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Ye H, Tu N, Wu Z, He S, Zhao Y, Yue M, Hong M. Identification of bacteria and fungi responsible for litter decomposition in desert steppes via combined DNA stable isotope probing. Front Microbiol 2024; 15:1353629. [PMID: 38525080 PMCID: PMC10957780 DOI: 10.3389/fmicb.2024.1353629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/28/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction Soil microorganisms play crucial roles in determining the fate of litter in desert steppes because their activities constitute a major component of the global carbon (C) cycle. Human activities lead to increased ecosystem nitrogen (N) deposition, which has unpredictable impacts on soil microorganism diversity and functions. Nowadays, it is necessary to further study the succession of these microorganisms in the process of litter decomposition in desert steppe, and explore the effect of N deposition on this process. This issue is particularly important to resolve because it contributes to the broader understanding of nutrient cycling processes in desert steppes. Methods In this study, DNA stable isotope probing (DNA-SIP) was used to study changes in soil bacterial and fungal community composition and function during 8 weeks of culture of 13C-labeled litter in desert steppes. Results The results were as follows: (1) Actinomycetota, Pseudomonadota, and Ascomycota are the main microorganisms involved in litter decomposition in desert steppes; (2) N deposition (50 kg ha-1 year-1) significantly increased the relative abundance of some microorganisms involved in the decomposition process; and (3) N deposition likely promotes litter decomposition in desert steppes by increasing the abundances of N cycles bacteria (usually carrying GH family functional genes). Discussion These findings contribute to a deeper understanding of the C assimilation mechanisms associated with litter residue production, emphasizing the importance of extensive C utilization.
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Affiliation(s)
- He Ye
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Nare Tu
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Zhendan Wu
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Shilong He
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Yu Zhao
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Mei Yue
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
| | - Mei Hong
- Key Laboratory of Soil Quality and Nutrient Resources, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Agricultural Ecological Security and Green Development, Universities of Inner Mongolia Autonomous Region, Hohhot, China
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Chen J, Chen X, Zhu Y, Yan S, Xie S. New insights into bioaugmented removal of sulfamethoxazole in sediment microcosms: degradation efficiency, ecological risk and microbial mechanisms. Microbiome 2024; 12:43. [PMID: 38424602 PMCID: PMC10903153 DOI: 10.1186/s40168-023-01741-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/18/2023] [Indexed: 03/02/2024]
Abstract
BACKGROUND Bioaugmentation has the potential to enhance the ability of ecological technology to treat sulfonamide-containing wastewater, but the low viability of the exogenous degraders limits their practical application. Understanding the mechanism is important to enhance and optimize performance of the bioaugmentation, which requires a multifaceted analysis of the microbial communities. Here, DNA-stable isotope probing (DNA-SIP) and metagenomic analysis were conducted to decipher the bioaugmentation mechanisms in stabilization pond sediment microcosms inoculated with sulfamethoxazole (SMX)-degrading bacteria (Pseudomonas sp. M2 or Paenarthrobacter sp. R1). RESULTS The bioaugmentation with both strains M2 and R1, especially strain R1, significantly improved the biodegradation rate of SMX, and its biodegradation capacity was sustainable within a certain cycle (subjected to three repeated SMX additions). The removal strategy using exogenous degrading bacteria also significantly abated the accumulation and transmission risk of antibiotic resistance genes (ARGs). Strain M2 inoculation significantly lowered bacterial diversity and altered the sediment bacterial community, while strain R1 inoculation had a slight effect on the bacterial community and was closely associated with indigenous microorganisms. Paenarthrobacter was identified as the primary SMX-assimilating bacteria in both bioaugmentation systems based on DNA-SIP analysis. Combining genomic information with pure culture evidence, strain R1 enhanced SMX removal by directly participating in SMX degradation, while strain M2 did it by both participating in SMX degradation and stimulating SMX-degrading activity of indigenous microorganisms (Paenarthrobacter) in the community. CONCLUSIONS Our findings demonstrate that bioaugmentation using SMX-degrading bacteria was a feasible strategy for SMX clean-up in terms of the degradation efficiency of SMX, the risk of ARG transmission, as well as the impact on the bacterial community, and the advantage of bioaugmentation with Paenarthrobacter sp. R1 was also highlighted. Video Abstract.
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Affiliation(s)
- Jianfei Chen
- Fujian Key Laboratory of Pollution Control & Resource Reuse, College of Environmental and Resource Sciences, Fujian Normal University, Fuzhou, 350007, China
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Ying Zhu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuang Yan
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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Ishizaki Y, Kurisu F, Furumai H, Kasuga I. Autotrophic growth activity of complete ammonia oxidizers in an upflow biological contact filter for drinking water treatment. Lett Appl Microbiol 2023; 76:ovad105. [PMID: 37679291 DOI: 10.1093/lambio/ovad105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/24/2023] [Accepted: 09/05/2023] [Indexed: 09/09/2023]
Abstract
Biological filters effectively remove ammonium from drinking water via nitrification. In a pilot-scale upflow biological contact filter (U-BCF), complete ammonia oxidizers (comammox), which are capable of oxidizing ammonia to nitrate in one cell, were more abundant than ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). However, little information is available on the contribution of comammox to nitrification. In this study, we evaluated the autotrophic growth activity of comammox associated with biological activated carbon (BAC) in a U-BCF by DNA-stable isotope probing (DNA-SIP). BAC samples collected from the U-BCF were continuously fed mineral medium containing 0.14 mg N L-1 ammonium and 12C- or 13C-labeled bicarbonate for 20 days. DNA-SIP analysis revealed that comammox (clades A and B) as well as AOA assimilated bicarbonate after 10 days of incubation, proving that dominant comammox could contribute to nitrification. Contrarily, AOB remained inactive throughout the observation period. Amplicon sequencing of the 13C-labeled DNA fractions of comammox revealed that specific genotypes other than the most dominant genotype in the original sample were more enriched under the incubation condition for the DNA-SIP experiment. Thus, dominant genotypes of comammox in a U-BCF might utilize organic nitrogen to fuel nitrification in ammonia-limited environments.
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Affiliation(s)
- Yuta Ishizaki
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Bunkyo, Tokyo 113-8656, Japan
| | - Futoshi Kurisu
- Research Center for Water Environment Technology, Graduate School of Engineering, The University of Tokyo, Bunkyo, Tokyo 113-8656, Japan
| | - Hiroaki Furumai
- Research and Development Initiative, Chuo University, Bunkyo, Tokyo 112-8551, Japan
| | - Ikuro Kasuga
- Department of Urban Engineering, Graduate School of Engineering, The University of Tokyo, Bunkyo, Tokyo 113-8656, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, Meguro, Tokyo 153-8904, Japan
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Xu R, Kolton M, Tao W, Sun X, Su P, Huang D, Zhang M, Yang Z, Guo Z, Gao H, Wang Q, Li B, Chen C, Sun W. Anaerobic selenite-reducing bacteria and their metabolic potentials in Se-rich sediment revealed by the combination of DNA-stable isotope probing, metagenomic binning, and metatranscriptomics. J Hazard Mater 2023; 457:131834. [PMID: 37327607 DOI: 10.1016/j.jhazmat.2023.131834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 06/04/2023] [Accepted: 06/09/2023] [Indexed: 06/18/2023]
Abstract
Microorganisms play a critical role in the biogeochemical cycling of selenium (Se) in aquatic environments, particularly in reducing the toxicity and bioavailability of selenite (Se(IV)). This study aimed to identify putative Se(IV)-reducing bacteria (SeIVRB) and investigate the genetic mechanisms underlying Se(IV) reduction in anoxic Se-rich sediment. Initial microcosm incubation confirmed that Se(IV) reduction was driven by heterotrophic microorganisms. DNA stable-isotope probing (DNA-SIP) analysis identified Pseudomonas, Geobacter, Comamonas, and Anaeromyxobacter as putative SeIVRB. High-quality metagenome-assembled genomes (MAGs) affiliated with these four putative SeIVRB were retrieved. Annotation of functional gene indicated that these MAGs contained putative Se(IV)-reducing genes such as DMSO reductase family, fumarate and sulfite reductases. Metatranscriptomic analysis of active Se(IV)-reducing cultures revealed significantly higher transcriptional levels of genes associated with DMSO reductase (serA/PHGDH), fumarate reductase (sdhCD/frdCD), and sulfite reductase (cysDIH) compared to those in cultures not amended with Se(IV), suggesting that these genes played important roles in Se(IV) reduction. The current study expands our knowledge of the genetic mechanisms involved in less-understood anaerobic Se(IV) bio-reduction. Additinally, the complementary abilities of DNA-SIP, metagenomics, and metatranscriptomics analyses are demonstrated in elucidating the microbial mechanisms of biogeochemical processes in anoxic sediment.
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Affiliation(s)
- Rui Xu
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, PR China; National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Max Kolton
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Wan Tao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Pingzhou Su
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Duanyi Huang
- College of Environmental Science and Engineering, Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Miaomiao Zhang
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Zhaohui Yang
- College of Environmental Science and Engineering, Key Laboratory of Environmental Biology and Pollution Control (Ministry of Education), Hunan University, Changsha 410082, PR China
| | - Zhaohui Guo
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, PR China
| | - Hanbing Gao
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha 410083, PR China
| | - Qi Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China
| | - Chengyu Chen
- College of Natural Resources and Environment, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, South China Agricultural University, Guangzhou 510642, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, PR China; School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control (Ministry of Education), Henan Normal University, Xinxiang 453007, PR China.
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Bao J, Li J, Jiang L, Mei W, Song M, Huang D, Luo C, Zhang G. New insight into the mechanism underlying the effect of biochar on phenanthrene degradation in contaminated soil revealed through DNA-SIP. J Hazard Mater 2022; 438:129466. [PMID: 35803194 DOI: 10.1016/j.jhazmat.2022.129466] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Biochar has been widely used for the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil, but its mechanism of influencing PAH biodegradation remains unclear. Here, DNA-stable isotope probing coupled with high-throughput sequencing was employed to assess its influence on phenanthrene (PHE) degradation, the active PHE-degrading microbial community and PAH-degradation genes (PAH-RHDα). Our results show that both Low-BC and High-BC (soils amended with 1 % and 4 % w/w biochar, respectively) treatments significantly decreased PHE biodegradation and bioavailable concentrations with a dose-dependent effect compared to Non-BC treatment (soils without biochar). This result could be attributed to the immobilisation of PHE and alteration of the composition and abundance of the PHE-degrading microbial consortium by biochar. Active PHE degraders were identified, and those in the Non-BC, Low-BC and High-BC microcosms differed taxonomically. Sphaerobacter, unclassified Diplorickettsiaceae, Pseudonocardia, and Planctomyces were firstly linked with PHE biodegradation. Most importantly, the abundances of PHE degraders and PAH-RHDα genes in the 13C-enriched DNA fractions of biochar-amended soils were greatly attenuated, and were significantly positively correlated with PHE biodegradation. Our findings provide a novel perspective on PAH biodegradation mechanisms in biochar-treated soils, and expand the understanding of the biodiversity of microbes involved in PAH biodegradation in the natural environment.
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Affiliation(s)
- Jiangqiao Bao
- Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China
| | - Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China.
| | - Longfei Jiang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
| | - Weiping Mei
- Institute of Eco-Environmental Research, Institute of Beibu Gulf Marine Industry, Guangxi Academy of Sciences, Nanning 530007, China
| | - Mengke Song
- Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China
| | - Deyin Huang
- Guangdong Institute of Eco-environmental and Soil sciences, Guangdong Academy of Sciences, Guangzhou 510650, Guangdong, China
| | - Chunling Luo
- Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China.
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou 510640, China
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Xu R, Huang D, Sun X, Zhang M, Wang D, Yang Z, Jiang F, Gao P, Li B, Sun W. Diversity and Metabolic Potentials of As(III)-Oxidizing Bacteria in Activated Sludge. Appl Environ Microbiol 2021; 87:e0176921. [PMID: 34756059 DOI: 10.1128/AEM.01769-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Biological arsenite [As(III)] oxidation is an important process in the removal of toxic arsenic (As) from contaminated water. However, the diversity and metabolic potentials of As(III)-oxidizing bacteria (AOB) responsible for As(III) oxidation in wastewater treatment facilities are not well documented. In this study, two groups of bioreactors inoculated with activated sludge were operated under anoxic or oxic conditions to treat As-containing synthetic wastewater. Batch tests of inoculated sludges from the bioreactors further indicated that microorganisms could use nitrate or oxygen as electron acceptors to stimulate biological As(III) oxidation, suggesting the potentials of this process in wastewater treatment facilities. In addition, DNA-based stable isotope probing (DNA-SIP) was performed to identify the putative AOB in the activated sludge. Bacteria associated with Thiobacillus were identified as nitrate-dependent AOB, while bacteria associated with Hydrogenophaga were identified as aerobic AOB in activated sludge. Metagenomic binning reconstructed a number of high-quality metagenome-assembled genomes (MAGs) associated with the putative AOB. Functional genes encoding As resistance, As(III) oxidation, denitrification, and carbon fixation were identified in these MAGs, suggesting their potentials for chemoautotrophic As(III) oxidation. In addition, the presence of genes encoding secondary metabolite biosynthesis and extracellular polymeric substance metabolism in these MAGs may facilitate the proliferation of these AOB in activated sludge and enhance their capacity for As(III) oxidation. IMPORTANCE AOB play an important role in the removal of toxic arsenic from wastewater. Most of the AOB have been isolated from natural environments. However, knowledge regarding the structure and functional roles of As(III)-oxidizing communities in wastewater treatment facilities is not well documented. The combination of DNA-SIP and metagenomic binning provides an opportunity to elucidate the diversity of in situ AOB community inhabiting the activated sludges. In this study, the putative AOB responsible for As(III) oxidation in wastewater treatment facilities were identified, and their metabolic potentials, including As(III) oxidation, denitrification, carbon fixation, secondary metabolite biosynthesis, and extracellular polymeric substance metabolism, were investigated. This observation provides an understanding of anoxic and/or oxic AOB during the As(III) oxidation process in wastewater treatment facilities, which may contribute to the removal of As from contaminated water.
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Yi Y, Wang H, Chen Y, Gou M, Xia Z, Hu B, Nie Y, Tang Y. Identification of Novel Butyrate- and Acetate-Oxidizing Bacteria in Butyrate-Fed Mesophilic Anaerobic Chemostats by DNA-Based Stable Isotope Probing. Microb Ecol 2020; 79:285-298. [PMID: 31263981 DOI: 10.1007/s00248-019-01400-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/11/2019] [Indexed: 06/09/2023]
Abstract
Butyrate is one of the most important intermediates during anaerobic digestion of protein wastewater, and its oxidization is considered as a rate-limiting step during methane production. However, information on syntrophic butyrate-oxidizing bacteria (SBOB) is limited due to the difficulty in isolation of pure cultures. In this study, two anaerobic chemostats fed with butyrate as the sole carbon source were operated at different dilution rates (0.01/day and 0.05/day). Butyrate- and acetate-oxidizing bacteria in both chemostats were investigated, combining DNA-Stable Isotope Probing (DNA-SIP) and 16S rRNA gene high-throughput sequencing. The results showed that, in addition to known SBOB, Syntrophomonas, other species of unclassified Syntrophomonadaceae were putative butyrate-oxidizing bacteria. Species of Mesotoga, Aminivibrio, Acetivibrio, Desulfovibrio, Petrimonas, Sedimentibacter, unclassified Anaerolineae, unclassified Synergistaceae, unclassified Spirochaetaceae, and unclassified bacteria may contribute to acetate oxidation from butyrate metabolism. Among them, the ability of butyrate oxidation was unclear for species of Sedimentibacter, unclassified Synergistaceae, unclassified Spirochaetaceae, and unclassified bacteria. These results suggested that more unknown species participated in the degradation of butyrate. However, the corresponding function and pathway for butyrate or acetate oxidization of these labeled species need to be further investigated.
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Affiliation(s)
- Yue Yi
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - HuiZhong Wang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - YaTing Chen
- Institute for Disaster Management and Reconstruction, Sichuan University-The Hong Kong Polytechnic University, No. 122 Huanghe Middle Road Section 1, Shuangliu District, Chengdu, 610027, Sichuan, China
| | - Min Gou
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China.
| | - ZiYuan Xia
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
| | - Bin Hu
- College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, China
| | - Yong Nie
- College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing, 100871, China
| | - YueQin Tang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, 610065, Sichuan, China
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Pornkulwat P, Kurisu F, Soonglerdsongpha S, Banjongproo P, Srithep P, Limpiyakorn T. Incorporation of 13C-HCO 3- by ammonia-oxidizing archaea and bacteria during ammonia oxidation of sludge from a municipal wastewater treatment plant. Appl Microbiol Biotechnol 2018; 102:10767-77. [PMID: 30343425 DOI: 10.1007/s00253-018-9436-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/23/2018] [Accepted: 10/07/2018] [Indexed: 10/28/2022]
Abstract
Ammonia-oxidizing archaea (AOA) have recently been proposed as potential players for ammonia removal in wastewater treatment plants (WWTPs). However, there is little evidence directly showing the contribution of AOA to ammonia oxidation in these engineered systems. In this study, DNA-stable isotope probing (DNA-SIP) with labeled 13C-HCO3- was introduced to sludge from a municipal WWTP. Quantitative PCR demonstrated that AOA amoA genes outnumbered AOB amoA genes in this WWTP sludge. AOA amoA gene sequence analysis revealed that AOA present in this WWTP were specific to one subcluster within the group 1.1b Thaumarchaeota. When ammonia was supplied to DNA-SIP incubation, the DNA-SIP profiles demonstrated the incorporation of the 13C into AOA and AOB. However, the 13C was not found to be assimilated into both microorganisms in the incubation without ammonia. Specific primers were designed to target amoA genes of AOA belonging to the subcluster found in this WWTP. Applying the primers to DNA-SIP experiment revealed that AOA of this subcluter most likely utilized inorganic carbon during ammonia oxidation under the studied conditions.
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Srithep P, Pornkulwat P, Limpiyakorn T. Contribution of ammonia-oxidizing archaea and ammonia-oxidizing bacteria to ammonia oxidation in two nitrifying reactors. Environ Sci Pollut Res Int 2018; 25:8676-8687. [PMID: 29322393 DOI: 10.1007/s11356-017-1155-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 12/26/2017] [Indexed: 05/04/2023]
Abstract
In this study, two laboratory nitrifying reactors (NRI and NRII), which were seeded by sludge from different sources and operated under different operating conditions, were found to possess distinct dominant ammonia-oxidizing microorganisms. Ammonia-oxidizing archaeal (AOA) amoA genes outnumbered ammonia-oxidizing bacterial (AOB) amoA genes in reactor NRI, while only AOB amoA genes were detectable in reactor NRII. The AOA amoA gene sequences retrieved from NRI were characterized within the Nitrososphaera sister cluster of the group 1.1b Thaumarchaeota. Two inhibitors for ammonia oxidation, allylthiourea (ATU) and 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), were applied individually and as a mixture to observe the ammonia-oxidizing activity of both microorganisms in the reactors' sludge. The results indicated that AOA and AOB jointly oxidized ammonia in NRI, while AOB played the main role in ammonia oxidation in NRII. DNA-stable isotope probing with labeled 13C-HCO3- was performed on NRI sludge. Incorporation of 13C into AOA and AOB implied that both microorganisms may perform autotrophy during ammonia oxidation. Taken together, the results from this study provide direct evidence demonstrating the contribution of AOA and AOB to ammonia oxidation in the nitrifying reactors.
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Affiliation(s)
- Papitchaya Srithep
- International Program in Hazardous Substance and Environmental Management, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Research Program in Hazardous Substance Management in Agricultural Industry, Center of Excellence on Hazardous Substance Management, Bangkok, Thailand
| | - Preeyaporn Pornkulwat
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Tawan Limpiyakorn
- Research Program in Hazardous Substance Management in Agricultural Industry, Center of Excellence on Hazardous Substance Management, Bangkok, Thailand.
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok, 10330, Thailand.
- Research Unit Control of Emerging Micropollutants in Environment, Chulalongkorn University, Bangkok, Thailand.
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Niu J, Kasuga I, Kurisu F, Furumai H, Shigeeda T. Evaluation of autotrophic growth of ammonia-oxidizers associated with granular activated carbon used for drinking water purification by DNA-stable isotope probing. Water Res 2013; 47:7053-7065. [PMID: 24200001 DOI: 10.1016/j.watres.2013.07.056] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/25/2013] [Accepted: 07/04/2013] [Indexed: 06/02/2023]
Abstract
Nitrification is an important biological function of granular activated carbon (GAC) used in advanced drinking water purification processes. Newly discovered ammonia-oxidizing archaea (AOA) have challenged the traditional understanding of ammonia oxidation, which considered ammonia-oxidizing bacteria (AOB) as the sole ammonia-oxidizers. Previous studies demonstrated the predominance of AOA on GAC, but the contributions of AOA and AOB to ammonia oxidation remain unclear. In the present study, DNA-stable isotope probing (DNA-SIP) was used to investigate the autotrophic growth of AOA and AOB associated with GAC at two different ammonium concentrations (0.14 mg N/L and 1.4 mg N/L). GAC samples collected from three full-scale drinking water purification plants in Tokyo, Japan, had different abundance of AOA and AOB. These samples were fed continuously with ammonium and (13)C-bicarbonate for 14 days. The DNA-SIP analysis demonstrated that only AOA assimilated (13)C-bicarbonate at low ammonium concentration, whereas AOA and AOB exhibited autotrophic growth at high ammonium concentration. This indicates that a lower ammonium concentration is preferable for AOA growth. Since AOA could not grow without ammonium, their autotrophic growth was coupled with ammonia oxidation. Overall, our results point towards an important role of AOA in nitrification in GAC filters treating low concentration of ammonium.
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Affiliation(s)
- Jia Niu
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo, Tokyo 113-8656, Japan.
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