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Iqbal MM, Nishimura M, Tsukamoto Y, Yoshizawa S. Changes in microbial community structure related to biodegradation of eelgrass (Zostera marina). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172798. [PMID: 38688366 DOI: 10.1016/j.scitotenv.2024.172798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 04/21/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
Seagrass meadows produce organic carbon and deposit it on the seabed through the decaying process. Microbial activity is closely related to the process of eelgrass death and collapse. We investigated the microbial community structure of eelgrass during the eelgrass decomposition process by using a microcosm containing raw seawater and excised eelgrass leaves collected from a Zostera marina bed in Futtsu, Chiba Prefecture, Japan. The fast-growing microbes (i.e., Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia) rapidly adhered to the eelgrass leaf surface and proliferated in the first two weeks but gradually decreased the relative abundance as the months moved on. On the other hand, the slow-growing microbes (i.e., Cytophagia, Anaerolineae, Thaumarchaeota, and Actinobacteria) became predominant over the eelgrass surface late in the culture experiment (120, 180 days). The fast-growing groups of Gammaproteobacteria and Flavobacteriia appear to be closely related to the initial decomposition of eelgrass, especially the rapid decomposition of leaf-derived biopolymers. Changes in nitrogen content due to the bacterial rapid consumption of readily degradable organic carbon induced changes in the community structure at the early stage of eelgrass decomposition. In addition, shifts in the C/N ratio were driven by microbial community changes during later decomposition phases.
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Affiliation(s)
- Md Mehedi Iqbal
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan; Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8563, Japan.
| | - Masahiko Nishimura
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Yuya Tsukamoto
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan; Department of Natural Environmental Studies, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8563, Japan.
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Wu J, Zhan M, Yuan L, Zhu Y, Lin W, Luo J. Sealing solid agar in serum bottles for rapid isolation and long-term preservation of chemoautotrophic ammonia-oxidizing bacteria. WATER RESEARCH 2024; 260:121916. [PMID: 38875857 DOI: 10.1016/j.watres.2024.121916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/06/2024] [Accepted: 06/08/2024] [Indexed: 06/16/2024]
Abstract
Ammonia-oxidizing bacteria (AOB) are ubiquitous on the earth and have broad applications in bioremediation. However, the number of their species with standing in nomenclature and deposited in Microbial Culture Collections still remains low. Moreover, only a few novel species have been reported over the last decades. In this study, we sealed agar in serum bottles to develop a kind of solid agar plate with the oxygen concentration in the headspace maintained at low levels. By using these plates, eight AOB isolates including two novel species were obtained. When AOB cells were grown on the sealed solid agar plates, the time to form visible colonies was largely reduced and the maximum diameter of colonies reached 2 mm, which makes the process of AOB isolation rapid and efficient. Based on five AOB isolates, the headspace oxygen concentration had a significant influence on AOB growth either on solid plate or in liquid culture. Especially, when grown under 21 % O2, the number of colonies formed on solid agar plates was very low and sometimes no visible colony formed. Besides the application on AOB isolation, the sealed solid agar plate was also effective for the enumeration and preservation of AOB cells. When preserved under room temperature for more than ten months, the AOB colonies on the plate could still be recovered. This method provides a feasible way to isolate more novel AOB species from the environment and deposit more species in Microbial Culture Collections.
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Affiliation(s)
- Jiajie Wu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Manjun Zhan
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Lingling Yuan
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Yueyue Zhu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Weitie Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; MOE Joint International Research Laboratory of Synthetic Biology and Medicine, South China University of Technology, Guangzhou 510006, PR China.
| | - Jianfei Luo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; MOE Joint International Research Laboratory of Synthetic Biology and Medicine, South China University of Technology, Guangzhou 510006, PR China.
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3
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Shan X, Wang J, Du M, Tian Z. Inhibitory effect of marine Bacillus sp. and its biomineralization on the corrosion of X65 steel in offshore oilfield produced water. Bioelectrochemistry 2024; 157:108659. [PMID: 38330530 DOI: 10.1016/j.bioelechem.2024.108659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
The issue of material failure attributed to microbiologically influenced corrosion (MIC) is escalating in seriousness. Microorganisms not only facilitate corrosion but certain beneficial microorganisms also impede its occurrence. This study explored the impact of marine B. velezensis on the corrosion behavior of X65 steel in simulated offshore oilfield produced water. B. velezensis exhibited rapid growth in the initial stages, and the organic acid metabolites were found to promote corrosion. Subsequently, there was an increase in cross-linked "networked" biofilms products, a significant rise in the prismatic shape of corrosion products, and a tendency for continuous development in the middle and late stages. The organic/inorganic mineralized film layer formed on the surface remained consistently complete. Metabolic products of amino acid corrosion inhibitors were also observed to be adsorbed into the film. B. velezensis altered the kinetics of the X65 steel cathodic reaction, resulting in a deceleration of the electrochemical reaction rate. The mineralization induced by B. velezensis effectively slowed down the corrosion rate of X65 steel.
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Affiliation(s)
- Xueyan Shan
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Jian Wang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Min Du
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China.
| | - Zhiyu Tian
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
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Fang J, Sheng Z, Liu J, Li C, Lyu T, Wang Z, Zhang H. Interference of microplastics on autotrophic microbiome in paddy soils: Shifts in carbon fixation rate, structure, abundance, co-occurrence, and assembly process. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134783. [PMID: 38824776 DOI: 10.1016/j.jhazmat.2024.134783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/20/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
Autotrophic microorganisms play a crucial role in soil CO2 assimilation. Although microplastic pollution is recognized as a significant global concern, its precise impact on carbon sequestration by autotrophic microorganisms in agroecosystem soil remains poorly understood. This study conducted microcosm experiments to explore how conventional polystyrene (PS) and biodegradable poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) microplastics affect carbon fixation rates (CFRs) and the community characteristics of soil autotrophic microorganisms in paddy agroecosystems. The results showed that compared with the control groups, 0.5 % and 1 % microplastic treatments significantly reduced soil CFRs by 11.8 - 24.5 % and 18.7 - 32.3 %, respectively. PS microplastics exerted a stronger inhibition effect on CFRs than PHBV microplastics in bulk soil. However, no significant difference was observed in the inhibition of CFRs by both types of microplastics in rhizosphere soils. Additionally, PS and PHBV microplastics altered the structure of autotrophic microbial communities, resulting in more stochastically dominated assembly and looser, more fragile coexistence networks compared to control groups. Moreover, microplastics drove the changes in autotrophic microbial carbon fixation primarily through their direct interference and the indirect effect by increasing soil organic carbon levels. Our findings enhance the understanding and predictive capabilities regarding the impacts of microplastic pollution on carbon sinks in agricultural soils.
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Affiliation(s)
- Jiaohui Fang
- School of Life Sciences, Qufu Normal University, Qufu 273100, China
| | - Zihao Sheng
- School of Life Sciences, Qufu Normal University, Qufu 273100, China
| | - Jian Liu
- Environment Research Institute, Shandong University, Qingdao 266237, China
| | - Changchao Li
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Tianshu Lyu
- School of Life Sciences, Qufu Normal University, Qufu 273100, China
| | - Zhenyang Wang
- School of Life Sciences, Qufu Normal University, Qufu 273100, China
| | - Honghai Zhang
- School of Life Sciences, Qufu Normal University, Qufu 273100, China.
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Ali A, Vishnivetskaya TA, Chauhan A. Comparative analysis of prokaryotic microbiomes in high-altitude active layer soils: insights from Ladakh and global analogues using In-Silico approaches. Braz J Microbiol 2024:10.1007/s42770-024-01365-3. [PMID: 38758507 DOI: 10.1007/s42770-024-01365-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/08/2024] [Indexed: 05/18/2024] Open
Abstract
The active layer is the portion of soil overlaying the permafrost that freezes and thaws seasonally. It is a harsh habitat in which a varied and vigorous microbial population thrives. The high-altitude active layer soil in northern India is a unique and important cryo-ecosystem. However, its microbiology remains largely unexplored. It represents a unique reservoir for microbial communities with adaptability to harsh environmental conditions. In the Changthang region of Ladakh, the Tsokar area is a high-altitude permafrost-affected area situated in the southern part of Ladakh, at a height of 4530 m above sea level. Results of the comparison study with the QTP, Himalayan, Alaskan, Russian, Canadian and Polar active layers showed that the alpha diversity was significantly higher in the Ladakh and QTP active layers as the environmental condition of both the sites were similar. Moreover, the sampling site in the Ladakh region was in a thawing condition at the time of sampling which possibly provided nutrients and access to alternative nitrogen and carbon sources to the microorganisms thriving in it. Analysis of the samples suggested that the geochemical parameters and environmental conditions shape the microbial alpha diversity and community composition. Further analysis revealed that the cold-adapted methanogens were present in the Ladakh, Himalayan, Polar and Alaskan samples and absent in QTP, Russian and Canadian active layer samples. These methanogens could produce methane at slow rates in the active layer soils that could increase the atmospheric temperature owing to climate change.
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Affiliation(s)
- Ahmad Ali
- Department of Zoology, Panjab University, Sector 14, 160014, Chandigarh, India
| | | | - Archana Chauhan
- Department of Zoology, Panjab University, Sector 14, 160014, Chandigarh, India.
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6
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Wang S, Lan B, Yu L, Xiao M, Jiang L, Qin Y, Jin Y, Zhou Y, Armanbek G, Ma J, Wang M, Jetten MSM, Tian H, Zhu G, Zhu YG. Ammonium-derived nitrous oxide is a global source in streams. Nat Commun 2024; 15:4085. [PMID: 38744837 PMCID: PMC11094135 DOI: 10.1038/s41467-024-48343-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Global riverine nitrous oxide (N2O) emissions have increased more than 4-fold in the last century. It has been estimated that the hyporheic zones in small streams alone may contribute approximately 85% of these N2O emissions. However, the mechanisms and pathways controlling hyporheic N2O production in stream ecosystems remain unknown. Here, we report that ammonia-derived pathways, rather than the nitrate-derived pathways, are the dominant hyporheic N2O sources (69.6 ± 2.1%) in agricultural streams around the world. The N2O fluxes are mainly in positive correlation with ammonia. The potential N2O metabolic pathways of metagenome-assembled genomes (MAGs) provides evidence that nitrifying bacteria contain greater abundances of N2O production-related genes than denitrifying bacteria. Taken together, this study highlights the importance of mitigating agriculturally derived ammonium in low-order agricultural streams in controlling N2O emissions. Global models of riverine ecosystems need to better represent ammonia-derived pathways for accurately estimating and predicting riverine N2O emissions.
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Affiliation(s)
- Shanyun Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bangrui Lan
- 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
| | - Manyi Xiao
- 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
| | - Yu Qin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yucheng Jin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yuting Zhou
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Gawhar Armanbek
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingchen Ma
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Manting Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Mike S M Jetten
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, AJ, 6525, the Netherlands
| | - Hanqin Tian
- Center for Earth System Science and Global Sustainability, Schiller Institute for Integrated Science and Society, Boston College, Chestnut Hill, MA, 02467, USA
- Department of Earth and Environmental Sciences, Boston College, Chestnut Hill, MA, 02467, USA
| | - Guibing Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - 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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7
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Xie L, Cheng J, Cao H, Yang F, Jiang M, Li M, Huang Q. Fast Bacterial Succession Associated with the Decomposition of Larix gmelinii Litter in Wudalianchi Volcano. Microorganisms 2024; 12:948. [PMID: 38792778 PMCID: PMC11123687 DOI: 10.3390/microorganisms12050948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/26/2024] Open
Abstract
In order to understand the role of microorganisms in litter decomposition and the nutrient cycle in volcanic forest ecosystems, the dominant forest species Larix gmelinii in the volcanic lava plateau of the Wudalianchi volcano was considered as the research object. We analyzed the response of bacterial community structure and diversity to litter decomposition for 1 year, with an in situ decomposition experimental design using litter bags and Illumina MiSeq high-throughput sequencing. The results showed that after 365 days, the litter quality residual rate of Larix gmelinii was 77.57%, and the litter N, P, C:N, C:P, and N:P showed significant differences during the decomposition period (p < 0.05). The phyla Cyanobacteria and the genus unclassified_o_Chloroplast were the most dominant groups in early decomposition (January and April). The phyla Proteobacteria, Actinobacteriota, and Acidobacteriota and the genera Massilia, Pseudomonas, and Sphingomona were higher in July and October. The microbial communities showed extremely significant differences during the decomposition period (p < 0.05), with PCoa, RDA, and litter QRR, C:P, and N as the main factors driving litter bacteria succession. Microbial functional prediction analysis showed that Chloroplasts were the major functional group in January and April. Achemoheterotrophy and aerobic chemoheterotrophy showed a significant decrease as litter decomposition progressed.
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Affiliation(s)
- Lihong Xie
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China; (L.X.); (J.C.); (H.C.); (F.Y.); (M.J.)
| | - Jiahui Cheng
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China; (L.X.); (J.C.); (H.C.); (F.Y.); (M.J.)
| | - Hongjie Cao
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China; (L.X.); (J.C.); (H.C.); (F.Y.); (M.J.)
| | - Fan Yang
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China; (L.X.); (J.C.); (H.C.); (F.Y.); (M.J.)
| | - Mingyue Jiang
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China; (L.X.); (J.C.); (H.C.); (F.Y.); (M.J.)
| | - Maihe Li
- Forest Dynamics, Swiss Federal Institute for Forest, Snow and Landscape Research, CH-8903 Birmensdorf, Switzerland;
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun 130024, China
- School of Life Science, Hebei University, Baoding 071002, China
| | - Qingyang Huang
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China; (L.X.); (J.C.); (H.C.); (F.Y.); (M.J.)
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Zhang A, Zhu M, Zheng Y, Tian Z, Mu G, Zheng M. The significant contribution of comammox bacteria to nitrification in a constructed wetland revealed by DNA-based stable isotope probing. BIORESOURCE TECHNOLOGY 2024; 399:130637. [PMID: 38548031 DOI: 10.1016/j.biortech.2024.130637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024]
Abstract
The discovery of Comammox bacteria (CMX) has changed our traditional concept towards nitrification, yet its role in constructed wetlands (CWs) remains unclear. This study investigated the contributions of CMX and two canonical ammonia-oxidizing microorganisms, ammonia-oxidizing bacteria (AOB) and archaea to nitrification in four regions (sediment, shoreside, adjacent soil, and water) of a typical CW using DNA-based stable isotope probing. The results revealed that CMX not only widely occurred in sediment and shoreside zones with high abundance (5.08 × 104 and 6.57 × 104 copies g-1 soil, respectively), but also actively participated in ammonia oxidation, achieving ammonia oxidation rates of 1.43 and 2.00 times that of AOB in sediment and shoreside, respectively. Phylogenetic analysis indicated that N. nitrosa was the dominant and active CMX species. These findings uncovered the crucial role of CMX in nitrification of sediment and shoreside, providing a new insight into nitrogen cycle of constructed wetlands.
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Affiliation(s)
- Anqi Zhang
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Mingyang Zhu
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yize Zheng
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Zhichao Tian
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Guangli Mu
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Maosheng Zheng
- Key Laboratory of Resources and Environmental Systems Optimization, Ministry of Education, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
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Xu Z, Gao X, Li G, Nghiem LD, Luo W, Zhang F. Microbial Sources and Sinks of Nitrous Oxide during Organic Waste Composting. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:7367-7379. [PMID: 38644786 DOI: 10.1021/acs.est.3c10341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Composting is widely used for organic waste management and is also a major source of nitrous oxide (N2O) emission. New insight into microbial sources and sinks is essential for process regulation to reduce N2O emission from composting. This study used genome-resolved metagenomics to decipher the genomic structures and physiological behaviors of individual bacteria for N2O sources and sinks during composting. Results showed that several nosZ-lacking denitrifiers in feedstocks drove N2O emission at the beginning of the composting. Such emission became negligible at the thermophilic stage, as high temperatures inhibited all denitrifiers for N2O production except for those containing nirK. The nosZ-lacking denitrifiers were notably enriched to increase N2O production at the cooling stage. Nevertheless, organic biodegradation limited energy availability for chemotaxis and flagellar assembly to restrain nirKS-containing denitrifiers for nitrate reduction toward N2O sources but insignificantly interrupt norBC- and nosZ-containing bacteria (particularly nosZ-containing nondenitrifiers) for N2O sinks by capturing N2O and nitric oxide (NO) for energy production, thereby reducing N2O emission at the mature stage. Furthermore, nosZII-type bacteria included all nosZ-containing nondenitrifiers and dominated N2O sinks. Thus, targeted strategies can be developed to restrict the physiological behaviors of nirKS-containing denitrifiers and expand the taxonomic distribution of nosZ for effective N2O mitigation in composting.
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Affiliation(s)
- Zhicheng Xu
- Key Laboratory of Plant-Soil Interactions of Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xingzu Gao
- Key Laboratory of Plant-Soil Interactions of Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Guoxue Li
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Long D Nghiem
- Centre for Technology in Water and Wastewater, University of Technology Sydney, Ultimo 2007, NSW, Australia
| | - Wenhai Luo
- Key Laboratory of Plant-Soil Interactions of Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, Suzhou 215128, China
| | - Fusuo Zhang
- Key Laboratory of Plant-Soil Interactions of Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
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10
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Chandra Sarker D, Bal Krishna KC, Ginige MP, Sathasivan A. Effective chloramine management without "burn" in biofilm affected nitrifying tanks using a low dose of copper. CHEMOSPHERE 2024; 354:141709. [PMID: 38484992 DOI: 10.1016/j.chemosphere.2024.141709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 01/19/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
This paper highlights the potential to effectively inhibit nitrification and restore chloramine levels using a low copper concentration in a biofilm-affected (surface-to-volume ratio 16 m-1) continuous-flow laboratory-scale chloraminated system. High nitrite and low chloramine containing tanks are always recovered with chlorine "burn" by water utilities. The "burn" is not only costly and operationally complex, but also compromises the water quality, public health, and customer relations. A laboratory system comprising five reactors connected in series was operated. Each reactor simulated conditions typically encountered in full-scale systems. Low amount of copper (0.1-0.2 mg-Cu L-1) was dosed once per day into nitrified reactors. At any given time, only one reactor was dosed with copper. Not only inhibition of nitrification, chloramine decay associated with bulk water, biofilm and sediments also improved. However, the improvement was quicker and more significant when the influent to the reactor contained a high chloramine and a low nitrite concentration. Ammonia oxidising microbes exhibited resilience when exposed to low copper and chloramine concentrations for an extended period. Chloramine decay due to planktonic microbes and chemical reactions in bulk water decreased more rapidly than decay attributed to biofilm and sediments. The concept "biostable residual chlorine" explained how copper and chloramine can inhibit nitrification. Once nitrification was inhibited, the chloramine supplied from upstream effectively continued to suppress downstream nitrification, and this effect lasted more than 50 days even at 22 °C. The findings could be used to develop short-term copper dosing strategies and prevent negative impacts of nitrification and breakpoint chlorination.
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Affiliation(s)
- Dipok Chandra Sarker
- Department of Civil and Construction Engineering, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - K C Bal Krishna
- School of Engineering, Design and Built Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Maneesha P Ginige
- CSIRO Environment, 147 Underwood Avenue, Floreat, WA, 6014, Australia
| | - Arumugam Sathasivan
- Department of Civil and Construction Engineering, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia; School of Engineering, Design and Built Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.
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11
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Chen T, Yang X, Zuo Z, Xu H, Yang X, Zheng X, He S, Wu X, Lin X, Li Y, Zhang Z. Shallow wet irrigation reduces nitrogen leaching loss rate in paddy fields by microbial regulation and lowers rate of downward migration of leaching water: a 15N-tracer study. FRONTIERS IN PLANT SCIENCE 2024; 15:1340336. [PMID: 38590742 PMCID: PMC10999577 DOI: 10.3389/fpls.2024.1340336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/08/2024] [Indexed: 04/10/2024]
Abstract
China consumes 35% of the world's fertilizer every year; however, most of the nitrogen fertilizers, which are essential for rice cultivation, are not used effectively. In this study, factors affecting the nitrogen leaching loss rate were studied in typical soil and rice varieties in South China. The effects of various irrigation measures on rice growth and nitrogen leaching loss were investigated by conducting experiments with eight groups. These groups included traditional irrigation (TI) and shallow wet irrigation (SWI). The TI is a common irrigation method for farmers in South China, maintaining a water layer of 5-8 cm depth. For SWI, after establishing a shallow water layer usually maintaining at 1-2 cm, paddy is irrigated when the field water level falls to a certain depth, then this process is then repeat as necessary. The nitrogen distribution characteristics were determined using 15N isotope tracing. In addition, the effects of nitrification, denitrification, and microbial composition on soil nitrogen transformation at different depths were studied by microbial functional gene quantification and high-throughput sequencing. The results revealed that in the SWI groups, the total nitrogen leaching loss rate reduced by 0.3-0.8% and the nitrogen use efficiency (NUE) increased by 2.18-4.43% compared with those in the TI groups. After the 15N-labeled nitrogen fertilizer was applied, the main pathways of nitrogen were found to be related to plant absorption and nitrogen residues. Furthermore, paddy soil ammonia-oxidizing archaea were more effective than ammonia-oxidizing bacteria for soil ammonia oxidation by SWI groups. The SWI measures increased the relative abundance of Firmicutes in paddy soil, enhancing the ability of rice to fix nitrogen to produce ammonium nitrogen, thus reducing the dependence of rice on chemical fertilizers. Moreover, SWI enhanced the relative abundance of nirS and nosZ genes within surface soil bacteria, thereby promoting denitrification in the surface soil of paddy fields. SWI also promoted ammonia oxidation and denitrification by increasing the abundance and activity of Proteobacteria, Nitrospirae, and Bacteroidetes. Collectively, SWI effectively reduced the nitrogen leaching loss rate and increase NUE.
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Affiliation(s)
- Tianyi Chen
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Xiaoming Yang
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Zheng Zuo
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Huijuan Xu
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Xingjian Yang
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Xiangjian Zheng
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Shuran He
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Xin Wu
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Xueming Lin
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Yongtao Li
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
| | - Zhen Zhang
- College of Natural Resources and Environment, Joint Institute for Environmental Research & Education, South China Agricultural University, Guangzhou, China
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12
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Niu R, Zhuang Y, Lali MN, Zhao L, Xie J, Xiong H, Wang Y, He X, Shi X, Zhang Y. Root Reduction Caused Directly or Indirectly by High Application of Nitrogen Fertilizer Was the Main Cause of the Decline in Biomass and Nitrogen Accumulation in Citrus Seedlings. PLANTS (BASEL, SWITZERLAND) 2024; 13:938. [PMID: 38611468 PMCID: PMC11013181 DOI: 10.3390/plants13070938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/07/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024]
Abstract
Citrus is the largest fruit crop around the world, while high nitrogen (N) application in citrus orchards is widespread in many countries, which results not only in yield, quality and environmental issues but also slows down the establishment of citrus canopies in newly cultivated orchards. Thus, the objective of this study was to investigate the physiological inhibitory mechanism of excessive N application on the growth of citrus seedlings. A pot experiment with the citrus variety Orah (Orah/Citrus junos) at four N fertilization rates (0, 50, 100, and 400 mg N/kg dry soil, denoted as N0, N50, N100, and N400, respectively) was performed to evaluate the changes of root morphology, biomass, N accumulation, enzyme activities, and so on. The results showed that the N400 application significantly reduced the total biomass (from 14.24 to 6.95 g/Plant), N accumulation (from 0.65 to 0.33 g/Plant) and N use efficiency (92.69%) in citrus seedlings when compared to the N100 treatment. The partial least squares pathway model further showed that the decline of biomass and N accumulation by high N application were largely attributed to the reduction of root growth through direct and indirect effects (the goodness of fit under the model was 0.733.) rather than just soil N transformation and activity of root N uptake. These results are useful to optimize N management through a synergistic N absorption and utilization by citrus seedlings.
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Affiliation(s)
- Runzheng Niu
- College of Resources and Environment, Southwest University, Chongqing 400716, China; (R.N.); (Y.Z.); (M.N.L.); (L.Z.); (J.X.); (H.X.); (Y.W.); (X.H.); (X.S.)
| | - Yuan Zhuang
- College of Resources and Environment, Southwest University, Chongqing 400716, China; (R.N.); (Y.Z.); (M.N.L.); (L.Z.); (J.X.); (H.X.); (Y.W.); (X.H.); (X.S.)
| | - Mohammad Naeem Lali
- College of Resources and Environment, Southwest University, Chongqing 400716, China; (R.N.); (Y.Z.); (M.N.L.); (L.Z.); (J.X.); (H.X.); (Y.W.); (X.H.); (X.S.)
- Department of Forestry and Natural Resources, Faculty of Agriculture, Bamyan University, Bamyan 1601, Afghanistan
| | - Li Zhao
- College of Resources and Environment, Southwest University, Chongqing 400716, China; (R.N.); (Y.Z.); (M.N.L.); (L.Z.); (J.X.); (H.X.); (Y.W.); (X.H.); (X.S.)
| | - Jiawei Xie
- College of Resources and Environment, Southwest University, Chongqing 400716, China; (R.N.); (Y.Z.); (M.N.L.); (L.Z.); (J.X.); (H.X.); (Y.W.); (X.H.); (X.S.)
| | - Huaye Xiong
- College of Resources and Environment, Southwest University, Chongqing 400716, China; (R.N.); (Y.Z.); (M.N.L.); (L.Z.); (J.X.); (H.X.); (Y.W.); (X.H.); (X.S.)
| | - Yuheng Wang
- College of Resources and Environment, Southwest University, Chongqing 400716, China; (R.N.); (Y.Z.); (M.N.L.); (L.Z.); (J.X.); (H.X.); (Y.W.); (X.H.); (X.S.)
| | - Xinhua He
- College of Resources and Environment, Southwest University, Chongqing 400716, China; (R.N.); (Y.Z.); (M.N.L.); (L.Z.); (J.X.); (H.X.); (Y.W.); (X.H.); (X.S.)
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing 400716, China; (R.N.); (Y.Z.); (M.N.L.); (L.Z.); (J.X.); (H.X.); (Y.W.); (X.H.); (X.S.)
| | - Yueqiang Zhang
- College of Resources and Environment, Southwest University, Chongqing 400716, China; (R.N.); (Y.Z.); (M.N.L.); (L.Z.); (J.X.); (H.X.); (Y.W.); (X.H.); (X.S.)
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13
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Zhou X, Xiao C, Zhang B, Chen T, Yang X. Effects of microplastics on carbon release and microbial community in mangrove soil systems. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133152. [PMID: 38056259 DOI: 10.1016/j.jhazmat.2023.133152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/08/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023]
Abstract
Mangrove ecosystems are major carbon sink biomes and also a sink of microplastics (MPs). The final enrichment of MPs in sediments may have a significant impact on the microbial community and carbon turnover in the soil. However, the effects of MP pollution on the mangrove soil microbial communities and carbon release remain unknown. Here, we conducted a manipulative incubation experiment by adding MPs to soil at different soil depths to examine the effect of enriched MPs on soil microorganisms and its function (i.e., decomposition of soil carbon). The results showed that the addition of MPs had no significant effect on the microbial diversity and CO2 cumulative emission in the topsoil but significantly increased CO2 release from the subsoil. The promoting effect of polylactide (PLA) on the release of CO2 from the subsoil was stronger than that of polyethylene (PE) and aging PE. In the subsoil, the activity of soil extracellular enzymes related to N acquisition increased with the MP addition, indicating an increase in microbial N deficiency. The subsoil was more sensitive to MPs because of the exacerbated nitrogen limitation. MP addition reduced the microbial diversity of the subsoil and altered soil microbial interactions. The increasing abundance of some microbial taxa, especially bacteria related to the sulfur cycle, indicated more active electron transfer and organic carbon mineralization in the subsoil. Our findings suggest that MP contamination has potential effects on microbial communities, nutrient cycling, and carbon release in mangrove soils that vary depending on soil depth.
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Affiliation(s)
- Xu Zhou
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing 100875, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)
| | - Cunde Xiao
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing 100875, China
| | - Bingwei Zhang
- Zhuhai Branch of State Key Laboratory of Earth Surface Processes and Resource Ecology, Beijing Normal University at Zhuhai, Zhuhai 519087, China
| | - Tao Chen
- MOE Key Laboratory of Theoretical Chemistry of Environment, School of Environment, South China Normal University, University Town, Guangzhou 510006, China
| | - Xiaofan Yang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Faculty of Geographical Science, Beijing Normal University, Beijing 100875, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou).
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14
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Peoples LM, Seixas MH, Evans KA, Bilbrey EM, Ranieri JR, Tappenbeck TH, Dore JE, Baumann A, Church MJ. Out of sight, but not out of season: Nitrifier distributions and population dynamics in a large oligotrophic lake. Environ Microbiol 2024; 26:e16616. [PMID: 38517638 DOI: 10.1111/1462-2920.16616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 03/08/2024] [Indexed: 03/24/2024]
Abstract
Nitrification is an important control on the form and distribution of nitrogen in freshwater ecosystems. However, the seasonality of nitrogen pools and the diversity of organisms catalyzing this process have not been well documented in oligotrophic lakes. Here, we show that nitrogen pools and nitrifying organisms in Flathead Lake are temporally and vertically dynamic, with nitrifiers displaying specific preferences depending on the season. While the ammonia-oxidizing bacteria (AOB) Nitrosomonadaceae and nitrite-oxidizing bacteria (NOB) Nitrotoga dominate at depth in the summer, the ammonia-oxidizing archaea (AOA) Nitrososphaerota and NOB Nitrospirota become abundant in the winter. Given clear seasonality in ammonium, with higher concentrations during the summer, we hypothesize that the succession between these two nitrifying groups may be due to nitrogen affinity, with AOB more competitive when ammonia concentrations are higher and AOA when they are lower. Nitrifiers in Flathead Lake share more than 99% average nucleotide identity with those reported in other North American lakes but are distinct from those in Europe and Asia, indicating a role for geographic isolation as a factor controlling speciation among nitrifiers. Our study shows there are seasonal shifts in nitrogen pools and nitrifying populations, highlighting the dynamic spatial and temporal nature of nitrogen cycling in freshwater ecosystems.
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Affiliation(s)
- Logan M Peoples
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Miranda H Seixas
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Kate A Evans
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Evan M Bilbrey
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, USA
| | - John R Ranieri
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Tyler H Tappenbeck
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - John E Dore
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - Adam Baumann
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Matthew J Church
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
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15
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Hou J, Zhu Y, Liu J, Lin L, Zheng M, Yang L, Wei W, Ni BJ, Chen X. Competitive enrichment of comammox Nitrospira in floccular sludge. WATER RESEARCH 2024; 251:121151. [PMID: 38246075 DOI: 10.1016/j.watres.2024.121151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
The discovery of complete ammonium oxidation (comammox) has subverted the traditional perception of two-step nitrification, which plays a key role in achieving biological nitrogen removal from wastewater. Floccular sludge-based treatment technologies are being applied at the majority of wastewater treatment plants in service where detection of various abundances and activities of comammox bacteria have been reported. However, limited efforts have been made to enrich and subsequently characterize comammox bacteria in floccular sludge. To this end, a lab-scale sequencing batch reactor (SBR) in the step-feeding mode was applied in this work to enrich comammox bacteria through controlling appropriate operational conditions (dissolved oxygen of 0.5 ± 0.1 g-O2/m3, influent ammonium of 40 g-N/m3 and uncontrolled longer sludge retention time). After 215-d operation, comammox bacteria gradually gained competitive advantages over counterparts in the SBR with a stable nitrification efficiency of 92.2 ± 2.2 %: the relative abundance of Nitrospira reached 42.9 ± 1.3 %, which was 13 times higher than that of Nitrosomonas, and the amoA gene level of comammox bacteria increased to 7.7 ± 2.1 × 106 copies/g-biomass, nearly 50 times higher than that of conventional ammonium-oxidizing bacteria. The enrichment of comammox bacteria, especially Clade A Candidatus Nitrospira nitrosa, in the floccular sludge led to (i) apparent affinity constants for ammonium and oxygen of 3.296 ± 0.989 g-N/m3 and 0.110 ± 0.004 g-O2/m3, respectively, and (ii) significantly low N2O and NO production, with emission factors being 0.136 ± 0.026 % and 0.023 ± 0.013 %, respectively.
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Affiliation(s)
- Jiaying Hou
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350116, China
| | - Ying Zhu
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350116, China
| | - Jinzhong Liu
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350116, China
| | - Limin Lin
- School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Linyan Yang
- School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wei Wei
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Xueming Chen
- College of Environment and Safety Engineering, Fuzhou University, Fuzhou 350116, China.
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16
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Jiang C, Wu J, Ye J, Hong Y. High throughput amplicon analysis reveals potential novel ammonia oxidizing prokaryotes in the eutrophic Jiaozhou Bay. MARINE POLLUTION BULLETIN 2024; 200:116046. [PMID: 38246016 DOI: 10.1016/j.marpolbul.2024.116046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/07/2023] [Accepted: 01/11/2024] [Indexed: 01/23/2024]
Abstract
Ammonia-oxidizing prokaryotes (AOPs) are the major contributors of ammonia oxidization with widely distribution. Here we investigated the phylogenetic diversity, community composition, and regulating factors of AOPs in Jiaozhou Bay (JZB) with high-throughput sequencing of amoA gene. Phylogenetic analysis showed most of the OTUs could not be clustered with any known AOPs, indicating there might exist putative novel AOPs. With new developed protocols for AOP community analysis, we confirmed that only 3 OTUs of ammonia-oxidizing archaea (AOA) could be affiliated to known Nitrosopumilaceae and Nitrososphaera, and the other OTUs were identified as novel AOA based on the threshold. All abstained OTUs of ammonia-oxidizing bacteria (AOB) were identified as novel clusters based on the threshold. Further analysis showed the novel AOPs had different distribution characteristics related to environmental factors. The high abundance and widespread distribution of these novel AOPs indicated that they played an important role in ammonia conversion in eutrophic JZB.
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Affiliation(s)
- Cuihong Jiang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
| | - Jiaqi Ye
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China.
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17
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Yang W, Cui H, Liu Q, Wang F, Liao H, Lu P, Qin S. Effect of nitrogen reduction by chemical fertilization with green manure (Vicia sativa L.) on soil microbial community, nitrogen metabolism and and yield of Uncaria rhynchophylla by metagenomics. Arch Microbiol 2024; 206:106. [PMID: 38363349 DOI: 10.1007/s00203-024-03839-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/24/2023] [Accepted: 01/06/2024] [Indexed: 02/17/2024]
Abstract
Uncaria rhynchophylla is an important herbal medicine, and the predominant issues affecting its cultivation include a single method of fertilizer application and inappropriate chemical fertilizer application. To reduce the use of inorganic nitrogen fertilization and increase the yield of Uncaria rhynchophylla, field experiments in 2020-2021 were conducted. The experimental treatments included the following categories: S1, no fertilization; S2, application of chemical NPK fertilizer; and S3-S6, application of chemical fertilizers and green manures, featuring nitrogen fertilizers reductions of 0%, 15%, 30%, and 45%, respectively. The results showed that a moderate application of nitrogen fertilizer when combined with green manure, can help alleviate soil acidification and increase urease activity. Specifically, the treatment with green manure provided in a 14.71-66.67% increase in urease activity compared to S2. Metagenomics sequencing results showed a decrease in diversity in S3, S4, S5, and S6 compared to S2, but the application of chemical fertilizer with green manure promoted an increase in the relative abundance of Acidobacteria and Chloroflexi. In addition, the nitrification pathway displayed a progressive augmentation in tandem with the reduction in nitrogen fertilizer and application of green manure, reaching its zenith at S5. Conversely, other nitrogen metabolism pathways showed a decline in correlation with diminishing nitrogen fertilizer dosages. The rest of the treatments showed an increase in yield in comparison to S1, S5 showing significant differences (p < 0.05). In summary, although S2 demonstrate the ability to enhance soil microbial diversity, it is important to consider the long-term ecological impacts, and S5 may be a better choice.
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Affiliation(s)
- Wansheng Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - HongHao Cui
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
- Institute of Soil Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Qian Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Fang Wang
- Guizhou Industry Polytechnic College, Guiyang, 550008, China
| | - Heng Liao
- Institute of Soil Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Ping Lu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
| | - Song Qin
- Institute of Soil Fertilizer, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
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18
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Xia Z, Jiang Z, Zhang T, Liu B, Jia M, Liu GH, Qi L, Wang H. Effects of sludge retention time (SRT) on nitrogen and phosphorus removal and the microbial community in an ultrashort-SRT activated sludge system. ENVIRONMENTAL RESEARCH 2024; 240:117510. [PMID: 37890826 DOI: 10.1016/j.envres.2023.117510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/14/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Abstract
The ultrashort-sludge retention time activate sludge (USAS) process is considered promising for the recovery of energy and resource from wastewater. In this study, we developed five USAS systems (with sludge retention time (SRT) of 0.5, 1, 2, 3, and 4 d), and investigated the nitrogen and phosphorus removal, as well as the microbial community, in the USAS systems. The results revealed that the activated sludge in the USAS system with a shorter SRT can capture more organic matter from wastewater, with organic matter mineralization, capture, and loss rates of 12.9-45.9, 42.4-62.3, and 18.2-24.8%, respectively. In addition, ammonia oxidization only occurred in the USAS systems with SRTs of 3 and 4 d, and all the USAS systems with different SRTs exhibited phosphorus-removal ability. The microbial community analysis results revealed that the relative abundance of nitrifying and denitrifying bacteria (such as Thauera) increased with an increase in the SRT.
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Affiliation(s)
- Zhiheng Xia
- Low-carbon Water Environment Technology Research Center, School of Environment & Natural Resources, Renmin University of China, Beijing, 100872, China.
| | - Zhao Jiang
- Low-carbon Water Environment Technology Research Center, School of Environment & Natural Resources, Renmin University of China, Beijing, 100872, China.
| | - Tongtong Zhang
- Low-carbon Water Environment Technology Research Center, School of Environment & Natural Resources, Renmin University of China, Beijing, 100872, China
| | - Binhua Liu
- Low-carbon Water Environment Technology Research Center, School of Environment & Natural Resources, Renmin University of China, Beijing, 100872, China
| | - Mengfei Jia
- Low-carbon Water Environment Technology Research Center, School of Environment & Natural Resources, Renmin University of China, Beijing, 100872, China
| | - Guo-Hua Liu
- Low-carbon Water Environment Technology Research Center, School of Environment & Natural Resources, Renmin University of China, Beijing, 100872, China
| | - Lu Qi
- Low-carbon Water Environment Technology Research Center, School of Environment & Natural Resources, Renmin University of China, Beijing, 100872, China
| | - Hongchen Wang
- Low-carbon Water Environment Technology Research Center, School of Environment & Natural Resources, Renmin University of China, Beijing, 100872, China.
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Akutsu Y, Fujiwara T, Suzuki R, Nishigaya Y, Yamazaki T. Juglone, a plant-derived 1,4-naphthoquinone, binds to hydroxylamine oxidoreductase and inhibits the electron transfer to cytochrome c554. Appl Environ Microbiol 2023; 89:e0129123. [PMID: 38009977 PMCID: PMC10734522 DOI: 10.1128/aem.01291-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/20/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Nitrification, the microbial conversion of ammonia to nitrate via nitrite, plays a pivotal role in the global nitrogen cycle. However, the excessive use of ammonium-based fertilizers in agriculture has disrupted this cycle, leading to groundwater pollution and greenhouse gas emissions. In this study, we have demonstrated the inhibitory effects of plant-derived juglone and related 1,4-naphthoquinones on the nitrification process in Nitrosomonas europaea. Notably, the inhibition mechanism is elucidated in which 1,4-naphthoquinones interact with hydroxylamine oxidoreductase, disrupting the electron transfer to cytochrome c554, a physiological electron acceptor. These findings support the notion that phytochemicals can impede nitrification by interfering with the essential electron transfer process in ammonia oxidation. The findings presented in this article offer valuable insights for the development of strategies aimed at the management of nitrification, reduction of fertilizer utilization, and mitigation of greenhouse gas emissions.
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Affiliation(s)
- Yukie Akutsu
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Takaaki Fujiwara
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Rintaro Suzuki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | | | - Toshimasa Yamazaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
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20
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Wang Y, Huang Y, Zeng Q, Liu D, An S. Biogeographic distribution of autotrophic bacteria was more affected by precipitation than by soil properties in an arid area. Front Microbiol 2023; 14:1303469. [PMID: 38173682 PMCID: PMC10761425 DOI: 10.3389/fmicb.2023.1303469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction Autotrophic bacteria play an important role in carbon dioxide fixation and are widespread in terrestrial ecosystems. However, the biogeographic patterns of autotrophic bacteria and the driving factors still remain poorly understood. Methods Herein, we conducted a 391-km north to south transect (mean annual precipitation <600 mm) survey in the Loess Plateau of China, to investigate the biogeographic distributions of autotrophic bacteria (RubisCO cbbL and cbbM genes) and the environmental drivers across different latitude sites with clear vegetational and climatic gradients. Results and discussion The soils in northern region with lower precipitation are dominated by grassland/forest, which is typically separated from the soils in southern region with higher precipitation. The community structure of autotrophic bacterial cbbL and cbbM genes generally differed between the soils in the southern and northern Loess Plateau, suggesting that precipitation and its related land use practices/ecosystem types, rather than local soil properties, are more important in shaping the soil autotrophic microorganisms. The cbbL-containing generalist OTUs were almost equally abundant across the northern and southern Loess Plateau, while the cbbM-containing bacterial taxa were more prevalent in the low precipitation northern region. Such differences indicate differentiate distribution patterns of cbbM- and cbbL-containing bacteria across the north to south transect. Our results suggest that the community composition and the differentiate distributions of soil cbbL- and cbbM-containing bacterial communities depend on precipitation and the related ecosystem types in the north to south transect in the Loess Plateau of China.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A & F University, Yangling, Shaanxi Province, China
| | - Yimei Huang
- College of Resources and Environment, Northwest A & F University, Yangling, Shaanxi Province, China
| | - Quanchao Zeng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Dong Liu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A & F University, Yangling, Shaanxi Province, China
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21
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Kolovou M, Panagiotou D, Süße L, Loiseleur O, Williams S, Karpouzas DG, Papadopoulou ES. Assessing the activity of different plant-derived molecules and potential biological nitrification inhibitors on a range of soil ammonia- and nitrite-oxidizing strains. Appl Environ Microbiol 2023; 89:e0138023. [PMID: 37916825 PMCID: PMC10686072 DOI: 10.1128/aem.01380-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/26/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Synthetic nitrification inhibitors are routinely used with nitrogen fertilizers to reduce nitrogen losses from agroecosystems, despite having drawbacks like poor efficiency, cost, and entry into the food chain. Plant-derived BNIs constitute a more environmentally conducive alternative. Knowledge on the activity of BNIs to soil nitrifiers is largely based on bioassays with a single Nitrosomonas europaea strain which does not constitute a dominant member of the community of ammonia-oxidizing microorganisms (AOM) in soil. We determined the activity of several plant-derived molecules reported as having activity, including the recently discovered maize-isolated BNI, zeanone, and its natural analog, 2-methoxy-1,4-naphthoquinone, on a range of ecologically relevant AOM and one nitrite-oxidizing bacterial culture, expanding our knowledge on the intrinsic inhibition potential of BNIs toward AOM and highlighting the necessity for a deeper understanding of the effect of BNIs on the overall soil microbiome integrity before their further use in agricultural settings.
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Affiliation(s)
- Maria Kolovou
- Department of Environmental Sciences, Laboratory of Environmental Microbiology, University of Thessaly, Larissa, Greece
| | - Dimitra Panagiotou
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
| | - Lars Süße
- Syngenta Crop Protection AG, Basel, Switzerland
| | | | | | - Dimitrios G. Karpouzas
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Larissa, Greece
| | - Evangelia S. Papadopoulou
- Department of Environmental Sciences, Laboratory of Environmental Microbiology, University of Thessaly, Larissa, Greece
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22
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Yang Y, Liu H, Zhang Y, Fang X, Zhong X, Lv J. Contribution of ammonia-oxidizing archaea and bacteria to nitrogen transformation in a soil fertilized with urea and organic amendments. Sci Rep 2023; 13:20722. [PMID: 38007550 PMCID: PMC10676402 DOI: 10.1038/s41598-023-44147-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/04/2023] [Indexed: 11/27/2023] Open
Abstract
The contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) is crucial for nitrogen transformation. The effects of four organic amendments (OAs) plus urea on soil nitrogen transformation and the contribution of the ammonia-oxidizing microbial community were investigated using an incubation experiment. The OAs plus urea treatments included pig manure plus urea (PM + U), wheat straw plus urea (WS + U), compost plus urea (CP + U) and improved-compost plus urea (IC + U), while no OAs and urea amended control was noted as CK. The abundance and composition of AOA and AOB were determined using high through-put sequencing. Compared with CK, the OA plus urea treatments significantly enhanced the amount of total mineralized nitrogen released during the incubation process. After incubation, the highest mineralized nitrogen and net nitrogen mineralization was under the PM + U treatment and the lowest was in the WS + U treatment. In conclusion, among all OA plus urea treatments, the microbial biomass nitrogen content was the highest in WS + U treatment and dissolved organic nitrogen content was the highest with the PM + U treatment. Additionally, the abundance of AOB was inhibited in comparison to that of AOA; however, AOB contributed more to nitrification than AOA. Soil NO3--N and dissolved organic nitrogen were the principal components influencing the distribution of AOA and AOB. The result illustrated that the OAs plus urea, especially PM plus urea promoted mineralization to produce more dissolved organic nitrogen and NH4+-N, thus accelerating the growth of AOB to strengthen nitrification in soil.
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Affiliation(s)
- Yajun Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Hexiang Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Yang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Xianhui Fang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Xianbao Zhong
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China
| | - Jialong Lv
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
- Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China, Ministry of Agriculture, Yangling, China.
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23
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Zhang W, Tao X, Hu Z, Kang E, Yan Z, Zhang X, Wang J. The driving effects of nitrogen deposition on nitrous oxide and associated gene abundances at two water table levels in an alpine peatland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 898:165525. [PMID: 37451456 DOI: 10.1016/j.scitotenv.2023.165525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Alpine peatlands are recognized as a weak or negligible source of nitrous oxide (N2O). Anthropogenic activities and climate change resulted in the altered water table (WT) levels and increased nitrogen (N) deposition, which could potentially transition this habitat into a N2O emission hotspot. However, the underlying mechanism related with the effects is still uncertain. Hence, we conducted a mesocosm experiment to address the response of growing-season N2O emissions and the gene abundances of nitrification (bacterial amoA) and denitrification (narG, nirS, norB and nosZ) to the increased N deposition (20 kg N ha-1 yr-1) at two WT levels (WT-30, 30 cm below soil surface; WT10, 10 cm above soil surface) in the Zoige alpine peatland, Qinghai-Tibetan Plateau. The results showed that the WT did not affect N2O emissions, and this was attributed with the limitation of soil NO3-. The higher WT level increased denitrification (narG and nirS gene abundance) resulting in the depletion of soil NO3-, but the consequent NO3- deficiency further limited denitrification, while the WT did not affect nitrification (bacterial amoA gene abundance). Meanwhile, the N deposition increased N2O emissions, regardless of WT levels. This was associated with the N-deposition induced increase in denitrification-related gene abundances of narG, nirS, norB and nosZ at WT-30 and narG at WT10. Additionally, the N2O emission factor assigned to N deposition was 1.3 % at WT-30 and 0.9 % at WT10, respectively. Our study provided comprehensive understanding of the mechanisms referring N2O emissions in response to the interactions between climate change and human disturbance from this high-altitude peatland.
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Affiliation(s)
- Wantong Zhang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Services and Restoration, Beijing 100091, China; Insititute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610218, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuping Tao
- Insititute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu 610218, China
| | - Zhengyi Hu
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Enze Kang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Services and Restoration, Beijing 100091, China
| | - Zhongqing Yan
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Services and Restoration, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba 624500, China
| | - Xiaodong Zhang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Services and Restoration, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba 624500, China
| | - Jinzhi Wang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing Key Laboratory of Wetland Services and Restoration, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba 624500, China.
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24
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Zou D, Chen J, Zhang C, Kao SJ, Liu H, Li M. Diversity and salinity adaptations of ammonia oxidizing archaea in three estuaries of China. Appl Microbiol Biotechnol 2023; 107:6897-6909. [PMID: 37702790 DOI: 10.1007/s00253-023-12761-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/22/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
Ammonia-oxidizing archaea (AOA) are ubiquitously found in diverse habitats and play pivotal roles in the nitrogen and carbon cycle, especially in estuarine and coastal environments. Despite the fact that the diversity and distribution of AOA are thought to be tightly linked to habitats, little is known about the relationship that underpins their genomic traits, adaptive potentials, and ecological niches. Here, we have characterized and compared the AOA community in three estuaries of China using metagenomics. AOA were the dominant ammonia oxidizers in the three estuaries. Through phylogenetic analyses, five major AOA groups were identified, including the Nitrosomarinus-like, Nitrosopumilus-like, Aestuariumsis-like, Nitrosarchaeum-like, and Nitrosopelagicus-like groups. Statistical analyses showed that the aquatic and sedimentary AOA communities were mainly influenced by spatial factors (latitude and water depth) and environmental factors (salinity, pH, and dissolved oxygen) in estuaries, respectively. Compared to AOA dwelling in terrestrial and marine habitats, estuarine AOA encoded more genes involved in glucose and amino acid metabolism, transport systems, osmotic control, and cell motility. The low proteome isoelectric points (pI), high content of acidic amino acids, and the presence of potassium ion and mechanosensitive channels suggest a "salt-in" strategy for estuarine AOA to counteract high osmolarity in their surroundings. Our findings have indicated potential adaptation strategies and highlighted their importance in the estuarine nitrogen and carbon cycles. KEY POINTS: • Spatial and environmental factors influence water and sediment AOA respectively. • Estuarine AOA share low proteome isoelectric value and high acid amino acids content. • AOA adaptation to estuaries is likely resulted from their unique genomic features.
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Affiliation(s)
- Dayu Zou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Jianfang Chen
- Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, 518000, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510000, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361000, China
| | - Hongbin Liu
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China.
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25
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Shi X, Tan W, Tang S, Ling Q, Tang C, Qin P, Luo S, Zhao Y, Yu F, Li Y. Metagenomics reveals taxon-specific responses of soil nitrogen cycling under different fertilization regimes in heavy metal contaminated soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118766. [PMID: 37579601 DOI: 10.1016/j.jenvman.2023.118766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/24/2023] [Accepted: 08/09/2023] [Indexed: 08/16/2023]
Abstract
Soil deficiency, cyclic erosion, and heavy metal pollution have led to fertility loss and ecological function decline in mining areas. Fertilization is an important way to rapidly replenish soil nutrients, which have a major influence on the soil nitrogen cycling process, but different fertilization regimes have different impacts on soil properties and microbial functional potentials. Here, metagenomic sequencing was used to investigate the different responses of key functional genes of microbial nitrogen cycling to fertilization regimes and explore the potential effects of soil physicochemical properties on the key functional genes. The results indicated that AC-HH (ammonium chloride-high frequency and concentration) treatment significantly increased the gene abundance of norC (13.40-fold), nirK (5.46-fold), and napA (5.37-fold). U-HH (urea-high frequency and concentration) treatment significantly increased the gene abundance of hao (6.24-fold), pmoA-amoA (4.32-fold) norC (7.00-fold), nosZ (3.69-fold), and nirK (6.88-fold). Functional genes were distributed differently among the 10 dominant phyla. The nifH and nifK genes were distributed only in Proteobacteria. The hao gene was distributed in Gemmatimonadetes, Nitrospirae and Proteobacteria. Fertilization regimes caused changes in functional redundancy in soil, and nirK and nirB, which are involved in denitrification, were present in different genera. Fertilization regimes with high frequency and high concentration were more likely to increase the gene abundance at the genus level. In summary, this study provides insights into the taxon-specific response of soil nitrogen cycling under different fertilization regimes, where changes in fertilization regimes affect microbial nitrogen cycling by altering soil physicochemical properties in a complex dynamic environment.
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Affiliation(s)
- Xinwei Shi
- 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
| | - Weilan Tan
- 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
| | - Shuting Tang
- 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
| | - Qiujie Ling
- 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
| | - Chijian Tang
- 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
| | - Peiqing Qin
- 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
| | - Shiyu Luo
- 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
| | - Yinjun Zhao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, 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.
| | - 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.
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26
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Kikuchi S, Fujitani H, Ishii K, Isshiki R, Sekiguchi Y, Tsuneda S. Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:404-416. [PMID: 37078228 PMCID: PMC10472526 DOI: 10.1111/1758-2229.13158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
Members of the genus Nitrosomonas are major ammonia oxidizers that catalyse the first step of nitrification in various ecosystems. To date, six subgenus-level clades have been identified. We have previously isolated novel ammonia oxidizers from an additional clade (unclassified cluster 1) of the genus Nitrosomonas. In this study, we report unique physiological and genomic properties of the strain PY1, compared with representative ammonia-oxidising bacteria (AOB). The apparent half-saturation constant for total ammonia nitrogen and maximum velocity of strain PY1 were 57.9 ± 4.8 μM NH3 + NH4 + and 18.5 ± 1.8 μmol N (mg protein)-1 h-1 , respectively. Phylogenetic analysis based on genomic information revealed that strain PY1 belongs to a novel clade of the Nitrosomonas genus. Although PY1 contained genes to withstand oxidative stress, cell growth of PY1 required catalase to scavenge hydrogen peroxide. Environmental distribution analysis revealed that the novel clade containing PY1-like sequences is predominant in oligotrophic freshwater. Taken together, the strain PY1 had a longer generation time, higher yield and required reactive oxygen species (ROS) scavengers to oxidize ammonia, compared with known AOB. These findings expand our knowledge of the ecophysiology and genomic diversity of ammonia-oxidising Nitrosomonas.
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Affiliation(s)
- Shuta Kikuchi
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Hirotsugu Fujitani
- Department of Biological SciencesChuo UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
| | - Kento Ishii
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
| | - Rino Isshiki
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Yuji Sekiguchi
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)IbarakiJapan
| | - Satoshi Tsuneda
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
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27
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Li J, Zhao C, Li C, Xue B, Wang S, Zhang X, Yang X, Shen Z, Bo L, He X, Qiu Z, Wang J. Multidrug-resistant plasmid RP4 increases NO and N 2O yields via the electron transport system in Nitrosomonas europaea ammonia oxidation. WATER RESEARCH 2023; 242:120266. [PMID: 37421866 DOI: 10.1016/j.watres.2023.120266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/19/2023] [Accepted: 06/23/2023] [Indexed: 07/10/2023]
Abstract
Antibiotic resistance genes (ARGs) have recently become an important public health problem and therefore several studies have characterized ARG composition and distribution. However, few studies have assessed their impact on important functional microorganisms in the environment. Therefore, our study sought to investigate the mechanisms through which multidrug-resistant plasmid RP4 affected the ammonia oxidation capacity of ammonia-oxidizing bacteria, which play a key role in the nitrogen cycle. The ammonia oxidation capacity of N. europaea ATCC25978 (RP4) was significantly inhibited, and NO and N2O were produced instead of nitrite. Our findings demonstrated that the decrease in electrons from NH2OH decreased the ammonia monooxygenase (AMO) activity, leading to a decrease in ammonia consumption. In the ammonia oxidation process, N. europaea ATCC25978 (RP4) exhibited ATP and NADH accumulation. The corresponding mechanism was the overactivation of Complex Ⅰ, ATPase, and the TCA cycle by the RP4 plasmid. The genes encoding TCA cycle enzymes related to energy generation, including gltA, icd, sucD, and NE0773, were upregulated in N. europaea ATCC25978 (RP4). These results demonstrate the ecological risks of ARGs, including the inhibition of the ammonia oxidation process and an increased production of greenhouse gases such as NO and N2O.
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Affiliation(s)
- Jia Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Chen Zhao
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Chenyu Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Bin Xue
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Shang Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xi Zhang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xiaobo Yang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhiqiang Shen
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Lin Bo
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China; Tiangong University, Tianjin, China
| | - Xinxin He
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhigang Qiu
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China.
| | - Jingfeng Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China.
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28
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Gulay A, Fournier G, Smets BF, Girguis PR. Proterozoic Acquisition of Archaeal Genes for Extracellular Electron Transfer: A Metabolic Adaptation of Aerobic Ammonia-Oxidizing Bacteria to Oxygen Limitation. Mol Biol Evol 2023; 40:msad161. [PMID: 37440531 PMCID: PMC10415592 DOI: 10.1093/molbev/msad161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/09/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023] Open
Abstract
Many aerobic microbes can utilize alternative electron acceptors under oxygen-limited conditions. In some cases, this is mediated by extracellular electron transfer (or EET), wherein electrons are transferred to extracellular oxidants such as iron oxide and manganese oxide minerals. Here, we show that an ammonia-oxidizer previously known to be strictly aerobic, Nitrosomonas communis, may have been able to utilize a poised electrode to maintain metabolic activity in anoxic conditions. The presence and activity of multiheme cytochromes in N. communis further suggest a capacity for EET. Molecular clock analysis shows that the ancestors of β-proteobacterial ammonia oxidizers appeared after Earth's atmospheric oxygenation when the oxygen levels were >10-4pO2 (present atmospheric level [PAL]), consistent with aerobic origins. Equally important, phylogenetic reconciliations of gene and species trees show that the multiheme c-type EET proteins in Nitrosomonas and Nitrosospira lineages were likely acquired by gene transfer from γ-proteobacteria when the oxygen levels were between 0.1 and 1 pO2 (PAL). These results suggest that β-proteobacterial EET evolved during the Proterozoic when oxygen limitation was widespread, but oxidized minerals were abundant.
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Affiliation(s)
- Arda Gulay
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Greg Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Barth F Smets
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby, Denmark
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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29
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Tan Q, Zhang G, Ding A, Bian Z, Wang X, Xing Y, Zheng L. Anthropogenic land-use activities within watersheds reduce comammox activity and diversity in rivers. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 338:117841. [PMID: 37003226 DOI: 10.1016/j.jenvman.2023.117841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/12/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
Nitrogen cycling plays a key role in maintaining river ecological functions which are threatened by anthropogenic activities. The newly discovered complete ammonia oxidation, comammox, provides novel insights into the ecological effects of nitrogen on that it oxidizes ammonia directly to nitrate without releasing nitrite as canonical ammonia oxidization conducted by AOA or AOB which is believed to play an important role in greenhouse gas generation. Theoretically, contribution of commamox, AOA and AOB to ammonia oxidization in rivers might be impacted by anthropogenic land-use activities through alterations in flow regime and nutrient input. While how land use pattern affects comammox and other canonical ammonia oxidizers remains elusive. In this study, we examined the ecological effects of land use practices on the activity and contribution of three distinctive groups of ammonia oxidizers (AOA, AOB, comammox) as well as the composition of comammox bacterial communities from 15 subbasins covering an area of 6166 km2 in North China. The results showed that comammox dominated nitrification (55.71%-81.21%) in less disturbed basins characterized by extensive forests and grassland, while AOB became the major player (53.83%-76.43%) in highly developed basins with drastic urban and agricultural development. In addition, increasing anthropogenic land use activities within the watershed lowered the alpha diversity of comammox communities and simplified the comammox network. Additionally, the alterations of NH4+-N, pH and C/N induced by land use change were found to be crucial drivers in determining the distribution and activity of AOB and comammox. Together, our findings cast a new light on aquatic-terrestrial linkages from the view of microorganism-mediated nitrogen cycling and can further be applied to target watershed land use management.
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Affiliation(s)
- Qiuyang Tan
- College of Water Science, Beijing Normal University, Beijing, 100875, China
| | - Guoyu Zhang
- Department of Environmental Engineering, School of Marine Science and Technology, Harbin Institute of Technology, Weihai, 264209, China
| | - Aizhong Ding
- College of Water Science, Beijing Normal University, Beijing, 100875, China
| | - Zhaoyong Bian
- College of Water Science, Beijing Normal University, Beijing, 100875, China
| | - Xue Wang
- College of Water Science, Beijing Normal University, Beijing, 100875, China
| | - Yuzi Xing
- College of Water Science, Beijing Normal University, Beijing, 100875, China
| | - Lei Zheng
- College of Water Science, Beijing Normal University, Beijing, 100875, China.
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Huang S, Guo T, Feng Z, Li B, Cai Y, Ouyang D, Gustave W, Ying C, Zhang H. Polyethylene and polyvinyl chloride microplastics promote soil nitrification and alter the composition of key nitrogen functional bacterial groups. JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131391. [PMID: 37043864 DOI: 10.1016/j.jhazmat.2023.131391] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/29/2023] [Accepted: 04/07/2023] [Indexed: 05/03/2023]
Abstract
Microplastics (MPs) contamination in soils seriously threatens agroecosystems globally. However, very few studies have been done on the effects of MPs on the soil nitrogen cycle and related functional microorganisms. To assess MP's impact on the soil nitrogen cycle and related functional bacteria, we carried out a one-month soil incubation experiment using typical acidic soil. The soil was amended with alfalfa meal and was spiked with 1% and 5% (mass percentage) of low-density polyethylene (LDPE) and polyvinyl chloride (PVC) MPs. Our results showed that both LDPE and PVC addition significantly increased soil nitrification rate and nitrate reductase activity, which could further promote soil denitrification. The relative abundance of diazotrophs, ammonium oxidizing, and denitrifying bacterial groups were significantly altered with MPs addition. Moreover, the MPs treatments greatly enhanced denitrifying bacteria richness. Redundancy analysis showed that nitrate reductase activity was the most significant factor affecting the soil functional bacterial community. Correlation analysis shows that Nitrosospira genus might be for the improvement of soil nitrification rate. Our results implied that MPs exposure could significantly affect the soil nitrogen cycling in farmland ecosystems by influencing essential nitrogen functional microorganisms and related enzymatic activities.
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Affiliation(s)
- Shunyin Huang
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Ting Guo
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Zhen Feng
- School of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Baochen Li
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Yimin Cai
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Da Ouyang
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Williamson Gustave
- School of Chemistry, Environmental & Life Sciences, University of The Bahamas, Nassau, New Providence, Bahamas
| | - Chengfei Ying
- School of Humanities and Law, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Haibo Zhang
- Zhejiang Provincial Key laboratory of Soil Contamination Bioremediation, School of Environment and Resources, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China.
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Chen L, Shi Y, Wang S, Sun M, Wang M, Ren X, Gao Z, Zhou Y, Zhang J, Zhuang W, Su X, Fu Y, Wu M. Temperature and phosphorus: the main environmental factors affecting the seasonal variation of soil bacterial diversity in Nansi Lake Wetland. Front Microbiol 2023; 14:1169444. [PMID: 37455734 PMCID: PMC10348425 DOI: 10.3389/fmicb.2023.1169444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/01/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction The soil bacteria promote the circulation conversion of lake nutrients and play an important role in maintaining the balance of the lake ecosystem. Few studies have investigated the association of seasonal variation in bacteria and environmental factors in inland freshwater lake wetlands. Nansi Lake is a large shallow freshwater lake in northern China. It is an important hub of the eastern route of the South-to-North Water Diversion Project. Methods In this study, bacterial 16S rRNA genes were used to analyze the variation of soil bacterial community diversity in Nansi Lake Wetland and its influencing factors in different seasons. Results It is showed that the phylum, family, and genus with the largest relative abundance in the soil of Nansi Lake Wetland are Proteobacteria, Nitrosomonadaceae, and MND1, respectively. There were significant seasonal differences in soil bacterial diversity in Nansi Lake Wetland, which was significantly higher in summer than in winter. Seasonal variation in environmental factors was significantly correlated with the variation in bacterial communities. Temperature and the content of available phosphorus may be the key factors influencing seasonal variation in bacterial diversity. Discussion The results of this study further enhance our understanding of the relationship between bacterial community diversity and environmental factors in the lake wetland ecosystem, which can provide scientific data for the conservation of Nansi Lake Wetland.
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Affiliation(s)
- Lei Chen
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Yuying Shi
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Shen Wang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Mengyao Sun
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Meng Wang
- Lunan Geo-Engineering Exploration Institute of Shandong Province, Yanzhou, Shandong, China
| | - Xiaoyue Ren
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Zenghao Gao
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Yiping Zhou
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Jie Zhang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Weijing Zhuang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Xinyue Su
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Yongchao Fu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Mengmeng Wu
- Shandong Freshwater Fisheries Research Institute, Jinan, Shandong, China
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Zheng S, Li J, Ye C, Xian X, Feng M, Yu X. Microbiological risks increased by ammonia-oxidizing bacteria under global warming: The neglected issue in chloraminated drinking water distribution system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 874:162353. [PMID: 36822432 DOI: 10.1016/j.scitotenv.2023.162353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
A rising outbreak of waterborne diseases caused by global warming requires higher microbial stability in the drinking water distribution system (DWDS). Chloramine disinfection is gaining popularity in this context due to its good persistent stability and fewer disinfection byproducts. However, the microbiological risks may be significantly magnified by ammonia-oxidizing bacteria (AOB) in distribution systems during global warming, which is rarely noticed. Hence, this work mainly focuses on AOB to explore its impact on water quality biosafety in the context of global warming. Research indicates that global warming-induced high temperatures can directly or indirectly promote the growth of AOB, thus leading to nitrification. Further, its metabolites or cellular residues can be used as substrates for the growth of heterotrophic bacteria (e.g., waterborne pathogens). Thus, biofilm may be more persistent in the pipelines due to the presence of AOB. Breakpoint chlorination is usually applied to control such situations. However, switching between this strategy and chloramine disinfection would result in even more severe nitrification and other adverse effects. Based on the elevated microbiological risks in DWDS, the following aspects should be paid attention to in future research: (1) to understand the response of nitrifying bacteria to high temperatures and the possible association between AOB and pathogenic growth, (2) to reveal the mechanisms of AOB-mediated biofilm formation under high-temperature stress, and (3) to develop new technologies to prevent and control the occurrence of nitrification in drinking water distribution system.
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Affiliation(s)
- Shikan Zheng
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Jianguo Li
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Chengsong Ye
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Xuanxuan Xian
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Mingbao Feng
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Xin Yu
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
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Meng S, Liang X, Peng T, Liu Y, Wang H, Huang T, Gu JD, Hu Z. Ecological distribution and function of comammox Nitrospira in the environment. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12557-6. [PMID: 37195422 DOI: 10.1007/s00253-023-12557-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/18/2023]
Abstract
Complete ammonia oxidizers (Comammox) are of great significance for studying nitrification and expanding the understanding of the nitrogen cycle. Moreover, Comammox bacteria are also crucial in natural and engineered environments due to their role in wastewater treatment and maintaining the flux of greenhouse gases to the atmosphere. However, only few studies are there regarding the Comammox bacteria and their role in ammonia and nitrite oxidation in the environment. This review mainly focuses on summarizing the genomes of Nitrospira in the NCBI database. Ecological distribution of Nitrospira was also reviewed and the influence of environmental parameters on genus Nitrospira in different environments has been summarized. Furthermore, the role of Nitrospira in carbon cycle, nitrogen cycle, and sulfur cycle were discussed, especially the comammox Nitrospira. In addition, the overviews of current research and development regarding comammox Nitrospira, were summarized along with the scope of future research. KEY POINTS: • Most of Comammox Nitrospira are widely distributed in both aquatic and terrestrial ecosystems, but it has been studied less frequently in the extreme environments. • Comammox Nitrospira can be involved in different nitrogen transformation process, but rarely involved in nitrogen fixation. • The stable isotope and transcriptome techniques are important methods to study the metabolic function of comammox Nitrospira.
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Affiliation(s)
- Shanshan Meng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Xueji Liang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Tao Peng
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Yongjin Liu
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Hui Wang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. China
| | - Tongwang Huang
- Department of Biology, Shantou University, Shantou, Guangdong, 515063, P.R. 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, P.R. China.
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Li D, Ren Z, Zhou Y, Jiang L, Zheng M, Liu G. Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations. Appl Environ Microbiol 2023; 89:e0004723. [PMID: 36912626 PMCID: PMC10056971 DOI: 10.1128/aem.00047-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/31/2023] [Indexed: 03/14/2023] Open
Abstract
Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.
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Affiliation(s)
- Deyong Li
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Zhichang Ren
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yangqi Zhou
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Lugao Jiang
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Guoqiang Liu
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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Zhao W, Bi X, Bai M, Wang Y. Research advances of ammonia oxidation microorganisms in wastewater: metabolic characteristics, microbial community, influencing factors and process applications. Bioprocess Biosyst Eng 2023; 46:621-633. [PMID: 36988685 DOI: 10.1007/s00449-023-02866-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
Ammonia oxidation carried out by ammonia-oxidizing microorganisms (AOMs) is a central step in the global nitrogen cycle. Aerobic AOMs comprise conventional ammonia-oxidizing bacteria (AOB), novel ammonia-oxidizing archaea (AOA), which could exist in complex and extreme conditions, and complete ammonia oxidizers (comammox), which directly oxidize ammonia to nitrate within a single cell. Anaerobic AOMs mainly comprise anaerobic ammonia-oxidizing bacteria (AnAOB), which can transform NH4+-N and NO2--N into N2 under anaerobic conditions. In this review, the unique metabolic characteristics, microbial community of AOMs and the influencing factors are discussed. Process applications of nitrification/denitrification, nitritation/denitrification, nitritation/anammox and partial denitrification/anammox in wastewater treatment systems are emphasized. The future development of nitrogen removal processes using AOMs is expected, enrichment of comammox facilitates the complete nitrification performance, inhibiting the activity of comammox and NOB could achieve stable nitritation, and additionally, AnAOB conducting the anammox process in municipal wastewater is a promising development direction.
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Affiliation(s)
- Weihua Zhao
- State and Local Joint Engineering Research Center of Municipal Wastewater Treatment and Resource Recycling, Qingdao University of Technology, Qingdao, 266033, People's Republic of China.
- School of Marine Science and Technology, Harbin Institute of Technology, Weihai, 264209, People's Republic of China.
- Qingdao University of Technology, Huangdao District, Qingdao, 266525, People's Republic of China.
| | - Xuejun Bi
- State and Local Joint Engineering Research Center of Municipal Wastewater Treatment and Resource Recycling, Qingdao University of Technology, Qingdao, 266033, People's Republic of China
| | - Meng Bai
- State and Local Joint Engineering Research Center of Municipal Wastewater Treatment and Resource Recycling, Qingdao University of Technology, Qingdao, 266033, People's Republic of China
| | - Yanyan Wang
- State and Local Joint Engineering Research Center of Municipal Wastewater Treatment and Resource Recycling, Qingdao University of Technology, Qingdao, 266033, People's Republic of China
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Yue X, Liu H, Wei H, Chang L, Gong Z, Zheng L, Yin F. Reactive and microbial inhibitory mechanisms depicting the panoramic view of pH stress effect on common biological nitrification. WATER RESEARCH 2023; 231:119660. [PMID: 36716566 DOI: 10.1016/j.watres.2023.119660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 01/03/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
pH is a crucial factor of microbial nitrification, which often combines with high-strength ammonium to influence nitrogen removal pathway in wastewater treatment. However, the detailed inhibitory mechanisms of pH stress are not sufficiently disclosed yet. In this study, the pH stress effect on nitrification was comprehensively studied by a set of experiments which identified the reactivity of nitrification processes and activity of nitrifiers, the time dependence of inhibition effect and the hybrid pH stress effect with ammonium. The results revealed two distinct inhibitory mechanisms dominating in alkaline and acid ranges. In alkaline range (pH > 8), pH stress causes physiological damages on microorganisms which is named as microbial inhibition. It has the features of less recoverability of nitrifiers, time-dependent inhibition effect and low pH-tolerance of nitrite oxidation bacteria. Free ammonia enhanced microbial inhibition and greatly promoted nitrite accumulation. A novel reactive inhibition mechanism dominated in acid range (pH < 7) was disclosed. It only impedes ammonia oxidation process (AOP) but not impair microbial activity obviously and the effect is time-independent. The mechanism was clarified from H+ transport because AOP involved H+ production. The H+ transport was impeded under acid stress owing to the decrease of pH gradient across cell membrane. The two mechanisms formed a panoramic view of pH stress effect on nitrification advancing the understanding of nitrifier adaptability and nitritation regulation in wastewater treatment processes.
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Affiliation(s)
- Xuehai Yue
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu 611756, China
| | - Hong Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Haotian Wei
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Lin Chang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Zhengjun Gong
- Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu 611756, China
| | - Lei Zheng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Fengjun Yin
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
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Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot. THE ISME JOURNAL 2023; 17:354-370. [PMID: 36536072 PMCID: PMC9938248 DOI: 10.1038/s41396-022-01345-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022]
Abstract
The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.
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Ecophysiological and Genomic Characterization of the Freshwater Complete Ammonia Oxidizer Nitrospira sp. Strain BO4. Appl Environ Microbiol 2023; 89:e0196522. [PMID: 36719237 PMCID: PMC9973019 DOI: 10.1128/aem.01965-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Complete ammonia oxidizers (comammox) are a group of ubiquitous chemolithoautotrophic bacteria capable of deriving energy from the oxidation of ammonia to nitrate via nitrite. Here, we present a study characterizing the comammox strain Nitrospira sp. BO4 using a combination of cultivation-dependent and molecular methods. The enrichment culture BO4 was obtained from the sediment of Lake Burr Oak, a mesotrophic lake in eastern Ohio. The metagenome of the enrichment culture was sequenced, and a metagenome-assembled genome (MAG) was constructed for Nitrospira sp. BO4. The closest characterized relative of Nitrospira sp. BO4 was "Candidatus Nitrospira kreftii." All genes for ammonia and nitrite oxidation, reductive tricarboxylic acid (TCA) cycle, and other pathways of the central metabolism were detected. Nitrospira sp. BO4 used ammonia and oxidized it to nitrate with nitrite as the intermediate. The culture grew on initial ammonium concentrations between 0.01 and 3 mM with the highest rates observed at the lowest ammonium concentrations. Blue light completely inhibited the growth of Nitrospira sp. BO4, while white light reduced the growth and red light had no effect on the growth. Nitrospira sp. BO4 did not grow on nitrite as its sole substrate. When supplied with ammonium and nitrite, the culture utilized nitrite after most of the ammonium was consumed. In summary, the genomic information of Nitrospira sp. BO4 coupled with the growth experiments shows that Nitrospira sp. BO4 is a freshwater comammox species. Future research will focus on further characterization of the niches of comammox in freshwater environments. IMPORTANCE Nitrification is a key process in the global nitrogen cycle. Complete ammonia oxidizers (comammox) were discovered recently, and only three enrichment cultures and one pure culture have been characterized with respect to activity and growth under different conditions. The cultivated comammox strains were obtained from engineered systems such as a recirculating aquaculture system and hot water pipes. Here, we present the first study characterizing a comammox strain obtained from a mesotrophic freshwater lake. In freshwater environments, comammox coexist with ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our results will help elucidate physiological characteristics of comammox and the distribution and niche differentiation of different ammonia oxidizers in freshwater environments.
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Ullah S, Ali I, Yang M, Zhao Q, Iqbal A, Wu X, Ahmad S, Muhammad I, Khan A, Adnan M, Yuan P, Jiang L. Partial Substitution of Urea with Biochar Induced Improvements in Soil Enzymes Activity, Ammonia-Nitrite Oxidizers, and Nitrogen Uptake in the Double-Cropping Rice System. Microorganisms 2023; 11:microorganisms11020527. [PMID: 36838492 PMCID: PMC9959172 DOI: 10.3390/microorganisms11020527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/09/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Biochar is an important soil amendment that can enhance the biological properties of soil, as well as nitrogen (N) uptake and utilization in N-fertilized crops. However, few studies have characterized the effects of urea and biochar application on soil biochemical traits and its effect on paddy rice. Therefore, a field trial was conducted in the early and late seasons of 2020 in a randomized complete block design with two N levels (135 and 180 kg ha-1) and four levels of biochar (0, 10, 20, and 30 t ha-1). The treatment combinations were as follows: 135 kg N ha-1 + 0 t B ha-1 (T1), 135 kg N ha-1 + 10 t B ha-1 (T2), 135 kg N ha-1 + 20 t B ha-1 (T3), 135 kg N ha-1 + 30 t B ha-1 (T4), 180 kg N ha-1 + 0 t B ha-1 (T5), 180 kg N ha-1 + 10 t B ha-1 (T6), 180 kg N ha-1 + 20 t B ha-1 (T7) and 180 kg N ha-1 + 30 t B ha-1 (T8). The results showed that soil amended with biochar had higher soil pH, soil organic carbon content, total nitrogen content, and mineral nitrogen (NH4+-N and NO3--N) than soil that had not been amended with biochar. In both seasons, the 20 t ha-1 and 30 t ha-1 biochar treatments had the highest an average concentrations of NO3--N (10.54 mg kg-1 and 10.25 mg kg-1, respectively). In comparison to soil that had not been treated with biochar, the average activity of the enzymes urease, polyphenol oxidase, dehydrogenase, and chitinase was, respectively, 25.28%, 14.13%, 67.76%, and 22.26% greater; however, the activity of the enzyme catalase was 15.06% lower in both seasons. Application of biochar considerably increased the abundance of ammonia-oxidizing bacteria (AOB), which was 48% greater on average in biochar-amended soil than in unamended soil. However, there were no significant variations in the abundances of ammonia-oxidizing archaea (AOA) or nitrite-oxidizing bacteria (NOB) across treatments. In comparison to soil that had not been treated with biochar, the average N content was 24.46%, 20.47%, and 19.08% higher in the stem, leaves, and panicles, respectively. In general, adding biochar at a rate of 20 to 30 t ha-1 with low-dose urea (135 kg N ha-1) is a beneficial technique for improving the nutrient balance and biological processes of soil, as well as the N uptake and grain yield of rice plants.
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Affiliation(s)
- Saif Ullah
- Key Laboratory of Crop Cultivation and Physiology, Guangxi University, Education Department of Guangxi, Nanning 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China
| | - Izhar Ali
- Key Laboratory of Crop Cultivation and Physiology, Guangxi University, Education Department of Guangxi, Nanning 530004, China
| | - Mei Yang
- Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning 530004, China
| | - Quan Zhao
- Key Laboratory of Crop Cultivation and Physiology, Guangxi University, Education Department of Guangxi, Nanning 530004, China
| | - Anas Iqbal
- Key Laboratory of Crop Cultivation and Physiology, Guangxi University, Education Department of Guangxi, Nanning 530004, China
| | - Xiaoyan Wu
- Key Laboratory of Crop Cultivation and Physiology, Guangxi University, Education Department of Guangxi, Nanning 530004, China
| | - Shakeel Ahmad
- Key Laboratory of Crop Cultivation and Physiology, Guangxi University, Education Department of Guangxi, Nanning 530004, China
| | - Ihsan Muhammad
- Key Laboratory of Crop Cultivation and Physiology, Guangxi University, Education Department of Guangxi, Nanning 530004, China
| | - Abdullah Khan
- Key Laboratory of Crop Cultivation and Physiology, Guangxi University, Education Department of Guangxi, Nanning 530004, China
| | - Muhammad Adnan
- Key Laboratory of Crop Cultivation and Physiology, Guangxi University, Education Department of Guangxi, Nanning 530004, China
| | - Pengli Yuan
- Key Laboratory of Crop Cultivation and Physiology, Guangxi University, Education Department of Guangxi, Nanning 530004, China
| | - Ligeng Jiang
- Key Laboratory of Crop Cultivation and Physiology, Guangxi University, Education Department of Guangxi, Nanning 530004, China
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, China
- Correspondence:
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Johnston J, Du Z, Behrens S. Ammonia-Oxidizing Bacteria Maintain Abundance but Lower amoA-Gene Expression during Cold Temperature Nitrification Failure in a Full-Scale Municipal Wastewater Treatment Plant. Microbiol Spectr 2023; 11:e0257122. [PMID: 36786623 PMCID: PMC10100873 DOI: 10.1128/spectrum.02571-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/21/2023] [Indexed: 02/15/2023] Open
Abstract
In this study, we explore the relationship between community structure and transcriptional activity of ammonia-oxidizing bacteria during cold temperature nitrification failure in three parallel full-scale sequencing batch reactors (SBRs) treating municipal wastewater. In the three reactors, ammonia concentrations increased with declines in wastewater temperature below 15°C. We quantified and sequenced 16S rRNA and ammonia monooxygenase (amoA) gene fragments in DNA and RNA extracts from activated sludge samples collected from the SBRs during the warmer seasons (summer and fall) and when water temperatures were below 15°C (winter and spring). Taxonomic community composition of amoA genes and transcripts did not vary much between the warmer and colder seasons. However, we observed significant differences in amoA transcript copy numbers between fall (highest) and spring (lowest). Ammonia-oxidizing bacteria of the genus Nitrosomonas sp. could maintain their population abundance despite lowering their amoA gene expression during winter and spring. In spite of relatively low population abundance, an amoA amplicon sequence variant (ASV) cluster identified as most similar to the amoA gene of Nitrosospira briensis showed the highest amoA transcript-to-gene ratio throughout all four seasons, indicating that some nitrifiers remain active at wastewater temperatures below 15°C. Our results show that 16S rRNA and amoA gene copy numbers are limited predictors of cell activity. To optimize function and performance of mixed community bioprocesses, we need to collect high-resolution quantitative transcriptomic and potentially proteomic data to resolve the response of individual species to changes in environmental parameters in engineered systems. IMPORTANCE The diverse microbial community of activated sludge used in biological treatment systems exhibits dynamic seasonal shifts in community composition and activity. Many wastewater treatment plants in temperate/continental climates experience seasonal cold temperature nitrification failure. "Seasonal nitrification failure" is the discharge of elevated concentrations of ammonia (greater than 4 mg/liter) with treated wastewater during the winter (influent wastewater temperatures below 13°C). This study aims at expanding our understanding of how ammonia-oxidizing bacteria in activated sludge change in activity and growth across seasons. We quantified the ammonia monooxygenase (amoA) gene and transcript copy numbers using real-time PCR and sequenced the amoA amplicons to reveal community structure and activity changes of nitrifying microbial populations during seasonal nitrification failure in three full-scale sequencing batch reactors (SRBs) treating municipal wastewater. Relevant findings presented in this study contribute to explain seasonal nitrification performance variability in SRBs.
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Affiliation(s)
- Juliet Johnston
- University of Minnesota, Department of Civil, Environmental, and Geo-Engineering, Minneapolis, Minnesota, USA
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, California, USA
| | - Zhe Du
- University of Minnesota, Department of Civil, Environmental, and Geo-Engineering, Minneapolis, Minnesota, USA
- Center for Environmental Health Risk Assessment and Research, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Sebastian Behrens
- University of Minnesota, Department of Civil, Environmental, and Geo-Engineering, Minneapolis, Minnesota, USA
- University of Minnesota, BioTechnology Institute, St. Paul, Minnesota, USA
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Grey A, Costeira R, Lorenzo E, O’Kane S, McCaul MV, McCarthy T, Jordan SF, Allen CCR, Kelleher BP. Geochemical properties of blue carbon sediments through an elevation gradient: study of an anthropogenically impacted coastal lagoon. BIOGEOCHEMISTRY 2023; 162:381-408. [PMID: 36873378 PMCID: PMC9971090 DOI: 10.1007/s10533-022-00974-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/06/2022] [Indexed: 06/18/2023]
Abstract
UNLABELLED Global research is showing that coastal blue carbon ecosystems are vulnerable to climate change driven threats including accelerated sea-level rise and prolonged periods of drought. Furthermore, direct anthropogenic impacts present immediate threats through deterioration of coastal water quality, land reclamation, long-term impact to sediment biogeochemical cycling. These threats will invariably alter the future efficacy of carbon (C) sequestration processes and it is imperative that currently existing blue carbon habitats be protected. Knowledge of underlying biogeochemical, physical and hydrological interactions occurring in functioning blue carbon habitats is essential for developing strategies to mitigate threats, and promote conditions to optimise C sequestration/storage. In this current work, we investigated how sediment geochemistry (0-10 cm depth) responds to elevation, an edaphic factor driven by long-term hydrological regimes consequently exerting control over particle sedimentation rates and vegetation succession. This study was performed in an anthropogenically impacted blue carbon habitat along a coastal ecotone encompassing an elevation gradient transect from intertidal sediments (un-vegetated and covered daily by tidal water), through vegetated salt marsh sediments (periodically covered by spring tides and flooding events), on Bull Island, Dublin Bay. We determined the quantity and distributions of bulk geochemical characteristics in sediments through the elevation gradient, including total organic carbon (TOC), total nitrogen (TN), total metals, silt, clay, and also, 16 individual polyaromatic hydrocarbon's (PAH's) as an indication of anthropogenic input. Elevation measurements for sample sites were determined on this gradient using a LiDAR scanner accompanied by an IGI inertial measurement unit (IMU) on board a light aircraft. Considering the gradient from the Tidal mud zone (T), through the low-mid marsh (M) to the most elevated upper marsh (H), there were significant differences between all zones for many measured environmental variables. The results of significance testing using Kruskal-Wallis analysis revealed, that %C, %N, PAH (µg/g), Mn (mg/kg), TOC:NH4 + and pH are significantly different between all zones on the elevation gradient. The highest values for all these variables exists (excluding pH which followed a reverse trend) in zone H, decreasing in zone M and lowest in the un-vegetated zone T. TC content is 16 fold higher overall in vegetated (3.43 -21.84%) than uninhabited (0.21-0.56%) sediments. TN was over 50 times higher (0.24-1.76%), more specifically increasing in % mass on approach to the upper salt marsh with distance from the tidal flats sediments zone T (0.002-0.05%). Clay and silt distributions were greatest in vegetated sediments, increasing in % content towards upper marsh zones The retention of water, metals, PAHs, mud, chloride ions, NH4 +, PO4 3- and SO4 2- increased with elevated C concentrations, concurrently where pH significantly decreased. Sediments were categorized with respect to PAH contamination where all SM samples were placed in the high polluted category. The results highlight the ability of Blue C sediments to immobilise increasing levels of C, N, and metals, and PAH with over time and with both lateral and vertical expansion. This study provides a valuable data set for an anthropogenically impacted blue carbon habitat predicted to suffer from sea-level rise and exponential urban development. GRAPHICAL ABSTRACT Summarized results from this study demonstrating the geochemical changes through an elevation gradient, with a transect encompassing intertidal sediments through supratidal salt marsh sediments within Bull Island's blue carbon lagoon zones. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10533-022-00974-0.
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Affiliation(s)
- Anthony Grey
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Ricardo Costeira
- The School of Biological Sciences, Queen’s University Belfast, Belfast, N. Ireland
| | - Emmaline Lorenzo
- Department of Chemistry, University of Kansas, Lawrence, KS 66045 USA
| | - Sean O’Kane
- National Centre for Geocomputation, Maynooth University, Kildare, Ireland
| | - Margaret V. McCaul
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin, Ireland
| | - Tim McCarthy
- National Centre for Geocomputation, Maynooth University, Kildare, Ireland
| | - Sean F. Jordan
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin, Ireland
| | | | - Brian P. Kelleher
- School of Chemical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
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Xu C, Wong VNL, Tuovinen A, Simojoki A. Effects of liming on oxic and anoxic N 2O and CO 2 production in different horizons of boreal acid sulfate soil and non-acid soil under controlled conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159505. [PMID: 36257417 DOI: 10.1016/j.scitotenv.2022.159505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
In acid sulfate (AS) soils, organic rich topsoil and subsoil horizons with highly variable acidity and moisture conditions and interconnected reactions of sulfur and nitrogen make them potential sources of greenhouse gases (GHGs). Subsoil liming can reduce the acidification of sulfidic subsoils in the field. However, the mitigation of GHG production in AS subsoils by liming, and the mechanisms involved, are still poorly known. We limed samples from different horizons of AS and non-AS soils to study the effects of liming on the N2O and CO2 production during a 56-day oxic and subsequent 72-h anoxic incubation. Liming to pH ≥ 7 decreased oxic N2O production by 97-98 % in the Ap1 horizon, 38-50 % in the Bg1 horizon, and 34-36 % in the BC horizon, but increased it by 136-208 % in the C horizon, respectively. Liming decreased anoxic N2O production by 86-94 % and 78-91 % in Ap1 and Bg1 horizons, but increased it by 100-500 % and 50-162 % in BC and C horizons, respectively. Liming decreased N2O/(N2O + N2) in anoxic denitrification in most horizons of both AS and non-AS soils. Liming significantly increased the cumulative oxic and anoxic CO2 production in AS soil, but less so in non-AS soil due to the initial high soil pH. Higher carbon and nitrogen contents in AS soil compared to non-AS soil agreed with the respectively higher cumulative oxic N2O production in all horizons, and the higher CO2 production in the subsoil horizons of all lime treatments. Overall, liming reduced the proportion of N2O in the GHGs produced in most soil horizons under oxic and anoxic conditions but reduced the total GHG production (as CO2 equivalents) only in the Ap1 horizon of both soils. The results suggest that liming of subsoils may not always effectively mitigate GHG emissions due to concurrently increased CO2 production and denitrification.
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Affiliation(s)
- Chang Xu
- School of Earth, Atmosphere and Environment, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Vanessa N L Wong
- School of Earth, Atmosphere and Environment, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Anna Tuovinen
- Department of Agricultural Sciences, University of Helsinki, P. O. Box 56 (Biocenter 1, Viikinkaari 9), FI-00014, Finland
| | - Asko Simojoki
- Department of Agricultural Sciences, University of Helsinki, P. O. Box 56 (Biocenter 1, Viikinkaari 9), FI-00014, Finland.
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Navarrete AA, Aburto F, González-Rocha G, Guzmán CM, Schmidt R, Scow K. Anthropogenic degradation alter surface soil biogeochemical pools and microbial communities in an Andean temperate forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158508. [PMID: 36063938 DOI: 10.1016/j.scitotenv.2022.158508] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 08/14/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
Soil microbial communities regulate a myriad of critical biogeochemical functions in forest ecosystems. Anthropogenic disturbances in natural forests could drive major shifts in plant and microbial communities resulting in substantial biogeochemical alterations. We evaluated the effect of anthropogenic disturbances in the soils of Andean temperate forests with different levels of degradation: i) mature forest (MF), ii) secondary forest (SF), iii) degraded forest (DF), and iv) deforested site converted into a prairie (DP). We quantified total soil carbon, nitrogen and phosphorous (TC, TN, and TP), and available nutrient stocks. The soil microbial community structure (i.e., composition, diversity, and abundance) was assessed under each condition from amplicon sequence variants (ASVs) obtained via NGS-Illumina sequencing and subsequent microbiome analysis. There were no significant differences in TC, TN, and TP across the forested states (MF, SF, DF). The deforested site condition presented significantly higher soil TC, TN, and TP and the lowest C:N, C:P, and N:P ratios. The DP soil microbiome was significantly more diverse in bacteria (D' = 0.47 ± 0.04); and fungi (H' = 5.11 ± 0.33). The bacterial microbiome was dominated by Proteobacteria (45.35 ± 0.89 %), Acidobacteria (20.73 ± 1.48 %), Actinobacteria (12.59 ± 0.34 %), and Bacteroidetes (7.32 ± 0.36 %) phyla in all sites. The soil fungal community was dominated by the phyla Ascomycota (42.11 ± 0.95 %), Mortierellomycota (28.74 ± 2.25 %), Basidiomycota (24.61 ± 0.52), and Mucoromycota (2.06 ± 0.43 %). Yet, there were significant differences at the genus level across conditions. Forest to prairie conversion facilitated the introduction of exotic bacterial and fungal taxa associated with agricultural activities and livestock grazing (∼50 % of DP core microbiome composed of unique ASVs). For example, the ammonia-oxidizing bacteria community emerged as a dominant group in the DP soils, along with a reduction in the ectomycorrhizal fungi community. The surface soil microbial community was surprisingly resistant to forest degradation and did not show a clear succession along the degradation gradient, but it was strongly altered after deforestation.
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Affiliation(s)
- Alejandro Atenas Navarrete
- Postgrado Facultad de Ciencias Forestales, Universidad de Concepción, Chile; Laboratorio de Investigación en Suelos, Aguas y Bosques (LISAB), Universidad de Concepción, Chile; Iniciativa Foresta Nativa, Universidad de Concepción, Concepción, Chile
| | - Felipe Aburto
- Soil and Crop Sciences Department, Texas A&M University, 370 Olsen Blvd. Heep Center, TX 77845, USA; Departamento de Planificación Territorial y Sistemas Urbanos, Facultad de Ciencias Ambientales, Universidad de Concepción, Chile.
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Facultad de Ciencias Biológicas, Universidad de Concepción, Chile
| | - Carolina Merino Guzmán
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, BIOREN, Universidad de La Frontera, Chile
| | - Radomir Schmidt
- Working Lands Innovation Center at the Institute of the Environment, University of California, Davis, USA
| | - Kate Scow
- Soil Microbial Ecology Lab, Department of Land, Air and Water Resources, University of California, Davis, USA
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Fan Y, Liu J, Liu Z, Hu X, Yu Z, Li Y, Chen X, Li L, Jin J, Wang G. Chitin amendments eliminate the negative impacts of continuous cropping obstacles on soil properties and microbial assemblage. FRONTIERS IN PLANT SCIENCE 2022; 13:1067618. [PMID: 36507440 PMCID: PMC9730418 DOI: 10.3389/fpls.2022.1067618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
Continuous cropping of soybean leads to soil environment deterioration and soil-borne disease exacerbation, which in turn limits the sustainability of agricultural production. Chitin amendments are considered promising methods for alleviating soybean continuous cropping obstacles; however, the underlying mechanisms of soil sickness reduction remain unclear. In this study, soil amendments with pure and crude chitin at different addition dosages were employed to treat diseased soil induced by continuous cropping of soybean for five years. Chitin amendments, especially crude chitin, remarkably increased soil pH, available phosphorus (AP), potassium (AK) and nitrate nitrogen ( NO 3 - -N) contents, and improved soybean plant growth and soil microbial activities (FDA). Additionally, chitin application significantly enriched the relative abundances of the potential biocontrol bacteria Sphingomonas, Streptomyces, and Bacillus and the fungi Mortierella, Purpureocillium, and Metarhizium while depleted those of the potential plant pathogens Fusarium, Cylindrocarpon and Paraphoma. Moreover, chitin amendments induced looser pathogenic subnetwork structures and less pathogenic cooperation with other connected microbial taxa in the rhizosphere soils. The structural equation model (SEM) revealed that pure and crude chitin amendments promoted soybean plant growth by indirectly regulating soil pH-mediated soil microbial activities and potentially beneficial microbes, respectively. Therefore, the reduction strategies for continuous cropping obstacles by adding pure and crude chitin were distinct; pure chitin amendments showed general disease suppression, while crude chitin exhibited specific disease suppression. Overall, chitin amendments could suppress potential plant pathogens and improve soil health, thereby promoting soybean growth, which provides new prospects for cultivation practices to control soybean continuous cropping obstacles.
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Affiliation(s)
- Yanli Fan
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhuxiu Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojing Hu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhenhua Yu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Yansheng Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xueli Chen
- Heilongjiang Academy of Black Soil Conservation and Utilization, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Lujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Jian Jin
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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Zhang X, Shan X, Fu H, Sun Z. Effects of artificially-simulated acidification on potential soil nitrification activity and ammonia oxidizing microbial communities in greenhouse conditions. PeerJ 2022; 10:e14088. [PMID: 36213504 PMCID: PMC9536323 DOI: 10.7717/peerj.14088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/29/2022] [Indexed: 01/20/2023] Open
Abstract
Background Nitrification can lead to large quantities of nitrate leaching into the soil during vegetable production, which may result in soil acidification in a greenhouse system. A better understanding is needed of the nitrification process and its microbial mechanisms in soil acidification. Materials and Methods A simulated acidification experiment with an artificially manipulated pH environment (T1: pH 7.0; T2: pH 6.5; T3: pH 6.0; T4: pH 5.5; T5: pH 4.5) was conducted in potted tomatoes grown in greenhouse conditions. The abundance and community structures of ammonia oxidizers under different pH environment were analyzed using q-PCR and high-throughput sequencing methods, respectively. Results and discussions Soil acidification was accompanied by a reduction of soil organic matter (SOM), total nitrogen (TN), NH3 concentration, and enzyme activities. The abundance of ammonia-oxidizing archaea (AOA) in the soil was higher than that of ammonia-oxidizing bacteria (AOB) in soils with a pH of 6.93 to 5.33. The opposite trend was observed when soil pH was 4.21. In acidified soils, the dominant strain of AOB was Nitrosospira, while the dominant strain of AOA was Nitrososphaera. The abundance and community structure of ammonia oxidizers were mainly affected by soil pH, NH4 + content, and microbial biomass. Soil nitrification activity (PNA) has a relationship with both AOA and AOB, in which the abundance of AOA was the crucial factor affecting PNA. Conclusions PNA was co-dominated by AOA and AOB in soils with simulated acidification. Changes of soil pH, NH4 +, and microbial biomass caused by acidification were the main factors for the differences in the ammonia-oxidizing microbial community in greenhouse soils. Under acidic conditions (pH < 5), the pH significantly inhibited nitrification and had a strong negative effect on the production of tomatoes in greenhouse conditions.
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Bai Z, Zheng L, Bai Z, Jia A, Wang M. Long-term cultivation alter soil bacterial community in a forest-grassland transition zone. Front Microbiol 2022; 13:1001781. [PMID: 36246280 PMCID: PMC9557053 DOI: 10.3389/fmicb.2022.1001781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Changes in land use types can significantly affect soil porperties and microbial community composition in many areas. However, the underlying mechanism of shift in bacterial communities link to soil properties is still unclear. In this study, Illumina high-throughput sequencing was used to analyze the changes of soil bacterial communities in different land use types in a forest-grassland transition zone, North China. There are two different land use types: grassland (G) and cultivated land (CL). Meanwhile, cultivated land includes cultivated of 10 years (CL10) or 20 years (CL20). Compared with G, CL decreased soil pH, SOC and TN, and significantly increased soil EC, P and K, and soil properties varied significantly with different cultivation years. Grassland reclamation increases the diversity of bacterial communities, the relative abundance of Proteobacteria, Gemmatimonadetes and Bacteroidetes increased, while that of Actinobacteria, Acidobacteria, Rokubacteria and Verrucomicrobia decreased. However, the relative abundance of Proteobacteria decreased and the relative abundance of Chloroflexi and Nitrospirae increased with the increase of cultivated land years. Mantel test and RDA analysis showed that TP, AP, SOC and EC were the main factors affecting the diversity of composition of bacterial communities. In conclusion, soil properties and bacterial communities were significantly altered after long-term cultivation. This study provides data support for land use and grassland ecological protection in this region.
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Zhou X, Lee J, Yun J, Kim J, Yang Y, Kang H. Distinct Nitrification Rates and Nitrifiers in Needleleaf and Evergreen Broadleaf Forest Soils. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02110-9. [PMID: 36151339 DOI: 10.1007/s00248-022-02110-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Research on niche specialization in the microbial communities of ammonia oxidizers is important for assessing the consequences of vegetation shift on nitrogen (N) cycling. In this study, soils were sampled from three tree stands (needleleaf, mixed, and evergreen broadleaf) from the Hannam experimental forest in South Korea in spring (May 2019), summer (August 2019), autumn (November 2019), and winter (January 2020). Quantitative polymerase chain reaction (qPCR) and high-throughput sequencing were used to measure the abundance and community structure of various nitrifiers: ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) as well as complete ammonia oxidizers (comammox). Nitrification rates and total ammonia oxidizer abundance were significantly higher in needleleaf forest soil than those in other forest stands, and they were lowest in evergreen broadleaf forest soil. Comammox clade B was most abundant in needleleaf and evergreen broadleaf forest soils, while AOA were significantly more abundant in mixed forest soil. The abundances of comammox clade B and AOA were negatively correlated with dissolved organic carbon. Phylogenetic analysis showed that NT-alpha and NS-gamma-2.3.2 were the most abundant AOA lineages in all the samples. The seasonal of AOA, AOB, and comammox varied with the sites, suggesting the need to examine the combinations of environmental factors when considering the effects of seasonal changes in the environment. Overall, the results suggest that potential vegetation shifts in forest ecosystems might affect nitrification activities by regulating the abundance and community structure of ammonia oxidizers.
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Affiliation(s)
- Xue Zhou
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
- College of Agricultural Science and Engineering, Hohai University, Nanjing, China
| | - Jaehyun Lee
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
| | - Jeongeun Yun
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
| | - Jinhyun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
| | - Yerang Yang
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul, Korea.
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48
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Chow C, Padda KP, Puri A, Chanway CP. An Archaic Approach to a Modern Issue: Endophytic Archaea for Sustainable Agriculture. Curr Microbiol 2022; 79:322. [PMID: 36125558 DOI: 10.1007/s00284-022-03016-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/31/2022] [Indexed: 11/03/2022]
Abstract
Archaea have existed for over 3.5 billion years, yet they were detected in the plant endosphere only in the recent past and still, not much is known about them. Archaeal endophytes may be important microorganisms for sustainable agriculture, particularly in the face of climate change and increasing food demand due to population growth. Recent advances in culture-independent methods of research have revealed a diverse abundance of archaea from the phyla Euryarchaeota, Crenarchaeaota, and Thaumarchaeota globally that are associated with significant crops such as maize, rice, coffee, and olive. Novel insights into the plant microbiome have revealed specific genes in archaea that may be involved in numerous plant metabolic functions including amino acid production and phytohormone modulation. This is the first review article to address what is known about archaea as endophytes, including their patterns of colonization and abundance in various parts of different crop plants grown under diverse environmental conditions. This review aims to facilitate mainstream discussions and encourage future research regarding the occurrence and role of endophytic archaea in plants, particularly in relation to agricultural applications.
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Affiliation(s)
- Chanelle Chow
- Department of Biology, Faculty of Science, University of British Columbia, Vancouver, Canada
| | - Kiran Preet Padda
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, Canada.,School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Akshit Puri
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland. .,UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Chris P Chanway
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, Canada
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49
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Liu B, Lin W, Huang S, Sun Q, Yin H, Luo J. Removal of Mg 2+ inhibition benefited the growth and isolation of ammonia-oxidizing bacteria: An inspiration from bacterial interaction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155923. [PMID: 35577082 DOI: 10.1016/j.scitotenv.2022.155923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Ammonia-oxidizing bacteria (AOB) play an important role in the global nitrogen cycle and have broad applications in the nitrogen removal from wastewater. However, the AOB species are sensitive to environmental factors and usually form tight relationships with other microbes, making the AOB isolation and maintenance are difficult and time-consuming. In this study, the relationship that occurred between AOB and their bacterial partners was found to be able to improve the ammonia oxidation; during the co-cultivation, the magnesium ions (Mg2+) with removal rate as high as 36.7% was removed from culture medium by the concomitant bacterial species, which was regarded as the main reason for improving ammonia oxidation. During the pure cultivation of AOB isolate, when the concentration of Mg2+ reduced to low levels, the ammonia-oxidizing activity was more than 5 times and the amoA gene expression was more than 12 times higher than that grown in the initial culture medium. Based on a newly designed culture medium, the ammonia oxidation of AOB isolate grown in liquid culture was significantly promoted and the visible AOB colonies with much more number and larger diameter were observed to form on agar plates. With the addition of high concentration of calcium carbonate (CaCO3), AOB colonies could be easily and specifically identified by following the hydrolytic zones that formed around AOB colonies. Another AOB isolates were successively obtained from different samples and within a short time, suggesting the feasibility and effectivity of this culture medium and strategy on the AOB isolation from environments.
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Affiliation(s)
- Buchan Liu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Weitie Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; MOE Joint International Research Laboratory of Synthetic Biology and Medicine, South China University of Technology, Guangzhou 510006, PR China
| | - Shenxi Huang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Qiuyun Sun
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Hao Yin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Jianfei Luo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; MOE Joint International Research Laboratory of Synthetic Biology and Medicine, South China University of Technology, Guangzhou 510006, PR China.
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50
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Sampara P, Luo Y, Lin X, Ziels RM. Integrating Genome-Resolved Metagenomics with Trait-Based Process Modeling to Determine Biokinetics of Distinct Nitrifying Communities within Activated Sludge. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11670-11682. [PMID: 35929783 PMCID: PMC9387530 DOI: 10.1021/acs.est.2c02081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Conventional bioprocess models for wastewater treatment are based on aggregated bulk biomass concentrations and do not incorporate microbial physiological diversity. Such a broad aggregation of microbial functional groups can fail to predict ecosystem dynamics when high levels of physiological diversity exist within trophic guilds. For instance, functional diversity among nitrite-oxidizing bacteria (NOB) can obfuscate engineering strategies for their out-selection in activated sludge (AS), which is desirable to promote energy-efficient nitrogen removal. Here, we hypothesized that different NOB populations within AS can have different physiological traits that drive process performance, which we tested by estimating biokinetic growth parameters using a combination of highly replicated respirometry, genome-resolved metagenomics, and process modeling. A lab-scale AS reactor subjected to a selective pressure for over 90 days experienced resilience of NOB activity. We recovered three coexisting Nitrospira population genomes belonging to two sublineages, which exhibited distinct growth strategies and underwent a compositional shift following the selective pressure. A trait-based process model calibrated at the NOB genus level better predicted nitrite accumulation than a conventional process model calibrated at the NOB guild level. This work demonstrates that trait-based modeling can be leveraged to improve our prediction, control, and design of functionally diverse microbiomes driving key environmental biotechnologies.
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