Cold-adapted Exiguobacterium sibiricum K1 as a potential bioinoculant in cold regions: Physiological and genomic elucidation of biocontrol and plant growth promotion

The scarcity of soil nutrient availability under cold conditions of Himalayan regions needs a sustainable approach for better crop yields. The cold-adapted bacteria, Exiguobacterium sibiricum K1, with the potential to produce several plant growth-promoting (PGP) attributes, nitrogen fixation, indole acetic acid production, phosphate and potassium solubilization at 10 °C can provide an opportunity to promote crop yield improvement in an eco-friendly way under cold conditions. The bacterium also exhibited biocontrol activity against two phytopathogens and produced siderophore (53.0 ± 0.5 % psu). The strain's PGP properties were investigated using a spinach-based bioassay under controlled conditions. The bacterized seeds showed a notable increase in germination rate (23.2 %), shoot length (65.3 %), root length (56.6 %), leaf area (73.7 %), number of leaflets (65.2 %), and dry matter (65.2 %). Additionally, the leaf analysis indicated elevated chlorophyll pigments, i.e., chlorophyll a (55.5 %), chlorophyll b (42.8 %), carotenoids (35.2 %), percentage radical scavenging activity (47.4 %), and leaf nutrient uptake such as nitrogen (23.4 %), calcium (60.8 %), potassium (62.3 %), and magnesium (28.9 %). Moreover, the whole-genome sequencing and genome mining endorsed various biofertilisation-related genes, including genes for potassium and phosphate solubilization, iron and nitrogen acquisition, carbon dioxide fixation, and biocontrol ability of Exiguobacterium sibiricum K1. Overall, this study highlights the role of Exiguobacterium sibiricum K1 as a potential bioinoculant for improving crop yield under cold environments.

Association between organic nitrogen substrates and the optical purity of D-lactic acid during the fermentation by Sporolactobacillus terrae SBT-1

The development of biotechnological lactic acid production has attracted attention to the potential production of an optically pure isomer of lactic acid, although the relationship between fermentation and the biosynthesis of highly optically pure D-lactic acid remains poorly understood. Sporolactobacillus terrae SBT-1 is an excellent D-lactic acid producer that depends on cultivation conditions. Herein, three enzymes responsible for synthesizing optically pure D-lactic acid, including D-lactate dehydrogenase (D-LDH; encoded by ldhDs), L-lactate dehydrogenase (L-LDH; encoded by ldhLs), and lactate racemase (Lar; encoded by larA), were quantified under different organic nitrogen sources and concentration to study the relationship between fermentation conditions and synthesis pathway of optically pure lactic acid. Different organic nitrogen sources and concentrations significantly affected the quantity and quality of D-lactic acid produced by strain SBT-1 as well as the synthetic optically pure lactic acid pathway. Yeast extract is a preferred organic nitrogen source for achieving high catalytic efficiency of D-lactate dehydrogenase and increasing the transcription level of ldhA2, indicating that this enzyme plays a major role in D-lactic acid formation in S. terrae SBT-1. Furthermore, lactate racemization activity could be regulated by the presence of D-lactic acid. The results of this study suggest that specific nutrient requirements are necessary to achieve a stable and highly productive fermentation process for the D-lactic acid of an individual strain.

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.

Cellulonodin-2 and Lihuanodin: Lasso Peptides with an Aspartimide Post-Translational Modification

Lasso peptides are a family of ribosomally synthesized and post-translationally modified peptides (RiPPs) defined by their threaded structure. Besides the class-defining isopeptide bond, other post-translational modifications (PTMs) that further tailor lasso peptides have been previously reported. Using genome mining tools, we identified a subset of lasso peptide biosynthetic gene clusters (BGCs) that are colocalized with genes encoding protein l-isoaspartyl methyltransferase (PIMT) homologues. PIMTs have an important role in protein repair, restoring isoaspartate residues formed from asparagine deamidation to aspartate. Here we report a new function for PIMT enzymes in the post-translational modification of lasso peptides. The PIMTs associated with lasso peptide BGCs first methylate an l-aspartate side chain found within the ring of the lasso peptide. The methyl ester is then converted into a stable aspartimide moiety, endowing the lasso peptide ring with rigidity relative to its unmodified counterpart. We describe the heterologous expression and structural characterization of two examples of aspartimide-modified lasso peptides from thermophilic Gram-positive bacteria. The lasso peptide cellulonodin-2 is encoded in the genome of actinobacterium Thermobifida cellulosilytica, while lihuanodin is encoded in the genome of firmicute Lihuaxuella thermophila. Additional genome mining revealed PIMT-containing lasso peptide BGCs in 48 organisms. In addition to heterologous expression, we have reconstituted PIMT-mediated aspartimide formation in vitro, showing that lasso peptide-associated PIMTs transfer methyl groups very rapidly as compared to canonical PIMTs. Furthermore, in stark contrast to other characterized lasso peptide PTMs, the methyltransferase functions only on lassoed substrates.

Performance evaluation of a continuous packed bed bioreactor: Bio-kinetics and external mass transfer study

The biodegradation of naphthalene using low-density polyethylene (LDPE) immobilized Exiguobacterium sp. RKS3 (MG696729) in a packed bed bioreactor (PBBR) was studied. The performance of a continuous PBBR was evaluated at different inlet flow rates (IFRs) (20-100 mL/h) under 64 days of operation. The maximum naphthalene removal efficiency (RE) was found at low IFR, and it further decreased with increasing IFRs. In a continuous PBBR, the external mass transfer (EMT) aspect was analysed at various IFRs, and experimental data were interrelated between Colburn factor (J_D) and Reynolds number (N_Re) as [Formula: see text] . A new correlation [Formula: see text] was obtained to predict the EMT aspect of naphthalene biodegradation. Andrew-Haldane model was used to evaluate the bio-kinetic parameters of naphthalene degradation, and kinetic constant ν_max, J_s, and J_i were found as 0.386 per day, 13.6 mg/L, and 20.54 mg/L, respectively.

Inducible Antibacterial Activity in the Bacillales by Triphenyl Tetrazolium Chloride

The world is in the midst of an antimicrobial resistance crisis, driving a need to discover novel antibiotic substances. Using chemical cues as inducers to unveil a microorganism's full metabolic potential is considered a successful strategy. To this end, we investigated an inducible antagonistic behavior in multiple isolates of the order Bacillales, where large inhibition zones were produced against Ralstonia solanacearum only when grown in the presence of the indicator triphenyl tetrazolium chloride (TTC). This bioactivity was produced in a TTC-dose dependent manner. Escherichia coli and Staphylococcus sp. isolates were also inhibited by Bacillus sp. strains in TTC presence, to a lesser extent. Knockout mutants and transcriptomic analysis of B. subtilis NCIB 3610 cells revealed that genes from the L-histidine biosynthetic pathway, the purine, pyrimidine de novo synthesis and salvage and interconversion routes, were significantly upregulated. Chemical space studied through metabolomic analysis, showed increased presence of nitrogenous compounds in extracts from induced bacteria. The metabolites orotic acid and L-phenylalaninamide were tested against R. solanacearum, E. coli, Staphylococcus sp. and B. subtilis, and exhibited activity against pathogens only in the presence of TTC, suggesting a biotransformation of nitrogenous compounds in Bacillus sp. cells as the plausible cause of the inducible antagonistic behavior.

Mobilization and transformation of arsenic from ternary complex OM-Fe(III)-As(V) in the presence of As(V)-reducing bacteria

Organic matter (OM) was proved to have a high affinity for arsenic (As) in the presence of ferric iron (Fe(III)), the formed ternary complex OM-Fe(III)-As(V) were frequently studied before; however, the mobilization and transformation of As from OM-Fe(III)-As(V) in the presence of As(V)-reducing bacteria remains unclear. Two different strains (Desulfitobacterium sp. DJ-3, Exiguobacterium sp. DJ-4) were incubated with OM-Fe(III)-As(V) to assess the biotransformation of As and Fe. Results showed that Desulfitobacterium sp. DJ-3 could substantially stimulate the reduction and release of OM-Fe complexed As(V) and resulted in notable As(III) release (30 mg/L). The linear combination fitting result of k³-weighted As K-edge EXAFS spectra showed that 56% of OM-Fe-As(V) was transformed to OM-Fe-As(III) after 144 h. Besides, strain DJ-3 could also reduce OM complexed Fe(III), which lead to the decomposition of ternary complex and the release of 11.8 mg/g Fe(II), this microbial Fe(III) reduction process has resulted in 11% more As liberation from OM-Fe(III)-As(V) than without bacteria. In contrast, Exiguobacterium sp. DJ-4 could only reduce free As(V) but cannot stimulate As release from the complex. Our study provides the first evidence for microbial As reduction and release from ternary complex OM-Fe(III)-As(V), which could be of great importance in As geochemical circulation.

Steps Toward High-Performance PLA: Economical Production of d-Lactate Enabled by a Newly Isolated Sporolactobacillus terrae Strain

Optically pure d-lactate production has received much attention for its critical role in high-performance polylactic acid production. However, the current technology can hardly meet the comprehensive demand of industrialization on final titer, productivity, optical purity, and raw material costs. Here, an efficient d-lactate producer strain, Sporolactobacillus terrae (S. terrae) HKM-1, is isolated for d-lactate production. The strain HKM-1 shows extremely high d-lactate fermentative capability by using peanut meal, soybean meal, or corn steep liquor powder as a sole nitrogen source; the final titers (205.7 g L-1 , 218.9 g L-1 , and 193.9 g L-1 , respectively) and productivities (5.56 g L-1  h-1 , 5.34 g L-1  h-1 , and 3.73 g L-1  h-1 , respectively) of d-lactate reached the highest level ever reported. A comparative genomic analysis between S. terrae HKM-1 and previously reported d-lactate high-producing Sporolactobacillus inulinus (S. inulinus) CASD is conducted. The results show that many unrelated genetic features may contribute to the superior performance in d-lactate production of S. terrae HKM-1. This d-lactate producer HKM-1, along with its fermentation process, is promising for sustainable d-lactate production by using agro-industrial wastes.

Endo-symbiont mediated synthesis of gold nanobactericides and their activity against human pathogenic bacteria

Synthesis of gold nanobactericides (AuNBs) were achieved by treating 1mM chloroaurate with cell free supernatant of Aneurinibacillus migulanus. Formation of AuNBs was initially was monitored with change in colour to ruby red. Further confirmation was assessed with UV-visible spectra with maximum absorption occurring at 510nm. Transmission electron microscopy (TEM) analysis revealed the polydispersity of AuNBs with size distribution ranging from 10 to 60nm with an average size of 30nm. Crystalline nature was studied using X-ray diffraction which exhibited characteristic peaks indexed to Bragg's reflection at 2θ angle which confers (111), (200), (220), and (311) planes suggesting AuNBs were face-centred cubic. Fourier transform infrared spectroscopy (FTIR) analysis revealed absorption peaks occurring at 3341cm^-1, 1635cm^-1 and 670cm^-1 which corresponds to functional groups attributing to synthesis. The antibacterial efficacy of AuNBs was tested against selective human pathogenic bacteria and activity was measured as zone of inhibition by using disc and well diffusion. Bactericidal activity was interpreted with standard antibiotics gentamicin and kanamycin. Micro broth dilution assay expressed the minimal concentration of AuNBs to inhibit the growth of test pathogens. Highest activity was observed against Pseudomonas aeruginosa (MTCC 7903) with 21.00±0.57mm compared to other pathogens. The possible mode of action of AuNBs on DNA was carried out with in vitro assay as preliminary test against pathogenic DNA isolated from P. aeruginosa. Further studies will be interesting enough to reveal the exact interactive mechanism of AuNBs with DNA. Overall study contributes towards biogenic synthesis of AuNBs as one of the alternative in combating drug resistant pathogens.

Combined utilization of nutrients and sugar derived from wheat bran for d-Lactate fermentation by Sporolactobacillus inulinus YBS1-5

To decrease d-Lactate production cost, wheat bran, a low-cost waste of milling industry, was selected as the sole feedstock. First, the nutrients were recovered from wheat bran by acid protease hydrolysis. Then, cellulosic hydrolysates were prepared from protease-treated samples after acid pretreatment and enzymatic saccharification. The combined use of nutrients and hydrolysates as nitrogen and carbon sources for fermentation by S. inulinus YB1-5 resulted in d-Lactate levels of 99.5g/L, with an average production efficiency of 1.94g/L/h and a yield of 0.89g/g glucose. Moreover, fed-batch simultaneous saccharification and fermentation process at 40°C, 20% (w/v) solid loading and 20FPU/g solid cellulase concentration was obtained. d-Lactate concentrations, yield, productivity, and optical purity were 87.3g/L, 0.65g/g glucose, 0.81g/L/h and 99.1%, respectively. This study provided a feasible procedure that can help produce cellulosic d-Lactate using agricultural waste without external nutrient supplementation.

Tricalcium phosphate solubilization and nitrogen fixation by newly isolated Aneurinibacillus aneurinilyticus CKMV1 from rhizosphere of Valeriana jatamansi and its growth promotional effect

Aneurinibacillus aneurinilyticus strain CKMV1 was isolated from rhizosphere of Valeriana jatamansi and possessed multiple plant growth promoting traits like production of phosphate solubilization (260 mg/L), nitrogen fixation (202.91 nmol ethylene mL⁻¹ h⁻¹), indole-3-acetic acid (IAA) (8.1 μg/mL), siderophores (61.60%), HCN (hydrogen cyanide) production and antifungal activity. We investigated the ability of isolate CKMV1 to solubilize insoluble P via mechanism of organic acid production. High-performance liquid chromatography (HPLC) study showed that isolate CKMV1 produced mainly gluconic (1.34%) and oxalic acids. However, genetic evidences for nitrogen fixation and phosphate solubilization by organic acid production have been reported first time for A. aneurinilyticus strain CKMV1. A unique combination of glucose dehydrogenase (gdh) gene and pyrroloquinoline quinone synthase (pqq) gene, a cofactor of gdh involved in phosphate solubilization has been elucidated. Nitrogenase (nif H) gene for nitrogen fixation was reported from A. aneurinilyticus. It was notable that isolate CKMV1 exhibited highest antifungal against Sclerotium rolfsii (93.58%) followed by Fusarium oxysporum (64.3%), Dematophora necatrix (52.71%), Rhizoctonia solani (91.58%), Alternaria sp. (71.08%) and Phytophthora sp. (71.37%). Remarkable increase was observed in seed germination (27.07%), shoot length (42.33%), root length (52.6%), shoot dry weight (62.01%) and root dry weight (45.7%) along with NPK (0.74, 0.36, 1.82%) content of tomato under net house condition. Isolate CKMV1 possessed traits related to plant growth promotion, therefore, could be a potential candidate for the development of biofertiliser or biocontrol agent and this is the first study to include the Aneurinibacillus as PGPR.

D-Lactic acid production by Sporolactobacillus inulinus YBS1-5 with simultaneous utilization of cottonseed meal and corncob residue

d-Lactic acid, is an important organic acid produced from agro-industrial wastes by Sporolactobacillus inulinus YBS1-5 was investigated to reduce the raw material cost of fermentation. The YBS1-5 strain could produce d-lactic acid by using cottonseed meal as the sole nitrogen source. For efficient utilization, the cottonseed meal was enzymatically hydrolyzed and simultaneously utilized during d-lactic acid fermentation. Corncob residues are rich in cellulose and can be enzymatically hydrolyzed without pretreatment. The hydrolysate of this lignocellulosic waste could be utilized by strain YBS1-5 as a carbon source for d-lactic acid production. Under optimal conditions, a high d-lactic acid concentration (107.2g/L) was obtained in 7-L fed-batch fermenter, with an average productivity of 1.19g/L/h and a yield of 0.85g/g glucose. The optical purity of d-lactic acid in the broth was 99.2%. This study presented a new approach for low-cost production of d-lactic acid for an industrial application.

The D-Lactate Dehydrogenase from Sporolactobacillus inulinus Also Possessing Reversible Deamination Activity

Hydroxyacid dehydrogenases are responsible for the conversion of 2-keto acids to 2-hydroxyacids and have a wide range of biotechnological applications. In this study, a D-lactate dehydrogenase (D-LDH) from a Sporolactobacillus inulinus strain was experimentally verified to have both the D-LDH and glutamate dehydrogenase (GDH) activities (reversible deamination). The catalytic mechanism was demonstrated by identification of key residues from the crystal structure analysis and site-directed mutagenesis. The Arg²³⁴ and Gly⁷⁹ residues of this enzyme play a significant role in both D-LDH and GDH activities. His²⁹⁵ and Phe²⁹⁸ in DLDH744 were identified to be key residues for lactate dehydrogenase (LDH) activity only whereas Tyr¹⁰¹ is a unique residue that is critical for GDH activity. Characterization of the biochemical properties contributes to understanding of the catalytic mechanism of this novel D-lactate dehydrogenase enzyme.

Halotolerant PGPRs Prevent Major Shifts in Indigenous Microbial Community Structure Under Salinity Stress

The resilience of soil microbial populations and processes to environmental perturbation is of increasing interest as alteration in rhizosphere microbial community dynamics impacts the combined functions of plant-microbe interactions. The present study was conducted to investigate the effect of inoculation with halotolerant rhizobacteria Bacillus pumilus (STR2), Halomonas desiderata (STR8), and Exiguobacterium oxidotolerans (STR36) on the indigenous root-associated microbial (bacterial and fungal) communities in maize under non-saline and salinity stress. Plants inoculated with halotolerant rhizobacteria recorded improved growth as illustrated by significantly higher shoot and root dry weight and elongation in comparison to un-inoculated control plants under both non-saline and saline conditions. Additive main effect and multiplicative interaction ordination analysis revealed that plant growth promoting rhizobacteria (PGPR) inoculations as well as salinity are major drivers of microbial community shift in maize rhizosphere. Salinity negatively impacts microbial community as analysed through diversity indices; among the PGPR-inoculated plants, STR2-inoculated plants recorded higher values of diversity indices. As observed in the terminal-restriction fragment length polymorphism analysis, the inoculation of halotolerant rhizobacteria prevents major shift of the microbial community structure, thus enhancing the resilience capacity of the microbial communities.

Biodegradation of 4-chloroindole by Exiguobacterium sp. PMA

Exiguobacterium sp. PMA utilized 4-chloroindole as its sole source of carbon and energy. The effect of initial concentrations of substrate on the 4-chloroindole degradation was studied and observed that strain PMA was capable of degrading 4-chloroindole up to concentration of 0.5mM. The degradation pathway of 4-chloroindole was studied for Exiguobacterium sp. PMA based on metabolites identified by gas chromatography-mass spectrometry. 4-Chloroindole was initially dehalogenated to indole that was further degraded via isatin, anthranilic acid, and salicylic acid. The potential of strain PMA to degrade 4-chloroindole in soil was monitored using soil microcosms, and it was observed that the cells of strain PMA efficiently degraded 4-chloroindole in the soil. The results of microcosm studies show that strain PMA may be used for bioremediation of 4-chloroindole-contaminated sites. This is the first report of the bacterial degradation of 4-chloroindole.

Conversion of steam-exploded cedar into ethanol using simultaneous saccharification, fermentation and detoxification process

In this study, we investigated the simultaneous saccharification, fermentation and detoxification SSDF process of steam-exploded cedar using a detoxification microorganism, Ureibacillus thermosphaericus A1, to facilitate efficient ethanol production. Steam explosion was applied as a pretreatment before enzymatic saccharification followed by alcohol fermentation. The highest glucose conversion rate was observed in the sample pretreated with a steam pressure of 45atm for 5min. Alcohol production by a heat-tolerant yeast, Saccharomyces cerevisiae BA11, was inhibited strongly by inhibitory materials present in the steam-exploded cedar, such as formic acid, furfural, and 5-hydroxymethylfurfural. The maximum amount of ethanol, i.e., 0.155g ethanol/g dry steam-exploded cedar, which corresponded to 74% of the theoretical ethanol yield, was obtained using the SSDF when U. thermosphaericus A1 degraded the inhibitory materials. A fed batch SSDF culture, in which U. thermosphaericus A1 was used to maintain low concentrations of inhibitory materials, was effective for increasing the ethanol concentration.

Biodegradation of complex hydrocarbons in spent engine oil by novel bacterial consortium isolated from deep sea sediment

Complex hydrocarbon and aromatic compounds degrading marine bacterial strains were isolated from deep sea sediment after enrichment on spent engine (SE) oil. Phenotypic characterization and phylogenetic analysis of 16S rRNA gene sequences showed the isolates were related to members of the Pseudoalteromonas sp., Ruegeria sp., Exiguobacterium sp. and Acinetobacter sp. Biodegradation using 1% (v/v) SE oil with individual and mixed strains showed the efficacy of SE oil utilization within a short retention time. The addition of non-ionic surfactant 0.05% (v/v) Tween 80 as emulsifying agent enhanced the solubility of hydrocarbons and renders them more accessible for biodegradation. The degradation of several compounds and the metabolites formed during the microbial oxidation process were confirmed by Fourier transform infrared spectroscopy and Gas chromatography-mass spectrometry analyses. The potential of this consortium to biodegrade SE oil with and without emulsifying agent provides possible application in bioremediation of oil contaminated marine environment.

Biodegradation of shrimp biowaste by marine Exiguobacterium sp. CFR26M and concomitant production of extracellular protease and antioxidant materials: production and process optimization by response surface methodology

Twelve marine bacterial cultures were screened for extracellular protease activity, and the bacterium CFR26M which exhibited the highest activity on caseinate agar plate was identified as an Exiguobacterium sp. Significant amount of extracellular protease (5.9 ± 0.3 U/ml) and antioxidant materials, measured as 2,2'-diphenyl picrylhydrazyl (DPPH) radical scavenging activity (44.4 ± 0.5 %), was produced by CFR26M in submerged fermentation using a shrimp biowaste medium. Response surface methodology (RSM) was employed to optimize the process variables for maximum production of protease and antioxidant materials by CFR26M. Among the seven variables screened by two-level 2**(7-2) fractional factorial design, the concentration of shrimp biowaste, sugar, and phosphate was found to be significant (p ≤ 0.05). The optimum levels of these variables were determined by employing the central composite design (CCD) of RSM. The coefficient of determination (R (2)) values of 0.9039 and 0.8924 for protease and antioxidant, respectively, indicates the accuracy of the CCD models. The optimum levels of shrimp biowaste, sugar, and phosphate were 21.2, 10.5, and 2.3 % (w/v) for production of protease and 28.8, 12, and 0.32 % (w/v) for production of antioxidant material, respectively. The concentration of shrimp biowaste, sugar, and phosphate had linear and quadratic effect on both protease and antioxidant productions. RSM optimization yielded 6.3-fold increases in protease activity and 1.6-fold in antioxidant material production. The crude protease of CFR26M had a maximum activity at 32 ± 2 °C with pH 7.6. This is the first report on the use of marine Exiguobacterium sp. for concomitant production of protease and antioxidant materials from shrimp biowaste.

Principles of ion recognition in RNA: insights from the group II intron structures

Metal ions promote both RNA folding and catalysis, thus being essential in stabilizing the structure and determining the function of large RNA molecules, including group II introns. The latter are self-splicing metalloribozymes, containing a heteronuclear four-metal-ion center within the active site. In addition to these catalytic ions, group II introns bind many other structural ions, including delocalized ions that bind the RNA diffusively and well-ordered ions that bind the RNA tightly with high occupancy. The latter ions, which can be studied by biophysical methods, have not yet been analyzed systematically. Here, we compare crystal structures of the group IIC intron from Oceanobacillus iheyensis and classify numerous site-bound ions, which are primarily localized in the intron core and near long-range tertiary contacts. Certain ion-binding sites resemble motifs observed in known RNA structures, while others are idiosyncratic to the group II intron. Particularly interesting are (1) ions proximal to the active site, which may participate in splicing together with the catalytic four-metal-ion center, (2) organic ions that bind regions predicted to interact with intron-encoded proteins, and (3) unusual monovalent ions bound to GU wobble pairs, GA mismatches, the S-turn, the tetraloop-receptor, and the T-loop. Our analysis extends the general principles by which ions participate in RNA structural organization and it will aid in the determination and interpretation of future RNA structures.

Decolourisation of Acid Orange 7 recalcitrant auto-oxidation coloured by-products using an acclimatised mixed bacterial culture

This study focuses on the biodegradation of recalcitrant, coloured compounds resulting from auto-oxidation of Acid Orange 7 (AO7) in a sequential facultative anaerobic-aerobic treatment system. A novel mixed bacterial culture, BAC-ZS, consisting of Brevibacillus panacihumi strain ZB1, Lysinibacillus fusiformis strain ZB2, and Enterococcus faecalis strain ZL bacteria were isolated from environmental samples. The acclimatisation of the mixed culture was carried out in an AO7 decolourised solution. The acclimatised mixed culture showed 98 % decolourisation within 2 h of facultative anaerobic treatment using yeast extract and glucose as co-substrate. Subsequent aerobic post treatment caused auto-oxidation reaction forming dark coloured compounds that reduced the percentage decolourisation to 73 %. Interestingly, further agitations of the mixed culture in the solution over a period of 48 h significantly decolourise the coloured compounds and increased the decolourisation percentage to 90 %. Analyses of the degradation compounds using UV-visible spectrophotometer, Fourier transform infrared spectroscopy (FTIR) and high performance liquid chromatography (HPLC) showed complete degradation of recalcitrant AO7 by the novel BAC-ZS. Phytotoxicity tests using Cucumis sativus confirmed the dye solution after post aerobic treatment were less toxic compared to the parent dye. The quantitative real-time PCR revealed that E. faecalis strain ZL was the dominant strain in the acclimatised mix culture.

Microbial community structure in a thermophilic aerobic digester used as a sludge pretreatment process for the mesophilic anaerobic digestion and the enhancement of methane production

An effective two-stage sewage sludge digestion process, consisting of thermophilic aerobic digestion (TAD) followed by mesophilic anaerobic digestion (MAD), was developed for efficient sludge reduction and methane production. Using TAD as a biological pretreatment, the total volatile suspended solid reduction (VSSR) and methane production rate (MPR) in the MAD reactor were significantly improved. According to denaturing gradient gel electrophoresis (DGGE) analysis, the results indicated that the dominant bacteria species such as Ureibacillus thermophiles and Bacterium thermus in TAD were major routes for enhancing soluble organic matter. TAD pretreatment using a relatively short SRT of 1 day showed highly increased soluble organic products and positively affected an increment of bacteria populations which performed interrelated microbial metabolisms with methanogenic species in the MAD; consequently, a quantitative real-time PCR indicated greatly increased Methanosarcinales (acetate-utilizing methanogens) in the MAD, resulting in enhanced methane production.

Production of bioethanol from fermented sugars of sugarcane bagasse produced by lignocellulolytic enzymes of Exiguobacterium sp. VSG-1

Exiguobacterium sp. VSG-1 was isolated from the soil sample and characterized for the production of lignocellulolytic enzymes. Production of these enzymes by the strain VSG-1 was carried out using steam-exploded sugarcane bagasse (SCB) and found to secrete cellulase, pectinase, mannanase, xylanase, and tannase. The growth and enzyme production were found to be optimum at pH 9.0 and 37 °C. Upon steam explosion of SCB, the cellulose increased by 42 %, whereas hemicelluloses and lignin decreased by 40 and 62 %, respectively. Enzymatic hydrolysis of steam-exploded SCB yielded 640 g/l of total sugars. Fermentation of sugars produced from pretreated SCB was carried out by using Saccharomyces cerevisiae at pH 5.0 and 30 °C. The alcohol produced was calculated and found to be 62.24 g/l corresponding to 78 % of the theoretical yield of ethanol. Hence, the strain VSG-1 has an industrial importance for the production of fermentable sugars for biofuels.

Exiguobacterium oxidotolerans, a halotolerant plant growth promoting rhizobacteria, improves yield and content of secondary metabolites in Bacopa monnieri (L.) Pennell under primary and secondary salt stress

Brahmi (Bacopa monnieri), an integral component of Indian Ayurvedic medicine system, is facing a threat of extinction owing to the depletion of its natural populations. The present study investigates the prospective of exploitation of halotolerant plant growth promoting rhizobacteria (PGPR) in utilising the salt stressed soils for cultivation of B. monnieri. The effects of two salt tolerant PGPR, Bacillus pumilus (STR2) and Exiguobacterium oxidotolerans (STR36) on the growth and content of bacoside-A, an important pharmaceutical compound in B. monnieri, were investigated under primary and secondary salinity conditions. The herb yields of un-inoculated plants decreased by 48 % under secondary salinization and 60 % under primary salinization than the non salinised plants. Among the rhizobacteria treated plants, E. oxidotolerans recorded 109 and 138 %, higher herb yield than non-inoculated plants subjected to primary and secondary salinity respectively. E. oxidotolerans inoculated plants recorded 36 and 76 % higher bacoside-A content under primary and secondary salinity respectively. Higher levels of proline content and considerably lower levels of lipid peroxidation were noticed when the plants were inoculated with PGPR under all salinity regimes. From the results of this investigation, it can be concluded that, the treatments with salt tolerant PGPR can be a useful strategy in the enhancement of biomass yield and saponin contents in B. monnieri, as besides being an eco-friendly approach; it can also be instrumental in cultivation of B. monnieri in salt stressed environments.

Exiguobacterium oxidotolerans, a halotolerant plant growth promoting rhizobacteria, improves yield and content of secondary metabolites in Bacopa monnieri (L.) Pennell under primary and secondary salt stress

Brahmi (Bacopa monnieri), an integral component of Indian Ayurvedic medicine system, is facing a threat of extinction owing to the depletion of its natural populations. The present study investigates the prospective of exploitation of halotolerant plant growth promoting rhizobacteria (PGPR) in utilising the salt stressed soils for cultivation of B. monnieri. The effects of two salt tolerant PGPR, Bacillus pumilus (STR2) and Exiguobacterium oxidotolerans (STR36) on the growth and content of bacoside-A, an important pharmaceutical compound in B. monnieri, were investigated under primary and secondary salinity conditions. The herb yields of un-inoculated plants decreased by 48 % under secondary salinization and 60 % under primary salinization than the non salinised plants. Among the rhizobacteria treated plants, E. oxidotolerans recorded 109 and 138 %, higher herb yield than non-inoculated plants subjected to primary and secondary salinity respectively. E. oxidotolerans inoculated plants recorded 36 and 76 % higher bacoside-A content under primary and secondary salinity respectively. Higher levels of proline content and considerably lower levels of lipid peroxidation were noticed when the plants were inoculated with PGPR under all salinity regimes. From the results of this investigation, it can be concluded that, the treatments with salt tolerant PGPR can be a useful strategy in the enhancement of biomass yield and saponin contents in B. monnieri, as besides being an eco-friendly approach; it can also be instrumental in cultivation of B. monnieri in salt stressed environments.

The order Bacillales hosts functional homologs of the worrisome cfr antibiotic resistance gene

The cfr gene encodes the Cfr methyltransferase that methylates a single adenine in the peptidyl transferase region of bacterial ribosomes. The methylation provides resistance to several classes of antibiotics that include drugs of clinical and veterinary importance. This paper describes a first step toward elucidating natural residences of the worrisome cfr gene and functionally similar genes. Three cfr-like genes from the order Bacillales were identified from BLAST searches and cloned into plasmids under the control of an inducible promoter. Expression of the genes was induced in Escherichia coli, and MICs for selected antibiotics indicate that the cfr-like genes confer resistance to PhLOPSa (phenicol, lincosamide, oxazolidinone, pleuromutilin, and streptogramin A) antibiotics in the same way as the cfr gene. In addition, modification at A2503 on 23S rRNA was confirmed by primer extension. Finally, expression of the Cfr-like proteins was verified by SDS gel electrophoresis of whole-cell extracts. The work shows that cfr-like genes exist in the environment and that Bacillales are natural residences of cfr-like genes.

Purification and characterization of a solvent-stable protease from Geomicrobium sp. EMB2

A moderately haloalkaliphilic bacterium, Geomicrobium sp. EMB2, was isolated from the Sambhar Salt Lake located in the western part of India. It secreted an alkaline protease, which was stable and active in the presence of a wide range of organic solvents. The protease was purified by hydrophobic interaction chromatography on Phenyl Sepharose 6 Fast Flow matrix, and a 22.6-fold purification with 51.2% recovery was attained. The apparent molecular mass was estimated to be 38 kDa. The enzyme was stable in the pH range 6.0-12.0, the optimum being 10.0. The Km and Vmax towards casein were found to be 0.10 mM and 526 U/min, respectively. The protease was most active at 50 degrees C. It appeared to be serine type, owing to its sensitivity to phenylmethylsulphonyl fluoride (PMSF). It withstood a range of detergents and surfactants, and exhibited remarkable stability in the presence of solvents having a log P >2. The presence of NaCl or osmolytes exerted a protective effect and further enhanced the stability of the enzyme. These properties make this novel protease potentially useful for catalysis in non-aqueous medium.

Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) co-polymer production from a local isolate, Brevibacillus invocatus MTCC 9039

Accumulation of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] co-polymer by a local isolate, Brevibacillus invocatus MTCC 9039 under batch mode was investigated under glucose, acetate and propionate-supplemented conditions. Cells harvested at the stationary phase of growth depicted maximum accumulation of poly-3-hydroxybutyrate (PHB), i.e. 3% of dry cell weight (dcw) at pH 7.0 and temperature 30 degrees C at 48h of incubation. PHB accumulation reached up to 52% (dcw) under 3% glucose with 1% acetate supplementation. P(3HB-co-3HV) co-polymer synthesis was observed under propionate-supplemented condition, which reached up to 45% under 3% glucose with 1% propionate supplementation. Optimization of process parameters by response surface methodology (RSM) resulted into co-polymer accumulation up to 65% (dcw) at 2.08% glucose, 1.62% acetate, 0.75% propionate and 2.15 g l(-1) KH(2)PO(4) concentrations. This co-polymer exhibited comparable material properties with the commercial [P(3HB-co-3HV)] co-polymers, whereas the elasticity was tremendously high and could be comparable with polypropylene. Thus, B. invocatus MTCC 9039 is emerging as an interesting organism and could be exploited further for P(3HB-co-3HV) co-polymer production.

Cohnella damensis sp. nov., a motile xylanolytic bacteria isolated from a low altitude area in Tibet

A bacterial strain, 13-25(T) with xylanolytic activity isolated from a single present soil sample, was characterized with respect to its phenetic and phylogenetic characteristics. The cells of the isolate are gram staining variable rods. The predominant fatty acids are anteiso-C(15 : 0), C(16-0), and iso-C(16 : 0), the major respiratory quinone is menaquinone (MK-7), with a polar lipid profile with unknown aminophospholipids. The G+C content is 54.3 mol%. The 16S rRNA gene sequence analysis indicates that this organism belongs to the genus Cohnella, with Cohnella panacarvi as the closest phylogenetic neighbor. Low levels of 16S rRNA gene sequence similarity (<97.0%) with respect to other taxa with published names and the identification of distinctive phenetic features in the isolate indicate that the strain 13-25(T) represents a novel species of the genus Cohnella, for which the name Cohnella damensis sp. nov. is proposed. The type strain is 13-25(T) (=CCTCC AB 208103(T) =KCTC 13422(T)).