Recent discoveries and applications of Anoxybacillus

Production and biological activities of exopolysaccharides synthesized by thermophilic bacilli isolated from hot springs in Türkiye

Thermophilic bacteria able to produce exopolysaccharides (EPSs) have become attractive in recent years. EPSs synthesized by thermophiles are worth investigating due to their unexplored structural and biological properties. In this study, EPSs from thermophilic, Gram-positive bacterial isolates were purified and tested for their biological activities. A total of one hundred seven thermophilic bacteria were screened for their ability to produce exopolysaccharides. Nine isolates belonging to Geobacillus, Parageobacillus, Aeribacillus, and Anoxybacillus genera with highest EPS production were chosen, and purified EPSs (20, 61, 74, 76, 78, 89, 106, 134, and 261) were used for biological activity studies. EPS yields of selected thermophilic bacteria ranged between 117 and 419 mg/L. Among the tested EPSs, 61, 106, and 261 showed antibacterial effect against E. faecalis JH2-2 at a final concentration of 1.5 mg/mL. EPS samples had significant antioxidant capacity, especially EPS 134, with the highest DPPH radical scavenging activity of 100% at a concentration of 5 mg/mL and the strongest reducing power. EPS 20 showed the highest lipid peroxidation inhibition effect at a rate of 31%. EPSs displayed weak alpha-amylase inhibition activity when compared with standard acarbose. The prebiotic indices of EPSs 20, 61, 76, 89, 134, and 261 were found to be higher than that of inulin, a representative prebiotic carbohydrate for all tested lactic acid bacteria in the study. All examined EPSs inhibited the biofilms formed by various bacteria depending on the test strain. Results indicated that thermophilic EPSs had remarkable antioxidant, prebiotic, and antibiofilm activities. Therefore, EPSs characterized in this study may have technological applications in health and food fields.

Enhancement of the structure and biochemical function of cyclomaltodextrinase from the Anoxybacillus flavithermus ZNU-NGA with site-directed mutagenesis

This study was conducted to examine the role of the central domain of cyclomaltodextrinase in terms of stability, substrate specificity, becoming dodecameric form, and enzyme activity. To this end, H403R/L309V double-point mutation and T280Q single-point mutation were performed at the central domain and (β/α)8-barrel. The results indicated that the activity of the H403R/L309V mutant at the optimal pH and temperature increased by about 25% and 40%, respectively. Plus, the irreversible thermal inactivation of the H403R/L309V mutant at 60 °C and 160 min was approximately twice of the enzyme without mutation. Both mutants underwent significant structural change relative to the wild enzyme and subsequently a significant catalytic activity. However, the catalytic efficiency (kcat/Km) of the H403R/L309V mutant increased in the presence of beta- and gamma-cyclomaltodextrin substrates compared to the wild enzyme and T280Q mutant. As a result, by applying the L309V mutant and given the smaller size of the valine, leucine spatial inhibition in the wild protein seems to decline, and also it facilitates the substrate access to active site amino acids. Moreover, as gamma substrate is larger, eliminating the effect of spatial inhibition on this substrate has a greater effect on improving the catalytic activity of this enzyme.

Characterization and functional insights of the novel RC-type plasmid pAnox1 from Anoxybacillus gonensis 05S15

The plasmid pAnox1, isolated from Anoxybacillus gonensis 05S15, was sequenced and characterized as a circular, double-stranded DNA molecule of 1592 base pairs with a GC content of 40.01 %. Despite its cryptic nature and small genome, bioinformatic analyses identified conserved motifs associated with replication-related proteins, though BLAST searches revealed no significant homology with other plasmids. The plasmid genome contains five putative Open Reading Frames (ORFs), four palindromic sequences, and two direct repeats on both strands, suggesting regulatory roles. Electron microscopy and Southern hybridization studies confirmed that pAnox1 follows a Rolling Circle (RC) replication mode. The study further demonstrated that the plasmid encodes three distinct transcripts: ORF-1 and ORF-3 are oriented in the same direction, while ORF-5 is on the opposite strand. RACE and LACE analyses revealed transcript lengths of 903 bp for ORF1, 499 bp for ORF3, and 211 bp for ORF5. Quantitative real-time PCR estimated the relative copy number of pAnox1 at 127 ± 2 copies per chromosomal equivalent. This novel RC-type plasmid in the Anoxybacillus genome holds promise as a cloning and expression vector for biotechnological applications and in vivo protein engineering.

Untangling the adaptive strategies of thermophilic bacterium Anoxybacillus rupiensis TPH1 under low temperature

The present study investigates the low temperature tolerance strategies of thermophilic bacterium Anoxybacillus rupiensis TPH1, which grows optimally at 55 °C , by subjecting it to a temperature down-shift of 10 °C (45 °C) for 4 and 6 h followed by studying its growth, morphophysiological, molecular and proteomic responses. Results suggested that although TPH1 experienced increased growth inhibition, ROS production, protein oxidation and membrane disruption after 4 h of incubation at 45 °C yet maintained its DNA integrity and cellular structure through the increased expression of DNA damage repair and cell envelop synthesizing proteins and also progressively alleviated growth inhibition by 20% within two hours i.e., 6 h, by inducing the expression of antioxidative enzymes, production of unsaturated fatty acids, capsular and released exopolysaccharides and forming biofilm along with chemotaxis proteins. Conclusively, the adaptation of Anoxybacillus rupiensis TPH1 to lower temperature is mainly mediated by the synthesis of large numbers of defense proteins and exopolysaccharide rich biofilm formation.

Detergent-resistant α-amylase derived from Anoxybacillus karvacharensis K1 and its production based on whey

In the field of biotechnology, the utilization of agro-industrial waste for generating high-value products, such as microbial biomass and enzymes, holds significant importance. This study aimed to produce recombinant α-amylase from Anoxybacillus karvacharensis strain K1, utilizing whey as an useful growth medium. The purified hexahistidine-tagged α-amylase exhibited remarkable homogeneity, boasting a specific activity of 1069.2 U mg-1. The enzyme displayed its peak activity at 55 °C and pH 6.5, retaining approximately 70% of its activity even after 3 h of incubation at 55 °C. Its molecular weight, as determined via SDS-PAGE, was approximately 69 kDa. The α-amylase demonstrated high activity against wheat starch (1648.8 ± 16.8 U mg-1) while exhibiting comparatively lower activity towards cyclodextrins and amylose (≤ 200.2 ± 16.2 U mg-1). It exhibited exceptional tolerance to salt, withstanding concentrations of up to 2.5 M. Interestingly, metal ions and detergents such as sodium dodecyl sulfate (SDS), Triton 100, Triton 40, and Tween 80, 5,5'-dithio-bis-[2-nitrobenzoic acid (DNTB), β-mercaptoethanol (ME), and dithiothreitol (DTT) had no significant inhibitory effect on the enzyme's activity, and the presence of CaCl2 (2 mM) even led to a slight activation of the recombinant enzyme (1.4 times). The Michaelis constant (Km) and maximum reaction rate (Vmax), were determined using soluble starch as a substrate, yielding values of 1.2 ± 0.19 mg mL-1 and 1580.3 ± 183.7 μmol mg-1 protein min-1, respectively. Notably, the most favorable conditions for biomass and recombinant α-amylase production were achieved through the treatment of acid whey with β-glucosidase for 24 h.

Shaping the Microbial Landscape: Parasitoid-Driven Modifications of Bactrocera dorsalis Microbiota

Koinobiont endoparasitoids regulate the physiology of their hosts through altering host immuno-metabolic responses, processes which function in tandem to shape the composition of the microbiota of these hosts. Here, we employed 16S rRNA and ITS amplicon sequencing to investigate whether parasitization by the parasitoid wasps, Diachasmimorpha longicaudata (Ashmaed) (Hymenoptera: Braconidae) and Psyttalia cosyrae (Wilkinson) (Hymenoptera: Braconidae), induces gut dysbiosis and differentially alter the gut microbial (bacteria and fungi) communities of an important horticultural pest, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae). We further investigated the composition of bacterial communities of adult D. longicaudata and P. cosyrae to ascertain whether the adult parasitoids and parasitized host larvae share microbial taxa through transmission. We demonstrated that parasitism by D. longicaudata induced significant gut perturbations, resulting in the colonization and increased relative abundance of pathogenic gut bacteria. Some pathogenic bacteria like Stenotrophomonas and Morganella were detected in both the guts of D. longicaudata-parasitized B. dorsalis larvae and adult D. longicaudata wasps, suggesting a horizontal transfer of microbes from the parasitoid to the host. The bacterial community of P. cosyrae adult wasps was dominated by Arsenophonus nasoniae, whereas that of D. longicaudata adults was dominated by Paucibater spp. and Pseudomonas spp. Parasitization by either parasitoid wasp was associated with an overall reduction in fungal diversity and evenness. These findings indicate that unlike P. cosyrae which is avirulent to B. dorsalis, parasitization by D. longicaudata induces shifts in the gut bacteriome of B. dorsalis larvae to a pathobiont-dominated community. This mechanism possibly enhances its virulence against the pest, further supporting its candidacy as an effective biocontrol agent of this frugivorous tephritid fruit fly pest.

Thermophilic bacteria from Peruvian hot springs with high potential application in environmental biotechnology

Hot springs are extreme environments in which well-adapted microorganisms with biotechnological applications can thrive naturally. These thermal environments across Peruvian territory have, until now, remained poorly investigated. In this study, two hot springs, El Tragadero and Quilcate, located in Cajamarca (Peru) were selected in order to investigate the biotechnological potential of indigenous thermophilic bacteria. Enrichment and isolation processes were carried out using microbial mats, sediments, biofilms, and plastic polymers as samples. Screening for biosurfactants and siderophores production, as well as for polyethylene terephthalate (PET) hydrolysis was done using culture-dependent techniques. After molecular identification, Bacillus was found as the most abundant genus in both hot springs. Bacillus velezensis was found producing biosurfactants under high-level temperature. Anoxybacillus species (A. salavatliensis and A. gonensis) are here reported as siderophore-producing bacteria for the first time. Additionally, Brevibacillus and the less-known bacterium Tistrella mobilis were found demonstrating PET hydrolysis activity. Our study provides the first report of thermophilic bacteria isolated from Peruvian hot springs with biotechnological potential for the bioremediation of oil-, metal- and plastic-polluted environments.

Elevated abundance of Komagataeibacter results in a lower pH in kombucha production; insights from microbiomic and chemical analyses

Kombucha consumption has grown rapidly worldwide in the last decade, with production at both small- and large scales. The complex fermentation process involves both bacterial and yeast species, but little is known regarding the progression of microbial development during production. We explored the microbial diversity of multiple batches across two kombucha types, i. e commercial scale versus laboratory-made (hereafter "home") kombucha brew using metabarcoding to characterize both fungal and bacterial communities. We found the microbial community of the commercial kombucha brew to be more complex than that of the home brew. Furthermore, PERMANOVA uncovered significant compositional differences between the bacterial (F = 2.68, R2 = 0.23, p = 00.001) and fungal (F = 3.18, R2 = 0.26, p = 00.006) communities between batches. For the home brew, both alpha and beta diversity analyses revealed no significant differences between all batches and replicates. When the microbial diversity of the home and commercial kombucha types were directly compared, the former had higher proportions of Ammoniphilus and Komagataeibacter. The commercial kombucha on the other hand were high in Anoxybacillus, Methylobacterium and Sphingomonas. For the fungal communities, the most dominant fungal genera detected in both kombucha types were similar. Linear model revealed significant correlations between some microorganisms and the sugars and organic acids assayed in this study. For example, rising glucose levels correlated with an increase in the relative abundance of Komagataeibacter (F = 7.115, Adj. R2 = 0.44, p = 00.0003). We believe these results contribute towards achieving a better control of the kombucha fermentation process and may assist in targeted product diversification.

Highly stable and versatile α-amylase from Anoxybacillus vranjensis ST4 suitable for various applications

α-Amylase from the thermophilic bacterial strain Anoxybacillus vranjensis ST4 (AVA) was cloned into the pMALc5HisEk expression vector and successfully expressed and purified from the Escherichia coli ER2523 host strain. AVA belongs to the GH13_5 subfamily of glycoside hydrolases and has 7 conserved sequence regions (CSRs) distributed in three distinct domains (A, B, C). In addition, there is a starch binding domain (SBD) from the CBM20 family of carbohydrate binding modules (CBMs). AVA is a monomer of 66 kDa that achieves maximum activity at 60-80 °C and is active and stable over a wide pH range (4.0-9.0). AVA retained 50 % of its activity after 31 h of incubation at 60 °C and was resistant to a large number of denaturing agents. It hydrolyzed starch granules very efficiently, releasing maltose, maltotriose and maltopentaose as the main products. The hydrolysis rates of raw corn, wheat, horseradish, and potato starch, at a concentration of 10 %, were 87.8, 85.9, 93.0, and 58 %, respectively, at pH 8.5 over a 3 h period. This study showed that the high level of expression as well as the properties of this highly stable and versatile enzyme show all the prerequisites for successful application in industry.

The genus Anoxybacillus: an emerging and versatile source of valuable biotechnological products

Thermophilic and alkaliphilic microorganisms are unique organisms that possess remarkable survival strategies, enabling them to thrive on a diverse range of substrates. Anoxybacillus, a genus of thermophilic and alkaliphilic bacteria, encompasses 24 species and 2 subspecies. In recent years, extensive research has unveiled the diverse array of thermostable enzymes within this relatively new genus, holding significant potential for industrial and environmental applications. The biomass of Anoxybacillus has demonstrated promising results in bioremediation techniques, while the recently discovered metabolites have exhibited potential in medicinal experiments. This review aims to provide an overview of the key experimental findings related to the biotechnological applications utilizing bacteria from the Anoxybacillus genus.

Anoxybacillus: an overview of a versatile genus with recent biotechnological applications

The Bacillaceae family members are considered to be a good source of microbial factories for biotechnological processes. In contrast to Bacillus and Geobacillus, Anoxybacillus, which would be thermophilic and spore-forming group of bacteria, is a relatively new genus firstly proposed in the year of 2000. The development of thermostable microbial enzymes, waste management and bioremediation processes would be a crucial parameter in the industrial sectors. There has been increasing interest in Anoxybacillus strains for biotechnological applications. Therefore, various Anoxybacillus strains isolated from different habitats have been explored and identified for biotechnological and industrial purposes such as enzyme production, bioremediation and biodegradation of toxic compounds. Certain strains have ability to produce exopolysaccharides possessing biological activities including antimicrobial, antioxidant and anticancer. This current review provides past and recent discoveries regarding Anoxybacillus strains and their potential biotechnological applications in enzyme industry, environmental processes and medicine.

Environmental sporobiota: Occurrence, dissemination, and risks

Spore-forming bacteria known as sporobiota are widespread in diverse environments from terrestrial and aquatic habitats to industrial and healthcare systems. Studies on sporobiota have been mainly focused on food processing and clinical fields, while a large amount of sporobiota exist in natural environments. Due to their persistence and capabilities of transmitting virulence factors and antibiotic resistant genes, environmental sporobiota could pose significant health risks to humans. These risks could increase as global warming and environmental pollution has altered the life cycle of sporobiota. This review summarizes the current knowledge of environmental sporobiota, including their occurrence, characteristics, and functions. An interaction network among clinical-, food-related, and environment-related sporobiota is constructed. Recent and effective methods for detecting and disinfecting environmental sporobiota are also discussed. Key problems and future research needs for better understanding and reducing the risks of environmental sporobiota and sporobiome are proposed.

Can the Gut Microbiota Serve as a Guide to the Diagnosis and Treatment of Childhood Epilepsy?

BACKGROUND

To investigate the activity of the gut-brain axis in the pathogenesis of childhood epilepsy and to define biomarkers capable of assisting with determining new strategies in that context.

METHODS

Twenty children with epilepsy of "unknown etiology" and seven healthy controls in the same age group were included in the study. The groups were compared using a questionnaire. Stool samples were stored in tubes containing DNA/RNA Shield (Zymo Research) with a sterile swab. Sequencing was carried out using the MiSeq System (Illumina). The 16S rRNA sequencing of samples using next-generation sequencing involved V4 variable region polymerase chain reaction amplification concluded by 2 × 250-bp paired-end sequencing of amplicons and at least 50,000 reads (>Q30) per sample. DNA sequences were classified at the genus level using the Kraken program. Bioinformatics and statistical analysis were then performed.

RESULTS

Individuals' gut microbiota relative abundance values differed between the groups at the genus, order, class, family, and phylum levels. Flavihumibacter, Niabella, Anoxybacillus, Brevundimonas, Devosia, and Delftia were seen only in the control group, whereas Megamonas and Coriobacterium were observed only in the epilepsy group. The linear discriminant analysis effect size method identified 33 taxa as important in differentiating the groups.

CONCLUSIONS

We think that bacterial varieties (such as Megamonas and Coriobacterium) that differ between the two groups can be employed as useful biomarkers in the diagnosis and follow-up of epileptic patients. We also predict that, in addition to epilepsy treatment protocols, the restoration of eubiotic microbiota may increase the success of treatment.

Decoding whole genome of Anoxybacillus rupiensis TPH1 isolated from Tatapani hot spring, India and giving insight into bioremediation ability of TPH1 via heavy metals and azo dyes

A moderately thermophilic, gram-positive genomospecies Anoxybacillus rupiensis TPH1 was isolated from Tatapani hot spring, Chhattisgarh, India. Genome of 3.70 Mb with 42.3% GC subsumed 4131 CDSs, 65 tRNA, 5 rRNA, 35 AMR and 19 drug target genes. Further, comparative genomics of 19 Anoxybacillus spp. exhibited an open pan genome of 13102 genes along with core (10.62%), unique (43.5%) and accessory (45.9%) genes. Moreover, phylogenomic tree displayed clustering of Anoxybacillus spp. into two distinct clades where clade A species harbored larger genomes, more unique genes, CDS and hypothetical proteins than clade B species. Further, distribution of azoreductases showed FMN-binding NADPH azoreductase (AzoRed1) presence in clade A species only and FMN-binding NADH azoreductase (AzoRed2) harboring by species of both clades. Heavy metal resistance genes distribution showed omnipresence of znuA, copZ and arsC in both clades, dispersed presence of cbiM, czcD, merA and feoB over both clades and harboring of nikA and acr3 by few species of clade A only. Additionally, molecular docking of AzoRed1, AzoRed2, ZnuA, CopZ, Acr3, CbiM, CzcD, MerA and NikA with their respective ligands indicated high affinity and stable binding. Conclusively, present study provided insight into gene repertoire of genus Anoxybacillus and a basis for the potential application of this thermophile in bioremediation of azo dyes and heavy metals.

Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives

For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.

Comparative metagenomic analysis of human intervertebral disc nucleus pulposus and cartilaginous end plates

Study design

The diversity of microflora inhabiting endplate (EP) and nucleus pulposus (NP) tissues of human intervertebral disc (IVD) was profiled through NGS-supported 16S rRNA amplicon sequencing. Sixteen EP and their corresponding NP were excised from the brain-dead voluntary organ donors with no clinical history of low back pain, and 12 herniated and 8 degenerated NP tissues isolated from the patients undergoing spinal surgery were subjected to study the alteration in the microbial diversity.

Objective(s)

To understand in normal IVD, whether the colonization of bacteria to the NP is through the EP in discs with intact annulus fibrosus. To identify significantly differing microbial population(s) between normal and diseased IVD (NP).

Background of the study

There is increasing evidence for subclinical infection by fastidious low, growing bacteria to be a cause of disc degeneration. Although the presence of bacteria in NP has been reported well in literature, the source of bacteria is not clearly proved as the disc is avascular in healthy condition. Documentation of similar bacterial populations in the EP and NP may add proof that bacterial inoculation of NP occurs via the EP.

Materials and methods

Sixteen EP and their corresponding NP excised from brain-dead voluntary organ donors with no history of back pain and 20 diseased discs collected from patients undergoing microdiscectomy/fusion surgery were used for profiling microbiome through 16S rRNA amplicon sequencing using primers specific for V1-V9 hypervariable regions. Changes in bacterial diversity and abundance were analysed to identify the key microbial populations in normal IVD NP and EP tissues and those significantly altered in diseased IVD (NP).

Results

NP and EP shared a similar spectrum of microbiome but with varying abundance. The five dominant phyla identified were Proteobacteria, Firmicutes, Actinobacteria, OD1, and Bacteroidetes. Proteobacteria was found to be the most abundant phyla in both NP (62%) and EP (53%) of the normal IVD. This was followed by Firmicutes (16%), Actinobacteriota (11%), OD1 (Parcubacteria) (7.6%), and Bacteroidetes (2%) in NP and Firmicutes (23.4%), OD1 (Parcubacteria) (17.6%), Actinobacteriota (2.8%), and Bacteroidetes (2.6%) in EP, respectively. Under diseased conditions, Proteobacteria (68%) was dominant when compared with other phyla. However, there was no significant difference in the abundance of Proteobacteria between the normal and diseased discs. Interestingly, the other dominant phyla such as Firmicutes (Normal-NP: 16.2%; Diseased-NP: 4.02%) and Actinobacteria (Normal-NP: 11%; Diseased-NP: 0.99%) showed a significant reduction in degenerated discs. To understand the key microbial populations that are significantly altered during disease, correlation analysis was performed among the three phyla, which revealed a negative correlation in the ratio of Actinobacteria + Firmicutes vs. Proteobacteria (p = 0.001) in DD.

Conclusion

Results of our study clearly demonstrated a similar bacterial diversity but with varying abundance between the EP and NP, suggesting the existence of the endplate–nucleus pulposus axis in the normal IVD microbiome. Further, our results have indicated that the changes in the abundance of Actinobacteria + Firmicutes vs. Proteobacteria during DDD need further investigation.

Unraveling the Genomic Potential of the Thermophilic Bacterium Anoxybacillus flavithermus from an Antarctic Geothermal Environment

Antarctica is a mosaic of extremes. It harbors active polar volcanoes, such as Deception Island, a marine stratovolcano having notable temperature gradients over very short distances, with the temperature reaching up to 100 °C near the fumaroles and subzero temperatures being noted in the glaciers. From the sediments of Deception Island, we isolated representatives of the genus Anoxybacillus, a widely spread genus that is mainly encountered in thermophilic environments. However, the phylogeny of this genus and its adaptive mechanisms in the geothermal sites of cold environments remain unknown. To the best of our knowledge, this is the first study to unravel the genomic features and provide insights into the phylogenomics and metabolic potential of members of the genus Anoxybacillus inhabiting the Antarctic thermophilic ecosystem. Here, we report the genome sequencing data of seven A. flavithermus strains isolated from two geothermal sites on Deception Island, Antarctic Peninsula. Their genomes were approximately 3.0 Mb in size, had a G + C ratio of 42%, and were predicted to encode 3500 proteins on average. We observed that the strains were phylogenomically closest to each other (Average Nucleotide Identity (ANI) > 98%) and to A. flavithermus (ANI 95%). In silico genomic analysis revealed 15 resistance and metabolic islands, as well as genes related to genome stabilization, DNA repair systems against UV radiation threats, temperature adaptation, heat- and cold-shock proteins (Csps), and resistance to alkaline conditions. Remarkably, glycosyl hydrolase enzyme-encoding genes, secondary metabolites, and prophage sequences were predicted, revealing metabolic and cellular capabilities for potential biotechnological applications.

Ozone and Fenton oxidation affected the bacterial community and opportunistic pathogens in biofilms and effluents from GAC

Granular activated carbon (GAC) filtration impacts pathogen colonization and bacterial communities in drinking water. However, the effects of ozone and heterogeneous Fenton oxidation on microbial community composition, in particular opportunistic pathogens (OPs), and their metabolic potential in biofilms and effluents from GAC filtration are not fully understood. The results of our pilot-scale test indicated that Fenton-GAC filtration removed more dissolved organic carbon (DOC, 1.25 mg/L) than ozone-GAC filtration (0.98 mg/L). Excitation-emission matrix (EEM) results showed that Fenton-GAC removed more tyrosine-like proteins and fulvic acid-like materials, while ozone-GAC removed more humic acid-like compounds and tryptophan-like proteins. Illumina HiSeq analysis indicated that Curvibacter and Hydrogenophaga dominated in the Fenton-GAC biofilm, while Bradyrhizobium, Aquabacterium and Limnobacter were predominant in the ozone-GAC biofilm. Functional prediction suggested that the microbial functional gene related to glyoxylate and dicarboxylate metabolism (the pathway for carbohydrate metabolism) was higher in the Fenton-GAC biofilm, resulting in higher contents of protein in extracellular polymeric substances (EPS) in the Fenton-GAC biofilm. Therefore, there were fewer bacteria that detached from the biofilm into the water during the Fenton-GAC filtration process. The lower EPS content in the effluents from Fenton-GAC resulted in bacteria, including OPs, being easier to remove by chlorine. However, ozone oxidation removed more bacteria, including different OPs, than Fenton oxidation, which contributed to fewer bacteria and OPs in the effluents from ozone-GAC. Overall, our results provide a Fenton-GAC treatment process to remove DOC and control OPs in drinking water systems, the cost of which was comparable to that of ozone-GAC.

Mechanism that allows manno-oligosaccharide to promote cellulose degradation by the bacterial community and the composting of cow manure with straw

The new sugar source manno-oligosaccharide can regulate the structure of the microbial community. This study investigated the effects of adding manno-oligosaccharide at four different levels (0, 0.1%, 0.5%, and 1% w/w compost) to composting cow manure and straw on lignocellulose degradation and the bacterial community. Adding 0.5% manno-oligosaccharide had the greatest effects on accelerating the composting process, reducing its toxicity, and improving the stability of the product. After composting for 25 days, adding 0.5% manno-oligosaccharide decreased the hemicellulose, cellulose, and lignin contents to 2.25%, 11.25%, and 7.07%, respectively, compared with those under CK. Manno-oligosaccharide promoted the degradation of lignocellulose by increasing the abundances of Thermobifida, Streptomyces, and Luteimonas. In addition, manno-oligosaccharide inhibited pathogenic bacteria and increased the abundances of functional genes related to metabolism. Finally, adding 0.5% manno-oligosaccharide mainly affected the degradation of lignocellulose by enhancing the C/N ratio and the abundances of Streptomyces and the secretion system during composting according to redundancy analysis.

Genome Analysis of Celeribacter sp. PS-C1 Isolated from Sekinchan Beach in Selangor, Malaysia, Reveals Its β-Glucosidase and Licheninase Activities

A halophilic marine bacterial strain, PS-C1, was isolated from Sekinchan beach in Selangor, Malaysia. The 16S rRNA gene sequence analysis indicated that strain PS-C1 was associated with the genus Celeribacter. To date, there have been no reports on enzymes from the genus Celeribacter. The present study reports on the cellular features of Celeribacter sp. PS-C1, its annotated genome sequence, and comparative genome analyses of Celeribacter glycoside hydrolase (GH) enzymes. The genome of strain PS-C1 has a size of 3.87 Mbp and a G+C content of 59.10%, and contains 3739 protein-coding genes. Detailed analysis using the Carbohydrate-Active enZYmes (CAZy) database revealed that Celeribacter genomes harboured at least 12 putative genes encoding industrially important GHs that are grouped as cellulases, β-glucanases, hemicellulases, and starch-degrading enzymes. Herein, the potential applications of these enzymes are discussed. Furthermore, the activities of two types of GHs (β-glucosidase and licheninase) in strain PS-C1 were demonstrated. These findings suggest that strain PS-C1 could be a reservoir of novel GH enzymes for lignocellulosic biomass degradation.

Unveiling lignocellulolytic trait of a goat omasum inhabitant Klebsiella variicola strain HSTU-AAM51 in light of biochemical and genome analyses

Klebsiella variicola is generally known as endophyte as well as lignocellulose-degrading strain. However, their roles in goat omasum along with lignocellulolytic genetic repertoire are not yet explored. In this study, five different pectin-degrading bacteria were isolated from a healthy goat omasum. Among them, a new Klebsiella variicola strain HSTU-AAM51 was identified to degrade lignocellulose. The genome of the HSTU-AAM51 strain comprised 5,564,045 bp with a GC content of 57.2% and 5312 coding sequences. The comparison of housekeeping genes (16S rRNA, TonB, gyrase B, RecA) and whole-genome sequence (ANI, pangenome, synteny, DNA-DNA hybridization) revealed that the strain HSTU-AAM51 was clustered with Klebsiella variicola strains, but the HSTU-AAM51 strain was markedly deviated. It consisted of seventeen cellulases (GH1, GH3, GH4, GH5, GH13), fourteen beta-glucosidase (2GH3, 7GH4, 4GH1), two glucosidase, and one pullulanase genes. The strain secreted cellulase, pectinase, and xylanase, lignin peroxidase approximately 76-78 U/mL and 57-60 U/mL, respectively, when it was cultured on banana pseudostem for 96 h. The catalytically important residues of extracellular cellulase, xylanase, mannanase, pectinase, chitinase, and tannase proteins (validated 3D model) were bound to their specific ligands. Besides, genes involved in the benzoate and phenylacetate catabolic pathways as well as laccase and DiP-type peroxidase were annotated, which indicated the strain lignin-degrading potentiality. This study revealed a new K. variicola bacterium from goat omasum which harbored lignin and cellulolytic enzymes that could be utilized for the production of bioethanol from lignocelluloses.

Phylogenetic analysis of the bacterial Pro-Pro-endopeptidase domain reveals a diverse family including secreted and membrane anchored proteins

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Bacterial Pro-Pro-endopeptidase (PPEP) is the latest member of the metalloendopeptidase class (E.C. 3.4.24.89).

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PPEP homologs are found in two firmicutes orders, clostridiales and bacillales spread over 9 genera and more than 130 species.

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Some PPEP homologs have acquired additional anchor domains that bind noncovalently to various elements of the bacterial peptidoglycan cell wall.

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Prototype family members, PPEP-1 and PPEP-2, target bacterial surface adhesion proteins, but homologs could target other extracellular proteins.

Pro-Pro-endopeptidases (PPEP, EC 3.4.24.89) are secreted, zinc metalloproteases that have the unusual capacity to cleave a peptide bond between two prolines, a bond that is generally less sensitive to proteolytic cleavage. Two well studied members of the family are PPEP-1 and PPEP-2, produced by Clostridioides difficile, a human pathogen, and Paenibacillus alvei, a bee secondary invader, respectively. Both proteases seem to be involved in mediating bacterial adhesion by cleaving cell surface anchor proteins on the bacterium itself.

By using basic alignment and phylogenetic profiling analysis, this work shows that the complete family of proteins that contain a PPEP domain includes proteins from more than 130 species spread over 9 genera. These analyses also suggest that the PPEP domain spread through horizontal gene transfer events between species within the Firmicutes’ classes Bacilli and Clostridia. Bacterial species containing PPEP homologs are found in diverse habitats, varying from human pathogens and gut microbiota to free-living bacteria, which were isolated from various environments, including extreme conditions such as hot springs, desert soil and salt lakes.

The phylogenetic tree reveals the relationships between family members and suggests that smaller subgroups could share cleavage specificity, substrates and functional similarity. Except for PPEP-1 and PPEP-2, no cleavage specificity, specific physiological target, or function has been assigned for any of the other PPEP-family members. Some PPEP proteins have acquired additional domains that recognize and bind noncovalently to various elements of the bacterial peptidoglycan cell-wall, anchoring these PPEPs. Secreted or anchored to the cell-wall surface PPEP proteins seem to perform various functions.

Whole-Genome Sequence Data Analysis of Anoxybacillus kamchatkensis NASTPD13 Isolated from Hot Spring of Myagdi, Nepal

Anoxybacillus kamchatkensis NASTPD13 isolated from Paudwar hot spring of Myagdi, Nepal, upon morphological and biochemical analysis revealed to be Gram-positive, straight or slightly curved, rod-shaped, spore-forming, catalase, and oxidase-positive facultative anaerobes. It grows over a wide range of pH (5.0-11) and temperature (37-75°C), which showed growth in different reduced carbon sources such as starch raffinose, glucose, fructose, inositol, trehalose, sorbitol, mellobiose, and mannitol in aerobic conditions. Furthermore, the partial sequence obtained upon sequencing showed 99% sequence similarity in 16S rRNA gene sequence with A. kamchatkensis JW/VK-KG4 and was suggested to be Anoxybacillus kamchatkensis. Moreover, whole-genome analysis of NASTPD13 revealed 2,866,796 bp genome with a G+C content of 41.6%. Analysis of the genome revealed the presence of 102 RNA genes, which includes sequences coding for 19 rRNA and 79 tRNA genes. While the 16S rRNA gene sequence of strain NASTPD13 showed high similarity (>99%) to those of A. kamchatkensis JW/VK-KG4, RAST analysis of NASTPD13 genome suggested that A. kamchatkensis G10 is actually the closest neighbor in terms of sequence similarity. The genome annotation by RAST revealed various genes encoding glycoside hydrolases supporting that it can utilize several reduced carbon sources as observed and these genes could be important for carbohydrate-related industries. Xylanase pathway, particularly the genomic region encoding key enzymes for xylan depolymerization and xylose metabolism, further confirmed the presence of the complete gene in xylan metabolism. In addition, the complete xylose utilization gene locus analysis of NASTPD13 genome revealed all including D-xylose transport ATP-binding protein XylG and XylF, the xylose isomerase encoding gene XylA, and the gene XylB coding for a xylulokinase supported the fact that the isolate contains a complete set of genes related to xylan degradation, pentose transport, and metabolism. The results of the present study suggest that the isolated A. kamchatkensis NASTPD13 containing xylanase-producing genes could be useful in lignocellulosic biomass-utilizing industries where pentose polymers could also be utilized along with the hexose polymers.

Temperature management potentially affects carbon mineralization capacity and microbial community composition of a shallow aquifer

High-temperature aquifer thermal energy storage (HT-ATES) is a promising technique to reduce the CO2 footprint of heat supply in the frame of transitioning to renewable energies. However, HT-ATES causes temperature fluctuations in groundwater ecosystems potentially affecting important microbial-mediated ecosystem services. Hence, assessing the impact of increasing temperatures on the structure and functioning of aquifer microbiomes is crucial to evaluate potential environmental risks associated with HT-ATES. In this study, we investigated the effects of temperature variations (12-80°C) on microbial communities and their capacity to mineralize acetate in aerobically incubated sediment sampled from a pristine aquifer. Compared to natural conditions (12°C), increased acetate mineralization rates were observed at 25°C, 37°C and 45°C, whereas mineralization was decelerated at 60°C and absent at 80°C. Sequencing of 16S rRNA genes revealed that the bacterial diversity in acetate-amended and non-acetate-amended sediments decreased with rising temperatures. Distinct communities dominated by bacterial groups affiliated with meso- and thermophilic bacteria established at 45°C and 60°C, respectively, while the number of archaeal phylotypes decreased. The changes in microbial diversity observed at 45°C and 60°C indicate a potential loss of ecosystem functioning, functional redundancy and resilience, while heat storage at 80°C bears the risk of ecological collapse.

Characterization of Chemical and Bacterial Compositions of Dairy Wastewaters

The dairy industry produces large amounts of wastewater, including white and cleaning wastewater originating principally from rinsing and cleaning-in-place procedures. Their valorization into process water and non-fat milk solids, in the case of white wastewater, or the renewal of cleaning solutions could be achieved using pressure-driven membrane processes. However, it is crucial to determine the intrinsic characteristics of wastewaters, such as proximate composition and bacterial composition, to optimize their potential for valorization. Consequently, white and cleaning wastewaters were sampled from industrial-scale pasteurizers located in two different Canadian dairy processing plants. Bacterial profiles of dairy wastewaters were compared to those of tap waters, pasteurized skim milk and unused cleaning solutions. The results showed that the physicochemical characteristics as well as non-fat milk solids contents differed drastically between the two dairy plants due to different processing conditions. A molecular approach combining quantitative real-time polymerase chain reaction (qPCR) and metabarcoding was used to characterize the bacteria present in these solutions. The cleaning solutions did not contain sufficient genomic DNA for sequencing. In white wastewater, the bacterial contamination differed depending on the dairy plant (6.91 and 7.21 log10 16S gene copies/mL). Psychrotrophic Psychrobacter genus (50%) dominated white wastewater from plant A, whereas thermophilic Anoxybacillus genus (56%) was predominant in plant B wastewater. The use of cold or warm temperatures during the pasteurizer rinsing step in each dairy plant might explain this difference. The detailed characterization of dairy wastewaters described in this study is important for the dairy sector to clearly identify the challenges in implementing strategies for wastewater valorization.

Exopolysaccharide of Anoxybacillus pushchinoensis G11 has antitumor and antibiofilm activities

Exopolysaccharides (EPS/EPSs) possess several various applications in the food and pharmaceutical industries. This study was performed to investigate the biological (antibiofilm and antitumor), rheological (temperature, shear rate, and density) and chemical (solubility, carbohydrate and protein content, composition, molecular weight, functional group analysis, thermal analysis, X-ray diffraction pattern and scanning electron microscopy) properties of the EPS, which was purified from the locally isolated thermophilic bacterium Anoxybacillus pushchinoensis G11 (MN720646). EPS was found to have antibiofilm and antitumor [lung (A-549) and colon (Caco-2 and HT-29) cancer] activities. The viscosity of EPS showing Newtonian flow was temperature dependent. As chemical properties, the EPS was found to be a heteropolysaccharide containing arabinose (57%), fructose (26%), glucose (12%), and galactose (5%). EPS contained 93% carbohydrates and 1.08% protein. The molecular weight of EPS was determined as 75.5 kDa. The FTIR analysis confirmed the presence of sulfate ester (band at 1217 cm^-1), an indication of the antitumor effect. The EPS was semi-crystalline. It could maintain 36% of its weight at 800 °C and crystallization and melting temperatures were 221 and 255.6 °C. This is the first report on the EPS production potential and the biological activity of A. pushchinoensis.

Identification of Genome Sequences of Polyphosphate-Accumulating Organisms by Machine Learning

In the field of sewage treatment, the identification of polyphosphate-accumulating organisms (PAOs) usually relies on biological experiments. However, biological experiments are not only complicated and time-consuming, but also costly. In recent years, machine learning has been widely used in many fields, but it is seldom used in the water treatment. The present work presented a high accuracy support vector machine (SVM) algorithm to realize the rapid identification and prediction of PAOs. We obtained 6,318 genome sequences of microorganisms from the publicly available microbial genome database for comparative analysis (MBGD). Minimap2 was used to compare the genomes of the obtained microorganisms in pairs, and read the overlap. The SVM model was established using the similarity of the genome sequences. In this SVM model, the average accuracy is 0.9628 ± 0.019 with 10-fold cross-validation. By predicting 2,652 microorganisms, 22 potential PAOs were obtained. Through the analysis of the predicted potential PAOs, most of them could be indirectly verified their phosphorus removal characteristics from previous reports. The SVM model we built shows high prediction accuracy and good stability.

Verticillium dahliae Inoculation and in vitro Propagation Modify the Xylem Microbiome and Disease Reaction to Verticillium Wilt in a Wild Olive Genotype

Host resistance is the most practical, long-term, and economically efficient disease control measure for Verticillium wilt in olive caused by the xylem-invading fungus Verticillium dahliae (Vd), and it is at the core of the integrated disease management. Plant's microbiome at the site of infection may have an influence on the host reaction to pathogens; however, the role of xylem microbial communities in the olive resistance to Vd has been overlooked and remains unexplored to date. This research was focused on elucidating whether in vitro olive propagation may alter the diversity and composition of the xylem-inhabiting microbiome and if those changes may modify the resistance response that a wild olive clone shows to the highly virulent defoliating (D) pathotype of Vd. Results indicated that although there were differences in microbial communities among the different propagation methodologies, most substantial changes occurred when plants were inoculated with Vd, regardless of whether the infection process took place, with a significant increase in the diversity of bacterial communities when the pathogen was present in the soil. Furthermore, it was noticeable that olive plants multiplied under in vitro conditions developed a susceptible reaction to D Vd, characterized by severe wilting symptoms and 100% vascular infection. Moreover, those in vitro propagated plants showed an altered xylem microbiome with a decrease in total OTU numbers as compared to that of plants multiplied under non-aseptic conditions. Overall, 10 keystone bacterial genera were detected in olive xylem regardless of infection by Vd and the propagation procedure of plants (in vitro vs nursery), with Cutibacterium (36.85%), Pseudomonas (20.93%), Anoxybacillus (6.28%), Staphylococcus (4.95%), Methylobacterium-Methylorubrum (3.91%), and Bradyrhizobium (3.54%) being the most abundant. Pseudomonas spp. appeared as the most predominant bacterial group in micropropagated plants and Anoxybacillus appeared as a keystone bacterium in Vd-inoculated plants irrespective of their propagation process. Our results are the first to show a breakdown of resistance to Vd in a wild olive that potentially may be related to a modification of its xylem microbiome and will help to expand our knowledge of the role of indigenous xylem microbiome on host resistance, which can be of use to fight against main vascular diseases of olive.

Diversity and enzymatic potential of thermophilic bacteria associated with terrestrial hot springs in Algeria

This study aims to determine the diversity of culturable thermophilic bacteria isolated from eight terrestrial hot springs in Northeastern of Algeria using the conventional methods, SDS-PAGE fingerprinting of whole-cell proteins and 16S rRNA gene sequencing. In addition, their hydrolytic enzyme activities were also investigated. A total of 293 strains were isolated from the hot springs' water and sediment using different culture media. Overall, five distinct bacterial groups were characterized by whole-cell protein pattern analysis. Based on the 16S rRNA gene sequencing of 100 selected strains, the isolates were assigned to the following three major phyla: Firmicutes (93%), Deinococcus-Thermus (5%), and Actinobacteria (2%), which included 27 distinct species belonging to 12 different phylotypes, Aeribacillus, Aneurinibacillus, Anoxybacillus, Bacillus, Brevibacillus, Geobacillus, Laceyella, Meiothermus, Saccharomonospora, Thermoactinomyces, Thermobifida, and Thermus. The screening for nine extracellular enzymes showed that 65.87% of the isolates presented at least five types of enzyme activities, and 6.48% of strains combined all tested enzymes (amylase, cellulase, pectinase, esculinase, protease, gelatinase, lipase, lecithinase, and nuclease). It was found that Bacillus, Anoxybacillus, Aeribacillus, and Aneurinibacillus were the genera showing the highest activities. Likewise, the study showed an abundant and diverse thermophilic community with novel taxa presenting a promising source of thermozymes with important biotechnological applications. This study showed that a combined identification method using SDS-PAGE profiles of whole-cell proteins and subsequent 16S rRNA gene sequence analysis could successfully differentiate thermophilic bacteria from Algerian hot springs.

The extremophile Anoxybacillus sp. PC2 isolated from Brazilian semiarid region (Caatinga) produces a thermostable keratinase

The aim of this study was to select and identify thermophilic bacteria from Caatinga biome (Brazil) able to produce thermoactive keratinases and characterize the keratinase produced by the selected isolate. After enrichment in keratin culture media, an Anoxybacillus caldiproteolyticus PC2 was isolated. This thermotolerant isolate presents a remarkable feature producing a thermostable keratinase at 60°C. The partially purified keratinase, identified as a thermolysin-like peptidase, was active at a pH range of 5.0-10.0 with maximal activity at a temperature range of 50-80°C. The optimal activity was observed at pH 7.0 and 50-60°C. These characteristics are potentially useful for biotechnological purposes such as processing and bioconversion of keratin.

Characterization of Thermophilic Microorganisms in the Geothermal Water Flow of El Chichón Volcano Crater Lake

This study reports for the first time the isolation, identification and characterization of lipase-producing thermophilic strain from the geothermal water of the El Chichón volcano crater lake. Two strains were identified by 16S rRNA sequencing as Geobacillus jurassicus CHI2 and Geobacillus stearothermophilus CHI1. Results showed that G. jurassicus CHI2 is Gram-positive, able to ferment maltose, fructose and sucrose and to hydrolyze starch and casein; while G. stearothermophilus CHI1 showed to be Gram-variable, able to ferment maltose and fructose and to hydrolyze starch. Colonies of both strains presented irregular shape, umbilicated elevation of gummy texture and cells presented flagellar movement to survive in fluids with high temperature and mass gradients due to complex phenomena of heat and mass transfer present in the geothermal fluids. Lipase production for G. stearothermophilus CHI1 was also evaluated. It was found that this strain possesses a growth associated with extracellular lipase production with a high activity of 143 U/mL at 8.3 h of incubation time, superior to the activities reported for other microorganisms of genus Geobacillus; for this reason, it can be said that the thermal flow of the El Chichón volcano crater lake can be a useful source of lipase-producing thermophilic bacteria.

The sources and transmission routes of microbial populations throughout a meat processing facility

Microbial food spoilage is responsible for a considerable amount of waste and can cause food-borne diseases in humans, particularly in immunocompromised individuals and children. Therefore, preventing microbial food spoilage is a major concern for health authorities, regulators, consumers, and the food industry. However, the contamination of food products is difficult to control because there are several potential sources during production, processing, storage, distribution, and consumption, where microorganisms come in contact with the product. Here, we use high-throughput full-length 16S rRNA gene sequencing to provide insights into bacterial community structure throughout a pork-processing plant. Specifically, we investigated what proportion of bacteria on meat are presumptively not animal-associated and are therefore transferred during cutting via personnel, equipment, machines, or the slaughter environment. We then created a facility-specific transmission map of bacterial flow, which predicted previously unknown sources of bacterial contamination. This allowed us to pinpoint specific taxa to particular environmental sources and provide the facility with essential information for targeted disinfection. For example, Moraxella spp., a prominent meat spoilage organism, which was one of the most abundant amplicon sequence variants (ASVs) detected on the meat, was most likely transferred from the gloves of employees, a railing at the classification step, and the polishing tunnel whips. Our results suggest that high-throughput full-length 16S rRNA gene sequencing has great potential in food monitoring applications.

Metagenomic analysis revealed the succession of microbiota and metabolic function in corncob composting for preparation of cultivation medium for Pleurotus ostreatus

Metagenomic sequencing was used to reveal the dynamic changes in microbiota and the metabolic functions in corncob composting for preparing cultivation medium of Pleurotus ostreatus. Results showed that the changes of physicochemical properties lead to different dominant phylum at different stages of composting. Firmicutes replaced Proteobacteria as the dominant phylum at thermophilic stage. Correlation analysis indicated that the succession of microbiota was significantly affected by the C/N ratio, pH, temperature and organic matters in compost. The changes in community inevitably lead to the differences of metabolic functions. Metabolism analysis indicated that carbohydrate, lipid and amino acid metabolism were relatively higher in thermophilic stage. Conversely, the metabolism of starch, sucrose, galactose, ascorbate was mainly detected in the late stage. The metabolisms of different stages were driven by different microorganisms. Overall, these findings deepened our understanding of metabolic functions, and it is of great value to the metabolomics research of composting system.

Geothermal springs in Armenia and Nagorno-Karabakh: potential sources of hydrolase-producing thermophilic bacilli

In recent years, scientists have increasingly focused on the microbial diversity of high-altitude hot springs to explore the biotechnological applications of extremophiles. In this regard, a total of 107 thermophilic bacilli were isolated from 9 high-altitude mineralized geothermal springs (of temperatures ranging from 27.5 to 70 °C) located within the territory of Armenia and Nagorno-Karabakh. The isolated bacilli were phylogenetically profiled and studied for their potential to produce extracellular hydrolytic enzymes (protease, amylase, and lipase). The identification of isolates based on 16S rRNA gene sequences revealed their relationship to members of more than 22 distinct species, of 8 different genera, namely Aeribacillus, Anoxybacillus, Bacillus, Brevibacillus, Geobacillus, Parageobacillus, Paenibacillus and Ureibacillus. Bacillus licheniformis, Parageobacillus toebii and Anoxybacillus flavithermus were found to be the most abundant species in the springs that were studied. Some of the isolated bacilli shared less than 91-97% sequence identity with their closest match in GenBank, indicating that Armenian geothermal springs harbor novel bacilli, at least at the species level. 71% of the isolates actively produced at least one or more extracellular proteases, amylases, or lipases. In total, 22 strains (28.6%) were efficient producers of all three types of thermostable enzymes.

Distinct lung microbial community states in patients with pulmonary tuberculosis

An improved understanding of the lung microbiome may lead to better strategies to diagnose, treat, and prevent pulmonary tuberculosis (PTB). However, the characteristics of the lung microbiomes of patients with TB remain largely undefined. In this study, 163 bronchoalveolar lavage (BAL) samples were collected from 163 sputum-negative suspected PTB patients. Furthermore, 12 paired BAL samples were obtained from 12 Mycobacterium tuberculosis-positive (MTB+) patients before and after negative conversion following a two-month anti-TB treatment. The V3-V4 region of the 16S ribosomal RNA (rRNA) gene was used to characterize the microbial composition of the lungs. The results showed that the prevalence of MTB in the BAL samples was 42.9% (70/163) among the sputum-negative patients. The α-diversity of lung microbiota was significantly less diverse in MTB+ patients compared with Mycobacterium tuberculosis-negative (MTB-) patients. There was a significant difference in β-diversity between MTB+ and MTB- patients. MTB+ patients were enriched with Anoxybacillus, while MTB- patients were enriched with Prevotella, Alloprevotella, Veillonella, and Gemella. There was no significant difference between the Anoxybacillus detection rates of MTB+ and MTB- patients. The paired comparison between the BAL samples from MTB+ patients and their negative conversion showed that BAL negative-conversion microbiota had a higher α-diversity. In conclusion, distinct features of airway microbiota could be identified between samples from patients with and without MTB. Our results imply links between lung microbiota and different clinical groups of active PTB.

Mangrove soil as a source for novel xylanase and amylase as determined by cultivation-dependent and cultivation-independent methods

Xylanase and α-amylase enzymes participate in the degradation of organic matter, acting in hemicellulose and starch mineralization, respectively, and are in high demand for industrial use. Mangroves represent a promising source for bioprospecting enzymes due to their unique characteristics, such as fluctuations in oxic/anoxic conditions and salinity. In this context, the present work aimed to bioprospect xylanases from mangrove soil using cultivation-dependent and cultivation-independent methods. Through screening from a metagenomic library, three potentially xylanolytic clones were obtained and sequenced, and reads were assembled into contigs and annotated. The contig MgrBr135 was affiliated with the Planctomycetaceae family and was one of 30 ORFs selected for subcloning that demonstrated only amylase activity. Through the cultivation method, 38 bacterial isolates with xylanolytic activity were isolated. Isolate 11 showed an enzymatic index of 10.9 using the plate assay method. Isolate 39 achieved an enzyme activity of 0.43 U/mL using the colorimetric method with 3,5-dinitrosalicylic acid. Isolate 39 produced xylanase on culture medium with salinity ranging from 1.25 to 5%. Partial 16S rRNA gene sequencing identified isolates in the Bacillus and Paenibacillus genera. The results of this study highlight the importance of mangroves as an enzyme source and show that bacterial groups can be used for starch and hemicellulose degradation.

Dynamics of microbial contaminants is driven by selection during ethanol production

Brazil is the second largest ethanol producer in the world and largest using sugarcane feedstock. Bacteria contamination is one of the most important issues faced by ethanol producers that seek to increase production efficiency. Each step of production is a selection event due to the environmental and biological changes that occur. Therefore, we evaluated the influence of the selection arising from the ethanol production process on diversity and composition of bacteria. Our objectives were to test two hypotheses, (1) that species richness will decrease during the production process and (2) that lactic acid bacteria will become dominant with the advance of ethanol production. Bacterial community assemblage was accessed using 16S rRNA gene sequencing from 19 sequential samples. Temperature is of great importance in shaping microbial communities. Species richness increased between the decanter and must steps of the process. Low Simpson index values were recorded at the fermentation step, indicating a high dominance of Lactobacillus. Interactions between Lactobacillus and yeast may be impairing the efficiency of industrial ethanol production.

Structural and functional consequences of replacement of His403 with Arg near the catalytic site of Anoxybacillus flavithermus cyclomaltodextrinase

The hydrolytic activity of a thermophilic cyclomaltodextrinase (CMD) from Anoxybacillus flavithermus ZNU-NGA and a representative single mutant were investigated against soluble substrates including α-, β- and γ-cyclomaltodestrines (CDs). Based on the occurrence of arginine (Arg) at position 403 in some homologue proteins, His⁴⁰³ in Wild-type (WT) CMD was replaced with Arg (H403R variant) with site-directed mutagenesis procedures. According to bioinformatics data, Arg⁴⁰³ in mutant protein is located near Glu³⁵⁷ as one of the catalytic residues in a manner that they are able to create a medium-range attractive electrostatistic interaction. Structural studies by Far UV-CD showed that this mutation is accompanied by conversion of a small fraction of α-helix to β-form structure. Fluorescence data reveals that, the hydrophobic regions at the surface of protein, as the binding sites for ANS (8-Anilinonaphthalene-1-sulfonic acid) increase in mutant protein, demonstrating relative inflation of H403R variant compared with WT protein. However, the polarity of microenvironment around chromophores did not change upon mutation. Activity measurement in different ranges of pH and temperatures showed that the optimum values of pH and temperature in mutant enzyme is the same as WT enzyme, however; the activity at optimum points increased in H403R variant. It was also revealed that the H403R variant had slightly improved catalytic efficiency for γ-CD. The same value of activation parameters for both protein variants indicates that mutation does not alter the mechanism of catalysis during enzyme-substrate formation.

Identification of a novel protease from the thermophilic Anoxybacillus kamchatkensis M1V and its application as laundry detergent additive

A thermostable extracellular alkaline protease (called SAPA) was produced (4600 U/mL) by Anoxybacillus kamchatkensis M1V, purified to homogeneity, and biochemically characterized. SAPA is a monomer with a molecular mass of 28 kDa estimated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), Native-PAGE, casein-zymography, and size exclusion using high performance liquid chromatography (HPLC). The sequence of its NH₂-terminal amino-acid residues showed high homology with those of Bacillus proteases. The SAPA irreversible inhibition by diiodopropyl fluorophosphates (DFP) and phenylmethanesulfonyl fluoride (PMSF) confirmed its belonging to the serine proteases family. Optimal activity of SAPA was at pH 11 and 70 °C. The sapA gene was cloned and expressed in the extracellular fraction of E. coli. The highest sequence identity value (95%) of SAPA was obtained with peptidase S8 from Bacillus subtilis WT 168, but with 16 amino-acids of difference. The biochemical characteristics of the purified recombinant extracellular enzyme (called rSAPA) were analogous to those of native SAPA. Interestingly, rSAPA exhibit a degree of hydrolysis that were 1.24 and 2.6 than SAPB from Bacillus pumilus CBS and subtilisin A from Bacillus licheniformis, respectively. Furthermore, rSAPA showed a high detergent compatibility and an outstanding stain removal capacity compared to commercial enzymes: savinase™ 16L, type EX and alcalase™ Ultra 2.5 L.

Extreme environments: microbiology leading to specialized metabolites

The prevalence of multidrug-resistant microbial pathogens due to the continued misuse and overuse of antibiotics in agriculture and medicine is raising the prospect of a return to the preantibiotic days of medicine at the time of diminishing numbers of drug leads. The good news is that an increased understanding of the nature and extent of microbial diversity in natural habitats coupled with the application of new technologies in microbiology and chemistry is opening up new strategies in the search for new specialized products with therapeutic properties. This review explores the premise that harsh environmental conditions in extreme biomes, notably in deserts, permafrost soils and deep-sea sediments select for micro-organisms, especially actinobacteria, cyanobacteria and fungi, with the potential to synthesize new druggable molecules. There is evidence over the past decade that micro-organisms adapted to life in extreme habitats are a rich source of new specialized metabolites. Extreme habitats by their very nature tend to be fragile hence there is a need to conserve those known to be hot-spots of novel gifted micro-organisms needed to drive drug discovery campaigns and innovative biotechnology. This review also provides an overview of microbial-derived molecules and their biological activities focusing on the period from 2010 until 2018, over this time 186 novel structures were isolated from 129 representatives of microbial taxa recovered from extreme habitats.

Genomic analysis of a lignocellulose degrading strain from the underexplored genus Meridianimaribacter

The genus Meridianimaribacter is one of the least-studied genera within Cytophaga-Flavobacteria. To date, no genomic analysis of Meridianimaribacter has been reported. In this study, Meridianimaribacter sp. strain CL38, a lignocellulose degrading halophile was isolated from mangrove soil. The genome of strain CL38 was sequenced and analyzed. The assembled genome contains 17 contigs with 3.33 Mbp, a GC content of 33.13% and a total of 2982 genes predicted. Lignocellulose degrading enzymes such as cellulases (GH3, 5, 9, 16, 74 and 144), xylanases (GH43 and CE4) and mannanases (GH5, 26, 27 and 130) are encoded in the genome. Furthermore, strain CL38 demonstrated its ability to decompose empty fruit bunch, a lignocellulosic waste residue arising from palm oil industry. The genome information coupled with experimental studies confirmed the ability of strain CL38 to degrade lignocellulosic biomass. Therefore, Meridianimaribacter sp. strain CL38, with its halotolerance, could be useful for seawater based lignocellulosic biorefining.

Succession of organics metabolic function of bacterial community in response to addition of earthworm casts and zeolite in maize straw composting

Succession and metabolism functions of bacterial communities were determined in maize straw composting with earthworm casts and zeolite addition by using high-throughput sequencing, Biolog and PICRUSt. Results showed that earthworm casts and zeolite addition increased the temperature, decreased NH₄⁺ contents and affected bacterial community structure. The relative abundances of Firmicutes and Betaproteobacteria increased with earthworm casts and zeolite addition in the late stage. The abundances of genes related to carbohydrate metabolism, amino acid metabolism, and energy metabolism were increased by these two additives in the early stage, but decreased in the late stage. Network analysis demonstrated that members of Bacillaceae were identified as the keystone taxa. Temperature showed negative relationship with Georgenia, while NH₄⁺ exhibited positive associations with Georgenia, Devosia, Ruania and Mycobacterium. These results indicated that earthworm casts and zeolite addition benefitted the keystone species and enhanced the metabolism capacity of bacterial community, thereby improved the quality of compost.

Isolation and Partial Characterisation of Thermophilic Cellulolytic Bacteria from North Malaysian Tropical Mangrove Soil

This study reports the biodiversity of thermophilic cellulolytic bacterial strains that present in the north Malaysian mangrove ecosystem. Soil samples were collected at the four most northern state of Malaysia (Perak, Pulau Pinang, Kedah and Perlis). The samples obtained were first enriched in nutrient broth at 45°C and 55°C prior culturing in the carboxymethylcellulose (CMC) agar medium. Repeated streaking was performed on the CMC agar to obtain a pure culture of each isolate prior subjecting it to hydrolysis capacity testing. The isolates that showing the cellulolytic zone (halozone) were sent for 16S rRNA sequencing. Total seven isolates (two from Perak, three from Kedah, another two were from Perlis and Penang each) showed halozone. The isolate (KFX-40) from Kedah exhibited highest halozone of 3.42 ± 0.58, meanwhile, the one obtained from Perak (AFZ-0) showed the lowest hydrolysis capacity (2.61 ± 0.10). Based on 16S rRNA sequencing results, 5 isolates (AFY-40, AFZ-0, KFX-40, RFY-20, and PFX-40) were determined to be Anoxybacillus sp. The other two isolates were identified as Bacillus subtilis (KFY-40) and Paenibacillus dendritiformis (KFX-0). Based on growth curve, doubling time of Anoxybacillus sp. UniMAP-KB06 was calculated to be 32.3 min. Optimal cellulose hydrolysis temperature and pH of this strain were determined to be 55°C and 6.0 respectively. Addition of Mg²⁺ and Ca²⁺ were found to enhance the cellulase activity while Fe³⁺ acted as an enzyme inhibitor.

Influence of Calcium Ions on the Thermal Characteristics of α-amylase from Thermophilic Anoxybacillus sp. GXS-BL

BACKGROUND

α-Amylases are starch-degrading enzymes and used widely, the study on thermostability of α-amylase is a central requirement for its application in life science and biotechnology.

OBJECTIVE

In this article, our motivation is to study how the effect of Ca2+ ions on the structure and thermal characterization of α-amylase (AGXA) from thermophilic Anoxybacillus sp.GXS-BL.

METHODS

α-Amylase activity was assayed with soluble starch as the substrate, and the amount of sugar released was determined by DNS method. For AGXA with calcium ions and without calcium ions, optimum temperature (Topt), half-inactivation temperature (T50) and thermal inactivation (halflife, t1/2) was evaluated. The thermal denaturation of the enzymes was determined by DSC and CD methods. 3D structure of AGXA was homology modeled with α-amylase (5A2A) as the template.

RESULTS

With calcium ions, the values of Topt, T50, t1/2, Tm and ΔH in AGXA were significantly higher than those of AGXA without calcium ions, showing calcium ions had stabilizing effects on α-amylase structure with the increased temperature. Based on DSC measurements AGXA underwent thermal denaturation by adopting two-state irreversible unfolding processes. Based on the CD spectra, AGXA without calcium ions exhibited two transition states upon unfolding, including α- helical contents increasing, and the transition from α-helices to β-sheet structures, which was obviously different in AGXA with Ca2+ ions, and up to 4 Ca2+ ions were located on the inter-domain or intra-domain regions according to the modeling structure.

CONCLUSION

These results reveal that Ca2+ ions have pronounced influences on the thermostability of AGXA structure.

Association of Anoxybacillus sp. with acid off-flavor development in a spoiled, boiled, rice dish

Off-flavor is one of the most common food complaints. In this study, we demonstrated that acetic acid produced by Anoxybacillus sp. contamination of takikomi-gohan (boiled rice with sweet potato mixed in advance) was considered the causative agent of acid off-flavor development. First, we conducted whole genome sequencing of the bacterial strain (S1674) isolated from the remains of the contaminated takikomi-gohan, and phylogenetic analysis of k-mer diversity demonstrated that S1674 belongs to the Anoxybacillus genus. Gene expression analysis of S1674 RNA sequencing (RNA-seq) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) indicated that the genes encoding enzymes responsible for acetic acid formation, namely ackA1, eutD, pflA, pflB, and pykA, were upregulated in high-temperature cultures in Thermus medium supplemented with soluble starch. Additionally, we succeeded in reproducing the acid off-flavor by adding S1674 to boiled rice stored at 37 °C, 45 °C, and 60 °C. The most strongly detected organic acid was acetic acid, at the odor threshold value or more in both the air and condensation samples. Our findings suggest that some Anoxybacillus sp. produce acetic acid as a byproduct of carbohydrate metabolism, potentially causing the complaint of acid off-flavor even under high-temperature conditions in which other bacteria cannot survive.

Succession of organics metabolic function of bacterial community in swine manure composting

Organics metabolic function of bacterial communities was evaluated in 60 days composting of swine manure and pumice by using MiSeq sequencing, PICRUSt and Biolog tools. The diversity of bacterial communities significantly decreased during the first 10 days, and gradually increased in the cooling and curing phase. The PICRUSt and Biolog analysis indicated that carbohydrate, lipid and amino acids metabolisms were relatively higher in the thermophilic phases. Xenobiotics biodegradation and metabolism, lipid metabolism, terpenoids and polyketides and biosynthesis of other secondary metabolites were mainly detected in the curing phases. Canonical correspondence analysis (CCA) indicated that the succession of bacterial community and organics utilization characteristics were highly affected by the temperature, moisture and oxidation reduction potential (ORP) in the swine composting system.

Peculiarities and biotechnological potential of environmental adaptation by Geobacillus species

The genus Geobacillus comprises thermophilic bacilli capable of endospore formation. The members of this genus provide thermostable proteins and can be used in whole cell applications at elevated temperatures; therefore, these organisms are of biotechnological importance. While these applications have been described in previous reviews, the present paper highlights the environmental adaptations and genome diversifications of Geobacillus spp. and their applications in evolutionary-protein engineering. Despite their obligate thermophilic properties, Geobacillus spp. are widely distributed in nature. Because several isolates demonstrate remarkable properties for cell reproduction in their respective niches, they seem to exist not only as endospores but also as vegetative cells in diverse environments. This suggests their excellence in environmental adaptation via genome diversification; in fact, evidence suggests that Geobacillus spp. were derived from Bacillus spp. while diversifying their genomes via horizontal gene transfer. Moreover, when subjected to an environmental stressor, Geobacillus spp. diversify their genomes using inductive mutations and transposable elements to produce derivative cells that are adaptive to the stressor. Notably, inductive mutations in Geobacillus spp. occur more rapidly and frequently than the stress-induced mutagenesis observed in other microorganisms. Owing to this, Geobacillus spp. can efficiently generate mutant genes coding for thermostable enzyme variants from the thermolabile enzyme genes under appropriate selection pressures. This phenomenon provides a new approach to generate thermostable enzymes, termed as thermoadaptation-directed enzyme evolution, thereby expanding the biotechnological potentials of Geobacillus spp. In this review, we have discussed this approach using successful examples and major challenges yet to be addressed.