Comparative genome analysis of Bacillus velezensis reveals a potential for degrading lignocellulosic biomass

Seasonal Variations in the Structure and Function of the Gut Flora in Adult Male Rhesus Macaques Reared in Outdoor Colonies

The seasonal variations that occur in the gut microbiota of healthy adult rhesus monkeys kept in outdoor groups under conventional rearing patterns and how these variations are affected by environmental variables are relatively poorly understood. In this study, we collected 120 fecal samples from 30 adult male rhesus monkeys kept in outdoor groups across four seasons and recorded the temperature and humidity of the housing facilities, as well as the proportions of fruit and vegetables in their diet. A 16S rRNA sequencing analysis showed that the alpha diversity of the gut microbiota of the rhesus monkeys was higher in winter and spring than in summer and autumn. A principal coordinate analysis (PCoA) further demonstrated notable seasonal variations in the composition and functionality of the gut microbiota in the rhesus monkeys. The phyla Firmicutes and Bacteroidetes and the genus Prevotella 9 were the significantly dominant groups in all 120 fecal samples from the rhesus monkeys. A linear discriminant analysis (LDA) effect size (LEfSe) analysis (LDA > 4) indicated that at the phylum level, Firmicutes was significantly enriched in winter, Bacteroidetes was significantly enriched in summer, and Proteobacteria and Campylobacter were significantly enriched in spring. At the genus level, Helicobacter and Ralstonia were significantly enriched in spring; Prevotella 9, Streptococcus, and Prevotella were significantly enriched in summer; and UCG_005 was significantly enriched in autumn. The beneficial genera Lactobacillus, Limosilactobacillus, and Ligilactobacillus and the beneficial species Lactobacillus johnsonii, Limosilactobacillus reuteri, Ligilactobacillus murinus, and Lactobacillus amylovorus all showed the same seasonal trend; namely, their average relative abundance was markedly greater during the winter months compared to other seasons. Compared with other seasons, carbohydrate metabolic function was significantly upregulated in winter (p < 0.01), amino acid metabolic function was relatively increased in spring, and energy metabolic function and the metabolic function of cofactors and vitamins were significantly downregulated in winter and relatively upregulated in summer. A variance partitioning analysis (VPA) and redundancy analysis (RDA) showed that the proportions of fruits and vegetables in the diet, but not climatic factors (temperature and humidity), significantly influenced the seasonal changes in the gut microbiota. These variations were related to changes in the proportions of fruits and vegetables. This research presents novel findings regarding the influence of external environmental factors on the gastrointestinal environment of rhesus monkeys.

Microbial valorization of kraft black liquor for production of platform chemicals, biofuels, and value-added products: A critical review

The proper treatment and utilization of kraft black liquor, generated from the pulp and paper industry through the kraft pulping method, is required to reduce environmental impacts prior to the final disposal. It also improves the economic performance through the utilization of waste. Microbial valorization appears to demonstrates the dual benefits of waste management and resource recovery by providing an innovative solution to convert kraft black liquor into resource for reuse. A comprehensive review on the microbial valorization of kraft black liquor, describing the role in valorization and management, is still lacking in the literature, forming the rationale of this article. Thus, the present study reviews and systematically discusses the potential of utilizing microorganisms to valorize kraft black liquor as a sustainable feedstock to develop a numerous portfolio of platform chemicals, bioenergy, and other value-added products. This work contributes to sustainability and resource efficiency within the pulp and paper industry. The recent developments in utilization of synthetic biology tools and molecular techniques, including omics approaches for engineering novel microbial strains, for enhancing kraft black liquor valorization has been presented. This review explores how the better utilization of kraft black liquor in the pulp and paper industry contributes to achieving UN Sustainable Development Goals (SDGs), particularly clean water and sanitation (SDG 6) as well as the affordable and clean energy goal (SDG 7). The current review also addresses challenges related to toxicity, impurities, low productivity, and downstream processing that serve as obstacles to the progress of developing highly efficient bioproducts. The new directions for future research efforts to fill the critical knowledge gaps are proposed. This study concludes that by implementing microbial valorization techniques, the pulp and paper industry can transition from a linear to a circular bioeconomy and eco-friendly manage the kraft black liuor. This approach showed to be effective towards resource recovery, while simultaneously minimizing the environmental burden.

A scientific version of understanding "Why did the chickens cross the road"? - A guided journey through Bacillus spp. towards sustainable agriculture, circular economy and biofortification

The world, a famished planet with an overgrowing population, requires enormous food crops. This scenario compelled the farmers to use a high quantity of synthetic fertilizers for high food crop productivity. However, prolonged usage of chemical fertilizers results in severe adverse effects on soil and water quality. On the other hand, the growing population significantly consumes large quantities of poultry meats. Eventually, this produces a mammoth amount of poultry waste, chicken feathers. Owing to the protein value of the chicken feathers, these wastes are converted into protein hydrolysate and further extend their application as biostimulants for sustained agriculture. The protein profile of chicken feather protein hydrolysate (CFPH) produced through Bacillus spp. was the maximum compared to physical and chemical protein extraction methods. Several studies proved that the application of CFPH and active Bacillus spp. culture to soil and plants results in enhanced plant growth, phytochemical constituents, crop yield, soil nutrients, fertility, microbiome and resistance against diverse abiotic and biotic stresses. Overall, "CFPH - Jack of all trades" and "Bacillus spp. - an active camouflage to the surroundings where they applied showed profound and significant benefits to the plant growth under the most adverse conditions. In addition, Bacillus spp. coheres the biofortification process in plants through the breakdown of metals into metal ions that eventually increase the nutrient value of the food crops. However, detailed information on them is missing. This can be overcome by further real-world studies on rhizoengineering through a multi-omics approach and their interaction with plants. This review has explored the best possible and efficient strategy for managing chicken feather wastes into protein-rich CFPH through Bacillus spp. bioconversion and utilizing the CFPH and Bacillus spp. as biostimulants, biofertilizers, biopesticides and biofortificants. This paper is an excellent report on organic waste management, circular economy and sustainable agriculture research frontier.

Desilification of phytolith exacerbates the release of arsenic from rice straw

Arsenic (As) turnover in rice paddy agro-ecosystems has received much attention because As can enter the food chain through its accumulation in rice, thereby affecting human health. Returning straw to soil is a common practice to retain nutrients for soil and crops, but it also cycles As within the rice paddy field ecosystems. However, there is still a lack of detailed understanding of the fate of As in rice straw, and how or to what extent it is recycled back into the soil environment. This study aims to elucidate the relationship between the microstructure of rice straw and the release of As during rice straw decomposition. The microstructure of rice straw was found to comprise both organic and silica (phytolith) components. These two constituents are inter-embedded to form a composite-like structure that contains up to 6.48 mg As Kg-1. The 30-day batch experiments revealed that the biochemical release of As simultaneously depends upon the decomposition of the organic component and the desilicification of the silica component. Accompanying the release of As was the release of other elements such as Fe, Al, P and S. These elements can further interact with As to form less mobile compounds. The introduction of either Trichoderma harzianum or Bacillus velezensis was expected to accelerate the decomposition of rice straw, and enhance the silica dissolution, hence contributing to an increase in the As release. Despite these expectations, our observations showed the opposite effects. Microorganisms presumably have facilitated the change in solution chemistry or the inclusion of As into the newly-formed precipitates. The biochemical decomposition process can reduce straw particle size, while the negatively-charge surface will involve microsized straw particles in the electrostatic interaction, thereby favoring the dispersibility state. Therefore, the co-transport of micro-sized straw particles with As under field conditions should not be neglected.

Cellulase with Bacillus velezensis improves physicochemical characteristics, microbiota and metabolites of corn germ meal during two-stage co-fermentation

Corn germ meal (CGM) is one of the major byproducts of corn starch extraction. Although CGM has rich fiber content, it lacks good protein content and amino acid balance, and therefore cannot be fully utilized as animal feed. In this study, we investigated the processing effect of cellulase synergized with Bacillus velezensis on the nutritional value of pretreated CGM (PCGM) in two-stage solid-state fermentation (SSF). High-throughput sequencing technology was used to explore the dynamic changes in microbial diversity. The results showed that compared with four combinations of B. velezensis + Lactiplantibacillus plantarum (PCGM-BL), cellulase + L. plantarum (PCGM-CL),control group (PCGM-CK), and cellulase + B. velezensis + L. plantarum (PCGM-BCL), the fourth combination of PCGM-BCL significantly improved the nutritional characteristics of PCGM. After two-stage SSF (48 h), viable bacterial count and contents of crude protein (CP) and trichloroacetic acid-soluble protein (TCA-SP) all were increased in PCGM-BCL (p < 0.05), while the pH was reduced to 4.38 ± 0.02. In addition, compared with PCGM-BL, the cellulose degradation rate increased from 5.02 to 50.74%, increasing the amounts of short-chain fatty acids (216.61 ± 2.74 to 1727.55 ± 23.00 µg/g) and total amino acids (18.60 to 21.02%) in PCGM-BCL. Furthermore, high-throughput sequencing analysis revealed significant dynamic changes in microbial diversity. In the first stage of PCGM-BCL fermentation, Bacillus was the dominant genus (99.87%), which after 24 h of anaerobic fermentation changed to lactobacillus (37.45%). Kyoto Encylopaedia of Genes and Genomes (KEGG) metabolic pathway analysis revealed that the pathways related to the metabolism of carbohydrates, amino acids, cofactors, and vitamins accounted for more than 10% of the enriched pathways throughout the fermentation period. Concisely, we show that cellulase can effectively improve the nutritional value of PCGM when synergized with B. velezensis in two-stage SSF.

The gastrointestinal microbiome of browsing goats (Capra hircus)

Despite the growing interest in the ruminants' gastrointestinal tract (GIT) microbiomes' ability to degrade plant materials by animal husbandry and industrial sectors, only a few studies addressed browsing ruminants. The present work describes the taxonomic and functional profile of the bacterial and archaeal communities from five different gastrointestinal sections (rumen, omasum-abomasum, jejunum, cecum and colon) of browsing Capra hircus, by metabarcoding using 16S rRNA genes hypervariable regions. The bacterial communities across the GITs are mainly composed of Bacillota and Bacteroidota. Prevotella was the leading bacterial group found in the stomachs, Romboutsia in the jejuna, and Rikenellaceae_RC9_gut_group, Bacteroides, UCG-010_ge, UCG-005, and Alistipes in large intestines. The archaeal communities in the stomachs and jejuna revealed to be mainly composed of Methanobrevibacter, while in the large intestines its dominance is shared with Methanocorpusculum. Across the GITs, the main metabolic functions were related to carbohydrate, amino acid, and energy metabolisms. Significant differences in the composition and potential biological functions of the bacterial communities were observed among stomachs, jejuna and large intestines. In contrast, significant differences were observed among stomachs and jejuna verse large intestines for archaeal communities. Overall different regions of the GIT are occupied by different microbial communities performing distinct biological functions. A high variety of glycoside hydrolases (GHs) indispensable for degrading plant cell wall materials were predicted to be present in all the GIT sections.

Fermentation of NaHCO3-treated corn germ meal by Bacillus velezensis CL-4 promotes lignocellulose degradation and nutrient utilization

Sodium bicarbonate pretreatment and solid-state fermentation (SSF) were used to maximize the nutritional value of corn germ meal (CGM) by inoculating it with Bacillus velezensis CL-4 (isolated from chicken cecal contents and capable of degrading lignocellulose). Based on genome sequencing, B. velezensis CL-4 has a 4,063,558 bp ring chromosome and 46.27% GC content. Furthermore, genes associated with degradation of lignocellulose degradation were detected. Pretreatment of CGM (PCGM) with sodium bicarbonate (optimized to 0.06 g/mL) neutralized low pH. Fermented and pretreated CGM (FPCGM) contained more crude protein (CP), soluble protein of trichloroacetic acid (TCA-SP), and total amino acids (aa) than CGM and PCGM. Degradation rates of cellulose and hemicellulose were reduced by 21.33 and 71.35%, respectively, after 48 h fermentation. Based on electron microscopy, FPCGM destroys the surface structure and adds small debris of the CGM substrate, due to lignocellulose breakdown. Furthermore, 2-oxoadipic acid and dimethyl sulfone were the most important metabolites during pretreatment. Concentrations of adenosine, cytidine, guanosine, S-methyl-5'-thioadenosine, and adenine decreased significantly after 48 h fermentation, whereas concentrations of probiotics, enzymes, and fatty acids (including palmitic, 16-hydroxypalmitic, and linoleic acids) were significantly improved after fermentation. In conclusion, the novel pretreatment of CGM provided a proof of concept for using B. velezensis CL-4 to degrade lignocellulose components, improve nutritional characteristics of CGM, and expand CGM lignocellulosic biological feed production. KEY POINTS: • Sodium bicarbonate (baking soda) can be used as an economical and green additive to pretreat corn germ meal; • Fermentation with B. velezensis degrades the cellulose and hemicellulose component of corn germ meal and improves its feed quality; • As a novel qualified presumption of safety (QPS) strain, B. velezensis should have broad potential applications in food and feed industries.

Lignocellulose conversion of ensiled Caragana korshinskii Kom. facilitated by Pediococcus acidilactici and cellulases

To explore the biofuel production potential of Caragana korshinskii Kom., Pediococcus acidilactici and an exogenous fibrolytic enzyme were employed to investigate the fermentation profile, structural carbohydrates degradation, enzymatic saccharification and the dynamics of bacterial community of C. korshinskii silage. After 60 d of ensiling, all additives increased the fermentation quality. The highest lactic and acetic acids and lowest non-protein nitrogen (NPN) and ammonia nitrogen (NH₃ -N) were observed in P. acidilactici and Acremonium cellulase (PA + AC) treated silage. Additionally, all additives significantly increased the ferulic acid content and fibre degradability with the highest values obtained from PA + AC silage. The bacterial community in all silages was dominated by P. acidilactici throughout the entire fermentation process. The bacterial community was also modified by the silage additives exhibiting a relatively simple network of bacterial interaction characterized by a lower bacterial diversity in P. acidilactici (PA) treated silage. The highest 6-phospho-beta-glucosidase abundance was observed in PA-treated silage at the mid-later stage of ensiling. PA treatment exhibited lower structural carbohydrates degradation but performed better in lignocellulose conversion during enzymatic saccharification. These results indicated that pretreating C. korshinskii improved its silage quality and potential use as a lignocellulosic feedstock for the production of bio-product and biofuel.

Bacterial Transformation and Processing of Diatom-Derived Organic Matter: A Case Study for Skeletonema dohrnii

Bacterial transformation and processing of phytoplankton-derived organic matter are extremely important for the formation of ubiquitous organic matter (OM) in aquatic ecosystems. Heterotrophic bacteria convert OM into biomass and recycle inorganic components, contributing to the production of microbial food webs. While phytoplankton-derived organic matter is commonly studied, the transformation and processing of dissolved OM (DOM) and lysate OM (LOM) by culturable epiphytic bacteria remains poorly understood. In this study, cultivable epiphytic bacteria from the marine diatom, Skeletonema dohrnii, were isolated, purified, and identified. Three bacteria, Roseobacteria sp., Marinobacter sp., and Bacillus sp., were selected to study the transformation and processing of S. dohrnii-derived DOM and LOM using excitation-emission matrix (EEM) fluorescence methods, and bacterial abundance, dissolved organic carbon (DOC) concentration, and transparent exopolymer particle (TEP) content were measured. Meanwhile, the bacterial transformation of DOM and LOM was further evaluated by the fluorescence index, biological index, β/α, and humification index. The primary fluorophores, peak A (humic-like), peak C (humic-like), peak M (humic-like), peak B (protein-like), and peak T (tryptophan-like), were present in the sample. The fluorescence of DOM and LOM was dominated by protein-like signal that became increasingly humic-like over time, suggesting that more complex molecules (e.g., recalcitrant OM) are being produced. The fluorescence of DOM and LOM was dominated by a protein-like signal that became increasingly humic-like over time, suggesting that epiphytic bacteria produced more complex molecules. Results showed that the bacteria utilized LOM more rapidly than DOM. While the three bacteria transformed OM to different degrees, all were able to facilitate microbial reprocessing of OM into refractory OM.

Bioprospecting of microbial enzymes: current trends in industry and healthcare

Microbial enzymes have an indispensable role in producing foods, pharmaceuticals, and other commercial goods. Many novel enzymes have been reported from all domains of life, such as plants, microbes, and animals. Nonetheless, industrially desirable enzymes of microbial origin are limited. This review article discusses the classifications, applications, sources, and challenges of most demanded industrial enzymes such as pectinases, cellulase, lipase, and protease. In addition, the production of novel enzymes through protein engineering technologies such as directed evolution, rational, and de novo design, for the improvement of existing industrial enzymes is also explored. We have also explored the role of metagenomics, nanotechnology, OMICs, and machine learning approaches in the bioprospecting of novel enzymes. Overall, this review covers the basics of biocatalysts in industrial and healthcare applications and provides an overview of existing microbial enzyme optimization tools. KEY POINTS: • Microbial bioactive molecules are vital for therapeutic and industrial applications. • High-throughput OMIC is the most proficient approach for novel enzyme discovery. • Comprehensive databases and efficient machine learning models are the need of the hour to fast forward de novo enzyme design and discovery.

Comparative Genome Analysis Reveals Phylogenetic Identity of Bacillus velezensis HNA3 and Genomic Insights into Its Plant Growth Promotion and Biocontrol Effects

Bacillus velezensis HNA3, a potential plant growth promoter and biocontrol rhizobacterium, was isolated from plant rhizosphere soils in our previous work. Here, we sequenced the entire genome of the HNA3 strain and performed a comparative genome analysis. We found that HNA3 has a 3,929-kb chromosome with 46.5% GC content and 4,080 CDSs. We reclassified HNA3 as a Bacillus velezensis strain by core genome analysis between HNA3 and 74 previously defined Bacillus strains in the evolutionary tree. A comparative genomic analysis among Bacillus velezensis HNA3, Bacillus velezensis FZB42, Bacillus amyloliquefaciens DSM7, and Bacillus subtilis 168 showed that only HNA3 has one predicated secretory protein feruloyl esterase that catalyzes the hydrolysis of plant cell wall polysaccharides. The analysis of gene clusters revealed that whole biosynthetic gene clusters type Lanthipeptide was exclusively identified in HNA3 and might lead to the synthesis of new bioactive compounds. Twelve gene clusters were detected in HNA3 responsible for the synthesis of 14 secondary metabolites including Bacillaene, Fengycin, Bacillomycin D, Surfactin, Plipastatin, Mycosubtilin, Paenilarvins, Macrolactin, Difficidin, Amylocyclicin, Bacilysin, Iturin, Bacillibactin, Paenibactin, and others. HNA3 has 77 genes encoding for possible antifungal and antibacterial secreting carbohydrate active enzymes. It also contains genes involved in plant growth promotion, such as 11 putative indole acetic acid (IAA)-producing genes, spermidine and polyamine synthase genes, volatile compound producing genes, and multiple biofilm related genes. HNA3 also has 19 phosphatase genes involved in phosphorus solubilization. Our results provide insights into the genetic characteristics responsible for the bioactivities and potential application of HNA3 as plant growth-promoting strain in ecological agriculture.

IMPORTANCE This study is the primary initiative to identify Bacillus velezensis HNA3 whole genome sequence and reveal its genomic properties as an effective biocontrol agent against plant pathogens and a plant growth stimulator. HNA3 genetic profile can be used as a reference for future studies that can be applied as a highly effective biofertilizer and biofungicide inoculum to improve agriculture productivity. HNA3 reclassified in the phylogenetic tree which may be helpful for highly effective strain engineering and taxonomy. The genetic comparison among HNA3 and closely similar species B. velezensis FZB42, B. amyloliquefaciens DSM7, and B. subtilis 168 demonstrates some distinctive genetic properties of HNA3 and provides a basis for the genetic diversity of the Bacillus genus, which allows developing more effective eco-friendly resources for agriculture and separation of Bacillus velezensis as distinct species in the phylogenetic tree.

Genomic, Antimicrobial, and Aphicidal Traits of Bacillus velezensis ATR2, and Its Biocontrol Potential against Ginger Rhizome Rot Disease Caused by Bacillus pumilus

Ginger rhizome rot disease, caused by the pathogen Bacilluspumilus GR8, could result in severe rot of ginger rhizomes and heavily threaten ginger production. In this study, we identified and characterized a new Bacillus velezensis strain, designated ATR2. Genome analysis revealed B. velezensis ATR2 harbored a series of genes closely related to promoting plant growth and triggering plant immunity. Meanwhile, ten gene clusters involved in the biosynthesis of various secondary metabolites (surfactin, bacillomycin, fengycin, bacillibactin, bacilysin, difficidin, macrolactin, bacillaene, plantazolicin, and amylocyclicin) and two clusters encoding a putative lipopeptide and a putative phosphonate which might be explored as novel bioactive compounds were also present in the ATR2 genome. Moreover, B. velezensis ATR2 showed excellent antagonistic activities against multiple plant pathogenic bacteria, plant pathogenic fungi, human pathogenic bacteria, and human pathogenic fungus. B. velezensis ATR2 was also efficacious in control of aphids. The antagonistic compound from B. velezensis ATR2 against B.pumilus GR8 was purified and identified as bacillomycin D. In addition, B. velezensis ATR2 exhibited excellent biocontrol efficacy against ginger rhizome rot disease on ginger slices. These findings showed the potential of further applications of B. velezensis ATR2 as a biocontrol agent in agricultural diseases and pests management.

Current Advances in Microbial Production of Acetoin and 2,3-Butanediol by Bacillus spp

The growing need for industrial production of bio-based acetoin and 2,3-butanediol (2,3-BD) is due to both environmental concerns, and their widespread use in the food, pharmaceutical, and chemical industries. Acetoin is a common spice added to many foods, but also a valuable reagent in many chemical syntheses. Similarly, 2,3-BD is an indispensable chemical on the platform in the production of synthetic rubber, printing inks, perfumes, antifreeze, and fuel additives. This state-of-the-art review focuses on representatives of the genus Bacillus as prospective producers of acetoin and 2,3-BD. They have the following important advantages: non-pathogenic nature, unpretentiousness to growing conditions, and the ability to utilize a huge number of substrates (glucose, sucrose, starch, cellulose, and inulin hydrolysates), sugars from the composition of lignocellulose (cellobiose, mannose, galactose, xylose, and arabinose), as well as waste glycerol. In addition, these strains can be improved by genetic engineering, and are amenable to process optimization. Bacillus spp. are among the best acetoin producers. They also synthesize 2,3-BD in titer and yield comparable to those of the pathogenic producers. However, Bacillus spp. show relatively lower productivity, which can be increased in the course of challenging future research.

Enhanced Activity by Genetic Complementarity: Heterologous Secretion of Clostridial Cellulases by Bacillus licheniformis and Bacillus velezensis

To adapt to various ecological niches, the members of genus Bacillus display a wide spectrum of glycoside hydrolases (GH) responsible for the hydrolysis of cellulose and lignocellulose. Being abundant and renewable, cellulose-containing plant biomass may be applied as a substrate in second-generation biotechnologies for the production of platform chemicals. The present study aims to enhance the natural cellulase activity of two promising 2,3-butanediol (2,3-BD) producers, Bacillus licheniformis 24 and B. velezensis 5RB, by cloning and heterologous expression of cel8A and cel48S genes of Acetivibrio thermocellus. In B. licheniformis, the endocellulase Cel8A (GH8) was cloned to supplement the action of CelA (GH9), while in B. velezensis, the cellobiohydrolase Cel48S (GH48) successfully complemented the activity of endo-cellulase EglS (GH5). The expression of the natural and heterologous cellulase genes in both hosts was demonstrated by reverse-transcription PCR. The secretion of clostridial cellulases was additionally enhanced by enzyme fusion to the subtilisin-like signal peptide, reaching a significant increase in the cellulase activity of the cell-free supernatants. The results presented are the first to reveal the possibility of genetic complementation for enhancement of cellulase activity in bacilli, thus opening the prospect for genetic improvement of strains with an important biotechnological application.

Valorisation of wheat bran to produce natural pigments using selected microorganisms

Pigments are compounds with highly diverse structures and wide uses, which production is increasing worldwide. An eco-friendly method of bioproduction is to use the ability of some microorganisms to ferment on renewable carbon sources. Wheat bran (WB) is a cheap and abundant lignocellulosic co-product of low recalcitrance to biological conversion. Microbial candidates with theoretical ability to degrade WB were first preselected using specific databases. The microorganisms were Ashbya gossypii (producing riboflavin), Chitinophaga pinensis (producing flexirubin), Chromobacterium vaccinii (violacein) and Gordonia alkanivorans (carotenoids). Growth was shown for each on minimal salt medium supplemented with WB at 5 g.L^-1. Activities of the main enzymes consuming WB were measured, showing leucine amino-peptidase (up to 8.45 IU. mL^-1) and β-glucosidase activities (none to 6.44 IU. mL^-1). This was coupled to a FTIR (Fourier Transform Infra-Red) study of the WB residues that showed main degradation of the WB protein fraction for C. pinensis, C. vaccinii and G. alkanivorans. Production of the pigments on WB was assessed for all the strains except Ashbya, with values of production reaching up to 1.47 mg.L^-1. The polyphasic approach used in this study led to a proof of concept of pigment production from WB as a cheap carbon source.

Hemicellulosic biomass conversion by Moroccan hot spring Bacillus paralicheniformis CCMM B940 evidenced by glycoside hydrolase activities and whole genome sequencing

Thermophilic bacteria, especially from the genus Bacillus, constitute a huge potential source of novel enzymes that could be relevant for biotechnological applications. In this work, we described the cellulose and hemicellulose-related enzymatic activities of the hot spring Bacillus aerius CCMM B940 from the Moroccan Coordinated Collections of Microorganisms (CCMM), and revealed its potential for hemicellulosic biomass utilization. Indeed, B940 was able to degrade complex polysaccharides such as xylan and lichenan and exhibited activity towards carboxymethylcellulose. The strain was also able to grow on agriculture waste such as orange and apple peels as the sole carbon source. Whole-genome sequencing allowed the reclassification of CCMM B940 previously known as B. aerius into Bacillus paralicheniformis since the former species name has been rejected. The draft genome reported here is composed of 38 contigs resulting in a genome of 4,315,004 bp and an average G + C content of 45.87%, and is an important resource for illuminating the molecular mechanisms of carbohydrate metabolism. The annotated genomic sequences evidenced more than 52 genes encoding glycoside hydrolases and pectate lyases belonging to 27 different families of CAZymes that are involved in the degradation of plant cell wall carbohydrates. Genomic predictions in addition to in vitro experiments have revealed broad hydrolytic capabilities of the strain, thus reinforcing its relevance for biotechnology applications.

A Review on Bacterial Contribution to Lignocellulose Breakdown into Useful Bio-Products

Discovering novel bacterial strains might be the link to unlocking the value in lignocellulosic bio-refinery as we strive to find alternative and cleaner sources of energy. Bacteria display promise in lignocellulolytic breakdown because of their innate ability to adapt and grow under both optimum and extreme conditions. This versatility of bacterial strains is being harnessed, with qualities like adapting to various temperature, aero tolerance, and nutrient availability driving the use of bacteria in bio-refinery studies. Their flexible nature holds exciting promise in biotechnology, but despite recent pointers to a greener edge in the pretreatment of lignocellulose biomass and lignocellulose-driven bioconversion to value-added products, the cost of adoption and subsequent scaling up industrially still pose challenges to their adoption. However, recent studies have seen the use of co-culture, co-digestion, and bioengineering to overcome identified setbacks to using bacterial strains to breakdown lignocellulose into its major polymers and then to useful products ranging from ethanol, enzymes, biodiesel, bioflocculants, and many others. In this review, research on bacteria involved in lignocellulose breakdown is reviewed and summarized to provide background for further research. Future perspectives are explored as bacteria have a role to play in the adoption of greener energy alternatives using lignocellulosic biomass.

Nutritional quality improvement of soybean meal by Bacillus velezensis and Lactobacillus plantarum during two-stage solid- state fermentation

Bacillus velezensis is widely used for agricultural biocontrol, due to its ability to enhance plant growth while suppressing the growth of microbial pathogens. However, there are few reports on its application in fermented feed. Here, a two-stage solid-state fermentation process using Bacillus velezensis followed by Lactobacillus plantarum was developed to degrade antinutritional factors (ANFs) and improve soybean meal (SBM) nutrition for animal feed. The process was evaluated for performance in degrading SBM antinutritional factors, dynamic changes in physicochemical characteristics, microorganisms and metabolites. After two-stage fermentation, degradation rates of glycinin and β-conglycinin contents reached 78.60% and 72.89%, respectively. The pH of fermented SBM (FSBM) decreased to 4.78 ± 0.04 and lactic acid content reached 183.38 ± 4.86 mmol/kg. NSP-degrading enzymes (Non-starch polysaccharide, NSPases) and protease were detected from the fermented product, which caused the changed microstructure of SBM. Compared to uninoculated SBM, FSBM exhibited increased proportions of crude protein (51.97 ± 0.44% vs. 47.28 ± 0.34%), Ca, total phosphorus (P), and trichloroacetic acid-soluble protein (11.79 ± 0.13% vs. 5.07 ± 0.06%). Additionally, cellulose and hemicellulose proportions declined by 22.10% and 39.15%, respectively. Total amino acid content increased by 5.05%, while the difference of AA content between the 24 h, 48 h and 72 h of fermentation was not significant (P > 0.05). Furthermore, FSBM also showed antibacterial activity against Staphylococcus aureus and Escherichia coli. These results demonstrated that two-stage SBM fermentation process based on Bacillus velezensis 157 and Lactobacillus plantarum BLCC2-0015 is an effective approach to reduce ANFs content and improve the quality of SBM feed.

Novel research on nanocellulose production by a marine Bacillus velezensis strain SMR: a comparative study

Bacterial nanocellulose (BNC) is a nanofibrillar polymer that possesses unique characteristics such as high chemical purity, mechanical strength, flexibility, and absorbency. In addition, different bacterial strains can form nanocellulose (NC) in multiple shapes and sizes. This study describes the first report of a marine Bacillus strain that is able to synthesize NC. The strain identified as B. velezensis SMR based on 16S rDNA sequencing, produced highly structured NC, as confirmed by X-ray diffraction (XRD) and Scanning Electron Microscopic Analysis (SEM). In Hestrin-Schramm (HS) medium, B. velezensis SMR produced twice the quantity of BNC in comparison to the reference strain, G. xylinus ATCC 10245. The ability of B. velezensis SMR to produce NC using different industrial waste materials as growth media was tested. Growth in Ulva seaweed extract supported a 2.5-fold increase of NC production by B. velezensis SMR and a threefold increase in NC production by G. xylinus ATCC 10245. As proof of principle for the usability of NC from B. velezensis SMR, we successfully fabricated a BNC-based polyvinyl alcohol hydrogel (BNC-PVA) system, a promising material used in different fields of application such as medicine, food, and agriculture.

Bacillus velezensis: phylogeny, useful applications, and avenues for exploitation

Some members of the Bacillus velezensis (Bv) group (e.g., Bv FZB42T and AS3.43) were previously assigned grouping with B. subtilis and B. amyloliquefaciens, based on the fact that they shared a 99% DNA-DNA percentage phylogenetic similarity. However, hinging on current assessments of the pan-genomic reassignments, the differing phylogenomic characteristics of Bv from B. subtilis and B. amyloliquefaciens are now better understood. Within this re-grouping/reassignment, the various strains within the Bv share a close phylogenomic resemblance, and a number of these strains have received a lot of attention in recent years, due to their genomic robustness, and the growing evidence for their possible utilization in the agricultural industry for managing plant diseases. Only a few applications for their use medicinally/pharmaceutically, environmentally, and in the food industry have been reported, and this may be due to the fact that the majority of those strains investigated are those typically occurring in soil. Although the intracellular unique biomolecules of Bv strains have been revealed via in silico genome modeling and investigated using transcriptomics and proteomics, a further inquisition into the Bv metabolome using newer technologies such as metabolomics could elucidate additional applications of this economically relevant Bacillus species, beyond that of primarily the agricultural sector.

Selecting lipopeptide-producing, Fusarium-suppressing Bacillus spp.: Metabolomic and genomic probing of Bacillus velezensis NWUMFkBS10.5

The results of this study indicate that the maize rhizosphere remains a reservoir for microbial strains with unique beneficial properties. The study sought to provide an indigenous Bacillus strain with a bioprotective potential to alleviate maize fusariosis in South Africa. We selected seven Bacillus isolates (MORWBS1.1, MARBS2.7, VERBS5.5, MOREBS6.3, MOLBS8.5, MOLBS8.6, and NWUMFkBS10.5) with biosuppressive effects against two maize fungal pathogens (Fusarium graminearum and Fusarium culmorum) based on 16S rDNA gene characterization and lipopeptide gene analysis. The PCR analysis revealed that lipopeptide genes encoding the synthesis of iturin, surfactin, and fengycin might be responsible for their antifungal activities. Few of the isolates also showed possible biosurfactant capability, and their susceptibility to known antibiotics is indicative of their eco‐friendly attributes. In addition, in silico genomic analysis of our best isolate (Bacillus velezensis NWUMFkBS10.5) and characterization of its active metabolite with FTIR, NMR, and ESI‐Micro‐Tof MS confirmed the presence of valuable genes clusters and metabolic pathways. The versatile genomic potential of our Bacillus isolate emphasizes the continued relevance of Bacillus spp. in biological management of plant diseases.