Identification and Characterization of a Garlic Virus E Genome in Garlic (Allium sativum L.) Using High-Throughput Sequencing from India

Garlic (Allium sativum L.) plants exhibiting mosaics, deformation, and yellow stripes symptoms were identified in Meerut City, Uttar Pradesh, India. To investigate the viruses in the garlic samples, the method of high-throughput sequencing (HTS) was used. Complete genome of the garlic virus E (GarV-E) isolate (NCBI accession No. MW925710) was retrieved. The virus complete genome comprises 8450 nucleotides (nts), excluding the poly (A) tail at the 3′ terminus, with 5′ and 3′ untranslated regions (UTRs) of 99 and 384 nts, respectively, and ORFs encoding replicase with a conserved motif for RNA-dependent RNA polymerase (RdRP), TGB1, TGB2, TGB3, serine-rich protein, coat protein, and nucleic acid binding protein (NABP). The sequence homology shared 83.49–90.40% and 87.48–92.87% with those of GarV-E isolates available in NCBI at the nucleotide and amino acid levels, respectively. Phylogenetic analysis showed a close relationship of this isolate from India (MW925710) with GarV-E isolate YH (AJ292230) from Zhejiang, China. The presence of GarV-E was also confirmed by RT-PCR. The present study is the first report of GarV-E in garlic cultivar Yamuna Safed-3 grown in northern India. However, further studies are needed to confirm its role in symptom development, nationwide distribution, genetic diversity, and potential yield loss to the garlic in India.

Complete Genome Sequence of Pseudomonas Stutzeri S116 Provides Insights into the Mechanism of Microbial Fuel Cells

To identify suitable biocatalysts applied in microbial fuel cells (MFCs), Pseudomonas stutzeri S116 isolated from marine sludge was investigated, which possessed excellcent bioelectricity generation ability (BGA). Herein, P. stutzeri as a bioanode and biocathode achieved maximum output voltage (254.2 mV and 226.0 mV), and power density of (765 mW/m2 and 656.6 mW/m2). Complete genome sequencing of P. stutzeri was performed to reveal its potential microbial functions. The results exhibited that the strain was the ecologically dominant Pseudomonas, and its primary annotations were associated with energy production and conversion (6.84%), amino acid transport and metabolism (6.82%) and inorganic ion transport and metabolism (6.77%). The thirty-six genes involved in oxidative phosphorylation indicate that strain possesses an integrated electron transport chain. Moreover, many genes encoding redox mediators (mainly riboflavin and phenazine) were detected in the databases. Simultaneously, thiosulfate oxidization and dissimilatory nitrate reduction were annotated in the sulfur metabolism and nitrogen metabolism pathway. Gene function and cyclic voltammetry (CV) analysis indicated BGA of P. stutzeri probably was attributed to its cytochrome c and redox mediators, which enhance extracellular electron transfer (EET) rate.

Isolation and Complete Genome Sequence Analysis of Kosakonia cowanii Pa82, a Novel Pathogen Causing Bacterial Wilt on Patchouli

Pogostemon cablin (patchouli), an important medicinal and aromatic plant, is widely used in traditional Chinese medicine as well as in perfume industry. Patchouli plants are susceptible to bacterial wilt disease, which causes significant economic losses by reduction in yield and quality of the plant products. However, few studies focus on the pathogens causing bacterial wilt on patchouli. In this study, strain Pa82 was isolated from diseased patchouli plants with typical bacterial wilt symptoms in Guangdong province, China, and was confirmed to be a highly virulent pathogen of patchouli bacterial wilt. Comparative sequence analysis of 16S rRNA gene showed that the strain was closely related to Kosakonia sp. CCTCC M2018092 (99.9% similarity) and Kosakonia cowanii Esp_Z (99.8% similarity). Moreover, phylogenetic tree based on 16S rRNA gene sequences showed that the strain was affiliated with genus Kosakonia. Further, the whole genome of strain Pa82 was sequenced, and the sequences were assembled and annotated. The complete genome of the strain consists of one chromosome and three plasmids. Average nucleotide identity (ANI) and phylogenetic analysis revealed that the strain belongs to Kosakonia cowanii (designated Kosakonia cowanii Pa82). Virulence-related genes of the strain involved in adherence, biofilm formation, endotoxin and other virulence factors were predicted. Among them, vgrG gene that encodes one of the type VI secretion system components was functionally validated as a virulence factor in Kosakonia cowanii Pa82 through construction of Tn5 insertion mutants and identification of mutant defective in virulence.

Complete Genome Sequence of a Chemolithoautotrophic Iron-Oxidizing Bacterium, Acidithiobacillus ferrooxidans Strain NFP31, Isolated from Volcanic Ash Deposits on Miyake-Jima, Japan

The genome sequence of Acidithiobacillus ferrooxidans strain NFP31, which is a chemolithoautotrophic iron-oxidizing bacterium that inhabits acidified volcanic deposits on Mount Oyama, Miyake Island (Miyake-jima), Japan, was determined to identify the genetic characteristics associated with pioneer microbes in newly placed pyroclastic deposits.