Draft genome of the Arabidopsis thaliana phyllosphere bacterium, Williamsia sp. ARP1

Abstract

The Gram-positive actinomycete Williamsia sp. ARP1 was originally isolated from the Arabidopsis thaliana phyllosphere. Here we describe the general physiological features of this microorganism together with the draft genome sequence and annotation. The 4,745,080 bp long genome contains 4434 protein-coding genes and 70 RNA genes. To our knowledge, this is only the second reported genome from the genus Williamsia and the first sequenced strain from the phyllosphere. The presented genomic information is interpreted in the context of an adaptation to the phyllosphere habitat.Electronic supplementary materialThe online version of this article (doi:10.1186/s40793-015-0122-x) contains supplementary material, which is available to authorized users.

Temporal patterns inIxodes ricinusmicrobial communities: an insight into tick-borne microbe interactions

“…Assuming that the detection of both Wolbachia and Arsenophonus is probably due to the infection of ticks by I. hookeri, we hypothesize that Spiroplasma might be upregulated by the presence of the parasitoid in ticks and might act as a defensive response mechanism against I. hookeri, as previously mentioned in Drosophila melanogaster infested by two species of parasitoid wasps [88]. Nevertheless, we cannot rule out the hypothesis that, while identified in a large variety of tick species [47,54] [60,[94][95][96][97][98][99], and known to potentially infect ticks. The high connectivity displayed by these OTUs might reflect similar functions between OTUs adapted to contrasting environmental conditions (functional redundancy).…”

“…Furthermore, the fact that not all these studies used negative controls to identify potential contaminating OTUs and remove them from their datasets calls for caution in attempts to draw conclusions about these differences, particularly when we know that these OTUs can represent more than 50% of sequences detected in tick samples [22]. [6,12,16,18,19], were identified as bacteria present in the environment [57][58][59][60][61][62]. While very few of the above mentioned references reported performing negative controls while studying tick microbiota [12,19], it is important to keep in mind that some of these genera could also correspond to contaminants that may arise during extraction or amplification steps [22,30,[63][64][65].…”

Distinguishing nutrient‐dependent plant driven bacterial colonization patterns in alfalfa

“…While our endophyte culture collection is small, many of the members are found consistently in plant phyllosphere, root tissue and seed endophytes (Vorholt, ; Kaewkla and Franco, ; Stiefel et al ., ; Horn et al ., ; López et al ., ), as well as the 16S rRNA gene amplicon survey from the source material for our isolate collection (Figure S2). In one review, three of the eight genera represented in our synthetic community, Pantoea , Streptomyces and Arthrobacter were among the most abundant genera detected in the phyllosphere of both legumes (e.g.…”

“…A. thaliana and rice) (Vorholt, ). Six of the eight genera represented in our synthetic community were previously identified as M. sativa endophytes, and the other two, Williamsia and Oceanobacillus , were previously isolated from the phyllosphere and root endosphere of legume and non‐leguminous plants (Kaewkla and Franco, ; Stiefel et al ., ; Horn et al ., ; Yang et al ., ). Thus, our synthetic community is composed of M. sativa relevant bacteria.…”

Draft Genome Sequences of Two Novel Sub-Antarctic Williamsia Species

“…Nine species have been validly published to date (2). To assist in understanding the genetics of cold-tolerant oleaginous Williamsia species, the genomes of two Williamsia strains, 1135 and 1138, were shotgun sequenced.…”