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Cholet F, Agogué H, Ijaz UZ, Lachaussée N, Pineau P, Smith CJ. Low-abundant but highly transcriptionally active uncharacterised Nitrosomonas drive ammonia-oxidation in the Brouage mudflat, France. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174312. [PMID: 38936706 DOI: 10.1016/j.scitotenv.2024.174312] [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: 04/09/2024] [Revised: 06/03/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
Exploring differences in nitrification within adjacent sedimentary structures of ridges and runnels on the Brouage mudflat, France, we quantified Potential Nitrification Rates (PNR) alongside amoA genes and transcripts. PNR was lower in ridges (≈1.7 fold-lower) than runnels, despite higher (≈1.8 fold-higher) ammonia-oxidizing bacteria (AOB) abundance. However, AOB were more transcriptionally active in runnels (≈1.9 fold-higher). Sequencing of amoA genes and transcripts revealed starkly contrasting profiles with transcripts from ridges and runnels dominated (≈91 % in ridges and ≈98 % in runnels) by low abundant (≈4.6 % of the DNA community in runnels and ≈0.8 % in ridges) but highly active phylotypes. The higher PNR in runnels was explained by higher abundance of this group, an uncharacterised Nitrosomonas sp. cluster. This cluster is phylogenetically similar to other active ammonia-oxidizers with worldwide distribution in coastal environments indicating its potential, but previously overlooked, contribution to ammonia oxidation globally. In contrast DNA profiles were dominated by highly abundant but low-activity clusters phylogenetically distinct from known Nitrosomonas (Nm) and Nitrosospira (Ns). This cluster is also globally distributed in coastal sediments, primarily detected as DNA, and often classified as Nitrosospira or Nitrosomonas. We therefore propose to classify this cluster as Ns/Nm. Our work indicates that low abundant but highly active AOB could be responsible for the nitrification globally, while the abundant AOB Ns/Nm may not be transcriptionally active, and as such account for the lack of correlation between rate processes and gene abundances often reported in the literature. It also raises the question as to what this seemingly inactive group is doing?
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Affiliation(s)
- Fabien Cholet
- Advanced Research Centre, Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, 11 Chapel Lane G11 6EW, Glasgow, UK..
| | - Hélène Agogué
- LIENSs, UMR 7266, CNRS - La Rochelle Université, 2 Rue Olympe de Gouges, 17000, La Rochelle, France
| | - Umer Z Ijaz
- Advanced Research Centre, Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, 11 Chapel Lane G11 6EW, Glasgow, UK
| | - Nicolas Lachaussée
- LIENSs, UMR 7266, CNRS - La Rochelle Université, 2 Rue Olympe de Gouges, 17000, La Rochelle, France
| | - Philippe Pineau
- LIENSs, UMR 7266, CNRS - La Rochelle Université, 2 Rue Olympe de Gouges, 17000, La Rochelle, France
| | - Cindy J Smith
- Advanced Research Centre, Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, 11 Chapel Lane G11 6EW, Glasgow, UK
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Cai S, Lao Q, Chen C, Zhu Q, Chen F. The impact of algal blooms on promoting in-situ N 2O emissions: A case in Zhanjiang bay, China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 358:120935. [PMID: 38648725 DOI: 10.1016/j.jenvman.2024.120935] [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: 02/19/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
Under the influence of many factors, such as climate change, anthropogenic eutrophication, and the development of aquaculture, the area and frequency of algal blooms have showed an increasing trend worldwide, which has become a challenging issue at present. However, the coupled relationship between nitrous oxide (N2O) and algal blooms and the underlying mechanisms remain unclear. To address this issue, 15N isotope cultures and quantitative polymerase chain reaction (qPCR) experiments were conducted in Zhanjiang Bay during algal and non-algal bloom periods. The results showed that denitrification and nitrification-denitrification were the two processes responsible for the in-situ production of N2O during algal and non-algal bloom periods. Stable isotope rate cultivation experiments indicated that denitrification and nitrification-denitrification were promoted in the water during the algal bloom period. The in-situ production of N2O during the algal bloom period was three-fold that during the non-algal bloom period. This may be because fresh particulate organic matter (POM) from the organisms responsible for the algal bloom provides the necessary anaerobic and hypoxic environment for denitrification and nitrification-denitrification in the degradation environment. Additionally, a positive linear correlation between N2O concentrations and ammonia-oxidizing bacteria (AOB) and denitrifying bacteria (nirK and nirS) also supported the significant denitrification and nitrification-denitrification occurring in the water during the algal bloom period. However, the algal bloom changed the main process for the in-situ production of N2O, wherein it shifted from denitrification during the non-algal bloom period to nitrification-denitrification during the algal bloom period. The results of our study will improve our understanding of the processes responsible for the in-situ production of N2O during the algal bloom period, and can help formulate effective policies to mitigate N2O emissions in the bay.
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Affiliation(s)
- Shangjun Cai
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Qibin Lao
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Chunqing Chen
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Qingmei Zhu
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China; Key Laboratory for Coastal Ocean Variation and Disaster Prediction, Guangdong Ocean University, Zhanjiang, 524088, China; Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Fajin Chen
- College of Ocean and Meteorology, Guangdong Ocean University, Zhanjiang, 524088, China; School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, 524088, China; Key Laboratory for Coastal Ocean Variation and Disaster Prediction, Guangdong Ocean University, Zhanjiang, 524088, China; Key Laboratory of Climate, Resources and Environment in Continental Shelf Sea and Deep Sea of Department of Education of Guangdong Province, Guangdong Ocean University, Zhanjiang, 524088, China.
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3
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Mao Y, Wu J, Yang R, Ma Y, Ye J, Zhong J, Deng N, He X, Hong Y. Novel database for accA gene revealed a vertical variability pattern of autotrophic carbon fixation potential of ammonia oxidizing archaea in a permeable subterranean estuary. MARINE ENVIRONMENTAL RESEARCH 2024; 194:106342. [PMID: 38185001 DOI: 10.1016/j.marenvres.2024.106342] [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: 10/31/2023] [Revised: 12/26/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
The autotrophic carbon fixation pathway of ammonia-oxidizing archaea (AOA) was the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle, of which the acetyl-CoA carboxylase α-submit (accA) gene is widely recognized as the indicator. To date, there is no reference database or suitable cut-off value for operational taxonomic unit (OTU) clustering to analyze the diversity of AOA based on the accA gene. In this study, a reference database with 489 sequences was constructed, all the accA gene sequences was obtained from the AOA enrichment culture, pure culture and environmental samples. Additionally, the 79% was determined as the cut-off value for OTU clustering by comparing the similarity between the accA gene and the 16S rRNA gene. The developed method was verified by analyzing samples from the subterranean estuary and a vertical variation pattern of autotrophic carbon fixation potential of AOA was revealed. This study provided an effective method to analyze the diversity and autotrophic carbon fixation potential of AOA based on accA gene.
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Affiliation(s)
- Yixiang Mao
- 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.
| | - Ruotong Yang
- 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
| | - Yuexi Ma
- 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
| | - Jiarui Zhong
- 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
| | - Nanling Deng
- 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
| | - Xiang He
- 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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4
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Euler S, Jeffrey LC, Maher DT, Johnston SG, Sugimoto R, Tait DR. Microbiome mediating methane and nitrogen transformations in a subterranean estuary. Environ Microbiol 2024; 26:e16558. [PMID: 38115223 DOI: 10.1111/1462-2920.16558] [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: 01/30/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
Subterranean estuaries (STEs) are important coastal biogeochemical reactors facilitating unique niches for microbial communities. A common approach in determining STE greenhouse gas and nutrient fluxes is to use terrestrial endmembers, not accounting for microbially mediated transformations throughout the STE. As such, the microbial ecology and spatial distribution of specialists that cycle compounds in STEs remain largely underexplored. In this study, we applied 16S rRNA amplicon sequencing with paired biogeochemical characterisations to spatially evaluate microbial communities transforming greenhouse gases and nutrients in an STE. We show that methanogens are most prevalent at the terrestrial end (up to 2.81% relative abundance) concomitant to the highest porewater methane, carbon dioxide and dissolved organic carbon concentrations (0.41 ± 0.02 μM, 273.31 ± 6.05 μM and 0.51 ± 0.02 mM, respectively). Lower ammonium concentrations corresponded with abundant nitrifying and ammonia-oxidising prokaryotes in the mixing zone (up to 11.65% relative abundance). Methane, ammonium and dissolved organic carbon concentrations all decreased by >50% from the terrestrial to the oceanic end of the 15 m transect. This study highlights the STE's hidden microbiome zonation, as well as the importance of accounting for microbial transformations mitigating nutrient and greenhouse gas fluxes to the coastal ecosystems.
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Affiliation(s)
- Sebastian Euler
- Faculty of Science and Engineering, Southern Cross University, Lismore, Australia
| | - Luke C Jeffrey
- Faculty of Science and Engineering, Southern Cross University, Lismore, Australia
| | - Damien T Maher
- Faculty of Science and Engineering, Southern Cross University, Lismore, Australia
| | - Scott G Johnston
- Faculty of Science and Engineering, Southern Cross University, Lismore, Australia
| | - Ryo Sugimoto
- Faculty of Marine Science and Technology, Fukui Prefectural University, Fukui, Japan
| | - Douglas R Tait
- Faculty of Science and Engineering, Southern Cross University, Lismore, Australia
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5
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Wang X, Wang P, Wang C, Chen J, Hu B, Yuan Q, Du C, Xing X. Cascade damming impacts on microbial mediated nitrogen cycling in rivers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166533. [PMID: 37625716 DOI: 10.1016/j.scitotenv.2023.166533] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
Rivers display essential role in nitrogen (N) cycling in terrestrial and aquatic ecosystems, but now they are suffering from damming worldwide, especially from cascade damming. Despite of the importance of microorganisms in biogeochemical nutrient cycling, little attention has been paid to microbial functional biogeography under damming disturbances. Here, the Geochip microarray was applied to investigate the microbial mediated N cycling across the single-dammed Yarlung Tsangpo-Brahmaputra River and the cascade-dammed Lancang-Mekong River in southwest China. Our results showed that the N cycling processes (nitrogen fixation, ammonification, denitrification, nitrification and anammox) were stimulated in reservoirs in both rivers and the enhancement was inversely coupled with hydraulic retention time, but the recovery of N-cycling gene abundance in downstream of dam was intervened by cascade damming. Moreover, N-cycling gene composition was significantly altered in the single-dammed river, while no remarkable change was found in the cascade-dammed reaches. However, different from the unvaried gene composition, cascade damming intervened the recovery of N-cycling gene flow connectivity and resulted in the continuous decrease of connectivity in cascade damming reaches. In addition, in the single-dammed river, nutrients were the important drivers for variation in gene abundance, while they did not influence gene composition. Meanwhile, the abundance and composition of N-cycling genes in the cascade-dammed river were both significantly correlated to geographical parameters and water physical characteristics. Therefore, our study has vital implications for anticipating microbial functional response and biogeochemical feedback to ongoing cascade damming, contributing to the protection of river ecosystems under river regulation.
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Affiliation(s)
- Xun Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Peifang Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China.
| | - Chao Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Juan Chen
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Bin Hu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Qiusheng Yuan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Chenggong Du
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Huaiyin Normal University, Huai'an, Jiangsu 223300, China
| | - Xiaolei Xing
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
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6
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Wilson SJ, Song B, Anderson IC. Geochemical factors impacting nitrifying communities in sandy sediments. Environ Microbiol 2023; 25:3180-3191. [PMID: 37715648 DOI: 10.1111/1462-2920.16504] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/04/2023] [Indexed: 09/18/2023]
Abstract
Sandy sediment beaches covering 70% of non-ice-covered coastlines are important ecosystems for nutrient cycling along the land-ocean continuum. Subterranean estuaries (STEs), where groundwater and seawater meet, are hotspots for biogeochemical cycling within sandy beaches. The STE microbial community facilitates biogeochemical reactions, determining the fate of nutrients, including nitrogen (N), supplied by groundwater. Nitrification influences the fate of N, oxidising reduced dissolved inorganic nitrogen (DIN), making it available for N removal. We used metabarcoding of 16S rRNA genes and quantitative PCR (qPCR) of ammonia monooxygenase (amoA) genes to characterise spatial and temporal variation in STE microbial community structure and nitrifying organisms. We examined nitrifier diversity, distribution and abundance to determine how geochemical measurements influenced their distribution in STEs. Sediment microbial communities varied with depth (p-value = 0.001) and followed geochemical gradients in dissolved oxygen (DO), salinity, pH, dissolved inorganic carbon and DIN. Genetic potential for nitrification in the STE was evidenced by qPCR quantification of amoA genes. Ammonia oxidiser abundance was best explained by DIN, DO and pH. Our results suggest that geochemical gradients are tightly linked to STE community composition and nitrifier abundance, which are important to determine the fate and transport of groundwater-derived nutrients to coastal waters.
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Affiliation(s)
- Stephanie J Wilson
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, Virginia, USA
- Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, Virginia, USA
| | - Iris C Anderson
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, Virginia, USA
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Sarkar S, Kazarina A, Hansen PM, Ward K, Hargreaves C, Reese N, Ran Q, Kessler W, de Souza LF, Loecke TD, Sarto MVM, Rice CW, Zeglin LH, Sikes BA, Lee ST. Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566028. [PMID: 37987001 PMCID: PMC10659370 DOI: 10.1101/2023.11.08.566028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Background Global change has accelerated the nitrogen cycle. Soil nitrogen stock degradation by microbes leads to the release of various gases, including nitrous oxide (N2O), a potent greenhouse gas. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) participate in the soil nitrogen cycle, producing N2O. There are outstanding questions regarding the impact of environmental processes such as precipitation and land use legacy on AOA and AOB structurally, compositionally, and functionally. To answer these questions, we analyzed field soil cores and soil monoliths under varying precipitation profiles and land legacies. Results We resolved 28 AOA and AOB metagenome assembled genomes (MAGs) and found that they were significantly higher in drier environments and differentially abundant in different land use legacies. We further dissected AOA and AOB functional potentials to understand their contribution to nitrogen transformation capabilities. We identified the involvement of stress response genes, differential metabolic functional potentials, and subtle population dynamics under different environmental parameters for AOA and AOB. We observed that AOA MAGs lacked a canonical membrane-bound electron transport chain and F-type ATPase but possessed A/A-type ATPase, while AOB MAGs had a complete complex III module and F-type ATPase, suggesting differential survival strategies of AOA and AOB. Conclusions The outcomes from this study will enable us to comprehend how drought-like environments and land use legacies could impact AOA- and AOB-driven nitrogen transformations in soil.
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Affiliation(s)
- Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Anna Kazarina
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Paige M. Hansen
- PMH Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado USA
| | - Kaitlyn Ward
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | | | - Nicholas Reese
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Qinghong Ran
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Willow Kessler
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Ligia F.T. de Souza
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Terry D. Loecke
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
- Environmental Studies Program, University of Kansas, Lawrence, Kansas, USA
| | | | - Charles W. Rice
- Department of Agronomy, Kansas State University, Manhattan, Kansas, USA
| | - Lydia H. Zeglin
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Benjamin A. Sikes
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
| | - Sonny T.M. Lee
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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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: 16] [Impact Index Per Article: 16.0] [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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Mavi MS, Singh G, Choudhary OP, Dey D. Moderation of nitrogen availability through the application of pyrolyzed and unpyrolyzed organic materials in saline water irrigated soil. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:467. [PMID: 36917357 DOI: 10.1007/s10661-023-11052-9] [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: 09/26/2022] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Soil application of pyrolyzed biomass (biochar) has been proposed as an effective strategy for managing degraded land, but its limitations as a sole nutrient supplier discourage its widespread application as a soil amendment. Excessive use of saline water for irrigation leads to buildup of salts and other toxic ions, which cause a decline in the availability of essential nutrients due to negative effects on the mineralization process. Therefore, a long-term incubation experiment was conducted for 52 weeks to study the individual or combined impact of pyrolyzed [biochar derived from rice residue (RB)] and unpyrolyzed organic materials [rice residue (RR) and animal manure (AM)] on nitrogen (N) dynamics in soil irrigated with water of varying electrical conductivity (EC) (EC0.3 [non-saline canal water), EC10, and EC15 dS m-1 (saline)]. Increasing salinity had an adverse effect on N mineralization, reducing it by 20-70% during the incubation period. Irrespective of the EC, soil amended with AM showed greater and faster N mineralization than unamended control, while individual application of RB or RR showed immobilization of N during the early period of incubation. However, conjoint application of pyrolyzed (RB) and unpyrolyzed organic materials (RR or AM) showed enhanced mineralized N content (26-96%) compared with the sole biochar-amended soil irrigated with water of different EC levels. It was most likely due to the synergic effect of unpyrolyzed materials on the mineralization rate of biochar. On the other hand, the high cation exchange capacity, large surface area, and greater total porosity of the biochar may cause stronger adsorption of free NH4+-N released from the labile organic amendments, thereby moderating the N mineralization process under saline conditions. Therefore, it is recommended that biochar be used in conjunction with AM or RR to ensure the prolonged availability of N in a saline environment.
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Affiliation(s)
- Manpreet Singh Mavi
- Department of Soil Science, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Gurpreet Singh
- Department of Soil Science, Punjab Agricultural University, Ludhiana, 141004, India
| | - Om Parkash Choudhary
- Department of Soil Science, Punjab Agricultural University, Ludhiana, 141004, India
| | - Debomita Dey
- Department of Soil Science, Punjab Agricultural University, Ludhiana, 141004, India
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10
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Wang H, Liu X, Wang Y, Zhang S, Zhang G, Han Y, Li M, Liu L. Spatial and temporal dynamics of microbial community composition and factors influencing the surface water and sediments of urban rivers. J Environ Sci (China) 2023; 124:187-197. [PMID: 36182129 DOI: 10.1016/j.jes.2021.10.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 09/15/2021] [Accepted: 10/11/2021] [Indexed: 06/16/2023]
Abstract
The temporal and spatial characteristics of urban river bacterial communities help us understand the feedback mechanism of bacteria to changes in the aquatic environment. The Fuhe River plays an important role in determining the water ecological environment of Baiyangdian Lake. 16S rRNA gene sequencing was used to study the microbial distribution characteristics in the Fuhe River in different seasons. The results showed that some environmental factors of the surface water (ammonia nitrogen (NH3-N), total nitrogen (TN), and total phosphorus (TP)) were different on the spatial and temporal scales. Moreover, there were no seasonal differences in the contents of TN, TP, total organic carbon (TOC), or heavy metals in the sediments. The distributions of Cyanobacteria, Actinomycetes and Firmicutes in the water and Actinomycetes and Planctomycetes in the sediments differed significantly among seasons (P < 0.05). There were significant spatial differences in bacteria in the surface water, with the highest abundance of Proteobacteria recorded in the river along with the highest nutrient concentration, while the abundance of Bacteroidetes was higher in the upstream than the downstream. Microbial communities in the water were most sensitive to temperature (T) and the TP concentration (P < 0.01). Moreover, differences in the bacterial community were better explained by the content of heavy metals in the sediments than by the chemical characteristics. A PICRUSt metabolic inference analysis showed that the effect of high summer temperatures on the enzyme action led to an increase in the abundances of the metabolic-related genes of the river microorganisms.
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Affiliation(s)
- Hongjie Wang
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Xingchun Liu
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Yali Wang
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Shengqi Zhang
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Guangming Zhang
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300130, China
| | - Yangyang Han
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Mengxiang Li
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China
| | - Ling Liu
- College of Ecology and Environment, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Hebei Key Laboratory of Close-to-Nature Restoration Technology of Wetlands, Baoding 071002, China.
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11
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Woo Y, Cruz MC, Wuertz S. Selective Enrichment of Nitrososphaera viennensis-Like Ammonia-Oxidizing Archaea over Ammonia-Oxidizing Bacteria from Drinking Water Biofilms. Microbiol Spectr 2022; 10:e0184522. [PMID: 36445127 PMCID: PMC9769795 DOI: 10.1128/spectrum.01845-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 11/08/2022] [Indexed: 12/03/2022] Open
Abstract
Ammonia-oxidizing archaea (AOA) can oxidize ammonia to nitrite for energy gain. They have been detected in chloraminated drinking water distribution systems (DWDS) along with the more common ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). To date, no members of the AOA have been isolated or enriched from drinking water environments. To begin the investigation of the role of AOA in chloraminated DWDS, we developed a selective approach using biofilm samples from a full-scale operational network as inoculum. A Nitrososphaera viennensis-like AOA taxon was enriched from a mixed community that also included Nitrosomonas-like AOB while gradually scaling up the culture volume. Dimethylthiourea (DMTU) and pyruvate at 100 μM were added to promote the growth of AOA while inhibiting AOB. This resulted in the eventual washout of AOB, while NOB were absent after 2 or 3 rounds of amendment with 24 μM sodium azide. The relative abundance of AOA in the enrichment increased from 0.2% to 39.5% after adding DMTU and pyruvate, and further to 51.6% after filtration through a 0.45-μm pore size membrane, within a period of approximately 6 months. IMPORTANCE Chloramination has been known to increase the risk of nitrification episodes in DWDS due to the presence of ammonia-oxidizing microorganisms. Among them, AOB are more frequently detected than AOA. All publicly available cultures of AOA have been isolated from soil, marine or surface water environments, meaning they are allochthonous to DWDS. Hence, monochloramine exposure studies involving these strains may not accurately reflect their role in DWDS. The described method allows for the rapid enrichment of autochthonous AOA from drinking water nitrifying communities. The high relative abundance of AOA in the resulting enrichment culture reduces any confounding effects of co-existing heterotrophic bacteria when investigating the response of AOA to varied levels of monochloramine in drinking water.
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Affiliation(s)
- Yissue Woo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
| | - Mercedes Cecilia Cruz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore
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12
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Calvo-Martin E, Teira E, Álvarez-Salgado XA, Rocha C, Jiang S, Justel-Díez M, Ibánhez JSP. On the hidden diversity and niche specialization of the microbial realm of subterranean estuaries. Environ Microbiol 2022; 24:5859-5881. [PMID: 36054689 PMCID: PMC10087554 DOI: 10.1111/1462-2920.16160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/02/2022] [Indexed: 01/12/2023]
Abstract
Subterranean estuaries (STEs) modulate the chemical composition of continental groundwater before it reaches the coast, but their microbial community is poorly known. Here, we explored the microbial ecology of two neighbouring, yet contrasting STEs (Panxón and Ladeira STEs; Ría de Vigo, NW Iberian Peninsula). We investigated microbial composition (16S rRNA gene sequencing), abundance, heterotrophic production and their geochemical drivers. A total of 10,150 OTUs and 59 phyla were retrieved from porewater sampled during four surveys covering each STE seepage face. In both STEs, we find a very diverse microbial community composed by abundant cosmopolitans and locally restricted rare taxa. Porewater oxygen and dissolved organic matter are the main environmental predictors of microbial community composition. More importantly, the high variety of benthic microbiota links to biogeochemical processes of different elements in STEs. The oxygen-rich Panxón beach showed strong associations of the ammonium oxidizing archaea Nitrosopumilales with the heterotrophic community, thus acting as a net source of nitrogen to the coast. On the other hand, the prevailing anoxic conditions of Ladeira beach promoted the dominance of anaerobic heterotrophs related to the degradation of complex and aromatic compounds, such as Dehalococcoidia and Desulfatiglans, and the co-occurrence of methane oxidizers and methanogens.
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Affiliation(s)
- Elisa Calvo-Martin
- Organic Geochemistry Lab, Department of Oceanography, Instituto de Investigacións Mariñas, Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain.,PhD Program in Marine Science, Technology and Management, Universidade de Vigo, Vigo, Spain
| | - Eva Teira
- Departamento de Ecología y Biología Animal, Universidade de Vigo, Centro de Investigación Mariña da Universidade de Vigo (CIM-UVigo), Vigo, Spain
| | - Xosé Antón Álvarez-Salgado
- Organic Geochemistry Lab, Department of Oceanography, Instituto de Investigacións Mariñas, Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain
| | - Carlos Rocha
- School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
| | - Shan Jiang
- School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland.,State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Maider Justel-Díez
- Departamento de Ecología y Biología Animal, Universidade de Vigo, Centro de Investigación Mariña da Universidade de Vigo (CIM-UVigo), Vigo, Spain
| | - Juan Severino Pino Ibánhez
- Organic Geochemistry Lab, Department of Oceanography, Instituto de Investigacións Mariñas, Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain.,School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
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13
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Ruiz‐González C, Rodríguez‐Pie L, Maister O, Rodellas V, Alorda‐Keinglass A, Diego‐Feliu M, Folch A, Garcia‐Orellana J, Gasol JM. High spatial heterogeneity and low connectivity of bacterial communities along a Mediterranean subterranean estuary. Mol Ecol 2022; 31:5745-5764. [PMID: 36112071 PMCID: PMC9827943 DOI: 10.1111/mec.16695] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 01/13/2023]
Abstract
Subterranean estuaries are biogeochemically active coastal sites resulting from the underground mixing of fresh aquifer groundwater and seawater. In these systems, microbial activity can largely transform the chemical elements that may reach the sea through submarine groundwater discharge (SGD), but little is known about the microorganisms thriving in these land-sea transition zones. We present the first spatially-resolved characterization of the bacterial assemblages along a coastal aquifer in the NW Mediterranean, considering the entire subsurface salinity gradient. Combining bulk heterotrophic activity measurements, flow cytometry, microscopy and 16S rRNA gene sequencing we find large variations in prokaryotic abundances, cell size, activity and diversity at both the horizontal and vertical scales that reflect the pronounced physicochemical gradients. The parts of the transect most influenced by freshwater were characterized by smaller cells and lower prokaryotic abundances and heterotrophic production, but some activity hotspots were found at deep low-oxygen saline groundwater sites enriched in nitrite and ammonium. Diverse, heterogeneous and highly endemic communities dominated by Proteobacteria, Patescibacteria, Desulfobacterota and Bacteroidota were observed throughout the aquifer, pointing to clearly differentiated prokaryotic niches across these transition zones and little microbial connectivity between groundwater and Mediterranean seawater habitats. Finally, experimental manipulations unveiled large increases in community heterotrophic activity driven by fast growth of some rare and site-specific groundwater Proteobacteria. Our results indicate that prokaryotic communities within subterranean estuaries are highly heterogeneous in terms of biomass, activity and diversity, suggesting that their role in transforming nutrients will also vary spatially within these terrestrial-marine transition zones.
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Affiliation(s)
| | | | - Olena Maister
- Institut de Ciències del Mar (ICM‐CSIC)BarcelonaSpain
| | - Valentí Rodellas
- Institut de Ciència i Tecnologia Ambientals (ICTA‐UAB)Universitat Autònoma de BarcelonaBellaterraSpain
| | - Aaron Alorda‐Keinglass
- Institut de Ciència i Tecnologia Ambientals (ICTA‐UAB)Universitat Autònoma de BarcelonaBellaterraSpain
| | - Marc Diego‐Feliu
- Institut de Ciència i Tecnologia Ambientals (ICTA‐UAB)Universitat Autònoma de BarcelonaBellaterraSpain,Departament de FísicaUniversitat Autònoma de BarcelonaBellaterraSpain
| | - Albert Folch
- Department of Civil and Environmental EngineeringUniversitat Politècnica de CatalunyaBarcelonaSpain,Associated Unit: Hydrogeology Group (UPC‐CSIC)BarcelonaSpain
| | - Jordi Garcia‐Orellana
- Institut de Ciència i Tecnologia Ambientals (ICTA‐UAB)Universitat Autònoma de BarcelonaBellaterraSpain,Departament de FísicaUniversitat Autònoma de BarcelonaBellaterraSpain
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14
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Yang X, Yu X, He Q, Deng T, Guan X, Lian Y, Xu K, Shu L, Wang C, Yan Q, Yang Y, Wu B, He Z. Niche differentiation among comammox ( Nitrospira inopinata) and other metabolically distinct nitrifiers. Front Microbiol 2022; 13:956860. [PMID: 36187961 PMCID: PMC9515657 DOI: 10.3389/fmicb.2022.956860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Due to global change, increasing nutrient input to ecosystems dramatically affects the nitrogen cycle, especially the nitrification process. Nitrifiers including ammonia-oxidizing archaea (AOAs), ammonia-oxidizing bacteria (AOBs), nitrite-oxidizing bacteria (NOBs), and recently discovered complete ammonia oxidizers (comammoxs) perform nitrification individually or in a community. However, much remains to be learned about their niche differentiation, coexistence, and interactions among those metabolically distinct nitrifiers. Here, we used synthetic microbial ecology approaches to construct synthetic nitrifying communities (SNCs) with different combinations of Nitrospira inopinata as comammox, Nitrososphaera gargensis as AOA, Nitrosomonas communis as AOB, and Nitrospira moscoviensis as NOB. Our results showed that niche differentiation and potential interactions among those metabolically distinct nitrifiers were determined by their kinetic characteristics. The dominant species shifted from N. inopinata to N. communis in the N4 community (with all four types of nitrifiers) as ammonium concentrations increased, which could be well explained by the kinetic difference in ammonia affinity, specific growth rate, and substrate tolerance of nitrifiers in the SNCs. In addition, a conceptual model was developed to infer niche differentiation and possible interactions among the four types of nitrifiers. This study advances our understanding of niche differentiation and provides new strategies to further study their interactions among the four types of nitrifiers.
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Affiliation(s)
- Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, United States
| | - Ting Deng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Yingli Lian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Kui Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- College of Agronomy, Hunan Agricultural University, Changsha, China
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15
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Yang J, Li G, Sheng Y, Zhang F. Response and contribution of bacterial and archaeal communities to eutrophication in urban river sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119397. [PMID: 35513192 DOI: 10.1016/j.envpol.2022.119397] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/21/2022] [Accepted: 04/30/2022] [Indexed: 06/14/2023]
Abstract
Excessive loading of nitrogen (N) and phosphorus (P) that leads to eutrophication mutually interacts with sediment microbial community. To unravel the microbial community structures and interaction networks in the urban river sediments with the disturbance of N and P loadings, we used high-throughput sequencing analysis and ecological co-occurrence network methods to investigate the responses of diversity and community composition of bacteria and archaea and identify the keystone species in river sediments. The alpha-diversity of archaea significantly decreased with the increased total nitrogen (TN), whereas the operational taxonomic unit (OTU) number of bacteria increased with the increase of available phosphorus (AP). The beta-diversity of archaea and bacteria was more sensitive to N content than P content. The relative abundance of predominant bacterial and archaeal taxa varied differently in terms of different N and P contents. Complexity and connectivity of bacteria and archaea interaction networks showed significant variations with eutrophication, and competition between bacteria became more significant with the increase of N content. The sensitive and the highest connective species (keystone species) were identified for different N and P loadings. Total carbon (TC), water content (WC), microbial alpha-diversity and interaction networks played pivotal roles in the N and P transformation in urban river sediments.
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Affiliation(s)
- Juejie Yang
- School of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Guanghe Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Yizhi Sheng
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA
| | - Fang Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, State Environment Protection Key Laboratory of Microorganism Application and Risk Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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16
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Deterministic Factors Determine the Comammox Community Composition in the Pearl River Estuary Ecosystem. Microbiol Spectr 2022; 10:e0101622. [PMID: 35913204 PMCID: PMC9431512 DOI: 10.1128/spectrum.01016-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Complete ammonia oxidizers (comammox) have been widely detected in riverine and estuarine ecosystems. However, knowledge about the process of comammox community assembly from freshwater to marine environments is still limited. Here, based on deep sequencing, we investigated the community composition of comammox along a salinity gradient in the Pearl River Estuary (PRE), South China. Our results showed that comammox microorganisms in the PRE sediments were extremely diverse and displayed distinct distributional patterns between upstream and downstream habitats. Quantitative PCR demonstrated that comammox was the dominant ammonia-oxidizing microorganism (AOM) in the PRE upstream sediments, and ammonia-oxidizing archaea (AOA) dominated the PRE downstream sediments, while ammonia-oxidizing bacteria (AOB) were not dominant in any section of the PRE. Neutral modeling revealed that stochastic processes explained a limited part of the variation in the comammox community. The majority of beta nearest-taxon index values were higher than 2, indicating that comammox community assembly in the PRE sediments was better explained through a deterministic process than through a stochastic process. Salinity and total nitrogen were the most important contributing factors that shaped the comammox community. This study expanded the current knowledge of the diversity and niche preference of comammox in the estuarine ecosystem, and further enhances our understanding of the assembly of comammox community from freshwater to marine environments. IMPORTANCE Microbial communities are shaped by stochastic (emigration, immigration, birth, death, and genetic drift of species) and deterministic (e.g., environmental factors) processes. However, it remains unknown as to which type of process is more important in influencing the comammox community assembly from freshwater to marine environments. In this study, we compared the relative importance of stochastic and deterministic processes in shaping the assembly of the comammox community, which demonstrated that the deterministic process was more important in determining the community assembly patterns in the PRE ecosystem.
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17
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Ma Z, Gao L, Sun M, Liao Y, Bai S, Wu Z, Li J. Microbial Diversity in Groundwater and Its Response to Seawater Intrusion in Beihai City, Southern China. Front Microbiol 2022; 13:876665. [PMID: 35910635 PMCID: PMC9328385 DOI: 10.3389/fmicb.2022.876665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Seawater intrusion is a major concern commonly found in coastal aquifers worldwide. Because of the intense aquifer exploitation and land-based marine aquaculture in the coastal area of Beihai City, Guangxi Zhuang Autonomous Region, China, numerous underground aquifers in this area have been affected by seawater intrusion. However, the microbial communities in freshwater aquifers and their response to seawater intrusion are still unclear. In this study, groundwater from three aquifers was collected from three monitoring sites at different distances from the coastline in the coastal area of Beihai City, and the hydrochemical characteristics of these groundwater samples and the structure of the associated microbial communities were analyzed. The Cl- concentration of the samples indicated that seawater intrusion had occurred in the research area up to 1.5 km away from the coastline, but the monitoring site 2 km away from the coastline had yet to be affected. Statistical analysis showed that the bacterial communities in different groundwater aquifers were significantly correlated with the Cl- concentration, thereby suggesting that the extent of seawater intrusion might be one of the primary factors shaping bacterial composition in groundwater of this area, but the composition and distribution of archaea did not show a significant response to seawater intrusion and presented no apparent correlation with the Cl- concentration. α-, γ-Proteobacteria and Bacteroidota were the dominant bacterial lineages, accounting for about 58-95% of the bacterial communities. Meanwhile, the predominant archaeal taxa were mainly composed of Crenarchaeota, Nanoarchaeota, and Thermoplasmatota, as accounting for 83-100%. Moreover, there was significant spatial heterogeneity of microbial communities in the aquifers affected by varying degrees of seawater intrusion. The microbial communities inhabiting the unconfined aquifer were influenced by the geochemical fluctuation caused by seawater infiltration from land-based marine aquaculture ponds and the diffusion of eutrophic surface water. In contrast, changes in microbial community structure in the confined aquifers were closely related to the environmental gradient caused by different degrees of seawater intrusion. In addition, we also found that the tidal cycle did not significantly affect the structure of microbial communities inhabiting confined aquifers that had been long affected by seawater intrusion.
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Affiliation(s)
- Zhonglin Ma
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Long Gao
- Marine Geological Survey Institute of Guangxi Zhuang Autonomous Region, Beihai, China
| | - Mingxue Sun
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Yongjie Liao
- Marine Geological Survey Institute of Guangxi Zhuang Autonomous Region, Beihai, China
| | - Shijie Bai
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Zijun Wu
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
| | - Jiangtao Li
- State Key Laboratory of Marine Geology, Tongji University, Shanghai, China
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18
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Okamoto N, Keeling PJ, Leander BS, Tai V. Microbial communities in sandy beaches from the three domains of life differ by microhabitat and intertidal location. Mol Ecol 2022; 31:3210-3227. [PMID: 35364623 DOI: 10.1111/mec.16453] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/28/2022]
Abstract
The microbial communities of sandy beaches are poorly described despite the biogeochemical importance and ubiquity of these ecosystems. Using metabarcoding of the 16S and 18S rRNA genes, we investigated the diversity, microhabitats (with or between sand grains), and intertidal distributions of microorganisms (including meiofauna) from pristine sandy beaches in British Columbia, Canada, and hypothesized that abiotic variations due to microhabitat or intertidal gradients influences the distribution of microorganisms on local scales. Bacterial, archaeal, and protistan communities of the sand were clearly distinct from interstitial communities, and from planktonic communities of the overlying seawater, which correlated with differences in function and lifestyle, e.g., sulfur reduction and gliding motility. In contrast, meiofaunal communities could not be distinguished by sample type, suggesting that they are more frequently mobilized between these microhabitats. Across intertidal zones, high intertidal, mid intertidal, and low intertidal/swash communities were distinct and correlated with moisture, organic carbon and phosphate content, implying that the distribution of microorganisms is influenced by intertidal abiotic gradients. However, few taxa at the genus or species level individually contributed to this zonation pattern; rather, a unique combination of multiple microbial taxa was more likely responsible. Although significant differences in microbial community composition on sandy beaches can be attributed to microhabitat and intertidal gradients, further investigations are needed to assess community assembly processes, the consistency of these distributions, and the functions of the majority of the microorganisms observed in the sand and their effects on the biogeochemistry and ecology of sandy beaches.
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Affiliation(s)
- Noriko Okamoto
- University of British Columbia, Vancouver, British Columbia, Canada.,Hakai Institute, Quadra Island, British Columbia, Canada
| | | | - Brian S Leander
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Vera Tai
- University of British Columbia, Vancouver, British Columbia, Canada.,University of Western Ontario, London, Ontario, Canada
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19
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Korbel KL, Greenfield P, Hose GC. Agricultural practices linked to shifts in groundwater microbial structure and denitrifying bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150870. [PMID: 34627912 DOI: 10.1016/j.scitotenv.2021.150870] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/21/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Irrigation enhances the connectivity between the surface and groundwater by facilitating the transport of energy sources and oxygen. When combined with fertilisers, the impact on groundwater microbial communities and their interactions with nitrogen cycling in aquifers is poorly understood. This study examines the impact of different landuses (irrigated and non-irrigated) on groundwater microbial communities. A total of 38 wells accessing shallow aquifers in three sub-catchments of the Murray Darling Basin, Australia, were sampled for water chemistry and microbial community structure using environmental DNA (eDNA) techniques. All sub-catchments showed evidence of intense irrigation and groundwater contamination with total nitrogen, nitrates and phosphorus concentrations often well above background, with total nitrogen concentrations up to 70 mg/L and nitrate concentration up to 18 mg/L. Across sub-catchments there was high microbial diversity, with differences in community structure and function between catchments and landuses. Of the 1100 operational taxonomic units (OTUs) recorded, 47 OTUs were common across catchments with species from Woesearchaeota, Nitrospirales, Nitrosopumilales and Acidobacter taxonomic groups contributing greatly to groundwater microbial communities. Within non-irrigated sites, groundwaters contained similar proportions of nitrifying and denitrifying capable taxa, whereas irrigated sites had significantly higher abundances of microbes with nitrifying rather than denitrifying capabilities. Microbial diversity was lower in irrigated sites in the Macquarie catchment. These results indicate that irrigated landuses impact microbial community structure and diversity within groundwaters and suggest that the ratios of denitrifying to nitrifying capable microbes as well as specific orders (e.g., Nitrososphaerales) may be useful to indicate long-term nitrogen contamination of groundwaters. Such research is important for understanding the biogeochemical processes that are key predictors of redox state and contamination of groundwater by N species and other compounds. This will help to predict human impacts on groundwater microbial structure, diversity, and ecosystem functions, aiding the long-term management groundwater resources.
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Affiliation(s)
- K L Korbel
- Department of Biological Sciences, Macquarie University, Australia.
| | | | - G C Hose
- Department of Biological Sciences, Macquarie University, Australia
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20
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Martinez‐Rabert E, Smith CJ, Sloan WT, González‐Cabaleiro R. Biochemistry shapes growth kinetics of nitrifiers and defines their activity under specific environmental conditions. Biotechnol Bioeng 2022; 119:1290-1300. [PMID: 35092010 PMCID: PMC9303882 DOI: 10.1002/bit.28045] [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: 07/14/2021] [Revised: 11/22/2021] [Accepted: 12/01/2021] [Indexed: 11/14/2022]
Abstract
Is it possible to find trends between the parameters that define microbial growth to help us explain the vast microbial diversity? Through an extensive database of kinetic parameters of nitrifiers, we analyzed if the dominance of specific populations of nitrifiers could be predicted and explained. We concluded that, in general, higher growth yield (YXS) and ammonia affinity (a0NH3) and lower growth rate (µmax) are observed for ammonia‐oxidizing archaea (AOA) than bacteria (AOB), which would explain their considered dominance in oligotrophic environments. However, comammox (CMX), with the maximum energy harvest per mole of ammonia, and some AOB, have higher a0NH3 and lower µmax than some AOA. Although we were able to correlate the presence of specific terminal oxidases with observed oxygen affinities (a0O2) for nitrite‐oxidizing bacteria (NOB), that correlation was not observed for AOB. Moreover, the presumed dominance of AOB over NOB in O2‐limiting environments is discussed. Additionally, lower statistical variance of a0O2 values than for ammonia and nitrite affinities was observed, suggesting nitrogen limitation as a stronger selective pressure. Overall, specific growth strategies within nitrifying groups were not identified through the reported kinetic parameters, which might suggest that mostly, fundamental differences in biochemistry are responsible for underlying kinetic parameters.
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Affiliation(s)
- Eloi Martinez‐Rabert
- James Watt School of Engineering, Infrastructure and Environment, University of Glasgow, Rankine Building Glasgow G12 8LT UK
| | - Cindy J. Smith
- James Watt School of Engineering, Infrastructure and Environment, University of Glasgow, Rankine Building Glasgow G12 8LT UK
| | - William T. Sloan
- James Watt School of Engineering, Infrastructure and Environment, University of Glasgow, Rankine Building Glasgow G12 8LT UK
| | - Rebeca González‐Cabaleiro
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft The Netherlands
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21
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Metagenomic Insights into the Structure of Microbial Communities Involved in Nitrogen Cycling in Two Integrated Multitrophic Aquaculture (IMTA) Ponds. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10020171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The microbial structure and metabolic potential, particularly with regard to nitrogen (N) cycling, in integrated multitrophic aquaculture (IMTA) ponds with shrimp remain unclear. In this study, an analysis of microbial community taxonomic diversity and a metagenomic analysis of N-related genes were performed in a shrimp-crab pond (Penaeus japonicus-Portunus trituberculatus, SC) and a shrimp-crab-clam pond (P. japonicus-P. trituberculatus-Sinonovacula constricta, SCC) to evaluate microbial structure and N transformation capacities in these two shrimp IMTA ponds. The composition of the microbial communities was similar between SC and SCC, but the water and sediments shared few common members in either pond. The relative abundances of N cycling genes were significantly higher in sediment than in water in both SC and SCC, except for assimilatory nitrate reduction genes. The main drivers of the differences in the relative abundances of N cycling genes in SC and SCC were salinity and pH in water and the NO2− and NH4+ contents of pore water in sediment. These results indicate that the coculture of S. constricta in a shrimp-crab pond may result in decreased N cycling in sediment. The reduced N flux in the shrimp IMTA ponds primarily originates within the sediment, except for assimilatory nitrate reduction.
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22
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Zhao M, Tang X, Sun D, Hou L, Liu M, Zhao Q, Klümper U, Quan Z, Gu JD, Han P. Salinity gradients shape the nitrifier community composition in Nanliu River Estuary sediments and the ecophysiology of comammox Nitrospira inopinata. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 795:148768. [PMID: 34247082 DOI: 10.1016/j.scitotenv.2021.148768] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
The recent discovery of complete ammonia oxidizers (comammox), which convert ammonia to nitrate in a single organism, revolutionized the conventional understanding that two types of nitrifying microorganisms have to be involved in the nitrification process for more than 100 years. However, how different types of nitrifiers in response to salinity change remains largely unclear. This study not only investigated nitrifier community (including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), comammox and nitrite-oxidizing Nitrospira) in the Nanliu estuary to find the ecological relationship between salinity and functional communities and also studied the physiology of a typical comammox Nitrospira inopinata in response to a salinity gradient. Based on sequences retrieved with four sets of functional gene primes, comammox Nitrospira was in general, mainly composed of clade A, with a clear separation of clade A1 subgroup in all samples and clade A2 subgroup in low salinity ones. As expected, group I.1b and group I.1a AOA dominated the AOA community in low- and high-salinity samples, respectively. Nitrosomonas-AOB were detected in all samples while Nitrosospira-AOB were mainly found in relatively high-salinity samples. Regarding general Nitrospira, lineages II and IV were the major groups in most of the samples, while lineage I Nitrospira was only detected in low-salinity samples. Furthermore, the comammox pure culture of N. inopinata showed an optimal salinity at 0.5‰ and ceased to grow at 12.8‰ for ammonia oxidation, but remained active for nitrite oxidation. These results show new evidence regarding niche specificity of different nitrifying microorganisms modulated mainly by salinity, and also a clear response by comammox N. inopinata to a wide range of simulated salinity levels.
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Affiliation(s)
- Mengyue Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xiufeng Tang
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Dongyao Sun
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China
| | - Qiang Zhao
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Uli Klümper
- Institute for Hydrobiology, Technische Universität Dresden, 01062 Dresden, Germany
| | - Zhexue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, China
| | - Ping Han
- Key Laboratory of Geographic Information Science (Ministry of Education), School of Geographic Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China; Institute of Eco-Chongming, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062, China.
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23
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Huang L, Bae HS, Young C, Pain AJ, Martin JB, Ogram A. Campylobacterota dominate the microbial communities in a tropical karst subterranean estuary, with implications for cycling and export of nitrogen to coastal waters. Environ Microbiol 2021; 23:6749-6763. [PMID: 34472187 DOI: 10.1111/1462-2920.15746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 11/30/2022]
Abstract
Subterranean estuaries (STEs), the zones in which seawater and subsurface groundwater mix, are recognized as hotspots for biogeochemical reactions; however, little is known of the microbial communities that control many of those reactions. This study investigated the potential functions of microbes inhabiting a cenote and an offshore submarine spring (Pargos) in the near-coastal waters of the Yucatan Peninsula, Mexico. The inland cenote (Cenote Siete Bocas; C7B) is characterized by a chemocline that is host to an array of physicochemical gradients associated with microbial activities. The chemocline includes an increasing gradient in sulfide concentrations with depth and a decreasing gradient in nitrate concentrations. The microbial community within the chemocline was dominated by Sulfurimonas and Sulfurovum of the Campylobacteria, which are likely responsible for sulfide oxidation coupled with nitrate reduction. Although C7B has not been directly connected with Pargos Spring, water discharging from the spring has physicochemical characteristics and microbial community structures similar to C7B, strongly suggesting biogeochemical processing in the STE impacts groundwater composition prior to discharge. This work yields insight into the microbial communities and biogeochemical reactions in STEs in karstic aquifers and provides evidence for the importance of Campylobacteria in controlling nitrate concentrations exported to marine springs.
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Affiliation(s)
- Laibin Huang
- Soil and Water Science Department, University of Florida, Gainesville, FL, USA
| | - Hee-Sung Bae
- Soil and Water Science Department, University of Florida, Gainesville, FL, USA
| | - Caitlin Young
- Department of Geological Sciences, University of Florida, Gainesville, FL, USA
| | - Andrea J Pain
- Center for Environmental Science, Horn Point Laboratory, University of Maryland, Cambridge, MD, USA
| | - Jonathan B Martin
- Department of Geological Sciences, University of Florida, Gainesville, FL, USA
| | - Andrew Ogram
- Soil and Water Science Department, University of Florida, Gainesville, FL, USA
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24
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Nakagawa T, Koji M, Hosoyama A, Yamazoe A, Tsuchiya Y, Ueda S, Takahashi R, Stahl DA. Nitrosopumilus zosterae sp. nov., an autotrophic ammonia-oxidizing archaeon of phylum Thaumarchaeota isolated from coastal eelgrass sediments of Japan. Int J Syst Evol Microbiol 2021; 71. [PMID: 34406920 DOI: 10.1099/ijsem.0.004961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel mesophilic and aerobic ammonia-oxidizing archaeon of the phylum Thaumarchaeota, strain NM25T, was isolated from coastal eelgrass zone sediment sampled in Shimoda (Japan). The cells were rod-shaped with an S-layer cell wall. The temperature range for growth was 20-37 °C, with an optimum at 30 °C. The pH range for growth was pH 6.1-7.7, with an optimum at pH 7.1. The salinity range for growth was 5-40 %, with an optimum range of 15-32 %. Cells obtained energy from ammonia oxidation and used bicarbonate as a carbon source. Utilization of urea was not observed for energy generation and growth. Strain NM25T required a hydrogen peroxide scavenger, such as α-ketoglutarate, pyruvate or catalase, for sustained growth on ammonia. Growth of strain NM25T was inhibited by addition of low concentrations of some organic compounds and organic mixtures, including complete inhibition by glycerol, peptone and yeast extract. Phylogenetic analysis of four concatenated housekeeping genes (16S rRNA, rpoB, rpsI and atpD) and concatenated AmoA, AmoB, AmoC amino acid sequences indicated that the isolate is similar to members of the genus Nitrosopumilus. The closest relative is Nitrosopumilus ureiphilus PS0T with sequence similarities of 99.5 % for the 16S rRNA gene and 97.2 % for the amoA gene. Genome relatedness between strain NM25T and N. ureiphilus PS0T was assessed by average nucleotide identity and digital DNA-DNA hybridization, giving results of 85.4 and 40.2 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain NM25T represents a novel species of the genus Nitrosopumilus, for which the name sp. nov, is proposed. The type strain is NM25T (=NBRC 111181T=ATCC TSD-147T).
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Affiliation(s)
- Tatsunori Nakagawa
- College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan.,Department of Civil and Environmental Engineering, University of Washington, WA 98195, USA
| | - Mori Koji
- Department of Civil and Environmental Engineering, University of Washington, WA 98195, USA
| | - Akira Hosoyama
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu 292-0818, Japan
| | - Atsushi Yamazoe
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu 292-0818, Japan
| | - Yuki Tsuchiya
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu 292-0818, Japan
| | - Shingo Ueda
- College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan
| | - Reiji Takahashi
- College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa 252-0880, Japan
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, WA 98195, USA
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25
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Wang Y, Cui X, Chen F, He S. Cyclic utilization of reed litters to enhance nitrogen removal efficiency in simulated estuarine wetland. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:39071-39081. [PMID: 33745057 DOI: 10.1007/s11356-021-13485-6] [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: 10/25/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Reed is a common species in China's estuarine wetlands, contains high carbon and low nitrogen, and its litters have potential to be reused as external carbon source to achieve denitrification efficiency enhancement in estuarine wetlands. In this study, leaching experiments of reed leaf and stem under estuarine wetland salinity were conducted, and a certain amount of reed litters was then added into simulated estuarine wetlands under 0‰ and 7‰ salinity respectively. It was observed that reed litters had a higher release of total organic carbon (TOC) under 7‰ salinity than 0‰ salinity, and reed leaf litters released more TOC than stem litters did. Meantime, it was found that salinity had a more significant effect on TOC leached from stems than from leaves. In simulated estuarine wetlands, NO3--N removal rates were found to be improved about 20% under 7‰ salinity and 25% under 0‰ salinity in average after the addition of mixed litters, and almost no additional improvement in NO3--N removal was found after leaf-only litter addition compared with mixed litter addition. Besides, mixed litter addition could work two weeks longer than leaf-only litter addition. Moreover, the microbial community change was analyzed by high-throughput sequencing and found that litter addition could increase the denitrification-related genera and then increased the NO3--N removal efficiency. For simulated estuarine wetland, reed litter addition could achieve better nitrogen removal efficiency.
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Affiliation(s)
- Yanan Wang
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Xijun Cui
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Fanfan Chen
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Shengbing He
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Dong Chuan Road 800, Shanghai, 200240, People's Republic of China.
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26
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Wei H, Lin X. Shifts in the relative abundance and potential rates of sediment ammonia-oxidizing archaea and bacteria along environmental gradients of an urban river-estuary-adjacent sea continuum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 771:144824. [PMID: 33545473 DOI: 10.1016/j.scitotenv.2020.144824] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in N cycling in sediments globally. However, little is known about their ammonia oxidation rates along a river-estuary-sea continuum. In this study, we investigated how the potential ammonia oxidation rates (PARs) of AOA and AOB changed spatially along a continuum comprising three habitats: the Shanghai urban river network, the Yangtze Estuary, and the adjacent East China Sea, in summer and winter. The AOA and AOB PARs (0.53 ± 0.49 and 0.72 ± 0.69 μg N g-1 d-1, mean ± SD, respectively) and their amoA gene abundance (0.47 ± 0.85 × 106 and 2.4 ± 3.54 × 106 copies g-1, respectively) decreased along the continuum, particularly from the urban river to the estuary, driven by decreasing sediment total organic C and N and other correlated inorganic nutrients (e.g., NH4+) along the gradient of anthropogenic influences. These spatial patterns were consistent between the seasons. The urban river network, where the anthropogenic influences were strongest, saw the largest seasonal differences, as both AOA and AOB had higher PARs and abundance in summer than in winter. The ratios between AOA and AOB PARs (~0.87 ± 0.51) and gene abundances (~0.25 ± 0.24), however, were predominantly <1, indicating an AOB-dominated community. Comparing the different NH4+ consumption pathways, total aerobic oxidation accounted for 12-26% of the total consumption, with the largest proportion in the estuary, where the system was well oxygenated, and the lowest in the adjacent sea, where inorganic N was highly depleted. This study revealed the spatiotemporal patterns of AOA and AOB potential rates and gene abundance along gradients of human influences and identified organic matter and nutrients as key environmental factors that shaped the variation of AOA and AOB along the continuum.
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Affiliation(s)
- Hengchen Wei
- The University of Texas at Austin Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA
| | - Xianbiao Lin
- Laboratory of Microbial Ecology and Matter Cycles, School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; School of Geographic Sciences, Key Laboratory of Geographic Information Science of the Ministry of Education, East China Normal University, Shanghai 200241, China; Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Zhuhai 519000, China.
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27
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Diversity of soil nitrogen-fixing bacteria in the rhizosphere and non-rhizophere soils of Ebinur Lake Wetland. Arch Microbiol 2021; 203:3919-3932. [PMID: 34021386 DOI: 10.1007/s00203-021-02363-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
Ebinur Lake Wetland is an understudied desert wetland ecosystem, particularly regarding nitrogen cycling. This study aimed to ascertain the diversity and richness of nitrogen-fixing bacterial communities in the Ebinur Lake Wetland. The diversity of the nitrogen-fixing bacteria community of nifH genes from the rhizosphere and non-rhizosphere soils of four plants in different seasons were examined using Illumina HiSeq PE250 high-throughput sequencing technology. The correlation between soil environmental factors and diversity and richness of nitrogen-fixing bacteria was studied using the redundancy analysis (RDA). The results showed that the diversity of nitrogen-fixing bacteria in the rhizosphere soil of the constructive plants was higher than that in the non-rhizosphere soil; also, the diversity in July was higher than that in October and April. Geobacter, Pseudomonas and Bradyrhizobium were the dominant common bacteria in different samples of Ebinur Lake Wetland. The RDA showed that the total nitrogen, available potassium and available phosphoruswere significantly correlated with the diversity and richness of nitrogen-fixing bacteria. The diversity and community structure of nitrogen-fixing bacteria in soil samples also changed over time. The community structures of nitrogen-fixing bacteria in the rhizosphere and non-rhizosphere soils of the four plants were not the same during the same period. The correlation between soil environmental factors and the community structure and abundance of nitrogen-fixing bacteria can provide data basis and theoretical support for the degradation and restoration of Ebinur Lake Wetland.
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28
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Boey JS, Mortimer R, Couturier A, Worrallo K, Handley KM. Estuarine microbial diversity and nitrogen cycling increase along sand-mud gradients independent of salinity and distance. Environ Microbiol 2021; 24:50-65. [PMID: 33973326 DOI: 10.1111/1462-2920.15550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/22/2023]
Abstract
Estuaries are depositional environments prone to terrigenous mud sedimentation. While macrofaunal diversity and nitrogen retention are greatly affected by changes in sedimentary mud content, its impact on prokaryotic diversity and nitrogen cycling activity remains understudied. We characterized the composition of estuarine tidal flat prokaryotic communities spanning a habitat range from sandy to muddy sediments, while controlling for salinity and distance. We also determined the diversity, abundance and expression of ammonia oxidizers and N2 O-reducers within these communities by amoA and clade I nosZ gene and transcript analysis. Results show that prokaryotic communities and nitrogen cycling fractions were sensitive to changes in sedimentary mud content, and that changes in the overall community were driven by a small number of phyla. Significant changes occurred in prokaryotic communities and N2 O-reducing fractions with only a 3% increase in mud, while thresholds for ammonia oxidizers were less distinct, suggesting other factors are also important for structuring these guilds. Expression of nitrogen cycling genes was substantially higher in muddier sediments, and results indicate that the potential for coupled nitrification-denitrification became increasingly prevalent as mud content increased. Altogether, results demonstrate that mud content is a strong environmental driver of diversity and N-cycling dynamics in estuarine microbial communities.
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Affiliation(s)
- Jian Sheng Boey
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Redmond Mortimer
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Agathe Couturier
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand.,Ecole Supérieure de Biologie Biochimie Biotechnologies, Faculté des Sciences, Université Catholique de Lyon, Lyon, France
| | - Katie Worrallo
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Kim M Handley
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
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29
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Molecular characterization of bacteria and archaea in a bioaugmented zero-water exchange shrimp pond. SN APPLIED SCIENCES 2021. [DOI: 10.1007/s42452-021-04392-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
AbstractIn the zero-water exchange shrimp culture pond maintained with the application of indigenous bioaugmentor, low levels of total ammonia–nitrogen were reported, indicating the relevance of indigenous microbial communities. Sediments (0–5 cm layer) were sampled from the pond (85th day) and the bacterial and archaeal communities; specifically, the ammonia oxidizers (ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and anaerobic ammonia-oxidizing bacteria) in the sediment metagenome of the pond were analysed using the 16S rRNA and functional genes. Bacterial and archaeal 16S rRNA genes showed the relative abundance of Delta-Proteobacteria and Bacteroidetes groups performing sulphur respiration and organic matter degradation, archaeal groups of anaerobic sulphur respiring Crenarchaeotae, and chemolithoautotrophic ammonia oxidizers belonging to Thaumarchaeota. The presence of these diverse bacterial and archaeal communities denotes their significant roles in the cycling the carbon, nitrogen, and sulphur thereby bringing out efficient bioremediation in the bioaugmented zero-water exchange shrimp culture pond. Similarly, the functional gene-specific study showed the predominance of Nitrosomonas sp. (ammonia-oxidizing bacteria), Nitrosopumilus maritimus (ammonia-oxidizing archaea), and Candidatus Kuenenia (anaerobic ammonia-oxidizing bacteria) in the system, which points to their importance in the removal of accumulated ammonia. Thus, this study paves the way for understanding the microbial communities, specifically the ammonia oxidizers responsible for maintaining healthy and optimal environmental conditions in the bioaugmented zero-water exchange shrimp culture pond.
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30
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Ruiz-González C, Rodellas V, Garcia-Orellana J. The microbial dimension of submarine groundwater discharge: current challenges and future directions. FEMS Microbiol Rev 2021; 45:6128669. [PMID: 33538813 PMCID: PMC8498565 DOI: 10.1093/femsre/fuab010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/28/2021] [Indexed: 12/22/2022] Open
Abstract
Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, the microbial dimension of SGD remains poorly understood. SGD can influence marine microbial communities through supplying chemical compounds and microorganisms, and in turn, microbes at the land–ocean transition zone determine the chemistry of the groundwater reaching the ocean. However, compared with inland groundwater, little is known about microbial communities in coastal aquifers. Here, we review the state of the art of the microbial dimension of SGD, with emphasis on prokaryotes, and identify current challenges and future directions. Main challenges include improving the diversity description of groundwater microbiota, characterized by ultrasmall, inactive and novel taxa, and by high ratios of sediment-attached versus free-living cells. Studies should explore microbial dynamics and their role in chemical cycles in coastal aquifers, the bidirectional dispersal of groundwater and seawater microorganisms, and marine bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization and linking taxonomy to activity but also considering the entire groundwater–marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, microbial ecology) are needed to frame the study of terrestrial and aquatic microorganisms beyond the limits of their presumed habitats, and to foster our understanding of SGD processes and their influence in coastal biogeochemical cycles.
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Affiliation(s)
- Clara Ruiz-González
- Institut de Ciències del Mar (ICM-CSIC). Passeig Marítim de la Barceloneta 37-49, E08003 Barcelona, Spain
| | - Valentí Rodellas
- Institut de Ciència i Tecnologia Ambientals (ICTA-UAB), Universitat Autònoma de Barcelona, E08193 Bellaterra, Spain
| | - Jordi Garcia-Orellana
- Institut de Ciència i Tecnologia Ambientals (ICTA-UAB), Universitat Autònoma de Barcelona, E08193 Bellaterra, Spain.,Departament de Física, Universitat Autònoma de Barcelona, E08193 Bellaterra, Spain
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31
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Santos JP, Sousa AGG, Ribeiro H, Magalhães C. The Response of Estuarine Ammonia-Oxidizing Communities to Constant and Fluctuating Salinity Regimes. Front Microbiol 2020; 11:574815. [PMID: 33324363 PMCID: PMC7727400 DOI: 10.3389/fmicb.2020.574815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 11/02/2020] [Indexed: 01/04/2023] Open
Abstract
Aerobic nitrification is a fundamental nitrogen biogeochemical process that links the oxidation of ammonia to the removal of fixed nitrogen in eutrophicated water bodies. However, in estuarine environments there is an enormous variability of water physicochemical parameters that can affect the ammonia oxidation biological process. For instance, it is known that salinity can affect nitrification performance, yet there is still a lack of information on the ammonia-oxidizing communities behavior facing daily salinity fluctuations. In this work, laboratory experiments using upstream and downstream estuarine sediments were performed to address this missing gap by comparing the effect of daily salinity fluctuations with constant salinity on the activity and diversity of ammonia-oxidizing microorganisms (AOM). Activity and composition of AOM were assessed, respectively by using nitrogen stable isotope technique and 16S rRNA gene metabarcoding analysis. Nitrification activity was negatively affected by daily salinity fluctuations in upstream sediments while no effect was observed in downstream sediments. Constant salinity regime showed clearly higher rates of nitrification in upstream sediments while a similar nitrification performance between the two salinity regimes was registered in the downstream sediments. Results also indicated that daily salinity fluctuation regime had a negative effect on both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) community’s diversity. Phylogenetically, the estuarine downstream AOM were dominated by AOA (0.92–2.09%) followed by NOB (0.99–2%), and then AOB (0.2–0.32%); whereas NOB dominated estuarine upstream sediment samples (1.4–9.5%), followed by AOA (0.27–0.51%) and AOB (0.01–0.23%). Analysis of variance identified the spatial difference between samples (downstream and upstream) as the main drivers of AOA and AOB diversity. Our study indicates that benthic AOM inhabiting different estuarine sites presented distinct plasticity toward the salinity regimes tested. These findings help to improve our understanding in the dynamics of the nitrogen cycle of estuarine systems by showing the resilience and consequently the impact of different salinity regimes on the diversity and activity of ammonia oxidizer communities.
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Affiliation(s)
- João Pereira Santos
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal.,Department F.A. Forel for Environmental and Aquatic Sciences, Section of Earth and Environmental Sciences, Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland
| | - António G G Sousa
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal
| | - Hugo Ribeiro
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal.,Abel Salazar Institute of Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Catarina Magalhães
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Matosinhos, Portugal.,Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,School of Science & Engineering, University of Waikato, Hamilton, New Zealand.,Ocean Frontier Institute, Dalhousie University, Halitax, NS, Canada
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Chen X, Ye Q, Sanders CJ, Du J, Zhang J. Bacterial-derived nutrient and carbon source-sink behaviors in a sandy beach subterranean estuary. MARINE POLLUTION BULLETIN 2020; 160:111570. [PMID: 32861939 DOI: 10.1016/j.marpolbul.2020.111570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/01/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities in subterranean estuaries play important roles in the biogeochemical cycle. However, the microorganisms associated with biogeochemical behaviors in subterranean estuaries have received little attention. Here, the bacterial communities were compared between the fresh and saline groundwater in a subterranean estuary. Correlation analysis between bacterial groups and salinity indicated that different species represented different groundwater types. The key bacterial groups found along the subterranean estuaries have been shown to influence organic pollutant degradation and nitrate utilization. These species may be potential candidates for the in situ bioremediation of subterranean estuaries that are contaminated with pollutants. The utilization of nitrate and organic pollutants by bacteria in subterranean estuaries serves as a nitrate sink and inorganic carbon source. Our results show the role of bacteria in remediating pollutants through submarine groundwater discharge (SGD) to the coastal ocean, and specific species may be helpful in selecting reasonable groundwater end-members and reducing SGD uncertainties.
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Affiliation(s)
- Xiaogang Chen
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China; School of Engineering, Westlake University, Hangzhou 310024, China
| | - Qi Ye
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China.
| | - Christian J Sanders
- National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW 2450, Australia
| | - Jinzhou Du
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China; Institute of Eco-Chongming (IEC), Shanghai 202162, China
| | - Jing Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
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Mei X, Wang Y, Yang Y, Xu L, Wang Y, Guo Z, Shen W, Zhang Z, Ma M, Ding Y, Xiao Y, Yang X, Yin C, Guo W, Xu K, Wang C. Enhanced treatment of nitroaniline-containing wastewater by a membrane-aerated biofilm reactor: Simultaneous nitroaniline degradation and nitrogen removal. Sep Purif Technol 2020. [DOI: 10.1016/j.seppur.2020.117078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Zou D, Liu H, Li M. Community, Distribution, and Ecological Roles of Estuarine Archaea. Front Microbiol 2020; 11:2060. [PMID: 32983044 PMCID: PMC7484942 DOI: 10.3389/fmicb.2020.02060] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/05/2020] [Indexed: 12/04/2022] Open
Abstract
Archaea are diverse and ubiquitous prokaryotes present in both extreme and moderate environments. Estuaries, serving as links between the land and ocean, harbor numerous microbes that are relatively highly active because of massive terrigenous input of nutrients. Archaea account for a considerable portion of the estuarine microbial community. They are diverse and play key roles in the estuarine biogeochemical cycles. Ammonia-oxidizing archaea (AOA) are an abundant aquatic archaeal group in estuaries, greatly contributing estuarine ammonia oxidation. Bathyarchaeota are abundant in sediments, and they may involve in sedimentary organic matter degradation, acetogenesis, and, potentially, methane metabolism, based on genomics. Other archaeal groups are also commonly detected in estuaries worldwide. They include Euryarchaeota, and members of the DPANN and Asgard archaea. Based on biodiversity surveys of the 16S rRNA gene and some functional genes, the distribution and abundance of estuarine archaea are driven by physicochemical factors, such as salinity and oxygen concentration. Currently, increasing amount of genomic information for estuarine archaea is becoming available because of the advances in sequencing technologies, especially for AOA and Bathyarchaeota, leading to a better understanding of their functions and environmental adaptations. Here, we summarized the current knowledge on the community composition and major archaeal groups in estuaries, focusing on AOA and Bathyarchaeota. We also highlighted the unique genomic features and potential adaptation strategies of estuarine archaea, pointing out major unknowns in the field and scope for future research.
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Affiliation(s)
- Dayu Zou
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongbin Liu
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of Southern Marine Science & Engineering Guangdong Laboratory, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Meng Li
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
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Xie R, Rao P, Pang Y, Shi C, Li J, Shen D. Salt intrusion alters nitrogen cycling in tidal reaches as determined in field and laboratory investigations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 729:138803. [PMID: 32361438 DOI: 10.1016/j.scitotenv.2020.138803] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/06/2020] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Salinization is a growing problem throughout the world and poses a threat especially to freshwater ecosystems. However, much remains to be learned about the mechanisms by which salinity impacts microbially mediated biogeochemical processes. Elevated nitrogen (N) concentrations in estuarine ecosystems have led to their eutrophication, but the relationship between N transformation and the functional genes involved in the response to saltwater intrusion is poorly understood. Here, using the Minjiang River, a tidal river in southeastern China as an easily accessible natural laboratory, we conducted a 2-year field survey to investigate N speciation during ebb and flood tides. Then, in a laboratory experiment we simulated the varying degrees of salt intrusion that occur in natural tidal reaches. The microcosm study allowed quantitative assessments of N transformation and functional gene responses. The field surveys showed that concentrations of NH4+ rose during flood tides, while the concentrations of NO3- and total N fluctuated. In the microcosms, NO3- concentrations decreased in response to salt pulses, due to simultaneous declines in the abundance of genes responsible for nitrification and increases in the abundance of those involved in dissimilatory nitrate reduction to ammonium (DNRA). The elevated salinity led to increased yields of NH4+, a response that correlated positively with the abundance of nrfA genes, involved in DNRA. Furthermore, an increase in salinity promoted N2O accumulation during the denitrification process. Altogether, our study suggests that saltwater intrusion leads to a decrease in nitrification while favoring N transformation via denitrification and DNRA and that N2O accumulation in the water is dependent on the strength of the salt pulse.
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Affiliation(s)
- Rongrong Xie
- College of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China; Key Laboratory of Pollution Control and Resource Recycling of Fujian Province, Fujian Normal University, Fuzhou 350007, China; Section of Physical Oceanography and Instrumentation, Leibniz Institute for Baltic Sea Research, Warnemuende, D-18119 Rostock, Germany
| | - Peiyuan Rao
- College of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Yong Pang
- College of Environment, Hohai University, Nanjing 210098, China
| | - Chengchun Shi
- Fuzhou Research Academy of Environmental Sciences, Fuzhou 350013, China
| | - Jiabing Li
- College of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China; Key Laboratory of Pollution Control and Resource Recycling of Fujian Province, Fujian Normal University, Fuzhou 350007, China.
| | - Dandan Shen
- Section of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Warnemuende, D-18119 Rostock, Germany; Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden.
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Hampel JJ, McCarthy MJ, Aalto SL, Newell SE. Hurricane Disturbance Stimulated Nitrification and Altered Ammonia Oxidizer Community Structure in Lake Okeechobee and St. Lucie Estuary (Florida). Front Microbiol 2020; 11:1541. [PMID: 32754132 PMCID: PMC7366250 DOI: 10.3389/fmicb.2020.01541] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/12/2020] [Indexed: 01/01/2023] Open
Abstract
Nitrification is an important biological link between oxidized and reduced forms of nitrogen (N). The efficiency of nitrification plays a key role in mitigating excess N in eutrophic systems, including those with cyanobacterial harmful algal blooms (cyanoHABs), since it can be closely coupled with denitrification and removal of excess N. Recent work suggests that competition for ammonium (NH4+) between ammonia oxidizers and cyanoHABs can help determine microbial community structure. Nitrification rates and ammonia-oxidizing archaeal (AOA) and bacterial (AOB) community composition and gene abundances were quantified in Lake Okeechobee and St. Lucie Estuary in southern Florida (United States). We sampled during cyanobacterial (Microcystis) blooms in July 2016 and August 2017 (2 weeks before Hurricane Irma) and 10 days after Hurricane Irma made landfall. Nitrification rates were low during cyanobacterial blooms in Lake Okeechobee and St. Lucie Estuary, while low bloom conditions in St. Lucie Estuary coincided with greater nitrification rates. Nitrification rates in the lake were correlated (R2 = 0.94; p = 0.006) with AOA amoA abundance. Following the hurricane, nitrification rates increased by an order of magnitude, suggesting that nitrifiers outcompeted cyanobacteria for NH4+ under turbid, poor light conditions. After Irma, AOA and AOB abundances increased in St. Lucie Estuary, while only AOB increased in Lake Okeechobee. AOA sequences clustered into three major lineages: Nitrosopumilales (NP), Nitrososphaerales (NS), and Nitrosotaleales (NT). Many of the lake OTUs placed within the uncultured and uncharacterized NS δ and NT β clades, suggesting that these taxa are ecologically important along this eutrophic, lacustrine to estuarine continuum. After the hurricane, the AOA community shifted toward dominance by freshwater clades in St. Lucie Estuary and terrestrial genera in Lake Okeechobee, likely due to high rainfall and subsequent increased turbidity and freshwater loading from the lake into the estuary. AOB community structure was not affected by the disturbance. AOA communities were consistently more diverse than AOB, despite fewer sequences recovered, including new, unclassified, eutrophic ecotypes, suggesting a wider ecological biogeography than the oligotrophic niche originally posited. These results and other recent reports contradict the early hypothesis that AOB dominate ammonia oxidation in high-nutrient or terrestrial-influenced systems.
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Affiliation(s)
- Justyna J Hampel
- School of Ocean Science and Engineering, The University of Southern Mississippi, Ocean Springs, MS, United States.,Department of Earth and Environmental Sciences, Wright State University, Dayton, OH, United States
| | - Mark J McCarthy
- Department of Earth and Environmental Sciences, Wright State University, Dayton, OH, United States
| | - Sanni L Aalto
- Section for Aquaculture, The North Sea Research Centre, DTU Aqua, Technical University of Denmark, Hirtshals, Denmark
| | - Silvia E Newell
- Department of Earth and Environmental Sciences, Wright State University, Dayton, OH, United States
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Adyasari D, Hassenrück C, Montiel D, Dimova N. Microbial community composition across a coastal hydrological system affected by submarine groundwater discharge (SGD). PLoS One 2020; 15:e0235235. [PMID: 32598345 PMCID: PMC7323985 DOI: 10.1371/journal.pone.0235235] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/10/2020] [Indexed: 11/18/2022] Open
Abstract
Mobile Bay, the fourth largest estuary in the USA located in the northern Gulf of Mexico, is known for extreme hypoxia in the water column during dry season caused by NH4+-rich and anoxic submarine groundwater discharge (SGD). Nutrient dynamics in the coastal ecosystem point to potentially elevated microbial activities; however, little is known about microbial community composition and their functional roles in this area. In this study, we investigated microbial community composition, distribution, and metabolic prediction along the coastal hydrological compartment of Mobile Bay using 16S rRNA gene sequencing. We collected microbial samples from surface (river and bay water) and subsurface water (groundwater and coastal pore water from two SGD sites with peat and sandy lithology, respectively). Salinity was identified as the primary factor affecting the distribution of microbial communities across surface water samples, while DON and PO43- were the major predictor of community shift within subsurface water samples. Higher microbial diversity was found in coastal pore water in comparison to surface water samples. Gammaproteobacteria, Bacteroidia, and Oxyphotobacteria dominated the bacterial community. Among the archaea, methanogens were prevalent in the peat-dominated SGD site, while the sandy SGD site was characterized by a higher proportion of ammonia-oxidizing archaea. Cyanobium PCC-6307 and unclassified Thermodesulfovibrionia were identified as dominant taxa strongly associated with trends in environmental parameters in surface and subsurface samples, respectively. Microbial communities found in the groundwater and peat layer consisted of taxa known for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This finding suggested that microbial communities might also play a significant role in mediating nitrogen transformation in the SGD flow path and in affecting the chemical composition of SGD discharging to the water column. Given the ecological importance of microorganisms, further studies at higher taxonomic and functional resolution are needed to accurately predict chemical biotransformation processes along the coastal hydrological continuum, which influence water quality and environmental condition in Mobile Bay.
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Affiliation(s)
- Dini Adyasari
- Department of Biogeochemistry and Geology, Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | - Christiane Hassenrück
- Department of Biogeochemistry and Geology, Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | - Daniel Montiel
- Department of Geological Sciences, Coastal Hydrogeology Laboratory, University of Alabama, Alabama, AL, United States of America
- Geosyntec Consultants, Clearwater, FL, United States of America
| | - Natasha Dimova
- Department of Geological Sciences, Coastal Hydrogeology Laboratory, University of Alabama, Alabama, AL, United States of America
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38
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Yuan D, Wang W, Liu C, Xu L, Fei H, Wang X, Shen M, Wang S, Wang M, Zhu G. Source, contribution and microbial N-cycle of N-compounds in China fresh snow. ENVIRONMENTAL RESEARCH 2020; 183:109146. [PMID: 31991341 DOI: 10.1016/j.envres.2020.109146] [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: 09/16/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 06/10/2023]
Abstract
The importance and contribution of nitrogen compounds and the related microbial nitrogen cycling processes in fresh snow are not well understood under the current research background. We collected fresh snow samples from 21 cities that 80% are from China during 2016 and 2017. Principal component analysis showed that SO42- were in the first principal component, and N-compounds were the second. Furthermore, the main pollutant ions SO42- and NO3- were from anthropogenic sources, and SO42- contributed (61%) more to the pollution load than NO3- (29%), which were confirmed through a series of precipitation mechanism analysis. We selected five N-cycle processes (consist of oxidation and reduction processes) for molecular biology experiments, including Ammonia-oxidation process, Nitrite-oxidation process, Denitrification process, Anaerobic-ammoxidation process (Anammox) and Dissimilatory nitrate reduction to ammonium process (DNRA). Except ammonia-oxidizing archaeal (AOA) and bacterial (AOB) amoA genes (above 107 copies g-1), molecular assays of key functional genes in various nitrogen conversion processes showed a belowed detection limit number, and AOB abundance was always higher than AOA. The determination of the microbial transformation rate using the 15N-isotope tracer technique showed that the potential rate of five N-conversion processes was very low, which is basically consistent with the results from molecular biology studies. Taken together, our results illustrated that microbial nitrogen cycle processes are not the primary biological processes causing the pollution in China fresh snow.
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Affiliation(s)
- Dongdan Yuan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Municipal and Environmental Engineering, Jilin Jianzhu University, Changchun, 130118, China
| | - Weidong Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Chunlei Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Liya Xu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hexin Fei
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xiaoling Wang
- School of Municipal and Environmental Engineering, Jilin Jianzhu University, Changchun, 130118, China
| | - Mengnan Shen
- School of Municipal and Environmental Engineering, Jilin Jianzhu University, Changchun, 130118, China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Mengzi Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Municipal and Environmental Engineering, Jilin Jianzhu University, Changchun, 130118, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Vegetation-Dependent Response to Drought in Salt Marsh Ammonia-Oxidizer Communities. Microorganisms 2019; 8:microorganisms8010009. [PMID: 31861554 PMCID: PMC7022406 DOI: 10.3390/microorganisms8010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 11/17/2022] Open
Abstract
We investigated the impacts of drought on ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a salt marsh and compared the response to the total bacterial community. We analyzed abundance and community composition of amoA genes by QPCR and TRFLP, respectively, in three vegetation zones in 2014 (pre-drought), 2016 (drought), and 2017 (post-drought), and analyzed bacterial 16S rRNA genes by QPCR, TRFLP, and MiSeq analyses. AOA and AOB abundance in the Spartina patens zone increased significantly in 2016, while abundance decreased in the tall S. alterniflora zone, and showed little change in the short S. alterniflora zone. Total bacterial abundance declined annually in all vegetation zones. Significant shifts in community composition were detected in 2016 in two of the three vegetation zones for AOA and AOB, and in all three vegetation zones for total bacteria. Abundance and community composition of AOA and AOB returned to pre-drought conditions by 2017, while bacterial abundance continued to decline, suggesting that nitrifiers may be more resilient to drought than other bacterial communities. Finding vegetation-specific drought responses among N-cycling microbes may have broad implications for changes in N availability and marsh productivity, particularly if vegetation patterns continue to shift as predicted due to sea level rise.
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Zhao C, Liu S, Jiang Z, Wu Y, Cui L, Huang X, Macreadie PI. Nitrogen purification potential limited by nitrite reduction process in coastal eutrophic wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 694:133702. [PMID: 31386948 DOI: 10.1016/j.scitotenv.2019.133702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/16/2019] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
Coastal wetlands accumulate enormous quantities of nitrogen due to their position at the interface between land and sea and high trapping capacity. Fortunately, they have high nitrogen (N) purifying (removal) capacity, which means that they likely play an important role in mitigating against coastal eutrophication. However studies that empirically measure the degree to which wetlands purify nitrogen and their removal pathways (e.g. denitrification, anammox, plant uptake, microbial immobilization, etc.) are rare. In this study, the N purification potential (denitrification and anammox) and enzyme activities related to denitrification in different subtropical wetlands types were conducted in nitrogen-enriched wetlands of Daya Bay, Southern China. We found the average N purification rate was 11.4 μmol N·kg-1·h-1, with denitrification accounting for 84.2%-100% of the total N2 production in the wetlands of Daya Bay. The N purification potential in the wet season, subtidal areas and mangrove forests were generally observed to be higher than that in the dry season, high and low tidal areas, barren and estuary habitats, respectively. Correspondingly, these differences were mainly driven by the temperature, Eh and NH4-N, respectively. Additionally, the nitrate reductase (Nar) and nitrite reductase (Nir) activities tended to be similar among different seasons and tidal areas, however, Nir activity in mangrove forest was 1.5-fold and 2-fold of the estuarine and barren areas, respectively. Meanwhile, Nir showed a positive correlation with denitrification rate. These results indicate that NO2-N reduction, the key control mechanism for N purification, should be the rate-limiting step of the denitrification process in Daya Bay wetlands. Notably, mangroves could improve N removal rates by 48.0% compared to other wetlands. Therefore, protecting and restoring mangrove ecosystems could be an effective way to reduce the risk of coastal eutrophication.
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Affiliation(s)
- Chunyu Zhao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Lijun Cui
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Peter I Macreadie
- School of Life and Environmental Sciences, Faculty of Science Engineering and Built Environment, Deakin University, Burwood, Victoria 3125, Australia
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Bernhard AE, Chelsky A, Giblin AE, Roberts BJ. Influence of local and regional drivers on spatial and temporal variation of ammonia-oxidizing communities in Gulf of Mexico salt marshes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:825-834. [PMID: 31646752 DOI: 10.1111/1758-2229.12802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
We characterized ammonia-oxidizing archaea (AOA) and bacteria (AOB) from salt marsh sediments in the Gulf of Mexico over 5 years to identify environmental drivers of nitrifying community patterns following the Deepwater Horizon oil spill. Samples were collected from oiled and unoiled sites in July of 2012-2016 from 12 marshes spanning three regions on the Louisiana coast. No consistent oil effect was detected for either AOA or AOB abundance or community composition. At the local scale, abundance was correlated with changes in marsh elevation, suggesting that oxygen may be an important driver. Regional differences in abundance were best explained by salinity and soil moisture, while interannual variation may be more linked to changes in climate and Mississippi River discharge. Variation of AOA communities was correlated with organic sediment nutrients, while AOB communities were correlated with soil extractable nutrients. AOA and AOB diversity and AOB abundance decreased in 2014 in all regions, suggesting that broad-scale drivers, such as climate, may explain synchronous shifts throughout the coastal area. Our results provide insights about large-scale disturbances on nitrifying microbes in the Gulf of Mexico, and suggest that nitrogen cycling may be controlled primarily by local factors, but large-scale drivers might override these localized differences at times.
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Affiliation(s)
| | - Ariella Chelsky
- Louisiana Universities Marine Consortium, Chauvin, LA
- San Francisco Estuary Institute, Richmond, CA
| | - Anne E Giblin
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA
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Rajta A, Bhatia R, Setia H, Pathania P. Role of heterotrophic aerobic denitrifying bacteria in nitrate removal from wastewater. J Appl Microbiol 2019; 128:1261-1278. [PMID: 31587489 DOI: 10.1111/jam.14476] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 11/27/2022]
Abstract
With the increase in industrial and agricultural activities, a large amount of nitrogenous compounds are released into the environment, leading to nitrate pollution. The perilous effects of nitrate present in the environment pose a major threat to human and animal health. Bioremediation provides a cost-effective and environmental friendly method to deal with this problem. The process of aerobic denitrification can reduce nitrate compounds to harmless dinitrogen gas. This review provides a brief view of the exhaustive role played by aerobic denitrifiers for tackling nitrate pollution under different ecological niches and their dependency on various environmental parameters. It also provides an understanding of the enzymes involved in aerobic denitrification. The role of aerobic denitrification to solve the issues faced by the conventional method (aerobic nitrification-anaerobic denitrification) in treating nitrogen-polluted wastewaters is elaborated.
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Affiliation(s)
- A Rajta
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
| | - R Bhatia
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
| | - H Setia
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
| | - P Pathania
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
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43
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Nsenga Kumwimba M, Meng F. Roles of ammonia-oxidizing bacteria in improving metabolism and cometabolism of trace organic chemicals in biological wastewater treatment processes: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 659:419-441. [PMID: 31096373 DOI: 10.1016/j.scitotenv.2018.12.236] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/20/2018] [Accepted: 12/15/2018] [Indexed: 05/27/2023]
Abstract
While there has been a significant recent improvement in the removal of pollutants in natural and engineered systems, trace organic chemicals (TrOCs) are posing a major threat to aquatic environments and human health. There is a critical need for developing potential strategies that aim at enhancing metabolism and/or cometabolism of these compounds. Recently, knowledge regarding biodegradation of TrOCs by ammonia-oxidizing bacteria (AOB) has been widely developed. This review aims to delineate an up-to-date version of the ecophysiology of AOB and outline current knowledge related to biodegradation efficiencies of the frequently reported TrOCs by AOB. The paper also provides an insight into biodegradation pathways by AOB and transformation products of these compounds and makes recommendations for future research of AOB. In brief, nitrifying WWTFs (wastewater treatment facilities) were superior in degrading most TrOCs than non-nitrifying WWTFs due to cometabolic biodegradation by the AOB. To fully understand and/or enhance the cometabolic biodegradation of TrOCs by AOB, recent molecular research has focused on numerous crucial factors including availability of the compounds to AOB, presence of growth substrate (NH4-N), redox potentials, microorganism diversity (AOB and heterotrophs), physicochemical properties and operational parameters of the WWTFs, molecular structure of target TrOCs and membrane-based technologies, may all significantly impact the cometabolic biodegradation of TrOCs. Still, further exploration is required to elucidate the mechanisms involved in biodegradation of TrOCs by AOB and the toxicity levels of formed products.
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Affiliation(s)
- Mathieu Nsenga Kumwimba
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; Faculty of Agronomy, Department of Natural Resources and Environmental Management, University of Lubumbashi, Democratic Republic of the Congo
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China.
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Moradi S, Rasouli-Sadaghiani MH, Sepehr E, Khodaverdiloo H, Barin M. Soil nutrients status affected by simple and enriched biochar application under salinity conditions. ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:257. [PMID: 30929074 DOI: 10.1007/s10661-019-7393-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 03/13/2019] [Indexed: 06/09/2023]
Abstract
In order to study the effect of biochar application as simple and enriched, on the soil nutrients status in the salinity conditions, a research was conducted as a factorial arrangement based on completely randomized design (CRD) with three replicates. The biochar (grape pruning residues) was applied in three levels (0, 2% biochar, and 2% enriched biochar by rock phosphate and cow manure). Also, the salinity treatment was considered in three levels (2, 4.5, and 9 dSm-1). After treating the soil, it was incubated in polyethylene containers for a 70-day period at 25 °C and 70% field capacity moisture regime. The results showed that salinity significantly affected the soil pH, electrical conductivity (EC), calcium, magnesium, sodium, basal respiration, and nitrifying bacteria frequency (P < 0.001) and chloride concentration (P < 0.01). Also, the biochar significantly affected the pH, organic carbon, concentration of total nitrogen, phosphorous, solution potassium, sodium, iron, zinc, copper, basal respiration, and nitrifying bacteria frequency (P < 0.001) of the soil. The interaction effect of biochar and salinity levels was significant on soil sodium concentration (P < 0.01) and pH (P < 0.05). In comparison with the control treatment, the enriched biochar, decreased soil pH (about 1.4%) and increased the phosphorous, iron, and zinc up to 36%, 29%, and 36%, respectively and simple biochar increased the Nitrogen and Potassium up to 46% and 48%, respectively. In general, it was concluded that both types of the biochars lowered the sodium concentration of the soil in different salinity levels due to high potential of biochar for sodium absorption which this ability may be considered in saline soils remediation.
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Affiliation(s)
- Salahedin Moradi
- Soil Science, University of Urmia, Urmia, Iran.
- Agriculture Department, Payame Noor University, Tehran, Iran.
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45
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Wang X, Wang S, Shi G, Wang W, Zhu G. Factors driving the distribution and role of AOA and AOB in Phragmites communis
rhizosphere in riparian zone. J Basic Microbiol 2019; 59:425-436. [DOI: 10.1002/jobm.201800581] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/01/2018] [Accepted: 12/16/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaomin Wang
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Guoshuai Shi
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Weidong Wang
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing 100049 China
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46
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Zhou X, Li B, Guo Z, Wang Z, Luo J, Lu C. Niche Separation of Ammonia Oxidizers in Mudflat and Agricultural Soils Along the Yangtze River, China. Front Microbiol 2018; 9:3122. [PMID: 30619196 PMCID: PMC6305492 DOI: 10.3389/fmicb.2018.03122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/03/2018] [Indexed: 12/30/2022] Open
Abstract
Nitrification driven by ammonia oxidizers is a key step of nitrogen removal in estuarine environments. Spatial distribution characteristics of ammonia-oxidizers have been well understood in mudflats, but less studied in the agricultural soils next to mudflats, which also play an important role in nitrogen cycling of the estuarine ecosystem. In the present research, we investigated ammonia oxidizers' distributions along the Yangtze River estuary in Jiangsu Province, China, sampling soils right next to the estuary (mudflats) and the agricultural soils 100 m away. We determined the relationship between the abundance of amoA genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and the potential nitrification rates of the mudflats and agricultural soils. We also identified the environmental variables that correlated with the composition of the ammonia oxidizers' communities by 16S rRNA gene pyrosequencing. Results indicated that agricultural soils have significantly higher potential nitrification rates as well as the AOA abundance, and resulted in strong phylogenetic clustering only in AOA communities. The ammonia oxidizers' community compositions differed dramatically among the mudflat and agricultural sites, and stochasticity played a dominant role. The AOA communities were dominated by the Group 1.1a cluster at the mudflat, whereas the 54D9 and 29i4 clusters were dominant in agriculture soils. The dominant AOB communities in the mudflat were closely related to the Nitrosospira lineage, whereas the agricultural soils were dominated by the Nitrosomonas lineage. Soil organic matter and salinity were correlated with the ammonia oxidizers' community compositions.
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Affiliation(s)
- Xue Zhou
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
| | - Bolun Li
- School of Geographic Sciences, Nanjing University of Information Science and Technology, Nanjing, China
| | - Zhiying Guo
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Zhiyuan Wang
- Center for Eco-Environmental Research, Nanjing Hydraulic Research Institute, Nanjing, China
| | - Jian Luo
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Chunhui Lu
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing, China
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Huang S, Chen C, Jaffé PR. Seasonal distribution of nitrifiers and denitrifiers in urban river sediments affected by agricultural activities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:1282-1291. [PMID: 30045508 DOI: 10.1016/j.scitotenv.2018.06.116] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/08/2018] [Accepted: 06/10/2018] [Indexed: 05/26/2023]
Abstract
Nitrifiers and denitrifiers play a critical role in nitrogen removal in urban river sediments that are also affected by agricultural activities. However, the seasonal variations and vertical profile of these organisms in these river sediments are not well understood. In this study, the seasonal and depth (0 to 30 cm) distributions of the abundance and activity of nitrifiers and denitrifiers in sediments of the Pearl River in Guangzhou city were quantifying via qPCR and RT-qPCR according to various nitrifying and denitrifying functional genes, and their diversities were analyzed via high-throughput sequencing on an Illumina MiSeq platform. Results show that the distribution of nitrifiers and denitrifiers in these urban sediments were more abundant and active during the summer than winter; had distinct vertical distributions in the bacterial numbers and activity, with higher activity of the nirS gene (yearly averaged RNA:DNA 2.5% at 18 to 22 cm, vs. a yearly-depth average of 0.65%) but with lower overall numbers (yearly averaged 2.1 × 106 copies g-1 at 18 to 22 cm, vs. a yearly-depth average of 12.5 × 106 copies g-1); and their amoA and nosZ gene diversities in the sediments exhibited a correlation with the communities in nearby agricultural soils.
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Affiliation(s)
- Shan Huang
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ 08544, USA.
| | - Chen Chen
- South China Institute of Environmental Sciences, Ministry of Environmental Protection, Guangzhou, China
| | - Peter R Jaffé
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ 08544, USA
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48
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Mai YZ, Lai ZN, Li XH, Peng SY, Wang C. Structural and functional shifts of bacterioplanktonic communities associated with spatiotemporal gradients in river outlets of the subtropical Pearl River Estuary, South China. MARINE POLLUTION BULLETIN 2018; 136:309-321. [PMID: 30509812 DOI: 10.1016/j.marpolbul.2018.09.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 09/07/2018] [Accepted: 09/08/2018] [Indexed: 06/09/2023]
Abstract
In this study, we used high-throughput sequencing of 16S rRNA gene amplicons, to investigate the spatio-temporal variation in bacterial communities in surface-waters collected from eight major outlets of the Pearl River Estuary, South China. Betaproteobacteria were the most abundant class among the communities, followed by Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, and Acidimicrobiia. Generally, alpha-diversity increased in winter communities and the taxonomic diversity of bacterial communities differed with seasonal and spatial differences. Temperature, conductivity, salinity, pH and nutrients were the crucial environmental factors associated with shifts in the bacterial community composition. Furthermore, inferred community functions that were associated with amino acid, carbohydrate and energy metabolisms were lower in winter, whereas the relative abundance of inferred functions associated with membrane transport, bacterial motility proteins, and xenobiotics biodegradation and metabolism, were enriched in winter. These results provide new insights into the dynamics of bacterial communities within estuarine ecosystems.
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Affiliation(s)
- Yong-Zhan Mai
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Zi-Ni Lai
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
| | - Xin-Hui Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Song-Yao Peng
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Chao Wang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
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Ye F, Ma MH, Op den Camp HJM, Chatzinotas A, Li L, Lv MQ, Wu SJ, Wang Y. Different Recovery Processes of Soil Ammonia Oxidizers from Flooding Disturbance. MICROBIAL ECOLOGY 2018; 76:1041-1052. [PMID: 29644407 DOI: 10.1007/s00248-018-1183-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/26/2018] [Indexed: 06/08/2023]
Abstract
Understanding how microorganisms respond to environmental disturbance is one of the key focuses in microbial ecology. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are responsible for ammonia oxidation which is a crucial step in the nitrogen cycle. Although the physiology, distribution, and activity of AOA and AOB in soil have been extensively investigated, their recovery from a natural disturbance remains largely unknown. To assess the recovery capacities, including resistance and resilience, of AOA and AOB, soil samples were taken from a reservoir riparian zone which experienced periodically water flooding. The samples were classified into three groups (flooding, recovery, and control) for a high-throughput sequencing and quantitative PCR analysis. We used a relative quantitative index of both the resistance (RS) and resilience (RL) to assess the variation of gene abundance, alpha-diversity, and community composition. The AOA generally demonstrated a better recovery capability after the flooding disturbance compared to AOB. In particular, AOA were more resilient after the flooding disturbance. Taxa within the AOA and AOB showed different RS and RL values, with the most abundant taxa showing in general the highest RS indices. Soil NH4+ and Fe2+/Fe3+ were the main variables controlling the key taxa of AOA and AOB and probably influenced the resistance and resilience properties of AOA and AOB communities. The distinct mechanisms of AOA and AOB in maintaining community stability against the flooding disturbance might be linked to the different life-history strategies: the AOA community was more likely to represent r-strategists in contrast to the AOB community following a K-life strategy. Our results indicated that the AOA may play a vital role in ammonia oxidation in a fluctuating habitat and contribute to the stability of riparian ecosystem.
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Affiliation(s)
- Fei Ye
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mao-Hua Ma
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, 6525 AJ, the Netherlands
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany
- Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Lei Li
- Beijing Academy of Science and Technology, Beijing, 100048, China
| | - Ming-Quan Lv
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sheng-Jun Wu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China.
| | - Yu Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China.
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50
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Abstract
Submarine groundwater discharge (SGD) is a global and well-studied geological process by which groundwater of varying salinities enters coastal waters. SGD is known to transport bioactive solutes, including but not limited to nutrients (nitrogen, phosphorous, silica), gases (methane, carbon dioxide), and trace metals (iron, nickel, zinc). In addition, physical changes to the water column, such as changes in temperature and mixing can be caused by SGD. Therefore SGD influences both autotrophic and heterotrophic marine biota across all kingdoms of life. This paper synthesizes the current literature in which the impacts of SGD on marine biota were measured and observed by field, modeling, or laboratory studies. The review is grouped by organismal complexity: bacteria and phytoplankton, macrophytes (macroalgae and marine plants), animals, and ecosystem studies. Directions for future research about the impacts of SGD on marine life, including increasing the number of ecosystem assessment studies and including biological parameters in SGD flux studies, are also discussed.
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