Indirect Interspecies Regulation: Transcriptional and Physiological Responses of a Cyanobacterium to Heterotrophic Partnership Hans C. Bernstein, a,e Ryan S. McClure, a Vera Thiel, c Natalie C. Sadler, a Young-Mo Kim, a William B. Chrisler, a,b Eric A. Hill, a Donald A. Bryant, c,d Margaret F. Romine, a Janet K. Jansson, a Jim K. Fredrickson, a Alexander S. Beliaev a Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA a ; Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA b ; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA c ; Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA d ; The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, USA e ABSTRACT The mechanisms by which microbes interact in communities remain poorly understood. Here, we interrogated specific interactions between photoau- totrophic and heterotrophic members of a model consortium to infer mechanisms that mediate metabolic coupling and acclimation to partnership. This binary consor- tium was composed of a cyanobacterium, Thermosynechococcus elongatus BP-1, which supported growth of an obligate aerobic heterotroph, Meiothermus ruber strain A, by providing organic carbon, O 2 , and reduced nitrogen. Species-resolved transcriptomic analyses were used in combination with growth and photosynthesis kinetics to infer interactions and the environmental context under which they occur. We found that the efficiency of biomass production and resistance to stress induced by high levels of dissolved O 2 increased, beyond axenic performance, as a result of heterotrophic partnership. Coordinated transcriptional responses transcending both species were observed and used to infer specific interactions resulting from the synthesis and ex- change of resources. The cyanobacterium responded to heterotrophic partnership by altering expression of core genes involved with photosynthesis, carbon uptake/fixa- tion, vitamin synthesis, and scavenging of reactive oxygen species (ROS). IMPORTANCE This study elucidates how a cyanobacterial primary producer accli- mates to heterotrophic partnership by modulating the expression levels of key met- abolic genes. Heterotrophic bacteria can indirectly regulate the physiology of the photoautotrophic primary producers, resulting in physiological changes identified here, such as increased intracellular ROS. Some of the interactions inferred from this model system represent putative principles of metabolic coupling in phototrophic- heterotrophic partnerships. KEYWORDS consortia, cyanobacteria, heterotroph, microbial interactions, transcriptome I nterspecies microbial interactions are controlled by the genome-encoded functions belonging to individual organisms and from their responses to environmental cues. Community-level responses are a function of all species, including those in low abun- dance, and comprehensive analyses require species-level resolution (1). Most microbial communities in nature are structurally and functionally complex, and it is technically challenging to make species-specific observations of behavior. Hence, model microbial consortia, maintained under controlled environments, are attractive for interrogating Received 18 November 2016 Accepted 30 January 2017 Published 7 March 2017 Citation Bernstein HC, McClure RS, Thiel V, Sadler NC, Kim Y-M, Chrisler WB, Hill EA, Bryant DA, Romine MF, Jansson JK, Fredrickson JK, Beliaev AS. 2017. Indirect interspecies regulation: transcriptional and physiological responses of a cyanobacterium to heterotrophic partnership. mSystems 2: e00181-16. https://doi.org/10.1128/ mSystems.00181-16. Editor Mark J. Mandel, Northwestern University Feinberg School of Medicine Copyright © 2017 Bernstein et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Hans C. Bernstein, hans.bernstein@pnnl.gov. Cyanobacteria acclimate to heterotrophic partnership showing evidence of indirect interspecies regulation RESEARCH ARTICLE Ecological and Evolutionary Science crossm March/April 2017 Volume 2 Issue 2 e00181-16 msystems.asm.org 1 on December 5, 2017 by guest http://msystems.asm.org/ Downloaded from