-
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 -
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 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 -
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 -
Foods (Basel, Switzerland) May 2021Feruloyl esterase (FAE; EC 3.1.1.73) catalyzes the hydrolysis of the 4-hydroxy-3-methoxycinnamoyl group in an esterified sugar to assist in waste biomass degradation or...
Feruloyl esterase (FAE; EC 3.1.1.73) catalyzes the hydrolysis of the 4-hydroxy-3-methoxycinnamoyl group in an esterified sugar to assist in waste biomass degradation or to release ferulic acid (FA). An FAE-producing strain was isolated from humus soil samples and identified as SK52.001. The BpFAE gene from SK52.001 was speculated and heterogeneously expressed in WB800 for the first time. The enzyme exists as a monomer with 303 amino acids and a molecular mass of 33.6 kDa. Its specific activity was 377.9 ± 10.3 U/ (mg protein), using methyl ferulate as a substrate. It displays an optimal alkaline pH of 9.0, an optimal temperature of 50 °C, and half-lives of 1434, 327, 235, and 68 min at 50, 55, 60, and 65 °C, respectively. Moreover, the purified BpFAE released 4.98% FA of the alkali-acidic extractable FA from de-starched wheat bran (DSWB). When the DSWB was enzymatically degraded by the synergistic effect of the BpFAE and commercial xylanase, the FA amount reached 49.47%. It suggested that the alkaline BpFAE from SK52.001, which was heterologously expressed in WB800, possesses great potential for biomass degradation and achieving high-added value FA production from food by-products.
PubMed: 34071417
DOI: 10.3390/foods10061229 -
International Journal of Molecular... Jul 2021A 98.1 Kb genomic region from 15.1, a strain isolated as an entomopathogen toward , the Mediterranean fruit fly, has been characterised in search of potential virulence...
A 98.1 Kb genomic region from 15.1, a strain isolated as an entomopathogen toward , the Mediterranean fruit fly, has been characterised in search of potential virulence factors. The 98.1 Kb region shows a high number of phage-related protein-coding ORFs. Two regions with different phylogenetic origins, one with 28.7 Kb in size, highly conserved in strains, and one with 60.2 Kb in size, scarcely found in genomes are differentiated. The content of each region is thoroughly characterised using comparative studies. This study demonstrates that these two regions are responsible for the production, after mitomycin induction, of a phage-like particle that packages DNA from the host bacterium and a novel phage for , respectively. Both the phage-like particles and the novel phage are observed and characterised by TEM, and some of their structural proteins are identified by protein fingerprinting. In addition, it is found that the phage-like particle shows bacteriocin activity toward other strains. The effect of the phage-like particles and the phage in the toxicity of the strain toward is also evaluated.
Topics: Animals; Bacillus pumilus; Bacteriocins; Bacteriophages; Ceratitis capitata; Virulence Factors
PubMed: 34360927
DOI: 10.3390/ijms22158164 -
Genes Jul 2021The present study reports the isolation of antibacterial exhibiting () SF-4 from soil field. The genome of this strain SF-4 was sequenced and analyzed to acquire... (Comparative Study)
Comparative Study
The present study reports the isolation of antibacterial exhibiting () SF-4 from soil field. The genome of this strain SF-4 was sequenced and analyzed to acquire in-depth genomic level insight related to functional diversity, evolutionary history, and biosynthetic potential. The genome of the strain SF-4 harbor 12 Biosynthetic Gene Clusters (BGCs) including four Non-ribosomal peptide synthetases (NRPSs), two terpenes, and one each of Type III polyketide synthases (PKSs), hybrid (NRPS/PKS), lipopeptide, β-lactone, and bacteriocin clusters. Plant growth-promoting genes associated with de-nitrification, iron acquisition, phosphate solubilization, and nitrogen metabolism were also observed in the genome. Furthermore, all the available complete genomes of strains were used to highlight species boundaries and diverse niche adaptation strategies. Phylogenetic analyses revealed local diversification and indicate that strain SF-4 is a sister group to SAFR-032 and 150a. Pan-genome analyses of 12 targeted strains showed regions of genome plasticity which regulate function of these strains and proposed direct strain adaptations to specific habitats. The unique genome pool carries genes mostly associated with "biosynthesis of secondary metabolites, transport, and catabolism" (Q), "replication, recombination and repair" (L), and "unknown function" (S) clusters of orthologous groups (COG) categories. Moreover, a total of 952 unique genes and 168 exclusively absent genes were prioritized across the 12 genomes. While newly sequenced SF-4 genome consists of 520 accessory, 59 unique, and seven exclusively absent genes. The current study demonstrates genomic differences among 12 strains and offers comprehensive knowledge of the respective genome architecture which may assist in the agronomic application of this strain in future.
Topics: Anti-Bacterial Agents; Bacillus pumilus; Bacterial Proteins; Genome, Bacterial; Multigene Family; Peptide Synthases; Phylogeny
PubMed: 34356076
DOI: 10.3390/genes12071060 -
Microorganisms Jun 2023Due to their capacity to produce antimicrobial peptides that can prevent the growth of diseases, many spp. are beneficial to plants. In this study, we looked into the...
Due to their capacity to produce antimicrobial peptides that can prevent the growth of diseases, many spp. are beneficial to plants. In this study, we looked into the antagonistic activity of the 3-19 strain and its derivatives following targeted genome editing. Two peptide genes with antibacterial action, bacilysin () and bacteriocin (), and the F gene, which encodes the sigma factor of sporulation, were specifically inactivated using the CRISPR-Cas9 system in the genome of 3-19. Antibacterial activity against and decreased as a result of the inactivation of target genes in the 3-19 genome, with a noticeable effect against bacilysin. The growth dynamics of the culture changed when the , , and F genes were inactivated, and the altered strains had less proteolytic activity. An asporogenic mutant of 3-19 was obtained by inactivating the F gene. It has been proven that bacilysin plays a unique part in the development of 3-19's antagonistic action against soil microorganisms.
PubMed: 37375011
DOI: 10.3390/microorganisms11061508 -
Frontiers in Chemistry 2021CRISPR-associated Cas9 endonuclease (CRISPR/Cas9) systems are widely used to introduce precise mutations, such as knocking in/out at targeted genomic sites. Herein, we...
CRISPR-associated Cas9 endonuclease (CRISPR/Cas9) systems are widely used to introduce precise mutations, such as knocking in/out at targeted genomic sites. Herein, we successfully disrupted the transcription of multiple genes in LG3145 using a series of unspecific guide RNAs (gRNAs) and UgRNA:Cas9 system-assisted -box editing. The bases used as gRNAs shared 30-70% similarity with a consensus sequence, a acting element (-box) mediating carbon catabolite repression (CCR) of many genes in . This triggers -crRNA:Cas9 complex wobble cleavage up/downstream of sites in the promoters of multiple genes (up to 7), as confirmed by Sanger sequencing and next-generation sequencing (NGS). LG3145 displayed an obvious CCR release phenotype, including numerous secondary metabolites released into the culture broth, ∼ 1.67 g/L white flocculent protein, pigment overflow causing orange-coloured broth (absorbance = 309 nm), polysaccharide capsules appearing outside cells, improved sugar tolerance, and a two-fold increase in cell density. We assessed the relationship between carbon catabolite pathways and phenotype changes caused by unspecific UgRNA-directed site wobble editing. We propose a novel strategy for editing consensus targets at operator sequences that mediates transcriptional regulation in bacteria.
PubMed: 34434920
DOI: 10.3389/fchem.2021.717609