Communities of ammonia-oxidizing bacteria, ammonia-oxidizing archaea and nitrite-oxidizing bacteria in shrimp ponds

The communities of nitrifying microorganisms were identified in samples taken from six shrimp ponds in Thailand (five outdoor-earthen ponds and one indoor pond). The sequences of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and nitrite-oxidizing bacteria (NOB) were analyzed after specific PCR amplification of the 16S rRNA or amoA genes. Among the ammonia-oxidizing microorganisms, AOB appeared to be the most dispersed throughout the ponds, while AOA sequences were only retrieved from three ponds. The AOB found in the shrimp ponds belonged to only two AOB clusters, the Nitrosomonas sp. Nm143 cluster and Nitrosomonas marina cluster, which are reported with salt requirements. The majority of AOA sequences fell closer to group I.1a Thaumarcheota rather than group I.1b Thaumarcheota. For NOB, Nitrospira, but not Nitrobacter, were detected. NOB of sublineage II and IV Nitrospira, which were previously reported as salt tolerant and salt requirement NOB, were found to be common in the shrimp ponds. Insight into ammonia-oxidizing microorganisms, numbers of AOB and AOA amoA genes in two selected ponds (one outdoor-earthen ponds and one indoor pond) were quantified using qPCR. High numbers of AOA amoA genes were found in both ponds. The information obtained from this study clearly identifies the microorganisms responsible for nitrification in shrimp ponds.