1
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Schacksen PS, Nielsen JL. Unraveling the genetic potential of nitrous oxide reduction in wastewater treatment: insights from metagenome-assembled genomes. Appl Environ Microbiol 2024; 90:e0217723. [PMID: 39136491 PMCID: PMC11409646 DOI: 10.1128/aem.02177-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 07/22/2024] [Indexed: 09/19/2024] Open
Abstract
This study explores the genetic landscape of nitrous oxide (N2O) reduction in wastewater treatment plants (WWTPs) by profiling 1,083 high-quality metagenome-assembled genomes (HQ MAGs) from 23 Danish full-scale WWTPs. The focus is on the distribution and diversity of nitrous oxide reductase (nosZ) genes and their association with other nitrogen metabolism pathways. A custom pipeline for clade-specific nosZ gene identification with higher sensitivity revealed 503 nosZ sequences in 489 of these HQ MAGs, outperforming existing Kyoto Encyclopedia of Genes and Genomes (KEGG) module-based methods. Notably, 48.7% of the total 1,083 HQ MAGs harbored nosZ genes, with clade II being predominant, accounting for 93.7% of these genes. Taxonomic profiling highlighted the prevalence of nosZ-containing taxa within Bacteroidota and Pseudomonadota. Chloroflexota exhibited unexpected affiliations with both the sec and tat secretory pathways, and all were found to contain the accessory nosB gene, underscoring the importance of investigating the secretory pathway. The majority of non-denitrifying N2O reducers were found within Bacteroidota and Chloroflexota. Additionally, HQ MAGs with genes for dissimilatory nitrate reduction to ammonium and assimilatory nitrate reduction frequently co-occurred with the nosZ gene. Traditional primers targeting nosZ often focus on short-length amplicons. Therefore, we introduced custom-designed primer sets targeting near-full-length nosZ sequences. These new primers demonstrate efficacy in capturing diverse and well-characterized sequences, providing a valuable tool with higher resolution for future research. In conclusion, this comprehensive analysis enhances our understanding of N2O-reducing organisms in WWTPs, highlighting their potential as N2O sinks with the potential for optimizing wastewater treatment processes and mitigating greenhouse gas emissions. IMPORTANCE This study provides critical insights into the genetic diversity of nitrous oxide reductase (nosZ) genes and the microorganisms harboring them in wastewater treatment plants (WWTPs) by exploring 1,083 high-quality metagenome-assembled genomes (MAGs) from 23 Danish full-scale WWTPs. Despite the pivotal role of nosZ-containing organisms, their diversity remains largely unexplored in WWTPs. Our custom pipeline for detecting nosZ provides near-full-length genes with detailed information on secretory pathways and accessory nos genes. Using these genes as templates, we developed taxonomically diverse clade-specific primers that generate nosZ amplicons for phylogenetic annotation and gene-to-MAG linkage. This approach improves detection and expands the discovery of novel sequences, highlighting the prevalence of non-denitrifying N2O reducers and their potential as N2O sinks. These findings have the potential to optimize nitrogen removal processes and mitigate greenhouse gas emissions from WWTPs by fully harnessing the capabilities of the microbial communities.
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Affiliation(s)
| | - Jeppe Lund Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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2
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Mao TQ, Zhang Y, Ou YF, Li XF, Zheng YL, Liang X, Liu M, Hou LJ, Dong HP. Temperature differentially regulates estuarine microbial N 2O production along a salinity gradient. WATER RESEARCH 2024; 267:122454. [PMID: 39293343 DOI: 10.1016/j.watres.2024.122454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 09/04/2024] [Accepted: 09/13/2024] [Indexed: 09/20/2024]
Abstract
Nitrous oxide (N2O) is atmospheric trace gas that contributes to climate change and affects stratospheric and ground-level ozone concentrations. Ammonia oxidizers and denitrifiers contribute to N2O emissions in estuarine waters. However, as an important climate factor, how temperature regulates microbial N2O production in estuarine water remains unclear. Here, we have employed stable isotope labeling techniques to demonstrate that the N2O production in estuarine waters exhibited differential thermal response patterns between nearshore and offshore regions. The optimal temperatures (Topt) for N2O production rates (N2OR) were higher at nearshore than offshore sites. 15N-labeled nitrite (15NO2-) experiments revealed that at the nearshore sites dominated by ammonia-oxidizing bacteria (AOB), the thermal tolerance of 15N-N2OR increases with increasing salinity, suggesting that N2O production by AOB-driven nitrifier denitrification may be co-regulated by temperature and salinity. Metatranscriptomic and metagenomic analyses of enriched water samples revealed that the denitrification pathway of AOB is the primary source of N2O, while clade II N2O-reducers dominated N2O consumption. Temperature regulated the expression patterns of nitrite reductase (nirK) and nitrous oxide reductase (nosZ) genes from different sources, thereby influencing N2O emissions in the system. Our findings contribute to understanding the sources of N2O in estuarine waters and their response to global warming.
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Affiliation(s)
- Tie-Qiang Mao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Yong Zhang
- College of Environmental and Resource Sciences, College of Carbon Neutral Modern Industry, Fujian Key Laboratory of Pollution Control and Resource Recycling, Fujian Normal University, Fuzhou 350117, China
| | - Ya-Fei Ou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Xiao-Fei Li
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Yan-Ling Zheng
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai 200241, China
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China.
| | - Hong-Po Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China.
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3
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Kong Z, Wang H, Wang H, Man S, Yan Q. Magnetite-mediated shifts in denitrifying consortia in bioelectrochemical system: Insights into species selection and metabolic dynamics. WATER RESEARCH 2024; 262:122132. [PMID: 39053208 DOI: 10.1016/j.watres.2024.122132] [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: 05/02/2024] [Revised: 07/10/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
Conductive materials, such as magnetite, are recognized for their ability to enhance electron transfer and stimulate microbial metabolic activities. This study aimed to elucidate the metabolic potential and species interactions of dominant microbial species within complex communities influenced by magnetite. It indicated that the optimal dosage of magnetite at 4.5 mg/cm², would significantly improve denitrification efficiency and then reduce the time for removing 50 mg/L nitrate by 24.33 %. This enhancement was attributed to the reduced charge transfer resistance and the promoted formation of extracellular polymeric substances (EPS) facilitated by magnetite. Metagenomic analysis revealed that magnetite addition mitigated the competition among truncated denitrifiers for downstream nitrogen species, diminished the contribution of bacteria with complete nitrogen metabolism pathways to denitrification, and fostered a transition towards co-denitrification through interspecies cooperation, consequently leading to decreased nitrite accumulation and increased tolerance to nitrate shock loads. Furthermore, an in-depth study on a key species, Geobacter anodireducens JN93 within the bioelectrochemical system revealed that while magnetite with varying Fe(II) and Fe(III) ratios improved denitrification performance, the metabolic potential of Geobacter sp. varied for different nitrogen metabolism pathways. Collectively, this research provides insights into the microecological effects of magnetite on denitrifying consortia by shifting interspecific interactions via enhanced electron transfer.
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Affiliation(s)
- Ziang Kong
- School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - He Wang
- School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - Han Wang
- School of Environment and Ecology, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi 214122, China
| | - Shuaishuai Man
- School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - Qun Yan
- School of Environment and Ecology, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou 215011, China.
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4
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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.
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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.
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5
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Sennett LB, Roco CA, Lim NYN, Yavitt JB, Dörsch P, Bakken LR, Shapleigh JP, Frostegård Å. Determining how oxygen legacy affects trajectories of soil denitrifier community dynamics and N 2O emissions. Nat Commun 2024; 15:7298. [PMID: 39181870 PMCID: PMC11344836 DOI: 10.1038/s41467-024-51688-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024] Open
Abstract
Denitrification - a key process in the global nitrogen cycle and main source of the greenhouse gas N2O - is intricately controlled by O2. While the transition from aerobic respiration to denitrification is well-studied, our understanding of denitrifier communities' responses to cyclic oxic/anoxic shifts, prevalent in natural and engineered systems, is limited. Here, agricultural soil is exposed to repeated cycles of long or short anoxic spells (LA; SA) or constant oxic conditions (Ox). Surprisingly, denitrification and N2O reduction rates are three times greater in Ox than in LA and SA during a final anoxic incubation, despite comparable bacterial biomass and denitrification gene abundances. Metatranscriptomics indicate that LA favors canonical denitrifiers carrying nosZ clade I. Ox instead favors nosZ clade II-carrying partial- or non-denitrifiers, suggesting efficient partnering of the reduction steps among organisms. SA has the slowest denitrification progression and highest accumulation of intermediates, indicating less functional coordination. The findings demonstrate how adaptations of denitrifier communities to varying O2 conditions are tightly linked to the duration of anoxic episodes, emphasizing the importance of knowing an environment's O2 legacy for accurately predicting N2O emissions originating from denitrification.
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Affiliation(s)
- Louise B Sennett
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Constance A Roco
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Natalie Y N Lim
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Joseph B Yavitt
- Department of Natural Resources, Cornell University, Ithaca, NY, USA
| | - Peter Dörsch
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway
| | | | - Åsa Frostegård
- Faculty of Chemistry, Biotechnology, and Food Sciences, Norwegian University of Life Sciences, Norwegian University of Life Sciences, Ås, Norway.
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6
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Crocker K, Lee KK, Chakraverti-Wuerthwein M, Li Z, Tikhonov M, Mani M, Gowda K, Kuehn S. Environmentally dependent interactions shape patterns in gene content across natural microbiomes. Nat Microbiol 2024; 9:2022-2037. [PMID: 38977908 PMCID: PMC11386527 DOI: 10.1038/s41564-024-01752-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 06/03/2024] [Indexed: 07/10/2024]
Abstract
Sequencing surveys of microbial communities in hosts, oceans and soils have revealed ubiquitous patterns linking community composition to environmental conditions. While metabolic capabilities restrict the environments suitable for growth, the influence of ecological interactions on patterns observed in natural microbiomes remains uncertain. Here we use denitrification as a model system to demonstrate how metagenomic patterns in soil microbiomes can emerge from pH-dependent interactions. In an analysis of a global soil sequencing survey, we find that the abundances of two genotypes trade off with pH; nar gene abundances increase while nap abundances decrease with declining pH. We then show that in acidic conditions strains possessing nar fail to grow in isolation but are enriched in the community due to an ecological interaction with nap genotypes. Our study provides a road map for dissecting how associations between environmental variables and gene abundances arise from environmentally modulated community interactions.
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Affiliation(s)
- Kyle Crocker
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA
- Center for Living Systems, The University of Chicago, Chicago, IL, USA
| | - Kiseok Keith Lee
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA
- Center for Living Systems, The University of Chicago, Chicago, IL, USA
| | - Milena Chakraverti-Wuerthwein
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA
- Center for Living Systems, The University of Chicago, Chicago, IL, USA
- Biophysical Sciences Graduate Program, The University of Chicago, Chicago, IL, USA
| | - Zeqian Li
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA
- Department of Physics, The University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mikhail Tikhonov
- Department of Physics, Washington University in St. Louis, St. Louis, MO, USA
| | - Madhav Mani
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, USA
- National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago, Chicago, IL, USA
| | - Karna Gowda
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA.
| | - Seppe Kuehn
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA.
- Center for Living Systems, The University of Chicago, Chicago, IL, USA.
- National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago, Chicago, IL, USA.
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7
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Hiis EG, Vick SHW, Molstad L, Røsdal K, Jonassen KR, Winiwarter W, Bakken LR. Unlocking bacterial potential to reduce farmland N 2O emissions. Nature 2024; 630:421-428. [PMID: 38811724 PMCID: PMC11168931 DOI: 10.1038/s41586-024-07464-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024]
Abstract
Farmed soils contribute substantially to global warming by emitting N2O (ref. 1), and mitigation has proved difficult2. Several microbial nitrogen transformations produce N2O, but the only biological sink for N2O is the enzyme NosZ, catalysing the reduction of N2O to N2 (ref. 3). Although strengthening the NosZ activity in soils would reduce N2O emissions, such bioengineering of the soil microbiota is considered challenging4,5. However, we have developed a technology to achieve this, using organic waste as a substrate and vector for N2O-respiring bacteria selected for their capacity to thrive in soil6-8. Here we have analysed the biokinetics of N2O reduction by our most promising N2O-respiring bacterium, Cloacibacterium sp. CB-01, its survival in soil and its effect on N2O emissions in field experiments. Fertilization with waste from biogas production, in which CB-01 had grown aerobically to about 6 × 109 cells per millilitre, reduced N2O emissions by 50-95%, depending on soil type. The strong and long-lasting effect of CB-01 is ascribed to its tenacity in soil, rather than its biokinetic parameters, which were inferior to those of other strains of N2O-respiring bacteria. Scaling our data up to the European level, we find that national anthropogenic N2O emissions could be reduced by 5-20%, and more if including other organic wastes. This opens an avenue for cost-effective reduction of N2O emissions for which other mitigation options are lacking at present.
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Affiliation(s)
- Elisabeth G Hiis
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Silas H W Vick
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Lars Molstad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Kristine Røsdal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Wilfried Winiwarter
- International Institute for Applied Systems Analysis, Laxenburg, Austria
- Institute of Environmental Engineering, University of Zielona Góra, Zielona Góra, Poland
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
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8
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Ceballos-Escalera A, Pous N, Bañeras L, Balaguer MD, Puig S. Advancing towards electro-bioremediation scaling-up: On-site pilot plant for successful nitrate-contaminated groundwater treatment. WATER RESEARCH 2024; 256:121618. [PMID: 38663208 DOI: 10.1016/j.watres.2024.121618] [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: 12/10/2023] [Revised: 03/26/2024] [Accepted: 04/14/2024] [Indexed: 05/12/2024]
Abstract
The potential of nitrate electro-bioremediation has been fully demonstrated at the laboratory scale, although it has not yet been fully implemented due to the challenges associated with scaling-up bioelectrochemical reactors and their on-site operation. This study describes the initial start-up and subsequent stable operation of an electro-bioremediation pilot plant for the treatment of nitrate-contaminated groundwater on-site (Navata site, Spain). The pilot plant was operated under continuous flow mode for 3 months, producing an effluent suitable for drinking water in terms of nitrates and nitrites (<50 mg NO3- L-1; 0 mg NO2- L-1). A maximum nitrate removal rate of 0.9 ± 0.1 kg NO3- m-3 d-1 (efficiency 82 ± 18 %) was achieved at a cathodic hydraulic retention time (HRTcat) of 2.0 h with a competitive energy consumption of 4.3 ± 0.4 kWh kg-1 NO3-. Under these conditions, the techno-economic analysis estimated an operational cost of 0.40 € m-3. Simultaneously, microbiological analyses revealed structural heterogeneity in the reactor, with denitrification functionality concentrated predominantly from the centre to the upper section of the reactor. The most abundant groups were Pseudomonadaceae, Rhizobiaceae, Gallionellaceae, and Xanthomonadaceae. In conclusion, this pilot plant represents a significant advancement in implementing this technology on a larger scale, validating its effectiveness in terms of nitrate removal and cost-effectiveness. Moreover, the results validate the electro-bioremediation in a real environment and encourage further investigation of its potential as a water treatment.
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Affiliation(s)
- Alba Ceballos-Escalera
- LEQUiA, Institute of the Environment, University of Girona, C/ Maria Aurèlia Capmany, 69, E-17003, Girona, Spain
| | - Narcís Pous
- LEQUiA, Institute of the Environment, University of Girona, C/ Maria Aurèlia Capmany, 69, E-17003, Girona, Spain
| | - Lluis Bañeras
- Group of Environmental Microbial Ecology, Institute of Aquatic Ecology, University of Girona, C/ Maria Aurèlia Capmany, 40, E-17003, Girona, Spain
| | - M Dolors Balaguer
- LEQUiA, Institute of the Environment, University of Girona, C/ Maria Aurèlia Capmany, 69, E-17003, Girona, Spain
| | - Sebastià Puig
- LEQUiA, Institute of the Environment, University of Girona, C/ Maria Aurèlia Capmany, 69, E-17003, Girona, Spain.
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9
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Chen L, Xiang H, Zhou LT, Zhang YQ, Ding YC, Wu D, Zhu NW, Zhang YF, Feng HJ. Low-voltage stimulated denitrification performance of high-salinity wastewater using halotolerant microorganisms. BIORESOURCE TECHNOLOGY 2024; 401:130688. [PMID: 38604298 DOI: 10.1016/j.biortech.2024.130688] [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: 01/18/2024] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Nitrate is a common contaminant in high-salinity wastewater, which has adverse effects on both the environment and human health. However, conventional biological treatment exhibits poor denitrification performance due to the high-salinity shock. In this study, an innovative approach using an electrostimulating microbial reactor (EMR) was explored to address this challenge. With a low-voltage input of 1.2 V, the EMR reached nitrate removal kinetic parameter (kNO3-N) of 0.0166-0.0808 h-1 under high-salinities (1.5 %-6.5 %), which was higher than that of the microbial reactor (MR) (0.0125-0.0478 h-1). The mechanisms analysis revealed that low-voltage significantly enhanced microbial salt-in strategy and promoted the secretion of extracellular polymeric substances. Halotolerant denitrification microorganisms (Pseudomonas and Nitratireductor) were also enriched in EMR. Moreover, the EMR achieved a NO3-N removal efficiency of 73.64 % in treating high-salinity wastewater (salinity 4.69 %) over 18-cycles, whereas the MR only reached 54.67 %. In summary, this study offers an innovative solution for denitrification of high-salinity wastewater.
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Affiliation(s)
- Long Chen
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang, China; International Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development, Zhejiang Gongshang University, Hangzhou 310012, Zhejiang, China
| | - Hai Xiang
- College of Environment and Resources, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China
| | - Li-Ting Zhou
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang, China; International Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development, Zhejiang Gongshang University, Hangzhou 310012, Zhejiang, China
| | - Yan-Qing Zhang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang, China; International Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development, Zhejiang Gongshang University, Hangzhou 310012, Zhejiang, China
| | - Yang-Cheng Ding
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang, China; College of Environment and Resources, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China; International Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development, Zhejiang Gongshang University, Hangzhou 310012, Zhejiang, China
| | - Di Wu
- Center for Environmental and Energy Research (CEER) - Engineering of Materials via Catalysis and Characterization, Ghent University Global Campus, 119-5 Songdomunhwa-Ro, Yeonsu-Gu, Incheon 406-840, South Korea
| | - Nan-Wen Zhu
- Shanghai Engineering Research Center of Solid Waste Treatment and Resource Recovery, School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi-Feng Zhang
- Department of Environmental and Resource Engineering, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Hua-Jun Feng
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, Zhejiang, China; College of Environment and Resources, Zhejiang A&F University, Hangzhou 311300, Zhejiang, China; International Science and Technology Cooperation Platform for Low-Carbon Recycling of Waste and Green Development, Zhejiang Gongshang University, Hangzhou 310012, Zhejiang, China.
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10
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Awala SI, Gwak JH, Kim Y, Jung MY, Dunfield PF, Wagner M, Rhee SK. Nitrous oxide respiration in acidophilic methanotrophs. Nat Commun 2024; 15:4226. [PMID: 38762502 PMCID: PMC11102522 DOI: 10.1038/s41467-024-48161-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/22/2024] [Indexed: 05/20/2024] Open
Abstract
Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic and even anoxic environments. Despite possessing denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we show that acidophilic methanotrophs can respire nitrous oxide (N2O) and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. We study two strains that possess N2O reductase genes: Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6. We show that N2O respiration supports growth of Methylacidiphilum caldifontis at an extremely acidic pH of 2.0, exceeding the known physiological pH limits for microbial N2O consumption. Methylocella tundrae simultaneously consumes N2O and CH4 in suboxic conditions, indicating robustness of its N2O reductase activity in the presence of O2. Furthermore, in O2-limiting conditions, the amount of CH4 oxidized per O2 reduced increases when N2O is added, indicating that Methylocella tundrae can direct more O2 towards methane monooxygenase. Thus, our results demonstrate that some methanotrophs can respire N2O independently or simultaneously with O2, which may facilitate their growth and survival in dynamic environments. Such metabolic capability enables these bacteria to simultaneously reduce the release of the key greenhouse gases CO2, CH4, and N2O.
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Affiliation(s)
- Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
- Center for Ecology and Environmental Toxicology, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Yongman Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Man-Young Jung
- Interdisciplinary Graduate Programme in Advance Convergence Technology and Science, Jeju National University, Jeju, Republic of Korea
- Department of Science Education, Jeju National University, Jeju, Republic of Korea
- Jeju Microbiome Center, Jeju National University, Jeju, Republic of Korea
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea.
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11
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He G, Chen G, Xie Y, Swift CM, Ramirez D, Cha G, Konstantinidis KT, Radosevich M, Löffler FE. Sustained bacterial N 2O reduction at acidic pH. Nat Commun 2024; 15:4092. [PMID: 38750010 PMCID: PMC11096178 DOI: 10.1038/s41467-024-48236-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024] Open
Abstract
Nitrous oxide (N2O) is a climate-active gas with emissions predicted to increase due to agricultural intensification. Microbial reduction of N2O to dinitrogen (N2) is the major consumption process but microbial N2O reduction under acidic conditions is considered negligible, albeit strongly acidic soils harbor nosZ genes encoding N2O reductase. Here, we study a co-culture derived from acidic tropical forest soil that reduces N2O at pH 4.5. The co-culture exhibits bimodal growth with a Serratia sp. fermenting pyruvate followed by hydrogenotrophic N2O reduction by a Desulfosporosinus sp. Integrated omics and physiological characterization revealed interspecies nutritional interactions, with the pyruvate fermenting Serratia sp. supplying amino acids as essential growth factors to the N2O-reducing Desulfosporosinus sp. Thus, we demonstrate growth-linked N2O reduction between pH 4.5 and 6, highlighting microbial N2O reduction potential in acidic soils.
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Affiliation(s)
- Guang He
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Gao Chen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Yongchao Xie
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Cynthia M Swift
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Diana Ramirez
- Department of Microbiology, The University of Tennessee Knoxville, Knoxville, TN, 37996, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gyuhyon Cha
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | | | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Frank E Löffler
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA.
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA.
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA.
- Department of Microbiology, The University of Tennessee Knoxville, Knoxville, TN, 37996, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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12
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Yang S, Hou LJ, Dong HP, Zhang JW, Gao DZ, Li XF, Zheng YL, Liang X, Liu M. Natural chalcopyrite mitigates nitrous oxide emissions in sediment from coastal wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168766. [PMID: 38008310 DOI: 10.1016/j.scitotenv.2023.168766] [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: 08/30/2023] [Revised: 10/29/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
Coastal wetlands are one of the most important natural sources of nitrous oxide (N2O). Previous studies have shown that copper-containing chemicals are able to reduce N2O emissions from these ecosystems. However, these chemicals may harm organisms present in coastal waters and sediment, and disturb the ecological balance of these areas. Here, we first investigated the physiological characteristics and genetic potential of denitrifying bacteria isolated from coastal wetlands. Based on an isolated denitrifier carrying a complete denitrification pathway, we tested the effect of the natural mineral chalcopyrite on N2O production by the bacteria. The results demonstrated that chalcopyrite addition lowers N2O emissions from the bacteria while increasing its N2 production rate. Among the four denitrification genes of the isolate, only nosZ gene expression was significantly upregulated following the addition of 2 mg L-1 chalcopyrite. Furthermore, chalcopyrite was applied to coastal wetland sediments. The N2O flux was significantly reduced in 50-100 mg L-1 chalcopyrite-amended sets relative to the controls. Notably, the dissolved Cu concentration in chalcopyrite-amended sediment remained within the limit set by the National Sewage Treatment Discharge Standard. qPCR and metagenomic analysis revealed that the abundance of N2O-reducing bacteria with the nosZ or nirK + nosZ genotype increased significantly in the chalcopyrite-amended groups relative to the controls, suggesting their active involvement in the reduction of N2O emissions. Our findings offer valuable insights for the use of natural chalcopyrite in large-scale field applications to reduce N2O emissions.
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Affiliation(s)
- Sai Yang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China.
| | - Hong-Po Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China.
| | - Jia-Wei Zhang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Deng-Zhou Gao
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Xiao-Fei Li
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Yan-Ling Zheng
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai 200241, China
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13
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Zhang L, Zhao H, Qin S, Hu C, Shen Y, Qu B, Bai Y, Liu B. Genome-Resolved Metagenomics and Denitrifying Strain Isolation Reveal New Insights into Microbial Denitrification in the Deep Vadose Zone. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2323-2334. [PMID: 38267389 DOI: 10.1021/acs.est.3c06466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
The heavy use of nitrogen fertilizer in intensive agricultural areas often leads to nitrate accumulation in subsurface soil and nitrate contamination in groundwater, which poses a serious risk to public health. Denitrifying microorganisms in the subsoil convert nitrate to gaseous forms of nitrogen, thereby mitigating the leaching of nitrate into groundwater. Here, we investigated denitrifying microorganisms in the deep vadose zone of a typical intensive agricultural area in China through microcosm enrichment, genome-resolved metagenomic analysis, and denitrifying bacteria isolation. A total of 1000 metagenome-assembled genomes (MAGs) were reconstructed, resulting in 98 high-quality, dereplicated MAGs that contained denitrification genes. Among them, 32 MAGs could not be taxonomically classified at the genus or species level, indicating that a broader spectrum of taxonomic groups is involved in subsoil denitrification than previously recognized. A denitrifier isolate library was constructed by using a strategy combining high-throughput and conventional cultivation techniques. Assessment of the denitrification characteristics of both the MAGs and isolates demonstrated the dominance of truncated denitrification. Functional screening revealed the highest denitrification activity in two complete denitrifiers belonging to the genus Pseudomonas. These findings greatly expand the current knowledge of the composition and function of denitrifying microorganisms in subsoils. The constructed isolate library provided the first pool of subsoil-denitrifying microorganisms that could facilitate the development of microbe-based technologies for nitrate attenuation in groundwater.
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Affiliation(s)
- Linqi Zhang
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Huicheng Zhao
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Shuping Qin
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Chunsheng Hu
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Yanjun Shen
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Baoyuan Qu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Binbin Liu
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- Xiong'an Institute of Innovation, Chinese Academy of Sciences, Xiong'an 071700, China
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14
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LaSarre B, Morlen R, Neumann GC, Harwood CS, McKinlay JB. Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired. Appl Environ Microbiol 2024; 90:e0174123. [PMID: 38078768 PMCID: PMC10807417 DOI: 10.1128/aem.01741-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/04/2023] [Indexed: 01/25/2024] Open
Abstract
Denitrification is a form of anaerobic respiration wherein nitrate (NO3-) is sequentially reduced via nitrite (NO2-), nitric oxide, and nitrous oxide (N2O) to dinitrogen gas (N2) by four reductase enzymes. Partial denitrifying bacteria possess only one or some of these four reductases and use them as independent respiratory modules. However, it is unclear if partial denitrifiers sense and respond to denitrification intermediates outside of their reductase repertoire. Here, we tested the denitrifying capabilities of two purple nonsulfur bacteria, Rhodopseudomonas palustris CGA0092 and Rhodobacter capsulatus SB1003. Each had denitrifying capabilities that matched their genome annotation; CGA0092 reduced NO2- to N2, and SB1003 reduced N2O to N2. For each bacterium, N2O reduction could be used both for electron balance during growth on electron-rich organic compounds in light and for energy transformation via respiration in darkness. However, N2O reduction required supplementation with a denitrification intermediate, including those for which there was no associated denitrification enzyme. For CGA0092, NO3- served as a stable, non-catalyzable molecule that was sufficient to activate N2O reduction. Using a β-galactosidase reporter, we found that NO3- acted, at least in part, by stimulating N2O reductase gene expression. In SB1003, NO2- but not NO3- activated N2O reduction, but NO2- was slowly removed, likely by a promiscuous enzyme activity. Our findings reveal that partial denitrifiers can still be subject to regulation by denitrification intermediates that they cannot use.IMPORTANCEDenitrification is a form of microbial respiration wherein nitrate is converted via several nitrogen oxide intermediates into harmless dinitrogen gas. Partial denitrifying bacteria, which individually have some but not all denitrifying enzymes, can achieve complete denitrification as a community by cross-feeding nitrogen oxide intermediates. However, the last intermediate, nitrous oxide (N2O), is a potent greenhouse gas that often escapes, motivating efforts to understand and improve the efficiency of denitrification. Here, we found that at least some partial denitrifying N2O reducers can sense and respond to nitrogen oxide intermediates that they cannot otherwise use. The regulatory effects of nitrogen oxides on partial denitrifiers are thus an important consideration in understanding and applying denitrifying bacterial communities to combat greenhouse gas emissions.
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Affiliation(s)
- Breah LaSarre
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Ryan Morlen
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Gina C. Neumann
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Caroline S. Harwood
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - James B. McKinlay
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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15
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Freeman CN, Russell JN, Yost CK. Temporal metagenomic characterization of microbial community structure and nitrogen modification genes within an activated sludge bioreactor system. Microbiol Spectr 2024; 12:e0283223. [PMID: 38018980 PMCID: PMC10783093 DOI: 10.1128/spectrum.02832-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 10/18/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Wastewater treatment plays an essential role in minimizing negative impacts on downstream aquatic environments. Microbial communities are known to play a vital role in the wastewater treatment process, particularly in the removal of nitrogen and phosphorus, which can be especially damaging to aquatic ecosystems. There is limited understanding of how these microbial communities may change in response to fluctuating temperatures or how seasonality may impact their ability to participate in the treatment process. The findings of this study indicate that the microbial communities of wastewater are relatively stable both compositionally and functionally across fluctuating temperatures.
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Affiliation(s)
- Claire N. Freeman
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Chris K. Yost
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
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16
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Khanal A, Han SR, Lee JH, Oh TJ. Comparative Genome Analysis of Polar Mesorhizobium sp. PAMC28654 to Gain Insight into Tolerance to Salinity and Trace Element Stress. Microorganisms 2024; 12:120. [PMID: 38257947 PMCID: PMC10820077 DOI: 10.3390/microorganisms12010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
In this study, Mesorhizobium sp. PAMC28654 was isolated from a soil sample collected from the polar region of Uganda. Whole-genome sequencing and comparative genomics were performed to better understand the genomic features necessary for Mesorhizobium sp. PAMC28654 to survive and thrive in extreme conditions and stresses. Additionally, diverse sequence analysis tools were employed for genomic investigation. The results of the analysis were then validated using wet-lab experiments. Genome analysis showed trace elements' resistant proteins (CopC, CopD, CzcD, and Acr3), exopolysaccharide (EPS)-producing proteins (ExoF and ExoQ), and nitrogen metabolic proteins (NarG, NarH, and NarI). The strain was positive for nitrate reduction. It was tolerant to 100 mM NaCl at 15 °C and 25 °C temperatures and resistant to multiple trace elements (up to 1 mM CuSO4·5H2O, 2 mM CoCl2·6H2O, 1 mM ZnSO4·7H2O, 0.05 mM Cd(NO3)2·4H2O, and 100 mM Na2HAsO4·7H2O at 15 °C and 0.25 mM CuSO4·5H2O, 2 mM CoCl2·6H2O, 0.5 mM ZnSO4·7H2O, 0.01 mM Cd(NO3)2·4H2O, and 100 mM Na2HAsO4·7H2O at 25 °C). This research contributes to our understanding of bacteria's ability to survive abiotic stresses. The isolated strain can be a potential candidate for implementation for environmental and agricultural purposes.
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Affiliation(s)
- Anamika Khanal
- Genome-Based Bio-IT Convergence Institute, Asan 31460, Republic of Korea; (A.K.); (S.-R.H.)
- Bio Big Data-Based Chungnam Smart Clean Research Leader Training Program, SunMoon University, Asan 31460, Republic of Korea
| | - So-Ra Han
- Genome-Based Bio-IT Convergence Institute, Asan 31460, Republic of Korea; (A.K.); (S.-R.H.)
- Bio Big Data-Based Chungnam Smart Clean Research Leader Training Program, SunMoon University, Asan 31460, Republic of Korea
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 31460, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Materials, Korea Polar Research Institute, Incheon 21990, Republic of Korea;
| | - Tae-Jin Oh
- Genome-Based Bio-IT Convergence Institute, Asan 31460, Republic of Korea; (A.K.); (S.-R.H.)
- Bio Big Data-Based Chungnam Smart Clean Research Leader Training Program, SunMoon University, Asan 31460, Republic of Korea
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 31460, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan 31460, Republic of Korea
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17
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Sun Y, Yin Y, He G, Cha G, Ayala-del-Río HL, González G, Konstantinidis KT, Löffler FE. pH selects for distinct N 2O-reducing microbiomes in tropical soil microcosms. ISME COMMUNICATIONS 2024; 4:ycae070. [PMID: 38808123 PMCID: PMC11131594 DOI: 10.1093/ismeco/ycae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/27/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Abstract
Nitrous oxide (N2O), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by N2O reductase (NosZ). Bacteria with NosZ activity have been studied at circumneutral pH but the microbiology of low pH N2O reduction has remained elusive. Acidic (pH < 5) tropical forest soils were collected in the Luquillo Experimental Forest in Puerto Rico, and microcosms maintained with low (0.02 mM) and high (2 mM) N2O assessed N2O reduction at pH 4.5 and 7.3. All microcosms consumed N2O, with lag times of up to 7 months observed in microcosms with 2 mM N2O. Comparative metagenome analysis revealed that Rhodocyclaceae dominated in circumneutral microcosms under both N2O feeding regimes. At pH 4.5, Peptococcaceae dominated in high-N2O, and Hyphomicrobiaceae in low-N2O microcosms. Seventeen high-quality metagenome-assembled genomes (MAGs) recovered from the N2O-reducing microcosms harbored nos operons, with all eight MAGs derived from acidic microcosms carrying the Clade II type nosZ and lacking nitrite reductase genes (nirS/K). Five of the eight MAGs recovered from pH 4.5 microcosms represent novel taxa indicating an unexplored N2O-reducing diversity exists in acidic tropical soils. A survey of pH 3.5-5.7 soil metagenome datasets revealed that nosZ genes commonly occur, suggesting broad distribution of N2O reduction potential in acidic soils.
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Affiliation(s)
- Yanchen Sun
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Present address: Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States
| | - Yongchao Yin
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Present address: Department of Biology, Antimicrobial Discovery Center, Northeastern University, Boston, MA 02148, United States
| | - Guang He
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
| | - Gyuhyon Cha
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | | | - Grizelle González
- USDA Forest Service, International Institute of Tropical Forestry, San Juan 00926, Puerto Rico
| | | | - Frank E Löffler
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN 37996, United States
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18
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Wang K, Li J, Gu X, Wang H, Li X, Peng Y, Wang Y. How to Provide Nitrite Robustly for Anaerobic Ammonium Oxidation in Mainstream Nitrogen Removal. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:21503-21526. [PMID: 38096379 DOI: 10.1021/acs.est.3c05600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Innovation in decarbonizing wastewater treatment is urgent in response to global climate change. The practical implementation of anaerobic ammonium oxidation (anammox) treating domestic wastewater is the key to reconciling carbon-neutral management of wastewater treatment with sustainable development. Nitrite availability is the prerequisite of the anammox reaction, but how to achieve robust nitrite supply and accumulation for mainstream systems remains elusive. This work presents a state-of-the-art review on the recent advances in nitrite supply for mainstream anammox, paying special attention to available pathways (forward-going (from ammonium to nitrite) and backward-going (from nitrate to nitrite)), key controlling strategies, and physiological and ecological characteristics of functional microorganisms involved in nitrite supply. First, we comprehensively assessed the mainstream nitrite-oxidizing bacteria control methods, outlining that these technologies are transitioning to technologies possessing multiple selective pressures (such as intermittent aeration and membrane-aerated biological reactor), integrating side stream treatment (such as free ammonia/free nitrous acid suppression in recirculated sludge treatment), and maintaining high activity of ammonia-oxidizing bacteria and anammox bacteria for competing oxygen and nitrite with nitrite-oxidizing bacteria. We then highlight emerging strategies of nitrite supply, including the nitrite production driven by novel ammonia-oxidizing microbes (ammonia-oxidizing archaea and complete ammonia oxidation bacteria) and nitrate reduction pathways (partial denitrification and nitrate-dependent anaerobic methane oxidation). The resources requirement of different mainstream nitrite supply pathways is analyzed, and a hybrid nitrite supply pathway by combining partial nitrification and nitrate reduction is encouraged. Moreover, data-driven modeling of a mainstream nitrite supply process as well as proactive microbiome management is proposed in the hope of achieving mainstream nitrite supply in practical application. Finally, the existing challenges and further perspectives are highlighted, i.e., investigation of nitrite-supplying bacteria, the scaling-up of hybrid nitrite supply technologies from laboratory to practical implementation under real conditions, and the data-driven management for the stable performance of mainstream nitrite supply. The fundamental insights in this review aim to inspire and advance our understanding about how to provide nitrite robustly for mainstream anammox and shed light on important obstacles warranting further settlement.
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Affiliation(s)
- Kaichong Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Siping Road, Shanghai 200092, P. R. China
| | - Jia Li
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Siping Road, Shanghai 200092, P. R. China
| | - Xin Gu
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Siping Road, Shanghai 200092, P. R. China
| | - Han Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Siping Road, Shanghai 200092, P. R. China
| | - Xiang Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, P. R. China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Engineering Research Center of Beijing, Beijing University of Technology, Beijing 100124, P. R. China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P. R. China
- Shanghai Institute of Pollution Control and Ecological Security, Siping Road, Shanghai 200092, P. R. China
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19
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Wang X, Xiang B, Li J, Zhang M, Frostegard A, Bakken L, Zhang X. Using adaptive and aggressive N 2O-reducing bacteria to augment digestate fertilizer for mitigating N 2O emissions from agricultural soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166284. [PMID: 37586512 DOI: 10.1016/j.scitotenv.2023.166284] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023]
Abstract
Nitrous oxide (N2O) emitted from agricultural soils destroys stratospheric ozone and contributes to global warming. A promising approach to reduce emissions is fertilizing the soil using organic wastes augmented by non-denitrifying N2O-reducing bacteria (NNRB). To realize this potential, we need a suite of NNRB strains that fulfill several criteria: efficient reduction of N2O, ability to grow in organic waste, and ability to survive in farmland soil. In this study, we enriched such organisms by sequential anaerobic batch incubations with N2O and reciprocating inoculation between the sterilized substrates of anaerobic manure digestate and soils. 16S rDNA amplicon sequencing and metagenomics analysis showed that a cluster of bacteria containing nosZ genes encoding N2O-reductase, was enriched during the incubation process. Strains of several dominant members were then isolated and characterized, and three of them were found to harbor the nosZ gene but none of the other denitrifying genes, thus qualifying as NNRB. The selected isolates were tested for their capacities to reduce N2O emissions from three different typical Chinese farmland soils. The results indicated the significant mitigation effect of these isolates, even in very acidic red soil. In conclusion, this study demonstrated a strategy to engineer the soil microbiome with promising NNRB with high adaptability to livestock manure digestate as well as different agricultural soils, which would be suitable for developing novel fertilizer for farmland application to efficiently mitigate the N2O emissions from agricultural soils.
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Affiliation(s)
- Xinhui Wang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Baoyu Xiang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ji Li
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Menghui Zhang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Asa Frostegard
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Aas, Norway
| | - Lars Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, N-1432 Aas, Norway
| | - Xiaojun Zhang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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20
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Crocker K, Lee KK, Chakraverti-Wuerthwein M, Li Z, Tikhonov M, Mani M, Gowda K, Kuehn S. Global patterns in gene content of soil microbiomes emerge from microbial interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.542950. [PMID: 38014336 PMCID: PMC10680560 DOI: 10.1101/2023.05.31.542950] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Microbial metabolism sustains life on Earth. Sequencing surveys of communities in hosts, oceans, and soils have revealed ubiquitous patterns linking the microbes present, the genes they possess, and local environmental conditions. One prominent explanation for these patterns is environmental filtering: local conditions select strains with particular traits. However, filtering assumes ecological interactions do not influence patterns, despite the fact that interactions can and do play an important role in structuring communities. Here, we demonstrate the insufficiency of the environmental filtering hypothesis for explaining global patterns in topsoil microbiomes. Using denitrification as a model system, we find that the abundances of two characteristic genotypes trade-off with pH; nar gene abundances increase while nap abundances decrease with declining pH. Contradicting the filtering hypothesis, we show that strains possessing the Nar genotype are enriched in low pH conditions but fail to grow alone. Instead, the dominance of Nar genotypes at low pH arises from an ecological interaction with Nap genotypes that alleviates nitrite toxicity. Our study provides a roadmap for dissecting how global associations between environmental variables and gene abundances arise from environmentally modulated community interactions.
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Affiliation(s)
- Kyle Crocker
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA
| | - Kiseok Keith Lee
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA
| | | | - Zeqian Li
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA
- Department of Physics, The University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mikhail Tikhonov
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Madhav Mani
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Karna Gowda
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA
| | - Seppe Kuehn
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL 60637, USA
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21
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Zhou M, Guan X, Deng T, Hu R, Qian L, Yang X, Wu B, Li J, He Q, Shu L, Yan Q, He Z. Synthetic phylogenetically diverse communities promote denitrification and stability. ENVIRONMENTAL RESEARCH 2023; 231:116184. [PMID: 37207729 DOI: 10.1016/j.envres.2023.116184] [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: 03/07/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/21/2023]
Abstract
Denitrification is an important process of the global nitrogen cycle as some of its intermediates are environmentally important or related to global warming. However, how the phylogenetic diversity of denitrifying communities affects their denitrification rates and temporal stability remains unclear. Here we selected denitrifiers based on their phylogenetic distance to construct two groups of synthetic denitrifying communities: one closely related (CR) group with all strains from the genus Shewanella and the other distantly related (DR) group with all constituents from different genera. All synthetic denitrifying communities (SDCs) were experimentally evolved for 200 generations. The results showed that high phylogenetic diversity followed by experimental evolution promoted the function and stability of synthetic denitrifying communities. Specifically, the productivity and denitrification rates were significantly (P < 0.05) higher with Paracocus denitrificans as the dominant species (since the 50th generation) in the DR community than those in the CR community. The DR community also showed significantly (t = 7.119, df = 10, P < 0.001) higher stability through overyielding and asynchrony of species fluctuations, and showed more complementarity than the CR group during the experimental evolution. This study has important implications for applying synthetic communities to remediate environmental problems and mitigate greenhouse gas emissions.
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Affiliation(s)
- Min Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiaotong Guan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ting Deng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Lu Qian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Juan Li
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Qiang He
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
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22
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Garrido-Amador P, Stortenbeker N, Wessels HJCT, Speth DR, Garcia-Heredia I, Kartal B. Enrichment and characterization of a nitric oxide-reducing microbial community in a continuous bioreactor. Nat Microbiol 2023; 8:1574-1586. [PMID: 37429908 PMCID: PMC10390337 DOI: 10.1038/s41564-023-01425-8] [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: 02/09/2023] [Accepted: 06/14/2023] [Indexed: 07/12/2023]
Abstract
Nitric oxide (NO) is a highly reactive and climate-active molecule and a key intermediate in the microbial nitrogen cycle. Despite its role in the evolution of denitrification and aerobic respiration, high redox potential and capacity to sustain microbial growth, our understanding of NO-reducing microorganisms remains limited due to the absence of NO-reducing microbial cultures obtained directly from the environment using NO as a substrate. Here, using a continuous bioreactor and a constant supply of NO as the sole electron acceptor, we enriched and characterized a microbial community dominated by two previously unknown microorganisms that grow at nanomolar NO concentrations and survive high amounts (>6 µM) of this toxic gas, reducing it to N2 with little to non-detectable production of the greenhouse gas nitrous oxide. These results provide insight into the physiology of NO-reducing microorganisms, which have pivotal roles in the control of climate-active gases, waste removal, and evolution of nitrate and oxygen respiration.
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Affiliation(s)
| | | | - Hans J C T Wessels
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daan R Speth
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Boran Kartal
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- School of Science, Constructor University, Bremen, Germany.
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23
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Ciccarese D, Tantawi O, Zhang IH, Plata D, Babbin AR. Microscale dynamics promote segregated denitrification in diatom aggregates sinking slowly in bulk oxygenated seawater. COMMUNICATIONS EARTH & ENVIRONMENT 2023; 4:275. [PMID: 38665198 PMCID: PMC11041763 DOI: 10.1038/s43247-023-00935-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 07/18/2023] [Indexed: 04/28/2024]
Abstract
Sinking marine particles drive the biological pump that naturally sequesters carbon from the atmosphere. Despite their small size, the compartmentalized nature of particles promotes intense localized metabolic activity by their bacterial colonizers. Yet the mechanisms promoting the onset of denitrification, a metabolism that arises once oxygen is limiting, remain to be established. Here we show experimentally that slow sinking aggregates composed of marine diatoms-important primary producers for global carbon export-support active denitrification even among bulk oxygenated water typically thought to exclude anaerobic metabolisms. Denitrification occurs at anoxic microsites distributed throughout a particle and within microns of a particle's boundary, and fluorescence-reporting bacteria show nitrite can be released into the water column due to segregated dissimilatory reduction of nitrate and nitrite. Examining intact and broken diatoms as organic sources, we show slowly leaking cells promote more bacterial growth, allow particles to have lower oxygen, and generally support greater denitrification.
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Affiliation(s)
- Davide Ciccarese
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Omar Tantawi
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Irene H. Zhang
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
- Program in Microbiology, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Desiree Plata
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Andrew R. Babbin
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA USA
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24
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Amarnath K, Narla AV, Pontrelli S, Dong J, Reddan J, Taylor BR, Caglar T, Schwartzman J, Sauer U, Cordero OX, Hwa T. Stress-induced metabolic exchanges between complementary bacterial types underly a dynamic mechanism of inter-species stress resistance. Nat Commun 2023; 14:3165. [PMID: 37258505 PMCID: PMC10232422 DOI: 10.1038/s41467-023-38913-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/19/2023] [Indexed: 06/02/2023] Open
Abstract
Metabolic cross-feeding plays vital roles in promoting ecological diversity. While some microbes depend on exchanges of essential nutrients for growth, the forces driving the extensive cross-feeding needed to support the coexistence of free-living microbes are poorly understood. Here we characterize bacterial physiology under self-acidification and establish that extensive excretion of key metabolites following growth arrest provides a collaborative, inter-species mechanism of stress resistance. This collaboration occurs not only between species isolated from the same community, but also between unrelated species with complementary (glycolytic vs. gluconeogenic) modes of metabolism. Cultures of such communities progress through distinct phases of growth-dilution cycles, comprising of exponential growth, acidification-triggered growth arrest, collaborative deacidification, and growth recovery, with each phase involving different combinations of physiological states of individual species. Our findings challenge the steady-state view of ecosystems commonly portrayed in ecological models, offering an alternative dynamical view based on growth advantages of complementary species in different phases.
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Affiliation(s)
- Kapil Amarnath
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Avaneesh V Narla
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Sammy Pontrelli
- Institute of Molecular and Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Jiajia Dong
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
- Department of Physics and Astronomy, Bucknell University, Lewisburg, PA, 17837, USA
| | - Jack Reddan
- Division of Biological Sciences, U.C. San Diego, La Jolla, CA, 92093, USA
| | - Brian R Taylor
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Tolga Caglar
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA
| | - Julia Schwartzman
- Department of Civil and Environmental Engineering, MIT, Cambridge, MA, 02139, USA
| | - Uwe Sauer
- Institute of Molecular and Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, MIT, Cambridge, MA, 02139, USA
| | - Terence Hwa
- Department of Physics, U.C. San Diego, La Jolla, CA, 92093-0319, USA.
- Division of Biological Sciences, U.C. San Diego, La Jolla, CA, 92093, USA.
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25
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Shi M, Song C, Xie L, Zhang G, Wei Z. Role in aromatic metabolites biodegradation and adverse implication of denitrifying microbiota in kitchen waste composting. ENVIRONMENTAL MICROBIOME 2023; 18:44. [PMID: 37254173 DOI: 10.1186/s40793-023-00496-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 04/21/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Understanding the functional diversity, composition, and dynamics of microbiome is critical for quality in composting. Denitrifying microbiota, possessing multiple metabolic pathways simultaneously. Denitrification-based biodegradation of aromatic metabolites has been widely applied in the bioremediation of sediments. However, role in biodegradation of denitrifying microbiota in kitchen waste composting remain unclear. In this study, microbiome and metabolome were used to comprehensively decipher the relationship of denitrifying microbiota and aromatic metabolites, and its implication in kitchen waste (KW) composting. RESULTS This study was investigated by adjusting moisture content 60% as control test (CK), 70% as denitrification test (DE). In addition, one tests referred as DE + C, which received 10% of biochar to amend denitrification. Results indicated the quantities of denitrification genes narG were 1.22 × 108 copies/g in DE at the 55th day, which were significantly higher than that in CK and DE + C (P < 0.05). Similarly, the abundance of nirK gene also significantly increased in DE (P < 0.05). The relative abundance of denitrification-related microbes in DE was higher than that in CK, DE + C could weaken their abundance. Metabolomics results demonstrated that metabolites were downgraded in aromatic amino acid and catechin metabolic pathways in DE, which were identified as precursors to synthesis key product fulvic acid. The concentrations of fulvic acid dramatically decreased 21.05 mg/g in DE comparison with CK. Biochar addition alleviated the biodegradation of aromatic metabolites and reduced the utilization of fulvic acid. Integrative analyses of metabolomics and microbiome suggested that the microbiota involved in nitrite reduction pathway was vital for the biodegradation aromatic metabolites. Mantel test verified that NO3--N, moisture content, eta, environmental factors were important drivers behind the changes in the denitrifying microbiota biodegradation function. CONCLUSION The data confirm the biodegradation function of denitrifying microbiota led to the loss of core product fulvic acid in KW composting, which highlighted the adverse role and implication of denitrification for composting humification. Control of denitrification with biochar was recommended to improve composting quality.
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Affiliation(s)
- Mingzi Shi
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
- College of Life Science, Henan Agricultural University, Zhengzhou, 450000, China
| | - Caihong Song
- College of Life Science, Liaocheng University, Liaocheng, 252000, China
| | - Lina Xie
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Guogang Zhang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China
| | - Zimin Wei
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, 300387, China.
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26
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Abada A, Beiralas R, Narvaez D, Sperfeld M, Duchin-Rapp Y, Lipsman V, Yuda L, Cohen B, Carmieli R, Ben-Dor S, Rocha J, Huang Zhang I, Babbin AR, Segev E. Aerobic bacteria produce nitric oxide via denitrification and promote algal population collapse. THE ISME JOURNAL 2023:10.1038/s41396-023-01427-8. [PMID: 37173383 DOI: 10.1038/s41396-023-01427-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/23/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023]
Abstract
Microbial interactions govern marine biogeochemistry. These interactions are generally considered to rely on exchange of organic molecules. Here we report on a novel inorganic route of microbial communication, showing that algal-bacterial interactions between Phaeobacter inhibens bacteria and Gephyrocapsa huxleyi algae are mediated through inorganic nitrogen exchange. Under oxygen-rich conditions, aerobic bacteria reduce algal-secreted nitrite to nitric oxide (NO) through denitrification, a well-studied anaerobic respiratory mechanism. The bacterial NO is involved in triggering a cascade in algae akin to programmed cell death. During death, algae further generate NO, thereby propagating the signal in the algal population. Eventually, the algal population collapses, similar to the sudden demise of oceanic algal blooms. Our study suggests that the exchange of inorganic nitrogen species in oxygenated environments is a potentially significant route of microbial communication within and across kingdoms.
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Affiliation(s)
- Adi Abada
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Roni Beiralas
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Delia Narvaez
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Martin Sperfeld
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Yemima Duchin-Rapp
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Valeria Lipsman
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Lilach Yuda
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Bar Cohen
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Raanan Carmieli
- Depertment of Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Department of Life Science Core Facilities, The Weizmann Institute of Science, Rehovot, Israel
| | - Jorge Rocha
- CIDEA Consortium Conacyt-Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Mexico
| | - Irene Huang Zhang
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew R Babbin
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Einat Segev
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel.
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27
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Denitrification by Bradyrhizobia under Feast and Famine and the Role of the bc1 Complex in Securing Electrons for N 2O Reduction. Appl Environ Microbiol 2023; 89:e0174522. [PMID: 36662572 PMCID: PMC9972998 DOI: 10.1128/aem.01745-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Rhizobia living as microsymbionts inside nodules have stable access to carbon substrates, but also must survive as free-living bacteria in soil where they are starved for carbon and energy most of the time. Many rhizobia can denitrify, thus switch to anaerobic respiration under low O2 tension using N-oxides as electron acceptors. The cellular machinery regulating this transition is relatively well known from studies under optimal laboratory conditions, while little is known about this regulation in starved organisms. It is, for example, not known if the strong preference for N2O- over NO3- reduction in bradyrhizobia is retained under carbon limitation. Here, we show that starved cultures of a Bradyrhizobium strain with respiration rates 1 to 18% of well-fed cultures reduced all available N2O before touching provided NO3-. These organisms, which carry out complete denitrification, have the periplasmic nitrate reductase NapA but lack the membrane-bound nitrate reductase NarG. Proteomics showed similar levels of NapA and NosZ (N2O reductase), excluding that the lack of NO3- reduction was due to low NapA abundance. Instead, this points to a metabolic-level phenomenon where the bc1 complex, which channels electrons to NosZ via cytochromes, is a much stronger competitor for electrons from the quinol pool than the NapC enzyme, which provides electrons to NapA via NapB. The results contrast the general notion that NosZ activity diminishes under carbon limitation and suggest that bradyrhizobia carrying NosZ can act as strong sinks for N2O under natural conditions, implying that this criterion should be considered in the development of biofertilizers. IMPORTANCE Legume cropped farmlands account for substantial N2O emissions globally. Legumes are commonly inoculated with N2-fixing bacteria, rhizobia, to improve crop yields. Rhizobia belonging to Bradyrhizobium, the microsymbionts of several economically important legumes, are generally capable of denitrification but many lack genes encoding N2O reductase and will be N2O sources. Bradyrhizobia with complete denitrification will instead act as sinks since N2O-reduction efficiently competes for electrons over nitrate reduction in these organisms. This phenomenon has only been demonstrated under optimal conditions and it is not known how carbon substrate limitation, which is the common situation in most soils, affects the denitrification phenotype. Here, we demonstrate that bradyrhizobia retain their strong preference for N2O under carbon starvation. The findings add basic knowledge about mechanisms controlling denitrification and support the potential for developing novel methods for greenhouse gas mitigation based on legume inoculants with the dual capacity to optimize N2 fixation and minimize N2O emission.
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28
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Ding K, Xu L, Chen Y, Li W, Chai X, Dai X, Wu B. Mechanistic insights into polyhydroxyalkanoate-enhanced denitrification capacity of microbial community: Evolution of community structure and intracellular electron transfer of nitrogen metabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159147. [PMID: 36183769 DOI: 10.1016/j.scitotenv.2022.159147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Denitrification is the key driving force of nitrogen cycle in surface water and plays an important role in eutrophication water remediation. Compared with some other common carbon sources, such as glucose and sodium acetate, polyhydroxyalkanoates (PHAs) were found to have the distinguished advantages in screening specific denitrifying bacteria of natural surface water bodies. In this study, the large ensembles of taxa were obtained from surface water samples and then sub-cultured with PHA or glucose as the sole carbon source. The microbial community that could be screened by PHA was identified, and the environmental functions of these bacteria were analyzed. At the genus level, the main communities regulated by PHA included Pseudomonas (56.30 %), Acinetobacter (27.75 %), Flavobacterium (10.19 %) and Comamonas (3.14 %), which all had good denitrification ability. The changes in carbon source, nitrogen source and biomass (expressed by DNA) were simultaneously monitored when culturing the model strain (P. stuzeri) with PHA or glucose. Compared with the glucose group, less PHA was consumed to remove the same amount of nitrate within a shorter incubation time, and there was no significant difference in bacterial growth with PHA or glucose as the carbon source (glucose:ΔN:ΔC:ΔDNA = 1:18:0.072; PHA:ΔN:ΔC:ΔDNA = 1:11:0.063). PHA improved the denitrification efficiency by increasing the expression of NarGHI, NirB, NirK and NorB, i.e., the key enzymes in the denitrification process. In addition, PHA accelerated the assimilating rate of extracellular nitrate by bacteria through increasing the expression of NarK. Finally, PHA-regulated electron transfer during denitrification was studied by observing the changes in NADH and NAD+. PHA could use a large proportion of NADH to offer electrons for denitrification, which increased the rate of denitrification. Improved mechanistic insights into the PHA-enhanced denitrification capacity of the microbial community can provide novel options for the in-situ remediation of eutrophic surface water.
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Affiliation(s)
- Ke Ding
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Linge Xu
- Hydrochina Huadong Engineering Corporation Limited, 201 Gaojiao Road, Hangzhou, 311122, China
| | - Yulin Chen
- Shanghai Municipal Engineering Design Institute (Group) Co., Ltd, 901 Zhongshan North 2nd Road, Shanghai 200092, China
| | - Wenxuan Li
- NUS Environmental Research Institute, National University of Singapore, 5A Engineering Drive 1, #02-01 T-Lab Building, 117411 Singapore, Singapore
| | - Xiaoli Chai
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Boran Wu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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Chen L, Li W, Zhao Y, Zhang S, Meng L. Mechanism of sulfur-oxidizing inoculants and nitrate on regulating sulfur functional genes and bacterial community at the thermophilic compost stage. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 326:116733. [PMID: 36372033 DOI: 10.1016/j.jenvman.2022.116733] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/05/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
The emission of H2S odors predominantly occurred at the thermophilic phase of composting, which could cause odorous gas pollution and reduce the fertilizer value of composting products. And sulfur-oxidizing bacteria (SOB) possess oxidative capacities for inorganic sulfur compounds with nitrate applied as electron acceptors. Therefore, this study aimed to assess the effectiveness of combined additives (SOB inoculants and nitrate) on the bacterial community diversity, sulfur-oxidizing gene abundances, and metabolic function prediction at the thermophilic stage of sewage sludge composting. The highest sulfate contents were increased by 1.02-1.34 folds, and the abundances of the sulfur-oxidizing genes (sqr, pdo, sox, and sor) were also enhanced by adding the combined additives. Network patterns revealed a strengthened interaction of inoculants and sulfur functional genes. Microbial functional pathways predicted higher metabolic levels of carbohydrate and amino acid metabolisms with the addition of combined additives, and the predicted relative abundances of sulfur metabolism and nitrogen metabolism were increased by 19.3 ± 2.5% and 24.7 ± 4.1%, respectively. Heatmap analysis showed that the SOB might have a competitive advantage over the indigenous denitrifying bacteria in using nitrate for biochemical reactions. Correlation analyses suggested that sulfur-oxidizing efficacy could be indirectly affected by the environmental parameters through changing the structure of bacterial community. These findings provide new insights toward an optimized inoculation strategy of using SOB and nitrate to enhance sulfur preservation and modulate the bacterial communities at the thermophilic phase of sewage sludge composting.
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Affiliation(s)
- Li Chen
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Weiguang Li
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Yi Zhao
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Shumei Zhang
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, China
| | - Liqiang Meng
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, China
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Wilbert SA, Newman DK. The contrasting roles of nitric oxide drive microbial community organization as a function of oxygen presence. Curr Biol 2022; 32:5221-5234.e4. [PMID: 36306787 PMCID: PMC9772256 DOI: 10.1016/j.cub.2022.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 08/15/2022] [Accepted: 10/05/2022] [Indexed: 12/23/2022]
Abstract
Microbial assemblages are omnipresent in the biosphere, forming communities on the surfaces of roots and rocks and within living tissues. These communities can exhibit strikingly beautiful compositional structures, with certain members reproducibly occupying particular spatiotemporal microniches. Despite this reproducibility, we lack the ability to explain these spatial patterns. We hypothesize that certain spatial patterns in microbial communities may be explained by the exchange of redox-active metabolites whose biological function is sensitive to microenvironmental gradients. To test this, we developed a simple community consisting of synthetic Pseudomonas aeruginosa strains with a partitioned denitrification pathway: a strict consumer and strict producer of nitric oxide (NO), a key pathway intermediate. Because NO can be both toxic or beneficial depending on the amount of oxygen present, this system provided an opportunity to investigate whether dynamic oxygen gradients can tune metabolic cross-feeding and fitness outcomes in a predictable fashion. Using a combination of genetic analysis, controlled growth environments, and imaging, we show that oxygen availability dictates whether NO cross-feeding is deleterious or mutually beneficial and that this organizing principle maps to the microscale. More generally, this work underscores the importance of considering the double-edged and microenvironmentally tuned roles redox-active metabolites can play in shaping microbial communities.
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Affiliation(s)
- Steven A Wilbert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA.
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31
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Gowda K, Kuehn S. Microbial biofilms: An ecological tale of Jekyll and Hyde. Curr Biol 2022; 32:R1349-R1351. [PMID: 36538887 DOI: 10.1016/j.cub.2022.10.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The molecules of life can be double-edged, performing both beneficial and detrimental roles depending on the environmental context. New work reveals how the Jekyll and Hyde nature of nitric oxide shapes complexity in microbial biofilms, from ecological interactions to spatial structure.
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Affiliation(s)
- Karna Gowda
- Department of Ecology and Evolution and Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA
| | - Seppe Kuehn
- Department of Ecology and Evolution and Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA.
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32
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Zhang Q, Xu X, Zhang R, Shao B, Fan K, Zhao L, Ji X, Ren N, Lee DJ, Chen C. The mixed/mixotrophic nitrogen removal for the effective and sustainable treatment of wastewater: From treatment process to microbial mechanism. WATER RESEARCH 2022; 226:119269. [PMID: 36279615 DOI: 10.1016/j.watres.2022.119269] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/25/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Biological nitrogen removal (BNR) is one of the most important environmental concerns in the field of wastewater treatment. The conventional BNR process based on heterotrophic nitrogen removal (HeNR) is suffering from several limitations, including external carbon source dependence, excessive sludge production, and greenhouse gas emissions. Through the mediation of autotrophic nitrogen removal (AuNR), mixed/mixotrophic nitrogen removal (MixNR) offers a viable solution to the optimization of the BNR process. Here, the recent advance and characteristics of MixNR process guided by sulfur-driven autotrophic denitrification (SDAD) and anammox are summarized in this review. Additionally, we discuss the functional microorganisms in different MixNR systems, shedding light on metabolic mechanisms and microbial interactions. The significance of MixNR for carbon reduction in the BNR process has also been noted. The knowledge gaps and the future research directions that may facilitate the practical application of the MixNR process are highlighted. Overall, the prospect of the MixNR process is attractive, and this review will provide guidance for the future implementation of MixNR process as well as deciphering the microbially metabolic mechanisms.
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Affiliation(s)
- Quan Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Room 1433, Harbin, Heilongjiang 150090, China
| | - Xijun Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Room 1433, Harbin, Heilongjiang 150090, China
| | - Ruochen Zhang
- School of Civil and Transportation Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Bo Shao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Room 1433, Harbin, Heilongjiang 150090, China
| | - Kaili Fan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Room 1433, Harbin, Heilongjiang 150090, China
| | - Lei Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Room 1433, Harbin, Heilongjiang 150090, China
| | - Xiaoming Ji
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Room 1433, Harbin, Heilongjiang 150090, China
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-li, 32003, Taiwan
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Room 1433, Harbin, Heilongjiang 150090, China.
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Preparation for Denitrification and Phenotypic Diversification at the Cusp of Anoxia: a Purpose for N 2O Reductase Vis-à-Vis Multiple Roles of O 2. Appl Environ Microbiol 2022; 88:e0105322. [PMID: 36250705 PMCID: PMC9642011 DOI: 10.1128/aem.01053-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Adaptation to anoxia by synthesizing a denitrification proteome costs metabolic energy, and the anaerobic respiration conserves less energy per electron than aerobic respiration. This implies a selective advantage of the stringent O2 repression of denitrification gene transcription, which is found in most denitrifying bacteria. In some bacteria, the metabolic burden of adaptation can be minimized further by phenotypic diversification, colloquially termed "bet-hedging," where all cells synthesize the N2O reductase (NosZ) but only a minority synthesize nitrite reductase (NirS), as demonstrated for the model strain Paracoccus denitrificans. We hypothesized that the cells lacking NirS would be entrapped in anoxia but with the possibility of escape if supplied with O2 or N2O. To test this, cells were exposed to gradual O2 depletion or sudden anoxia and subsequent spikes of O2 and N2O. The synthesis of NirS in single cells was monitored by using an mCherry-nirS fusion replacing the native nirS, and their growth was detected as dilution of green, fluorescent fluorescein isothiocyanate (FITC) stain. We demonstrate anoxic entrapment due to e--acceptor deprivation and show that O2 spiking leads to bet-hedging, while N2O spiking promotes NirS synthesis and growth in all cells carrying NosZ. The cells rescued by the N2O spike had much lower respiration rates than those rescued by the O2 spike, however, which could indicate that the well-known autocatalytic synthesis of NirS via NO production requires O2. Our results bring into relief a fitness advantage of pairing restrictive nirS expression with universal NosZ synthesis in energy-limited systems. IMPORTANCE Denitrifying bacteria have evolved elaborate regulatory networks securing their respiratory metabolism in environments with fluctuating oxygen concentrations. Here, we provide new insight regarding their bet-hedging in response to hypoxia, which minimizes their N2O emissions because all cells express NosZ, reducing N2O to N2, while a minority express NirS + Nor, reducing NO2- to N2O. We hypothesized that the cells without Nir were entrapped in anoxia, without energy to synthesize Nir, and that they could be rescued by short spikes of O2 or N2O. We confirm such entrapment and the rescue of all cells by an N2O spike but only a fraction by an O2 spike. The results shed light on the role of O2 repression in bet-hedging and generated a novel hypothesis regarding the autocatalytic nirS expression via NO production. Insight into the regulation of denitrification, including bet-hedging, holds a clue to understanding, and ultimately curbing, the escalating emissions of N2O, which contribute to anthropogenic climate forcing.
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Oba K, Suenaga T, Kuroiwa M, Riya S, Terada A. Exploring the Functions of Efficient Canonical Denitrifying Bacteria as N 2O Sinks: Implications from 15N Tracer and Transcriptome Analyses. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11694-11706. [PMID: 35917165 DOI: 10.1021/acs.est.2c02119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In denitrifying reactors, canonical complete denitrifying bacteria reduce nitrate (NO3-) to nitrogen via N2O. However, they can also produce N2O under certain conditions. We used a 15N tracer method, in which 15N-labeled NO3-/nitrite (NO2-) and nonlabeled N2O were simultaneously supplied with organic electron donors to five canonical complete denitrifying bacteria affiliated with either Clade I or Clade II nosZ. We calculated their NO3-, NO2-, and N2O consumption rates. The Clade II nosZ bacterium Azospira sp. strain I13 had the highest N2O consumption rate (3.47 ± 0.07 fmol/cell/h) and the second lowest NO3- consumption rate (0.20 ± 0.03 fmol/cell/h); hence, it is a N2O sink. A change from peptone- to acetate/citrate-based organic electron donors increased the NO3- consumption rate by 4.8 fold but barely affected the N2O consumption rate. Electron flow was directed to N2O rather than NO3- in Azospira sp. strain I13 and Az. oryzae strain PS only exerting a N2O sink but to NO3- in the Clade I nosZ N2O-reducing bacteria Pseudomonas stutzeri strain JCM 5965 and Alicycliphilus denitrificans strain I51. Transcriptome analyses revealed that the genotype could not fully describe the phenotype. The results show that N2O production and consumption differ among canonical denitrifying bacteria and will be useful for developing N2O mitigation strategies.
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Affiliation(s)
- Kohei Oba
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Toshikazu Suenaga
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-Cho, Fuchu, Tokyo 185-8538, Japan
- Department of Chemical Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-hiroshima, Hiroshima 739-8527, Japan
| | - Megumi Kuroiwa
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
| | - Shohei Riya
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-Cho, Fuchu, Tokyo 185-8538, Japan
| | - Akihiko Terada
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-Cho, Koganei, Tokyo 184-8588, Japan
- Global Innovation Research Institute, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-Cho, Fuchu, Tokyo 185-8538, Japan
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35
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The NtrYX Two-Component System of Paracoccus denitrificans Is Required for the Maintenance of Cellular Iron Homeostasis and for a Complete Denitrification under Iron-Limited Conditions. Int J Mol Sci 2022; 23:ijms23169172. [PMID: 36012437 PMCID: PMC9409073 DOI: 10.3390/ijms23169172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 02/08/2023] Open
Abstract
Denitrification consists of the sequential reduction of nitrate to nitrite, nitric oxide, nitrous oxide, and dinitrogen. Nitrous oxide escapes to the atmosphere, depending on copper availability and other environmental factors. Iron is also a key element because many proteins involved in denitrification contain iron-sulfur or heme centers. The NtrYX two-component regulatory system mediates the responses in a variety of metabolic processes, including denitrification. A quantitative proteomic analysis of a Paracoccus denitrificans NtrY mutant grown under denitrifying conditions revealed the induction of different TonB-dependent siderophore transporters and proteins related to iron homeostasis. This mutant showed lower intracellular iron content than the wild-type strain, and a reduced growth under denitrifying conditions in iron-limited media. Under iron-rich conditions, it releases higher concentrations of siderophores and displayes lower nitrous oxide reductase (NosZ) activity than the wild-type, thus leading to nitrous oxide emission. Bioinformatic and qRT-PCR analyses revealed that NtrYX is a global transcriptional regulatory system that responds to iron starvation and, in turn, controls expression of the iron-responsive regulators fur, rirA, and iscR, the denitrification regulators fnrP and narR, the nitric oxide-responsive regulator nnrS, and a wide set of genes, including the cd1-nitrite reductase NirS, nitrate/nitrite transporters and energy electron transport proteins.
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36
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Wu Q, Ji M, Yu S, Li J, Wu X, Ju X, Liu B, Zhang X. Distinct Denitrifying Phenotypes of Predominant Bacteria Modulate Nitrous Oxide Metabolism in Two Typical Cropland Soils. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02085-7. [PMID: 35918440 DOI: 10.1007/s00248-022-02085-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Denitrifying nitrous oxide (N2O) emissions in agroecosystems result from variations in microbial composition and soil properties. However, the microbial mechanisms of differential N2O emissions in agricultural soils are less understood. In this study, microcosm experiments using two main types of Chinese cropland soil were conducted with different supplements of nitrate and glucose to simulate the varying nitrogen and carbon conditions. The results show that N2O accumulation in black soil (BF) was significantly higher than that in fluvo-aquic soil (FF) independent of nitrogen and carbon. The abundance of most denitrifying genes was significantly higher in FF, but the ratios of genes responsible for N2O production (nirS and nirK) to the gene responsible for N2O reduction (nosZ) did not significantly differ between the two soils. However, the soils showed obvious discrepancies in denitrifying bacterial communities, with a higher abundance of N2O-generating bacteria in BF and a higher abundance of N2O-reducing bacteria in FF. High accumulation of N2O was verified by the bacterial isolates of Rhodanobacter predominated in BF due to a lack of N2O reduction capacity. The dominance of Castellaniella and others in FF led to a rapid reduction in N2O and thus less N2O accumulation, as demonstrated when the corresponding isolate was inoculated into the studied soils. Therefore, the different phenotypes of N2O metabolism of the distinct denitrifiers predominantly colonized the two soils, causing differing N2O accumulation. This knowledge would help to develop a strategy for mitigating N2O emissions in agricultural soils by regulating the phenotypes of N2O metabolism.
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Affiliation(s)
- Qiaoyu Wu
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mengmeng Ji
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Siyu Yu
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ji Li
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaogang Wu
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaotang Ju
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Binbin Liu
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021, China
| | - Xiaojun Zhang
- State Key Laboratory of Microbial Metabolism, and Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Karaoz U, Brodie EL. microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes. FRONTIERS IN BIOINFORMATICS 2022; 2:918853. [PMID: 36304272 PMCID: PMC9580909 DOI: 10.3389/fbinf.2022.918853] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2023] Open
Abstract
Remote sensing approaches have revolutionized the study of macroorganisms, allowing theories of population and community ecology to be tested across increasingly larger scales without much compromise in resolution of biological complexity. In microbial ecology, our remote window into the ecology of microorganisms is through the lens of genome sequencing. For microbial organisms, recent evidence from genomes recovered from metagenomic samples corroborate a highly complex view of their metabolic diversity and other associated traits which map into high physiological complexity. Regardless, during the first decades of this omics era, microbial ecological research has primarily focused on taxa and functional genes as ecological units, favoring breadth of coverage over resolution of biological complexity manifested as physiological diversity. Recently, the rate at which provisional draft genomes are generated has increased substantially, giving new insights into ecological processes and interactions. From a genotype perspective, the wide availability of genome-centric data requires new data synthesis approaches that place organismal genomes center stage in the study of environmental roles and functional performance. Extraction of ecologically relevant traits from microbial genomes will be essential to the future of microbial ecological research. Here, we present microTrait, a computational pipeline that infers and distills ecologically relevant traits from microbial genome sequences. microTrait maps a genome sequence into a trait space, including discrete and continuous traits, as well as simple and composite. Traits are inferred from genes and pathways representing energetic, resource acquisition, and stress tolerance mechanisms, while genome-wide signatures are used to infer composite, or life history, traits of microorganisms. This approach is extensible to any microbial habitat, although we provide initial examples of this approach with reference to soil microbiomes.
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Affiliation(s)
- Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Eoin L. Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
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Zhang Z, Zhang Y, Shi Z, Chen Y. Linking Genome-Centric Metagenomics to Kinetic Analysis Reveals the Regulation Mechanism of Hydroxylamine in Nitrite Accumulation of Biological Denitrification. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:10317-10328. [PMID: 35761213 DOI: 10.1021/acs.est.2c01914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Given hydroxylamine accumulation in various nitrification systems and its potential mechanism in regulating the subsequent denitrification process were unraveled in this study. Hydroxylamine (>0.5 mgN/L) immediately induced nitrite accumulation of activated sludge by inhibiting the activities of nitrite reductases and their electron transport modules (Complex III and cytochrome c). Moreover, long-term exposure to 0.5-2.5 mgN/L hydroxylamine accelerated the functional transformation from denitrification to denitratation under low C/N conditions. However, genome-centric metagenomics indicated that a genotypic complete rather than truncated denitrifier Thauera aminoaromatica TJ127 was enriched and mainly responsible for acetate storage and nitrate reduction of the denitratation community. Interestingly, its enrichment resulted in nitrite production and reduction sequentially but reduced nitrate only to nitrite under carbon-limited conditions (C/N ≤ 3.0). Thus, it showed higher tolerance to hydroxylamine than the concurrent phenotype denitrifiers in activated sludge. Moreover, due to its higher anoxic storage capability in the feast phase, this enrichment became highly specialized by decreasing the feast/famine ratio, and thus a satisfactory denitratation performance was still maintained without hydroxylamine. These results suggested that the transient release of hydroxylamine from nitrification may interfere with subsequent denitrification metabolism, but its continuous accumulation is beneficial for achieving denitratation, which could steadily provide nitrite for mainstream anammox.
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Affiliation(s)
- Zhengzhe Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yu Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Zhijian Shi
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai 200438, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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Valk LC, Peces M, Singleton CM, Laursen MD, Andersen MH, Mielczarek AT, Nielsen PH. Exploring the microbial influence on seasonal nitrous oxide concentration in a full-scale wastewater treatment plant using metagenome assembled genomes. WATER RESEARCH 2022; 219:118563. [PMID: 35594748 DOI: 10.1016/j.watres.2022.118563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Nitrous oxide is a highly potent greenhouse gas and one of the main contributors to the greenhouse gas footprint of wastewater treatment plants (WWTP). Although nitrous oxide can be produced by abiotic reactions in these systems, biological N2O production resulting from the imbalance of nitrous oxide production and reduction by microbial populations is the dominant cause. The microbial populations responsible for the imbalance have not been clearly identified, yet they are likely responsible for strong seasonal nitrous oxide patterns. Here, we examined the seasonal nitrous oxide concentration pattern in Avedøre WWTP alongside abiotic parameters, the microbial community composition based on 16S rRNA gene sequencing and already available metagenome-assembled genomes (MAGs). We found that the WWTP parameters could not explain the observed pattern. While no distinct community changes between periods of high and low dissolved nitrous oxide concentrations were determined, we found 26 and 28 species with positive and negative correlations to the seasonal N2O concentrations, respectively. MAGs were identified for 124 species (approximately 31% mean relative abundance of the community), and analysis of their genomic nitrogen transformation potential could explain this correlation for four of the negatively correlated species. Other abundant species were also analysed for their nitrogen transformation potential. Interestingly, only one full-denitrifier (Candidatus Dechloromonas phosphorivorans) was identified. 59 species had a nosZ gene predicted, with the majority identified as a clade II nosZ gene, mainly from the phylum Bacteroidota. A correlation of MAG-derived functional guilds with the N2O concentration pattern showed that there was a small but significant negative correlation with nitrite oxidizing bacteria and species with a nosZ gene (N2O reducers (DEN)). More research is required, specifically long-term activity measurements in relation to the N2O concentration to increase the resolution of these findings.
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Affiliation(s)
- Laura Christina Valk
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Miriam Peces
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Caitlin Margaret Singleton
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Mads Dyring Laursen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | | | | | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark.
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Pessi IS, Viitamäki S, Virkkala AM, Eronen-Rasimus E, Delmont TO, Marushchak ME, Luoto M, Hultman J. In-depth characterization of denitrifier communities across different soil ecosystems in the tundra. ENVIRONMENTAL MICROBIOME 2022; 17:30. [PMID: 35690846 PMCID: PMC9188126 DOI: 10.1186/s40793-022-00424-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N2O). However, the microorganisms involved in the cycling of N2O in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of N2O, we aimed at investigating differences in community structure across different soil ecosystems in the tundra. RESULTS We analysed 1.4 Tb of metagenomic data from soils in northern Finland covering a range of ecosystems from dry upland soils to water-logged fens and obtained 796 manually binned and curated metagenome-assembled genomes (MAGs). We then searched for MAGs harbouring genes involved in denitrification, an important process driving N2O emissions. Communities of potential denitrifiers were dominated by microorganisms with truncated denitrification pathways (i.e., lacking one or more denitrification genes) and differed across soil ecosystems. Upland soils showed a strong N2O sink potential and were dominated by members of the Alphaproteobacteria such as Bradyrhizobium and Reyranella. Fens, which had in general net-zero N2O fluxes, had a high abundance of poorly characterized taxa affiliated with the Chloroflexota lineage Ellin6529 and the Acidobacteriota subdivision Gp23. CONCLUSIONS By coupling an in-depth characterization of microbial communities with in situ measurements of N2O fluxes, our results suggest that the observed spatial patterns of N2O fluxes in the tundra are related to differences in the composition of denitrifier communities.
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Affiliation(s)
- Igor S. Pessi
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS), Yliopistonkatu 3, 00014 Helsinki, Finland
| | - Sirja Viitamäki
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - Anna-Maria Virkkala
- Woodwell Climate Research Center, 149 Woods Hole Road, Falmouth, MA 02540-1644 USA
- Department of Geosciences and Geography, University of Helsinki, Gustaf Hällströmin katu 2, 00014 Helsinki, Finland
| | - Eeva Eronen-Rasimus
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
- Marine Research Centre, Finnish Environment Institute (SYKE), Agnes Sjöbergin katu 2, 00790 Helsinki, Finland
| | - Tom O. Delmont
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d’Evry, Université Paris-Saclay, 91057 Evry, France
| | - Maija E. Marushchak
- Department of Biological and Environmental Science, University of Jyväskylä, 40014 Jyväskylä, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Miska Luoto
- Department of Geosciences and Geography, University of Helsinki, Gustaf Hällströmin katu 2, 00014 Helsinki, Finland
| | - Jenni Hultman
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
- Helsinki Institute of Sustainability Science (HELSUS), Yliopistonkatu 3, 00014 Helsinki, Finland
- Natural Resources Institute Finland (LUKE), Latokartanonkaari 9, 00790 Helsinki, Finland
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Sun S, Bi X, Yang B, Zhang W, Zhang X, Sun S, Xiao J, Yang Y, Huang Z. Nitrite removal by Acinetobacter sp.TX: a candidate of curbing N 2O emission. ENVIRONMENTAL TECHNOLOGY 2022; 43:2300-2309. [PMID: 33427603 DOI: 10.1080/09593330.2021.1874543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/01/2021] [Indexed: 06/12/2023]
Abstract
The nitrite removal pathway in Acinetobacter sp. TX5 was explored through the key gene identification and the corresponding enzyme purification, after which the capability to reduce nitrite by immobilized beads was investigated in a fixed-bed reactor. Results revealed that a nosZ gene encoding nitrous oxide reductase (N2OR) exists in TX5 cells, and a N2OR responsible for the reduction of N2O to N2 was purified successfully with a molecular weight of 70.05 kDa, a purification fold of 16.30 and a recovery rate of 5.17%. For TX5 immobilization, the optimal values of polyvinyl alcohol (PVA), spent mushroom substrate (SMS) and Aci (TX5) obtained by response surface methodology (RSM) were 6.32%, 2.92% and 4.57%, respectively. In a fixed-bed reactor packed with immobilized TX5, the removal efficiency (RE) achieved 90% (at 50 h) for NO2--N and 85% (at 96 h) for total nitrogen (TN). On the basis of these results, a nitrite removal pathway in TX5 was proposed. Overall, Acinetobacter sp. TX5 might be a promising candidate for nitrite removal with an ability to suppress N2O accumulation.
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Affiliation(s)
- Shuqian Sun
- College of Life Science, Fujian Agriculture and Forestry University, Fuhzou, People's Republic of China
| | - Xiaohui Bi
- College of Life Science, Fujian Agriculture and Forestry University, Fuhzou, People's Republic of China
| | - Bin Yang
- College of Life Science, Fujian Agriculture and Forestry University, Fuhzou, People's Republic of China
| | - Weihong Zhang
- College of Life Science, Fujian Agriculture and Forestry University, Fuhzou, People's Republic of China
| | - Xinyu Zhang
- College of Life Science, Fujian Agriculture and Forestry University, Fuhzou, People's Republic of China
| | - Shujing Sun
- College of Life Science, Fujian Agriculture and Forestry University, Fuhzou, People's Republic of China
| | - Jibo Xiao
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People's Republic of China
- Wenzhou Chuangyuan Environment Technology Co. Ltd., Wenzhou, People's Republic of China
| | - Yunlong Yang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, People's Republic of China
| | - Zhida Huang
- Wenzhou Institute of Industry & Science, Wenzhou, People's Republic of China
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42
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Synergistic Inorganic Carbon and Denitrification Genes Contributed to Nitrite Accumulation in a Hydrogen-Based Membrane Biofilm Reactor. Bioengineering (Basel) 2022; 9:bioengineering9050222. [PMID: 35621500 PMCID: PMC9137978 DOI: 10.3390/bioengineering9050222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
Partial denitrification, the termination of NO3−-N reduction at nitrite (NO2−-N), has received growing interest for treating wastewaters with high ammonium concentrations, because it can be coupled to anammox for total-nitrogen removal. NO2− accumulation in the hydrogen (H2)-based membrane biofilm reactor (MBfR) has rarely been studied, and the mechanisms behind its accumulation have not been defined. This study aimed at achieving the partial denitrification with H2-based autotrophic reducing bacteria in a MBfR. Results showed that by increasing the NO3− loading, increasing the pH, and decreasing the inorganic-carbon concentration, a nitrite transformation rate higher than 68% was achieved. Community analysis indicated that Thauera and Azoarcus became the dominant genera when partial denitrification was occurring. Functional genes abundances proved that partial denitrification to accumulate NO2− was correlated to increases of gene for the form I RuBisCo enzyme (cbbL). This study confirmed the feasibility of autotrophic partial denitrification formed in the MBfR, and revealed the inorganic carbon mechanism in MBfR denitrification.
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43
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Vuong P, Moreira-Grez B, Wise MJ, Whiteley AS, Kumaresan D, Kaur P. From Rags to Enriched: Metagenomic Insights into Ammonia-oxidizing Archaea Following Ammonia Enrichment of a Denuded Oligotrophic Soil Ecosystem. Environ Microbiol 2022; 24:3097-3110. [PMID: 35384236 PMCID: PMC9545067 DOI: 10.1111/1462-2920.15994] [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: 11/26/2021] [Accepted: 03/28/2022] [Indexed: 11/29/2022]
Abstract
Stored topsoil acts as a microbial inoculant for ecological restoration of land after disturbance, but the altered circumstances frequently create unfavorable conditions for microbial survival. Nitrogen cycling is a critical indicator for ecological success and this study aimed to investigate the cornerstone taxa driving the process. Previous in-silico studies investigating stored topsoil discovered persistent archaeal taxa with the potential for re-establishing ecological activity. Ammonia oxidization is the limiting step in nitrification and as such, ammonia oxidizing archaea (AOA) can be considered as the one of the gatekeepers for the re-establishment of the nitrogen cycle in disturbed soils. Semi-arid soil samples were enriched with ammonium sulfate to promote the selective enrichment of ammonia oxidizers for targeted genomic recovery, and to investigate the microbial response of the microcosm to nitrogen input. Ammonia addition produced an increase in AOA population, particularly within the genus Candidatus Nitrosotalea, from which metagenome-assembled genomes (MAGs) were successfully recovered. The Ca. Nitrosotalea archaeon candidates' ability to survive in extreme conditions and rapidly respond to ammonia input makes it a potential bioprospecting target for application in ecological restoration of semi-arid soils and the recovered MAGs provide a metabolic blueprint for developing potential strategies towards isolation of these acclimated candidates. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Paton Vuong
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
| | - Benjamin Moreira-Grez
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
| | - Michael J Wise
- School of Physics, Mathematics and Computing, University of Western Australia, Perth, Australia.,The Marshall Centre of Infectious Diseases, School of Biological Sciences, The University of Western Australia, Perth, Australia
| | - Andrew S Whiteley
- Centre for Environment & Life Sciences, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Floreat, Australia
| | - Deepak Kumaresan
- School of Biological Sciences, Queen's University of Belfast, Belfast, UK
| | - Parwinder Kaur
- UWA School of Agriculture & Environment, University of Western Australia, Perth, Australia
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Jones CM, Putz M, Tiemann M, Hallin S. Reactive nitrogen restructures and weakens microbial controls of soil N2O emissions. Commun Biol 2022; 5:273. [PMID: 35347224 PMCID: PMC8960841 DOI: 10.1038/s42003-022-03211-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 03/02/2022] [Indexed: 12/20/2022] Open
Abstract
AbstractThe global surplus of reactive nitrogen (Nr) in agricultural soils is accelerating nitrous oxide (N2O) emission rates, and may also strongly influence the microbial controls of this greenhouse gas resulting in positive feedbacks that further exacerbate N2O emissions. Yet, the link between legacy effects of Nr on microbial communities and altered regulation of N2O emissions is unclear. By examining soils with legacies of Nr-addition from 14 field experiments with different edaphic backgrounds, we show that increased potential N2O production is associated with specific phylogenetic shifts in communities of frequently occurring soil microbes. Inputs of Nr increased the complexity of microbial co-association networks, and altered the relative importance of biotic and abiotic predictors of potential N2O emissions. Our results provide a link between the microbial legacy of Nr addition and increased N2O emissions by demonstrating that biological controls of N2O emissions were more important in unfertilized soils and that these controls are weakened by increasing resource levels in soil.
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45
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Gopalakrishnappa C, Gowda K, Prabhakara KH, Kuehn S. An ensemble approach to the structure-function problem in microbial communities. iScience 2022; 25:103761. [PMID: 35141504 PMCID: PMC8810406 DOI: 10.1016/j.isci.2022.103761] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The metabolic activity of microbial communities plays a primary role in the flow of essential nutrients throughout the biosphere. Molecular genetics has revealed the metabolic pathways that model organisms utilize to generate energy and biomass, but we understand little about how the metabolism of diverse, natural communities emerges from the collective action of its constituents. We propose that quantifying and mapping metabolic fluxes to sequencing measurements of genomic, taxonomic, or transcriptional variation across an ensemble of diverse communities, either in the laboratory or in the wild, can reveal low-dimensional descriptions of community structure that can explain or predict their emergent metabolic activity. We survey the types of communities for which this approach might be best suited, review the analytical techniques available for quantifying metabolite fluxes in communities, and discuss what types of data analysis approaches might be lucrative for learning the structure-function mapping in communities from these data.
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Affiliation(s)
| | - Karna Gowda
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA
| | - Kaumudi H. Prabhakara
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA
| | - Seppe Kuehn
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
- Center for the Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA
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46
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Zhuang JL, Sun X, Zhao WQ, Zhang X, Zhou JJ, Ni BJ, Liu YD, Shapleigh JP, Li W. The anammox coupled partial-denitrification process in an integrated granular sludge and fixed-biofilm reactor developed for mainstream wastewater treatment: Performance and community structure. WATER RESEARCH 2022; 210:117964. [PMID: 34959064 DOI: 10.1016/j.watres.2021.117964] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/29/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
This study describes an integrated granular sludge and fixed-biofilm (iGB) reactor innovatively designed to carry out the anammox/partial-denitrification (A/PD) process for nitrogen removal with mainstream municipal wastewater. The iGB-A/PD reactor consists of anammox granules inoculated in the lower region of reactor and an acclimated fixed-biofilm positioned in the upper region. Compared to the other reported A/PD systems for mainstream wastewater treatment, this iGB-A/PD reactor is notable due to its higher quality effluent with a total inorganic nitrogen (TIN) of ∼3 mg•L-1 and operation at a high nitrogen removal rate (NRR) of 0.8 ± 0.1 kg-N•m-3•d-1. Reads-based metatranscriptomic analysis found that the expression values of hzsA and hdh, key genes associated with anammox, were much higher than other functional genes on nitrogen conversion, confirming the major roles of the anammox bacteria in nitrogen bio-removal. In both regions of the reactor, the nitrate reduction genes (napA/narG) had expression values of 56-99 RPM, which were similar to that of the nitrite reduction genes (nirS/nirK). The expression reads from genes for dissimilatory nitrate reduction to ammonium (DNRA), nrfA and nirB, were unexpectedly high, and were over the half of the levels of reads from genes required for nitrate reduction. Kinetic assays confirmed that the granules had an anammox activity of 16.2 g-NH4+-N•kg-1-VSS•d-1 and a nitrate reduction activity of 4.1 g-N•kg-1-VSS•d-1. While these values were changed to be 4.9 g- NH4+-N•kg-1-VSS•d-1and 4.3 g-N•kg-1-VSS•d-1 respectively in the fixed-biofilm. Mass flux determination found that PD and DNRA was responsible for ∼50% and ∼25% of nitrate reduction, respectively, in the whole reactor, consistent with high effluent quality and treatment efficiency via a nitrite loop. Metagenomic binning analysis revealed that new and unidentified anammox species, affiliated with Candidatus Brocadia, were the dominant anammox organisms. Myxococcota and Planctomycetota were the principal organisms associated with the PD and DNRA processes, respectively.
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Affiliation(s)
- Jin-Long Zhuang
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Xu Sun
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Wei-Qi Zhao
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Xu Zhang
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Jia-Jia Zhou
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China
| | - Bing-Jie Ni
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, Australia
| | - Yong-Di Liu
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - James P Shapleigh
- Department of Microbiology, Cornell University, Ithaca, United States
| | - Wei Li
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, East China University of Science and Technology, Shanghai, China; State Environmental Protection Key Laboratory of Environmental Risk Assessment and Control on Chemical Process, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China; State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, China.
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47
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Genomic structure predicts metabolite dynamics in microbial communities. Cell 2022; 185:530-546.e25. [PMID: 35085485 DOI: 10.1016/j.cell.2021.12.036] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 07/16/2021] [Accepted: 12/21/2021] [Indexed: 12/21/2022]
Abstract
The metabolic activities of microbial communities play a defining role in the evolution and persistence of life on Earth, driving redox reactions that give rise to global biogeochemical cycles. Community metabolism emerges from a hierarchy of processes, including gene expression, ecological interactions, and environmental factors. In wild communities, gene content is correlated with environmental context, but predicting metabolite dynamics from genomes remains elusive. Here, we show, for the process of denitrification, that metabolite dynamics of a community are predictable from the genes each member of the community possesses. A simple linear regression reveals a sparse and generalizable mapping from gene content to metabolite dynamics for genomically diverse bacteria. A consumer-resource model correctly predicts community metabolite dynamics from single-strain phenotypes. Our results demonstrate that the conserved impacts of metabolic genes can predict community metabolite dynamics, enabling the prediction of metabolite dynamics from metagenomes, designing denitrifying communities, and discovering how genome evolution impacts metabolism.
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48
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Wei W, Hu X, Yang S, Wang K, Zeng C, Hou Z, Cui H, Liu S, Zhu L. Denitrifying halophilic archaea derived from salt dominate the degradation of nitrite in salted radish during pickling. Food Res Int 2022; 152:110906. [DOI: 10.1016/j.foodres.2021.110906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/27/2021] [Accepted: 12/13/2021] [Indexed: 11/04/2022]
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49
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Duffner C, Kublik S, Fösel B, Frostegård Å, Schloter M, Bakken L, Schulz S. Genotypic and phenotypic characterization of hydrogenotrophic denitrifiers. Environ Microbiol 2022; 24:1887-1901. [PMID: 35106904 DOI: 10.1111/1462-2920.15921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
Stimulating litho-autotrophic denitrification in aquifers with hydrogen is a promising strategy to remove excess NO3 - , but it often entails accumulation of the cytotoxic intermediate NO2 - and the greenhouse gas N2 O. To explore if these high NO2 - and N2 O concentrations are caused by differences in the genomic composition, the regulation of gene transcription or the kinetics of the reductases involved, we isolated hydrogenotrophic denitrifiers from a polluted aquifer, performed whole-genome sequencing and investigated their phenotypes. We therefore assessed the kinetics of NO2 - , NO, N2 O, N2 and O2 as they depleted O2 and transitioned to denitrification with NO3 - as the only electron acceptor and hydrogen as the electron donor. Isolates with a complete denitrification pathway, although differing intermediate accumulation, were closely related to Dechloromonas denitrificans, Ferribacterium limneticum or Hydrogenophaga taeniospiralis. High NO2 - accumulation was associated with the reductases' kinetics. While available, electrons only flowed towards NO3 - in the narG-containing H. taeniospiralis but flowed concurrently to all denitrification intermediates in the napA-containing D. denitrificans and F. limneticum. The denitrification regulator RegAB, present in the napA strains, may further secure low intermediate accumulation. High N2 O accumulation only occurred during the transition to denitrification and is thus likely caused by delayed N2 O reductase expression.
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Affiliation(s)
- Clara Duffner
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Bärbel Fösel
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Michael Schloter
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Lars Bakken
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
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50
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Frostegård Å, Vick SHW, Lim NYN, Bakken LR, Shapleigh JP. Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N 2O emissions and nitrite accumulation in soil. THE ISME JOURNAL 2022; 16:26-37. [PMID: 34211102 PMCID: PMC8692524 DOI: 10.1038/s41396-021-01045-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/07/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022]
Abstract
Soil pH is a key controller of denitrification. We analysed the metagenomics/transcriptomics and phenomics of two soils from a long-term liming experiment, SoilN (pH 6.8) and un-limed SoilA (pH 3.8). SoilA had severely delayed N2O reduction despite early transcription of nosZ (mainly clade I), encoding N2O reductase, by diverse denitrifiers. This shows that post-transcriptionally hampered maturation of the NosZ apo-protein at low pH is a generic phenomenon. Identification of transcript reads of several accessory genes in the nos cluster indicated that enzymes for NosZ maturation were present across a range of organisms, eliminating their absence as an explanation for the failure to produce a functional enzyme. nir transcript abundances (for NO2- reductase) in SoilA suggest that low NO2- concentrations in acidic soils, often ascribed to abiotic degradation, are primarily due to biological activity. The accumulation of NO2- in neutral soil was ascribed to high nar expression (nitrate reductase). The -omics results revealed dominance of nirK over nirS in both soils while qPCR showed the opposite, demonstrating that standard primer pairs only capture a fraction of the nirK pool. qnor encoding NO reductase was strongly expressed in SoilA, implying an important role in controlling NO. Production of HONO, for which some studies claim higher, others lower, emissions from NO2- accumulating soil, was estimated to be ten times higher from SoilA than from SoilN. The study extends our understanding of denitrification-driven gas emissions and the diversity of bacteria involved and demonstrates that gene and transcript quantifications cannot always reliably predict community phenotypes.
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Affiliation(s)
- Åsa Frostegård
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
| | - Silas H W Vick
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Natalie Y N Lim
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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