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Wang X, Zhang L, Gu J, Feng Y, He K, Jiang H. Effects of soil solarization combined with manure-amended on soil ARGs and microbial communities during summer fallow. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 333:121950. [PMID: 37279818 DOI: 10.1016/j.envpol.2023.121950] [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: 02/18/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/08/2023]
Abstract
Soil solarization (SS) is a technique for managing pathogens and weeds, which involves covering with transparent plastic to increase soil temperature during summer fallow (SF). However, SS also alters the diversity of bacterial communities. Therefore, during SF, various organic modifiers are used in combination with SS to improve its efficacy. Organic amendments may contain antibiotic resistance genes (ARGs). Greenhouse vegetable production (GVP) soils are vital to ensure food security and ecological balance. However, comprehensive study on the effects of SS combined with different types of manure on ARGs in GVP soils during SF remains unclear. Therefore, this study employed high-throughput qPCR to explore the effects of different organic amendments combined with SS on the abundance changes of ARGs and mobile genetic elements (MGEs) in GVP soils during SF. The abundance and diversity of ARGs and MGEs in GVP soils with different manure fertilization and SS decreased during SF. Horizontal gene transfer via MGEs (especially integrases 45.80%) induced by changes in environmental factors (NO3--N 14.7% and NH4+-N) was the main factor responsible for the changes in ARGs. Proteobacteria (14.3%) and Firmicutes were the main potential hosts of ARGs. Network analysis suggested that Ornithinimicrobium, Idiomarina and Corynebacterium had positive correlations with aminoglycosides, MLSB, and tetracycline resistance genes. These results provide new insights to understand the fate of ARGs in the GVP soils by manure-amended combined with SS during SF, which may help to reduce the spread of ARGs.
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Affiliation(s)
- Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Li Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China; Shaanxi Engineering Research Center of Utilization of Agricultural Waste Resources, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yucheng Feng
- Department of C, rop, Soil & Environmental Sciences (formerly Agronomy and Soils), Auburn University, Auburn, AL36849, USA
| | - Kai He
- Tobacco Monopoly Bureau (Branch), Longhui, Shaoyang, Hunan, 422208, China
| | - Haihong Jiang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Haber Z, Wilhelmi MDMR, Fernández-Bayo JD, Harrold DR, Stapleton JJ, Toubiana D, VanderGheynst JS, Blumwald E, Simmons CW, Sade N, Achmon Y. The effect of circular soil biosolarization treatment on the physiology, metabolomics, and microbiome of tomato plants under certain abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:1009956. [PMID: 36426148 PMCID: PMC9679285 DOI: 10.3389/fpls.2022.1009956] [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: 08/02/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Soil biosolarization (SBS) is an alternative technique for soil pest control to standard techniques such as soil fumigation and soil solarization (SS). By using both solar heating and fermentation of organic amendments, faster and more effective control of soilborne pathogens can be achieved. A circular economy may be created by using the residues of a given crop as organic amendments to biosolarize fields that produce that crop, which is termed circular soil biosolarization (CSBS). In this study, CSBS was employed by biosolarizing soil with amended tomato pomace (TP) residues and examining its impact on tomato cropping under conditions of abiotic stresses, specifically high salinity and nitrogen deficiency. The results showed that in the absence of abiotic stress, CSBS can benefit plant physiological performance, growth and yield relative to SS. Moreover, CSBS significantly mitigated the impacts of abiotic stress conditions. The results also showed that CSBS impacted the soil microbiome and plant metabolome. Mycoplana and Kaistobacter genera were found to be positively correlated with benefits to tomato plants health under abiotic stress conditions. Conversely, the relative abundance of the orders RB41, MND1, and the family Ellin6075 and were negatively correlated with tomato plants health. Moreover, several metabolites were significantly affected in plants grown in SS- and CSBS-treated soils under abiotic stress conditions. The metabolite xylonic acid isomer was found to be significantly negatively correlated with tomato plants health performance across all treatments. These findings improve understanding of the interactions between CSBS, soil ecology, and crop physiology under abiotic stress conditions.
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Affiliation(s)
- Zechariah Haber
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | | | - Jesus D. Fernández-Bayo
- Department of Food Science and Technology, University of California, Davis, CA, United States
| | - Duff R. Harrold
- Department of Food Science and Technology, University of California, Davis, CA, United States
| | - James J. Stapleton
- Statewide Integrated Pest Management Program, University of California Kearney Agricultural Research and Extension Center, Parlier, CA, United States
| | - David Toubiana
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Jean S. VanderGheynst
- College of Engineering, University of Massachusetts Dartmouth, Dartmouth, MA, United States
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, CA, United States
| | - Christopher W. Simmons
- Department of Food Science and Technology, University of California, Davis, CA, United States
| | - Nir Sade
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Yigal Achmon
- Biotechnology and Food Engineering, Guangdong Technion - Israel Institute of Technology, Shantou, Guangdong, China
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, Israel
- Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, Shantou, Guangdong, China
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Cuartero J, Pascual JA, Vivo JM, Özbolat O, Sánchez-Navarro V, Weiss J, Zornoza R, Martínez-Mena M, García E, Ros M. Melon/cowpea intercropping pattern influenced the N and C soil cycling and the abundance of soil rare bacterial taxa. Front Microbiol 2022; 13:1004593. [PMID: 36419434 PMCID: PMC9676475 DOI: 10.3389/fmicb.2022.1004593] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
The high use of pesticides, herbicides, and unsustainable farming practices resulted in losses of soil quality. Sustainable farming practices such as intercropping could be a good alternative to traditional monocrop, especially using legumes such as cowpea (Vigna unguiculata L. Walp). In this study, different melon and cowpea intercropping patterns (melon mixed with cowpea in the same row (MC1); alternating one melon row and one cowpea row (MC2); alternating two melon rows and one cowpea row (MC3)) were assayed to study the intercropping effect on soil bacterial community through 16S rRNA region in a 3-year experiment. The results indicated that intercropping showed high content of total organic carbon, total nitrogen and ammonium, melon yield, and bacterial diversity as well as higher levels of beneficial soil microorganisms such a Pseudomonas, Aeromicrobium, Niastella, or Sphingomonas which can promote plant growth and plant defense against pathogens. Furthermore, intercropping showed a higher rare taxa diversity in two (MC1 and MC2) out of the three intercropping systems. In addition, N-cycling genes such as nirB, nosZ, and amoA were more abundant in MC1 and MC2 whereas the narG predicted gene was far more abundant in the intercropping systems than in the monocrop at the end of the 3-year experiment. This research fills a gap in knowledge about the importance of soil bacteria in an intercropping melon/cowpea pattern, showing the benefits to yield and soil quality with a decrease in N fertilization.
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Affiliation(s)
- Jessica Cuartero
- Centre of Edaphology and Applied Biology of the Segura (CSIC), University Campus of Espinardo, Murcia, Spain
| | - Jose Antonio Pascual
- Centre of Edaphology and Applied Biology of the Segura (CSIC), University Campus of Espinardo, Murcia, Spain
| | - Juana-María Vivo
- Department of Statistics and Operations Research, CMN & IMIB-Arrixaca, University of Murcia, Murcia, Spain
| | - Onurcan Özbolat
- Institute of Plant Biotechnology, Plaza del Hospital s/n, Technical University of Cartagena, Cartagena, Spain
| | - Virginia Sánchez-Navarro
- Institute of Plant Biotechnology, Plaza del Hospital s/n, Technical University of Cartagena, Cartagena, Spain
| | - Julia Weiss
- Institute of Plant Biotechnology, Plaza del Hospital s/n, Technical University of Cartagena, Cartagena, Spain
| | - Raúl Zornoza
- Institute of Plant Biotechnology, Plaza del Hospital s/n, Technical University of Cartagena, Cartagena, Spain
- Department of Agricultural Science, Polytechnic University of Cartagena, Cartagena, Spain
| | - María Martínez-Mena
- Centre of Edaphology and Applied Biology of the Segura (CSIC), University Campus of Espinardo, Murcia, Spain
| | - Eloisa García
- Centre of Edaphology and Applied Biology of the Segura (CSIC), University Campus of Espinardo, Murcia, Spain
| | - Margarita Ros
- Centre of Edaphology and Applied Biology of the Segura (CSIC), University Campus of Espinardo, Murcia, Spain
- *Correspondence: Margarita Ros
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Fernandez-Bayo J, Achmon Y, Guerrero MDM, Di Gioia F. Editorial: Upcycling organic waste for the sustainable management of soilborne pests and pathogens in agri-food systems. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.1012789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Gandariasbeitia M, López-Pérez JA, Juaristi B, Larregla S. Sunflower Seed Husk as Promising By-Product for Soil Biodisinfestation Treatments and Fertility Improvement in Protected Lettuce Crop. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.901654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
One of the major challenges in biodisinfestation treatments against soilborne pathogens is the selection of the proper organic amendments and mixture features. The use of agro-industrial by-products is a sustainable alternative with proven efficacy, but the availability has to be considered in terms of location and quantity. Sunflower seed is one of the five major oil crops widely cultivated and the husk constitutes a significant part that is discarded. This by-product brings together the features to be considered an interesting organic amendment in agricultural soils because of its lignocellulose content, but no references have been found in this field. In this study, sunflower seed husk was used with fresh cow manure in biodisinfestation treatments, alone or combined with other by-products (rapeseed cake, beer bagasse and wheat bran). The assay was performed in summer in a commercial greenhouse with significant yield losses in lettuce crops caused by the root-knot nematode Meloidogyne incognita. Four different amendment mixtures were applied which included 3kg/m2 cow manure, as common waste, and 1 kg/m2 of by-products (dry weight), considering 6mgC/g soil in all treatments but different C/N ratio (23, 29, 31, 34) and by-products. Data was collected in three moments: (i) before and (ii) after biodisinfestation treatments and (iii) after harvesting the first crop after biodisinfestations. Crop damage was assessed through root galling index and the number of eggs in roots. The effects on the pathogen population and the whole soil nematode community were assessed along with some physicochemical and soil microbiological variables (respiration rate, microbial organic C, water-soluble organic C and physiological profile of heterotrophic bacteria through Biolog Ecoplates™). All treatments reported effectiveness in disease control without significant differences among them, but among times. However, soil temperatures during biodisinfestations were higher at higher C/N ratios and fertility variables also increased in these cases, mainly in the treatment with husk as the only by-product. Sunflower seed husk proved to be an interesting source of organic C to improve both biodisinfestation treatments and soil fertility in humid temperate climate zones.
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Wei Z, Ahmed Mohamed T, Zhao L, Zhu Z, Zhao Y, Wu J. Microhabitat drive microbial anabolism to promote carbon sequestration during composting. BIORESOURCE TECHNOLOGY 2022; 346:126577. [PMID: 34923079 DOI: 10.1016/j.biortech.2021.126577] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Transforming organic waste into stable carbon by composting is an eco-friendly way. However, the complex environment, huge microbial community and complicated metabolic of composting have limited the directional transformation of organic carbon, which is also not conducive to the fixation of organic carbon. Therefore, this review is based on the formation of humus, a stable by-product of composting, to expound how to promote carbon fixation by increasing the yield of humus. Firstly, we have clarified the transformation regularity of organic matter during composting. Meanwhile, the microhabitat factors affecting microbial catabolism and anabolism were deeply analyzed, in order to provide a theoretical basis for the micro habitat regulation of directional transformation of organic matter during composting. Given that, a method to adjust the directional humification and stabilization of organic carbon has been proposed. Hoping the rapid reduction and efficient stabilization of organic waste can be realized according to this method.
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Affiliation(s)
- Zimin Wei
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Taha Ahmed Mohamed
- College of Life Science, Northeast Agricultural University, Harbin 150030, China; Soil, Water and Environment Research Institute, Agricultural Research Center, Giza, Egypt
| | - Li Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zechen Zhu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yue Zhao
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Junqiu Wu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
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Fernandez-Bayo JD, Simmons CW, VanderGheynst JS. Characterization of digestate microbial community structure following thermophilic anaerobic digestion with varying levels of green and food wastes. ACTA ACUST UNITED AC 2020; 47:1031-1044. [DOI: 10.1007/s10295-020-02326-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/20/2020] [Indexed: 12/23/2022]
Abstract
Abstract
The properties of digestates generated through anaerobic digestion are influenced by interactions between the digester microbial communities, feedstock properties and digester operating conditions. This study investigated the effect of varying initial feedstock carbon to nitrogen (C/N) ratios on digestate microbiota and predicted abundance of genes encoding lignocellulolytic activity. The C/N ratio had a significant impact on the digestate microbiome. Feedstocks with intermediate C/N ratio (20–27) (where higher biomethane potential was observed) showed higher relative abundance of archaea compared to feedstocks with C/N ratios at 17 and 34. Within microbial networks, four microbial clusters and eight connector microorganisms changed significantly with the C/N ratio (P < 0.05). Feedstocks with C/N < 23 were richer in organisms from the family Thermotogaceae and genus Caldicoprobacter and enhanced potential for degradation of maltose, galactomannans, melobiose and lactose. This study provides new insights into how anaerobic digestion conditions relate to the structure and functional potential of digester microbial communities, which may be relevant to both digester performance and subsequent utilization of digestates for composting or amending soil.
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Affiliation(s)
- Jesus D Fernandez-Bayo
- grid.27860.3b 0000 0004 1936 9684 Department of Biological and Agricultural Engineering University of California One Shields Ave. 95616 Davis CA USA
- grid.27860.3b 0000 0004 1936 9684 Department of Food Science and Technology University of California One Shields Ave. 95616 Davis CA USA
| | - Christopher W Simmons
- grid.27860.3b 0000 0004 1936 9684 Department of Food Science and Technology University of California One Shields Ave. 95616 Davis CA USA
| | - Jean S VanderGheynst
- grid.27860.3b 0000 0004 1936 9684 Department of Biological and Agricultural Engineering University of California One Shields Ave. 95616 Davis CA USA
- grid.266686.a 0000000102217463 Department of Bioengineering University of Massachusetts Dartmouth MA USA
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Bellini A, Ferrocino I, Cucu MA, Pugliese M, Garibaldi A, Gullino ML. A Compost Treatment Acts as a Suppressive Agent in Phytophthora capsici - Cucurbita pepo Pathosystem by Modifying the Rhizosphere Microbiota. FRONTIERS IN PLANT SCIENCE 2020; 11:885. [PMID: 32670324 PMCID: PMC7327441 DOI: 10.3389/fpls.2020.00885] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 05/29/2020] [Indexed: 05/05/2023]
Abstract
Phytophthora capsici Leonian (PHC) is a filamentous pathogen oomycete that causes root, fruit, foliar and crown rot over a wide host range, including the economically and nutritionally important summer squash (Cucurbita pepo var. cylindrica L.) crop. PHC chemical control strategies are difficult to adopt, due to the limited number of registered chemicals that are permitted and the scalar harvest system. For these reasons, other strategies, such as the use of waste-based composts that can act as suppressive agents against several soilborne pathogens, have been studied intensively. It is well known that compost's microbiota plays an important role to confer its suppressive ability. In this study, four different composts were analyzed with both 16S rRNA gene and 18S rRNA gene real-time PCR amplification and with 26S gene amplicon-based sequencing; the total abundance of the bacterial and fungal communities was found to be higher compared to literature, thus confirming that the four composts were a good inoculum source for agricultural applications. The core mycobiota was mainly composed of 31 genera; nevertheless, it was possible to observe a clear predominance of the same few taxa in all the composts. The four composts were then tested, at different concentrations (1-10-20% v/v), to establish their ability to confer suppressiveness to the Phytophthora capsici (PHC) - Cucurbita pepo pathosystem in controlled greenhouse pot trials. A total of 12 compost mixtures were considered, and of these, one (Trichoderma-enriched compost at 10% v/v) was able to statistically reduce the disease incidence caused by PHC (by 50% compared to the untreated control). Hence, the microbiota composition of the most effective compost treatment was investigated and compared with untreated and chemical (metalaxyl) controls. Mycobiota sequencing showed genera differences between the three treatments, with relative abundances of several fungal genera that were significantly different among the samples. Moreover, PCA analyses clustered the compost treatment differently from the chemical and the untreated controls. These findings suggest that suppressive activity of a compost is strictly influenced by its microbiota and the applied dosage, but the ability to induce a shaping in the rhizosphere microbial composition is also required.
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Affiliation(s)
- Alessio Bellini
- AGROINNOVA – Centre of Competence for the Innovation in the Agro-Environmental Sector, University of Turin, Turin, Italy
- Agricultural, Forestry and Food Sciences Department (DISAFA), University of Turin, Turin, Italy
| | - Ilario Ferrocino
- Agricultural, Forestry and Food Sciences Department (DISAFA), University of Turin, Turin, Italy
| | - Maria Alexandra Cucu
- AGROINNOVA – Centre of Competence for the Innovation in the Agro-Environmental Sector, University of Turin, Turin, Italy
| | - Massimo Pugliese
- AGROINNOVA – Centre of Competence for the Innovation in the Agro-Environmental Sector, University of Turin, Turin, Italy
- Agricultural, Forestry and Food Sciences Department (DISAFA), University of Turin, Turin, Italy
- AgriNewTech s.r.l., Turin, Italy
| | - Angelo Garibaldi
- AGROINNOVA – Centre of Competence for the Innovation in the Agro-Environmental Sector, University of Turin, Turin, Italy
| | - Maria Lodovica Gullino
- AGROINNOVA – Centre of Competence for the Innovation in the Agro-Environmental Sector, University of Turin, Turin, Italy
- Agricultural, Forestry and Food Sciences Department (DISAFA), University of Turin, Turin, Italy
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