Transcriptional Response of the Archaeal Ammonia Oxidizer Nitrosopumilus maritimus to Low and Environmentally Relevant Ammonia Concentrations

ABSTRACTThe ability of chemoautotrophic ammonia-oxidizing archaea to compete for ammonia among marine microorganisms at low ambient concentrations has been in part attributed to their extremely high affinity for ammonia, but as yet there is no mechanistic understanding of supporting metabolism. We examined transcription of selected genes for anabolic functions (CO2fixation, ammonia transport, and cell wall synthesis) and a central catabolic function (ammonia oxidation) in the thaumarchaeonNitrosopumilus maritimusSCM1 growing at two ammonia concentrations, as measured by combined ammonia and ammonium, one well above theKmfor ammonia oxidation (∼500 μM) and the other well below theKm(<10 nM). Transcript levels were generally immediately and differentially repressed when cells transitioned from ammonia-replete to ammonia-limiting conditions. Transcript levels for ammonia oxidation, CO2fixation, and one of the ammonia transport genes were approximately the same at high and low ammonia availability. Transcripts for all analyzed genes decreased with time in the complete absence of ammonia, but with various rates of decay. The new steady-state mRNA levels established are presumably more reflective of the natural physiological state of ammonia-oxidizing archaea and offer a reference for interpreting message abundance patterns in the natural environment.

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Competition for Ammonia Influences the Structure of Chemotrophic Communities in Geothermal Springs

Applied and Environmental Microbiology ◽

10.1128/aem.02577-13 ◽

2013 ◽

Vol 80 (2) ◽

pp. 653-661 ◽

Cited By ~ 22

Author(s):

Trinity L. Hamilton ◽

Evangeline Koonce ◽

Alta Howells ◽

Jeff R. Havig ◽

Talia Jewell ◽

...

Keyword(s):

Nitrogen Fixation ◽

Acetylene Reduction ◽

Ammonia Oxidation ◽

Hot Spring ◽

Transcript Levels ◽

Content Type ◽

Geothermal Springs ◽

Ammonia Oxidizing Archaea ◽

Nitrite Production ◽

N Pool

ABSTRACTSource waters sampled from Perpetual Spouter hot spring (pH 7.03, 86.4°C), Yellowstone National Park, WY, have low concentrations of total ammonia, nitrite, and nitrate, suggesting nitrogen (N) limitation and/or tight coupling of N cycling processes. Dominant small-subunit rRNA sequences in Perpetual Spouter source sediments are closely affiliated with the ammonia-oxidizing archaeon “CandidatusNitrosocaldus yellowstonii” and the putatively nitrogen-fixing (diazotrophic) bacteriumThermocrinis albus, respectively, suggesting that these populations may interact at the level of the bioavailable N pool, specifically, ammonia. This hypothesis was evaluated by using a combination of geochemical, physiological, and transcriptomic analyses of sediment microcosms. Amendment of microcosms with allylthiourea, an inhibitor of ammonia oxidation, decreased rates of acetylene reduction (a proxy for N2fixation) and nitrite production (a proxy for ammonia oxidation) and decreased transcript levels of structural genes involved in both nitrogen fixation (nifH) and ammonia oxidation (amoA). In contrast, amendment of microcosms with ammonia stimulated nitrite production and increasedamoAtranscript levels while it suppressed rates of acetylene reduction and decreasednifHtranscript levels. Sequencing of amplifiednifHandamoAtranscripts from native sediments, as well as microcosms, at 2 and 4 h postamendment, indicates that the dominant and responsive populations involved in ammonia oxidation and N2fixation are closely affiliated withCa. Nitrosocaldus yellowstonii andT. albus, respectively. Collectively, these results suggest that ammonia-oxidizing archaea, such asCa. Nitrosocaldus yellowstonii, have an apparent affinity for ammonia that is higher than that of the diazotrophs present in this ecosystem. Depletion of the bioavailable N pool through the activity of ammonia-oxidizing archaea likely represents a strong selective pressure for the inclusion of organisms capable of nitrogen fixation in geothermal communities. These observations help to explain the strong pattern in the codistribution of ammonia-oxidizing archaea and diazotrophs in circumneutral-to-alkaline geothermal springs.

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The Putative APSES Transcription Factor RgdA Governs Growth, Development, Toxigenesis, and Virulence in Aspergillus fumigatus

mSphere ◽

10.1128/msphere.00998-20 ◽

2020 ◽

Vol 5 (6) ◽

Author(s):

Sang-Cheol Jun ◽

Yong-Ho Choi ◽

Min-Woo Lee ◽

Jae-Hyuk Yu ◽

Kwang-Soo Shin

Keyword(s):

Transcription Factor ◽

Aspergillus Fumigatus ◽

Molecular Mechanisms ◽

Pathogenic Fungus ◽

Mrna Levels ◽

Transcript Levels ◽

Content Type ◽

Asexual Sporulation ◽

Human Pathogenic Fungus ◽

Growth Development

ABSTRACT The APSES transcription factor (TF) in Aspergillus species is known to govern diverse cellular processes, including growth, development, and secondary metabolism. Here, we investigated functions of the rgdA gene (Afu3g13920) encoding a putative APSES TF in the opportunistic human-pathogenic fungus Aspergillus fumigatus. The rgdA deletion resulted in significantly decreased hyphal growth and asexual sporulation. Consistently, transcript levels of the key asexual developmental regulators abaA, brlA, and wetA were decreased in the ΔrgdA mutant compared to those in the wild type (WT). Moreover, ΔrgdA resulted in reduced spore germination rates and elevated transcript levels of genes associated with conidium dormancy. The conidial cell wall hydrophobicity and architecture were changed, and levels of the RodA protein were decreased in the ΔrgdA mutant. Comparative transcriptomic analyses revealed that the ΔrgdA mutant showed higher mRNA levels of gliotoxin (GT)-biosynthetic genes and GT production. While the ΔrgdA mutant exhibited elevated production of GT, ΔrgdA strains showed reduced virulence in the mouse model. In addition, mRNA levels of genes associated with the cyclic AMP (cAMP)-protein kinase A (PKA) signaling pathway and the SakA mitogen-activated protein (MAP) kinase pathway were increased in the ΔrgdA mutant. In summary, RgdA plays multiple roles in governing growth, development, GT production, and virulence which may involve attenuation of PKA and SakA signaling. IMPORTANCE Immunocompromised patients are susceptible to infections with the opportunistic human-pathogenic fungus Aspergillus fumigatus. This fungus causes systemic infections such as invasive aspergillosis (IA), which is one of the most life-threatening fungal diseases. To control this serious disease, it is critical to identify new antifungal drug targets. In fungi, the transcriptional regulatory proteins of the APSES family play crucial roles in controlling various biological processes, including mating, asexual sporulation and dimorphic growth, and virulence traits. This study found that a putative APSES transcription factor, RgdA, regulates normal growth, asexual development, conidium germination, spore wall architecture and hydrophobicity, toxin production, and virulence in A. fumigatus. Better understanding the molecular mechanisms of RgdA in human-pathogenic fungi may reveal a novel antifungal target for future drug development.

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Nitrogen and Oxygen Isotope Effects of Ammonia Oxidation by Thermophilic Thaumarchaeota from a Geothermal Water Stream

Applied and Environmental Microbiology ◽

10.1128/aem.00250-16 ◽

2016 ◽

Vol 82 (15) ◽

pp. 4492-4504 ◽

Cited By ~ 14

Author(s):

Manabu Nishizawa ◽

Sanae Sakai ◽

Uta Konno ◽

Nozomi Nakahara ◽

Yoshihiro Takaki ◽

...

Keyword(s):

Oxygen Isotope ◽

Ammonia Oxidation ◽

Isotope Effects ◽

Isotope Ratios ◽

Oxidation Activity ◽

Content Type ◽

Ammonia Oxidizing Archaea ◽

Nitrogen Pools ◽

Archaeal Ammonia Oxidation

ABSTRACTAmmonia oxidation regulates the balance of reduced and oxidized nitrogen pools in nature. Although ammonia-oxidizing archaea have been recently recognized to often outnumber ammonia-oxidizing bacteria in various environments, the contribution of ammonia-oxidizing archaea is still uncertain due to difficulties in thein situquantification of ammonia oxidation activity. Nitrogen and oxygen isotope ratios of nitrite (δ15NNO2−and δ18ONO2−, respectively) are geochemical tracers for evaluating the sources and thein siturate of nitrite turnover determined from the activities of nitrification and denitrification; however, the isotope ratios of nitrite from archaeal ammonia oxidation have been characterized only for a few marine species. We first report the isotope effects of ammonia oxidation at 70°C by thermophilicThaumarchaeotapopulations composed almost entirely of “CandidatusNitrosocaldus.” The nitrogen isotope effect of ammonia oxidation varied with ambient pH (25‰ to 32‰) and strongly suggests the oxidation of ammonia, not ammonium. The δ18O value of nitrite produced from ammonia oxidation varied with the δ18O value of water in the medium but was lower than the isotopic equilibrium value in water. Because experiments have shown that the half-life of abiotic oxygen isotope exchange between nitrite and water is longer than 33 h at 70°C and pH ≥6.6, the rate of ammonia oxidation by thermophilicThaumarchaeotacould be estimated using δ18ONO2−in geothermal environments, where the biological nitrite turnover is likely faster than 33 h. This study extended the range of application of nitrite isotopes as a geochemical clock of the ammonia oxidation activity to high-temperature environments.IMPORTANCEBecause ammonia oxidation is generally the rate-limiting step in nitrification that regulates the balance of reduced and oxidized nitrogen pools in nature, it is important to understand the biological and environmental factors underlying the regulation of the rate of ammonia oxidation. The discovery of ammonia-oxidizing archaea (AOA) in marine and terrestrial environments has transformed the concept that ammonia oxidation is operated only by bacterial species, suggesting that AOA play a significant role in the global nitrogen cycle. However, the archaeal contribution to ammonia oxidation in the global biosphere is not yet completely understood. This study successfully identified key factors controlling nitrogen and oxygen isotopic ratios of nitrite produced from thermophilicThaumarchaeotaand elucidated the applicability and its limit of nitrite isotopes as a geochemical clock of ammonia oxidation rate in nature. Oxygen isotope analysis in this study also provided new biochemical information on archaeal ammonia oxidation.

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The Staphylococcus aureus Protein-Coding GenegdpSModulatessarSExpression via mRNA-mRNA Interaction

Infection and Immunity ◽

10.1128/iai.00159-15 ◽

2015 ◽

Vol 83 (8) ◽

pp. 3302-3310 ◽

Cited By ~ 5

Author(s):

Chuan Chen ◽

Xu Zhang ◽

Fei Shang ◽

Haipeng Sun ◽

Baolin Sun ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Environmental Changes ◽

Wide Spectrum ◽

Protein A ◽

Mrna Levels ◽

Site Mutation ◽

Transcript Levels ◽

Content Type ◽

Ggdef Domain ◽

Domain Protein

Staphylococcus aureusis an important Gram-positive pathogen responsible for numerous diseases ranging from localized skin infections to life-threatening systemic infections. The virulence ofS. aureusis essentially determined by a wide spectrum of factors, including cell wall-associated proteins and secreted toxins that are precisely controlled in response to environmental changes. GGDEF domain protein fromStaphylococcus(GdpS) is the only conserved staphylococcal GGDEF domain protein that is involved not in c-di-GMP synthesis but in the virulence regulation ofS. aureusNCTC8325. Our previous study showed that the inactivation ofgdpSgenerates an extensive change of virulence factors together with, in particular, a major Spa (protein A) surface protein. As reported,sarSis a direct positive regulator ofspa. The decreased transcript levels ofsarSin thegdpSmutant compared with the parental NCTC8325 strain suggest thatgdpSaffectsspathrough interaction withsarS. In this study, site mutation and complementary experiments showed that the translation product ofgdpSwas not involved in the regulation of transcript levels ofsarS. We found thatgdpSfunctioned through direct RNA-RNA base pairing with the 5′ untranslated region (5′UTR) ofsarSmRNA and that a putative 18-nucleotide region played a significant role in the regulatory process. Furthermore, the mRNA half-life analysis ofsarSin thegdpSmutant showed thatgdpSpositively regulates the mRNA levels ofsarSby contributing to the stabilization ofsarSmRNA, suggesting thatgdpSmRNA may regulatespaexpression in an RNA-dependent pathway.

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Ecophysiological Characterization of Ammonia-Oxidizing Archaea and Bacteria from Freshwater

Applied and Environmental Microbiology ◽

10.1128/aem.00432-12 ◽

2012 ◽

Vol 78 (16) ◽

pp. 5773-5780 ◽

Cited By ~ 113

Author(s):

Elizabeth French ◽

Jessica A. Kozlowski ◽

Maitreyee Mukherjee ◽

George Bullerjahn ◽

Annette Bollmann

Keyword(s):

Growth Rates ◽

Ammonia Oxidation ◽

Light Exposure ◽

Enrichment Culture ◽

Ammonia Oxidizing Bacteria ◽

Content Type ◽

Ammonia Oxidizing Archaea ◽

Group I ◽

Nitrosomonas Oligotropha

ABSTRACTAerobic biological ammonia oxidation is carried out by two groups of microorganisms, ammonia-oxidizing bacteria (AOB) and the recently discovered ammonia-oxidizing archaea (AOA). Here we present a study using cultivation-based methods to investigate the differences in growth of three AOA cultures and one AOB culture enriched from freshwater environments. The strain in the enriched AOA culture belong to thaumarchaeal group I.1a, with the strain in one enrichment culture having the highest identity with “CandidatusNitrosoarchaeum koreensis” and the strains in the other two representing a new genus of AOA. The AOB strain in the enrichment culture was also obtained from freshwater and had the highest identity to AOB from theNitrosomonas oligotrophagroup (Nitrosomonascluster 6a). We investigated the influence of ammonium, oxygen, pH, and light on the growth of AOA and AOB. The growth rates of the AOB increased with increasing ammonium concentrations, while the growth rates of the AOA decreased slightly. Increasing oxygen concentrations led to an increase in the growth rate of the AOB, while the growth rates of AOA were almost oxygen insensitive. Light exposure (white and blue wavelengths) inhibited the growth of AOA completely, and the AOA did not recover when transferred to the dark. AOB were also inhibited by blue light; however, growth recovered immediately after transfer to the dark. Our results show that the tested AOB have a competitive advantage over the tested AOA under most conditions investigated. Further experiments will elucidate the niches of AOA and AOB in more detail.

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Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical spongeIanthella basta

10.1101/527234 ◽

2019 ◽

Cited By ~ 1

Author(s):

Florian U. Moeller ◽

Nicole S. Webster ◽

Craig W. Herbold ◽

Faris Behnam ◽

Daryl Domman ◽

...

Keyword(s):

Ammonia Oxidation ◽

Indirect Evidence ◽

Marine Sponges ◽

Ammonia Oxidizer ◽

Filter Feeding ◽

Ammonia Oxidizing Archaea ◽

Branched Chain Amino Acid ◽

Direct Demonstration ◽

Branched Chain

SummaryMarine sponges represent one of the few eukaryotic groups that frequently harbor symbiotic members of theThaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However, in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of ammonia-oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine spongeIanthella bastausing metaproteogenomics, fluorescencein situhybridization, qPCR and isotope-based functional assays. “CandidatusNitrosospongia bastadiensis” is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia inI. bastathat surprisingly does not harbor nitrite-oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system, represent important adaptations of AOA to life within these ancient filter-feeding animals.Originality-Significance StatementMany marine sponges harbor symbiotic members of theThaumarchaeota, but there is generally only indirect evidence available about their functional role within these filter-feeding animals. Furthermore, the specific adaptations of thaumarchaeal symbionts to their sponge hosts are incompletely understood. In this study, we thoroughly characterized a thaumarchaeal symbiont residing in the reef spongeIanthella bastaand demonstrate by using a combination of molecular tools and isotope techniques, that it is the only ammonia-oxidizer in its host. In contrast to other sponges,I. bastadoes not contain nitrite-oxidizing microbes and thus excretes considerable amounts of nitrite. Furthermore, using metagenomics and metaproteomics we reveal important adaptations of this symbiont, that represents a new genus within theThaumarchaeota, and conclude that it most likely lives as a mixotroph in its sponge host.

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The Response of Estuarine Ammonia-Oxidizing Communities to Constant and Fluctuating Salinity Regimes

Frontiers in Microbiology ◽

10.3389/fmicb.2020.574815 ◽

2020 ◽

Vol 11 ◽

Author(s):

João Pereira Santos ◽

António G. G. Sousa ◽

Hugo Ribeiro ◽

Catarina Magalhães

Keyword(s):

Ammonia Oxidation ◽

Estuarine Sediments ◽

Ammonia Oxidizer ◽

Rrna Gene ◽

Ammonia Oxidizing Bacteria ◽

Salinity Regime ◽

Salinity Fluctuation ◽

Ammonia Oxidizing Archaea ◽

Negative Effect ◽

The Impact

Aerobic nitrification is a fundamental nitrogen biogeochemical process that links the oxidation of ammonia to the removal of fixed nitrogen in eutrophicated water bodies. However, in estuarine environments there is an enormous variability of water physicochemical parameters that can affect the ammonia oxidation biological process. For instance, it is known that salinity can affect nitrification performance, yet there is still a lack of information on the ammonia-oxidizing communities behavior facing daily salinity fluctuations. In this work, laboratory experiments using upstream and downstream estuarine sediments were performed to address this missing gap by comparing the effect of daily salinity fluctuations with constant salinity on the activity and diversity of ammonia-oxidizing microorganisms (AOM). Activity and composition of AOM were assessed, respectively by using nitrogen stable isotope technique and 16S rRNA gene metabarcoding analysis. Nitrification activity was negatively affected by daily salinity fluctuations in upstream sediments while no effect was observed in downstream sediments. Constant salinity regime showed clearly higher rates of nitrification in upstream sediments while a similar nitrification performance between the two salinity regimes was registered in the downstream sediments. Results also indicated that daily salinity fluctuation regime had a negative effect on both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) community’s diversity. Phylogenetically, the estuarine downstream AOM were dominated by AOA (0.92–2.09%) followed by NOB (0.99–2%), and then AOB (0.2–0.32%); whereas NOB dominated estuarine upstream sediment samples (1.4–9.5%), followed by AOA (0.27–0.51%) and AOB (0.01–0.23%). Analysis of variance identified the spatial difference between samples (downstream and upstream) as the main drivers of AOA and AOB diversity. Our study indicates that benthic AOM inhabiting different estuarine sites presented distinct plasticity toward the salinity regimes tested. These findings help to improve our understanding in the dynamics of the nitrogen cycle of estuarine systems by showing the resilience and consequently the impact of different salinity regimes on the diversity and activity of ammonia oxidizer communities.

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A Mesophilic, Autotrophic, Ammonia-Oxidizing Archaeon of Thaumarchaeal Group I.1a Cultivated from a Deep Oligotrophic Soil Horizon

Applied and Environmental Microbiology ◽

10.1128/aem.03730-13 ◽

2014 ◽

Vol 80 (12) ◽

pp. 3645-3655 ◽

Cited By ~ 46

Author(s):

Man-Young Jung ◽

Soo-Je Park ◽

So-Jeong Kim ◽

Jong-Geol Kim ◽

Jaap S. Sinninghe Damsté ◽

...

Keyword(s):

Carbon Fixation ◽

Ammonia Oxidation ◽

Soil Horizon ◽

Ammonia Oxidizer ◽

Rrna Gene ◽

Soil Nitrification ◽

Content Type ◽

Niche Adaptation ◽

Group I ◽

Terrestrial Environments

ABSTRACTSoil nitrification plays an important role in the reduction of soil fertility and in nitrate enrichment of groundwater. Various ammonia-oxidizing archaea (AOA) are considered to be members of the pool of ammonia-oxidizing microorganisms in soil. This study reports the discovery of a chemolithoautotrophic ammonia oxidizer that belongs to a distinct clade of nonmarine thaumarchaeal group I.1a, which is widespread in terrestrial environments. The archaeal strain MY2 was cultivated from a deep oligotrophic soil horizon. The similarity of the 16S rRNA gene sequence of strain MY2 to those of other cultivated group I.1a thaumarchaeota members, i.e.,Nitrosopumilus maritimusand “CandidatusNitrosoarchaeum koreensis,” is 92.9% for both species. Extensive growth assays showed that strain MY2 is chemolithoautotrophic, mesophilic (optimum temperature, 30°C), and neutrophilic (optimum pH, 7 to 7.5). The accumulation of nitrite above 1 mM inhibited ammonia oxidation, while ammonia oxidation itself was not inhibited in the presence of up to 5 mM ammonia. The genome size of strain MY2 was 1.76 Mb, similar to those ofN. maritimusand “Ca. Nitrosoarchaeum koreensis,” and the repertoire of genes required for ammonia oxidation and carbon fixation in thaumarchaeal group I.1a was conserved. A high level of representation of conserved orthologous genes for signal transduction and motility in the noncore genome might be implicated in niche adaptation by strain MY2. On the basis of phenotypic, phylogenetic, and genomic characteristics, we propose the name “CandidatusNitrosotenuis chungbukensis” for the ammonia-oxidizing archaeal strain MY2.

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Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities

10.1101/2021.03.02.433310 ◽

2021 ◽

Author(s):

Man-Young Jung ◽

Christopher J. Sedlacek ◽

K. Dimitri Kits ◽

Anna J. Mueller ◽

Sung-Keun Rhee ◽

...

Keyword(s):

Ammonia Oxidation ◽

Oxidation Kinetic ◽

Ammonia Oxidizer ◽

Substrate Affinity ◽

Kinetic Properties ◽

Ammonia Oxidizing Bacteria ◽

Ammonia Oxidizers ◽

Kinetic Measurements ◽

Ammonia Oxidizing Archaea ◽

Wide Range

AbstractNitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co- occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest substrate affinity of any characterized AOA, which are similar to previously determined affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values strongly supports the hypothesis that – like for AOB – ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.

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Competition of Ammonia-Oxidizing Archaea and Bacteria from Freshwater Environments

Applied and Environmental Microbiology ◽

10.1128/aem.01038-21 ◽

2021 ◽

Author(s):

Elizabeth French ◽

Jessica A. Kozlowski ◽

Annette Bollmann

Keyword(s):

Ammonia Oxidation ◽

Heterotrophic Bacteria ◽

Ammonia Oxidizer ◽

Ammonium Concentration ◽

Natural Environments ◽

Ammonia Oxidizing Bacteria ◽

Ammonia Oxidizers ◽

Batch Cultures ◽

Freshwater Systems ◽

Ammonia Oxidizing Archaea

In the environment, nutrients are rarely available in constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater systems, ammonia-oxidizing archaea (AOA) and bacteria (AOB) compete with heterotrophic bacteria, photosynthetic microorganisms, and each other for ammonium, which AOA and AOB utilize as their sole source of energy and nitrogen. We investigated the competition between highly enriched cultures of an AOA (AOA-AC1) and an AOB (AOB-G5-7) for ammonium. Based on the amoA gene, the newly enriched archaeal ammonia oxidizer in AOA-AC1 was closely related to Nitrosotenuis spp. and the bacterial ammonia oxidizer in AOB-G5-7, Nitrosomonas sp. Is79, belonged to the Nitrosomonas oligotropha group ( Nitrosomonas cluster 6a). Growth experiments in batch cultures showed that AOB-G5-7 had higher growth rates than AOA-AC1 at higher ammonium concentrations. During chemostat competition experiments under ammonium-limiting conditions, AOA-AC1 dominated the cultures, while AOB-G5-7 decreased in abundance. In batch cultures, the outcome of the competition between AOA and AOB was determined by the initial ammonium concentrations. AOA-AC1 was the dominant ammonia oxidizer at an initial ammonium concentration of 50 μM and AOB-G5-7 at 500 μM. These findings indicate that, during direct competition, AOA-AC1 was able to use ammonium that was unavailable to AOB-G5-7, while AOB-G5-7 dominated at higher ammonium concentrations. The results are in strong accordance with environmental survey data suggesting that AOA are mainly responsible for ammonia oxidation under more oligotrophic conditions, whereas AOB dominate under eutrophic conditions. Importance Nitrification is an important process in the global nitrogen cycle. The first step - ammonia oxidation to nitrite – can be carried out by Ammonia-oxidizing Archaea (AOA) and Ammonia-oxidizing Bacteria (AOB). In many natural environments, these ammonia oxidizers coexist. Therefore, it is important to understand the population dynamics in response to increasing ammonium concentrations. Here, we study the competition between AOA and AOB enriched from freshwater systems. The results demonstrate that AOA are more abundant in systems with low ammonium availabilities and AOB when the ammonium availability increases. These results will help to predict potential shifts in community composition of ammonia oxidizers in the environment due to changes in ammonium availability.

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