Draft Genome Sequence of Bacillus toyonensis Strain GM18, Isolated from Agricultural Soil

ABSTRACT Bacillus toyonensis is a recently described species related to Bacillus cereus and Bacillus thuringiensis. The GM18 strain previously identified as B. thuringiensis is now classified as B. toyonensis based on the RNA 16S sequence and whole-genome average nucleotide identity. The genome analysis revealed the presence of insecticide, nematicide, and antitumoral proteins.

Tetracycline Resistant Genes as Bioindicators of Water Pollution

The current study aimed to investigate the prevalence of tetracycline resistant bacteria isolated from different water samples and the genes responsible for this resistance. Two hundred fifty isolates were isolated from different water samples from two different locations. Isolates were obtained from El-Zamalek site was (n =110) and from Rod El-Farag site was (n = 140). A hundred isolates out of 250 bacterial isolates (40%) were resistant to tetracycline at a concentration of 16 μg/ml. Only 31 (31%) were selected due to their resistance to (32 μg/ml) tetracycline for identification. All selected isolates were identified according to biochemical and the 16S sequence techniques. The 16S rDNA gene sequences of the bacterial isolates which were reported in this study were submitted to the NCBI database. Of the 31 isolates were analyzed by Polymerase Chain Reaction (PCR), results showed that 41.9 % (13/31) harbored tet A gene, 74.2% (23/31) carried tet D gene, while 12.9 % (4/31) carried tet M gene. Whereas tet B, tet C and tet O were not detected. Twenty-one isolates (67.7%) harbored a single tet gene, five isolates (16.1%) harbored two different tet genes while three isolates (9.7 %) harbored three different tet genes. Moreover, two isolates were free from any tested tet genes.

Chitinophaga vietnamensis sp. nov., a multi-drug resistant bacterium infecting humans

We describe a new multidrug resistant Chitinophaga species that was isolated from patients with type 2 diabetes in Vietnam. Strain BD 01T was cultivated in 2017 from a blood sample of a patient suffering from bacteremia. Strain VP 7442 was isolated in 2018 from a pleural fluid sample of a patient who had presented with lung abscess and pleural effusion. Both strains are aerobic, Gram-negative, non-motile and non-spore-forming. The 16S rRNA gene sequences of both strains are 100 % similar and share a highest 16S sequence identity with Chitinophaga polysaccharea MRP-15T of 97.42 %. Their predominant fatty acid is iso-C15 : 0 (73.8 % for strain BD 01T and 79.8 % for strain VP 7442). The draft genome sizes of strains BD 01T and VP 7442 are 6 308 408 and 6 308 579 bp, respectively. They are resistant to beta-lactams, aminoglycosides, fluoroquinolones, metronidazole, fosfomycin, vancomycin and macrolides, and exhibit 20 and 18 antimicrobial resistance-related genes, respectively. Using the multiphasic taxonogenomic approach, we propose that strains BD 01T (=CSUR P9622=VTCC 70981) and VP 7442 (=CSUR P9623=VTCC 70982) represent a new species, for which we propose the name Chitinophaga vietnamensis sp. nov. Strain BD 01T was chosen as type strain of C. vietnamensis sp. nov.

Natural hybridization between two species of green Anoles: morphological and genetic evidence

Anoles are a group of lizards that offer a wide range of opportunities to study different biological topics. In this work, we examined some aspects of the morphology from 139 individuals of green anoles collected in urban parks of Santo Domingo and the Distrito Nacional. We investigated evidence of hybridization between the two Hispaniola endemic species Anolis chlorocyanus and A. cyanostictus and the introduced species A. porcatus. We categorized the individuals in pure species and intermediates based on their phenotype. Additionally, mitochondrial 16S sequence data was generated from the collected specimens, to compare molecular and phenotypic species assignments. We consider the general congruence between both data sets in most but inconsistency in a few specimens as evidence for hybridization between the two endemic species. However, we did not find evidence of hybridization between any of these species and the introduced species A. porcatus. Nevertheless, the continuous expansion of the distribution of this invasive species possibly will have drastic negative consequences for the populations of the endemic species.

Identification of Gastrointestinal Microbiota in Hawaiian Green Turtles (Chelonia mydas)

Green turtles ( Chelonia mydas) have a hindgut fermentation digestive tract, which uses cellulolytic microbes to break down plant matter in the cecum and proximal colon. Previous studies on bacterial communities of green turtles have not identified in situ hindgut microbiota, and never before in Hawaiian green turtles, which comprise an isolated metapopulation. Fresh samples using sterile swabs were taken from five locations along the gastrointestinal tracts of eight green turtles that had required euthanization. Bacteria were cultured, aerobically and anaerobically, on nutrient agar and four differential and selective media. Samples at three sections along the gastrointestinal tracts of two green turtles were analyzed using 16S metagenomics on an Ion Torrent Personal Genome Machine. More than half of the 4 532 104 sequences belonged to the phylum Firmicutes, followed by Bacteroidetes and Proteobacteria, which are characteristic of herbivore gut microbiota. Some microbiota variation existed between turtles and among gastrointestinal sections. The 16S sequence analysis provided a better representation of the total gastrointestinal bacterial community, much of which cannot be cultured using traditional microbial techniques. These metagenomic analyses serve as a foundation for a better understanding of the microbiome of green turtles in the Hawaiian Islands and elsewhere.

A new method for quantitative detection of Lactobacillus casei based on casx gene and its application

Background The traditional method of bacterial identification based on 16S rRNA is a widely used and very effective detection method, but this method still has some deficiencies, especially in the identification of closely related strains. A high homology with little differences is mostly observed in the 16S sequence of closely related bacteria, which results in difficulty to distinguish them by 16S rRNA-based detection method. In order to develop a rapid and accurate method of bacterial identification, we studied the possibility of identifying bacteria with other characteristic fragments without the use of 16S rRNA as detection targets. Results We analyzed the potential of using cas (CRISPR-associated proteins) gene as a target for bacteria detection. We found that certain fragment located in the casx gene was species-specific and could be used as a specific target gene. Based on these fragments, we established a TaqMan MGB Real-time PCR method for detecting bacteria. We found that the method used in this study had the advantages of high sensitivity and good specificity. Conclusions The casx gene-based method of bacterial identification could be used as a supplement to the conventional 16 s rRNA-based detection method. This method has an advantage over the 16 s rRNA-based detection method in distinguishing the genetic relationship between closely-related bacteria, such as subgroup bacteria, and can be used as a supplement to the 16 s rRNA-based detection method.

Integrative taxonomy reveals first country record of Hyalinobatrachium mondolfii Señaris and Ayarzagüena 2001, and distribution range extensions for Cochranella nola Harvey 1996, and Rulyrana spiculata Duellman 1976 (Anura: Centrolenidae) in Peru

We used an integrative taxonomy approach to investigate the taxonomic identity of several populations of glassfrogs from Peru, which are notoriously challenging to identify due to their overall similarity in morphology and coloration. We relied on comparisons of morphology, bioacoustics, and partial fragments of 16S rRNA DNA sequences. We report for the first time the presence of Hyalinobatrachium mondolfii in Peru, being this the southernmost locality known for the species. Likewise, we update and extend the distribution ranges of Rulyrana spiculata and Cochranella nola in the Andes of Peru, provide a 16S sequence of a topotype of R. spiculata, and confirm its presence in Bolivia. For all three species, we increase the current knowledge on their geographic distribution and genetic and phenotypic variation.

Is Anopheles gambiae a natural host of Wolbachia?

Wolbachia (Alphaproteobacteria, Rickettsiales) is an intraovarially-transmitted symbiont of insects able to exert striking phenotypes, including reproductive manipulations and pathogen blocking. These phenotypes make Wolbachia a promising tool to combat mosquito-borne diseases. Although Wolbachia is present in the majority of terrestrial arthropods, including many disease vectors, it was considered absent from Anopheles gambiae mosquitos, the main vectors of malaria in sub-Saharan Africa. In 2014, Wolbachia sequences were detected in A. gambiae samples collected in Burkina Faso. Subsequently, similar evidence came from collections all over Africa, revealing a high Wolbachia 16S sequence diversity, low abundance, and a lack of congruence between host and symbiont phylogenies. Here, we reanalyze and discuss recent evidence on the presence of Wolbachia sequences in A. gambiae. We find that although detected at increasing frequencies, the unusual properties of these Wolbachia sequences render them insufficient to diagnose natural infections in A. gambiae. Future studies should focus on uncovering the origin of Wolbachia sequence variants in Anopheles and seeking sequence-independent evidence for this new symbiosis. Understanding the ecology of Anopheles mosquitos and their interactions with Wolbachia will be key in designing successful, integrative approaches to limit malaria spread. Although the prospect of using Wolbachia to fight malaria is intriguing, the newly discovered strains do not bring it closer to realization.SignificanceAnopheles gambiae mosquitos are the main vectors of malaria, threatening around half of the world’s population. The bacterial symbiont Wolbachia can interfere with disease transmission by other important insect vectors, but until recently it was thought to be absent from natural A. gambiae populations. Here, we critically analyze the genomic, metagenomic, PCR, imaging and phenotypic data presented in support of the presence of natural Wolbachia infections in A. gambiae. We find that they are insufficient to diagnose Wolbachia infections and argue for the need of obtaining robust data confirming basic Wolbachia characteristics in this system. Determining Wolbachia infection status of Anopheles is critical due to its potential to influence Anopheles population structure and Plasmodium transmission.

Searching for Molecular Markers to Differentiate Bombus terrestris (Linnaeus) Subspecies in the Iberian Peninsula

Bumblebees (genus Bombus Latreille) are pollinator insects of great ecological and economic importance, which commercial use for pollination has increased since the 80s. However, the introduction of foreign Bombus terrestris (Linnaeus) has resulted in a decline of native bumblebee populations in Japan, Chile or Argentina among others. To study the potential introgression of commercial B. terrestris into the Iberian endemic subspecies Bombus terrestris lusitanicus Krüger, it is necessary to find a precise molecular marker that differentiates both subspecies. For this purpose, comparative analyses were carried out between B. t. lusitanicus and B. t. terrestris (Linnaeus) from Spain and from Belgium by sequencing the nuclear genes elongation factor 1-α and arginine kinase and the mitochondrial gene 16S ribosomal RNA, and genotyping with eleven microsatellite loci. No differentiation was observed at the nuclear level, but haplotypes found within the 16S sequence correlated with the morphological characterization of the subspecies. In a case study including individuals sampled before the establishment of bumblebee rearing companies and others from recent samplings, we detected hybrid individuals (those with non-matching morphological subspecies and 16S haplotype) more frequently in the south supporting the naturalization of commercial B. t. terrestris and introgression events between both subspecies. This marker should be used in Iberian populations with the aim to support management and conservation actions in endemic populations of B. t. lusitanicus.

Three new earthworm species of the tokioensis-group in the genus Amynthas (Oligochaeta: Megascolecidae) from Guangxi Province, China

Three new species of the genus Amynthas are described from Guangxi Province, China. They are named A. dissimilis sp. nov., A. anteporus sp. nov. and A. marsupiformis sp. nov. All of them have two pairs of spermathecal pores in 6/7–7/8, and belong to the tokioensis-group. Their morphological characteristics are compared to similar species in tokioensis-group from China and other Asian countries. In addition, the mitochondrial COI and 12S-tRNA-Val-16S sequence of three new species were determined, then pairwise distances between species were calculated. Both morphological and molecular evidences could easily distinguish the new species from earthworms previously reported in the tokioensis-group.