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Centella asiatica is a traditional herbaceous plant with numerous beneficial effects, widely known for its medicinal and cosmetic applications. Maximizing its growth can lead to beneficial effects, by focusing on the use of its active compounds. The use of plant growth-promoting rhizobacteria (PGPR) is known to be an alternative to chemical fertilizers. In this study, we used the PGPR Priestia megaterium HY-01 to increase the yield of C. asiatica. In vitro assays showed that HY-01 exhibited plant growth-promoting activities (IAA production, denitrification, phosphate solubilization, and urease activity). Genomic analyses also showed that the strain has plant growth-promoting-related genes that corroborate with the different PGP activities found in the assays. This strain was subsequently used in field experiments to test its effectiveness on the growth of C. asiatica. After four months of application, leaf and root samples were collected to measure the plant growth rate. Moreover, we checked the rhizosphere microbiome between the treated and non-treated plots. Our results suggest that treatment with Hyang-yak-01 not only improved the growth of C. asiatica (leaf length, leaf weight, leaf width, root length, root width, and chlorophyll content) but also influenced the rhizosphere microbiome. Biodiversity was higher in the treated group, and the bacterial composition was also different from the control group.

Quorum sensing (QS) enables bacteria to organize gene expression programs, thereby coordinating collective behaviors. It involves the production, release, and population-wide detection of extracellular signaling molecules. The cellular processes regulated by QS in bacteria are diverse and may be used in mutualistic coordination or in response to changing environmental conditions. Here, we focused on the influence of the QS-dependent genes of our model bacterial strain Serratia fonticola GS2 on potential plant growth promoting (PGP) activities including indole-3-acetic acid (IAA) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, and biofilm formation. Based on genomic and phenotypic experimental data we identified and investigated the function of QS genes in the genome of the model strain. Our gene deletion study confirmed the biological functionality of the QS auto-inducer (gloI) and receptor (gloR) on potential PGP activities of GS2. A transcriptomic approach was also undertaken to understand the role of QS genes in regulation of genes primarily involved in PGP activities (IAA, ACC deaminase activity, and biofilm formation). Both transcriptomic and phenotypic data revealed that the QS-deletion mutants had considerably less PGP activities, as compared to the wild type. In addition, in vivo plant experiments showed that plants treated with GS2 had significantly higher growth rates than plants treated with the QS-deletion mutants. Overall, our results showed how QS-dependent genes regulate the potential PGP activities of GS2. This information may be helpful in understanding the relationship between QS-dependent genes and the PGP activity of bacteria, which aid in the production of practical bio-fertilizers for plant growth promotion.

Environmental factors can influence the composition of gut microbiota, but understanding the combined effect of lifestyle factors on adult gut microbiota is limited. Here, we investigated whether changes in the modifiable lifestyle factors, such as cigarette smoking, alcohol consumption, sleep duration, physical exercise, and body mass index affected the gut microbiota of Korean navy trainees. The navy trainees were instructed to stop smoking and alcohol consumption and follow a sleep schedule and physical exercise regime for eight weeks. For comparison, healthy Korean civilians, who had no significant change in lifestyles for eight weeks were included in this study. A total of 208 fecal samples were collected from navy trainees (n = 66) and civilians (n = 38) at baseline and week eight. Gut flora was assessed by sequencing the highly variable region of the 16S rRNA gene. The α-and β -diversity of gut flora of both the test and control groups were not significantly changed after eight weeks. However, there was a significant difference among individuals. Smoking had a significant impact in altering α-diversity. Our study showed that a healthy lifestyle, particularly cessation of smoking, even in short periods, can affect the gut microbiome by enhancing the abundance of beneficial taxa and reducing that of harmful taxa.

In the anaerobic process, fat-oil-grease (FOG) is hydrolysed to long-chain fatty acids (LCFAs) and glycerol (GLYC), which are then used as substrates to produce biogas. The increase in FOG and LCFAs inhibits methanogenesis, and so far, most work investigating this inhibition has been carried out when FOG or LCFAs were used as co-substrates. In the current work, the inhibition of methanogenesis by FOG, LCFAs and GLYC was investigated when used as sole substrates. To gain more insight on the dynamics of this process, the change of microbial community was analysed using 16S rRNA gene amplicon sequencing. The results indicate that, as the concentrations of cooking olive oil (CO, which represents FOG) and LCFAs increase, methanogenesis is inhibited. For instance, at 0.01 g. L-1 of FOG, the rate of biogas formation was around 8 ml.L-1.day-1, and this decreased to = 45°C and NaCl > 3% led to a significant decrease in the rate of biogas formation. Microbial community analyses were carried out from samples from 3 different bioreactors (CO, OLEI and GLYC), on day 1, 5 and 15. In each bioreactor, microbial communities were dominated by Proteobacteria, Firmicutes and Bacteroidetes phyla. The most important families were Enterobacteriaceae, Pseudomonadaceae and Shewanellaceae (Proteobacteria phylum), Clostridiacea and Ruminococcaceae (Firmicutes) and Porphyromonadaceae and Bacteroidaceae (Bacteroidetes). In CO bioreactor, Proteobacteria bacteria decreased over time, while those of OLEI and GLYC bioreactors increased. A more pronounced increase in Bacteroidetes and Firmicutes were observed in CO bioreactor. The methanogenic archaea Methanobacteriaceae and Methanocorpusculaceae were identified. This analysis has shown that a set of microbial population is selected as a function of the substrate.

Variable region analysis of 16S rRNA gene sequences is the most common tool in bacterial taxonomic studies. Although used for distinguishing bacterial species, its use remains limited due to the presence of variable copy numbers with sequence variation in the genomes. In this study, 16S rRNA gene sequences, obtained from completely assembled whole genome and Sanger electrophoresis sequencing of cloned PCR products from Serratia fonticola GS2, were compared. Sanger sequencing produced a combination of sequences from multiple copies of 16S rRNA genes. To determine whether the variant copies of 16S rRNA genes affected Sanger sequencing, two ratios (5:5 and 8:2) with different concentrations of cloned 16S rRNA genes were used; it was observed that the greater the number of copies with similar sequences the higher its chance of amplification. Effect of multiple copies for taxonomic classification of 16S rRNA gene sequences was investigated using the strain GS2 as a model. 16S rRNA copies with the maximum variation had 99.42% minimum pairwise similarity and this did not have an effect on species identification. Thus, PCR products from genomes containing variable 16S rRNA gene copies can provide sufficient information for species identification except from species which have high similarity of sequences in their 16S rRNA gene copies like the case of Bacillus thuringiensis and Bacillus cereus. In silico analysis of 1,616 bacterial genomes from long-read sequencing was also done. The average minimum pairwise similarity for each phylum was reported with their average genome size and average "unique copies" of 16S rRNA genes and we found that the phyla Proteobacteria and Firmicutes showed the highest amount of variation in their copies of their 16S rRNA genes. Overall, our results shed light on how the variations in the multiple copies of the 16S rRNA genes of bacteria can aid in appropriate species identification.

Many Bacillus species are among the plant growth-promoting rhizobacteria (PGPR) that promote the growth of many different plant species. This study aimed to investigate the effects of Bacillus thuringiensis KNU-07 on the growth of pepper plants and the soil microbiota. We also designed primers specific for the strain KNU-07 to monitor the population in pepper-cultivated soil. Accordingly, a strain-specific primer pair was designed using a database constructed from 16,160 complete bacterial genomes. We employed quantitative PCR (qPCR) to track the abundance of the strain KNU-07 introduced into pepper-cultivated soil using the strain-specific primers. Our study revealed that the strain was found to possess plant growth-promoting (PGP) activities, and it promoted the growth of pepper plants. The soil bacterial community structure due to the application of the PGPR strain was significantly changed after six weeks post-inoculation. In addition, based on qPCR analysis, the population of the introduced strain declined over time. In this study, application of a PGPR strain increased the growth of pepper plants and changed the soil bacterial community structure. The successful results of monitoring of a bacterial strain’s population using a single strain-specific primer pair can provide important information about the quantification of bio-inoculants under non-sterile soil conditions.

Macrophthalmus japonicus is located in the Macrophthalmidae family, but genetic research about the whole mitochondrial genome in Macrophthalmidae family doesn’t exist. Here, we report the first complete mitochondrial genome from M. japonicus, which is composed of 16,170 base pair (bp) containing 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and A + T rich region. The overall nucleotide composition of M. japonicus was G + C: 33.6%, A + T: 66.4% with a strong AT bias. The phylogenetic relationship using whole mitochondrial genome showed that M. japonicus was closest with Eriocheir japonica although their respective families are different.

The larva of Galleria mellonella is widely used as a model organism for in vivo toxicology and pathogenicity testing. Here, we report complete sequence of the mitochondrial genome (mitogenome) from G. mellonella, which is comprised of 15,320 base pairs encoding 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and an A + T rich region. The overall base composition was G + C: 19.6%, A + T: 80.4%, with an apparent AT bias. Phylogenetic analysis using whole mitogenome revealed that G. mellonella was closely related to Corcyra cephalonica, which is in the same Pyralidae family.

Pyrhila pisum is known as leucosiid crab. So far, there is no study about whole mitochondrial genome in Leucosiidae family. Here, we report first the complete sequence of the mitochondrial genome from P. pisum, which is composed of 15,516 base pair encoding 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and A + T-rich region. The nucleotide composition of P. pisum was G + C: 25.5%, A + T: 74.5%, with a strong AT bias. In phylogenetic analysis using whole mitogenome, it was figured out that P. pisum was closely related to Sesarma neglectum but their family is different.

Panax ginseng is a well-known medicinal plant that achieves strong resistance against plant pathogens while growing in the wild. Due to the high market demand for ginseng as a health food source, ginseng cultivation is prevalent in South Korea. However, continuous monocropping creates problems like irregular growth or vulnerability to crop diseases. Quorum sensing (QS) deals with the intracellular communication of bacteria and plays a role in dynamic changes in the soil microbiome. Here, we investigated how acyl-homoserine lactone (AHL) signaling molecules in QS (C8, C10, and C12) improve plant growth and induce shifts in the soil microbiome. To assess the effects, we recorded root and shoot growth of ginseng seedlings and checked the changes in the soil microbiome during different time points (0, 2, 4, and 8) after 8 weeks of growth. We observed that soils treated with N-decanoyl-L-homoserine lactone (C10) showed the most pronounced effects. Very striking was that C10 had the lowest alpha diversity. Using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2), we observed a high number of QS-related functional genes, with the highest count occurring in the untreated planted soil (W). Together with the known direct and beneficial effects of AHLs on plant development, AHLs treated mono-cropped soil showed trends in the microbiome community.