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Chisholm C, Di H, Cameron K, Podolyan A, Shen J, Zhang L, Sirisena K, Godsoe W. Contrasting response of comammox Nitrospira, ammonia oxidising bacteria, and archaea to soil pH and nitrogen inputs. Sci Total Environ 2024; 924:171627. [PMID: 38471592 DOI: 10.1016/j.scitotenv.2024.171627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
This study aimed to investigate the effect of soil pH change, and nitrogen amendment on ammonia oxidiser abundance and comammox Nitrospira community composition. The experimental design used soil mesocosms placed in a temperature-controlled incubator for 90 days. A Templeton silt loam was used as its physiochemical properties are typical of the region's dairy farms. The results showed that comammox Nitrospira clade B preferred the natural (pH 6.1-6.2) soil pH with no applied nitrogen. Furthermore, synthetic urine (N700) decreased the abundance of comammox Nitrospira clade B. This may have been because the large amounts of available ammonia in the N700 treatments inhibited the growth of comammox Nitrospira. These results suggest that while comammox Nitrospira clade B are present in New Zealand dairy farm soils, but their role in nitrification in the very high nitrogen environment under a urine patch in grazed pastures may be limited. Further research is needed to confirm this. In contrast to comammox, the AOB community (dominated by Nitrosospira) responded positively to the application of synthetic urine. The response was greatest in the high pH soil (7.1), followed by the natural and then the low pH (4.9) soils. This may be due to the difference in ammonia availability. At high pH, the ammonia/ammonium equilibrium favours ammonia production. Calculated ammonia availability in the N700 treatments accurately predicted the AOB amoA gene abundance. Interestingly, the AOA community abundance (which was predominantly made up of Thaumarchaeota group I.1b clade E) seemed to prefer the natural and high pH soils over the low pH. This may be due to the specific lineage of AOA present. AOA did not respond to the application of nitrogen.
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Affiliation(s)
- C Chisholm
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - H Di
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand.
| | - K Cameron
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - A Podolyan
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - J Shen
- Fujian Normal University, China
| | - L Zhang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, China
| | - K Sirisena
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - W Godsoe
- Department of Pest Management and Conservation, Lincoln University, New Zealand
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Zhang Z, Bo L, Wang S, Li C, Zhang X, Xue B, Yang X, He X, Shen Z, Qiu Z, Zhao C, Wang J. Multidrug-resistant plasmid RP4 inhibits the nitrogen removal capacity of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and comammox in activated sludge. Environ Res 2024; 242:117739. [PMID: 38007076 DOI: 10.1016/j.envres.2023.117739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/09/2023] [Accepted: 11/17/2023] [Indexed: 11/27/2023]
Abstract
In wastewater treatment plants (WWTPs), ammonia oxidation is primarily carried out by three types of ammonia oxidation microorganisms (AOMs): ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and comammox (CMX). Antibiotic resistance genes (ARGs), which pose an important public health concern, have been identified at every stage of wastewater treatment. However, few studies have focused on the impact of ARGs on ammonia removal performance. Therefore, our study sought to investigate the effect of the representative multidrug-resistant plasmid RP4 on the functional microorganisms involved in ammonia oxidation. Using an inhibitor-based method, we first evaluated the contributions of AOA, AOB, and CMX to ammonia oxidation in activated sludge, which were determined to be 13.7%, 41.1%, and 39.1%, respectively. The inhibitory effects of C2H2, C8H14, and 3,4-dimethylpyrazole phosphate (DMPP) were then validated by qPCR. After adding donor strains to the sludge, fluorescence in situ hybridization (FISH) imaging analysis demonstrated the co-localization of RP4 plasmids and all three AOMs, thus confirming the horizontal gene transfer (HGT) of the RP4 plasmid among these microorganisms. Significant inhibitory effects of the RP4 plasmid on the ammonia nitrogen consumption of AOA, AOB, and CMX were also observed, with inhibition rates of 39.7%, 36.2%, and 49.7%, respectively. Moreover, amoA expression in AOB and CMX was variably inhibited by the RP4 plasmid, whereas AOA amoA expression was not inhibited. These results demonstrate the adverse environmental effects of the RP4 plasmid and provide indirect evidence supporting plasmid-mediated conjugation transfer from bacteria to archaea.
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Affiliation(s)
- Zhaohui Zhang
- School of Environmental Science and Engineering, Tiangong University, State Key Laboratory of Separation Membranes and Membrane Processes, Binshui West Road 399, Xiqing District, Tianjin, 300387, China.
| | - Lin Bo
- School of Environmental Science and Engineering, Tiangong University, State Key Laboratory of Separation Membranes and Membrane Processes, Binshui West Road 399, Xiqing District, Tianjin, 300387, China; Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Shang Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Chenyu Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Xi Zhang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Bin Xue
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Xiaobo Yang
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China
| | - Xinxin He
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Zhiqiang Shen
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Zhigang Qiu
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China
| | - Chen Zhao
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China.
| | - Jingfeng Wang
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, 300050, China.
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Ding F, He T, Qi X, Zhang H, An L, Xu S, Zhang X. Comammox Nitrospira dominates the nitrification in artificial coniferous forest soils of the Qilian Mountains. Sci Total Environ 2024; 906:167653. [PMID: 37806577 DOI: 10.1016/j.scitotenv.2023.167653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
Complete ammonia oxidizers (Comammox, CMX) are a newly discovered and important component of the nitrogen cycle. While CMX Nitrospira has been detected in various ecosystems, few studies so far have focused on the relative contribution and co-occurrence network of ammonia oxidizing archaea (AOA), bacteria (AOB), and CMX Nitrospira in artificial forest ecosystems (tree plantations). We evaluated the dynamics of composition, co-occurrence patterns and contribution of soil microbial nitrifiers to nitrification in soil of various tree species with different ages in the Qilian Mountains employing the space for time substitution approach, quantitative PCR and high-throughput sequencing technology. Generally, plantation development significantly reduced soil potential nitrification rates. Inhibition experiments and modular analysis showed that AOA played leading roles in nitrification of abandoned farmland and 17-year-old Hippophae rhamnoides, whereas CMX Nitrospira dominated in 36-year-old Picea crassifolia, 36-year-old Picea crassifolia and Larix gmelinii mixed plantation, and 50-year-old Picea crassifolia. The dominant AOA and CMX Nitrospira lineages in all samples were Group I.1b and Clade B, respectively. The assembly of nitrifier community was governed by stochastic processes, in which dispersal limitation made a significant contribution. The nitrifiers coexist in a mutualistic manner, albeit with possible functional redundancy, while the modular analysis revealed the aggregation pattern of the four modules in different artificial forests' soil. The Mantel test showed that modular formation is mainly affected by NH4+ and SOM. These results broaden our current understanding of the relation between CMX Nitrospira and canonical ammonia oxidizers in terrestrial ecosystems, and provide empirical evidence for not only niche differentiation, but also the relative contribution and co-occurrence patterns of nitrifying communities in an artificial forest ecosystem.
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Affiliation(s)
- Fan Ding
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Tianjiao He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Xing'e Qi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Hui Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China; The College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Shijian Xu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Xinfang Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, China.
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Lu Y, Cheung S, Koh XP, Xia X, Jing H, Lee P, Kao SJ, Gan J, Dai M, Liu H. Active degradation-nitrification microbial assemblages in the hypoxic zone in a subtropical estuary. Sci Total Environ 2023; 904:166694. [PMID: 37660824 DOI: 10.1016/j.scitotenv.2023.166694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 08/06/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
In 2017 summer, we observed widespread bottom hypoxia at the lower estuary of the Pearl River estuary (PRE). Our previous study noticed that AOA and bacteria were highly abundant and clustered within the hypoxia zone. Moreover, nitrification and respiration rates were also evidently higher in these hypoxic waters. These observations prompt us to investigate whether these two oxygen-consuming microorganisms have symbiotic relationships and whether specific groups consistently coexist and form ecological-meaningful associations. In this study, we use network analysis to investigate the presence and active communities (DNA-RNA) based on bacterial and AOA communities sequencing (inferred from the 16S rRNA and amoA gene, respectively) to gain more insight into ecological-meaningful associations. We observed a highly diverse and active bacterial community in the hypoxia zone. The RNA networks were more modulized than the corresponding DNA networks, indicating that the active communities were better parsed into functional microbial assemblages. The network topology revealed that Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia, Cyanobacteria (Synechococcales), and AOA sublineages were module hubs and connectors, indicating that they were the keystone taxa of the microbial communities. The hub-subnetwork further showed robust co-occurrence between Gammaproteobacteria, Bacteroidetes (Flavobacteriales), Alphaproteobacteria (Rhodobacterales and Rhodospirillales), Marinimicrobia with AOA sublineages, and Nitrospinae (presumably NOB) reflecting the formation of Degradation-Nitrification (sequential oxidation of Organic matter degradation to ammonia, then nitrate) microbial assemblage in the hypoxia zone. The subnetworks revealed AOA ecotype-specific modularization and niche partitioning of different AOA sublineages. Interestingly, the recurring co-occurrence of nitrifiers assemblage in the RNA subnetworks (SCM1-like-II (AOA) and Nitrospinae OTUs (NOB) suggests an active interaction via nitrite exchange. The Degradation-Nitrification microbial assemblage may contribute substantially to the oxygen consumption in the hypoxia formation in PRE. Our results provide new insight into the functional microbial assemblages, which is worth further investigation on their ecological implication in estuarine waters.
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Affiliation(s)
- Yanhong Lu
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen, Guangdong; Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong; Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, Guangdong; Shenzhen Marine Development and Promotion Center, Shenzhen, Guangdong.
| | - Shunyan Cheung
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
| | - Xiu Pei Koh
- Division of Environment and Sustainability, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan
| | - Puiyin Lee
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian
| | - Jianping Gan
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Minhan Dai
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong; Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong Kong.
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Xiang Y, Zhou T, Deng S, Shao Z, Liu Y, He Q, Chai H. Nitrite improved nitrification efficiency and enriched ammonia-oxidizing archaea and bacteria in the simultaneous nitrification and denitrification process. Water Res X 2023; 21:100204. [PMID: 38098882 PMCID: PMC10719579 DOI: 10.1016/j.wroa.2023.100204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/18/2023] [Accepted: 10/02/2023] [Indexed: 12/17/2023]
Abstract
Simultaneous nitrification and denitrification (SND) is effective and energy-saving for wastewater treatment. As an inevitable intermediate product in the SND process, nitrite affects the efficiency of ammonia oxidation and the composition of nitrifiers. To investigate the impact of nitrite on ammonia oxidation efficiency, two reactors performing SND were respectively operated without nitrite (R1 as control) and with 20 mg N/L nitrite addition (R2 as experimental). The total nitrogen removal efficiency was 74.5% in R1 while 99.0% in R2. With nitrite addition (i.e., 20 mg N/L), the ammonia removal rate in R2 increased to 4.5 times of that in R1. The ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) contributed to respective around 46.9% and 41.8% ammonia removal in R2 based on the results of experiments with specific inhibitors. The number of respective AOA and AOB ammonia monooxygenase gene (amoA) copies increased by 280 and 30 times due to nitrite addition, according to the qPCR results. The high-throughput sequencing results illustrated the increase of dominant AOB species from 0.40% in R1 to 1.59% in R2 and the phylogenetic tree analysis revealed a close link to Nitrosospira multiformis. These results indicated that the ammonia removal efficiency was improved and AOA/AOB were enriched by nitrite addition. The specific nitrite reductases in AOA and AOB boosted the adaptation of nitrite addition. This study demonstrated the positive impacts of nitrite addition on the ammonia removal efficiency and rate in the SND process.
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Affiliation(s)
- Yu Xiang
- School of Architecture and Civil Engineering, Xihua University, Chengdu 610039, China
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Tengzhi Zhou
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Siping Deng
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Zhiyu Shao
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Yiwen Liu
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Qiang He
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Hongxiang Chai
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), College of Environment and Ecology, Chongqing University, Chongqing 400045, China
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Li L, Zhao C, Wang X, Tan Y, Wang X, Liu X, Guo B. Effects of nitrification and urease inhibitors on ammonia-oxidizing microorganisms, denitrifying bacteria, and greenhouse gas emissions in greenhouse vegetable fields. Environ Res 2023; 237:116781. [PMID: 37517488 DOI: 10.1016/j.envres.2023.116781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
Soil microorganisms and N cycling are important components of biogeochemical cycling processes. In addition, the study of the effects of nitrification and urease inhibitors on N and microorganisms in greenhouse vegetable fields is essential to reducing N loss and greenhouse gas emissions. The effects of nitrification inhibitors [2-chloro-6-(trichloromethyl) pyridine (CP), dicyandiamide (DCD)], and urease inhibitor [N-(n-butyl) thiophosphoric triamide (NBPT)] on soil inorganic N (NH4+-N, NO2--N and NO3--N) concentrations and the production rates of greenhouse gases (N2O, CH4, and CO2) in greenhouse vegetable fields were investigated via indoor incubation experiments. Polymerase chain reaction amplification and high-throughput sequencing technology (Illumina Miseq) were used to explore the community structure and abundance changes of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and denitrifying bacteria (nirK and nirS). The results showed that CP and DCD obviously inhibited NH4+-N conversion, and NO2--N, and NO3--N accumulation, NBPT slowed down urea hydrolysis and NH4+-N production, and the apparent nitrification rates of soil were in the following order: NBPT > DCD > DCD + NBPT > CP + NBPT > CP. Compared with urea treatment, the peak N2O production rate of inhibitor treatment decreased by 73.30-99.30%, and the production rate of CH4 and CO2 decreased by more than 66.16%. DCD and CP reduced the abundance of AOA and AOB, respectively. Furthermore, NBPT hindered the growth of ammonia-oxidizing microorganisms and nirS-type denitrifying bacteria, and urea and nitrification inhibitors were detrimental to the growth of Ensifer and Sinorhizobium in the nirK community. Nitrification and urease inhibitors can effectively slow down nitrification and greenhouse gas emissions, reduce N loss and improve soil quality by inhibiting the growth of ammonia-oxidizing microorganisms and denitrifying bacteria.
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Affiliation(s)
- Luzhen Li
- Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Changsheng Zhao
- Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China.
| | - Xinghua Wang
- Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Yu Tan
- Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Xiaokai Wang
- Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Xuzhen Liu
- Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Beibei Guo
- Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
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Godfrey B, Li B, Gottshall E, Brysons S, Abrahamson B, Winkler M. Co-immobilization of AOA strains with anammox bacteria in three different synthetic bio-granules maintained under two substrate-level conditions. Chemosphere 2023; 342:140192. [PMID: 37722534 DOI: 10.1016/j.chemosphere.2023.140192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/28/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023]
Abstract
Hydrogel encapsulation of ammonium oxidizing archaea (AOA) along with anammox bacteria holds potential to enable mainstream partial nitritation (PN)-anammox process attributing to AOA's high affinity to ammonia and oxygen. This study explored the growth of AOA and anammox in hydrogel-based synthetic biogranules by testing two AOA strains, three types of hydrogel beads and two substrate levels, to identify the optimal combination favoring the concomitant growth of AOA and anammox. The AOA Nitrososphaera viennensis (AOA-NV) exhibited higher abundance (10-2.3±0.6 AOA/16S) than the AOA-DW (10-4.7±0.8 AOA/16S) during the entire experimental period. Amongst the three types of hydrogel beads, the PVA-SA-BaCl2 (140 days) and PVA-SA-H3BO3 beads (>180 days) exhibited better long-term structural stability than the PEGDMA-SA-CaCl2 beads. The PVA-SA-H3BO3 beads exhibited the best long-term stability and both the PVA/SA BaCl2 and PVA-SA-H3BO3 beads had comparable ability to retain AOA, anammox and the overall microbial community. Substrate conditions rather than the bead type primarily controlled the microbial community structure. Modest substrate concentrations (1 mM NH4+-N in the feed and 0.8 mg/L dissolved oxygen (DO) in the reactor during aeration phase) followed by low substrate conditions (0.1 mM NH4+-N and 0.2 mg DO/L) both supported the growth of AOA and anammox, while the low substrate condition also suppressed the growth of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB), with AOA /AOB and anammox/NOB ratio of 0.7 and 0.4 at moderate substrate condition and 16.5 and 2.6 at low substrate condition.
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Affiliation(s)
- Bruce Godfrey
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA, 98195, USA
| | - Bo Li
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA, 98195, USA.
| | - Ekaterina Gottshall
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA, 98195, USA
| | - Samuel Brysons
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA, 98195, USA
| | - Britt Abrahamson
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA, 98195, USA
| | - Mari Winkler
- University of Washington, Department of Civil & Environmental Engineering, Seattle, WA, 98195, USA
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Han L, Qin H, Wang J, Yao D, Zhang L, Guo J, Zhu B. Immediate response of paddy soil microbial community and structure to moisture changes and nitrogen fertilizer application. Front Microbiol 2023; 14:1130298. [PMID: 37547687 PMCID: PMC10400893 DOI: 10.3389/fmicb.2023.1130298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 06/23/2023] [Indexed: 08/08/2023] Open
Abstract
Water and fertilizer managements are the most common practices to maximize crop yields, and their long-term impact on soil microbial communities has been extensively studied. However, the initial response of microbes to fertilization and soil moisture changes remains unclear. In this study, the immediate effects of nitrogen (N)-fertilizer application and moisture levels on microbial community of paddy soils were investigated through controlled incubation experiments. Amplicon sequencing results revealed that moisture had a stronger influence on the abundance and community composition of total soil bacteria, as well as ammonia oxidizing-archaea (AOA) and -bacteria (AOB). Conversely, fertilizer application noticeably reduced the connectivity and complexity of the total bacteria network, and increasing moisture slightly exacerbated these effects. NH4+-N content emerged as a significant driving force for changes in the structure of the total bacteria and AOB communities, while NO3--N content played more important role in driving shifts in AOA composition. These findings indicate that the initial responses of microbial communities, including abundance and composition, and network differ under water and fertilizer managements. By providing a snapshot of microbial community structure following short-term N-fertilizer and water treatments, this study contributes to a better understanding of how soil microbes respond to long-term agriculture managements.
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Affiliation(s)
- Linrong Han
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi’an, China
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Hongling Qin
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Jingyuan Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- College of Resources and Environment, Hunan Agricultural University, Changsha, China
| | - Dongliang Yao
- College of Resources and Environment, Hunan Agricultural University, Changsha, China
- College of Biodiversity, Conservation Southwest Forestry University, Kunming, China
| | - Leyan Zhang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
- College of Resources and Environment, Hunan Agricultural University, Changsha, China
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi’an, China
| | - Baoli Zhu
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
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Quintana-Vehí A, Martínez M, Zamora MJ, Rodríguez A, Vassena R, Miguel-Escalada I, Popovic M. Significant differences in efficiency between two commonly used ionophore solutions for assisted oocyte activation ( AOA): a prospective comparison of ionomycin and A23187. J Assist Reprod Genet 2023:10.1007/s10815-023-02833-9. [PMID: 37247099 DOI: 10.1007/s10815-023-02833-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/18/2023] [Indexed: 05/30/2023] Open
Abstract
PURPOSE Despite the success of ICSI in treating severe male factor infertile patients, total fertilization failure (FF) still occurs in around 1-3% of ICSI cycles. To overcome FF, the use of calcium ionophores has been proposed to induce oocyte activation and restore fertilization rates. However, assisted oocyte activation (AOA) protocols and ionophores vary between laboratories, and the morphokinetic development underlying AOA remains understudied. METHODS A prospective single-center cohort study involving 81 in vitro matured metaphase-II oocytes from 66 oocyte donation cycles artificially activated by A23187 (GM508 CultActive, Gynemed) (n=42) or ionomycin (n=39). Parthenogenesis was induced, and morphokinetic parameters (tPNa, tPNf, t2-t8, tSB, and tB) were compared between the 2 study groups and a control group comprising 39 2PN-zygotes from standard ICSI cycles. RESULTS Ionomycin treatment resulted in higher activation rates compared to A23187 (38.5% vs 23.8%, p=0.15). Importantly, none of the A23187-activated parthenotes formed blastocysts. When evaluating the morphokinetic dynamics between the two ionophores, we found that tPNa and tPNf were significantly delayed in the group treated by A23187 (11.84 vs 5.31, p=0.002 and 50.15 vs 29.69, p=0.005, respectively). t2 was significantly delayed in A23187-activated parthenotes when compared to the double heterologous control embryo group. In contrast, the morphokinetic development of ionomycin-activated parthenotes was comparable to control embryos (p>0.05). CONCLUSION Our results suggest that A23187 leads to lower oocyte activation rates and profoundly affects morphokinetic timings and preimplantation development in parthenotes. Despite our limited sample size and low parthenote competence, standardization and further optimization of AOA protocols may allow wider use and improved outcomes for FF cycles.
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Affiliation(s)
| | - M Martínez
- Clínica EUGIN, C/ Balmes 236, 08006, Barcelona, Spain
| | - M J Zamora
- Clínica EUGIN, C/ Balmes 236, 08006, Barcelona, Spain
| | | | - R Vassena
- Eugin Group, 08006, Barcelona, Spain
| | | | - M Popovic
- Eugin Group, 08006, Barcelona, Spain
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10
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Hou G, Wazir ZG, Liu J, Wang G, Rong F, Xu Y, Li M, Liu K, Liu A, Liu H, Wang F. Effects of sulfadiazine and Cu on soil potential nitrification and ammonia-oxidizing archaea and bacteria communities across different soils. Front Microbiol 2023; 14:1153199. [PMID: 37256053 PMCID: PMC10225667 DOI: 10.3389/fmicb.2023.1153199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 03/10/2023] [Indexed: 06/01/2023] Open
Abstract
Introduction Sulfadiazine (SDZ) and copper (Cu) are frequently detected in agricultural soils, but little is known on their single or combined impact on ammonia oxidizing microbial community and function across different soils. Methods In this study, a microcosm was conducted to distinguish the microbial ecotoxicity of SDZ and Cu across different soils by analyzing soil potential nitrification rate (PNR) and the amoA gene sequences. Results The results showed that the single spiking of SDZ caused a consistent decrease of soil PNR among three tested soils, but no consistent synergistic inhibition of SDZ and Cu was observed across these soils. Moreover, across three tested soils, the distinct responses to the single or joint exposure of SDZ and Cu were found in amoA gene abundance, and diversity as well as the identified genus taxa of ammonia-oxidizing archaea (AOA) and bacteria (AOB). Meanwhile, only the specific genus taxa of AOA or AOB consistently corresponded to the variation of soil PNR across different treated soils. The further principal component analysis (PCA) exhibited that the variable influence of SDZ and Cu on ammonia oxidizing microbial community and function was greatly dependent on soil type. Discussion Therefore, in addition to ecological functionality and the specific prokaryotic taxa, soil microbial ecotoxicity of SDZ and Cu also was dependent on edaphic factors derived from soil types. This study proposes an integrative assessment of soil properties and multiple microbial targets to soil contamination management.
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Affiliation(s)
- Guoqin Hou
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Zafran Gul Wazir
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Jing Liu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Guizhen Wang
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Fangxu Rong
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, China
| | - Yuzhi Xu
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo, China
| | - Mingyue Li
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo, China
| | - Kai Liu
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo, China
| | - Aijv Liu
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo, China
| | - Hongliang Liu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong, China
| | - Fayuan Wang
- School of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao, China
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11
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Chisholm C, Di HJ, Cameron K, Podolyan A, Shah A, Hsu L, Shen J. Soil moisture is a primary driver of comammox Nitrospira abundance in New Zealand soils. Sci Total Environ 2023; 858:159961. [PMID: 36343813 DOI: 10.1016/j.scitotenv.2022.159961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/31/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
The objectives of this study were to investigate the abundance and community composition of comammox Nitrospira under: (i) pasture-based dairy farms from different regions, and (ii) different land uses from the same region and soil type. The results clearly showed that comammox Nitrospira were most abundant (3.0 × 106 copies) under the west coast dairy farm conditions, where they were also significantly more abundant than canonical ammonia oxidisers. This was also true in the Canterbury dairy farm. The six land uses investigated were pine monoculture, a long term no input ecological trial, sheep + beef and Dairy, both irrigated and non-irrigated. It was concluded that comammox Nitrospira was most abundant under the irrigated dairy farm (2.7 × 106 copies). Contrary to the current industry opinion, the relatively high abundance of comammox Nitrospira under fertile irrigated dairy land suggests that comammox Nitrospira found in terrestrial ecosystems may be copiotrophic. it was also determined that comammox Nitrospira was more abundant under irrigated land use than their non-irrigated counterparts, suggesting that soil moisture is a key environmental parameter influencing comammox abundance. Comammox abundance was also positively correlated with annual rainfall, further supporting this theory. Phylogenetic analysis of the comammox Nitrospira detected determined that 17 % of the comammox community belonged to a newly distinguished subclade, clade B.2. The remaining 83 % belonged to clade B.1. No sequences from clade A were found.
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Affiliation(s)
- Chris Chisholm
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - Hong J Di
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand.
| | - Keith Cameron
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - Andriy Podolyan
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - Anish Shah
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
| | - Lisa Hsu
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, 7647, Christchurch, New Zealand
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12
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Wu Z, Wang Y, Liu C, Yin N, Hu Z, Shen L, Islam ARMT, Wei Z, Chen S. Characteristics of soil N 2O emission and N 2O-producing microbial communities in paddy fields under elevated CO 2 concentrations. Environ Pollut 2023; 318:120872. [PMID: 36529344 DOI: 10.1016/j.envpol.2022.120872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
The effects of elevated carbon dioxide (CO2) concentration (e[CO2]) on nitrous oxide (N2O) emissions from paddy fields and the microbial processes involved in N2O emissions have recently received much attention. Ammonia-oxidizing microorganisms and denitrifying bacteria dominate the production of N2O in paddy soils. To better understand the dynamics of N2O production under e[CO2], a field experiment was conducted after five years of CO2 fumigation based on three treatments: CK (ambient atmospheric CO2), T1 (CK + increase of 40 ppm per year until 200 ppm), and T2 (CK + 200 ppm). N2O fluxes, soil physicochemical properties, and N2O production potential were quantified during the rice-growth period. The functional gene abundance and community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were analyzed using quantitative polymerase chain reaction (qPCR) and those of ammonia-denitrifying bacteria (nirS- and nirK-type) were analyzed using Illumina MiSeq sequencing. N2O emissions decreased by 173% and 41% under the two e[CO2] treatments during grain filling and milk ripening, respectively (P < 0.05). N2O emissions increased by 279% and 172% in the T2 treatment compared with T1 during the tillering and milk-ripening stages, respectively (P < 0.05). Furthermore, the N2O production potential was significantly higher in the CK treatment than in T1 and T2 during the elongation stage. The N2O production potential and abundance of AOA amoA genes in T1 treatment were significantly lower than those in CK treatment during the high N2O emission phase caused by mid-season drainage (P < 0.05). Although nirK- and nirS-type denitrifying bacteria community structure and diversity did not respond significantly (P > 0.05) to e[CO2], the abundance of nirK-type denitrifying bacteria significantly affected the N2O flux (P < 0.05). Linear regression analysis showed that the N2O production potential, AOA amoA gene abundance, and nirK gene abundance explained 47.2% of the variation in N2O emissions. In addition, soil nitrogen (N) significantly affected the nirK- and nirS-type denitrifier communities. Overall, our results revealed that e[CO2] suppressed N2O emissions, which was closely associated with the abundance of AOA amoA and nirK genes (P < 0.05).
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Affiliation(s)
- Zhurong Wu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Yuanyuan Wang
- School of Life Science, Huaiyin Normal University, Huaian, 223001, China
| | - Chao Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Nan Yin
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Zhenghua Hu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, 210044, China.
| | - Lidong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - A R M Towfiqul Islam
- Department of Disaster Management, Begum Rokeya University, Rangpur, 5400, Bangladesh
| | - Zhaowei Wei
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Shutao Chen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, 210044, China
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13
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Zhang T, Zhang P, Kalathas P, Wang G, Liu H. A Machine Learning Approach to Improve Ranging Accuracy with AoA and RSSI. Sensors (Basel) 2022; 22:6404. [PMID: 36080862 PMCID: PMC9459702 DOI: 10.3390/s22176404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/12/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
Ranging accuracy is a critical parameter in time-based indoor positioning systems. Indoor environments often have complex structures, which make centimeter-level-accurate ranging a challenging task. This study proposes a new distance measurement method to decrease the ranging error in multipath environment. Our method uses an artificial neural network that utilizes the received signal strength indicator along with a signal's angle of arrival to calculate the line-of-sight distance. This combination results in a significant reduction of the error caused by multipath effects that common RSSI-based methods suffer from. It outperforms traditional ranging methods while the implementation complexity is kept low.
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Affiliation(s)
- Tingwei Zhang
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Peng Zhang
- School of Software & Microelectronics, Peking University, Beijing 100871, China
| | - Paris Kalathas
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Guangxin Wang
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Huaping Liu
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
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14
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Zhao H, Zhang L. Metagenome-assembled Genomes of Six Novel Ammonia-oxidizing Archaea ( AOA) from Agricultural Upland Soil. Microbes Environ 2022; 37. [PMID: 35965098 PMCID: PMC9530722 DOI: 10.1264/jsme2.me22035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA), key players in agricultural upland soil nitrification, convert soil ammonium to nitrite. The microbial oxidation of ammonia to nitrite is an important part of the global biogeochemical nitrogen cycle. In the present study, we recovered six novel AOA metagenome-assembled genomes (MAGs) containing genes for carbon (C) fixation and nitrogen (N) metabolism by using a deep shotgun metagenomic sequencing strategy. We also found that these AOA MAGs possessed cobalamin synthesis genes, suggesting that AOA are vitamin suppliers in agricultural upland soil. Collectively, the present results deepen our understanding of the metabolic potential and phylogeny of AOA in agroecosystems.
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Affiliation(s)
- Huicheng Zhao
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences.,University of Chinese Academy of Sciences
| | - Linqi Zhang
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences.,University of Chinese Academy of Sciences
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15
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Meng S, Peng T, Wang H, Huang T, Gu JD, Hu Z. Evaluation of PCR primers for detecting the distribution of nitrifiers in mangrove sediments. Appl Microbiol Biotechnol 2022; 106:5811-5822. [PMID: 35941255 DOI: 10.1007/s00253-022-12104-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/28/2022]
Abstract
Ammonia-oxidizing archaea and ammonia-oxidizing bacteria (AOA and AOB), complete ammonia oxidizers (Comammox), and nitrite-oxidizing bacteria (NOB) play a crucial role in the nitrification process during the nitrogen cycle. However, their occurrence and diversity in mangrove ecosystems are still not fully understood. Here, a total of 11 pairs of PCR primers were evaluated to study the distribution and abundances of these nitrifiers in rhizosphere and non-rhizosphere sediments of a mangrove ecosystem. The amplification efficiency of these 11 pairs of primers was first evaluated and their performances were found to vary considerably. The CamoA-19F/CamoA-616R primer pair was suitable for the amplification of AOA in mangrove sediments, especially on the surface of rhizosphere sediments. Primer pair amoA1F/amoA2R was better for the characterization of novel AOB in the bacterial community of non-rhizosphere sediments of mangroves. In contrast, primer nxrB169F/nxrB638R showed a low abundance of NOB in mangrove sediments (except for R1). Comammox bacteria were abundant and diverse in mangrove sediments, as indicated by both the amoB gene for Comammox clade A and the amoA gene for Comammox Nitrospira clade B. However, the amoA gene for Comammox Nitrospira clade A was not successful in detecting them in the mangrove sediments. Furthermore, 568 operational taxonomic units (OTUs) were obtained by generating a clone library and a high abundance of OTUs was correlated with ammonium, pH, NO2-, and NO3-. Comammox and Comammox Nitrospira were identified by phylogenetic tree analysis, indicating that mangrove sediments harbor newly discovered nitrifiers. Additionally, many AOA and NOB were mainly distributed in the surface layer of the rhizosphere, whereas AOB and Comammox Nitrospira were in the subsurface of non-rhizosphere, as determined by qPCR analysis. Collectively, our findings highlight the limitations of some primers for the identification of specific nitrifying bacteria. Therefore, primers must be carefully selected to gain accurate insights into the ecological distribution of nitrifiers in mangroves. KEY POINTS: • Several sets of PCR primers perform well for the detection of nitrifiers in mangroves. • Mangroves are an important source of newly discovered nitrifiers. • Ammonium, pH, NO2-, and NO3- are important shapers of nitrifier communities in mangroves.
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Affiliation(s)
- Shanshan Meng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China
| | - Hui Wang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong, 511458, Guangzhou, People's Republic of China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, Shantou, 515063, Guangdong, China.,Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, Shantou, 515063, Guangdong, China
| | - Zhong Hu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, People's Republic of China. .,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong, 511458, Guangzhou, People's Republic of China.
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16
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Zhu G, Wang X, Wang S, Yu L, Armanbek G, Yu J, Jiang L, Yuan D, Guo Z, Zhang H, Zheng L, Schwark L, Jetten MSM, Yadav AK, Zhu YG. Towards a more labor-saving way in microbial ammonium oxidation: A review on complete ammonia oxidization (comammox). Sci Total Environ 2022; 829:154590. [PMID: 35306060 DOI: 10.1016/j.scitotenv.2022.154590] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
In the Anthropocene, nitrogen pollution is becoming an increasing challenge for both mankind and the Earth system. Microbial nitrogen cycling begins with aerobic nitrification, which is also the key rate-limiting step. For over a century, it has been accepted that nitrification occurs sequentially involving ammonia oxidation, which produces nitrite followed by nitrite oxidation, generating nitrate. This perception was changed by the discovery of comammox Nitrospira bacteria and their metabolic pathway. In addition, this also provided us with new knowledge concerning the complex nitrogen cycle network. In the comammox process, ammonia can be completely oxidized to nitrate in one cell via the subsequent activity of the enzyme complexes, ammonia monooxygenase, hydroxylamine dehydrogenase, and nitrite oxidodreductase. Over the past five years, research on comammox made great progress. However, there still exist a lot of questions, including how much does comammox contribute to nitrification? How large is the diversity and are there new strains to be discovered? Do comammox bacteria produce the greenhouse gas N2O, and how or to which extent may they contribute to global climate change? The above four aspects are of great significance on the farmland nitrogen management, aquatic environment restoration, and mitigation of global climate change. As large number of comammox bacteria and pathways have been detected in various terrestrial and aquatic ecosystems, indicating that the comammox process may exert an important role in the global nitrogen cycle.
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Affiliation(s)
- Guibing Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiaomin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanyun Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Longbin Yu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gawhar Armanbek
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jie Yu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Liping Jiang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongdan Yuan
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Zhongrui Guo
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hanrui Zhang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lei Zheng
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Lorenz Schwark
- Institute for Geosciences, University of Kiel, 24118 Kiel, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud University Nijmegen, 36525 AJ Nijmegen, the Netherlands
| | - Asheesh Kumar Yadav
- Department of Environment and Sustainability, CSIR-Institute of Minerals and Materials Technology, Bhubaneswar 751013, India
| | - Yong-Guan Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Ye H, Tang C, Cao Y, Li X, Huang P. Contribution of ammonia-oxidizing archaea and bacteria to nitrification under different biogeochemical factors in acidic soils. Environ Sci Pollut Res Int 2022; 29:17209-17222. [PMID: 34661841 DOI: 10.1007/s11356-021-16887-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Nitrification in soils is an essential process that involves archaeal and bacterial ammonia-oxidizers. Despite its importance, the relative contributions of soil factors to the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and their nitrification performances are seldom discussed. The aim of this study was to determine the effects of AOA and AOB abundance and different environmental conditions (pH, TC, TN, moisture, and temperature) on nitrification performance. The soils of the long-term fertilized tea orchards and forests were sampled in the field, and nitrification experiments were conducted in the laboratory. The acid soils were collected from the field and used in laboratory incubation experiments to calculate the nitrification rate, including the net nitrification rate (NN rate), nitrification potential (NP), and nitrification kinetics. The basic parameters, different forms of nitrogen content, and AOA and AOB amoA gene copies were also analyzed. Compared with the forest soil, the tea orchard soil had a lower pH and higher nitrogen content (p < 0.05). The AOA and AOB abundance in the soils of the forests and tea orchards were pH-dependent. The NN rate and NP had good relationships with AOA or AOB in the forest soil; however, poor relationships were observed in the tea orchard soil. When pH < 4, the performances of AOA and AOB were restricted by pH and the environment, especially in long-term fertilized farmlands. Long-term fertilization can cause soil acidification, which regulates the abundance of AOA and AOB and their nitrifying ability. The soil environment rather than AOA or AOB could control nitrification in long-term fertilized farmlands with a pH below 4. These findings could improve fertilization efficiency and control nutrient runoff in hilly agricultural ecosystems.
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Affiliation(s)
- Huijun Ye
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510006, China
| | - Changyuan Tang
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510006, China
- School of Geography and Planning, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Yingjie Cao
- School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China.
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, 510006, China.
- Southern Laboratory of Ocean Science and Engineering, Guangdong, Zhuhai, 519000, China.
| | - Xing Li
- Wuhan Institute of Technology, Wuhan, 430000, China
| | - Pinyi Huang
- School of Geography and Planning, Sun Yat-Sen University, Guangzhou, 510006, China
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18
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Lin YP, Ansari A, Wunderlich RF, Lur HS, Ngoc-Dan Cao T, Mukhtar H. Assessing the influence of environmental niche segregation in ammonia oxidizers on N 2O fluxes from soil and sediments. Chemosphere 2022; 289:133049. [PMID: 34838835 DOI: 10.1016/j.chemosphere.2021.133049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/18/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Understanding the environmental niche segregation of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and its impact on their relative contributions to nitrification and nitrous oxide (N2O) production is essential for predicting N2O dynamics within an ecosystem. Here, we used ammonia oxidizer-specific inhibitors to measure the differential contributions of AOA and AOB to potential ammonia oxidization (PAO) and N2O fluxes over pH (4.0-9.0) and temperature (10-45 °C) gradients in five soils and three wetland sediments. AOA and AOB activities were differentiated using PTIO (2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide), 1-octyne, and acetylene. We used square root growth (SQRT) and macromolecular rate theory (MMRT) models to estimate cardinal temperatures and thermodynamic characteristics for AOA- and AOB-dominated PAO and N2O fluxes. We found that AOA and AOB occupied different niches for PAO, and soil temperature was the major determinant of niche specialization. SQRT and MMRT models predicted a higher optimum temperature for AOA-dominated PAO and N2O fluxes compared with those of AOB. Additionally, PAO was dominated by AOA in acidic conditions, whereas both AOA- and AOB-dominated N2O fluxes decreased with increasing pH. Consequently, net N2O fluxes (AOA and AOB) under acidic conditions were approximately one to three-fold higher than those observed in alkaline conditions. Moreover, structural equation and linear regression modeling confirmed a significant positive correlation (R2 = 0.45, p < 0.01) between PAO and N2O fluxes. Collectively, these results show the influence of ammonia oxidizer responses to temperature and pH on nitrification-driven N2O fluxes, highlighting the potential for mitigating N2O emissions via pH manipulation.
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Affiliation(s)
- Yu-Pin Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan
| | - Andrianto Ansari
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan
| | | | - Huu-Sheng Lur
- Department of Agronomy, National Taiwan University, Taiwan
| | - Thanh Ngoc-Dan Cao
- Graduate Institute of Environmental Engineering, National Taiwan University, Taiwan
| | - Hussnain Mukhtar
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taiwan.
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19
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Tian L, Chen L, Xu Z, Chen Z. An Angle Recognition Algorithm for Tracking Moving Targets Using WiFi Signals with Adaptive Spatiotemporal Clustering. Sensors (Basel) 2021; 22:276. [PMID: 35009819 PMCID: PMC8749511 DOI: 10.3390/s22010276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
An angle estimation algorithm for tracking indoor moving targets with WiFi is proposed. First, phase calibration and static path elimination are proposed and performed on the collected channel state information signals from different antennas. Then, the angle of arrival information is obtained with the joint estimation algorithm of the angle of arrival (AOA) and time of flight (TOF). To deal with the multipath effects, we adopt the DBscan spatiotemporal clustering algorithm with adaptive parameters. In addition, the time-continuous angle of arrival information is obtained by interpolating and supplementing points to extract the dynamic signal paths better. Finally, the least-squares method is used for linear fitting to obtain the final angle information of a moving target. Experiments are conducted with the tracking data set presented with Tsinghua's Widar 2.0. The results show that the average angle estimation error with the proposed algorithm is smaller than Widar2.0. The average angle error is about 7.18° in the classroom environment, 3.62° in the corridor environment, and 12.16° in the office environment; they are smaller than the errors of the existing system.
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Affiliation(s)
- Liping Tian
- School of Physics and Information Engineering, Fuzhou University, Fuzhou 350008, China; (L.T.); (Z.X.); (Z.C.)
| | - Liangqin Chen
- School of Physics and Information Engineering, Fuzhou University, Fuzhou 350008, China; (L.T.); (Z.X.); (Z.C.)
| | - Zhimeng Xu
- School of Physics and Information Engineering, Fuzhou University, Fuzhou 350008, China; (L.T.); (Z.X.); (Z.C.)
| | - Zhizhang Chen
- School of Physics and Information Engineering, Fuzhou University, Fuzhou 350008, China; (L.T.); (Z.X.); (Z.C.)
- Department of Electrical and Computer Engineering, Dalhousie University, Halifax, NC B3J 1Z1, Canada
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20
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Zhao M, Tang X, Sun D, Hou L, Liu M, Zhao Q, Klümper U, Quan Z, Gu JD, Han P. Salinity gradients shape the nitrifier community composition in Nanliu River Estuary sediments and the ecophysiology of comammox Nitrospira inopinata. Sci Total Environ 2021; 795:148768. [PMID: 34247082 DOI: 10.1016/j.scitotenv.2021.148768] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
The recent discovery of complete ammonia oxidizers (comammox), which convert ammonia to nitrate in a single organism, revolutionized the conventional understanding that two types of nitrifying microorganisms have to be involved in the nitrification process for more than 100 years. However, how different types of nitrifiers in response to salinity change remains largely unclear. This study not only investigated nitrifier community (including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), comammox and nitrite-oxidizing Nitrospira) in the Nanliu estuary to find the ecological relationship between salinity and functional communities and also studied the physiology of a typical comammox Nitrospira inopinata in response to a salinity gradient. Based on sequences retrieved with four sets of functional gene primes, comammox Nitrospira was in general, mainly composed of clade A, with a clear separation of clade A1 subgroup in all samples and clade A2 subgroup in low salinity ones. As expected, group I.1b and group I.1a AOA dominated the AOA community in low- and high-salinity samples, respectively. Nitrosomonas-AOB were detected in all samples while Nitrosospira-AOB were mainly found in relatively high-salinity samples. Regarding general Nitrospira, lineages II and IV were the major groups in most of the samples, while lineage I Nitrospira was only detected in low-salinity samples. Furthermore, the comammox pure culture of N. inopinata showed an optimal salinity at 0.5‰ and ceased to grow at 12.8‰ for ammonia oxidation, but remained active for nitrite oxidation. These results show new evidence regarding niche specificity of different nitrifying microorganisms modulated mainly by salinity, and also a clear response by comammox N. inopinata to a wide range of simulated salinity levels.
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Affiliation(s)
- Mengyue Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiufeng Tang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Dongyao Sun
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Qiang Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, 01062 Dresden, Germany
| | - Zhexue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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21
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Zhou X, Li B, Wei J, Ye Y, Xu J, Chen L, Lu C. Temperature Influenced the Comammox Community Composition in Drinking Water and Wastewater Treatment Plants. Microb Ecol 2021; 82:870-884. [PMID: 33665721 DOI: 10.1007/s00248-021-01724-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Nitrification is a pivotal step applied in water engineered systems for nitrogen removal. Temperature variation due to seasonal changes is a great challenge for maintaining nitrogen removal efficiency in water engineered ecosystems by affecting nitrifier activities. Research on the abundance, activity, and metabolic characteristics of nitrifiers can provide information for selecting suitable design parameters to ensure efficient nitrogen removal in different seasons. To date, the temperature-related niche separation of comammox, a newly discovered nitrifier with potential high-growth yield, has been rarely investigated. This study addressed the distribution of comammox and canonical nitrifying guilds in drinking water treatment plants (DWTPs) and wastewater treatment plants (WWTPs) in different seasons. qPCR-based surveys showed that comammox ubiquitously distributed and greatly outnumbered other ammonia-oxidizing prokaryotes in both DWTPs and WWTPs, except in Aug samples from DWTPs, suggesting the potential competitive advantage of AOA in summer. The nitrificans-like comammox and nitrosa-like comammox comprised the majority of the comammox community in DWTPs and WWTPs, respectively, and COD and NH4+ concentrations significantly contributed to the distinct comammox phylotype distribution between DWTPs and WWTPs. The temperature-related distribution pattern of the comammox community was observed at each site. Moreover, the network complex of comammox communities was highest in Dec at all the sites, possibly contributing to the survival of comammox community in low temperature conditions.
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Affiliation(s)
- Xue Zhou
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, Jiangsu Province, China
- Yangtze Institute for Conservation and Development, Hohai University, Nanjing, 210098, Jiangsu Province, China
- State key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, Jiangsu Province, China
| | - Bolun Li
- School of Geographic Sciences, Nanjing University of Information Science and Technology, Nanjing, 210044, Jiangsu Province, China
| | - Jun Wei
- Power China Huadong Engineering Corporation Limited, Hangzhou, 311122, Jiangsu Province, China
| | - Yu Ye
- Yangtze Institute for Conservation and Development, Hohai University, Nanjing, 210098, Jiangsu Province, China
- State key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, Jiangsu Province, China
| | - Junzeng Xu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, Jiangsu Province, China
- State key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, Jiangsu Province, China
| | - Lina Chen
- College of Agricultural Science and Engineering, Hohai University, Nanjing, 210098, Jiangsu Province, China
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, Jiangsu Province, China
| | - Chunhui Lu
- Yangtze Institute for Conservation and Development, Hohai University, Nanjing, 210098, Jiangsu Province, China.
- State key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, 210098, Jiangsu Province, China.
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22
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Sun P, Zhao Z, Fan P, Chen W, Ruan Y, Wang Q. Ammonia- and Nitrite-Oxidizing Bacteria are Dominant in Nitrification of Maize Rhizosphere Soil Following Combined Application of Biochar and Chemical Fertilizer. Front Microbiol 2021; 12:715070. [PMID: 34675894 PMCID: PMC8524134 DOI: 10.3389/fmicb.2021.715070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
Autotrophic nitrification is regulated by canonical ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB). To date, most studies have focused on the role of canonical ammonia oxidizers in nitrification while neglecting the NOB. In order to understand the impacts of combined biochar and chemical fertilizer addition on nitrification and associated nitrifiers in plant rhizosphere soil, we collected rhizosphere soil from a maize field under four different treatments: no fertilization (CK), biochar (B), chemical nitrogen (N) + phosphorus (P) + potassium (K) fertilizers (NPK), and biochar + NPK fertilizers (B + NPK). The potential nitrification rate (PNR), community abundances, and structures of AOA, AOB, complete ammonia-oxidizing bacteria (Comammox Nitrospira clade A), and Nitrobacter- and Nitrospira-like NOB were measured. Biochar and/or NPK additions increased soil pH and nutrient contents in rhizosphere soil. B, NPK, and B + NPK treatments significantly stimulated PNR and abundances of AOB, Comammox, and Nitrobacter- and Nitrospira-like NOB, with the highest values observed in the B + NPK treatment. Pearson correlation and random forest analyses predicted more importance of AOB, Comammox Nitrospira clade A, and Nitrobacter- and Nitrospira-like NOB abundances over AOA on PNR. Biochar and/or NPK additions strongly altered whole nitrifying community structures. Redundancy analysis (RDA) showed that nitrifying community structures were significantly affected by pH and nutrient contents. This research shows that combined application of biochar and NPK fertilizer has a positive effect on improving soil nitrification by affecting communities of AOB and NOB in rhizosphere soil. These new revelations, especially as they related to understudied NOB, can be used to increase efficiency of agricultural land and resource management.
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Affiliation(s)
- Ping Sun
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Ziting Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Pingshan Fan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Wei Chen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Yunze Ruan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Qing Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
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23
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Wang YF, Gu JD, Dick RP, Han W, Yang HX, Liao HQ, Zhou Y, Meng H. Distribution of ammonia-oxidizing archaea and bacteria along an engineered coastal ecosystem in subtropical China. Ecotoxicology 2021; 30:1769-1779. [PMID: 33432457 DOI: 10.1007/s10646-020-02327-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/25/2020] [Indexed: 06/12/2023]
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the crucial players in nitrogen cycle. Both AOA and AOB were examined along a gradient of human activity in a coastal ecosystem from intertidal zone, grassland, and Casuarina equisetifolia forest to farmland. Results showed that the farmland soils had noticeably higher nitrate-N, available P than soils in the other three sites. Generally, AOA and AOB community structures varied across sites. The farmland mainly had Nitrosotalea-like AOA, intertidal zone was dominated by Nitrosopumilus AOA, while grassland and C. equisetifolia forest primarily harbored Nitrososphaera-like AOA. The farmland and C. equisetifolia forest owned Nitrosospira-like AOB, intertidal zone possessed Nitrosomonas-like AOB, and no AOB was detected in the grassland. AOA abundance was significantly greater than AOB in this coastal ecosystem (p < 0.05, n = 8). AOB diversity and abundance in the farmland were significantly higher than those in the other three sites (p < 0.05, n = 2). The biodiversity and abundance of AOA were not significantly correlated with any soil property (p < 0.05, n = 8). However, the diversity of AOB was significantly correlated with pH, available P and total P (p < 0.05, n = 6). The abundance of AOB was significantly correlated with pH, nitrite, available N, available P and total P (p < 0.05, n = 6). This study suggested that the community structures of AOA and AOB vary in the different parts in the bio-engineered coastal ecosystem and agricultural activity appears to influence these nitrifiers.
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Affiliation(s)
- Yong-Feng Wang
- Institute of Environment and Ecology, Institute of Environmental Health and Ecological Security, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, PR China.
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, 233 Guangshan 1st Road, Guangzhou, PR China.
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, 515063, PR China
| | - Richard P Dick
- School of Environment and Natural Resources, The Ohio State University, 2021 Coffey Road, Columbus, OH, 43210-1085, USA
| | - Wei Han
- Agro-Technical Station of Shandong Province, Jinan, PR China
| | - Hui-Xiao Yang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, 233 Guangshan 1st Road, Guangzhou, PR China
| | - Huan-Qin Liao
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, 233 Guangshan 1st Road, Guangzhou, PR China
| | - Yi Zhou
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, 233 Guangshan 1st Road, Guangzhou, PR China.
| | - Han Meng
- School of Environment, Nanjing Normal University, Nanjing, 210023, PR China
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24
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Hu J, Zhao Y, Yao X, Wang J, Zheng P, Xi C, Hu B. Dominance of comammox Nitrospira in soil nitrification. Sci Total Environ 2021; 780:146558. [PMID: 33765470 DOI: 10.1016/j.scitotenv.2021.146558] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/09/2021] [Accepted: 03/14/2021] [Indexed: 06/12/2023]
Abstract
The first and limiting step of nitrification is catalyzed by ammonia-oxidizing archaea (AOA) and bacteria (AOB). Recently, complete ammonia oxidizers (comammox Nitrospira) have been discovered to perform complete nitrification in one cell, yet their role in soil nitrification is still unclear. This study investigated the abundance and contribution of aerobic ammonia oxidizers in typical soil habitats, and assessed the role of comammox Nitrospira in ammonia-oxidizing communities. The results showed that comammox Nitrospira were dominant in 70% of the samples and their abundance displayed a significant positive correlation with nitrification potential. The median amoA gene transcription level of comammox Nitrospira exceeded that of AOA and AOB in in-situ soils. The abundance of comammox Nitrospira was negatively correlated with soil pH, dominating in 84% of soil samples with pH < 6.17. The results challenge the role of AOA and AOB in soils, highlighting the importance of comammox Nitrospira in soil nitrification, especially in acid soils. This work supports better understanding and regulation of the soil nitrogen cycle.
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Affiliation(s)
- Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
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25
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Srikanthasamy T, Barot S, Koffi FK, Tambosco K, Marcangeli Y, Carmignac D, N'Dri AB, Gervaix J, Le Roux X, Lata J. Short-term impact of fire on the total soil microbial and nitrifier communities in a wet savanna. Ecol Evol 2021; 11:9958-9969. [PMID: 34367552 PMCID: PMC8328428 DOI: 10.1002/ece3.7661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 11/21/2022] Open
Abstract
Savannas are characterized by the coexistence of grasses and trees. Fires are critical for their coexistence, because they decrease the survival of tree seedlings and saplings and their recruitment to the adult stage. In some humid savannas, perennial grasses inhibit nitrification and trees stimulate nitrification, which likely favors coexistence between trees and grasses. However, fires may influence plant capacity to control nitrogen cycling, which could subsequently influence tree-grass coexistence and savanna nitrogen budget. Therefore, we sampled soil in a humid savanna of Ivory Coast under the dominant nitrification-inhibiting grass species and the dominant nitrification-stimulating tree species and under bare soil before and after (i.e., 5 days) fire during the long dry season. We quantified the total microbial and nitrifier abundances and transcriptional activities and the nitrification enzyme activity. Fire decreased soil water content, probably by increasing evaporation and, maybe, by triggering the growth of grasses, and increased soil ammonium availability likely due to ash deposition and increased mineralization. Fire did not impact the total archaeal, bacterial, or fungal abundances, or that of the nitrifiers. Fire did not impact archaeal transcriptional activity and increased bacterial and fungal total transcriptional activities. In contrast, fire decreased the archaeal nitrifier transcriptional activities and the nitrification enzymatic activity, likely due to the often reported resumption of the growth of nitrification-inhibiting grasses quickly after the fire (and the subsequent increase in root exudation). These results pave the way for a better understanding of the short-term effects of fire on nitrogen cycling and tree-grass competition for nitrogen.
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Affiliation(s)
- Tharaniya Srikanthasamy
- Sorbonne Université, Université de ParisUPECCNRSINRAEIRDUMR 7618Institute of Ecology and Environmental Sciences – Paris, iEES ParisParisFrance
| | - Sébastien Barot
- IRDSorbonne UniversitéCNRSINRAEUniversité de ParisUPECUMR 7618Institute of Ecology and Environmental Sciences – Paris, iEES‐ParisParisFrance
| | - Fulgence K. Koffi
- UFR‐SN / Research Station of Lamto (CRE)Research Pole Environment and Sustainable Development, Nangui Abrogoua University (ex University of Abobo‐Adjamé), Abidjan, Côte d'IvoireAbidjanIvory Coast
| | - Kevin Tambosco
- Sorbonne Université, Université de ParisUPECCNRSINRAEIRDUMR 7618Institute of Ecology and Environmental Sciences – Paris, iEES ParisParisFrance
| | - Yoan Marcangeli
- Sorbonne Université, Université de ParisUPECCNRSINRAEIRDUMR 7618Institute of Ecology and Environmental Sciences – Paris, iEES ParisParisFrance
| | - David Carmignac
- Sorbonne Université, Université de ParisUPECCNRSINRAEIRDUMR 7618Institute of Ecology and Environmental Sciences – Paris, iEES ParisParisFrance
| | - Aya Brigitte N'Dri
- UFR‐SN / Research Station of Lamto (CRE)Research Pole Environment and Sustainable Development, Nangui Abrogoua University (ex University of Abobo‐Adjamé), Abidjan, Côte d'IvoireAbidjanIvory Coast
| | - Jonathan Gervaix
- INRACNRSUniversité de LyonUniversité Lyon 1Laboratoire d'Ecologie MicrobienneUMR INRA 1418UMR CNRS 5557VilleurbanneFrance
| | - Xavier Le Roux
- INRACNRSUniversité de LyonUniversité Lyon 1Laboratoire d'Ecologie MicrobienneUMR INRA 1418UMR CNRS 5557VilleurbanneFrance
| | - Jean‐Christophe Lata
- Sorbonne Université, Université de ParisUPECCNRSINRAEIRDUMR 7618Institute of Ecology and Environmental Sciences – Paris, iEES ParisParisFrance
- Department of Geoecology and GeochemistryInstitute of Natural ResourcesTomsk Polytechnic UniversityTomskRussia
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26
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Kitamura R, Kozaki T, Ishii K, Iigo M, Kurokura T, Yamane K, Maeda I, Iwabuchi K, Saito T. Utilizing Cattle Manure Compost Increases Ammonia Monooxygenase A Gene Expression and Ammonia-oxidizing Activity of Both Bacteria and Archaea in Biofiltration Media for Ammonia Deodorization. Microbes Environ 2021; 36. [PMID: 33907062 PMCID: PMC8209447 DOI: 10.1264/jsme2.me20148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Malodorous emissions are a crucial and inevitable issue during the decomposition of biological waste and contain a high concentration of ammonia. Biofiltration technology is a feasible, low-cost, energy-saving method that reduces and eliminates malodors without environmental impact. In the present study, we evaluated the effectiveness of compost from cattle manure and food waste as deodorizing media based on their removal of ammonia and the expression of ammonia-oxidizing genes, and identified the bacterial and archaeal communities in these media. Ammonia was removed by cattle manure compost, but not by food waste compost. The next-generation sequencing of 16S ribosomal RNA obtained from cattle manure compost revealed the presence of ammonia-oxidizing bacteria (AOB), including Cytophagia, Alphaproteobacteria, and Gammaproteobacteria, and ammonia-oxidizing archaea (AOA), such as Thaumarchaeota. In cattle manure compost, the bacterial and archaeal ammonia monooxygenase A (amoA) genes were both up-regulated after exposure to ammonia (fold ratio of 14.2±11.8 after/before), and the bacterial and archaeal communities were more homologous after than before exposure to ammonia, which indicates the adaptation of these communities to ammonia. These results suggest the potential of cattle manure compost as an efficient biological deodorization medium due to the activation of ammonia-oxidizing microbes, such as AOB and AOA, and the up-regulation of their amoA genes.
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Affiliation(s)
- Rika Kitamura
- Center for Bioscience Research and Education, Utsunomiya University
| | - Toshinori Kozaki
- Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology
| | | | - Masayuki Iigo
- Department of Applied Biological Chemistry, Faculty of Agriculture, Utsunomiya University
| | - Takeshi Kurokura
- Department of Agrobiology and Bioresources, Faculty of Agriculture, Utsunomiya University
| | - Kenji Yamane
- Department of Agrobiology and Bioresources, Faculty of Agriculture, Utsunomiya University
| | - Isamu Maeda
- Department of Applied Biological Chemistry, Faculty of Agriculture, Utsunomiya University
| | - Kazunori Iwabuchi
- Department of Bioresource and Environmental Engineering, Faculty of Agriculture, Hokkaido University
| | - Takahiro Saito
- Department of Environmental Engineering, Faculty of Agriculture, Utsunomiya University
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Li Y, Liang Y, Zhang H, Liu Y, Zhu J, Xu J, Zhou Z, Ma J, Liu K, Yu F. Variation, distribution, and diversity of canonical ammonia-oxidizing microorganisms and complete-nitrifying bacteria in highly contaminated ecological restoration regions in the Siding mine area. Ecotoxicol Environ Saf 2021; 217:112274. [PMID: 33930771 DOI: 10.1016/j.ecoenv.2021.112274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 04/12/2021] [Accepted: 04/18/2021] [Indexed: 06/12/2023]
Abstract
Canonical ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and complete-nitrifying bacteria (comammox) exist in a variety of ecosystems. However, little is known about AOA, AOB and comammox or their contributions to nitrification in the soils of heavily degraded and acidic mine regions. In the present study, the activity, richness, diversity and distribution patterns of AOA, AOB and comammox in the Siding mine area were investigated. Nemerow's multifactor pollution index (PN) values indicated that the soil in all three areas in the Siding mine area was highly contaminated by Cd, Pb, Zn, Mn and Cu. The AOA, AOB and comammox amoA gene copy numbers exhibited significant positive correlations with Pb and Zn levels and PN values, which indicated that the populations of AOA, AOB and comammox underwent adaptation and reproduction in response to pollution from multiple metals in the Siding mine area. Among them, the abundance of AOA was the highest, and AOA may survive better than AOB and comammox under such severely pollution-stressed and ammonia-limited conditions. The phyla Thaumarchaeota and Crenarchaeota may play vital roles in the soil ammonia oxidation process. Unlike AOA, AOB may use soil available phosphorus to help them compete for NH3 and other limiting nutrients with AOA and heterotrophs. Moreover, soil organic matter was the main factor influencing the species diversity of AOB, the β-diversity of AOB and comammox, and the community composition of AOA, AOB and comammox. Our research will help to explain the role and importance of AOA, AOB and comammox in the different ecological restoration regions in the Siding mine area.
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Affiliation(s)
- Yi Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004 Guilin, China; Innovation Institute of Sustainable Development, Guangxi Normal University, 541004 Guilin, China
| | - Ying Liang
- College of Environment and Resources, Guangxi Normal University, 541004 Guilin, China
| | - Haichun Zhang
- College of Life Science, Guangxi Normal University, 541004 Guilin, China
| | - Yuan Liu
- College of Environment and Resources, Guangxi Normal University, 541004 Guilin, China
| | - Jing Zhu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004 Guilin, China
| | - Jie Xu
- College of Life Science, Guangxi Normal University, 541004 Guilin, China
| | - Zhenming Zhou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004 Guilin, China
| | - Jiangming Ma
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Life Science, Guangxi Normal University, 541004 Guilin, China; Innovation Institute of Sustainable Development, Guangxi Normal University, 541004 Guilin, China
| | - Kehui Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Life Science, Guangxi Normal University, 541004 Guilin, China; Innovation Institute of Sustainable Development, Guangxi Normal University, 541004 Guilin, China.
| | - Fangming Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, China; College of Environment and Resources, Guangxi Normal University, 541004 Guilin, China; Innovation Institute of Sustainable Development, Guangxi Normal University, 541004 Guilin, China.
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Liu X, Shao Y, Dong Y, Dong M, Xu Z, Hu X, Liu A. Response of ammonia-oxidizing archaea and bacteria to sulfadiazine and copper and their interaction in black soils. Environ Sci Pollut Res Int 2021; 28:11357-11368. [PMID: 33123879 DOI: 10.1007/s11356-020-11356-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
The large-scale development of animal husbandry and the wide agricultural application of livestock manure lead to more and more serious co-pollution of heavy metals and antibiotics in soil. In this study, two common feed additives, copper (Cu) and sulfadiazine (SDZ), were selected as target pollutants to evaluate the toxicity and interaction of antibiotics and heavy metals on ammonia oxidizers diversity, potential nitrification rate (PNR), and enzymatic activity in black soils. The results showed that soil enzyme activity was significantly inhibited by single Cu pollution, but the toxicity could be reduced by introducing low-concentration SDZ (5 mg · kg-1), which showed an antagonistic effect between Cu and SDZ (5 mg · kg-1), while the combined toxicity of high-concentration SDZ (10 mg · kg-1) and Cu were strengthened compared with the single Cu contamination on soil enzymes. In contrast, soil PNR was more sensitive to single Cu pollution and its combined pollution with SDZ than the enzyme activity. Real-time fluorescence quota PCR and Illumina Hiseq/Miseq sequencing results showed that ammonia-oxidizing archaea (AOA) was decreased in C2 (200 mg · kg-1 Cu treatment) and ammonia-oxidizing bacteria (AOB) was obviously stimulated in soil contaminated in C2, while in S5 (5 mg · kg-1 SDZ treatment), AOB was decreased; both AOA and AOB were significantly decreased at gene level in soils with combined pollutants (C2S5, 200 mg · kg-1 Cu combined with 5 mg · kg-1 SDZ). So, it can be concluded that combined pollution can cause more serious toxicity on the enzymatic activity, PNR, and ammonia-oxidizing microorganisms in soil through the synergistic effect between heavy metals and antibiotics pollutants.
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Affiliation(s)
- Xijuan Liu
- College of Agricultural engineering and Food science, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Yifei Shao
- College of Agricultural engineering and Food science, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Yuanpeng Dong
- College of Agricultural engineering and Food science, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Mengyang Dong
- College of Agricultural engineering and Food science, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Ziwen Xu
- College of Agricultural engineering and Food science, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Xinxin Hu
- College of Resources and Environmental engineering, Shandong University of Technology, Zibo, 255049, People's Republic of China
| | - Aiju Liu
- College of Resources and Environmental engineering, Shandong University of Technology, Zibo, 255049, People's Republic of China.
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Semedo M, Lopes E, Baptista MS, Oller-Ruiz A, Gilabert J, Tomasino MP, Magalhães C. Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific. Front Microbiol 2021; 12:624071. [PMID: 33732221 PMCID: PMC7959781 DOI: 10.3389/fmicb.2021.624071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/01/2021] [Indexed: 12/21/2022] Open
Abstract
Nitrification is a vital ecosystem function in the open ocean that regenerates inorganic nitrogen and promotes primary production. Recent studies have shown that the ecology and physiology of nitrifying organisms is more complex than previously postulated. The distribution of these organisms in the remote oligotrophic ocean and their interactions with the physicochemical environment are relatively understudied. In this work, we aimed to evaluate the depth profile of nitrifying archaea and bacteria in the Eastern North Pacific Subtropical Front, an area with limited biological surveys but with intense trophic transferences and physicochemical gradients. Furthermore, we investigated the dominant physicochemical and biological relationships within and between ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) as well as with the overall prokaryotic community. We used a 16S rRNA gene sequencing approach to identify and characterize the nitrifying groups within the first 500 m of the water column and to analyze their abiotic and biotic interactions. The water column was characterized mainly by two contrasting environments, warm O2-rich surface waters with low dissolved inorganic nitrogen (DIN) and a cold O2-deficient mesopelagic layer with high concentrations of nitrate (NO3–). Thaumarcheotal AOA and bacterial NOB were highly abundant below the deep chlorophyll maximum (DCM) and in the mesopelagic. In the mesopelagic, AOA and NOB represented up to 25 and 3% of the total prokaryotic community, respectively. Interestingly, the AOA community in the mesopelagic was dominated by unclassified genera that may constitute a novel group of AOA highly adapted to the conditions observed at those depths. Several of these unclassified amplicon sequence variants (ASVs) were positively correlated with NO3– concentrations and negatively correlated with temperature and O2, whereas known thaumarcheotal genera exhibited the opposite behavior. Additionally, we found a large network of positive interactions within and between putative nitrifying ASVs and other prokaryotic groups, including 13230 significant correlations and 23 sub-communities of AOA, AOB, NOB, irrespective of their taxonomic classification. This study provides new insights into our understanding of the roles that AOA may play in recycling inorganic nitrogen in the oligotrophic ocean, with potential consequences to primary production in these remote ecosystems.
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Affiliation(s)
- Miguel Semedo
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Eva Lopes
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Mafalda S Baptista
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Ainhoa Oller-Ruiz
- Department of Chemical & Environmental Engineering, Universidad Politécnica de Cartagena (UPCT), Cartagena, Spain
| | - Javier Gilabert
- Department of Chemical & Environmental Engineering, Universidad Politécnica de Cartagena (UPCT), Cartagena, Spain
| | - Maria Paola Tomasino
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal.,Faculty of Sciences, University of Porto, Porto, Portugal.,School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
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Zhao Y, Hu J, Yang W, Wang J, Jia Z, Zheng P, Hu B. The long-term effects of using nitrite and urea on the enrichment of comammox bacteria. Sci Total Environ 2021; 755:142580. [PMID: 33059137 DOI: 10.1016/j.scitotenv.2020.142580] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/25/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
The discovery of complete ammonia oxidizer (comammox) was a breakthrough in the study of nitrification. However, slow growth of comammox bacteria makes it challenging to distinguish them from traditional ammonia oxidizing microorganisms. Genomic data indicated that comammox bacteria encoded genes that can metabolize urea and had higher nitrite tolerance, which could only be found in several ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This implies that using nitrite and urea as nitrogen sources may accelerate comammox bacteria's enrichment efficiency. In this study, two reactors using nitrite and urea as substrates, respectively, were operated for 390 days. At the end of cultivation, the reactor fed with urea exhibited higher nitrification potential than the reactor fed with nitrite. Comammox bacteria outcompeted AOA and AOB, regardless of whether they were cultured with nitrite or urea. Using nitrite can improve the proportion of comammox amoA to total amoA of 92%, while using urea may increase the proportion of comammox bacteria among total bacteria to 14.2%. Metagenomic results implied that nitrite was converted to ammonia by nitrate reduction and absorbed by comammox bacteria. On the other hand, urea may be directly utilized as substrate. These results demonstrated that using different nitrogen sources caused niche differentiation of comammox bacteria, AOA, and AOB. Using nitrite can increase the relative abundance of comammox amoA to total amoA, while using urea can increase the quantity of comammox amoA. Comammox bacteria were dominant among ammonia oxidizing microorganisms for both nitrite and urea cultures.
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Affiliation(s)
- Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Weiling Yang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China; Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
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31
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Martínez M, Durban M, Santaló J, Rodríguez A, Vassena R. Assisted oocyte activation effects on the morphokinetic pattern of derived embryos. J Assist Reprod Genet 2021; 38:531-7. [PMID: 33405007 DOI: 10.1007/s10815-020-02025-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/26/2020] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVE Assisted oocyte activation (AOA) can restore fertilization rates after IVF/ICSI cycles with fertilization failure. AOA is an experimental technique, and its downstream effects remain poorly characterized. Clarifying the relationship between AOA and embryo, morphokinetics could offer complementary insights into the quality and viability of the embryos obtained with this technique. The aim of this study is to compare the preimplantation morphokinetic development of embryos derived from ICSI-AOA (experimental group) vs. ICSI cycles (control group). METHODS A retrospective cohort study was carried out with 141 embryos from fresh oocyte donation cycles performed between 2013 and 2017; 41 embryos were derived from 7 ICSI-AOA cycles and 100 embryos from 18 ICSI cycles. Morphokinetic development of all embryos was followed using a time-lapse system. RESULTS We show that embryos from both groups develop similarly for most milestones, with the exception of the time of second polar body extrusion (tPB2) and the time to second cell division (t3). CONCLUSIONS We conclude that ionomycin mediated AOA does not seem to affect the morphokinetic pattern of preimplantation embryo development, despite the alterations found in tPB2 and t3, which could directly reflect the use of a Ca2+ ionophore as a transient and quick non-physiologic increase of free intracytoplasmic Ca2+.
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32
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Long R, Wang M, Yang QY, Hu SQ, Zhu LX, Jin L. Risk of birth defects in children conceived by artificial oocyte activation and intracytoplasmic sperm injection: a meta-analysis. Reprod Biol Endocrinol 2020; 18:123. [PMID: 33308238 PMCID: PMC7731535 DOI: 10.1186/s12958-020-00680-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/06/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Whether artificial oocyte activation (ICSI-AOA) will increase the risk of birth defects remains controversial. Thus, we performed this study to evaluate the risk of birth defects and further compare the incidence of different birth defects types (chromosomal aberrations and non-chromosomal aberrations) in children conceived by ICSI-AOA and conventional intracytoplasmic sperm injection (ICSI) in an enlarged sample size. METHOD A comprehensive review of the literatures comparing birth defects in children conceived by ICSI-AOA and conventional ICSI by October 2020 was performed in PubMed, Embase, Cochrane Libraries, Web of Science, and Chinese databases including China National Knowledge Infrastructure, China Biology Medicine disc and Wan Fang. Risk ratios (RR) and 95% confidence intervals (CI) were calculated. RESULTS Five studies were included in the final analysis. Compared with conventional ICSI, ICSI-AOA did not increase the birth defects rate (RR = 1.27, 95%CI 0.70-2.28) of children. Furthermore, in a subgroup analysis, birth defects were classified into two types (chromosomal aberrations and non-chromosomal aberrations) in four studies and no statistical difference were revealed. CONCLUSION Our analysis indicates that ICSI-AOA represents no significant difference in the prevalence of major birth defects or types of birth defects (chromosomal aberrations and non-chromosomal aberrations) comparing with conventional ICSI. This conclusion may provide clinicians evidence-based support in patient counseling and instruction of the application and safety concern about ICSI-AOA.
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Affiliation(s)
- Rui Long
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, 430030, China
| | - Meng Wang
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, 430030, China
| | - Qi Yu Yang
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, 430030, China
| | - Shi Qiao Hu
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, 430030, China
| | - Li Xia Zhu
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, 430030, China.
| | - Lei Jin
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, 430030, China.
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Cardona Barberán A, Boel A, Vanden Meerschaut F, Stoop D, Heindryckx B. Diagnosis and Treatment of Male Infertility-Related Fertilization Failure. J Clin Med 2020; 9:E3899. [PMID: 33271815 DOI: 10.3390/jcm9123899] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/22/2022] Open
Abstract
Infertility affects approximately 15% of reproductive-aged couples worldwide, of which up to 30% of the cases are caused by male factors alone. The origin of male infertility is mostly attributed to sperm abnormalities, of which many are caused by genetic defects. The development of intracytoplasmic sperm injection (ICSI) has helped to circumvent most male infertility conditions. However, there is still a challenging group of infertile males whose sperm, although having normal sperm parameters, are unable to activate the oocyte, even after ICSI treatment. While ICSI generally allows fertilization rates of 70 to 80%, total fertilization failure (FF) still occurs in 1 to 3% of ICSI cycles. Phospholipase C zeta (PLCζ) has been demonstrated to be a critical sperm oocyte activating factor (SOAF) and the absence, reduced, or altered forms of PLCζ have been shown to cause male infertility-related FF. The purpose of this review is to (i) summarize the current knowledge on PLCζ as the critical sperm factor for successful fertilization, as well as to discuss the existence of alternative sperm-induced oocyte activation mechanisms, (ii) describe the diagnostic tests available to determine the cause of FF, and (iii) summarize the beneficial effect of assisted oocyte activation (AOA) to overcome FF.
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Landreau M, Byson SJ, You H, Stahl DA, Winkler MKH. Effective nitrogen removal from ammonium-depleted wastewater by partial nitritation and anammox immobilized in granular and thin layer gel carriers. Water Res 2020; 183:116078. [PMID: 32623243 DOI: 10.1016/j.watres.2020.116078] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/24/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
This study investigates the effect of physicochemical conditions on the partial nitritation and anammox treatment by immobilized ammonia oxidizers under ammonium-deplete conditions. The impact of oxygen and temperature was studied by measuring the activity of immobilized aerobic and anaerobic ammonia-oxidizing organisms (Ammonia-oxidizing bacteria (AOB) and archaea (AOA), and Anammox bacteria) embedded in polyvinyl alcohol - sodium alginate (PVA-SA) beads and in thin layer poly-ethylene glycol hydrogels. Beads and flat hydrogels were incubated in a fluidized bed reactor (FBR) and in two flow cells, respectively. Both systems were fed with synthetic wastewater (15 mg N-NH4+/L) at different temperatures (20 °C and/or 30 °C) and different dissolved oxygen (DO) concentrations (0.1, 0.3, 0.5 and/or 1 mg/L) over 152 and 207 days, respectively. The FBR system had a maximum removal rate of 1.7 g-N/m3/d at 0.1 mg O2/L, corresponding to 80% removal efficiency, while a high aerobic ammonia-oxidizing activity but a partial oxygen inhibition of Anammox bacteria were observed at higher DO concentrations. In both flow cells, nitrogen removal efficiency was highest (80%) at 30 °C and 1 mg O2/L while removal was less favorable at lower DO and lower temperature. Our results indicate a potential use of hydrogel beads for an energy efficient technology with reduced aeration demand for treating low ammonia wastewater, while layered hydrogels are a possible first step for biological treatments of wastewater using tangential flow. In addition, we provide blueprint drawings of the flow cells, which may be used to 3D-print the apparatus for other applications.
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Affiliation(s)
- Matthieu Landreau
- Department of Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA.
| | - Samuel J Byson
- Department of Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA
| | - HeeJun You
- Department of Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA
| | - Mari K H Winkler
- Department of Civil and Environmental Engineering, University of Washington, 201 More Hall, Box 352700, Seattle, WA, 98195-2700, USA
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35
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Hampel JJ, McCarthy MJ, Aalto SL, Newell SE. Hurricane Disturbance Stimulated Nitrification and Altered Ammonia Oxidizer Community Structure in Lake Okeechobee and St. Lucie Estuary (Florida). Front Microbiol 2020; 11:1541. [PMID: 32754132 PMCID: PMC7366250 DOI: 10.3389/fmicb.2020.01541] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/12/2020] [Indexed: 01/01/2023] Open
Abstract
Nitrification is an important biological link between oxidized and reduced forms of nitrogen (N). The efficiency of nitrification plays a key role in mitigating excess N in eutrophic systems, including those with cyanobacterial harmful algal blooms (cyanoHABs), since it can be closely coupled with denitrification and removal of excess N. Recent work suggests that competition for ammonium (NH4+) between ammonia oxidizers and cyanoHABs can help determine microbial community structure. Nitrification rates and ammonia-oxidizing archaeal (AOA) and bacterial (AOB) community composition and gene abundances were quantified in Lake Okeechobee and St. Lucie Estuary in southern Florida (United States). We sampled during cyanobacterial (Microcystis) blooms in July 2016 and August 2017 (2 weeks before Hurricane Irma) and 10 days after Hurricane Irma made landfall. Nitrification rates were low during cyanobacterial blooms in Lake Okeechobee and St. Lucie Estuary, while low bloom conditions in St. Lucie Estuary coincided with greater nitrification rates. Nitrification rates in the lake were correlated (R2 = 0.94; p = 0.006) with AOA amoA abundance. Following the hurricane, nitrification rates increased by an order of magnitude, suggesting that nitrifiers outcompeted cyanobacteria for NH4+ under turbid, poor light conditions. After Irma, AOA and AOB abundances increased in St. Lucie Estuary, while only AOB increased in Lake Okeechobee. AOA sequences clustered into three major lineages: Nitrosopumilales (NP), Nitrososphaerales (NS), and Nitrosotaleales (NT). Many of the lake OTUs placed within the uncultured and uncharacterized NS δ and NT β clades, suggesting that these taxa are ecologically important along this eutrophic, lacustrine to estuarine continuum. After the hurricane, the AOA community shifted toward dominance by freshwater clades in St. Lucie Estuary and terrestrial genera in Lake Okeechobee, likely due to high rainfall and subsequent increased turbidity and freshwater loading from the lake into the estuary. AOB community structure was not affected by the disturbance. AOA communities were consistently more diverse than AOB, despite fewer sequences recovered, including new, unclassified, eutrophic ecotypes, suggesting a wider ecological biogeography than the oligotrophic niche originally posited. These results and other recent reports contradict the early hypothesis that AOB dominate ammonia oxidation in high-nutrient or terrestrial-influenced systems.
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Affiliation(s)
- Justyna J Hampel
- School of Ocean Science and Engineering, The University of Southern Mississippi, Ocean Springs, MS, United States.,Department of Earth and Environmental Sciences, Wright State University, Dayton, OH, United States
| | - Mark J McCarthy
- Department of Earth and Environmental Sciences, Wright State University, Dayton, OH, United States
| | - Sanni L Aalto
- Section for Aquaculture, The North Sea Research Centre, DTU Aqua, Technical University of Denmark, Hirtshals, Denmark
| | - Silvia E Newell
- Department of Earth and Environmental Sciences, Wright State University, Dayton, OH, United States
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Shi Y, Jiang Y, Wang S, Wang X, Zhu G. Biogeographic distribution of comammox bacteria in diverse terrestrial habitats. Sci Total Environ 2020; 717:137257. [PMID: 32065897 DOI: 10.1016/j.scitotenv.2020.137257] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
Comammox, the microbial group capable of completely oxidizing ammonia to nitrate, challenged the traditional two-step nitrification process where ammonia is oxidized by ammonia-oxidizing archaea (AOA) and bacteria (AOB), and nitrite by nitrite-oxidizing bacteria (NOB). However, the distribution of comammox bacteria in various habitats and their potential environmental drivers remain poorly understood. Using qPCR and high-throughput sequencing approach, we analyzed the abundance and community patterns of comammox from 38 samples taken from five different habitat types including paddy fields in Shaoguan and Antu, the wheat fields, river, and grassland in the Qinghai-Tibet Plateau, and the fringe and central riparian zones of Chaohu Lake of China during winter and summer. Comammox bacteria were detected in all samples, with Ca. N. nitrificans dominating the community, followed by Ca. N. nitrosa. Generally, in paddy fields of Shaoguan and Antu, ammonia (NH4+) was the key factor affecting comammox bacteria. However, in wheat fields, river and grassland of the Qinghai-Tibet Plateau, altitude was the strongest factor affecting comammox bacteria. In Chaohu Lake, comammox bacteria showed temporal heterogeneity, being higher in winter than summer, especially in the fringe riparian zone. Our results suggest that comammox is widespread in diverse habitats and exhibit niche partitioning, and can be affected by different environmental factors that may vary by habitat.
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Affiliation(s)
- Yao Shi
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yingying Jiang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Life Science, Shenyang Normal University, Shenyang 110034, China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Wang C, Tang S, He X, Ji G. The abundance and community structure of active ammonia-oxidizing archaea and ammonia-oxidizing bacteria shape their activities and contributions in coastal wetlands. Water Res 2020; 171:115464. [PMID: 31926374 DOI: 10.1016/j.watres.2019.115464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/19/2019] [Accepted: 12/31/2019] [Indexed: 06/10/2023]
Abstract
Aerobic ammonia oxidation, an important part of the global nitrogen cycle, is thought to be jointly driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in coastal wetlands. However, the activities and contributions of AOA and AOB in coastal wetlands have remained largely unknown. Here, we investigated the oxidation capability of AOA and AOB in four types of typical coastal wetlands (paddy, estuary, shallow and reed wetland) in the Bohai region in China using DNA-based stable-isotope probing (DNA-SIP), quantitative PCR and high-throughput sequencing techniques. We found that the community structure of AOB varied substantially, and the AOA structure was more stable across different coastal wetlands. The rate of AOA was 0.12, 0.84, 0.45 and 0.93 μg N g-1 soil d-1 in paddy, estuary, shallow and reed wetlands, and the rate of AOB was 5.61, 10.72, 0.74 and 1.16 μg N g-1 soil d-1, respectively. We found that the contribution of AOA gradually increased from paddy to estuary to shallow wetland and finally to reed wetland, with values of 2.03%, 7.25%, 37.53% and 44.51%, respectively. Our results provide new insight into the mechanisms of the differences in activities and the contributions of AOA and AOB in different coastal wetlands, and our findings may contribute to further understanding of the global nitrogen cycle.
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Affiliation(s)
- Chen Wang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Shuangyu Tang
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Xiangjun He
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing, 100871, China.
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Reyes C, Hodgskiss LH, Baars O, Kerou M, Bayer B, Schleper C, Kraemer SM. Copper limiting threshold in the terrestrial ammonia oxidizing archaeon Nitrososphaera viennensis. Res Microbiol 2020; 171:134-142. [PMID: 31991171 DOI: 10.1016/j.resmic.2020.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 11/25/2022]
Abstract
Ammonia oxidizing archaea (AOA) inhabiting soils have a central role in the global nitrogen cycle. Copper (Cu) is central to many enzymes in AOA including ammonia monooxygenase (AMO), the enzyme involved in the first step of ammonia oxidation. This study explored the physiological response of the AOA soil isolate, Nitrososphaera viennensis (EN76T) to Cu-limiting conditions in order to approach its limiting threshold under laboratory conditions. The chelator TETA (1,4,8,11-tetraazacyclotetradecane N, N', N″, N‴-tetraacetic acid hydrochloride hydrate) with selective affinity for Cu2+ was used to lower bioavailable Cu2+ in culture experiments as predicted by thermodynamic speciation calculations. Results show that N. viennensis is Cu-limited at concentrations ≤10-15 mol L-1 free Cu2+ compared to standard conditions (10-12 mol L-1). This Cu2+ limiting threshold is similar to pure cultures of denitrifying bacteria and other AOA and AOB inhabiting soils, freshwaters and sewage (<10-16 mol L-1), and lower than pure cultures of the marine AOA Nitrosopumilus maritimus (<10-12.7 mol L-1), which also possesses a high amount of Cu-dependent enzymes.
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Affiliation(s)
- Carolina Reyes
- University of Vienna, EDGE- Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, UZA2, 1090, Vienna, Austria; University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Logan H Hodgskiss
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Oliver Baars
- North Carolina State University, Department of Entomology and Plant Pathology, 840 Main Campus Drive, Raleigh, NC, 27695, USA.
| | - Melina Kerou
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Barbara Bayer
- Department of Limnology and Bio-Oceanography, Division of Bio-Oceanography, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Christa Schleper
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, UZA1, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
| | - Stephan M Kraemer
- University of Vienna, EDGE- Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, Althanstrasse 14, UZA2, 1090, Vienna, Austria; University of Vienna, Environmental Science Research Network (ESRN), Faculty for Geosciences, Geography and Astronomy, Althanstrasse 14, UZA2, 1090, Vienna, Austria.
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Yang Y, Pan J, Zhou Z, Wu J, Liu Y, Lin JG, Hong Y, Li X, Li M, Gu JD. Complex microbial nitrogen-cycling networks in three distinct anammox-inoculated wastewater treatment systems. Water Res 2020; 168:115142. [PMID: 31605831 DOI: 10.1016/j.watres.2019.115142] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 08/02/2019] [Accepted: 09/29/2019] [Indexed: 05/05/2023]
Abstract
Microbial nitrogen removal mediated by anaerobic ammonium oxidation (anammox) are cost-effective, yet it is time-consuming to accumulate the slow-growing anammox bacteria in conventional wastewater treatment plants (WWTPs). Inoculation of anammox enriched pellets is an effective way to establish anammox and achieve shortcut nitrogen removal in full-scale WWTPs. However, little is known about the complex microbial nitrogen-cycling networks in these anammox-inoculated WWTPs. Here, we applied metagenomic and metatranscriptomic tools to study the microbial nitrogen removal in three conventional WWTPs, which have been inoculated exogenous anammox pellets, representing partial-nitrification anammox (PNA) and nitrification-denitrification nitrogen removal processes. In the PNA system of Bali (BL), ammonia was partially oxidized by ammonia-oxidizing bacteria (AOB) Nitrosomonas and the oxidized nitrite and the remaining ammonium were directly converted to N2 by anammox bacteria Ca. Brocadia and Ca. Kuenenia. In the nitrification-denitrification system of Wenshan (WS), ammonia-oxidizing archaea (AOA) Thaumarchaeota unexpectedly dominated the nitrifying community in the presence of AOB Nitrosomonas. Meanwhile, the biomass yield of Ca. Brocadia was likely inhibited by the high biodegradable organic compound input and limited by substrate competitions from AOA, AOB, complete ammonia oxidizers (comammox) Nitrospira, nitrite-oxidizing bacteria (NOB) Nitrospira, and heterotrophic denitrifiers. Unexpectedly, comammox Nitrospira was the predominant nitrifier in the presence of AOB Nitrosomonas in the organic carbon-rich nitrification-denitrification system of Linkou (LK). These results clearly showed that distinct active groups were working in concert for an effective nitrogen removal in different WWTPs. This study confirmed the feasibility of anammox application in ammonium-rich systems by direct inoculation of the exogenous anammox pellets and improved our understanding of microbial nitrogen cycling in anammox-driven conventional WWTPs from both physiochemical and omics perspectives.
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Affiliation(s)
- Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Jiapeng Wu
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Institute of Environmental Research at Greater Bay, Guangzhou University, Guangzhou, 510006, People's Republic of China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, People's Republic of China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Jih-Gaw Lin
- Institute of Environmental Engineering, National Chiao Tung University, 1001 University Road, Hsinchu City, 30010, Taiwan
| | - Yiguo Hong
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Institute of Environmental Research at Greater Bay, Guangzhou University, Guangzhou, 510006, People's Republic of China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, People's Republic of China
| | - Xiaoyan Li
- Department of Civil and Environmental Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People's Republic of China.
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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Shi Y, Liu X, Zhang Q. Effects of combined biochar and organic fertilizer on nitrous oxide fluxes and the related nitrifier and denitrifier communities in a saline-alkali soil. Sci Total Environ 2019; 686:199-211. [PMID: 31176819 DOI: 10.1016/j.scitotenv.2019.05.394] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 04/19/2019] [Accepted: 05/25/2019] [Indexed: 06/09/2023]
Abstract
This study intended to evaluate the combined effects of both biochar and organic fertilizer on nitrous oxide (N2O) fluxes and composition of nitrifier and denitrifier of saline-alkali soil. Therefore, four different treatments such as CK (only chemical fertilizer), B (only biochar), M (only organic fertilizer), BM (B:M = 1:1) were used in this experiment. The results showed that N2O emissions were decreased in B and BM treatments compare to the control. In contrast, N2O emissions were highest before day 12 but lowest after day 19 in M treatment compare to the control. Application of biochar, organic fertilizer and biochar plus organic fertilizer decreased the nirS and nirK genes copies and enhanced the nosZ gene copies which resulting in the lower N2O fluxes. The ammonia-oxidizing bacteria (AOB) amoA and nirK genes copies were significantly increased by organic fertilizer before day 12, leading to high N2O emissions. The genera Nitrosospira (AOB) and Nitrososphaera (ammonia-oxidizing archaea, AOA) assumed absolute superiority. Additionally, Nitrosospira (AOB) was also appeared in nirK-type denitrifiers, illustrating denitrification was carried out by nitrifiers. The genera Azospirillum (nirS), Burkholderia (nosZ) and Polymorphum (nosZ) were dominant in CK. There was only one dominant genus, Mesorhizobium (nosZ) in the B treatment. The genera Mesorhizobium (nirK), Azoarcus (nirS), Kocuria (nirS) and Pseudomonas (nosZ) occupied the main status in the M treatment. The relative abundance of Rhodanobacter (nirS) and Azospirillum (nosZ) were higher in the BM treatment compared with other treatments. Soil water content (SWC), pH, NH4+-N and NO3--N were the main factors affecting AOB and denitrifiers, which influencing N2O emissions. Overall, combined application of biochar and organic fertilizer can reduce the N2O emission where AOB and nirK-type denitrifier were the main contributors to the N2O emission.
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Affiliation(s)
- Yulong Shi
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xingren Liu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Qingwen Zhang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Wang J, Wang J, Rhodes G, He JZ, Ge Y. Adaptive responses of comammox Nitrospira and canonical ammonia oxidizers to long-term fertilizations: Implications for the relative contributions of different ammonia oxidizers to soil nitrogen cycling. Sci Total Environ 2019; 668:224-233. [PMID: 30852199 DOI: 10.1016/j.scitotenv.2019.02.427] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 06/09/2023]
Abstract
The new discovery of complete ammonia oxidizers (comammox), single organisms capable of oxidizing ammonia into nitrate, redefined the traditional view of nitrification. However, little is known about the relative contributions of comammox and other nitrifiers to nitrification, particularly in agricultural soils with long-term intensive input of nutrients. Herein, we investigated the communities of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and comammox Nitrospira in agricultural soils under nutrients input gradient of nitrogen (0-675 kg N ha-1 year-1), phosphorus (0-405 kg P2O5 ha-1 year-1), and potassium (0-675 kg K2O ha-1 year-1) fertilizers for 19 years. The results showed that N and K fertilizers input significantly (P < 0.05) increased the AOB-amoA gene abundance, while AOA were not as sensitive as AOB. The comammox-amoA gene copies were increased in all fertilizer treatments and was significantly correlated (P < 0.05) with the amount of N fertilizer added. Terminal restriction fragment length polymorphism (T-RFLP) combined with clone-library assays of comammox-amoA gene showed that increasing gradient of nutrients input increased the relative abundance of 73 bp T-RF (assigned to Clade A) but decreased the relative abundance of 198 bp T-RF (representing Clade B). Correlation analyses and stepwise linear regression analyses demonstrated that AOB were the dominate contributors to soil potential nitrification, while comammox Nitrospira did not play a significant role (P > 0.05). This study provided insights into the adaptive responses of comammox Nitrospira and canonical ammonia oxidizers to long-term fertilizations and their relative contributions to potential nitrification in arable soils.
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Affiliation(s)
- Jichen Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianlei Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Geoff Rhodes
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Nguyen NM, Tran LC, Safaei F, Phung SL, Vial P, Huynh N, Cox A, Harada T, Barthelemy J. Performance Evaluation of Non-GPS Based Localization Techniques under Shadowing Effects. Sensors (Basel) 2019; 19:E2633. [PMID: 31185660 DOI: 10.3390/s19112633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/24/2019] [Accepted: 06/06/2019] [Indexed: 11/17/2022]
Abstract
Non-GPS localization has gained much interest from researchers and industries recently because GPS might fail to meet the accuracy requirements in shadowing environments. The two most common range-based non-GPS localization methods, namely Received Signal Strength Indicator (RSSI) and Angle-of-Arrival (AOA), have been intensively mentioned in the literature over the last decade. However, an in-depth analysis of the weighted combination methods of AOA and RSSI in shadowing environments is still missing in the state-of-the-art. This paper proposes several weighted combinations of the two RSSI and AOA components in the form of pAOA + qRSSI, devises the mathematical model for analyzing shadowing effects, and evaluates these weighted combination localization methods from both accuracy and precision perspectives. Our simulations show that increasing the number of anchors does not necessarily improve the precision and accuracy, that the AOA component is less susceptible to shadowing than the RSSI one, and that increasing the weight of the AOA component and reducing that of the RSSI component help improve the accuracy and precision at high Signal-to-Noise Ratios (SNRs). This observation suggests that some power control algorithm could be used to increase automatically the transmitted power when the channel experiences large shadowing to maintain a high SNR, thus guaranteeing both accuracy and precision of the weighted combination localization techniques.
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Purohit P, Palamthodi S, Lele SS. Effect of karwanda ( Carissa congesta Wight) and sugar addition on physicochemical characteristics of ash gourd ( Benincasa hispida) and bottle gourd ( Langenaria siceraria) based beverages. J Food Sci Technol 2019; 56:1037-45. [PMID: 30906061 DOI: 10.1007/s13197-019-03570-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 12/26/2018] [Accepted: 01/01/2019] [Indexed: 10/27/2022]
Abstract
There is a clear trend towards increasing consumption of juices as they can reduce imbalance of redox potential and provide necessary health benefits to consumers. Levels of karwanda (Carissa congesta Wight) and vegetable juices were varied to prepare nine different formulations of ash gourd-karwanda (AgK) and bottle gourd-karwanda blends (BgK) of higher nutritive, sensory qualities and storability. Total polyphenols (TP), antioxidant activity (AOA), total soluble solids and acidity were increased significantly (p ≤ 0.05) with addition of karwanda. AgK blend (35:35) and BgK blend (35:30) were selected based on their higher overall acceptability, TP and AOA. AgK blends had higher α-amylase (31%) while BgK blends had higher α-glucosidase (43%) inhibitory activities. Concentration of TP and anthocyanins decreased significantly (p < 0.05), AOA remained unchanged and anti-inflammatory activities decreased (33-38%) in AgK and BgK blends during accelerated storage at 50 °C for 12 days. Addition of sugar in BgK blend decreased stability of TP (11%), flavonoids (31%) and anthocyanins (8%). During in vitro gastrointestinal digestion, TP, flavonoids and anthocyanins reduction rate was significantly higher for BgK blend with sugar.
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Marques ELS, Dias JCT, Gross E, Silva ABCE, de Moura SR, Rezende RP. Purple Sulfur Bacteria Dominate Microbial Community in Brazilian Limestone Cave. Microorganisms 2019; 7:E29. [PMID: 30678083 DOI: 10.3390/microorganisms7020029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/11/2019] [Accepted: 01/13/2019] [Indexed: 11/16/2022] Open
Abstract
The mineralogical composition of caves makes the environment ideal for inhabitation by microbes. However, the bacterial diversity in the cave ecosystem remains largely unexplored. In this paper, we described the bacterial community in an oxic chamber of the Sopradeira cave, an iron-rich limestone cave, in the semiarid region of Northeast Brazil. The microbial population in the cave samples was studied by 16S rDNA next-generation sequencing. A type of purple sulfur bacteria (PSB), Chromatiales, was found to be the most abundant in the sediment (57%), gravel-like (73%), and rock samples (96%). The predominant PSB detected were Ectothiorhodospiraceae, Chromatiaceae, and Woeseiaceae. We identified the PSB in a permanently aphotic zone, with no sulfur detected by energy-dispersive X-ray (EDX) spectroscopy. The absence of light prompted us to investigate for possible nitrogen fixing (nifH) and ammonia oxidizing (amoA) genes in the microbial samples. The nifH gene was found to be present in higher copy numbers than the bacterial-amoA and archaeal-amoA genes, and archaeal-amoA dominated the ammonia-oxidizing community. Although PSB dominated the bacterial community in the samples and may be related to both nitrogen-fixing and ammonia oxidizing bacteria, nitrogen-fixing associated gene was the most detected in those samples, especially in the rock. The present work demonstrates that this cave is an interesting hotspot for the study of ammonia-oxidizing archaea and aphotic PSB.
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Xia F, Wang JG, Zhu T, Zou B, Rhee SK, Quan ZX. Ubiquity and Diversity of Complete Ammonia Oxidizers (Comammox). Appl Environ Microbiol 2018; 84:e01390-18. [PMID: 30315079 PMCID: PMC6275355 DOI: 10.1128/aem.01390-18] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022] Open
Abstract
The discovery of complete ammonia oxidizers (comammox) refutes the century-old paradigm that nitrification requires the activity of two types of microbes. Determining the distribution and abundance of comammox in various environments is important for revealing the ecology of microbial nitrification within the global nitrogen cycle. In this study, the ubiquity and diversity of comammox were analyzed for samples from different types of environments, including soil, sediment, sludge, and water. The results of a two-step PCR using highly degenerate primers (THDP-PCR) and quantitative real-time PCR (qPCR) supported the relatively high abundance of comammox in nearly half of all samples tested, sometimes even outnumbering canonical ammonia-oxidizing bacteria (AOB). In addition, a relatively high proportion of comammox in tap and coastal water samples was confirmed via analysis of metagenomic data sets in public databases. The diversity of comammox was estimated by comammox-specific partial nested PCR amplification of the ammonia monooxygenase subunit A (amoA) gene, and phylogenetic analysis of comammox AmoA clearly showed a split of clade A into clades A.1 and A.2, with the proportions of clades A.1, A.2, and B differing among the various environmental samples. Moreover, compared to the amoA genes of AOB and ammonia-oxidizing archaea (AOA), the comammox amoA gene exhibited higher diversity indices. The ubiquitous distribution and high diversity of comammox indicate that they are likely overlooked contributors to nitrification in various ecosystems.IMPORTANCE The discovery of complete ammonia oxidizers (comammox), which oxidize ammonia to nitrate via nitrite, refutes the century-old paradigm that nitrification requires the activity of two types of microbes and redefines a key process in the biogeochemical nitrogen cycle. Understanding the functional relationships between comammox and other nitrifiers is important for ecological studies on the nitrogen cycle. Therefore, the diversity and contribution of comammox should be considered during ecological analyses of nitrifying microorganisms. In this study, a ubiquitous and highly diverse distribution of comammox was observed in various environmental samples, similar to the distribution of canonical ammonia-oxidizing bacteria. The proportion of comammox was relatively high in coastal water and sediment samples, whereas it was nearly undetectable in open-ocean samples. The ubiquitous distribution and high diversity of comammox indicate that these microorganisms might be important contributors to nitrification.
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Affiliation(s)
- Fei Xia
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Jian-Gong Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Ting Zhu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Bin Zou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, Republic of Korea
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
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Arce MI, von Schiller D, Bengtsson MM, Hinze C, Jung H, Alves RJE, Urich T, Singer G. Drying and Rainfall Shape the Structure and Functioning of Nitrifying Microbial Communities in Riverbed Sediments. Front Microbiol 2018; 9:2794. [PMID: 30519221 PMCID: PMC6250940 DOI: 10.3389/fmicb.2018.02794] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/30/2018] [Indexed: 11/13/2022] Open
Abstract
Non-flow periods in fluvial ecosystems are a global phenomenon. Streambed drying and rewetting by sporadic rainfalls could drive considerable changes in the microbial communities that govern stream nitrogen (N) availability at different temporal and spatial scales. We performed a microcosm-based experiment to investigate how dry period duration (DPD) (0, 3, 6, and 9 weeks) and magnitude of sporadic rewetting by rainfall (0, 4, and 21 mm applied at end of dry period) affected stocks of N in riverbed sediments, ammonia-oxidizing bacteria (AOB) and archaea (AOA) and rates of ammonia oxidation (AO), and emissions of nitrous oxide (N2O) to the atmosphere. While ammonium (NH4 +) pool size decreased, nitrate (NO3 -) pool size increased in sediments with progressive drying. Concomitantly, the relative and absolute abundance of AOB and, especially, AOA (assessed by 16S rRNA gene sequencing and quantitative PCR of ammonia monooxygenase genes) increased, despite an apparent decrease of AO rates with drying. An increase of N2O emissions occurred at early drying before substantially dropping until the end of the experiment. Strong rainfall of 21 mm increased AO rates and NH4 + in sediments, whereas modest rainfall of 4 mm triggered a notable increase of N2O fluxes. Interestingly, such responses were detected only after 6 and 9 weeks of drying. Our results demonstrate that progressive drying drives considerable changes in in-stream N cycling and the associated nitrifying microbial communities, and that sporadic rainfall can modulate these effects. Our findings are particularly relevant for N processing and transport in rivers with alternating dry and wet phases - a hydrological scenario expected to become more important in the future.
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Affiliation(s)
- Maria Isabel Arce
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Daniel von Schiller
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Mia M. Bengtsson
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christian Hinze
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Hoseung Jung
- Integrative Research Institute on Transformations of Human-Environment Systems (IRI THESys), Humboldt University of Berlin, Berlin, Germany
| | - Ricardo J. Eloy Alves
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Gabriel Singer
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
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47
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Kruglova A, Mikola A, Gonzalez-Martinez A, Vahala R. Effect of sulfadiazine and trimethoprim on activated sludge performance and microbial community dynamics in laboratory-scale membrane bioreactors and sequencing batch reactors at 8°C. Biotechnol Prog 2018; 35:e2708. [PMID: 30294885 DOI: 10.1002/btpr.2708] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 06/28/2018] [Indexed: 11/12/2022]
Abstract
The effect of antibiotics sulfadiazine and trimethoprim on activated sludge operated at 8°C was investigated. Performance and microbial communities of sequencing batch reactors (SBRs) and Membrane Bioreactors (MBRs) were compared before and after the exposure of antibiotics to the synthetic wastewater. The results revealed irreversible negative effect of these antibiotics in environmentally relevant concentrations on nitrifying microbial community of SBR activated sludge. In opposite, MBR sludge demonstrated fast adaptation and more stable performance during the antibiotics exposure. Dynamics of microbial community was greatly affected by presence of antibiotics. Bacteria from classes Betaproteobacteria and Bacteroidetes demonstrated the potential to develop antibiotic resistance in both wastewater treatment systems while Actinobacteria disappeared from all of the reactors after 60 days of antibiotics exposure. Altogether, results showed that operational parameters such as sludge retention time (SRT) and reactor configuration had great effect on microbial community composition of activated sludge and its vulnerability to antibiotics. Operation at long SRT allowed archaea, including ammonium oxidizing species (AOA) such as Nitrososphaera viennensis to grow in MBRs. AOA could have an important role in stable nitrification performance of MBR-activated sludge as a result of tolerance of archaea to antibiotics. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2708, 2019.
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Affiliation(s)
| | - Anna Mikola
- Dept. of Built Environment, Aalto University, Espoo, Finland
| | | | - Riku Vahala
- Dept. of Built Environment, Aalto University, Espoo, Finland
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48
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Lan T, Suter H, Liu R, Yuan S, Chen D. Effects of nitrification inhibitors on gross N nitrification rate, ammonia oxidizers, and N 2O production under different temperatures in two pasture soils. Environ Sci Pollut Res Int 2018; 25:28344-28354. [PMID: 30083899 DOI: 10.1007/s11356-018-2873-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
Australian pasture soil for cattle and sheep industries constitutes the principal land use with considerable N fertilizer consumption, which is one of the causes of local environmental problems. Nitrification plays a key role in regulating soil inorganic N concentration and its environmental diffusion. The effects of different nitrification inhibitors (NIs) on gross N nitrification (ngross) rate and N2O production under different temperatures in pasture soils remain unclear. A laboratory incubation experiment was conducted to determine the effect of NIs (dicyandiamide [DCD], 3,4-dimethylpyrazole phosphate [DMPP], and 3-methylpyrazol and 1H-1,2,4-triazol [3MP + TZ]) on N2O emissions, ngross and net N nitrification (nnet) rates, and the abundance of ammonia oxidizers, namely, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), in two Australian pasture soils incubated at temperatures of 15, 25, and 35 °C. All NIs reduced both ngross and nnet rates and N2O production rate from the two pasture soils but to different extents. The inhibitory rates of NIs on ngross and nnet reached 6.80-63.8 and 5.91-62.3%, respectively, whereas that on N2O production rate totaled 4.5-41.4% in the tested soils. NIs reduced nitrification and N2O production by inhibiting the growth of AOB rather than AOA. The inhibitory effects of NIs were temperature-dependent, that is, decreasing with increasing temperature from 15 to 35 °C. In general, DMPP performed better than DCD and 3MP + TZ at 15 and 35 °C, whereas DCD performed more effectively than the other two NIs at 25 °C. Our results suggest that the utilization of NIs will depend on the conditions present, especially soil temperature. Additionally, AOB is the target of inhibition when mitigating nitrification and N2O emission by applying NIs in pasture soils.
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Affiliation(s)
- Ting Lan
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Faculty of Veterinary and Agriculture Science, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Helen Suter
- Faculty of Veterinary and Agriculture Science, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Rui Liu
- Faculty of Veterinary and Agriculture Science, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Shu Yuan
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Deli Chen
- Faculty of Veterinary and Agriculture Science, University of Melbourne, Melbourne, VIC, 3010, Australia
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49
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Marshall A, Phillips L, Longmore A, Tang C, Heidelberg K, Mele P. Primer selection influences abundance estimates of ammonia oxidizing archaea in coastal marine sediments. Mar Environ Res 2018; 140:90-95. [PMID: 29891388 DOI: 10.1016/j.marenvres.2018.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 06/01/2018] [Accepted: 06/03/2018] [Indexed: 06/08/2023]
Abstract
Quantification of the α-subunit of ammonia monooxygenase (amoA) through PCR is an established technique for estimating the abundance of ammonia oxidizing archaea (AOA) in environmental samples. This study quantified AOA with two established primer sets in 1 cm increments from the sediment surface (0-1 cm) to a depth of 10 cm at two locations within Port Phillip Bay (PPB), Australia. Primer choice had a significant effect on within sample estimates of AOA with copy numbers ranging from 102 to 104 copies per ng DNA. Variation in AOA abundance patterns with increasing sediment depth were site and primer specific. Sequence mismatches between the primer binding region of the isolated amoA sequences from PPB and Nitrosopumilus maritimus SCM1 were identified and may explain the high variation identified between primer estimates. Our results highlight the need for testing multiple primer pairs that target different regions of the AOA amoA sequence prior to large-scale marine sediment environmental studies.
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Affiliation(s)
- Alexis Marshall
- La Trobe University, AgriBio Centre for AgriBiosciences, 5 Ring Road, Bundoora, Australia; Department of Economic Development, Jobs, Transport and Resources, AgriBio, Centre for AgriBiosciences, 5 Ring Road, Bundoora, Australia.
| | - Lori Phillips
- Agriculture and AgriFood Canada, Harrow Research and Development Centre, Harrow, Ontario, Canada
| | - Andrew Longmore
- Centre for Aquatic Pollution Identification and Management, Melbourne University, Parkville, Australia
| | - Caixian Tang
- La Trobe University, AgriBio Centre for AgriBiosciences, 5 Ring Road, Bundoora, Australia
| | - Karla Heidelberg
- The University of Southern California, Department of Biology, Los Angeles, CA, 90089, USA
| | - Pauline Mele
- La Trobe University, AgriBio Centre for AgriBiosciences, 5 Ring Road, Bundoora, Australia; Department of Economic Development, Jobs, Transport and Resources, AgriBio, Centre for AgriBiosciences, 5 Ring Road, Bundoora, Australia
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50
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Lin Y, Ye G, Luo J, Di HJ, Liu D, Fan J, Ding W. Nitrosospira Cluster 8a Plays a Predominant Role in the Nitrification Process of a Subtropical Ultisol under Long-Term Inorganic and Organic Fertilization. Appl Environ Microbiol 2018; 84:e01031-18. [PMID: 30006397 DOI: 10.1128/AEM.01031-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/04/2018] [Indexed: 11/20/2022] Open
Abstract
Long-term effects of inorganic and organic fertilization on nitrification activity (NA) and the abundances and community structures of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated in an acidic Ultisol. Seven treatments applied annually for 27 years comprised no fertilization (control), inorganic NPK fertilizer (N), inorganic NPK fertilizer plus lime (CaCO3) (NL), inorganic NPK fertilizer plus peanut straw (NPS), inorganic NPK fertilizer plus rice straw (NRS), inorganic NPK fertilizer plus radish (NR), and inorganic NPK fertilizer plus pig manure (NPM). In nonfertilized soil, the abundance of AOA was 1 order of magnitude higher than that of AOB. Fertilization reduced the abundance of AOA but increased that of AOB, especially in the NL treatment. The AOA communities in the control and the N treatments were dominated by the Nitrososphaera and B1 clades but shifted to clade A in the NL and NPM treatments. Nitrosospira cluster 8a was found to be the most dominant AOB in all treatments. NA was primarily regulated by soil properties, especially soil pH, and the interaction with AOB abundance explained up to 73% of the variance in NA. When NL soils with neutral pH were excluded from the analysis, AOB abundance, especially the relative abundance of Nitrosospira cluster 8a, was positively associated with NA. In contrast, there was no association between AOA abundance and NA. Overall, our data suggest that Nitrosospira cluster 8a of AOB played an important role in the nitrification process in acidic soil following long-term inorganic and organic fertilization.IMPORTANCE The nitrification process is an important step in the nitrogen (N) cycle, affecting N availability and N losses to the wider environment. Ammonia oxidation, which is the first and rate-limiting step of nitrification, was widely accepted to be mainly regulated by AOA in acidic soils. However, in this study, nitrification activity was correlated with the abundance of AOB rather than that of AOA in acidic Ultisols. Nitrosospira cluster 8a, a phylotype of AOB which preferred warm temperatures, and low soil pH played a predominant role in the nitrification process in the test Ultisols. Our results also showed that long-term application of lime or pig manure rather than plant residues altered the community structure of AOA and AOB. Taken together, our findings contribute new knowledge to the understanding of the nitrification process and ammonia oxidizers in subtropical acidic Ultisol under long-term inorganic and organic fertilization.
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