Publications

4642

Health, growth, fruit production, and fruit quality of citrus crops are severely affected by tree infection with Candidatus Liberibacter asiaticus (CLas) and subsequent development of the disease huanglongbing (HLB). The use of HLB-tolerant rootstocks is one strategy that is used to ameliorate the effects of HLB in commercial production. Although there is a clear long-term rootstock effect to improve tree performance, such field trials take many years for establishment and evaluation, and this long time-period is very limiting to expeditious evaluation of new rootstocks. In this study, we have conducted a 50-week greenhouse experiment to evaluate rootstock influences on Valencia sweet orange tree response to CLas infection. The infection of trees with CLas reduced scion and rootstock growth, increased leaf yellowing, and reduced the number of leaves per tree and leaf area, regardless of rootstock. There were clear rootstock influences on some traits during the 50-week study. In general, infected trees on US-942 rootstock had lower CLas root titers, less reduction of the number of leaves, less reduction of leaf area, and less leaf yellowing, as compared with some of the other rootstocks. The 50-week greenhouse evaluation method provided results that corresponded well with results from long-term field testing, indicating this may be a useful tool to accelerate evaluation and selection of new rootstocks, as well as in testing other HLB management strategies.

Abstract Objectives In order to characterize a river-associated, enriched microbiome capable of degrading an anthraquinone dye from the oil blue family, as well as assessing its functional potential, we performed a taxa-specific metagenomic deconvolution analysis based on contact probability maps at the chromosomal level. This study will allow associating the genomic content of “Candidatus Afipia apatlaquensis” strain IBT-C3 with its phenotypic potential in the context of bioremediation of textile dyes. We anticipate that this resource will be very useful in comparative genomic clinical studies, contributing to understanding the genomic basis of Afipia pathogenicity. Data description Here, we report the first draft genome sequence of “Candidatus Afipia apatlaquensis” sp. nov., strain IBT-C3, obtained by deconvolution of a textile-dye degrader microbiome in Mexico. The genome composite was deconvoluted using a Hi-C proximity ligation method. Whole-genome-based comparisons and phylogenomics reconstruction indicate that strain IBT-C3 represents a new species of the genus Afipia. The assembly completeness was 92.5% with 5,604,749 bp in length and 60.72% G+C content. The genome complement of IBT-C3 suggests a functional potential for decolorization of textile dyes, contrasting with previous reports of Afipia genus focused on its pathogenic potential.

Abstract Background Anaerobic ammonium oxidizing bacteria (anammox bacteria) are contributing significantly to the nitrogen cycle and are successfully used in wastewater treatment. Due to the lack of complete genomes in the databases, little is known about the stability and variability of their genomes and how the genomes evolve in response to changing environments. Results Here we report the complete genome of the anammox bacterium “Candidatus Kuenenia stuttgartiensis” strain CSTR1 which was enriched planktonically in a semi-continuous stirred-tank reactor. A comparison of the genome of strain CSTR1 with the genome of “Ca. Kuenenia stuttgartiensis” MBR1 and the draft genome of KUST showed > 99% average nucleotide identity among all. Rearrangements of large genomic regions were observed, most of which were associated with transposase genes. Phylogenetic analysis suggests that strain MBR1 is more distantly related to the other two strains. Proteomic analysis of actively growing cells of strain CSTR1 (growth rate ~ 0.33 d− 1) failed to detect the annotated cytochrome cd1-type nitrite reductase (NirS) although in total 1189 proteins were found in the proteome. Yet, this NirS was expressed when strain CSTR1 was under stress or starvation (growth rate < 0.06 d− 1). We also observed large sequence shifts in the strongly expressed S-layer protein compared to other “Ca. Kuenenia” strains, indicating the formation of hybrids of genes encoding the surface proteins. Conclusions “Ca. Kuenenia” strains appear to be relatively stable in their basic physiological traits, but show high variability in overall genome structure and surface proteins.

Sec-delivered effector 1 (SDE1) from the huanglongbing (HLB)-associated bacterium ‘Candidatus Liberibacter asiaticus’ was previously characterized as an inhibitor of defense-related, papain-like cysteine proteases in vitro and in planta. Here, we investigated the contributions of SDE1 to HLB progression. We found that SDE1 expression in the model plant Arabidopsis thaliana caused severe yellowing in mature leaves, reminiscent of both ‘Ca. L. asiaticus’ infection symptoms and accelerated leaf senescence. Induction of senescence signatures was also observed in the SDE1-expressing A. thaliana lines. These signatures were apparent in older leaves but not in seedlings, suggesting an age-associated effect. Furthermore, independent lines of transgenic Citrus paradisi (L.) Macfadyen (Duncan grapefruit) that express SDE1 exhibited hypersusceptibility to ‘Ca. L. asiaticus’. Similar to A. thaliana, transgenic citrus expressing SDE1 showed altered expression of senescence-associated genes, but only after infection with ‘Ca. L. asiaticus’. These findings suggest that SDE1 is a virulence factor that contributes to HLB progression, likely by inducing premature or accelerated senescence in citrus. This work provides new insight into HLB pathogenesis. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Specific scopeThis Standard describes a national regulatory control system for the bacterial pathogen ‘Candidatus Liberibacter solanacearum’ and its vector Bactericera cockerelli when regulated as quarantine pests. It also covers measures to reduce the risk of ‘Ca. L. solanacearum’ spreading to potato production systems when listed as a regulated nonquarantine pest (RNQP) on seed potatoFor the EPPO A1 listed pests recommended for regulation as quarantine pests B. cockerelli and ‘Ca. L. solanacearum’ (Solanaceae haplotypes, i.e. non‐European haplotypes, such as haplotypes A and B), the Standard describes measures to achieve: Exclusion from the EPPO region of B. cockerelli, which is an efficient vector of ‘Ca. L. solanacearum’ within solanaceous crops (e.g. potato, tomato) Eradication of incursions of B. cockerelli Exclusion from the EPPO region of non‐European haplotypes of ‘Ca. L. solanacearum’ Eradication of incursions of non‐European haplotypes of ‘Ca. L. solanacearum’. Although reference will only be made to the non‐European haplotypes A and B, the Standard would also apply to new non‐European haplotypes of ‘Ca. L. solanacearum’ which may have different host ranges or which may be vectored more efficiently by psyllids which are widespread in the region.For the haplotypes which are not recommended for regulation as quarantine pests but are recommended for regulation as RNQPs on seed potato (i.e. European haplotypes, such as C, D and E), the Standard describes measures (specified in Appendix 4) to reduce the risk of spread to potato production systems to achieve: Exclusion of European haplotypes of ‘Ca. L. solanacearum’ from the potato production system Suppression of European haplotypes of ‘Ca. L. solanacearum’ in potato production systems where they are present. Although reference will only be made to haplotypes C, D and E, Appendix 4 would also apply to new European haplotypes of ‘Ca. L. solanacearum’.SpecificapprovalFirst approved in 2017‐09. Revised in 2020‐09.

Phytoplasmas have been associated with a disease that affects trees of at least 11 species from different botanic families in Bogotá, Colombia. ‘Candidatus Phytoplasma asteris’ and ‘Candidatus Phytoplasma fraxini’ are the major groups of phytoplasma in the area of Bogotá. In this study, the genetic diversity within ‘Ca. P. asteris’ and ‘Ca. P. fraxini’ was studied in five urban tree species: Croton species (Euphorbiaceae), Fraxinus uhdei (Oleaceae), Magnolia grandiflora (Magnoliaceae), Populus nigra (Salicaceae) and Quercus humboldtii (Fagaceae). Analyses of the 16S rRNA gene using nested PCR, RFLP and sequencing showed that phytoplasmas of ‘Ca. P. asteris’ could be assigned to: subgroup 16SrI-B; a new subgroup named 16SrI-AF, with a restriction pattern similar to that of 16SrI-B; and a new subgroup named 16SrI-AG, with a restriction pattern similar to that of 16SrI-K and 16SrI-AH with a restriction pattern similar to that of 16SrI-AC. ‘Ca. P. fraxini’ isolates belonged to a new subgroup named 16SrVII-G, with a restriction pattern similar to that of 16SrVII-A. To complement the identification of the phytoplasma strains, we amplified nonribosomal genes such as leuS and secA. Unexpectedly, it was observed that in 16 trees in which 16S rRNA gene analysis showed the presence of ‘Ca. P. fraxini’ only, the leuS or secA primers amplified sequences exclusively affiliated to ‘Ca. P. asteris. In those plants, sequences belonging to ‘Ca. P. fraxini’ leuS or secA genes were not amplified. The present work contributes to the identification of novel strains of both species in Colombia, and supports previous suggestions that phytoplasmas in South America are highly variable.

Summary Holobiont phenotype results from a combination of host and symbiont genotypes as well as from prevailing environmental conditions that alter the relationships among symbiotic members. Corals exemplify this concept, where shifts in the algal symbiont community can lead to some corals becoming more or less thermally tolerant. Despite linkage between coral bleaching and disease, the roles of symbiotic bacteria in holobiont resistance and susceptibility to disease remains less well understood. This study thus characterizes the microbiome of disease‐resistant and ‐susceptible Acropora cervicornis coral genotypes (hereafter referred to simply as ‘genotypes’) before and after high temperature‐mediated bleaching. We found that the intracellular bacterial parasite ‘ Ca. Aquarickettsia rohweri’ was strikingly abundant in disease‐susceptible genotypes. Disease‐resistant genotypes, however, had notably more diverse and even communities, with correspondingly low abundances of ‘ Ca. Aquarickettsia’ . Bleaching caused a dramatic reduction of ‘ Ca. Aquarickettsia’ within disease‐susceptible corals and led to an increase in bacterial community dispersion, as well as the proliferation of opportunists. Our data support the hypothesis that ‘ Ca. Aquarickettsia’ species increase coral disease risk through two mechanisms: (i) the creation of host nutritional deficiencies leading to a compromised host‐symbiont state and (ii) the opening of niche space for potential pathogens during thermal stress.