Expanding the environmental virome: Infection profile in a native rainforest tree species

Abstract

Agroforestry systems (AFS) for cocoa production combine traditional land-use practices with local biodiversity conservation, resulting in both ecological and agricultural benefits. The cacao-cabruca AFS model is widely implemented in regions of the Brazilian Atlantic Forest. Carpotroche brasiliensis (Raddi) A. Gray (Achariaceae) is a tree found in cabruca landscapes that is often used for reforestation and biotechnological applications. Despite its importance, we still lack information about viruses circulating in C. brasiliensis, particularly considering the possibility of spillover that could affect cocoa production. In our study, we analyzed the Carpotroche brasiliensis virome from Atlantic Forest and cacao-cabruca AFS regions using metatranscriptomics from several vegetative and reproductive organs. Our results revealed a diverse virome detecting near-complete or partial coding sequences of single- and double-stranded DNA and RNA viruses classified into at least six families (Botourmiaviridae, Bromoviridae, Caulimoviridae, Genomoviridae, Mitoviridae, and Rhabdoviridae) plus unclassified elements. We described with high confidence the near-complete and the partial genomes of two tentative novel viruses: Carpotroche-associated ilarvirus and Carpotroche-associated genomovirus, respectively. Interestingly, we also described sequences likely derived from a rhabdovirus, which could represent a novel member of the genus Gammanucleorhabdovirus. We observed higher viral diversity in cacao-cabruca AFS and reproductive organs of C. brasiliensis with preferential tropism to fruits, which could directly affect production. Altogether, our results provide data to better understand the virome in this unexplored agroecological interface, such as cacao-cabruca AFS and forest ecosystem, providing information on the aspects of virus–plant interactions.

33rd Brazilian Society for Virology (SBV) 2022 Annual Meeting

“…Metavirome analysis of Carpotroche brasiliensis (Raddi) A. Gray (Achariaceae) in agroecological interface reveals viral diversity in cacao-cabruca agroforestry systems and in regions of the Brazilian Atlantic Forest [15] Mônica Cristina de M. Silva (Instituto Evandro Chagas, MS) Metagenomic analysis of the viral microbiota of Amazonian rivers located in the northeastern region of Pará state, Brazil [16] Talita Bastos Machado (UFMG, MG) Discovery and characterization of Cedratvirus pambiensis: a 1 micrometer giant virus infecting amoebas [17] Basic Virology 1…”

“…Metavirome analysis of Carpotroche brasiliensis (Raddi) A. Gray (Achariaceae) reveals a new virus from the genus Gammanucleorhabdovirus (Rhabdoviridae, -ssRNA) [31] Ivair José de Morais Júnior (UNB, DF) * Whole genome analyses suggest that potato and pepper PVY isolates are distinctly evolving [32] Basic Virology 2…”

The RNA virosphere: How big and diverse is it?

“…Despite Sanger sequencing's low throughput, this novel survey approach revealed a diverse array of highly‐divergent ‘picorna‐like’ RNA viruses that were likely infecting marine phytoplankton. A decade later, sequencing technologies had advanced sufficiently to enable the exploration of diverse environments, often via mining RdRp sequences in RNA‐seq data derived from (i) biotic samples (including holobiont, unicellular, and multicellular organisms), such as invertebrates (Li et al, 2015 ; Shi et al, 2016 ; Vieira et al, 2022b ; Wu et al, 2020 ), vertebrates (Shi et al, 2018 ), plants (Roossinck, 2012 ; Vieira et al, 2022a ), protists (Cai et al, 2012 ; Charon et al, 2022 , 2020 , 2021 ; Lachnit et al, 2015 ; Nagasaki et al, 2004 ; Sasai et al, 2018 ; Shirai et al, 2008 ; Tai et al, 2003 ; Tomaru et al 2004 , 2009 , 2012 ), and fungi (Deakin et al, 2017 ; Marzano et al, 2016 ) and (ii) environmental samples, such as faeces (Krishnamurthy et al, 2016 ), sediments (Callanan et al, 2020 ), soils (Hillary et al, 2022 ; Starr et al, 2019 ; Wu et al, 2021 ), rivers (French et al, 2022 ), and seawater from specific sites (Culley et al, 2003 , 2006 , 2014 ; Djikeng et al, 2009 ; Steward et al, 2013 ; Urayama et al, 2018 ; Vlok et al, 2019 ; Wolf et al, 2020 ) and from geographic locations representing the entire global oceans (Dominguez‐Huerta et al, 2022 ; Zayed et al, 2022 ). The environments most explored for RNA viruses during these two decades are aquatic (e.g., marine, sewage, and riverine), providing us with the first insights into their ecology, evolution of their viral inhabitants, and methodological challenges associated with characterizing specific natural ecosystems (Culley, 2018 ; Liao et al, ...…”