Bacillus flavothermus, a newly isolated facultative thermophile

Detection of risk areas in dairy powder processes: The development of thermophilic spore forming bacteria taking into account their growth limits

Anoxybacillus flavithermus, Geobacillus stearothermophilus and Bacillus licheniformis are the main contaminants found in dairy powders. These spore-forming thermophilic bacteria, rarely detected in raw milk, persist, and grow during the milk powder manufacturing process. Moreover, in the form of spores, these species resist and concentrate in the powders during the processes. The aim of this study was to determine the stages of the dairy powder manufacturing processes that are favorable to the growth of such contaminants. A total of 5 strains were selected for each species as a natural contaminant of dairy pipelines in order to determine the minimum and maximum growth enabling values for temperature, pH, and aw and their optimum growth rates in milk. These growth limits were combined with the environmental conditions of temperature, pH and aw encountered at each step of the manufacture of whole milk, skim milk and milk protein concentrate powders to estimate growth capacities using cardinal models and the Gamma concept. These simulations were used to theoretically calculate the population sizes reached for the different strains studied at each stage in between two successive cleaning in place procedures. This approach highlights the stages at which risk occurs for the development of spore-forming thermophilic bacterial species. During the first stages of production, i.e. pre-treatment, pasteurization, standardization and pre-heating before concentration, physico-chemical conditions encountered are suitable for the development and growth of A. flavithermus, G. stearothermophilus and B. licheniformis. During the pre-heating stage and during the first effects in the evaporators, the temperature conditions appear to be the most favorable for the growth of G. stearothermophilus. The temperatures in the evaporator during the last evaporator effects are favorable for the growth of B. licheniformis. In the evaporation stage, low water activity severely limits the development of A. flavithermus.

A Novel Thermostable and Processive Reverse Transcriptase from a Group II Intron of Anoxybacillus flavithermus

Reverse transcriptases (RTs) are a family of enzymes that synthesize DNA using an RNA template and are involved in retrovirus propagation and telomere lengthening. In vitro, RTs are widely applied in various methods, including RNA-seq, RT-PCR, and RT-LAMP. Thermostable RTs from bacterial group II introns are promising tools for biotechnology due to their higher thermostability, fidelity, and processivity compared to commonly used M-MuLV RT and its mutants. However, the diversity of group II intron-encoded RTs is still understudied. In this work, we biochemically characterized a novel RT from a thermophilic bacterium, Anoxybacillus flavithermus, which was isolated from a hot spring in New Zealand and has an optimal growth temperature of around 60 °C. The cloned RT, named Afl RT, retained approximately 40% of the specific activity after a 45 min incubation at 50 °C. The optimal pH was 8.5, the optimal temperature was between 45 and 50 °C, and Mn2+ ions were found to be an optimal cofactor. The processivity analysis with MS2 phage gRNA (3569 b) demonstrated that Afl RT elongated fully up to 36% of the template molecules. In reverse transcription and RT-qLAMP, the enzyme allowed up to 10 copies of MS2 phage genomic RNA to be detected per reaction. Thus, Afl RT holds great potential for a variety of practical applications that require the use of thermostable and processive RTs.

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.

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.

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.

Chromogenicity of aerobic spore-forming bacteria of the Bacillaceae family isolated from different ecological niches and physiographic zones

To determine the distribution patterns of pigmented bacteria of the Bacilaceae family in different physiographic zones and ecological niches, we recovered 787 isolates from 185 environmental samples (including the areas with radiation pollution). Among the strains obtained, 149 pigmented representatives were detected, which synthesized intracellular and extracellular pigments of yellow, red, pink, and dark colors. In compliance with physiological, biochemical, and chemotaxonomic features, the isolates were identified as 7 species of the Bacilaceae family. We demonstrated that the ability to synthesize pigments significantly depended on the culture medium composition. According to the color of the colonies, the absorption spectra of pigment extracts, their physicochemical properties, and the implementation of several qualitative tests, the pigmented isolates were divided into ten groups. The relative number of pigmented strains in the physiographic zone was consistent with the total level of solar radiation for the year. Most pigmented members of the Bacillaceae family were recovered from deserts and semi-deserts, and fewest of them originated from mixed forests. We show that among the studied ecological niches, pigmented strains were most often isolated from the phyllosphere and aquatic environment and least often from soils. However, the isolates from soils and aquatic environments exhibited a greater diversity of pigmentation, and a lesser variety of colored strains was obtained from the phyllosphere and the gastrointestinal tract of animals. We established that the quantitative and qualitative composition of pigmented isolates from the areas with radiation contamination differed significantly from those coming from the natural radiation background.

Anoxybacillus karvacharensis sp. nov., a novel thermophilic bacterium isolated from the Karvachar geothermal spring in Nagorno-Karabakh

Twelve thermophilic Anoxybacillus strains were isolated from sediment and water samples from a Karvachar hot spring located in the northern part of Nagorno-Karabakh. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, one of the isolates, designated strain K1^T, was studied in detail. The cells are straight, motile rods that are 0.2–0.4×2.3–7.2 µm in size. The strain is a Gram-stain-positive, moderately thermophilic facultative anaerobe with an optimum growth temperature of 60–65 °C and a growth temperature range of 45–70 °C. Growth of strain K1^T was observed at pH 6–11 (optimum, pH 8–9) and was inhibited in the presence of NaCl concentrations above 2.5 % (optimum, 1–1.5 %). The isolate could utilize a wide variety of carbon sources, including d-arabinose, d-ribose, d-galactose, d-fructose, d-mannitol, maltose, aesculin, melibiose, sucrose, trehalose, raffinose, amidone, glycogen, turanose, d-lyxose, d-tagatose, potassium gluconate and 2-keto-gluconate. The strain was able to hydrolyse starch, casein and gelatin, was positive for oxidase and catalase, and reduced nitrate to nitrite, but was negative for H₂S production. Production of urease and indole was not observed. The major cellular fatty acids were C_15 : 0 iso, C_16 : 0 and C_17 : 0 iso (52.5, 13.6 and 19.6 % of total fatty acids, respectively). Strain K1^T shares >99 % 16S rRNA sequence similarity and a genomic average nucleotide identity value of 94.5 % with its closest relative, Anoxybacillus flavithermus DSM 2641^T, suggesting that it represents a separate and novel species, for which the name Anoxybacillus karvacharensis sp. nov. is proposed. The type strain of Anoxybacillus karvacharensis is K1^T (=DSM 106524^T=KCTC 15807^T).

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.

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.

Exploring functional core bacteria in fermentation of a traditional Chinese food, Aspergillus-type douchi

Douchi is a type of traditional Chinese flavoring food that has been used for thousands of years and is produced by multispecies solid-state fermentation. However, the correlation between the flavor, the microbiota, and the functional core microbiota in Aspergillus-type douchi fermentation remains unclear. In this study, Illumina MiSeq sequencing and chromatography were used to investigate the bacterial community and flavor components in Aspergillus-type douchi fermentation. The dominant phyla were Firmicutes, Proteobacteria, and Actinobacteria, and the dominant genera were Weissella, Bacillus, Anaerosalibacter, Lactobacillus, Staphylococcus, and Enterococcus. A total of 58 flavor components were detected during fermentation, including two alcohols, 14 esters, five pyrazines, three alkanes, four aldehydes, three phenols, six acids, and five other compounds. Bidirectional orthogonal partial least square modeling showed that Corynebacterium_1, Lactococcus, Atopostipes, Peptostreptococcus, norank_o__AKYG1722, Truepera, Gulosibacter, norank_f__Actinomycetaceae, and unclassified_f__Rhodobacteraceae are the functional core microbiota responsible for the formation of the flavor components during douchi fermentation. This is the first study to investigate the functional core microbiota in douchi fermentation using Illumina MiSeq sequencing and chromatographic techniques. Our findings extend our understanding of the relationships between flavor, the microbiota, and the functional core microbiota during Aspergillus-type douchi fermentation.

Complete Genome Sequence of Anoxybacillus flavithermus Strain 52-1A Isolated from a Heat-Processed Powdered Milk Concentrate

The thermophilic spore-forming bacterium Anoxybacillus flavithermus is responsible for powdered milk product spoilage, and its presence in dairy processing environments is a concern. Here, the complete genome sequence of the A. flavithermus strain 52-1A isolated from a heat-processed powdered milk product concentrate in Switzerland is presented.

Identification and sequence analyses of novel lipase encoding novel thermophillic bacilli isolated from Armenian geothermal springs

BACKGROUND

Among the huge diversity of thermophilic bacteria mainly bacilli have been reported as active thermostable lipase producers. Geothermal springs serve as the main source for isolation of thermostable lipase producing bacilli. Thermostable lipolytic enzymes, functioning in the harsh conditions, have promising applications in processing of organic chemicals, detergent formulation, synthesis of biosurfactants, pharmaceutical processing etc.

RESULTS

In order to study the distribution of lipase-producing thermophilic bacilli and their specific lipase protein primary structures, three lipase producers from different genera were isolated from mesothermal (27.5-70 °C) springs distributed on the territory of Armenia and Nagorno Karabakh. Based on phenotypic characteristics and 16S rRNA gene sequencing the isolates were identified as Geobacillus sp., Bacillus licheniformis and Anoxibacillus flavithermus strains. The lipase genes of isolates were sequenced by using initially designed primer sets. Multiple alignments generated from primary structures of the lipase proteins and annotated lipase protein sequences, conserved regions analysis and amino acid composition have illustrated the similarity (98-99%) of the lipases with true lipases (family I) and GDSL esterase family (family II). A conserved sequence block that determines the thermostability has been identified in the multiple alignments of the lipase proteins.

CONCLUSIONS

The results are spreading light on the lipase producing bacilli distribution in geothermal springs in Armenia and Nagorno Karabakh. Newly isolated bacilli strains could be prospective source for thermostable lipases and their genes.

Genome Sequence of Anoxybacillus flavithermus Strain AK1, a Thermophile Isolated from a Hot Spring in Saudi Arabia

Anoxybacillus flavithermus strain AK1 was isolated from Al-Ain Alhara, a thermal hot spring located 50 km southeast of the city of Gazan, Saudi Arabia (16°56'N, 43°15'E). The sequenced and annotated genome is 2,630,664 bp and encodes 2,799 genes.

Chemolithoautotrophic arsenite oxidation by a thermophilic Anoxybacillus flavithermus strain TCC9-4 from a hot spring in Tengchong of Yunnan, China

A new facultative chemolithoautotrophic arsenite (As^III)-oxidizing bacterium TCC9-4 was isolated from a hot spring microbial mat in Tengchong of Yunnan, China. This strain could grow with As^III as an energy source, CO₂–HCO₃^- as a carbon source and oxygen as the electron acceptor in a minimal salts medium. Under chemolithoautotrophic conditions, more than 90% of 100 mg/L As^III could be oxidized by the strain TCC9-4 in 36 h. Temperature was an important environmental factor that strongly influenced the As^III oxidation rate and As^III oxidase (Aio) activity; the highest Aio activity was found at the temperature of 40∘C. Addition of 0.01% yeast extract enhanced the growth significantly, but delayed the As^III oxidation. On the basis of 16S rRNA phylogenetic sequence analysis, strain TCC9-4 was identified as Anoxybacillus flavithermus. To our best knowledge, this is the first report of arsenic (As) oxidation by A. flavithermus. The Aio gene in TCC9-4 might be quite novel relative to currently known gene sequences. The results of this study expand our current understanding of microbially mediated As oxidation in hot springs.

Draft Genome Sequence of Anoxybacillus flavithermus Strain 25, Isolated from the Garga Hot Spring in the Barguzin Valley, Baikal Region, Russian Federation

Anoxybacillus flavithermus strain 25 was isolated from a sediment sample from the Garga hot spring in the Barguzin Valley, Baikal Region, Russian Federation (54°19'3.72″N, 110°59'38.4″E). The sequenced and annotated genome is 2,838,680 bp and encodes 3,009 genes.

Non-contiguous finished genome sequence of Anoxybacillus flavithermus subsp. yunnanensis type strain (E13(T)), a strictly thermophilic and organic solvent-tolerant bacterium

Anoxybacillus flavithermus subsp. yunnanensis is the only strictly thermophilic bacterium that is able to tolerate a broad range of toxic solvents at its optimal temperature of 55-60°C. The type strain E13(T) was isolated from water-sediment slurries collected from a hot spring. This study presents the draft genome sequence of A. flavithermus subsp. yunnanensis E13(T) and its annotation. The 2,838,393bp long genome (67 contigs) contains 3,035 protein-coding genes and 85 RNA genes, including 10 rRNA genes, and no plasmids. The genome information has been used to compare with the genomes from A. flavithermus subsp. flavithermus strains.

Analysis of anoxybacillus genomes from the aspects of lifestyle adaptations, prophage diversity, and carbohydrate metabolism

Species of Anoxybacillus are widespread in geothermal springs, manure, and milk-processing plants. The genus is composed of 22 species and two subspecies, but the relationship between its lifestyle and genome is little understood. In this study, two high-quality draft genomes were generated from Anoxybacillus spp. SK3-4 and DT3-1, isolated from Malaysian hot springs. De novo assembly and annotation were performed, followed by comparative genome analysis with the complete genome of Anoxybacillus flavithermus WK1 and two additional draft genomes, of A. flavithermus TNO-09.006 and A. kamchatkensis G10. The genomes of Anoxybacillus spp. are among the smaller of the family Bacillaceae. Despite having smaller genomes, their essential genes related to lifestyle adaptations at elevated temperature, extreme pH, and protection against ultraviolet are complete. Due to the presence of various competence proteins, Anoxybacillus spp. SK3-4 and DT3-1 are able to take up foreign DNA fragments, and some of these transferred genes are important for the survival of the cells. The analysis of intact putative prophage genomes shows that they are highly diversified. Based on the genome analysis using SEED, many of the annotated sequences are involved in carbohydrate metabolism. The presence of glycosyl hydrolases among the Anoxybacillus spp. was compared, and the potential applications of these unexplored enzymes are suggested here. This is the first study that compares Anoxybacillus genomes from the aspect of lifestyle adaptations, the capacity for horizontal gene transfer, and carbohydrate metabolism.

Anoxybacillus suryakundensis sp. nov, a moderately thermophilic, alkalitolerant bacterium isolated from hot spring at Jharkhand, India

Four closely related facultative anaerobe, moderately thermophilic, Gram positive rods (JS1(T), JS5, JS11, and JS15) were isolated from sediment samples from a hot spring at Suryakund, Jharkhand, India. Colonies were pale yellow, rough surface with uneven edges on TSA after 72 h incubation. Heterotrophic growth was observed at 40-60°C and pH 5.5-11.5; optimum growth occurred at 55°C and pH 7.5. 16S rRNA gene sequence analysis revealed the strains belong to genus Anoxybacillus. DNA-DNA homology values among strains were above 70% and showed distinct ERIC and REP PCR profile. On the basis of morphology and biochemical characteristics, strain JS1(T) was studied further. Strain JS1(T) showed 99.30% sequence similarity with A. flavithermus subsp. yunnanensis, 99.23% with A. mongoliensis, 99.16% with A. eryuanensis, 98.74% with A. flavithermus subsp. flavithermus, 98.54% with A. tengchongensis, 98.51% with A. pushchinoensis, 97.91% with A. thermarum, 97.82% with A. kaynarcensis, 97.77% with A. ayderensis and A. kamchatkensis, 97.63% with A. salavatliensis, 97.55% with A. kestanbolensis, 97.48% with A. contaminans, 97.27% with A. gonensis and 97.17% with A. voinovskiensis. In 16S rRNA secondary structure based phylogenetic comparison, strain JS1(T) was clustered with Anoxybacillus eryuanensis, A. mongoliensis, and A. flavithermus subsp. yunnanensis and showed 15 species specific base substitutions with maximum variability in helix 6. Moreover, DNA-DNA relatedness between JS1(T) and the closely related type strains were well below 70%. The DNA G+C content was 42.1 mol%. The major fatty acids were C(15:0 iso), C(16:0 iso) and C(17:0iso). The polar lipids were a phosphatidylgylycerol, a diphosphatidylglycerol, a phosphatidylethnolamine, a phosphatidylcholine, a phosphatidyl monomethylethanolamine and four unknown lipids. Based on polyphasic approach, strain JS1(T) represent a novel species of the genus Anoxybacillus for which Anoxybacillus suryakundensis sp. nov. is proposed. The type strain is JS1(T) (= DSM 27374(T) = LMG 27616(T) =JCM19211(T)).

Draft Genome Sequence of a Thermophilic Member of the Bacillaceae, Anoxybacillus flavithermus Strain Kn10, Isolated from the Kan-nawa Hot Spring in Japan

Here, we report the draft genome sequence of the Anoxybacillus flavithermus Kn10 strain (NBRC 109594), isolated from a water drain of the Kan-nawa Hot Spring in Japan. The draft genome sequence is composed of 90 contigs for 2,772,624 bp with 41.6% G+C content and contains 2,883 protein-coding genes and 80 tRNA genes.

Draft genome sequence of the thermophilic bacterium Anoxybacillus kamchatkensis G10

Anoxybacillus kamchatkensis G10 is a spore-forming thermophilic bacterium isolated from a hot spring in Indonesia. Here, we report the draft genome sequence of A. kamchatkensis G10 that may reveal insights into aerobic/anaerobic metabolisms and carbon utilization in moderate thermophiles.

Recent discoveries and applications of Anoxybacillus

The Bacillaceae family members are a good source of bacteria for bioprocessing and biotransformation involving whole cells or enzymes. In contrast to Bacillus and Geobacillus, Anoxybacillus is a relatively new genus that was proposed in the year 2000. Because these bacteria are alkali-tolerant thermophiles, they are suitable for many industrial applications. More than a decade after the first report of Anoxybacillus, knowledge accumulated from fundamental and applied studies suggests that this genus can serve as a good alternative in many applications related to starch and lignocellulosic biomasses, environmental waste treatment, enzyme technology, and possibly bioenergy production. This current review provides the first summary of past and recent discoveries regarding the isolation of Anoxybacillus, its medium requirements, its proteins that have been characterized and cloned, bioremediation applications, metabolic studies, and genomic analysis. Comparisons to some other members of Bacillaceae and possible future applications of Anoxybacillus are also discussed.

Bacillus thermoglucosidasius sp. nov., a New Species of Obligately Thermophilic Bacilli

A group of 6 strains of obligately thermophilic spore-formers is described as a novel species named Bacillus thermoglucosidasius. The strains are strictly aerobic, neutrophilic, amylolytic, Gram-positive, azide sensitive, produce terminally swollen sporangia and exo-oligo-1,6-glucosidase in large amounts. Strain KP 1006 (DSM 2542) is designated as the type strain. Growth occurs at temperatures from 42°C to 69°C with an optimum at 61-63°C, and at an initial pH of 6.5-8.5. The guanine + cytosine content of DNA, estimated by thermal DNA denaturation, is 45-46 mol%.

Isolation and characterization of pullulan-degrading Anoxybacillus species isolated from Malaysian hot springs

Two thermophilic bacteria (SK3-4 and DT3-1) were isolated from the Sungai Klah (SK) and Dusun Tua (DT) hot springs in Malaysia. The cells from both strains were rod-shaped, stained Gram positive and formed endospores. The optimal growth of both strains was observed at 55 degrees C and pH 7. Strain DT3-1 exhibited a higher tolerance to chloramphenicol (100 microg ml(-1)) but showed a lower tolerance to sodium chloride (2%, w/v) compared to strain SK3-4. Phylogenetic analysis based on 16S rRNA gene sequences revealed that both strains belong to the genus Anoxybacillus. High concentrations of 15:0 iso in the fatty acid profiles support the conclusion that both strains belong to the genus Anoxybacillus and exhibit unique fatty acid compositions and percentages compared to other Anoxybacillus species. The DNA G + C contents were 42.0 mol% and 41.8 mol% for strains SK3-4 and DT3-1, respectively. Strains SK3-4 and DT3-1 were able to degrade pullulan and to produce maltotriose and glucose, respectively, as their main end products. Based on phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequences, and the DNA G + C content, we propose that strains SK3-4 and DT3-1 are new pullulan-degrading Anoxybacillus strains.

RAPD-based screening for spore-forming bacterial populations in Uruguayan commercial powdered milk

The occurrence of spore-forming bacteria in powdered milk is of concern to the dairy industry due to potential deleterious effects including those resulting from proteolytic and lipolytic activities. Twenty-two powdered milk samples representative of spring and summer production obtained from Uruguayan retail stores were analyzed for type and number of thermophilic and spore-forming bacterial species. Bacillus licheniformis isolates were found to be the most prominent milk powder contaminant followed by Anoxybacillus flavithermus representing 71.5 to 84% of the total microflora. Geobacillus stearothermophilus, however, was not found. B. licheniformis strains F and G were both found in this study but strain F was the prevalent isolate representing 98.9% of the total isolates of this species. A. flavithermus isolates corresponded to strain C in accordance with 16S rRNA gene sequence analysis, however, in contrast with other reports, the RAPD profiles showed three characteristic bands at approximately 650, 1000 and 1650 bp, but lacking a band at 1250 bp. A third group of isolates was identified corresponding to members of a Bacillus subtilis group and Bacillus megaterium. Isolates designated B. licheniformis, A. flavithermus, B. megaterium and the B. subtilis group represented 89.1 to 93.6% of those analyzed, and depended on previous heat treatment and incubation temperatures of the plates. The remaining isolates were Bacillus pumilus and unidentified spore-formers.

Anoxybacillus tengchongensis sp. nov. and Anoxybacillus eryuanensis sp. nov., facultatively anaerobic, alkalitolerant bacteria from hot springs

Two novel thermophilic, spore-forming bacterial strains, T-11(T) and E-112(T), were isolated from hot springs in Tengchong and Eryuan counties of Yunnan province in south-west China. The strains were Gram-stain-positive rods, occurring singly or in chains. Growth of strain T-11(T) was observed between 30 and 75 °C (optimum 50 °C) and at pH 7-11 (optimum pH 8.5), while the temperature range for strain E-112(T) was 35-70 °C (optimum 55 °C) and the pH range was 7.0-11.0 (optimum pH 8.0). The DNA G+C contents of strains T-11(T) and E-112(T) were 41.1 and 42.6 mol%, respectively. On the basis of 16S rRNA gene sequence similarity, the two strains were shown to be related most closely to Anoxybacillus species. The chemotaxonomic characteristics [predominant isoprenoid quinone menaquinone 7 (MK-7); major fatty acids iso-C(15 : 0) and iso-C(17 : 0)] also supported the affiliation of strains T-11(T) and E-112(T) to the genus Anoxybacillus. The results of DNA-DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains T-11(T) and E-112(T) from Anoxybacillus species with validly published names. Strains T-11(T) and E-112(T) therefore represent two novel species, for which the names Anoxybacillus tengchongensis sp. nov. (type strain T-11(T) =CCTCC AB209237(T) =KCTC 13721(T)) and Anoxybacillus eryuanensis sp. nov. (type strain E-112(T) =CCTCC AB209236(T) =KCTC 13720(T)) are proposed.

Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1

BACKGROUND

Gram-positive bacteria of the genus Anoxybacillus have been found in diverse thermophilic habitats, such as geothermal hot springs and manure, and in processed foods such as gelatin and milk powder. Anoxybacillus flavithermus is a facultatively anaerobic bacterium found in super-saturated silica solutions and in opaline silica sinter. The ability of A. flavithermus to grow in super-saturated silica solutions makes it an ideal subject to study the processes of sinter formation, which might be similar to the biomineralization processes that occurred at the dawn of life.

RESULTS

We report here the complete genome sequence of A. flavithermus strain WK1, isolated from the waste water drain at the Wairakei geothermal power station in New Zealand. It consists of a single chromosome of 2,846,746 base pairs and is predicted to encode 2,863 proteins. In silico genome analysis identified several enzymes that could be involved in silica adaptation and biofilm formation, and their predicted functions were experimentally validated in vitro. Proteomic analysis confirmed the regulation of biofilm-related proteins and crucial enzymes for the synthesis of long-chain polyamines as constituents of silica nanospheres.

CONCLUSIONS

Microbial fossils preserved in silica and silica sinters are excellent objects for studying ancient life, a new paleobiological frontier. An integrated analysis of the A. flavithermus genome and proteome provides the first glimpse of metabolic adaptation during silicification and sinter formation. Comparative genome analysis suggests an extensive gene loss in the Anoxybacillus/Geobacillus branch after its divergence from other bacilli.

Thermophilic aerobic granular biomass for enhanced settleability

Aerobic biological wastewater treatment at thermophilic (ca. 55 degrees C) temperatures notoriously produces biomass that flocculates poorly or not at all. Contrary to this, thermophilic aerobic biomass that settled well in sequencing batch reactors was cultured with sludge volume index (SVI) values as low as 60mL/g. A mixture of granular and flocculant biomass resulted when closed reactors were sparged with recirculated reactor headspace gas containing some air, whereas a conventionally aerated control reactor sparged with air alone contained dispersed growth that did not flocculate. Maximum granule diameter was from 1.2 to 1.9mm, and granule resistance to disintegration was comparable to aerobic mesophilic granules. Two bacteria were isolated and identified as Anoxybacillus flavothermus and Pseudoxanthomonas taiwanensis as determined by partial 16S rDNA sequencing. Anoxybacilli species are alkaliphilic or alkalitolerant, with the type species having an obligate requirement for carbonate, even when grown on glucose. We postulate that high alkalinity and CO(2) may select for a population of aerobic thermophilies that flocculates and granulates.

Anoxybacillus kamchatkensis sp. nov., a novel thermophilic facultative aerobic bacterium with a broad pH optimum from the Geyser valley, Kamchatka

A facultative aerobic, moderately thermophilic, spore forming bacterium, strain JW/VK-KG4 was isolated from an enrichment culture obtained from the Geyser valley, a geo-thermally heated environment located in the Kamchatka peninsula (Far East region of Russia). The cells were rod shaped, motile, peritrichous flagellated stained Gram positive and had a Gram positive type cell wall. Aerobically, the strain utilized a range of carbohydrates including glucose, fructose, trehalose, proteinuous substrates, and pectin as well. Anaerobically, only carbohydrates are utilized. When growing on carbohydrates, the strain required yeast extract and vitamin B(12). Anaerobically, glucose was fermented to lactate as main product and acetate, formate, ethanol as minor products. Aerobically, even in well-aerated cultures (agitated at 500 rpm), glucose oxidation was incomplete and lactate and acetate were found in culture supernatants as by-products. Optimal growth of the isolate was observed at pH(25 C) 6.8-8.5 and 60 degrees C. The doubling times on glucose at optimal growth conditions were 34 min (aerobically) and 40 min (anaerobically). The G+C content was 42.3 mol% as determined by T(m) assay. Sequence analysis of the 16S rRNA gene indicated an affiliation of strain JW/VK-KG4 with Anoxybacillus species. Based on its morphology, physiology, phylogenetic relationship and its low DNA-DNA homology with validly published species of Anoxybacillus, it is proposed that strain JW/VK-KG4 represents a new species in the genus Anoxybacillus as A. kamchatkensis sp. nov. The type strain for the novel species is JW/VK-KG4(T) (=DSM 14988, =ATCC BAA-549). The GenBank accession number for the 16S rDNA sequence is AF510985.

Anoxybacillus voinovskiensis sp. nov., a moderately thermophilic bacterium from a hot spring in Kamchatka

A novel moderately thermophilic bacterium, strain TH13T, was isolated from a hot spring in Kamchatka. It was found to be a Gram-positive, facultative aerobe; the straight, non-motile rods grew at 30-64 degrees C (optimum 54 degrees C). The isolate was positive for catalase and oxidase tests and reduced nitrate to nitrite, but was negative for H2S production and growth in more than 3% NaCl (w/v). The isolate grew at pH 7-8, but not at pH values higher than 9. The DNA G+C content was 43.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain TH13T was a member of the genus Anoxybacillus. DNA-DNA hybridization revealed a low relatedness (less than 30.2%) between the isolate and its close phylogenetic neighbours Anoxybacillus pushchinoensis and Anoxybacillus flavithermus. On the basis of phenotypic characteristics, phylogenetic data and DNA-DNA hybridization data, it was concluded that the isolate merited classification as a novel species, for which the name Anoxybacillus voinovskiensis sp. nov. is proposed. The type strain of this species is TH13T (=NCIMB 13956T=JCM 12111T).

A RAPD-based survey of thermophilic bacilli in milk powders from different countries

Twenty-eight milk powders from 18 different countries were examined for the number and type of contaminating thermophilic bacilli. Of 742 isolates examined, 96.8% were assigned to the same strains of bacilli as previously found in New Zealand powders. The dominant isolate was Anoxybacillus flavithermus strain C followed by Bacillus licheniformis strain F. The former was also prevalent in New Zealand powders and the results demonstrate that A. flavithermus represents a widespread contaminant, seemingly ubiquitous in factories producing milk powder. The presence of thermophilic strains of Geobacillus stearothermophilus and to a lesser extent of Bacillus subtilis in milk powders was reconfirmed.

Aerobic growth of Anoxybacillus pushchinoensis K1(T): emended descriptions of A. pushchinoensis and the genus Anoxybacillus

In this work, corrections are made to the descriptions of the species Anoxybacillus pushchinoensis corrig. and the genus ANOXYBACILLUS: Experiments to determine the relationship of A. pushchinoensis K1(T) to oxygen showed that it was capable of aerobic growth, but preferred to grow anaerobically. During aerobic growth, the redox indicator resazurin was reduced as a result of hydrogen gas production. The facultatively anaerobic nature of K1(T) was ascertained by cultivation in aerobic liquid medium, where growth began at the bottom of the tube. The anaerobic nature of K1(T) was also indicated by a negative catalase reaction. This work is submitted to correct the description of the species A. pushchinoensis from obligate anaerobe to aerotolerant anaerobe and to emend the description of the genus Anoxybacillus from obligate anaerobes or facultative anaerobes to aerotolerant anaerobes or facultative anaerobes.

A RAPD-based comparison of thermophilic bacilli from milk powders

The similarity of strains of thermophilic Geobacillus stearothermophilus (formerly Bacillus stearothermophilus), Anoxybacillus flavithermus (formerly Bacillus flavothermus), Bacillus licheniformis and Bacillus subtilis isolated from separate milk powder production runs from multiple factories was examined using a random amplified polymorphic DNA (RAPD) protocol. As a result of the analysis of the RAPD fingerprints and data relating to general growth and biochemical tests, over 98% of the 1470 isolates examined (grown at 55 degrees C) were assigned to the species G. stearothermophilus, A. flavithermus, B. licheniformis and B. subtilis. The G. stearothermophilus isolates were identified as being nearly identical to G. stearothermophilus (DSMZ 22; equivalent to ATCC 12980), or G. stearothermophilus var. calidolactis (DSMZ 1550). Three groups of isolates were found to be related to A. flavithermus (DSMZ 2641) by partial small ribosomal subunit (16S) sequence comparisons and shown to be interrelated by RAPD analyses with multiple primer sets. The thermophilic isolates of B. licheniformis were positively identified by comparison with type strains of B. licheniformis DSMZ 13 and DSMZ 8785. All of the B. subtilis strains shared bands in their RAPD profiles and were similar to a common B. subtilis type strain (DSMZ 10 and DSMZ 347). Overall, the most common and prevalent group of strains (group A) was demonstrated to be closely related to G. stearothermophilus (DSMZ 22).

Improved amplification of microbial DNA from blood cultures by removal of the PCR inhibitor sodium polyanetholesulfonate

Molecular methods are increasingly used to identify microbes in clinical samples. A common technical problem with PCR is failed amplification due to the presence of PCR inhibitors. Initial attempts at amplification of the bacterial 16S rRNA gene from inoculated blood culture media failed for this reason. The inhibitor persisted, despite numerous attempts to purify the DNA, and was identified as sodium polyanetholesulfonate (SPS), a common additive to blood culture media. Like DNA, SPS is a high-molecular-weight polyanion that is soluble in water but insoluble in alcohol. Accordingly, SPS tends to copurify with DNA. An extraction method was designed for purification of DNA from blood culture media and removal of SPS. Blood culture media containing human blood and spiked with Escherichia coli was subjected to an organic extraction procedure with benzyl alcohol, and removal of SPS was documented spectrophotometrically. Successful amplification of the extracted E. coli 16S rRNA gene was achieved by adding 5 microliter of undiluted processed sample DNA to a 50-microliter PCR mixture. When using other purification methods, the inhibitory effect of SPS could be overcome only by dilution of these samples. By our extraction technique, even uninoculated blood culture media were found to contain bacterial DNA when they were subjected to broad-range 16S rRNA gene consensus PCR. We conclude that the blood culture additive SPS is a potent inhibitor of PCR, is resistant to removal by traditional DNA purification methods, but can be removed by a benzyl alcohol extraction protocol that results in improved PCR performance.

Characterization of the xylanases from the new isolated thermophilic xylan-degrading Bacillus thermoleovorans strain K-3d and Bacillus flavothermus strain LB3A

Three strictly aerobic strains (K-1, K-3d and K-4) were isolated from a hot-spring in Kobe, Japan, and a facultative anaerobic strain LB3A was isolated from sediments collected from the alkaline Lake Bogoria, Kenya. All strains were thermophilic and capable of growth on xylan. On the basis of morphological, physiological and phylogenetic studies the new aerobic isolates resemble the thermophilic species Bacillus thermoleovorans while the facultative anaerobic isolate LB3A resembles the facultative anaerobic thermophilic species Bacillus flavothermus. When grown on xylan as sole carbon source, all isolates produce thermoactive xylanases, Xylanases from strains K-3d and LB3A are active at temperatures between 40 and 90 degrees C and pH values between 5.0 and 9.0. Applying SDS-PAGE the crude xylanase complex of isolate K-3d was shown to be composed of two active bands, with molecular masses of 40 and 69 kDa. The crude xylanase complex of isolate LB3A, on the other hand, is composed of at least four activity bands with molecular masses ranging from 80 to 130 kDa. Due to the product pattern of xylan hydrolysis both enzymes are classified as endoxylanases. The xylanolytic enzyme system of isolate K-3d produces xylotriose, xylotetraose and larger xylooligosacharides, whereas the xylanases from isolate LB3A release xylotetraose as the major product of hydrolysis.

Cultivation of aerobic chemoorganotrophic proteobacteria and gram-positive bacteria from a hot spring microbial mat

The diversity of aerobic chemoorganotrophic bacteria inhabiting the Octopus Spring cyanobacterial mat community (Yellowstone National Park) was examined by using serial-dilution enrichment culture and a variety of enrichment conditions to cultivate the numerically significant microbial populations. The most abundant bacterial populations cultivated from dilutions to extinction were obtained from enrichment flasks which contained 9.0 x 10(2) primary producer (Synechococcus spp.) cells in the inoculum. Two isolates exhibited 16S rRNA nucleotide sequences typical of beta-proteobacteria. One of these isolates contained a 16S rRNA sequence identical to a sequence type previously observed in the mat by molecular retrieval techniques. Both are distantly related to a new sequence directly retrieved from the mat and contributed by a beta-proteobacterial community member. Phenotypically diverse gram-positive isolates genetically similar to Bacillus flavothermus were obtained from a variety of dilutions and enrichment types. These isolates exhibited identical 16S rRNA nucleotide sequences through a variable region of the molecule. Of the three unique sequences observed, only one had been previously retrieved from the mat, illustrating both the inability of the cultivation methods to describe the composition of a microbial community and the limitations of the ability of molecular retrieval techniques to describe populations which may be less abundant in microbial communities.