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Franco GC, Leiva J, Nand S, Lee DM, Hajkowski M, Dick K, Withers B, Soto L, Mingoa BR, Acholonu M, Hutchins A, Neely L, Anand A. Soil Microbial Communities and Wine Terroir: Research Gaps and Data Needs. Foods 2024; 13:2475. [PMID: 39200402 PMCID: PMC11354026 DOI: 10.3390/foods13162475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 09/02/2024] Open
Abstract
Microbes found in soil can have a significant impact on the taste and quality of wine, also referred to as wine terroir. To date, wine terroir has been thought to be associated with the physical and chemical characteristics of the soil. However, there is a fragmented understanding of the contribution of vineyard soil microbes to wine terroir. Additionally, vineyards can play an important role in carbon sequestration since the promotion of healthy soil and microbial communities directly impacts greenhouse gas emissions in the atmosphere. We review 24 studies that explore the role of soil microbial communities in vineyards and their influence on grapevine health, grape composition, and wine quality. Studies spanning 2015 to 2018 laid a foundation by exploring soil microbial biogeography in vineyards, vineyard management effects, and the reservoir function of soil microbes for grape-associated microbiota. On the other hand, studies spanning 2019 to 2023 appear to have a more specific and targeted approach, delving into the relationships between soil microbes and grape metabolites, the microbial distribution at different soil depths, and microbial influences on wine flavor and composition. Next, we identify research gaps and make recommendations for future work. Specifically, most of the studies utilize targeted sequencing (16S, 26S, ITS), which only reveals community composition. Utilizing high-throughput omics approaches such as shotgun sequencing (to infer function) and transcriptomics (for actual function) is vital to determining the specific mechanisms by which soil microbes influence grape chemistry. Going forward, understanding the long-term effects of vineyard management practices and climate change on soil microbiology, grapevine trunk diseases, and the role of bacteriophages in vineyard soil and wine-making would be a fruitful investigation. Overall, the studies presented shed light on the importance of soil microbiomes and their interactions with grapevines in shaping wine production. However, there are still many aspects of this complex ecosystem that require further exploration and understanding to support sustainable viticulture and enhance wine quality.
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Affiliation(s)
- Gabriela Crystal Franco
- Department of Biology, College of Science and Engineering, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA; (G.C.F.); (J.L.); (S.N.); (D.M.L.); (M.H.); (K.D.); (B.W.); (L.S.); (B.-R.M.); (M.A.)
| | - Jasmine Leiva
- Department of Biology, College of Science and Engineering, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA; (G.C.F.); (J.L.); (S.N.); (D.M.L.); (M.H.); (K.D.); (B.W.); (L.S.); (B.-R.M.); (M.A.)
| | - Sanjiev Nand
- Department of Biology, College of Science and Engineering, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA; (G.C.F.); (J.L.); (S.N.); (D.M.L.); (M.H.); (K.D.); (B.W.); (L.S.); (B.-R.M.); (M.A.)
| | - Danica Marvi Lee
- Department of Biology, College of Science and Engineering, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA; (G.C.F.); (J.L.); (S.N.); (D.M.L.); (M.H.); (K.D.); (B.W.); (L.S.); (B.-R.M.); (M.A.)
| | - Michael Hajkowski
- Department of Biology, College of Science and Engineering, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA; (G.C.F.); (J.L.); (S.N.); (D.M.L.); (M.H.); (K.D.); (B.W.); (L.S.); (B.-R.M.); (M.A.)
| | - Katherine Dick
- Department of Biology, College of Science and Engineering, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA; (G.C.F.); (J.L.); (S.N.); (D.M.L.); (M.H.); (K.D.); (B.W.); (L.S.); (B.-R.M.); (M.A.)
| | - Brennan Withers
- Department of Biology, College of Science and Engineering, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA; (G.C.F.); (J.L.); (S.N.); (D.M.L.); (M.H.); (K.D.); (B.W.); (L.S.); (B.-R.M.); (M.A.)
| | - LuzMaria Soto
- Department of Biology, College of Science and Engineering, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA; (G.C.F.); (J.L.); (S.N.); (D.M.L.); (M.H.); (K.D.); (B.W.); (L.S.); (B.-R.M.); (M.A.)
| | - Benjamin-Rafael Mingoa
- Department of Biology, College of Science and Engineering, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA; (G.C.F.); (J.L.); (S.N.); (D.M.L.); (M.H.); (K.D.); (B.W.); (L.S.); (B.-R.M.); (M.A.)
| | - Michael Acholonu
- Department of Biology, College of Science and Engineering, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA; (G.C.F.); (J.L.); (S.N.); (D.M.L.); (M.H.); (K.D.); (B.W.); (L.S.); (B.-R.M.); (M.A.)
| | - Amari Hutchins
- Department of Biology, Howard University, 2400 6th St NW, Washington, DC 20059, USA;
| | - Lucy Neely
- Neely Winery, Spring Ridge Vineyard, 555 Portola Road, Portola Valley, CA 94028, USA;
| | - Archana Anand
- Department of Biology, College of Science and Engineering, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA; (G.C.F.); (J.L.); (S.N.); (D.M.L.); (M.H.); (K.D.); (B.W.); (L.S.); (B.-R.M.); (M.A.)
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Han S, Ji X, Huang L, Liu G, Ye J, Wang A. Effects of aftercrop tomato and maize on the soil microenvironment and microbial diversity in a long-term cotton continuous cropping field. Front Microbiol 2024; 15:1410219. [PMID: 39101036 PMCID: PMC11295657 DOI: 10.3389/fmicb.2024.1410219] [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: 03/31/2024] [Accepted: 06/17/2024] [Indexed: 08/06/2024] Open
Abstract
Long-term continuous cropping affects the soil microecological community and leads to nutrient imbalances, which reduces crop yields, and crop rotation can increase soil productivity. To study the effects of the cultivation of tomato (Solanum lycopersicum) and corn (Zea mays) on the microbial community, physical and chemical factors and the structure of aggregates in cotton (Gossypium hirsutum) long-term continuous cropping soils were examined. Four cropping patterns were established, including one continuous cropping pattern and three crop rotation patterns, and the diversity of the soil microecological community was measured using high-throughput sequencing. The physical and chemical properties of different models of soil were measured, and the soil aggregate structure was determined by dry and wet sieving. Planting of aftercrop tomato and corn altered the bacterial community of the cotton continuous soil to a lesser extent and the fungal community to a greater extent. In addition, continuous cropping reduced the diversity and richness of the soil fungal community. Different aftercrop planting patterns showed that there were very high contents of soil organic carbon and organic matter in the cotton-maize rotation model, while the soil aggregate structure was the most stable in the corn-cotton rotation model. Planting tomato in continuous cropping cotton fields has a greater effect on the soil microbial community than planting maize. Therefore, according to the characteristics of different succeeding crop planting patterns, the damage of continuous cropping of cotton to the soil microenvironment can be alleviated directionally, which will enable the sustainable development of cotton production.
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Affiliation(s)
- Shouyan Han
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
- Key Laboratory of Oasis Town and Mountain-basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, Xinjiang, China
| | - Xiaohui Ji
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
- Key Laboratory of Oasis Town and Mountain-basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, Xinjiang, China
| | - Liwen Huang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
- Key Laboratory of Oasis Town and Mountain-basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, Xinjiang, China
| | - Gaijie Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
- Key Laboratory of Oasis Town and Mountain-basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, Xinjiang, China
| | - Jingyi Ye
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
- Key Laboratory of Oasis Town and Mountain-basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, Xinjiang, China
| | - Aiying Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
- Key Laboratory of Oasis Town and Mountain-basin System Ecology, Xinjiang Production and Construction Corps, Shihezi, Xinjiang, China
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Chavez M, Viscardi S, Ruiz MJ, Sans-Serramitjana E, Durán P. CLI: A new protocol for the isolation of Lactic Acid Bacteria from complex plant samples. J Microbiol Methods 2024; 221:106937. [PMID: 38648958 DOI: 10.1016/j.mimet.2024.106937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024]
Abstract
Lactic Acid Bacteria (LAB) are predominantly probiotic microorganisms and the most are Generally Recognized As Safe (GRAS). LAB inhabit in the human gut ecosystem and are largely found in fermented foods and silage. In the last decades, LAB have also has been found in plant microbiota as a new class of microbes with probiotic activity to plants. For this reason, today the scientific interest in the study and isolation of LAB for agronomic application has increased. However, isolation protocols from complex samples such as plant tissues are scarce and inefficient. In this study, we developed a new protocol (CLI, Complex samples LAB Isolation) which yields purified LAB from plants. The sensitivity of CLI protocol was sufficient to isolate representative microorganisms of LAB genera (i.e. Leuconostoc, Lactococcus and Enterococcus). CLI protocol consists on five steps: i) sample preparation and pre-incubation in 1% sterile peptone at 30 °C for 24-48 h; ii) Sample homogenization in vortex by 10 min; iii) sample serial dilution in quarter-strength Ringer solution, iv) incubation in MRS agar plates with 0.2% of sorbic acid, with 1% of CaCO3, O2 < 15%, at pH 5.8 and 37 °C for 48 h.; v) Selection of single colonies with LAB morphology and CaCO3-solubilization halo. Our scientific contribution is that CLI protocol could be used for several complex samples and represents a useful method for further studies involving native LAB.
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Affiliation(s)
- Mariannys Chavez
- Doctoral Program in Natural Bioresource Sciences, Universidad de La Frontera, Temuco 4811230, Chile; Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Sharon Viscardi
- Núcleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, P.O. Box 15-D, Temuco 4813302, Chile; Laboratorio de Investigación Interdisciplinaria en Microbiología Aplicada, Departamento de Procesos Diagnóstico y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Manuel Montt 56, Temuco, La Araucanía, Chile
| | - María José Ruiz
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Eulàlia Sans-Serramitjana
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile; Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile
| | - Paola Durán
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile; Biocontrol Research Laboratory, Universidad de La Frontera, Temuco 4811230, Chile; Facultad de Ciencias Agropecuarias y Medioambiente, Departamento de Producción Agropecuaria, Universidad de La Frontera, Temuco 4811230, Chile.
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de Sousa RDSDR, Lima GVS, Garcias JT, Gomes GDO, Mateus JR, Madeira LDPDS, Seldin L, Rogez HLG, Marques JM. The Microbial Community Structure in the Rhizosphere of Theobroma cacao L. and Euterpe oleracea Mart. Is Influenced by Agriculture System in the Brazilian Amazon. Microorganisms 2024; 12:398. [PMID: 38399802 PMCID: PMC10892126 DOI: 10.3390/microorganisms12020398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 02/25/2024] Open
Abstract
This study tested the hypothesis that cocoa monoculture (MS) and cocoa-açai agroforestry systems (AFS) may influence the microbial community structure and populations of plant growth-promoting bacteria (PGPR). Accordingly, the aim was to analyze the microbial community structure and PGPR populations in different agroecosystems in the Brazilian Amazon. To achieve this, the rhizosphere microbial community of cocoa and açai plants in both Amazonian seasons (dry and rainy) was analyzed using culture-dependent (PGPR screening) and -independent methods [PCR-DGGE based on rrs, alp, nifH gene, and intergenic region (ITS) of fungi]. Concerning PGPR screening, out of 48 isolated bacterial strains, 25% were capable of siderophore production, 29% of mineralized organic phosphate, 8% of inorganic phosphate solubilization, and 4% of indole acetic acid production. Moreover, 17% of isolates could inhibit the growth of various phytopathogenic fungi. Statistical analyses of DGGE fingerprints (p < 0.05) showed that bacterial and fungal community structures in the rhizosphere were influenced by the seasons, supporting the results of the physicochemical analysis of the environment. Furthermore, as hypothesized, microbial communities differed statistically when comparing the MS and AFS. These findings provide important insights into the influence of climate and cultivation systems on soil microbial communities to guide the development of sustainable agricultural practices.
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Affiliation(s)
- Rosiane do Socorro dos Reis de Sousa
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Giulia Victória Silva Lima
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Josinete Torres Garcias
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Graziane de Oliveira Gomes
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Jackeline Rossetti Mateus
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Rio de Janeiro, Brazil; (J.R.M.); (L.S.)
| | - Lucimar Di Paula dos Santos Madeira
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Rio de Janeiro, Brazil; (J.R.M.); (L.S.)
| | - Hervé Louis Ghislain Rogez
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Joana Montezano Marques
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Rio de Janeiro, Brazil; (J.R.M.); (L.S.)
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Kotlova ER, Senik SV, Pozhvanov GA, Prokopiev IA, Boldyrev IA, Manzhieva BS, Amigud EY, Puzanskiy RK, Khakulova AA, Serebryakov EB. Uptake and Metabolic Conversion of Exogenous Phosphatidylcholines Depending on Their Acyl Chain Structure in Arabidopsis thaliana. Int J Mol Sci 2023; 25:89. [PMID: 38203257 PMCID: PMC10778594 DOI: 10.3390/ijms25010089] [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: 11/16/2023] [Revised: 12/11/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024] Open
Abstract
Fungi and plants are not only capable of synthesizing the entire spectrum of lipids de novo but also possess a well-developed system that allows them to assimilate exogenous lipids. However, the role of structure in the ability of lipids to be absorbed and metabolized has not yet been characterized in detail. In the present work, targeted lipidomics of phosphatidylcholines (PCs) and phosphatidylethanolamines (PEs), in parallel with morphological phenotyping, allowed for the identification of differences in the effects of PC molecular species introduced into the growth medium, in particular, typical bacterial saturated (14:0/14:0, 16:0/16:0), monounsaturated (16:0/18:1), and typical for fungi and plants polyunsaturated (16:0/18:2, 18:2/18:2) species, on Arabidopsis thaliana. For comparison, the influence of an artificially synthesized (1,2-di-(3-(3-hexylcyclopentyl)-propanoate)-sn-glycero-3-phosphatidylcholine, which is close in structure to archaeal lipids, was studied. The phenotype deviations stimulated by exogenous lipids included changes in the length and morphology of both the roots and leaves of seedlings. According to lipidomics data, the main trends in response to exogenous lipid exposure were an increase in the proportion of endogenic 18:1/18:1 PC and 18:1_18:2 PC molecular species and a decrease in the relative content of species with C18:3, such as 18:3/18:3 PC and/or 16:0_18:3 PC, 16:1_18:3 PE. The obtained data indicate that exogenous lipid molecules affect plant morphology not only due to their physical properties, which are manifested during incorporation into the membrane, but also due to the participation of exogenous lipid molecules in the metabolism of plant cells. The results obtained open the way to the use of PCs of different structures as cellular regulators.
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Affiliation(s)
- Ekaterina R. Kotlova
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
| | - Svetlana V. Senik
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
| | - Gregory A. Pozhvanov
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
- Department of Botany and Ecology, Faculty of Biology, Herzen State Pedagogical University, 191186 Saint-Petersburg, Russia
| | - Ilya A. Prokopiev
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
| | - Ivan A. Boldyrev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Bairta S. Manzhieva
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
| | - Ekaterina Ya. Amigud
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
- Department of Botany and Ecology, Faculty of Biology, Herzen State Pedagogical University, 191186 Saint-Petersburg, Russia
| | - Roman K. Puzanskiy
- Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint-Petersburg, Russia; (S.V.S.); (G.A.P.); (I.A.P.); (B.S.M.); (E.Y.A.); (R.K.P.)
| | - Anna A. Khakulova
- Chemical Analysis and Materials Research Core Facility Center, Reseach Park, Saint-Petersburg State University, 199034 Saint-Petersburg, Russia; (A.A.K.); (E.B.S.)
| | - Evgeny B. Serebryakov
- Chemical Analysis and Materials Research Core Facility Center, Reseach Park, Saint-Petersburg State University, 199034 Saint-Petersburg, Russia; (A.A.K.); (E.B.S.)
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Dumonceaux T. Composition and Dynamics of Plant- and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems. Microorganisms 2023; 11:1782. [PMID: 37512954 PMCID: PMC10384853 DOI: 10.3390/microorganisms11071782] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Peter Kropotkin (1842-1921) is well known as an anarchist intellectual, an amiable mass of contradictions who loved humanity and was highly regarded in academic and intellectual circles, yet also penned "fiery peans to violence" in Le Révolté, the anarchist journal he established with Elisée Reclus in the 1870s [...].
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Affiliation(s)
- Tim Dumonceaux
- Agriculture and Agri-Food Canada Saskatoon Research and Development Centre, Saskatoon, SK S7N 0X2, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
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Assessing Impacts of Transgenic Plants on Soil Using Functional Indicators: Twenty Years of Research and Perspectives. PLANTS 2022; 11:plants11182439. [PMID: 36145839 PMCID: PMC9503467 DOI: 10.3390/plants11182439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/23/2022] [Accepted: 09/15/2022] [Indexed: 11/23/2022]
Abstract
Assessment of the effects of transgenic plants on microbiota and soil fertility is an important part of the overall assessment of their biosafety. However, the environmental risk assessment of genetically modified plants has long been focused on the aboveground effects. In this review, we discuss the results of two decades of research on the impact of transgenic plants on the physicochemical properties of soil, its enzyme activities and microbial biomass. These indicators allow us to assess both the short-term effects and long-term effects of cultivating transgenic plants. Most studies have shown that the effect of transgenic plants on the soil is temporary and inconsistent. Moreover, many other factors, such as the site location, weather conditions, varietal differences and management system, have a greater impact on soil quality than the transgenic status of the plants. In addition to the effects of transgenic crop cultivation, the review also considers the effects of transgenic plant residues on soil processes, and discusses the future prospects for studying the impact of genetically modified plants on soil ecosystems.
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Farooq MS, Wang X, Uzair M, Fatima H, Fiaz S, Maqbool Z, Rehman OU, Yousuf M, Khan MR. Recent trends in nitrogen cycle and eco-efficient nitrogen management strategies in aerobic rice system. FRONTIERS IN PLANT SCIENCE 2022; 13:960641. [PMID: 36092421 PMCID: PMC9453445 DOI: 10.3389/fpls.2022.960641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Rice (Oryza sativa L.) is considered as a staple food for more than half of the global population, and sustaining productivity under a scarcity of resources is challenging to meet the future food demands of the inflating global population. The aerobic rice system can be considered as a transformational replacement for traditional rice, but the widespread adaptation of this innovative approach has been challenged due to higher losses of nitrogen (N) and reduced N-use efficiency (NUE). For normal growth and developmental processes in crop plants, N is required in higher amounts. N is a mineral nutrient and an important constituent of amino acids, nucleic acids, and many photosynthetic metabolites, and hence is essential for normal plant growth and metabolism. Excessive application of N fertilizers improves aerobic rice growth and yield, but compromises economic and environmental sustainability. Irregular and uncontrolled use of N fertilizers have elevated several environmental issues linked to higher N losses in the form of nitrous oxide (N2O), ammonia (NH3), and nitrate (NO3 -), thereby threatening environmental sustainability due to higher warming potential, ozone depletion capacities, and abilities to eutrophicate the water resources. Hence, enhancing NUE in aerobic rice has become an urgent need for the development of a sustainable production system. This article was designed to investigate the major challenge of low NUE and evaluate recent advances in pathways of the N cycle under the aerobic rice system, and thereby suggest the agronomic management approaches to improve NUE. The major objective of this review is about optimizing the application of N inputs while sustaining rice productivity and ensuring environmental safety. This review elaborates that different soil conditions significantly shift the N dynamics via changes in major pathways of the N cycle and comprehensively reviews the facts why N losses are high under the aerobic rice system, which factors hinder in attaining high NUE, and how it can become an eco-efficient production system through agronomic managements. Moreover, it explores the interactive mechanisms of how proper management of N cycle pathways can be accomplished via optimized N fertilizer amendments. Meanwhile, this study suggests several agricultural and agronomic approaches, such as site-specific N management, integrated nutrient management (INM), and incorporation of N fertilizers with enhanced use efficiency that may interactively improve the NUE and thereby plant N uptake in the aerobic rice system. Additionally, resource conservation practices, such as plant residue management, green manuring, improved genetic breeding, and precision farming, are essential to enhance NUE. Deep insights into the recent advances in the pathways of the N cycle under the aerobic rice system necessarily suggest the incorporation of the suggested agronomic adjustments to reduce N losses and enhance NUE while sustaining rice productivity and environmental safety. Future research on N dynamics is encouraged under the aerobic rice system focusing on the interactive evaluation of shifts among activities and diversity in microbial communities, NUE, and plant demands while applying N management measures, which is necessary for its widespread adaptation in face of the projected climate change and scarcity of resources.
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Affiliation(s)
- Muhammad Shahbaz Farooq
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Hira Fatima
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Zubaira Maqbool
- Institute of Soil Science, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Obaid Ur Rehman
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
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9
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Florent P, Cauchie HM, Herold M, Jacquet S, Ogorzaly L. Soil pH, Calcium Content and Bacteria as Major Factors Responsible for the Distribution of the Known Fraction of the DNA Bacteriophage Populations in Soils of Luxembourg. Microorganisms 2022; 10:1458. [PMID: 35889177 PMCID: PMC9321959 DOI: 10.3390/microorganisms10071458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages participate in soil life by influencing bacterial community structure and function, biogeochemical cycling and horizontal gene transfer. Despite their great abundance, diversity, and importance in microbial processes, they remain little explored in environmental studies. The influence of abiotic factors on the persistence of bacteriophages is now recognized; however, it has been mainly studied under experimental conditions. This study aimed to determine whether the abiotic factors well-known to influence bacteriophage persistence also control the natural distribution of the known DNA bacteriophage populations. To this end, soil from eight study sites including forests and grasslands located in the Attert River basin (Grand Duchy of Luxembourg) were sampled, covering different soil and land cover characteristics. Shotgun metagenomics, reference-based bioinformatics and statistical analyses allowed characterising the diversity of known DNA bacteriophage and bacterial communities. After combining soil properties with the identified DNA bacteriophage populations, our in-situ study highlighted the influence of pH and calcium cations on the diversity of the known fraction of the soil DNA bacteriophages. More interestingly, significant relationships were established between bacteriophage and bacterial populations. This study provides new insights into the importance of abiotic and biotic factors in the distribution of DNA bacteriophages and the natural ecology of terrestrial bacteriophages.
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Affiliation(s)
- Perrine Florent
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), 4422 Belvaux, Luxembourg; (P.F.); (H.-M.C.); (M.H.)
- Faculté des Sciences, de la Technologie et de la Communication (FSTC), Doctoral School in Science and Engineering (DSSE), University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Henry-Michel Cauchie
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), 4422 Belvaux, Luxembourg; (P.F.); (H.-M.C.); (M.H.)
| | - Malte Herold
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), 4422 Belvaux, Luxembourg; (P.F.); (H.-M.C.); (M.H.)
| | - Stéphan Jacquet
- INRAE, UMR CARRTEL, Université Savoie Mont Blanc, 74200 Thonon-les-Bains, France;
| | - Leslie Ogorzaly
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), 4422 Belvaux, Luxembourg; (P.F.); (H.-M.C.); (M.H.)
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