Application of a Novel Functional Gene Microarray to Probe the Functional Ecology of Ammonia Oxidation in Nitrifying Activated Sludge

Abstract

We report on the first study trialling a newly-developed, functional gene microarray (FGA) for characterising bacterial and archaeal ammonia oxidisers in activated sludge. Mixed liquor (ML) and media biofilm samples from a full-scale integrated fixed-film activated sludge (IFAS) plant were analysed with the FGA to profile the diversity and relative abundance of ammonia-oxidising archaea and bacteria (AOA and AOB respectively). FGA analyses of AOA and AOB communities revealed ubiquitous distribution of AOA across all samples – an important finding for these newly-discovered and poorly characterised organisms. Results also revealed striking differences in the functional ecology of attached versus suspended communities within the IFAS reactor. Quantitative assessment of AOB and AOA functional gene abundance revealed a dominance of AOB in the ML and approximately equal distribution of AOA and AOB in the media-attached biofilm. Subsequent correlations of functional gene abundance data with key water quality parameters suggested an important functional role for media-attached AOB in particular for IFAS reactor nitrification performance and indicate possible functional redundancy in some IFAS ammonia oxidiser communities. Results from this investigation demonstrate the capacity of the FGA to resolve subtle ecological shifts in key microbial communities in nitrifying activated sludge and indicate its value as a tool for better understanding the linkages between the ecology and performance of these engineered systems.

The Diversity of Nitrogen-Cycling Microbial Genes in a Waste Stabilization Pond Reveals Changes over Space and Time that Is Uncoupled to Changing Nitrogen Chemistry

“…1). A functional gene array (FGA) is an ideal approach because it allows an efficient and targeted search for N-cycling microbes [9]. Because FGAs are a rapid and cost-effective method for detecting microbes and their functional genes from virtually any sample, they can be applied to a wide array of sample types [9,10].…”

“…A functional gene array (FGA) is an ideal approach because it allows an efficient and targeted search for N-cycling microbes [9]. Because FGAs are a rapid and cost-effective method for detecting microbes and their functional genes from virtually any sample, they can be applied to a wide array of sample types [9,10]. For example, FGA studies investigating nitrogen cycling associated with harmful cyanobacterial and dinoflagellate blooms in freshwater and marine environments showed that genes and bacteria driving N cycling were spatially and temporally dynamic [11,12].…”

“…Similarly, the environment can also determine the abundance of different functional groups of N-cycling microbes. For example, ammonia oxidisers (AamoA and BamoA) are competitive under low oxygen conditions and low NH 4 + -N concentrations [9,[13][14][15][16]. Thus, it is not surprising that wastewater physicochemistry and the N substrate concentration can influence the dominance of functional microbial groups.…”

“…Comparisons of numerous worldwide studies on N removal and transformation in WSPs show how the changing environmental conditions influence the N-cycling process and microbes involved [3,[17][18][19][20][21]. These studies show that shifting environmental conditions over space and time changed the N transformation along with the microbial community and diversity because N-cycling microbes were habitat specific [9]. Genes associated with nitrogencycling pathways include as follows: nrfA, DNRA (dissimilatory NO 3 reduction to NH 3 ); nosZ, denitrification; hszA, anammox; nifH, nitrogen fixation; AamoA and BamoA, ammonia oxidation; nxrB, nitrite oxidation.…”

“…Because of a lack of understanding of the N-cycling communities, previous wastewater systems were developed without considering the key microbes involved in N treatment. Consideration of N-cycling groups was further confounded by the complicated relationship bacteria and archaea have with the surrounding physical environment and chemical substrates they use [ 9 ]. It is well established that the physical environment can influence N-cycling transformation pathways.…”