The incidence of tomato-infecting begomoviruses has sharply increased in Brazil following the introduction of the B biotype of the whitefly vector in the early 1990s. Five definitive species and six tentative species have been described since then. Here, we report the detection of members of an additional six novel species, three in tomato and three infecting weeds that are commonly associated with tomato fields: Blainvillea rhomboidea, Sida rhombifolia and Sida micrantha. Tomato and weed samples were collected in two major tomato-growing regions of southeastern Brazil in 2005 and 2007. Two of the novel viruses were present in tomato plants collected in Paty do Alferes, Rio de Janeiro state. Three novel viruses were present in weed samples collected in Coimbra, Minas Gerais state. One virus was present in tomato samples collected at both locations. Genome features indicate that all six species are typical New World, bipartite begomoviruses. However, the viruses belonging to two of the novel species did not cluster with the Brazilian viruses in a phylogenetic tree. These species could represent a distinct lineage of New World begomoviruses, found in Brazil for the first time.

Biodiversity underlies ecosystem functioning. While aboveground biodiversity is often well studied, the belowground microbiome, in particular protists, remains largely unknown. Indeed, holistic insights into soil microbiome structures in natural soils, especially in hyperdiverse biomes such as the Brazilian Cerrado, remain unexplored. Here, we study the soil microbiome across four major vegetation zones of the Cerrado, ranging from grass-dominated to tree-dominated vegetation with a focus on protists. We show that protist taxon richness increases towards the tree-dominated climax vegetation. Early successional habitats consisting of primary grass vegetation host most potential plant pathogens and least animal parasites. Using network analyses combining protist with prokaryotic and fungal sequences, we show that microbiome complexity increases towards climax vegetation. Together, this suggests that protists are key microbiome components and that vegetation succession towards climax vegetation is stimulated by higher loads of animal and plant pathogens. At the same time, an increase in microbiome complexity towards climax vegetation might enhance system stability.

Local chlorotic spots resembling early lesions characteristic of citrus leprosis (CL) were observed in leaves of two sweet orange (Citrus sinensis L.) trees in Teresina, State of Piauí, Brazil, in early 2017. However, despite the similarities, these spots were generally larger than those of a typical CL and showed rare or no necrosis symptoms. In symptomatic tissues, transmission electron microscopy revealed the presence of viroplasms in the nuclei of the infected parenchymal cells and rod-shaped particles with an average size of approximately 40 × 100 nm, resembling those typically observed during infection by dichorhaviruses. A bipartite genome of the putative novel virus, tentatively named citrus chlorotic spot virus (CiCSV) (RNA1 = 6,518 nucleotides [nt] and RNA2 = 5,987 nt), revealed the highest nucleotide sequence identity values with the dichorhaviruses coffee ringspot virus strain Lavras (73.8%), citrus leprosis virus N strain Ibi1 (58.6%), and orchid fleck virus strain So (56.9%). In addition to citrus, CiCSV was also found in local chlorotic lesions on leaves of the ornamental plant beach hibiscus (Talipariti tiliaceum (L.) Fryxell). Morphological characterization of mites recovered from the infected plants revealed at least two different types of Brevipalpus. One of them corresponds to Brevipalpus yothersi. The other is slightly different from B. yothersi mites but comprises traits that possibly place it as another species. A mix of the two mite types collected on beach hibiscus successfully transmitted CiCSV to arabidopsis plants but additional work is required to verify whether both types of flat mite may act as viral vectors. The current study reveals a newly described dichorhavirus associated with a citrus disease in the northeastern region of Brazil.

The taxonomy of the genus Colletotrichum has undergone various changes. These alterations arise from the use of modern molecular tools. Currently, Colletotrichum species are grouped into complexes. Species of Colletotrichum associated with diseases in lima bean have been investigated very little. In Brazil, anthracnose in lima bean has often been associated with Colletotrichum truncatum, but only morphological characteristics have been used for identification purposes. In this study, samples of lima bean with symptoms of spots on the leaves and pods have been collected in Piauí and Alagoas states. Comparisons of morphological characteristics revealed nine isolates with cylindrical or curved conidia. The ITS region and partial sequences of GAPDH, β-tubulin and Actin regions were amplified by PCR, sequenced and submitted to multilocus phylogenetic analysis. The isolates analyzed grouped with reference specimens from Colletotrichum truncatum, C. cliviae and C. fructicola. All isolates were pathogenic to 25-day-old lima bean seedlings. Therefore, this work confirms the pathogenicity of C. truncatum to lima bean and for the first time records the occurrence of C. cliviae and C. fructicola as pathogens of this host in Brazil.

The complete genomic sequences of two cowpea aphid-borne mosaic virus (CABMV) isolates from Brazil, MG-Avr from passion fruit (which also infects cowpea), and BR1 from peanut (which also infects cowpea, but not passion fruit), were determined. Their nucleotide sequences are 89% identical and display 85% identity to that of CABMV-Z. Both isolates have the typical potyvirus genome features. P3 and VPg are the most conserved proteins, with 99% amino acid sequence identity between the two isolates, and P1 is the most variable, with 50% identity. A significant variation exists at the 5'-end of the genome between the Brazilian isolates and CABMV-Z. However, this variation does not correlate with the biological properties of these three isolates.