scholarly journals Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ian M. Clark ◽  
David J. Hughes ◽  
Qingling Fu ◽  
Maïder Abadie ◽  
Penny R. Hirsch
Keyword(s):  
Phylogenetic Diversity ◽  
Arable Soil ◽  
Nitrifying Bacteria ◽  
Anammox Bacteria ◽  
Ammonia Oxidizing Archaea ◽  
Wheat Cultivation ◽  
Soil Metagenome ◽  
Nitrite Oxidizing Bacteria ◽  
Bare Fallow ◽  
Field Plots

AbstractThe abundance and phylogenetic diversity of functional genes involved in nitrification were assessed in Rothamsted field plots under contrasting management regimes—permanent bare fallow, grassland, and arable (wheat) cultivation maintained for more than 50 years. Metagenome and metatranscriptome analysis indicated nitrite oxidizing bacteria (NOB) were more abundant than ammonia oxidizing archaea (AOA) and bacteria (AOB) in all soils. The most abundant AOA and AOB in the metagenomes were, respectively, Nitrososphaera and Ca. Nitrososcosmicus (family Nitrososphaeraceae) and Nitrosospira and Nitrosomonas (family Nitrosomonadaceae). The most abundant NOB were Nitrospira including the comammox species Nitrospira inopinata, Ca. N. nitrificans and Ca. N. nitrosa. Anammox bacteria were also detected. Nitrospira and the AOA Nitrososphaeraceae showed most transcriptional activity in arable soil. Similar numbers of sequences were assigned to the amoA genes of AOA and AOB, highest in the arable soil metagenome and metatranscriptome; AOB amoA reads included those from comammox Nitrospira clades A and B, in addition to Nitrosomonadaceae. Nitrification potential assessed in soil from the experimental sites (microcosms amended or not with DCD at concentrations inhibitory to AOB but not AOA), was highest in arable samples and lower in all assays containing DCD, indicating AOB were responsible for oxidizing ammonium fertilizer added to these soils.

scholarly journals Ammonia-oxidizing archaea are integral to nitrogen cycling in a highly fertile agricultural soil

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Laibin Huang ◽  
Seemanti Chakrabarti ◽  
Jennifer Cooper ◽  
Ana Perez ◽  
Sophia M. John ◽  
...  
Keyword(s):  
Nitrogen Cycle ◽  
Agricultural Soil ◽  
Agricultural Soils ◽  
Ammonia Oxidizing Bacteria ◽  
Central Process ◽  
Soil Nitrification ◽  
Plant Nitrogen ◽  
Ammonia Oxidizing Archaea ◽  
Activity Measurements ◽  
Nitrite Oxidizing Bacteria

AbstractNitrification is a central process in the global nitrogen cycle, carried out by a complex network of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Nitrification is responsible for significant nitrogen leaching and N2O emissions and thought to impede plant nitrogen use efficiency in agricultural systems. However, the actual contribution of each nitrifier group to net rates and N2O emissions remain poorly understood. We hypothesized that highly fertile agricultural soils with high organic matter mineralization rates could allow a detailed characterization of N cycling in these soils. Using a combination of molecular and activity measurements, we show that in a mixed AOA, AOB, and comammox community, AOA outnumbered low diversity assemblages of AOB and comammox 50- to 430-fold, and strongly dominated net nitrification activities with low N2O yields between 0.18 and 0.41 ng N2O–N per µg NOx–N in cropped, fallow, as well as native soil. Nitrification rates were not significantly different in plant-covered and fallow plots. Mass balance calculations indicated that plants relied heavily on nitrate, and not ammonium as primary nitrogen source in these soils. Together, these results imply AOA as integral part of the nitrogen cycle in a highly fertile agricultural soil.

Investigation of aerobic and anaerobic ammonium-oxidising bacteria presence in a small full-scale wastewater treatment system comprised by UASB reactor and three polishing ponds

2010 ◽  
Vol 61 (3) ◽  
pp. 737-743 ◽  
Author(s):  
J. C. Araujo ◽  
M. M. S. Correa ◽  
E. C. Silva ◽  
A. P. Campos ◽  
V. M. Godinho ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Ammonia Removal ◽  
Treatment System ◽  
Nitrifying Bacteria ◽  
Uasb Reactor ◽  
Anammox Bacteria ◽  
Fluorescence In Situ Hybridisation ◽  
Probable Number ◽  
Sediment Samples ◽  
Wastewater Treatment System

This work applied PCR amplification method and Fluorescence in situ hybridisation (FISH) with primers and probes specific for the anammox organisms and aerobic ammonia-oxidising β-Proteobacteria in order to detect these groups in different samples from a wastewater treatment system comprised by UASB reactor and three polishing (maturation) ponds in series. Seven primer pairs were used in order to detect Anammox bacteria. Positive results were obtained with three of them, suggesting that Anammox could be present in polishing pond sediments. However, Anammox bacteria were not detected by FISH, indicating that they were not present in sediment samples, or they could be present but below FISH detection limit. Aerobic ammonia- and nitrite-oxidising bacteria were verified in water column samples through Most Probable Number (MPN) analysis, but they were not detected in sediment samples by FISH. Ammonia removal efficiencies occurred systematically along the ponds (24, 32, and 34% for polishing pond 1, 2, and 3, respectively) but the major reaction responsible for this removal is still unclear. Some nitrification might have occurred in water samples because some nitrifying bacteria were present. Also Anammox reaction might have occurred because Anammox genes were detected in the sediments, but probably this reaction was too low to be noticed. It is important also to consider that some of the ammonia removal observed might be related to NH3 stripping, associated with the pH increase resulting from the intensive photosynthetic activity in the ponds (mechanism under investigation). Therefore, it can be concluded that more than one mechanism (or reaction) might be involved in the ammonia removal in the polishing ponds investigated in this study.

scholarly journals Operational modifications for the development of nitrifying bacteria in a large-scale biological aerated filter and its impact on wastewater treatment

2018 ◽  
Vol 78 (8) ◽  
pp. 1704-1714 ◽  
Author(s):  
François-René Bourgeois ◽  
Frédéric Monette ◽  
Daniel G. Cyr
Keyword(s):  
Large Scale ◽  
Oxygen Demand ◽  
Bacterial Biofilm ◽  
Nitrifying Bacteria ◽  
Nitrification Rate ◽  
Total Biomass ◽  
Ammonia Oxidizing Bacteria ◽  
Operational Conditions ◽  
Nitrite Oxidizing Bacteria ◽  
Aerated Filter

Abstract To develop a better understanding for fixed biomass processes, the development of a nitrifying bacterial biofilm, as well as the performance of treatment during modifications to operational conditions of a full-scale submerged biological filter were examined. The development of the nitrifying biofilm was investigated at four depth levels (1, 2, 4 and 5 feet). The result of bacterial subpopulations analyzed by qPCR relative to the physico-chemical parameters of the wastewater during the various tests (sustained aeration, modified backwash parameters and inflow restriction) revealed an increase of the relative presence of nitrifying microorganisms throughout the biofilm (especially for nitrite oxidizing bacteria (NOB)), but this was not necessarily accompanied by a better nitrification rate. The highest observed nitrification rate was 49% of removal in the test cell during backwashing conditions, whereas the relative ammonia oxidizing bacteria (AOB) population was 0.032% and NOB was 0.008% of the total biomass collected. The highest percentage of nitrifying bacteria observed (0.034% AOB and 0.18% NOB) resulted in a nitrification rate of 21%. The treatment of organic matter determined by measuring the chemical and biochemical oxygen demand (COD, CBOD5) was improved.

scholarly journals Investigating the chemolithoautotrophic and formate metabolism of Nitrospira moscoviensis by constraint-based metabolic modeling and 13C-tracer analysis

2021 ◽  
Author(s):  
Christopher E. Lawson ◽  
Aniela B. Mundinger ◽  
Hanna Koch ◽  
Tyler B. Jacobson ◽  
Coty A. Weathersby ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Metabolic Networks ◽  
Metabolic Model ◽  
Scale Model ◽  
Nitrifying Bacteria ◽  
Metabolomic Analysis ◽  
A Genome ◽  
Nitrite Oxidizing Bacteria ◽  
Genome Scale ◽  
Nitrospira Moscoviensis

AbstractNitrite-oxidizing bacteria belonging to the genus Nitrospira mediate a key step in nitrification and play important roles in the biogeochemical nitrogen cycle and wastewater treatment. While these organisms have recently been shown to exhibit metabolic flexibility beyond their chemolithoautotrophic lifestyle, including the use of simple organic compounds to fuel their energy metabolism, the metabolic networks controlling their autotrophic and mixotrophic growth remain poorly understood. Here, we reconstructed a genome-scale metabolic model for Nitrospira moscoviensis (iNmo686) and used constraint-based analysis to evaluate the metabolic networks controlling autotrophic and formatotrophic growth on nitrite and formate, respectively. Subsequently, proteomic analysis and 13C-tracer experiments with bicarbonate and formate coupled to metabolomic analysis were performed to experimentally validate model predictions. Our findings support that N. moscoviensis uses the reductive tricarboxylic acid cycle for CO2 fixation. We also show that N. moscoviensis can indirectly use formate as a carbon source by oxidizing it first to CO2 followed by reassimilation, rather than direct incorporation via the reductive glycine pathway. Our study offers the first measurements of Nitrospira’s in vivo central carbon metabolism and provides a quantitative tool that can be used for understanding and predicting their metabolic processes.ImportanceNitrospira are globally abundant nitrifying bacteria in soil and aquatic ecosystems and wastewater treatment plants, where they control the oxidation of nitrite to nitrate. Despite their critical contribution to nitrogen cycling across diverse environments, detailed understanding of their metabolic network and prediction of their function under different environmental conditions remains a major challenge. Here, we provide the first constraint-based metabolic model of N. moscoviensis representing the ubiquitous Nitrospira lineage II and subsequently validate this model using proteomics and 13C-tracers combined with intracellular metabolomic analysis. The resulting genome-scale model will serve as a knowledge base of Nitrospira metabolism and lays the foundation for quantitative systems biology studies of these globally important nitrite- oxidizing bacteria.

Communities of ammonia-oxidizing bacteria, ammonia-oxidizing archaea and nitrite-oxidizing bacteria in shrimp ponds

2014 ◽  
Vol 65 (1) ◽  
pp. 267-278 ◽  
Author(s):  
Papitchaya Srithep ◽  
Bongkoch Khinthong ◽  
Thanasita Chodanon ◽  
Sorawit Powtongsook ◽  
Wiboonlak Pungrasmi ◽  
...  
Keyword(s):  
Ammonia Oxidizing Bacteria ◽  
Shrimp Ponds ◽  
Ammonia Oxidizing Archaea ◽  
Nitrite Oxidizing Bacteria

Biological Treatment of High Ammonium Content Urban Landfill Leachate Using an Anaerobic-Aerobic Process

2013 ◽  
Vol 781-784 ◽  
pp. 2095-2099
Author(s):  
Hong Wei Sun ◽  
Yong Jun You ◽  
Ying Guo
Keyword(s):  
Landfill Leachate ◽  
Inhibitory Effect ◽  
Nitrifying Bacteria ◽  
Anaerobic Sludge ◽  
Nitrite Accumulation ◽  
Fish Analysis ◽  
Free Nitrous Acid ◽  
Nitrite Oxidizing Bacteria ◽  
Anaerobic Sludge Blanket

Biological system consisting of an up-flow anaerobic sludge blanket (UASB) and anoxic-oxic (A/O) reactor was applied to treat high ammonium content urban landfill leachate. Inhibitory effect of free ammonia (FA) and free nitrous acid (FNA) on nitrifying bacteria activity was used to achieve nitrogen removal via nitrite pathway in the A/O. Results demonstrated that removed efficiencies of COD, total nitrogen (TN) and NH4+-N were 95.3%, 84.6 %and 99.2%, respectively. Stable nitrite pathway with above 90% nitrite accumulation was successfully achieved in the A/O reactor by synergetic inhibition of FA and FNA on the activity of nitrite oxidizing bacteria (NOB). Moreover, Fluorescence in situ hybridization (FISH) analysis showed that AOB was dominant microorganism.

Autotrophic nitrogen removal in sequencing batch biofilm reactors at different oxygen supply modes

2008 ◽  
Vol 58 (10) ◽  
pp. 1889-1894 ◽  
Author(s):  
C. Wantawin ◽  
J. Juateea ◽  
P. L. Noophan ◽  
J. Munakata-Marr
Keyword(s):  
Nitrogen Removal ◽  
Nitrogen Loss ◽  
Ammonia Concentration ◽  
Anammox Bacteria ◽  
Ammonia Oxidizing Bacteria ◽  
Intermittent Aeration ◽  
Biofilm Reactors ◽  
Air Supply ◽  
Nitrite Oxidizing Bacteria ◽  
Sequencing Batch Biofilm Reactors

Conventional nitrification-denitrification treatment is a common way to treat nitrogen in wastewater, but this process is costly for low COD/N wastewaters due to the addition of air and external carbon-source. However, ammonia may alternatively be converted to dinitrogen gas by autotrophic bacteria utilizing aerobically autotrophically produced nitrite as an electron acceptor under anoxic conditions. Lab-scale sequencing batch biofilm reactors (SBBRs) inoculated with normal nitrifying sludge were employed to study the potential of an oxygen-limited autotrophic nitrification-denitrification process initiated with typical nitrifying sludge for treating a synthetic ammonia wastewater devoid of organic carbon in one step. The ring-laced fibrous carrier (length 0.32 m, surface area 3.4 m2/m) was fixed vertically in a 3 L reactor. Two different air supply modes were applied:continuous aeration to control dissolved oxygen at 1.5 mg/L and intermittent aeration. High nitrogen removals of more than 50% were obtained in both SBBRs. At an ammonia loading of 0.882 gm N/m2-day [hydraulic retention time (HRT) of 24 hr], the SBBR continuously aerated to 1.5 mg DO/L had slightly higher nitrogen removal (64%) than the intermittently alternated SBBR (55%). The main form of residual nitrogen in the effluent was ammonia, at concentrations of 25 mg/L and 37 mg N/L in continuous and intermittent aeration SBBRs, respectively. Ammonia was completely consumed when ammonia loading was reduced to 0.441 gm N/m2-day [HRT extended to 48 hr]. The competitive use of nitrite by aerobic nitrite oxidizing bacteria (ANOB) with anaerobic ammonia-oxidizing bacteria (anammox bacteria) during the expanded aeration period under low remaining ammonia concentration resulted in higher nitrate production and lower nitrogen loss in the continuous aeration SBBR than in the intermittent aeration SBBR. The nitrogen removal efficiencies in SBBRs with continuous and alternating aerated were 80% and 86% respectively. Specific microorganisms in the biofilm were characterized using fluorescence in situ hybridization. Aerobic ammonia-oxidizing bacteria (AAOB) occurred side by side with putative anammox bacteria (cells hybridizing with probe AMX820) throughout the biofilm, though ANOB were rarely detected.

scholarly journals Nitrogen removal via a single-stage PN–Anammox process in a novel combined biofilm reactor

2017 ◽  
Vol 77 (6) ◽  
pp. 1483-1492 ◽  
Author(s):  
Yue-mei Han ◽  
Feng-xia Liu ◽  
Xiao-fei Xu ◽  
Zhuo Yan ◽  
Zhi-jun Liu
Keyword(s):  
Total Nitrogen ◽  
Nitrogen Removal ◽  
Ammonia Oxidation ◽  
Biofilm Reactor ◽  
Nitrifying Bacteria ◽  
Anammox Bacteria ◽  
Ammonia Oxidizing Bacteria ◽  
High Ammonia ◽  
Total Nitrogen Removal ◽  
Anammox Process

Abstract This study developed a partial nitrification (PN) and anaerobic ammonia oxidation (Anammox) process for treating high-ammonia wastewater using an innovative biofilm system in which ammonia oxidizing bacteria grew on fluidized Kaldnes (K1) carriers and Anammox bacteria grew on fixed acryl resin carriers. The airlift loop biofilm reactor (ALBR) was stably operated for more than 4 months under the following conditions: 35 ± 2 °C, pH 7.5–8.0 and dissolved oxygen (DO) of 0.5–3.5 mg/L. The results showed that the total nitrogen removal efficiency reached a maximum of 75% and the total nitrogen removal loading rate was above 0.4 kg/(d·m3). DO was the most efficient control parameter in the mixed biofilm system, and values below 1.5 mg/L were observed in the riser zone for the PN reaction, while values below 0.8 mg/L were observed in the downer zone for the Anammox reaction. Scanning electron microscopy and Fluorescence In Situ Hybridization images showed that most of the nitrifying bacteria were distributed on the K1 carriers and most of the Anammox bacteria were distributed within the acryl resin carriers. Therefore, the results indicate that the proposed combined biofilm system is easy to operate and efficient for the treatment of high-ammonia wastewater.

scholarly journals Effects of Different Land-use Types on Active Autotrophic Ammonia and Nitrite Oxidizers in Cinnamon Soils

2021 ◽  
Author(s):  
Xinli Wang ◽  
Yun Wang ◽  
Fei Zhu ◽  
Chi Zhang ◽  
Peiyao Wang ◽  
...  
Keyword(s):  
Land Use ◽  
Forest Soil ◽  
Community Composition ◽  
Organic Matter Content ◽  
Soil Dna ◽  
Ammonia Oxidizing Archaea ◽  
Vegetable Soil ◽  
Land Use Types ◽  
Nitrite Oxidizing Bacteria ◽  
Greenhouse Vegetable

Land-use types with different disturbance gradients show many variations in soil properties, but the effects of different land-use types on soil nitrifying communities and their ecological implications remain poorly understood. Using 13CO2-DNA-based stable isotope probing (DNA-SIP), we examined the relative importance and active community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite-oxidizing bacteria (NOB) in soils under three land-use types, forest, cropland, and greenhouse vegetable soil, representing three interference gradients. Soil net nitrification rate was in the order forest soil > cropland soil > greenhouse vegetable soil. DNA-SIP showed that active AOA outcompeted AOB in the forest soil, whereas AOB outperformed AOA in the cropland and greenhouse vegetable soils. Cropland soil was richer in NOB than in AOA and AOB. Phylogenetic analysis revealed that ammonia oxidation in the forest soil was predominantly catalyzed by the AOA Nitrosocosmicus franklandus cluster within the group 1.1b lineage. The 13C-labeled AOB were overwhelmingly dominated by Nitrosospira cluster 3 in the cropland soil. The active AOB Nitrosococcus watsonii lineage was observed in the greenhouse vegetable soil, and it played an important role in nitrification. Active NOB communities were closely affiliated with Nitrospira in the forest and cropland soils, and with Nitrolancea and Nitrococcus in the greenhouse vegetable soil. Canonical correlation analysis showed that soil pH and organic matter content significantly affected the active nitrifier community composition. These results suggest that land-use types with different disturbance gradients alter the distribution of active nitrifier communities by affecting soil physicochemical properties. IMPORTANCE Nitrification plays an important role in the soil N cycle, and land-use management has a profound effect on soil nitrifiers. It is unclear how different gradients of land use affect active ammonia-oxidizing archaea and bacteria and nitrite-oxidizing bacteria. Our research is significant because we determined the response of nitrifiers to human disturbance, which will greatly improve our understanding of the niche of nitrifiers and the differences in their physiology.

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