1
|
Fan Y, Zhou Z, Liu F, Qian L, Yu X, Huang F, Hu R, Su H, Gu H, Yan Q, He Z, Wang C. The vertical partitioning between denitrification and dissimilatory nitrate reduction to ammonium of coastal mangrove sediment microbiomes. WATER RESEARCH 2024; 262:122113. [PMID: 39032335 DOI: 10.1016/j.watres.2024.122113] [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: 03/22/2024] [Revised: 07/13/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
Mangrove aquatic ecosystems receive substantial nitrogen (N) inputs from both land and sea, playing critical roles in modulating coastal N fluxes. The microbially-mediated competition between denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in mangrove sediments significantly impacts the N fate and transformation processes. Despite their recognized role in N loss or retention in surface sediments, how these two processes vary with sediment depths and their influential factors remain elusive. Here, we employed a comprehensive approach combining 15N isotope tracer, quantitative PCR (qPCR) and metagenomics to verify the vertical dynamics of denitrification and DNRA across five 100-cm mangrove sediment cores. Our results revealed a clear vertical partitioning, with denitrification dominated in 0-30 cm sediments, while DNRA played a greater role with increasing depths. Quantification of denitrification and DNRA functional genes further explained this phenomenon. Taxonomic analysis identified Pseudomonadota as the primary denitrification group, while Planctomycetota and Pseudomonadota exhibited high proportion in DNRA group. Furthermore, genome-resolved metagenomics revealed multiple salt-tolerance strategies and aromatic compound utilization potential in denitrification assemblages. This allowed denitrification to dominate in oxygen-fluctuating and higher-salinity surface sediments. However, the elevated C/N in anaerobic deep sediments favored DNRA, tending to generate biologically available NH4+. Together, our results uncover the depth-related variations in the microbially-mediated competition between denitrification and DNRA, regulating N dynamics in mangrove ecosystems.
Collapse
Affiliation(s)
- Yijun Fan
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhengyuan Zhou
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Fei Liu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Lu Qian
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaoli Yu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Fangjuan Huang
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Ruiwen Hu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Hualong Su
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Hang Gu
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Qingyun Yan
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
| | - Cheng Wang
- School of Environmental Science and Engineering, Marine Synthetic Ecology Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
| |
Collapse
|
2
|
Dai Z, Zhang N, Wang F, Li Y, Peng J, Xiang T, Zhao X, Yang S, Cao W. Loss of microbial functional diversity following Spartina alterniflora invasion reduces the potential of carbon sequestration and nitrogen removal in mangrove sediments-from a gene perspective. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 365:121569. [PMID: 38914045 DOI: 10.1016/j.jenvman.2024.121569] [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: 03/24/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/26/2024]
Abstract
Mangrove ecosystems play an important role in carbon (C) sequestration and nitrogen (N) removal. Although Spartina alterniflora has successively invaded native mangrove habitats during the preceding two decades, the effects of this invasion on the microbial functional potential involved in nutrient cycling remain unclear. In this study, metagenomic sequencing was used to investigate microbial C and N cycling in sediments derived from S. alterniflora and three native mangrove species (Kandelia obovata, Avicennia marina, and Aegiceras corniculatum). Greater differences in functional profiles of C and N cycling-related genes were observed between S. alterniflora and mangrove sediments than between different mangrove sediments. Functional diversity was lower in S. alterniflora sediments than in native mangrove sediments. The growth of Thaumarchaeota and Proteobacteria, was enhanced due to their resilience to diversity loss, while the growth of oligotrophs, such as Chloroflexi and Firmicutes, was inhibited in S. alterniflora sediments. Compared to mangrove sediments, the abundance of genes involved in C fixation and methane production was lower in S. alterniflora sediments. However, S. alterniflora significantly increased the gene abundance of pmo which controlled the oxidation process of CH4 to carbon dioxide. Additionally, genes involved in nitrification were enriched, whereas genes involved in N reduction processes, such as denitrification and dissimilatory nitrate reduction to ammonium, N immobilization, and N mineralization, were depleted in S. alterniflora sediments compared to mangrove sediments. Partial least squares regression models demonstrated that the decrease in soil organic C and increase in pH after S. alterniflora invasion induced the loss of microbial functional diversity, which was the main driver of changes in the abundances of genes involved in C and N cycling. Overall, our findings indicate that S. alterniflora invasion modifies the microbial functional profile of nutrient cycling in native mangrove ecosystems and potentially weakens the capacity of mangroves to sequester carbon and remove nitrogen.
Collapse
Affiliation(s)
- Zetao Dai
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Ning Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Feifei Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yujie Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Jiarui Peng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Tao Xiang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Xiaoyu Zhao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Shengchang Yang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Wenzhi Cao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China.
| |
Collapse
|
3
|
Stoodley P, Toelke N, Schwermer C, de Beer D. Bioenergetics of simultaneous oxygen and nitrate respiration and nitric oxide production in a Pseudomonas aeruginosa agar colony biofilm. Biofilm 2024; 7:100181. [PMID: 38425549 PMCID: PMC10902143 DOI: 10.1016/j.bioflm.2024.100181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/09/2024] [Accepted: 02/01/2024] [Indexed: 03/02/2024] Open
Abstract
Pseudomonas aeruginosa is a biofilm forming pathogen commonly associated with infection of the cystic fibrosis (CF) lung, chronic wounds and indwelling medical devices. P. aeruginosa is a facultative aerobe that can use nitrate (NO3-) found in healthy and infected tissues and body fluids to generate energy through denitrification. Further, P. aeruginosa the expression of denitrification genes has been found in specimens from people with CF. The main aim of this study was to determine the relative energy contribution of oxygen (O2) respiration and denitrification in single Pseudomonas aeruginosa PAO1 biofilm colonies under different O2 concentrations to estimate the possible relative importance of these metabolic processes in the context of biofilm infections. We showed that the used strain PAO1 in biofilms denitrified with nitrous oxide (N2O), and not nitrogen (N2), as the end product in our incubations. From simultaneous O2 and N2O microprofiles measured with high spatial resolution by microsensors in agar colony biofilms under air, N2 and pure O2, the rates of aerobic respiration and denitrification were calculated and converted to ATP production rates. Denitrification occurred both in the oxic and anoxic zones, and became increasingly dominant with decreasing O2 concentrations. At O2 concentrations characteristic for tissues and wounds (20-60 μM), denitrification was responsible for 50% of the total energy conservation in the biofilm. In addition the formation of nitric oxide (NO), a precursor of N2O and an important regulator of many cellular processes, was strongly influenced by the local O2 concentrations. NO production was inhibited under pure O2, present under anoxia (∼1 μM) and remarkably high (up to 6 μM) under intermediate O2 levels, which can be found in infected tissues. Possible impacts of such NO levels on both the host and the biofilm bacteria are discussed.
Collapse
Affiliation(s)
- Paul Stoodley
- National Centre for Advanced Tribology at Southampton, (NCATS), Mechanical Engineering, University of Southampton, Southampton, SO17 1BJ, UK
- Department of Microbial Infection and Immunity, Department of Orthopaedics, The Ohio State University, 716 Biomedical Research Tower (BRT), 460 W 12th Ave, Columbus OH, 43210, United States
| | - Nina Toelke
- Max Planck Institute for Marine Microbiology (MPI), Microsensor Group and Molecular Ecology Group, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Carsten Schwermer
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349, Oslo, Norway
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology (MPI), Microsensor Group and Molecular Ecology Group, Celsiusstrasse 1, D-28359, Bremen, Germany
| |
Collapse
|
4
|
Roothans N, Gabriëls M, Abeel T, Pabst M, van Loosdrecht MCM, Laureni M. Aerobic denitrification as an N2O source from microbial communities. THE ISME JOURNAL 2024; 18:wrae116. [PMID: 38913498 PMCID: PMC11272060 DOI: 10.1093/ismejo/wrae116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/26/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas of primarily microbial origin. Oxic and anoxic emissions are commonly ascribed to autotrophic nitrification and heterotrophic denitrification, respectively. Beyond this established dichotomy, we quantitatively show that heterotrophic denitrification can significantly contribute to aerobic nitrogen turnover and N2O emissions in complex microbiomes exposed to frequent oxic/anoxic transitions. Two planktonic, nitrification-inhibited enrichment cultures were established under continuous organic carbon and nitrate feeding, and cyclic oxygen availability. Over a third of the influent organic substrate was respired with nitrate as electron acceptor at high oxygen concentrations (>6.5 mg/L). N2O accounted for up to one-quarter of the nitrate reduced under oxic conditions. The enriched microorganisms maintained a constitutive abundance of denitrifying enzymes due to the oxic/anoxic frequencies exceeding their protein turnover-a common scenario in natural and engineered ecosystems. The aerobic denitrification rates are ascribed primarily to the residual activity of anaerobically synthesised enzymes. From an ecological perspective, the selection of organisms capable of sustaining significant denitrifying activity during aeration shows their competitive advantage over other heterotrophs under varying oxygen availabilities. Ultimately, we propose that the contribution of heterotrophic denitrification to aerobic nitrogen turnover and N2O emissions is currently underestimated in dynamic environments.
Collapse
Affiliation(s)
- Nina Roothans
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Minke Gabriëls
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, van Mourik Broekmanweg 6, Delft 2628 XE, the Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, United States
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Michele Laureni
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
- Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
| |
Collapse
|
5
|
Qian L, Yu X, Gu H, Liu F, Fan Y, Wang C, He Q, Tian Y, Peng Y, Shu L, Wang S, Huang Z, Yan Q, He J, Liu G, Tu Q, He Z. Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes. MICROBIOME 2023; 11:71. [PMID: 37020239 PMCID: PMC10074775 DOI: 10.1186/s40168-023-01501-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH4), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches. RESULTS Our results showed that the metabolic pathways involved in CH4, N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly (P < 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0-15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N2O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly (P < 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH4 oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments. CONCLUSIONS In addition to offering a perspective on the vertical distribution of microbially driven CH4, N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N2O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change. Video Abstract.
Collapse
Affiliation(s)
- Lu Qian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Hang Gu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Fei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Yijun Fan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qiang He
- Department of Civil and Environmental Engineering, the University of Tennessee, Knoxville, TN 37996 USA
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Yisheng Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Shanquan Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Zhijian Huang
- School of Marine Science, Sun Yat-Sen University, Zhuhai, 519080 China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Jianguo He
- School of Life Science, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Guangli Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237 China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, 510006 China
| |
Collapse
|
6
|
Bourceau OM, Ferdelman T, Lavik G, Mussmann M, Kuypers MMM, Marchant HK. Simultaneous sulfate and nitrate reduction in coastal sediments. ISME COMMUNICATIONS 2023; 3:17. [PMID: 36882570 PMCID: PMC9992702 DOI: 10.1038/s43705-023-00222-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 03/09/2023]
Abstract
The oscillating redox conditions that characterize coastal sandy sediments foster microbial communities capable of respiring oxygen and nitrate simultaneously, thereby increasing the potential for organic matter remineralization, nitrogen (N)-loss and emissions of the greenhouse gas nitrous oxide. It is unknown to what extent these conditions also lead to overlaps between dissimilatory nitrate and sulfate respiration. Here, we show that sulfate and nitrate respiration co-occur in the surface sediments of an intertidal sand flat. Furthermore, we found strong correlations between dissimilatory nitrite reduction to ammonium (DNRA) and sulfate reduction rates. Until now, the nitrogen and sulfur cycles were assumed to be mainly linked in marine sediments by the activity of nitrate-reducing sulfide oxidisers. However, transcriptomic analyses revealed that the functional marker gene for DNRA (nrfA) was more associated with microorganisms known to reduce sulfate rather than oxidise sulfide. Our results suggest that when nitrate is supplied to the sediment community upon tidal inundation, part of the sulfate reducing community may switch respiratory strategy to DNRA. Therefore increases in sulfate reduction rate in-situ may result in enhanced DNRA and reduced denitrification rates. Intriguingly, the shift from denitrification to DNRA did not influence the amount of N2O produced by the denitrifying community. Our results imply that microorganisms classically considered as sulfate reducers control the potential for DNRA within coastal sediments when redox conditions oscillate and therefore retain ammonium that would otherwise be removed by denitrification, exacerbating eutrophication.
Collapse
Affiliation(s)
- O M Bourceau
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - T Ferdelman
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - G Lavik
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - M Mussmann
- University of Vienna, Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Djerassiplatz 1, A-1030, Vienna, Austria
| | - M M M Kuypers
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - H K Marchant
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
- University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359, Bremen, Germany.
| |
Collapse
|
7
|
Grenier V, Gonzalez E, Brereton NJB, Pitre FE. Dynamics of bacterial and archaeal communities during horse bedding and green waste composting. PeerJ 2023; 11:e15239. [PMID: 37159830 PMCID: PMC10163874 DOI: 10.7717/peerj.15239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 03/28/2023] [Indexed: 05/11/2023] Open
Abstract
Organic waste decomposition can make up substantial amounts of municipal greenhouse emissions during decomposition. Composting has the potential to reduce these emissions as well as generate sustainable fertilizer. However, our understanding of how complex microbial communities change to drive the chemical and biological processes of composting is still limited. To investigate the microbiota associated with organic waste decomposition, initial composting feedstock (Litter), three composting windrows of 1.5 months (Young phase), 3 months (Middle phase) and 12 months (Aged phase) old, and 24-month-old mature Compost were sampled to assess physicochemical properties, plant cell wall composition and the microbial community using 16S rRNA gene amplification. A total of 2,612 Exact Sequence Variants (ESVs) included 517 annotated as putative species and 694 as genera which together captured 57.7% of the 3,133,873 sequences, with the most abundant species being Thermobifida fusca, Thermomonospora chromogena and Thermobifida bifida. Compost properties changed rapidly over time alongside the diversity of the compost community, which increased as composting progressed, and multivariate analysis indicated significant variation in community composition between each time-point. The abundance of bacteria in the feedstock is strongly correlated with the presence of organic matter and the abundance of plant cell wall components. Temperature and pH are the most strongly correlated parameters with bacterial abundance in the thermophilic and cooling phases/mature compost respectively. Differential abundance analysis revealed 810 ESVs annotated as species significantly varied in relative abundance between Litter and Young phase, 653 between the Young and Middle phases, 1182 between Middle and Aged phases and 663 between Aged phase and mature Compost. These changes indicated that structural carbohydrates and lignin degrading species were abundant at the beginning of the thermophilic phase, especially members of the Firmicute and Actinobacteria phyla. A high diversity of species capable of putative ammonification and denitrification were consistently found throughout the composting phases, whereas a limited number of nitrifying bacteria were identified and were significantly enriched within the later mesophilic composting phases. High microbial community resolution also revealed unexpected species which could be beneficial for agricultural soils enriched with mature compost or for the deployment of environmental and plant biotechnologies. Understanding the dynamics of these microbial communities could lead to improved waste management strategies and the development of input-specific composting protocols to optimize carbon and nitrogen transformation and promote a diverse and functional microflora in mature compost.
Collapse
Affiliation(s)
- Vanessa Grenier
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de Recherche en Biologie Végétale, Montréal, Québec, Canada
| | - Emmanuel Gonzalez
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Canadian Centre for Computational Genomics, McGill Genome Centre, McGill University, Montréal, Québec, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Nicholas JB Brereton
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Frederic E. Pitre
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
- Institut de Recherche en Biologie Végétale, Montréal, Québec, Canada
- Montreal Botanical Garden, Montréal, Québec, Canada
| |
Collapse
|
8
|
Zhang N, Zhang Y, Bohu T, Wu S, Bai Z, Zhuang X. Nitrogen Removal Characteristics and Constraints of an Alphaproteobacteria with Potential for High Nitrogen Content Heterotrophic Nitrification-Aerobic Denitrification. Microorganisms 2022; 10:microorganisms10020235. [PMID: 35208689 PMCID: PMC8879992 DOI: 10.3390/microorganisms10020235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 01/09/2023] Open
Abstract
The discovery of heterotrophic nitrification-aerobic denitrification (HN-AD) microorganisms has opened a new window for wastewater treatment. The underlying mechanism of HN-AD, however, is not fully understood because of the phylogenetic diversity of HN-AD microbes. The isolation and characterization of new HN-AD microorganisms are encouraging for furthering the understanding of this process. In this study, we found an Alphaproteobacteria isolate W30 from a historically polluted river in China through an HN-AD microbes screening process, which we identified as Pannonibacter sp. A potential HN-AD pathway for W30 was proposed based on N conversion analyses and the successful amplification of the entire denitrification gene series. The isolate exhibited high efficiency of aerobic inorganic nitrogen transformation, which accounted for 97.11% of NH4+-N, 100% of NO3−-N, and 99.98% of NO2−-N removal with a maximum linear rate of 10.21 mg/L/h, 10.46 mg/L/h, and 10.77 mg/L/h, respectively. Assimilation rather than denitrification was the main mechanism for the environmental nitrogen depletion mediated by W30. The effect of environmental constraints on aerobic NO3−-N removal were characterized, following a membrane bioreactor effluent test under an oxic condition. Compared to known Alphaproteobacterial HN-AD microbes, we showed that Pannonibacter sp. W30 could deplete nitrogen with no NO2−-N or NO3−-N accumulation in the HN-AD process. Therefore, the application of Pannonibacter sp. W30 has the potential for developing a felicitous HN-AD technology to treat N-laden wastewater at the full-scale level.
Collapse
Affiliation(s)
- Nan Zhang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (N.Z.); (Y.Z.); (S.W.); (Z.B.)
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiting Zhang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (N.Z.); (Y.Z.); (S.W.); (Z.B.)
- School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Tsing Bohu
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Taipa, Macao
- CNSA Macau Center for Space Exploration and Science, Taipa, Macao
- CSIRO Mineral Resources, Australian Resources and Research Centre, Kensington, WA 6151, Australia
- Correspondence: (T.B.); (X.Z.)
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (N.Z.); (Y.Z.); (S.W.); (Z.B.)
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (N.Z.); (Y.Z.); (S.W.); (Z.B.)
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- Xiongan Institute of Innovation, Xiongan New Area, Baoding 071000, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (N.Z.); (Y.Z.); (S.W.); (Z.B.)
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (T.B.); (X.Z.)
| |
Collapse
|
9
|
Wang W, Wang X, Shu X, Wang B, Li H, Zhang Q. Denitrification of Permeable Sand Sediment in a Headwater River Is Mainly Influenced by Water Chemistry, Rather Than Sediment Particle Size and Heterogeneity. Microorganisms 2021; 9:2202. [PMID: 34835328 PMCID: PMC8624688 DOI: 10.3390/microorganisms9112202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/08/2021] [Accepted: 10/19/2021] [Indexed: 12/03/2022] Open
Abstract
Sediment particle size and heterogeneity play an important role in sediment denitrification through direct and indirect effects on, for example, the material exchange rate, environmental gradients, microbial biomass, and grazing pressure. However, these effects have mostly been observed in impermeable sediments. On the other hand, the material exchange of permeable sediments is dominated by advection instead of diffusion, with the exchange or transport rates exceeding those of diffusion by two orders of magnitude relative to impermeable sediments. The impact of permeable sediment particle size and heterogeneity on denitrification remains poorly understood, especially at the millimeter scale. Here, we conducted an in situ control experiment in which we sorted sand sediment into four homogeneous-particle-sizes treatments and four heterogeneous treatments. Each treatment was deployed, in replicate, within the riffle in three different river reaches with contrasting physicochemical characteristics. After incubating for three months, sediment denitrifier communities (nirS, nirK, nosZ), denitrification gene abundances (nirS, nirK, nosZ), and denitrification rates in all treatments were measured. We found that most of the denitrifying microbes in permeable sediments were unclassified denitrifying microbes, and particle size and heterogeneity were not significantly correlated with the functional gene abundances or denitrification rates. Water chemistry was the key controlling factor for the denitrification of permeable sediments. Water NO3--N directly regulated the denitrification rate of permeable sediments, instead of indirectly regulating the denitrification rate of sediments by affecting the chemical characteristics of the sediments. Our study fills a knowledge gap of denitrification in permeable sediment in a headwater river and highlights that particle size and heterogeneity are less important for permeable sediment denitrification.
Collapse
Affiliation(s)
- Weibo Wang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (X.S.); (H.L.)
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| | - Xu Wang
- College of Science, Tibet University, Lhasa 850000, China;
| | - Xiao Shu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (X.S.); (H.L.)
| | - Baoru Wang
- Hengyang Key Laboratory of Soil Pollution Control and Remediation, Resource Environment and Safety Engineering College, University of South China, Hengyang 421001, China;
| | - Hongran Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (X.S.); (H.L.)
| | - Quanfa Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (X.S.); (H.L.)
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China
| |
Collapse
|
10
|
Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments. ISME JOURNAL 2021; 16:750-763. [PMID: 34584214 PMCID: PMC8857189 DOI: 10.1038/s41396-021-01111-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 01/04/2023]
Abstract
The microbial community composition and biogeochemical dynamics of coastal permeable (sand) sediments differs from cohesive (mud) sediments. Tide- and wave-driven hydrodynamic disturbance causes spatiotemporal variations in oxygen levels, which select for microbial generalists and disrupt redox cascades. In this work, we profiled microbial communities and biogeochemical dynamics in sediment profiles from three sites varying in their exposure to hydrodynamic disturbance. Strong variations in sediment geochemistry, biogeochemical activities, and microbial abundance, composition, and capabilities were observed between the sites. Most of these variations, except for microbial abundance and diversity, significantly correlated with the relative disturbance level of each sample. In line with previous findings, metabolically flexible habitat generalists (e.g., Flavobacteriaceae, Woeseaiceae, Rhodobacteraceae) dominated in all samples. However, we present evidence that aerobic specialists such as ammonia-oxidizing archaea (Nitrosopumilaceae) were more abundant and active in more disturbed samples, whereas bacteria capable of sulfate reduction (e.g., uncultured Desulfobacterales), dissimilatory nitrate reduction to ammonium (DNRA; e.g., Ignavibacteriaceae), and sulfide-dependent chemolithoautotrophy (e.g., Sulfurovaceae) were enriched and active in less disturbed samples. These findings are supported by insights from nine deeply sequenced metagenomes and 169 derived metagenome-assembled genomes. Altogether, these findings suggest that hydrodynamic disturbance is a critical factor controlling microbial community assembly and biogeochemical processes in coastal sediments. Moreover, they strengthen our understanding of the relationships between microbial composition and biogeochemical processes in these unique environments.
Collapse
|
11
|
Wang W, Hu M, Shu X, Li H, Qi W, Yang Y, Zhang Q. Microbiome of permeable sandy substrate in headwater river is shaped by water chemistry rather than grain size and heterogeneity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146552. [PMID: 34030307 DOI: 10.1016/j.scitotenv.2021.146552] [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: 12/30/2020] [Revised: 03/06/2021] [Accepted: 03/13/2021] [Indexed: 06/12/2023]
Abstract
The reservoir of microbial communities within the soil and the sediment performs many ecological functions and offers many ecosystem services. It has been suggested that its diversity and community structure could be explained by different grain size and heterogeneity. However, most of these conclusions come from studies conducted in terrestrial soil, impermeable marine and freshwater sediment (substrate). It remains to be seen whether these conclusions hold true in permeable substrate, especially in headwater river ecosystems. To address this, a field experiment was aimed to evaluate the link between grain median size and distribution heterogeneity and microbial diversity and community structure. Permeable substrate with gradient grain sizes and heterogeneities was inoculated in a headwater river in central China, while the diversity and community composition of the total microbial community and three denitrifier communities were investigated by high throughput sequencing three months later. The total microbial community was sequenced by 16S rRNA, a marker for taxonomic diversity. Three denitrifier communities were sequenced using three functional gene markers: nirK, nirS, and nosZ. The result showed that both the diversity and community structure of the total microbial community and three denitrifier communities were determined by water chemistry rather than grain size and size distribution heterogeneity, although grain size and heterogeneity positively influenced the nutrient concentrations of the substrate. Compared to the total microbial community, denitrification functional groups had more unique species proportions, indicating that functional genes were more sensitive to environmental change than the 16S rRNA gene. Our study fills a gap in understanding microbial communities in permeable sediment in a headwater river and highlights the less importance of grain size and heterogeneity on mm-scale in shaping the diversity and structure of microbiome.
Collapse
Affiliation(s)
- Weibo Wang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.
| | - Mingming Hu
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, Beijing 10038, China; Department of Water Ecology and Environment, China Institute of Water Resources and Hydropower Research, Beijing 10038, China
| | - Xiao Shu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Hua Li
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wenhua Qi
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yuyi Yang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Quanfa Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.
| |
Collapse
|
12
|
Wu J, Hong Y, Wilson SJ, Song B. Microbial nitrogen loss by coupled nitrification to denitrification and anammox in a permeable subterranean estuary at Gloucester Point, Virginia. MARINE POLLUTION BULLETIN 2021; 168:112440. [PMID: 33971455 DOI: 10.1016/j.marpolbul.2021.112440] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/29/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
The nitrogen (N) loss processes have not been well examined in subterranean estuaries (STEs) between land and sea. We utilized a 15N isotope tracer method, q-PCR, and high-throughput sequencing to reveal the activities, abundances, and community compositions of N loss communities in a STE in Gloucester Point, Virginia, US. The highest activities, abundances and diversity of denitrifiers and anammox bacteria were detected at 50-60 cm depth in the aerobic-anaerobic transition zone (AATZ) characterized by sharp redox gradients. nirS-denitrifiers and anammox bacteria were affiliated to 10 different clusters and three genera, respectively. Denitrification and anammox played equal roles with an estimated N loss of 13.15 mmol N m-3 day-1. A positive correlation between ammonia oxidizing prokaryote abundances and DO as well as NOx- suggested that nitrification produces NOx- which supports the hotspot of denitrification and anammox within the AATZ. Overall, these results highlight the roles of N loss communities in STEs.
Collapse
Affiliation(s)
- Jiapeng Wu
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China; School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China.
| | - Stephanie J Wilson
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, USA
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, USA.
| |
Collapse
|
13
|
Ammonia-oxidizing archaea have similar power requirements in diverse marine oxic sediments. ISME JOURNAL 2021; 15:3657-3667. [PMID: 34158628 PMCID: PMC8630020 DOI: 10.1038/s41396-021-01041-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 11/08/2022]
Abstract
Energy/power availability is regarded as one of the ultimate controlling factors of microbial abundance in the deep biosphere, where fewer cells are found in habitats of lower energy availability. A critical assumption driving the proportional relationship between total cell abundance and power availability is that the cell-specific power requirement keeps constant or varies over smaller ranges than other variables, which has yet to be validated. Here we present a quantitative framework to determine the cell-specific power requirement of the omnipresent ammonia-oxidizing archaea (AOA) in eight sediment cores with 3-4 orders of magnitude variations of organic matter flux and oxygen penetration depth. Our results show that despite the six orders of magnitude variations in the rates and power supply of nitrification and AOA abundances across these eight cores, the cell-specific power requirement of AOA from different cores and depths overlaps within the narrow range of 10-19-10-17 W cell-1, where the lower end may represent the basal power requirement of microorganisms persisting in subseafloor sediments. In individual cores, AOA also exhibit similar cell-specific power requirements, regardless of the AOA population size or sediment depth/age. Such quantitative insights establish a relationship between the power supply and the total abundance of AOA, and therefore lay a foundation for a first-order estimate of the standing stock of AOA in global marine oxic sediments.
Collapse
|
14
|
Schutte CA, Huanca-Valenzuela P, Lavik G, Marchant HK, de Beer D. Advection Drives Nitrate Past the Microphytobenthos in Intertidal Sands, Fueling Deeper Denitrification. Front Microbiol 2021; 12:556268. [PMID: 34220727 PMCID: PMC8250833 DOI: 10.3389/fmicb.2021.556268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/10/2021] [Indexed: 11/18/2022] Open
Abstract
Nitrification rates are low in permeable intertidal sand flats such that the water column is the primary source of nitrate to the sediment. During tidal inundation, nitrate is supplied to the pore space by advection rather than diffusion, relieving the microorganisms that reside in the sand from nitrate limitation and supporting higher denitrification rates than those observed under diffusive transport. Sand flats are also home to an abundant community of benthic photosynthetic microorganisms, the microphytobenthos (MPB). Diatoms are an important component of the MPB that can take up and store high concentrations of nitrate within their cells, giving them the potential to alter nitrate availability in the surrounding porewater. We tested whether nitrate uptake by the MPB near the sediment surface decreases its availability to denitrifiers along deeper porewater flow paths. In laboratory experiments, we used NOx (nitrate + nitrite) microbiosensors to confirm that, in the spring, net NOx consumption in the zone of MPB photosynthetic activity was stimulated by light. The maximum potential denitrification rate, measured at high spatial resolution using microsensors with acetylene and nitrate added, occurred below 1.4 cm, much deeper than light-induced NOx uptake (0.13 cm). Therefore, the shallower MPB had the potential to decrease NOx supply to the deeper sediments and limit denitrification. However, when applying a realistic downward advective flow to sediment from our study site, NOx always reached the depths of maximum denitrification potential, regardless of light availability or season. We conclude that during tidal inundation porewater advection overwhelms any influence of shallow NOx uptake by the MPB and drives water column NOx to the depths of maximum denitrification potential.
Collapse
Affiliation(s)
- Charles A Schutte
- Microsensors Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Gaute Lavik
- Biogeochemistry Department, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Hannah K Marchant
- Biogeochemistry Department, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Dirk de Beer
- Microsensors Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| |
Collapse
|
15
|
Boey JS, Mortimer R, Couturier A, Worrallo K, Handley KM. Estuarine microbial diversity and nitrogen cycling increase along sand-mud gradients independent of salinity and distance. Environ Microbiol 2021; 24:50-65. [PMID: 33973326 DOI: 10.1111/1462-2920.15550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/22/2023]
Abstract
Estuaries are depositional environments prone to terrigenous mud sedimentation. While macrofaunal diversity and nitrogen retention are greatly affected by changes in sedimentary mud content, its impact on prokaryotic diversity and nitrogen cycling activity remains understudied. We characterized the composition of estuarine tidal flat prokaryotic communities spanning a habitat range from sandy to muddy sediments, while controlling for salinity and distance. We also determined the diversity, abundance and expression of ammonia oxidizers and N2 O-reducers within these communities by amoA and clade I nosZ gene and transcript analysis. Results show that prokaryotic communities and nitrogen cycling fractions were sensitive to changes in sedimentary mud content, and that changes in the overall community were driven by a small number of phyla. Significant changes occurred in prokaryotic communities and N2 O-reducing fractions with only a 3% increase in mud, while thresholds for ammonia oxidizers were less distinct, suggesting other factors are also important for structuring these guilds. Expression of nitrogen cycling genes was substantially higher in muddier sediments, and results indicate that the potential for coupled nitrification-denitrification became increasingly prevalent as mud content increased. Altogether, results demonstrate that mud content is a strong environmental driver of diversity and N-cycling dynamics in estuarine microbial communities.
Collapse
Affiliation(s)
- Jian Sheng Boey
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Redmond Mortimer
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Agathe Couturier
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand.,Ecole Supérieure de Biologie Biochimie Biotechnologies, Faculté des Sciences, Université Catholique de Lyon, Lyon, France
| | - Katie Worrallo
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| | - Kim M Handley
- School of Biological Sciences, Faculty of Science, University of Auckland, Auckland, New Zealand
| |
Collapse
|
16
|
Outer membrane vesicles mediated horizontal transfer of an aerobic denitrification gene between Escherichia coli. Biodegradation 2021; 32:435-448. [PMID: 33886019 DOI: 10.1007/s10532-021-09945-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
Bacterial genetic material can be horizontally transferred between microorganisms via outer membrane vesicles (OMVs) released by bacteria. Up to now, the application of vesicle-mediated horizontal transfer of "degrading genes" in environmental remediation has not been reported. In this study, the nirS gene from an aerobic denitrification bacterium, Pseudomonas stutzeri, was enclosed in a pET28a plasmid, transformed into Escherichia coli (E. coli) DH5α and expressed in E. coli BL21. The E. coli DH5α released OMVs containing the recombination plasmid pET28a-nirS-EGFP. When compared with the free pET28a-nirS-EGFP plasmid's inability to transform, nirS in OMVs could be transferred into E. coli BL21 with the transformation frequency of 2.76 × 106 CFU/g when the dosage of OMVs was 200 µg under natural conditions, and nirS could express successfully in recipient bacteria. Furthermore, the recipient bacteria that received OMVs containing pET28a-nirS-EGFP could produce 18.16 U/mL activity of nitrite reductase.
Collapse
|
17
|
Quantifying potential N turnover rates in hypersaline microbial mats by 15N tracer techniques. Appl Environ Microbiol 2021; 87:AEM.03118-20. [PMID: 33579680 PMCID: PMC8091114 DOI: 10.1128/aem.03118-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial mats, due to stratification of the redox zones, have a potential to include a complete N cycle, however an attempt to evaluate a complete N cycle in these ecosystems has not been yet made. In this study, occurrence and rates of major N cycle processes were evaluated in intact microbial mats from Elkhorn Slough, Monterey Bay, CA, USA, and Baja California Sur, Mexico under oxic and anoxic conditions using 15N-labeling techniques. All of the major N transformation pathways, with the exception of anammox, were detected in both microbial mats. Nitrification rates were found to be low at both sites for both seasons investigated. The highest rates of ammonium assimilation were measured in Elkhorn Slough mats in April and corresponded to high in situ ammonium concentration in the overlying water. Baja mats featured higher ammonification than ammonium assimilation rates and this, along with their higher affinity for nitrate compared to ammonium and low dissimilatory nitrate reduction to ammonium rates, characterized their differences from Elkhorn Slough mats. Nitrogen fixation rates in Elkhorn Slough microbial mats were found to be low implying that other processes such as recycling and assimilation from water are main sources of N for these mats at the times sampled. Denitrification in all of the mats was incomplete with nitrous oxide as end product and not dinitrogen. Our findings highlight N cycling features not previously quantified in microbial mats and indicate a need of further investigations in these microbial ecosystems.Importance: Nitrogen is essential for life. The nitrogen cycle on Earth is mediated by microbial activity and has had a profound impact on both the atmosphere and the biosphere throughout geologic time. Microbial mats, present in many modern environments, have been regarded as living records of the organisms, genes, and phylogenies of microbes, as they are one of the most ancient ecosystems on Earth. While rates of major nitrogen metabolic pathways have been evaluated in a number of ecosystems, it remains elusive in microbial mats. In particular it is unclear what factors affect nitrogen cycling in these ecosystems and how morphological differences between mats impact nitrogen transformations. In this study we investigate nitrogen cycling in two microbial mats having morphological differences. Our findings provide insight for further understanding of biogeochemistry and microbial ecology of microbial mats.
Collapse
|
18
|
Müller B, Thoma R, Baumann KBL, Callbeck CM, Schubert CJ. Nitrogen removal processes in lakes of different trophic states from on-site measurements and historic data. AQUATIC SCIENCES 2021; 83:37. [PMID: 33785997 PMCID: PMC7946664 DOI: 10.1007/s00027-021-00795-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Freshwater lakes are essential hotspots for the removal of excessive anthropogenic nitrogen (N) loads transported from the land to coastal oceans. The biogeochemical processes responsible for N removal, the corresponding transformation rates and overall removal efficiencies differ between lakes, however, it is unclear what the main controlling factors are. Here, we investigated the factors that moderate the rates of N removal under contrasting trophic states in two lakes located in central Switzerland. In the eutrophic Lake Baldegg and the oligotrophic Lake Sarnen, we specifically examined seasonal sediment porewater chemistry, organic matter sedimentation rates, as well as 33-year of historic water column data. We find that the eutrophic Lake Baldegg, which contributed to the removal of 20 ± 6.6 gN m-2 year-1, effectively removed two-thirds of the total areal N load. In stark contrast, the more oligotrophic Lake Sarnen contributed to 3.2 ± 4.2 gN m-2 year-1, and had removed only one-third of the areal N load. The historic dataset of the eutrophic lake revealed a close linkage between annual loads of dissolved N (DN) and removal rates (NRR = 0.63 × DN load) and a significant correlation of the concentration of bottom water nitrate and removal rates. We further show that the seasonal increase in N removal rates of the eutrophic lake correlated significantly with seasonal oxygen fluxes measured across the water-sediment interface (R2 = 0.75). We suggest that increasing oxygen enhances sediment mineralization and stimulates nitrification, indirectly enhancing denitrification activity. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s00027-021-00795-7.
Collapse
Affiliation(s)
- Beat Müller
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Raoul Thoma
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Kathrin B. L. Baumann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Cameron M. Callbeck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Carsten J. Schubert
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| |
Collapse
|
19
|
Abstract
Nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) colonize diverse anoxic environments, including soil subsurface, groundwater, and wastewater. NRB and SRB compete for resources, and their interplay has major implications on the global cycling of nitrogen and sulfur species, with undesirable outcomes in some contexts. Competition between nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) for resources in anoxic environments is generally thought to be governed largely by thermodynamics. It is now recognized that intermediates of nitrogen and sulfur cycling (e.g., hydrogen sulfide, nitrite, etc.) can also directly impact NRB and SRB activities in freshwater, wastewater, and sediment and therefore may play important roles in competitive interactions. Here, through comparative transcriptomic and metabolomic analyses, we have uncovered mechanisms of hydrogen sulfide- and cysteine-mediated inhibition of nitrate respiratory growth for the NRB Intrasporangium calvum C5. Specifically, the systems analysis predicted that cysteine and hydrogen sulfide inhibit growth of I. calvum C5 by disrupting distinct steps across multiple pathways, including branched-chain amino acid (BCAA) biosynthesis, utilization of specific carbon sources, and cofactor metabolism. We have validated these predictions by demonstrating that complementation with BCAAs and specific carbon sources relieves the growth inhibitory effects of cysteine and hydrogen sulfide. We discuss how these mechanistic insights give new context to the interplay and stratification of NRB and SRB in diverse environments. IMPORTANCE Nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) colonize diverse anoxic environments, including soil subsurface, groundwater, and wastewater. NRB and SRB compete for resources, and their interplay has major implications on the global cycling of nitrogen and sulfur species, with undesirable outcomes in some contexts. For instance, the removal of reactive nitrogen species by NRB is desirable for wastewater treatment, but in agricultural soils, NRB can drive the conversion of nitrates from fertilizers into nitrous oxide, a potent greenhouse gas. Similarly, the hydrogen sulfide produced by SRB can help sequester and immobilize toxic heavy metals but is undesirable in oil wells where competition between SRB and NRB has been exploited to suppress hydrogen sulfide production. By characterizing how reduced sulfur compounds inhibit growth and activity of NRB, we have gained systems-level and mechanistic insight into the interplay of these two important groups of organisms and drivers of their stratification in diverse environments.
Collapse
|
20
|
Yuan H, Huang S, Yuan J, You Y, Zhang Y. Characteristics of microbial denitrification under different aeration intensities: Performance, mechanism, and co-occurrence network. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:141965. [PMID: 32911146 DOI: 10.1016/j.scitotenv.2020.141965] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/09/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
This study aimed to explore how dissolved oxygen (DO) affected the characteristics and mechanisms of denitrification in mixed bacterial consortia. We analyzed denitrification efficiency, intracellular nicotinamide adenine dinucleotide (NADH), relative expression of functional genes, and potential co-occurrence network of microorganisms. Results showed that the total nitrogen (TN) removal rates at different aeration intensities (0.00, 0.25, 0.63, and 1.25 L/(L·min)) were 0.93, 1.45, 0.86, and 0.53 mg/(L·min), respectively, which were higher than previously reported values for pure culture. The optimal aeration intensity was 0.25 L/(L·min), at which the maximum NADH accumulation rate and highest relative abundance of napA, nirK, and nosZ were achieved. With increased aeration intensity, the amount of electron flux to nitrate decreased and nitrate assimilation increased. On one hand, nitrate reduction was primarily inhibited by oxygen through competition for electron donors of a certain single strain. On the other hand, oxygen was consumed rapidly by bacteria by stimulating carbon metabolism to create an optimal denitrification niche for denitrifying microorganisms. Denitrification was performed via inter-genus cooperation (competitive interactions and symbiotic relationships) between keystone taxa (Azoarcus, Paracoccus, Thauera, Stappia, and Pseudomonas) and other heterotrophic bacteria (OHB) in aeration reactors. However, in the non-aeration case, which was primarily carried out based on intra-genus syntrophy within genus Propionivibrio, the co-occurrence network constructed the optimal niche contributing to the high TN removal efficiency. Overall, this study enhanced our knowledge about the molecular ecological mechanisms of aerobic denitrification in mixed bacterial consortia and has theoretical guiding significance for further practical application.
Collapse
Affiliation(s)
- Haiguang Yuan
- School of Environment and Energy, South China University of Technology, Higher Education Mega Center, Guangzhou 510006, PR China; Guangdong Ecological Environment Control Engineering Technology Research Center, South China University of Technology, Higher Education Mega Center, Guangzhou 510006, PR China
| | - Shaobin Huang
- School of Environment and Energy, South China University of Technology, Higher Education Mega Center, Guangzhou 510006, PR China; Guangdong Ecological Environment Control Engineering Technology Research Center, South China University of Technology, Higher Education Mega Center, Guangzhou 510006, PR China; State Key Laboratory of Pulp and Paper Engineering, Plant Micro/Nano Fiber Research Center, South China University of Technology, Guangzhou 510640, PR China.
| | - Jianqi Yuan
- School of Environment and Energy, South China University of Technology, Higher Education Mega Center, Guangzhou 510006, PR China; Guangdong Ecological Environment Control Engineering Technology Research Center, South China University of Technology, Higher Education Mega Center, Guangzhou 510006, PR China
| | - Yingying You
- School of Environment and Energy, South China University of Technology, Higher Education Mega Center, Guangzhou 510006, PR China; Guangdong Ecological Environment Control Engineering Technology Research Center, South China University of Technology, Higher Education Mega Center, Guangzhou 510006, PR China
| | - Yongqing Zhang
- School of Environment and Energy, South China University of Technology, Higher Education Mega Center, Guangzhou 510006, PR China
| |
Collapse
|
21
|
Qiao Z, Hu S, Wu Y, Sun R, Liu X, Chan J. Changes in the fluorescence intensity, degradability, and aromaticity of organic carbon in ammonium and phenanthrene-polluted aquatic ecosystems. RSC Adv 2021; 11:1066-1076. [PMID: 35423689 PMCID: PMC8693519 DOI: 10.1039/d0ra08655j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 11/27/2020] [Indexed: 11/21/2022] Open
Abstract
Mixed cultures were established by a sediment to investigate the changes in organic carbon (C) in a combined ammonium and phenanthrene biotransformation process in aquatic ecosystems. The microorganisms in the sediment demonstrated significant ammonium-N and phenanthrene biotransformation capacity with removal efficiencies of 99.96% and 99.99%, respectively. The changes in the organic C characteristics were evaluated by the fluorescence intensity, degradability (humification index (HIX) and UV absorbance at 254 nm (A254)), aromaticity (specific UV absorbance at 254 nm (SUVA254) and fluorescence index (FI)). Compared with C2 (the second control), the lower values of fluorescence intensity (after the 15th d), HIX (after the 8th d), A254 (after the 11th d), and SUVA254 (after the 8th d) and the higher FI value (after the 8th d) in ammonium and phenanthrene-fed mixed cultures (N_PHE) suggest that aromatic structures and some condensed molecules were easier to break down in N_PHE. Similar results were obtained from Fourier transformation infrared spectroscopy (FTIR) and nuclear magnetic resonance (1H NMR) spectra. Changes in organic C characteristics may be due to two key organisms Massilia and Azohydromonas. The biodiversity also suggested that the selective pressure of ammonium and phenanthrene is the decisive factor for changes in organic C characteristics. This study will shed light on theoretical insights into the interaction of N and aromatic compounds in aquatic ecosystems. Mixed cultures were established by a sediment to investigate the changes in organic carbon (C) in a combined ammonium and phenanthrene biotransformation process in aquatic ecosystems.![]()
Collapse
Affiliation(s)
- Zixia Qiao
- Department of Applied Chemistry
- Northwestern Polytechnical University
- Xi'an 710129
- China
| | - Sihai Hu
- Department of Applied Chemistry
- Northwestern Polytechnical University
- Xi'an 710129
- China
| | - Yaoguo Wu
- Department of Applied Chemistry
- Northwestern Polytechnical University
- Xi'an 710129
- China
| | - Ran Sun
- Department of Applied Chemistry
- Northwestern Polytechnical University
- Xi'an 710129
- China
| | - Xiaoyan Liu
- Department of Applied Chemistry
- Northwestern Polytechnical University
- Xi'an 710129
- China
| | - Jiangwei Chan
- Department of Applied Chemistry
- Northwestern Polytechnical University
- Xi'an 710129
- China
| |
Collapse
|
22
|
Qiao Z, Sun R, Wu Y, Hu S, Liu X, Chan J, Mi X. Characteristics and metabolic pathway of the bacteria for heterotrophic nitrification and aerobic denitrification in aquatic ecosystems. ENVIRONMENTAL RESEARCH 2020; 191:110069. [PMID: 32828759 DOI: 10.1016/j.envres.2020.110069] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/11/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
The present study investigated the nitrogen removal characteristics and metabolic pathway of bacteria in aquatic ecosystem, with a focus on heterotrophic nitrification and aerobic denitrification. The bacteria demonstrated significant heterotrophic nitrification and aerobic denitrification capacity. The highest ammonium-N, nitrate-N, and nitrite-N removal efficiencies were 95.31 ± 0.11%, 98.91 ± 0.05%, and 98.79 ± 0.09%, respectively. The Monod model was used to estimate the maximum rate of substrate utilization (Rmo) and the half-saturation concentration (Ks) for the two substrates, i.e., ammonium and nitrate. The kinetic coefficients were 3.34 mg/L/d (Rmo) and 30.59 mg/L (Ks) for ammonium-N, respectively, and 14.23 mg/L/d (Rmo) and 215.24 mg/L (Ks) for nitrate-N, respectively. The effects of initial nitrogen (ammonium-N or nitrate-N) concentration, temperature, and dissolved oxygen (DO) on nitrogen removal rate were investigated using response surface methodology (RSM), and the optimal conditions for nitrogen removal were determined. The principal nitrogen removal pathway of the bacteria was proposed as complete heterotrophic nitrification and aerobic denitrification, which was performed by six key genera: Arthrobacter, Pseudomonas, Rhodococcus, Bacillus, Massilia, and Rhizobium. Chryseobacterium and other denitrifying species may also reduce nitrification products (NOX-) via aerobic denitrification.
Collapse
Affiliation(s)
- Zixia Qiao
- Department of Applied Chemistry, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Ran Sun
- Department of Applied Chemistry, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Yaoguo Wu
- Department of Applied Chemistry, Northwestern Polytechnical University, Xi'an, 710129, China.
| | - Sihai Hu
- Department of Applied Chemistry, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Xiaoyan Liu
- Department of Applied Chemistry, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Jiangwei Chan
- Department of Applied Chemistry, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Xiaohui Mi
- Department of Applied Chemistry, Northwestern Polytechnical University, Xi'an, 710129, China
| |
Collapse
|
23
|
Xie R, Rao P, Pang Y, Shi C, Li J, Shen D. Salt intrusion alters nitrogen cycling in tidal reaches as determined in field and laboratory investigations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 729:138803. [PMID: 32361438 DOI: 10.1016/j.scitotenv.2020.138803] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/06/2020] [Accepted: 04/17/2020] [Indexed: 06/11/2023]
Abstract
Salinization is a growing problem throughout the world and poses a threat especially to freshwater ecosystems. However, much remains to be learned about the mechanisms by which salinity impacts microbially mediated biogeochemical processes. Elevated nitrogen (N) concentrations in estuarine ecosystems have led to their eutrophication, but the relationship between N transformation and the functional genes involved in the response to saltwater intrusion is poorly understood. Here, using the Minjiang River, a tidal river in southeastern China as an easily accessible natural laboratory, we conducted a 2-year field survey to investigate N speciation during ebb and flood tides. Then, in a laboratory experiment we simulated the varying degrees of salt intrusion that occur in natural tidal reaches. The microcosm study allowed quantitative assessments of N transformation and functional gene responses. The field surveys showed that concentrations of NH4+ rose during flood tides, while the concentrations of NO3- and total N fluctuated. In the microcosms, NO3- concentrations decreased in response to salt pulses, due to simultaneous declines in the abundance of genes responsible for nitrification and increases in the abundance of those involved in dissimilatory nitrate reduction to ammonium (DNRA). The elevated salinity led to increased yields of NH4+, a response that correlated positively with the abundance of nrfA genes, involved in DNRA. Furthermore, an increase in salinity promoted N2O accumulation during the denitrification process. Altogether, our study suggests that saltwater intrusion leads to a decrease in nitrification while favoring N transformation via denitrification and DNRA and that N2O accumulation in the water is dependent on the strength of the salt pulse.
Collapse
Affiliation(s)
- Rongrong Xie
- College of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China; Key Laboratory of Pollution Control and Resource Recycling of Fujian Province, Fujian Normal University, Fuzhou 350007, China; Section of Physical Oceanography and Instrumentation, Leibniz Institute for Baltic Sea Research, Warnemuende, D-18119 Rostock, Germany
| | - Peiyuan Rao
- College of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China
| | - Yong Pang
- College of Environment, Hohai University, Nanjing 210098, China
| | - Chengchun Shi
- Fuzhou Research Academy of Environmental Sciences, Fuzhou 350013, China
| | - Jiabing Li
- College of Environmental Science and Engineering, Fujian Normal University, Fuzhou 350007, China; Key Laboratory of Pollution Control and Resource Recycling of Fujian Province, Fujian Normal University, Fuzhou 350007, China.
| | - Dandan Shen
- Section of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Warnemuende, D-18119 Rostock, Germany; Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden.
| |
Collapse
|
24
|
Characteristics and Driving Factors of the Aerobic Denitrifying Microbial Community in Baiyangdian Lake, Xiong'an New Area. Microorganisms 2020; 8:microorganisms8050714. [PMID: 32403444 PMCID: PMC7284800 DOI: 10.3390/microorganisms8050714] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 11/30/2022] Open
Abstract
Here, the ion-exchangeable form of nitrogen (IEF-N), weak-acid extractable form of nitrogen (WAEF-N), strong-alkali extractable form of nitrogen (SAEF-N), strong-oxidant extractable form of nitrogen (SOEF-N), residue nitrogen (Res-N), and total nitrogen (TN) showed spatial differences, and most of the sediment nitrogen fractions exhibited positive correlations in Baiyangdian Lake. High-throughput sequencing analysis revealed that the aerobic denitrification microbial community was composed of proteobacteria (42.04%–99.08%) and unclassified_bacteria (0.92%–57.92%). Moreover, the microbial community exhibited significant differences (R2 = 0.4422, P < 0.05) on the basis of the adonis analysis. T(temperature), Moisture content (MC), sediment total phosphorus (STP), ion-exchangeable form of ammonia (IEF-NH4+-N), weak-acid extractable form of ammonia (WAEF-NH4+-N), weak-acid extractable form of nitrate (WAEF-NO3−-N), and strong-alkali extractable form of ammonia (SAEF-NH4+-N) were the dominant environmental factors and explained 11.1%, 8.2%, 10.7%, 6.9%, 9.3%, 8.1%, 10.5%, 7.5%, and 7% variation, respectively, of the total variation in the microbial community. Furthermore, the network analysis showed that symbiotic relationships accounted for a major percentage of the microbial networks. The keystone aerobic denitrifying bacteria belonged to Comamonas, Rhodobacter, Achromobacter, Aeromonas, Azoarcus, Leptothrix_Burkholderiales, Pseudomonas, Thauera, unclassified_Burkholderiales, and unclassified_bacteria. The composition of the keystone aerobic denitrifying microbial community also exhibited significant differences (R2 = 0.4534, P < 0.05) on the basis of the adonis analysis. T, STP, IEF-NH4+-N, ion-exchangeable form of nitrate (IEF-NO3−-N), WAEF-NO3−-N, SAEF-NH4+-N, and TN were the dominant environmental factors that explained 8.4%, 6.2%, 4.6%, 5.9%, 5.9%, 4.5%, and 9.4% variation, respectively, of the total variation in the keystone aerobic denitrifying microbial community. The systematic investigation could provide a theoretical foundation for the evolution mechanism of the aerobic denitrifying microbial community in Baiyangdian Lake.
Collapse
|
25
|
Ahmerkamp S, Marchant HK, Peng C, Probandt D, Littmann S, Kuypers MMM, Holtappels M. The effect of sediment grain properties and porewater flow on microbial abundance and respiration in permeable sediments. Sci Rep 2020; 10:3573. [PMID: 32107429 PMCID: PMC7046789 DOI: 10.1038/s41598-020-60557-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 02/13/2020] [Indexed: 11/08/2022] Open
Abstract
Sandy sediments cover 50-60% of the continental shelves and are highly efficient bioreactors in which organic carbon is remineralized and inorganic nitrogen is reduced to N2. As such they seem to play an important role, buffering the open ocean from anthropogenic nitrogen inputs and likely remineralizing the vast amounts of organic matter formed in the highly productive surface waters. To date however, little is known about the interrelation between porewater transport, grain properties and microbial colonization and the consequences for remineralization rates in sandy sediments. To constrain the effect of theses factors on remineralization in silicate sands, we incubated North Sea sediments in flow-through reactors after separating into five different grain size fractions. Bulk sediment and sediment grain properties were measured along with microbial colonization and cell abundances, oxygen consumption and denitrification rates. Volumetric oxygen consumption ranged from 14 to 77 µmol O2 l-1 h-1 while nitrogen-loss via denitrification was between 3.7 and 8.4 µmol N l-1 h-1. Oxygen consumption and denitrification rates were linearly correlated to the microbial cell abundances, which ranged from 2.9 to 5.4·108 cells cm-3. We found, that cell abundance and consumption rates in sandy sediments are influenced (i) by the surface area available for microbial colonization and (ii) by the exposure of these surfaces to the solute-supplying porewater flow. While protective structures such as cracks and depressions promote microbial colonization, the oxygen demand is only met by good ventilation of these structures, which is supported by a high sphericity of the grains. Based on our results, spherical sand grains with small depressions, i.e. golf ball like structures, provide the optimal supporting mineral structure for microorganisms on continental shelves.
Collapse
Affiliation(s)
- Soeren Ahmerkamp
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany.
- Marum Center for Marine Environmental Sciences, Bremen, Germany.
| | - Hannah K Marchant
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany
| | - Chao Peng
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany
- University Tübingen, Center for Applied Geoscience, Geomicrobiology, Geschwister-Scholl-Platz, 72074, Tübingen, Germany
| | - David Probandt
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany
| | - Marcel M M Kuypers
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany
| | - Moritz Holtappels
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359, Bremen, Germany
- Marum Center for Marine Environmental Sciences, Bremen, Germany
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| |
Collapse
|
26
|
Wang S, Pi Y, Jiang Y, Pan H, Wang X, Wang X, Zhou J, Zhu G. Nitrate reduction in the reed rhizosphere of a riparian zone: From functional genes to activity and contribution. ENVIRONMENTAL RESEARCH 2020; 180:108867. [PMID: 31708170 DOI: 10.1016/j.envres.2019.108867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/27/2019] [Accepted: 10/27/2019] [Indexed: 06/10/2023]
Abstract
The increased nitrogen (N) fertilizer usage caused substantial nitrate (NO3-) leaching into groundwater and eutrophication in downstream aquatic systems. Riparian zones positioned as the link interfaces of terrestrial and aquatic environments are effective in NO3- removal. However, the microbial mechanisms regulating NO3- reduction in riparian zones are still unclear. In this study, four microbial NO3- reduction processes were explored in fine-scale riparian soil horizons by isotopic tracing technique, qPCR of functional gene, high-throughput amplicon sequencing, and phylogenetic molecular ecological network analysis. Interestingly, anaerobic ammonium oxidation (anammox) contributed to NO3- removal of up to 48.2% only in waterward sediments but not in landward soil. Denitrification was still the most significant contributor to NO3- reduction (32.0-91.8%) and N-losses (51.7-100%). Additionally, dissimilatory nitrate reduction to ammonium (DNRA) played a key role in NO3- reduction (4.4-67.5%) and was even comparable to denitrification. Community structure analysis of denitrifying, anammox, and DNRA bacterial communities targeting the related functional gene showed that spatial heterogeneity played a greater role than both temporal and soil type (rhizosphere and non-rhizosphere soil) variability in microbial community structuring. Denitrification and DNRA communities were diverse, and their activities did not depend on gene abundance but were significantly related to organic matter, suggesting that gene abundance alone was insufficient in assessing their activity in riparian zones. Based on networks, DNRA plays a keystone role among the microbial NO3- reducers. As the last line of defense in the interception of terrestrial NO3-, these findings contribute to our understanding of NO3- removal mechanisms in riparian zones, and could potentially be exploited to reduce the diffusion of NO3- pollution.
Collapse
Affiliation(s)
- Shanyun Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yanxia Pi
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yingying Jiang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Huawei Pan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xiaoxia Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xiaomin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jiemin Zhou
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Guibing Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
27
|
Wang S, Wang W, Zhao S, Wang X, Hefting MM, Schwark L, Zhu G. Anammox and denitrification separately dominate microbial N-loss in water saturated and unsaturated soils horizons of riparian zones. WATER RESEARCH 2019; 162:139-150. [PMID: 31260829 DOI: 10.1016/j.watres.2019.06.052] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 06/09/2019] [Accepted: 06/19/2019] [Indexed: 06/09/2023]
Abstract
Fertilized agroecosystems may show considerable leaching of the mobile nitrogen (N) compound NO3-, which pollutes groundwater and causes eutrophication of downstream waterbodies. Riparian buffer zones, positioned between terrestrial and aquatic environments, effectively remove NO3- and serve as a hotspot for N2O emissions. However, microbial processes governing NO3- reduction in riparian zones still remain largely unclear. This study explored the underlying mechanisms of various N-loss processes in riparian soil horizons using isotopic tracing techniques, molecular assays, and high-throughput sequencing. Both anaerobic ammonium oxidation (anammox) and denitrification activity were maximized in the riparian fringe rather than in the central zones. Denitrifying anaerobic methane oxidation (damo) process was not detected. Interestingly, both contrasting microbial habitats were separated by a groundwater table, which forms an important biogeochemical interface. Denitrification dominated cumulative N-losses in the upper unsaturated soil, while anammox dominated the lower oxic saturated soil horizons. Archaeal and bacterial ammonium oxidation that couple dissimilatory nitrate reduction to ammonium (DNRA) with a high cell-specific rate promoted anammox even further in oxic subsurface horizons. High-throughput sequencing and network analysis showed that the anammox rate positively correlated with Candidatus 'Kuenenia' (4%), rather than with the dominant Candidatus 'Brocadia'. The contribution to N-loss via anammox increased significantly with the water level, which was accompanied by a significant reduction of N2O emission (∼39.3 ± 10.6%) since N-loss by anammox does not cause N2O emissions. Hence, water table management in riparian ecotones can be optimized to reduce NO3- pollution by shifting from denitrification to the environmentally friendly anammox pathway to mitigate greenhouse gas emissions.
Collapse
Affiliation(s)
- Shanyun Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Weidong Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Siyan Zhao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xiaomin Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Mariet M Hefting
- Ecology and Biodiversity Group, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Lorenz Schwark
- Institute for Geosciences, University of Kiel, Kiel, Germany
| | - Guibing Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
28
|
Zhou S, Zhang Y, Huang T, Liu Y, Fang K, Zhang C. Microbial aerobic denitrification dominates nitrogen losses from reservoir ecosystem in the spring of Zhoucun reservoir. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:998-1010. [PMID: 30266057 DOI: 10.1016/j.scitotenv.2018.09.160] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
The mechanism and factors influencing nitrogen loss in the Zhoucun reservoir were explored during the spring. The results showed that the nitrate and total nitrogen concentration decreased from 1.84 ± 0.01 mg/L and 2.34 ± 0.06 mg/L to 0.06 ± 0.01 mg/L and 0.48 ± 0.09 mg/L, respectively. Meanwhile, the nitrate and total nitrogen removal rate reached 97.02% ± 0.25 and 79.38% ± 3.32, respectively. Moreover, the abundance of nirS gene and aerobic denitrification bacteria increased from 1.04-3.38 × 103 copies/mL and 0.71 ± 0.22 × 102 cfu/mL to 5.36-5.81 × 103 copies/mL and 8.64 ± 2.08 × 103 cfu/mL, respectively. The low MW fractions of DOM (<5 kDa) increased from 0.94 ± 0.02 mg/L in February to 1.51 ± 0.09 mg/L in April. E3/E4 and absorption spectral slope ratio (SR) showed that fulvic acid accounted for the main proportion with autochthonous characteristics. These findings were consistent with the fluorescence components and fluorescence characteristic indices based on EEM-PARAFAC. Meanwhile, the microbial metabolism activity increased significantly from February to April, which contributed to the cycle of nutrients within the reservoir water system. Moreover, the abundance of the bacterial species involved in denitrification (Exiguobacterium, Brevundimonas, Deinococcus, Paracoccus, and Pseudomonas) increased significantly. The relative abundance of KOs related to nitrogen metabolism, were initially increased and then decreased. Specifically, K02567 (napA) represented the main proportion of KOs related to denitrification. The abundance of napA-type denitrifying bacteria (Dechloromonas, Pseudomonas, Azospira, Rhodopseudomonas, Aeromonas, Zobellella, Sulfuritalea, Bradyrhizobium, Achromobacter, Enterobacter, Thauera, and Magnetospirillum) increased significantly during the period of nitrogen loss. Furthermore, the levels of nitrate, T, DO, and AWCD were the most important factors affecting the N-functional bacteria composition. The systematic investigation of the nitrogen loss would provide a theoretical foundation for the remediation of the water reservoir via aerobic denitrification in the future.
Collapse
Affiliation(s)
- Shilei Zhou
- Pollution Prevention Biotechnology Laboratory of Hebei Province, School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Yiran Zhang
- Pollution Prevention Biotechnology Laboratory of Hebei Province, School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Tinglin Huang
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture & Technology, Xi'an 710055, China.
| | - Yanfang Liu
- Pollution Prevention Biotechnology Laboratory of Hebei Province, School of Environmental Science and Engineering, Hebei University of Science and Technology, Shijiazhuang 050018, China
| | - Kaikai Fang
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture & Technology, Xi'an 710055, China
| | - Chunhua Zhang
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture & Technology, Xi'an 710055, China
| |
Collapse
|
29
|
Hong Y, Wu J, Wilson S, Song B. Vertical Stratification of Sediment Microbial Communities Along Geochemical Gradients of a Subterranean Estuary Located at the Gloucester Beach of Virginia, United States. Front Microbiol 2019; 9:3343. [PMID: 30687299 PMCID: PMC6336712 DOI: 10.3389/fmicb.2018.03343] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/27/2018] [Indexed: 11/17/2022] Open
Abstract
Subterranean estuaries (STEs) have been recognized as important ecosystems for the exchange of materials between the land and sea, but the microbial players of biogeochemical processes have not been well examined. In this study, we investigated the bacterial and archaeal communities within 10 cm depth intervals of a permeable sediment core (100 cm in length) collected from a STE located at Gloucester Point (GP-STE), VA, United States. High throughput sequencing of 16S rRNA genes and subsequent bioinformatics analyses were conducted to examine the composition, diversity, and potential functions of the sediment communities. The community composition varied significantly from the surface to a depth of 100 cm with up to 13,000 operational taxonomic units (OTUs) based on 97% sequence identities. More than 95% of the sequences consisted of bacterial OTUs, while the relative abundances of archaea, dominated by Crenarchaea, gradually increased with sediment core depth. Along the redox gradients of GP-STE, differential distribution of ammonia- and methane-oxidizing, denitrifying, and sulfate reducing bacteria was observed as well as methanogenic archaea based on predicted microbial functions. The aerobic-anaerobic transition zone (AATZ) had the highest diversity and abundance of microorganisms, matching with the predicted functional diversity. This indicates the AATZ as a hotspot of biogeochemical processes of STEs. The physical and geochemical gradients in different depths have attributed to vertical stratification of microbial community composition and function in the GP-STE.
Collapse
Affiliation(s)
- Yiguo Hong
- College of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Jiapeng Wu
- College of Environmental Science and Engineering, Guangzhou University, Guangzhou, China
| | - Stephanie Wilson
- Department of Biological Sciences, College of William & Mary, Virginia Institute of Marine Science, Gloucester Point, VA, United States
| | - Bongkeun Song
- Department of Biological Sciences, College of William & Mary, Virginia Institute of Marine Science, Gloucester Point, VA, United States
| |
Collapse
|
30
|
Hong Y, Wu J, Guan F, Yue W, Long A. Nitrogen removal in the sediments of the Pearl River Estuary, China: Evidence from the distribution and forms of nitrogen in the sediment cores. MARINE POLLUTION BULLETIN 2019; 138:115-124. [PMID: 30660252 DOI: 10.1016/j.marpolbul.2018.11.040] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 11/07/2018] [Accepted: 11/16/2018] [Indexed: 06/09/2023]
Abstract
In this study, the spatial distribution and forms of nitrogen in sediment cores collected from the Pearl River Estuary were analyzed. Exchangeable nitrogen (Nex) comprised only a small proportion of total nitrogen (Ntot), with a mean of 3.54% in the sediment cores. NH4+ was the main form of Nex. No obvious change was observed in the vertical content of fixed ammonia (Nfix) in the sediments, and the mean Nfix in all five sediment cores was 141.23 mg·kg-1. The organic nitrogen (Norg), strongly related to organic carbon (Corg), was the main form in Ntot. The dissolved inorganic nitrogen in sediment pore water was much lower than that in estuarine water and no significant variation was observed from upstream to downstream. Our results indicated that most nitrogen deposited on surface sediments from overlying water was rapidly removed by a series of microbial processes, reducing the extent of nitrogen returning to overlying waters.
Collapse
Affiliation(s)
- Yiguo Hong
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, PR China.
| | - Jiapeng Wu
- State Key Laboratory of Tropical Oceanography (LTO), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Fengjie Guan
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, PR China
| | - Weizhong Yue
- State Key Laboratory of Tropical Oceanography (LTO), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Aimin Long
- State Key Laboratory of Tropical Oceanography (LTO), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| |
Collapse
|
31
|
Zhang Y, Douglas GB, Kaksonen AH, Cui L, Ye Z. Microbial reduction of nitrate in the presence of zero-valent iron. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 646:1195-1203. [PMID: 30235605 DOI: 10.1016/j.scitotenv.2018.07.112] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
Abstract
Microbial reduction of nitrate in the presence of zero-valent iron (ZVI) was evaluated in anoxic shake flasks to assess the feasibility of ZVI-facilitated biological nitrate removal. Nitrate was completely reduced within 3days in the presence of both ZVI and microorganisms (ZVI-M). In contrast, only 75% of the nitrate was reduced in the presence of ZVI but without microbial inoculum. Nitrate removal was affected by ZVI-M flasks initial pH, nitrate concentration and ZVI dosage. Nitrate removal in the inoculated ZVI flasks system could be divided into two phases: adaptation phase and log phase which could be described by first-order kinetic equations. The analysis of bacterial communities in the inoculated flasks in the absence and presence of ZVI, indicated that the addition of ZVI increased the relative abundance of Methylotenera spp., Alcaligenes eutrophus, Pseudomonas spp. which might play an important role in nitrogen removal. The presence of ZVI could enhance biological denitrification through four mechanisms: the biological reduction of nitrate with 1) electrons derived directly from ZVI; 2) with hydrogen released from ZVI; 3) with Fe2+ released from ZVI; and 4) with acetate generated by homoacetogens which utilize H2 released from ZVI.
Collapse
Affiliation(s)
- Yiping Zhang
- Department of Environmental Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Grant B Douglas
- CSIRO Land and Water, Centre for Environment and Life Sciences, Private Bag 5, Wembley, 6913, WA, Australia
| | - Anna H Kaksonen
- CSIRO Land and Water, Centre for Environment and Life Sciences, Private Bag 5, Wembley, 6913, WA, Australia
| | - Lili Cui
- Hebei Energy and Environmental Engineering, Hebei Institute of Architectural Engineering, Zhangjiakou, Hebei 075000, China
| | - Zhengfang Ye
- Department of Environmental Engineering, Peking University, The Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China.
| |
Collapse
|
32
|
Dyksma S, Lenk S, Sawicka JE, Mußmann M. Uncultured Gammaproteobacteria and Desulfobacteraceae Account for Major Acetate Assimilation in a Coastal Marine Sediment. Front Microbiol 2018; 9:3124. [PMID: 30619197 PMCID: PMC6305295 DOI: 10.3389/fmicb.2018.03124] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 12/03/2018] [Indexed: 11/13/2022] Open
Abstract
Acetate is a key intermediate in anaerobic mineralization of organic matter in marine sediments. Its turnover is central to carbon cycling, however, the relative contribution of different microbial populations to acetate assimilation in marine sediments is unknown. To quantify acetate assimilation by in situ abundant bacterial populations, we incubated coastal marine sediments with 14C-labeled acetate and flow-sorted cells that had been labeled and identified by fluorescence in situ hybridization. Subsequently, scintillography determined the amount of 14C-acetate assimilated by distinct populations. This approach fostered a high-throughput quantification of acetate assimilation by phylogenetically identified populations. Acetate uptake was highest in the oxic-suboxic surface layer for all sorted bacterial populations, including deltaproteobacterial sulfate-reducing bacteria (SRB), which accounted for up to 32% of total bacterial acetate assimilation. We show that the family Desulfobulbaceae also assimilates acetate in marine sediments, while the more abundant Desulfobacteraceae dominated acetate assimilation despite lower uptake rates. Unexpectedly, members of Gammaproteobacteria accounted for the highest relative acetate assimilation in all sediment layers with up to 31–62% of total bacterial acetate uptake. We also show that acetate is used to build up storage compounds such as polyalkanoates. Together, our findings demonstrate that not only the usual suspects SRB but a diverse bacterial community may substantially contribute to acetate assimilation in marine sediments. This study highlights the importance of quantitative approaches to reveal the roles of distinct microbial populations in acetate turnover.
Collapse
Affiliation(s)
- Stefan Dyksma
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences, Emden, Germany
| | - Sabine Lenk
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Joanna E Sawicka
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marc Mußmann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| |
Collapse
|
33
|
Zhou S, Xia C, Huang T, Zhang C, Fang K. Seasonal variation of potential denitrification rate and enhanced denitrification performance via water-lifting aeration technology in a stratified reservoir-A case study of Zhoucun reservoir. CHEMOSPHERE 2018; 211:1123-1136. [PMID: 30223328 DOI: 10.1016/j.chemosphere.2018.08.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 08/04/2018] [Accepted: 08/09/2018] [Indexed: 06/08/2023]
Abstract
Zhoucun reservoir is one of the major water resources in Zao Zhuang city, northern China. The seasonal distribution of surface sediment denitrification rate and enhanced performance of denitrification via water-lifting aeration technology were explored using the acetylene-inhibition technique. Surface sediment denitrification rates ranged from 2.57 ± 1.32 to 923.90 ± 86.81 nmol N2/(g dw·h), with the highest rates in November (ANOVA, p < 0.05) and significantly low rates in June, July, and August (ANOVA, p < 0.05), mainly because of the seasonal differences in nitrate concentration, water temperature, and sediment total nitrogen (STN). Meanwhile, the N2/(N2+N2O) ratio (83.44-91.70% for the highest sediment denitrification period) indicated that N2 accounted for a majority of denitrification. Correlation analysis between various environmental factors and denitrification was conducted, and nitrate concentration, STN, low molecular weight organic carbon, the number of aerobic denitrifying bacteria, and the environmental parameters of oxidation-reduction potential (ORP), pH, electrical conductivity (EC), and chlorophyll a (Chl-a) presented significant relationships during the entire study period. On the basis of the multiple regression model, nitrate and low molecular weight organic carbon concentration were the most influential factors on denitrification variability. Moreover, the denitrification rates of the surface sediment clearly increased, from 5.28 to 13.22 nmol N2/(g dw·h) to 1117.02-3129.47 nmol N2/(g dw·h), which were higher than those in the non-operating year. This suggests that the denitrification in the sediment system could be enhanced in situ by water-lifting and aeration technology in the reservoir ecosystem.
Collapse
Affiliation(s)
- Shilei Zhou
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China.
| | - Chao Xia
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China
| | - Tinglin Huang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China.
| | - Chunhua Zhang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China
| | - Kaikai Fang
- Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, PR China
| |
Collapse
|
34
|
Marchant HK, Tegetmeyer HE, Ahmerkamp S, Holtappels M, Lavik G, Graf J, Schreiber F, Mussmann M, Strous M, Kuypers MMM. Metabolic specialization of denitrifiers in permeable sediments controls N 2 O emissions. Environ Microbiol 2018; 20:4486-4502. [PMID: 30117262 DOI: 10.1111/1462-2920.14385] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 08/10/2018] [Accepted: 08/12/2018] [Indexed: 11/28/2022]
Abstract
Coastal oceans receive large amounts of anthropogenic fixed nitrogen (N), most of which is denitrified in the sediment before reaching the open ocean. Sandy sediments, which are common in coastal regions, seem to play an important role in catalysing this N-loss. Permeable sediments are characterized by advective porewater transport, which supplies high fluxes of organic matter into the sediment, but also leads to fluctuations in oxygen and nitrate concentrations. Little is known about how the denitrifying communities in these sediments are adapted to such fluctuations. Our combined results indicate that denitrification in eutrophied sandy sediments from the world's largest tidal flat system, the Wadden Sea, is carried out by different groups of microorganisms. This segregation leads to the formation of N2 O which is advectively transported to the overlying waters and thereby emitted to the atmosphere. At the same time, the production of N2 O within the sediment supports a subset of Flavobacteriia which appear to be specialized on N2 O reduction. If the mechanisms shown here are active in other coastal zones, then denitrification in eutrophied sandy sediments may substantially contribute to current marine N2 O emissions.
Collapse
Affiliation(s)
| | - Halina E Tegetmeyer
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | | | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jon Graf
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Frank Schreiber
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,ETH Zurich, Swiss Federal Institute of Technology, Department of Environmental Systems Science, Zurich, Switzerland.,Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Environmental Microbiology, Dübendorf, Switzerland.,Division of Biodeterioration and Reference Organisms, Department of Materials and Environment, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Marc Mussmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marc Strous
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | |
Collapse
|
35
|
Liu J, Shen Z, Yan T, Yang Y. Source identification and impact of landscape pattern on riverine nitrogen pollution in a typical urbanized watershed, Beijing, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 628-629:1296-1307. [PMID: 30045551 DOI: 10.1016/j.scitotenv.2018.02.161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/13/2018] [Accepted: 02/13/2018] [Indexed: 05/14/2023]
Abstract
This study explored the sources of nitrate and the impact of landscape pattern on nitrogen pollution in the highly urbanized Beiyun River Watershed, China during 2016 by applying a dual stable isotope approach (δ15N-NO3-and δ18O-NO3-) combined with multiple statistical analyses. The sources of riverine nitrate principally originated from manure and sewage, nitrification of soil nitrogen, fertilizer nitrification, and atmospheric deposition. A Bayesian model was used to estimate the source contributions and results showed that manure and sewage were the major contributors to river nitrate with combined proportions of 77.59% and 89.57% in the rainy season and the dry season, respectively. Results from multiple stepwise regression indicated that the typical artificial land use types and landscape configuration metrics reflecting landscape fragmentation related well with riverine nitrogen variables for different seasons (R2>0.6). Industrial land, unused land and patch density of built-up land and road were positively correlated with riverine nitrogen over seasons, whereas the interspersion and juxtaposition index of forest land was negatively related with nitrate. Regulating built-up land and unused land, connecting forest land with other land use types and diminishing discharges of industrial and domestic wastewater would be effective ways to improve urban river water quality.
Collapse
Affiliation(s)
- Jin Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Zhenyao Shen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China.
| | - Tiezhu Yan
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| | - Yucong Yang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, PR China
| |
Collapse
|
36
|
Wang S, Wang W, Liu L, Zhuang L, Zhao S, Su Y, Li Y, Wang M, Wang C, Xu L, Zhu G. Microbial Nitrogen Cycle Hotspots in the Plant-Bed/Ditch System of a Constructed Wetland with N 2O Mitigation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6226-6236. [PMID: 29750509 DOI: 10.1021/acs.est.7b04925] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Artificial microbial nitrogen (N) cycle hotspots in the plant-bed/ditch system were developed and investigated based on intact core and slurry assays measurement using isotopic tracing technology, quantitative PCR and high-throughput sequencing. By increasing hydraulic retention time and periodically fluctuating water level in heterogeneous riparian zones, hotspots of anammox, nitrification, denitrification, ammonium (NH4+) oxidation, nitrite (NO2-) oxidation, nitrate (NO3-) reduction and DNRA were all stimulated at the interface sediments, with the abundance and activity being about 1-3 orders of magnitude higher than those in nonhotspots. Isotopic pairing experiments revealed that in microbial hotspots, nitrite sources were higher than the sinks, and both NH4+ oxidation (55.8%) and NO3- reduction (44.2%) provided nitrite for anammox, which accounted for 43.0% of N-loss and 44.4% of NH4+ removal in riparian zones but did not involve nitrous oxide (N2O) emission risks. High-throughput analysis identified that bacterial quorum sensing mediated this anammox hotspot with B.fulgida dominating the anammox community, but it was B. anammoxidans and Jettenia sp. that contributed more to anammox activity. In the nonhotspot zones, the NO2- source (NO3- reduction dominated) was lower than the sink, limiting the effects on anammox. The in situ N2O flux measurement showed that the microbial hotspot had a 27.1% reduced N2O emission flux compared with the nonhotspot zones.
Collapse
Affiliation(s)
- Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
| | - Weidong Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
| | - Lu Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
| | - Linjie Zhuang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
| | - Siyan Zhao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yu Su
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yixiao Li
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
| | - Mengzi Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
| | - Cheng Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Liya Xu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences , Chinese Academy of Sciences , Beijing , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
| |
Collapse
|
37
|
Perujo N, Romaní AM, Sanchez-Vila X. Bilayer Infiltration System Combines Benefits from Both Coarse and Fine Sands Promoting Nutrient Accumulation in Sediments and Increasing Removal Rates. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5734-5743. [PMID: 29672036 DOI: 10.1021/acs.est.8b00771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Infiltration systems are treatment technologies based on water percolation through porous media where biogeochemical processes take place. Grain size distribution (GSD) acts as a driver of these processes and their rates and influences nutrient accumulation in sediments. Coarse sands inhibit anaerobic reactions such as denitrification and could constrain nutrient accumulation in sediments due to smaller specific surface area. Alternatively, fine sands provide higher nutrient accumulation but need a larger area available to treat the same volume of water; furthermore, they are more susceptible to bioclogging. Combining both sand sizes in a bilayer system would allow infiltrating a greater volume of water and the occurrence of aerobic/anaerobic processes. We studied the performance of a bilayer coarse-fine system compared to a monolayer fine one-by triplicate-in an outdoor infiltration experiment to close the C-N-P cycles simultaneously in terms of mass balances. Our results confirm that the bilayer coarse-fine GSD promotes nutrient removal by physical adsorption and biological assimilation in sediments, and further it enhances biogeochemical process rates (2-fold higher than the monolayer system). Overall, the bilayer coarse-fine system allows treating a larger volume of water per surface unit achieving similar removal efficiencies as the fine system.
Collapse
Affiliation(s)
- N Perujo
- Department of Civil and Environmental Engineering , Universitat Politècnica de Catalunya (UPC) , Jordi Girona 1-3 , 08034 Barcelona , Spain
- Hydrogeology Group (UPC-CSIC) , Universitat Politècnica de Catalunya (UPC) , 08034 Barcelona , Spain
- GRECO-Institute of Aquatic Ecology , Universitat de Girona , 17003 Girona , Spain
| | - A M Romaní
- GRECO-Institute of Aquatic Ecology , Universitat de Girona , 17003 Girona , Spain
| | - X Sanchez-Vila
- Department of Civil and Environmental Engineering , Universitat Politècnica de Catalunya (UPC) , Jordi Girona 1-3 , 08034 Barcelona , Spain
- Hydrogeology Group (UPC-CSIC) , Universitat Politècnica de Catalunya (UPC) , 08034 Barcelona , Spain
| |
Collapse
|
38
|
Zeng J, Chen M, Zheng M, Qiu Y, He W, He Y, Liu X. Effects of particles on potential denitrification in the coastal waters of the Beibu Gulf in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 624:1274-1286. [PMID: 29929240 DOI: 10.1016/j.scitotenv.2017.12.192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/16/2017] [Accepted: 12/17/2017] [Indexed: 06/08/2023]
Abstract
Although the influence of suspended particulate matter (SPM) on denitrifying activity has been identified in river waters recently through metabolic incubations and community gene analysis, the regulations of SPM to denitrification in marine systems are still poorly understood. In the present study, the effects of suspended particle properties (including concentration, composition and size) on potential denitrification were explored in the coastal Beibu Gulf water columns based on a series of 15N-labeled incubations under artificial anaerobic condition. A gradient of oxygen (O2) concentrations was also manipulated in the incubated seawaters to test the sensitivity of denitrification to O2 exposure. According to our experiments, potential denitrification was the dominant pathway for N2 production with major contribution (>60%) recovered from the particle-associated (PA) fraction. The Highest rate occurred in the benthic nepheloid layer, where high particle content induced by sediment resuspension were observed, suggesting that resuspended particles may act as a hot spot for marine nitrogen (N) loss. Both content and lability of particulate organic carbon (POC) were tightly related to the denitrification rates, with denitrification enhanced by autochthonous POC fractions more significantly. The PA denitrification was higher on small particles (1.2-10μm) compared to the large ones (>10μm), probably due to larger specific surface area and higher specific POC content in small particles. O2 suppressed denitrifying activity for both bulk water samples and PA fractions. Although in situ denitrifying activity should be minor or neglected because of high-O2 inhibition, the novel findings of particle effects on anaerobic denitrification can still be applied to hypoxic marine environments. Our research also implies that resuspended particles from sediment may act as a hot spot for N loss, and therefore to be a first step toward future studies in high particle loaded marine regimes.
Collapse
Affiliation(s)
- Jian Zeng
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Min Chen
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China.
| | - Minfang Zheng
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Yusheng Qiu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Wentao He
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Yingxue He
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Xiao Liu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| |
Collapse
|
39
|
Jiang S, Ibánhez JSP, Rocha C. Influence of labile dissolved organic matter on nitrate reduction in a seepage face. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:10654-10667. [PMID: 29392604 DOI: 10.1007/s11356-018-1302-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 01/15/2018] [Indexed: 06/07/2023]
Abstract
Seepage faces, the outer rim of subterranean estuaries, are an important reaction node for SGD-borne nitrate (NO3-) on a global scale. Labile dissolved organic matter (DOM) has been suggested to be a key factor constraining the NO3- removal rate in aquifer systems. To determine whether and to what extent the availability of labile DOM affects benthic NO3- reduction in seepage faces, a series of flow-through reactor (FTR) experiments with sandy sediment collected from a seepage face was conducted under oxic conditions. Experimental results revealed that the addition of labile DOM (glucose) to porewater did not trigger a significant enhancement in NO3- reduction rate. In contrast, the aerobic respiration was boosted from ca. 50 to 90 μmol dm-3 sediment h-1 by glucose amendments, accounting for approximately 70% consumption of the labile DOM pool. This rapid consumption may increase the NO3- reducing capability within the sediment, but only indirectly. Together with fluorescent DOM (FDOM) analyses, it can be inferred that NO3- reducers tend to choose sediment organic matter the prime electron donor under the experimental conditions. As a result, enrichment of DOM in seepage faces, depending on composition, might only stimulate aerobic respiration and nitrification, thus promoting the increase of ensuing NO3- fluxes to adjacent coastal waters.
Collapse
Affiliation(s)
- Shan Jiang
- Biogeochemistry Research Group, Geography Department, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland.
| | - J Severino P Ibánhez
- Biogeochemistry Research Group, Geography Department, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Carlos Rocha
- Biogeochemistry Research Group, Geography Department, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| |
Collapse
|
40
|
Methane stimulates massive nitrogen loss from freshwater reservoirs in India. Nat Commun 2018; 9:1265. [PMID: 29593290 PMCID: PMC5871758 DOI: 10.1038/s41467-018-03607-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/28/2018] [Indexed: 11/08/2022] Open
Abstract
The fate of the enormous amount of reactive nitrogen released to the environment by human activities in India is unknown. Here we show occurrence of seasonal stratification and generally low concentrations of dissolved inorganic combined nitrogen, and high molecular nitrogen (N2) to argon ratio, thus suggesting seasonal loss to N2 in anoxic hypolimnia of several dam-reservoirs. However, 15N-experiments yielded low rates of denitrification, anaerobic ammonium oxidation and dissimilatory nitrate reduction to ammonium-except in the presence of methane (CH4) that caused ~12-fold increase in denitrification. While nitrite-dependent anaerobic methanotrophs belonging to the NC10 phylum were present, previously considered aerobic methanotrophs were far more abundant (up to 13.9%) in anoxic hypolimnion. Methane accumulation in anoxic freshwater systems seems to facilitate rapid loss of reactive nitrogen, with generally low production of nitrous oxide (N2O), through widespread coupling between methanotrophy and denitrification, potentially mitigating eutrophication and emissions of CH4 and N2O to the atmosphere.
Collapse
|
41
|
Mori F, Umezawa Y, Kondo R, Wada M. Effects of bottom-water hypoxia on sediment bacterial community composition in a seasonally hypoxic enclosed bay (Omura Bay, West Kyushu, Japan). FEMS Microbiol Ecol 2018; 94:4951600. [DOI: 10.1093/femsec/fiy053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 03/21/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fumiaki Mori
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo 1-14, Nagasaki, Nagasaki 852-8521, Japan
| | - Yu Umezawa
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo 1-14, Nagasaki, Nagasaki 852-8521, Japan
- Department of Environmental Science on Biosphere, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Ryuji Kondo
- Department of Marine Science and Technology, Fukui Prefectural University, Fukui 917-0003, Japan
| | - Minoru Wada
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Bunkyo 1-14, Nagasaki, Nagasaki 852-8521, Japan
| |
Collapse
|
42
|
Yazdani Foshtomi M, Leliaert F, Derycke S, Willems A, Vincx M, Vanaverbeke J. The effect of bio-irrigation by the polychaete Lanice conchilega on active denitrifiers: Distribution, diversity and composition of nosZ gene. PLoS One 2018; 13:e0192391. [PMID: 29408934 PMCID: PMC5800672 DOI: 10.1371/journal.pone.0192391] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 01/23/2018] [Indexed: 11/18/2022] Open
Abstract
The presence of large densities of the piston-pumping polychaete Lanice conchilega can have important consequences for the functioning of marine sediments. It is considered both an allogenic and an autogenic ecosystem engineer, affecting spatial and temporal biogeochemical gradients (oxygen concentrations, oxygen penetration depth and nutrient concentrations) and physical properties (grain size) of marine sediments, which could affect functional properties of sediment-inhabiting microbial communities. Here we investigated whether density-dependent effects of L. conchilega affected horizontal (m-scale) and vertical (cm-scale) patterns in the distribution, diversity and composition of the typical nosZ gene in the active denitrifying organisms. This gene plays a major role in N2O reduction in coastal ecosystems as the last step completing the denitrification pathway. We showed that both vertical and horizontal composition and richness of nosZ gene were indeed significantly affected when large densities of the bio-irrigator were present. This could be directly related to allogenic ecosystem engineering effects on the environment, reflected in increased oxygen penetration depth and oxygen concentrations in the upper cm of the sediment in high densities of L. conchilega. A higher diversity (Shannon diversity and inverse Simpson) of nosZ observed in patches with high L. conchilega densities (3,185-3,440 ind. m-2) at deeper sediment layers could suggest a downward transport of NO3- to deeper layers resulting from bio-irrigation as well. Hence, our results show the effect of L. conchilega bio-irrigation activity on denitrifying organisms in L. conchilega reefs.
Collapse
Affiliation(s)
- Maryam Yazdani Foshtomi
- Marine Biology Research Group, Biology Department, Ghent University, Ghent, Belgium
- CeMoFE, Ghent University, Ghent, Belgium
| | - Frederik Leliaert
- Marine Biology Research Group, Biology Department, Ghent University, Ghent, Belgium
- Botanic Garden Meise, Meise, Belgium
| | - Sofie Derycke
- Marine Biology Research Group, Biology Department, Ghent University, Ghent, Belgium
- Aquatic Environment and Quality, Institute for Agricultural and Fisheries Research (ILVO), Ostend, Belgium
| | - Anne Willems
- CeMoFE, Ghent University, Ghent, Belgium
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Magda Vincx
- Marine Biology Research Group, Biology Department, Ghent University, Ghent, Belgium
| | - Jan Vanaverbeke
- Marine Biology Research Group, Biology Department, Ghent University, Ghent, Belgium
- Marine Ecology and Management, Operational Directorate Natural Environment (OD Nature), Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| |
Collapse
|
43
|
Liu S, Chen Q, Ma T, Wang M, Ni J. Genomic insights into metabolic potentials of two simultaneous aerobic denitrification and phosphorus removal bacteria, Achromobacter sp. GAD3 and Agrobacterium sp. LAD9. FEMS Microbiol Ecol 2018; 94:4834001. [DOI: 10.1093/femsec/fiy020] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 01/31/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Shufeng Liu
- Department of Environmental Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Qian Chen
- Department of Environmental Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Tao Ma
- Department of Environmental Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| | - Ming Wang
- Yellow River Institute of Hydraulic Research, Zhengzhou 450003, China
| | - Jinren Ni
- Department of Environmental Engineering, Peking University; Key Laboratory of Water and Sediment Sciences, Ministry of Education, Beijing 100871, China
| |
Collapse
|
44
|
Coates CJ, Wyman M. A denitrifying community associated with a major, marine nitrogen fixer. Environ Microbiol 2017; 19:4978-4992. [PMID: 29194965 DOI: 10.1111/1462-2920.14007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 11/15/2017] [Accepted: 11/21/2017] [Indexed: 12/11/2022]
Abstract
The diazotrophic cyanobacterium, Trichodesmium, is an integral component of the marine nitrogen cycle and contributes significant amounts of new nitrogen to oligotrophic, tropical/subtropical ocean surface waters. Trichodesmium forms macroscopic, fusiform (tufts), spherical (puffs) and raft-like colonies that provide a pseudobenthic habitat for a host of other organisms including marine invertebrates, microeukaryotes and numerous other microbes. The diversity and activity of denitrifying bacteria found in association with the colonies was interrogated using a series of molecular-based methodologies targeting the gene encoding the terminal step in the denitrification pathway, nitrous oxide reductase (nosZ). Trichodesmium spp. sampled from geographically isolated ocean provinces (the Atlantic Ocean, the Red Sea and the Indian Ocean) were shown to harbor highly similar, taxonomically related communities of denitrifiers whose members are affiliated with the Roseobacter clade within the Rhodobacteraceae (Alphaproteobacteria). These organisms were actively expressing nosZ in samples taken from the mid-Atlantic Ocean and Red Sea implying that Trichodesmium colonies are potential sites of nitrous oxide consumption and perhaps earlier steps in the denitrification pathway also. It is proposed that coupled nitrification of newly fixed N is the most likely source of nitrogen oxides supporting nitrous oxide cycling within Trichodesmium colonies.
Collapse
Affiliation(s)
- Christopher J Coates
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK.,Department of Biosciences, College of Science, Swansea University, Swansea SA2 8PP, Wales, UK
| | - Michael Wyman
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
| |
Collapse
|
45
|
Removal of Nitrogen and COD from Reclaimed Water during Long-Term Simulated Soil Aquifer Treatment System under Different Hydraulic Conditions. WATER 2017. [DOI: 10.3390/w9100786] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
46
|
Diversity of culturable aerobic denitrifying bacteria in the sediment, water and biofilms in Liangshui River of Beijing, China. Sci Rep 2017; 7:10032. [PMID: 28855587 PMCID: PMC5577267 DOI: 10.1038/s41598-017-09556-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/24/2017] [Indexed: 01/17/2023] Open
Abstract
Aerobic denitrification is a process reducing the nitrate into gaseous nitrogen forms in the presence of oxygen gas, which makes the nitrification and denitrification performed simultaneously. However, little was known on the diversity of the culturable aerobic denitrifying bacteria in the surface water system. In this study, 116 strains of aerobic denitrifying bacteria were isolated from the sediment, water and biofilm samples in Liangshui River of Beijing. These bacteria were classified into 14 genera based on the 16 S rDNA, such as Pseudomonas, Rheinheimera, and Gemmobacter. The Pseudomonas sp., represented by the Pseudomonas stutzeri, Pseudomonas mendocina and Pseudomonas putida, composed the major culturable aerobic denitrifiers of the river, followed by Ochrobactrum sp. and Rheinheimera sp. The PCA plot showed the unclassified Pseudomonas sp. and Rheinheimera pacifica preferred to inhabit in biofilm phase while one unclassified Ochrobactrum sp. and Pseudomonas resinovorans had higher abundance in the sediment. In the overlying water, the Pseudomonas stutzeri and Ochrobactrum rhizosphaerae were found to have higher abundance, indicating these aerobic denitrifiers had different habitat-preferable characteristics among the 3 phases of river system. The findings may help select the niche to isolate the aerobic denitrifiers and facilitate the bioaugmentation-based purification of the nitrate polluted surface water.
Collapse
|
47
|
Marchant HK, Ahmerkamp S, Lavik G, Tegetmeyer HE, Graf J, Klatt JM, Holtappels M, Walpersdorf E, Kuypers MMM. Denitrifying community in coastal sediments performs aerobic and anaerobic respiration simultaneously. THE ISME JOURNAL 2017; 11:1799-1812. [PMID: 28463234 PMCID: PMC5520038 DOI: 10.1038/ismej.2017.51] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 02/08/2017] [Accepted: 03/03/2017] [Indexed: 01/20/2023]
Abstract
Nitrogen (N) input to the coastal oceans has increased considerably because of anthropogenic activities, however, concurrent increases have not occurred in open oceans. It has been suggested that benthic denitrification in sandy coastal sediments is a sink for this N. Sandy sediments are dynamic permeable environments, where electron acceptor and donor concentrations fluctuate over short temporal and spatial scales. The response of denitrifiers to these fluctuations are largely unknown, although previous observations suggest they may denitrify under aerobic conditions. We examined the response of benthic denitrification to fluctuating oxygen concentrations, finding that denitrification not only occurred at high O2 concentrations but was stimulated by frequent switches between oxic and anoxic conditions. Throughout a tidal cycle, in situtranscription of genes for aerobic respiration and denitrification were positively correlated within diverse bacterial classes, regardless of O2 concentrations, indicating that denitrification gene transcription is not strongly regulated by O2 in sandy sediments. This allows microbes to respond rapidly to changing environmental conditions, but also means that denitrification is utilized as an auxiliary respiration under aerobic conditions when imbalances occur in electron donor and acceptor supply. Aerobic denitrification therefore contributes significantly to N-loss in permeable sediments making the process an important sink for anthropogenic N-inputs.
Collapse
Affiliation(s)
| | | | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Halina E Tegetmeyer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Jon Graf
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Judith M Klatt
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Geomicrobiology Laboratory, Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor MI, USA
| | - Moritz Holtappels
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
- Marum—Centre for Marine Environmental Science, Bremen, Germany
| | - Eva Walpersdorf
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | |
Collapse
|
48
|
Impacts of chemical gradients on microbial community structure. ISME JOURNAL 2017; 11:920-931. [PMID: 28094795 PMCID: PMC5363838 DOI: 10.1038/ismej.2016.175] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 10/25/2016] [Accepted: 11/08/2016] [Indexed: 12/05/2022]
Abstract
Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.
Collapse
|
49
|
Wittorf L, Bonilla-Rosso G, Jones CM, Bäckman O, Hulth S, Hallin S. Habitat partitioning of marine benthic denitrifier communities in response to oxygen availability. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:486-492. [PMID: 26929183 DOI: 10.1111/1758-2229.12393] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/27/2015] [Accepted: 02/12/2016] [Indexed: 06/05/2023]
Abstract
Denitrification is of global significance for the marine nitrogen budget and the main process for nitrogen loss in coastal sediments. This facultative anaerobic respiratory pathway is modular in nature and the final step, the reduction of nitrous oxide (N2 O), is performed by microorganisms with a complete denitrification pathway as well as those only capable of N2 O reduction. Fluctuating oxygen availability is a significant driver of denitrification in sediments, but the effects on the overall N2 O-reducing community that ultimately controls the emission of N2 O from marine sediments is not well known. To investigate the effects of different oxygen regimes on N2 O reducing communities, coastal marine surface sediment was incubated in microcosms under oxic, anoxic or oscillating oxygen conditions in the overlying water for 137 days. Quantification of the genetic potential for denitrification, anammox and respiratory ammonification indicated that denitrification supported nitrogen removal in these sediments. Furthermore, denitrifiers with a complete pathway were identified as the dominant community involved in N2 O reduction, rather than organisms that are only N2 O reducers. Specific lineages within each group were associated with different oxygen regimes suggesting that oxygen availability in the overlying water is associated with habitat partitioning of N2 O reducers in coastal marine surface sediments.
Collapse
Affiliation(s)
- Lea Wittorf
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Germán Bonilla-Rosso
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christopher M Jones
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ola Bäckman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Stefan Hulth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
50
|
Zhou S, Huang T, Ngo HH, Zhang H, Liu F, Zeng M, Shi J, Qiu X. Nitrogen removal characteristics of indigenous aerobic denitrifiers and changes in the microbial community of a reservoir enclosure system via in situ oxygen enhancement using water lifting and aeration technology. BIORESOURCE TECHNOLOGY 2016; 214:63-73. [PMID: 27128190 DOI: 10.1016/j.biortech.2016.04.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 04/13/2016] [Accepted: 04/15/2016] [Indexed: 06/05/2023]
Abstract
Indigenous aerobic denitrifiers of a reservoir system were enhanced in situ by water lifting and aeration technology. Nitrogen removal characteristics and changes in the bacterial community were investigated. Results from a 30-day experiment showed that the TN in the enhanced water system decreased from 1.08-2.02 to 0.75-0.91mg/L and that TN removal rates varied between 21.74% and 52.54% without nitrite accumulation, and TN removal rate of surface sediments reached 41.37±1.55%. The densities of aerobic denitrifiers in the enhanced system increased. Furthermore, the enhanced system showed a clear inhibition of Fe, Mn, and P performances. Community analysis using Miseq showed that diversity was higher in the in situ oxygen enhanced system than in the control system. In addition, the microbial composition was significantly different between systems. It can be concluded that in situ enhancement of indigenous aerobic denitrifiers is very effective in removing nitrogen from water reservoir systems.
Collapse
Affiliation(s)
- Shilei Zhou
- Key Lab of Northwest Water Resources, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Tinglin Huang
- Key Lab of Northwest Water Resources, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Huu Hao Ngo
- School of Civil and Environmental Engineering, Faculty of Engineering and Information Technology, University of Technology Sydney, NSW 2007, Australia
| | - Haihan Zhang
- Key Lab of Northwest Water Resources, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Fei Liu
- Key Lab of Northwest Water Resources, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Mingzheng Zeng
- Key Lab of Northwest Water Resources, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Jianchao Shi
- Key Lab of Northwest Water Resources, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Xiaopeng Qiu
- Key Lab of Northwest Water Resources, Environment and Ecology, Ministry of Education, Xi'an University of Architecture and Technology, Xi'an 710055, China
| |
Collapse
|