Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea.

Ammonia-oxidizing bacteria (AOB) have long been considered key to the removal of nitrogen in activated sludge bioreactors. Culture-independent molecular analyses have established that AOB lineages in bioreactors are dynamic, but the underlying operational or environmental factors are unclear. Furthermore, the contribution of ammonia-oxidizing archaea (AOA) to nitrogen removal in bioreactors has not been studied. To this end, we investigated the abundance of AOA and AOB as well as correlations between dynamics in AOB lineages and operational parameters at a municipal wastewater treatment plant sampled weekly over a 1 year period. Quantitative PCR measurements of bacterial and archaeal ammonia monooxygenase subunit A (amoA) genes revealed that the bacterial homologue predominated by at least three orders of magnitude in all samples. Archaeal amoA was only detectable in approximately 15% of these samples. Using terminal restriction fragment length polymorphism analysis, we monitored AOB lineages based on amoA genes. The Nitrosomonas europaea lineage and a novel Nitrosomonas-like cluster were the dominant AOB signatures, with a Nitrosospira lineage present at lower relative abundance. These lineages exhibited strong temporal oscillations, with one becoming sequentially dominant over the other. Using non-metric multidimensional scaling and redundancy analyses, we tested correlations between terminal restriction fragment length polymorphism profiles and 20 operational and environmental parameters. The redundancy analyses indicated that the dynamics of AOB lineages correlated most strongly with temperature, dissolved oxygen and influent nitrite and chromium. The Nitrosospira lineage signal had a strong negative correlation to dissolved oxygen and temperature, while the Nitrosomonas-like (negative correlations) and N. europaea lineages (positive correlations) were inversely linked (relative to one another) to influent nitrite and chromium. Overall, this study suggests that AOA may be minor contributors to ammonia oxidation in highly aerated activated sludge, and provides insight into parameters controlling the diversity and dominance of AOB lineages within bioreactors during periods of stable nitrification.

[1]  F. Villa,et al.  The Effect of Copper on The Structure of the Ammonia-Oxidizing Microbial Community in an Activated Sludge Wastewater Treatment Plant , 2009, Microbial Ecology.

[2]  Annika C. Mosier,et al.  Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. , 2008, Environmental microbiology.

[3]  C. Schleper,et al.  The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. , 2008, Environmental microbiology.

[4]  J. Prosser,et al.  Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. , 2008, Environmental microbiology.

[5]  Yong-guan Zhu,et al.  Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. , 2008, Environmental microbiology.

[6]  A. Boehm,et al.  Shifts in the relative abundance of ammonia-oxidizing bacteria and archaea across physicochemical gradients in a subterranean estuary. , 2008, Environmental microbiology.

[7]  J. Beman,et al.  Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California , 2008, The ISME Journal.

[8]  M. Könneke,et al.  Cultivation of a Thermophilic Ammonia Oxidizing Archaeon Synthesizing Crenarchaeol , 2022 .

[9]  V. Kunin,et al.  A bacterial metapopulation adapts locally to phage predation despite global dispersal. , 2008, Genome research.

[10]  Karen L. Adair,et al.  Evidence that Ammonia-Oxidizing Archaea are More Abundant than Ammonia-Oxidizing Bacteria in Semiarid Soils of Northern Arizona, USA , 2008, Microbial Ecology.

[11]  C. Criddle,et al.  Correlation of patterns of denitrification instability in replicated bioreactor communities with shifts in the relative abundance and the denitrification patterns of specific populations , 2007, The ISME Journal.

[12]  J. Hollibaugh,et al.  Ammonia oxidation and ammonia-oxidizing bacteria and archaea from estuaries with differing histories of hypoxia , 2007, The ISME Journal.

[13]  M. Hermansson,et al.  Effects of environmental conditions on the nitrifying population dynamics in a pilot wastewater treatment plant. , 2007, Environmental microbiology.

[14]  Ming-Gang Xu,et al.  Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. , 2007, Environmental microbiology.

[15]  Katie Bloor,et al.  Experimental demonstration of chaotic instability in biological nitrification , 2007, The ISME Journal.

[16]  Yoriko Sakamoto,et al.  Effects of ammonium and nitrite on communities and populations of ammonia-oxidizing bacteria in laboratory-scale continuous-flow reactors. , 2007, FEMS microbiology ecology.

[17]  D. Noguera,et al.  Characterization of two ammonia‐oxidizing bacteria isolated from reactors operated with low dissolved oxygen concentrations , 2007, Journal of applied microbiology.

[18]  M. Kuypers,et al.  New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation , 2007, The ISME Journal.

[19]  R. Amann,et al.  Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea , 2007, Proceedings of the National Academy of Sciences.

[20]  Slil Siripong,et al.  Diversity study of nitrifying bacteria in full-scale municipal wastewater treatment plants. , 2007, Water research.

[21]  W. Verstraete,et al.  Real-time PCR assay for the simultaneous quantification of nitrifying and denitrifying bacteria in activated sludge , 2007, Applied Microbiology and Biotechnology.

[22]  Takako Sasaki,et al.  Molecular analysis of ammonia-oxidizing bacteria community in intermittent aeration sequencing batch reactors used for animal wastewater treatment. , 2006, Environmental microbiology.

[23]  T. Urich,et al.  Archaea predominate among ammonia-oxidizing prokaryotes in soils , 2006, Nature.

[24]  Marc Strous,et al.  Archaeal nitrification in the ocean , 2006, Proceedings of the National Academy of Sciences.

[25]  C. Criddle,et al.  Occurrence of Ammonia-Oxidizing Archaea in Wastewater Treatment Plant Bioreactors , 2006, Applied and Environmental Microbiology.

[26]  T P Curtis,et al.  Towards the design of diversity: stochastic models for community assembly in wastewater treatment plants. , 2006, Water science and technology : a journal of the International Association on Water Pollution Research.

[27]  C. Schleper,et al.  Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle? , 2006, Trends in microbiology.

[28]  S. Nee,et al.  Quantifying the roles of immigration and chance in shaping prokaryote community structure. , 2006, Environmental microbiology.

[29]  P. de Vos,et al.  Failure of the ammonia oxidation process in two pharmaceutical wastewater treatment plants is linked to shifts in the bacterial communities , 2005, Journal of applied microbiology.

[30]  Tong Zhang,et al.  Effect of pH change on the performance and microbial community of enhanced biological phosphate removal process. , 2005, Biotechnology and bioengineering.

[31]  J. Beman,et al.  Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[32]  Thomas P. Curtis,et al.  Agreement between Theory and Measurement in Quantification of Ammonia-Oxidizing Bacteria , 2005, Applied and Environmental Microbiology.

[33]  M. Könneke,et al.  Isolation of an autotrophic ammonia-oxidizing marine archaeon , 2005, Nature.

[34]  K. Gilbride,et al.  Nitrification in activated sludge batch reactors is linked to protozoan grazing of the bacterial population. , 2005, Canadian journal of microbiology.

[35]  D. Stahl,et al.  Loss of diversity of ammonia-oxidizing bacteria correlates with increasing salinity in an estuary system. , 2005, Environmental microbiology.

[36]  G. Sayler,et al.  Emergence of Competitive Dominant Ammonia-Oxidizing Bacterial Populations in a Full-Scale Industrial Wastewater Treatment Plant , 2005, Applied and Environmental Microbiology.

[37]  B. Ward,et al.  Community level analysis: genetic and biogeochemical approaches to investigate community composition and function in aerobic ammonia oxidation. , 2005, Methods in enzymology.

[38]  C. Field,et al.  Ammonia-oxidizing bacteria respond to multifactorial global change. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[39]  T. Limpiyakorn,et al.  Distribution of ammonia-oxidizing bacteria in sewage activated sludge: analysis based on 16S rDNA sequence. , 2004, Water science and technology : a journal of the International Association on Water Pollution Research.

[40]  D. Noguera,et al.  Evaluating the effect of dissolved oxygen on ammonia-oxidizing bacterial communities in activated sludge. , 2004, Water research.

[41]  C. Braak,et al.  Canonical correspondence analysis and related multivariate methods in aquatic ecology , 1995, Aquatic Sciences.

[42]  G. Sayler,et al.  Molecular assessment of ammonia- and nitrite-oxidizing bacteria in full-scale activated sludge wastewater treatment plants. , 2003, Water science and technology : a journal of the International Association on Water Pollution Research.

[43]  Michael Wagner,et al.  16S rRNA and amoA-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads. , 2003, International journal of systematic and evolutionary microbiology.

[44]  Werner Liesack,et al.  Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers. , 2003, Environmental microbiology.

[45]  L. Raskin,et al.  Diversity and dynamics of microbial communities in engineered environments and their implications for process stability. , 2003, Current opinion in biotechnology.

[46]  Jan Lepš,et al.  Multivariate Analysis of Ecological Data using CANOCO , 2003 .

[47]  J. Lamerdin,et al.  Complete Genome Sequence of the Ammonia-Oxidizing Bacterium and Obligate Chemolithoautotroph Nitrosomonas europaea , 2003, Journal of bacteriology.

[48]  A. K. Rowan,et al.  Composition and diversity of ammonia-oxidising bacterial communities in wastewater treatment reactors of different design treating identical wastewater. , 2003, FEMS microbiology ecology.

[49]  G. Sayler,et al.  Real-time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant. , 2003, Environmental science & technology.

[50]  T. Liebig,et al.  Effect of carbon dioxide on nitrification rates , 2003, Bioprocess and biosystems engineering.

[51]  S. Tsuneda,et al.  Community analysis of nitrifying bacteria in an advanced and compact Gappei-Johkasou by FISH and PCR-DGGE. , 2002, Water science and technology : a journal of the International Association on Water Pollution Research.

[52]  I. Head,et al.  The effect of C/N ratio on ammonia oxidising bacteria community structure in a laboratory nitrification-denitrification reactor. , 2002, Water science and technology : a journal of the International Association on Water Pollution Research.

[53]  J. Regan,et al.  Molecular analysis of ammonia-oxidizing bacterial populations in aerated-anoxic orbal processes. , 2002, Water science and technology : a journal of the International Association on Water Pollution Research.

[54]  Michael Wagner,et al.  Bacterial community composition and function in sewage treatment systems. , 2002, Current opinion in biotechnology.

[55]  J. Etxebarria,et al.  A comparison of five rapid direct toxicity assessment methods to determine toxicity of pollutants to activated sludge. , 2002, Chemosphere.

[56]  G. Sayler,et al.  Quantification of Nitrosomonas oligotropha-Like Ammonia-Oxidizing Bacteria and Nitrospira spp. from Full-Scale Wastewater Treatment Plants by Competitive PCR , 2002, Applied and Environmental Microbiology.

[57]  H. Koops,et al.  Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species , 2001 .

[58]  R. Amann,et al.  Community Structure and Activity Dynamics of Nitrifying Bacteria in a Phosphate-Removing Biofilm , 2001, Applied and Environmental Microbiology.

[59]  G. Kowalchuk,et al.  Shifts in the dominant populations of ammonia-oxidizing ß subclass Proteobacteria along the eutrophic Schelde estuary , 2001 .

[60]  K. Fujie,et al.  Effects of temperature on biodegradation characteristics of organic pollutants and microbial community in a solid phase aerobic bioreactor treating high strength organic wastewater. , 2001, Water science and technology : a journal of the International Association on Water Pollution Research.

[61]  G. Kowalchuk,et al.  Ammonia-oxidizing bacteria: a model for molecular microbial ecology. , 2001, Annual review of microbiology.

[62]  M. Wagner,et al.  Phylogeny of All Recognized Species of Ammonia Oxidizers Based on Comparative 16S rRNA and amoA Sequence Analysis: Implications for Molecular Diversity Surveys , 2000, Applied and Environmental Microbiology.

[63]  Craig S. Criddle,et al.  Flexible Community Structure Correlates with Stable Community Function in Methanogenic Bioreactor Communities Perturbed by Glucose , 2000, Applied and Environmental Microbiology.

[64]  J. Kristjánsson,et al.  Influence of Sulfide and Temperature on Species Composition and Community Structure of Hot Spring Microbial Mats , 2000, Applied and Environmental Microbiology.

[65]  Suiying Huang,et al.  How Stable Is Stable? Function versus Community Composition , 1999, Applied and Environmental Microbiology.

[66]  R. Conrad,et al.  Effect of Temperature on Structure and Function of the Methanogenic Archaeal Community in an Anoxic Rice Field Soil , 1999, Applied and Environmental Microbiology.

[67]  D. Stahl,et al.  Molecular and modeling analyses of the structure and function of nitrifying activated sludge , 1999 .

[68]  D. Arp,et al.  Loss of Ammonia Monooxygenase Activity in Nitrosomonas europaea upon Exposure to Nitrite , 1998, Applied and Environmental Microbiology.

[69]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[70]  W. Liesack,et al.  The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations , 1997, Applied and environmental microbiology.

[71]  M. Strous,et al.  Effects of aerobic and microaerobic conditions on anaerobic ammonium-oxidizing (anammox) sludge , 1997, Applied and environmental microbiology.

[72]  R. H. Økland.  Are ordination and constrained ordination alternative or complementary strategies in general ecological studies , 1996 .

[73]  P. Nielsen.  Adsorption of ammonium to activated sludge , 1996 .

[74]  K. Schleifer,et al.  In situ Identification of Ammonia-oxidizing Bacteria , 1995 .

[75]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[76]  K. R. Clarke,et al.  Non‐parametric multivariate analyses of changes in community structure , 1993 .

[77]  M. Stenstrom,et al.  EFFECTS OF OXYGEN TRANSPORT LIMITATION ON NITRIFICATION IN THE ACTIVATED SLUDGE PROCESS , 1991 .

[78]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[79]  R. Loehr,et al.  Inhibition of nitrification by ammonia and nitrous acid. , 1976, Journal - Water Pollution Control Federation.