Ruegeria pomeroyi masters of nutrient cycling in the plankton: degradation of purines in the plankton

Marine Roseobacter clades (MRC) are very successful members of the bacterioplankton and this is can be attributed by their immense metabolic versatility, implementing them in a many biogeochemical processes. Purines are widespread and an important source of dissolved organic nitrogen in the marine environment, they are present in nucleic acids hence why they are widely distributed in the marine environment. As it was previously known that bacterioplankton in estuarine waters rapidly degrade purines, it was put forward that the metabolically versatile MRC maybe also be able to degrade purines.

Cunliffe 2016, explored weather Ruegeria pomeroyi, were able to degrade xanthine (a purine base found in the tissue and fluids of humans and other organisms), various methods firstly xanthine dehydrogenase activity was measured, then total RNA form bacteria grown on marine ammonium mineral salts (MAMS) media (with, glucose and xanthine, xanthine and ammonium and xanthine only, added glucose for the control)

Total RNA was extracted and the rRNA depleted, RNAseq libraries were prepared from mRNA enriched samples. An average of 71,891,358 reads where generated per library and 99.74% could be mapped. Putative gene functions were determined using a few resources, KEGG BRENDA, UniProt (online resources). It was fund that they contained the putative genes xdhB and xdhA which together encode xanthine dehydrogenase, an analysis on data from the TARA ocean studies revealed xdhB is present is prominent in open ocean bacterioplankton.

To ensure that the XDH was active in the bacteria were gown in media with xanthine (which is very insoluble and can be seen on in the media) and as the bacteria grew the media became clear indicating the xanthine had been degraded.

Cell free protein extraction from R. pomeroyi grown in liquid media under 4 conditions 1) glucose and ammonia (GA), glucose and xanthine (GX), xanthine and ammonia (XG) and xanthine only (XX) was used to determine transcription (XDH expression). In all the treatments with xanthine the transcription of the putative genes for the xanthine degradation pathway were upregulated when compared to GA. These included not only xanthine dehydrogenase but also SPO1781, SPO0876 and SPOO873 which all play a role in the purine catabolism pathway, where allonate is converted to glyocylate and ammonia via ureidcyicine and ureidoglyclate which appears to be the pathway that is significantly unregulated in R. pomeroyi. Upregulation of these genes is most significant when xanthine was the only carbon source.

This paper has some great ecological implications, it was previously known that R. pomeroyi and MRC have great metabolic versatility but the ‘discovery’ of their putative catabolic pathway for xanthine (purines) again solidifies the huge capability of MCR. A new link between roseobacter and phytoplankton in which the roseobacter can utilize purines from phytoplankton producing ammonia in which can be used by phytoplankton. This represents a very ecologically important link between phytoplankton and bacterioplankton, especially in times of low nitrate levels in the environment.

This paper illustrates the strength of transcriptional studies especially of marine bacteria which can be extremely difficult to culture, these studies help revel new functions that were previously unknown, and allows us to make links in the nutrient cycles in the marine environment.

Reviewed paper:  

Cunliffe, M. (2015) ‘Purine catabolic pathway revealed by transcriptomics in the model marine bacterium Ruegeria pomeroyi DSS-3’, FEMS Microbiology Ecology, 92(1), p. fiv150. doi: 10.1093/femsec/fiv150. https://www.ncbi.nlm.nih.gov/pubmed/26613749