Soil

Environmental Microbiology, 2008

Ammonia oxidation, as the first step in the nitrification process, plays a central role in the global cycling of nitrogen. Although bacteria are traditionally considered to be responsible for ammonia oxidation, a role for archaea has been suggested by data from metagenomic studies and by the isolation of a marine, autotrophic, ammonia-oxidizing, non-thermophilic crenarchaeon. Evidence for ammonia oxidation by non-thermophilic crenarchaea in marine and terrestrial environments is largely based on abundance of bacterial and archaeal ammonia monooxygenase (amo) genes, rather than activity. In this study, we have determined the influence of temperature on the response of ammonia-oxidizing bacteria and archaea in nitrifying soil microcosms using two approaches, involving analysis of transcriptional activity of 16S rRNA genes and of a key functional gene, amoA, which encodes ammonia monooxygenase subunit A. There was little evidence of changes in relative abundance or transcriptional activity of ammoniaoxidizing bacteria during nitrification. In contrast, denaturing gradient gel electrophoresis analysis of crenarchaeal 16S rRNA and crenarchaeal amoA genes provided strong evidence of changes in community structure of active archaeal ammonia oxidizers. Community structure changes were similar during incubation at different temperatures and much of the activity was due to a group of non-thermophilic crenarchaea associated with subsurface and marine environments, rather than soil. The findings suggest a role for crenarchaea in soil nitrification and that further information is required on their biogeography.

Journal of Soils and Sediments, 2012

Purpose Acidic red soils account for 21% of land area in China and contain low ammonia concentration due to ionization to ammonium. The unusual high affinity for ammonia of marine Nitrosopumilus maritimus and acidophilic soil Nitrosotalea devanaterra has suggested that ammonia-oxidizing archaea (AOA) may have greater selective advantage over ammonia-oxidizing bacteria (AOB) in ammonia-limited environment because ammonia rather than ammonium is thought to be the actual substrate for oxidation. The aim of this study was to assess whether nitrification activity can be attributed to AOA and/or AOB by relating community structures of AOA and AOB to nitrification activity in acidic red soils in southern China. Materials and methods In this study, the composition and abundance of AOA community were investigated in acidic red soils of coniferous Pinus forest, broad-leaf Cinnamomum forest, bush forest (BF), and a 30-year agricultural field converted from bush forest (BFA). The composition of AOA based on archaeal amoA genes were analyzed by denaturant gradient gel electrophoresis, and the abundances of AOA communities were determined by real-time quantitative polymerase chain reaction, while soil nitrification activity was measured using 15 N pool enrichment technique. Results and discussion 15 N pool enrichment technique indicated nitrification activity in acidic red soils, but AOB were not detected. The absence of AOB in acidic red soils could be well explained by the low ammonia concentration ranging from 17.8 to 34.3 nM, which is far below the known threshold values required to support the growth of AOB in culture. Nitrification activity change coupled well with abundance and composition changes of archaeal amoA genes, particularly for acidic BF and BFA soils. Phylogenetic analysis demonstrated that the putatively active AOA were related to amoA transcripts in a hot spring within the soil Crenarchaeota group 1.1b lineage. Conclusions These results suggest that AOA play important roles in ammonia oxidation in acidic red soils tested in this study.

Fems Microbiology Ecology - FEMS MICROBIOL ECOL, 2009

Autotrophic ammonia-oxidizing bacteria were considered to be responsible for the majority of ammonia oxidation in soil until the recent discovery of the autotrophic ammonia-oxidizing archaea. To assess the relative contributions of bacterial and archaeal ammonia oxidizers to soil ammonia oxidation, their growth was analysed during active nitrification in soil microcosms incubated for 30 days at 30 °C, and the effect of an inhibitor of ammonia oxidation (acetylene) on their growth and soil nitrification kinetics was determined. Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial ammonia oxidizer 16S rRNA genes did not detect any change in their community composition during incubation, and quantitative PCR (qPCR) analysis of bacterial amoA genes indicated a small decrease in abundance in control and acetylene-containing microcosms. DGGE fingerprints of archaeal amoA and 16S rRNA genes demonstrated changes in the relative abundance of specific crenarchaeal phylotypes during active nitrification. Growth was also indicated by increases in crenarchaeal amoA gene copy number, determined by qPCR. In microcosms containing acetylene, nitrification and growth of the crenarchaeal phylotypes were suppressed, suggesting that these crenarchaea are ammonia oxidizers. Growth of only archaeal but not bacterial ammonia oxidizers occurred in microcosms with active nitrification, indicating that ammonia oxidation was mostly due to archaea in the conditions of the present study.

Fems Microbiology Ecology, 2010

Nitrification is a key process of the nitrogen (N) cycle in soil with major environmental implications. The recent discovery of ammonia-oxidizing archaea (AOA) questions the traditional assumption of the dominant role of ammonia-oxidizing bacteria (AOB) in nitrification. We investigated AOB and AOA growth and nitrification rate in two different layers of three grassland soils treated with animal urine substrate and a nitrification inhibitor [dicyandiamide (DCD)]. We show that AOB were more abundant in the topsoils than in the subsoils, whereas AOA were more abundant in one of the subsoils. AOB grew substantially when supplied with a high dose of urine substrate, whereas AOA only grew in the Controls without the urine-N substrate. AOB growth and the amoA gene transcription activity were significantly inhibited by DCD. Nitrification rates were much higher in the topsoils than in the subsoils and were significantly related to AOB abundance, but not to AOA abundance. These results suggest that AOB and AOA prefer different soil N conditions to grow: AOB under high ammonia (NH3) substrate and AOA under low NH3 substrate conditions.

Microbes and Environments, 2011

Soil type is one of the key factors affecting soil microbial communities. With regard to ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), however, it has not been determined how soil type affects their community size and soil nitrification activity. Here we quantitatively analyzed the ammonia monooxygenase genes (amoA) of these ammonia oxidizers in fields with three different soil types (Low-humic Andosol [LHA], Gray Lowland Soil [GLS], and Yellow Soil [YS]) under common cropping conditions, and assessed the relationships between soil nitrification activity and the abundance of each amoA. Nitrification activity of LHA was highest, followed by that of GLS and YS; this order was consistent with that for the abundance of AOB amoA. Abundance of AOB amoA showed temporal variation, which was similar to that observed in nitrification activity, and a strong relationship (adjusted R 2 =0.742) was observed between the abundance of AOB amoA and nitrification activity. Abundance of AOA amoA also exhibited a significant relationship (adjusted R 2 =0.228) with nitrification activity, although this relationship was much weaker. Our results indicate that soil type affects the community size of AOA and AOB and the resulting nitrification activity, and that AOB are major contributors to nitrification in soils, while AOA are partially responsible.

FEMS Microbiology Ecology, 2000

Autotrophic ammonia-oxidizing bacteria were considered to be responsible for the majority of ammonia oxidation in soil until the recent discovery of the autotrophic ammonia-oxidizing archaea. To assess the relative contributions of bacterial and archaeal ammonia oxidizers to soil ammonia oxidation, their growth was analysed during active nitrification in soil microcosms incubated for 30 days at 30 1C, and the effect of an inhibitor of ammonia oxidation (acetylene) on their growth and soil nitrification kinetics was determined. Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial ammonia oxidizer 16S rRNA genes did not detect any change in their community composition during incubation, and quantitative PCR (qPCR) analysis of bacterial amoA genes indicated a small decrease in abundance in control and acetylene-containing microcosms. DGGE fingerprints of archaeal amoA and 16S rRNA genes demonstrated changes in the relative abundance of specific crenarchaeal phylotypes during active nitrification. Growth was also indicated by increases in crenarchaeal amoA gene copy number, determined by qPCR. In microcosms containing acetylene, nitrification and growth of the crenarchaeal phylotypes were suppressed, suggesting that these crenarchaea are ammonia oxidizers. Growth of only archaeal but not bacterial ammonia oxidizers occurred in microcosms with active nitrification, indicating that ammonia oxidation was mostly due to archaea in the conditions of the present study.

The ISME Journal, 2013

The functioning of Arctic soil ecosystems is crucially important for global climate, and basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and its availability is strongly dependent on nitrification. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH 3) oxidation. Eleven Arctic soils were analyzed through a polyphasic approach, integrating determination of gross nitrification rates, qualitative and quantitative marker gene analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and enrichment of AOA in laboratory cultures. AOA were the only NH 3 oxidizers detected in five out of 11 soils and outnumbered AOB in four of the remaining six soils. The AOA identified showed great phylogenetic diversity and a multifactorial association with the soil properties, reflecting an overall distribution associated with tundra type and with several physico-chemical parameters combined. Remarkably, the different gross nitrification rates between soils were associated with five distinct AOA clades, representing the great majority of known AOA diversity in soils, which suggests differences in their nitrifying potential. This was supported by selective enrichment of two of these clades in cultures with different NH 3 oxidation rates. In addition, the enrichments provided the first direct evidence for NH 3 oxidation by an AOA from an uncharacterized Thaumarchaeota-AOA lineage. Our results indicate that AOA are functionally heterogeneous and that the selection of distinct AOA populations by the environment can be a determinant for nitrification activity and N availability in soils.

Microbial Ecology, 2021

Ammonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in low pH soils. This study aimed to investigate the effect of different fertilisation histories on community composition and activity of acidophilic AOA in soils. High-throughput sequencing of ammonia monooxygenase gene (amoA) was performed on six low pH agricultural plots originating from the same soil but amended with different types of fertilisers for over 20 years and nitrification rates in those soils were measured. In these fertilised acidic soils, nitrification was likely dominated by Nitrososphaerales AOA and ammonia-oxidising bacteria, while Ca. Nitrosotaleaceae AOA activity was non-significant. Within Nitrososphaerales AOA, commun...

Soil ammonia-oxidizing archaea (AOA) are highly abundant and play an important role in the nitrogen cycle. In addition, AOA have a significant impact on soil quality. Nitrite produced by AOA and further oxidized to nitrate can cause nitrogen loss from soils, surface and groundwater contamination, and water eutrophication. The AOA discovered to date are classified in the phylum Thaumarchaeota. Only a few archaeal genomes are available in databases. As a result, AOA genes are not well annotated, and it is difficult to mine and identify archaeal genes within metagenomic libraries. Nevertheless, 16S rRNA and comparative analysis of ammonia monooxygenase sequences show that soils can vary greatly in the relative abundance of AOA. In some soils, AOA can comprise more than 10% of the total prokaryotic community. In other soils, AOA comprise less than 0.5% of the community. Many approaches have been used to measure the abundance and diversity of this group including DGGE, T-RFLP, q-PCR, and DNA sequencing. AOA have been studied across different soil types and various ecosystems from the Antarctic dry valleys to the tropical forests of South America to the soils near Mount Everest. Different studies have identified multiple soil factors that trigger the abundance of AOA. These factors include pH, concentration of available ammonia, organic matter content, moisture content, nitrogen content, clay content, as well as other triggers. Land use management appears to have a major effect on the abundance of AOA in soil, which may be the result of nitrogen fertilizer used in agricultural soils. This review summarizes the published results on this topic and suggests future work that will increase our understanding of how soil management and edaphoclimatic factors influence AOA.

Soil Biology & Biochemistry, 2017

Soil ammonia-oxidizing bacteria and archaea (AOB and AOA) convert ammonium/ammonia to nitrite in the process of nitrification. However, the potentially differential responses of these AO to substrate and temperature and the effects of conventional and organic nitrogen management on these responses remains poorly understood. We determined the response of nitrification to ammonium substrate concentration and temperature using an AOB specific inhibitor to distinguish the contribution of AOB and AOA to nitrification. Soils were sampled from cornfield plots that had been treated for four years with contrasting nitrogen sources: control (no additional N), ammonium sulfate at two rates and compost. Nitrification potential and net rates were stimulated for one month after fertilization with ammonium sulfate compared to relatively lower and stable rates in control and compost treated soils. For soils that had been fertilized with ammonium sulfate, the proportion of nitrification mediated by AOB in slurry assays was over 90% at 1.0 mM but less than 50% at 0.01 mM. Kinetic analysis showed maximum nitrification activity (V max) for AOB ranged from 0.32 to 4.8 mmol N kg À1 d À1 with a half saturation constant (K m) of 14e160 mM ammonium; parameters were higher for soils from ammonium sulfate treated plots. V max and K m for AOA averaged 0.24 mmol N kg À1 d À1 and 4.28 mM ammonium with no effect of field treatment. The proportion of nitrification due to AOA was lowest at 5 C, increased with temperature, and was near to 100% at 50 C; optimum temperature was 41 C for AOA versus 31 C for AOB. Understanding the kinetic and temperature response of microbes responsible for nitrification may allow ecosystem models to include these populations as dynamic components driving nitrogen flux.