Biochemical and molecular characterization of Bacillus pumilus isolated from coastal environment in Cochin, India

Bacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation

Background

Members of the Bacillus pumilus group (abbreviated as the Bp group) are quite diverse and ubiquitous in marine environments, but little is known about correlation with their terrestrial counterparts. In this study, 16 marine strains that we had isolated before were sequenced and comparative genome analyses were performed with a total of 52 Bp group strains. The analyses included 20 marine isolates (which included the 16 new strains) and 32 terrestrial isolates, and their evolutionary relationships, differentiation, and environmental adaptation.

Results

Phylogenomic analysis revealed that the marine Bp group strains were grouped into three species: B. pumilus, B. altitudinis and B. safensis. All the three share a common ancestor. However, members of B. altitudinis were observed to cluster independently, separating from the other two, thus diverging from the others. Consistent with the universal nature of genes involved in the functioning of the translational machinery, the genes related to translation were enriched in the core genome. Functional genomic analyses revealed that the marine-derived and the terrestrial strains showed differences in certain hypothetical proteins, transcriptional regulators, K⁺ transporter (TrK) and ABC transporters. However, species differences showed the precedence of environmental adaptation discrepancies. In each species, land specific genes were found with possible functions that likely facilitate survival in diverse terrestrial niches, while marine bacteria were enriched with genes of unknown functions and those related to transcription, phage defense, DNA recombination and repair.

Conclusion

Our results indicated that the Bp isolates show distinct genomic features even as they share a common core. The marine and land isolates did not evolve independently; the transition between marine and non-marine habitats might have occurred multiple times. The lineage exhibited a priority effect over the niche in driving their dispersal. Certain intra-species niche specific genes could be related to a strains adaptation to its respective marine or terrestrial environment(s). In summary, this report describes the systematic evolution of 52 Bp group strains and will facilitate future studies toward understanding their ecological role and adaptation to marine and/or terrestrial environments.

Persistence of fecal indicator bacteria associated with zooplankton in a tropical estuary-west coast of India

In a study carried out during 2014, bacteria associated with zooplankton in the Zuari estuary were three to four orders of magnitude higher in abundance than in seawater. The live zooplankton carried much more bacterial load compared with the carcasses, and the fecal pellets harbored the highest density of bacteria, i.e., 8 × 10¹³ CFU cm^-3. The diversity of bacteria was higher in live zooplankton and also in seawater. But the activity of the zooplankton-associated bacteria was much higher compared with the free-living ones. Most of the associated bacteria belonged to the genus Enterobacter, Pseudomonas, Aeromonas, and Bacillus. In growth experiments, Aeromonas and Bacillus were found to have lower salinity optima than Enterobacter (20 psu) and Vibrio and Pseudomonas (normal seawater salinity). Better growth of bacteria was observed in the medium containing the diatom Chaetoceros sp. than Navicula sp. Bacterial isolates were also able to survive in oligotrophic conditions and produce optimum biomass in 2 days at salinity 5 psu, but in freshwater, the bacteria took a week's time to attain the optima. At salinities 0-35, the bacteria survived even for 3 months without nutrient addition, indicating resilience in these bacteria and mechanisms to persist in the estuaries even in adverse conditions.

The role of pH on the biological struvite production in digested sludge dewatering liquors

Struvite production mediated by bacteria has opened up a new route for phosphorus recovery from wastewater streams but its application to digested sludge dewatering liquors is not yet well understood. This study investigates the growth and biological struvite production of selected bacteria in wastewater liquors with pHs between 5.7 to 9.1. The bacterial growth was assessed through flow cytometry. Bacillus pumilus, Halobacterium salinarum and Brevibacterium antiquum remained viable at pHs between 5.7 to 9.1 but B. antiquum was able to grow at pHs between 7.3 to 7.8. Further analysis allowed the identification of crystals as struvite in tests between pH 7.3 to 8.3. All strains were capable of producing struvite at a range of pHs, but the highest production of 135-198 mg/L was observed for pHs between 7.3 to 8.3. At pHs > 8.3, precipitation of struvite and calcium compounds was observed in inoculated and non-inoculated tests. This study demonstrates that biological struvite production can occur at a wide range of pHs, hence significantly different from chemical struvite precipitation that occurs at pH > 8.3, making it a potentially viable process for phosphorus recovery as struvite from wastewater streams and sludge liquors without strict pH control.

Isolation and Characterization of Bacteria Colonizing Acartia tonsa Copepod Eggs and Displaying Antagonist Effects against Vibrio anguillarum, Vibrio alginolyticus and Other Pathogenic Strains

Copepods represent a major source of food for many aquatic species of commercial interest for aquaculture such as mysis shrimp and early stages of fishes. For the purpose of this study, the culturable mesophilic bacterial flora colonizing Acartia tonsa copepod eggs was isolated and identified. A total of 175 isolates were characterized based on their morphological and biochemical traits. The majority of these isolates (70%) were Gram-negative bacteria. Matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) was used for rapid identification of bacterial isolates. Here, 58% of isolates were successfully identified at the genus level and among them, 54% were identified at the species level. These isolates belong to 12 different genera and 29 species. Five strains, identified as Bacillus pumilus, named 18 COPS, 35A COPS, 35R COPS, 38 COPS, and 40A COPS, showed strong antagonisms against several potential fish pathogens including Vibrio alginolyticus, V. anguillarum, Listeria monocytogenes, and Staphylococcus aureus. Furthermore, using a differential approach, we show that the antimicrobial activity of the 35R COPS strain is linked primarily to the production of antimicrobial compounds of the amicoumacin family, as demonstrated by the specific UV-absorbance and the MS/MS fragmentation patterns of these compounds.

Rhizobacterial characterization for quality control of eucalyptus biogrowth promoter products

Plant growth-promoting rhizobacteria strains from special formulations have been used to optimize eucalyptus cutting production. To undertake quality control for the formulated products, the rhizobacterial strains should be characterized to assess their purity and authentication. In the present study, we characterized nine strains of rhizobacteria, including three Bacillus subtilis (S1, S2 and 3918), two Pseudomonas sp. (MF4 and FL2), P. putida (MF2), P. fulva (Ca), Frateuria aurantia (R1), and Stenotrophomonas maltophilia (CIIb). The strains were differentiated by colony morphology after 24 h of incubation in three different solid state culture media (glucose-nutritive agar, 523 medium and yeast extract-mannitol agar), sensitivity to a panel of 28 antibiotics (expressed according to the formation of inhibition halos of bacterial growth in the presence of antibiotics), and PCR-RFLP profiles of the 16S rDNA gene produced using nine restriction enzymes. It was possible to differentiate all nine strains of rhizobacteria using their morphological characteristics and sensitivity to antibiotics. The molecular analysis allowed us to separate the strains CIIb, FL2 and R1 from the strains belonging to the genera Bacillus and Pseudomonas. By using these three methods concomitantly, we were able to determine strain purity and perform the authentication.

Antimicrobial Activities of Bacteria Associated with the Brown Alga Padina pavonica

Macroalgae belonging to the genus Padina are known to produce antibacterial compounds that may inhibit growth of human- and animal pathogens. Hitherto, it was unclear whether this antibacterial activity is produced by the macroalga itself or by secondary metabolite producing epiphytic bacteria. Here we report antibacterial activities of epiphytic bacteria isolated from Padina pavonica (Peacocks tail) located on northern coast of Tunisia. Eighteen isolates were obtained in pure culture and tested for antimicrobial activities. Based on the 16S rRNA gene sequences the isolates were closely related to Proteobacteria (12 isolates; 2 Alpha- and 10 Gammaproteobacteria), Firmicutes (4 isolates) and Actinobacteria (2 isolates). The antimicrobial activity was assessed as inhibition of growth of 12 species of pathogenic bacteria (Aeromonas salmonicida, A. hydrophila, Enterobacter xiangfangensis, Enterococcus faecium, Escherichia coli, Micrococcus sp., Salmonella typhimurium, Staphylococcus aureus, Streptococcus sp., Vibrio alginoliticus, V. proteolyticus, V. vulnificus) and one pathogenic yeast (Candida albicans). Among the Firmicutes, isolate P8, which is closely related to Bacillus pumilus, displayed the largest spectrum of growth inhibition of the pathogenic bacteria tested. The results emphasize the potential use of P. pavonica associated antagonistic bacteria as producers of novel antibacterial compounds.

Purification and characterization of [Formula: see text]-mannanase from Bacillus pumilus (M27) and its applications in some fruit juices

Thermo alkaline mannanase was purified from the bacteria of Bacillus pumilus (M27) using the techniques of ammonium sulphate precipitation, DEAE-Sephadex ion exchange chromatography and Sephacryl S200 gel filtration chromatography with 111-fold and 36 % yield. It was determined that the enzyme had 2 sub-units including 35 kDa and 55 kDa in gel filtration chromatography and SDS-PAGE electrophoresis systems. The optimum pH and temperature was determined as 8 and 60 °C, respectively. It was also noticed that the enzyme did not lose its activity at a wide interval such as pH 3-11 and at high temperatures such as 90 °C. Additionally, the effects of some metal ions on the mannanase enzyme activity. Moreover, the clarifying efficiency of purified mannanase enzyme with some fruit juices such as orange, apricot, grape and apple was also investigated. Enzymatic treatment was carried out with 1 mL L(-1) of purified mannanase for 1 h at 60 °C. It was determined that the highest pure enzyme was efficient upon clarifying the apple juice at 154 % rate.

Phylogenetic diversity of the Bacillus pumilus group and the marine ecotype revealed by multilocus sequence analysis

Bacteria closely related to Bacillus pumilus cannot be distinguished from such other species as B. safensis, B. stratosphericus, B. altitudinis and B. aerophilus simply by 16S rRNA gene sequence. In this report, 76 marine strains were subjected to phylogenetic analysis based on 7 housekeeping genes to understand the phylogeny and biogeography in comparison with other origins. A phylogenetic tree based on the 7 housekeeping genes concatenated in the order of gyrB-rpoB-pycA-pyrE-mutL-aroE-trpB was constructed and compared with trees based on the single genes. All these trees exhibited a similar topology structure with small variations. Our 79 strains were divided into 6 groups from A to F; Group A was the largest and contained 49 strains close to B. altitudinis. Additional two large groups were presented by B. safensis and B. pumilus respectively. Among the housekeeping genes, gyrB and pyrE showed comparatively better resolution power and may serve as molecular markers to distinguish these closely related strains. Furthermore, a recombinant phylogenetic tree based on the gyrB gene and containing 73 terrestrial and our isolates was constructed to detect the relationship between marine and other sources. The tree clearly showed that the bacteria of marine origin were clustered together in all the large groups. In contrast, the cluster belonging to B. safensis was mainly composed of bacteria of terrestrial origin. Interestingly, nearly all the marine isolates were at the top of the tree, indicating the possibility of the recent divergence of this bacterial group in marine environments. We conclude that B. altitudinis bacteria are the most widely spread of the B. pumilus group in marine environments. In summary, this report provides the first evidence regarding the systematic evolution of this bacterial group, and knowledge of their phylogenetic diversity will help in the understanding of their ecological role and distribution in marine environments.