Genetic characterization of biohydrogen-producing purple non-sulfur bacteria Rhodobacter johrii MAY2 isolate via whole genome analysis.

Purple non-sulfur bacteria (PNSB) are a diverse group of bacteria studied for various possible applications. They are commonly surveyed in bioenergy research as they produce biohydrogen, a candidate for clean alternative energy. This study aimed to assess the biohydrogen production ability and genetically characterize a high biohydrogen-producing PNSB (MAY2) isolated from Los Baños, Laguna, Philippines via whole genome sequencing (WGS). MAY2, when grown in mixed volatile fatty acids, produced biogas with 38% hydrogen. WGS results revealed that the isolate is positively classified under the genus Rhodobacter johrii. Also, 82 genetic hallmarks for biohydrogen production were found in the isolated genome which are involved in the production of key enzymes and proteins relevant to the photofermentative and hydrogen regulation pathways. Its nitrogenase gene cluster is stringently regulated by two genes, nifA and rofN, whose function and expression are easily affected by several environmental factors.

Dataset on CRISPR/Cas9 system targeting hydrogenase genes in Rhodobacter johrii MAY2 isolate.

This dataset contains the gene sequences of the small and large sub-unit of the hydrogenase enzyme obtained from the annotated genome of Rhodobacter johrii MAY2. The whole genome sequence of the isolate was performed using SEED genome viewer on the Rapid Annotation using the Subsystem Technology (RAST) platform. Concurrently, guide RNA sequences and primers were meticulously crafted using the CHOPCHOP v.3.0 web tool, specifically designed for the precise editing and amplification of the target genes. The primers were optimized via gradient PCR to determine appropriate amplification conditions. Furthermore, the guide RNA was tested via in-vitro cleavage assay, gauging its efficacy in cleaving the intended target genes. The dataset, including the optimization and the cleavage assay, was deposited in Mendeley Data with DOI no: 10.17632/rcx3mcssnx.2.

Attachment of potential cultivable primo-colonizing bacteria and its implications on the fate of low-density polyethylene (LDPE) plastics in the marine environment.

Plastics released in the environment become suitable matrices for microbial attachment and colonization. Plastics-associated microbial communities interact with each other and are metabolically distinct from the surrounding environment. However, pioneer colonizing species and their interaction with the plastic during initial colonization are less described. Marine sediment bacteria from sites in Manila Bay were isolated via a double selective enrichment method using sterilized low-density polyethylene (LDPE) sheets as the sole carbon source. Ten isolates were identified to belong to the genera Halomonas, Bacillus, Alteromonas, Photobacterium, and Aliishimia based on 16S rRNA gene phylogeny, and majority of the taxa found exhibit a surface-associated lifestyle. Isolates were then tested for their ability to colonize polyethylene (PE) through co-incubation with LDPE sheets for 60 days. Growth of colonies in crevices, formation of cell-shaped pits, and increased roughness of the surface indicate physical deterioration. Fourier-transform infrared (FT-IR) spectroscopy revealed significant changes in the functional groups and bond indices on LDPE sheets separately co-incubated with the isolates, demonstrating that different species potentially target different substrates of the photo-oxidized polymer backbone. Understanding the activity of primo-colonizing bacteria on the plastic surface can provide insights on the possible mechanisms used to make plastic more bioavailable for other species, and their implications on the fate of plastics in the marine environment.

Detection of Salmonella enterica subsp. enterica via Quenching of Unincorporated Amplification Signal Reporters in Loop-Mediated Isothermal Amplification.

Salmonella enterica is a major cause of diarrheal diseases in developing countries where timely surveillance and proper clinical management are inadequate. In this study, a rapid and cheap method of detecting S. enterica DNA was developed by employing the Quenching of Unincorporated Amplification Signal Reporters in Loop-Mediated Isothermal Amplification (QUASR LAMP) platform. QUASR LAMP provides a closed-tube, target-specific endpoint detection of pathogens, wherein results can be analyzed visually through an LED transilluminator and verified through agarose gel electrophoresis. Based on the chromosomal SopD gene, primers and probes were first designed, then screened. The assay was subsequently optimized so that the presence of S. enterica is determined by incubating the extracted DNA at 65°C for only 60 minutes. The assay was repeatable and can be performed by simply using a thermal cycler or even a dry bath incubator. S. enterica positives appear bright yellow green when viewed through a yellow filter excited with blue LED. The developed assay had an in silico and in vitro specificity towards Salmonella enterica subsp. enterica serovars with a limit of detection of 104 copies per microliter. The Salmonella QUASR LAMP assay has the potential for food and environmental applications. Chiefly, as an alternative to traditional microbiology and PCR, this QUASR LAMP assay can be used for point-of-care salmonellosis testing of clinical specimens in low-resource settings.

Draft Genome Sequences of Six Bacteria Isolated from the Benham Bank, Philippine Rise, Philippines.

We report here the draft genome sequences of six bacteria isolated from the near-bottom waters and surface sediments of the Benham Bank, Philippine Rise, Philippines. These genome sequences represent candidate novel species and/or strains from the families Flavobacteriaceae and Dermacoccaceae and the genera Idiomarina, Bacillus, and Vibrio.

Draft Genome Sequence of Bacillus lehensis M136, Isolated from the Manleluag Hyperalkaline Spring in Pangasinan, Philippines.

Here, we report the draft whole-genome sequence of Bacillus lehensis M136, isolated from a hyperalkaline spring located in Pangasinan, Philippines. From 24 scaffolds, the total genome assembly length is 3,985,437 bp. Industrially important genes like cyclodextrin glycosyltransferase (CGTase) and proteases were detected in this draft genome.