Genome drafts of Pseudogracilibacillus spp. from soil and sediment of Mount Makiling, a dormant volcano in the Philippines.

We present the draft whole-genome sequences of Pseudogracilibacillus spp. isolated from the soils and sediments of Sipit Creek located at Mount Makiling, a dormant volcano in the southern part of Luzon Island, Philippines. This Pseudogracilibacillus spp. genome report extends the body of knowledge on a lesser-known genus of Bacillaceae.

Devosia yakushimensis sp. nov., isolated from root nodules of Pueraria lobata (Willd.) Ohwi.

A Gram-negative, strictly aerobic bacterium, comprising non-endospore-forming motile rods (1.2-2.0 microm x 0.4-0.6 microm) with polar flagellae was isolated from root nodules of the leguminous plant Pueraria lobata (Willd.) Ohwi growing on the coast of Yakushima Island, Kagoshima Prefecture, Japan. The novel strain, designated Yak96B(T), grew at an optimum pH of 7.0 and an optimum temperature of 28 degrees C. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the new strain was closely related to Devosia neptuniae J1(T) and Devosia chinhatensis IPL18(T), with sequence similarities of 98.1 % and 97.8 %, respectively. However, the DNA-DNA relatedness values of strain Yak96B(T) with D. neptuniae LMG 21357(T) and D. chinhatensis CCM 7426(T) were 53.6 % and 34 %, respectively. The DNA G+C content of strain Yak96B(T) was 65.3 mol%, the predominant isoprenoid quinone was Q10 (85 %) and the polar lipids were phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids (>5 %) were 11-methyl C(18 : 1)omega7c (35.0 %), C(16 : 0) (22.4 %), C(18 : 1)omega7c (21.8 %), C(19 : 0) cyclo omega8c (6.8 %) and C(18 : 0) (5.4 %). The infection/nodulation test was negative and nifH and nodD genes were not detected. Based on its chemotaxonomic and physiological characteristics, strain Yak96B(T) represents a novel species of the genus Devosia, for which the name Devosia yakushimensis sp. nov. is proposed. The type strain is Yak96B(T) (=KCTC 22147(T)=NBRC 103855(T)=LMG 24299(T)).

Differential detection of vibrios pathogenic to shrimp by multiplex PCR.

The research was focused on the multiplex polymerase chain reaction (PCR) differential detection of shrimp pathogens Vibrio harveyi, Vibrio campbellii and isolates from a variant strain of Vibrio (referred to as Philippine Vibrio isolates in this study) exhibiting characteristics distinct from these two species. Sequence alignment of the hemolysin gene from type strains Vibrio harveyi (NBRC 15634) and Vibrio campbellii (NBRC 15631), as well as 10 variant Philippine Vibrio isolates, was performed in order to design a set of hemolysin-targeted primers for the specific detection of the Philippine Vibrio isolates. Primer PNhemo amplified a 320-bp hemolysin gene fragment of the Philippine Vibrio isolates in PCR using 65 degrees C annealing temperature, but did not amplify the target gene fragment in type strains V. harveyi and V. campbellii. Another new primer (VcatoxR) targeting the toxR gene was designed for the specific detection of type strain V. campbellii under stringent 65 degrees C annealing temperature. PCR using VcatoxR primer resulted in the specific amplification of a 245-bp V. campbellii toxR fragment. The simultaneous use of three primer sets in PCR, including PNhemo and VcatoxR (the two new primers designed in this study), and a primer VhtoxR (previously reported for the specific detection of V. harveyi), resulted in differential profiles with 390-bp, 245-bp, and 320-bp amplicons for V. harveyi, V. campbellii, and variant Philippine Vibrio isolates, respectively. Presence of all three types of Vibrio shrimp pathogens in the sample could be detected with a multiplex PCR profile containing all the expected size amplicons.