Complexity and local specificity of the virome associated with tospovirus-transmitting thrips species.

Frankliniella occidentalis (western flower thrips=WFT) and Thrips tabaci (onion thrips=OT) are insect species that greatly impact horticultural crops through direct damage and their efficient vectoring of tomato spotted wilt virus and iris yellow spot virus. In this study we collected thrips of these species from 12 field populations in various regions in Italy. We also included one field population of Neohydatothrips variabilis (soybean thrips=ST) from the U.S.A. Total RNAseq from high-throughput sequencing (HTS) was used to assemble the virome and then we assigned putative viral contigs to each thrips sample by qRT-PCR. Excluding plant and fungal viruses, we were able to identify 61 viral segments, corresponding to 41 viruses: 14 were assigned to WFT, 17 to OT, one from ST and 9 viruses could not be assigned to any species based on our stringent criteria. All these viruses are putative representative of new species (with only the exception of a sobemo-like virus that is 100% identical to a virus recently characterized in ST) and some belong to new higher-ranking taxa. These additions to the viral phylogeny suggest previously undescribed evolutionary niches. Most of the Baltimore’s classes of RNA viruses were present (positive- and minus- strand and dsRNA viruses), but only one DNA virus was identified in our collection. Repeated sampling in a subset of locations in 2019 and 2020 and further virus characterization in a subset of four thrips populations maintained in laboratory allowed us to provide evidence of a locally persistent thrips core virome that characterizes each population. IMPORTANCE Harnessing the insect microbiome can result in new approaches to contain their populations or the damage they cause vectoring viruses of medical, veterinary, or agricultural importance. Persistent insect viruses are a neglected component of their microbiota. Here for the first time, we characterize the virome associated with the two model systems for tospovirus-transmitting thrips species, of utmost importance for the direct and indirect damage they cause to a number of different crops. The thrips virome here characterized includes several novel viruses, that in some cases reveal previously undescribed clades. More importantly, some of the viruses we describe are part of a core virome that is specific and consistently present in distinct geographical locations monitored over the years, hinting at a possible mutualistic symbiotic relationship with their host.

Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses

Soybean thrips (Neohydatothrips variabilis) are one of the most efficient vectors of soybean vein necrosis virus, which can cause severe necrotic symptoms in sensitive soybean plants. To determine which other viruses are associated with soybean thrips, the metatranscriptome of soybean thrips, collected by the Midwest Suction Trap Network during 2018, was analyzed. Contigs assembled from the data revealed a remarkable diversity of virus-like sequences. Of the 181 virus-like sequences identified, 155 were novel and associated primarily with taxa of arthropod-infecting viruses, but sequences similar to plant and fungus-infecting viruses were also identified. The novel viruses were predicted to have positive-sense RNA, negative-stranded RNA, double-stranded RNA, and single-stranded DNA genomes. The assembled sequences included 100 contigs that represented at least 95% coverage of a virus genome or genome segment. Sequences represented 12 previously described arthropod viruses including eight viruses reported from Hubei Province in China, and 12 plant virus sequences of which six have been previously described. The presence of diverse populations of plant viruses within soybean thrips suggests they feed on and acquire viruses from multiple host plant species that could be transmitted to soybean. Assessment of the virome of soybean thrips provides, for the first time, information on the diversity of viruses present in thrips.

Evaluation of Soybean for Resistance to Neohyadatothrips variabilis (Thysanoptera: Thripidae) Noninfected and Infected With Soybean Vein Necrosis Virus

Soybean vein necrosis virus (SVNV) was first identified in Arkansas and Tennessee in 2008 and is now known to be widespread in the United States and Canada. Multiple species of thrips transmit this and other tospoviruses with Neohydatothrips variabilis (Beach) (soybean thrips) cited as the most efficient vector for SVNV. In this study, 18 soybean, Glycine max (L.) Merr., genotypes were evaluated in four experiments by infesting plants with noninfected and SVNV-infected thrips using choice and no-choice assays. In both choice experiments with noninfected and SVNV-infected thrips, the lowest number of immature soybean thrips occurred on plant introductions (PIs) 229358 and 604464 while cultivars Williams 82 and Williamsfield Illini 3590N supported higher counts of mature thrips. The counts between the two assays (noninfected and SVNV-infected thrips) were positively correlated. In both no-choice experiments with noninfected and SVNV-infected thrips, counts of thrips did not differ by soybean genotypes. Further studies are needed to characterize the inheritance and mechanisms involved in the resistance found in the choice assay.

A Survey of Thrips (Thysanoptera) Species Infesting Cotton Seedlings in Alabama, Arkansas, Georgia, Louisiana, Mississippi, and Tennessee

The common species of thrips that are considered pests of cotton, Gossypium hirsutum (L.), include flower thrips, Frankliniella tritici (Fitch); tobacco thrips, Frankliniella fusca (Hinds); western flower thrips, Frankliniella occidentalis (Pergande); onion thrips, Thrips tabaci (Lindeman); and soybean thrips, Neohydatothrips variabilis (Beach). Thrips feeding on cotton seedlings can inhibit plant growth, reduce plant stand, delay crop maturity, and reduce seed-cotton yield. Surveys were conducted in Alabama, Arkansas, Georgia, Louisiana, Mississippi, and Tennessee to determine the thrips species infesting cotton seedlings during 1996 to 1999. Cotton seedlings were sampled weekly between 7 and 48 days after plant emergence at one to four field sites in each state. Over 12,000 thrips adults were collected using plant washing procedures with 9,005 individuals mounted on slides, and identified to species. The tobacco thrips was the most common species collected in all states, except Georgia, and comprised at least 63% of the thrips adults in all instances, except four. The occurrence of flower thrips and soybean thrips was variable; however, neither species accounted for more than 21% of thrips identified in each state. Western flower thrips accounted for less than 15% of adults collected in all instances except two (28% and 30%) in Louisiana. Also, individual specimens of Thrips nigropilosus Uzel and Anophothrips obscurus Müller were collected in Alabama, and several specimens of Microcephalothrips abdominalis (Crawford) were collected in Arkansas and Louisiana.

Population Distribution of Flower Thrips and the Western Flower Thrips (Thysanoptera: Thripidae) in Nectarines and their Relative Association with Injury to Fruit in the Southeastern United States2

Thrips populations and injury attributed to thrips feeding on fruit surfaces was monitored in unsprayed middle Georgia nectarines during 1986 – 1988. The flower thrips, Frankliniella tritici (Fitch), the western flower thrips, Frankliniella occidentalis (Pergande), and the soybean thrips, Neohydatothrips variabilis (Beach), were the most abundant thrips species recovered from the orchard. Their relative abundance changed each year. The western flower thrips particularly appears to be most damaging in causing russeting on fruit surfaces. Silvering injury was caused by either or both of the flower thrips and coincided with peak populations of adults at or near final fruit swell. Soybean thrips caused little or no injury to fruit. None of the above mentioned flower thrips species were recovered from various weed and grass species in and near the nectarine orchard during two years of overwintering studies.