Draft genome sequences of Bacillus pumilus 36R ATNSAL and B. safensis 13L LOBSAL, two potential candidate probiotic strains for shrimp aquaculture.

OBJECTIVES: This work aimed to isolate bacterial strains with antagonist activity against Vibrio parahaemolyticus, the causative agent of acute hepatopancreatic necrosis disease (VPAHPND) that was isolated from outbreaks in Mexico. Here, we report the draft genome sequences of two antagonistic strains, isolated from saline sediment in Sonora, Mexico. METHODS: Cross-streak and well diffusion tests were employed to find the bacterial strains with higher inhibitory activity against VPAHPND. The whole genomes of B. pumilus 36R ATNSAL and B. safensis 13L LOBSAL were sequenced using Ion TorrentTM (PGM) and Illumina MiseqTM platforms, respectively. Annotation was performed using the RAST server, and the genes involved in the biosynthesis of bacterial secondary metabolites were predicted using antiSMASH. RESULTS: Two bacterial isolates, B. safensis 13L LOBSAL and B. pumilus 36R ATNSAL, were chosen based on their strong antagonistic profiles. The genome of 36R ATNSAL was 3.94 Mbp in length and contained 3824 genes and a total of 4116 coding sequences (CDSs); the genome of 13L LOBSAL was 3.68 Mbp and contained 3619 genes and 3688 CDSs. Twenty-eight and 32 biosynthetic gene clusters responsible for putative antimicrobial metabolite production were identified in 36R ATNSAL and 13L LOBSAL, respectively. CONCLUSIONS: The two strains 13L LOBSAL and 36R ATNSAL showed excellent probiotic profiles in vitro. The genome sequences will help with the mining and reconstruction of metabolic pathways in Bacillus strains. Genome sequence-guided strain improvement could augment the probiotic potential of Bacillus strains for applications in shrimp aquaculture.

Implementation and Evaluation of Open-Source Hardware to Monitor Water Quality in Precision Aquaculture.

Precision aquaculture is a new field that allows farmers to have better control over aquaculture processes, facilitating decision-making and improving efficiency. The implementation and evaluation of a low-cost water-quality monitoring system based on open-source hardware, which is easy to rebuild for scientific applications, is reported in this paper. The proposed system measures temperature, dissolved oxygen, and pH, taking records and sending information through a wireless protocol (ZigBee) to a graphical user interface which can display information numerically and graphically, as well as simultaneously storing the information in a database. These variables are very important for aquaculture, as they have a direct influence on critical culture parameters such as growth and survival. Although it is a low-cost system, it offers good quality data and demonstrates efficiency for its use in precision aquaculture.

Stenamoeba dejonckheerei sp. nov., a Free-Living Amoeba Isolated from a Thermal Spring.

Two amoeboid organisms were obtained from water samples taken from a thermal spring, "Agua Caliente", in Northwestern Mexico. The isolates were obtained when samples were cultivated at 37 °C on non-nutrient agar coated with Escherichia coli. The initial identification of the isolates was performed morphologically using light microscopy. The samples were found to have trophozoite morphology consistent with members of the genus Stenamoeba, a genus derived in 2007 from within the abolished polyphyletic genus Platyamoeba. Further analysis was performed by sequencing PCR products obtained using universal eukaryotic primers for the small subunit ribosomal ribonucleic acid (SSU rRNA) gene. Sequencing primers were designed to allow the comparison of the 18S rRNA gene sequences of the new isolates with previous sequences reported for Stenamoeba. Phylogenetic relationships among sequences from Stenamoeba were determined using Maximum Likelihood analysis. The results showed the two "Agua Caliente" sequences to be closely related, while clearly separating them from those of other Stenamoeba taxa. The degrees of sequence differentiation from other taxa were considered sufficient to allow us to propose that the Mexican isolates represent a new species.

Draft genome sequence of Pseudoalteromonas piscicida strain 36Y_RITHPW, a hypersaline seawater isolate from the south coast of Sonora, Mexico.

OBJECTIVES: This study reports the draft genome sequence of Pseudoalteromonas piscicida strain 36Y_RITHPW, a marine Gammaproteobacteria that synthesises bioactive compounds with antagonistic activity against Vibrio parahaemolyticus, a multidrug-resistant strain that is the causative agent of acute hepatopancreatic necrosis disease (AHPND), reported in shrimp farm outbreaks from Asia to Mexico with mortality rates of 80-100%. METHODS: The genome of P. piscicida 36Y_RITHPW was sequenced with an Ion Torrent™ Personal Genome Machine™ (PGM) platform. A total of 606805 reads were constructed for a 308.48Mbp and 33.5×coverage. A high-quality draft assembly and ordering of contigs was obtained with Mauve. The annotation was obtained with RAST and antiSMASH. RESULTS: The genome size consists of 5.15Mbp, with a total of 4548 genes, 4217 protein-coding sequences and a GC content of 43.3%. Several resistance genes as well as other genes involved in the production of bacteriocins and ribosomally synthesised antibacterial peptides are also present. CONCLUSIONS: Mining of this draft genome provides valuable information to explain the antagonistic capacity of P. piscicida 36Y_RITHPW, a useful strain as a potential probiotic in shrimp aquaculture against pathogenic V. parahaemolyticus.

Potentially pathogenic genera of free-living amoebae coexisting in a thermal spring.

Little is known about the prevalence of Balamuthia mandrillaris within the environment due to its difficult isolation, but once an axenic culture is established, it is relatively easy to maintain. As most of the time researchers are interested mainly in isolating B. mandrillaris from environmental samples, the flora that accompanies it becomes second in importance. Therefore, this study aimed to determine which potentially pathogenic free-living amoebae, in addition to B. mandrillaris, could be found co-inhabiting a source of natural thermal water called "Agua Caliente" (Mexico), where this amoeba has previously been detected twice by molecular methods. A third sampling from this same source was carried out to try to isolate B. mandrillaris and other free-living amoebae using 37 and 45 °C as isolation temperatures. For PCR techniques, specific primers were used for B. mandrillaris, Naegleria fowleri, and Acanthamoeba species, plus a universal primer set for the eukaryotic 18S SSU rRNA gene for other isolated amoebae. PCR products were sequenced for final identification. 42 strains of the primary isolate were obtained, but only 34 could be kept in culture. Of them, 23 strains were identified as Naegleria lovaniensis, eight strains as Acanthamoeba jacobsi, two strains as Stenamoeba sp. and only one was identified as Vermamoeba vermiformis. The isolation of B. mandrillaris was once again not successful, but the presence of potentially pathogenic and nonpathogenic free-living amoebae is reported for the first time in this type of water in Mexico thanks to molecular methodology.

Draft Genome Sequence of White Spot Syndrome Virus Isolated from Cultured Litopenaeus vannamei in Mexico.

The first genome sequence of a Mexican white spot syndrome virus is presented here. White spot syndrome is a shrimp pandemic virus that has devastated production in Mexico for more than 10 years. The availability of this genome will greatly aid epidemiological studies worldwide, contributing to the molecular diagnostic and disease prevention in shrimp farming.