibacillus sphaericus was dominant for urea degradation. S. cerevisiae degraded 18% and L. sphaericus degraded 13% of urea in their corresponding single cultures, whereas they degraded 56% of urea in coculture after 12 h. Compared to single cultures, transcription of CAR1, DAL2, and argA, which are related to urea biosynthesis, decreased by 51, 36, and 69% in coculture, respectively. Transcription of DUR1 and ureA, which are related to urea degradation, increased by 227 and 70%, respectively. Thus, coexistence of the two strains promoted degradation of urea via transcriptional regulation of genes related to urea metabolism.

Capture and Release of tRNA by the T-Loop Receptor in the Function of the T-Box Riboswitch

In Gram-positive bacteria, the tRNA-dependent T-box riboswitch system regulates expression of amino acid biosynthetic and aminoacyl-tRNA synthetase genes through a transcription attenuation mechanism. Binding of uncharged tRNA "closes" the switch, allowing transcription read-through. Structural studies of the 100-nucleotide stem I domain reveal tRNA utilizes base pairing and stacking interactions to bind the stem, but little is known structurally about the 180-nucleotide riboswitch core (stem I, stem III, and antiterminator stem) in complex with tRNA or the mechanism of coupling of the intermolecular binding domains crucial to T-box function. Here we utilize solution structural and biophysical methods to characterize the interplay of the different riboswitch-tRNA contact points using Bacillus subtilis and Oceanobacillus iheyensis glycyl T-box and T-box:tRNA constructs. The data reveal that tRNA:riboswitch core binding at equilibrium involves only Specifier-anticodon and antiterminator-acceptor stem pairing. The elbow:platform stacking interaction observed in studies of the T-box stem I domain is released after pairing between the acceptor stem and the bulge in the antiterminator helix. The results are consistent with the model of T-box riboswitch:tRNA function in which tRNA is captured by stem I of the nascent mRNA followed by stabilization of the antiterminator helix and the paused transcription complex.

A genome-scale metabolic reconstruction of Lysinibacillus sphaericus unveils unexploited biotechnological potentials

The toxic lineage (TL) of Lysinibacillus sphaericus has been extensively studied because of its potential biotechnological applications in biocontrol of mosquitoes and bioremediation of toxic metals. We previously proposed that L. sphaericus TL should be considered as a novel species based on a comparative genomic analysis. In the current work, we constructed the first manually curated metabolic reconstruction for this species on the basis of the available genomes. We elucidated the central metabolism of the proposed species and, beyond confirming the reported experimental evidence with genomic a support, we found insights to propose novel applications and traits to be considered in further studies. The strains belonging to this lineage exhibit a broad repertory of genes encoding insecticidal factors, some of them remain uncharacterized. These strains exhibit other unexploited biotechnological important traits, such as lactonases (quorum quenching), toxic metal resistance, and potential for aromatic compound degradation. In summary, this study provides a guideline for further research aimed to implement this organism in biocontrol and bioremediation. Similarly, we highlighted the unanswered questions to be responded in order to gain a deeper understanding of the L. sphaericus TL biology.

Non-ureolytic calcium carbonate precipitation by Lysinibacillus sp. YS11 isolated from the rhizosphere of Miscanthus sacchariflorus

Although microbially induced calcium carbonate precipitation (MICP) through ureolysis has been widely studied in environmental engineering fields, urea utilization might cause environmental problems as a result of ammonia and nitrate production. In this study, many non-ureolytic calcium carbonate-precipitating bacteria that induced an alkaline environment were isolated from the rhizosphere of Miscanthus sacchariflorus near an artificial stream and their ability to precipitate calcium carbonate minerals with the absence of urea was investigated. MICP was observed using a phase-contrast microscope and ion-selective electrode. Only Lysinibacillus sp. YS11 showed MICP in aerobic conditions. Energy dispersive X-ray spectrometry and X-ray diffraction confirmed the presence of calcium carbonate. Field emission scanning electron microscopy analysis indicated the formation of morphologically distinct minerals around cells under these conditions. Monitoring of bacterial growth, pH changes, and Ca²⁺ concentrations under aerobic, hypoxia, and anaerobic conditions suggested that strain YS11 could induce alkaline conditions up to a pH of 8.9 and utilize 95% of free Ca²⁺ only under aerobic conditions. Unusual Ca²⁺ binding and its release from cells were observed under hypoxia conditions. Biofilm and extracellular polymeric substances (EPS) formation were enhanced during MICP. Strain YS11 has resistance at high pH and in high salt concentrations, as well as its spore-forming ability, which supports its potential application for self-healing concrete.

Kinetic and thermodynamic properties of alginate lyase and cellulase co-produced by Exiguobacterium species Alg-S5

In an effort to screen out the alginolytic and cellulolytic bacteria from the putrefying invasive seaweed Sargassum species accumulated off Barbados' coast, a potent bacterial strain was isolated. This bacterium, which simultaneously produced alginate lyase and cellulase, was identified as Exiguobacterium sp. Alg-S5 via the phylogenetic approach targeting the 16S rRNA gene. The co-produced alginate lyase and cellulase exhibited maximal enzymatic activity at pH 7.5 and at 40°C and 45°C, respectively. The Km and Vmax values recorded as 0.91mg/mL and 21.8U/mg-protein, respectively, for alginate lyase, and 10.9mg/mL and 74.6U/mg-protein, respectively, for cellulase. First order kinetic analysis of the thermal denaturation of the co-produced alginate lyase and cellulase in the temperature range from 40°C to 55°C revealed that both the enzymes were thermodynamically efficient by displaying higher activation energy and enthalpy of denaturation. These enzymatic properties indicate the potential industrial importance of this bacterium in algal biomass conversion. This appears to be the first report on assessing the efficacy of a bacterium for the co-production of alginate lyase and cellulase.

Rhizoremediation of cadmium-contaminated soil associated with hydroxamate siderophores isolated from Cd-resistant plant growth-promoting Dietzia maris and Lysinibacillus strains

In search of multitrait plant growth-promoting (PGP) inoculants, we introduced two cadmium-resistant bacterial strains, C4 (PG), C5 (WB), and their consortium C6 (PG × WB) isolated from metal-contaminated industrial waste-fed canal near West Bengal. The test isolates were biochemically characterized and screened in vitro for siderophore production. The infrared spectra revealed the hydroxamate nature of the siderophore produced. Further in green house, siderophore-based seed inoculation with selected PGP isolates exhibited stimulatory effects on seed germination (up to 85.4%), chlorophyll index (22.9 spad unit), shoot and root length (70% and 62.7%), tiller numbers (38.82%), spikelet numbers (52.2%), straw yield (62.2%), grain yield (76.1%), total dry matter of root and shoot (55.56% and 64.4%, respectively), and grain yields (76.1%) of tested wheat cultivars. The 16S rRNA sequencing identified strain PG and WB as Dietzia maris and Lysinibacillus sp. strains. Furthermore, inoculation of C6 (consortium) in both cultivar UP-2565 and KS-227 showed maximum Cd sorption capacity in roots (38.3% and 67.1%) and shoots (68.4% and 67.5%), respectively. Both the strains and their consortium showed a great potential to increase the growth and yield of wheat cultivars, which can also be utilized for rhizoremediation process.

DGGE diversity of manganese mine samples and isolation of a Lysinibacillus sp. efficient in removal of high Mn (II) concentrations

Manganese contamination has become a serious environmental problem in the world and bacterial removal plays an important role in global cycling of manganese. In this study, microorganism distribution within samples from a manganese mine was analyzed with PCR-DGGE technology. The results suggested that Manganese oxidizing bacteria (such as Bacillus, Hyphomicrobiaceae and Erythrobacter) were dominant in the soil. In addition, a Lysinibacillus sp. Isolate, strain MK-1, revealed robust growth at high Mn(II) concentrations up to 1 mM. At that concentration, 55.94% of added Mn(II) was oxidized and 36.23% of the Mn(II) was adsorbed by MK-1(total manganese removal reached 94.67%) after 7 days of culturing. By measuring its metabolic process, the great role of biological adsorption was found. Additionally, the spectroscopic result demonstrated that Mn(III) was an intermediate during the biological oxidation process. These findings increase the knowledge of biological manganese removal mechanisms and show some potentials to the operation of manganese treatment.

Marinococcus salis sp., nov., a moderately halophilic bacterium isolated from a salt marsh

A novel Gram-stain-positive, coccoid-shaped, facultative anaerobic, motile and halophilic bacterium strain 5M^T was isolated from Surajbari in India. Based on the 16S rRNA gene sequence analysis, it was identified as belonging to the genus Marinococcus and was most closely related to Marinococcus luteus KCTC 13214^T (99.3 %, sequence similarity), Marinococcus halotolerans KCTC 19045^T (99.0 %), Marinococcus halophilus LMG 17439^T (98.8 %) and Marinococcus tarijensis LMG 26930^T (98.7 %). However, the DNA-DNA relatedness of strain 5M^T with M. luteus KCTC 13214^T, M. halotolerans KCTC 19045^T, M. halophilus LMG 17439^T and M. tarijensis LMG 26930^T was 42.6 ± 0.8, 48.6 ± 0.8, 40.9 ± 0.8 and 39.8 ± 0.9 %, respectively. Strain 5M^T grows optimally at 5 % (w/v) NaCl, pH 7.5-8.5 and 37 °C. The cell-wall peptidoglycan of strain 5M^T contains meso-diaminopimelic acid. Polar lipids of the strain 5M^T include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a phospholipid and two unknown lipids. The predominant isoprenoid quinone was MK-7. DNA G+C content was 48.9 mol%, and anteiso-C_15:0 (40.9 %) was the predominant fatty acid. The results of phylogenetic, biochemical tests and chemotaxonomic allowed a clear differentiation of strain 5M^T from all of its nearest phylogenetic neighbours, which represents a novel member of the genus Marinococcus, for which the name Marinococcus salis sp., nov., is proposed. The type strain is 5M^T (=KCTC 33743^T = LMG 29101^T = CGMCC 1.15385^T).

Lysinibacillus endophyticus sp. nov., an indole-3-acetic acid producing endophytic bacterium isolated from corn root (Zea mays cv. Xinken-5)

A Gram-positive, aerobic, motile, rod-shaped bacterium, designated strain C9(T), was isolated from surface sterilised corn roots (Zea mays cv. Xinken-5) and found to be able to produce indole-3-acetic acid. A polyphasic taxonomic study was carried out to determine the status of strain C9(T). The major cellular fatty acids were found to contain iso-C15:0, anteiso-C15:0 and anteiso-C17:0, and the only menaquinone was identified as MK-7. The polar lipid profile was found to contain diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and an unidentified lipid. The cell wall peptidoglycan was found to be of the A4α L-Lys-D-Asp type and the whole cell sugar was found to be glucose. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain C9(T) belongs to the genus Lysinibacillus and is closely related to Lysinibacillus chungkukjangi NBRC 108948(T) (98.1 % similarity) and Lysinibacillus sinduriensis DSM 27595(T) (98.0 %). However, the low levels of DNA-DNA relatedness and some differential phenotypic characteristics allowed the strain to be distinguished from its close relatives. Therefore, it is concluded that strain C9(T) represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus endophyticus sp. nov. is proposed. The type strain is C9(T) (=DSM 100506(T) = CGMCC 1.15291(T)).

Microcosm-based interaction studies between members of two ecophysiological groups of bioemulsifier producer and a hydrocarbon degrader from the Indian intertidal zone

Isolates were obtained from intertidal zone site samples from all five western and one eastern coastal states of India and were screened. These ecophysiological groups of aerobic, mesophilic, heterotrophic, sporulating, and bioemulsifier-producing bacteria were from Planococcaceae and Bacillaceae. This is the first report of bioemulsifier production by Sporosarcina spp., Lysinibacillus spp., B. thuringiensis, and B. flexus. In this group, Solibacillus silvestris AM1 was found to produce the highest emulsification activity (62.5 %EI) and the sample that yielded it was used to isolate the ecophysiological group of non-bioemulsifier-producing, hydrocarbon-degrading bacteria (belonging to Chromatiales and Bacillales). These yielded hitherto unreported degrader, Rheinheimera sp. CO6 which was selected for the interaction studies (in a microcosm) with bioemulsifier-producing S. silvestris AM1. The gas chromatographic study of these microcosm experiments revealed increased degradation of benzene, toluene, and xylene (BTX) and the growth of Rheinheimera sp. CO6 in the presence of bioemulsifier produced by S. silvestris AM1. Enhancement of the growth of S. silvestris AM1 in the presence of Rheinheimera sp. CO6 was observed possibly due to reduced toxicity of BTX suggesting mutualistic association between the two. This study elucidates the presence and interaction between enhancers and degraders in a hydrocarbon-contaminated intertidal zone and contributes to the knowledge during application of the two in remediation processes.

Bacteria-based polythene degradation products: GC-MS analysis and toxicity testing

Polythene degradation leads to the production of various by-products depending upon the type of degradation process. The polythene degradation products (PEDP) in the culture supernatant of the two bacteria (Lysinibacillus fusiformis strain VASB14/WL and Bacillus cereus strain VASB1/TS) were analyzed with GC-MS technique. The major by-products in the PEDP in the culture supernatant of L. fusiformis strain VASB14/WL (1,2,3,4 tetra methyl benzene) and B. cereus strain VASB1/TS (1,2,3 trimethyl benzene, 1 ethyl 3,5-dimethyl benzene, 1,4 di methyl 2 ethyl benzene, and dibutyl phthalate) dissolved in diethyl ether were recorded. To assess the environmental applicability of polythene degradation using L. fusiformis strain VASB14/WL and B. cereus strain VASB1/TS at in vitro level. The effect of PEDP produced after 2 months of regular shaking at room temperature on both plants and animal system was studied. No significant decrease in the percent seed germination was recorded with the PEDP of both the bacteria. PEDP produced by L. fusiformis strain VASB14/WL did not report any significant change in germination index (GI) at 10 and 25 %, but least GI (39.66 ± 13.94) was documented at 50 % concentration of PEDP. Highest elongation inhibition rate (53.83 ± 15.71) of Sorghum was also recorded with L. fusiformis and at the same concentration.

Distribution and diversity of biosurfactant-producing bacteria in a wastewater treatment plant

The distribution and diversity of culturable biosurfactant-producing bacteria were investigated in a wastewater treatment plant (WWTP) using the Shannon and Simpson's indices. Twenty wastewater samples were analysed, and from 667 isolates obtained, 32 were classified as biosurfactant producers as they reduced the surface tension of the culture medium (71.1 mN/m), with the lowest value of 32.1 mN/m observed. Certain isolates also formed stable emulsions with diesel, kerosene and mineral oils. The 16S ribosomal RNA (rRNA) analysis classified the biosurfactant producers into the Aeromonadaceae, Bacillaceae, Enterobacteriaceae, Gordoniaceae and the Pseudomonadaceae families. In addition, numerous isolates carried the surfactin 4'-phosphopantetheinyl transferase (sfp), rhamnosyltransferase subunit B (rhlB) and bacillomycin C (bamC) genes involved in the biosynthesis of surfactin, rhamnolipid and bacillomycin, respectively. While, biosurfactant-producing bacteria were found at all sampling points in the WWTP, the Simpson's diversity (1 - D) and the Shannon-Weaver (H) indices revealed an increase in bacterial diversity in the influent samples (0.8356 and 2.08), followed by the effluent (0.8 and 1.6094) and then the biological trickling filter (0.7901 and 1.6770) samples. Numerous biosurfactant-producing bacteria belonging to diverse genera are thus present throughout a WWTP.

[Microbiological characteristics of a Lysinibacillus strain isolated from Populous euphratica]

OBJECTIVE

The aim of this study was to identify the microbiological characteristics of a Lysinibacillus strain isolated from storage liquid in the stems of Populus euphratica trees.

METHODS

Bacterial morphology and cultivation characteristics were studied by conventional cultivation and dyeing method. Biochemical characteristics, fatty acid components, menaquinone, polar lipids, phylogenetic analyses of 16S rRNA, determination of (G + C) mol% content and DNA- DNA hybridization were studied by polyphasic taxonomic approach.

RESULTS

Strain ML-64 is Gram-positive, endospore-forming and rod-shaped. Colonies are pale-yellow, circular and entire margin. Temperature range for growth is between 10 and 45 degrees C (optimum at 37 degrees C ). The pH range for growth is between 6. 0 and 9.0 (optimum at 7.0). NaCl concentration range for growth is between 0 and 6% (optimum 3% ). Cells were positive for lipid esterase, Arginine dihydrolase, urease and Voges-Proskauer test. No sugars were fermented in the API 50CH strips. L-Serine, Methyl Pyruvate, α-Keto-Butyric, Acetoacetic Acid were oxidized. Resistant to polymyxin b (30 μg), novobiocin (30 μg), peillin G (10 U). 16S rRNA gene sequence demonstrated that strain ML-64 was closely related to Lysinibacillus chungkukjangi 2RL3-2T (100%) , Lysinibacillus sinduriensis BLB-1T (99.1%). DNA-DNA relatedness were 82% and 50. 9% with Lysinibacillus chungkukjangi 2RL3-2T and Lysinibacillus massiliensis CIP108446T, respectively. The genomic DNA G + C content of strain ML-64 was 36. 8% (mol). Major fatty acids were iso-C,,, (55. 05% ) and anteiso-C15,0 (20. 70% ). The predominant menaquinone is MK-7. Based on the phenotypic phylogenetic and genotypic analyses, the strain ML-64 is concluded to represent a new mutant strain of the Lysinibacillus chungkukjangi species, GenBank accession number is KC609752.

CONCLUSION

As an endophytic bacterium of Populus euphratica, genomic structure of the strain ML-64 was greatly differentiated from the closest strain L. chungkukjangi, and suitably adapted to the endophytic environment of Populus euphratica.

Conductive iron oxide minerals accelerate syntrophic cooperation in methanogenic benzoate degradation

Recent studies have suggested that conductive iron oxide minerals can facilitate syntrophic metabolism of the methanogenic degradation of organic matter, such as ethanol, propionate and butyrate, in natural and engineered microbial ecosystems. This enhanced syntrophy involves direct interspecies electron transfer (DIET) powered by microorganisms exchanging metabolic electrons through electrically conductive minerals. Here, we evaluated the possibility that conductive iron oxides (hematite and magnetite) can stimulate the methanogenic degradation of benzoate, which is a common intermediate in the anaerobic metabolism of aromatic compounds. The results showed that 89-94% of the electrons released from benzoate oxidation were recovered in CH4 production, and acetate was identified as the only carbon-bearing intermediate during benzoate degradation. Compared with the iron-free controls, the rates of methanogenic benzoate degradation were enhanced by 25% and 53% in the presence of hematite and magnetite, respectively. This stimulatory effect probably resulted from DIET-mediated methanogenesis in which electrons transfer between syntrophic partners via conductive iron minerals. Phylogenetic analyses revealed that Bacillaceae, Peptococcaceae, and Methanobacterium are potentially involved in the functioning of syntrophic DIET. Considering the ubiquitous presence of iron minerals within soils and sediments, the findings of this study will increase the current understanding of the natural biological attenuation of aromatic hydrocarbons in anaerobic environments.

Therapeutic intervention and molecular characterizations of bacteriocin producing Lysinibacillus sp., nov., isolated from food sample

Many bacteriocins from Lactobacilli have been reported as immunostimulatory, preservatives, anticancerous and biocontroling. However, antimicrobial potential of Lysinibacillus is not much reported. In this study, an attempt was made to isolate and anticipate therapeutic potential of Lysinibacillus from spoiled food sample. We screened 125 Lactobacilli for their antagonistic nature against food borne and disease causing bacterial and fungal pathogens. Among them, one Bacillus was phenotypically, and 16S rRNA based, molecularly identified as Lysinibacillus species given with accession numbers JX416855 in NCBI. The type strain JX416855 has shown the 99% identity with the Lysinibacillus fusiformis, Lysinibacillus sphaericus and Lysinibacillus xylanilyticus. It was amylase, protease, gelatinase, nitrate reductase and urease negative and catalase positive. The growth conditions and bacteriocin activity were found optimum with MRS media at pH 7-10, Temp-35-40°C and salt tolerance at 1-3% which was optimized with MRS broth at pH 7.4, 37 °C, 1.5% NaCl for 48 h in shaking conditions @ 100 rpm. The isolate showed broad-spectrum antibacterial activity against gram positive (10-13 mm) and gram-negative (20mm) bacteria. It also strongly inhibited to fungus Aspergillus, Fusarium and Trichoderma. Bacteriocin from 60% ammonium sulphate fraction strongly inhibited to gram-negative R. planticola and Pseudomonas aeruginosa, which showed three protein bands of high molecular weight (nearly 40-70 kD) by SDS-PAGE analysis.