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Gene regulatory networks allow single cells to adopt a wide range of different phenotypes in response to changes in environmental conditions. The ecological implications of these cellular computations are poorly understood, and they are largely absent from models of microbial community assembly. Here, we highlight a number of examples where ecological interactions are or may be affected by cellular computations. Our review identifies specific opportunities for integrating cellular decision-making into mathematical models of microbe-microbe interactions and community assembly. We argue that incorporating cellular decision-making into microbial ecology will be critical in order to gain a quantitative understanding of microbial biogeography.

In analyzing grapevine clones infected with grapevine red blotch associated virus, we identified a small number of isometric particles of approximately 30 nm in diameter from an enriched fraction of leaf extract. A dominant protein of 25 kDa was isolated from this fraction using SDS-PAGE and was identified by mass spectrometry as belonging to grapevine asteroid mosaic associated virus (GAMaV). Using a combination of three methods RNA-Seq, sRNA-Seq, and Sanger sequencing of RT- and RACE-PCR products, we obtained a full-length genome sequence consisting of 6719 nucleotides without the poly(A) tail. The virus possesses all of the typical conserved functional domains concordant with the genus Marafivirus and lies evolutionarily between citrus sudden death associated virus and oat blue dwarf virus. A large shift in RNA-Seq coverage coincided with the predicted location of the subgenomic RNA involved in coat protein (CP) expression. Genus wide sequence alignments confirmed the cleavage motif LxG(G/A) to be dominant between the helicase and RNA dependent RNA polymerase (RdRp), and the RdRp and CP domains. A putative overlapping protein (OP) ORF lacking a canonical translational start codon was identified with a reading frame context more consistent with the putative OPs of tymoviruses and fig fleck associated virus than with those of marafiviruses. BLAST analysis of the predicted GAMaV OP showed a unique relatedness to the OPs of members of the genus Tymovirus .