The diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the sediment of the Pearl River Estuary were investigated by cloning and quantitative real-time polymerase chain reaction (qPCR). From one sediment sample S16, 36 AOA OTUs (3% cutoff) were obtained from three clone libraries constructed using three primer sets for amoA gene. Among the 36 OTUs, six were shared by all three clone libraries, two appeared in two clone libraries, and the other 28 were only recovered in one of the libraries. For AOB, only seven OTUs (based on 16S rRNA gene) and eight OTUs (based on amoA gene) were obtained, showing lower diversity than AOA. The qPCR results revealed that AOA amoA gene copy numbers ranged from 9.6 × 106 to 5.1 × 107 copies per gram of sediment and AOB amoA gene ranged from 9.5 × 104 to 6.2 × 105 copies per gram of sediment, indicating that the dominant ammonia-oxidizing microorganisms in the sediment of the Pearl River Estuary were AOA. The terminal restriction fragment length polymorphism results showed that the relative abundance of AOB species in the sediment samples of different salinity were significantly different, indicating that salinity might be a key factor shaping the AOB community composition.Electronic supplementary materialThe online version of this article (doi:10.1007/s00253-011-3107-8) contains supplementary material, which is available to authorized users.

Aims:  Characterization of the ammonia‐oxidizing archaea (AOA) community in activated sludge from a nitrogen removal bioreactor and wastewater treatment plants (WWTPs). Methods and Results:  Three primer sets specific for ammonia mono‐oxygenase α‐subunit (amoA) were used to construct clone libraries for activated sludge sample from a nitrogen removal bioreactor. One primer set resulted in strong nonspecific PCR products. The other two clone libraries retrieved both shared and unique AOA amoA sequences. One primer set was chosen to study the AOA communities of activated sludge samples from Shatin and Stanley WWTPs. In total, 18 AOA amoA sequences were recovered and compared to the previous reported sequences. A phylogenetic analysis indicated that sequences found in this study fell into three clusters. Conclusions:  Different primers resulted in varied AOA communities from the same sample. The AOA found from Hong Kong WWTPs were closely similar to those from sediment and soil, but distinct from those from activated sludge in other places. A comparison of clone libraries between Shatin WWTP and bioreactor indicated the AOA community significantly shifted only after 30‐day enrichment. Significance and Impact of the Study:  This study confirmed the occurrence of AOA in a laboratory scale nitrogen removal bioreactor and Hong Kong WWTPs treating saline or freshwater wastewater. AOA communities found in this study were significantly different from those found in other places. To retrieve diverse AOA communities from environmental samples, a combination of different primers for the amoA gene is needed.

Using ammonia monooxygenase α-subunit (amoA) gene and 16S rRNA gene, the community structure and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in a nitrogen-removing reactor, which was operated for five phases, were characterized and quantified by cloning, terminal restriction fragment length polymorphism (T-RFLP), and quantitative polymerase chain reaction (qPCR). The results suggested that the dominant AOB in the reactor fell to the genus Nitrosomonas, while the dominant AOA belonged to Crenarchaeotal Group I.1a in phylum Crenarchaeota. Real-time PCR results demonstrated that the levels of AOB amoA varied from 2.9 × 103 to 2.3 × 105 copies per nanogram DNA, greatly (about 60 times) higher than those of AOA, which ranged from 1.7 × 102 to 3.8 × 103 copies per nanogram DNA. This indicated the possible leading role of AOB in the nitrification process in this study. T-RFLP results showed that the AOB community structure significantly shifted in different phases while AOA only showed one major peak for all the phases. The analyses also suggested that the AOB community was more sensitive than that of AOA to operational conditions, such as ammonia loading and dissolved oxygen.

Many soft-bodied sessile marine invertebrates such as sponges and soft corals defend themselves against fouling directly through the production of antifouling compounds, or indirectly through regulating the epibiotic microbes that affect larval settlement. In this study, 10beta-formamidokalihinol-A and kalihinol A were isolated and purified from the marine sponge Acanthella cavernosa (Dendy). The results indicated that both compounds inhibited the growth of bacteria isolated from the natural environment whereas kalihinol A suppressed larval settlement of a major fouling polychaete, Hydroides elegans with an EC50 of 0.5 microg ml(-1). Kalihinol A was incorporated in Phytagel that was exposed to the bacterial consortia in natural seawater for biofilm formation. Biofilms that developed on the Phytagel surfaces were analysed for bacterial abundance and bacterial species composition using a DNA fingerprinting technique, terminal restriction fragment length polymorphism (T-RFLP). The results showed that kalihinol A only slightly reduced bacterial abundance (t-test, p = 0.0497), but modified the bacterial species composition of the biofilms. Inhibition of H. elegans larval settlement was observed when biofilms developed under the influence of kalihinol A were exposed to larvae, suggesting that compounds like kalihinol A from the sponge A. cavernosa may change bacterial community composition on the sponge surface, which in turn, modulates larval settlement of fouling organisms.