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Bhaduri D, Sihi D, Bhowmik A, Verma BC, Munda S, Dari B. A review on effective soil health bio-indicators for ecosystem restoration and sustainability. Front Microbiol 2022; 13:938481. [PMID: 36060788 PMCID: PMC9428492 DOI: 10.3389/fmicb.2022.938481] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/29/2022] [Indexed: 11/30/2022] Open
Abstract
Preventing degradation, facilitating restoration, and maintaining soil health is fundamental for achieving ecosystem stability and resilience. A healthy soil ecosystem is supported by favorable components in the soil that promote biological productivity and provide ecosystem services. Bio-indicators of soil health are measurable properties that define the biotic components in soil and could potentially be used as a metric in determining soil functionality over a wide range of ecological conditions. However, it has been a challenge to determine effective bio-indicators of soil health due to its temporal and spatial resolutions at ecosystem levels. The objective of this review is to compile a set of effective bio-indicators for developing a better understanding of ecosystem restoration capabilities. It addresses a set of potential bio-indicators including microbial biomass, respiration, enzymatic activity, molecular gene markers, microbial metabolic substances, and microbial community analysis that have been responsive to a wide range of ecosystem functions in agricultural soils, mine deposited soil, heavy metal contaminated soil, desert soil, radioactive polluted soil, pesticide polluted soil, and wetland soils. The importance of ecosystem restoration in the United Nations Sustainable Development Goals was also discussed. This review identifies key management strategies that can help in ecosystem restoration and maintain ecosystem stability.
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Affiliation(s)
- Debarati Bhaduri
- ICAR-National Rice Research Institute, Cuttack, India
- *Correspondence: Debarati Bhaduri
| | - Debjani Sihi
- Department of Environmental Sciences, Emory University, Atlanta, GA, United States
| | - Arnab Bhowmik
- Department of Natural Resources and Environmental Design, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
- Arnab Bhowmik
| | - Bibhash C. Verma
- Central Rainfed Upland Rice Research Station (ICAR-NRRI), Hazaribagh, India
| | | | - Biswanath Dari
- Agriculture and Natural Resources, Cooperative Extension at North Carolina Agricultural and Technical State University, Greensboro, NC, United States
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Wang T, Duan Y, Liu G, Shang X, Liu L, Zhang K, Li J, Zou Z, Zhu X, Fang W. Tea plantation intercropping green manure enhances soil functional microbial abundance and multifunctionality resistance to drying-rewetting cycles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:151282. [PMID: 34757096 DOI: 10.1016/j.scitotenv.2021.151282] [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: 07/12/2021] [Revised: 10/11/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
Climate change leads to more serious drying-rewetting alternation disturbance, which furtherly affects soil ecosystem function and agriculture production. Intercropping green manure, as an ancient agricultural practice, can improve the physical, chemical, and biological fertility of soil in tea plantation. However, the effects of intercropping green manure on soil multifunctional resistance to drying-rewetting disturbance in tea plantation has not been reported. In this study, the effects of different green manure practices over four years (tea plant monoculture, tea plant and soybean intercropping, tea plant and soybean + milk vetch intercropping) on soil multifunctionality resistance to drying-rewetting cycles, and the pivotal influencing factors were investigated. We used quantitative PCR array and analysis of multiple enzyme activities to characterize the abundance of functional genes and ecosystem multifunctionality, respectively. Compared with tea plantation monoculture, tea plant intercropping soybean and soybean + milk vetch significantly increased multifunctionality resistance by 12.07% and 25.86%, respectively. Random forest analysis indicated that rather than the diversity, the abundance of functional genes was the major drive of multifunctionality resistance. The structure equation model further proved that tea plantation intercropping green manure could improve the abundance of C cycling related functional genes mediated by soil properties, and ultimately increased multifunctionality resistance to drying-rewetting disturbance. Therefore, tea plantation intercropping green manure is an effective approach to maintain the multifunctionality resistance, which is conducive to maintain the soil nutrient supply capacity and tea production under the disturbance of drying-rewetting alternation.
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Affiliation(s)
- Ting Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Duan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Guodong Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaowen Shang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Lefeng Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kexin Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinqiu Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongwei Zou
- Department of Plant Science, University of Manitoba, Winnipeg R3T2N2, Canada
| | - Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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Granados-Chinchilla F, Arias-Andrés MDJ, Fernández Montes de Oca ML, Rodríguez C. Effect of the veterinary ionophore monensin on the structure and activity of a tropical soil bacterial community. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2019; 55:127-134. [PMID: 31588829 DOI: 10.1080/03601234.2019.1673612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Monensin (MON) is a coccidiostat used as a growth promoter that can reach the environment through fertilization with manure from farm animals. To verify whether field-relevant concentrations of this drug negatively influence the structure and activity of tropical soil bacteria, plate counts, CO2 efflux measurements, phospholipid fatty acids (PLFA) and community-level physiological profiling (CLPP) profiles were obtained for soil microcosms exposed to 1 or 10 mg kg-1 of MON across 11 days. Although 53% (1 mg kg-1) to 40% (10 mg kg-1) of the MON concentrations added to the microcosms dissipated within 5 days, a subtle concentration-dependent decrease in the number of culturable bacteria (<1 log CFU g-1), reduced (-20 to -30%) or exacerbated (+25%) soil CO2 effluxes, a marked shift of non-bacterial fatty acids, and altered respiration of amines (1.22-fold decrease) and polymers (1.70-fold increase) were noted in some of the treatments. These results suggest that MON quickly killed some microorganisms and that the surviving populations were selected and metabolically stimulated. Consequently, MON should be monitored in agronomic and environmental systems as part of One Health efforts.
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Affiliation(s)
| | - María de Jesús Arias-Andrés
- Instituto Regional de Estudios en Sustancias Tóxicas (IRET), Universidad Nacional de Costa Rica, Heredia, Costa Rica
| | | | - César Rodríguez
- Centro de Investigación en Enfermedades Tropicales (CIET) and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
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Domeignoz-Horta LA, Philippot L, Peyrard C, Bru D, Breuil MC, Bizouard F, Justes E, Mary B, Léonard J, Spor A. Peaks of in situ N 2 O emissions are influenced by N 2 O-producing and reducing microbial communities across arable soils. GLOBAL CHANGE BIOLOGY 2018; 24:360-370. [PMID: 28752605 DOI: 10.1111/gcb.13853] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/03/2017] [Indexed: 05/22/2023]
Abstract
Agriculture is the main source of terrestrial N2 O emissions, a potent greenhouse gas and the main cause of ozone depletion. The reduction of N2 O into N2 by microorganisms carrying the nitrous oxide reductase gene (nosZ) is the only known biological process eliminating this greenhouse gas. Recent studies showed that a previously unknown clade of N2 O-reducers (nosZII) was related to the potential capacity of the soil to act as a N2 O sink. However, little is known about how this group responds to different agricultural practices. Here, we investigated how N2 O-producers and N2 O-reducers were affected by agricultural practices across a range of cropping systems in order to evaluate the consequences for N2 O emissions. The abundance of both ammonia-oxidizers and denitrifiers was quantified by real-time qPCR, and the diversity of nosZ clades was determined by 454 pyrosequencing. Denitrification and nitrification potential activities as well as in situ N2 O emissions were also assessed. Overall, greatest differences in microbial activity, diversity, and abundance were observed between sites rather than between agricultural practices at each site. To better understand the contribution of abiotic and biotic factors to the in situ N2 O emissions, we subdivided more than 59,000 field measurements into fractions from low to high rates. We found that the low N2 O emission rates were mainly explained by variation in soil properties (up to 59%), while the high rates were explained by variation in abundance and diversity of microbial communities (up to 68%). Notably, the diversity of the nosZII clade but not of the nosZI clade was important to explain the variation of in situ N2 O emissions. Altogether, these results lay the foundation for a better understanding of the response of N2 O-reducing bacteria to agricultural practices and how it may ultimately affect N2 O emissions.
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Affiliation(s)
| | - Laurent Philippot
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | | | - David Bru
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | | | - Florian Bizouard
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Eric Justes
- AGIR, INPT, INP-PURPAN, INRA, Université de Toulouse, Toulouse, France
| | | | | | - Ayme Spor
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté, Dijon, France
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Mundepi A, Norton J, Cabrera M, Franklin D, Habteselassie MY. Ammonia Oxidizers in a Grazing Land with a History of Poultry Litter Application. JOURNAL OF ENVIRONMENTAL QUALITY 2017; 46:994-1002. [PMID: 28991982 DOI: 10.2134/jeq2017.04.0156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Poultry litter (PL) is widely applied on grazing lands in Georgia. However, it is not clear how its long-term use affects soil microorganisms and their function. We examined changes in activity and community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a grazing land with a history of PL application and compared it to treatment with urea ammonium nitrate (UAN). Soil samples (0-15 cm) were collected in 2009 (after 15 yr of PL application) and in 2013 (after 2 yr of no application). The abundance and community composition of ammonia oxidizers (AO) were determined with molecular techniques that targeted Nitrification potential (NP) was used for measuring their activity. Abundance of AO was significantly higher in PL (7.41 and 7.10 log copies g soil for AOB and AOA, respectively) than in UAN plots (6.82 and 6.50 log copies g soil for AOB and AOA, respectively) in 2009. This is consistent with NP, which was higher in PL (0.78 mg NO -N kg h) than in UAN (0.50 mg NO-N kg h) plots in 2009. The abundance of AO and NP decreased in 2013. There was no treatment effect on the composition of AO. Correlation analysis suggested that AOB were functionally more important than AOA, indicating the need to target AOB for efficient management of N in PL-receiving soils. Overall, the difference in nitrification between PL and UAN was mainly caused by the change in AO abundance rather than composition, and AO were not negatively affected by an increase in PL-derived trace metal concentrations.
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Waldrip HM, Todd RW, Parker DB, Cole NA, Rotz CA, Casey KD. Nitrous Oxide Emissions from Open-Lot Cattle Feedyards: A Review. JOURNAL OF ENVIRONMENTAL QUALITY 2016; 45:1797-1811. [PMID: 27898789 DOI: 10.2134/jeq2016.04.0140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nitrous oxide (NO) emissions from concentrated animal feeding operations, including cattle feedyards, have become an important research topic. However, there are limitations to current measurement techniques, uncertainty in the magnitude of feedyard NO fluxes, and a lack of effective mitigation methods. The objective of this review was to assess NO emission from cattle feedyards, including comparison of measured and modeled emission rates, discussion of measurement methods, and evaluation of mitigation options. Published annual per capita flux rates for beef cattle feedyards and open-lot dairies were highly variable and ranged from 0.002 to 4.3 kg NO animal yr. On an area basis, published emission rates ranged from 0 to 41 mg NO m h. From these studies and Intergovernmental Panel on Climate Change emission factors, calculated daily per capita NO fluxes averaged 18 ± 10 g NO animal d (range, 0.04-67 g NO animal d). This variation was due to inconsistency in measurement techniques as well as irregularity in NO production and emission attributable to management, animal diet, and environmental conditions. Based on this review, it is clear that the magnitude and dynamics of NO emissions from open-lot cattle systems are not well understood. Further research is required to quantify feedyard NO fluxes and develop cost-effective mitigation methods.
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Singer AC, Shaw H, Rhodes V, Hart A. Review of Antimicrobial Resistance in the Environment and Its Relevance to Environmental Regulators. Front Microbiol 2016; 7:1728. [PMID: 27847505 PMCID: PMC5088501 DOI: 10.3389/fmicb.2016.01728] [Citation(s) in RCA: 373] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/17/2016] [Indexed: 01/25/2023] Open
Abstract
The environment is increasingly being recognized for the role it might play in the global spread of clinically relevant antibiotic resistance. Environmental regulators monitor and control many of the pathways responsible for the release of resistance-driving chemicals into the environment (e.g., antimicrobials, metals, and biocides). Hence, environmental regulators should be contributing significantly to the development of global and national antimicrobial resistance (AMR) action plans. It is argued that the lack of environment-facing mitigation actions included in existing AMR action plans is likely a function of our poor fundamental understanding of many of the key issues. Here, we aim to present the problem with AMR in the environment through the lens of an environmental regulator, using the Environment Agency (England’s regulator) as an example from which parallels can be drawn globally. The issues that are pertinent to environmental regulators are drawn out to answer: What are the drivers and pathways of AMR? How do these relate to the normal work, powers and duties of environmental regulators? What are the knowledge gaps that hinder the delivery of environmental protection from AMR? We offer several thought experiments for how different mitigation strategies might proceed. We conclude that: (1) AMR Action Plans do not tackle all the potentially relevant pathways and drivers of AMR in the environment; and (2) AMR Action Plans are deficient partly because the science to inform policy is lacking and this needs to be addressed.
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Affiliation(s)
| | - Helen Shaw
- Department for Environment, Food and Rural Affairs London, UK
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Zhu X, Silva LCR, Doane TA, Wu N, Horwath WR. Quantifying the effects of green waste compost application, water content and nitrogen fertilization on nitrous oxide emissions in 10 agricultural soils. JOURNAL OF ENVIRONMENTAL QUALITY 2013; 42:912-918. [PMID: 23673959 DOI: 10.2134/jeq2012.0445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Common management practices, such as the application of green waste compost, soil moisture manipulation, and nitrogen fertilization, affect nitrous oxide (NO) emissions from agricultural soils. To expand our understanding of how soils interact with these controls, we studied their effects in 10 agricultural soils. Application of compost slightly increased NO emissions in soils with low initial levels of inorganic N and low background emission. For soils in which compost caused a decrease in emission, this decrease was larger than any of the observed increases in the other soils. The five most important factors driving emission across all soils, in order of increasing importance, were native dissolved organic carbon (DOC), treatment-induced change in DOC, native inorganic N, change in pH, and soil iron (Fe). Notable was the prominence of Fe as a regulator of NO emission. In general, compost is a viable amendment, considering the agronomic benefits it provides against the risk of producing a small increase in NO emissions. However, if soil properties and conditions are taken into account, management can recognize the potential effect of compost and thereby reduce NO emissions from susceptible soils, particularly by avoiding application of compost under wet conditions and together with ammonium fertilizer.
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Ammonia oxidation pathways and nitrifier denitrification are significant sources of N2O and NO under low oxygen availability. Proc Natl Acad Sci U S A 2013; 110:6328-33. [PMID: 23576736 DOI: 10.1073/pnas.1219993110] [Citation(s) in RCA: 249] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The continuous increase of nitrous oxide (N2O) abundance in the atmosphere is a global concern. Multiple pathways of N2O production occur in soil, but their significance and dependence on oxygen (O2) availability and nitrogen (N) fertilizer source are poorly understood. We examined N2O and nitric oxide (NO) production under 21%, 3%, 1%, 0.5%, and 0% (vol/vol) O2 concentrations following urea or ammonium sulfate [(NH4)2SO4] additions in loam, clay loam, and sandy loam soils that also contained ample nitrate. The contribution of the ammonia (NH3) oxidation pathways (nitrifier nitrification, nitrifier denitrification, and nitrification-coupled denitrification) and heterotrophic denitrification (HD) to N2O production was determined in 36-h incubations in microcosms by (15)N-(18)O isotope and NH3 oxidation inhibition (by 0.01% acetylene) methods. Nitrous oxide and NO production via NH3 oxidation pathways increased as O2 concentrations decreased from 21% to 0.5%. At low (0.5% and 3%) O2 concentrations, nitrifier denitrification contributed between 34% and 66%, and HD between 34% and 50% of total N2O production. Heterotrophic denitrification was responsible for all N2O production at 0% O2. Nitrifier denitrification was the main source of N2O production from ammonical fertilizer under low O2 concentrations with urea producing more N2O than (NH4)2SO4 additions. These findings challenge established thought attributing N2O emissions from soils with high water content to HD due to presumably low O2 availability. Our results imply that management practices that increase soil aeration, e.g., reducing compaction and enhancing soil structure, together with careful selection of fertilizer sources and/or nitrification inhibitors, could decrease N2O production in agricultural soils.
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Saunders OE, Fortuna AM, Harrison JH, Cogger CG, Whitefield E, Green T. Gaseous nitrogen and bacterial responses to raw and digested dairy manure applications in incubated soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:11684-11692. [PMID: 22971014 DOI: 10.1021/es301754s] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A study was conducted under laboratory conditions to compare rates of nitrous oxide (N(2)O) and ammonia (NH(3)) emissions when soil was amended with anaerobically digested dairy manure slurry containing <30% food byproducts, raw dairy manure slurry, or urea. Slurries were applied via surface and subsurface methods. A second objective was to correlate genes regulating nitrification and denitrification with rates of N(2)O production, slurry treatment, and application method. Ammonia volatilization from incubated soil ranged from 140 g kg(-1) of total N applied in digested slurry to 230 g kg(-1) in urea. Subsurface application of raw dairy manure slurry decreased ammonia volatilization compared with surface application. Anaerobic digestion increased N(2)O production. Cumulative N(2)O loss averaged 27 g kg(-1) of total N applied for digested slurry, compared with 5 g kg(-1) for raw dairy slurry. Genes of interest included a 16S rRNA gene selective for β-subgroup proteobacterial ammonia-oxidizers, amoA, narG, and nosZ quantified with quantitative polymerase chain reaction (qPCR) and real-time polymerase chain reaction (RT-PCR). Application of anaerobically digested slurry increased nitrifier and denitrifier gene copies that correlated with N(2)O production. Expression of all genes measured via mRNA levels was affected by N applications to soil. This study provides new information linking genetic markers in denitrifier and nitrifier populations to N(2)O production.
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Affiliation(s)
- Olivia E Saunders
- Department of Crop and Soil Science, Washington State University, Pullman, Washington 99164-6420, USA
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