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International Journal of Molecular... Nov 2023Drought stress is a significant threat to agricultural productivity and poses challenges to plant survival and growth. Research into microbial plant biostimulants faces...
Drought stress is a significant threat to agricultural productivity and poses challenges to plant survival and growth. Research into microbial plant biostimulants faces difficulties in understanding complicated ecological dynamics, molecular mechanisms, and specificity; to address these knowledge gaps, collaborative efforts and innovative strategies are needed. In the present study, we investigated the potential role of (S1T13) as a microbial plant biostimulant to enhance drought tolerance in . We assessed the impact of S1T13 on Col-0 wild-type (WT) and mutant plants under drought conditions. Our results revealed that the inoculation of S1T13 significantly contributed to plant vigor, with notable improvements observed in both genotypes. To elucidate the underlying mechanisms, we studied the role of ROS and their regulation by antioxidant genes and enzymes in plants inoculated with S1T13. Interestingly, the inoculation of S1T13 enhanced the activities of GSH, SOD, POD, and PPO by 33, 35, 41, and 44% in WT and 24, 22, 26, and 33% in , respectively. In addition, S1T13 upregulated the expression of antioxidant genes. This enhanced antioxidant machinery played a crucial role in neutralizing ROS and protecting plant cells from oxidative damage during drought stress. Furthermore, we investigated the impact of S1T13 on ABA and drought-stress-responsive genes. Similarly, S1T13 modulated the production of ABA and expression of , , , and by 31, 42, 37, 41, and 42% in WT and 20, 29, 27, 38, and 29% in . The improvement in plant vigor, coupled with the induction of the antioxidant system and modulation of ABA, indicates the pivotal role of S1T13 in enhancing the drought stress tolerance of the plants. Conclusively, the current study provides valuable insights for the application of multitrait S1T13 as a novel strain to improve drought stress tolerance in plants and could be added to the consortium of biofertilizers.
Topics: Arabidopsis; Antioxidants; Droughts; Reactive Oxygen Species; Stress, Physiological; Arabidopsis Proteins; Plants, Genetically Modified; Gene Expression Regulation, Plant; Abscisic Acid; Plant Proteins
PubMed: 38068913
DOI: 10.3390/ijms242316590 -
Pathogens (Basel, Switzerland) Jun 2022The increasing prevalence of crop-threatening root-knot nematodes (RKNs) has stimulated extensive research to discover effective nematicides. A highly focused strategy...
The increasing prevalence of crop-threatening root-knot nematodes (RKNs) has stimulated extensive research to discover effective nematicides. A highly focused strategy for accomplishing this is the development of biocontrol agents by a variety of soilborne microorganisms, as different bacterial metabolites have demonstrated promising nematicidal activities. In this study, we characterized the nematicidal and suppressive activity of a bacterial isolate against the agriculturally important RKN and the model nematode , and the main -toxic metabolite of the strain. After a preliminary screening of 22 bacterial isolates with a corrected mortality (CM) of whole-cell culture greater than 50% against from different RKN-incident soils in China, a total of 14 isolates with CM of the supernatant of culture suspension (SCS) higher than 50% against both and were rescreened. An isolate with the highest CM of 86.1% and 95.0% for and , respectively, was further identified as the species via morphological examination, physiological and biochemical assays and alignment analysis of 16S rRNA gene sequences. The SCS of this strain, namely, MB756, exhibited synchronous killing activity along with significant detrimental effects on the growth, brood size, and locomotion of . The effects of heat treatment, pH, inoculations, and protease K proteolysis on the CM of MB756 SCS were evaluated. A major -toxic substance in the MB756 SCS was assayed and identified using thin-layer chromatography, column chromatography and high-performance liquid chromatography with a mass spectrometer, and it was preliminarily identified as 2-ethylhexan-1-ol, with a molecular formula of CHO and a molecular weight of 130.3 Da.
PubMed: 35745562
DOI: 10.3390/pathogens11060708 -
Current Microbiology May 2016When the genomes of Caulobacter isolates NA1000 and K31 were compared, numerous genome rearrangements were observed. In contrast, similar comparisons of closely related...
When the genomes of Caulobacter isolates NA1000 and K31 were compared, numerous genome rearrangements were observed. In contrast, similar comparisons of closely related species of other bacterial genera revealed nominal rearrangements. A phylogenetic analysis of the 16S rRNA indicated that K31 is more closely related to Caulobacter henricii CB4 than to other known Caulobacters. Therefore, we sequenced the CB4 genome and compared it to all of the available Caulobacter genomes to study genome rearrangements, discern the conservation of the NA1000 essential genome, and address concerns about using 16S rRNA to group Caulobacter species. We also sequenced the novel bacteria, Brevundimonas DS20, a representative of the genus most closely related to Caulobacter and used it as part of an outgroup for phylogenetic comparisons. We expected to find that there would be fewer rearrangements when comparing more closely related Caulobacters. However, we found that relatedness was not correlated with the amount of observed "genome scrambling." We also discovered that nearly all of the essential genes previously identified for C. crescentus are present in the other Caulobacter genomes and in the Brevundimonas genomes as well. However, a few of these essential genes were only found in NA1000, and some were missing in a combination of one or more species, while other proteins were 100 % identical across species. Also, phylogenetic comparisons of highly conserved genomic regions revealed clades similar to those identified by 16S rRNA-based phylogenies, verifying that 16S rRNA sequence comparisons are a valid method for grouping Caulobacters.
Topics: Alphaproteobacteria; Caulobacter; DNA, Bacterial; Evolution, Molecular; Genome, Bacterial; Phylogeny; RNA, Ribosomal, 16S
PubMed: 26750121
DOI: 10.1007/s00284-015-0964-x -
Frontiers in Microbiology 2022The deep terrestrial biosphere hosts vast sessile rock surface communities and biofilms, but thus far, mostly planktic communities have been studied. We enriched deep...
The deep terrestrial biosphere hosts vast sessile rock surface communities and biofilms, but thus far, mostly planktic communities have been studied. We enriched deep subsurface microbial communities on mica schist in microcosms containing bedrock groundwater from the depth of 500 m from Outokumpu, Finland. The biofilms were visualized using scanning electron microscopy, revealing numerous different microbial cell morphologies and attachment strategies on the mica schist surface, e.g., bacteria with outer membrane vesicle-like structures, hair-like extracellular extensions, and long tubular cell structures expanding over hundreds of micrometers over mica schist surfaces. Bacterial communities were analyzed with amplicon sequencing showing that , , and genera dominated communities after 8-40 months of incubation. A total of 21 metagenome assembled genomes from sessile rock surface metagenomes identified genes involved in biofilm formation, as well as a wide variety of metabolic traits indicating a high degree of environmental adaptivity to oligotrophic environment and potential for shifting between multiple energy or carbon sources. In addition, we detected ubiquitous organic carbon oxidation and capacity for arsenate and selenate reduction within our rocky MAGs. Our results agree with the previously suggested interaction between the deep subsurface microbial communities and the rock surfaces, and that this interaction could be crucial for sustaining life in the harsh anoxic and oligotrophic deep subsurface of crystalline bedrock environment.
PubMed: 35300483
DOI: 10.3389/fmicb.2022.826048 -
BioMed Research International 2022The relationship between urinary system tumors and urothelial microorganisms remains unexplored. This study is aimed at exploring the relationship between urinary flora...
The relationship between urinary system tumors and urothelial microorganisms remains unexplored. This study is aimed at exploring the relationship between urinary flora and urinary tumors and identifying potential biomarkers for urinary tumors and new targets for prevention. We included four healthy adults (control group) and six patients diagnosed with urinary tract tumors (tumor group). In both groups, 10 and 50 ml clean middle urine samples were reserved. The 10 ml samples were analyzed (including pH, specific gravity, and leukocytes) using an automatic urine analyzer, and the 50 ml samples were analyzed by DNA extraction, 16S rRNA gene amplification, and high-throughput sequencing. The correlation between routine urine analysis and sequencing results was also analyzed. Testing using the DESeq2 method showed that, at the order level, there were significant differences in the abundance of Caulobacterales between the urinary flora of the two groups ( < 0.05); family level, , , and ( < 0.05); genus level, , , , , , , and ( < 0.05). LEfSe analysis found specific bacteria at the genus level in the urinary flora of the tumor group, namely, (genus Digestiflora) ( < 0.001) and Varibaculum ( < 0.001). Further correlation analysis showed that both species were positively correlated with the urine pH ( < 0.05). PICRUSt analysis showed significant differences in the two functional pathways of cell transformation and metabolism ( < 0.05). Combined with the results of bioinformatics analysis, some differential bacteria may be new biomarkers for urologic tumors, and there may be a correlation between urine pH and tumor occurrence. However, large-scale prospective studies and in vitro and in vivo experiments are required to further test and verify these findings.
Topics: Actinomycetaceae; Adult; Bacteria; Clostridiales; Humans; Prospective Studies; RNA, Ribosomal, 16S; Urinary Tract; Urologic Neoplasms
PubMed: 35872872
DOI: 10.1155/2022/9368687 -
Frontiers in Cell and Developmental... 2022The development of new biomarkers for human male infertility is crucial to improve the diagnosis and the prognosis of this disease. Recently, seminal microbiota was...
The development of new biomarkers for human male infertility is crucial to improve the diagnosis and the prognosis of this disease. Recently, seminal microbiota was shown to be related to sperm quality parameters, suggesting an effect in human fertility and postulating it as a biomarker candidate. However, its relationship to sperm DNA integrity has not been studied yet. The aim of the present study is to characterize the seminal microbiota of a western Mediterranean population and to evaluate its relationship to sperm chromatin integrity parameters, and oxidative stress. For that purpose, 14 samples from sperm donors and 42 samples from infertile idiopathic patients were obtained and were analyzed to assess the composition of the microbiota through full-length gene sequencing (Illumina MiSeq platform). Microbial diversity and relative abundances were compared to classic sperm quality parameters (macroscopic semen parameters, motility, morphology and concentration), chromatin integrity (global DNA damage, double-stranded DNA breaks and DNA protamination status) and oxidative stress levels (oxidation-reduction potential). The seminal microbiota observed of these samples belonged to the phyla , , and . The most abundant genera were , , , , , , , , , and . To our knowledge, this is the first detection of genus in seminal samples. Two clusters of microbial profiles were built based on a clustering analysis, and specific genera were found with different frequencies in relation to seminal quality defects. The abundances of several bacteria negatively correlate with the sperm global DNA fragmentation, most notably , and . The latter two were also associated with higher sperm motility and additionally with lower oxidative-reduction potential. , and correlated with reduced chromatin protamination status and increased double-stranded DNA fragmentation. These effects on DNA integrity coincide in many cases with the metabolism or enzymatic activities of these genera. Significant differences between fertile and infertile men were found in the relative presence of the family and the , and genera, which supports its possible involvement in male fertility. Our findings sustain the hypothesis that the seminal microbiome has an effect on male fertility.
PubMed: 35837328
DOI: 10.3389/fcell.2022.937157 -
Microorganisms Apr 2023is broadly distributed in terrestrial and aquatic environments and has various biological activities. In this study, we found that exhibited nematicidal activity...
is broadly distributed in terrestrial and aquatic environments and has various biological activities. In this study, we found that exhibited nematicidal activity against the plant root-knot nematode, . A total of 42 volatile organic compounds (VOCs) from were identified using gas chromatography-mass spectrometry (GC-MS). The nematicidal activity of the 10 main VOCs was tested against . Butyl butanoate (4 µL) caused the mortality of 80.13% of after 4 h. The nematicidal activity of an additional 38 butyl-butyrate-like volatile esters was also investigated. Of these, seven had strong nematicidal activity against , five of which showed egg-hatching inhibitory activity. This study is the first to report that butyl butanoate, ethyl 2-methylbutanoate, ethyl 4-methylpentanoate, ethyl pent-4-enoate, and methyl undecanoate have nematicidal activity against . The results indicated that could serve as a candidate microorganism for the biocontrol of plant root-knot nematodes, showing that volatile esters have great potential as nematicides.
PubMed: 37110389
DOI: 10.3390/microorganisms11040966 -
Frontiers in Microbiology 2021The development of salinity affects 7% of the world's land surface, acting as a major constraint to crop productivity. This study attempted to use the co-evolving...
The development of salinity affects 7% of the world's land surface, acting as a major constraint to crop productivity. This study attempted to use the co-evolving endophytes of peanut to alleviate salinity stress and enhance the yield of peanut. Diverse and different tissue colonizing endophytes were isolated from peanut and screened by seed germination bioassay imposing gradients of salinity, with two cultivars TG37A (susceptible) and GG2 (moderately resistant), in potted conditions using saline irrigation water. Finally, nine endophytes capable of producing IAA and ACC-deaminase, promoting root growth and yield in potted conditions were selected for further evaluation in field conditions. They were evaluated with saline water (1.5-2.0 dS/m) in saline soil with susceptible cultivar TG37A. Simultaneously, three endophytes ( J22N; SEN15N; and sp. REN51N) were evaluated with two cultivars, GG2 and TG37A, during rainy and post-rainy seasons with elevated salinity. The application of endophytes like J22N and sp. REN51N enhanced the pod and haulm yield of peanuts by 14-19% across cultivars, salinity, and seasons. In addition, there was significant modulation in parameters like relative water content; production of enzymes like superoxide dismutase (SOD), glutathione reductase (GR), catalase (CAT), ascorbate peroxidase (APX), lipid peroxidase (POD), and HO content in leaf; and uptake of potassium. The activities of the enzymes involved in scavenging reactive oxygen species (ROS) increased with salinity, and further increased with endophytes like J22N, SEN15N, and sp. REN51N. There was an enhanced accumulation of proline, reduced level of phenol and HO, and enhanced uptake of potassium with the inoculation of endophytes. This improved scavenging capacity of plants by endophytic modulation of ROS scavengers, uptake of K, production of ACC deaminase and IAA, root and biomass growth, modulation in relative water content, and enhanced accumulation of osmoprotectant might be the reasons of alleviation of salinity stress. Endophytes could have alleviated salinity stress in peanuts, indicating the mechanisms and potential of peanuts at the field level. These endophytes could be applied to bring agricultural sustainability to salinity-affected areas in the future. Furthermore, few genera viz. , , , , and were observed in peanut tissue for the first time.
PubMed: 33936008
DOI: 10.3389/fmicb.2021.650771 -
Frontiers in Plant Science 2022Dioecious plant species have a high genetic variation that is important for coping with or adapting to environmental stress through natural selection. Intensive studies...
Dioecious plant species have a high genetic variation that is important for coping with or adapting to environmental stress through natural selection. Intensive studies have reported dimorphism morphism in morphology, physiology, as well as biotic and abiotic stress responses in dioecious plants. Here, we demonstrated the dimorphism of metabolic profile and the preference of some microorganisms in the roots and rhizosphere soils of male and female papaya. The metabolic composition of roots were significantly different between the males and females. Some sex hormones occurred in the differential metabolites in roots and rhizosphere soils. For example, testosterone was up-regulated in male papaya roots and rhizosphere soils, whereas norgestrel was up-regulated in the female papaya roots, indicating a possible balance in papaya roots to control the sexual differentiation. Plant hormones such as BRs, JAs, SA and GAs were also detected among the differential metabolites in the roots and rhizosphere soils of dioecious papaya. In addition, some metabolites that have medicinal values, such as ecliptasaponin A, crocin, berberine and sapindoside A were also expressed differentially between the two sexes. Numerous differential metabolites from the papaya roots were secreted in the soil, resulting in the differences in microbial community structure in the roots and rhizosphere soils. Some nitrogen-fixing bacteria such as ---, and were enriched in the male papaya roots or rhizosphere soils. While and , which utilize organic matters, were enriched in the roots or rhizosphere soils of the female papaya. Some differences in the fungi abundance were also observed in both male and female papaya roots. These findings uncovered the effect of sex types on the metabolic and microbiota differences in roots and rhizosphere soils in papaya and will lead to investigations of underlining genomic and molecular mechanisms.
PubMed: 36311075
DOI: 10.3389/fpls.2022.991114 -
Applied and Environmental Microbiology Jul 2021Metagenomic studies about cocoa fermentation have mainly reported on the analysis of short reads for determination of operational taxonomic units. However, it is also...
Metagenomic studies about cocoa fermentation have mainly reported on the analysis of short reads for determination of operational taxonomic units. However, it is also important to determine metagenome-assembled genomes (MAGs), which are genomes deriving from the assembly of metagenomics. For this research, all the cocoa metagenomes from public databases were downloaded, resulting in five data sets: one from Ghana and four from Brazil. In addition, approaches were used to describe putative phenotypes and the metabolic potential of MAGs. A total of 17 high-quality MAGs were recovered from these microbiomes, as follows: (i) for fungi, ( = 1); (ii) lactic acid bacteria, Limosilactobacillus fermentum ( = 5), Liquorilactobacillus cacaonum ( = 1), Liquorilactobacillus nagelli ( = 1), Leuconostoc pseudomesenteroides ( = 1), and Lactiplantibacillus plantarum subsp. ( = 1); (iii) acetic acid bacteria, Acetobacter senegalensis ( = 2) and Kozakia baliensis ( = 1); and (iv) Bacillus subtilis ( = 1), Brevundimonas sp. ( = 2), and Pseudomonas sp. ( = 1). Medium-quality MAGs were also recovered from cocoa microbiomes, including some that, to our knowledge, were not previously detected in this environment (Liquorilactobacillus vini, Komagataeibacter saccharivorans, and Komagataeibacter maltaceti) and others previously described (Fructobacillus pseudoficulneus and Acetobacter pasteurianus). Taken together, the MAGs were useful for providing an additional description of the microbiome of cocoa fermentation, revealing previously overlooked microorganisms, with prediction of key phenotypes and biochemical pathways. The production of chocolate starts with the harvesting of cocoa fruits and the spontaneous fermentation of the seeds in a microbial succession that depends on yeasts, lactic acid bacteria, and acetic acid bacteria in order to eliminate bitter and astringent compounds present in the raw material, which will be further roasted and grinded to originate the cocoa powder that will enter the food processing industry. The microbiota of cocoa fermentation is not completely known, and yet it advanced from culture-based studies to the advent of next-generation DNA sequencing, with the generation of a myriad of data that need bioinformatic approaches to be properly analyzed. Although the majority of metagenomic studies have been based on short reads (operational taxonomic units), it is also important to analyze entire genomes to determine more precisely possible ecological roles of different species. Metagenome-assembled genomes (MAGs) are very useful for this purpose; here, MAGs from cocoa fermentation microbiomes are described, and the possible implications of their phenotypic and metabolic potentials are discussed.
Topics: Bacteria; Cacao; Chocolate; Fermentation; Fungi; Metagenome; Microbiota; Phylogeny; Seeds
PubMed: 34105982
DOI: 10.1128/AEM.00584-21