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Lim J, Wehmeyer H, Heffner T, Aeppli M, Gu W, Kim PJ, Horn MA, Ho A. Resilience of aerobic methanotrophs in soils; spotlight on the methane sink under agriculture. FEMS Microbiol Ecol 2024; 100:fiae008. [PMID: 38327184 PMCID: PMC10872700 DOI: 10.1093/femsec/fiae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 02/09/2024] Open
Abstract
Aerobic methanotrophs are a specialized microbial group, catalyzing the oxidation of methane. Disturbance-induced loss of methanotroph diversity/abundance, thus results in the loss of this biological methane sink. Here, we synthesized and conceptualized the resilience of the methanotrophs to sporadic, recurring, and compounded disturbances in soils. The methanotrophs showed remarkable resilience to sporadic disturbances, recovering in activity and population size. However, activity was severely compromised when disturbance persisted or reoccurred at increasing frequency, and was significantly impaired following change in land use. Next, we consolidated the impact of agricultural practices after land conversion on the soil methane sink. The effects of key interventions (tillage, organic matter input, and cover cropping) where much knowledge has been gathered were considered. Pairwise comparisons of these interventions to nontreated agricultural soils indicate that the agriculture-induced impact on the methane sink depends on the cropping system, which can be associated to the physiology of the methanotrophs. The impact of agriculture is more evident in upland soils, where the methanotrophs play a more prominent role than the methanogens in modulating overall methane flux. Although resilient to sporadic disturbances, the methanotrophs are vulnerable to compounded disturbances induced by anthropogenic activities, significantly affecting the methane sink function.
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Affiliation(s)
- Jiyeon Lim
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Helena Wehmeyer
- Nestlè Research, Route du Jorat 57, CH 1000 Lausanne 26, Switzerland
| | - Tanja Heffner
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Meret Aeppli
- Environmental Engineering Institute IIE-ENAC, Laboratory SOIL, Ecole Polytechnique Fédérale de Lausanne (EPFL), Valais Wallis, CH 1950 Sion, Switzerland
| | - Wenyu Gu
- Environmental Engineering Institute IIE-ENAC, Laboratory MICROBE, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH 1015 Lausanne, Switzerland
| | - Pil Joo Kim
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Marcus A Horn
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Adrian Ho
- Nestlè Research, Route du Jorat 57, CH 1000 Lausanne 26, Switzerland
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Duan N, Radosevich M, Zhuang J, DeBruyn JM, Staton M, Schaeffer SM. Identification of Novel Viruses and Their Microbial Hosts from Soils with Long-Term Nitrogen Fertilization and Cover Cropping Management. mSystems 2022; 7:e0057122. [PMID: 36445691 DOI: 10.1128/msystems.00571-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Soils are the largest organic carbon reservoir and are key to global biogeochemical cycling, and microbes are the major drivers of carbon and nitrogen transformations in the soil systems. Thus, virus infection-induced microbial mortality could impact soil microbial structure and functions. In this study, we recovered 260 viral operational taxonomic units (vOTUs) in samples collected from soil taken from four nitrogen fertilization (N-fertilization) and cover-cropping practices at an experimental site under continuous cotton production evaluating conservation agricultural management systems for more than 40 years. Only ~6% of the vOTUs identified were clustered with known viruses in the RefSeq database using a gene-sharing network. We found that 14% of 260 vOTUs could be linked to microbial hosts that cover key carbon and nitrogen cycling taxa, including Acidobacteriota, Proteobacteria, Verrucomicrobiota, Firmicutes, and ammonia-oxidizing archaea, i.e., Nitrososphaeria (phylum Thermoproteota). Viral diversity, community structure, and the positive correlation between abundance of a virus and its host indicate that viruses and microbes are more sensitive to N-fertilization than cover-cropping treatment. Viruses may influence key carbon and nitrogen cycling through control of microbial function and host populations (e.g., Chthoniobacterales and Nitrososphaerales). These findings provide an initial view of soil viral ecology and how it is influenced by long-term conservation agricultural management. IMPORTANCE Bacterial viruses are extremely small and abundant particles that can control the microbial abundance and community composition through infection, which gradually showed their vital roles in the ecological process to influence the nutrient flow. Compared to the substrate control, less is known about the influence of soil viruses on microbial community function, and even less is known about microbial and viral diversity in the soil system. To obtain a more complete knowledge of microbial function dynamics, the interaction between microbes and viruses cannot be ignored. To fully understand this process, it is fundamental to get insight into the correlation between the diversity of viral communities and bacteria which could induce these changes.
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Lombardo S, Restuccia A, Abbate C, Anastasi U, Fontanazza S, Scavo A, Guarnaccia P, La Malfa S, Pandino G, Mauromicale G. Trifolium subterraneum cover cropping for improving the nutritional status of a Mediterranean apricot orchard. J Sci Food Agric 2021; 101:3767-3777. [PMID: 33300619 DOI: 10.1007/s13593-021-00721-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/18/2020] [Accepted: 12/02/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND The utilization of Trifolium subterraneum L. cover crops may represent an innovative and efficient option in low-input and organic farming, especially in Mediterranean agroecosystems where low and irregular rainfall require frequent soil tillage and use of herbicides to reduce moisture losses and weed competitiveness. Since imbalances of soil macro- and micro-nutrients due to cover cropping establishment could be responsible for numerous problems in specialized orchards, such as disturbances in the normal tree growth and quality of fruits, the objective of this study was to investigate, the cumulative effects of a 3-years established T. subterraneum cover cropping, compared with a spontaneous flora and a conventional management (as a control), on the levels of mineral nutrients in the apricot leaves and fruits. RESULTS Our findings indicated that T. subterraneum cover cropping tended to stimulate higher leaf macro- and micro-nutrients content than conventional management and flora spontaneous cover cropping. In addition, the presence of T. subterraneum cover cropping, especially with the incorporation of dead mulches into the soil, increased the content of potassium (K), nitrogen (N), calcium (Ca), iron (Fe) and manganese (Mn) in apricot fruits. CONCLUSION Taking also into account the effects of T. subterraneum cover cropping on both the reduction of soil weed and enhancement of bacteria communities involved in the soil N-cycle, we may suggest its application in Mediterranean orchards as an eco-friendly alternative to synthetic herbicides for weed control and mineral N fertilizers, while enhancing the apricot tree nutritional status and fruit quality. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Sara Lombardo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Alessia Restuccia
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Cristina Abbate
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Umberto Anastasi
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Stefania Fontanazza
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Aurelio Scavo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Paolo Guarnaccia
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Stefano La Malfa
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Gaetano Pandino
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Giovanni Mauromicale
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
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Lombardo S, Restuccia A, Abbate C, Anastasi U, Fontanazza S, Scavo A, Guarnaccia P, La Malfa S, Pandino G, Mauromicale G. Trifolium subterraneum cover cropping for improving the nutritional status of a Mediterranean apricot orchard. J Sci Food Agric 2021; 101:3767-3777. [PMID: 33300619 DOI: 10.1002/jsfa.11009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/18/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND The utilization of Trifolium subterraneum L. cover crops may represent an innovative and efficient option in low-input and organic farming, especially in Mediterranean agroecosystems where low and irregular rainfall require frequent soil tillage and use of herbicides to reduce moisture losses and weed competitiveness. Since imbalances of soil macro- and micro-nutrients due to cover cropping establishment could be responsible for numerous problems in specialized orchards, such as disturbances in the normal tree growth and quality of fruits, the objective of this study was to investigate, the cumulative effects of a 3-years established T. subterraneum cover cropping, compared with a spontaneous flora and a conventional management (as a control), on the levels of mineral nutrients in the apricot leaves and fruits. RESULTS Our findings indicated that T. subterraneum cover cropping tended to stimulate higher leaf macro- and micro-nutrients content than conventional management and flora spontaneous cover cropping. In addition, the presence of T. subterraneum cover cropping, especially with the incorporation of dead mulches into the soil, increased the content of potassium (K), nitrogen (N), calcium (Ca), iron (Fe) and manganese (Mn) in apricot fruits. CONCLUSION Taking also into account the effects of T. subterraneum cover cropping on both the reduction of soil weed and enhancement of bacteria communities involved in the soil N-cycle, we may suggest its application in Mediterranean orchards as an eco-friendly alternative to synthetic herbicides for weed control and mineral N fertilizers, while enhancing the apricot tree nutritional status and fruit quality. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Sara Lombardo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Alessia Restuccia
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Cristina Abbate
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Umberto Anastasi
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Stefania Fontanazza
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Aurelio Scavo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Paolo Guarnaccia
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Stefano La Malfa
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Gaetano Pandino
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Giovanni Mauromicale
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
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Bhowmik A, Cloutier M, Ball E, Bruns MA. Underexplored microbial metabolisms for enhanced nutrient recycling in agricultural soils. AIMS Microbiol 2017; 3:826-845. [PMID: 31294192 PMCID: PMC6604955 DOI: 10.3934/microbiol.2017.4.826] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/21/2017] [Indexed: 01/03/2023] Open
Abstract
Worldwide, arable soils have been degraded through erosion and exhaustive cultivation, and substantial proportions of fertilizer nutrients are not taken up by crops. A central challenge in agriculture is to understand how soils and resident microbial communities can be managed to deliver nutrients to crops more efficiently with minimal losses to the environment. Throughout much of the twentieth century, intensive farming has caused substantial loss of organic matter and soil biological function. Today, more farmers recognize the importance of protecting soils and restoring organic matter through reduced tillage, diversified crop rotation, cover cropping, and increased organic amendments. Such management practices are expected to foster soil conditions more similar to those of undisturbed, native plant-soil systems by restoring soil biophysical integrity and re-establishing plant-microbe interactions that retain and recycle nutrients. Soil conditions which could contribute to desirable shifts in microbial metabolic processes include lower redox potentials, more diverse biogeochemical gradients, higher concentrations of labile carbon, and enrichment of carbon dioxide (CO2) and hydrogen gas (H2) in soil pores. This paper reviews recent literature on generalized and specific microbial processes that could become more operational once soils are no longer subjected to intensive tillage and organic matter depletion. These processes include heterotrophic assimilation of CO2; utilization of H2 as electron donor or reactant; and more diversified nitrogen uptake and dissimilation pathways. Despite knowledge of these processes occurring in laboratory studies, they have received little attention for their potential to affect nutrient and energy flows in soils. This paper explores how soil microbial processes could contribute to in situ nutrient retention, recycling, and crop uptake in agricultural soils managed for improved biological function.
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Affiliation(s)
- Arnab Bhowmik
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA 16802, USA
| | - Mara Cloutier
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA 16802, USA.,Dual-Title Graduate Program in Biogeochemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Emily Ball
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA 16802, USA
| | - Mary Ann Bruns
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA 16802, USA.,Dual-Title Graduate Program in Biogeochemistry, The Pennsylvania State University, University Park, PA 16802, USA.,Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA 16802, USA
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