Phototrophicity and Genomic Composition in Plant-Associated Sphingomonas faeni Strains

Solar radiation impacts most life forms on Earth by acting as a energy source or a regulatory signal. However, relatively little is still known about phototrophic potential and strategies of environmental bacteria beyond Cyanobacteria. This study explores the phototrophy related genomic diversity of Sphingomonas faeni strains from Arctic and sub-Arctic regions. We analyzed the genomes of 25 plant-associated S.faeni strains isolated from Vaccinium myrtillus , Oxyria digyna , Vaccinium vitis-idaea , and Bistorta vivipara , along with a reference S. faeni genome MA-olki. The strains showed diversity both in overall genome level but also in phototrophic capabilities: Seven strains were identified as aerobic anoxygenic phototrophic (AAP) bacteria with a complete photosynthetic gene cluster, 16 strains contained Xanthorhodopsin (XR) genes, and three strains were non-phototrophic, possessing no AAP or XR genes. The AAP strains were found exclusive from Vaccinium hosts. O. digyna contained only XR containing strains and B. vivipara showed XR genes and one non-phototrophic strain. V. vitis-idaea hosted strains for all three different phototrophy categories. Phylogenetic analyses using 16S rRNA gene and whole genome alignments showed AAP positive strains forming a tight phylogenetic group. We found no strong evidence of horizontal gene transfer of photosynthetic gene cluster. XR strains and non-phototrophic strains clustered into three different subgroups. Phototrophic strains had more photoreceptors, and AAP strains exhibited dual copies of the 5-aminolevulinic acid (5-ALA) gene within the photosynthetic gene cluster (PGC). Our genomic analysis suggests a relationship between phototrophic strategies and host plant specificity.