Virus community structuring is shaped by habitat heterogeneity and resource utilisation strategies

After decades of disconcerted research, we still recognise large gaps in the understanding of mechanisms that govern disease dynamics in complex biological communities. To determine how spatial structuring of plant communities caused by anthropic disturbance affects resource utilisation traits of viruses, we combine high-throughput, network, and metacommunity approaches. We find that the disturbance gradient corresponded to network modules and habitat specificity exhibited by a majority of viruses. Communities were connected through key hub species of either generalist viruses or high potential host reservoirs. Spatial dependencies were evident in regression models of species richness and correlations between metacommunity structure and both host range and transmission mode at finer spatial resolutions. We propose that virus community assembly is influenced by variation in niche opportunities. Distinctions in virus community composition caused by resource compartmentalisation can be use..., We conducted 78 collections at 23 sampling sites between July 2015 and June 2017 in the Vega del Tajo-Tajuña agricultural region of the south-central plateau of the Iberian Peninsula.
Total RNA extractions were conducted for the detection of all virus genome types (+ssRNA, -ssRNA, dsRNA, ssDNA, and dsDNA). Individual RNA extracts were pooled by plant species and collection (i.e., a single instance of sampling at a study site) to obtain a single preparation for HTS. Together, the HTS sample comprised 323 libraries of 2,037 pooled individual samples.
High throughput sequencing was outsourced (CRG, Barcelona, Spain; http://www.crg.eu/). All library preparation included a step for rRNA depletion. Paired-end reads of 125 or 150 nt. were sequenced on Illumina HiSeq platforms. All reads were provided with Phred quality scores greater or equal to Q30. The trimming of adapter contamination was conducted using cutadapt v1.8.3.
To standardise the counts of OTUs, the following pipeline was applied ..., A text editor or Microsoft Excel can be used to open the data.