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Gios E, Verbruggen E, Audet J, Burns R, Butterbach-Bahl K, Espenberg M, Fritz C, Glatzel S, Jurasinski G, Larmola T, Mander Ü, Nielsen C, Rodriguez AF, Scheer C, Zak D, Silvennoinen HM. Unraveling microbial processes involved in carbon and nitrogen cycling and greenhouse gas emissions in rewetted peatlands by molecular biology. BIOGEOCHEMISTRY 2024; 167:609-629. [PMID: 38707517 PMCID: PMC11068585 DOI: 10.1007/s10533-024-01122-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 01/22/2024] [Indexed: 05/07/2024]
Abstract
Restoration of drained peatlands through rewetting has recently emerged as a prevailing strategy to mitigate excessive greenhouse gas emissions and re-establish the vital carbon sequestration capacity of peatlands. Rewetting can help to restore vegetation communities and biodiversity, while still allowing for extensive agricultural management such as paludiculture. Belowground processes governing carbon fluxes and greenhouse gas dynamics are mediated by a complex network of microbial communities and processes. Our understanding of this complexity and its multi-factorial controls in rewetted peatlands is limited. Here, we summarize the research regarding the role of soil microbial communities and functions in driving carbon and nutrient cycling in rewetted peatlands including the use of molecular biology techniques in understanding biogeochemical processes linked to greenhouse gas fluxes. We emphasize that rapidly advancing molecular biology approaches, such as high-throughput sequencing, are powerful tools helping to elucidate the dynamics of key biogeochemical processes when combined with isotope tracing and greenhouse gas measuring techniques. Insights gained from the gathered studies can help inform efficient monitoring practices for rewetted peatlands and the development of climate-smart restoration and management strategies. Supplementary Information The online version contains supplementary material available at 10.1007/s10533-024-01122-6.
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Affiliation(s)
- Emilie Gios
- NINA, Norwegian Institute for Nature Research, PO Box 5685, Torgarden, NO-7485 Trondheim, Norway
| | - Erik Verbruggen
- Plants and Ecosystems Research Group, Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk, 2610 Antwerp, Belgium
| | - Joachim Audet
- Department of Ecoscience, Aarhus University, C.F. Møllers Allé, 8000 Aarhus, Denmark
| | - Rachel Burns
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Klaus Butterbach-Bahl
- Institute of Meteorology and Climate Research, Atmospheric Environmental Research, Karlsruhe Institute of Technology, 82467 Garmisch-Partenkirchen, Germany
- Department of Agroecology, Pioneer Center for Research in Sustainable Agricultural Futures (Land-CRAFT), Aarhus University, 8000 Aarhus, Denmark
| | - Mikk Espenberg
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 St., Vanemuise, 51003 Tartu, Estonia
| | - Christian Fritz
- Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Stephan Glatzel
- Department of Geography and Regional Research, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Gerald Jurasinski
- Faculty of Agriculture and Environment, Landscape Ecology and Site Evaluation, University of Rostock, Justus-von-Liebig-Weg 6, 18059 Rostock, Germany
- Department of Maritime Systems, Faculty of Interdisciplinary Research, University of Rostock, Albert- Einstein-Straße 3, 18059 Rostock, Germany
| | - Tuula Larmola
- Natural Resources Institute Finland (Luke), 00790 Helsinki, Finland
| | - Ülo Mander
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 St., Vanemuise, 51003 Tartu, Estonia
| | - Claudia Nielsen
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Blichers Alle 20, 8830 Tjele, Denmark
- CBIO, Centre for Circular Bioeconomy, Aarhus University, 8830 Tjele, Denmark
| | - Andres F. Rodriguez
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Blichers Alle 20, 8830 Tjele, Denmark
| | - Clemens Scheer
- Institute of Meteorology and Climate Research, Atmospheric Environmental Research, Karlsruhe Institute of Technology, 82467 Garmisch-Partenkirchen, Germany
| | - Dominik Zak
- Department of Ecoscience, Aarhus University, C.F. Møllers Allé, 8000 Aarhus, Denmark
- Department of Ecohydrology and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, Germany
| | - Hanna M. Silvennoinen
- NINA, Norwegian Institute for Nature Research, PO Box 5685, Torgarden, NO-7485 Trondheim, Norway
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Huda N, Rana MR, Huq MA, Al-Mamun A, Rahman ST, Alam MK, Rahman MM. Understanding vermicompost and organic manure interactions: impact on toxic elements, nitrification activity, comammox Nitrospira inopinata, and archaea/bacteria. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:355. [PMID: 38466496 DOI: 10.1007/s10661-024-12491-8] [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] [Accepted: 02/19/2024] [Indexed: 03/13/2024]
Abstract
Vermicompost is a substantial source of nutrients, promotes soil fertility, and maintains or increases soil organic matter levels. Potentially toxic elements (PTEs) in vermicompost impact on nitrification activity. However, it is yet unknown how vermicompost affects nitrifying bacteria and archaea, comammox Nitrospira inopinata (complete ammonia oxidizers), net nitrification rates (NNRs), and PTEs. The effects of vermicompost application on NNRs, potential nitrification rates (NPs), PTEs, and the abundances of comammox N. inopinata bacteria, nitrite-oxidizing bacteria (NOB), and ammonia-oxidizing bacteria (AOB)/archaea (AOA) were studied. NNRs and NPs were significantly higher (p < 0.05) in fresh cow-dung vermicompost (stored for 40 days) as compared with other organic manure. The level of PTEs (Cu2+, Fe2+, Pb2+, Cd2+, and Zn2+) was significantly lower (p < 0.05) in vermicompost as compared with compost of waste material with Trichoderma and cow dung. Comammox N. inopinata, NOB, AOB, and AOA were significantly higher (p < 0.05) in stored cow-dung vermicompost (more than 1 year) as compared with other organic manure. The results of the scatterplot matrix analysis suggested that Fe2+, total nitrogen (TN), soil organic carbon (SOC), and total carbon (TC) were linearly correlated (p < 0.001) with NNRs and NPs in vermicompost and organic manure. Similarly, comammox N. inopinata bacteria, NOB, AOB, and AOA were linearly correlated (p < 0.001) with NNR and NP. These results indicated that vermicompost promoted nitrification activity by increasing microbial diversity and abundance, supplying nutrients and organic matter for microbial growth, and facilitating complex microbial interactions. It may be concluded that the influence of vermicompost, which played a great role in PTE concentration reduction, increased chemical, and biological properties, increased the growth rate of nitrifying bacteria/archaea and the nitrogen cycle.
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Affiliation(s)
- Nazmul Huda
- Agricultral and Environmental Lab, Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Md Rasel Rana
- Agricultral and Environmental Lab, Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Md Amdadul Huq
- Department of Food and Nutrition, College of Biotechnology and Natural Resources, Chung-Ang University, Anseong-Si, Gyeonggi-Do, 17546, Republic of Korea
| | - Abdullah Al-Mamun
- Agricultral and Environmental Lab, Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Shabiha Tasbir Rahman
- Agricultral and Environmental Lab, Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Md Khasrul Alam
- Agricultral and Environmental Lab, Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - M Mizanur Rahman
- Agricultral and Environmental Lab, Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh.
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Bulseco AN, Murphy AE, Giblin AE, Tucker J, Sanderman J, Bowen JL. Marsh sediments chronically exposed to nitrogen enrichment contain degraded organic matter that is less vulnerable to decomposition via nitrate reduction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:169681. [PMID: 38163591 DOI: 10.1016/j.scitotenv.2023.169681] [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: 10/11/2023] [Revised: 12/23/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
Blue carbon habitats, including salt marshes, can sequester carbon at rates that are an order of magnitude greater than terrestrial forests. This ecosystem service may be under threat from nitrate (NO3-) enrichment, which can shift the microbial community and stimulate decomposition of organic matter. Despite efforts to mitigate nitrogen loading, salt marshes continue to experience chronic NO3- enrichment, however, the long-term consequence of this enrichment on carbon storage remains unclear. To investigate the effect of chronic NO3- exposure on salt marsh organic matter decomposition, we collected sediments from three sites across a range of prior NO3- exposure: a relatively pristine marsh, a marsh enriched to ~70 μmol L-1 NO3- in the flooding seawater for 13 years, and a marsh enriched between 100 and 1000 μmol L-1 for 40 years from wastewater treatment effluent. We collected sediments from 20 to 25 cm depth and determined that sediments from the most chronically enriched site had less bioavailable organic matter and a distinct assemblage of active microbial taxa compared to the other two sites. We also performed a controlled anaerobic decomposition experiment to test whether the legacy of NO3- exposure influenced the functional response to additional NO3-. We found significant changes to microbial community composition resulting from experimental NO3- addition. Experimental NO3- addition also increased microbial respiration in sediments collected from all sites. However, sediments from the most chronically enriched site exhibited the smallest increase, the lowest rates of total NO3- reduction by dissimilatory nitrate reduction to ammonium (DNRA), and the highest DNF:DNRA ratios. Our results suggest that chronic exposure to elevated NO3- may lead to residual pools of organic matter that are less biologically available for decomposition. Thus, it is important to consider the legacy of nutrient exposure when examining the carbon cycle of salt marsh sediments.
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Affiliation(s)
- Ashley N Bulseco
- Marine Science Center, Northeastern University, Nahant, MA, USA; Department of Biological Sciences, University of New Hampshire, Durham, NH, USA
| | - Anna E Murphy
- Marine Science Center, Northeastern University, Nahant, MA, USA; INSPIRE Environmental, Newport, RI, USA
| | - Anne E Giblin
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Jane Tucker
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | | | - Jennifer L Bowen
- Marine Science Center, Northeastern University, Nahant, MA, USA.
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Martínez-Colón M, Capparelli MV, Kolb D, Moulatlet GM. Trophic transfer mechanisms of potentially toxic elements from sediment and plant leaves (Rhizophora mangle) to fiddler crabs (Minuca rapax) (). MARINE POLLUTION BULLETIN 2023; 197:115786. [PMID: 37988967 DOI: 10.1016/j.marpolbul.2023.115786] [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: 09/01/2023] [Revised: 10/23/2023] [Accepted: 11/11/2023] [Indexed: 11/23/2023]
Abstract
To assess "bottom-up" to "top-down" trophic transfer, we analyze As, Cd, Co, Cr, Cu, Hg, Ni, Se, Zn, Fe, and Mn from two sediment chemical fractions (exchangeable and organic-bound), red mangrove (Rhizophora mangle) leaves, and fiddler crab (M. rapax) soft tissues from Isla del Carmen, Yucatán Peninsula. Both mechanisms were observed indictive that R. mangle and M. rapax indeed bioaccumulated the toxic elements from the different matrices with the latter being a macro-concentrator only for Cu and Zn. Although the modified Geo-accumulation factor (combined exchangeable and organic matter fractions) suggested that the studied sites are practically "uncontaminated", Hg is the only toxic element to be having a "moderately to strongly" impact. Data shows how M. rapax had progressively bioaccumulated Hg, but no biomagnification could be corroborated given that the fiddler crab behaved as a de-concentrator.
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Affiliation(s)
- Michael Martínez-Colón
- School of the Environment, Florida A&M University, 1515 S MLK Boulevard, Tallahassee, FL 32307, United States of America.
| | - Mariana V Capparelli
- Estación el Carmen, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Carretera Carmen-Puerto Real Km. 9.5, C. P 24157 Ciudad del Carmen, Campeche, México.
| | - Daniel Kolb
- School of the Environment, Florida A&M University, 1515 S MLK Boulevard, Tallahassee, FL 32307, United States of America
| | - Gabriel M Moulatlet
- Red de Biología Evolutiva, Instituto de Ecología, A.C., Xalapa, Veracruz, México
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Yang S, Dong M, Lu H, Cai Z, Ge M, Xing J, Huang H, Huang Y, Sun G, Zhou S, Xu M. Explaining nitrogen turnover in sediments and water through variations in microbial community composition and potential function. CHEMOSPHERE 2023; 344:140379. [PMID: 37827459 DOI: 10.1016/j.chemosphere.2023.140379] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 09/20/2023] [Accepted: 10/05/2023] [Indexed: 10/14/2023]
Abstract
Anthropogenic activities greatly impact nitrogen (N) biogeochemical cycling in aquatic ecosystems. High N concentrations in coastal aquaculture waters threaten fishery production and aquaculture ecosystems and have become an urgent problem to be solved. Existing microbial flora and metabolic potential significantly regulate N turnover in aquatic ecosystems. To clarify the contribution of microorganisms to N turnover in sediment and water, we investigated three types of aquaculture ecosystems in coastal areas of Guangdong, China. Nitrate nitrogen (NO3--N) was the dominant component of total nitrogen in the sediment (interstitial water, 90.4%) and water (61.6%). This finding indicates that NO3--N (1.67-2.86 mg/L and 2.98-7.89 mg/L in the sediment and water) is a major pollutant in aquaculture ecosystems. In water, the relative abundances of assimilation nitrogen reduction and aerobic denitrifying bacteria, as well as the metabolic potentials of nitrogen fixation and dissimilated nitrogen in fish monoculture, were only 61.0%, 31.5%, 47.5%, and 27.2% of fish and shrimp polyculture, respectively. In addition, fish-shrimp polyculture reduced NO3--N content (2.86 mg/L) compared to fish monoculture (7.89 mg/L), which was consistent with changes in aerobic denitrification and nitrate assimilation, suggesting that polyculture could reduce TN concentrations in water bodies and alleviate nitrogen pollution risks. Further analysis via structural equation modeling (SEM) revealed that functional pathways (36% and 31%) explained TN changes better than microbial groups in sediment and water (13% and 11%), suggesting that microbial functional capabilities explain TN better than microbial community composition and other factors (pH, O2, and aquaculture type). This study enhances our understanding of nitrogen pollution characteristics and microbial community and functional capabilities related to sediment-water nitrogen turnover in three types of aquaculture ecosystems, which can contribute to the preservation of healthy coastal ecosystems.
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Affiliation(s)
- Shan Yang
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Meijun Dong
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Huibin Lu
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Zhipeng Cai
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Meng Ge
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Jia Xing
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Haobin Huang
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Youda Huang
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Guoping Sun
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Shaofeng Zhou
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Meiying Xu
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
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Sun X, Tan E, Wang B, Gan Z, Yang J, Han J, Zhang X, Kao SJ, King G, Dong H, Jiang H. Salinity change induces distinct climate feedbacks of nitrogen removal in saline lakes. WATER RESEARCH 2023; 245:120668. [PMID: 37776589 DOI: 10.1016/j.watres.2023.120668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/19/2023] [Accepted: 09/24/2023] [Indexed: 10/02/2023]
Abstract
Current estimations of nitrogen biogeochemical cycling and N2O emissions in global lakes as well as predictions of their future changes are overrepresented by freshwater datasets, while less consideration is given to widespread saline lakes with different salinity (representing salinization or desalinization). Here, we show that N2O production by denitrification is the main process of reactive nitrogen (Nr, the general abbreviations of NH4+-N, NO2--N and NO3--N) removal in hypersaline lake sediments (e.g. Lake Chaka). The integration of our field measurements and literature data shows that in response to natural salinity decrease, potential Nr removal increases while N2O production decreases. Furthermore, denitrification-induced N2 production exhibits higher salinity sensitivity than denitrification-induced N2O production, suggesting that the contribution of N2O to Nr removal decreases with decreasing salinity. This field-investigation-based salinity response model of Nr removal indicates that under global climate change, saline lakes in the process of salinization or desalination may have distinct Nr removal and climate feedback effects: salinized lakes tend to generate a positive climate feedback, while desalinated lakes show a negative feedback. Therefore, salinity change should be considered as an important factor in assessing future trend of N2O emissions from lakes under climate change.
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Affiliation(s)
- Xiaoxi Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China; Key Laboratory of Salt Lake Geology and Environment of Qinghai Province, Qinghai Institute of Salt Lakes, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Xining 810008, China
| | - Ehui Tan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Zixuan Gan
- College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA 95616-5270, United States of America
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Jibin Han
- Key Laboratory of Salt Lake Geology and Environment of Qinghai Province, Qinghai Institute of Salt Lakes, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Xining 810008, China
| | - Xiying Zhang
- Key Laboratory of Salt Lake Geology and Environment of Qinghai Province, Qinghai Institute of Salt Lakes, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Xining 810008, China
| | - Shuh-Ji Kao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China
| | - Gary King
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China; Frontiers Science Center for Deep-time Digital Earth, China University of Geosciences (Beijing), Beijing 100083, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China; Key Laboratory of Salt Lake Geology and Environment of Qinghai Province, Qinghai Institute of Salt Lakes, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Xining 810008, China; Frontiers Science Center for Deep-time Digital Earth, China University of Geosciences (Beijing), Beijing 100083, China.
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7
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Booth JM, Fusi M, Marasco R, Daffonchio D. The microbial landscape in bioturbated mangrove sediment: A resource for promoting nature-based solutions for mangroves. Microb Biotechnol 2023. [PMID: 37209285 PMCID: PMC10364319 DOI: 10.1111/1751-7915.14273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/25/2023] [Accepted: 04/30/2023] [Indexed: 05/22/2023] Open
Abstract
Globally, soils and sediments are affected by the bioturbation activities of benthic species. The consequences of these activities are particularly impactful in intertidal sediment, which is generally anoxic and nutrient-poor. Mangrove intertidal sediments are of particular interest because, as the most productive forests and one of the most important stores of blue carbon, they provide global-scale ecosystem services. The mangrove sediment microbiome is fundamental for ecosystem functioning, influencing the efficiency of nutrient cycling and the abundance and distribution of key biological elements. Redox reactions in bioturbated sediment can be extremely complex, with one reaction creating a cascade effect on the succession of respiration pathways. This facilitates the overlap of different respiratory metabolisms important in the element cycles of the mangrove sediment, including carbon, nitrogen, sulphur and iron cycles, among others. Considering that all ecological functions and services provided by mangrove environments involve microorganisms, this work reviews the microbial roles in nutrient cycling in relation to bioturbation by animals and plants, the main mangrove ecosystem engineers. We highlight the diversity of bioturbating organisms and explore the diversity, dynamics and functions of the sediment microbiome, considering both the impacts of bioturbation. Finally, we review the growing evidence that bioturbation, through altering the sediment microbiome and environment, determining a 'halo effect', can ameliorate conditions for plant growth, highlighting the potential of the mangrove microbiome as a nature-based solution to sustain mangrove development and support the role of this ecosystem to deliver essential ecological services.
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Affiliation(s)
- Jenny M Booth
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Coastal Research Group, Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Marco Fusi
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre for Conservation and Restoration Science, School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK
- Joint Nature Conservation Committee, Peterborough, UK
| | - Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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8
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Xiong G, Zhu X, Wu J, Liu M, Yang Y, Zeng X. Seawater intrusion alters nitrogen cycling patterns through hydrodynamic behavior and biochemical reactions: Based on Bayesian isotope mixing model and microbial functional network. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 867:161368. [PMID: 36621512 DOI: 10.1016/j.scitotenv.2022.161368] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/07/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Seawater intrusion is a global coastal environmental issue of great concern and significantly impacts the regional biogeochemical environment and material cycles, including nitrogen cycling. To reveal the mechanism of seawater intrusion altering nitrogen cycling patterns through hydrodynamic behavior and biochemical reactions, the Bayesian mixing model (δ15N-NO3- and δ18O-NO3-) and 16S rDNA gene amplicon sequencing are used to establish nitrogen cycling pathways and microbial functional network. The results show that the nitrate in the coastal groundwater is from manure and septic waste (M&S, over 44 %), soil organic nitrogen (SON, over 20 %), and nitrogen fertilizer (FN, over 16 %). The hydrological interaction has promoted the coupling between material cycling and microbial community in the coastal groundwater systems. Among them, precipitation infiltration has caused the gradual decrease of specific microbes along the flow direction, such as Lactobacillus, Acinetobacter, Bifidobacterium, etc. And seawater intrusion has caused the mutations of specific microbes (Planktomarina, Clade_Ia, Wenyingzhuangia, Glaciecola, etc.) and convergence of microbial community at the salt-freshwater interface in the aquifer. In the coastal intruded aquifer systems, the nitrogen cycling pattern can be divided into oxidation and reduction processes. The oxidation process involves the enhancement of nitrification while the weakening of denitrification and anammox with the increase of aquifer depth. The reduction process consists of the enhancement of denitrification and anammox while the erosion of nitrification and ammonification with increased seawater intrusion. In addition, seawater intrusion can mitigate nitrate contamination by promoting denitrification and anammox in coastal areas.
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Affiliation(s)
- Guiyao Xiong
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Xiaobin Zhu
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China.
| | - Jichun Wu
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China.
| | - Mengwen Liu
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
| | - Yun Yang
- School of Earth Sciences and Engineering, Hohai University, Nanjing 211100, China
| | - Xiankui Zeng
- Key Laboratory of Surficial Geochemistry of Ministry of Education, School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China
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9
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Akter R, Mukhles MB, Rahman MM, Rana MR, Huda N, Ferdous J, Rahman F, Rafi MH, Biswas SK. Effect of pesticides on nitrification activity and its interaction with chemical fertilizer and manure in long-term paddy soils. CHEMOSPHERE 2022; 304:135379. [PMID: 35716712 DOI: 10.1016/j.chemosphere.2022.135379] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/12/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Effect of pesticides on nitrification activity and its interaction among heavy metal concentrations (HMCs), antibiotic resistance genes (ARGs), and ammonia monooxygenase (amoA) genes of long-term paddy soils is little known. The aim was to study the effect of pesticides on net nitrification rate (NR), potential nitrification rate (NP), HMCs, ARGs (sulI, sulII, tetO, and tetQ), and amoA (amoA-AOA, amoA-AOB, and amoA-NOB) genes in long-term treated paddy soils. NR and NP were significantly decreased (p < 0.05), whereas HMCs (Pb2+, Cu2+, Zn2+, and Fe3+) were a significantly increased (p < 0.05) in chemical fertilizer with pesticide treated paddy soils as compared with chemical fertilizer treated paddy soils. The scatter plot matrix indicated that total carbon (TC), soil organic carbon (SOC), total nitrogen (TN), and Fe were linearly correlated with NR and NP in long-term treated paddy soils. ARGs and amoA genes were significantly decreased (p < 0.05) in chemical fertilizer and manure with pesticide treated paddy soils. Overall, the result indicated the response of pesticide and their combination of manure with pesticide interaction present in long-term paddy soils, which will play a great role in the control uses of pesticides, manure, and chemical fertilizers in paddy soils and protect the nitrogen cycle as well as environment.
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Affiliation(s)
- Rehena Akter
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Muntaha Binte Mukhles
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - M Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh.
| | - Md Rasel Rana
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Nazmul Huda
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Jannatul Ferdous
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Fahida Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Meherab Hossain Rafi
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
| | - Sudhangshu Kumar Biswas
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia, 7003, Bangladesh
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10
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Ooi SK, Barry A, Lawrence BA, Elphick CS, Helton AM. Vegetation zones as indicators of denitrification potential in salt marshes. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2630. [PMID: 35403778 PMCID: PMC9539531 DOI: 10.1002/eap.2630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/18/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Salt marsh vegetation zones shift in response to large-scale environmental changes such as sea-level rise (SLR) and restoration activities, but it is unclear if they are good indicators of soil nitrogen removal. Our goal was to characterize the relationship between denitrification potential and salt marsh vegetation zones in tidally restored and tidally unrestricted coastal marshes, and to use vegetation zones to extrapolate how SLR may influence high marsh denitrification at the landscape scale. We conducted denitrification enzyme activity assays on sediment collected from three vegetation zones expected to shift in distribution due to SLR and tidal flow restoration across 20 salt marshes in Connecticut, USA (n = 60 sampling plots) during the summer of 2017. We found lower denitrification potential in short-form Spartina alterniflora zones (mean, 95% CI: 4, 3-6 mg N h-1 m-2 ) than in S. patens (25, 15-36 mg N h-1 m-2 ) and Phragmites australis (56, 16-96 mg N h-1 m-2 ) zones. Vegetation zone was the single best predictor and explained 52% of the variation in denitrification potential; incorporating restoration status and soil characteristics (soil salinity, moisture, and ammonium) did not improve model fit. Because denitrification potential did not differ between tidally restored and unrestricted marshes, we suggest landscape-scale changes in denitrification after tidal restoration are likely to be associated with shifts in vegetation, rather than differences driven by restoration status. Sea-level-rise-induced hydrologic changes are widely observed to shift high marsh dominated by S. patens to short-form S. alterniflora. To explore the implications of this shift in dominant high marsh vegetation, we paired our measured mean denitrification potential rates with projections of high marsh loss from SLR. We found that, under low and medium SLR scenarios, predicted losses of denitrification potential due to replacement of S. patens by short-form S. alterniflora were substantially larger than losses due to reduced high marsh land area alone. Our results suggest that changes in vegetation zones can serve as landscape-scale predictors of the response of denitrification rates to rapid changes occurring in salt marshes.
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Affiliation(s)
- Sean Khan Ooi
- Department of Natural Resources and the EnvironmentUniversity of ConnecticutStorrsConnecticutUSA
| | - Aidan Barry
- Department of Natural Resources and the EnvironmentUniversity of ConnecticutStorrsConnecticutUSA
| | - Beth A. Lawrence
- Department of Natural Resources and the EnvironmentUniversity of ConnecticutStorrsConnecticutUSA
- Center for Environmental Sciences and EngineeringUniversity of ConnecticutStorrsConnecticutUSA
| | - Chris S. Elphick
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticutUSA
- Center of Biological RiskUniversity of ConnecticutStorrsConnecticutUSA
| | - Ashley M. Helton
- Department of Natural Resources and the EnvironmentUniversity of ConnecticutStorrsConnecticutUSA
- Center for Environmental Sciences and EngineeringUniversity of ConnecticutStorrsConnecticutUSA
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11
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Capparelli MV, Martínez-Colón M, Lucas-Solis O, Valencia-Castañeda G, Celis-Hernández O, Ávila E, Moulatlet GM. Can the bioturbation activity of the fiddler crab Minuca rapax modify the distribution of microplastics in sediments? MARINE POLLUTION BULLETIN 2022; 180:113798. [PMID: 35665620 DOI: 10.1016/j.marpolbul.2022.113798] [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: 03/09/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Fiddler crabs are known as "eco-engineers" who maintain habitat health through sediment bioturbation. They regularly interact with microplastics (MPs) due to their contact with the sediment. In this study we compared MPs concentration between burrows and pellets resulting from bioturbation, and MPs bioaccumulation in the soft tissues of Minuca rapax (Smith, 1870), along a gradient of urbanization in Isla del Carmen, southern Gulf of Mexico. Overall, MPs shape and color in the pellets and in the tissues reflected those of the burrow's sediments. MPs were more abundant and diverse in burrows (9 ± 12 MPs.g-1) than in pellets (5 ± 5 MPs.g-1) or in the soft tissues (1.3 ± 1.2 MPs.g-1). Bioturbation can concentrate MPs in pellets and tissues, depending on the MPs contamination and urbanization level. M. rapax is an important structuring agent of sedimentary MPs, showing a strong top-down translocation of MPs in subtropical tidal flats.
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Affiliation(s)
- Mariana V Capparelli
- Estación El Carmen, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Carretera Carmen-Puerto Real Km. 9.5, CP 24157 Ciudad del Carmen, Campeche, Mexico.
| | - Michael Martínez-Colón
- School of the Environment, Florida A&M University, 1515 S MLK Boulevard, Tallahassee, FL 32307, United States of America
| | - Oscar Lucas-Solis
- Facultad de Ciencias de la Tierra y Agua, Universidad Regional Amazónica Ikiam, 150150 Tena, Napo, Ecuador
| | - Gladys Valencia-Castañeda
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de Mexico, Unidad Académica Mazatlán, Mexico
| | - Omar Celis-Hernández
- Estación El Carmen, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Carretera Carmen-Puerto Real Km. 9.5, CP 24157 Ciudad del Carmen, Campeche, Mexico; Dirección de Cátedras CONACYT, Av. Insurgentes Sur 1582, Alcaldía Benito Juárez 03940, Ciudad de México, Mexico
| | - Enrique Ávila
- Estación El Carmen, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Carretera Carmen-Puerto Real Km. 9.5, CP 24157 Ciudad del Carmen, Campeche, Mexico
| | - Gabriel M Moulatlet
- Red de Biología Evolutiva, Instituto de Ecología, A.C., Xalapa, Veracruz, Mexico
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12
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Fusi M, Booth JM, Marasco R, Merlino G, Garcias-Bonet N, Barozzi A, Garuglieri E, Mbobo T, Diele K, Duarte CM, Daffonchio D. Bioturbation Intensity Modifies the Sediment Microbiome and Biochemistry and Supports Plant Growth in an Arid Mangrove System. Microbiol Spectr 2022; 10:e0111722. [PMID: 35647697 PMCID: PMC9241789 DOI: 10.1128/spectrum.01117-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/06/2022] [Indexed: 01/04/2023] Open
Abstract
In intertidal systems, the type and role of interactions among sediment microorganisms, animals, plants and abiotic factors are complex and not well understood. Such interactions are known to promote nutrient provision and cycling, and their dynamics and relationships may be of particular importance in arid microtidal systems characterized by minimal nutrient input. Focusing on an arid mangrove ecosystem on the central Red Sea coast, we investigated the effect of crab bioturbation intensity (comparing natural and manipulated high levels of bioturbation intensity) on biogeochemistry and bacterial communities of mangrove sediments, and on growth performance of Avicennia marina, over a period of 16 months. Along with pronounced seasonal patterns with harsh summer conditions, in which high sediment salinity, sulfate and temperature, and absence of tidal flooding occur, sediment bacterial diversity and composition, sediment physicochemical conditions, and plant performance were significantly affected by crab bioturbation intensity. For instance, bioturbation intensity influenced components of nitrogen, carbon, and phosphate cycling, bacterial relative abundance (i.e., Bacteroidia, Proteobacteria and Rhodothermi) and their predicted functionality (i.e., chemoheterotrophy), likely resulting from enhanced metabolic activity of aerobic bacteria. The complex interactions among bacteria, animals, and sediment chemistry in this arid mangrove positively impact plant growth. We show that a comprehensive approach targeting multiple biological levels provides useful information on the ecological status of mangrove forests. IMPORTANCE Bioturbation is one of the most important processes that governs sediment biocenosis in intertidal systems. By facilitating oxygen penetration into anoxic layers, bioturbation alters the overall sediment biogeochemistry. Here, we investigate how high crab bioturbation intensity modifies the mangrove sediment bacterial community, which is the second largest component of mangrove sediment biomass and plays a significant role in major biogeochemical processes. We show that the increase in crab bioturbation intensity, by ameliorating the anoxic condition of mangrove sediment and promoting sediment bacterial diversity in favor of a beneficial bacterial microbiome, improves mangrove tree growth in arid environments. These findings have significant implications because they show how crabs, by farming the mangrove sediment, can enhance the overall capacity of the system to sustain mangrove growth, fighting climate change.
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Affiliation(s)
- Marco Fusi
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre for Conservation and Restoration Science, School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Jenny Marie Booth
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Coastal Research Group, Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Ramona Marasco
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Giuseppe Merlino
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Neus Garcias-Bonet
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Alan Barozzi
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Elisa Garuglieri
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Tumeka Mbobo
- National Research Foundation-South African Institute for Aquatic Biodiversity Institute, Makhanda, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - Karen Diele
- Centre for Conservation and Restoration Science, School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Carlos M. Duarte
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- Division of Biological and Environmental Science and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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13
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Rolando JL, Kolton M, Song T, Kostka JE. The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA. MICROBIOME 2022; 10:37. [PMID: 35227326 PMCID: PMC8886783 DOI: 10.1186/s40168-021-01187-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/25/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Salt marshes are dominated by the smooth cordgrass Spartina alterniflora on the US Atlantic and Gulf of Mexico coastlines. Although soil microorganisms are well known to mediate important biogeochemical cycles in salt marshes, little is known about the role of root microbiomes in supporting the health and productivity of marsh plant hosts. Leveraging in situ gradients in aboveground plant biomass as a natural laboratory, we investigated the relationships between S. alterniflora primary productivity, sediment redox potential, and the physiological ecology of bulk sediment, rhizosphere, and root microbial communities at two Georgia barrier islands over two growing seasons. RESULTS A marked decrease in prokaryotic alpha diversity with high abundance and increased phylogenetic dispersion was found in the S. alterniflora root microbiome. Significantly higher rates of enzymatic organic matter decomposition, as well as the relative abundances of putative sulfur (S)-oxidizing, sulfate-reducing, and nitrifying prokaryotes correlated with plant productivity. Moreover, these functional guilds were overrepresented in the S. alterniflora rhizosphere and root core microbiomes. Core microbiome bacteria from the Candidatus Thiodiazotropha genus, with the metabolic potential to couple S oxidation with C and N fixation, were shown to be highly abundant in the root and rhizosphere of S. alterniflora. CONCLUSIONS The S. alterniflora root microbiome is dominated by highly active and competitive species taking advantage of available carbon substrates in the oxidized root zone. Two microbially mediated mechanisms are proposed to stimulate S. alterniflora primary productivity: (i) enhanced microbial activity replenishes nutrients and terminal electron acceptors in higher biomass stands, and (ii) coupling of chemolithotrophic S oxidation with carbon (C) and nitrogen (N) fixation by root- and rhizosphere-associated prokaryotes detoxifies sulfide in the root zone while potentially transferring fixed C and N to the host plant. Video Abstract.
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Affiliation(s)
- Jose L Rolando
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Max Kolton
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion, University of the Negev, Beer Sheva, Israel
| | - Tianze Song
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Joel E Kostka
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA.
- Georgia Institute of Technology, School of Earth and Atmospheric Sciences, Atlanta, GA, 30332, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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14
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Jones SF, Schutte CA, Roberts BJ, Thorne KM. Seasonal impoundment management reduces nitrogen cycling but not resilience to surface fire in a tidal wetland. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 303:114153. [PMID: 34875564 DOI: 10.1016/j.jenvman.2021.114153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 10/25/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Hydrology and salinity regimes of many impounded wetlands are manipulated to provide seasonal habitats for migratory waterfowl, with little-known consequences for ecosystem structure and function. Managed hydrology can alter ecosystems by directly changing soil properties and processes and by influencing plant community dynamics. Additionally, management history may influence ecosystem response to disturbance, including fires. To better understand how wetland management regime influences ecosystem response to disturbance, we quantified elevation, soil nitrogen concentrations and process rates, and plant community structure and diversity in a natural experiment following the 2018 Branscombe Fire. We measured paired burned-unburned patches in both tidally-influenced and managed, seasonally-impounded wetlands in Suisun Marsh, California, USA. Unburned ecosystem structure and nutrient cycling differed by wetland management history; unburned impounded wetlands were ∼1 m lower in elevation and plant community composition was dominated by succulents whereas the unburned tidal wetland was dominated by graminoids. Unburned impounded wetland soil nitrogen cycling (potential nitrification and denitrification) rates were <28% of those measured in unburned tidal wetland soils and soil extractable nitrate, ammonium, and dissolved inorganic phosphorus concentrations were also substantially lower in unburned impounded than unburned tidal wetlands. Despite these differences in pre-disturbance (i.e., unburned) conditions, all soil processes recovered to baseline levels within 6 months after surface fire, and we found no evidence of plant community change 1 year after fire in either wetland management type. Overall, water management history exerted stronger control on ecosystem processes and structure than surface fire disturbance. Low extractable soil nitrate and potential denitrification rates may indicate limitation of soil nitrogen removal in impounded wetlands, with implications for downstream environmental quality and eutrophication across managed landscapes.
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Affiliation(s)
- Scott F Jones
- U.S. Geological Survey, Western Ecological Research Center, Davis, CA, USA.
| | | | | | - Karen M Thorne
- U.S. Geological Survey, Western Ecological Research Center, Davis, CA, USA
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15
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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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16
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Wang DQ, Zhou CH, Nie M, Gu JD, Quan ZX. Abundance and niche specificity of different types of complete ammonia oxidizers (comammox) in salt marshes covered by different plants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 768:144993. [PMID: 33736320 DOI: 10.1016/j.scitotenv.2021.144993] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 06/12/2023]
Abstract
The recently discovered complete ammonia oxidizers (comammox), which are ubiquitous in various natural and artificial ecosystems, have led to a paradigm shift in our understanding of aerobic nitrification. The coastal salt marsh covered by various plant species is an important ecosystem to link nitrogen cycles of terrestrial and marine environments; however, the distribution and structure of comammox in such ecosystems have not been clearly investigated. Here, we applied quantitative PCR and partial nested-PCR to investigate the abundance and community composition of comammox in salt marsh sediment samples covered by three plant types along the southern coastline of China. Our results showed a predominance of comammox clade A in majority of the samples, suggesting their ubiquity and the important role they play in nitrification in salt marsh ecosystems. However, variations by the sites were found when comparing the abundance of subclades of comammox clade A. Redundancy analysis demonstrated a coexistence pattern by comammox clade A.1 with ammonia-oxidizing archaea and comammox clade A.2 with canonical ammonia-oxidizing bacteria, indicating their differences in potential niche preference. However, the abundance of comammox clade B was lower than that of comammox clade A and other ammonia oxidizers in most samples. Moreover, pH and salinity were found to be the most significant factors affecting comammox community structures, suggesting their roles in driving niche partitioning of comammox, whereas plant types did not show a significant effect on the comammox community structure. Our study provided insights into the abundance, community diversity, and niche partitions of comammox, broadening the current understanding of the relationship of comammox with other ammonia oxidizers in salt marsh ecosystems.
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Affiliation(s)
- Dan-Qi Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Chen-Hao Zhou
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Ming Nie
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Ji-Dong Gu
- Environmental Engineering, Guangdong Technion Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, People's Republic of China
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China.
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17
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Yin Z, Yang X, Wang X, Wang S. Effects of operating conditions on microbial consortium of the heterotrophic ammonia oxidation process. BIORESOURCE TECHNOLOGY 2021; 328:124823. [PMID: 33592544 DOI: 10.1016/j.biortech.2021.124823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to investigate the ammonia removal by the consortium mainly comprising of ammonia-oxidizing bacteria under different initial pH, temperatures and stress of heavy metals. The results showed that the consortium exhibited a strong adaptation for broad pH ranging from 5 to 9. When the temperature dropped to 15℃, its ammonium removal and nitrate accumulation rates decreased by 72.23% and 95.12%, respectively. Meanwhile, the temperature correction coefficients of the ammonium removal and nitrate accumulation rates reached the maximum. In addition, the consortium could survive in the solutions containing 0-1.0 mg·L-1 Cu2+ and 0-5.0 mg·L-1 Fe3+. Moreover, the inhibition of free nitrous acid (FNA) against nitrite oxidation activity was found to be much more significant than that low-temperature treatment. Microbial diversity analysis showed that the bacterial community structure was shift significantly by the temperature drop, especially change the abundance of Nitrosomonas, Paracoccus, Pseudomonas and Nitrospirae.
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Affiliation(s)
- Zhikai Yin
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai 200433, PR China
| | - Xiaolong Yang
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai 200433, PR China
| | - Xingyu Wang
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai 200433, PR China
| | - Shoubing Wang
- Department of Environmental Science and Engineering, Fudan University, 2005 Songhu Road, Shanghai 200433, PR China.
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18
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Li N, Nie M, Li B, Wu J, Zhao J. Contrasting effects of the aboveground litter of native Phragmites australis and invasive Spartina alterniflora on nitrification and denitrification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:144283. [PMID: 33387763 DOI: 10.1016/j.scitotenv.2020.144283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/29/2020] [Accepted: 11/29/2020] [Indexed: 06/12/2023]
Abstract
Aboveground litter inputs from plants are among the most important pathways for carbon and nutrient fluxes to the soil. Previous studies on the effects of aboveground litter from invasive plants on ecosystem processes have primarily focused on biogeochemical cycling processes such as C and N mineralization, whereas the effects of aboveground litter from invasive plants on nitrogen removal processes are not well understood. In this study, the effects of the aboveground litter of native Phragmites australis and exotic Spartina alterniflora on soil nitrification and denitrification were compared. Results showed that the removal of the aboveground litter of both species had no effect on nitrification or denitrification in the early growth phase. However, after aboveground litter removal in the late growth phase, nitrification and denitrification in the P. australis stands decreased by 41.18% and 25.11%, respectively, whereas no such changes were observed in the S. alterniflora stands. These results indicate that the impacts of aboveground litter on nitrification and denitrification are species-specific. The aboveground litter from indigenous P. australis affected the SOC content and then indirectly affected nitrification or denitrification, and these effects were clearer in the late growth phase. Although other studies have reported that the invasive S. alterniflora have strong impacts on nitrogen removal processes, our study showed that the aboveground litter from S. alterniflora did not alter nitrification or denitrification, which indicates that other pathways may play important roles in nitrogen removal processes than its aboveground litter does.
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Affiliation(s)
- Niu Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ming Nie
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Bo Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jihua Wu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jiayuan Zhao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200433, China.
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Bernhard AE, Beltz J, Giblin AE, Roberts BJ. Biogeography of ammonia oxidizers in New England and Gulf of Mexico salt marshes and the potential importance of comammox. ISME COMMUNICATIONS 2021; 1:9. [PMID: 36717686 PMCID: PMC9723745 DOI: 10.1038/s43705-021-00008-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 02/03/2023]
Abstract
Few studies have focused on broad scale biogeographic patterns of ammonia oxidizers in coastal systems, yet understanding the processes that govern them is paramount to understanding the mechanisms that drive biodiversity, and ultimately impact ecosystem processes. Here we present a meta-analysis of 16 years of data of ammonia oxidizer abundance, diversity, and activity in New England (NE) salt marshes and 5 years of data from marshes in the Gulf of Mexico (GoM). Potential nitrification rates were more than 80x higher in GoM compared to NE marshes. However, nitrifier abundances varied between regions, with ammonia-oxidizing archaea (AOA) and comammox bacteria significantly greater in GoM, while ammonia-oxidizing bacteria (AOB) were more than 20x higher in NE than GoM. Total bacterial 16S rRNA genes were also significantly greater in GoM marshes. Correlation analyses of rates and abundance suggest that AOA and comammox are more important in GoM marshes, whereas AOB are more important in NE marshes. Furthermore, ratios of nitrifiers to total bacteria in NE were as much as 80x higher than in the GoM, suggesting differences in the relative importance of nitrifiers between these systems. Communities of AOA and AOB were also significantly different between the two regions, based on amoA sequences and DNA fingerprints (terminal restriction fragment length polymorphism). Differences in rates and abundances may be due to differences in salinity, temperature, and N loading between the regions, and suggest significantly different N cycling dynamics in GoM and NE marshes that are likely driven by strong environmental differences between the regions.
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Affiliation(s)
- A E Bernhard
- Department of Biology, Connecticut College, New London, CT, USA.
| | - J Beltz
- Department of Biology, Connecticut College, New London, CT, USA
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - A E Giblin
- Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - B J Roberts
- Louisiana Universities Marine Consortium, Chauvin, LA, USA
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20
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Kolton M, Rolando JL, Kostka JE. Elucidation of the rhizosphere microbiome linked to Spartina alterniflora phenotype in a salt marsh on Skidaway Island, Georgia, USA. FEMS Microbiol Ecol 2020; 96:5813622. [PMID: 32227167 DOI: 10.1093/femsec/fiaa026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 03/23/2020] [Indexed: 01/04/2023] Open
Abstract
Smooth cordgrass, Spartina alterniflora, dominates salt marshes on the east coast of the United States. While the physicochemical cues affecting S. alterniflora productivity have been studied intensively, the role of plant-microbe interactions in ecosystem functioning remains poorly understood. Thus, in this study, the effects of S. alterniflora phenotype on the composition of archaeal, bacterial, diazotrophic and fungal communities were investigated. Overall, prokaryotic communities were more diverse and bacteria were more abundant in the areas colonized by the tall plant phenotype in comparison to those of short plant phenotype. Diazotrophic methanogens (Methanomicrobia) preferentially colonized the area of the short plant phenotype. Putative iron-oxidizing Zetaproteobacteria and sulfur-oxidizing Campylobacteria were identified as indicator species in the rhizosphere of tall and short plant phenotypes, respectively. Finally, while diazotrophic populations shaped microbial interactions in the areas colonized by the tall plant phenotype, fungal populations filled this role in the areas occupied by the short plant phenotype. The results here demonstrate that S. alterniflora phenotype and proximity to the root zone are selective forces dictating microbial community assembly. Results further reveal that reduction-oxidation chemistry is a major factor driving the selection of belowground microbial populations in salt marsh habitats.
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Affiliation(s)
- Max Kolton
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - José L Rolando
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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21
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Yu J, Zhang Y, Zhong J, Ding H, Zheng X, Wang Z, Zhang Y. Water-level alterations modified nitrogen cycling across sediment-water interface in the Three Gorges Reservoir. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:25886-25898. [PMID: 31713142 DOI: 10.1007/s11356-019-06656-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Water-level regime alteration-associated redox fluctuation plays a primary role in governing exchange and transformation of nitrogen (N) in water-level fluctuation zones (WLFZs), while few understanding of how hydrological regimes under reservoir operation affected N cycling across the sediment-water interface (SWI), giving rise to uncertainties in reservoir N nutrient management. Batch microcosm simulation experiments with intact sediment cores from WLFZs of the Three Gorges Reservoir (TGR) were conducted for 24 days to identify holistic flooding-drying process mechanism on N-cycling patterns. Our results showed a distinct transition of N-cycling mode across the SWI, shifting from biological denitrogen loss dominated in initial period of flooding to enhance endogenous N retention. A dramatic source-sink switch of nitrous oxide (N2O) occurred in the first 1.5 days during the flooding period. However, combined accelerating migration of NH4+-N from sediment to overlying water, and subsequently enhanced transformation of NH4+-N to NO3--N formed from flooding to drying rotation, thereby increasing N loading to overlying water. The reason for this investigation could be attributed to intensive N loss through coupled nitrification and denitrification in oxic-anoxic microenvironments after flooding. With oxygen replenishment from atmosphere during drying phase, persistent ammonification of organic N in sediments provided sufficient source of NH4+-N for the formation of NO3--N fraction in a more oxic overlying water. Therefore, water-level regime alteration by reservoir operation was capable of weakening N removal from water body and lengthening internal N turnover time across redox-variable SWI. These findings elucidate new understanding of holistic hydrological regime mechanisms on N cycling across SWI and provide insight to biogenic N nutrient management for improving the green credentials of hydroelectric reservoir.
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Affiliation(s)
- Juhua Yu
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, China.
| | - Yushu Zhang
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, China.
| | - Jicheng Zhong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Hong Ding
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, China
| | - Xiangzhou Zheng
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, China
| | - Zhiyuan Wang
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research Institute, Nanjing, 210029, China
| | - Yinlong Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
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22
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Moncada C, Hassenrück C, Gärdes A, Conaco C. Microbial community composition of sediments influenced by intensive mariculture activity. FEMS Microbiol Ecol 2019; 95:5289376. [PMID: 30649441 DOI: 10.1093/femsec/fiz006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/10/2019] [Indexed: 12/22/2022] Open
Abstract
Marine aquaculture is a major industry that supports the economy in many countries, including the Philippines. However, excess feeds and fish waste generated by mariculture activities contribute an immense nutrient load to the environment that can affect the underlying sediment. To better understand these impacts, we compared the physicochemical characteristics and microbial community composition of sediments taken at a fish cage and an off cage site in Bolinao, Philippines. Sediments and pore water at the fish cage site showed evidence of greater organic enrichment relative to the off cage site. Under these conditions, we found lower relative abundance of dissimilatory sulfate reductase and nitrite reductase genes, suggesting shifts in prevalent nutrient cycling processes. This is further supported by 16S rRNA gene sequencing that revealed differences in the community composition between sites. Fish cage sediments favored the growth of taxa that thrive in anaerobic, organic carbon-enriched environments, such as members of class Anaerolineae, which can potentially serve as bioindicators of eutrophication in sediments. This study demonstrates that intensive mariculture activity can cause eutrophic sediment conditions that influence microbial community structure and function.
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Affiliation(s)
- Chyrene Moncada
- Marine Science Institute, University of the Philippines Diliman, Velasquez Street, Quezon City 1101, Philippines
| | - Christiane Hassenrück
- Tropical Marine Microbiology Group, Leibniz Centre for Tropical Marine Research, Fahrenheitstraße 6, 283 59 Bremen, Germany
| | - Astrid Gärdes
- Tropical Marine Microbiology Group, Leibniz Centre for Tropical Marine Research, Fahrenheitstraße 6, 283 59 Bremen, Germany
| | - Cecilia Conaco
- Marine Science Institute, University of the Philippines Diliman, Velasquez Street, Quezon City 1101, Philippines
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23
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Caffrey JM, Bonaglia S, Conley DJ. Short exposure to oxygen and sulfide alter nitrification, denitrification, and DNRA activity in seasonally hypoxic estuarine sediments. FEMS Microbiol Lett 2019; 366:5266299. [PMID: 30596977 PMCID: PMC6343015 DOI: 10.1093/femsle/fny288] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/14/2018] [Indexed: 02/03/2023] Open
Abstract
Increased organic loading to sediments from eutrophication often results in hypoxia, reduced nitrification and increased production of hydrogen sulfide, altering the balance between nitrogen removal and retention. We examined the effect of short-term exposure to various oxygen and sulfide concentrations on sediment nitrification, denitrification and DNRA from a chronically hypoxic basin in Roskilde Fjord, Denmark. Surprisingly, nitrification rates were highest in the hypoxic and anoxic treatments (about 5 μmol cm−3 d−1) and the high sulfide treatment was not significantly different than the oxic treatment. Denitrification in the hypoxic treatment was highest at 1.4 μmol cm−3 d−1 and significantly higher than the high sulfide treatment. For DNRA, the rate in high sulfide treatment was 2 μmol cm−3 d−1. This was significantly higher than all oxygen treatments that were near zero. In this system, nitrifiers rapidly recovered from conditions typically considered inhibiting, while denitrifiers had a more muted response. DNRA bacteria appear to depend on sulfide for nitrate reduction. Anammox was insignificant. Thus, in estuaries and coastal systems that experience short-term variations in oxygen and sulfide, capabilities of microbial communities are more diverse and tolerant of suboptimal conditions than some paradigms suggest.
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Affiliation(s)
- Jane M Caffrey
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, 11000 University Parkway, Pensacola, FL 32514, USA
| | - Stefano Bonaglia
- Department of Geology, Lund University, Solvegatan 12, SE-223 62 Lund, Sweden
| | - Daniel J Conley
- Department of Geology, Lund University, Solvegatan 12, SE-223 62 Lund, Sweden
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24
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Dale H, Taylor JD, Solan M, Lam P, Cunliffe M. Polychaete mucopolysaccharide alters sediment microbial diversity and stimulates ammonia-oxidising functional groups. FEMS Microbiol Ecol 2018; 95:5247715. [DOI: 10.1093/femsec/fiy234] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/12/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Harriet Dale
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Joe D Taylor
- School of Environment and Life Sciences, University of Salford, The Crescent, Salford, M5 4WT, UK
| | - Martin Solan
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Phyllis Lam
- Ocean and Earth Science, University of Southampton, Waterfront Campus, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
- Marine Biology and Ecology Research Group, School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK
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25
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26
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Urakawa H, Rajan S, Feeney ME, Sobecky PA, Mortazavi B. Ecological response of nitrification to oil spills and its impact on the nitrogen cycle. Environ Microbiol 2018; 21:18-33. [DOI: 10.1111/1462-2920.14391] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 08/11/2018] [Accepted: 08/17/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Hidetoshi Urakawa
- Department of Marine and Ecological Sciences Florida Gulf Coast University Fort Myers FL, 33965 USA
| | - Suja Rajan
- Department of Biological Sciences University of Alabama Tuscaloosa AL, 35487 USA
| | - Megan E. Feeney
- Department of Marine and Ecological Sciences Florida Gulf Coast University Fort Myers FL, 33965 USA
| | - Patricia A. Sobecky
- Department of Biological Sciences University of Alabama Tuscaloosa AL, 35487 USA
| | - Behzad Mortazavi
- Department of Biological Sciences University of Alabama Tuscaloosa AL, 35487 USA
- Dauphin Island Sea Lab Dauphin Island AL, 36528 USA
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27
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Angell JH, Peng X, Ji Q, Craick I, Jayakumar A, Kearns PJ, Ward BB, Bowen JL. Community Composition of Nitrous Oxide-Related Genes in Salt Marsh Sediments Exposed to Nitrogen Enrichment. Front Microbiol 2018; 9:170. [PMID: 29483902 PMCID: PMC5816060 DOI: 10.3389/fmicb.2018.00170] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 01/25/2018] [Indexed: 11/13/2022] Open
Abstract
Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated profiles of microbial communities and communities of micro-organisms containing specific nitrogen cycling genes that encode several enzymes (amoA, norB, nosZ) related to nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms involved in the production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that previously measured rates of nitrous oxide production and consumption are likely the result of changes in community structure, not simply changes in microbial activity.
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Affiliation(s)
- John H. Angell
- Biology Department, University of Massachusetts Boston, Boston, MA, United States
| | - Xuefeng Peng
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Qixing Ji
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Ian Craick
- Biology Department, University of Massachusetts Boston, Boston, MA, United States
| | - Amal Jayakumar
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Patrick J. Kearns
- Biology Department, University of Massachusetts Boston, Boston, MA, United States
| | - Bess B. Ward
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Jennifer L. Bowen
- Biology Department, University of Massachusetts Boston, Boston, MA, United States
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28
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Wang W, Dudel EG. Nitrogen species coupled with transpiration enhance Fe plaque assisted aquatic uranium removal via rhizofiltration of Phragmites australis Trin ex Steud. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2018; 181:138-146. [PMID: 29150188 DOI: 10.1016/j.jenvrad.2017.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 08/27/2017] [Accepted: 11/07/2017] [Indexed: 06/07/2023]
Abstract
The influences of N species and transpiration on the Fe plaque (IP) formation and related aquatic U rhizofiltration had not revealed yet, especially when these factors were co-existed. It was evaluated in a mesocosm experiment in the condition of respective ammonium (NH4+)/nitrate (NO3-) cultivation of Phragmites australis Trin ex Steud. coupled with different transpiration rates (TRs). The results suggested that the enhanced transpiration of P. australis improved the aquatic U rhizofiltration in both NO3- and NH4+ rich milieus. However, the NO3- dependent oxidizing milieu restricted aquatic U uptake by the root of P. australis (up to 47.6 ± 1.8 mg kg-1 under high TR) via IP assisted rhizofiltration. The high aquatic U availability and limited IP formation in NO3- rich milieu benefited the U retention within root tissue. On the contrary, the aquatic U rhizofiltration (up to 62.1 ± 1.0 mg kg-1 under high TR) was enhanced under NH4+ dependent reductive milieu. It was mainly contributed by U retention within IP. The area related U accumulation in different N species cultured roots was enhanced but did not significantly different under higher TR condition. The result suggested that the supplied NH4+ coupled with enhanced transpiration was supposed to be more optimized option for IP assisted aquatic U rhizofiltration via P. australis.
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Affiliation(s)
- Weiqing Wang
- Institute of Plant and Wood Chemistry, Dresden University of Technology, Pienner Strasse 19, D-01737 Tharandt, Germany.
| | - E Gert Dudel
- Institute of Plant and Wood Chemistry, Dresden University of Technology, Pienner Strasse 19, D-01737 Tharandt, Germany
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29
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Nacke H, Schöning I, Schindler M, Schrumpf M, Daniel R, Nicol GW, Prosser JI. Links between seawater flooding, soil ammonia oxidiser communities and their response to changes in salinity. FEMS Microbiol Ecol 2017; 93:4563574. [DOI: 10.1093/femsec/fix144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 10/23/2017] [Indexed: 11/13/2022] Open
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30
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Duff AM, Zhang LM, Smith CJ. Small-scale variation of ammonia oxidisers within intertidal sediments dominated by ammonia-oxidising bacteria Nitrosomonas sp. amoA genes and transcripts. Sci Rep 2017; 7:13200. [PMID: 29038459 PMCID: PMC5643298 DOI: 10.1038/s41598-017-13583-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/25/2017] [Indexed: 11/08/2022] Open
Abstract
While numerous studies have investigated the abundance of ammonia oxidising bacteria and archaea (AOB/AOA) via the ammonia monooxygenase gene amoA, less is known about their small-scale variation and if amoA gene abundance equates to activity. Here we present a spatial and temporal study of ammonia oxidation in two small intertidal bays, Rusheen and Clew bay, Ireland. Potential Nitrification Rate (PNR) was ten-fold higher in Rusheen bay (Clew: 0.27 ± SD 0.55; Rusheen: 2.46 ± SD 3.4 NO2- µg-1 g-1 day-1, P < 0.001) than in Clew bay but amoA gene abundances were similar between bays, and comparable to those in other coastal ecosystems. Within bays AOB genes increased towards the muddy sediments and were positively correlated with PNR and pH. Less spatial variation was observed in AOA abundances which nevertheless positively correlated with pH and temperature and negatively with salinity and ammonia. Transcriptionally active AOB and AOA were quantified from all sites in Rusheen bay, February 2014, following the general trends observed at DNA level. AOB phylotypes predominantly from the known Nitrosomonas group were distributed across the bay, while Nitrosomonas group B phylotypes were absent from low salinity sites. AOA genes and transcripts were primarily affiliated with Thaumarchaeota group I.1a.
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Affiliation(s)
- Aoife M Duff
- Microbiology, School of Natural Sciences, NUI Galway, Galway, Ireland
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Science, Chinese Academy of Sciences, 18 Shuangqing Rd., Haidan Beijing, 100085, P.R. China
| | - Cindy J Smith
- Microbiology, School of Natural Sciences, NUI Galway, Galway, Ireland.
- Infrastructure and Environment, School of Engineering, University of Glasgow, Glasgow, United Kingdom.
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31
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Hinshaw SE, Tatariw C, Flournoy N, Kleinhuizen A, Taylor C, Sobecky PA, Mortazavi B. Vegetation Loss Decreases Salt Marsh Denitrification Capacity: Implications for Marsh Erosion. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:8245-8253. [PMID: 28616973 DOI: 10.1021/acs.est.7b00618] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Salt marshes play a key role in removing excess anthropogenic nitrogen (N) loads to nearshore marine ecosystems through sediment microbial processes such as denitrification. However, in the Gulf of Mexico, the loss of marsh vegetation because of human-driven disturbances such as sea level rise and oil spills can potentially reduce marsh capacity for N removal. To investigate the effect of vegetation loss on ecosystem N removal, we contrasted denitrification capacity in marsh and subtidal sediments impacted by the Deepwater Horizon oil spill using a combination of 29N2 and 30N2 production (isotope pairing), denitrification potential measurements (acetylene block), and quantitative polymerase chain reaction (qPCR) of functional genes in the denitrification pathway. We found that, on average, denitrification capacity was 4 times higher in vegetated sediments because of a combination of enhanced nitrification and higher organic carbon availability. The abundance of nirS-type denitrifers indicated that marsh vegetation regulates the activity, rather than the abundance, of denitrifier communities. We estimated that marsh sediments remove an average of 3.6 t N km-2 y-1 compared to 0.9 t N km-2 y-1 in unvegetated sediments. Overall, our findings indicate that marsh loss results in a substantial loss of N removal capacity in coastal ecosystems.
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Affiliation(s)
- Sarra E Hinshaw
- University of Alabama , Department of Biological Sciences, Tuscaloosa, Alabama 35487, United States
- Dauphin Island Sea Lab, 101 Bienville Blvd Dauphin Island, Dauphin Island, Alabama 36528, United States
| | - Corianne Tatariw
- University of Alabama , Department of Biological Sciences, Tuscaloosa, Alabama 35487, United States
- Dauphin Island Sea Lab, 101 Bienville Blvd Dauphin Island, Dauphin Island, Alabama 36528, United States
| | - Nikaela Flournoy
- University of Alabama , Department of Biological Sciences, Tuscaloosa, Alabama 35487, United States
| | - Alice Kleinhuizen
- University of Alabama , Department of Biological Sciences, Tuscaloosa, Alabama 35487, United States
- Dauphin Island Sea Lab, 101 Bienville Blvd Dauphin Island, Dauphin Island, Alabama 36528, United States
| | - Caitlin Taylor
- University of Alabama , Department of Biological Sciences, Tuscaloosa, Alabama 35487, United States
| | - Patricia A Sobecky
- University of Alabama , Department of Biological Sciences, Tuscaloosa, Alabama 35487, United States
| | - Behzad Mortazavi
- University of Alabama , Department of Biological Sciences, Tuscaloosa, Alabama 35487, United States
- Dauphin Island Sea Lab, 101 Bienville Blvd Dauphin Island, Dauphin Island, Alabama 36528, United States
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Kim SH, Lee JS, Hyun JH. Extremely high sulfate reduction, sediment oxygen demand and benthic nutrient flux associated with a large-scale artificial dyke and its implication to benthic-pelagic coupling in the Yeongsan River estuary, Yellow Sea. MARINE POLLUTION BULLETIN 2017; 120:126-135. [PMID: 28499584 DOI: 10.1016/j.marpolbul.2017.04.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 04/25/2017] [Accepted: 04/26/2017] [Indexed: 06/07/2023]
Abstract
We investigated environmental impact of large-scale dyke on the sediment geochemistry, sulfate reduction rates (SRRs), sediment oxygen demand (SOD) and potential contribution of benthic nutrient flux (BNF) to primary production in the Yeongsan River estuary, Yellow Sea. The sediment near the dyke (YE1) with high organic carbon (Corg) content (>4%, dry wt.) was characterized by extremely high SOD (327mmolm-2d-1) and SRRs (91-140mmolm-2d-1). The sulfate reduction accounted for 73% of Corg oxidation, and was responsible for strikingly high concentrations of NH4+ (7.7mM), PO43- (67μM) and HS- (487μM) in pore water. The BNF at YE1 accounted for approximately 200% of N and P required for primary production in the water column. The results present one of the most extreme cases that the construction of an artificial dyke may have profound impacts on the biogeochemical and ecological processes in coastal ecosystems.
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Affiliation(s)
- Sung-Han Kim
- Department of Marine Sciences and Convergent Technology, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do 15588, South Korea
| | - Jae Seong Lee
- Division of Marine Chemistry and Geochemistry, Korea Institute of Ocean Science & Technology, 787 Haean-ro, Sangnok-gu, Ansan, Gyeonggi-do 15627, South Korea
| | - Jung-Ho Hyun
- Department of Marine Sciences and Convergent Technology, Hanyang University, 55 Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi-do 15588, South Korea.
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Yang WH, Silver WL. Gross nitrous oxide production drives net nitrous oxide fluxes across a salt marsh landscape. GLOBAL CHANGE BIOLOGY 2016; 22:2228-2237. [PMID: 26718748 DOI: 10.1111/gcb.13203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/15/2015] [Indexed: 06/05/2023]
Abstract
Sea level rise will change inundation regimes in salt marshes, altering redox dynamics that control nitrification - a potential source of the potent greenhouse gas, nitrous oxide (N2 O) - and denitrification, a major nitrogen (N) loss pathway in coastal ecosystems and both a source and sink of N2 O. Measurements of net N2 O fluxes alone yield little insight into the different effects of redox conditions on N2 O production and consumption. We used in situ measurements of gross N2 O fluxes across a salt marsh elevation gradient to determine how soil N2 O emissions in coastal ecosystems may respond to future sea level rise. Soil redox declined as marsh elevation decreased, with lower soil nitrate and higher ferrous iron in the low marsh compared to the mid and high marshes (P < 0.001 for both). In addition, soil oxygen concentrations were lower in the low and mid-marshes relative to the high marsh (P < 0.001). Net N2 O fluxes differed significantly among marsh zones (P = 0.009), averaging 9.8 ± 5.4 μg N m(-2) h(-1) , -2.2 ± 0.9 μg N m(-2) h(-1) , and 0.67 ± 0.57 μg N m(-2) h(-1) in the low, mid, and high marshes, respectively. Both net N2 O release and uptake were observed in the low and high marshes, but the mid-marsh was consistently a net N2 O sink. Gross N2 O production was highest in the low marsh and lowest in the mid-marsh (P = 0.02), whereas gross N2 O consumption did not differ among marsh zones. Thus, variability in gross N2 O production rates drove the differences in net N2 O flux among marsh zones. Our results suggest that future studies should focus on elucidating controls on the processes producing, rather than consuming, N2 O in salt marshes to improve our predictions of changes in net N2 O fluxes caused by future sea level rise.
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Affiliation(s)
- Wendy H Yang
- Ecosystem Sciences Division, Department of Environmental Science, Policy and Management, University of California, 130 Mulford Hall #3114, Berkeley, CA, 94720, USA
| | - Whendee L Silver
- Ecosystem Sciences Division, Department of Environmental Science, Policy and Management, University of California, 130 Mulford Hall #3114, Berkeley, CA, 94720, USA
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Yu J, Fan C, Zhong J, Zhang L, Zhang L, Wang C, Yao X. Effects of sediment dredging on nitrogen cycling in Lake Taihu, China: Insight from mass balance based on a 2-year field study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:3871-3883. [PMID: 26499196 DOI: 10.1007/s11356-015-5517-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/28/2015] [Indexed: 06/05/2023]
Abstract
Sediment dredging can permanently remove pollutants from an aquatic ecosystem, which is considered an effective approach to aquatic ecosystem restoration. In this work, a 2-year field simulation test was carried out to investigate the effect of dredging on nitrogen cycling across the sediment-water interface (SWI) in Lake Taihu, China. The results showed that simulated dredging applied to an area rich in total organic carbon (TOC) and total nitrogen (TN) slightly reduced the NH4(+)-N release from sediments while temporarily enhanced the NH4(+)-N release in an area with lower TOC and/or TN (in the first 180 days), although the application had a limited effect on the fluxes of NO2(-)-N and NO3(-)-N in both areas. Further analysis indicated that dredging induced decreases in nitrification, denitrification, and anaerobic ammonium oxidation (anammox) in sediments, notably by 76.9, 49.0, and 89.9%, respectively, in the TOC and/or TN-rich area. Therefore, dredging slowed down nitrogen cycling rates in sediments but did not increase N loading to overlying water. The main reason for the above phenomenon could be attributed to the removal of the surface sediments enriched with more TOC and/or TN (compared with the bottom sediments). Overall, to minimize internal N pollution, dredging may be more applicable to nutrient-rich sediments.
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Affiliation(s)
- Juhua Yu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Number 73 Beijing East Road, 210008, Nanjing, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengxin Fan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Number 73 Beijing East Road, 210008, Nanjing, People's Republic of China
| | - Jicheng Zhong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Number 73 Beijing East Road, 210008, Nanjing, People's Republic of China.
| | - Lu Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Number 73 Beijing East Road, 210008, Nanjing, People's Republic of China
| | - Lei Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Number 73 Beijing East Road, 210008, Nanjing, People's Republic of China
| | - Changhui Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Number 73 Beijing East Road, 210008, Nanjing, People's Republic of China
| | - Xiaolong Yao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Number 73 Beijing East Road, 210008, Nanjing, People's Republic of China
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Fan H, Bolhuis H, Stal LJ. Nitrification and Nitrifying Bacteria in a Coastal Microbial Mat. Front Microbiol 2015; 6:1367. [PMID: 26648931 PMCID: PMC4664649 DOI: 10.3389/fmicb.2015.01367] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/17/2015] [Indexed: 11/13/2022] Open
Abstract
The first step of nitrification, the oxidation of ammonia to nitrite, can be performed by ammonia-oxidizing archaea (AOA) or ammonium-oxidizing bacteria (AOB). We investigated the presence of these two groups in three structurally different types of coastal microbial mats that develop along the tidal gradient on the North Sea beach of the Dutch barrier island Schiermonnikoog. The abundance and transcription of amoA, a gene encoding for the alpha subunit of ammonia monooxygenase that is present in both AOA and AOB, were assessed and the potential nitrification rates in these mats were measured. The potential nitrification rates in the three mat types were highest in autumn and lowest in summer. AOB and AOA amoA genes were present in all three mat types. The composition of the AOA and AOB communities in the mats of the tidal and intertidal stations, based on the diversity of amoA, were similar and clustered separately from the supratidal microbial mat. In all three mats AOB amoA genes were significantly more abundant than AOA amoA genes. The abundance of neither AOB nor AOA amoA genes correlated with the potential nitrification rates, but AOB amoA transcripts were positively correlated with the potential nitrification rate. The composition and abundance of amoA genes seemed to be partly driven by salinity, ammonium, temperature, and the nitrate/nitrite concentration. We conclude that AOB are responsible for the bulk of the ammonium oxidation in these coastal microbial mats.
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Affiliation(s)
- Haoxin Fan
- Department of Marine Microbiology, Royal Netherlands Institute for Sea Research Yerseke, Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology, Royal Netherlands Institute for Sea Research Yerseke, Netherlands
| | - Lucas J Stal
- Department of Marine Microbiology, Royal Netherlands Institute for Sea Research Yerseke, Netherlands ; Department of Aquatic Microbiology, Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam, Netherlands
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Diepens NJ, Dimitrov MR, Koelmans AA, Smidt H. Molecular Assessment of Bacterial Community Dynamics and Functional End Points during Sediment Bioaccumulation Tests. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:13586-13595. [PMID: 26466173 DOI: 10.1021/acs.est.5b02992] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Whole sediment toxicity tests play an important role in environmental risk assessment of organic chemicals. It is not clear, however, to what extent changing microbial community composition and associated functions affect sediment test results. We assessed the development of bacterial communities in artificial sediment during a 28 day bioaccumulation test with polychlorinated biphenyls, chlorpyrifos, and four marine benthic invertebrates. DGGE and 454-pyrosequencing of PCR-amplified 16S rRNA genes were used to characterize bacterial community composition. Abundance of total bacteria and selected genes encoding enzymes involved in important microbially mediated ecosystem functions were measured by qPCR. Community composition and diversity responded most to the time course of the experiment, whereas organic matter (OM) content showed a low but significant effect on community composition, biodiversity and two functional genes tested. Moreover, OM content had a higher influence on bacterial community composition than invertebrate species. Medium OM content led to the highest gene abundance and is preferred for standard testing. Our results also indicated that a pre-equilibration period is essential for growth and stabilization of the bacterial community. The observed changes in microbial community composition and functional gene abundance may imply actual changes in such functions during tests, with consequences for exposure and toxicity assessment.
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Affiliation(s)
- Noël J Diepens
- Aquatic Ecology and Water Quality Management Group, Wageningen University , P.O Box 47, 6700 AA, Wageningen, The Netherlands
| | - Mauricio R Dimitrov
- Aquatic Ecology and Water Quality Management Group, Wageningen University , P.O Box 47, 6700 AA, Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University , Dreijenplein 10, 6703 HB Wageningen, The Netherlands
| | - Albert A Koelmans
- Aquatic Ecology and Water Quality Management Group, Wageningen University , P.O Box 47, 6700 AA, Wageningen, The Netherlands
- IMARES, Institute for Marine Resources & Ecosystem Studies, Wageningen UR , P.O. Box 68, 1970 AB IJmuiden, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University , Dreijenplein 10, 6703 HB Wageningen, The Netherlands
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Yuan J, Ding W, Liu D, Kang H, Freeman C, Xiang J, Lin Y. Exotic Spartina alterniflora invasion alters ecosystem-atmosphere exchange of CH4 and N2O and carbon sequestration in a coastal salt marsh in China. GLOBAL CHANGE BIOLOGY 2015; 21:1567-1580. [PMID: 25367159 DOI: 10.1111/gcb.12797] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 09/30/2014] [Indexed: 06/04/2023]
Abstract
Coastal salt marshes are sensitive to global climate change and may play an important role in mitigating global warming. To evaluate the impacts of Spartina alterniflora invasion on global warming potential (GWP) in Chinese coastal areas, we measured CH4 and N2O fluxes and soil organic carbon sequestration rates along a transect of coastal wetlands in Jiangsu province, China, including open water; bare tidal flat; and invasive S. alterniflora, native Suaeda salsa, and Phragmites australis marshes. Annual CH4 emissions were estimated as 2.81, 4.16, 4.88, 10.79, and 16.98 kg CH4 ha(-1) for open water, bare tidal flat, and P. australis, S. salsa, and S. alterniflora marshes, respectively, indicating that S. alterniflora invasion increased CH4 emissions by 57-505%. In contrast, negative N2O fluxes were found to be significantly and negatively correlated (P < 0.001) with net ecosystem CO2 exchange during the growing season in S. alterniflora and P. australis marshes. Annual N2O emissions were 0.24, 0.38, and 0.56 kg N2O ha(-1) in open water, bare tidal flat and S. salsa marsh, respectively, compared with -0.51 kg N2O ha(-1) for S. alterniflora marsh and -0.25 kg N2O ha(-1) for P. australis marsh. The carbon sequestration rate of S. alterniflora marsh amounted to 3.16 Mg C ha(-1) yr(-1) in the top 100 cm soil profile, a value that was 2.63- to 8.78-fold higher than in native plant marshes. The estimated GWP was 1.78, -0.60, -4.09, and -1.14 Mg CO2 eq ha(-1) yr(-1) in open water, bare tidal flat, P. australis marsh and S. salsa marsh, respectively, but dropped to -11.30 Mg CO2 eq ha(-1) yr(-1) in S. alterniflora marsh. Our results indicate that although S. alterniflora invasion stimulates CH4 emissions, it can efficiently mitigate increases in atmospheric CO2 and N2O along the coast of China.
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Affiliation(s)
- Junji Yuan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 10049, China
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Bernhard AE, Dwyer C, Idrizi A, Bender G, Zwick R. Long-term impacts of disturbance on nitrogen-cycling bacteria in a New England salt marsh. Front Microbiol 2015; 6:46. [PMID: 25699033 PMCID: PMC4316780 DOI: 10.3389/fmicb.2015.00046] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/13/2015] [Indexed: 12/02/2022] Open
Abstract
Recent studies on the impacts of disturbance on microbial communities indicate communities show differential responses to disturbance, yet our understanding of how different microbial communities may respond to and recover from disturbance is still rudimentary. We investigated impacts of tidal restriction followed by tidal restoration on abundance and diversity of denitrifying bacteria, ammonia-oxidizing bacteria (AOB), and ammonia-oxidizing archaea (AOA) in New England salt marshes by analyzing nirS and bacterial and archaeal amoA genes, respectively. TRFLP analysis of nirS and betaproteobacterial amoA genes revealed significant differences between restored and undisturbed marshes, with the greatest differences detected in deeper sediments. Additionally, community patterns indicated a potential recovery trajectory for denitrifiers. Analysis of archaeal amoA genes, however, revealed no differences in community composition between restored and undisturbed marshes, but we detected significantly higher gene abundance in deeper sediment at restored sites. Abundances of nirS and betaproteobacterial amoA genes were also significantly greater in deeper sediments at restored sites. Porewater ammonium was significantly higher at depth in restored sediments compared to undisturbed sediments, suggesting a possible mechanism driving some of the community differences. Our results suggest that impacts of disturbance on denitrifying and ammonia-oxidizing communities remain nearly 30 years after restoration, potentially impacting nitrogen-cycling processes in the marsh. We also present data suggesting that sampling deeper in sediments may be critical for detecting disturbance effects in coastal sediments.
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Affiliation(s)
| | - Courtney Dwyer
- Biology Department, Connecticut College, New London, CT USA
| | - Adrian Idrizi
- Biology Department, Connecticut College, New London, CT USA
| | | | - Rachel Zwick
- Biology Department, Connecticut College, New London, CT USA
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Ochoa-Izaguirre MJ, Soto-Jiménez MF. Variability in nitrogen stable isotope ratios of macroalgae: consequences for the identification of nitrogen sources. JOURNAL OF PHYCOLOGY 2015; 51:46-65. [PMID: 26986258 DOI: 10.1111/jpy.12250] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 07/30/2014] [Indexed: 06/05/2023]
Abstract
In our research, we collected and analyzed numerous macroalgal specimens (738) for isotopic analysis sampled over a year at monthly intervals across 20 sites within the Urías lagoon complex, a typical subtropical coastal ecosystem located in the Gulf of California. We quantified and characterized (chemically and isotopically) the N loads received by Urías throughout a year. We studied the spatial-temporal variation of the chemical forms and isotopic signals of the available N in the water column, and we monitored in situ different environmental variables and other hydrodynamic parameters. Multiple N sources (e.g., atmospheric, sewage, seafood processing, agriculture and aquaculture effluents) and biogeochemical reactions related to the N cycle (e.g., ammonia volatilization, nitrification and denitrification) co-occurring across the ecosystem, result in a mixture of chemical species and isotopic compositions of available N in the water column. Increased variability was observed in the δ(15) N values of macroalgae (0.41‰-22.67‰). Based on our results, the variation in δ(15) N was best explained by spatio-temporal changes in available N and not necessarily related to the N sources. The variability was also explained by the differences in macroalgal biology among functional groups, species and/or individuals. Although the δ(15) N-macroalgae technique was a useful tool to identify N sources, its application in coastal ecosystems receiving multiple N sources, with changing environmental conditions influencing biogeochemical processes, and high diversity of ephemeral macroalgal species, could be less sensitive and have less predictive power.
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Affiliation(s)
- María Julia Ochoa-Izaguirre
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Unidad Académica Mazatlán, Apdo. Postal 811, Mazatlán, Sinaloa, 82040, México
- Facultad de Ciencias del Mar, Universidad Autónoma de Sinaloa, Paseo Claussen s/n, Apdo. Postal 610, Mazatlán, Sinaloa, 82000, México
| | - Martín F Soto-Jiménez
- Unidad Académica Mazatlán, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México (UAM-ICMyL-UNAM), Apdo. Postal 811, Mazatlán, Sinaloa, 82040, México
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Damashek J, Smith JM, Mosier AC, Francis CA. Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine delta. Front Microbiol 2015; 5:743. [PMID: 25620958 PMCID: PMC4287051 DOI: 10.3389/fmicb.2014.00743] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/08/2014] [Indexed: 11/17/2022] Open
Abstract
Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California's Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the extensive discharge of ammonium into the Sacramento River has altered this ecosystem by vastly increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. This debate surrounding ammonium inputs highlights the importance of understanding the rates of, and controls on, nitrogen (N) cycling processes across the delta. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (which codes for the α-subunit of ammonia monooxygenase). There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB) outnumbering ammonia-oxidizing archaea (AOA) only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The benthic ammonia oxidizers in this nutrient-rich aquatic ecosystem may be important players in its overall nutrient cycling, and their community structure and biogeochemical function appear related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways, including benthic nitrification, is a critical step toward understanding how such ecosystems respond to the changing environmental conditions wrought by human development and climate change.
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Affiliation(s)
- Julian Damashek
- Department of Environmental Earth System Science, Stanford University Stanford, CA, USA
| | - Jason M Smith
- Department of Environmental Earth System Science, Stanford University Stanford, CA, USA
| | - Annika C Mosier
- Department of Environmental Earth System Science, Stanford University Stanford, CA, USA
| | - Christopher A Francis
- Department of Environmental Earth System Science, Stanford University Stanford, CA, USA
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Yang WH, Traut BH, Silver WL. Microbially mediated nitrogen retention and loss in a salt marsh soil. Ecosphere 2015. [DOI: 10.1890/es14-00179.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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amoA Gene abundances and nitrification potential rates suggest that benthic ammonia-oxidizing bacteria and not Archaea dominate N cycling in the Colne Estuary, United Kingdom. Appl Environ Microbiol 2014; 81:159-65. [PMID: 25326303 DOI: 10.1128/aem.02654-14] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase (amoA) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 μmol N grams dry weight [gdw](-1) day(-1) in June, increasing to 37.4 μmol N gdw(-1) day(-1) in January). At the estuary head, the nitrification potential was 4.3 μmol N gdw(-1) day(-1) in June, increasing to 11.7 μmol N gdw(-1) day(-1) in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOB amoA gene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally. Nitrosomonas spp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOA amoA gene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possibly Nitrosomonas spp.) were of major significance in nitrification.
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ISNANSETYO ALIM, GETSU SAI, SEGUCHI MASAHIRO, KORIYAMA MASUMI. Independent Effects of Temperature, Salinity, Ammonium Concentration and pH on Nitrification Rate of the Ariake Seawater Above Mud Sediment. HAYATI JOURNAL OF BIOSCIENCES 2014. [DOI: 10.4308/hjb.21.1.21] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Horel A, Bernard RJ, Mortazavi B. Impact of crude oil exposure on nitrogen cycling in a previously impacted Juncus roemerianus salt marsh in the northern Gulf of Mexico. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:6982-6993. [PMID: 24510533 DOI: 10.1007/s11356-014-2599-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 01/26/2014] [Indexed: 06/03/2023]
Abstract
This study investigated potential nitrogen fixation, net nitrification, and denitrification responses to short-term crude oil exposure that simulated oil exposure in Juncus roemerianus salt marsh sediments previously impacted following the Deepwater Horizon accident. Temperature as well as crude oil amount and type affected the nitrogen cycling rates. Total nitrogen fixation rates increased 44 and 194 % at 30 °C in 4,000 mg kg(-1) tar ball and 10,000 mg kg(-1) moderately weathered crude oil treatments, respectively; however, there was no difference from the controls at 10 and 20 °C. Net nitrification rates showed production at 20 °C and consumption at 10 and 30 °C in all oil treatments and controls. Potential denitrification rates were higher than controls in the 10 and 30 ºC treatments but responded differently to the oil type and amount. The highest rates of potential denitrification (12.7 ± 1.0 nmol N g(-1) wet h(-1)) were observed in the highly weathered 4,000 mg kg(-1) oil treatment at 30 °C, suggesting increased rates of denitrification during the warmer summer months. These results indicate that the impacts on nitrogen cycling from a recurring oil spill could depend on the time of the year as well as the amount and type of oil contaminating the marsh. The study provides evidence for impact on nitrogen cycling in coastal marshes that are vulnerable to repeated hydrocarbon exposure.
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Affiliation(s)
- Agota Horel
- Department of Biological Sciences, University of Alabama, PO Box 870344, Tuscaloosa, AL, 35487, USA,
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Stauffert M, Duran R, Gassie C, Cravo-Laureau C. Response of archaeal communities to oil spill in bioturbated mudflat sediments. MICROBIAL ECOLOGY 2014; 67:108-119. [PMID: 24057322 DOI: 10.1007/s00248-013-0288-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 09/03/2013] [Indexed: 06/02/2023]
Abstract
The response of archaeal community to oil spill with the combined effect of the bioturbation activity of the polychaetes Hediste diversicolor was determined in mudflat sediments from the Aber-Benoît basin (Brittany, French Atlantic coast), maintained in microcosms. The dynamics of the archaeal community was monitored by combining comparative terminal restriction fragment length polymorphism (T-RFLP) fingerprints and sequence library analyses based on 16S rRNA genes and 16S cDNA. Methanogens were also followed by targeting the mcrA gene. Crenarchaeota were always detected in all communities irrespective of the addition of H. diversicolor and/or oil. In the presence of oil, modifications of archaeal community structures were observed. These modifications were more pronounced when H. diversicolor was added resulting in a more diverse community especially for the Euryarchaeota and Thaumarchaeota. The analysis of mcrA transcripts showed a specific structure for each condition since the beginning of the experiment. Overall, oiled microcosms showed different communities irrespective of H. diversicolor addition, while similar hydrocarbon removal capacities were observed.
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Affiliation(s)
- Magalie Stauffert
- Equipe Environnement et Microbiologie, IPREM - UMR CNRS 5254, Université de Pau et des Pays de l'Adour, BP 1155, 64013, Pau Cedex, France
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46
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Curado G, Rubio-Casal AE, Figueroa E, Grewell BJ, Castillo JM. Native plant restoration combats environmental change: development of carbon and nitrogen sequestration capacity using small cordgrass in European salt marshes. ENVIRONMENTAL MONITORING AND ASSESSMENT 2013; 185:8439-8449. [PMID: 23591677 DOI: 10.1007/s10661-013-3185-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Accepted: 03/26/2013] [Indexed: 06/02/2023]
Abstract
Restoration of salt marshes is critical in the context of climate change and eutrophication of coastal waters because their vegetation and sediments may act as carbon and nitrogen sinks. Our primary objectives were to quantify carbon (C) and nitrogen (N) stocks and sequestration rates in restored marshes dominated by Spartina maritima to provide support for restoration and management strategies that may offset negative aspects of eutrophication and climate change in estuarine ecosystems. Sediment C content was between ca. 13 mg C g(-1)and sediment N content was ca. 1.8 mg N g(-1). The highest C content for S. maritima was recorded in leaves and stems (ca. 420 mg C g(-1)) and the lowest in roots (361 ± 4 mg C g(-1)). S. maritima also concentrated more N in its leaves (31 ± 1 mg N g(-1)) than in other organs. C stock in the restored marshes was 29.6 t C ha(-1); ca. 16 % was stored in S. maritima tissues. N stock was 3.6 t N ha(-1), with 8.3 % stored in S. maritima. Our results showed that the S. maritima restored marshes, 2.5 years after planting, were sequestering atmospheric C and, therefore, provide some mitigation for global warming. Stands are also capturing nitrogen and reducing eutrophication. The concentrations of C and N contents in sediments, and cordgrass relative cover of 62 %, and low below-ground biomass (BGB) suggest restored marshes can sequester more C and N. S. maritima plantations in low marshes replace bare sediments and invasive populations of exotic Spartina densiflora and increase the C and N sequestration capacity of the marsh by increasing biomass production and accumulation.
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Affiliation(s)
- Guillermo Curado
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Ap. 1095, 41080, Sevilla, Spain
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47
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Le Roux X, Schmid B, Poly F, Barnard RL, Niklaus PA, Guillaumaud N, Habekost M, Oelmann Y, Philippot L, Salles JF, Schloter M, Steinbeiss S, Weigelt A. Soil environmental conditions and microbial build-up mediate the effect of plant diversity on soil nitrifying and denitrifying enzyme activities in temperate grasslands. PLoS One 2013; 8:e61069. [PMID: 23613785 PMCID: PMC3629084 DOI: 10.1371/journal.pone.0061069] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Accepted: 03/05/2013] [Indexed: 11/18/2022] Open
Abstract
Random reductions in plant diversity can affect ecosystem functioning, but it is still unclear which components of plant diversity (species number - namely richness, presence of particular plant functional groups, or particular combinations of these) and associated biotic and abiotic drivers explain the observed relationships, particularly for soil processes. We assembled grassland communities including 1 to 16 plant species with a factorial separation of the effects of richness and functional group composition to analyze how plant diversity components influence soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively), the abundance of nitrifiers (bacterial and archaeal amoA gene number) and denitrifiers (nirK, nirS and nosZ gene number), and key soil environmental conditions. Plant diversity effects were largely due to differences in functional group composition between communities of identical richness (number of sown species), though richness also had an effect per se. NEA was positively related to the percentage of legumes in terms of sown species number, the additional effect of richness at any given legume percentage being negative. DEA was higher in plots with legumes, decreased with increasing percentage of grasses, and increased with richness. No correlation was observed between DEA and denitrifier abundance. NEA increased with the abundance of ammonia oxidizing bacteria. The effect of richness on NEA was entirely due to the build-up of nitrifying organisms, while legume effect was partly linked to modified ammonium availability and nitrifier abundance. Richness effect on DEA was entirely due to changes in soil moisture, while the effects of legumes and grasses were partly due to modified nitrate availability, which influenced the specific activity of denitrifiers. These results suggest that plant diversity-induced changes in microbial specific activity are important for facultative activities such as denitrification, whereas changes in microbial abundance play a major role for non-facultative activities such as nitrification.
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Affiliation(s)
- Xavier Le Roux
- Université de Lyon, INRA, CNRS, Université Lyon 1, Microbial Ecology Centre, UMR 5557 CNRS, USC 1364 INRA, Villeurbanne, France.
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48
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Peng X, Yando E, Hildebrand E, Dwyer C, Kearney A, Waciega A, Valiela I, Bernhard AE. Differential responses of ammonia-oxidizing archaea and bacteria to long-term fertilization in a New England salt marsh. Front Microbiol 2013; 3:445. [PMID: 23346081 PMCID: PMC3551258 DOI: 10.3389/fmicb.2012.00445] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 12/31/2012] [Indexed: 11/13/2022] Open
Abstract
Since the discovery of ammonia-oxidizing archaea (AOA), new questions have arisen about population and community dynamics and potential interactions between AOA and ammonia-oxidizing bacteria (AOB). We investigated the effects of long-term fertilization on AOA and AOB in the Great Sippewissett Marsh, Falmouth, MA, USA to address some of these questions. Sediment samples were collected from low and high marsh habitats in July 2009 from replicate plots that received low (LF), high (HF), and extra high (XF) levels of a mixed NPK fertilizer biweekly during the growing season since 1974. Additional untreated plots were included as controls (C). Terminal restriction fragment length polymorphism analysis of the amoA genes revealed distinct shifts in AOB communities related to fertilization treatment, but the response patterns of AOA were less consistent. Four AOB operational taxonomic units (OTUs) predictably and significantly responded to fertilization, but only one AOA OTU showed a significant pattern. Betaproteobacterial amoA gene sequences within the Nitrosospira-like cluster dominated at C and LF sites, while sequences related to Nitrosomonas spp. dominated at HF and XF sites. We identified some clusters of AOA sequences recovered primarily from high fertilization regimes, but other clusters consisted of sequences recovered from all fertilization treatments, suggesting greater physiological diversity. Surprisingly, fertilization appeared to have little impact on abundance of AOA or AOB. In summary, our data reveal striking patterns for AOA and AOB in response to long-term fertilization, and also suggest a missing link between community composition and abundance and nitrogen processing in the marsh.
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Affiliation(s)
- Xuefeng Peng
- Department of Biology, Connecticut College New London, CT, USA
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49
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Beman JM, Bertics VJ, Braunschweiler T, Wilson JM. Quantification of ammonia oxidation rates and the distribution of ammonia-oxidizing Archaea and Bacteria in marine sediment depth profiles from Catalina Island, California. Front Microbiol 2012; 3:263. [PMID: 22837756 PMCID: PMC3403348 DOI: 10.3389/fmicb.2012.00263] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 07/04/2012] [Indexed: 11/28/2022] Open
Abstract
Microbial communities present in marine sediments play a central role in nitrogen biogeochemistry at local to global scales. Along the oxidation–reduction gradients present in sediment profiles, multiple nitrogen cycling processes (such as nitrification, denitrification, nitrogen fixation, and anaerobic ammonium oxidation) are active and actively coupled to one another – yet the microbial communities responsible for these transformations and the rates at which they occur are still poorly understood. We report pore water geochemical (O2, NH4+, and NO3−) profiles, quantitative profiles of archaeal and bacterial amoA genes, and ammonia oxidation rate measurements, from bioturbated marine sediments of Catalina Island, California. Across triplicate sediment cores collected offshore at Bird Rock (BR) and within Catalina Harbor (CH), oxygen penetration (0.24–0.5 cm depth) and the abundance of amoA genes (up to 9.30 × 107 genes g–1) varied with depth and between cores. Bacterial amoA genes were consistently present at depths of up to 10 cm, and archaeal amoA was readily detected in BR cores, and CH cores from 2008, but not 2007. Although detection of DNA is not necessarily indicative of active growth and metabolism, ammonia oxidation rate measurements made in 2008 (using isotope tracer) demonstrated the production of oxidized nitrogen at depths where amoA was present. Rates varied with depth and between cores, but indicate that active ammonia oxidation occurs at up to 10 cm depth in bioturbated CH sediments, where it may be carried out by either or both ammonia-oxidizing archaea and bacteria.
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Affiliation(s)
- J M Beman
- School of Natural Sciences, University of California, Merced, Merced, CA, USA
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50
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Jung J, Yeom J, Han J, Kim J, Park W. Seasonal changes in nitrogen-cycle gene abundances and in bacterial communities in acidic forest soils. J Microbiol 2012; 50:365-73. [PMID: 22752898 DOI: 10.1007/s12275-012-1465-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 02/28/2012] [Indexed: 11/26/2022]
Abstract
The abundance of genes related to the nitrogen biogeochemical cycle and the microbial community in forest soils (bacteria, archaea, fungi) were quantitatively analyzed via real-time PCR using 11 sets of specific primers amplifying nifH, bacterial amoA, archaeal amoA, narG, nirS, nirK, norB, nosZ, bacterial 16S rRNA gene, archaeal 16S rRNA gene, and the ITS sequence of fungi. Soils were sampled from Bukhan Mountain from September of 2010 to July of 2011 (7 times). Bacteria were the predominant microbial community in all samples. However, the abundance of archaeal amoA was greater than bacterial amoA throughout the year. The abundances of nifH, nirS, nirK, and norB genes changed in a similar pattern, while narG and nosZ appeared in sensitive to the environmental changes. Clone libraries of bacterial 16S rRNA genes were constructed from summer and winter soil samples and these revealed that Acidobacteria was the most predominant phylum in acidic forest soil environments in both samples. Although a specific correlation of environmental factor and gene abundance was not verified by principle component analysis, our data suggested that the combination of biological, physical, and chemical characteristics of forest soils created distinct conditions favoring the nitrogen biogeochemical cycle and that bacterial communities in undisturbed acidic forest soils were quite stable during seasonal change.
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Affiliation(s)
- Jaejoon Jung
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 136-713, Republic of Korea
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