ammonia oxidizing bacteria
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2022 ◽  
Author(s):  
Barbara Bayer ◽  
Kelsey McBeain ◽  
Craig A Carlson ◽  
Alyson E Santoro

Nitrifying microorganisms, including ammonia-oxidizing archaea, ammonia-oxidizing bacteria and nitrite-oxidizing bacteria, are the most abundant chemoautotrophs in the ocean and play an important role in the global carbon cycle by fixing dissolved inorganic carbon (DIC) into biomass. The release of organic compounds by these microbes is less well known but may represent an as-yet unaccounted source of dissolved organic carbon (DOC) available to heterotrophic marine food webs. Here, we provide measurements of cellular carbon and nitrogen quotas, DIC fixation yields and DOC release of ten phylogenetically diverse marine nitrifiers grown in multiple culture conditions. All investigated strains released DOC during growth, making up on average 5-15% of the fixed DIC. Neither substrate concentration nor temperature affected the proportion of fixed DIC released as DOC, but release rates varied between closely related species. Our results also indicate previous studies may have underestimated DIC fixation yields of marine nitrite oxidizers due to partial decoupling of nitrite oxidation from CO2 fixation, and due to lower observed yields in artificial compared to natural seawater medium. The results of this study provide values for biogeochemical models of the global carbon cycle, and help to further constrain the implications of nitrification-fueled chemoautotrophy for marine food-web functioning and the biological sequestration of carbon in the ocean.


Author(s):  
Changqing Guo ◽  
Hongmei Wang ◽  
Dianbo Zou ◽  
Yue Wang ◽  
Xiaori Han

Abstract Purpose Nitrification inhibitor plays an important regulatory role in inhibiting the nitrification of ammonium in soils. However, most of nitrification inhibitors lack the sustainable effects in suppressing the nitrification of ammonium. In this study, a novel DMS nitrification inhibitor was prepared and tested to explore its lasting effect of nitrification suppression in black soil. Materials and methods Both culture experiments and field trial were performed in black soils. Three kinds of nitrification inhibitors (NIs), dicyandiamide (DCD) with low bioactivity, 3,4-dimethylpyrazole phosphate (DMPP) with high bioactivity, and a novel 3,4-dimethylpyrazole sulfate zinc (DMS) with long half-life, were applied into soils, respectively, and the abundance changes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated; then, the accumulation changes of inorganic nitrogen, nitrogen use efficiency, and crop yields were furtherly evaluated. Results and discussions A novel DMS nitrification inhibitor with high activity and long half-life maintained a persistent effect of nitrification suppression, and remarkably increased the accumulation of ammonium nitrogen in soil, thus improving nitrogen use efficiency and crop yields. This study implies that lowering the nitrogen loss of nitrification-triggered in soil is of great importance for improving nitrogen use efficiency. Conclusions This study provided an insight into the sustainable nitrification suppression of a novel DMS nitrification inhibitor under excessive application of nitrogen fertilizer in black soils. Compared with improving the activity, reasonably prolonging the validity of nitrification inhibitors in soil is a more important strategy increasing the sustainable effects of nitrification inhibition, and the survival period of nitrification inhibitors in soil should be a crucial factor improving nitrogen use efficiency.


Author(s):  
Liang Qi ◽  
Ling Li ◽  
Lin Yin ◽  
Wen Zhang

Abstract Carbon sources of cellulose plants are the promising materials that enhancing the activities of denitrifying bacteria in the groundwater system. To further verify the denitrification performance of cellulose plants and the main factors of affecting the denitrifying system, six cellulose plants from agricultural wastes (wood chip, corn cob, rice husk, corn straw, wheat straw, and sugar cane) were selected for bioavailable organic matter leaching experiments, carbon denitrification experiments, functional bacteria identification, and analysis experiments. The results show that the extracts of cellulose plants contain a mixed carbon sources system including small molecular organic acids, sugars, nitrogen-containing organic components, and esters. The qPCR results showed that the denitrifying bacteria had obvious advantages compare to anaerobic ammonia-oxidizing bacteria during the stable period; the denitrification experiment showed that each of six cellulose plants removed more than 80% of nitrogen, and the denitrification rates reached 1.00–2.00 mg N cm−3·d−1. The supplement of cellulose plants promotes the metabolism rate of denitrifying bacteria, and the additional denitrifying bacteria have little effect on nitrate removal. In summary, the expected denitrification reaction occurred in the cellulose plant system, which is suitable as a carbon source material for water body nitrogen pollution remediation.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12592
Author(s):  
Jialin Hu ◽  
Jonathan D. Richwine ◽  
Patrick D. Keyser ◽  
Lidong Li ◽  
Fei Yao ◽  
...  

Background Fertilizer 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. Methods In 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. Results Nitrosospira 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).


2021 ◽  
Author(s):  
P. Maza-Márquez ◽  
M. D. Lee ◽  
A. M. Detweiler ◽  
B. M. Bebout

AbstractMicrobial mats are modern analogues of the first ecosystems on the Earth. As extant representatives of microbial communities where free oxygen may have first been available on a changing planet, they offer an ecosystem within which to study the evolution of biogeochemical cycles requiring and inhibited by oxygen. Here, we report the distribution of genes involved in nitrogen metabolism across a vertical oxygen gradient at 1 mm resolution in a microbial mat using quantitative PCR (qPCR), retro-transcribed qPCR (RT-qPCR) and metagenome sequencing. Vertical patterns in the presence and expression of nitrogen cycling genes, corresponding to oxygen requiring and non-oxygen requiring nitrogen metabolism, could be seen across gradients of dissolved oxygen and ammonium. Metagenome analysis revealed that genes annotated as hydroxylamine dehydrogenase (proper enzyme designation EC 1.7.2.6, hao) and hydroxylamine reductase (hcp) were the most abundant nitrogen metabolism genes in the mat. The recovered hao genes encode hydroxylamine dehydrogenase EC 1.7.2.6 (HAO) proteins lacking the tyrosine residue present in aerobic ammonia oxidizing bacteria (AOB). Phylogenetic analysis confirmed that those proteins were more closely related to ɛHao protein present in Campylobacterota lineages (previously known as Epsilonproteobacteria) rather than oxidative HAO of AOB. BLAST analysis of some transcribed proteins indicated that they likely functioned as a nitrate reductase. The presence of hao sequences related with ɛHao protein, as well as numerous hcp genes encoding a prismane protein, suggest the presence of a nitrogen cycling pathway previously described in Nautilia profundicola as ancestral to the most commonly studied present day nitrogen cycling pathways.


Geoderma ◽  
2021 ◽  
Vol 404 ◽  
pp. 115395
Author(s):  
Yongxin Lin ◽  
Hang-Wei Hu ◽  
Guiping Ye ◽  
Jianbo Fan ◽  
Weixin Ding ◽  
...  

2021 ◽  
Vol 12 ◽  
Author(s):  
Shimin Lu ◽  
Xingguo Liu ◽  
Chong Liu ◽  
Guofeng Cheng ◽  
Runfeng Zhou ◽  
...  

The excessive ammonia produced in pond aquaculture processes cannot be ignored. In this review, we present the distribution and diversity of ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing bacteria (AnAOB) in the pond environment. Combined with environmental conditions, we analyze the advantages of AOA and AnAOB in aquaculture water treatment and discuss the current situation of pond water treatment engineering involving these microbes. AOA and AnAOB play an important role in the nitrogen removal process of aquaculture pond water, especially in seasonal low temperatures and anoxic sediment layers. Finally, we prospect the application of bioreactors to purify pond aquaculture water using AOA and AnAOB, in autotrophic nitrogen removal, which can reduce the production of greenhouse gases (such as nitrous oxide) and is conducive to the development of environmentally sustainable pond aquaculture.


2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Chen Lyu ◽  
Na Li ◽  
Ming Li ◽  
Yiyan Lyu ◽  
Zhaoying Liu ◽  
...  

It is crucial to explore new methods to deal with ammonia pollution in hog barns. In this experiment, ammonia gas generated from the decomposition of nitrogenous organic matter, such as feed and manure in hog barns, was studied. Growing environmental parameters monitored included temperature, humidity, and ammonia nitrogen concentration. For 92 days between March and May, ammonia emissions were characterized by monitoring and collecting the ammonia concentration during the selected time. The results showed that the average temperature in the hog house was 18.2 ± 2.7°C, the humidity was 62.7 ± 0.3%, and the average ammonia concentration range was 17.7∼23.1 mg m−3. The collected ammonia-nitrogen-containing wastewater that entered the denitrification device showed 173, 232, 201, and 280 mgNH4-N/L, respectively. An integrated denitrification device with anaerobic ammonia-oxidizing bacteria as a functional strain was used for denitrification treatment. Through the change of ion concentration in the incoming and outgoing water, an 85.5% average denitrification efficiency was calculated according to the denitrification reaction chemical formula. Thus, the results presented here provide data support for the future use of microbial denitrification equipment to treat ammonia in hog houses.


AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jing Lu ◽  
Yiguo Hong ◽  
Ying Wei ◽  
Ji-Dong Gu ◽  
Jiapeng Wu ◽  
...  

AbstractAnaerobic ammonium oxidation (anammox) process has been acknowledged as an environmentally friendly and time-saving technique capable of achieving efficient nitrogen removal. However, the community of nitrification process in anammox-inoculated wastewater treatment plants (WWTPs) has not been elucidated. In this study, ammonia oxidation (AO) and nitrite oxidation (NO) rates were analyzed with the incubation of activated sludge from Xinfeng WWTPs (Taiwan, China), and the community composition of nitrification communities were investigated by high-throughput sequencing. Results showed that both AO and NO had strong activity in the activated sludge. The average rates of AO and NO in sample A were 6.51 µmol L−1 h−1 and 6.52 µmol L−1 h−1, respectively, while the rates in sample B were 14.48 µmol L−1 h−1 and 14.59 µmol L−1 h−1, respectively. The abundance of the nitrite-oxidizing bacteria (NOB) Nitrospira was 0.89–4.95 × 1011 copies/g in both samples A and B, the abundance of ammonia-oxidizing bacteria (AOB) was 1.01–9.74 × 109 copies/g. In contrast, the abundance of ammonia-oxidizing archaea (AOA) was much lower than AOB, only with 1.28–1.53 × 105 copies/g in samples A and B. The AOA community was dominated by Nitrosotenuis, Nitrosocosmicus, and Nitrososphaera, while the AOB community mainly consisted of Nitrosomonas and Nitrosococcus. The dominant species of Nitrospira were Candidatus Nitrospira defluvii, Candidatus Nitrospira Ecomare2 and Nitrospira inopinata. In summary, the strong nitrification activity was mainly catalyzed by AOB and Nitrospira, maintaining high efficiency in nitrogen removal in the anammox-inoculated WWTPs by providing the substrates required for denitrification and anammox processes.


2021 ◽  
Author(s):  
Michelle M McKnight ◽  
Josh D Neufeld

Nitrification by aquarium biofilters transforms toxic ammonia waste (NH3/NH4+) to less toxic nitrate (NO3-) via nitrite (NO2-). Ammonia oxidation is mediated by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the recently discovered complete ammonia oxidizing (comammox) Nitrospira. Prior to the discovery of comammox Nitrospira, previous research revealed that AOA dominate among ammonia oxidizers in freshwater biofilters. Here, we characterized the composition of aquarium filter microbial communities and quantified the abundance of all three known groups of ammonia oxidizers. Aquarium biofilter and water samples were collected from representative freshwater and saltwater systems in Southwestern Ontario, Canada. Using extracted DNA, we performed 16S rRNA gene sequencing and quantitative PCR (qPCR) to assess community composition and quantify the abundance of amoA genes, respectively. Our results show that aquarium biofilter microbial communities were consistently represented by putative heterotrophs of the Proteobacteria and Bacteroides phyla, with distinct profiles associated with fresh versus saltwater biofilters. Among nitrifiers, comammox Nitrospira amoA genes were detected in all 38 freshwater aquarium biofilter samples and were the most abundant ammonia oxidizer in 30 of these samples, with the remaining biofilters dominated by AOA, based on amoA gene abundances. In saltwater biofilters, AOA or AOB were differentially abundant, with no comammox Nitrospira detected. These results demonstrate that comammox Nitrospira play an important role in biofilter nitrification that has been previously overlooked and such microcosms are useful for exploring the ecology of nitrification for future research.


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