Nitrogen utilization by marine prokaryotes revealed using stable isotope probing coupled with tag sequencing (Tag-SIP)

Nitrogen (N) can greatly influence microbial community structure and productivity through both its availability and form, but the role of specific organisms in the uptake of N remains poorly characterized. Most studies to date seeking to identify agents of N assimilation have been correlative, indirectly linking activity measurements (e.g., NO3- uptake) with the presence/absence of biological markers, particularly functional genes and their transcripts. Here, next-generation tag sequencing was successfully coupled with stable isotope probing (Tag-SIP) to assess the ability of individual phylotypes to assimilate a particular N source. Our results demonstrate evidence of nitrate assimilation by organisms previously believed to lack the genes required for this process, including Prochlorococcus and the heterotrophic clades SAR11 and the Archaeal Marine Group II (MG-II). Furthermore, Tag-SIP revealed functional heterogeneity, i.e. different levels of N assimilation within clades of organisms, possibly reflecting niche partitioning by ecotypes.