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Frontiers in Microbiology 2022Plant Growth-Promoting Bacteria (PGPB) are a promising alternative to conventional fertilization. One of the most interesting PGPB strains, among the spore-forming... (Review)
Review
Plant Growth-Promoting Bacteria (PGPB) are a promising alternative to conventional fertilization. One of the most interesting PGPB strains, among the spore-forming bacteria of the phylum Firmicutes, is . It is a bacterial species that inhabits a wide range of environments and shows resistance to abiotic stresses. So far, several PGPB strains of have been described, including LZP02, JPVS11, TUAT-1, TRS-3, and EU927414. These strains have been shown to produce a wide range of phytohormones and other plant growth-promoting substances. Therefore, they can affect various plant properties, including biometric traits, substance content (amino acids, proteins, fatty acids), and oxidative enzymes. Importantly, based on a study with WP8, it can be concluded that this bacterial species stimulates plant growth when the native microbiota of the inoculated soil is altered. However, there is still a lack of research with deeper insights into the structure of the native microbial community (after application), which would provide a better understanding of the functioning of this bacterial species in the soil and thus increase its effectiveness in promoting plant growth.
PubMed: 36620067
DOI: 10.3389/fmicb.2022.1069053 -
Microorganisms Sep 2021Mature and stable intestinal microbiota in chickens is essential for health and production. Slow development of microbiota in young chickens prolongs the precarious...
Mature and stable intestinal microbiota in chickens is essential for health and production. Slow development of microbiota in young chickens prolongs the precarious period before reaching mature configuration. Whether probiotics can play a role in the early maturation of intestinal microbiota is unknown. To address this, day-old chicks were assigned into six groups: NC (basal diet), PC (virginiamycin), low (BPL) and high-dose (BPH) of and low (BSL) and high-dose (BSH) of . Cecal contents at days 7, 14, 28 and 42 were used to analyze the treatment and time effects on the diversity and composition of microbiota. Overall, the alpha diversity was significantly decreased in the NC group between days 7 and 14, while this decline was prevented in the probiotic (BSL and BSH) and even reversed in the BPH group. The beta-diversity showed significant responses of microbial communities to probiotics in first two weeks of life. Analyses of the abundance of microbiota reflected that members of the family Ruminococcaceae (, , , and ), which were dominant in mature microbiota, were significantly higher in abundance at day 14 in the probiotic groups. Conversely, the abundance of genera within the family Lachnospiraceae (, and ) was dominant in early dynamic microbiota but was significantly lower in the probiotic groups at day 14. The and abundance was higher, while the Enterobacteriaceae abundance was lower in the probiotic groups. In summary, the probiotics efficiently helped the cecal microbiota reach mature configuration earlier in life. These results could be used for the future manipulation of microbiota from the perspective of improving poultry performance.
PubMed: 34576794
DOI: 10.3390/microorganisms9091899 -
Frontiers in Microbiology 2021Members of the group (abbreviated as the group) are quite diverse and ubiquitous in marine environments, but little is known about correlation with their terrestrial...
BACKGROUND
Members of the group (abbreviated as the 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 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 group strains were grouped into three species: , and . All the three share a common ancestor. However, members of 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 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 group strains and will facilitate future studies toward understanding their ecological role and adaptation to marine and/or terrestrial environments.
PubMed: 34025591
DOI: 10.3389/fmicb.2021.571212 -
Frontiers in Microbiology 2023Plant growth-promoting bacteria are one of the most interesting methods of controlling fungal phytopathogens. These bacteria can participate in biocontrol via a variety... (Review)
Review
Plant growth-promoting bacteria are one of the most interesting methods of controlling fungal phytopathogens. These bacteria can participate in biocontrol via a variety of mechanisms including lipopeptide production, hydrolytic enzymes (e.g., chitinase, cellulases, glucanase) production, microbial volatile organic compounds (mVOCs) production, and induced systemic resistance (ISR) triggering. Among the bacterial genera most frequently studied in this aspect are spp. including . Due to the range of biocontrol traits, is one of the most interesting members of spp. that can be used in the biocontrol of fungal phytopathogens. So far, a number of strains that exhibit biocontrol properties against fungal phytopathogens have been described, e.g., HR10, PTB180, SS-10.7, MCB-7, INR7, SE52, SE34, SE49, RST25, JK-SX001, and KUDC1732. strains are capable of suppressing phytopathogens such as , , , , , and . Importantly, can promote plant growth regardless of whether it alters the native microbiota or not. However, in order to increase its efficacy, research is still needed to clarify the relationship between the native microbiota and . Despite that, it can already be concluded that strains are good candidates to be environmentally friendly and commercially effective biocontrol agents.
PubMed: 37560520
DOI: 10.3389/fmicb.2023.1194606 -
Microorganisms May 2021The study aimed to evaluate the metabolism and resistance to the gastrointestinal tract conditions of UAMX (BP-UAMX) isolated from overweight individuals using genomic...
The study aimed to evaluate the metabolism and resistance to the gastrointestinal tract conditions of UAMX (BP-UAMX) isolated from overweight individuals using genomic tools. Specifically, we assessed its ability to metabolize various carbon sources, its resistance to low pH exposure, and its growth in the presence of bile salts. The genomic and bioinformatic analyses included the prediction of gene and protein metabolic functions, a pan-genome and phylogenomic analysis. BP-UAMX survived at pH 3, while bile salts (0.2-0.3% ) increased its growth rate. Moreover, it showed the ability to metabolize simple and complex carbon sources (glucose, starch, carboxymethyl-cellulose, inulin, and tributyrin), showing a differentiated electrophoretic profile. Genome was assembled into a single contig, with a high percentage of genes and proteins associated with the metabolism of amino acids, carbohydrates, and lipids. Antibiotic resistance genes were detected, but only one beta-Lactam resistance protein related to the inhibition of peptidoglycan biosynthesis was identified. The pan-genome of BP-UAMX is still open with phylogenetic similarities with other of human origin. Therefore, BP-UAMX seems to be adapted to the intestinal environment, with physiological and genomic analyses demonstrating the ability to metabolize complex carbon sources, the strain has an open pan-genome with continuous evolution and adaptation.
PubMed: 34067853
DOI: 10.3390/microorganisms9051076 -
Microbial Cell Factories Feb 2021Microbial surfactants called biosurfactants, thanks to their high biodegradability, low toxicity and stability can be used not only in bioremediation and oil processing,...
BACKGROUND
Microbial surfactants called biosurfactants, thanks to their high biodegradability, low toxicity and stability can be used not only in bioremediation and oil processing, but also in the food and cosmetic industries, and even in medicine. However, the high production costs of microbial surfactants and low efficiency limit their large-scale production. This requires optimization of management conditions, including the possibility of using waste as a carbon source, such as food processing by-products. This papers describes the production and characterization of the biosurfactant obtained from the endophytic bacterial strain Bacillus pumilus 2A grown on various by-products of food processing and its potential applications in supporting plant growth. Four different carbon and nitrogen sources, pH, inoculum concentration and temperature were optimized within Taguchi method.
RESULTS
Optimization of bioprocess within Taguchi method and experimental analysis revealed that the optimal conditions for biosurfactant production were brewer's spent grain (5% w/v), ammonium nitrate (1% w/v), pH of 6, 5% of inoculum, and temperature at 30 °C, leading to 6.8 g/L of biosurfactant. Based on gas chromatography-mass spectrometry and Fourier transform infrared spectroscopy analysis produced biosurfactant was determined as glycolipid. Obtained biosurfactant has shown high and long term thermostability, surface tension of 47.7 mN/m, oil displacement of 8 cm and the emulsion index of 69.11%. The examined glycolipid, used in a concentration of 0.2% significantly enhanced growth of Phaseolus vulgaris L. (bean), Raphanus L. (radish), Beta vulgaris L. (beetroot).
CONCLUSIONS
The endophytic Bacillus pumilus 2A produce glycolipid biosurfactant with high and long tem thermostability, what makes it useful for many purposes including food processing. The use of brewer's spent grain as the sole carbon source makes the production of biosurfactants profitable, and from an environmental point of view, it is an environmentally friendly way to remove food processing by products. Glycolipid produced by endophytic Bacillus pumilus 2A significantly improve growth of Phaseolus vulgaris L. (bean), Raphanus L. (radish), Beta vulgaris L. (beetroot). Obtained results provide new insight to the possible use of glycolipids as plant growth promoting agents.
Topics: Bacillus pumilus; Beta vulgaris; Endophytes; Phaseolus; Raphanus; Surface-Active Agents
PubMed: 33557838
DOI: 10.1186/s12934-021-01533-2 -
Foods (Basel, Switzerland) May 2022A novel laccase gene isolated from TCCC 11568 was expressed, and the recombinant laccase (rLAC) displayed maximal activity at 80 °C and at pH 6.0 against ABTS. rLAC...
A novel laccase gene isolated from TCCC 11568 was expressed, and the recombinant laccase (rLAC) displayed maximal activity at 80 °C and at pH 6.0 against ABTS. rLAC maintained its structural integrity at a high temperature (355 K) compared to its tertiary structure at a low temperature (325 K), except for some minor adjustments of certain loops. However, those adjustments were presumed to be responsible for the formation of a more open access aisle that facilitated the binding of ABTS in the active site, resulting in a shorter distance between the catalytic residue and the elevated binding energy. Additionally, rLAC showed good thermostability (≤70 °C) and pH stability over a wide range (3.0-10.0), and displayed high efficiency in decolorizing azo dyes that are applicable to the food industry. This work will improve our knowledge on the relationship of structure-function for thermophilic laccase, and provide a candidate for dye effluent treatment in the food industry.
PubMed: 35626959
DOI: 10.3390/foods11101387 -
Microbial Cell Factories Aug 2023Despite being necessary, copper is a toxic heavy metal that, at high concentrations, harms the life system. The parameters that affect the bioreduction and biosorption...
BACKGROUND
Despite being necessary, copper is a toxic heavy metal that, at high concentrations, harms the life system. The parameters that affect the bioreduction and biosorption of copper are highly copper-resistant bacteria.
RESULTS
In this work, the ability of the bacterial biomass, isolated from black shale, Wadi Nakheil, Red Sea, Egypt, for Cu attachment, was investigated. Two Cu resistance Bacillus species were isolated; Bacillus pumilus OQ931870 and Bacillus subtilis OQ931871. The most tolerant bacterial isolate to Cu was B. pumilus. Different factors on Cu biosorption were analyzed to estimate the maximum conditions for Cu biosorption. The q for Cu by B. pumilus and B. subtilis determined from the Langmuir adsorption isotherm was 11.876 and 19.88 mg. g, respectively. According to r, the biosorption equilibrium isotherms close-fitting with Langmuir and Freundlich model isotherm. Temkin isotherm fitted better to the equilibrium data of B. pumilus and B. subtilis adsorption. Additionally, the Dubinin-Radushkevich (D-R) isotherm suggested that adsorption mechanism of Cu is predominately physisorption.
CONCLUSION
Therefore, the present work indicated that the biomass of two bacterial strains is an effective adsorbent for Cu removal from aqueous solutions.
Topics: Copper; Bacillus subtilis; Bacillus pumilus; Egypt; Indian Ocean; Adsorption; Kinetics; Hydrogen-Ion Concentration; Biomass
PubMed: 37573310
DOI: 10.1186/s12934-023-02166-3 -
Frontiers in Microbiology 2022plays an important role in industrial application and biocontrol activities, as well as causing humans and plants disease, leading to economic losses and biosafety...
plays an important role in industrial application and biocontrol activities, as well as causing humans and plants disease, leading to economic losses and biosafety concerns. However, until now, the pathogenesis and underlying mechanisms of strains remain unclear. In our previous study, one representative isolate of named HM-7 has been recovered and proved to be the causal agent of fruit rot on muskmelon (). Herein, we present a complete and annotated genome sequence of HM-7 that contains 4,111 coding genes in a single 3,951,520 bp chromosome with 41.04% GC content. A total of 3,481 genes were functionally annotated with the GO, COG, and KEGG databases. Pan-core genome analysis of HM-7 and 20 representative strains, as well as six closely related species, discovered 740 core genes and 15,205 genes in the pan-genome of 21 strains, in which 485 specific-genes were identified in HM-7 genome. The average nucleotide identity (ANI), and whole-genome-based phylogenetic analysis revealed that HM-7 was most closely related to the C4, GR8, MTCC-B6033, TUAT1 and SH-B11 strains, but evolutionarily distinct from other strains in . Collinearity analysis of the six similar strains showed high levels of synteny but also several divergent regions for each strains. In the HM-7 genome, we identified 484 genes in the carbohydrate-active enzymes (CAZyme) class, 650 genes encoding virulence factors, and 1,115 genes associated with pathogen-host interactions. Moreover, three HM-7-specific regions were determined, which contained 424 protein-coding genes. Further investigation of these genes showed that 19 pathogenesis-related genes were mainly associated with flagella formation and secretion of toxic products, which might be involved in the virulence of strain HM-7. Our results provided detailed genomic and taxonomic information for the HM-7 strain, and discovered its potential pathogenic mechanism, which lay a foundation for developing effective prevention and control strategies against this pathogen in the future.
PubMed: 36419435
DOI: 10.3389/fmicb.2022.1008648 -
Journal of Global Antimicrobial... Dec 2022This work aimed to isolate bacterial strains with antagonist activity against Vibrio parahaemolyticus, the causative agent of acute hepatopancreatic necrosis disease...
OBJECTIVES
This work aimed to isolate bacterial strains with antagonist activity against Vibrio parahaemolyticus, the causative agent of acute hepatopancreatic necrosis disease (VP) that was isolated from outbreaks in Mexico. Here, we report the draft genome sequences of two antagonistic strains, isolated from saline sediment in Sonora, Mexico.
METHODS
Cross-streak and well diffusion tests were employed to find the bacterial strains with higher inhibitory activity against VP. The whole genomes of B. pumilus 36R ATNSAL and B. safensis 13L LOBSAL were sequenced using Ion Torrent (PGM) and Illumina Miseq platforms, respectively. Annotation was performed using the RAST server, and the genes involved in the biosynthesis of bacterial secondary metabolites were predicted using antiSMASH.
RESULTS
Two bacterial isolates, B. safensis 13L LOBSAL and B. pumilus 36R ATNSAL, were chosen based on their strong antagonistic profiles. The genome of 36R ATNSAL was 3.94 Mbp in length and contained 3824 genes and a total of 4116 coding sequences (CDSs); the genome of 13L LOBSAL was 3.68 Mbp and contained 3619 genes and 3688 CDSs. Twenty-eight and 32 biosynthetic gene clusters responsible for putative antimicrobial metabolite production were identified in 36R ATNSAL and 13L LOBSAL, respectively.
CONCLUSIONS
The two strains 13L LOBSAL and 36R ATNSAL showed excellent probiotic profiles in vitro. The genome sequences will help with the mining and reconstruction of metabolic pathways in Bacillus strains. Genome sequence-guided strain improvement could augment the probiotic potential of Bacillus strains for applications in shrimp aquaculture.
Topics: Animals; Bacillus pumilus; Penaeidae; Vibrio parahaemolyticus; Aquaculture; Probiotics; Bacillus
PubMed: 36272706
DOI: 10.1016/j.jgar.2022.10.002