Screening potential insect vectors in a museum biorepository reveals undiscovered diversity of plant pathogens in natural areas

Molecular Identification and Characterization of Novel Taxonomic Subgroups and New Host Plants in 16SrI and 16SrII Group Phytoplasmas and Their Evolutionary Diversity on Hainan Island, China

Phytoplasmas are a group of plant prokaryotic pathogens distributed worldwide. To comprehensively reveal the diversity of the pathogens and the diseases they cause on Hainan, a tropical island with abundant biodiversity in China, a survey of phytoplasmal diseases was performed from 2009 to 2022. Herein, molecular identification and genetic analysis were conducted based on the conserved genes of phytoplasmas. The results indicated that phytoplasmas could be detected in 138 samples from 18 host plants among 215 samples suspected to be infected by the pathogens. The phytoplasma strains from 27 diseased samples of 4 host plants belonged to the 16SrI group and the strains from 111 samples of 14 hosts belonged to the 16SrII group. Among them, 12 plants, including important tropical cash crops such as Phoenix dactylifera, cassava, sugarcane, and Piper nigrum, were first identified as hosts of phytoplasmas on Hainan Island. Based on BLAST and iPhyClassifier analyses, seven novel 16Sr subgroups were proposed to describe the relevant phytoplasma strains, comprising the 16SrI-AP, 16SrI-AQ, and 16SrI-AR subgroups within the 16SrI group and the 16SrII-Y, 16SrII-Z, 16SrII-AB, and 16SrII-AC subgroups within the 16SrII group. Genetic variation and phylogenetic analysis indicated that the phytoplasma strains identified in this study and those reported previously on Hainan Island mainly belong to four 16Sr groups (including I, II, V, and XXXII) and could infect 44 host plants, among which the 16SrI and 16SrII groups were the prevalent 16Sr groups associated with 43 host plant species. The diversity of host plants infected by the phytoplasmas made it difficult to monitor and control their related diseases. Therefore, strengthening inspection and quarantine during the introduction and transit of the related phytoplasmal host crops would effectively curb the spread and prevalence of the phytoplasmas and their related lethal diseases.

Pathogen prospecting of museums: Reconstructing malaria epidemiology

Malaria is a disease of global significance. Ongoing changes to the earth's climate, antimalarial resistance, insecticide resistance, and socioeconomic decline test the resilience of malaria prevention programs. Museum insect specimens present an untapped resource for studying vector-borne pathogens, spurring the question: Do historical mosquito collections contain Plasmodium DNA, and, if so, can museum specimens be used to reconstruct the historical epidemiology of malaria? In this Perspective, we explore molecular techniques practical to pathogen prospecting, which, more broadly, we define as the science of screening entomological museum specimens for human, animal, or plant pathogens. Historical DNA and pathogen prospecting provide a means of describing the coevolution of human, vector, and parasite, informing the development of insecticides, diagnostics, therapeutics, and vaccines.

Phylogenetic Analysis of Two New Mitochondrial Genomes of Singapora shinshana and Seriana bacilla from the Karst Region of Southwest China

Leafhoppers have been identified as a serious threat to different plants. To explore the characteristics of mitogenomes and reveal the phylogenetic positions of two species in the Typhlocybinae, complete mitogenomes of Singapora shinshana and Seriana bacilla were sequenced and annotated for the first time with lengths of 15,402 bp and 15,383 bp, respectively. The two mitogenomes contained 13 PCGs, 22 tRNA genes and 2 rRNA genes. The genome content, gene order, nucleotide composition, codon usage and amino acid composition are similar to those of other typical mitogenomes of Typhlocybinae. All 13 PCGs started with ATN codons, except for atp8 (TTA) and nad5 (TTG). All tRNAs were folded into a typical cloverleaf secondary structure, except for tRNA-Ser1 and tRNA-Val. Moreover, phylogenetic trees were constructed and analyzed based on all the PCGs from 42 mitogenomes using maximum likelihood (ML) and Bayesian inference (BI) methods. The results supported that eleven subfamilies are all monophyletic groups, S. shinshana and S. bacilla are members of Erythroneurini, but S. shinshana and the genus Empoascanara have a very close relationship with ((((Empoascanara sipra+ Empoascanara wengangensis) + Empoascanara dwalata) + Empoascanara gracilis) + S. shinshana), and S. bacilla is closely related to the genus Mitjaevia ((Mitjaevia dworakowskae + Mitjaevia shibingensis) + S. bacilla). These results provide valuable information for future study of evolutionary relationships in Typhlocybinae.

Phylogenetic Triage and Risk Assessment: How to Predict Emerging Phytoplasma Diseases

Phytoplasma diseases pose a substantial threat to diverse crops of agricultural importance. Management measures are usually implemented only after the disease has already occurred. Early detection of such phytopathogens, prior to disease outbreak, has rarely been attempted, but would be highly beneficial for phytosanitary risk assessment, disease prevention and mitigation. In this study, we present the implementation of a recently proposed proactive disease management protocol (DAMA: Document, Assess, Monitor, Act) for a group of vector-borne phytopathogens. We used insect samples collected during a recent biomonitoring program in southern Germany to screen for the presence of phytoplasmas. Insects were collected with malaise traps in different agricultural settings. DNA was extracted from these mass trap samples and subjected to PCR-based phytoplasma detection and mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding. Phytoplasma DNA was detected in two out of the 152 insect samples analyzed. Phytoplasma identification was performed using iPhyClassifier based on 16S rRNA gene sequence and the detected phytoplasmas were assigned to 'Candidatus Phytoplasma asteris'-related strains. Insect species in the sample were identified by DNA metabarcoding. By using established databases, checklists, and archives, we documented historical associations and records of phytoplasmas and its hosts in the study region. For the assessment in the DAMA protocol, phylogenetic triage was performed in order to determine the risk for tri-trophic interactions (plant-insect-phytoplasma) and associated disease outbreaks in the study region. A phylogenetic heat map constitutes the basis for risk assessment and was used here to identify a minimum number of seven leafhopper species suggested to be monitored by stakeholders in this region. A proactive stance in monitoring changing patterns of association between hosts and pathogens can be a cornerstone in capabilities to prevent future phytoplasma disease outbreaks. To the best of our knowledge, this is the first time that the DAMA protocol has been applied in the field of phytopathology and vector-borne plant diseases.

Characterizing the Vector Data Ecosystem

A growing body of information on vector-borne diseases has arisen as increasing research focus has been directed towards the need for anticipating risk, optimizing surveillance, and understanding the fundamental biology of vector-borne diseases to direct control and mitigation efforts. The scope and scale of this information, in the form of data, comprising database efforts, data storage, and serving approaches, means that it is distributed across many formats and data types. Data ranges from collections records to molecular characterization, geospatial data to interactions of vectors and traits, infection experiments to field trials. New initiatives arise, often spanning the effort traditionally siloed in specific research disciplines, and other efforts wane, perhaps in response to funding declines, different research directions, or lack of sustained interest. Thusly, the world of vector data - the Vector Data Ecosystem - can become unclear in scope, and the flows of data through these various efforts can become stymied by obsolescence, or simply by gaps in access and interoperability. As increasing attention is paid to creating FAIR (Findable Accessible Interoperable, and Reusable) data, simply characterizing what is 'out there', and how these existing data aggregation and collection efforts interact, or interoperate with each other, is a useful exercise. This study presents a snapshot of current vector data efforts, reporting on level of accessibility, and commenting on interoperability using an illustration to track a specimen through the data ecosystem to understand where it occurs for the database efforts anticipated to describe it (or parts of its extended specimen data).

Guilt by Association: DNA Barcoding-Based Identification of Potential Plant Hosts of Phytoplasmas from Their Insect Carriers

Phytoplasmas are small phloem-restricted and insect-transmissible bacteria that infect many plant species, including important crops and ornamental plants, causing severe economic losses. Our previous studies screened phytoplasmas in hundreds of leafhoppers collected from natural habitats worldwide and identified multiple genetically different phytoplasmas in seven leafhopper species (potential insect vectors). As an initial step toward determining the impact of these phytoplasmas on the ecosystem, ribulose 1,5-biphosphate carboxylase large subunit (rbcL), a commonly used plant DNA barcoding marker, was employed to identify the plant species that the phytoplasma-harboring leafhoppers feed on. The DNA of 17 individual leafhoppers was PCR amplified using universal rbcL primers. PCR products were cloned, and five clones per amplicon were randomly chosen for Sanger sequencing. Moreover, Illumina high-throughput sequencing on selected PCR products was conducted and confirmed no missing targets in Sanger sequencing. The nucleotide BLAST results revealed 14 plant species, including six well-known plant hosts of phytoplasmas such as tomato, alfalfa, and maize. The remaining species have not been documented as phytoplasma hosts, expanding our knowledge of potential plant hosts. Notably, the DNA of tomato and maize (apparently cultivated in well-managed croplands) was detected in some phytoplasma-harboring leafhopper species sampled in non-crop lands, suggesting the spillover/spillback risk of phytoplasma strains between crop and non-crop areas. Furthermore, our results indicate that barcoding (or metabarcoding) is a valuable tool to study the three-way interactions among phytoplasmas, plant hosts, and vectors. The findings contribute to a better understanding of phytoplasma host range, host shift, and disease epidemiology.

Use of mammalian museum specimens to test hypotheses about the geographic expansion of Lyme disease in the southeastern United States

Lyme disease, caused primarily in North America by the bacterium Borrelia burgdorferi sensu stricto, is the most frequently reported vector-borne disease in North America and its geographic extent is increasing in all directions from foci in the northeastern and north central United States. Several southeastern states, including Virginia and North Carolina, have experienced large increases in Lyme disease incidence in the past two decades, with the biggest changes in incidence occurring in the western portion of each state. We tested the hypothesis that B. burgdorferi s.s. was present in western Virginia and North Carolina Peromyscus leucopus populations prior to the recent emergence of Lyme disease. Specifically, we examined archived P. leucopus museum specimens, sampled between 1900 and 2000, for B. burgdorferi s.s. DNA. After confirming viability of DNA extracted from ear punch biopsies from P. leucopus study skins collected between 1945 and 2000 in 19 Virginia counties and 17 North Carolina counties, we used qPCR of two species-specific loci to test for the presence of B. burgdorferi s.s. DNA. Ten mice, all collected from the Eastern Shore of Virginia in 1989, tested positive for presence of B. burgdorferi; all of the remaining 344 specimens were B. burgdorferi-negative. Our results suggest that B. burgdorferi s.s was not common in western Virginia or North Carolina prior to the emergence of Lyme disease cases in the past two decades. Rather, the emergence of Lyme disease in this region has likely been driven by the relatively recent expansion of B. burgdorferi s.s. in southward-moving ticks and reservoir hosts in the mountainous counties of these two states.

Comparison of Traditional and Next-Generation Approaches for Uncovering Phytoplasma Diversity, with Discovery of New Groups, Subgroups and Potential Vectors

Simple Summary

Phytoplasmas are bacteria transmitted by insects that cause severe diseases in many plants, including crops, worldwide. Most phytoplasma research focuses on the epidemiology of phytoplasma-associated diseases in agriculture, and relatively few efforts have been made to survey phytoplasma diversity in natural areas. We compared traditional methods for detecting and identifying phytoplasmas with a new method based on next-generation DNA sequencing and found that the next-generation method performs as well, or better, for identifying phytoplasmas in DNA extracted from plant-feeding insects. Using this method, we report several new country/region records and insect associations for known phytoplasmas, three new designated phytoplasma subgroups and three possible new groups.

Abstract

Despite several decades’ effort to detect and identify phytoplasmas (Mollicutes) using PCR and Sanger sequencing focusing on diseased plants, knowledge of phytoplasma biodiversity and vector associations remains highly incomplete. To improve protocols for documenting phytoplasma diversity and ecology, we used DNA extracted from phloem-feeding insects and compared traditional Sanger sequencing with a next-generation sequencing method, Anchored Hybrid Enrichment (AHE) for detecting and characterizing phytoplasmas. Among 22 of 180 leafhopper samples that initially tested positive for phytoplasmas using qPCR, AHE yielded phytoplasma 16Sr sequences for 20 (19 complete and 1 partial sequence) while Sanger sequencing yielded sequences for 16 (11 complete and 5 partial). AHE yielded phytoplasma sequences for an additional 7 samples (3 complete and 4 partial) that did not meet the qPCR threshold for phytoplasma positivity or yielded non-phytoplasma sequences using Sanger sequencing. This suggests that AHE is more efficient for obtaining phytoplasma sequences. Twenty-three samples with sufficient data were classified into eight 16Sr subgroups (16SrI-B, I-F, I-AO, III-U, V-C, IX-J, XI-C, XXXVII-A), three new subgroups (designated as 16SrVI-L, XV-D, XI-G) and three possible new groups. Our results suggest that screening phloem-feeding insects using qPCR and AHE sequencing may be the most efficient method for discovering new phytoplasmas.

Metatranscriptomic Assessment of the Microbial Community Associated With the Flavescence dorée Phytoplasma Insect Vector Scaphoideus titanus

Phytoplasmas are insect-borne pathogenic bacteria that cause major economic losses to several crops worldwide. The dynamic microbial community associated with insect vectors influences several aspects of their biology, including their vector competence for pathogens. Unraveling the diversity of the microbiome of phytoplasma insect vectors is gaining increasing importance in the quest to develop novel microbe-based pest control strategies that can minimize the use of insecticides for better environmental quality. The leafhopper Scaphoideus titanus is the primary vector of the Flavescence dorée phytoplasma, a quarantine pest which is dramatically affecting the main grape-growing European countries. In this study, the RNA-Seq data, which were previously used for insect virus discovery, were further explored to assess the composition of the whole microbial community associated with insects caught in the wild in both its native (the United States) and invasive (Europe) areas. The first de novo assembly of the insect transcriptome was used to filter the host sequencing reads. The remaining ones were assembled into contigs and analyzed by blastx to provide the taxonomic identification of the microorganisms associated with S. titanus, including the non-bacterial components. By comparing the transcriptomic libraries, we could differentiate the stable and consistent associations from the more ephemeral and flexible ones. Two species appeared to be universal to the core microbiome of S. titanus: the obligate bacterial symbiont Candidatus Sulcia muelleri and an Ophiocordyceps-allied fungus distantly related to yeast-like symbionts described from other hemipterans. Bacteria of the genus Cardinium have been identified as another dominant member of the microbiome, but only in the European specimens. Although we are yet to witness how the interplay among the microorganisms influences the vector competence of S. titanus, this unbiased in silico characterization of its microbiome is paramount for identifying the naturally occurring targets for new biocontrol strategies to counteract Flavescence dorée spread in Europe.

Food security and emerging infectious disease: risk assessment and risk management

Climate change, emerging infectious diseases (EIDs) and food security create a dangerous nexus. Habitat interfaces, assumed to be efficient buffers, are being disrupted by human activities which in turn accelerate the movement of pathogens. EIDs threaten directly and indirectly availability and access to nutritious food, affecting global security and human health. In the next 70 years, food-secure and food-insecure countries will face EIDs driving increasingly unsustainable costs of production, predicted to exceed national and global gross domestic products. Our modern challenge is to transform this business as usual and embrace an alternative vision of the biosphere formalized in the Stockholm paradigm (SP). First, a pathogen-centric focus shifts our vision of risk space, determining how pathogens circulate in realized and potential fitness space. Risk space and pathogen exchange are always heightened at habitat interfaces. Second, apply the document-assess-monitor-act (DAMA) protocol developing strategic data for EID risk, to be translated, synthesized and broadcast as actionable information. Risk management is realized through targeted interventions focused around information exchanged among a community of scientists, policy practitioners of food and public health security and local populations. Ultimately, SP and DAMA protect human rights, supporting food security, access to nutritious food, health interventions and environmental integrity.