Publications

4369

Citrus Decline Disease was recently reported to affect several citrus species in Iran when grafted on a local rootstock variety, Bakraee. Preliminary studies found “Candidatus Phytoplasma aurantifoliae” and “Candidatus Liberibacter asiaticus” as putative etiological agents, but were not ultimately able to determine which one, or if an association of both, were causing the disease. The current study has the aim of characterizing the microbiota of citrus plants that are either asymptomatic, showing early symptoms, or showing late symptoms through amplification of the V1–V3 region of 16S rRNA gene using an Illumina sequencer in order to (i) clarify the etiology of the disease, and (ii) describe the microbiota associated to different symptom stages. Our results suggest that liberibacter may be the main pathogen causing Citrus Decline Disease, but cannot rule out the possibility of phytoplasma being involved as well. The characterization of microbiota shows that the leaves show only two kinds of communities, either symptomatic or asymptomatic, while roots show clear distinction between early and late symptoms. These results could lead to the identification of bacteria that are related to successful plant defense response and, therefore, to immunity to the Citrus Decline Disease.

Abstract Dissimilatory perchlorate reduction is an anaerobic respiratory pathway that in communities might be influenced by metabolic interactions. Because the genes for perchlorate reduction are horizontally transferred, previous studies have been unable to identify uncultivated perchlorate-reducing populations. Here we recovered metagenome-assembled genomes from perchlorate-reducing sediment enrichments and employed a manual scaffolding approach to reconstruct gene clusters for perchlorate reduction found within mobile genetic elements. De novo assembly and binning of four enriched communities yielded 48 total draft genomes. In addition to canonical perchlorate reduction gene clusters and taxa, a new type of gene cluster with an alternative perchlorate reductase was identified. Phylogenetic analysis indicated past exchange between these gene clusters, and the presence of plasmids with either gene cluster shows that the potential for gene transfer via plasmid persisted throughout enrichment. However, a majority of genomes in each community lacked perchlorate reduction genes. Putative chlorate-reducing or sulfur-reducing populations were dominant in most communities, supporting the hypothesis that metabolic interactions might result from perchlorate reduction intermediates and byproducts. Other populations included a novel phylum-level lineage (Ca. Muirbacteria) and epibiotic prokaryotes with no known role in perchlorate reduction. These results reveal unexpected genetic diversity, suggest that perchlorate-reducing communities involve substantial metabolic interactions, and encourage expanded strategies to further understand the evolution and ecology of this metabolism.

ABSTRACTCandidatus Ornithobacterium hominissp. nov. represents a new member of the Flavobacteriaceae detected in 16S rRNA gene surveys from Southeast Asia, Africa and Australia. It frequently colonises the infant nasopharynx at high proportional abundance, and we demonstrate its presence in 42% of nasopharyngeal swabs from 12 month old children in the Maela refugee camp in Thailand. The species, a Gram negative bacillus, has not yet been cultured but the cells can be identified in mixed samples by fluorescent hybridisation. Here we report seven genomes assembled from metagenomic data, two to improved draft standard. The genomes are approximately 1.9Mb, sharing 62% average amino acid identity with the only other member of the genus, the bird pathogenOrnithobacterium rhinotracheale.The draft genomes encode multiple antibiotic resistance genes, competition factors,Flavobacterium johnsoniae-like gliding motility genes and a homolog of thePasteurella multocidamitogenic toxin. Intra- and inter-host genome comparison suggests that colonisation with this bacterium is both persistent and strain exclusive.