Publications

4861

AbstractHuanglongbing (HLB; yellow shoot disease) is a severe worldwide infectious disease for citrus family plants. The pathogenCandidatus Liberibacter asiaticus(CLas) is an alphapro-teobacterium of theRhizobiaceaefamily that has been identified as the cause. The virulence of CLas has been attributed, in part, to prophage encoded genes. Prophage and prophage like elements have been identified in 12 of the 15 CLas available genomes, and are classified into three prophage types. Here, we re-examined all 15 CLas genomes using ade novoprediction approach and expanded the number of prophage like elements from 16 to 33. Further, we find that all CLas contain at least one prophage-like sequence. Comparative analysis reveals a prevalent, albeit previously unknown, prophage-like sequence type that is a remnant of an integrated prophage. Notably, this remnant prophage is found in the Ishi-1 CLas strain that had previously been reported as lacking prophages. Our findings provide both a resource and new insights into the evolutionary relationship between phage and CLas pathogenicity.

The systematics of single‐celled cyanobacteria represents a major challenge due to morphological convergence and application of various taxonomic concepts. The genus Cyanothece is one of the most problematic cases, as the name has been applied to oval‐shaped coccoid cyanobacteria lacking sheaths with little regard to their phylogenetic position and details of morphology and ultrastructure. Hereby we analyze an extensive set of complementary genetic and phenotypic evidence to disentangle the relationships among these cyanobacteria. We provide diagnostic characters to separate the known genera Cyanothece, Gloeothece, and Aphanothece, and provide a valid description for Crocosphaera gen. nov. We describe two new genera, Rippkaea and Zehria, to characterize two distinct phylogenetic lineages outside the previously known genera. We further describe 13 new species in total including Cyanothece svehlovae, Gloeothece aequatorialis, G. aurea, G. bryophila, G. citriformis, G. reniformis, Gloeothece tonkinensis, G. verrucosa, Crocosphaera watsonii, C. subtropica, C. chwakensis, Rippkaea orientalis, and Zehria floridana to recognize the intrageneric diversity as rendered by polyphasic analysis. We discuss the close relationship of free‐living cyanobacteria from the Crocosphaera lineage to nitrogen‐fixing endosymbionts of marine algae. The current study includes several experimental strains (Crocosphaera and “Cyanothece”) important for the study of diazotrophy and the global oceanic nitrogen cycle, and provides evidence suggesting ancestral N2‐fixing capability in the chroococcalean lineage.

Western X (WX) disease, caused by ‘Candidatus Phytoplasma pruni’, is a devastating disease of sweet cherry resulting in the production of small, bitter-flavored fruits that are unmarketable. Escalation of WX disease in Washington State prompted the development of a rapid detection assay based on recombinase polymerase amplification (RPA) to facilitate timely removal and replacement of diseased trees. Here, we report on a reliable RPA assay targeting putative immunodominant protein coding regions that showed comparable sensitivity to polymerase chain reaction (PCR) in detecting ‘Ca. Phytoplasma pruni’ from crude sap of sweet cherry tissues. Apart from the predominant strain of ‘Ca. Phytoplasma pruni’, the RPA assay also detected a novel strain of phytoplasma from several WX-affected trees. Multilocus sequence analyses using the immunodominant protein A (idpA), imp, rpoE, secY, and 16S ribosomal RNA regions from several ‘Ca. Phytoplasma pruni’ isolates from WX-affected trees showed that this novel phytoplasma strain represents a new subgroup within the 16SrIII group. Examination of high-throughput sequencing data from total RNA of WX-affected trees revealed that the imp coding region is highly expressed, and as supported by quantitative reverse transcription PCR data, it showed higher RNA transcript levels than the previously proposed idpA coding region of ‘Ca. Phytoplasma pruni’.

Phytoplasmas are cell-wall-less bacteria that cause diseases in approximately 1,000 plant species. ‘Candidatus Phytoplasma pyri’, the causal agent of pear decline, induces various symptoms on its hosts, leading to weakening and dieback of the plants, reduced fruit size and yield, and, consequently, considerable financial losses in all pear-growing areas. Fighting this disease requires a reliable and inexpensive method for pathogen detection in propagation material as well as plant stocks in orchards and breeding facilities. Here, we present a field-suitable detection protocol for ‘Ca. P. pyri’ based on loop-mediated isothermal amplification (LAMP) targeting the phytoplasmal 16S ribosomal DNA sequence. The combination of a simplified sample preparation method based on sodium hydroxide and colorimetric visualization of LAMP results enables a laboratory-independent pathogen detection. The detection limit is comparable with analysis by polymerase chain reaction; however, the pear decline LAMP detection method is superior in terms of ease of use, cost, and time effectiveness for obtaining results.

There is accumulating evidence that root system collapse is a primary symptom associated with Huanglongbing (HLB)-induced tree decline, especially for commercial sweet orange and grapefruit trees on Swingle and Carrizo rootstocks. Maintaining root health is imperative to keep trees productive in an HLB-endemic environment. Preliminary greenhouse and field studies have shown that HLB-impacted trees had secondary and micronutrient deficiencies that were much greater in the roots than in the leaves, and that treatments containing three-times the recommended dose of manganese (Mn) improved tree health and growth and increased feeder root density in greenhouse trees. These results suggested that trees in an HLB-endemic environment have higher specific micronutrient requirements than those currently recommended. To test this hypothesis, established Vernia sweet orange grafted onto rough lemon rootstock trees were divided into eight supplemental CRF nutrition treatments (including two-times and four-times the recommended doses of Mn and boron) using a randomized complete block design in a commercial grove in St. Cloud, FL. The following supplemental nutrition treatments were used: no extra nutrition (control); Harrell’s–St. Helena mix 0.9 kg per tree; Harrell’s with 32 g of Florikan polycoated sodium borate (PSB) per tree; Harrell’s with 90 g of TigerSul® Mn sulfate (MS) per tree; Harrell’s with 32 g of PSB and 90 g of MS per tree; 180 g of MS per tree; 64 g of PSB per tree; and 180 g of MS plus 64 g of PSB per tree applied every 6 months since Fall 2015. Leaf and soil nutritional analyses were performed in Mar. 2017, Sept. 2017, and May 2018; a quantitative polymerase chain reaction was performed for Candidatus Liberibacter asiaticus (CLas) titer estimation in Nov. 2017. Significantly higher cycle threshold (Ct) values indicating reduced CLas bacterial populations were observed in trees that received the higher doses of Mn, especially those receiving four-times the recommended dosage of Mn (180 g Mn). Many trees exhibited Ct values of 32 or more, indicating a nonactive infection. Fruit yields of these trees were also increased. No significant differences in juice characteristics, canopy volume, and trunk section area were found between control plants and plants treated with 180 g Mn. Soil and leaf nutrients B, K, Mn, and Zn were significantly different among treatments at various times during the study. Our results strongly suggest that overdoses of Mn can suppress CLas bacterial titers in sweet orange trees on rough lemon rootstock, thus providing a therapeutic effect that can help restore tree health and fruit yields. This response was not observed when Mn and B were combined in the overdose, suggesting an antagonistic effect from B on Mn metabolism. When an overdose of Mn is used, biological functions and tree tolerance lost due to nutritional imbalances caused by HLB might be restored. Further studies are needed to elucidate which metabolic pathways are altered by comparing overdosed and conventionally fertilized HLB-impacted trees and to determine if the observed therapeutic effects can be achieved in trees grafted to other important commercial rootstocks.