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Frontiers in Microbiology 2024A new strain of xanthan-degrading bacteria identified as sp. has been isolated from a xanthan thickener for food production. The strain was able to utilize xanthan as...
A new strain of xanthan-degrading bacteria identified as sp. has been isolated from a xanthan thickener for food production. The strain was able to utilize xanthan as the only carbon source and to reduce the viscosity of xanthan-containing medium during cultivation. Comparative analysis of the secretomes of sp. after growth on different media led to the identification of a xanthanase designated as Xan9, which was isolated after recombinant production in . Xan9 could efficiently degrade the β-1,4-glucan backbone of xanthan after previous removal of pyruvylated mannose residues from the ends of the native xanthan side chains by xanthan lyase treatment (XLT-xanthan). Compared with xanthanase from , xanthanase Xan9 had a different module composition at the N- and C-terminal ends. The main putative oligosaccharides released from XLT-xanthan by Xan9 cleavage were tetrasaccharides and octasaccharides. To explore the functions of the N- and C-terminal regions of the enzyme, truncated variants lacking some of the non-catalytic modules (Xan9-C, Xan9-N, Xan9-C-N) were produced. Enzyme assays with the purified deletion derivatives, which all contained the catalytic glycoside hydrolase family 9 (GH9) module, demonstrated substantially reduced specific activity on XLT-xanthan of Xan9-C-N compared with full-length Xan9. The C-terminal module of Xan9 was found to represent a novel carbohydrate-binding module of family CBM66 with binding affinity for XLT-xanthan, as was shown by native affinity polyacrylamide gel electrophoresis in the presence of various polysaccharides. The only previously known binding function of a CBM66 member is exo-type binding to the non-reducing fructose ends of the β-fructan polysaccharides inulin and levan.
PubMed: 38596379
DOI: 10.3389/fmicb.2024.1386552 -
Canadian Journal of Veterinary Research... Apr 2024Honey bees can be affected by a variety of pathogens, which impacts their vital role as pollinators in agriculture. A cross-sectional study was conducted in southwestern...
Honey bees can be affected by a variety of pathogens, which impacts their vital role as pollinators in agriculture. A cross-sectional study was conducted in southwestern Quebec to: i) estimate the prevalence of 11 bee pathogens; ii) assess the agreement between beekeeper suspicion of a disease and laboratory detection of the causative pathogen; and iii) explore the association between observed clinical signs and pathogen detection in a colony. A total of 242 colonies in 31 apiaries owned by 15 beekeepers was sampled in August 2017. The prevalence of detection was estimated as 48% for colonies and 93% for apiaries. The apparent prevalence of colonies infected by spp. and was estimated as 40% and 21%, respectively. At least 180 colonies were tested by polymerase chain reaction (PCR) for deformed wing virus (DWV), acute-Kashmir-Israeli complex (AKI complex), and black queen cell virus (BQCV), which were detected in 33%, 9%, and 95% of colonies, respectively. , and were not detected. Varroasis was suspected by beekeepers in 14 of the 15 beekeeping operations in which the mite was detected. However, no correlation was found between suspected European foulbrood and detection of or between suspected nosemosis and detection of spp. Colony weakness was associated with spore counts of at least 0.5 × 10 per bee. was more frequently detected in colonies showing scattered brood.
Topics: Bees; Animals; Quebec; Cross-Sectional Studies; Prevalence; RNA Viruses; Enterococcaceae
PubMed: 38595951
DOI: No ID Found -
Frontiers in Microbiology 2024In recent years, bacterial-based biocontrol agents (BCA) have become a new trend for the control of fungal diseases such as fusarium wilt that seriously threaten the...
In recent years, bacterial-based biocontrol agents (BCA) have become a new trend for the control of fungal diseases such as fusarium wilt that seriously threaten the yield and quality of cucumber, which are transmitted through infested soil and water. This study was set out with the aim of figuring the mechanism of the isolated rhizobacterial strain PJH16 in preventing f. sp. (). Biocontrol and growth-promoting experiments revealed that bacterial strain causes effective inhibition of the fungal disease through a significant growth-promoting ability of plants, and had activities of β-1,3-glucanase, cellulase, amylase and protease. It could produce siderophore and indole-3-acetic acid, too. Using the high-throughput sequencing tool PacBio Sequel II system and the database annotation, the bacterial strain was identified as PJH16 and contained genes encoding for presence of biofilm formation, antimicrobial peptides, siderophores and hydrolyases. From comparing data between the whole genome of PJH16 with four closely related strains, findings revealed markedly the subtle differences in their genome sequences and proposed new antifungal substances present in PJH16. Therefore, PJH16 could be utilized in bioengineering a microbial formulation for application as biocontrol agent and bio-stimulant, in the future.
PubMed: 38591040
DOI: 10.3389/fmicb.2024.1359263 -
Frontiers in Microbiology 2024L. is a versatile edible plant that is widely explored due to its medicinal properties and as a key element in intercropping systems. Its growth could be improved by...
L. is a versatile edible plant that is widely explored due to its medicinal properties and as a key element in intercropping systems. Its growth could be improved by the use of biofertilizers that can enhance nutrient uptake by the plant or provide tolerance to different abiotic and biotic stresses. In a previous study, 101 endophytes isolated from roots showed more than three plant growth-promoting (PGP) features , such as phosphate mineralization/solubilization, production of siderophores, antimicrobial substances and indole-related compounds, and presence of the gene. To provide sustainable alternatives for biofertilization, the genomes of two promising endophytes-CAPE95 and CAPE238-were sequenced to uncover metabolic pathways related to biofertilization. Greenhouse experiments were conducted with 216 seeds and 60 seedlings, half co-inoculated with the endophytes (treatment) and half inoculated with 1X PBS (control), and the impact of the co-inoculation on the plant's bacteriome was accessed through 16S rRNA gene metabarcoding. The strains CAPE95 and CAPE238 were taxonomically assigned as and , respectively. Metabolic pathways related to the enhancement of nutrient availability (nitrogen fixation, sulfate-sulfur assimilation), biosynthesis of phytohormones (indole-3-acetic acid precursors) and antimicrobial substances (bacilysin, paenibacillin) were found in their genomes. The experiments showed that treated seeds exhibited faster germination, with a 20.3% higher germination index than the control on the eleventh day of the experiment. Additionally, treated seedlings showed significantly higher plant height and leaf diameters ( < 0.05). The bacterial community of the treated plants was significantly different from that of the control plants ( < 0.001) and showed a higher richness and diversity of species (Chao and Shannon indexes, < 0.001). A higher relative abundance of potential synergistic PGP bacteria was also shown in the bacteriome of the treated plants, such as and . For the first time, co-inoculation of and was shown to have great potential for application as a biofertilizer to plants. The bacterial consortium used here could also be explored in other plant species in the future.
PubMed: 38585693
DOI: 10.3389/fmicb.2024.1356891 -
Applied Microbiology and Biotechnology Apr 2024Oleanane-type ginsenosides are a class of compounds with remarkable pharmacological activities. However, the lack of effective preparation methods for specific rare...
Oleanane-type ginsenosides are a class of compounds with remarkable pharmacological activities. However, the lack of effective preparation methods for specific rare ginsenosides has hindered the exploration of their pharmacological properties. In this study, a novel glycoside hydrolase PlGH3 was cloned from Paenibacillus lactis 154 and heterologous expressed in Escherichia coli. Sequence analysis revealed that PlGH3 consists of 749 amino acids with a molecular weight of 89.5 kDa, exhibiting the characteristic features of the glycoside hydrolase 3 family. The enzymatic characterization results of PlGH3 showed that the optimal reaction pH and temperature was 8 and 50 °C by using p-nitrophenyl-β-D-glucopyranoside as a substrate, respectively. The K and k values towards ginsenoside Ro were 79.59 ± 3.42 µM and 18.52 s, respectively. PlGH3 exhibits a highly specific activity on hydrolyzing the 28-O-β-D-glucopyranosyl ester bond of oleanane-type saponins. The mechanism of hydrolysis specificity was then presumably elucidated through molecular docking. Eventually, four kinds of rare oleanane-type ginsenosides (calenduloside E, pseudoginsenoside RP1, zingibroside R1, and tarasaponin VI) were successfully prepared by biotransforming total saponins extracted from Panax japonicus. This study contributes to understanding the mechanism of enzymatic hydrolysis of the GH3 family and provides a practical route for the preparation of rare oleanane-type ginsenosides through biotransformation. KEY POINTS: • The glucose at C-28 in oleanane-type saponins can be directionally hydrolyzed. • Mechanisms to interpret PlGH3 substrate specificity by molecular docking. • Case of preparation of low-sugar alternative saponins by directed hydrolysis.
Topics: Ginsenosides; Glycoside Hydrolases; Molecular Docking Simulation; Saponins; Escherichia coli; Esters; Oleanolic Acid; Paenibacillus
PubMed: 38573330
DOI: 10.1007/s00253-024-13109-2 -
Scientific Reports Apr 2024Cellulose-degrading microorganisms hold immense significance in utilizing cellulose resources efficiently. The screening of natural cellulase bacteria and the...
Cellulose-degrading microorganisms hold immense significance in utilizing cellulose resources efficiently. The screening of natural cellulase bacteria and the optimization of fermentation conditions are the hot spots of research. This study meticulously screened cellulose-degrading bacteria from mixed soil samples adopting a multi-step approach, encompassing preliminary culture medium screening, Congo red medium-based re-screening, and quantification of cellulase activity across various strains. Particularly, three robust cellulase-producing strains were identified: A24 (MT740356.1 Brevibacillus borstelensis), A49 (MT740358.1 Bacillus cereus), and A61 (MT740357.1 Paenibacillus sp.). For subsequent cultivation experiments, the growth curves of the three obtained isolates were monitored diligently. Additionally, optimal CMCase production conditions were determined, keeping CMCase activity as a key metric, through a series of single-factor experiments: agitation speed, cultivation temperature, unit medium concentration, and inoculum volume. Maximum CMCase production was observed at 150 rpm/37 °C, doubling the unit medium addition, and a 5 mL inoculation volume. Further optimization was conducted using the selected isolate A49 employing response surface methodology. The software model recommended a 2.21fold unit medium addition, 36.11 °C temperature, and 4.91 mL inoculant volume for optimal CMCase production. Consequently, three parallel experiments were conducted based on predicted conditions consistently yielding an average CMCase production activity of 15.63 U/mL, closely aligning with the predicted value of 16.41 U/mL. These findings validated the reliability of the model and demonstrated the effectiveness of optimized CMCase production conditions for isolate A49.
Topics: Bacillus cereus; Cellulose; Reproducibility of Results; Cellulase; Paenibacillus; Fermentation
PubMed: 38565929
DOI: 10.1038/s41598-024-58540-7 -
Microorganisms Mar 2024Alfalfa ( L.), a forage legume known for its moderate salt-alkali tolerance, offers notable economic and ecological benefits and aids in soil amelioration when...
Alfalfa ( L.), a forage legume known for its moderate salt-alkali tolerance, offers notable economic and ecological benefits and aids in soil amelioration when cultivated in saline-alkaline soils. Nonetheless, the limited stress resistance of alfalfa could curtail its productivity. This study investigated the salt tolerance and growth-promoting characteristics (in vitro) of four strains of plant growth-promoting rhizobacteria (PGPR) that were pre-selected, as well as their effects on alfalfa at different growth stages (a pot experiment). The results showed that the selected strains belonged to the genera (HL3), (HL6 and HG12), and (HG24). All four strains exhibited the ability to solubilize phosphate and produce indole-3-acetic acid (IAA) and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. Among them, except for strain HG24, the other strains could tolerate 9% NaCl stress. Treatment with 100 mM NaCl consistently decreased the IAA production levels of the selected strains, but inconsistent changes (either enhanced or reduced) in terms of phosphate solubilization, ACC deaminase, and exopolysaccharides (EPS) production were observed among the strains. During the various growth stages of alfalfa, PGPR exhibited different growth-promoting effects: at the seedling stage, they enhanced salt tolerance through the induction of physiological changes; at the flowering stage, they promoted growth through nutrient acquisition. The current findings suggest that strains HL3, HL6, and HG12 are effective microbial inoculants for alleviating salt stress in alfalfa plants in arid and semi-arid regions. This study not only reveals the potential of indigenous salt-tolerant PGPR in enhancing the salt tolerance of alfalfa but also provides new insights into the mechanisms of action of PGPR.
PubMed: 38543667
DOI: 10.3390/microorganisms12030616 -
Heliyon Mar 2024In water-stressed regions, treated acid mine drainage (AMD) water for irrigated agriculture is a potential solution to address freshwater scarcity. However, a...
Unlocking water potential in drylands: Quicklime and fly ash enhance soil microbiome structure, ecological networks and function in acid mine drainage water-irrigated agriculture.
In water-stressed regions, treated acid mine drainage (AMD) water for irrigated agriculture is a potential solution to address freshwater scarcity. However, a significant knowledge gap exists on the short and long-term effects of treated AMD water on soil health. This study used high-throughput Illumina sequencing and predictive metagenomic profiling to investigate the impact of untreated AMD (AMD), quicklime- (A1Q and A2Q) and quicklime and fly ash-treated AMD water (AFQ) irrigation on soil bacterial diversity, co-occurrence networks and function. Results showed that untreated AMD water significantly increased soil acidity, electrical conductivity (EC), sulfate (SO), and heavy metals (HM), including reduced microbial diversity, disrupted interaction networks, and functional capacity. pH, EC, Cu, and Pb were identified as key environmental factors shaping soil microbial diversity and structure. Predominantly, , , KB913035, , and , known for their adaptability to acidic conditions and metal resistance, were abundant in AMD soils. However, soils irrigated with treated AMD water exhibited significantly reduced acidity (pH > 6.5), HM and SO levels, with an enrichment of a balanced bacterial taxa associated with diverse functions related to soil health and agricultural productivity. These taxa included , , , , , , , , , and Moreover, treated AMD water contributed to higher connectivity and balance within soil bacterial co-occurrence networks compared to untreated AMD water. These results show that quicklime/fly ash treatments can help lessen impacts of AMD water on soil microbiome and health, suggesting its potential for irrigated agriculture in water-scarce regions.
PubMed: 38533070
DOI: 10.1016/j.heliyon.2024.e27985 -
Microbial Biotechnology Mar 2024Paenibacillus polymyxa is a non-pathogenic, Gram-positive bacterium endowed with a rich and versatile metabolism. However interesting, this bacterium has been seldom...
Paenibacillus polymyxa is a non-pathogenic, Gram-positive bacterium endowed with a rich and versatile metabolism. However interesting, this bacterium has been seldom used for bioproduction thus far. In this study, we engineered P. polymyxa for isobutanol production, a relevant bulk chemical and next-generation biofuel. A CRISPR-Cas9-based genome editing tool facilitated the chromosomal integration of a synthetic operon to establish isobutanol production. The 2,3-butanediol biosynthesis pathway, leading to the main fermentation product of P. polymyxa, was eliminated. A mutant strain harbouring the synthetic isobutanol operon (kdcA from Lactococcus lactis, and the native ilvC, ilvD and adh genes) produced 1 g L isobutanol under microaerobic conditions. Improving NADPH regeneration by overexpression of the malic enzyme subsequently increased the product titre by 50%. Network-wide proteomics provided insights into responses of P. polymyxa to isobutanol and revealed a significant metabolic shift caused by alcohol production. Glucose-6-phosphate 1-dehydrogenase, the key enzyme in the pentose phosphate pathway, was identified as a bottleneck that hindered efficient NADPH regeneration through this pathway. Furthermore, we conducted culture optimization towards cultivating P. polymyxa in a synthetic minimal medium. We identified biotin (B7), pantothenate (B5) and folate (B9) to be mutual essential vitamins for P. polymyxa. Our rational metabolic engineering of P. polymyxa for the production of a heterologous chemical sheds light on the metabolism of this bacterium towards further biotechnological exploitation.
Topics: Paenibacillus polymyxa; Carbon; NADP; Oxidation-Reduction; Paenibacillus; Metabolic Engineering; Butanols
PubMed: 38529712
DOI: 10.1111/1751-7915.14438 -
Ecology and Evolution Mar 2024Prolonged water stress can shift rhizoplane microbial communities, yet whether plant phylogenetic relatedness or drought tolerance predicts microbial responses is poorly...
Prolonged water stress can shift rhizoplane microbial communities, yet whether plant phylogenetic relatedness or drought tolerance predicts microbial responses is poorly understood. To explore this question, eight members of the clade with varying affinity to serpentine soil were subjected to three watering regimes. Rhizoplane bacterial communities were characterized using 16S rRNA gene amplicon sequencing and we compared the impact of watering treatment, soil affinity, and plant species identity on bacterial alpha and diversity. We determined which taxa were enriched among drought treatments using DESeq2 and identified features of soil affinity using random forest analysis. We show that water stress has a greater impact on microbial community structure than soil affinity or plant identity, even within a genus. Drought reduced alpha diversity overall, but plant species did not strongly differentiate alpha diversity. Watering altered the relative abundance of bacterial genera within Proteobacteria, Firmicutes, Bacteroidetes, Planctomycetes, and Acidobacteria, which responded similarly in the rhizoplane of most plant species. In addition, bacterial communities were more similar when plants received less water. was identified as a feature of affinity to serpentine soil while , , , and were features associated with affinity to nonserpentine soils among . The homogenizing effect of drought on microbial communities and the increasing prevalence of Gram-negative bacteria across all plant species suggest that effects of water stress on root-associated microbiome structure may be predictable among closely related plant species that inhabit very different soil environments. The functional implications of observed changes in microbiome composition remain to be studied.
PubMed: 38529025
DOI: 10.1002/ece3.11174