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Comparison of Rhizospheric and Endophytic Bacterial Compositions between Netted and Oriental Melons.Microbiology Spectrum Feb 2023To elucidate the biological mechanism of formation of the netted pattern in melons, the characteristics of the soil bacterial community structure in the rhizosphere and...
To elucidate the biological mechanism of formation of the netted pattern in melons, the characteristics of the soil bacterial community structure in the rhizosphere and of the endophytic bacteria in the stems of netted melons were analyzed. High-throughput sequencing technology was used for the analysis of plant stem and soil samples collected from netted melons (NM) and oriental melons (OM). At the phylum level, Acidobacteria, Dependentiae, and Chloroflexi were the dominant endophytic bacteria in the stems of NM only. In addition, at the genus level, the soil bacteria enriched in the rhizospheres of NM and OM were different. Five unique dominant bacterial genera, including , , , , and , were the dominant soil bacteria unique to the rhizosphere of NM. In contrast, Mycobacterium and were the dominant soil bacteria in the rhizosphere of OM. Moreover, , , , , , , , , , , , , and were the dominant endophytic bacteria in the stems of NM. In contrast, , , , , , and were the dominant endophytic bacteria in the stems of OM. The specific substances (enzymes, proteins, endogenous hormones, etc.) secreted by unique rhizospheric and endophytic bacteria, such as and , may activate the promoters of genes. Therefore, the expression of genes can be regulated by unique rhizospheric and endophytic bacteria for formation or nonformation of netting in melons. The study of the differential structures and functions of rhizospheric and endophytic bacterial communities between netted melon and oriental melon treatments is investigated. Our findings make a significant contribution to the literature because they are the first step in coupling the study of rhizospheric and endophytic microbial community structure to reticulation formation in netted melon. Further, we believe that this research appears to be meaningful because it provides new insights into the mechanisms of reticulation formation in netted melon in modern agricultural production.
Topics: Agriculture; Soil; Bacillus; Microbiota; Flavobacterium; Soil Microbiology
PubMed: 36622169
DOI: 10.1128/spectrum.04027-22 -
International Journal of Environmental... Dec 2022Fermented foods play an important role in the human diet and particularly so in under-resourced environments where cold preservation is not attainable due to irregular...
Fermented foods play an important role in the human diet and particularly so in under-resourced environments where cold preservation is not attainable due to irregular supply of electricity. Fermented foods are reported to support gut health by contributing probiotics. The purpose of this study was to investigate the microbial diversity and metabolic potential of spontaneous millet fermentation. The literature in the field was reviewed and analyses were conducted on publicly available Sequence Read Archive (SRA) datasets. Quality analysis was performed with FastQC, and operational taxonomic units (OTUs) were generated using Quantitative Insights Into Microbial Ecology (QIIME2) and Divisive Amplicon Denoising Algorithm (DADA2) pipelines with Greengenes as the reference database. Metagenomics and pathways analysis were performed with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2). Statistical analysis and visualization were accomplished with Statistical Analysis of Metagenomic Profiles (STAMP). At the family taxonomic level, there were differences in the relative abundances of the dominant taxa of bacteria that are involved in the spontaneous fermentation of millet namely , , , , and . was the dominant family in one dataset. The incidence of and suggest the probiotic characteristics of fermented millet. The datasets were collected with fermentations that were mediated by autochthonous microorganisms and the presence of some potential pathogens such as , , , , , and which suggest the need for standardization of fermentation approaches. The genomes show the potential to synthesize metabolites such as essential amino acids and vitamins, suggesting that the respective fermented foods can be further optimized to enhance nutritional benefits.
Topics: Humans; Fermentation; Micronutrients; Phylogeny; Bacteria; Microbiota; Edible Grain; Trace Elements
PubMed: 36554499
DOI: 10.3390/ijerph192416621 -
Biology Dec 2022The influence of climate change on microbial communities inhabiting the sparsely vegetated patterned ground soils that are widespread across the High Arctic is poorly...
The influence of climate change on microbial communities inhabiting the sparsely vegetated patterned ground soils that are widespread across the High Arctic is poorly understood. Here, in a four-year experiment on Svalbard, we warmed patterned ground soil with open top chambers and biannually irrigated the soil to predict the responses of its microbial community to rising temperatures and precipitation. A 1 °C rise in summertime soil temperature caused 44% and 78% increases in CO efflux and CH consumption, respectively, and a 32% increase in the frequency of bacterial 16S ribosomal RNA genes. Bacterial alpha diversity was unaffected by the treatments, but, of the 40 most frequent bacterial taxa, warming caused 44-45% reductions in the relative abundances of a sp. and sp. and 33-91% increases in those of a sp. and a member of the . Warming did not influence the frequency of fungal internal transcribed spacer 2 copies, and irrigation had no effects on the measured variables. Our study suggests rapid changes to the activities and abundances of microbes, and particularly bacteria, in High Arctic patterned ground soils as they warm. At current rates of soil warming on Svalbard (0.8 °C per decade), we anticipate that similar effects to those reported here will manifest themselves in the natural environment by approximately the mid 2030s.
PubMed: 36552329
DOI: 10.3390/biology11121819 -
BMC Microbiology Dec 2022The microbiome in the insect reproductive tract is poorly understood. Our previous study demonstrated the presence of Lactobacillus spp. in female moths, but their...
BACKGROUND
The microbiome in the insect reproductive tract is poorly understood. Our previous study demonstrated the presence of Lactobacillus spp. in female moths, but their distribution and function remain unclear. Lactobacillus spp. are known as the 'healthy' vaginal microbiome in humans.
RESULTS
Here, we studied the microbiome in the reproductive system (RS) and gut of Spodoptera frugiperda using 16S rDNA sequences. The obtained 4315 bacterial OTUs were classified into 61 phyla and 642 genera, with Proteobacteria, Firmicutes and Bacteroidota being the top three dominant phyla and Enterococcus and Asaia being dominant genera in most samples. Mating dramatically increased the abundance of pathogens or pathogenic functions in the gut, while in the RS, the change range was trivial. Taxonomy assignment identified thirteen Lactobacillus spp. in S. frugiperda, with Lactobacillus crustorum and Lactobacillus murinus showing high abundance. Three species found in S. frugiperda, namely L. reuteri, L. plantarum and L. brevis, have also been identified as human 'healthy' vaginal bacterial species. Lactobacillus spp. showed higher abundance in the RS of virgin females and lower abundance in the RS of virgin males and the gut of virgin females. Mating reduced their abundance in the RS of females but increased their abundance in the RS of males, especially in males mated with multiple females. The RS of virgin females and of multiple mated males were very similar in terms of composition and abundance of Lactobacillus species, with Lactobacillus crustorum showing much higher abundance in both tissues, potentially due to sexual transmission.
CONCLUSIONS
Lactobacillus spp. showed high abundance and diversity in the RS of female moths. The higher abundance of Lactobacillus spp. in the RS of female moths and the similarity of Lactobacillus species in female moths with human 'healthy' vaginal Lactobacillus spp. suggest that these bacterial strains are also an important microbiome in the RS of female moths.
Topics: Male; Animals; Humans; Female; Gastrointestinal Microbiome; Moths; Lactobacillus; Vagina; Acetobacteraceae
PubMed: 36536275
DOI: 10.1186/s12866-022-02724-6 -
Microbial Cell Factories Dec 2022The global market for sweeteners is increasing, and the food industry is constantly looking for new low-caloric sweeteners. The natural sweetener 5-keto-D-fructose is...
BACKGROUND
The global market for sweeteners is increasing, and the food industry is constantly looking for new low-caloric sweeteners. The natural sweetener 5-keto-D-fructose is one such candidate. 5-Keto-D-fructose has a similar sweet taste quality as fructose. Developing a highly efficient 5-keto-D-fructose production process is key to being competitive with established sweeteners. Hence, the 5-keto-D-fructose production process was optimised regarding titre, yield, and productivity.
RESULTS
For production of 5-keto-D-fructose with G. oxydans 621H ΔhsdR pBBR1-p264-fdhSCL-ST an extended-batch fermentation was conducted. During fructose feeding, a decreasing respiratory activity occurred, despite sufficient carbon supply. Oxygen and second substrate limitation could be excluded as reasons for the decreasing respiration. It was demonstrated that a short period of oxygen limitation has no significant influence on 5-keto-D-fructose production, showing the robustness of this process. Increasing the medium concentration increased initial biomass formation. Applying a fructose feeding solution with a concentration of approx. 1200 g/L, a titre of 545 g/L 5-keto-D-fructose was reached. The yield was with 0.98 g/g close to the theoretical maximum. A 1200 g/L fructose solution has a viscosity of 450 mPa∙s at a temperature of 55 °C. Hence, the solution itself and the whole peripheral feeding system need to be heated, to apply such a highly concentrated feeding solution. Thermal treatment of highly concentrated fructose solutions led to the formation of 5-hydroxymethylfurfural, which inhibited the 5-keto-D-fructose production. Therefore, fructose solutions were only heated to about 100 °C for approx. 10 min. An alternative feeding strategy was investigated using solid fructose cubes, reaching the highest productivities above 10 g/L/h during feeding. Moreover, the scale-up of the 5-keto-D-fructose production to a 150 L pressurised fermenter was successfully demonstrated using liquid fructose solutions (745 g/L).
CONCLUSION
We optimised the 5-keto-D-fructose production process and successfully increased titre, yield and productivity. By using solid fructose, we presented a second feeding strategy, which can be of great interest for further scale-up experiments. A first scale-up of this process was performed, showing the possibility for an industrial production of 5-keto-D-fructose.
Topics: Gluconobacter oxydans; Fructose; Fermentation; Sweetening Agents; Oxygen
PubMed: 36496372
DOI: 10.1186/s12934-022-01980-5 -
Scientific Reports Nov 2022Bacterial nanocellulose (BC) is a highly versatile biopolymer currently pursued as a material of choice in varied themes of biomedical and material science research...
Bacterial nanocellulose (BC) is a highly versatile biopolymer currently pursued as a material of choice in varied themes of biomedical and material science research fields. With the aim to extend the biotechnological applications, the genetic tractability of the BC producers within the Komagataeibacter genus and its potential as an alternative host chassis in synthetic biology have been extensively studied. However, such studies have been largely focused on the model Komagataeibacter spp. Here, we present a novel K. intermedius strain capable of utilizing glucose, and glycerol sources for biomass and BC synthesis. Genome assembly identified one bacterial cellulose synthetase (bcs) operon containing the complete gene set encoding the BC biogenesis machinery (bcsI) and three additional copies (bcsII-IV). Investigations on the genetic tractability confirmed plasmid transformation, propagation of vectors with pBBR1 and p15A origin of replications and constitutive and inducible induction of recombinant protein in K. intermedius ENS15. This study provides the first report on the genetic tractability of K. intermedius, serving as starting point towards future genetic engineering of this strain.
Topics: Acetobacteraceae; Genetic Engineering; Synthetic Biology; Biomass
PubMed: 36443480
DOI: 10.1038/s41598-022-24735-z -
Applied and Environmental Microbiology Dec 2022Plant growth-promoting (PGP) bacteria are important to the development of sustainable agricultural systems. PGP microbes that fix atmospheric nitrogen (diazotrophs)...
Plant growth-promoting (PGP) bacteria are important to the development of sustainable agricultural systems. PGP microbes that fix atmospheric nitrogen (diazotrophs) could minimize the application of industrially derived fertilizers and function as a biofertilizer. The bacterium Gluconacetobacter diazotrophicus is a nitrogen-fixing PGP microbe originally discovered in association with sugarcane plants, where it functions as an endophyte. It also forms endophyte associations with a range of other agriculturally relevant crop plants. G. diazotrophicus requires microaerobic conditions for diazotrophic growth. We generated a transposon library for G. diazotrophicus and cultured the library under various growth conditions and culture medium compositions to measure fitness defects associated with individual transposon inserts (transposon insertion sequencing [Tn-seq]). Using this library, we probed more than 3,200 genes and ascertained the importance of various genes for diazotrophic growth of this microaerobic endophyte. We also identified a set of essential genes. Our results demonstrate a succinct set of genes involved in diazotrophic growth for G. diazotrophicus, with a lower degree of redundancy than what is found in other model diazotrophs. The results will serve as a valuable resource for those interested in biological nitrogen fixation and will establish a baseline data set for plant free growth, which could complement future studies related to the endophyte relationship.
Topics: Symbiosis; Gluconacetobacter; Nitrogen Fixation; Nitrogen
PubMed: 36374093
DOI: 10.1128/aem.01241-22 -
Journal of Microbiology and... Nov 2022Bacterial cellulose (BC) is gaining attention as a carbon-neutral alternative to plant cellulose, and as a means to prevent deforestation and achieve a carbon-neutral...
Bacterial cellulose (BC) is gaining attention as a carbon-neutral alternative to plant cellulose, and as a means to prevent deforestation and achieve a carbon-neutral society. However, the high cost of fermentation media for BC production is a barrier to its industrialization. In this study, chestnut shell (CS) hydrolysates were used as a carbon source for the BC-producing bacteria strain, ATCC 53524. To evaluate the suitability of the CS hydrolysates, major inhibitors in the hydrolysates were analyzed, and BC production was profiled during fermentation. CS hydrolysates (40 g glucose/l) contained 1.9 g/l acetic acid when applied directly to the main medium. As a result, the BC concentration at 96 h using the control group and CS hydrolysates was 12.5 g/l and 16.7 g/l, respectively (1.3-fold improved). In addition, the surface morphology of BC derived from CS hydrolysates revealed more densely packed nanofibrils than the control group. In the microbial BC production using CS, the hydrolysate had no inhibitory effect during fermentation, suggesting it is a suitable feedstock for a sustainable and eco-friendly biorefinery. To the best of our knowledge, this is the first study to valorize CS by utilizing it in BC production.
Topics: Gluconacetobacter xylinus; Cellulose; Fermentation; Carbon; Glucose
PubMed: 36310363
DOI: 10.4014/jmb.2208.08022 -
Microbial Cell Factories Oct 2022Adipic acid (AA) is one of the most important industrial chemicals used mainly for the production of Nylon 6,6 but also for making polyurethanes, plasticizers, and...
BACKGROUND
Adipic acid (AA) is one of the most important industrial chemicals used mainly for the production of Nylon 6,6 but also for making polyurethanes, plasticizers, and unsaturated polyester resins, and more recently as a component in the biodegradable polyester poly(butylene adipate terephthalate) (PBAT). The main route for AA production utilizes benzene as feedstock and generates copious amounts of the greenhouse gas NO. Hence, alternative clean production routes for AA from renewable bio-based feedstock are drawing increasing attention. We have earlier reported the potential of Gluconobacter oxydans cells to oxidize 1,6-hexanediol, a potentially biobased diol to AA.
RESULTS
The present report involves a study on the effect of different parameters on the microbial transformation of 1,6-hexanediol to adipic acid, and subsequently testing the process on a larger lab scale for achieving maximal conversion and yield. Comparison of three wild-type strains of G. oxydans DSM50049, DSM2003, and DSM2343 for the whole-cell biotransformation of 10 g/L 1,6-hexanediol to adipic acid in batch mode at pH 7 and 30 °C led to the selection of G. oxydans DSM50049, which showed 100% conversion of the substrate with over 99% yield of adipic acid in 30 h. An increase in the concentrations of the substrate decreased the degree of conversion, while the product up to 25 g/L in batch and 40 g/L in fed-batch showed no inhibition on the conversion. Moreover, controlling the pH of the reaction at 5-5.5 was required for the cascade oxidation reactions to work. Cell recycling for the biotransformation resulted in a significant decrease in activity during the third cycle. Meanwhile, the fed-batch mode of transformation by intermittent addition of 1,6-hexanediol (30 g in total) in 1 L scale resulted in complete conversion with over 99% yield of adipic acid (approximately 37 g/L). The product was recovered in a pure form using downstream steps without the use of any solvent.
CONCLUSION
A facile, efficient microbial process for oxidation of 1,6-hexanediol to adipic acid, having potential for scale up was demonstrated. The entire process is performed in aqueous medium at ambient temperatures with minimal greenhouse gas emissions. The enzymes involved in catalyzing the oxidation steps are currently being identified.
Topics: Gluconobacter oxydans; Greenhouse Gases; Adipates; Polyesters
PubMed: 36307807
DOI: 10.1186/s12934-022-01947-6 -
Frontiers in Microbiology 2022Acetic acid bacteria (AAB) are Gram-negative obligate aerobics in Acetobacteraceae family. Producing acetic acid and brewing vinegars are one of the most important...
Acetic acid bacteria (AAB) are Gram-negative obligate aerobics in Acetobacteraceae family. Producing acetic acid and brewing vinegars are one of the most important industrial applications of AAB, attributed to their outstanding ability to tolerate the corresponding stresses. Several unique acid resistance (AR) mechanisms in AAB have been revealed previously. However, their overall AR strategies are still less-comprehensively clarified. Consequently, omics analysis was widely performed for a better understanding of this field. Among them, transcriptome has recently obtained more and more attention. However, most currently reported transcriptomic studies were conducted under lab conditions and even in low-acidity environment, which may be unable to completely reflect the conditions that AAB confront under industrialized vinegar-brewing processes. In this study, we performed an RNA-Seq transcriptomic analysis concerning AAB's AR mechanisms during a continuous and periodical industrial submerged vinegar fermentation process, where a single AAB strain performed the fermentation and the acetic acid concentration fluctuated between ~8% and ~12%, the highest acidity as far we know for transcriptomic studies. Samples were directly taken from the initial (CK), mid, and final stages of the same period of the on-going fermentation. 16S rRNA sequence analysis indicated the participation of in the fermentation. Transcriptomic results demonstrated that more genes were downregulated than upregulated at both mid and final stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrich analysis reflected that the upregulated genes mainly carried out tricarboxylic acid cycle and oxidative phosphorylation processes, probably implying a considerable role of acetic acid overoxidation in AR during fermentation. Besides, upregulation of riboflavin biosynthesis pathway and two NAD-dependent succinate-semialdehyde dehydrogenase-coding genes suggested a critical role of succinate oxidation in AR. Meanwhile, downregulated genes were mainly ribosomal protein-coding ones, reflecting that the adverse impact on ribosomes initiates at the transcription level. However, it is ambiguous whether the downregulation is good for stress responding or it actually reflects the stress. Furthermore, we also assumed that the fermentation stages may have a greater effect on gene expression than acidity. Additionally, it is possible that some physiological alterations would affect the AR to a larger extent than changes in gene expression, which suggests the combination of molecular biology and physiology research will provide deeper insight into the AR mechanisms in AAB.
PubMed: 36246236
DOI: 10.3389/fmicb.2022.956729