1
|
Zhang R, Qu Z, Yang W, Li J, Wang L, Liu Q, Zhang D, Qiao T, Zhao Y. Evaluating annual soil carbon emissions under biochar-added farmland subjecting from freeze-thaw cycle. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 365:121506. [PMID: 38901319 DOI: 10.1016/j.jenvman.2024.121506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/29/2024] [Accepted: 06/15/2024] [Indexed: 06/22/2024]
Abstract
Straw biochar is a commonly recognized agricultural amendment that can improve soil quality and reduce carbon emissions while sequestering soil carbon. However, the mechanisms underlying biochar's effects on annual soil carbon emissions in seasonally frozen soil areas and intrinsic drivers have not been clarified. Here, a 2-y field experiment was conducted to investigate the effects of different biochar dosages (0, 15, and 30, t ha-1; B0 (CK), B15, and B30, respectively) on carbon emissions (CO2 and CH4) microbial colony count, and soil-environment factors. The study period was the full annual cycle, including the freeze-thaw period (FTP) and the crop growth period (CP). Structural equation modeling (SEM) was developed to reveal the key drivers and potential mechanisms of biochar on carbon emissions. Biochar application reduced soil carbon emissions, with the reduction rate positively related to the biochar application rate (B30 best). During FTP, the reduction rate was 11.5% for CO2 and 48.2% for CH4. During CP, the reduction rate was 17.9% for CO2 and 34.5% for CH4. Overall, compared with CK, B30 treatment had a significant effect on reducing total soil carbon emissions (P < 0.05), with an average decrease of 16.7% during the two-year test period. The study also showed that for soils with continuous annual cycles (FTP and CP), carbon emissions were best observed from 10:00-13:00. After two years of freeze-thaw cycling, biochar continued to improve soil physical and chemical properties, thereby increasing soil microbial colony count. Compared with B0, the B30 treatment significantly increased the total colony count by 74.3% and 263.8% during FTP and CP (P < 0.05). Structural equation modeling (SEM) indicated that, with or without biochar application, the soil physicochemical properties directly or indirectly affected soil CO2 and CH4 emission fluxes through microbial colony count. The total effects of biochar application on CO2 emission fluxes were 0.50 (P < 0.05) and 0.64 (P < 0.01), respectively, but there was no significant effect on CH4 emission fluxes (P > 0.05). Among them, soil water content (SWC), soil temperature (ST) and soil organic carbon (SOC) were the main environmental determinants of CO2 emission fluxes during the FTP and CP. The total effects were 0.57, 0.65, and 0.53, respectively. For CH4, SWC, soil salinity (SS) and actinomycete colony count were the main environmental factors affecting its emission. The total effects were 0.50, 0.45, 0.44, respectively. For freeze-thaw alternating soils, the application of biochar is a feasible option for addressing climate change through soil carbon sequestration and greenhouse gas emissions mitigation. Soil water-heat-salt-fertilization and microbial communities are important for soil carbon emissions as the reaction matrix and main participants of soil carbon and nitrogen biochemical transformation.
Collapse
Affiliation(s)
- Ruxin Zhang
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Zhongyi Qu
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China; Autonomous Region Collaborative Innovation Center for Integrated Management of Water Resources and Water Environment in the Inner Mongolia Reaches of the Yellow River, Hohhot, 010018, China.
| | - Wei Yang
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, 010018, China; Autonomous Region Collaborative Innovation Center for Integrated Management of Water Resources and Water Environment in the Inner Mongolia Reaches of the Yellow River, Hohhot, 010018, China.
| | - Junjie Li
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Liping Wang
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China; Autonomous Region Collaborative Innovation Center for Integrated Management of Water Resources and Water Environment in the Inner Mongolia Reaches of the Yellow River, Hohhot, 010018, China
| | - Qi Liu
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Dongliang Zhang
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Tian Qiao
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yibo Zhao
- College of Water Conservancy and Civil Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| |
Collapse
|
2
|
Etiope G, Ciotoli G, Benà E, Mazzoli C, Röckmann T, Sivan M, Squartini A, Laemmel T, Szidat S, Haghipour N, Sassi R. Surprising concentrations of hydrogen and non-geological methane and carbon dioxide in the soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174890. [PMID: 39032737 DOI: 10.1016/j.scitotenv.2024.174890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 07/17/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
Due to its potential use as a carbon-free energy resource with minimal environmental and climate impacts, natural hydrogen (H2) produced by subsurface geochemical processes is today the target of intensive research. In H2 exploration practices, bacteria are thought to swiftly consume H2 and, therefore, small near-surface concentrations of H2, even orders of 102 ppmv in soils, are considered a signal of active migration of geological gas, potentially revealing underground resources. Here, we document an extraordinary case of a widespread occurrence of H2 (up to 1 vol%), together with elevated concentrations of CH4 and CO2 (up to 51 and 27 vol%, respectively), in aerated meadow soils along Italian Alps valleys. Based on current literature, this finding would be classified as a discovery of pervasive and massive geological H2 seepage. Nevertheless, an ensemble of gas geochemical and soil microbiological analyses, including bulk and clumped CH4 isotopes, radiocarbon of CH4 and CO2, and DNA and mcrA gene quantitative polymerase chain reaction analyses, revealed that H2 was only coupled to modern microbial gas. The H2-CO2-CH4-H2S association, wet soil proximity, and the absence of other geogenic gases in soils and springs suggest that H2 derives from near-surface fermentation, rather than geological degassing. H2 concentrations up to 1 vol% in soils are not conclusive evidence of deep gas seepage. This study provides a new reference for the potential of microbial H2, CH4 and CO2 in soils, to be considered in H2 exploration guidelines and soil carbon and greenhouse-gas cycle research.
Collapse
Affiliation(s)
- G Etiope
- Istituto Nazionale di Geofisica e Vulcanologia, Sezione Roma 2, Rome, Italy; Faculty of Environmental Science and Engineering, Babes-Bolyai University, Cluj-Napoca, Romania.
| | - G Ciotoli
- Istituto Nazionale di Geofisica e Vulcanologia, Sezione Roma 2, Rome, Italy; Consiglio Nazionale delle Ricerche, Istituto di Geologia Ambientale e Geoingegneria, Monterotondo, Italy
| | - E Benà
- Dipartimento di Geoscienze, Università di Padova, Padova, Italy
| | - C Mazzoli
- Dipartimento di Geoscienze, Università di Padova, Padova, Italy
| | - T Röckmann
- Institute for Marine and Atmospheric Research Utrecht, Utrecht University, the Netherlands
| | - M Sivan
- Institute for Marine and Atmospheric Research Utrecht, Utrecht University, the Netherlands
| | - A Squartini
- Department of Agronomy, Food, Natural Res., Animals and Environment, Università di Padova, Padova, Italy
| | - T Laemmel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences & Oeschger Center for Climate Change Research, University of Bern, Bern, Switzerland
| | - S Szidat
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences & Oeschger Center for Climate Change Research, University of Bern, Bern, Switzerland
| | - N Haghipour
- Geological Institute & Laboratory of Ion Beam Physics, ETHZ, Zurich, Switzerland
| | - R Sassi
- Dipartimento di Geoscienze, Università di Padova, Padova, Italy
| |
Collapse
|
3
|
Wang D, Candry P, Hunt KA, Flinkstrom Z, Shi Z, Liu Y, Wofford NQ, McInerney MJ, Tanner RS, De Leόn KB, Zhou J, Winkler MKH, Stahl DA, Pan C. Metaproteomics-informed stoichiometric modeling reveals the responses of wetland microbial communities to oxygen and sulfate exposure. NPJ Biofilms Microbiomes 2024; 10:55. [PMID: 38961111 PMCID: PMC11222425 DOI: 10.1038/s41522-024-00525-5] [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: 01/04/2024] [Accepted: 06/07/2024] [Indexed: 07/05/2024] Open
Abstract
Climate changes significantly impact greenhouse gas emissions from wetland soil. Specifically, wetland soil may be exposed to oxygen (O2) during droughts, or to sulfate (SO42-) as a result of sea level rise. How these stressors - separately and together - impact microbial food webs driving carbon cycling in the wetlands is still not understood. To investigate this, we integrated geochemical analysis, proteogenomics, and stoichiometric modeling to characterize the impact of elevated SO42- and O2 levels on microbial methane (CH4) and carbon dioxide (CO2) emissions. The results uncovered the adaptive responses of this community to changes in SO42- and O2 availability and identified altered microbial guilds and metabolic processes driving CH4 and CO2 emissions. Elevated SO42- reduced CH4 emissions, with hydrogenotrophic methanogenesis more suppressed than acetoclastic. Elevated O2 shifted the greenhouse gas emissions from CH4 to CO2. The metabolic effects of combined SO42- and O2 exposures on CH4 and CO2 emissions were similar to those of O2 exposure alone. The reduction in CH4 emission by increased SO42- and O2 was much greater than the concomitant increase in CO2 emission. Thus, greater SO42- and O2 exposure in wetlands is expected to reduce the aggregate warming effect of CH4 and CO2. Metaproteomics and stoichiometric modeling revealed a unique subnetwork involving carbon metabolism that converts lactate and SO42- to produce acetate, H2S, and CO2 when SO42- is elevated under oxic conditions. This study provides greater quantitative resolution of key metabolic processes necessary for the prediction of CH4 and CO2 emissions from wetlands under future climate scenarios.
Collapse
Affiliation(s)
- Dongyu Wang
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Pieter Candry
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Kristopher A Hunt
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Zachary Flinkstrom
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Zheng Shi
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Yunlong Liu
- School of Computer Science, University of Oklahoma, Norman, OK, USA
| | - Neil Q Wofford
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | | | - Ralph S Tanner
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Kara B De Leόn
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- School of Computer Science, University of Oklahoma, Norman, OK, USA
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Chongle Pan
- School of Biological Sciences, University of Oklahoma, Norman, OK, USA.
- School of Computer Science, University of Oklahoma, Norman, OK, USA.
| |
Collapse
|
4
|
Halim MA, Bieser JMH, Thomas SC. Large, sustained soil CO 2 efflux but rapid recovery of CH 4 oxidation in post-harvest and post-fire stands in a mixedwood boreal forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172666. [PMID: 38653415 DOI: 10.1016/j.scitotenv.2024.172666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
The net effect of forest disturbances, such as fires and harvesting, on soil greenhouse gas fluxes is determined by their impacts on both biological and physical factors, as well as the temporal dynamics of these effects post-disturbance. Although harvesting and fire may have distinct effects on soil carbon (C) dynamics, the temporal patterns in soil CO2 and CH4 fluxes and the potential differences between types of disturbances, remain poorly characterized in boreal forests. In this study, we measured soil CO2 and CH4 fluxes using a off-axis integrated cavity output spectroscopy system in snow-free seasons over two years in post-harvest and post-fire chronosequence sites within a mixedwood boreal forest in northwestern Ontario, Canada. Soil CO2 efflux showed a post-disturbance peak, with differing dynamics depending on the disturbance type: post-harvest stands exhibited a nearly tenfold increase (from ∼1 to ∼11 μmol CO2.m-2.s-1) from 1 to 9-10 years post-disturbance, followed by a steep decline; post-fire stands showed a more gradual increase, peaking at ∼6-7.2 μmol CO2.m-2.s-1 after ∼12-15 years. The youngest post-harvest stands were net sources of CH4,whereas post-fire stands were never net CH4 sources. In both disturbance types, the strength of the CH4 sink increased with stand age, approaching ∼2.4 nmol.m-2.s-1 by 15 years post-disturbance. Volumetric water content, bulk density, litter depth, and pH were significant predictors of CO2 fluxes; for CH4 fluxes, litter depth, pH, and the interaction of VWC and soil temperature were significant predictors in both disturbance types, with EC also showing a relationship in post-harvest stands. Our findings indicate that while soil CH4 oxidation rapidly recovers following disturbance, both post-harvest and post-fire stands show a multi-decade release of soil CO2 that is too large to be offset by C gains over this period.
Collapse
Affiliation(s)
- Md Abdul Halim
- Institute of Forestry and Conservation, University of Toronto, 33 Willcocks Street, M5S 3B3 Toronto, Canada; Department of Forestry and Environmental Science, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.
| | - Jillian M H Bieser
- Institute of Forestry and Conservation, University of Toronto, 33 Willcocks Street, M5S 3B3 Toronto, Canada
| | - Sean C Thomas
- Institute of Forestry and Conservation, University of Toronto, 33 Willcocks Street, M5S 3B3 Toronto, Canada
| |
Collapse
|
5
|
Wu Y, Gao J, Li M, Xie F, Li W, Wu X, Gao Q, Zhang Y. Sensitive Detection of OCS Using Thermal Conversion Combined with Spectral Reconstruction Filtering Differential Optical Absorption Spectroscopy. Anal Chem 2024; 96:8696-8704. [PMID: 38751030 DOI: 10.1021/acs.analchem.4c00943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Carbonyl sulfide (OCS) is a toxic gas produced during industrial processes that poses risks to both human health and industrial equipment. Therefore, detecting OCS concentrations plays a crucial role in early hazard warning. This paper presents an online system for detecting OCS at the ppb level using thermal conversion and spectral reconstruction filtering differential optical absorption spectroscopy (SRF-DOAS). First, OCS, which is not suitable for DOAS due to its weak absorption characteristics, is completely transformed into SO2 with strong absorption characteristics under high-temperature conditions. Then, the spectral reconstruction filtering method (SRF) is proposed to eliminate the noise and interference. The core idea of the method is to arrange the spectrum according to the spectral intensity from small to large rather than wavelength, reconstructing the spectrum into a new spectrum with linear characteristics. The reconstructed spectrum can remove noise and interference by linear fitting and retain the characteristic of SO2 oscillation absorption. Next, we demonstrate the ability of the reconstructed spectral method to remove noise and interference by comparing the spectra of the inverse-reconstructed gas mixture and SO2. The relative deviation of 0.88% at 100 ppb and detection limit of 7.26 ppb*m for OCS were obtained using the SRF-DOAS method. Finally, the reliability of the system was confirmed by measurements of OCS concentrations in mixture gas of OCS and air, as well as in human exhaled breath.
Collapse
Affiliation(s)
- Yongqi Wu
- School of Electrical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Jie Gao
- School of Electrical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Mu Li
- School of Electrical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Fei Xie
- School of Electrical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Wenbo Li
- School of Electrical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Xijun Wu
- School of Electrical Engineering, Yanshan University, Qinhuangdao 066004, China
| | - Qiang Gao
- State Key Laboratory of Engines, School of Tianjin University, Tianjin 300072, China
| | - Yungang Zhang
- School of Electrical Engineering, Yanshan University, Qinhuangdao 066004, China
| |
Collapse
|
6
|
Pereira-Mora L, Guerrero LD, Erijman L, Fernández-Scavino A. Tartrate fermentation with H 2 production by a new member of Sporomusaceae enriched from rice paddy soil. Appl Environ Microbiol 2024; 90:e0235123. [PMID: 38517167 PMCID: PMC11026083 DOI: 10.1128/aem.02351-23] [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: 01/22/2024] [Accepted: 03/03/2024] [Indexed: 03/23/2024] Open
Abstract
In rice paddies, soil and plant-derived organic matter are degraded anaerobically to methane (CH4), a powerful greenhouse gas. The highest rate of methane emission occurs during the reproductive stage of the plant when mostly dicarboxylic acids are exudated by the roots. The emission of methane at this stage depends largely on the cooperative interaction between dicarboxylic acid-fermenting bacteria and methanogenic archaea in the rhizosphere. The fermentation of tartrate, one of the major acids exudated, has been scarcely explored in rice paddy soils. In this work, we characterized an anaerobic consortium from rice paddy soil composed of four bacterial strains, whose principal member (LT8) can ferment tartrate, producing H2 and acetate. Tartrate fermentation was accelerated by co-inoculation with a hydrogenotrophic methanogen. The assembled genome of LT8 possesses a Na+-dependent oxaloacetate decarboxylase and shows that this bacterium likely invests part of the H2 produced to reduce NAD(P)+ to assimilate C from tartrate. The phylogenetic analysis of the 16S rRNA gene, the genome-based classification as well as the average amino acid identity (AAI) indicated that LT8 belongs to a new genus within the Sporomusaceae family. LT8 shares a few common features with its closest relatives, for which tartrate degradation has not been described. LT8 is limited to a few environments but is more common in rice paddy soils, where it might contribute to methane emissions from root exudates.IMPORTANCEThis is the first report of the metabolic characterization of a new anaerobic bacterium able to degrade tartrate, a compound frequently associated with plants, but rare as a microbial metabolite. Tartrate fermentation by this bacterium can be coupled to methanogenesis in the rice rhizosphere where tartrate is mainly produced at the reproductive stage of the plant, when the maximum methane rate emission occurs. The interaction between secondary fermentative bacteria, such as LT8, and methanogens could represent a fundamental step in exploring mitigation strategies for methane emissions from rice fields. Possible strategies could include controlling the activity of these secondary fermentative bacteria or selecting plants whose exudates are more difficult to ferment.
Collapse
Affiliation(s)
- Luciana Pereira-Mora
- Laboratorio de Ecología Microbiana y Microbiología Ambiental, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Graduate Program in Chemistry, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Unidad Asociada de Microbiología del Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Leandro D. Guerrero
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres” (INGEBI-CONICET), Buenos Aires, Argentina
| | - Leonardo Erijman
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres” (INGEBI-CONICET), Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ana Fernández-Scavino
- Laboratorio de Ecología Microbiana y Microbiología Ambiental, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| |
Collapse
|
7
|
Gios E, Verbruggen E, Audet J, Burns R, Butterbach-Bahl K, Espenberg M, Fritz C, Glatzel S, Jurasinski G, Larmola T, Mander Ü, Nielsen C, Rodriguez AF, Scheer C, Zak D, Silvennoinen HM. Unraveling microbial processes involved in carbon and nitrogen cycling and greenhouse gas emissions in rewetted peatlands by molecular biology. BIOGEOCHEMISTRY 2024; 167:609-629. [PMID: 38707517 PMCID: PMC11068585 DOI: 10.1007/s10533-024-01122-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 01/22/2024] [Indexed: 05/07/2024]
Abstract
Restoration of drained peatlands through rewetting has recently emerged as a prevailing strategy to mitigate excessive greenhouse gas emissions and re-establish the vital carbon sequestration capacity of peatlands. Rewetting can help to restore vegetation communities and biodiversity, while still allowing for extensive agricultural management such as paludiculture. Belowground processes governing carbon fluxes and greenhouse gas dynamics are mediated by a complex network of microbial communities and processes. Our understanding of this complexity and its multi-factorial controls in rewetted peatlands is limited. Here, we summarize the research regarding the role of soil microbial communities and functions in driving carbon and nutrient cycling in rewetted peatlands including the use of molecular biology techniques in understanding biogeochemical processes linked to greenhouse gas fluxes. We emphasize that rapidly advancing molecular biology approaches, such as high-throughput sequencing, are powerful tools helping to elucidate the dynamics of key biogeochemical processes when combined with isotope tracing and greenhouse gas measuring techniques. Insights gained from the gathered studies can help inform efficient monitoring practices for rewetted peatlands and the development of climate-smart restoration and management strategies. Supplementary Information The online version contains supplementary material available at 10.1007/s10533-024-01122-6.
Collapse
Affiliation(s)
- Emilie Gios
- NINA, Norwegian Institute for Nature Research, PO Box 5685, Torgarden, NO-7485 Trondheim, Norway
| | - Erik Verbruggen
- Plants and Ecosystems Research Group, Department of Biology, University of Antwerp, Universiteitsplein 1, Wilrijk, 2610 Antwerp, Belgium
| | - Joachim Audet
- Department of Ecoscience, Aarhus University, C.F. Møllers Allé, 8000 Aarhus, Denmark
| | - Rachel Burns
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Klaus Butterbach-Bahl
- Institute of Meteorology and Climate Research, Atmospheric Environmental Research, Karlsruhe Institute of Technology, 82467 Garmisch-Partenkirchen, Germany
- Department of Agroecology, Pioneer Center for Research in Sustainable Agricultural Futures (Land-CRAFT), Aarhus University, 8000 Aarhus, Denmark
| | - Mikk Espenberg
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 St., Vanemuise, 51003 Tartu, Estonia
| | - Christian Fritz
- Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Stephan Glatzel
- Department of Geography and Regional Research, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Gerald Jurasinski
- Faculty of Agriculture and Environment, Landscape Ecology and Site Evaluation, University of Rostock, Justus-von-Liebig-Weg 6, 18059 Rostock, Germany
- Department of Maritime Systems, Faculty of Interdisciplinary Research, University of Rostock, Albert- Einstein-Straße 3, 18059 Rostock, Germany
| | - Tuula Larmola
- Natural Resources Institute Finland (Luke), 00790 Helsinki, Finland
| | - Ülo Mander
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, 46 St., Vanemuise, 51003 Tartu, Estonia
| | - Claudia Nielsen
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Blichers Alle 20, 8830 Tjele, Denmark
- CBIO, Centre for Circular Bioeconomy, Aarhus University, 8830 Tjele, Denmark
| | - Andres F. Rodriguez
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Blichers Alle 20, 8830 Tjele, Denmark
| | - Clemens Scheer
- Institute of Meteorology and Climate Research, Atmospheric Environmental Research, Karlsruhe Institute of Technology, 82467 Garmisch-Partenkirchen, Germany
| | - Dominik Zak
- Department of Ecoscience, Aarhus University, C.F. Møllers Allé, 8000 Aarhus, Denmark
- Department of Ecohydrology and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, Germany
| | - Hanna M. Silvennoinen
- NINA, Norwegian Institute for Nature Research, PO Box 5685, Torgarden, NO-7485 Trondheim, Norway
| |
Collapse
|
8
|
Wei W, Shi X, Wang M, Zhou Z. Manure application maintained the CO 2 fixation activity of soil autotrophic bacteria but changed its ecological characteristics in an entisol of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169630. [PMID: 38154636 DOI: 10.1016/j.scitotenv.2023.169630] [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: 11/14/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023]
Abstract
The response of soil autotrophs to anthropogenic activities has attracted increasing attention against the background of global change. Here, three entisol plots under different fertilizing regimes, including no fertilization (CK), manure (M), and a combined application of chemical fertilizer and manure (NPKM) were selected, and then the soil RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) activity and cbbl (gene encoding the large subunit of RubisCO) composition were measured to indicate the activity and community of autotrophic bacteria, respectively. The results revealed that the RubisCO activity of CK showed no difference from that of M but was significantly higher than that of NPKM. The CK and M had the lowest and highest soil cbbl abundance, respectively. The α-diversity of soil cbbl-carrying bacteria showed no significant difference among these treatments, whereas they showed significantly different community structures of cbbl-carrying bacteria. Meanwhile, compared with CK, M had significantly lower abundances of bacterial species with the functions of nitrogen fixation (Azoarcus sp.KH32C) or detoxification (Methylibium petroleiphilum), indicating that manure application might have an inhibiting potential to some beneficial autotrophic bacterial species in this entisol.
Collapse
Affiliation(s)
- Wanling Wei
- College of Resources and Environment, Southwest University, Chongqing 400715, China; Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing 400715, China; The National Monitoring Base for Purple Soil Fertility and Fertilizer Efficiency, Southwest University, Chongqing 400715, China
| | - Mingxia Wang
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Zhifeng Zhou
- College of Resources and Environment, Southwest University, Chongqing 400715, China.
| |
Collapse
|
9
|
Yao X, Wang J, He M, Liu Z, Zhao Y, Li Y, Chi T, Zhu L, Zheng P, Jetten MSM, Hu B. Methane-dependent complete denitrification by a single Methylomirabilis bacterium. Nat Microbiol 2024; 9:464-476. [PMID: 38228857 DOI: 10.1038/s41564-023-01578-6] [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: 04/25/2023] [Accepted: 12/08/2023] [Indexed: 01/18/2024]
Abstract
Methane-dependent nitrate and nitrite removal in anoxic environments is thought to rely on syntrophy between ANME-2d archaea and bacteria in the genus 'Candidatus Methylomirabilis'. Here we enriched and purified a single Methylomirabilis from paddy soil fed with nitrate and methane, which is capable of coupling methane oxidation to nitrate reduction via nitrite to dinitrogen independently. Isotope labelling showed that this bacterium we name 'Ca. Methylomirabilis sinica' stoichiometrically performed methane-dependent complete nitrate reduction to dinitrogen gas. Multi-omics analyses collectively demonstrated that 'M. sinica' actively expressed a well-established pathway for this process, especially including nitrate reductase Nap. Furthermore, 'M. sinica' exhibited a higher nitrate affinity than most denitrifiers, implying its competitive fitness under oligotrophic nitrogen-limited conditions. Our findings revise the paradigm of methane-dependent denitrification performed by two organisms, and the widespread presence of 'M. sinica' in public databases suggests that the coupling of methane oxidation and complete denitrification in single cells substantially contributes to global methane and nitrogen budgets.
Collapse
Affiliation(s)
- Xiangwu Yao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Mingyue He
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Zishu Liu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yuxiang Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Yufen Li
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Taolve Chi
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Lin Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Baolan Hu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, China.
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China.
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
| |
Collapse
|
10
|
Garvin ZK, Abades SR, Trefault N, Alfaro FD, Sipes K, Lloyd KG, Onstott TC. Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert. THE ISME JOURNAL 2024; 18:wrae062. [PMID: 38625060 PMCID: PMC11094475 DOI: 10.1093/ismejo/wrae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/29/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
High-elevation arid regions harbor microbial communities reliant on metabolic niches and flexibility to survive under biologically stressful conditions, including nutrient limitation that necessitates the utilization of atmospheric trace gases as electron donors. Geothermal springs present "oases" of microbial activity, diversity, and abundance by delivering water and substrates, including reduced gases. However, it is unknown whether these springs exhibit a gradient of effects, increasing their impact on trace gas-oxidizers in the surrounding soils. We assessed whether proximity to Polloquere, a high-altitude geothermal spring in an Andean salt flat, alters the diversity and metabolic structure of nearby soil bacterial populations compared to the surrounding cold desert. Recovered DNA and metagenomic analyses indicate that the spring represents an oasis for microbes in this challenging environment, supporting greater biomass with more diverse metabolic functions in proximal soils that declines sharply with radial distance from the spring. Despite the sharp decrease in biomass, potential rates of atmospheric hydrogen (H2) and carbon monoxide (CO) uptake increase away from the spring. Kinetic estimates suggest this activity is due to high-affinity trace gas consumption, likely as a survival strategy for energy/carbon acquisition. These results demonstrate that Polloquere regulates a gradient of diverse microbial communities and metabolisms, culminating in increased activity of trace gas-oxidizers as the influence of the spring yields to that of the regional salt flat environment. This suggests the spring holds local importance within the context of the broader salt flat and potentially represents a model ecosystem for other geothermal systems in high-altitude desert environments.
Collapse
Affiliation(s)
- Zachary K Garvin
- Department of Geosciences, Princeton University, Princeton, NJ 08544, United States
| | - Sebastián R Abades
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, 8580745, Santiago, Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, 8580745, Santiago, Chile
| | - Fernando D Alfaro
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, 8580745, Santiago, Chile
| | - Katie Sipes
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
- Department of Environmental Science, Aarhus University, 4000, Roskilde, Denmark
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ 08544, United States
| |
Collapse
|
11
|
Kitz F, Wachter H, Spielmann F, Hammerle A, Wohlfahrt G. Root and rhizosphere contribution to the net soil COS exchange. PLANT AND SOIL 2023; 498:325-339. [PMID: 38665878 PMCID: PMC11039419 DOI: 10.1007/s11104-023-06438-0] [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: 06/20/2023] [Accepted: 12/02/2023] [Indexed: 04/28/2024]
Abstract
Background and aims Partitioning the measured net ecosystem carbon dioxide (CO2) exchange into gross primary productivity (GPP) and ecosystem respiration remains a challenge, which scientists try to tackle by using the properties of the trace gas carbonyl sulfide (COS). Its similar pathway into and within the leaf makes it a potential photosynthesis proxy. The application of COS as an effective proxy depends, among other things, on a robust inventory of potential COS sinks and sources within ecosystems. While the soil received some attention during the last couple of years, the role of plant roots is mostly unknown. In our study, we investigated the effects of live roots on the soil COS exchange. Methods An experimental setup was devised to measure the soil and the belowground plant parts of young beech trees observed over the course of 9 months. Results During the growing season, COS emissions were significantly lower when roots were present compared to chambers only containing soil, while prior to the growing season, with photosynthetically inactive trees, the presence of roots increased COS emissions. The difference in the COS flux between root-influenced and uninfluenced soil was fairly constant within each month, with diurnal variations in the COS flux driven primarily by soil temperature changes rather than the presence or absence of roots. Conclusion While the mechanisms by which roots influence the COS exchange are largely unknown, their contribution to the overall ground surface COS exchange should not be neglected when quantifying the soil COS exchange. Supplementary Information The online version contains supplementary material available at 10.1007/s11104-023-06438-0.
Collapse
Affiliation(s)
- Florian Kitz
- Universität Innsbruck, Institut für Ökologie, Sternwartestraße 15, Innsbruck, 6020 Austria
| | - Herbert Wachter
- Universität Innsbruck, Institut für Ökologie, Sternwartestraße 15, Innsbruck, 6020 Austria
| | - Felix Spielmann
- Universität Innsbruck, Institut für Ökologie, Sternwartestraße 15, Innsbruck, 6020 Austria
| | - Albin Hammerle
- Universität Innsbruck, Institut für Ökologie, Sternwartestraße 15, Innsbruck, 6020 Austria
| | - Georg Wohlfahrt
- Universität Innsbruck, Institut für Ökologie, Sternwartestraße 15, Innsbruck, 6020 Austria
| |
Collapse
|
12
|
Liang K, Qi J, Zhang X, Emmett B, Johnson JMF, Malone RW, Moglen GE, Venterea RT. Simulated nitrous oxide emissions from multiple agroecosystems in the U.S. Corn Belt using the modified SWAT-C model. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 337:122537. [PMID: 37709120 DOI: 10.1016/j.envpol.2023.122537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/19/2023] [Accepted: 09/08/2023] [Indexed: 09/16/2023]
Abstract
Agriculture is a major source of nitrous oxide (N2O) emissions into the atmosphere. However, assessing the impacts of agricultural conservation practices, land use change, and climate adaptation measures on N2O emissions at a large scale is a challenge for process-based model applications. Here, we integrated six N2O emission algorithms for the nitrification processes and seven N2O emission algorithms for the denitrification process into the Soil and Water Assessment Tool-Carbon (SWAT-C). We evaluated the different combinations of methods in simulating N2O emissions under corn (Zea mays L.) production systems with various conservation practices, including fertilization, tillage, and crop rotation (represented by 14 experimental treatments and 83 treatment-years) at five experimental sites across the U.S. Midwest. The SWAT-C model exhibited wide variability in simulating daily average N2O emissions across treatment-years with different method configurations, as indicated by the ranges of R2, NSE, and BIAS (0.04-0.68, -1.78-0.60, and -0.94-0.001, respectively). Our results indicate that the denitrification process has a stronger impact on N2O emissions than the nitrification process. The best performing N2O emission algorithms are those rooted in the CENTURY model, which considers soil pH and respiration effects that were overlooked by other algorithms. The optimal N2O emission algorithm explained about 63% of the variability of annual average N2O emissions, with NSE and BIAS of 0.60 and -0.033, respectively. The model can reasonably represent the impacts of agricultural conservation practices on N2O emissions. We anticipate that the improved SWAT-C model, with its flexible configurations and robust modeling and assessment capabilities, will provide a valuable tool for studying and managing N2O emissions from agroecosystems.
Collapse
Affiliation(s)
- Kang Liang
- Earth System Science Interdisciplinary Center, University of Maryland, College Park, MD, 20740, USA
| | - Junyu Qi
- Earth System Science Interdisciplinary Center, University of Maryland, College Park, MD, 20740, USA
| | - Xuesong Zhang
- USDA-ARS Hydrology and Remote Sensing Laboratory, Beltsville, MD, 20705, USA.
| | - Bryan Emmett
- USDA-ARS National Laboratory for Agriculture and the Environment, Ames, IA, 50011, USA
| | - Jane M F Johnson
- USDA-ARS North Central Soil Conservation Research Laboratory, Morris, MN, 56267, USA
| | - Robert W Malone
- USDA-ARS National Laboratory for Agriculture and the Environment, Ames, IA, 50011, USA
| | - Glenn E Moglen
- USDA-ARS Hydrology and Remote Sensing Laboratory, Beltsville, MD, 20705, USA
| | - Rodney T Venterea
- USDA-ARS, Soil and Water Management Unit, St. Paul, MN, 55108, USA; Department of Soil, Water and Climate, University of Minnesota-Twin Cities, St. Paul, MN, 55108, USA
| |
Collapse
|
13
|
Ma LC, Zhao HQ, Wu LB, Cheng ZL, Liu C. Impact of the microbiome on human, animal, and environmental health from a One Health perspective. SCIENCE IN ONE HEALTH 2023; 2:100037. [PMID: 39077043 PMCID: PMC11262275 DOI: 10.1016/j.soh.2023.100037] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 08/21/2023] [Indexed: 07/31/2024]
Abstract
The microbiome encompasses the genomes of the microorganisms that inhabit specific environments. One Health is an emerging concept, recognised as a cohesive, harmonising approach aimed at sustainably improving the well-being of humans, animals, and the environment. The microbiome plays a crucial role in the One Health domain, facilitating interactions among humans, animals, and the environment, along with co-evolution, co-development, co-metabolism, and co-regulation with their associated humans and animals. In addition, the microbiome regulates environmental health through interactions with plant microbiota, which actively participate in substance cycling (particularly the carbon and nitrogen cycles) and influence the overall energy flow in the biosphere. Moreover, antibiotic resistance genes present in microbiota can lead to widespread drug resistance in both humans and animals. This review explores the impact of the microbiome on humans, animals, and the environment, highlighting the significance of focusing on this field in One Health research.
Collapse
Affiliation(s)
- Ling-chao Ma
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- One Health Centre, Shanghai Jiao Tong University and the University of Edinburgh, Shanghai, China
| | - Han-qing Zhao
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- One Health Centre, Shanghai Jiao Tong University and the University of Edinburgh, Shanghai, China
| | - Logan Blair Wu
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- One Health Centre, Shanghai Jiao Tong University and the University of Edinburgh, Shanghai, China
- Population Health & Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Zi-le Cheng
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- One Health Centre, Shanghai Jiao Tong University and the University of Edinburgh, Shanghai, China
| | - Chang Liu
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
14
|
Silva TM, Waked D, Bastos AC, Gomes GL, Veras Closs JG, Tonin FG, Rossignolo JA, do Valle Marques K, Veras MM. A custom, low-cost, continuous flow chamber built for experimental Sargassum seaweed decomposition and exposure of small rodents to generated gaseous products. Heliyon 2023; 9:e18787. [PMID: 37636446 PMCID: PMC10448417 DOI: 10.1016/j.heliyon.2023.e18787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/29/2023] Open
Abstract
Since 2011, Sargassum events have increased in frequency along the Caribbean and Atlantic coasts. The accumulation and decomposition of large amounts of Sargassum seaweed on beaches pose socio-economic, ecological, and health risks due to the emission of hydrogen sulfide (H2S), methane, and ammonia. However, limited research exists on the emission processes and the health effects of subchronic and chronic exposure to low levels of H2S. Additionally, the absence of emission factor data for Sargassum decomposition on-site makes health risk assessments challenging. This study aimed to create a custom chamber to simulate real-world Sargassum decomposition, exposing experimental animals to the generated gases. Metal content was analyzed, and emission rates were estimated in a controlled environment. The decomposition-exposure system replicated reported environmental gas emissions from the Caribbean region, except for NH3. H2S bursts were observed during the decomposition process at intervals of 2-10 days, with higher frequency associated with larger masses of decomposing Sargassum. The decomposed gas was transferred to the exposure chamber, resulting in an 80-87% reduction in H2S concentration. The maximum H2S emission was 156 ppm, with a concentration ranging from 50.4 to 56.5 ppm. An estimated emission rate of 7-8 g/h for H2S was observed, and significant levels of lead, arsenic, and aluminum were found in beached Sargassum from the northeast coast of Brazil. This study's developed model provides an opportunity to investigate the effects and risks to human health associated with exposure to gases produced during the environmental decomposition of Sargassum seaweed.
Collapse
Affiliation(s)
- Thamires Moraes Silva
- Laboratório de Patologia Ambiental e Experimental (LIM05- LPAE), Hospital Das Clínicas Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Dunia Waked
- Laboratório de Patologia Ambiental e Experimental (LIM05- LPAE), Hospital Das Clínicas Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Ana Clara Bastos
- Laboratório de Patologia Ambiental e Experimental (LIM05- LPAE), Hospital Das Clínicas Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Gabriel Leandro Gomes
- Laboratório de Patologia Ambiental e Experimental (LIM05- LPAE), Hospital Das Clínicas Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - José Guilherme Veras Closs
- Laboratório de Patologia Ambiental e Experimental (LIM05- LPAE), Hospital Das Clínicas Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Fernando Gustavo Tonin
- Department of Biosystems Engineering, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Brazil
| | - João Adriano Rossignolo
- Department of Biosystems Engineering, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Brazil
| | | | - Mariana Matera Veras
- Laboratório de Patologia Ambiental e Experimental (LIM05- LPAE), Hospital Das Clínicas Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
Inayat A, Rocha-Meneses L, Ayoub M, Ullah S, Abdullah AZ, Naqvi SR, Bhat AH. Influence of Co 3O 4-based catalysts on N 2O catalytic decomposition and NO conversion. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27371-w. [PMID: 37170050 DOI: 10.1007/s11356-023-27371-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/27/2023] [Indexed: 05/13/2023]
Abstract
This study investigated the effect of different Co3O4-based catalysts on the catalytic decomposition of nitrous oxide (N2O) and on nitric oxide (NO) conversion. The experiments were carried out using various reaction temperatures, alkaline solutions, pH, mixing conditions, aging times, space velocities, impregnation loads, and compounds. The results showed that Co3O4 catalysts prepared by precipitation methods have the highest catalytic activity and N2O conversion, even at low reaction temperatures, while the commercial nano and powder forms of Co3O4 (CS) have the lowest performance. The catalysts become inactive at temperatures below 400 °C, and their activity is strongly influenced by the mixing temperature. Samples without stirring during the aging process have higher catalytic activity than those with stirring, even at low reaction temperatures (200-300 °C). The catalytic activity of Co3O4 PM1 decreases with low W/F values and low reaction temperatures. Additionally, the catalyst's performance tends to increase with the reduction process. The study suggests that cobalt-oxide-based catalysts are effective in N2O catalytic decomposition and NO conversion. The findings may be useful in the design and optimization of catalytic systems for N2O and NO control. The results obtained provide important insights into the development of highly efficient, low-cost, and sustainable catalysts for environmental protection.
Collapse
Affiliation(s)
- Abrar Inayat
- Department of Sustainable and Renewable Energy Engineering, University of Sharjah, 27272, Sharjah, United Arab Emirates
- Biomass & Bioenergy Research Group, Center for Sustainable Energy and Power Systems Research, Research Institute of Sciences and Engineering, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Lisandra Rocha-Meneses
- Technology Innovation Institute, Renewable and Sustainable Energy Research Center, Masdar City, P.O. Box: 9639, Abu Dhabi, United Arab Emirates.
| | - Muhammad Ayoub
- Department of Chemical Engineering, Universiti Teknologi PETRONAS, 32610, Perak, Malaysia
| | - Sami Ullah
- Department of Chemistry, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
| | - Ahmad Z Abdullah
- School of Chemical Engineering, Universiti Sains Malaysia, 14300, Pinang, Malaysia
| | - Salman R Naqvi
- School of Chemical and Materials Engineering, National University of Science and Technology, Islamabad, Pakistan
| | - Aamir H Bhat
- Department of Fundamental and Applied Sciences, Universiti Teknologi PETRONAS, 32610, Perak, Malaysia
| |
Collapse
|
17
|
Schoelmerich MC. Aerobic marine bacteria can use H 2 for growth. Trends Microbiol 2023; 31:554-555. [PMID: 37055295 DOI: 10.1016/j.tim.2023.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/15/2023]
Abstract
Molecular hydrogen (H2) and carbon monoxide (CO) are ubiquitously available in the Earth's oceans, yet their low dissolved concentrations seemed unlikely to support microbial growth. Lappan, Shelley, Islam et al. now report that dissolved H2 supports the growth of diverse aerobic marine bacteria in the oceans.
Collapse
|
18
|
Anthony TL, Szutu DJ, Verfaillie JG, Baldocchi DD, Silver WL. Carbon-sink potential of continuous alfalfa agriculture lowered by short-term nitrous oxide emission events. Nat Commun 2023; 14:1926. [PMID: 37024458 PMCID: PMC10079834 DOI: 10.1038/s41467-023-37391-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 03/15/2023] [Indexed: 04/08/2023] Open
Abstract
Alfalfa is the most widely grown forage crop worldwide and is thought to be a significant carbon sink due to high productivity, extensive root systems, and nitrogen-fixation. However, these conditions may increase nitrous oxide (N2O) emissions thus lowering the climate change mitigation potential. We used a suite of long-term automated instrumentation and satellite imagery to quantify patterns and drivers of greenhouse gas fluxes in a continuous alfalfa agroecosystem in California. We show that this continuous alfalfa system was a large N2O source (624 ± 28 mg N2O m2 y-1), offsetting the ecosystem carbon (carbon dioxide (CO2) and methane (CH4)) sink by up to 14% annually. Short-term N2O emissions events (i.e., hot moments) accounted for ≤1% of measurements but up to 57% of annual emissions. Seasonal and daily trends in rainfall and irrigation were the primary drivers of hot moments of N2O emissions. Significant coherence between satellite-derived photosynthetic activity and N2O fluxes suggested plant activity was an important driver of background emissions. Combined data show annual N2O emissions can significantly lower the carbon-sink potential of continuous alfalfa agriculture.
Collapse
Affiliation(s)
- Tyler L Anthony
- Ecosystem Science Division, Department of Environmental Science, Policy and Management, University of California at Berkeley, 130 Mulford Hall, Berkeley, CA, 94720, USA.
| | - Daphne J Szutu
- Ecosystem Science Division, Department of Environmental Science, Policy and Management, University of California at Berkeley, 130 Mulford Hall, Berkeley, CA, 94720, USA
| | - Joseph G Verfaillie
- Ecosystem Science Division, Department of Environmental Science, Policy and Management, University of California at Berkeley, 130 Mulford Hall, Berkeley, CA, 94720, USA
| | - Dennis D Baldocchi
- Ecosystem Science Division, Department of Environmental Science, Policy and Management, University of California at Berkeley, 130 Mulford Hall, Berkeley, CA, 94720, USA
| | - Whendee L Silver
- Ecosystem Science Division, Department of Environmental Science, Policy and Management, University of California at Berkeley, 130 Mulford Hall, Berkeley, CA, 94720, USA
| |
Collapse
|
19
|
Zhang H, Zhang X, Chen M, Deng X, Pei Y, Zhang J, Chen H, Yang S. Biochar Can Improve Absorption of Nitrogen in Chicken Manure by Black Soldier Fly. Life (Basel) 2023; 13:life13040938. [PMID: 37109467 PMCID: PMC10144396 DOI: 10.3390/life13040938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/26/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
(1) Background: There is growing interest in using insects to treat nutrient-rich organic wastes, such as the black soldier fly (BSF), one of the most efficient organic waste recyclers for upcycling nutrients into the food system. Although biochar (BC) was shown to enhance nutrient retention and the final product quality during the composting of livestock and poultry manure in many previous studies, little information is available on the effect of BC on livestock manure bioconversion by black soldier fly larvae (BSFL). (2) Methods: This study investigated the effect of adding a small amount of BC to chicken manure (CM) on the bioconversion system of the black soldier fly (including N2O and NH3 emissions and the final distribution of nitrogen during the treatment process). (3) Results: The lowest N2O and NH3 emission and highest residual nitrogen in the substrate were observed in the 15% BC treatment. The highest bioconversion rate of CM (8.31%) and the peak of larval biomass was obtained in the 5% BC treatment. (4) Conclusions: The results demonstrate the feasibility of adding 5% BC to reduce pollution and achieve a satisfactory BSFL-based CM bioconversion efficiency.
Collapse
Affiliation(s)
- Haixu Zhang
- Department of Microbiology, College of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou 450002, China
| | - Xilu Zhang
- Department of Microbiology, College of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou 450002, China
| | - Mengxiao Chen
- Department of Microbiology, College of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou 450002, China
| | - Xin Deng
- Department of Microbiology, College of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou 450002, China
| | - Yaxin Pei
- Department of Microbiology, College of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou 450002, China
| | - Jiran Zhang
- Department of Microbiology, College of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou 450002, China
| | - Hongge Chen
- Department of Microbiology, College of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou 450002, China
| | - Sen Yang
- Department of Microbiology, College of Life Sciences, Henan Agricultural University, Key Laboratory of Agricultural Microbial Enzyme Engineering (Ministry of Agriculture), Zhengzhou 450002, China
| |
Collapse
|
20
|
Miralles-Robledillo JM, Martínez-Espinosa RM, Pire C. Analysis of the external signals driving the transcriptional regulation of the main genes involved in denitrification in Haloferax mediterranei. Front Microbiol 2023; 14:1109550. [PMID: 37007523 PMCID: PMC10062603 DOI: 10.3389/fmicb.2023.1109550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 02/21/2023] [Indexed: 03/18/2023] Open
Abstract
Haloferax mediterranei is the model microorganism for the study of the nitrogen cycle in haloarchaea. This archaeon not only assimilate N-species such as nitrate, nitrite, or ammonia, but also it can perform denitrification under low oxygen conditions, using nitrate or nitrite as alternative electron acceptors. However, the information currently available on the regulation of this alternative respiration in this kind of microorganism is scarce. Therefore, in this research, the study of haloarchaeal denitrification using H. mediterranei has been addressed by analyzing the promoter regions of the four main genes of denitrification (narGH, nirK, nor, and nosZ) through bioinformatics, reporter gene assays under oxic and anoxic conditions and by site-directed mutagenesis of the promoter regions. The results have shown that these four promoter regions share a common semi-palindromic motif that plays a role in the control of the expression levels of nor and nosZ (and probably nirK) genes. Regarding the regulation of the genes under study, it has been concluded that nirK, nor, and nosZ genes share some expression patterns, and therefore their transcription could be under the control of the same regulator whereas nar operon expression displays differences, such as the activation by dimethyl sulfoxide with respect to the expression in the absence of an electron acceptor, which is almost null under anoxic conditions. Finally, the study with different electron acceptors demonstrated that this haloarchaea does not need complete anoxia to perform denitrification. Oxygen concentrations around 100 μM trigger the activation of the four promoters. However, a low oxygen concentration per se is not a strong signal to activate the promoters of the main genes involved in this pathway; high activation also requires the presence of nitrate or nitrite as final electron acceptors.
Collapse
Affiliation(s)
- Jose María Miralles-Robledillo
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Alicante, Spain
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Alicante, Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Alicante, Spain
- *Correspondence: Carmen Pire,
| |
Collapse
|
21
|
Schaedel M, Ishii S, Wang H, Venterea R, Paul B, Mutimura M, Grossman J. Temporal assessment of N-cycle microbial functions in a tropical agricultural soil using gene co-occurrence networks. PLoS One 2023; 18:e0281442. [PMID: 36787300 PMCID: PMC9928094 DOI: 10.1371/journal.pone.0281442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/24/2023] [Indexed: 02/15/2023] Open
Abstract
Microbial nitrogen (N) cycling pathways are largely responsible for producing forms of N that are available for plant uptake or lost from the system as gas or leachate. The temporal dynamics of microbial N pathways in tropical agroecosystems are not well defined, even though they are critical to understanding the potential impact of soil conservation strategies. We aimed to 1) characterize temporal changes in functional gene associations across a seasonal gradient, 2) identify keystone genes that play a central role in connecting N cycle functions, and 3) detect gene co-occurrences that remained stable over time. Soil samples (n = 335) were collected from two replicated field trials in Rwanda between September 2020 and March 2021. We found high variability among N-cycle gene relationships and network properties that was driven more by sampling timepoint than by location. Two nitrification gene targets, hydroxylamine oxidoreductase and nitrite oxidoreductase, co-occurred across all timepoints, indicating that they may be ideal year-round targets to limit nitrification in rainfed agricultural soils. We also found that gene keystoneness varied across time, suggesting that management practices to enhance N-cycle functions such as the application of nitrification inhibitors could be adapted to seasonal conditions. Our results mark an important first step in employing gene networks to infer function in soil biogeochemical cycles, using a tropical seasonal gradient as a model system.
Collapse
Affiliation(s)
- Marie Schaedel
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States of America
- * E-mail:
| | - Satoshi Ishii
- Department of Soil, Water, & Climate, University of Minnesota, St. Paul, MN, United States of America
- BioTechnology Institute, St Paul, MN, United States of America
| | - Hao Wang
- Department of Soil, Water, & Climate, University of Minnesota, St. Paul, MN, United States of America
| | - Rodney Venterea
- Department of Soil, Water, & Climate, University of Minnesota, St. Paul, MN, United States of America
- USDA-ARS, Soil & Water Management Research Unit, St. Paul, MN, United States of America
| | - Birthe Paul
- Tropical Forages Program, International Center for Tropical Agriculture, Nairobi, Kenya
| | - Mupenzi Mutimura
- Department of Animal Production, Rwanda Agriculture Board, Kigali, Rwanda
| | - Julie Grossman
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States of America
| |
Collapse
|
22
|
Wu Z, Wang Y, Liu C, Yin N, Hu Z, Shen L, Islam ARMT, Wei Z, Chen S. Characteristics of soil N 2O emission and N 2O-producing microbial communities in paddy fields under elevated CO 2 concentrations. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120872. [PMID: 36529344 DOI: 10.1016/j.envpol.2022.120872] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
The effects of elevated carbon dioxide (CO2) concentration (e[CO2]) on nitrous oxide (N2O) emissions from paddy fields and the microbial processes involved in N2O emissions have recently received much attention. Ammonia-oxidizing microorganisms and denitrifying bacteria dominate the production of N2O in paddy soils. To better understand the dynamics of N2O production under e[CO2], a field experiment was conducted after five years of CO2 fumigation based on three treatments: CK (ambient atmospheric CO2), T1 (CK + increase of 40 ppm per year until 200 ppm), and T2 (CK + 200 ppm). N2O fluxes, soil physicochemical properties, and N2O production potential were quantified during the rice-growth period. The functional gene abundance and community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were analyzed using quantitative polymerase chain reaction (qPCR) and those of ammonia-denitrifying bacteria (nirS- and nirK-type) were analyzed using Illumina MiSeq sequencing. N2O emissions decreased by 173% and 41% under the two e[CO2] treatments during grain filling and milk ripening, respectively (P < 0.05). N2O emissions increased by 279% and 172% in the T2 treatment compared with T1 during the tillering and milk-ripening stages, respectively (P < 0.05). Furthermore, the N2O production potential was significantly higher in the CK treatment than in T1 and T2 during the elongation stage. The N2O production potential and abundance of AOA amoA genes in T1 treatment were significantly lower than those in CK treatment during the high N2O emission phase caused by mid-season drainage (P < 0.05). Although nirK- and nirS-type denitrifying bacteria community structure and diversity did not respond significantly (P > 0.05) to e[CO2], the abundance of nirK-type denitrifying bacteria significantly affected the N2O flux (P < 0.05). Linear regression analysis showed that the N2O production potential, AOA amoA gene abundance, and nirK gene abundance explained 47.2% of the variation in N2O emissions. In addition, soil nitrogen (N) significantly affected the nirK- and nirS-type denitrifier communities. Overall, our results revealed that e[CO2] suppressed N2O emissions, which was closely associated with the abundance of AOA amoA and nirK genes (P < 0.05).
Collapse
Affiliation(s)
- Zhurong Wu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Yuanyuan Wang
- School of Life Science, Huaiyin Normal University, Huaian, 223001, China
| | - Chao Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Nan Yin
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Zhenghua Hu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, 210044, China.
| | - Lidong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - A R M Towfiqul Islam
- Department of Disaster Management, Begum Rokeya University, Rangpur, 5400, Bangladesh
| | - Zhaowei Wei
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Shutao Chen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, School of Applied Meteorology, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| |
Collapse
|
23
|
Malvoisin B, Brunet F. Barren ground depressions, natural H 2 and orogenic gold deposits: Spatial link and geochemical model. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:158969. [PMID: 36162584 DOI: 10.1016/j.scitotenv.2022.158969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/19/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
A review of the localities in continental rocks where H2-rich gases have been reported, showed that they are mainly located near orogenic gold deposits. Two types of geomorphological features known as markers of gas venting in sedimentary basins were also systematically observed near orogenic gold deposits on satellite images. They consist in both barren ground depressions and high densities of small (<20 m in diameter) circular- and comet-shaped white spots in 32 and 7 localities, respectively. Point pattern analysis revealed that the white spots are self-organized, and similar to previously described vegetation patterns associated with termite mounds and fairy circles. We proposed a geochemical model to account for this relationship between orogenic gold deposits, H2 emanations and geomorphological features. Fe‑carbonates are ubiquitous mineral products associated with gold mineralization. They can further dissolve in the presence of aqueous fluid due to their high reactivity below 200 °C to produce magnetite and up to ∼1 mol H2 per kg of rock along with ∼3 mol/kg CO2. This process induces a solid volume decrease of 50 %. Therefore, we propose that Fe‑carbonate dissolution is (1) the primary source of H2 in orogenic gold deposit areas, and (2) involved in the formation of the geomorphological structures reported here, providing a new framework to understand their seemingly complex formation. Ground depressions and white spots are possible tools for gold exploration. Actually, we identified four new areas where we suspect possible orogenic gold deposits. The association between H2-rich gas and ground depressions was also made near other formations containing Fe‑carbonates such as iron formations and carbonatites. This suggests that H2 production through Fe‑carbonate dissolution is not restricted to gold deposits. The global H2 production in crustal rocks associated with Fe‑carbonate alteration is estimated to 3 × 105 mol/yr.
Collapse
Affiliation(s)
- Benjamin Malvoisin
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, IRD, Univ. Gustave Eiffel, ISTerre, 38000 Grenoble, France.
| | - Fabrice Brunet
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, IRD, Univ. Gustave Eiffel, ISTerre, 38000 Grenoble, France
| |
Collapse
|
24
|
Bandekar M, Ramaiah N, Seleyi SC, Nazareth DR, Kekäläinen J. Diversity and Quantitative Detection of Clade I Type nosZ Denitrifiers in the Arabian Sea Oxygen Minimum Zone. Microbes Environ 2023; 38. [PMID: 36696991 PMCID: PMC10037096 DOI: 10.1264/jsme2.me22056] [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] [Indexed: 01/27/2023] Open
Abstract
A significant amount of nitrous oxide (N2O) is effluxed into the atmosphere as a result of marine denitrification in the Arabian Sea (AS) oxygen minimum zone (OMZ). An assessment of temporal variations in the diversity and abundance of nosZ denitrifiers was performed to establish the relative importance of these bacteria in denitrification. Sampling was conducted at the Arabian Sea Time Series (ASTS) location and a quantitative PCR (qPCR) ana-lysis was performed. We detected a high abundance of the nosZ gene at core OMZ depths (250 m and 500 m), indicating the occurrence of denitrification in the AS-OMZ. The maximum abundance of the nosZ gene was observed during the Spring Intermonsoon (SIM) at 250 m (1.32×106 copies L-1) and 500 m (1.50×106 copies L-1). Sequencing ana-lysis showed that nosZ denitrifiers belonged to the classes Alpha-, Beta-, and Gammaproteobacteria. Taxonomic ana-lysis revealed that most OTUs were affiliated with Pseudomonas, Rhodopseudomonas, and Bradyrhizobium. Diversity indices and richness estimators confirmed a higher diversity of nosZ denitrifiers at 250 m than at 500 m during all three seasons. The present results also indicated that dissolved oxygen (DO) and total organic carbon (TOC) are critical factors influencing the diversity and abundance of the nosZ-denitrifying bacterial community.
Collapse
Affiliation(s)
- Mandar Bandekar
- Biological Oceanography Division, CSIR-National Institute of Oceanography
- Department of Environmental and Biological Sciences, University of Eastern Finland
| | - Nagappa Ramaiah
- Biological Oceanography Division, CSIR-National Institute of Oceanography
| | - Seyieleno C Seleyi
- Biological Oceanography Division, CSIR-National Institute of Oceanography
| | - Delcy R Nazareth
- Biological Oceanography Division, CSIR-National Institute of Oceanography
| | - Jukka Kekäläinen
- Department of Environmental and Biological Sciences, University of Eastern Finland
| |
Collapse
|
25
|
Wang Y, Sun Y, Chen L, Shao H, Zeng Y, Zeng Y, Tang F, Cai J, Huang S. Interactive effects of water management and liming on CH 4 emissions and rice cadmium uptake in an acid paddy soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:13551-13559. [PMID: 36136195 DOI: 10.1007/s11356-022-23162-x] [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: 02/17/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Rice agriculture is both an important source of the potent greenhouse gas methane (CH4) and a bioaccumulator of cadmium (Cd), which is hazardous to human health. Avoiding flooding during rice production is effective for reducing CH4 emissions, but it increases rice Cd uptake. Although lime application decreases Cd concentration in rice grains, it is not clear whether combining appropriate water management with liming can simultaneously reduce CH4 emissions and Cd uptake in rice paddies. Thus, a pot experiment was performed to investigate the interactive effects of water management (F: continuous flooding, FDF: flooding - midseason drainage - flooding, FDI: flooding - midseason drainage - intermittent irrigation) and lime application on CH4 emissions and rice Cd uptake in an acid paddy soil spiked with Cd. Results showed that neither water management nor liming significantly affected grain yield. Overall, liming reduced CH4 emissions by 42.2%. Compared to F, the FDF and FDI treatments reduced CH4 emissions by 43.5% and 54.2%, respectively. Liming reduced CH4 emissions by 32.6% under F, but with a greater decrease of 48.6% and 52.7% under FDF and FDI, respectively. Overall, liming reduced rice Cd uptake by an average of 47.3%. Compared to FDI, F and FDF significantly reduced Cd uptake by 84.0% and 75.1%, respectively, but there was no significant difference between F and FDF. Liming did not significantly affect Cd uptake under F and FDF, whereas liming reduced Cd uptake by 55.9% under FDI. These results suggest that maintaining flooding following midseason drainage can help in reducing rice Cd uptake, though slightly promoting CH4 emissions. Therefore, we recommend FDF combined with liming to mitigate CH4 emissions without increasing rice Cd uptake in acid paddy soils.
Collapse
Affiliation(s)
- Yong Wang
- Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yanni Sun
- Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Le Chen
- Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Hua Shao
- Soil and Fertilization Technology Extension Station of Jiangxi Province, Nanchang, 330046, China
| | - Yanhua Zeng
- Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yongjun Zeng
- Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Feiyu Tang
- Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Junhuo Cai
- Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shan Huang
- Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang, 330045, China.
| |
Collapse
|
26
|
Global Environment: Climate and Microorganisms. Environ Microbiol 2023. [DOI: 10.1007/978-3-662-66547-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
|
27
|
Hogendoorn C, Pol A, de Graaf R, White PB, Mesman R, van Galen PM, van Alen TA, Cremers G, Jansen RS, Jetten MSM, Op den Camp HJM. " Candidatus Hydrogenisulfobacillus filiaventi" strain R50 gen. nov. sp. nov., a highly efficient producer of extracellular organic compounds from H 2 and CO 2. Front Microbiol 2023; 14:1151097. [PMID: 37032882 PMCID: PMC10080006 DOI: 10.3389/fmicb.2023.1151097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
Production of organic molecules is largely depending on fossil fuels. A sustainable alternative would be the synthesis of these compounds from CO2 and a cheap energy source, such as H2, CH4, NH3, CO, sulfur compounds or iron(II). Volcanic and geothermal areas are rich in CO2 and reduced inorganic gasses and therefore habitats where novel chemolithoautotrophic microorganisms for the synthesis of organic compounds could be discovered. Here we describe "Candidatus Hydrogenisulfobacillus filiaventi" R50 gen. nov., sp. nov., a thermoacidophilic, autotrophic H2-oxidizing microorganism, that fixed CO2 and excreted no less than 0.54 mol organic carbon per mole fixed CO2. Extensive metabolomics and NMR analyses revealed that Val, Ala and Ile are the most dominant form of excreted organic carbon while the aromatic amino acids Tyr and Phe, and Glu and Lys were present at much lower concentrations. In addition to these proteinogenic amino acids, the excreted carbon consisted of homoserine lactone, homoserine and an unidentified amino acid. The biological role of the excretion remains uncertain. In the laboratory, we noticed the production under high growth rates (0.034 h-1, doubling time of 20 h) in combination with O2-limitation, which will most likely not occur in the natural habitat of this strain. Nevertheless, this large production of extracellular organic molecules from CO2 may open possibilities to use chemolithoautotrophic microorganisms for the sustainable production of important biomolecules.
Collapse
Affiliation(s)
- Carmen Hogendoorn
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Arjan Pol
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Rob de Graaf
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Paul B. White
- Department of Synthetic Organic Chemistry, IMM, Radboud University, Nijmegen, Netherlands
| | - Rob Mesman
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Peter M. van Galen
- Department of Systems Chemistry, IMM, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Theo A. van Alen
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Geert Cremers
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Robert S. Jansen
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Mike S. M. Jetten
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Huub J. M. Op den Camp
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
- *Correspondence: Huub J. M. Op den Camp,
| |
Collapse
|
28
|
Yang X, Tang S, Ni K, Shi Y, Yi X, Ma Q, Cai Y, Ma L, Ruan J. Long-term nitrogen addition increases denitrification potential and functional gene abundance and changes denitrifying communities in acidic tea plantation soil. ENVIRONMENTAL RESEARCH 2023; 216:114679. [PMID: 36326541 DOI: 10.1016/j.envres.2022.114679] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/03/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The response of soil denitrification to nitrogen (N) addition in the acidic and perennial agriculture systems and its underlying mechanisms remain poorly understood. Therefore, a long-term (12 years) field trial was conducted to explore the effects of different N application rates on the soil denitrification potential (DP), functional genes, and denitrifying microbial communities of a tea plantation. The study found that N application to the soil significantly increased the DP and the absolute abundance of denitrifying genes, such as narG, nirK, norB, and nosZ. The diversity of denitrifying communities (genus level) significantly decreased with increasing N rates. Moreover, the denitrifying communities composition significantly differed among the soils with different rates of N fertilization. Further variance partitioning analysis (VPA) revealed that the soil (39.04%) and pruned litter (32.53%) properties largely contributed to the variation in the denitrifying communities. Dissolved organic carbon (DOC) and soil pH, pruned litter's total crude fiber (TCF) content and total polyphenols to total N ratio (TP/TN), and narG and nirK abundance significantly (VIP >1.0) influenced the DP. Finally, partial least squares path modeling (PLS-PM) revealed that N addition indirectly affected the DP by changing specific soil and pruned litter properties and functional gene abundance. Thus, the findings suggest that tea plantation is a major source of N2O emissions that significantly enhance under N application and provide theoretical support for N fertilizer management in an acidic tea plantation system.
Collapse
Affiliation(s)
- Xiangde Yang
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Sheng Tang
- Ministry of Education Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Kang Ni
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Yuanzhi Shi
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Xiaoyun Yi
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Qingxu Ma
- Ministry of Education Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yanjiang Cai
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Lifeng Ma
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China.
| | - Jianyun Ruan
- Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China.
| |
Collapse
|
29
|
Zhang J, Zhao S, Liu Y, Liang H, Wang T, Zhao Y, Zhao Q, Peng T. Differences in methane and nitrous oxide emissions and soil bacteria communities between straw return methods in central China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:1167-1175. [PMID: 35915302 DOI: 10.1007/s11356-022-21883-7] [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: 03/10/2022] [Accepted: 07/02/2022] [Indexed: 06/15/2023]
Abstract
It is well recognized that straw return (SR) can improve soil fertility and soil organic carbon (SOC) storage. Increasing planting density and reducing nitrogen fertilizer application is considered an effective cultivation technique for japonica rice in central and northern China. However, few are known about the mechanisms of differences between wheat SR with rice planting densification and N reduction (SRD) and wheat SR on greenhouse gas emissions and soil bacteria communities in central China. A 2-year experiment was conducted to evaluate the effects of SR and SRD compared with straw removal (NS) on methane (CH4) and nitrous oxide (N2O) emission, rice yield, and soil properties in Henan Province, China, in 2019 and 2020. We found that SRD increased SOC, available phosphorous (AP), and available potassium (AK) compared to SR and NS in 2019 and 2020. The mean CH4 flux was positively correlated with SOC, and the cumulative CH4 emissions of SR and SRD plots were significantly higher than those of NS plots. No significant difference in cumulative CH4 emissions was detected between the SR and SRD treatments. N2O emissions were significantly lower under SRD than SR. SRD significantly affected soil bacteria diversity and composition at a depth of 0-15 cm. The relative abundance of Bacteroidota in SRD soil was 1.37- and 3.73-fold higher than that in NS and SR soils, respectively. The relative abundance of nitrate reduction-related operational taxonomic units enriched under SRD was significantly lower than that under SR, indicating that lower nitrate reduction of N2O production was induced by soil bacteria under SRD. N partial factor productivity was 21.4% and 28.5% higher under SRD than SR in 2019 and 2020, respectively. Our results suggest that SRD decreased soil bacteria N2O emissions; increased SOC, AP, and AK; and improved N fertilizer use efficiency, thereby improving rice yield in central China.
Collapse
Affiliation(s)
- Jing Zhang
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Biology, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
| | - Shuaibing Zhao
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Biology, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
| | - Ye Liu
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Biology, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
| | - He Liang
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Biology, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
| | - Tongtong Wang
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Biology, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
| | - Yafan Zhao
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Biology, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
| | - Quanzhi Zhao
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Biology, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
| | - Ting Peng
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice Biology, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China.
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China.
| |
Collapse
|
30
|
Yang X, Huang X, Cheng J, Cheng Z, Yang Q, Hu L, Xu J, He Y. Diversity-triggered bottom-up trophic interactions impair key soil functions under lindane pollution stress. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120293. [PMID: 36183873 DOI: 10.1016/j.envpol.2022.120293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/29/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
A growing amount of evidence suggests that microbial diversity loss may have negative effects on soil ecosystem function. However, less attention has been paid to the determinants of the relationship between community diversity and soil functioning under pollution stress. Here we manipulated microbial diversity to observe how biotic and abiotic factors influenced soil multi-functions (e.g. lindane degradation, soil respiration and nutrient cycling). Results showed that protist community was more sensitive to dilution, pollution stress, and sodium acetate addition than bacterial and fungal community. Acetate addition accelerated the lindane removal. Any declines in microbial diversity reduced the specialized soil processes (NO3-N production, and N2O flux), but increased soil respiration rate. Dilution led to a significant increase in consumers-bacterial and fungi-bacterial interaction as evidenced by co-occurrence network, which possibly played roles in maintaining microbiome stability and resilience. Interestingly, pollution stress and resource availability weaken the relationship between microbial diversity and soil functions through the bottom-up trophic interaction and environmental preference of soil microbiome. Overall, this work provides experimental evidence that loss in microbial diversity, accompanied with changes in trophic interactions mediated biotic and abiotic factors, could have important consequences for specialized soil functioning in farmland ecosystems.
Collapse
Affiliation(s)
- Xueling Yang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Xiaowei Huang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Jie Cheng
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Zhongyi Cheng
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Qi Yang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Lingfei Hu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China.
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Yan He
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| |
Collapse
|
31
|
Lumactud RA, Gorim LY, Thilakarathna MS. Impacts of humic-based products on the microbial community structure and functions toward sustainable agriculture. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.977121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Humic-based products (HPs) are carbon-rich organic amendments in the forms of extracted humic substances from manure, compost, and raw and extracted forms of lignites, coals and peats. HPs are widely used in agriculture and have beneficial effects on plants. While the agronomic benefits of HPs have been widely reported, information on their impact on the soil microbial community composition and functions is lacking, despite claims made by companies of humic substances as biostimulants. In this review, we explored published research on microbial responses with HPs application in an agronomic context. Although research data are sparse, current results suggest indirect impacts of HPs on microbial community composition and activities. HPs application changes the physico-chemical properties of the soil and influence root exudation, which in turn impact the microbial structure and function of the soil and rhizosphere. Application of HPs to the soil as biostimulants seemed to favor plant/soil beneficial bacterial community composition. HPs impacts on microbial activities that influence soil biogeochemical functioning remain unclear; existing data are also inconsistent and contradictory. The structural properties of HPs caused inconsistencies in their reported impacts on soil properties and plants. The sources of HPs and forms (whether extracted or raw), soil type, geographic location, crop species, and management strategies, among others, affect microbial communities affecting HPs efficacy as biostimulants. A more holistic approach to research encompassing multiple influential factors and leveraging the next-generation sequencing technology is needed to unravel the impacts of HPs on the soil microbiome. Addressing these knowledge gaps facilitates sustainable and efficient use of HPs as organic agricultural amendments reducing the use of chemical fertilizers.
Collapse
|
32
|
Nijman TPA, Lemmens M, Lurling M, Kosten S, Welte C, Veraart AJ. Phosphorus control and dredging decrease methane emissions from shallow lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 847:157584. [PMID: 35882339 DOI: 10.1016/j.scitotenv.2022.157584] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Freshwater ecosystems are an important source of the greenhouse gas methane (CH4), and their emissions are expected to increase due to eutrophication. Two commonly applied management techniques to reduce eutrophication are the addition of phosphate-binding lanthanum modified bentonite (LMB, trademark Phoslock©) and dredging, but their effect on CH4 emissions is still poorly understood. Here, this study researched how LMB and dredging affected CH4 emissions using a full-factorial mesocosm design monitored for 18 months. The effect was tested by measuring diffusive and ebullitive CH4 fluxes, plant community composition, methanogen and methanotroph activity and community composition, and a range of physicochemical water and sediment variables. LMB addition decreased total CH4 emissions, while dredging showed a trend towards decreasing CH4 emissions. Total CH4 emissions in all mesocosms were much higher in the summer of the second year, likely because of higher algal decomposition and organic matter availability. First, LMB addition lowered CH4 emissions by decreasing P-availability, which reduced coverage of the floating fern Azolla filiculoides, and thereby prevented anoxia and decreased surface water NH4+ concentrations, lowering CH4 production rates. Second, dredging decreased CH4 emissions in the first summer, possibly it removed the methanogenic community, and in the second year by preventing autumn and winter die-off of the rooted macrophyte Potamogeton cripsus. Finally, methanogen community composition was related to surface water NH4+ and O2, and porewater total phosphorus, while methanotroph community composition was related to organic matter content. To conclude, LMB addition and dredging not only improve water quality, but also decrease CH4 emissions, mitigating climate change.
Collapse
Affiliation(s)
- Thomas P A Nijman
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands.
| | - Maxime Lemmens
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Miquel Lurling
- Aquatic Ecology & Water Quality Management Group, Department of Environmental Sciences, Wageningen University, Droevendaalsesteeg 3a, 6708 PB Wageningen, the Netherlands
| | - Sarian Kosten
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Cornelia Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| |
Collapse
|
33
|
Homology modeling and virtual characterization of cytochrome c nitrite reductase (NrfA) in three model bacteria responsible for short-circuit pathway, DNRA in the terrestrial nitrogen cycle. World J Microbiol Biotechnol 2022; 38:168. [DOI: 10.1007/s11274-022-03352-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/04/2022] [Indexed: 11/26/2022]
|
34
|
Wang N, Zhu X, Zuo Y, Liu J, Yuan F, Guo Z, Zhang L, Sun Y, Gong C, Song C, Xu X. Metagenomic evidence of suppressed methanogenic pathways along soil profile after wetland conversion to cropland. Front Microbiol 2022; 13:930694. [PMID: 36204618 PMCID: PMC9530824 DOI: 10.3389/fmicb.2022.930694] [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: 04/28/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Wetland conversion to cropland substantially suppresses methane (CH4) emissions due to the strong suppression of methanogenesis, which consists of various pathways. In this study, we evaluated the cultivation impacts on four predominant CH4 production pathways, including acetate, carbon dioxide (CO2), methylamines, and methanol, in a wetland and cultivated cropland in northeastern China. The results showed significant suppression of CH4 production potential and the abundance of genes for all four methanogenic pathways in cropland. The consistency between CH4 production and methanogenesis genes indicates the robustness of genomic genes in analyzing methanogenesis. The suppression effects varied across seasons and along soil profiles, most evident in spring and 0 to 30 cm layers. The acetate pathway accounted for 55% in wetland vs. 70% in the cropland of all functional genes for CH4 production; while the other three pathways were stronger in response to cultivation, which presented as stronger suppressions in both abundance of functional genes (declines are 52% of CO2 pathway, 68% of methanol pathway, and 62% of methylamines pathway, vs. 19% of acetate pathway) and their percentages in four pathways (from 20 to 15% for CO2, 15 to 9% for methylamines, and 10 to 6% for methanol pathway vs. 55 to 70% for acetate pathway). The structural equation models showed that substrate availability was most correlated with CH4 production potential in the wetland, while the positive correlations of acetate, CO2, and methylamine pathways with CH4 production potential were significant in the cropland. The quantitative responses of four CH4 production pathways to land conversion reported in this study provide benchmark information for validating the CH4 model in simulating CH4 cycling under land use and land cover change.
Collapse
Affiliation(s)
- Nannan Wang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- *Correspondence: Nannan Wang
| | - Xinhao Zhu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yunjiang Zuo
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jianzhao Liu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fenghui Yuan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, United States
| | - Ziyu Guo
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Lihua Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Ying Sun
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Chao Gong
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Changchun Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Xiaofeng Xu
- Biology Department, San Diego State University, San Diego, CA, United States
- Xiaofeng Xu
| |
Collapse
|
35
|
Meier AB, Oppermann S, Drake HL, Schmidt O. The root zone of graminoids: A niche for H2-consuming acetogens in a minerotrophic peatland. Front Microbiol 2022; 13:978296. [PMID: 35992704 PMCID: PMC9391049 DOI: 10.3389/fmicb.2022.978296] [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: 06/25/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
The importance of acetogens for H2 turnover and overall anaerobic degradation in peatlands remains elusive. In the well-studied minerotrophic peatland fen Schlöppnerbrunnen, H2-consuming acetogens are conceptualized to be largely outcompeted by iron reducers, sulfate reducers, and hydrogenotrophic methanogens in bulk peat soil. However, in root zones of graminoids, fermenters thriving on rhizodeposits and root litter might temporarily provide sufficient H2 for acetogens. In the present study, root-free peat soils from around the roots of Molinia caerulea and Carex rostrata (i.e., two graminoids common in fen Schlöpnnerbrunnen) were anoxically incubated with or without supplemental H2 to simulate conditions of high and low H2 availability in the fen. In unsupplemented soil treatments, H2 concentrations were largely below the detection limit (∼10 ppmV) and possibly too low for acetogens and methanogens, an assumption supported by the finding that neither acetate nor methane substantially accumulated. In the presence of supplemental H2, acetate accumulation exceeded CH4 accumulation in Molinia soil whereas acetate and methane accumulated equally in Carex soil. However, reductant recoveries indicated that initially, additional unknown processes were involved either in H2 consumption or the consumption of acetate produced by H2-consuming acetogens. 16S rRNA and 16S rRNA gene analyses revealed that potential acetogens (Clostridium, Holophagaceae), methanogens (Methanocellales, Methanobacterium), iron reducers (Geobacter), and physiologically uncharacterized phylotypes (Acidobacteria, Actinobacteria, Bacteroidetes) were stimulated by supplemental H2 in soil treatments. Phylotypes closely related to clostridial acetogens were also active in soil-free Molinia and Carex root treatments with or without supplemental H2. Due to pronounced fermentation activities, H2 consumption was less obvious in root treatments, and acetogens likely thrived on root organic carbon and fermentation products (e.g., ethanol) in addition to H2. Collectively, the data highlighted that in fen Schlöppnerbrunnen, acetogens are associated to graminoid roots and inhabit the peat soil around the roots, where they have to compete for H2 with methanogens and iron reducers. Furthermore, the study underscored that the metabolically flexible acetogens do not rely on H2, potentially a key advantage over other H2 consumers under the highly dynamic conditions characteristic for the root-zones of graminoids in peatlands.
Collapse
Affiliation(s)
- Anja B. Meier
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Sindy Oppermann
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Harold L. Drake
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Oliver Schmidt
- Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
- *Correspondence: Oliver Schmidt,
| |
Collapse
|
36
|
Graf DRH, Jones CM, Zhao M, Hallin S. Assembly of root-associated N2O-reducing communities of annual crops is governed by selection for nosZ clade I over clade II. FEMS Microbiol Ecol 2022; 98:6655980. [PMID: 35927461 PMCID: PMC9397574 DOI: 10.1093/femsec/fiac092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 05/20/2022] [Accepted: 08/02/2022] [Indexed: 11/14/2022] Open
Abstract
The rhizosphere is a hotspot for denitrification. The nitrous oxide (N2O) reductase among denitrifiers and nondenitrifying N2O reducers is the only known N2O sink in the biosphere. We hypothesized that the composition of root-associated N2O-reducing communities when establishing on annual crops depend on soil type and plant species, but that assembly processes are independent of these factors and differ between nosZ clades I and II. Using a pot experiment with barley and sunflower and two soils, we analyzed the abundance, composition, and diversity of soil and root-associated N2O reducing communities by qPCR and amplicon sequencing of nosZ. Clade I was more abundant on roots compared to soil, while clade II showed the opposite. In barley, this pattern coincided with N2O availability, determined as potential N2O production rates, but for sunflower no N2O production was detected in the root compartment. Root and soil nosZ communities differed in composition and phylogeny-based community analyses indicated that assembly of root-associated N2O reducers was driven by the interaction between plant and soil type, with inferred competition being more influential than habitat selection. Selection between clades I and II in the root/soil interface is suggested, which may have functional consequences since most clade I microorganisms can produce N2O.
Collapse
Affiliation(s)
- Daniel R H Graf
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Christopher M Jones
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| | - Ming Zhao
- Department of Plant Biology, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden
| |
Collapse
|
37
|
Kanukollu S, Remus R, Rücker AM, Buchen-Tschiskale C, Hoffmann M, Kolb S. Methanol utilizers of the rhizosphere and phyllosphere of a common grass and forb host species. ENVIRONMENTAL MICROBIOME 2022; 17:35. [PMID: 35794633 PMCID: PMC9258066 DOI: 10.1186/s40793-022-00428-y] [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: 08/06/2021] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Managed grasslands are global sources of atmospheric methanol, which is one of the most abundant volatile organic compounds in the atmosphere and promotes oxidative capacity for tropospheric and stratospheric ozone depletion. The phyllosphere is a favoured habitat of plant-colonizing methanol-utilizing bacteria. These bacteria also occur in the rhizosphere, but their relevance for methanol consumption and ecosystem fluxes is unclear. Methanol utilizers of the plant-associated microbiota are key for the mitigation of methanol emission through consumption. However, information about grassland plant microbiota members, their biodiversity and metabolic traits, and thus key actors in the global methanol budget is largely lacking. RESULTS We investigated the methanol utilization and consumption potentials of two common plant species (Festuca arundinacea and Taraxacum officinale) in a temperate grassland. The selected grassland exhibited methanol formation. The detection of 13C derived from 13C-methanol in 16S rRNA of the plant microbiota by stable isotope probing (SIP) revealed distinct methanol utilizer communities in the phyllosphere, roots and rhizosphere but not between plant host species. The phyllosphere was colonized by members of Gamma- and Betaproteobacteria. In the rhizosphere, 13C-labelled Bacteria were affiliated with Deltaproteobacteria, Gemmatimonadates, and Verrucomicrobiae. Less-abundant 13C-labelled Bacteria were affiliated with well-known methylotrophs of Alpha-, Gamma-, and Betaproteobacteria. Additional metagenome analyses of both plants were consistent with the SIP results and revealed Bacteria with methanol dehydrogenases (e.g., MxaF1 and XoxF1-5) of known but also unusual genera (i.e., Methylomirabilis, Methylooceanibacter, Gemmatimonas, Verminephrobacter). 14C-methanol tracing of alive plant material revealed divergent potential methanol consumption rates in both plant species but similarly high rates in the rhizosphere and phyllosphere. CONCLUSIONS Our study revealed the rhizosphere as an overlooked hotspot for methanol consumption in temperate grasslands. We further identified unusual new but potentially relevant methanol utilizers besides well-known methylotrophs in the phyllosphere and rhizosphere. We did not observe a plant host-specific methanol utilizer community. Our results suggest that our approach using quantitative SIP and metagenomics may be useful in future field studies to link gross methanol consumption rates with the rhizosphere and phyllosphere microbiome.
Collapse
Affiliation(s)
- Saranya Kanukollu
- Microbial Biogeochemistry, RA1 Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Rainer Remus
- Isotope Biogeochemistry and Gas Fluxes, RA1 Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | | | - Caroline Buchen-Tschiskale
- Isotope Biogeochemistry and Gas Fluxes, RA1 Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
- Present Address: Johann Heinrich von Thünen-Institut, Institute of Climate-Smart Agriculture, Braunschweig, Germany
| | - Mathias Hoffmann
- Isotope Biogeochemistry and Gas Fluxes, RA1 Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, RA1 Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
- Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
| |
Collapse
|
38
|
Song L, Zang S, Lin L, Lu B, Sun C, Jiao Y, Wang H. Responses of nitrous oxide fluxes to autumn freeze-thaw cycles in permafrost peatlands of the Da Xing'an Mountains, Northeast China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:31700-31712. [PMID: 35013975 DOI: 10.1007/s11356-022-18545-z] [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: 07/13/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Climate warming has intensified changes of permafrost freeze-thaw process and postponed the starting period of soil freezing, which significantly affected the processes of N2O production and emission from the soils. However, responses of soil N2O fluxes to freeze-thaw cycles (FTCS) during autumn freezing period in permafrost peatlands in field remain unclear. Therefore, the static chamber-GC techniques were used to explore the effects of autumn FTCS on N2O fluxes in the three permafrost peatlands [Calamagrostis angustifolia peatland (CA), Larix gmelini-Sphagnum swamp (LS), and Eriophorum vaginatum peatland (EV)] in Da Xing'an Mountains, Northeast China, from September to November 2019. The response peaks of N2O fluxes to autumn FTCS in CA (29.22 ± 14.90 μg m-2 h-1) and EV (19.70 ± 7.26 μg m-2 h-1) occurred in the autumn FTCS prophase, whereas LS (11.33 ± 0.90 μg m-2 h-1) appeared in the autumn FTCS metaphase. CA (394.90 μg m-2) and EV (497.82 μg m-2) acted as a N2O source, and LS (- 1321.43 μg m-2) was a N2O sink. The effects of autumn FTCS on N2O fluxes were significantly different (p < 0.001) in the three permafrost peatlands. N2O emissions during autumn FTCS were mainly driven by soil NH4+-N0-50 cm, DOC30-40 cm and 40-50 cm content and soil NO3--N0-50 cm content. The results implied that autumn FTCS could stimulate soil N2O emissions in permafrost peatlands and confirmed the important contribution of N2O emissions during autumn FTCS to annual nitrogen budget. This study could improve the accuracy of regional estimates of annual nitrogen budget.
Collapse
Affiliation(s)
- Liquan Song
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, 150025, China
- Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China
| | - Shuying Zang
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, 150025, China.
- Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China.
| | - Lin Lin
- College of Foreign Languages, Jiamusi University, Jiamusi, 154007, China
| | - Boquan Lu
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, 150025, China
- Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China
| | - Chaofeng Sun
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, 150025, China
- Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China
| | - Yaqing Jiao
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, 150025, China
- Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China
| | - Hanxi Wang
- Heilongjiang Province Key Laboratory of Geographical Environment Monitoring and Spatial Information Service in Cold Regions, Harbin Normal University, Harbin, 150025, China.
- Heilongjiang Province Collaborative Innovation Center of Cold Region Ecological Safety, Harbin, 150025, China.
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, Jingyue Street 2555, Changchun, 130117, China.
| |
Collapse
|
39
|
Oshiki M, Toyama Y, Suenaga T, Terada A, Kasahara Y, Yamaguchi T, Araki N. N 2O Reduction by Gemmatimonas aurantiaca and Potential Involvement of Gemmatimonadetes Bacteria in N 2O Reduction in Agricultural Soils. Microbes Environ 2022; 37. [PMID: 35418546 PMCID: PMC9530729 DOI: 10.1264/jsme2.me21090] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Agricultural soil is the primary N2O sink limiting the emission of N2O gas into the atmosphere. Although Gemmatimonadetes bacteria are abundant in agricultural soils, limited information is currently available on N2O reduction by Gemmatimonadetes bacteria. Therefore, the effects of pH and temperature on N2O reduction activities and affinity constants for N2O reduction were examined by performing batch experiments using an isolate of Gemmatimonadetes bacteria, Gemmatimonas aurantiaca (NBRC100505T). G. aurantiaca reduced N2O at pH 5–9 and 4–50°C, with the highest activity being observed at pH 7 and 30°C. The affinity constant of G. aurantiaca cells for N2O was 4.4 μM. The abundance and diversity of the Gemmatimonadetes 16S rRNA gene and nosZ encoding nitrous oxide reductase in agricultural soil samples were also investigated by quantitative PCR (qPCR) and amplicon sequencing analyses. Four N2O-reducing agricultural soil samples were assessed, and the copy numbers of the Gemmatimonadetes 16S rRNA gene (clades G1 and G3), nosZ DNA, and nosZ mRNA were 8.62–9.65×108, 5.35–7.15×108, and 2.23–4.31×109 copies (g dry soil)–1, respectively. The abundance of the nosZ mRNA of Gemmatimonadetes bacteria and OTU91, OUT332, and OTU122 correlated with the N2O reduction rates of the soil samples tested, suggesting N2O reduction by Gemmatimonadetes bacteria. Gemmatimonadetes 16S rRNA gene reads affiliated with OTU4572 and OTU3759 were predominant among the soil samples examined, and these Gemmatimonadetes OTUs have been identified in various types of soil samples.
Collapse
Affiliation(s)
- Mamoru Oshiki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College.,Division of Environmental Engineering, Faculty of Engineering, Hokkaido University
| | - Yuka Toyama
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
| | | | - Akihiko Terada
- Department of Applied Physics and Chemical Engineering, Tokyo University of Agriculture and Technology
| | | | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology
| | - Nobuo Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College
| |
Collapse
|
40
|
Greening C, Grinter R. Microbial oxidation of atmospheric trace gases. Nat Rev Microbiol 2022; 20:513-528. [PMID: 35414013 DOI: 10.1038/s41579-022-00724-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2022] [Indexed: 02/06/2023]
Abstract
The atmosphere has recently been recognized as a major source of energy sustaining life. Diverse aerobic bacteria oxidize the three most abundant reduced trace gases in the atmosphere, namely hydrogen (H2), carbon monoxide (CO) and methane (CH4). This Review describes the taxonomic distribution, physiological role and biochemical basis of microbial oxidation of these atmospheric trace gases, as well as the ecological, environmental, medical and astrobiological importance of this process. Most soil bacteria and some archaea can survive by using atmospheric H2 and CO as alternative energy sources, as illustrated through genetic studies on Mycobacterium cells and Streptomyces spores. Certain specialist bacteria can also grow on air alone, as confirmed by the landmark characterization of Methylocapsa gorgona, which grows by simultaneously consuming atmospheric CH4, H2 and CO. Bacteria use high-affinity lineages of metalloenzymes, namely hydrogenases, CO dehydrogenases and methane monooxygenases, to utilize atmospheric trace gases for aerobic respiration and carbon fixation. More broadly, trace gas oxidizers enhance the biodiversity and resilience of soil and marine ecosystems, drive primary productivity in extreme environments such as Antarctic desert soils and perform critical regulatory services by mitigating anthropogenic emissions of greenhouse gases and toxic pollutants.
Collapse
Affiliation(s)
- Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. .,Securing Antarctica's Environmental Future, Monash University, Clayton, Victoria, Australia. .,Centre to Impact AMR, Monash University, Clayton, Victoria, Australia.
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| |
Collapse
|
41
|
Buzzard V, Thorne D, Gil-Loaiza J, Cueva A, Meredith LK. Sensitivity of soil hydrogen uptake to natural and managed moisture dynamics in a semiarid urban ecosystem. PeerJ 2022; 10:e12966. [PMID: 35317075 PMCID: PMC8934528 DOI: 10.7717/peerj.12966] [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: 07/09/2021] [Accepted: 01/28/2022] [Indexed: 01/11/2023] Open
Abstract
The North American Monsoon season (June-September) in the Sonoran Desert brings thunderstorms and heavy rainfall. These rains bring cooler temperature and account for roughly half of the annual precipitation making them important for biogeochemical processes. The intensity of the monsoon rains also increase flooding in urban areas and rely on green infrastructure (GI) stormwater management techniques such as water harvesting and urban rain gardens to capture runoff. The combination of increased water availability during the monsoon and water management provide a broad moisture regime for testing responses in microbial metabolism to natural and managed soil moisture pulses in drylands. Soil microbes rely on atmospheric hydrogen (H2) as an important energy source in arid and semiarid landscapes with low soil moisture and carbon availability. Unlike mesic ecosystems, transient water availability in arid and semiarid ecosystems has been identified as a key limiting driver of microbe-mediated H2 uptake. We measured soil H2 uptake in rain gardens exposed to three commonly used water harvesting practices during the monsoon season in Tucson AZ, USA. In situ static chamber measurements were used to calculate H2 uptake in each of the three water harvesting treatments passive (stormwater runoff), active (stored rooftop runoff), and greywater (used laundry water) compared to an unaltered control treatment to assess the effects of water management practices on soil microbial activity. In addition, soils were collected from each treatment and brought to the lab for an incubation experiment manipulating the soil moisture to three levels capturing the range observed from field samples. H2 fluxes from all treatments ranged between -0.72 nmol m-2 s-1 and -3.98 nmol m-2 s-1 over the monsoon season. Soil H2 uptake in the greywater treatment was on average 53% greater than the other treatments during pre-monsoon, suggesting that the increased frequency and availability of water in the greywater treatment resulted in higher H2 uptake during the dry season. H2 uptake was significantly correlated with soil moisture (r = -0.393, p = 0.001, df = 62) and temperature (r = 0.345, p = 0.005, df = 62). Our findings suggest that GI managed residential soils can maintain low levels of H2 uptake during dry periods, unlike unmanaged systems. The more continuous H2 uptake associated with GI may help reduce the impacts of drought on H2 cycling in semiarid urban ecosystems.
Collapse
Affiliation(s)
- Vanessa Buzzard
- School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, United States
| | - Dana Thorne
- School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, United States
| | - Juliana Gil-Loaiza
- School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, United States
| | - Alejandro Cueva
- Biosphere2, University of Arizona, Oracle, Arizona, United States
| | - Laura K. Meredith
- School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, United States,BIO5 Institute, University of Arizona, Tucson, Arizona, United States
| |
Collapse
|
42
|
Zhang Q, Tang J, Angel R, Wang D, Hu X, Gao S, Zhang L, Tang Y, Zhang X, Koide RT, Yang H, Sun Q. Soil Properties Interacting With Microbial Metagenome in Decreasing CH 4 Emission From Seasonally Flooded Marshland Following Different Stages of Afforestation. Front Microbiol 2022; 13:830019. [PMID: 35283824 PMCID: PMC8905362 DOI: 10.3389/fmicb.2022.830019] [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: 12/06/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Wetlands are the largest natural source of terrestrial CH4 emissions. Afforestation can enhance soil CH4 oxidation and decrease methanogenesis, yet the driving mechanisms leading to these effects remain unclear. We analyzed the structures of communities of methanogenic and methanotrophic microbes, quantification of mcrA and pmoA genes, the soil microbial metagenome, soil properties and CH4 fluxes in afforested and non-afforested areas in the marshland of the Yangtze River. Compared to the non-afforested land use types, net CH4 emission decreased from bare land, natural vegetation and 5-year forest plantation and transitioned to net CH4 sinks in the 10- and 20-year forest plantations. Both abundances of mcrA and pmoA genes decreased significantly with increasing plantation age. By combining random forest analysis and structural equation modeling, our results provide evidence for an important role of the abundance of functional genes related to methane production in explaining the net CH4 flux in this ecosystem. The structures of methanogenic and methanotrophic microbial communities were of lower importance as explanatory factors than functional genes in terms of in situ CH4 flux. We also found a substantial interaction between functional genes and soil properties in the control of CH4 flux, particularly soil particle size. Our study provides empirical evidence that microbial community function has more explanatory power than taxonomic microbial community structure with respect to in situ CH4 fluxes. This suggests that focusing on gene abundances obtained, e.g., through metagenomics or quantitative/digital PCR could be more effective than community profiling in predicting CH4 fluxes, and such data should be considered for ecosystem modeling.
Collapse
Affiliation(s)
- Qian Zhang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jie Tang
- Hunan Academy of Forestry, Changsha, China
| | - Roey Angel
- Soil and Water Research Infrastructure and Institute of Soil Biology, Biology Centre, Czech Academy of Sciences (CAS), České Budějovice, Czechia
| | - Dong Wang
- Institute of Forest Ecology, Environment and Nature Conservation, Chinese Academy of Forestry, Beijing, China
| | - Xingyi Hu
- Hubei Academy of Forestry, Wuhan, China
| | - Shenghua Gao
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Lei Zhang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yuxi Tang
- Hunan Academy of Forestry, Changsha, China
| | - Xudong Zhang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Roger T. Koide
- Department of Biology, Brigham Young University, Provo, UT, United States
| | - Haishui Yang
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Qixiang Sun
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| |
Collapse
|
43
|
Oceguera-Contreras E, Aguilar-Juarez O, Oseguera-Galindo D, Macías-Barragán J, Ortiz-Torres G, Luisa Pita-López M, Domínguez J, Titov I, Kamen A. Establishment of the upstream processing for renewable production of hydrogen using vermicomposting-tea and molasses as substrate. WASTE MANAGEMENT (NEW YORK, N.Y.) 2022; 139:279-289. [PMID: 34995855 DOI: 10.1016/j.wasman.2021.12.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
This study aimed to establish the optimal operational conditions for hydrogen production using vermicomposting-tea and sugarcane molasses as substrate. The experiments were carried out by triplicate in 110 ml serological bottles, a Box-Behnken design of experiments was performed in anaerobic dark conditions. The maximal hydrogen production (HP), hydrogen production rate (HPR), and hydrogen yield (HY) attained were 1021.0 mlL-1, 5.32 mlL-1h-1, and 60.3 mlLH2-1/gTCC, respectively. The statistical model showed that the optimal operational conditions for pH, molasses concentration, and temperature were 6.5; 30 % (v/v) and 25 °C. The bioreactor run showed 17.202 L of hydrogen, 0.58 Lh-1, and 77.2 mlH2gTCC-1 For HP, HPR, and HY. Chemometric analysis for the volatile fatty acids obtained at the fermentation showed that only two principal components are required to explain 90 % of the variance. The representative pathways for hydrogen production were acetic and butyric acids. This study established the operational conditions for the upstream processing amenable to pilot and industrial-scale operations. Our results add value to molasses within the circular economy for hydrogen production using a novel consortium from vermicompost.
Collapse
Affiliation(s)
- Edén Oceguera-Contreras
- Laboratorio de Sistemas Biológicos, Centro Universitario de los Valles, Universidad de Guadalajara. Carretera Guadalajara-Ameca km. 45.5, C.P. 46600. Ameca, Jalisco, México.
| | - Oscar Aguilar-Juarez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Avenida de los normalistas No. 800, Colinas de la Normal, C.P. 4470, Guadalajara, Jalisco, México
| | - David Oseguera-Galindo
- Laboratorio de Sistemas Biológicos, Centro Universitario de los Valles, Universidad de Guadalajara. Carretera Guadalajara-Ameca km. 45.5, C.P. 46600. Ameca, Jalisco, México
| | - José Macías-Barragán
- Laboratorio de Sistemas Biológicos, Centro Universitario de los Valles, Universidad de Guadalajara. Carretera Guadalajara-Ameca km. 45.5, C.P. 46600. Ameca, Jalisco, México
| | - Gerardo Ortiz-Torres
- Laboratorio de Mecatrónica, Centro Universitario de los Valles, Universidad de Guadalajara, Carretera Guadalajara-Ameca km. 45.5, C.P. 46600. Ameca, Jalisco, México
| | - María Luisa Pita-López
- Centro de Investigación en Biología Molecular de las Enfermedades Crónicas (CIBIMEC). Centro Universitario del Sur, Universidad de Guadalajara, Av. Enrique Arreola Silva No. 883, C.P. 49000. Zapotlán el Grande, Jalisco, México
| | - Jorge Domínguez
- Departamento de Ecología e Bioloxía Animal (GEA), Universidad de Vigo. As lagoas Marcosende, Vigo E-36310, Vigo, España
| | - Igor Titov
- Technological Institute of Information and Electronic Radio, Vladimir University, 600026, Vladimir st, Gorki d. 87, Vladimir, Russia
| | - Amine Kamen
- Department of Bioengineering, 3480 Rue University, McConnell Engineering Building, McGill University, Montreal, QC H3A OE9, Canada
| |
Collapse
|
44
|
Cecchetti AR, Stiegler AN, Gonthier EA, Bandaru SRS, Fakra SC, Alvarez-Cohen L, Sedlak DL. Fate of Dissolved Nitrogen in a Horizontal Levee: Seasonal Fluctuations in Nitrate Removal Processes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2770-2782. [PMID: 35077168 DOI: 10.1021/acs.est.1c07512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Horizontal levees are a nature-based approach for removing nitrogen from municipal wastewater effluent while simultaneously providing additional benefits, such as flood control. To assess nitrogen removal mechanisms and the efficacy of a horizontal levee, we monitored an experimental system receiving nitrified municipal wastewater effluent for 2 years. Based on mass balances and microbial gene abundance data, we determined that much of the applied nitrogen was most likely removed by heterotrophic denitrifiers that consumed labile organic carbon from decaying plants and added wood chips. Fe(III) and sulfate reduction driven by decay of labile organic carbon also produced Fe(II) sulfide minerals. During winter months, when heterotrophic activity was lower, strong correlations between sulfate release and nitrogen removal suggested that autotrophic denitrifiers oxidized Fe(II) sulfides using nitrate as an electron acceptor. These trends were seasonal, with Fe(II) sulfide minerals formed during summer fueling denitrification during the subsequent winter. Overall, around 30% of gaseous nitrogen losses in the winter were attributable to autotrophic denitrifiers. To predict long-term nitrogen removal, we developed an electron-transfer model that accounted for the production and consumption of electron donors. The model indicated that the labile organic carbon released from wood chips may be capable of supporting nitrogen removal from wastewater effluent for several decades with sulfide minerals, decaying vegetation, and root exudates likely sustaining nitrogen removal over a longer timescale.
Collapse
Affiliation(s)
- Aidan R Cecchetti
- Department of Civil and Environmental Engineering, University of California at Berkeley, Berkeley, California 94720, United States
- ReNUWIt Engineering Research Center, University of California at Berkeley, Berkeley, California 94720, United States
| | - Angela N Stiegler
- Department of Civil and Environmental Engineering, University of California at Berkeley, Berkeley, California 94720, United States
- ReNUWIt Engineering Research Center, University of California at Berkeley, Berkeley, California 94720, United States
| | - Emily A Gonthier
- Department of Civil and Environmental Engineering, University of California at Berkeley, Berkeley, California 94720, United States
- ReNUWIt Engineering Research Center, University of California at Berkeley, Berkeley, California 94720, United States
| | - Siva R S Bandaru
- Department of Civil and Environmental Engineering, University of California at Berkeley, Berkeley, California 94720, United States
| | - Sirine C Fakra
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lisa Alvarez-Cohen
- Department of Civil and Environmental Engineering, University of California at Berkeley, Berkeley, California 94720, United States
- ReNUWIt Engineering Research Center, University of California at Berkeley, Berkeley, California 94720, United States
| | - David L Sedlak
- Department of Civil and Environmental Engineering, University of California at Berkeley, Berkeley, California 94720, United States
- ReNUWIt Engineering Research Center, University of California at Berkeley, Berkeley, California 94720, United States
| |
Collapse
|
45
|
Hu J, Richwine JD, Keyser PD, Li L, Yao F, Jagadamma S, DeBruyn JM. Ammonia-oxidizing bacterial communities are affected by nitrogen fertilization and grass species in native C 4 grassland soils. PeerJ 2022; 9:e12592. [PMID: 35003922 PMCID: PMC8684740 DOI: 10.7717/peerj.12592] [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: 09/14/2021] [Accepted: 11/12/2021] [Indexed: 11/20/2022] Open
Abstract
Background Fertilizer addition can contribute to nitrogen (N) losses from soil by affecting microbial populations responsible for nitrification. However, the effects of N fertilization on ammonia oxidizing bacteria under C4 perennial grasses in nutrient-poor grasslands are not well studied. Methods In this study, a field experiment was used to assess the effects of N fertilization rate (0, 67, and 202 kg N ha−1) and grass species (switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii)) on ammonia-oxidizing bacterial (AOB) communities in C4 grassland soils using quantitative PCR, quantitative reverse transcription-PCR, and high-throughput amplicon sequencing of amoA genes. Results Nitrosospira were dominant AOB in the C4 grassland soil throughout the growing season. N fertilization rate had a stronger influence on AOB community composition than C4 grass species. Elevated N fertilizer application increased the abundance, activity, and alpha-diversity of AOB communities as well as nitrification potential, nitrous oxide (N2O) emission and soil acidity. The abundance and species richness of AOB were higher under switchgrass compared to big bluestem. Soil pH, nitrate, nitrification potential, and N2O emission were significantly related to the variability in AOB community structures (p < 0.05).
Collapse
Affiliation(s)
- Jialin Hu
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Jonathan D Richwine
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States of America
| | - Patrick D Keyser
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States of America
| | - Lidong Li
- Agroecosystem Management Research Unit, USDA-Agricultural Research Service, Lincoln, NE, United States of America
| | - Fei Yao
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Sindhu Jagadamma
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| |
Collapse
|
46
|
Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils. Proc Natl Acad Sci U S A 2021; 118:2025322118. [PMID: 34732568 DOI: 10.1073/pnas.2025322118] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 12/11/2022] Open
Abstract
Numerous diverse microorganisms reside in the cold desert soils of continental Antarctica, though we lack a holistic understanding of the metabolic processes that sustain them. Here, we profile the composition, capabilities, and activities of the microbial communities in 16 physicochemically diverse mountainous and glacial soils. We assembled 451 metagenome-assembled genomes from 18 microbial phyla and inferred through Bayesian divergence analysis that the dominant lineages present are likely native to Antarctica. In support of earlier findings, metagenomic analysis revealed that the most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen to support aerobic respiration and sometimes carbon fixation. Surprisingly, however, hydrogen oxidation in this region was catalyzed primarily by a phylogenetically and structurally distinct enzyme, the group 1l [NiFe]-hydrogenase, encoded by nine bacterial phyla. Through gas chromatography, we provide evidence that both Antarctic soil communities and an axenic Bacteroidota isolate (Hymenobacter roseosalivarius) oxidize atmospheric hydrogen using this enzyme. Based on ex situ rates at environmentally representative temperatures, hydrogen oxidation is theoretically sufficient for soil communities to meet energy requirements and, through metabolic water production, sustain hydration. Diverse carbon monoxide oxidizers and abundant methanotrophs were also active in the soils. We also recovered genomes of microorganisms capable of oxidizing edaphic inorganic nitrogen, sulfur, and iron compounds and harvesting solar energy via microbial rhodopsins and conventional photosystems. Obligately symbiotic bacteria, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also present. We conclude that microbial diversity in Antarctic soils reflects the coexistence of metabolically flexible mixotrophs with metabolically constrained specialists.
Collapse
|
47
|
Bay SK, Waite DW, Dong X, Gillor O, Chown SL, Hugenholtz P, Greening C. Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient. THE ISME JOURNAL 2021; 15:3339-3356. [PMID: 34035443 PMCID: PMC8528921 DOI: 10.1038/s41396-021-01001-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/16/2021] [Accepted: 04/28/2021] [Indexed: 02/04/2023]
Abstract
Desert soils harbour diverse communities of aerobic bacteria despite lacking substantial organic carbon inputs from vegetation. A major question is therefore how these communities maintain their biodiversity and biomass in these resource-limiting ecosystems. Here, we investigated desert topsoils and biological soil crusts collected along an aridity gradient traversing four climatic regions (sub-humid, semi-arid, arid, and hyper-arid). Metagenomic analysis indicated these communities vary in their capacity to use sunlight, organic compounds, and inorganic compounds as energy sources. Thermoleophilia, Actinobacteria, and Acidimicrobiia were the most abundant and prevalent bacterial classes across the aridity gradient in both topsoils and biocrusts. Contrary to the classical view that these taxa are obligate organoheterotrophs, genome-resolved analysis suggested they are metabolically flexible, with the capacity to also use atmospheric H2 to support aerobic respiration and often carbon fixation. In contrast, Cyanobacteria were patchily distributed and only abundant in certain biocrusts. Activity measurements profiled how aerobic H2 oxidation, chemosynthetic CO2 fixation, and photosynthesis varied with aridity. Cell-specific rates of atmospheric H2 consumption increased 143-fold along the aridity gradient, correlating with increased abundance of high-affinity hydrogenases. Photosynthetic and chemosynthetic primary production co-occurred throughout the gradient, with photosynthesis dominant in biocrusts and chemosynthesis dominant in arid and hyper-arid soils. Altogether, these findings suggest that the major bacterial lineages inhabiting hot deserts use different strategies for energy and carbon acquisition depending on resource availability. Moreover, they highlight the previously overlooked roles of Actinobacteriota as abundant primary producers and trace gases as critical energy sources supporting productivity and resilience of desert ecosystems.
Collapse
Affiliation(s)
- Sean K Bay
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.
| | - David W Waite
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sde Boker, Israel
| | - Steven L Chown
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.
| |
Collapse
|
48
|
The Fallow Period Plays an Important Role in Annual CH4 Emission in a Rice Paddy in Southern Brazil. SUSTAINABILITY 2021. [DOI: 10.3390/su132011336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Paddy fields are significant anthropogenic sources of methane (CH4) emissions. In southern Brazil, rice is grown in lowland flooded areas once a year, followed by a long fallow period. This study aimed to measure CH4 fluxes in a rice paddy field in southern Brazil during the rice-growing season of 2015/2016 and the following fallow period. The fluxes were estimated using the eddy covariance (EC) technique and soil chamber (SC). Diurnal and seasonal variations of CH4 fluxes and potential meteorological drivers were analyzed. The CH4 fluxes showed distinct diurnal variations in each analyzed subperiod (vegetative, reproductive, pre-harvest, no rice, and land preparation), characterized by a single-peak diurnal pattern. The variables that most influenced methane emissions were air and surface temperatures. In the growing season, the rice vegetative stage was responsible for most of the measured emissions. The accumulated annual emission estimated was 44.88 g CH4 m−2 y−1, being 64% (28.50 g CH4 m−2) due to the rice-growing season and 36% (16.38 g CH4 m−2) due to the fallow period. These results show the importance of including fallow periods in strategies to mitigate methane emissions in flood irrigated rice-growing areas.
Collapse
|
49
|
Su C, Zhu W, Kang R, Quan Z, Liu D, Huang W, Shi Y, Chen X, Fang Y. Interannual and seasonal variabilities in soil NO fluxes from a rainfed maize field in the Northeast China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117312. [PMID: 33992903 DOI: 10.1016/j.envpol.2021.117312] [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: 12/16/2020] [Revised: 04/18/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
Nitric oxide (NO) plays a critical role in atmospheric chemistry and also is a precursor of nitrate, which affects particle matter formation and nitrogen deposition. Agricultural soil has been recognized as a main source of atmospheric NO. However, quantifying the NO fluxes emitted from croplands remains a challenge and in situ long-term measurements of NO are still limited. In this study, we used an automated sampling system to measure NO fluxes with a high temporal resolution over two years (April 2017 to March 2019) from a rainfed maize field in the Northeast China. The cumulative annual NO emissions were 8.9 and 2.3 kg N ha-1 in year 1 (April 2017 to March 2018) and year 2 (April 2018 to March 2019), respectively. These interannual differences were largely related to different weather conditions encountered. In year 1, a month-long drought before and after the seeding and fertilizing reduced plant N uptake and dramatically increased soil N concentration. The following moderate rainfalls promoted large amount of NO emissions, which remained high until late September. The NO fluxes in both years showed clearer seasonal patterns, being highest after fertilizer application in summer, and lowest in winter. The seasonal patterns of NO fluxes were mainly controlled by soil available N concentrations and soil temperatures. The contribution of NO fluxes during the spring freeze-thaw in both years was no more than 0.2% of the annual NO budget, indicating that the freeze-thaw effect on agricultural NO emissions was minimal. In addition, with high-resolution monitoring, we found that soil not only act as a NO source but also a sink. Long-term and high-resolution measurements help us better understand the diurnal, seasonal, and annual dynamics of NO emissions, build more accurate models and better estimate global NO budget and develop more effective policy responses to global climate change.
Collapse
Affiliation(s)
- Chenxia Su
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China; College of Sources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weixing Zhu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China; Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, NY, 13902, USA
| | - Ronghua Kang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China; Key Laboratory of Isotope Techniques and Applications, Shenyang, 110016, China
| | - Zhi Quan
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China; Key Laboratory of Isotope Techniques and Applications, Shenyang, 110016, China
| | - Dongwei Liu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China; Key Laboratory of Isotope Techniques and Applications, Shenyang, 110016, China
| | - Wentao Huang
- College of Land and Environment, Shenyang Agricultural University, Shenyang, Liaoning, 110866, China
| | - Yi Shi
- CAS Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Xin Chen
- CAS Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Yunting Fang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China; Key Laboratory of Isotope Techniques and Applications, Shenyang, 110016, China.
| |
Collapse
|
50
|
Chen D, Xavier C, Clusius P, Nieminen T, Roldin P, Qi X, Pichelstorfer L, Kulmala M, Rantala P, Aalto J, Sarnela N, Kolari P, Keronen P, Rissanen MP, Taipale D, Foreback B, Baykara M, Zhou P, Boy M. A modelling study of OH, NO 3 and H 2SO 4 in 2007-2018 at SMEAR II, Finland: analysis of long-term trends. ENVIRONMENTAL SCIENCE: ATMOSPHERES 2021; 1:449-472. [PMID: 34604756 PMCID: PMC8459646 DOI: 10.1039/d1ea00020a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/13/2021] [Indexed: 11/21/2022]
Abstract
Major atmospheric oxidants (OH, O3 and NO3) dominate the atmospheric oxidation capacity, while H2SO4 is considered as a main driver for new particle formation. Although numerous studies have investigated the long-term trend of ozone in Europe, the trends of OH, NO3 and H2SO4 at specific sites are to a large extent unknown. The one-dimensional model SOSAA has been applied in several studies at the SMEAR II station and has been validated by measurements in several projects. Here, we applied the SOSAA model for the years 2007-2018 to simulate the atmospheric chemical components, especially the atmospheric oxidants OH and NO3, as well as H2SO4 at SMEAR II. The simulations were evaluated with observations from several shorter and longer campaigns at SMEAR II. Our results show that daily OH increased by 2.39% per year and NO3 decreased by 3.41% per year, with different trends of these oxidants during day and night. On the contrary, daytime sulfuric acid concentrations decreased by 2.78% per year, which correlated with the observed decreasing concentration of newly formed particles in the size range of 3-25 nm with 1.4% per year at SMEAR II during the years 1997-2012. Additionally, we compared our simulated OH, NO3 and H2SO4 concentrations with proxies, which are commonly applied in case a limited number of parameters are measured and no detailed model simulations are available.
Collapse
Affiliation(s)
- Dean Chen
- Institute for Atmospheric and Earth System Research/Physics, University of Helsinki P.O. Box 64 00014 Helsinki Finland
| | - Carlton Xavier
- Institute for Atmospheric and Earth System Research/Physics, University of Helsinki P.O. Box 64 00014 Helsinki Finland
| | - Petri Clusius
- Institute for Atmospheric and Earth System Research/Physics, University of Helsinki P.O. Box 64 00014 Helsinki Finland
| | - Tuomo Nieminen
- Institute for Atmospheric and Earth System Research/Physics, University of Helsinki P.O. Box 64 00014 Helsinki Finland .,Institute for Atmospheric and Earth System Research/Forest Sciences, University of Helsinki P.O. Box 64 00014 Helsinki Finland
| | - Pontus Roldin
- Division of Nuclear Physics, Department of Physics, Lund University P.O. Box 118 SE-22100 Lund Sweden
| | - Ximeng Qi
- Joint International Research Laboratory of Atmospheric and Earth System Sciences, School of Atmospheric Sciences, Nanjing University Nanjing 210023 China
| | - Lukas Pichelstorfer
- Institute for Atmospheric and Earth System Research/Physics, University of Helsinki P.O. Box 64 00014 Helsinki Finland
| | - Markku Kulmala
- Institute for Atmospheric and Earth System Research/Physics, University of Helsinki P.O. Box 64 00014 Helsinki Finland .,Joint International Research Laboratory of Atmospheric and Earth System Sciences, School of Atmospheric Sciences, Nanjing University Nanjing 210023 China
| | - Pekka Rantala
- Institute for Atmospheric and Earth System Research/Physics, University of Helsinki P.O. Box 64 00014 Helsinki Finland
| | - Juho Aalto
- Institute for Atmospheric and Earth System Research/Physics, University of Helsinki P.O. Box 64 00014 Helsinki Finland
| | - Nina Sarnela
- Institute for Atmospheric and Earth System Research/Physics, University of Helsinki P.O. Box 64 00014 Helsinki Finland
| | - Pasi Kolari
- Institute for Atmospheric and Earth System Research/Physics, University of Helsinki P.O. Box 64 00014 Helsinki Finland
| | - Petri Keronen
- Institute for Atmospheric and Earth System Research/Physics, University of Helsinki P.O. Box 64 00014 Helsinki Finland
| | - Matti P Rissanen
- Aerosol Physics Laboratory, Physics Unit, Faculty of Engineering and Natural Sciences, Tampere University Tampere Finland
| | - Ditte Taipale
- Institute for Atmospheric and Earth System Research/Physics, University of Helsinki P.O. Box 64 00014 Helsinki Finland
| | - Benjamin Foreback
- Institute for Atmospheric and Earth System Research/Physics, University of Helsinki P.O. Box 64 00014 Helsinki Finland
| | - Metin Baykara
- Institute for Atmospheric and Earth System Research/Physics, University of Helsinki P.O. Box 64 00014 Helsinki Finland .,Climate and Marine Sciences Department, Eurasia Institute of Earth Sciences, Istanbul Technical University Maslak 34469 Istanbul Turkey
| | - Putian Zhou
- Institute for Atmospheric and Earth System Research/Physics, University of Helsinki P.O. Box 64 00014 Helsinki Finland
| | - Michael Boy
- Institute for Atmospheric and Earth System Research/Physics, University of Helsinki P.O. Box 64 00014 Helsinki Finland
| |
Collapse
|