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Yoon S, Heo H, Han H, Song DU, Bakken LR, Frostegård Å, Yoon S. Suggested role of NosZ in preventing N 2O inhibition of dissimilatory nitrite reduction to ammonium. mBio 2023; 14:e0154023. [PMID: 37737639 PMCID: PMC10653820 DOI: 10.1128/mbio.01540-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/31/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) is a microbial energy-conserving process that reduces NO3 - and/or NO2 - to NH4 +. Interestingly, DNRA-catalyzing microorganisms possessing nrfA genes are occasionally found harboring nosZ genes encoding nitrous oxide reductases, i.e., the only group of enzymes capable of removing the potent greenhouse gas N2O. Here, through a series of physiological experiments examining DNRA metabolism in one of such microorganisms, Bacillus sp. DNRA2, we have discovered that N2O may delay the transition to DNRA upon an oxic-to-anoxic transition, unless timely removed by the nitrous oxide reductases. These observations suggest a novel explanation as to why some nrfA-possessing microorganisms have retained nosZ genes: to remove N2O that may otherwise interfere with the transition from O2 respiration to DNRA.
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Affiliation(s)
- Sojung Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Hokwan Heo
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Heejoo Han
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Dong-Uk Song
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Lars R. Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Sukhwan Yoon
- Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
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2
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Jiang X, Liu C, Cai J, Hu Y, Shao K, Tang X, Gong Y, Yao X, Xu Q, Gao G. Relationships between environmental factors and N-cycling microbes reveal the indirect effect of further eutrophication on denitrification and DNRA in shallow lakes. WATER RESEARCH 2023; 245:120572. [PMID: 37688860 DOI: 10.1016/j.watres.2023.120572] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 08/23/2023] [Accepted: 09/01/2023] [Indexed: 09/11/2023]
Abstract
Traditional views indicate that eutrophication and subsequent algal blooms favor denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in lake ecosystems. However, lakes tend to show an increasing propensity for inorganic nitrogen (N) limitation as they become more eutrophic. Thus, the influence of further eutrophication on denitrification and DNRA in eutrophic lakes are unclear due to the uncertainty of N availability. To fill this gap, we investigated the genes abundance (AOA, AOB, nirS, nirK and nrfA) and the composition of N-cycling microbes through quantitative PCR and 16S rRNA sequencing analysis, respectively, in 15 shallow eutrophic lakes of the Yangtze-Huaihe River basin, China. The results indicated that denitrification and DNRA rates could be modulated mainly by their functional gene abundances (nirS, nirK and nrfA), followed by the environmental factors (sediment total organic carbon and nitrogen). Denitrification rates significantly increased from slightly to highly eutrophic lakes, but DNRA rates were not. An explanation is that nitrification provided ample nitrate for denitrification, and this cooperative interaction was indicated by the positive correlation of their gene abundances. In addition, Pseudomonas and Anaeromyxobacter was the dominant genus mediated denitrification and DNRA, showing the potential to perform facultative anaerobic and strict anaerobic nitrate reduction, respectively. High level of dissolved oxygen might favor the facultatively aerobic denitrifiers over the obligately anaerobic fermentative DNRA bacteria in these shallow lakes. Chlorophyll a had a weak but positive effect on the gene abundances for nitrification (AOA and AOB). Further eutrophication had an indirect effect on denitrification and DNRA rates through modulating the genes abundances of N-cycling microbes.
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Affiliation(s)
- Xingyu Jiang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Changqing Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Cai
- Xiangyang Polytechnic, Xiangyang 441050, China
| | - Yang Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yi Gong
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiaolong Yao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qiujin Xu
- Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China.
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Marshall AJ, Phillips L, Longmore A, Hayden HL, Heidelberg KB, Tang C, Mele P. Temporal profiling resolves the drivers of microbial nitrogen cycling variability in coastal sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159057. [PMID: 36174701 DOI: 10.1016/j.scitotenv.2022.159057] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Here we describe the potential for sediment microbial nitrogen-cycling gene (DNA) and activity (RNA) abundances to spatially resolve coastal areas impacted by seasonal variability in external nutrient inputs. Three sites were chosen within a nitrogen-limited embayment, Port Phillip Bay (PPB), Australia that reflect variability in both proximity to external nutrient inputs and the dominant form of available nitrogen. At three sediment depths (0-1; 1-5; 5-10 cm) across a 2 year study key genes involved in nitrification (archaeal amoA and bacterial β-amoA), nitrite reduction (clade I nirS and cluster I nirK, archaeal nirK-a), anaerobic oxidation of ammonium (anammox 16S rRNA phylogenetic marker) and nitrogen fixation (nifH) were quantified. Sediments impacted by a dominance of organic nitrogen inputs were characterised at all time-points and to sediment depths of 10 cm by the highest transcript abundances of archaeal amoA and archaeal nirk-a. Proximity to a dominance of external nitrate inputs was associated with the highest transcript abundances of nirS which temporally co-varied with seasonal changes in sediment nitrate. Sediments isolated from external inputs displayed the greatest depth-specific decrease in quantifiable transcript abundances. In these isolated sediments bacterial β-amoA transcripts were temporally associated with increased sediment ammonium levels. Across this nitrogen limited system variability in the abundance of bacterial β-amoA, archaeal amoA, archaeal nirk-a or nirS transcripts from the sediment surface (0-1 and 5 cm) demonstrated a capacity to improve our ability to monitor coastal zones impacted by anthropogenic nitrogen inputs. Specifically, the spatial detection sensitivity of bacterial β-amoA transcripts could be developed as a metric to determine spatiotemporal impacts of large external loading events. This temporal study demonstrates a capacity for microbial activity metrics to facilitate coastal management strategies through greater spatial resolution of areas impacted by external nutrient inputs.
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Affiliation(s)
- Alexis J Marshall
- La Trobe University, AgriBio Centre for AgriBiosciences, 5 Ring Road Bundoora, Australia; Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, 5 Ring Road Bundoora, Australia.
| | - Lori Phillips
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, 5 Ring Road Bundoora, Australia
| | - Andrew Longmore
- Centre for Aquatic Pollution Identification and Management, Melbourne University, Parkville, Australia
| | - Helen L Hayden
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, 5 Ring Road Bundoora, Australia
| | - Karla B Heidelberg
- The University of Southern California, Department of Biology, Los Angeles, CA 90089, United States of America
| | - Caixian Tang
- La Trobe University, AgriBio Centre for AgriBiosciences, 5 Ring Road Bundoora, Australia
| | - Pauline Mele
- La Trobe University, AgriBio Centre for AgriBiosciences, 5 Ring Road Bundoora, Australia; Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, 5 Ring Road Bundoora, Australia
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4
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Liu C, Xia J, Cui Q, Zhang D, Liu M, Hou L, Gao D. Crab bioturbation affects competition between microbial nitrogen removal and retention in estuarine and coastal wetlands. ENVIRONMENTAL RESEARCH 2022; 215:114280. [PMID: 36103926 DOI: 10.1016/j.envres.2022.114280] [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: 06/22/2022] [Revised: 08/19/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
As the important benthic animal in coastal wetlands, crab bioturbation may significantly affect the nitrogen (N) budgets by regulating microbial N transformation processes. However, the response of interaction between different microbial N processes to crab bioturbation remains poorly understood. Here, a 30-day microcosmic experiment was conducted using sediment collected from the Yangtze Estuary wetland, followed by the determination of temporal variations of physicochemical parameters, N removal (denitrification plus anammox, which is defined as N2 production) and retention rates (nitrate dissimilatory reduction to ammonium, DNRA) as well as relevant gene abundances in response to different crabs densities. The results showed that crab bioturbation simultaneously promoted the rates of N2 production and DNRA processes. These two process rates were positively associated with the intensity of crab bioturbation, which was supported by molecular analysis of relevant functional gene abundance. Crab bioturbation was more beneficial to DNRA than N2 production. Due to this disproportionate stimulation, crab bioturbation increased the importance of DNRA, indicating that N retention was becoming more significant under crab bioturbation in estuarine and coastal wetlands. The variations of sediment total organic carbon and oxygen availability driven by crab bioturbation were the critical factors mediating the changes in microbial N removal and retention. Overall, our findings highlighted that crab bioturbation can affect the N budgets in estuarine and coastal wetlands by altering the competition between microbial N removal and retention.
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Affiliation(s)
- Cheng Liu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China; Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou, Shandong, 256600, China
| | - Jiangbao Xia
- Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou, Shandong, 256600, China
| | - Qian Cui
- Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou, Shandong, 256600, China
| | - Dongjie Zhang
- Shandong Key Laboratory of Eco-Environmental Science for the Yellow River Delta, Binzhou University, Binzhou, Shandong, 256600, China
| | - Min Liu
- School of Geographic Sciences, East China Normal University, Shanghai, 200241, China; Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University, Shanghai, 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Dengzhou Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.
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5
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Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments. mSystems 2022; 7:e0051622. [PMID: 35861508 PMCID: PMC9426555 DOI: 10.1128/msystems.00516-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Rivers have a significant role in global carbon and nitrogen cycles, serving as a nexus for nutrient transport between terrestrial and marine ecosystems. Although rivers have a small global surface area, they contribute substantially to worldwide greenhouse gas emissions through microbially mediated processes within the river hyporheic zone. Despite this importance, research linking microbial and viral communities to specific biogeochemical reactions is still nascent in these sediment environments. To survey the metabolic potential and gene expression underpinning carbon and nitrogen biogeochemical cycling in river sediments, we collected an integrated data set of 33 metagenomes, metaproteomes, and paired metabolomes. We reconstructed over 500 microbial metagenome-assembled genomes (MAGs), which we dereplicated into 55 unique, nearly complete medium- and high-quality MAGs spanning 12 bacterial and archaeal phyla. We also reconstructed 2,482 viral genomic contigs, which were dereplicated into 111 viral MAGs (vMAGs) of >10 kb in size. As a result of integrating gene expression data with geochemical and metabolite data, we created a conceptual model that uncovered new roles for microorganisms in organic matter decomposition, carbon sequestration, nitrogen mineralization, nitrification, and denitrification. We show how these metabolic pathways, integrated through shared resource pools of ammonium, carbon dioxide, and inorganic nitrogen, could ultimately contribute to carbon dioxide and nitrous oxide fluxes from hyporheic sediments. Further, by linking viral MAGs to these active microbial hosts, we provide some of the first insights into viral modulation of river sediment carbon and nitrogen cycling. IMPORTANCE Here we created HUM-V (hyporheic uncultured microbial and viral), an annotated microbial and viral MAG catalog that captures strain and functional diversity encoded in these Columbia River sediment samples. Demonstrating its utility, this genomic inventory encompasses multiple representatives of dominant microbial and archaeal phyla reported in other river sediments and provides novel viral MAGs that can putatively infect these. Furthermore, we used HUM-V to recruit gene expression data to decipher the functional activities of these MAGs and reconstruct their active roles in Columbia River sediment biogeochemical cycling. Ultimately, we show the power of MAG-resolved multi-omics to uncover interactions and chemical handoffs in river sediments that shape an intertwined carbon and nitrogen metabolic network. The accessible microbial and viral MAGs in HUM-V will serve as a community resource to further advance more untargeted, activity-based measurements in these, and related, freshwater terrestrial-aquatic ecosystems.
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6
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Omics-based ecosurveillance for the assessment of ecosystem function, health, and resilience. Emerg Top Life Sci 2022; 6:185-199. [PMID: 35403668 PMCID: PMC9023019 DOI: 10.1042/etls20210261] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 12/15/2022]
Abstract
Current environmental monitoring efforts often focus on known, regulated contaminants ignoring the potential effects of unmeasured compounds and/or environmental factors. These specific, targeted approaches lack broader environmental information and understanding, hindering effective environmental management and policy. Switching to comprehensive, untargeted monitoring of contaminants, organism health, and environmental factors, such as nutrients, temperature, and pH, would provide more effective monitoring with a likely concomitant increase in environmental health. However, even this method would not capture subtle biochemical changes in organisms induced by chronic toxicant exposure. Ecosurveillance is the systematic collection, analysis, and interpretation of ecosystem health-related data that can address this knowledge gap and provide much-needed additional lines of evidence to environmental monitoring programs. Its use would therefore be of great benefit to environmental management and assessment. Unfortunately, the science of ‘ecosurveillance’, especially omics-based ecosurveillance is not well known. Here, we give an overview of this emerging area and show how it has been beneficially applied in a range of systems. We anticipate this review to be a starting point for further efforts to improve environmental monitoring via the integration of comprehensive chemical assessments and molecular biology-based approaches. Bringing multiple levels of omics technology-based assessment together into a systems-wide ecosurveillance approach will bring a greater understanding of the environment, particularly the microbial communities upon which we ultimately rely to remediate perturbed ecosystems.
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7
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Shah RM, Hillyer KE, Stephenson S, Crosswell J, Karpe AV, Palombo EA, Jones OAH, Gorman D, Bodrossy L, van de Kamp J, Bissett A, Whiteley AS, Steven ADL, Beale DJ. Functional analysis of pristine estuarine marine sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 781:146526. [PMID: 33798899 DOI: 10.1016/j.scitotenv.2021.146526] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
Traditional environmental monitoring techniques are well suited to resolving acute exposure effects but lack resolution in determining subtle shifts in ecosystem functions resulting from chronic exposure(s). Surveillance with sensitive omics-based technologies could bridge this gap but, to date, most omics-based environmental studies have focused on previously degraded environments, identifying key metabolic differences resulting from anthropogenic perturbations. Here, we apply omics-based approaches to pristine environments to establish blueprints of microbial functionality within healthy estuarine sediment communities. We collected surface sediments (n = 50) from four pristine estuaries along the Western Cape York Peninsula of Far North Queensland, Australia. Sediment microbiomes were analyzed for 16S rRNA amplicon sequences, central carbon metabolism metabolites and associated secondary metabolites via targeted and untargeted metabolic profiling methods. Multivariate statistical analyses indicated heterogeneity among all the sampled estuaries, however, taxa-function relationships could be established that predicted community metabolism potential. Twenty-four correlated gene-metabolite pathways were identified and used to establish sediment microbial blueprints of essential carbon metabolism and amino acid biosynthesis that were positively correlated with community metabolic function outputs (2-oxisocapraote, tryptophan, histidine citrulline and succinic acid). In addition, an increase in the 125 KEGG genes related to metal homeostasis and metal resistance was observed, although, none of the detected metabolites related to these specific genes upon integration. However, there was a correlation between metal abundance and functional genes related to Fe and Zn metabolism. Our results establish a baseline microbial blueprint for the pristine sediment microbiome, one that drives important ecosystem services and to which future ecosurveillance monitoring can be compared.
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Affiliation(s)
- Rohan M Shah
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia; Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Katie E Hillyer
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia
| | - Sarah Stephenson
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Lucas Heights, NSW 2234, Australia
| | - Joseph Crosswell
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia
| | - Avinash V Karpe
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, School of Science, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Oliver A H Jones
- Australian Centre for Research on Separation Science (ACROSS), School of Science, RMIT University, Bundoora West Campus, PO Box 71, Bundoora, VIC 3083, Australia
| | - Daniel Gorman
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Indian Ocean Marine Research Centre, Crawley, WA 6009, Australia
| | - Levente Bodrossy
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | - Jodie van de Kamp
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Battery Point, TAS 7004, Australia
| | - Andrew S Whiteley
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Floreat, WA 6014, Australia
| | - Andy D L Steven
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, QLD 4102, Australia.
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Guo H, Han S, Lee DJ. Genomic studies on natural and engineered aquatic denitrifying eco-systems: A research update. BIORESOURCE TECHNOLOGY 2021; 326:124740. [PMID: 33497924 DOI: 10.1016/j.biortech.2021.124740] [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: 12/26/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
Excess nitrogenous compounds in municipal or industrial wastewaters can stimulate growth of denitrifying bacteria, in return, to convert potentially hazardous nitrate to inorganic nitrogen gas. To explore the community structure, distributions and succession of functional strains, and their interactions with other microbial communities, contemporary studies were performed based on detailed genomic analysis. This mini-review updated contemporary genomic studies on denitrifying genes in natural and engineered aquatic systems, with the constructed wetlands being the demonstrative system for the latter. Prospects for the employment of genomic studies on denitrifying systems for process design, optimization and development of novel denitrifying processes were discussed.
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Affiliation(s)
- Hongliang Guo
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Song Han
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; College of Technology and Engineering, National Taiwan Normal University, Taipei 10610, Taiwan; College of Engineering, Tunghai University, Taichung 40070, Taiwan.
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9
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Clarke LJ, Jones PJ, Ammitzboll H, Barmuta LA, Breed MF, Chariton A, Charleston M, Dakwa V, Dewi F, Eri R, Fountain-Jones NM, Freeman J, Kendal D, McDougal R, Raes EJ, Sow SLS, Staples T, Sutcliffe B, Vemuri R, Weyrich LS, Flies EJ. Mainstreaming Microbes across Biomes. Bioscience 2020. [DOI: 10.1093/biosci/biaa057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
Bacteria, fungi, and other microorganisms in the environment (i.e., environmental microbiomes) provide vital ecosystem services and affect human health. Despite their importance, public awareness of environmental microbiomes has lagged behind that of human microbiomes. A key problem has been a scarcity of research demonstrating the microbial connections across environmental biomes (e.g., marine, soil) and between environmental and human microbiomes. We show in the present article, through analyses of almost 10,000 microbiome papers and three global data sets, that there are significant taxonomic similarities in microbial communities across biomes, but very little cross-biome research exists. This disconnect may be hindering advances in microbiome knowledge and translation. In this article, we highlight current and potential applications of environmental microbiome research and the benefits of an interdisciplinary, cross-biome approach. Microbiome scientists need to engage with each other, government, industry, and the public to ensure that research and applications proceed ethically, maximizing the potential benefits to society.
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Affiliation(s)
- Laurence J Clarke
- Institute for Marine and Antarctic Studies, and LJC is also affiliated with the Antarctic Climate and Ecosystems Cooperative Research Centre, University of Tasmania, in Hobart, Australia
| | - Penelope J Jones
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Hans Ammitzboll
- School of Natural Sciences, University of Tasmania, Hobart, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Australia
| | - Leon A Barmuta
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Martin F Breed
- College of Scienceand Engineering, Flinders University, Adelaide, Australia, and with the Healthy Urban Microbiome Initiative (www.HUMIglobal.org) in the United Kingdom
| | - Anthony Chariton
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | | | - Vongai Dakwa
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia
| | - Fera Dewi
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia
| | - Rajaraman Eri
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Australia
| | | | - Jules Freeman
- Scion, part of the New Zealand Forest Research Institute Ltd., Rotorua, New Zealand
| | - Dave Kendal
- Research Centre for Marine and Fisheries Product Processing and Biotechnology, Ministry of Marine Affairs and Fisheries, Jakarta, Indonesia
- School of Technology, Environments, and Design, University of Tasmania, Hobart, Australia
| | - Rebecca McDougal
- Scion, part of the New Zealand Forest Research Institute Ltd., Rotorua, New Zealand
| | - Eric J Raes
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Australia
| | - Swan Li San Sow
- Institute for Marine and Antarctic Studies, and LJC is also affiliated with the Antarctic Climate and Ecosystems Cooperative Research Centre, University of Tasmania, in Hobart, Australia
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation, Hobart, Australia
| | - Timothy Staples
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia, and with the School of Biological Sciences, University of Queensland, Brisbane, Australia. RV is also affiliated with the Department of Comparative Medicine, in the School of Medicine, at Wake Forest Baptist Medical Center, in Winston-Salem, North Carolina
| | - Brodie Sutcliffe
- Department of Biological Sciences, Macquarie University, Sydney, Australia
| | - Ravichandra Vemuri
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Australia
| | - Laura S Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, Australia, and with the Department of Anthropology at The Pennsylvania State University, in University Park, Pennsylvania
| | - Emily J Flies
- School of Natural Sciences, University of Tasmania, Hobart, Australia
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