Novel microbial fermentation for the preparation of iron-chelating scallop skirts peptides-its profile, identification, and possible binding mode

Iron chelating peptides have been widely utilized as iron supplements due to their excellent absorption capacity, However, the high cost and cumbersome manufacturing process of these peptides significantly limit their industrial application. In this study, fermentation was used for the first time to prepare iron chelating peptides. Bacillus altitudinis 3*1-3 was selected as the most suitable strain from 50 strains. The hydrolysates of fermented scallop skirts showed excellent iron-chelating capacity (9.39 mg/g). Aspartic acid, glutamic acid, and histidine are crucial for the binding of peptides to ferrous ions. The heptapeptide (FEDPEFE) forms six binding bonds with ferrous irons. Compared with ferrous sulfate, peptide-ferrous chelate showed more stability in salt solution and simulated gastrointestinal juice (p < 0.05). Furthermore, the fermentation method could save >50% of the cost compared with the enzymatic method. The results can provide a theoretical basis for the preparation of ferrous-chelated peptides using the fermentation method.

A pan-genomic assessment: Delving into the genome of the marine epiphyte Bacillus altitudinis strain 19_A and other very close Bacillus strains from multiple environments

Marine macroalgae are the habitat of epiphytic bacteria and provide several conditions for a beneficial biological interaction to thrive. Although Bacillus is one of the most abundant epiphytic genera, genomic information on marine macroalgae-associated Bacillus species remains scarce. In this study, we further investigated our previously published genome of the epiphytic strain Bacillus altitudinis 19_A to find features that could be translated to potential metabolites produced by this microorganism, as well as genes that play a role in its interaction with its macroalgal host. To achieve this goal, we performed a pan-genome analysis of Bacillus sp. and a codon bias assessment, including the genome of the strain Bacillus altitudinis 19_A and 29 complete genome sequences of closely related Bacillus strains isolated from soil, marine environments, plants, extreme environments, air, and food. This genomic analysis revealed that Bacillus altitudinis 19_A possessed unique genes encoding proteins involved in horizontal gene transfer, DNA repair, transcriptional regulation, and bacteriocin biosynthesis. In this comparative analysis, codon bias was not associated with the habitat of the strains studied. Some accessory genes were identified in the Bacillus altitudinis 19_A genome that could be related to its epiphytic lifestyle, as well as gene clusters for the biosynthesis of a sporulation-killing factor and a bacteriocin, showing their potential as a source of antimicrobial peptides. Our results provide a comprehensive view of the Bacillus altitudinis 19_A genome to understand its adaptation to the marine environment and its potential as a producer of bioactive compounds.

Dark fermentation of pretreated hydrolysates of pineapple fruit waste for the production of biohydrogen using bacteria isolated from wastewater sources

In the present study, both acidic and alkaline hydrolysate of pineapple waste was utilised for the production of biohydrogen using locally isolated bacterial strains. The bacteria were isolated from different wastewater sources and were identified as Proteus mirabilis, Pseudomonas aeruginosa, Bacillus altitudinus, Bacillus subtilis, Paenibacillus alvei, and Lysinibacillus sphaericus. Experimental results showed that the highest biohydrogen yield of 836.33 ± 48.02 mL H2 was produced from alkaline hydrolysate with Bacillus altitudinis during the 96thhr of fermentation. Among the different bacterial strains, B. altitudinis showed higher H2 production. Comparatively alkaline hydrolysates exhibited a higher yield of hydrogen than acidic hydrolysates. The final pH of the experiment was found to be in acidic range. The total VFA concentration ranged between 930 ± 207.85 mg/L to 3050 ± 476.97 mg/L. Both sugar degradation and COD reduction were more than 80% in the acidic and alkaline hydrolysates while the lowest sugar degradation and COD reduction were observed for the untreated biomass. The rationale behind this study was to convert the waste biomass into energy by utilising the potential of native bacterial communities.

Production of Pumilarin and a Novel Circular Bacteriocin, Altitudin A, by Bacillus altitudinis ECC22, a Soil-Derived Bacteriocin Producer

The rise of antimicrobial resistance poses a significant global health threat, necessitating urgent efforts to identify novel antimicrobial agents. In this study, we undertook a thorough screening of soil-derived bacterial isolates to identify candidates showing antimicrobial activity against Gram-positive bacteria. A highly active antagonistic isolate was initially identified as Bacillus altitudinis ECC22, being further subjected to whole genome sequencing. A bioinformatic analysis of the B. altitudinis ECC22 genome revealed the presence of two gene clusters responsible for synthesizing two circular bacteriocins: pumilarin and a novel circular bacteriocin named altitudin A, alongside a closticin 574-like bacteriocin (CLB) structural gene. The synthesis and antimicrobial activity of the bacteriocins, pumilarin and altitudin A, were evaluated and validated using an in vitro cell-free protein synthesis (IV-CFPS) protocol coupled to a split-intein-mediated ligation procedure, as well as through their in vivo production by recombinant E. coli cells. However, the IV-CFPS of CLB showed no antimicrobial activity against the bacterial indicators tested. The purification of the bacteriocins produced by B. altitudinis ECC22, and their evaluation by MALDI-TOF MS analysis and LC-MS/MS-derived targeted proteomics identification combined with massive peptide analysis, confirmed the production and circular conformation of pumilarin and altitudin A. Both bacteriocins exhibited a spectrum of activity primarily directed against other Bacillus spp. strains. Structural three-dimensional predictions revealed that pumilarin and altitudin A may adopt a circular conformation with five- and four-α-helices, respectively.

Biocontrol potential of endophytic bacterium Bacillus altitudinis GS-16 against tea anthracnose caused by Colletotrichum gloeosporioides

Background

As one of the main pathogens causing tea anthracnose disease, Colletotrichum gloeosporioides has brought immeasurable impact on the sustainable development of agriculture. Given the adverse effects of chemical pesticides to the environment and human health, biological control has been a focus of the research on this pathogen. Bacillus altitudinis GS-16, which was isolated from healthy tea leaves, had exhibited strong antagonistic activity against tea anthracnose disease.

Methods

The antifungal mechanism of the endophytic bacterium GS-16 against C. gloeosporioides 1-F was determined by dual-culture assays, pot experiments, cell membrane permeability, cellular contents, cell metabolism, and the activities of the key defense enzymes.

Results

We investigated the possible mechanism of strain GS-16 inhibiting 1-F. In vitro, the dual-culture assays revealed that strain GS-16 had significant antagonistic activity (92.03%) against 1-F and broad-spectrum antifungal activity in all tested plant pathogens. In pot experiments, the disease index decreased to 6.12 after treatment with GS-16, indicating that strain GS-16 had a good biocontrol effect against tea anthracnose disease (89.06%). When the PE extract of GS-16 treated mycelial of 1-F, the mycelial appeared deformities, distortions, and swelling by SEM observations. Besides that, compared with the negative control, the contents of nucleic acids, protein, and total soluble sugar of GS-16 group were increased significantly, indicating that the PE extract of GS-16 could cause damage to integrity of 1-F. We also found that GS-16 obviously destroyed cellular metabolism and the normal synthesis of cellular contents. Additionally, treatment with GS-16 induced plant resistance by increasing the activities of the key defense enzymes PPO, SOD, CAT, PAL, and POD.

Conclusions

We concluded that GS-16 could damage cell permeability and integrity, destroy the normal synthesis of cellular contents, and induce plant resistance, which contributed to its antagonistic activity. These findings indicated that strain GS-16 could be used as an efficient microorganism for tea anthracnose disease caused by C. gloeosporioides.

Production and characterization of novel thermostable CotA-laccase from Bacillus altitudinis SL7 and its application for lignin degradation

Laccases are multi-copper oxidases and found in ligninolytic bacteria catalyzing the oxidation of both phenolic and non-phenolic compounds, however its application in lignin degradation suffers due to low oxidation rate, which have intensified the search for new laccases. In the present study, spore coat A protein (CotA) encoding gene having laccase like activity from Bacillus altitudinis SL7 (CotA-SL7) was cloned and expressed in Escherichia coli. The purified CotA-SL7 was active at wide range of temperature and pH with optimum activity at 55 °C and pH 5.0. The kinetic parameters of CotA-SL7 was determined with Km, Vmax, and kcat values 0.4 mM, 2777 μmol/min/mg, and 5194 s-1, respectively. Molecular docking revealed the presence of Pro, Phe, Asp, Asn, His, and Ile residues at the active site taking part in the oxidation of ABTS. The purified CotA-SL7 reduced lignin contents by 31 % and changes in lignin structure were analyzed through fourier transformed infrared spectroscopy (FTIR), scanning electron microsscopy (SEM) and gas chromatography mass-spectrometry (GC-MS). The appearance of low molecular size compounds clearly indicates the cleavage of lignin polymer and opening of the benzene ring by purified CotA-SL7. Thus, high catalytic efficiency of CotA-SL7 makes it a suitable bio-catalyst for remediation of lignin contaminated wastewater from pulp and paper industries with clear insights into lignin degradation at molecular level.

Bioherbicidal potential of Bacillus altitudinis D30202 on Avena fatua L.: a whole-genome sequencing analysis

Avena fatua L. (wild oat) is one of the most harmful gramineous weeds that can affect the yield and quality of infiltrating crops. Bacillus altitudinis D30202 exhibits an excellent biocontrol activity against wild oat. To elucidate the biocontrol mechanisms of B. altitudinis D30202, the genome structure of this strain was assessed via whole-genome sequencing analysis. We predicted and analyzed secondary metabolite synthesis gene clusters to elucidate the mechanisms underlying the biocontrol of weeds. The whole-genome sequencing data indicated that B. altitudinis D30202 had the genome size and GC content of 3,777,154 bp and 41.32%, respectively, and 3809 coding genes were identified. Moreover, this strain could generate several compounds with bioherbicidal activity, including 4-hydroxy-3-methoxycinnamic acid and two indole derivatives. Bioinformatics prediction and comparative genomic analysis revealed that the strain had 6 secondary metabolite gene clusters. Furthermore, the taxonomic position of B. altitudinis D30202 was assessed, confirming its uniqueness and novelty within the Bacillus genus. Comparative genomic analysis showed differences in gene distribution, suggesting potential adaptations to different environments. In conclusion, B. altitudinis D30202 possesses a genome with unique characteristics, encoding enzymes and pathways related to herbicidal potential and biocontrol. This study provides a reference basis for understanding the molecular mechanisms of weed inhibition.

Bacterial Metal-Scavengers Newly Isolated from Indonesian Gold Mine-Impacted Area: Bacillus altitudinis MIM12 as Novel Tools for Bio-Transformation of Mercury

Selikat river, located in the north part of Bengkulu Province, Indonesia, has critical environmental and ecological issues of contamination by mercury due to artisanal small-scale gold mining (ASGM) activities. The present study focused on the identification and bioremediation efficiency of the mercury-resistant bacteria (MRB) isolated from ASGM-impacted areas in Lebong Tambang village, Bengkulu Province, and analyzed their merA gene function in transforming Hg2+ to Hg0. Thirty-four MRB isolates were isolated, and four out of the 34 isolates exhibited not only the highest degree of resistance to Hg (up to 200 ppm) but also to cadmium (Cd), chromium (Cr), copper (Cu), and lead (Pb). Further analysis shows that all four selected isolates harbor a merA operon-encoded mercuric ion (Hg2+) reductase enzyme, with the Hg bioremediation efficiency varying from 71.60 to 91.30%. Additionally, the bioremediation efficiency for Cd, Cr, Cu, and Pb ranged from 54.36 to 98.37%. Among the 34, two isolates identified as Bacillus altitudinis possess effective and superior multi-metal degrading capacity up to 91.30% for Hg, 98.07% for Cu, and 54.36% for Cr. A pilot-scale study exhibited significant in situ bioremediation of Hg from gold mine tailings of 82.10 and 95.16% at 4- and 8-day intervals, respectively. Interestingly, translated nucleotide blast against bacteria and Bacilli merA sequence databases suggested that B. altitudinis harbor merA gene is the first case among Bacilli with the possibility exhibits a novel mechanism of bioremediation, considering our new finding. This study is the first to report the structural and functional Hg-resistant bacterial diversity of unexplored ASGM-impacted areas, emphasizing their biotechnological potential as novel tools for the biological transformation and adsorption of mercury and other toxic metals.

[Isolation and identification of a polyester-polyurethane degrading bacterium Bacillus altitudinis YX8-1]

Although polyurethane (PUR) plastics play important roles in daily life, its wastes bring serious environmental pollutions. Biological (enzymatic) degradation is considered as an environmentally friendly and low-cost method for PUR waste recycling, in which the efficient PUR-degrading strains or enzymes are crucial. In this work, a polyester PUR-degrading strain YX8-1 was isolated from the surface of PUR waste collected from a landfill. Based on colony morphology and micromorphology observation, phylogenetic analysis of 16S rDNA and gyrA gene, as well as genome sequence comparison, strain YX8-1 was identified as Bacillus altitudinis. The results of high performance liquid chromatography (HPLC) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) showed that strain YX8-1 was able to depolymerize self-synthesized polyester PUR oligomer (PBA-PU) to produce a monomeric compound 4, 4'-methylene diphenylamine. Furthermore, strain YX8-1 was able to degrade 32% of the commercialized polyester PUR sponges within 30 days. This study thus provides a strain capable of biodegradation of PUR waste, which may facilitate the mining of related degrading enzymes.

Screening, identification, and characterization of lipase-producing halotolerant Bacillus altitudinis Ant19 from Antarctic soil

Potent lipase-producing and halotolerant Bacillus altitudinis Ant19 strain was screened and isolated from Antarctic soil. The isolate showed broad-range lipase activity against different lipid substrates. Presence of lipase activity was confirmed by PCR amplification and sequencing of the lipase gene from Ant19. The study attempted to establish the use of crude extracellular lipase extract as cheap alternative to purified enzyme by characterizing the crude lipase activity and testing it in certain practical applications. Crude lipase extract from Ant19 showed high stability at 5-28 ℃ (> 97%), while lipase activity was noted in a wide temperature range of 20-60 ℃ (> 69%), with optimum activity at 40 ℃ (117.6%). The optimum lipolytic activity was noted at pH 8 with good activity and stability in alkaline conditions (pH 7-10). Moreover, the lipase activity was substantially stable in various solvents, commercial detergents, and surfactants. It retained 97.4% activity in 1% solution of commercial Nirma detergent. Besides, it was non-regiospecific, and active against substrates having different fatty acid chain lengths with preference for shorter chain length. Further, the crude lipase enhanced the oil stain removal efficiency of commercial detergent from 52 to 77.9%, while 66% oil stain was removed using crude lipase alone. Immobilization process improved the storage stability of crude lipase for 90 days. In our knowledge, it is the first study on characterization of lipase activity from B. altitudinis, which has promising applications in various fields.

Genome sequence analysis and characterization of Bacillus altitudinis B12, a polylactic acid- and keratin-degrading bacterium

Keratin-rich wastes, mainly in the form of feathers, are recalcitrant residues generated in high amounts as by-products in chicken farms and food industry. Polylactic acid (PLA) is the second most common biodegradable polymer found in commercial plastics, which is not easily degraded by microbial activity. This work reports the 3.8-Mb genome of Bacillus altitudinis B12, a highly efficient PLA- and keratin-degrading bacterium, with potential for environmental friendly biotechnological applications in the feed, fertilizer, detergent, leather, and pharmaceutical industries. The whole genome sequence of B. altitudinis B12 revealed that this strain (which had been previously misclassified as Bacillus pumilus B12) is closely related to the B. altitudinis strains ER5, W3, and GR-8. A total of 4056 coding sequences were annotated using the RAST server, of which 2484 are core genes of the pan genome of B. altitudinis and 171 are unique to this strain. According to the sequence analysis, B. pumilus B12 has a predicted secretome of 353 proteins, among which a keratinase and a PLA depolymerase were identified by sequence analysis. The presence of these two enzymes could explain the characterized PLA and keratin biodegradation capability of the strain.

Adding value to rice straw waste for high-level xylanase production using a new isolate of Bacillus altitudinis RS3025

An investigation was carried out using rice straw as a low-cost substrate to study the optimization of xylanase production using a newly identified endospore-forming bacterium, Bacillus altitudinis RS3025. The highest xylanase activity was achieved using 2% rice straw (pretreated with 2% NaOH at 100 °C) at pH 7.0, 37 °C temperature, and with 72-h incubation time. Under the optimized conditions, xylanase activity reached 2518.51 U/mL, which was 11.56-fold higher than the activity under the initial conditions using untreated rice straw as substrate. Enzymatic hydrolysis of the rice straw using crude xylanase of B. altitudinis RS3025 demonstrated the hydrolyzation efficiency of the rice straw waste, especially alkaline rice straw. The highest level of released reducing sugars was 149.78 mg/g substrate. The study demonstrated the successful utilization of rice straw waste for high-level xylanase production using B. altitudinis RS3025 and reducing sugar production using low-cost crude enzyme, which has the advantages of reducing the processing cost and environmental concerns associated with rice straw waste management.

Complete genome sequence analysis of a plant growth-promoting phylloplane Bacillus altitudinis FD48 offers mechanistic insights into priming drought stress tolerance in rice

Bacillus altitudinis FD48 is a multifunctional plant growth-promoting bacterium isolated from the phylloplane of rice and survives at --10 bars of osmotic potential (--1.0 MPa). It also serves as an ideal PGPM against drought stress by triggering antioxidant defense mechanisms in rice. To further unravel the genetic determinants of osmotic stress tolerance and plant growth-promoting traits, the whole genome sequence of FD48 was compared with its related strains. The whole genome analysis revealed a single chromosome with a total length of 3,752,533 bp (3.7 Mb) and an average G + C ratio of 41.19%. A total of 4029 genes were predicted, of which 3964 (98.4%) were protein-encoding genes (PEGs) and 65 (1.6%) were non-protein-coding genes. The interaction of FD48 with the host plants is associated with many chemotactic and motility-related genes. The ability of FD48 to colonize plants and maintain plant growth under adverse environmental conditions was evidenced by the presence of genes for plant nutrient acquisition, phytohormone synthesis, trehalose, choline, and glycine betaine biosynthesis, microbial volatile organic compounds (acetoin synthesis), heat and cold shock chaperones, translation elongation factor TU (Ef-Tu), siderophore production, DEAD/DEAH boxes, and non- ribosomal peptide synthase clusters (bacilysin, fengycin, and bacitracin). This study sheds light on the drought stress-resilient mechanism, metabolic pathways and potential activity, and plant growth-promoting traits of B. altitudinis FD48 at the genetic level.

Biofertilizer Based on Biochar and Metal-Tolerant Plant Growth Promoting Rhizobacteria Alleviates Copper Impact on Morphophysiological Traits in Brassica napus L

Metal tolerant plant growth-promoting (PGP) rhizobacteria are promising for enhancing plant productivity under copper (Cu) stress. Present pot scale experiment was conducted on Brassica napus L. to check the efficiency of rhizobacteria isolated from the rhizosphere of Tussilago farfara L. growing on Cu-contaminated soils. Out of fifty Cu tolerant strains, three isolates which showed multiple PGP traits such as indole-3-acetic acid (IAA) synthesis, phosphate (PS) solubilization, siderophore and ammonia production were identified preliminarily by morphological and physiological characteristics followed by 16S rRNA gene sequencing. The best Bacillus altitudinis strain TF16a which showed IAA: 15.5 mg L-1, PS: 215 mg L-1, siderophore halo zone ratio of 3.0 with high ammonia production was selected to prepare a biochar-based biofertilizer (BF). Seedling test showed maximum growth of B. napus shoot and root in presence of 5% of BF and this concentration was selected for further experiment. The pot experiment included four treatments: control (soil), 100Cu (100 mg Cu kg-1 soil), 5%BF (v/v), and 5%BF+100Cu, which were carried out for 30 days, after which the morphological, physiological, and biochemical parameters of B. napus were studied. The Cu treatment caused its accumulation in shoot and root up to 16.9 and 30.4 mg kg-1 DW, respectively, and increased malondialdehyde (MDA) content by 20%. Application of BF with copper led to the decrease in the Cu accumulation by 20% for shoot and 28% for root while MDA content was the same as in the control. Both treatments of BF with and without Cu increased chlorophyll a and b content by 1.3 times on average as well as non-enzymatic antioxidants such as soluble phenolic compounds (1.3 times) and free proline (1.6 times). Moreover, BF + Cu led to the increase in the biomass of shoot and root by 30 and 60%, respectively, while there was no significant effect on the growth characteristics of plants after the addition of BF without Cu. The study elucidates that BF based on B.altitudinis strain TF16a and biochar can be a promising bioformulation which could increase rapeseed growth under the moderate Cu concentration in soil.

Nematicidal activity of volatile organic compounds produced by Bacillus altitudinis AMCC 1040 against Meloidogyne incognita

The application of nematicidal microorganisms and their virulence factors provides more opportunities to control root-knot nematodes. Bacillus altitudinis AMCC 1040, previously isolated from suppressive soils, showed significant nematicidal activity, and in this study, nematicidal substances produced by Bacillus altitudinis AMCC 1040 were investigated. The results of the basic properties of active substances showed that these compounds have good thermal stability and passage, are resistant to acidic environment and sensitive to alkaline conditions. Further analysis showed that it is a volatile component. Using HS-SPME-GC/MS, the volatile compounds produced by Bacillus altitudinis AMCC 1040 were identified and grouped into four major categories: ethers, alcohols, ketone, and organic acids, comprising a total of eight molecules. Six of them possess nematicidal activities, including 2,3-butanedione, acetic acid, 2-isopropoxy ethylamine, 3-methylbutyric acid, 2-methylbutyric acid and octanoic acid. Our results further our understanding of the effects of Bacillus altitudinis and its nematicidal metabolites on the management of Meloidogyne incognita and may help in finding less toxic nematicides to control root knot nematodes.

Comprehensive Genomic Analysis of the Endophytic Bacillus altitudinis Strain GLB197, a Potential Biocontrol Agent of Grape Downy Mildew

Bacillus has been extensively studied for agricultural application as a biocontrol agent. B. altitudinis GLB197, an endophytic bacterium isolated from grape leaves, exhibits distinctive inhibition to grape downy mildew based on unknown mechanisms. To determine the genetic traits involved in the mechanism of biocontrol and host-interaction traits, the genome sequence of GLB197 was obtained and further analyzed. The genome of B. altitudinis GLB197 consisted of one plasmid and a 3,733,835-bp circular chromosome with 41.56% G + C content, containing 3,770 protein-coding genes. Phylogenetic analysis of 17 Bacillus strains using the concatenated 1,226 single-copy core genes divided into different clusters was conducted. In addition, average nucleotide identity (ANI) values indicate that the current taxonomy of some B. pumilus group strains is incorrect. Comparative analysis of B. altitudinis GLB197 proteins with other B. altitudinis strains identified 3,157 core genes. Furthermore, we found that the pan-genome of B. altitudinis is open. The genome of B. altitudinis GLB197 contains one nonribosomal peptide synthetase (NRPS) gene cluster which was annotated as lichenysin. Interestingly, the cluster in B. altitudinis has two more genes than other Bacillus strains (lgrD and lgrB). The two genes were probably obtained via horizontal gene transfer (HGT) during the evolutionary process from Brevibacillus. Taken together, these observations enable the future application of B. altitudinis GLB197 as a biocontrol agent for control of grape downy mildew and promote our understanding of the beneficial interactions between B. altitudinis GLB197 and plants.

Bacillus Cyclic Lipopeptides Iturin and Fengycin Control Rice Blast Caused by Pyricularia oryzae in Potting and Acid Sulfate Soils by Direct Antagonism and Induced Systemic Resistance

Rice monoculture in acid sulfate soils (ASSs) is affected by a wide range of abiotic and biotic constraints, including rice blast caused by Pyricularia oryzae. To progress towards a more sustainable agriculture, our research aimed to screen the biocontrol potential of indigenous Bacillus spp. against blast disease by triggering induced systemic resistance (ISR) via root application and direct antagonism. Strains belonging to the B. altitudinis and B. velezensis group could protect rice against blast disease by ISR. UPLC-MS and marker gene replacement methods were used to detect cyclic lipopeptide (CLiP) production and construct CLiPs deficient mutants of B. velezensis, respectively. Here we show that the CLiPs fengycin and iturin are both needed to elicit ISR against rice blast in potting soil and ASS conditions. The CLiPs surfactin, iturin and fengycin completely suppressed P. oryzae spore germination resulting in disease severity reduction when co-applied on rice leaves. In vitro microscopic assays revealed that iturin and fengycin inhibited the mycelial growth of the fungus P. oryzae, while surfactin had no effect. The capacity of indigenous Bacillus spp. to reduce rice blast by direct and indirect antagonism in ASS conditions provides an opportunity to explore their usage for rice blast control in the field.

Endophytic Bacillus altitudinis Strain Uses Different Novelty Molecular Pathways to Enhance Plant Growth

The identification and use of endophytic bacteria capable of triggering plant growth is an important aim in sustainable agriculture. In nature, plants live in alliance with multiple plant growth-promoting endophytic microorganisms. In the current study, we isolated and identified a new endophytic bacterium from a wild plant species Glyceria chinensis (Keng). The bacterium was designated as a Bacillus altitudinis strain using 16S rDNA sequencing. The endophytic B. altitudinis had a notable influence on plant growth. The results of our assays revealed that the endophytic B. altitudinis raised the growth of different plant species. Remarkably, we found transcriptional changes in plants treated with the bacterium. Genes such as maturase K, tetratricopeptide repeat-like superfamily protein, LOB domain-containing protein, and BTB/POZ/TAZ domain-containing protein were highly expressed. In addition, we identified for the first time an induction in the endophytic bacterium of the major facilitator superfamily transporter and DNA gyrase subunit B genes during interaction with the plant. These new findings show that endophytic B. altitudinis could be used as a favourable candidate source to enhance plant growth in sustainable agriculture.

Endophytic Bacillus altitudinis WR10 alleviates Cu toxicity in wheat by augmenting reactive oxygen species scavenging and phenylpropanoid biosynthesis

Soil copper (Cu) pollution severely stunts crops growth and limits sustainable agri-food production. Many microbes are widely used for remediation of polluted soil, including Cu pollution. In this study, the potential of an endophytic Bacillus altitudinis WR10 to protect wheat from Cu stress and the molecular mechanisms were investigated using hydroponic model. The Cu resistance assay showed B. altitudinis WR10 can resist up to 2 mM Cu and remove about 74% Cu in medium after 24 h of fermentation. Co-culture study demonstrated WR10 increased roots length and dry weight in wheat seedlings under 50 μM Cu. These results indicated that WR10 was a Cu-resistant strain and reduced Cu toxicity in wheat. Transcriptome data and biochemical tests of wheat roots indicated that WR10 alleviated Cu toxicity through enhancing peroxidases (PODs) gene expression and activity to remove excess hydrogen peroxide (H₂O₂) and down-regulating glutathione S-transferases (GSTs) to increase glutathione (GSH) level. Moreover, enrichment and pathway analysis indicated WR10 regulated the expression of genes involved in phenylpropanoid biosynthesis, which may improve phenolic acids accumulation for protecting plant cells from Cu toxicity. Overall, this study revealed that B. altitudinis WR10 alleviated Cu toxicity in wheat via augmenting reactive oxygen species scavenging and phenylpropanoid biosynthesis.

Isolation of ammonia gas-tolerant extremophilic bacteria and their application to the elimination of malodorous gas emitted from outdoor heat-treated toilets

Ammonia gas-tolerant extremophilic bacteria capable of growing in atmospheres containing up to 4000 ppm of gaseous ammonia were isolated. These bacteria were capable of growing in nutrient broth containing high concentrations of ammonia water, with growth in medium augmented with 0.1-0.2% ammonia exceeding that in medium without ammonia. The minimal inhibitory concentration of ammonia in the medium was 0.5%. The isolated ammonia gas-tolerant bacterium was moderately alkaliphilic, with optimum growth was observed at pH 9. DNA sequence analysis of the 16SrRNA gene revealed that the isolated bacterium was Bacillus lentus. Furthermore, extremophilic bacteria cultured in a 1300 ppm ammonia gas atmosphere on agar medium containing no nitrogen sources were observed to use ammonia gas for growth. These bacteria were identified as Paenibacillus lentus and Bacillus altitudinis based on 16SrRNA gene sequence analysis. The deodorizing effect of ammonia odor by the isolated bacteria immobilized on sawdust was evaluated. The findings showed that forcing ammonia gas through a column containing B. altitudinis immobilized on sawdust reduced the concentration of ammonia gas by 30% compared to columns containing sawdust only. The isolated bacteria immobilized on wood sawdust lost the capacity deodorization after drying, but this function could be restored with increased moisture. The ammonia gas-tolerant extremophilic bacteria immobilized on sawdust show considerable potential for use in ameliorating malodors associated with outdoor heat-treated toilets.

Bioprospecting of a Novel Plant Growth-Promoting Bacterium Bacillus Altitudinis KP-14 for Enhancing Miscanthus × giganteus Growth in Metals Contaminated Soil

Simple Summary

Marginal land represents poor soil with low agricultural characteristics and crop productivity, which is sometimes additionally contaminated. The exploitation of marginal land for normal agriculture is not possible but it suitable for cultivation of energy crops, especially Miscanthus × giganteus (Mxg), however, the harvest biomass value in such land is lower. The produced Mxg biomass can be converted to alternative energy like biofuel and biogas, or used for production of other value-added products like insulation fibers, building materials or paper, etc. It is well known fact that plant growth-promoting bacteria are beneficial for stimulating the overall development of plants even under stress conditions. In the current study, a number of strains were isolated from the metal-contaminated post-mining land, identified, biochemically characterized, and evaluated for abiotic stress tolerance: pH, temperature, salinity, and heavy metal (lead). Among different isolates, the multiple abiotic stress-tolerant plant growth-promoting bacteria Bacillus altitudinis KP-14 showed the best properties. Its effect on the growth of Mxg under the severe stress of metal-contaminated soil was evaluated. It was found that selected bacterial strain KP-14 significantly enhanced the biomass production. The overall results suggested that B. altitudinis KP-14 can be recommended as a potent biofertilizer for marginal lands.

Abstract

Use of plant growth-promoting bacteria (PGPB) for cultivation of the biofuel crop Miscanthus × giganteus (Mxg) in post-military and post-mining sites is a promising approach for the bioremediation of soils contaminated by metals. In the present study, PGPB were isolated from contaminated soil and screened for tolerance against abiotic stresses caused by salinity, pH, temperature, and lead (Pb). Selected strains were further assessed and screened for plant growth-promoting attributes. The isolate showing the most potential, Bacillus altitudinis KP-14, was tested for enhancement of Mxg growth in contaminated soil under greenhouse conditions. It was found to be highly tolerant to diverse abiotic stresses, exhibiting tolerance to salinity (0–15%), pH (4–8), temperature (4–50 °C), and Pb (up to 1200 ppm). The association of B. altitudinis KP-14 with Mxg resulted in a significant (p ≤ 0.001) impact on biomass enhancement: the total shoot and dry root weights were significantly enhanced by 77.7% and 55.5%, respectively. The significant enhancement of Mxg biomass parameters by application of B. altitudinis KP-14 strongly supports the use of this strain as a biofertilizer for the improvement of plant growth in metal-contaminated soils.

Biochemical and molecular characterization of an acido-thermostable endo-chitinase from Bacillus altitudinis KA15 for industrial degradation of chitinous waste

This paper reports the isolation and identification of an acido-thermostable chitinase (ChiA-Ba43) which was purified, from the culture liquid of Bacillus altitudinis strain KA15, and characterized. Purification of ChiA-Ba43 produced a 69.6-fold increase in the specific activity (120,000 U/mg) of the chitinase, with a yield of 51% using colloidal chitin as substrate. ChiA-Ba43 was found to be a monomeric protein with a molecular mass of 43,190.05 Da as determined by MALDI-TOF/MS. N-terminal sequence of the first 27 amino-acids (aa) of ChiA-Ba43 displayed homology to chitinases from other Bacillus species. Interestingly, ChiA-Ba43 exhibited optimum pH and temperature of 4-5.5 and 85 °C, respectively. Thin-layer chromatography (TLC) showed that the final hydrolyzed products of the enzyme from chitin-oligosaccharides and colloidal chitin are a mixture of (GlcNAc)₂, (GlcNAc)₃, (GlcNAc)₄, and (GlcNAc)₅, which indicates that ChiA-Ba43 possesses an endo-acting function. More interestingly, compared to ChiA-Mt45, ChiA-Hh59, Chitodextrinase®, N-acetyl-β-glucosaminidase®, and ChiA-65, ChiA-Ba43 demonstrated a high level of catalytic efficiency and outstanding tolerance towards various organic solvents. The chiA-Ba43 gene (1332 bp) encoding ChiA-Ba43 (409 aa) was cloned, sequenced, and expressed in Escherichia coli strain HB101. The biochemical properties of the recombinant chitinase (rChiA-Ba43) were equivalent to those of the natively expressed enzyme. These properties make ChiA-Ba43 an ideal candidate for industrial bioconversion of chitinous waste.

Statistical optimization of culture conditions of mesophillic gamma-glutamyl transpeptidase from Bacillus altitudinis IHB B1644

Microbial gamma-glutamyl transpeptidase (GGT) is a key enzyme in production of several γ-glutamyl compounds with food and pharmaceutical applications. Bacterial GGTs are not commercially available in the market owing to their low production from various sources. Thus, the study was focused on achieving the higher GGT production from B. altitudinis IHB B1644 by optimizing the culture conditions using one-variable-at-a-time (OVAT) strategy. A mesophillic temperature of 28 °C, agitation 200 rpm and neutral pH 7 were found to be optimal for higher GGT titre. Among the medium components, the monosaccharide glucose served as the best carbon source over disaccharides, and yeast extract was the preferred organic nitrogen source over inorganic nitrogen sources. The statistical approaches (Plakett-Burman and response surface methodology) were further employed for the optimization of medium components. Medium composition: 0.1% w/v glucose, 0.3% w/v yeast extract, 0.03% w/v magnesium sulphate, 0.20% w/v potassium dihydrogen phosphate and 2.5% w/v sodium chloride with inoculum size (1% v/v) was suitable for higher GGT titres (449 U ml^-1). Time kinetics showed the stability of enzyme up to 96 h of incubation suggesting its application in the industrial use. The proposed strategy resulted in 2.6-fold increase in the GGT production compared to that obtained in the unoptimized medium. The results demonstrated that RSM was fitting to identify the optimum production conditions and this finding should be of great importance for commercial GGT production.

Microbiological Insights into the Stress-Alleviating Property of an Endophytic Bacillus altitudinis WR10 in Wheat under Low-Phosphorus and High-Salinity Stresses

An indole-3-acetic acid producing Bacillus altitudinis WR10 was previously isolated from the root of wheat (Triticum aestivum L.). In this study, the strain WR10 was used for relieving abiotic stresses in wheat under low phosphorus and high saline in hydroponic co-culture models. Significantly, strain WR10 improved wheat seed relative germination rate under salinity stress (200/400 mM NaCl) and the root dry weight in wheat seedlings under phosphorus stress (10 μM KH2PO3) when insoluble phosphates are available. To provide insights into its abiotic stress-alleviating properties, the strain was characterized further. WR10 grows well under different culture conditions. Particularly, WR10 resists salt (12% NaCl) and hydrolyzes both inorganic and organic insoluble phosphates. WR10 uses many plant-derived substrates as sole carbon and energy sources. It produces catalase, amylase, phosphatase, phytase, reductase, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. In addition, WR10 possesses long peritrichous flagella, and its biofilm formation, as well as phytase production, is induced by abiotic stresses. Overall, the salinity-alleviating property of WR10 in wheat can be attributed to its inherent tolerance to NaCl, formation of biofilm, and production of enzymes, like catalase, amylase, and ACC deaminase. Meanwhile, B. altitudinis WR10 reduces low-phosphorus stress in wheat by production of phosphatases and phytases in the presence of insoluble phosphates.

Antagonistic activities of volatiles produced by two Bacillus strains against Monilinia fructicola in peach fruit

BACKGROUND

Brown rot caused by Monilinia fructicola is one of most serious diseases of postharvest peach fruit. The objective of this study was to select effective antagonistic bacteria against Monilinia fructicola and evaluate the effects of these strains against brown rot.

RESULTS

Four bacterial strains producing inhibitory volatile gas against Monilinia fructicola were isolated from the peach rhizosphere soil. The volatiles produced by 12a (Bacillus vallismortis) and 14b (Bacillus altitudinis) showed considerable antagonistic activities. Monilinia fructicola showed 80.3% and 68.4% mycelial growth inhibition and cell damage in the presence of strains 12a and 14b, respectively. The inhibition rate of brown rot in peach fruit fumigated with the culture solution of 12a or 14b reached 77.1% and 50.0%, respectively. The volatile compounds produced by 12a and 14b were identified according to gas chromatographic-mass spectrometric analysis. Among them, 6-methyl-2-heptanone and 2-pentylfuran completely inhibited mycelial growth at 100 µL L^-1 concentration. Cedrol showed strong inhibitory activity against mycelial growth at 100 µg L^-1 and isodecyl methacrylate inhibited growth at high concentration. The inhibition rate of the 50 µL L^-1 artificial mixture of these four volatiles was 59.3% in vitro.

CONCLUSION

These results indicate that the two antagonistic bacteria and some volatiles produced by them have potential value in controlling brown rot in harvested peach fruit. © 2018 Society of Chemical Industry.

Physicochemical characterization of pectinase activity from Bacillus spp. and their accessory role in synergism with crude xylanase and commercial cellulase in enzyme cocktail mediated saccharification of agrowaste biomass

AIM

The aim of this study was to evaluate the physicochemical properties of the crude pectinase activity from three Bacillus isolates of ruminant dung origin and study their synergism with crude xylanases from the same Bacillus spp. and a commercial cellulase to evaluate their accessory role in improved biomass saccharification.

METHODS AND RESULTS

Pectinolytic crude culture filtrate obtained from three ruminant dung isolates, Bacillus safensis M35, Bacillus altitudinis R31 and Bacillus altitudinis J208, on crude pectin containing medium possessed polygalacturonate hydrolase, pectate lyase and pectin lyase activities. Studies regarding their stability under various temperature and pH conditions revealed their mild acidic to alkaline and mesophilic nature with enzyme activity falling within the pH range 6·0-9·0 and temperature range 30-60°C. The pectinase activity was categorized as endolytic as it brought about ~50% reduction in relative viscosity of pectic polymer within initial 10 min of incubation. Synergism of pectinase activity with crude xylanase activities and/or commercial cellulase was clearly demonstrated as ~1·6 to ~1·9-fold increase in agrowaste biomass saccharification was obtained confirming the role of pectinases as accessory enzymes.

CONCLUSION

Synergism of the broad-spectrum endopectinase activity obtained from three Bacillus isolates with accessory crude xylanases from the same isolates and commercial cellulase enhanced the agrowaste saccharification and confirmed the accessory role of crude pectinase as they formed an efficient enzyme cocktail functioning in a contributive manner for improvement of agrowaste biomass saccharification.

SIGNIFICANCE AND IMPACT OF THE STUDY

Mesophilic crude endopectinases obtained from Bacillus spp. isolated from ruminant dung possessed activity in broad pH and temperature ranges as well as broad substrate specificity. Moreover, their synergism with crude xylanase and Primfast^® 200 cellulase demonstrated the potential to form efficient enzyme cocktail for application in plant biomass saccharification process.

Molecular and biochemical characterization of a thermostable keratinase from Bacillus altitudinis RBDV1

A thermostable keratinase designated as KBALT was purified from Bacillus altitudinis RBDV1 from a poultry farm in Gujarat, India. The molecular weight of the native KBALT (nKBALT) purified using ammonium sulfate and ion exchange and gel permeation chromatography with a 40% yield and 80-fold purification was estimated to be ~ 43 kDa. The gene for KBALT was successfully cloned, sequenced and expressed in Escherichia coli. Recombinant KBALT (rKBALT) when purified using a single step Ni-NTA His affinity chromatography achieved a yield of 38.20% and a 76.4-fold purification. Comparison of the deduced amino acid sequence of rKBALT with known proteases of Bacillus species and inhibitory effect of PMSF suggest that rKBALT was a subtilisin-like serine protease. Both native and rKBALT exhibited higher activity at 85 °C and pH 8.0 in the presence of Mg²⁺, Mn²⁺, Zn²⁺, Ba²⁺ and Fe³⁺ metal ions. Interestingly, 70% of their activity was retained at temperatures ranging from 35 to > 95 °C. The keratinolytic activity of both nKBALT and rKBALT was enhanced in the presence of reducing agents. They exhibited broad substrate specificity towards various protein substrates. KBALT was determined for its kinetic properties by calculating its K_m (0.61 mg/ml) and V_max (1673 U/mg/min) values. These results suggest KBALT as a robust and promising contender for enzymatic processing of keratinous wastes in waste processing plants.

Fish Scales as Potential Substrate for Production of Alkaline Protease and Amino Acid Rich Aqua Hydrolyzate by Bacillus altitudinis GVC11

Fish processing industries generate large quantities of fish scales as processing waste, if not treated leading to environmental pollution. Fish scales are hard to degrade, hence cause difficulty in waste management. In this context present study was made to utilize fish scales as substrate for the production of alkaline protease by Bacillus altitudinis GVC11 and subsequently amino acid rich aqua hydrolyzate. B. altitudinis GVC11 efficiently utilized five types of fish scales as substrates and produced maximum alkaline protease using Labeo rohita (28,150 U/mL) followed by Catla catla (23,320 U/mL) at 48 h and Cyprinus carpio (17,146 U/mL) Mugil cephalus (18,917 U/mL), Cirrhinus mrigala (12,430 U/mL) at 72 h. The HPLC analysis of protein hydrolyzate obtained after fermentation was enriched in essential amino acids, leucine, isoleucine, phenylalanine, lysine and non-essential amino acids, tyrosine, arginine and cysteine which can be used as animal feed supplement and organic fertilizer.

Engineering of a thermostable β-1,3-1,4-glucanase from Bacillus altitudinis YC-9 to improve its catalytic efficiency

BACKGROUND

Error-prone polymerase chain reaction (PCR) is frequently used in directed evolution of enzymes to modify their quality. In this study, error-prone PCR was used to improve the catalytic efficiency of β-1,3-1,4-glucanase from Bacillus altitudinis YC-9.

RESULTS

By screening, the mutant Glu-3060 with higher activity was selected among 5000 transformants. After induction with isopropyl β-D-1-thiogalactopyranoside (IPTG), the activity of the mutant Glu-3060 reached 474.6 U mL(-1), resulting in a 48.6% increment of the parent enzyme activity. Research on the characterization of the mutated enzyme showed the optimal pH of the mutated enzyme to be 5.0, which is lower than the parent enzyme, but thermal stability was almost the same between them. Sequence analysis of the mutated enzyme revealed that three amino acids were changed compared with the parent enzyme, including K142N, Q203L and N214D.

CONCLUSION

The three-dimensional structure predicted by SWISS-MODEL of the mutated enzyme Glu-3060 showed that the substitution of three amino acids had an effect on the catalytic activity, stability and optimal pH of the enzyme, through changing the charge properties or electron density, forming secondary keys, the acidity of the amino acids and the side chain group. The sum effects of all the factors were increased activity of the mutated enzyme and decreased optimal pH, while the same thermostability was maintained, thereby increasing the suitability of the enzyme for industrial use.

Three-step procedure for preparation of pure Bacillus altitudinis ribonuclease

Ribonucleases are considered as promising tools for anticancer treatment due to their selective cytotoxicity against tumor cells. We investigated a new RNase from Bacillus altitudinis termed BALNASE (B. altitudinis RNase). Balnase is a close homolog of the well-known cytotoxic binase, differing by only one amino acid residue: nonpolar hydrophobic alanine at position 106 in the balnase molecule is replaced by a polar uncharged threonine in binase. The most exciting question is how the physico-chemical properties and biological effects of RNase might be changed by A106T substitution. Here, we have developed a chromatography-based rapid and modern technique for the purification of this new RNase which allowed us to get a protein sample of high quality with specific activity of 1.2 × 10(6) units in preparative amounts, suitable for further investigation of its biological properties.