Plant DNA detection from grasshopper guts: A step-by-step protocol, from tissue preparation to obtaining plant DNA sequences

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.

Diverse Host Plants of the First Instars of the Invasive Lycorma delicatula: Insights from eDNA Metabarcoding

Identification of host plants of the invasive spotted lanternfly, Lycorma delicatula (Hemiptera: Fulgoridae), has been the focus of many studies. While the adults and late nymphs are relatively easy to observe on plants and to use for molecular gut-content analysis, studying the early instars is more challenging. This study is the continuation of our ongoing efforts to determine the host range for each developmental stage of L. delicatula. In the present study, we focused exclusively on the first nymphal instars, and we used a novel approach, utilizing "bulk" DNA extracts for DNA metabarcoding of nymphal gut contents, to identify all the detectable plants that the nymphs had ingested prior to being collected. We were able to obtain high-quality amplicons (up to 406 bp) of a portion of the rbcL gene and detect 27 unique ingested plant species belonging to 17 families. Both native and introduced plants with the prevalence of trees and grasses were present among the ingested plants. We also identified 13 novel host plants that have not been previously reported for L. delicatula on the U.S. territory. The results from our study have important applications for developing effective programs on early monitoring of invasive L. delicatula.

Response of Five Miscanthus sinensis Cultivars to Grasshopper Herbivory: Implications for Monitoring of Invasive Grasses in Protected Areas

Introduced grasses can aggressively expand their range and invade native habitats, including protected areas. Miscanthus sinensis is an introduced ornamental grass with 100+ cultivars of various invasive potential. Previous studies have demonstrated that the invasive potential of M. sinensis cultivars may be linked to seed viability, and some of the physiological traits, such as growth rate. Little is known, however, about whether these traits are associated with response of M. sinensis to insect herbivory, and whether plant tolerance and resistance to herbivory vary among its cultivars; which, in turn, can contribute to the invasive potential of some of M. sinensis cultivars. To address this issue, in our study we explored the response of five cultivars of M. sinensis to herbivory by Melanoplus grasshoppers. We demonstrated that plant responses varied among the cultivars during a season; all the cultivars, but “Zebrinus”, demonstrated a significant increase in plant tolerance by the end of the growing season regardless of the amount of sustained leaf damage. Different patterns in plant responses from “solid green” and “striped/spotted” varieties were recorded, with the lowest plant resistance detected for “Autumn Anthem” in the cage experiment. Our results have important applications for monitoring low-risk invaders in protected areas, as well as for biotic resistance of native communities to invasive grasses.

Two new invasive Ips bark beetles (Coleoptera: Curculionidae) in mainland China and their potential distribution in Asia

BACKGROUND

Ips is a bark beetle genus of 45 species, many of which are pests of conifer forests and plantations under stress. Twelve Ips species are recorded from China and presumably native there. From 2016 to 2018, specimens suspected to be Ips calligraphus and Ips grandicollis, were collected from traps with ethanol as a sole lure in Zhuhai, Guangdong, China. Both species originate in North America and infest various species of native or introduced pines. Since Ips species are known to cause or exacerbate problems in pine plantations, and a regional survey using traps baited with attractants were implemented in this study to investigate the extent of the introduction.

RESULTS

Both I. calligraphus and I. grandicollis have been collected repeatedly from several traps with Ips attractants in Zhuhai, Guangdong, China since 2016. Potential distributions of these two species in Asia, inferred using MaxEnt, is extensive, given the high projected environmental suitability in North America, South America, Mediterranean Europe, Northern Africa, and Eastern Asia. The host plant of I. calligraphus from Zhuhai was identified as slash pine Pinus elliottii using DNA barcoding of gut contents from trapped individuals.

CONCLUSION

This is the first report of the establishment of two American pine bark beetles, I. calligraphus and I. grandicollis in continental Asia. The gut content of both species suggests that these pest feeds on a non-native host. Whether the two species present high-risk to Asian forests will become clear with more research on their interactions with native pines.

Choosing an Effective PCR-Based Approach for Diet Analysis of Insect Herbivores: A Systematic Review

Identification of ingested plant species using polymerase chain reaction (PCR)-based methods is an increasingly useful yet challenging approach to accurately determine the diet composition of insect herbivores and thus their trophic interactions. A typical process of detection of DNA of ingested plants involves the choice of a DNA extraction method, a genomic target region, and/or the best approach for an accurate plant species identification. The wide range of available techniques makes the choice of the most appropriate method for an accurately and timely identification of ingested plants from insect guts difficult. In our study, we reviewed the commonly used PCR-based approaches in studies published from 1977 to 2019, to provide researchers with the information on the tools which have been shown to be effective for obtaining and identifying ingested plants. Our results showed that among five insect orders used in the retrieved studies Coleoptera and Hemiptera were prevalent (33 and 28% of all the records, respectively). In 79% of the studies a DNA barcoding approach was employed. In a substantial number of studies Qiagen DNA extraction kits and CTAB protocol were used (43 and 23%, respectively). Of all records, 65% used a single locus as a targeted plant DNA fragment; trnL, rbcL, and ITS regions were the most frequently used loci. Sequencing was the dominant type of among DNA verification approaches (70% of all records). This review provides important information on the availability of successfully used PCR-based approaches to identify ingested plant DNA in insect guts, and suggests potential directions for future studies on plant-insect trophic interactions.

Detecting Ingested Host Plant DNA in Potato Leafhopper (Hemiptera: Cicadellidae): Potential Use of Molecular Markers for Gut Content Analysis

Detection of host plant DNA from sap-feeding insects can be challenging due to potential low concentration of ingested plant DNA. Although a few previous studies have demonstrated the possibility of detecting various fragments of plant DNA from some sap-feeders, there are no protocols available for potato leafhopper, Empoasca fabae (Harris) (Hemiptera: Cicadellidae), a significant agricultural pest. In this study we focused on optimizing a DNA-based method for host plant identification of E. fabae and investigating the longevity of the ingested plant DNA as one of the potential applications of the protocol. We largely utilized and modified our previously developed PCR-based method for detecting host plant DNA from grasshopper and the spotted lanternfly gut contents. We have demonstrated that the trnL (UAA) gene can be successfully utilized for detecting ingested host plant DNA from E. fabae and determining plant DNA longevity. The developed protocol is a relatively quick and low-cost method for detecting plant DNA from E. fabae. It has a number of important applications-from determining host plants and dispersal of E. fabae to developing effective pest management strategies.

Identification of Edible Short- and Long-Horned Grasshoppers and Their Host Plants in East Africa

There is a paucity of information on the edible grasshoppers and their host plants in East Africa. This study adopted morphological and molecular analysis to identify edible grasshoppers in Kenya and Uganda. The associated host plants were identified through molecular analysis of the gut contents of the grasshoppers. The cytochrome b and 16s gene primers were used for grasshopper DNA analysis; while matK gene primers were used for plant DNA analysis. All long-horned grasshoppers sampled were identified as Ruspolia differens (Serville) (Orthoptera: Tettigonidae); whereas short-horned grasshoppers were identified as Acanthacris ruficornis (Fabricius) (Orthoptera: Acrididae) and Cyrtacanthacris tatarica (L.) (Orthoptera: Acrididae). Host plants of A. ruficornis were Achyranthes aspera (L.), Centella virgata L.f. Drude, Digitaria gayana (Kunth), Galinsoga quadriradiata Ruiz and Pavon, and Triumfetta pilosa Roth; whereas those of C. tatarica were Alysicarpus rugosus (Willd.) DC and Teramnus uncinatus (L.) SW. Host plants of R. differens were Ageratum conyzoides (L.), Citrus depressa Hayata, Cynodon dactylon (L.), D. gayana, Eragrostis mexicana Hornem, Eucalyptus saligna SM., Indigofera arrecta Hochst. ex A. Rich., Persicaria nepalensis (L.), and Sorghum halepense (L.). Information on the host plants of edible grasshoppers can help in the development of their mass rearing protocols.

Use of Molecular Gut Content Analysis to Decipher the Range of Food Plants of the Invasive Spotted Lanternfly, Lycorma delicatula

Spotted lanternfly, Lycorma delicatula (Hemiptera: Fulgoridae), is an introduced highly invasive insect pest in the US that poses a significant risk to forestry and agriculture. Assessing and predicting plant usage of the lanternfly has been challenging, and little is known regarding the lanternfly nymph association with its host plants. In this study, we focused on: (a) providing a protocol for using molecular markers for food plant identification of L. delicatula; (b) determining whether the ingested plant DNA corresponds with DNA of the plants from which the lanternfly was collected; and, (c) investigating the spectrum of ingested plants. We utilized gut contents of third and fourth instar nymphs that were collected from multiple plants; we isolated ingested plant DNA and identified consumed plants. We demonstrated that (a) up to 534 bp of the rbcL gene from ingested plants can be detected in L. delicatula guts, (b) ingested plants in ~93% of the nymphs did not correspond with the plants from which the nymphs were collected, and (c) both introduced and native plants, as well as woody and non-woody plants, were ingested. This information will aid effective the monitoring and management of the lanternfly, as well as predict the lanternfly host plants with range expansion.

Applying and refining DNA analysis to determine the identity of plant material extracted from the digestive tracts of katydids

Background

Feeding habits are central to animal ecology, but it is often difficult to characterize the diet of organisms that are arboreal, nocturnal, rare, or highly mobile. Genetic analysis of gut contents is a promising approach for expanding our understanding of animal feeding habits. Here, we adapt a laboratory protocol for extracting and sequencing plant material from gut contents and apply it to Neotropical forest katydids (Orthoptera: Tettigoniidae) on Barro Colorado Island (BCI) in Panama.

Methods

Our approach uses three chloroplast primer sets that were previously developed to identify vegetation on BCI. We describe the utility and success rate of each primer set. We then test whether there is a significant difference in the amplification and sequencing success of gut contents based on the size or sex of the katydid, the time of day that it was caught, and the color of the extracted gut contents.

Results

We find that there is a significant difference in sequencing success as a function of gut color. When extracts were yellow, green, or colorless the likelihood of successfully amplifying DNA ranged from ~30–60%. When gut extracts were red, orange, or brown, amplification success was exceptionally low (0–8%). Amplification success was also higher for smaller katydids and tended to be more successful in katydids that were captured earlier in the night. Strength of the amplified product was indicative of the likelihood of sequencing success, with strong bands having a high likelihood of success. By anticipating which samples are most likely to succeed, we provide information useful for estimating the number of katydids that need to be collected and minimizing the costs of purifying, amplifying, and sequencing samples that are unlikely to succeed. This approach makes it possible to understand the herbivory patterns of these trophically important katydids and can be applied more broadly to understand the diet of other tropical herbivores.

Should I Eat or Should I Go? Acridid Grasshoppers and Their Novel Host Plants: Potential for Biotic Resistance

Novel, non-coevolved associations between introduced plants and native insect herbivores may lead to changes in trophic interactions in native communities, as well as to substantial economic problems. Although some studies in invasion ecology demonstrated that native herbivores can preferentially feed on introduced plants and therefore contribute to the biotic resistance of native communities to plant invasions, the role of acridid grasshoppers as native generalist insect herbivores is largely overlooked. This systematic review aimed to identify patterns of grasshopper feeding preferences for native versus introduced plants and, consequently, a potential of grasshoppers to provide biotic resistance of native communities. The analysis of 63 records of feeding preference trials for 28 North-American grasshopper species (retrieved from 2146 studies published during 1967⁻2017) has demonstrated a preference of grasshoppers for introduced host plants, and identified 12 preferred introduced plants with high or middle invasive ranks. A significant effect of the life stage (p < 0.001), but not the experimental environment, plant material, and measurements, on grasshopper preferences for introduced plants was also detected. Overall, results suggest a potential of acridid grasshoppers to contribute to the biotic resistance of native communities. The review also provides methodological recommendations for future experimental studies on grasshopper-host plant interactions.

Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada

Their relatively slow rates of molecular evolution, as well as frequent exposure to hybridization and introgression, often make it difficult to discriminate species of vascular plants with the standard barcode markers (rbcL, matK, ITS2). Previous studies have examined these constraints in narrow geographic or taxonomic contexts, but the present investigation expands analysis to consider the performance of these gene regions in discriminating the species in local floras at sites across Canada. To test identification success, we employed a DNA barcode reference library with sequence records for 96% of the 5108 vascular plant species known from Canada, but coverage varied from 94% for rbcL to 60% for ITS2 and 39% for matK. Using plant lists from 27 national parks and one scientific reserve, we tested the efficacy of DNA barcodes in identifying the plants in simulated species assemblages from six biogeographic regions of Canada using BLAST and mothur. Mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) were strong predictors of barcode performance for different plant families and genera, and both metrics supported ITS2 as possessing the highest genetic diversity. All three genes performed strongly in assigning the taxa present in local floras to the correct genus with values ranging from 91% for rbcL to 97% for ITS2 and 98% for matK. However, matK delivered the highest species discrimination (~81%) followed by ITS2 (~72%) and rbcL (~44%). Despite the low number of plant taxa in the Canadian Arctic, DNA barcodes had the least success in discriminating species from this biogeographic region with resolution ranging from 36% with rbcL to 69% with matK. Species resolution was higher in the other settings, peaking in the Woodland region at 52% for rbcL and 87% for matK. Our results indicate that DNA barcoding is very effective in identifying Canadian plants to a genus, and that it performs well in discriminating species in regions where floristic diversity is highest.