Whole genome sequence data of Paenibacillus tyrfis YSS-72.2.G2, a chitinolytic bacterium newly isolated from a National Park of Vietnam.

Paenibacillus tyrfis YSS-72.2.G2 is a soil chitinolytic bacterium newly isolated from Yok Don National Park of Vietnam. Our previous results demonstrated that this bacterium was a strong chitinase producer, possessed plant growth promotion, and had high activity against phytopathogenic fungi. However, the genome sequence of this strain is unknown. This work aimed to establish data on the genome sequence of P. tyrfis YSS-72.2.G2 and its chitinase system for further assessments regarding biocontrol mechanisms and plant growth promotion. The P. tyrfis YSS-72.2.G2 genome is 7,756,121 bp in size and 53.4 % G+C. It harbors 6,948 protein-coding genes, 5 rRNA genes, 82 tRNA genes, 4 ncRNA genes, 99 pseudo genes, and 5 CRISPR arrays. Genes involved in heavy metal resistance (5 genes), iron acquisition (5 genes), and IAA biosynthesis (5 genes) were predicted in the genome. There were 234 carbohydrate-active enzymes found in this genome; among them, 13 enzymes possibly possess activity against phytopathogens. Chitin-degrading system of YSS-72.2.G2 contains 15 chitinolytic enzymes. In addition, 28 gene clusters coding for antimicrobial metabolites were identified, of these, 14 show no sequence similarities to the known clusters. The raw sequences were submitted to the Sequence Read Archive on the National Center for Biotechnology Information with accession number PRJNA946889. The genome sequence of P. tyrfis YSS-72.2.G2 has been deposited in the DDBJ/GenBank/EMBL database under accession number NZ_BSDJ00000000. Data provide insight into the genomic information of strain YSS-72.2.G2. This is the first work reporting data on the genome sequence of P. tyrfis isolated from Vietnam.

Data on gene cloning, expression, purification, and characterization of the glycoside hydrolase family 11 from Bacillus velezensis.

Bacillus velezensis RB.IBE29 is a chitinolytic bacterium originally isolated from the rhizospheric soil of black pepper grown in Vietnam. This bacterium is a strong biocontrol agent against plant pathogens and possesses a novel chitinase system. Genome sequences available in CAZy database revealed B. velezensis possesses one gene encoding xylanase belonging to glycoside hydrolase family 11; however, this enzyme has yet to be un-experimentally characterized. In this work, xyA gene was isolated from the genomic DNA of strain RB.IBE29 and cloned in Escherichia coli DH5α cells using the pUC19 vector. Sequencing analysis showed that the ORF of xyA contains 642 bp and encodes the deduced xylanase with 213 aa and 23.27 kDa. The domain structure of the enzyme has a signal peptide and a family 11 catalytic domain. xyA (without peptide sequence) was successfully expressed in E. coli BL21-CodonPlus (DE3)-RIPL cells using the pColdII vector and purified using the HisTrap FF column. Purified recombinant xylanase degraded xylan substrates, had the highest hydrolytic activity at 55°C in 20 mM sodium phosphate buffer (pH 6.0), and MgCl2, CoCl2, and MnCl2 enhanced the enzymatic activity. Nucleotide sequence of xyA was submitted to the DDBJ/GenBank/EMBL under accession number LC779040. This is the first data on the gene cloning, expression, purification, and characterization of the glycoside hydrolase family 11 from B. velezensis.

Novel resources of chitinolytic bacteria isolated from Yok Don National Park, Vietnam.

AIMS: This study focused on the isolation and characterization of chitinolytic bacteria from Yok Don National Park, Vietnam for future studies regarding biofertilizers and biocontrol agents. METHODS AND RESULTS: Chitinolytic bacteria were isolated from soils and chitin flakes soaked in river water at the National Park. On the basis of the halo zones caused by colloidal chitin degradation and colony morphologies, 12 chitinolytic strains were chosen from 15 700 isolates for various examinations. Findings from 16S rDNA analysis indicated that among these strains, 10 could be identified as different species, and the remaining 2 showed less identity to known species and genera. The 12 bacteria possess numerous properties concerning plant growth promotion and/or phytopathogenic biocontrol. Paenibacillus chitinolyticus YSY-3.1, which exhibited the highest chitinase activity and remarkable properties for plant growth, was chosen for sequencing and draft genome analysis. The results showed that the genome is 6571 781 bp in length with 6194 coding sequences, 52.2% G + C, and 96.53% ANI value. It harbors the chitinolytic system comprising 22 enzymes. Among these enzymes, PcChiQ has a loop structure different from that of known family 19 chitinases, PcChiA contains two GH18 catalytic domains rarely found in microorganisms, and PcChiF contains three GH18 catalytic domains that have never been reported. CONCLUSIONS: The 12 identified chitinolytic bacteria exhibit great potential for further studies on plant growth-promoting and/or biocontrol properties. Among these bacteria, two strains might be good candidates for next examinations concerning novel species and/or genera, and strain YSY-3.1 could possess a novel chitinolytic system.

Metagenomic next-generation sequencing of the microbiome dataset from the surface water sample collected from Serepok River in Yok Don National Park, Vietnam.

The Central Highlands region is considered as the center with the highest biodiversity in Vietnam because it has the majority of national parks such as Yok Don, Chu Yang Sin, Bidoup-Nui Ba, Ta Dung, Chu Mon Ray, and Kon Ka Kinh and nature reserves such as Ngoc Linh, Kon Chu Rang, Ea So, Nam Ka, and Nam Nung with different ecosystems [1]. Of the national parks and nature reserves, Yok Don has the most different ecosystem. Yok Don is the second biggest national park, and it is the only national park that conserves dry deciduous dipterocarp forests in Vietnam [2]. Presently, the decrease in forest area and global warming have led to the continuous reduction in microbial resources in this region. Thus, a dataset of the soil microbiome in this region has been established to explore microbial resources for conservation and further application in sustainable agricultural production in this region [3]; however, to the best of our knowledge, a dataset of water microbiome remains unknown. This work presented a microbiome dataset from surface water samples collected from Serepok River in Yok Don National Park, Vietnam. Metagenomic next-generation sequencing was used to characterize microbial communities in the sample. The raw sequence in this work was uploaded in Fastq format on NCBI, which can be accessed at https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA853090. This metagenome dataset can provide valuable information on surface water microbial communities and their functionality. It can also be used for further studies on the conservation and application of indigenous microbial resources for sustainable crop production in this region.

Analysis of endophytic microbiome dataset from roots of black pepper (Piper nigrum L.) cultivated in the Central Highlands region, Vietnam using 16S rRNA gene metagenomic next-generation sequencing.

Vietnam is the most prominent black pepper producer and exporter in the world. In 2020, the cultivated area of black pepper in Vietnam was 132.000 hectares and its production was 270.000 tons, in which the Central Highlands region took about 70% of both the cultivated area and production [1]. Hence, this region is thought to be the capital of black pepper cultivation and production in Vietnam. Numerous researches have investigated biodiversity and collected various beneficial endophytic bacteria from this plant in this region; however, traditional methods only were used to isolate such bacteria [2], [3], [4], [5]. Therefore, these studies have a limitation to providing insight into the profiles of the endophytic microorganism dataset in the black pepper plant. Most recently, our work based on the 16S rRNA gene amplicon sequencing revealed an insight into profiles of microbial diversity and its functionality from the sample collected from a forest in this region; however, that work was just focused on soil microbiome dataset from the dry deciduous dipterocarp forest in Yok Don national park [6]. To our knowledge, a dataset of endophytic microbiome of black pepper plant cultivated in the Central Highlands remains unclear. This report presents a dataset of the endophytic microbiome from a representative sample combined from five different root samples of black pepper (Vinh Linh local variety) cultivated in the Central Highlands of Vietnam using 16S rRNA gene metagenomic next-generation sequencing. The dataset in this work can provide information on the endophytic microbial diversity and its functionality. It can also be useful for developing cultivation techniques by applying endophytic microbial genetic resources for sustainable black pepper production in the Central Highlands, Vietnam, towards the nutrient need in different stages of development and growth.

Expression, purification, and basic properties of a novel domain structure possessing chitinase from Escherichia coli carrying the family 18 chitinase gene of Bacillus velezensis strain RB.IBE29.

BACKGROUND: Bacillus velezensis possesses numerous chitinolytic enzymes; however, not much is known about the role of its chitinase molecules. METHODS AND RESULTS: In this study, the chiA gene, which encodes a novel domain structure possessing family 18 chitinase from B. velezensis RB.IBE29, was expressed successfully in Escherichia coli BL21-CodonPlus (DE3)-RIPL using the pColdII expression vector. The recombinant protein, rBvChiA, was purified using the HisTrap FF column. Purified rBvChiA showed hydrolytic activity against insoluble chitin and bound to chitinous substrates. In addition, the purified recombinant enzyme displayed remarkable inhibition effects on the spore germination of Fusarium falciforme and the egg hatch of root-knot nematodes (Meloidogyne spp.), which are the main causes of black pepper diseases in the Central Highlands region, Vietnam. CONCLUSION: The current work results might enable further studies to develop novel chitinase A and strain RB.IBE29 as a natural fungicide and nematicide for sustainable black pepper production and other crops in the Central Highlands, Vietnam. This is the second report describing chitinase from B. velezensis based on the experimental data.

Molecular analysis of genes involved in chitin degradation from the chitinolytic bacterium Bacillus velezensis.

Bacillus velezensis RB.IBE29 is a potent biocontrol agent with high chitinase activity isolated from the rhizosphere of black pepper cultivated in the Central Highlands, Vietnam. Genome sequences revealed that this species possesses some GH18 chitinases and AA10 protein(s); however, these enzymes have not been experimentally characterized. In this work, three genes were identified from the genomic DNA of this bacterium and cloned in Escherichia coli. Sequence analysis exhibited that the ORF of chiA consists of 1,203 bp and encodes deduced 45.46 kDa-chitinase A of 400 aa. The domain structure of chitinase A is composed of a CBM 50 domain at the N-terminus and a catalytic domain at the C-terminus. The ORF of chiB includes 1,263 bp and encodes deduced 47.59 kDa-chitinase B of 420 aa. Chitinase B consists of two CBM50 domains at the N-terminus and a catalytic domain at the C-terminus. The ORF of lpmo10 is 621 bp and encodes a deduced 22.44 kDa-AA10 protein, BvLPMO10 of 206 aa. BvLPMO10 contains a signal peptide and an AA10 catalytic domain. Chitinases A and B were grouped into subfamily A of family 18 chitinases. Amino acid sequences in their catalytic domains lack aromatic residues (Trp, Phe, Tyr) probably involved in processivity and substrate binding compared with well-known bacterial GH18 chitinases. chiB was successfully expressed in E. coli. Purified rBvChiB degraded insoluble chitin and was responsible for inhibition of fungal spore-germination and egg hatching of plant-parasitic nematode. This is the first report describing the analysis of the chitinase system from B. velezensis.

Soil microbiome dataset from Yok Don national park in the Central Highlands region of Vietnam.

The Central Highlands region contains most of the national parks in Vietnam with different ecosystems, including the national parks of Kon Ka Kinh, Chu Mon Ray, Chu Yang Sin, Yok Don, Bidoup-Nui Ba, and Ta Dung. Thus, this region is considered a center with the highest biodiversity in Vietnam [1]. Among the national parks, Yok Don is unique in its conservation of the dry deciduous dipterocarp forest. Furthermore, Yok Don is the second-largest park in Vietnam; it has the most different ecosystem compared with other national parks in this region [2]. Although some studies have investigated biodiversity preservation in the region, some other studies have only dealt with medicinal plants, lichens, and the rhizospheric bacteria of cultivated black pepper [1,[3], [4], [5]. To the best of our knowledge, no research on the microbial communities in Yok Don national park and in the Central Highlands has been reported. At present, global warming and a decrease in the forest area in the Central Highlands have led to the ongoing reduction in biodiversity and microbial resources. The current study reports the microbiome dataset from the soil sample collected in Yok Don national park. Metagenomic next-generation sequencing was used to characterize the microbial communities in the sample. The metagenome dataset generated provides information on microbial diversity and its functionality and can be useful for further studies on the conservation and use of microbial genetic resources in this region.