Ammonia-oxidizing Bacterial Communities Research Articles

Insights into the spatial distributions of bacteria, archaea, ammonia-oxidizing bacteria and archaea communities in sediments of Daya Bay, northern South China Sea

Microbe plays an important role in the biogeochemical cycles of the coastal waters. However, comprehensive information about the microbe in the gulf waters is lacking. This study employed high-throughput sequencing and quantitative PCR (qPCR) to investigate the distribution patterns of bacterial, archaeal, ammonia-oxidizing bacterial (AOB), and archaeal (AOA) communities in Daya Bay. Community compositions and principal coordinates analysis (PCoA) exhibited significant spatial characteristics in the diversity and distributions of bacteria, archaea, AOB, and AOA. Notably, various microbial taxa (bacterial, archaeal, AOB, and AOA) exhibited significant differences in different regions, playing crucial roles in nitrogen, sulfur metabolism, and organic carbon mineralization. Canonical correlation analysis (CCA) or redundancy analysis (RDA) indicated that environmental parameters such as temperature, salinity, nitrate, total nitrogen, silicate, and phosphate strongly influenced the distributions of bacterial, archaeal, AOB, and AOA. This study deepens the understanding of the composition and ecological function of prokaryotes in the bay.

Ammonia-Oxidizing Bacterial Communities in Tilapia Pond Systems and the Influencing Factors

This study investigated ammonia-oxidizing bacterial communities in water and surface sediments of three tilapia ponds and their relationship with differences in the ponds, monthly variations in the water, and the physico-chemical parameters. Samples were collected from ponds with different stocking densities, after which DNA was extracted, 16S rRNA genes were amplified, the Illumina high-throughput sequencing was performed, and then the Silva and FunGene databases were used to investigate the ammonia-oxidizing bacterial communities. In total, 308,488 valid reads (144,931 in water and 163,517 in sediment) and 240 operational taxonomic units (207 in water and 225 in sediment) were obtained. Further analysis showed that the five genera of Nitrosospira, Nitrosococcus, Nitrosomonas, Proteobacteria_unclassified, and Nitrosomonadaceae_unclassified were distributed not only in the water, but also in surface sediments of all three ponds. Further, not only the abundance of these five genera, but also their diversities were affected by monthly variations in the water and by sediment differences among the ponds. Moreover, the total nitrogen (TN), nitrate, total phosphorus (TP), and sulphate were the main factors influencing the ammonia-oxidizing bacterial communities in the water, whereas TP was the main influencing factor in the sediments. Moreover, the parameter changes, especially those caused by differences in the ponds, were closely related to the cultivation management (stocking density and feed coefficients).

Ammonia-oxidizing bacterial communities are affected by nitrogen fertilization and grass species in native C4 grassland soils.

BackgroundFertilizer addition can contribute to nitrogen (N) losses from soil by affecting microbial populations responsible for nitrification. However, the effects of N fertilization on ammonia oxidizing bacteria under C4 perennial grasses in nutrient-poor grasslands are not well studied.MethodsIn this study, a field experiment was used to assess the effects of N fertilization rate (0, 67, and 202 kg N ha−1) and grass species (switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii)) on ammonia-oxidizing bacterial (AOB) communities in C4 grassland soils using quantitative PCR, quantitative reverse transcription-PCR, and high-throughput amplicon sequencing of amoA genes.ResultsNitrosospira were dominant AOB in the C4 grassland soil throughout the growing season. N fertilization rate had a stronger influence on AOB community composition than C4 grass species. Elevated N fertilizer application increased the abundance, activity, and alpha-diversity of AOB communities as well as nitrification potential, nitrous oxide (N2O) emission and soil acidity. The abundance and species richness of AOB were higher under switchgrass compared to big bluestem. Soil pH, nitrate, nitrification potential, and N2O emission were significantly related to the variability in AOB community structures (p < 0.05).

Yak Excreta Application Alter Nitrification by Regulating the Ammonia-Oxidizing Bacterial Communities in Wetland Soils

Yak Excreta Application Alter Nitrification by Regulating the Ammonia-Oxidizing Bacterial Communities in Wetland Soils

Spatial variability pattern of the anaerobic ammonia-oxidizing bacterial community across a salinity gradient from river to ocean

In natural habitats, the diversity of anaerobic ammonia-oxidizing (anammox) bacteria could be affected by multiple environmental variables. In this study, we investigated the distribution of the anammox bacterial community in surface sediment from the Dongjiang River (riverine sediment, DJ) to the Pearl River Estuary (estuarine sediment, PRE) and then to the South China Sea (coastal sediment, SCS). The results revealed evident differences in the structural diversity of anammox bacteria in three different habitats. Candidatus Brocadia accounted for approximately 90% of the total anammox bacteria in DJ, conversely, Ca. Scalindua dominated in the SCS. Nevertheless, Ca. Scalindua, Ca. Brocadia and Ca. Kuenenia coexisted in the PRE. The qPCR results indicated that anammox bacterial 16S rRNA gene abundance ranged from 2.23 × 105 to 1.19 × 107 copies g-1 of wet weight, but no significant correlation was found between the abundances and environmental variables (p > 0.05). The relative abundances of Ca. Brocadia gradually decreased with increasing salinity, and Ca. Scalindua showed the opposite trend, suggesting that salinity was a crucial factor in sculpturing the community composition of anammox bacteria in natural environments. Ca. Brocadia should be able to live in freshwater ecosystems, but it can also tolerate a certain level of salinity. Ca. Scalindua was halophilic anammox bacterium and exists only in saline environments. Ca. Kuenenia could adapt to a wide range of salinity and preferred to live in high DIN level conditions according to our search. The distribution pattern of anammox bacteria may be the result of microbial migration and long-term adaptation to salinity.

Comparison of the Total, Diazotrophic and Ammonia-Oxidizing Bacterial Communities Between Under Organic and Conventional Greenhouse Farming.

Organic greenhouse farming is an innovative system that may maintain a high yield and healthy agroecosystem. There have been no rigorous studies on the comparison of total and nitrogen-cycling bacterial community in vegetable soils between organic and conventional farming management at large scale. A survey of bacterial community and nitrogen cycles from soils under organic and conventional greenhouse farming was performed at 30 sites, covering seven soil types with 4 to 18 years of organic farming history. Communities of the total, diazotrophs and ammonia-oxidizing bacteria were studied with high-throughput sequencing of the 16S rRNA, nifH and amoA genes, respectively. Organic greenhouse farming did not influence alpha diversities. Beta diversities among the total (26/30) and diazotrophic (17/19) bacteria differed between farming systems, but compositional differences in ammonia-oxidizing bacteria between the two farming systems were only detected at 6 sites. Despite the effects of farming system on most bacterial genera were varied across different sites, organic greenhouse farming persistently selected for a few genera, possibly for the biodegradation of organic carbon with high molecular weight (Hyphomicrobium, Rubinisphaera, Aciditerrimonas, Planifilum, Phaselicystis, and Ohtaekwangia), but against putative ammonia oxidizing (Nitrosospira, Nitrosopumilus) and diazotrophic (Bradyrhizobium) bacterial genera, as determined by 16S rRNA analysis. Diazotrophic bacteria affiliated with nifH cluster 1J were preferentially associated with organic greenhouse farming, in contrast to Paenibacillus borealis. In summary, this study provides insights into the complex effects of organic greenhouse farming on the total, diazotrophic and ammonia oxidizing bacterial communities across different environmental context.

Ammonia-oxidizing bacterial and archaeal communities in tropical bioaugmented zero water exchange shrimp production systems

Ammonia oxidation is an important process in the removal of ammonia generated from feed and metabolic wastes in aquaculture systems. Considering the biogeochemical importance of ammonia oxidation in bioaugmented zero water exchange aquaculture systems, the diversity and abundance of bacterial and archaeal ammonia-oxidizing communities were analyzed in three selected ponds at different time intervals during the culture period, to unravel the key environmental factors influencing their distribution in the system. The diversity and abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in three tropical bioaugmented zero water exchange (ZWE) shrimp culture systems were analyzed using ammonia monooxygenase A (amoA) gene from the sediment metagenome during different phases of culture. The environmental factors associated with the variability in bacterial and archaeal amoA gene abundance and diversity were elucidated using RDA and Pearson correlation analysis. Ammonia-oxidizing archaea (AOA), Nitrosopumilus sp., Nitrosospharea sp., and ammonia-oxidizing bacteria (AOB), Nitrosomonas sp., were the dominant ammonia-oxidizing communities in the ZWE ponds studied. AOA shared 41 OTUs, and the maximum distribution was influenced by dissolved oxygen in the system, whereas AOB shared 4 OTUs. The copy numbers amoA gene determined using qPCR showed that the AOA amoA gene was 10- to 100-fold abundant than AOB amoA gene. Gene abundance of AOA was positively related to total organic carbon (TOC) and salinity of sediments, and the temperature had a negative impact on bacterial amoA gene abundance. The dissolved oxygen and TOC had a negative and redox potential a positive impact on the diversity of AOA, whereas pH had a negative impact on the diversity of AOB. The ammonia-oxidizing archaeal communities dominated the bioaugmented zero water exchange aquaculture systems compared to bacteria based on the abundance and diversity analysis using amoA gene sequence-based OTU analysis and gene copy numbers. Dissolved oxygen, total organic carbon, and Eh of the sediments contributed to the distribution and abundance of AOA group in the ZWE ponds. This study points to the importance of environmental management in these culture systems for maintaining ammonia-oxidizing populations for optimal ammonia removal. The relative contribution of the archaea and bacteria to ammonia oxidation in these systems is to be further resolved along with that of anammox and comammox bacteria, which would help to develop appropriate biostimulation or bioaugmentation strategies for the management of these sustainable aquaculture production systems.

Soil aggregate size and long-term fertilization effects on the function and community of ammonia oxidizers

Long-term field fertilization trials have suggested that reduced chemical nitrogen (N) plus organic fertilization can effectively reduce N loss without sacrificing crop yield, while the knowledge of how organic fertilizers regulate soil microorganisms and their function in N transformation are limited. In this study, the response of net nitrification rate and the ammonia-oxidizer community within soil aggregates to long-term combined organic N and reduced chemical N fertilization was evaluated to understand the underlying mechanism of the practice in mitigating soil N loss. The fertilization experiment included an unfertilized control; chemical N fertilizer (N), superphosphate (P) and potassium sulfate (K) fertilizer (NPK); NPK plus straw (NPKS); and NPK plus manure (NPKM). The results showed that the large macro-aggregates mass (>2 mm) in soil significantly increased from 34.1% in NPK to 47.2% in NPKS (P < 0.05). NPKS and NPKM both had positive effects on soil moisture retention, total N (TN), soil organic carbon (SOC), ammonium (NH4+-N) and nitrate (NO3−-N) accumulation, particularly within micro- (<0.25 mm) and small macro-aggregates. Compared with the NPK treatment, soil net nitrification rate (NNR) and ammonia-oxidizing bacterial (AOB) abundance decreased by 67.1% and 40.7% respectively under NPKS (P < 0.05), and the decrease mainly appeared in large macro-aggregate and micro-aggregates. The net nitrification rate was significantly correlated with ammonia-oxidizing archaea (AOA) abundance only in small macro-aggregates (r = 0.642, n = 12, P < 0.05). In contrast, NRR was positively correlated with AOB abundance within small macro- and micro-aggregate size classes (r values ranged from 0.654 to 0.813, P < 0.05). The community structure of AOB varied among different fertilization treatments, while AOA community differentiation was mainly dependent on aggregate size. The shift of the AOA and AOB communities corresponded with high moisture and lower ammonia content in the large macro-aggregates and were potentially responsible for the suppressed nitrification activity in the NPKS treatment. These results indicated that reduced chemical N plus organic fertilization is beneficial for increasing N concentration in large macro-aggregates.

Methane-generating ammonia oxidizing nitrifiers within bio-filters in aquaculture tanks

The discovery of aerobic and anammox bacteria capable of generating methane in bio-filters in freshwater aquaculture systems is generating interest in studies to understand the activity, diversity, distribution and roles of these environmental bacteria. In this study, we used microbial enrichment of bio-filters to assess their effect on water quality. Profiles of ammonia-oxidizing bacterial communities generated using nested PCR methods and DGGE were used to assess the expression of 16S rRNA genes using DNA sequencing. Five dominant ammonia-oxidizing bacterial strains–clones; KB.13, KB.15, KB.16, KB.17 and KB.18—were isolated and identified by phylogenetic analysis as environmental samples closely related to genera Methylobacillus, Stanieria, Nitrosomonas, and Heliorestis. The methyl ammonia-oxidizing microbes thereby found suggest a biochemical pathway involving electron donors and carbon sources, and all strains were functional in freshwater aquaculture systems. Environmental parameters including TN (2.69–20.43); COD (9.34–31.47); NH4+-N (0.44–11.78); NO2−N (0.00–3.67); NO3−N (0.05–1.82), mg/L and DO (1.47–10.31 µg/L) assessed varied in the ranges in the different tanks. Principal component analysis revealed that these water quality parameters significantly influenced the ammonia oxidizing microbial community composition. Temperature rises to about 40 °C significantly affected environmental characteristics—especially DO, TN and NH4+-N—and directly or indirectly affected the microbial communities. Although the nested PCR design was preferred due to its high sensitivity for amplifying specific DNA regions, a more concise method is recommended, as an equimolar mixture of degenerate PCR primer pairs, CTO189f-GC and CTO654r, never amplified only 16S rRNA of ammonia-oxidizing bacteria.

Evaluation of Ammonia Oxidizing Bacterial Community Structure of a Municipal Activated Sludge Plant by 454 High-Throughput Pyrosequencing

The ammonia oxidizing bacteria (AOB) community structure in a municipal wastewater treatment plant (WWTP) was monitored over the winter and summer periods. The AOB distribution in the full-scale WWTP was investigated using barcoded 454-pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. Using the quantitative polymerase chain reaction (qPCR) technique, the AOB population was quantified over 237 days. The plant operational parameters and its nitrification performance were also monitored. As revealed by pyrosequencing, majority of the identified AOB during the study were related to uncultured ammonia oxidizing bacteria, and Nitrosomonas oligotropha. Furthermore, it revealed higher AOB abundance during the summer which was 6 times more compared to winter. Substantial percentages of the reads from both seasons could not be assigned to any phylum, which suggests that vast population of novel, ecologically significant AOB species still inhabit the complex activated sludge communities unexploited. A significant seasonal variation in temperature (α = 0.05; P = < 0.0001) was recorded in the reactor with maximum temperature amplitude of 10.2 °C. The average nitrification rate recorded during the summer was 0.09 ± 0.03 g N-NH4+/g MLSS/d, whereas it was 0.04 ± 0.02 g N-NH4+/g MLSS/d during the winter. The nitrification rate of the plant had significant correlation with AOB population abundance (r = 0.70; P = 0.01) and temperature (α = 0.05; P = 0.0018). This study indicates that AOB diversity and population abundance were contributory factors to efficient nitrification in activated sludge system.

Ammonia-oxidizing bacteria and archaea within biofilters of a commercial recirculating marine aquaculture system

While biofilters are widely used to metabolize ammonia and other wastes in marine recirculating aquaculture systems, the ammonia-oxidizing bacterial and archaeal communities have not been characterized across a diversity of production systems. Using a metagenomics approach, we characterized the ammonia-oxidizing microbiological community of biofilters in a commercial recirculating marine aquaculture system producing hybrid grouper (Epinephelus lanceolatus × E. fuscoguttatus). Cloning and sequencing of the amoA gene showed that nitrifying bacteria included Nitrosomonas europea, N. stercoris, N. cryotolerans, N. eutropha, N. estuarii, eight strains of N. marina, and 15 strains not associated with described species. Nitrifying archaea included eight strains of Nitrosopumilus maritimus, N. koreensis, N. piranensis, N. adriaticus, undescribed congeners, and other undescribed archaea. The species composition of the bacterial and especially the archaeal communities was beyond that yet reported for aquaculture biofilters. While ammonia flux through the respective communities has yet to be estimated, the diverse environmental adaptations of the bacterial and archaeal communities suggest resilience of function under a range of environmental conditions.

Effects of microcystins contamination on soil enzyme activities and microbial community in two typical lakeside soils

A 30-day indoor incubation experiment was conducted to investigate the effects of different concentrations of microcystin (1, 10, 100 and 1000 μg eq. MC-LR L−1) on soil enzyme activity, soil respiration, physiological profiles, potential nitrification, and microbial abundance (total bacteria, total fungi, ammonia-oxidizing bacteria and archaea) in two lakeside soils in China (Soil A from the lakeside of Lake Poyanghu at Jiujiang; Soil B from the lakeside of Lake Taihu at Suzhou). Of the enzymes tested, only phenol oxidase activity was negatively affected by microcystin application. In contrast, dehydrogenase activity was stimulated in the 1000 μg treatment, and a stimulatory effect also occurred with soil respiration in contaminated soil. The metabolic profiles of the microbial communities indicated that overall carbon metabolic activity in the soils treated with high microcystin concentrations was inhibited, and high concentrations of microcystin also led to different patterns of potential carbon utilization. High microcystin concentrations (100, 1000 μg eq. MC-LR L−1 in Soil A; 10, 100 1000 μg eq. MC-LR L−1 in Soil B) significantly decreased soil potential nitrification rate. Furthermore, the decrease in soil potential nitrification rate was positively correlated with the decrease of the amoA gene abundance, which corresponds to the ammonia-oxidizing bacterial community. We conclude that application of microcystin-enriched irrigation water can significantly impact soil microbial community structure and function.

Soil texture modulates the response of ammonia-oxidizing prokaryotes to biochemical quality of organic inputs in tropical agricultural soils

Soil texture modulates the response of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to biochemical quality of organic inputs in tropical agricultural soils. To verify this assumption, we used the soil organic matter long-term field experiments in Kenya established on contrasting soils (i.e., clayey Humic Nitisol, sandy Ferric Alisol) in 2002. Since the start of the experiments, soils were continuously treated (4 Mg C ha−1 year−1) with biochemically different organic inputs including Tithonia diversifolia (TD; C/N ratio: 13, Lignin: 8.9%; Polyphenols: 1.7%), Calliandra calothyrsus (CC; 13; 13; 9.4) and Zea mays stover (ZM; 59; 5.4; 1.2). In 2013, soils (0–15 cm) were sampled at young growth (EC30) and flowering (EC60) stages of maize and subjected to DNA-based community analysis of AOB, AOA and 16S rRNA genes. Soil texture exerted stronger effects on the dynamics of the assayed genes than organic input quality with AOB being more responsive than AOA. Clayey soil with its predominant soil organic matter background and large surface area of clay minerals revealed generally higher AOB and AOA abundance than the sandy soil. In the sandy soil, N-rich TD and cellulose-rich ZM promoted AOB abundance, while it was decreased under CC due to N limitation induced by high contents of polyphenols and lignin. N limitation under ZM revealed a clear community differentiation of AOB between ZM versus TD and CC in the clayey soil. For the sandy soil, AOA community composition was distinct between CC versus TD and ZM. To provide a more detailed mechanistic understanding of active AOB and AOA in response to organic input quality, we recommend for prospective research RNA-based along with enzymatic analyses as complement to those shown in this study. This should be approached using controlled experiments to eliminate interfering environmental effects including rainfall and soil moisture, respectively.

Editorial: Linking Ecosystem Function to Microbial Diversity.

Editorial: Linking Ecosystem Function to Microbial Diversity.

Nitrogen removal performance and ammonia- and nitrite-oxidizing bacterial community analysis of a novel industrial waste-based biofilter

This study employed a newly developed treatment biofilter to remove high nitrogen (N) concentration from synthetic livestock wastewater combined with media containing neutralized used acid (NUA) and dewatered alum sludge (DAS). This biofilter was also utilized to investigate the spatial and temporal distributions of ammonia-oxidizing bacterial (AOB) and nitrite-oxidizing bacterial (NOB) communities and their active responses to effluent characteristics. Data were obtained from 210days of operations. Results showed that N removal was robust, with ammonia N and total N removal efficiencies of 59.8–82.1% and 57.5–74.9%, respectively. Denaturing gradient gel electrophoresis and sequence analyses revealed that the shift of AOB and NOB community structures in DAS was time dependent. These structures did not exhibit distinct differences in both media as depth varied. The retrieved AOB and NOB sequences from both media primarily belonged to Nitrosomonas, Nitrosovibrio, and Nitrobacter. The nitrification rates indicated that the change in AOB activity corresponded to the AOB community structure variation in the system. The peak was observed in DAS at the final time. By contrast, the NOB activity was inconsistent with the trend of its community structure. The AOB rate was positively related to the NOB rate. This finding suggested that AOB and NOB mutually promoted each other. The AOB and NOB activities of DAS rather than those of NUA appeared dependent on available nitrate from the effluent. Overall, these findings on AOB and NOB helped enhance further understanding on the efficient N removal of the NUA–DAS system.

Responses of ammonia-oxidizing bacterial communities to land-use and seasonal changes in Mollisols of Northeast China

In this study, AOB community was investigated over a 2-year period in cultivated Mollisols (0–20 cm) with three fertilizer treatments [no fertilizer (NoF), chemical fertilizer (CF) and chemical fertilizer plus manure (CFM)] and in an adjacent plot under natural restoration (NR). The crop rotation of maize, soybean and wheat was repeated every three years. The NR plot was abandoned agricultural land that was naturally revegetated with grasses. The AOB communities were characterized by clone sequencing of amoA gene targets, which encode ammonia monooxygenase subunit A. Phylogenetic analyses showed that the AOB communities in the Mollisols of Northeast China were related to defined groups, including clusters 1, 2, 3a, 3b, 9, and 10 in Nitrosospira and cluster 7 in Nitrosomonas. Nitrosospira cluster 3 was the most frequently recovered AOB in all treatments, and cluster 3a.2 and 3a.2-related sequences were common in cultivated soils. However, 12–27% of sequences were not related to any known AOB species, indicating a high diversity of AOB communities in Mollisols. There was a distinct AOB community in the NR plot and the cultivated plots, consistent with the hypothesis that land-use alters AOB community, and this appeared to be related to the soil pH. Cultivated soils with added N fertilizer had a greater frequency of clones in the Nitrosospira cluster 10 sequence type, but suppressed clones in the Nitrosospira cluster 3a.1 sequence type, whereas Nitrosomonas sequences were only recovered from the CFM treatment. The AOB clone frequency differed between the growing and non-growing seasons, possibly because the AOB communities were favoured by warm, moist soil conditions or the active plant rhizosphere during the growing season. The ecological implications of land-use change and seasonality on the contribution of these diverse AOB communities to primary production in Mollisols merits further attention.

Ammonia-oxidizing bacterial communities and shaping factors with different Phanerochaete chrysosporium inoculation regimes during agricultural waste composting

This research was conducted to determine the effects ofPhanerochaete chrysosporiuminoculation on the ammonia-oxidizing bacterial (AOB) communities during agricultural waste composting.

Effect of salinity on nitrification efficiency and structure of ammonia-oxidizing bacterial communities in a submerged fixed bed bioreactor

The effect of salt (NaCl) on biological nitrogen removal and community structure of ammonia-oxidizing bacteria (AOB) was investigated in a submerged fixed bed bioreactor (SFBBR). Influent wastewater was supplemented with NaCl at 0 (control), 3.7, 24.1 and 44.1g/L, and the rate of ammonia removal efficiency was measured by ion chromatography. The structure of the AOB community was profiled by 454-pyrosequencing, based on the amplification of partial ammonia-monooxygenase subunit A (amoA) genes. Salinity did not inhibit nitrification at 3.7g/L, while ammonia oxidation activity significantly decreased and nitrite was consequently accumulated in the SFBBR when the salt concentration was ⩾24.1g/L. The sequencing of amoA genes revealed that many of the OTUs found in the control experiment were still present at the full range of NaCl studied, while concentrations of 24.1 and 44.1g of NaCl/L promoted the emergence of new OTUs phylogenetically related to AOB described in saline environments.

Different effects of transgenic maize and nontransgenic maize on nitrogen-transforming archaea and bacteria in tropical soils.

The composition of the rhizosphere microbiome is a result of interactions between plant roots, soil, and environmental conditions. The impact of genetic variation in plant species on the composition of the root-associated microbiota remains poorly understood. This study assessed the abundances and structures of nitrogen-transforming (ammonia-oxidizing) archaea and bacteria as well as nitrogen-fixing bacteria driven by genetic modification of their maize host plants. The data show that significant changes in the abundances (revealed by quantitative PCR) of ammonia-oxidizing bacterial and archaeal communities occurred as a result of the maize host being genetically modified. In contrast, the structures of the total communities (determined by PCR-denaturing gradient gel electrophoresis) were mainly driven by factors such as soil type and season and not by plant genotype. Thus, the abundances of ammonia-oxidizing bacterial and archaeal communities but not structures of those communities were revealed to be responsive to changes in maize genotype, allowing the suggestion that community abundances should be explored as candidate bioindicators for monitoring the possible impacts of cultivation of genetically modified plants.

Spatiotemporal Relationships Between the Abundance, Distribution, and Potential Activities of Ammonia-Oxidizing and Denitrifying Microorganisms in Intertidal Sediments

The primary objective of this study was to gain an understanding of how key microbial communities involved in nitrogen cycling in estuarine sediments vary over a 12-month period. Furthermore, we sought to determine whether changes in the size of these communities are related to, or indicative of, seasonal patterns in fixed nitrogen dynamics in Elkhorn Slough--a small, agriculturally impacted estuary with a direct connection to Monterey Bay. We assessed sediment and pore water characteristics, abundance of functional genes for nitrification (bacterial and archaeal amoA, encoding ammonia monooxygenase subunit A) and denitrification (nirS and nirK, encoding nitrite reductase), and measurements of potential nitrification and denitrification activities at six sites. No seasonality in the abundance of denitrifier or ammonia oxidizer genes was observed. A strong association between potential nitrification activity and the size of ammonia-oxidizing bacterial communities was observed across the estuary. In contrast, ammonia-oxidizing archaeal abundances remained relatively constant in space and time. Unlike many other estuaries, salinity does not appear to regulate the distribution of ammonia-oxidizing communities in Elkhorn Slough. Instead, their distributions appear to be governed over two different time scales. Long-term niche characteristics selected for the gross size of archaeal and bacterial ammonia-oxidizing communities, yet covariation in their abundances between monthly samples suggests that they respond in a similar manner to short-term changes in their environment. Abundances of denitrifier and ammonia oxidizer genes also covaried, but site-specific differences in this relationship suggest differing levels of interaction (or coupling) between nitrification and denitrification.