Plant DNA viruses of the genus Begomovirus have been documented as the most genetically diverse in the family Geminiviridae and present a serious threat for global horticultural production, especially considering climate change. It is important to characterize naturally existing begomoviruses, since viral genetic diversity in non-cultivated plants could lead to future disease epidemics in crops. In this study, high-throughput sequencing (HTS) was employed to determine viral diversity of samples collected in a survey performed during 2012–2016 in seven states of Northern-Pacific Mexico, areas of diverse climatic conditions where different vegetable crops are subject to intensive farming. In total, 132 plant species, belonging to 34 families, were identified and sampled in the natural ecosystems surrounding cultivated areas (agro-ecological interface). HTS analysis and subsequent de novo assembly revealed a number of geminivirus-related DNA signatures with 80 to 100% DNA similarity with begomoviral sequences present in the genome databank. The analysis revealed DNA signatures corresponding to 52 crop-infecting and 35 non-cultivated-infecting geminiviruses that, interestingly, were present in different plant species. Such an analysis deepens our knowledge of geminiviral diversity and could help detecting emerging viruses affecting crops in different agro-climatic regions.

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Rhizospheric microbiota diversity of crops in agroecosystems is understudied in Mexico and worldwide. The aim of the present work was to explore the diversity of culturable bacteria in maize fields. A bacterial collection consisting of 11,520 purified isolates was created from the rhizosphere of maize plants. Genomic DNA was obtained from each isolate and a region of 16S rDNA was sequenced. The 16S rDNA amplicon sequences were analyzed and grouped into Operational Taxonomic Units (OTUs), allowing the assemblage of 7,077 bacterial isolates into 185 non-singleton OTUs. OTUs belonged to 19 bacterial genera within Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes Phyla; with Firmicutes as the richest Phylum comprising 146 OTUs and 6 genera, and being Bacillus the richest genus. The soil core-community of 28 OTUs belonging to Firmicutes and 1 OTU from Proteobacteria was identified. The work discusses the role that the different bacterial populations identified within the maize rhizosphere may play, their potential use for biotechnological purposes, and the importance of conservation of microbiological resources using bacterial collections.