Biology subjects

Olmedo-Velarde, A.

Publications and source records attributed to Olmedo-Velarde, A..

8 recordsLinked to original sources

bioRxiv2026

Genome-resolved metagenomics reveals conserved, flexible and emerging symbioses across global leafhoppers

BackgroundLeafhoppers are among the most important insect vectors of plant pathogens worldwide and depend on microbial symbionts to exploit nutrient-poor phloem diets. However, most studies of leafhopper-associated microbiota have focused on a limited number of taxa or marker-gene surveys, leaving the genomic diversity, ecological organization, and functional potential of these microbial communities poorly understood. Here, we generated the Global Leafhopper Microbiome Catalog by integrating genome-resolved metagenomics from 171 leafhopper species across 11 subfamilies and 13 countries, including the first microbiomes characterized from Arctic leafhoppers. ResultsDe novo assembly and genome reconstruction generated 337 high-quality non-redundant microbial genomes and 18.6 million non-redundant genes, substantially expanding the known microbial diversity associated with Cicadellidae, including several previously undescribed bacterial lineages. Comparative analyses revealed a recurrent modular microbiome architecture composed of: (i) a conserved core of obligate nutritional symbionts, dominated by Candidatus Karelsulcia and Candidatus Nasuia; (ii) a heterogeneous layer of secondary symbionts, including Wolbachia, Arsenophonus, Rickettsia, and Diplorickettsia; and (iii) a dynamic pool of environmentally acquired bacteria. While obligate symbionts remained highly conserved across divergent hosts, secondary and environmental taxa varied substantially among species and regions, suggesting repeated acquisition shaped by ecological filtering rather than host phylogeny alone. Comparative analyses between the specialist corn leafhopper Dalbulus maidis and the more polyphagous aster leafhopper Macrosteles quadrilineatus further showed that closely related vectors can maintain conserved ancestral symbionts while harboring markedly distinct accessory microbiomes. Arctic populations contained unique microbial assemblages enriched in functions associated with cold tolerance, oxidative stress, and reproductive manipulation. In addition, we identified numerous plant-associated bacteria, including phytoplasmas, spiroplasmas, Pantoea, and Erwinia, alongside taxa with predicted nutritional and plant growth-promoting functions. ConclusionsOur findings reveal that leafhopper microbiomes are structured through the interaction of ancient obligate symbioses and flexible environmentally responsive microbial layers. This work establishes a genome-resolved framework for understanding microbiome evolution in insect vectors and highlights the potential role of microbial community structure in host adaptation, pathogen ecology, and sustainable pest management.

microbiology↗

bioRxiv2026

Viromics in flat mites from Hawaii shows abundant arrays of viruses, expands the evolutionary origin of plant viruses, and provides a surveillance tool for Brevipalpus-transmitted viruses

Flat mites (Tenuipalpidae) are diverse phytophagous arthropods, among which Brevipalpus species are economically important pests capable of transmitting plant viruses. Brevipalpus-transmitted viruses (BTVs) cause localized infections in plants and are classified into two major groups based on cytopathology and genome organization: BTV-C (genera Cilevirus and Higrevirus, family Kitaviridae) and BTV-N (genus Dichorhavirus, family Rhabdoviridae). Despite their significance, the virome of tenuipalpid mite vectors remains poorly characterized. Using high-throughput sequencing (HTS), we analyzed virus populations associated with Brevipalpus and Dolichotetranychus mites collected from multiple plant hosts across two Hawaiian Islands. We identified a diverse assemblage of viral sequences affiliated with Kitaviridae, negeviruses, Picornavirales, Narnaviridae, Tombusviridae, Solemoviridae, Ourmiaviridae, Reoviridae, and Potyviridae. Near-complete genomes of citrus leprosis virus C2H and hibiscus green spot virus 2 (both BTV-C) were recovered, highlighting the utility of HTS-based viromics for surveillance of BTVs in mite vectors. In addition, multiple divergent virus-like contigs were identified based on viral hallmark genes and sequence divergence, including Brevipalpus-associated negevirus, Brevipalpus-associated bluner-like virus, and Dolichotetranychus-associated cile-like virus, all showing evolutionary affinities to BTV-C-related viruses. Phylogenetic analyses support evolutionary links between negeviruses and kitavirids, consistent with the hypothesis that Kitaviridae evolved from arthropod-associated ancestors. While some detected plant viruses may reflect ingestion rather than active replication in mites, this study establishes a robust framework for virome-based surveillance of tenuipalpid mites, advancing our understanding of plant virus evolution and supporting agricultural biosecurity and pest management efforts.

microbiology↗

bioRxiv2025

'Candidatus Phytoplasma zeae': community-driven delineation of the maize bushy stunt phytoplasma, a Dalbulus-transmitted corn pathogen confined to the Americas

A novel phytoplasma species, Candidatus Phytoplasma zeae, is proposed based on ecological distinctiveness, vector specificity, whole-genome comparisons, and community consensus. This phytoplasma is associated with maize bushy stunt (MBS) disease in corn (Zea mays) and is transmitted exclusively by Dalbulus maidis and D. elimatus, two leafhopper species endemic to the Americas, and has been reported in Brazil, Colombia, Mexico, Peru, and several U.S. states. Here we sequenced and assembled the genome of MBS phytoplasma strains from Brazil, and U.S. to describe and propose this new species. Although the 16S rRNA gene sequence of the proposed reference strain, MBSP-BRRS, shares >99% identity with that of Ca. Phytoplasma asteris, key nucleotide polymorphisms distinguish Ca. P. zeae from other 16SrI-related phytoplasma species. Average nucleotide identity (ANI) and average amino acid identity (AAI) values between Ca. P. zeae and Ca. P. asteris are 97.70-98.00% and 96.65-96.88%, respectively, both near the established species delineation thresholds. Comparative genomic analyses revealed unique gene clusters in Ca. P. zeae associated with amino acid transport, defense mechanisms, and protein turnover, which may contribute to its specialization in corn. The ecological profile of Ca. P. zeae, including its narrow host range and restricted geographic distribution, supports its recognition as a novel species under Rule c of the IRPCM guidelines. The designation Candidatus Phytoplasma zeae is therefore proposed by members of the research community who have studied this pathogen for over a decade, with the MBSP-BrazilRS strain serving as the reference.

microbiology↗

bioRxiv2025

The "Grove-First" Framework: Starting in the Grove to Find Therapies for Huanglongbing

Citrus greening disease, also known as huanglongbing (HLB), is the most serious vector-borne bacterial disease of citrus world-wide1,2. There is an immediate global need to provide the citrus industry with relief from HLB and a return to profitable citrus production. Standard screening methods for HLB therapeutic treatments typically involve various laboratory-based assays to select treatments with antimicrobial properties3, which then advance to greenhouse and eventually field testing in a workflow that takes multiple years. Unlike traditional lab-first screening, we present a design of experiments framework4,5, referred to as Grove-First, that rapidly screens treatments with regulatory-friendly profiles in commercial citrus groves using trunk injection to select treatments that improve tree health and fruit yield over the course of a single growing season. Using this framework, we identified candidate treatments with effects comparable to or better than the standard oxytetracycline (OTC) on visual tree-health and/or yield indices in an initial screen of HLB-positive 8-year-old Valencia sweet orange trees. Expanded trials in commercial citrus groves allowed us to validate the initial screening results at other locations and in other citrus varieties. Grove-First rapidly accelerated the identification and large-scale field testing of HLB therapies, some of which are available for growers to use immediately and others that require further field testing and/or regulatory actions.

plant biology↗

bioRxiv2024

Viral and bacterial plant pathogens suppress antiviral defense against flaviviruses in their insect vectors

A positive, single-stranded RNA virus member within the Flavivirus genus was identified and characterized infecting Myzus persicae. This new insect-specific virus (ISV), Myzus persicae flavivirus (MpFV), is 23,236 nucleotides in length and encodes a large polyprotein from a single open reading frame. Analysis of conserved domains showed that helicases, NS3-proteases, Fts-J methyltransferase, and an RNA-dependent RNA polymerase are present in the coded polyprotein. Aphid-infecting ISVs have been reported to interact with plant viruses within the vector, modulating its titer and manipulating aphid behavior and morphology. Small RNA (sRNA) profile analysis of the M. persicae sRNA profile demonstrated that the circulative plant virus, potato leafroll virus (PLRV), modified the aphid antiviral immunity against MpFV. Abundant sRNA reads matching MpFV were detected when aphids were fed on healthy plants, sucrose diet, and potato virus Y-infected plants. In contrast, no MpFV reads were detected in aphids that had acquired PLRV from infected plants or artificial diet sachets containing purified virions. While the titer of M. persicae densovirus (MpDNV) was previously reported to be regulated by expression of the PLRV silencing suppressor protein P0, P0 had no effect on MpFV titer in the aphid. MpFV was transmitted 100% vertically to the offspring, and exhibited tissue tropisms for the body rather than the head. By artificial diet assays, other aphid species, including Aphis gossypii (cotton aphid), Schizaphis graminum (greenbug aphid), Rhopalosiphum padi (bird cherry-oat aphid), and R. maidis (corn leaf aphid), acquired the MpFV. These findings further support the idea that PLRV suppresses aphid immunity against ISVs, suggest the existence of at least two distinct pathways for PLRV-induced aphid immune system modulation. To test whether other circulative plant pathogens suppress insect anti-viral immunity against insect-specific flaviviruses, we quantified the small RNA response of Diaphorina citri, vector of "Candidatus Liberibacter asiaticus" (CLas) associated with citrus greening disease and showed that CLas also suppresses D. citri anti-viral immunity against D. citri-like flavivirus (DcLFV). These data reveal an evolutionary conserved, unexpected role for diverse circulative plant pathogens in modulating anti-viral immunity in hemipteran vectors.

microbiology↗

bioRxiv2024

Data mining redefines the timeline and geographic spread of cotton leafroll dwarf virus

Cotton leafroll dwarf virus (CLRDV), a threat to the cotton industry, was first reported in the United States (US) as an emergent pathogen in 2017. Phylogenetic analysis supports the hypothesis that US CLRDV strains are genetically distinct from strains in South America and elsewhere, which is not consistent with the hypothesis that the virus is newly introduced into the country. Therefore, using database mining, we evaluated the timeline and geographic distribution of CLRDV in the country. We uncovered evidence that shows that CLRDV had been in the US for over a decade before its official first report. CLRDV sequences were detected in datasets derived from Mississippi in 2006, Louisiana in 2015, and California in 2018. Additionally, through field surveys of upland cotton in 2023, we confirmed that CLRDV is present in California, which had no prior reports of the virus. Viral sequences from these old and new datasets exhibited high nucleotide identities (>98%) with recently characterized US isolates, and phylogenetic analyses with their homologs placed these sequences within a US-specific clade, further supporting the earlier presence of CLRDV in the country. Moreover, potential new hosts, including another fiber crop, flax, were determined through data mining. Retrospective analysis suggests CLRDV presence in the US since at least 2006 (Mississippi). These findings necessitate a reevaluation of spread patterns, inoculum sources, symptomology variations, and control strategies. Our findings challenge the current understanding of the arrival and spread of CLRDV in the US, highlight the power of data mining for virus discovery, and underscore the need for further investigation into CLRDVs impact on US cotton.

plant biology↗

bioRxiv2023

Characterization of cotton virus A, a novel and distinct member of the genus Caulimovirus with endogenous viral elements in Gossypium spp.

The complete genome sequence of cotton virus A, a new virus infecting cotton (Gossypium spp.), was determined using high-throughput sequencing, PCR and rolling circle amplification. The 7,482-nt genome is a circular dsDNA molecule that codes for six open reading frames similar to other members of the Caulimovirus genus (family Caulimoviridae) but presenting key genome organization differences. P3, P5 and P6 are presumed movement, coat, and reverse transcriptase proteins, respectively. P1, P2 and P4 showed no homology to virus proteins. Endogenous viral elements were found in G. hirsutum and G. tomentosum, but not in G. barbadense, G. arboreum, or G. herbaceum.

plant biology↗

bioRxiv2020

Multiscale interactions between plant part and a steep environmental gradient determine plant microbial composition in a tropical watershed

Plant microbiomes are shaped by forces working at different spatial scales. Environmental factors determine a pool of potential symbionts while host physiochemical factors influence how those microbes associate with distinct plant tissues. Interactions between these scales, however, are seldom considered. Here we analyze epiphytic microbes from nine Hibiscus tiliaceus trees across a steep environmental gradient within a single Hawaiian watershed. At each location we sampled eight microhabitats: leaves, petioles, axils, stems, roots, and litter from the plant, as well as surrounding air and soil. While the composition of microbial communities is driven primarily by microhabitat, this variable predicted more than twice the compositional variance for bacteria compared to fungi. Fungal community compositional dissimilarity increased more rapidly along the gradient than did bacteria. Additionally, the spatial dynamics of fungal communities differed among plant parts, and these differences influenced the distribution patterns and range size of individual taxa. Within plants, microbes were compositionally nested such that aboveground communities contained a subset of the diversity found belowground. Our findings identify potential differences underlying the mechanisms shaping communities of fungi and bacteria associated with plants, and indicate an interaction between assembly mechanisms working simultaneously on different spatial scales.

microbiology↗