Publications

4719

Abstract The symbiont “Candidatus Aquarickettsia rohweri” infects a diversity of aquatic hosts. In the threatened Caribbean coral, Acropora cervicornis, Aquarickettsia proliferates in response to increased nutrient exposure, resulting in suppressed growth and increased disease susceptibility and mortality of coral. This study evaluated the extent, as well as the ecology and evolution of Aquarickettsia infecting threatened corals, Ac. cervicornis, and Ac. palmata and their hybrid (“Ac. prolifera”). Aquarickettsia was found in all acroporids, with coral host and geographic location impacting the infection magnitude. Phylogenomic and genome-wide single-nucleotide variant analysis of Aquarickettsia found phylogenetic clustering by geographic region, not by coral taxon. Analysis of Aquarickettsia fixation indices suggests multiple sequential infections of the same coral colony are unlikely. Furthermore, relative to other Rickettsiales species, Aquarickettsia is undergoing positive selection, with Florida populations experiencing greater positive selection relative to other Caribbean locations. This may be due in part to Aquarickettsia proliferating in response to greater nutrient stress in Florida, as indicated by greater in situ replication rates in these corals. Aquarickettsia was not found to significantly codiversify with either the coral animal or the coral’s algal symbiont (Symbiodinium “fitti”). Quantitative PCR analysis showed that gametes, larvae, recruits, and juveniles from susceptible, captive-reared coral genets were not infected with Aquarickettsia. Thus, horizontal transmission of Aquarickettsia via coral mucocytes or an unidentified host is more likely. The prevalence of Aquarickettsia in Ac. cervicornis and its high abundance in the Florida coral population suggests that coral disease mitigation efforts focus on preventing early infection via horizontal transmission.

AbstractThe black curry leaf psyllid, Diaphorina communis, is a host of the citrus pathogen, ‘Candidatus Liberibacter asiaticus’ (‘CLas’). However, there is a paucity of information on its biology; hence, this study was conducted to evaluate survival and development on citrus, in this instance mandarin (Citrus reticulata) and curry leaf (Bergera koenigii), and transmission of ‘CLas’. Given its similarity with the Asian citrus psyllid (Diaphorina citri), sequences of the COI and 16S genes were examined to see if they could distinguish molecularly between nymphs of these two species. Field and laboratory experiments showed that D. communis nymphs transferred to mandarin branches failed to survive. Adults could survive on flush growth of ‘CLas’‐infected mandarin trees; however, little oviposition took place, and the single resulting nymph did not survive to the second instar. These observations suggest that D. communis does not develop, or rarely develops on mandarin and possibly other Citrus spp. Curry leaf appears to be its preferred host, and complete development can take place, possibly exclusively, on this species. Studies on acquisition of ‘CLas’ by D. communis and possible transmission assessed in 2014 and 2015 using greenhouse‐grown curry leaf and mandarin seedlings with naturally infected mandarin stumps as a source of ‘CLas’ indicated a low acquisition rate of ‘CLas’. In addition, although D. communis can acquire ‘CLas’, it either cannot transmit it or transmission is limited, and the pathogen may not multiply within the insect. Phylogenetic analyses indicate that differences in COI and 16S regions may prove useful for differentiating between early instar D. communis and D. citri nymphs when fifth instar nymphs and adults are not present on host plants.

Summary Holosporales are an alphaproteobacterial lineage encompassing bacteria obligatorily associated with multiple diverse eukaryotes. For most representatives, little is known on the interactions with their hosts. In this study, we characterized a novel Holosporales symbiont of the ciliate Paramecium polycaryum . This bacterium inhabits the host cytoplasm, frequently forming quite large aggregates. Possibly due to such aggregates, host cells sometimes displayed lethal division defects. The symbiont was also able to experimentally stably infect another Paramecium polycaryum strain. The bacterium is phylogenetically related with symbionts of other ciliates and diplonemids, forming a putatively fast‐evolving clade within the family Holosporaceae . Similarly to many close relatives, it presents a very small genome (<600 kbp), and, accordingly, a limited predicted metabolism, implying a heavy dependence on Paramecium , thanks also to some specialized membrane transporters. Characterized features, including the presence of specific secretion systems, are overall suggestive of a mild parasitic effect on the host. From an evolutionary perspective, a potential ancestral trend towards pronounced genome reduction and possibly linked to parasitism could be inferred, at least among fast‐evolving Holosporaceae , with some lineage‐specific traits. Interestingly, similar convergent features could be observed in other host‐associated lineages, in particular Rickettsiales among Alphaproteobacteria .

AbstractThe Asian citrus psyllid, Diaphorina citri is an invasive insect 1 and a vector of ’Candidatus Liberibacter asiaticus’ (CLas), a bacterium whose growth in Citrus species results in citrus greening disease 2,3. Methods to enrich and sequence CLas from D. citri often rely on biased genome amplification 4 and nevertheless contain significant quantities of host DNA 5,6. To overcome these hurdles, we developed a simple pre-treatment DNase and filtration (hereafter PDF) protocol to directly sequence CLas and the complete, primarily uncultivable, microbiome from D. citri adults. The PDF protocol yielded CLas abundances upwards of 60% and enabled detection of 156 genetic variants in these strains compared to progenitor strains in Florida, which included prophage encoding regions with key functions in CLas pathogenesis, putative antibiotic resistance loci, and a single secreted effector. These variants suggest laboratory propagation of CLas may result in different phenotypic trajectories among laboratories, and may confound CLas physiology or therapeutic design and evaluation if these differences remain undocumented. Finally, we obtained genetic signatures affiliated with Citrus nuclear and organellar genomes, entomopathogenic fungal mitochondria, and commensal bacteria from laboratory-reared and field-collected D. citri adults. Hence, the PDF protocol can inform agricultural management strategies related to pathogen evolution 7, insect microbiome surveillance 8, antibiotic resistance screening 9, and gut content analysis 10.

A putative novel methanotrophic genus, Candidatus Methylumidiphilus (Methylococcales), was recently shown to be ubiquitous and one of the most abundant methanotrophic genera in water columns of oxygen-stratified lakes and ponds in boreal and subarctic areas. However, it has probably escaped detection in many previous studies that used 16S rRNA gene amplicon sequencing due to insufficient database coverage, as previously analysed metagenome-assembled genomes (MAGs) affiliated with Ca. Methylumidiphilus do not contain 16S rRNA genes. Therefore, we screened MAGs affiliated with the genus for their 16S rRNA gene sequences in a recently published lake and pond MAG data set. Among 66 MAGs classified as Ca. Methylumidiphilus (with completeness over 40% and contamination less than 5%) originating from lakes in Finland, Sweden and Switzerland as well as from ponds in Canada, we found 5 MAGs, each containing one 1532 bp sequence spanning the V1-V9 regions of the 16S rRNA gene. After removal of sequence redundancy, this resulted in 2 unique 16S rRNA gene sequences. These sequences represented 2 different putative species: Ca. Methylumidiphilus alinenensis (GenBank accession OK236221) and another unnamed species of Ca. Methylumidiphilus (GenBank accession OK236220). We suggest that including these 2 sequences in reference databases will enhance 16S rRNA gene-based detection of members of this genus from environmental samples.