Draft Genome Sequences of Shewanella sp. Strain UCD-FRSP16_17 and Nine Vibrio Strains Isolated from Abalone Feces

Vibrio cyclitrophicus phage encoding gene transfer agent fragment, representing a novel viral family

Vibrio is a prevalent bacterial genus in aquatic environments and exhibits diverse metabolic capabilities, playing a vital role in marine biogeochemical cycles. This study isolated a novel virus infecting Vibrio cyclitrophicus, vB_VviC_ZQ26, from coastal waters near Qingdao, China. The vB_VviC_ZQ26 comprises a linear double-stranded DNA genome with a length of 42,982 bp and a G + C content of 43.21 %, encoding 72 putative open reading frames (ORFs). Transmission electron microscope characterization indicates a siphoviral-morphology of vB_VviC_ZQ26. Nucleic-acids-wide analysis indicates a tetranucleotide frequency deviation for genomic segments encoding putative gene transfer agent protein (GTA) and coil-containing protein, implying divergent origins occurred in different parts of viral genomes. Phylogenetic and genome-content-based analysis suggest that vB_VviC_ZQ26 represents a novel vibriophage-specific family designated as Coheviridae. From the result of biogeographic analysis, Coheviridae is mainly colonized in the temperate and tropical epipelagic zones. This study describes a novel vibriophage infecting V. cyclitrophicus, shedding light on the evolutionary divergence of different parts of the viral genome and its ecological footprint in marine environments.

The degradation activities for three seaweed polysaccharides of Shewanella sp. WPAGA9 isolated from deep-sea sediments

Seaweed oligosaccharides possess great bioactivities. However, different microbial strains are required to degrade multiple polysaccharides due to their limited biodegradability, thereby increasing the cost and complexity of production. Shewanella sp. WPAGA9 was isolated from deep-sea sediments in this study. According to the genomic and biochemical analyses, the extracellular fermentation broth of WPAGA9 had versatile degradation abilities for three typical seaweed polysaccharides including agar, carrageenan, and alginate. The maximum enzyme activities of the extracellular fermentation broth of WPAGA9 were 71.63, 76.4, and 735.13 U/ml for the degradation of agar, alginate, and carrageenan, respectively. Moreover, multiple seaweed oligosaccharides can be produced by the extracellular fermentation broth of WPAGA9 under similar optimum conditions. Therefore, WPAGA9 can simultaneously degrade three types of seaweed polysaccharides under similar conditions, thereby greatly reducing the production cost of seaweed oligosaccharides. This finding indicates that Shewanella sp. WPAGA9 is an ideal biochemical tool for producing multiple active seaweed oligosaccharides at low costs and is also an important participant in the carbon cycle process of the deep-sea environment.

Combining Microbial Culturing With Mathematical Modeling in an Introductory Course-Based Undergraduate Research Experience

Quantitative techniques are a critical part of contemporary biology research, but students interested in biology enter college with widely varying quantitative skills and attitudes toward mathematics. Course-based undergraduate research experiences (CUREs) may be an early way to build student competency and positive attitudes. Here we describe the design, implementation, and assessment of an introductory quantitative CURE focused on halophilic microbes. In this CURE, students culture and isolate halophilic microbes from environmental and food samples, perform growth assays, then use mathematical modeling to quantify the growth rate of strains in different salinities. To assess how the course may impact students' future academic plans and attitudes toward the use of math in biology, we used pre- and post-quarter surveys. Students who completed the course showed more positive attitudes toward science learning and an increased interest in pursuing additional quantitative biology experiences. We argue that the classroom application of microbiology methods, combined with mathematical modeling using student-generated data, provides a degree of student ownership, collaboration, iteration, and discovery that makes quantitative learning both relevant and exciting to students.

Classification and structural insight into vibriolysin-like proteases of Vibrio pathogenicity

Vibriolysin-like proteases (VLPs) are important virulence agents in the arsenal of Vibrio causing instant cytotoxic effects during infection. Most of Vibrio secreted VLPs show serious pathogenicity, while some species of Vibrio with VLPs are non-pathogenic, like Vibrio tasmaniensis and Vibrio pacinii. To investigate the relation between VLPs and Vibrio pathogenicity, one phylogenetic tree of VLPs was constructed and compared consensus sequences at the N-terminus of VLPs. Based on these results, VLPs were defined into nine phylogenetic clades. Pathogenicity analysis of Vibrio showed that Vibrio species with VLPs III, VI, VII or VIII are serious pathogenic bacteria, while species with VLPs I, II, IV or IX are opportunistic pathogens. Multiple sequence alignment showed that the N-terminal 5-16 nucleotides of each clade are highly conservative. Topological analysis of VLPs exhibited the structural differences in N-terminal regions of each VLP clade. These results suggest that structure of N-terminus might play a key role in the pathogenicity of VLPs. Our findings give new insights into the classification of VLPs and the relationship between VLPs and Vibrio pathogenicity.

Complete genome sequence of the heavy metal resistant bacterium Agromyces aureus AR33T and comparison with related Actinobacteria

Agromyces aureus AR33^T is a Gram-positive, rod-shaped and motile bacterium belonging to the Microbacteriaceae family in the phylum Actinobacteria that was isolated from a former zinc/lead mining and processing site in Austria. In this study, the whole genome was sequenced and assembled combining sequences obtained from Illumina MiSeq and Sanger sequencing. The assembly resulted in the complete genome sequence which is 4,373,124 bp long and has a GC content of 70.1%. Furthermore, we performed a comparative genomic analysis with other related organisms: 6 Agromyces spp., 4 Microbacteriaceae spp. and 2 other members of the class Actinobacteria.