Novel primers for 16S rRNA-based archaeal community analyses in environmental samples

Detection of Ammonia-Oxidizing Archaea in Fish Processing Effluent Treatment Plants

“…AOB-amoA gene ranged from seven orders of magnitude (1.1 9 10 7 mg -1 sludge) to the levels of eight orders of magnitude (8.5 9 10 8 mg -1 sludge) in the effluent samples. Our results are in agreement with Gantner et al [12] who found the newly designed primer set ARC 340F and ARC 1000R to be the best and highly specific to archaea as it was able to cover 93, 97 and 70 % of Crenarchaeota, Euryarchaeota and Korarchaeota sequences respectively reported in the SILVA data base (http://www.arb-silva.de/). Furthermore they observed that, in silico tests of this primer combination revealed at least 38 % higher coverage for total archaea compared to other reported primers.…”

“…Furthermore they observed that, in silico tests of this primer combination revealed at least 38 % higher coverage for total archaea compared to other reported primers. Primer set ARC 344F/ARC915R was also found to be good as it could detect 52 and 86 % of total archaeal sequences by using probe match [12]. The majority of archaeal primers were designed prior to the differentiation of archaea as Nanoarchaeota, Geoarchaeota and Aigarchaeota sub-divisions [13] and hence archaeal specific primers need to be reassessed in the light of these novel taxonomic groups.…”

Distinct Communities of Free-Living and Copepod-Associated Microorganisms along a Salinity Gradient in Godthåbsfjord, West Greenland

“…In our study, we found Marine Group II (Euryarcheota) and only one DGGE band from Marine Group I (Crenarcheota), C. DZIALLAS ET AL. / 7 which could be due to biases in our primer system (Gantner et al, 2011) or sampling time as they were also found in low abundances in the prior summer (Alonso-Saez et al, 2008).…”

Optimization and microbial community analysis of anaerobic co-digestion of food waste and sewage sludge based on microwave pretreatment

“…While the abundance of archaeal community was much lower in comparison with bacterial community, archaeal community was specially analyzed using nested PCR. In the nested PCR approach, the specific archaeal community was firstly amplified using the primers Arch340F (5 0 -CCCTAYGGGGYGCASCAG-3 0 ) and Arch1000R (5 0 -GAGARGWRGTGCATGGCC-3 0 ) as described by Gantner et al (2011), and then the PCR product was used as a template in the second PCR using the primers Arch349F (5 0 -GYGCAS CAGKCGMGAAW-3 0 ) and Arch806R (5 0 -GGACTACVSGGGTATC TAAT-3 0 ) (Takai and Horikoshi, 2000). Barcodes unique to each sample were incorporated before the forward primers, which allowed the identification of each sample in a mixture for an Illumina sequencing run.…”