Rapid TaqMan-based Quantification of Chlorophyll d-containing

23 Reports of the chlorophyll (Chl) d-containing cyanobacterium Acaryochloris sp. in various habitats 24 have accumulated since its initial discovery in 1996. The majority of this evidence is based on 25 amplification of the gene coding for the 16S rRNA and due to the wide geographical distribution of 26 these sequences a global distribution of Acaryochloris sp. was suggested. Here we present a rapid, 27 reliable and cost-effective TaqMan-based qPCR assay that was developed for the specific detection 28 of Acaryochloris sp. in complex environmental samples. The probe showed detection limits of ~10 29 16S rRNA gene copy numbers based on standard curves consisting of plasmid inserts. DNA from 30 five Acaryochloris strains, i.e. MBIC11017, CCMEE5410, HICR111A, CRS and Awaji-1, 31 exhibited amplification efficiencies of >94% when tested in the TaqMan assay. When used on 32 complex natural communities, the TaqMan assay detected the presence of Acaryochloris sp. in four 33 out of eight samples of crustose coralline algae (CCA), collected from temperate and tropical 34 regions. In three out of these TaqMan-positive samples the presence of Chl d was confirmed via 35 HPLC and corresponding cell estimates of Acaryochloris sp. amounted to 7.6 x 103.0 x 10 per 36 mg of CCA. These numbers indicate a substantial contribution of Chl d-containing cyanobacteria to 37 primary productivity in endolithic niches. The new TaqMan assay allows quick and easy screening 38 of environmental samples for the presence of Acaryochloris sp. and is an important tool to further 39 resolve the global distribution and significance of this unique oxyphototroph. 40