Biology subjects

Rivarez, M. P. S.

Publications and source records attributed to Rivarez, M. P. S..

3 recordsLinked to original sources

bioRxiv2022

Diversity and pathobiology of an ilarvirus unexpectedly detected in diverse host plants and in global sequencing data

High-throughput sequencing (HTS) and sequence mining tools revolutionized virus detection and discovery in recent years and implementing them with classical plant virology techniques results to a powerful approach to characterize viruses. An example of a virus discovered through HTS is Solanum nigrum ilarvirus 1 (SnIV1) (family Bromoviridae), which was recently reported in various solanaceous plants from France, Slovenia, Greece, and South Africa. It was likewise detected in grapevines (Vitaceae) and several Fabaceae and Rosaceae plant species. Such a very diverse host association is atypical for ilarviruses, thus warranted further investigation. In this study, modern and classical virological tools were combined to accelerate the characterization of SnIV1. Through HTS-based virome surveys, mining of sequence read archive datasets, and literature search, SnIV1 was further identified from diverse plant and non-plant sources globally. SnIV1 isolates showed relatively low variability compared to other phylogenetically related ilarviruses. Phylogenetic analyses showed a distinct basal clade of isolates from Europe, while the rest formed clades of mixed geographic origin. Furthermore, systemic infection of SnIV1 in Solanum villosum and its mechanical and graft transmissibility to solanaceous species were demonstrated. Near identical SnIV1 genomes from the inoculum (S. villosum) and inoculated Nicotiana benthamiana were sequenced, thus partially fulfilling Kochs postulates. SnIV1 was shown to be seed-transmitted and potentially pollen-borne, has spherical virions, and possibly induces histopathological changes in infected N. benthamiana leaf tissues. Overall, this study provided information to better understand the diversity, distribution, and pathobiology of SnIV1, but whether it could emerge as a destructive pathogen remains uncertain. FundingO_LIEU Horizon 2020 Marie Skodowska-Curie Actions Innovative Training Network (H2020 MSCA-ITN) project no. GA 813542 C_LIO_LIAdministration of the Republic of Slovenia for Food Safety, Veterinary Sector and Plant Protection and Slovenian Research Agency (ARRS) funding no. P4-0165, P4-0407, J4-4553 C_LIO_LIBalik Scientist Program (Republic Act 11035) of the Department of Science and Technology- Philippine Council for Agriculture, Aquatic, and Natural Resources Research and Development (DOST-PCAARRD), Republic of the Philippines C_LIO_LIThe Belgian FPS Health Food Chain Safety and Environment under Project RT18/3 SEVIPLANT C_LI

microbiology↗

bioRxiv2022

In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem

BackgroundIn agroecosystems, viruses are well known to influence crop health and a few cause phytosanitary and economic problems, but their diversity in non-crop plants and role outside the disease perspective is less known. An extensive virome exploration that includes both crop and diverse weed plants is therefore needed to better understand roles of viruses in agroecosystems. Such unbiased exploration is possible through viromics, which could generate biological and ecological insights from immense high-throughput sequencing (HTS) data. ResultsHere, we implemented HTS-based viromics to explore viral diversity in tomatoes and weeds in farming areas at a nation-wide scale. We detected 125 viruses, including 79 novel species, wherein 65 were found exclusively in weeds. This spanned 21 higher-level plant virus taxa dominated by Potyviridae, Rhabdoviridae, and Tombusviridae, and four non-plant virus families. We detected viruses of non-plant hosts and viroid-like sequences, and demonstrated infectivity of a novel tobamovirus in plants of Solanaceae family. Diversities of predominant tomato viruses were variable, in some cases, comparable to that of global isolates of same species. We phylogenetically classified novel viruses, and showed links between a subgroup of phylogenetically-related rhabdoviruses to their taxonomically-related host plants. Ten classified viruses detected in tomatoes were also detected in weeds, which might indicate possible role of weeds as their reservoirs, and that these viruses could be exchanged between the two compartments. ConclusionsWe showed that even in relatively well studied agroecosystems, such as tomato farms, a large part of very diverse plant viromes can still be unknown and is mostly present in understudied non-crop plants. The overlapping presence of viruses in tomatoes and weeds implicate possible presence of virus reservoir and possible exchange between the weed and crop compartments, which may influence weed management decisions. The observed variability and widespread presence of predominant tomato viruses and the infectivity of a novel tobamovirus in solanaceous plants, provided foundation for further investigation of virus disease dynamics and their effect on tomato health. The extensive insights we generated from such in-depth agroecosystem virome exploration will be valuable in anticipating possible emergences of plant virus diseases, and would serve as baseline for further post-discovery characterization studies.

ecology↗

bioRxiv2019

Defense Biopriming and Antimicrobial Activity of Endophytic Bacteria and Associated Bacillus Species Contribute to Bacterial Crown Rot Tolerance in Papaya

The native plant microbiome is composed of diverse communities that influence its overall health, with some species known to promote plant growth and pathogen resistance. Here, we show the antimicrobial and growth promoting activities of autoclaved culture metabolites (ACMs) from native endophytic bacteria (NEB) in a papaya cultivar that is tolerant to bacterial crown rot (BCR) caused by Erwinia mallotivora. Initially, bacterial colonization in recovering tissues of this cultivar was observed before onset of tissue regeneration or regrowth. We further isolated and characterized these bacteria and were able to identify two culturable stem NEB under genera Kosakonia (EBW), related to Enterobacter, and Sphingomonas (EBY). We also identified root NEB (BN, BS and BT) under genus Bacillus. Inhibition assays indicated that ACMs from these NEB promptly (18-30h) and efficiently inhibited (60-65%) E. mallotivora proliferation in vitro. Interestingly, when ACMs from BN and EBW were inoculated in surface-sterilized papaya seeds, germination was variably retarded (20-60% reduction) depending on plant genotype, but plant biomass accumulation was significantly stimulated, at around two-fold increase. Moreover, greenhouse experiments show that ACMs from all isolates, especially EBW, significantly reduced BCR incidence and severity in susceptible genotype, at around two-fold. In general, our observations of pathogen antagonism, plant growth promotion leading to disease reduction by ACMs of native endophytic bacteria suggested its contribution to increased fitness of papaya and tolerance against the (re)emerging BCR disease.

plant biology↗