1
|
Saberi Riseh R, Gholizadeh Vazvani M, Vatankhah M, Kennedy JF. Chitin-induced disease resistance in plants: A review. Int J Biol Macromol 2024; 266:131105. [PMID: 38531527 DOI: 10.1016/j.ijbiomac.2024.131105] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/15/2024] [Accepted: 03/21/2024] [Indexed: 03/28/2024]
Abstract
Chitin is composed of N-acetylglucosamine units. Chitin a polysaccharide found in the cell walls of fungi and exoskeletons of insects and crustaceans, can elicit a potent defense response in plants. Through the activation of defense genes, stimulation of defensive compound production, and reinforcement of physical barriers, chitin enhances the plant's ability to defend against pathogens. Chitin-based treatments have shown efficacy against various plant diseases caused by fungal, bacterial, viral, and nematode pathogens, and have been integrated into sustainable agricultural practices. Furthermore, chitin treatments have demonstrated additional benefits, such as promoting plant growth and improving tolerance to abiotic stresses. Further research is necessary to optimize treatment parameters, explore chitin derivatives, and conduct long-term field studies. Continued efforts in these areas will contribute to the development of innovative and sustainable strategies for disease management in agriculture, ultimately leading to improved crop productivity and reduced reliance on chemical pesticides.
Collapse
Affiliation(s)
- Roohallah Saberi Riseh
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, 7718897111 Rafsanjan, Iran.
| | - Mozhgan Gholizadeh Vazvani
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, 7718897111 Rafsanjan, Iran
| | - Masoumeh Vatankhah
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, 7718897111 Rafsanjan, Iran
| | - John F Kennedy
- Chembiotech Laboratories Ltd, WR15 8FF Tenbury Wells, United Kingdom.
| |
Collapse
|
2
|
Anedo EO, Beesigamukama D, Mochoge B, Korir NK, Haukeland S, Cheseto X, Subramanian S, Kelemu S, Tanga CM. Evolving dynamics of insect frass fertilizer for sustainable nematode management and potato production. Front Plant Sci 2024; 15:1343038. [PMID: 38463573 PMCID: PMC10920244 DOI: 10.3389/fpls.2024.1343038] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/07/2024] [Indexed: 03/12/2024]
Abstract
Potato production faces major challenges from inadequate soil fertility, and nematode infestation, yet synthetic fertilizers and nematicides are costly and harmful to the environment. This study explored the potential of chitin-fortified black soldier fly-composted organic fertilizer (BSFCOF) as a multipurpose organic fertilizer amendment for enhancing potato yield and suppressing potato cyst nematodes (PCN). The BSFCOF was applied at a rate equivalent to 150 kg N ha-1 and fortified with chitin from black soldier fly pupal exuviae at inclusion rates equivalent to 0.5, 1, 2, 3, 4 and 5% chitin. Data were collected on potato growth characteristics, PCN population densities, and soil chemical properties for two growing cycles. Results showed that chitin fortified BSFCOF significantly improved potato growth parameters, chlorophyll concentration, marketable tuber yield and number of marketable tubers. The marketable tuber yield achieved using chitin-fortified BSFCOF was 70 - 362%, and 69 - 238% higher than the values achieved using unfertilized soil during the first and second growing cycles, respectively. Soil amendment with chitin-fortified BSFCOF significantly reduced the number of cysts per 200 g soil-1, number of eggs and J2 per cyst-1, eggs g-1 soil and reproduction rate by 32 - 87%, 9 - 92%, 31- 98% and 31 - 98%, respectively. The PCN suppression increased with chitin inclusion rates. There were significantly higher values for soil pH, ammonium nitrogen, nitrate nitrogen, available phosphorus, calcium, magnesium, potassium, and cation exchange capacity in soil amended with BSFCOF compared to unamended soil. This study demonstrates that BSFCOF fortified with 5% chitin is an effective soil enhancer with multiple benefits, including improved soil fertility, potato performance, and effective management of potato cyst nematodes.
Collapse
Affiliation(s)
- Emmanuel O. Anedo
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
- Department of Agricultural Science and Technology, Kenyatta University, Nairobi, Kenya
- Crop Research Operations Department, National Root Crops Research Institute, Umudike, Abia State, Nigeria
| | | | - Benson Mochoge
- Department of Agricultural Science and Technology, Kenyatta University, Nairobi, Kenya
| | - Nicholas K. Korir
- Department of Agricultural Science and Technology, Kenyatta University, Nairobi, Kenya
| | - Solveig Haukeland
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
- Division of Biotechnology and Plant Health, Norwegian Institute for Bioeconomy Research (NIBIO), Ås, Norway
| | - Xavier Cheseto
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | | | - Segenet Kelemu
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | | |
Collapse
|
3
|
Suwanchaikasem P, Nie S, Idnurm A, Selby‐Pham J, Walker R, Boughton BA. Effects of chitin and chitosan on root growth, biochemical defense response and exudate proteome of Cannabis sativa. Plant Environ Interact 2023; 4:115-133. [PMID: 37362423 PMCID: PMC10290428 DOI: 10.1002/pei3.10106] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/09/2023] [Accepted: 03/19/2023] [Indexed: 06/28/2023]
Abstract
Fungal pathogens pose a major threat to Cannabis sativa production, requiring safe and effective management procedures to control disease. Chitin and chitosan are natural molecules that elicit plant defense responses. Investigation of their effects on C. sativa will advance understanding of plant responses towards elicitors and provide a potential pathway to enhance plant resistance against diseases. Plants were grown in the in vitro Root-TRAPR system and treated with colloidal chitin and chitosan. Plant morphology was monitored, then plant tissues and exudates were collected for enzymatic activity assays, phytohormone quantification, qPCR analysis and proteomics profiling. Chitosan treatments showed increased total chitinase activity and expression of pathogenesis-related (PR) genes by 3-5 times in the root tissues. In the exudates, total peroxidase and chitinase activities and levels of defense proteins such as PR protein 1 and endochitinase 2 were increased. Shoot development was unaffected, but root development was inhibited after chitosan exposure. In contrast, chitin treatments had no significant impact on any defense parameters, including enzymatic activities, hormone quantities, gene expression levels and root secreted proteins. These results indicate that colloidal chitosan, significantly enhancing defense responses in C. sativa root system, could be used as a potential elicitor, particularly in hydroponic scenarios to manage crop diseases.
Collapse
Affiliation(s)
| | - Shuai Nie
- Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneMelbourneVictoria3052Australia
| | - Alexander Idnurm
- School of BioSciencesUniversity of MelbourneMelbourneVictoria3010Australia
| | - Jamie Selby‐Pham
- School of BioSciencesUniversity of MelbourneMelbourneVictoria3010Australia
- Cannabis and Biostimulants Research Group Pty LtdMelbourneVictoria3020Australia
| | - Robert Walker
- School of BioSciencesUniversity of MelbourneMelbourneVictoria3010Australia
| | - Berin A. Boughton
- School of BioSciencesUniversity of MelbourneMelbourneVictoria3010Australia
- Australian National Phenome CentreMurdoch UniversityPerthWestern Australia6150Australia
| |
Collapse
|
4
|
Barragán‐Fonseca KY, Rusman Q, Mertens D, Weldegergis BT, Peller J, Polder G, van Loon JJA, Dicke M. Insect exuviae as soil amendment affect flower reflectance and increase flower production and plant volatile emission. Plant Cell Environ 2023; 46:931-945. [PMID: 36514238 PMCID: PMC10107842 DOI: 10.1111/pce.14516] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Soil composition and herbivory are two environmental factors that can affect plant traits including flower traits, thus potentially affecting plant-pollinator interactions. Importantly, soil composition and herbivory may interact in these effects, with consequences for plant fitness. We assessed the main effects of aboveground insect herbivory and soil amendment with exuviae of three different insect species on visual and olfactory traits of Brassica nigra plants, including interactive effects. We combined various methodological approaches including gas chromatography/mass spectrometry, spectroscopy and machine learning to evaluate changes in flower morphology, colour and the emission of volatile organic compounds (VOCs). Soil amended with insect exuviae increased the total number of flowers per plant and VOC emission, whereas herbivory reduced petal area and VOC emission. Soil amendment and herbivory interacted in their effect on the floral reflectance spectrum of the base part of petals and the emission of 10 VOCs. These findings demonstrate the effects of insect exuviae as soil amendment on plant traits involved in reproduction, with a potential for enhanced reproductive success by increasing the strength of signals attracting pollinators and by mitigating the negative effects of herbivory.
Collapse
Affiliation(s)
- Katherine Y. Barragán‐Fonseca
- Laboratory of EntomologyWageningen University & ResearchWageningenThe Netherlands
- Grupo en Conservación y Manejo de Vida Silvestre, Instituto de Ciencias NaturalesUniversidad Nacional de ColombiaBogotáColombia
| | - Quint Rusman
- Laboratory of EntomologyWageningen University & ResearchWageningenThe Netherlands
| | - Daan Mertens
- Department of Entomology and NematologyUniversity of CaliforniaDavisCaliforniaUSA
| | | | - Joseph Peller
- Greenhouse HorticultureWageningen University & ResearchWageningenThe Netherlands
| | - Gerrit Polder
- Greenhouse HorticultureWageningen University & ResearchWageningenThe Netherlands
| | - Joop J. A. van Loon
- Laboratory of EntomologyWageningen University & ResearchWageningenThe Netherlands
| | - Marcel Dicke
- Laboratory of EntomologyWageningen University & ResearchWageningenThe Netherlands
| |
Collapse
|
5
|
Li L, Kaufmann M, Makechemu M, Van Poucke C, De Keyser E, Uyttendaele M, Zipfel C, Cottyn B, Pothier JF. Assessment of transcriptional reprogramming of lettuce roots in response to chitin soil amendment. Front Plant Sci 2023; 14:1158068. [PMID: 37089656 PMCID: PMC10115174 DOI: 10.3389/fpls.2023.1158068] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Chitin soil amendment is known to improve soil quality, plant growth and stress resilience, but the underlying mechanisms are not well understood. In this study, we monitored chitin's effect on lettuce physiology every two weeks through an eight-week growth period, analyzed the early transcriptional reprogramming and related metabolomic changes of lettuce, in response to crab chitin treatment in peat-based potting soil. In commercial growth conditions, chitin amendment still promoted lettuce growth, increased chlorophyll content, the number of leaves and crop head weight from week six. The flavonoid content in lettuce leaves was altered as well, showing an increase at week two but a decrease from week six. Transcriptomic analysis showed that over 300 genes in lettuce root were significantly differentially expressed after chitin soil treatment. Gene Ontology-term (GO) enrichment analysis revealed statistical overrepresentation of GO terms linked to photosynthesis, pigment metabolic process and phenylpropanoid metabolic process. Further analysis of the differentially expressed genes (DEGs) showed that the flavonoid pathway was mostly upregulated whereas the bifurcation of upstream phenylpropanoid pathway towards lignin biosynthesis was mostly downregulated. Metabolomic analysis revealed the upregulation of salicylic acid, chlorogenic acid, ferulic acid, and p-coumaric acid in chitin-treated lettuce seedlings. These phenolic compounds (PCs) mainly influence the phenylpropanoid biosynthesis pathway and may play important roles in plant defense reactions. Our results suggest that chitin soil amendments might activate induced resistance by priming lettuce plants and promote lettuce growth via transcriptional changes.
Collapse
Affiliation(s)
- Leilei Li
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- Department of Food Technology, Safety and Health, Ghent University, Ghent, Belgium
- *Correspondence: Joël F. Pothier, ; Leilei Li,
| | - Moritz Kaufmann
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Moffat Makechemu
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | | | - Ellen De Keyser
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Mieke Uyttendaele
- Department of Food Technology, Safety and Health, Ghent University, Ghent, Belgium
| | - Cyril Zipfel
- Department of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Bart Cottyn
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
- *Correspondence: Joël F. Pothier, ; Leilei Li,
| |
Collapse
|
6
|
Fan Y, Liu J, Liu Z, Hu X, Yu Z, Li Y, Chen X, Li L, Jin J, Wang G. Chitin amendments eliminate the negative impacts of continuous cropping obstacles on soil properties and microbial assemblage. Front Plant Sci 2022; 13:1067618. [PMID: 36507440 PMCID: PMC9730418 DOI: 10.3389/fpls.2022.1067618] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
Continuous cropping of soybean leads to soil environment deterioration and soil-borne disease exacerbation, which in turn limits the sustainability of agricultural production. Chitin amendments are considered promising methods for alleviating soybean continuous cropping obstacles; however, the underlying mechanisms of soil sickness reduction remain unclear. In this study, soil amendments with pure and crude chitin at different addition dosages were employed to treat diseased soil induced by continuous cropping of soybean for five years. Chitin amendments, especially crude chitin, remarkably increased soil pH, available phosphorus (AP), potassium (AK) and nitrate nitrogen ( NO 3 - -N) contents, and improved soybean plant growth and soil microbial activities (FDA). Additionally, chitin application significantly enriched the relative abundances of the potential biocontrol bacteria Sphingomonas, Streptomyces, and Bacillus and the fungi Mortierella, Purpureocillium, and Metarhizium while depleted those of the potential plant pathogens Fusarium, Cylindrocarpon and Paraphoma. Moreover, chitin amendments induced looser pathogenic subnetwork structures and less pathogenic cooperation with other connected microbial taxa in the rhizosphere soils. The structural equation model (SEM) revealed that pure and crude chitin amendments promoted soybean plant growth by indirectly regulating soil pH-mediated soil microbial activities and potentially beneficial microbes, respectively. Therefore, the reduction strategies for continuous cropping obstacles by adding pure and crude chitin were distinct; pure chitin amendments showed general disease suppression, while crude chitin exhibited specific disease suppression. Overall, chitin amendments could suppress potential plant pathogens and improve soil health, thereby promoting soybean growth, which provides new prospects for cultivation practices to control soybean continuous cropping obstacles.
Collapse
Affiliation(s)
- Yanli Fan
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhuxiu Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojing Hu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhenhua Yu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Yansheng Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xueli Chen
- Heilongjiang Academy of Black Soil Conservation and Utilization, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Lujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Jian Jin
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Guanghua Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| |
Collapse
|
7
|
Kama R, Javed Q, Liu Y, Li Z, Iqbal B, Diatta S, Sun J. Effect of Soil Type on Native Pterocypsela laciniata Performance under Single Invasion and Co-Invasion. Life (Basel) 2022; 12:life12111898. [PMID: 36431033 PMCID: PMC9695812 DOI: 10.3390/life12111898] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022]
Abstract
Native and invasive plant competition is usually controlled by the soil properties and the soil type underlying interspecific interactions. However, many uncertainties exist regarding the impact of soil type on native plant growth under single invasion and co-invasion despite the significant number of previous studies that focused on plant invasion. This study aims to elucidate the effects of soil type on the response of the native plant Pterocypsela laciniata under single invasion and co-invasion. Three different soils were used: natural soil, nutrient soil, and nutrient sterilized soil. The native P. laciniata was grown in monoculture and under single invasion and co-invasion with Solidago canadensis and Aster subulatus Michx. The results show that the native plant height and total biomass were 75% and 93.33% higher, respectively, in nutrient sterilized soil in monoculture than in natural and nutrient soil. In contrast, the native P. laciniata presents its best competitive ability in nutrient sterilized soil, being about 100% higher than in natural and nutrient soil under single invasion and co-invasion. However, no significant increase was observed in its growth parameters under co-invasion compared to single invasion. Conclusively, this study shows that nutrient soil sterilization positively affects native plant growth in monoculture and under single invasion, contrasting co-invasion in which more pronounced negative effects were observed on the native plant response.
Collapse
Affiliation(s)
- Rakhwe Kama
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
- Institute of Farmland Irrigation of CAAS, Xinxiang 453002, China
| | - Qaiser Javed
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yuan Liu
- Institute of Farmland Irrigation of CAAS, Xinxiang 453002, China
| | - Zhongyang Li
- Institute of Farmland Irrigation of CAAS, Xinxiang 453002, China
- National Research and Observation Station of Shangqiu Agro-Ecology System, Shangqiu 476000, China
| | - Babar Iqbal
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Sekouna Diatta
- Laboratory of Ecology, Faculty of Sciences and Technology, Cheikh Anta Diop University of Dakar, Dakar 50005, Senegal
| | - Jianfan Sun
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
- Correspondence: ; Tel./Fax: +86-511-887-9095
| |
Collapse
|
8
|
Trinchera A, Migliore M, Warren Raffa D, Ommeslag S, Debode J, Shanmugam S, Dane S, Babry J, Kivijarvi P, Kristensen HL, Lepse L, Salo T, Campanelli G, Willekens K. Can multi-cropping affect soil microbial stoichiometry and functional diversity, decreasing potential soil-borne pathogens? A study on European organic vegetable cropping systems. Front Plant Sci 2022; 13:952910. [PMID: 36237499 PMCID: PMC9552534 DOI: 10.3389/fpls.2022.952910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Crop diversification in spatial and temporal patterns can optimize the synchronization of nutrients plant demand and availability in soils, as plant diversity and soil microbial communities are the main drivers of biogeochemical C and nutrient cycling. The introduction of multi-cropping in organic vegetable production can represent a key strategy to ensure efficient complementation mediated by soil microbiota, including beneficial mycorrhizal fungi. This study shows the effect of the introduction of multi-cropping in five European organic vegetable systems (South-West: Italy; North-West: Denmark and Belgium; North-East: Finland and Latvia) on: (i) soil physicochemical parameters; (ii) soil microbial biomass stoichiometry; (iii) crop root mycorrhization; (iv) bacterial and fungal diversity and composition in crop rhizosphere; (v) relative abundance of selected fungal pathogens species. In each site, three cropping systems were considered: (1) crop 1-monocropping; (2) crop 2-monocropping; (3) crop 1-crop 2-intercropping or strip cropping. Results showed that, just before harvest, multi-cropping can increase soil microbial biomass amount and shape microbial community toward a predominance of some bacteria or fungi phyla, in the function of soil nutrient availability. We mainly observed a selection effect of crop type on rhizosphere microbiota. Particularly, Bacteroidetes and Mortierellomycota relative abundances in rhizosphere soil resulted in suitable ecological indicators of the positive effect of plant diversity in field, the first ones attesting an improved C and P cycles in soil and the second ones a reduced soil pathogens' pressure. Plant diversity also increased the root mycorrhizal colonization between the intercropped crops that, when properly selected, can also reduce the relative abundance of potential soil-borne pathogens, with a positive effect on crop productivity in long term.
Collapse
Affiliation(s)
- Alessandra Trinchera
- Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment, Rome, Italy
| | - Melania Migliore
- Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment, Rome, Italy
| | - Dylan Warren Raffa
- Council for Agricultural Research and Economics-Research Centre for Agriculture and Environment, Rome, Italy
| | - Sarah Ommeslag
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | | | - Sandra Dane
- Latvian Institute of Horticulture, LatHort, Dobeles Novads, Latvia
| | | | - Pirjo Kivijarvi
- LUKE (FI) Natural Resources Institute Finland, Helsinki, Finland
| | | | - Liga Lepse
- Latvian Institute of Horticulture, LatHort, Dobeles Novads, Latvia
| | - Tapio Salo
- LUKE (FI) Natural Resources Institute Finland, Helsinki, Finland
| | - Gabriele Campanelli
- Council for Agricultural Research and Economics-Research Centre for Vegetable and Ornamental Crops, Monsampolo del Tronto, Italy
| | - Koen Willekens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| |
Collapse
|
9
|
Barragán-Fonseca KY, Nurfikari A, van de Zande EM, Wantulla M, van Loon JJA, de Boer W, Dicke M. Insect frass and exuviae to promote plant growth and health. Trends Plant Sci 2022; 27:646-654. [PMID: 35248491 DOI: 10.1016/j.tplants.2022.01.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [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: 10/06/2021] [Revised: 12/28/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Beneficial soil microorganisms can contribute to biocontrol of plant pests and diseases, induce systemic resistance (ISR) against attackers, and enhance crop yield. Using organic soil amendments has been suggested to stimulate the abundance and/or activity of beneficial indigenous microbes in the soil. Residual streams from insect farming (frass and exuviae) contain chitin and other compounds that may stimulate beneficial soil microbes that have ISR and biocontrol activity. Additionally, changes in plant phenotype that are induced by beneficial microorganisms may directly influence plant-pollinator interactions, thus affecting plant reproduction. We explore the potential of insect residual streams derived from the production of insects as food and feed to promote plant growth and health, as well as their potential benefits for sustainable agriculture.
Collapse
Affiliation(s)
- Katherine Y Barragán-Fonseca
- Laboratory of Entomology, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands; Grupo en Conservación y Manejo de Vida Silvestre, Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Azkia Nurfikari
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; Soil Biology Group, Wageningen University & Research, 6700 AA Wageningen, The Netherlands
| | - Els M van de Zande
- Laboratory of Entomology, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands
| | - Max Wantulla
- Laboratory of Entomology, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands
| | - Joop J A van Loon
- Laboratory of Entomology, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; Soil Biology Group, Wageningen University & Research, 6700 AA Wageningen, The Netherlands
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University & Research, 6700 AA, Wageningen, The Netherlands.
| |
Collapse
|
10
|
Sun J, Li S, Fan C, Cui K, Tan H, Qiao L, Lu L. N-Acetylglucosamine Promotes Tomato Plant Growth by Shaping the Community Structure and Metabolism of the Rhizosphere Microbiome. Microbiol Spectr 2022; 10:e0035822. [PMID: 35665438 PMCID: PMC9241905 DOI: 10.1128/spectrum.00358-22] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/20/2022] [Indexed: 11/20/2022] Open
Abstract
Communication between plants and microorganisms is vital because it influences their growth, development, defense, propagation, and metabolism in achieving maximal fitness. N-acetylglucosamine (N-GlcNAc), the building block of bacterial and fungal cell walls, was first reported to promote tomato plant growth via stimulation of microorganisms typically known to dominate the tomato root rhizosphere, such as members of Proteobacteria and Actinobacteria. Using KEGG pathway analysis of the rhizosphere microbial operational taxonomic units, the streptomycin biosynthesis pathway was enriched in the presence of N-GlcNAc. The biosynthesis of 3-hydroxy-2-butanone (acetoin) and 2,3-butanediol, two foremost types of plant growth promotion-related volatile organic compounds, were activated in both Bacillus subtilis and Streptomyces thermocarboxydus strains when they were cocultured with N-GlcNAc. In addition, the application of N-GlcNAc increased indole-3-acetic acid production in a dose-dependent manner in strains of Bacillus cereus, Proteus mirabilis, Pseudomonas putida, and S. thermocarboxydus that were isolated from an N-GlcNAc-treated tomato rhizosphere. Overall, this study found that N-GlcNAc could function as microbial signaling molecules to shape the community structure and metabolism of the rhizosphere microbiome, thereby regulating plant growth and development and preventing plant disease through complementary plant-microbe interactions. IMPORTANCE While the benefits of using plant growth-promoting rhizobacteria (PGPRs) to enhance crop production have been recognized and studied extensively under laboratory conditions, the success of their application in the field varies immensely. More fundamentally explicit processes of positive, plant-PGPRs interactions are needed. The utilization of organic amendments, such as chitin and its derivatives, is one of the most economical and practical options for improving soil and substrate quality as well as plant growth and resilience. In this study, we observed that the chitin monomer N-GlcNAc, a key microbial signaling molecule produced through interactions between chitin, soil microbes, and the plants, positively shaped the community structure and metabolism of the rhizosphere microbiome of tomatoes. Our findings also provide a new direction for enhancing the benefits and stability of PGPRs in the field.
Collapse
Affiliation(s)
- Jiuyun Sun
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, People’s Republic of China
| | - Shuhua Li
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, People’s Republic of China
| | - Chunyang Fan
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, People’s Republic of China
| | - Kangjia Cui
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, People’s Republic of China
| | - Hongxiao Tan
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, People’s Republic of China
| | - Liping Qiao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, People’s Republic of China
| | - Laifeng Lu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, People’s Republic of China
| |
Collapse
|
11
|
Yurgel SN, Nadeem M, Cheema M. Microbial Consortium Associated with Crustacean Shells Composting. Microorganisms 2022; 10:1033. [PMID: 35630475 PMCID: PMC9145653 DOI: 10.3390/microorganisms10051033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
Soil microbes play an essential role in the biodegradation of crustacean shells, which is the process of sustainable bioconversion to chitin derivatives ultimately resulting in the promotion of plant growth properties. While a number of microorganisms with chitinolytic properties have been characterized, little is known about the microbial taxa that participate in this process either by active chitin degradation or by facilitation of this activity through nutritional cooperation and composting with the chitinolytic microorganisms. In this study, we evaluated the transformation of the soil microbiome triggered by close approximation to the green crab shell surface. Our data indicate that the microbial community associated with green crab shell matter undergoes significant specialized changes, which was reflected in a decreased fungal and bacterial Shannon diversity and evenness and in a dramatic alteration in the community composition. The relative abundance of several bacterial and fungal genera including bacteria Flavobacterium, Clostridium, Pseudomonas, and Sanguibacter and fungi Mortierella, Mycochlamys, and Talaromyces were increased with approximation to the shell surface. Association with the shell triggered significant changes in microbial cooperation that incorporate microorganisms that were previously reported to be involved in chitin degradation as well as ones with no reported chitinolytic activity. Our study indicates that the biodegradation of crab shells in soil incorporates a consortium of microorganisms that might provide a more efficient way for bioconversion.
Collapse
Affiliation(s)
- Svetlana N. Yurgel
- USDA-ARS, Grain Legume Genetics and Physiology Research Unit, Prosser, WA 99350, USA
| | - Muhammad Nadeem
- School of Science and the Environment, Grenfell Campus, Memorial University of Newfoundland and Labrador, Corner Brook, NL A2H 5G4, Canada; (M.N.); (M.C.)
| | - Mumtaz Cheema
- School of Science and the Environment, Grenfell Campus, Memorial University of Newfoundland and Labrador, Corner Brook, NL A2H 5G4, Canada; (M.N.); (M.C.)
| |
Collapse
|
12
|
Suwanchaikasem P, Idnurm A, Selby-Pham J, Walker R, Boughton BA. Root-TRAPR: a modular plant growth device to visualize root development and monitor growth parameters, as applied to an elicitor response of Cannabis sativa. Plant Methods 2022; 18:46. [PMID: 35397608 PMCID: PMC8994333 DOI: 10.1186/s13007-022-00875-1] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/14/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Plant growth devices, for example, rhizoponics, rhizoboxes, and ecosystem fabrication (EcoFAB), have been developed to facilitate studies of plant root morphology and plant-microbe interactions in controlled laboratory settings. However, several of these designs are suitable only for studying small model plants such as Arabidopsis thaliana and Brachypodium distachyon and therefore require modification to be extended to larger plant species like crop plants. In addition, specific tools and technical skills needed for fabricating these devices may not be available to researchers. Hence, this study aimed to establish an alternative protocol to generate a larger, modular and reusable plant growth device based on different available resources. RESULTS Root-TRAPR (Root-Transparent, Reusable, Affordable three-dimensional Printed Rhizo-hydroponic) system was successfully developed. It consists of two main parts, an internal root growth chamber and an external structural frame. The internal root growth chamber comprises a polydimethylsiloxane (PDMS) gasket, microscope slide and acrylic sheet, while the external frame is printed from a three-dimensional (3D) printer and secured with nylon screws. To test the efficiency and applicability of the system, industrial hemp (Cannabis sativa) was grown with or without exposure to chitosan, a well-known plant elicitor used for stimulating plant defense. Plant root morphology was detected in the system, and plant tissues were easily collected and processed to examine plant biological responses. Upon chitosan treatment, chitinase and peroxidase activities increased in root tissues (1.7- and 2.3-fold, respectively) and exudates (7.2- and 21.6-fold, respectively). In addition, root to shoot ratio of phytohormone contents were increased in response to chitosan. Within 2 weeks of observation, hemp plants exhibited dwarf growth in the Root-TRAPR system, easing plant handling and allowing increased replication under limited growing space. CONCLUSION The Root-TRAPR system facilitates the exploration of root morphology and root exudate of C. sativa under controlled conditions and at a smaller scale. The device is easy to fabricate and applicable for investigating plant responses toward elicitor challenge. In addition, this fabrication protocol is adaptable to study other plants and can be applied to investigate plant physiology in different biological contexts, such as plant responses against biotic and abiotic stresses.
Collapse
Affiliation(s)
| | - Alexander Idnurm
- School of BioSciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Jamie Selby-Pham
- School of BioSciences, University of Melbourne, Melbourne, VIC, 3010, Australia
- Nutrifield Pty Ltd, Melbourne, VIC, 3020, Australia
| | - Robert Walker
- School of BioSciences, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Berin A Boughton
- School of BioSciences, University of Melbourne, Melbourne, VIC, 3010, Australia
- Australian National Phenome Centre, Murdoch University, Perth, WA, 6150, Australia
| |
Collapse
|
13
|
Yanagawa A, Krishanti NPRA, Sugiyama A, Chrysanti E, Ragamustari SK, Kubo M, Furumizu C, Sawa S, Dara SK, Kobayashi M. Control of Fusarium and nematodes by entomopathogenic fungi for organic production of Zingiber officinale. J Nat Med 2022; 76:291-297. [PMID: 34609693 DOI: 10.1007/s11418-021-01572-4] [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: 08/01/2021] [Accepted: 09/21/2021] [Indexed: 10/20/2022]
Abstract
Ginger (genus Zingiber) is widely used as a spice and a medicinal herb worldwide and is the major ingredient of traditional local drinks such as jamu in Southeast Asia. Because ginger is frequently consumed, there is an increasing interest in organic ginger production without the use of synthetic agrochemicals. Recent studies have reported that certain kinds of entomopathogenic fungi (EPF) can establish endophytic- or mycorrhiza-like relationships with plants, thereby promoting plant growth and health, in addition to their typical role in crop protection as biological control agents. In this study, we explored the possibility of non-entomopathogenic effects of EPF Beauveria bassiana and Cordyceps fumosorosea on ginger plants (Zingiber officinale) via antagonism with Fusarium oxysporum or the parasitic nematode Meloidogyne incognita. The two EPF negatively affected the growth of F. oxysporum and survival of M. incognita in vitro. The application of EPF did not have any negative effect on the growth of ginger plants. Soil chemical properties were not different between the plots with or without EPF application, while the diversity of soil bacteria was observed to increase on application of EPF. At least C. fumosorosea appeared to persist in soil during the period of ginger cultivation. Thus, these EPF are potentially useful tools for producing chemical-free ginger.
Collapse
Affiliation(s)
- Aya Yanagawa
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, 611-0011, Japan
| | | | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, 611-0011, Japan
| | | | - Safendrri Komara Ragamustari
- Research Center for Biology, National Research and Innovation Agency - BRIN Cibinong Science Center, Cibinong, Bogor, 16911, Indonesia
| | - Minoru Kubo
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan
- Center for Digital Green-innovation, Nara Institute of Science and Technology, Nara, 630-0192, Japan
| | - Chihiro Furumizu
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan
- Graduate School of Medicine , Akita University, Akita, 010-8543, Japan
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan
| | - Surendra K Dara
- University of California Cooperative Extension, San Luis Obispo, CA, 93401, USA
| | - Masaru Kobayashi
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
| |
Collapse
|
14
|
Si J, Froussart E, Viaene T, Vázquez-Castellanos JF, Hamonts K, Tang L, Beirinckx S, De Keyser A, Deckers T, Amery F, Vandenabeele S, Raes J, Goormachtig S. Interactions between soil compositions and the wheat root microbiome under drought stress: From an in silico to in planta perspective. Comput Struct Biotechnol J 2021; 19:4235-4247. [PMID: 34429844 PMCID: PMC8353387 DOI: 10.1016/j.csbj.2021.07.027] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/29/2022] Open
Abstract
As wheat (Triticum aestivum) is an important staple food across the world, preservation of stable yields and increased productivity are major objectives in breeding programs. Drought is a global concern because its adverse impact is expected to be amplified in the future due to the current climate change. Here, we analyzed the effects of edaphic, environmental, and host factors on the wheat root microbiomes collected in soils from six regions in Belgium. Amplicon sequencing analysis of unplanted soil and wheat root endosphere samples indicated that the microbial community variations can be significantly explained by soil pH, microbial biomass, wheat genotype, and soil sodium and iron levels. Under drought stress, the biodiversity in the soil decreased significantly, but increased in the root endosphere community, where specific soil parameters seemingly determine the enrichment of bacterial groups. Indeed, we identified a cluster of drought-enriched bacteria that significantly correlated with soil compositions. Interestingly, integration of a functional analysis further revealed a strong correlation between the same cluster of bacteria and β-glucosidase and osmoprotectant proteins, two functions known to be involved in coping with drought stress. By means of this in silico analysis, we identified amplicon sequence variants (ASVs) that could potentially protect the plant from drought stress and validated them in planta. Yet, ASVs based on 16S rRNA sequencing data did not completely distinguish individual isolates because of their intrinsic short sequences. Our findings support the efforts to maintain stable crop yields under drought conditions through implementation of root microbiome analyses.
Collapse
Affiliation(s)
- Jiyeon Si
- Laboratory of Molecular Bacteriology. Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Center for Microbiology, VIB, 3000 Leuven, Belgium
- Medical Science Research Institute, School of Medicine, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Emilie Froussart
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 90e2 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | | | - Jorge F. Vázquez-Castellanos
- Laboratory of Molecular Bacteriology. Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Center for Microbiology, VIB, 3000 Leuven, Belgium
| | | | - Lin Tang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 90e2 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Stien Beirinckx
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 90e2 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | - Annick De Keyser
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 90e2 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
| | | | - Fien Amery
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | | | - Jeroen Raes
- Laboratory of Molecular Bacteriology. Department of Microbiology and Immunology, Rega Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
- Center for Microbiology, VIB, 3000 Leuven, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 90e2 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Gent, Belgium
- Corresponding author at: VIB-UGhent Center for Plant Systems Biology, 9052 Ghent, Belgium.
| |
Collapse
|
15
|
De Zutter N, Ameye M, Debode J, De Tender C, Ommeslag S, Verwaeren J, Vermeir P, Audenaert K, De Gelder L. Shifts in the rhizobiome during consecutive in planta enrichment for phosphate-solubilizing bacteria differentially affect maize P status. Microb Biotechnol 2021; 14:1594-1612. [PMID: 34021699 PMCID: PMC8313256 DOI: 10.1111/1751-7915.13824] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 04/09/2021] [Indexed: 12/13/2022] Open
Abstract
Phosphorus (P) is despite its omnipresence in soils often unavailable for plants. Rhizobacteria able to solubilize P are therefore crucial to avoid P deficiency. Selection for phosphate-solubilizing bacteria (PSB) is frequently done in vitro; however, rhizosphere competence is herein overlooked. Therefore, we developed an in planta enrichment concept enabling simultaneous microbial selection for P-solubilization and rhizosphere competence. We used an ecologically relevant combination of iron- and aluminium phosphate to select for PSB in maize (Zea mays L.). In each consecutive enrichment, plant roots were inoculated with rhizobacterial suspensions from plants that had grown in substrate with insoluble P. To assess the plants' P statuses, non-destructive multispectral imaging was used for quantifying anthocyanins, a proxy for maize's P status. After the third consecutive enrichment, plants supplied with insoluble P and inoculated with rhizobacterial suspensions showed a P status similar to plants supplied with soluble P. A parallel metabarcoding approach uncovered that the improved P status in the third enrichment coincided with a shift in the rhizobiome towards bacteria with plant growth-promoting and P-solubilizing capacities. Finally, further consecutive enrichment led to a functional relapse hallmarked by plants with a low P status and a second shift in the rhizobiome at the level of Azospirillaceae and Rhizobiaceae.
Collapse
Affiliation(s)
- Noémie De Zutter
- Laboratory of Applied Mycology and Phenomics (LAMP)Department of Plants and CropsFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
- Laboratory of Environmental BiotechnologyDepartment of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| | - Maarten Ameye
- Laboratory of Applied Mycology and Phenomics (LAMP)Department of Plants and CropsFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| | - Jane Debode
- Plant Sciences UnitFlanders Research Institute for AgricultureFisheries and Food (ILVO)Burgemeester Van Gansberghelaan 96MerelbekeB‐9820Belgium
| | - Caroline De Tender
- Plant Sciences UnitFlanders Research Institute for AgricultureFisheries and Food (ILVO)Burgemeester Van Gansberghelaan 96MerelbekeB‐9820Belgium
- Department of Applied Mathematics, Computer Science and StatisticsGhent UniversityKrijgslaan 281 S9GhentB‐9000Belgium
| | - Sarah Ommeslag
- Plant Sciences UnitFlanders Research Institute for AgricultureFisheries and Food (ILVO)Burgemeester Van Gansberghelaan 96MerelbekeB‐9820Belgium
| | - Jan Verwaeren
- Research Unit Knowledge‐based Systems (KERMIT)Department of Data Analysis and Mathematical ModelingGhent UniversityCoupure links 653GhentB‐9000Belgium
| | - Pieter Vermeir
- Laboratory of Chemical Analysis (LCA)Faculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| | - Kris Audenaert
- Laboratory of Applied Mycology and Phenomics (LAMP)Department of Plants and CropsFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| | - Leen De Gelder
- Laboratory of Environmental BiotechnologyDepartment of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityValentin Vaerwyckweg 1GhentB‐9000Belgium
| |
Collapse
|
16
|
Clocchiatti A, Hannula SE, Rizaludin MS, Hundscheid MPJ, klein Gunnewiek PJA, Schilder MT, Postma J, de Boer W. Impact of Cellulose-Rich Organic Soil Amendments on Growth Dynamics and Pathogenicity of Rhizoctonia solani. Microorganisms 2021; 9:microorganisms9061285. [PMID: 34204724 PMCID: PMC8231496 DOI: 10.3390/microorganisms9061285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 05/03/2021] [Revised: 05/25/2021] [Accepted: 06/03/2021] [Indexed: 01/04/2023] Open
Abstract
Cellulose-rich amendments stimulate saprotrophic fungi in arable soils. This may increase competitive and antagonistic interactions with root-infecting pathogenic fungi, resulting in lower disease incidence. However, cellulose-rich amendments may also stimulate pathogenic fungi with saprotrophic abilities, thereby increasing plant disease severity. The current study explores these scenarios, with a focus on the pathogenic fungus Rhizoctonia solani. Saprotrophic growth of R. solani on cellulose-rich materials was tested in vitro. This confirmed paper pulp as a highly suitable substrate for R. solani, whereas its performance on wood sawdusts varied with tree species. In two pot experiments, the effects of amendment of R. solani-infected soil with cellulose-rich materials on performance of beetroot seedlings were tested. All deciduous sawdusts and paper pulp stimulated soil fungal biomass, but only oak, elder and beech sawdusts reduced damping-off of beetroot. Oak sawdust amendment gave a consistent stimulation of saprotrophic Sordariomycetes fungi and of seedling performance, independently of the time between amendment and sowing. In contrast, paper pulp caused a short-term increase in R. solani abundance, coinciding with increased disease severity for beet seedlings sown immediately after amendment. However, damping-off of beetroot was reduced if plants were sown two or four weeks after paper pulp amendment. Cellulolytic bacteria, including Cytophagaceae, responded to paper pulp during the first two weeks and may have counteracted further spread of R. solani. The results showed that fungus-stimulating, cellulose-rich amendments have potential to be used for suppression of R. solani. However, such amendments require a careful consideration of material choice and application strategy.
Collapse
Affiliation(s)
- Anna Clocchiatti
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (M.S.R.); (M.P.J.H.); (P.J.A.k.G.)
- Correspondence: (A.C.); (W.d.B.)
| | - Silja Emilia Hannula
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands;
| | - Muhammad Syamsu Rizaludin
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (M.S.R.); (M.P.J.H.); (P.J.A.k.G.)
| | - Maria P. J. Hundscheid
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (M.S.R.); (M.P.J.H.); (P.J.A.k.G.)
| | - Paulien J. A. klein Gunnewiek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (M.S.R.); (M.P.J.H.); (P.J.A.k.G.)
| | - Mirjam T. Schilder
- Biointeractions and Plant Health, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (M.T.S.); (J.P.)
| | - Joeke Postma
- Biointeractions and Plant Health, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (M.T.S.); (J.P.)
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (M.S.R.); (M.P.J.H.); (P.J.A.k.G.)
- Soil Biology Group, Wageningen University, 6708 PB Wageningen, The Netherlands
- Correspondence: (A.C.); (W.d.B.)
| |
Collapse
|
17
|
Yoon JH, Kim SA, Shim WB, Seo DC, Choi S, Lee SY, Kim SR. Colonization of Listeria monocytogenes in potting soils as affected by bacterial community composition, storage temperature, and natural amendment. Food Sci Biotechnol 2021; 30:869-80. [PMID: 34249393 DOI: 10.1007/s10068-021-00925-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 05/05/2021] [Accepted: 05/25/2021] [Indexed: 10/21/2022] Open
Abstract
This study aimed to characterize the bacterial community of commercial potting soils with or without Listeria monocytogenes inoculation at 5-35 °C using 16S metagenomic sequencing and evaluate the effect of natural amendments on the reduction L. monocytogenes in non-sterile potting soils. An increase in the expected operational taxonomic units of each sample with or without L. monocytogenes was proportional to the increasing storage temperatures after 5 days. Biodiversity was distinct among all potting soils for Shannon and inverse Simpson indices, with the highest diversity being observed in a soil sample stored at 35 °C for 5 days with L. monocytogenes. An increase in richness and diversity of soil bacterial community structure positively correlated with less survival of the invading L. monocytogenes. Particularly, garlic extract was demonstrated as a promising soil-amendment substrate, reducing L. monocytogenes by ≥ 4.50 log CFU/g in potting soils stored at 35 °C. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-021-00925-9.
Collapse
|
18
|
Vandecasteele B, Amery F, Ommeslag S, Vanhoutte K, Visser R, Robbens J, De Tender C, Debode J. Chemically versus thermally processed brown shrimp shells or Chinese mitten crab as a source of chitin, nutrients or salts and as microbial stimulant in soilless strawberry cultivation. Sci Total Environ 2021; 771:145263. [PMID: 33545468 DOI: 10.1016/j.scitotenv.2021.145263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 10/05/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
Brown shrimp (Crangon crangon) shells and Chinese mitten crab (Eriocheir sinensis) were chemically demineralized and deproteinized (denoted as M1 to M4 for the shrimp shells and M5 to M7 for the Chinese mitten crab), and shrimp shells were torrefied at 200 to 300 °C (denoted as R200, R255, R300), and were compared with a commercially available chitin source (denoted as reference chitin). Based on their chemical characteristics, a selection of chitin sources was tested for their N mineralization capacity. The N release was high for the chemically treated shrimp shells and Chinese mitten crab, but not for the torrefied shrimp shells with or without acid treatment, indicating that treatment at 200 °C or higher resulted in low N availability. Interaction with nutrients was tested in a leaching experiment with limed peat for three thermally and two chemically processed shrimp shells and the reference chitin source. The K concentrations in the leachate for the chemically treated shrimp shells and the reference chitin were lower than for limed peat during fertigation. Irreversible K retention was observed for one source of chemically treated shrimp shells, and the reference chitin. The thermally treated shrimp shells had a significantly higher net release of P, Na and Cl than the treatment without chitin source. Three shrimp shell based materials (M4, R200 and R300) and the reference chitin were tested in a greenhouse trial with strawberry at a dose of 2 g/L limed peat. A very positive and significant effect on Botrytis cinerea disease suppression in the leaves was found for the reference chitin, M4 and R200 compared to the unamended control. The disease suppression of the 3 chitin sources was linked with an increase of the microbial biomass in the limed peat with 24% to 28% due to chitin decomposition and a 9-44% higher N uptake in the plants.
Collapse
Affiliation(s)
- Bart Vandecasteele
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burg. Van Gansberghelaan 109, 9820, Merelbeke, Belgium.
| | - Fien Amery
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burg. Van Gansberghelaan 109, 9820, Merelbeke, Belgium
| | - Sarah Ommeslag
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burg. Van Gansberghelaan 109, 9820, Merelbeke, Belgium
| | - Kaitlyn Vanhoutte
- Flanders Research Institute for Agriculture, Fisheries and Food, Animal Sciences Unit, Ankerstraat 1, 8400, Oostende, Belgium
| | - Rian Visser
- ECN part of TNO, Westerduinweg 3, 1755 ZG, Petten, the Netherlands
| | - Johan Robbens
- Flanders Research Institute for Agriculture, Fisheries and Food, Animal Sciences Unit, Ankerstraat 1, 8400, Oostende, Belgium
| | - Caroline De Tender
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burg. Van Gansberghelaan 109, 9820, Merelbeke, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 S9, 9000, Ghent, Belgium
| | - Jane Debode
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burg. Van Gansberghelaan 109, 9820, Merelbeke, Belgium
| |
Collapse
|
19
|
Babin D, Sommermann L, Chowdhury SP, Behr JH, Sandmann M, Neumann G, Nesme J, Sørensen SJ, Schellenberg I, Rothballer M, Geistlinger J, Smalla K, Grosch R. Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories. FEMS Microbiol Ecol 2021; 97:fiab027. [PMID: 33571366 DOI: 10.1093/femsec/fiab027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/09/2021] [Indexed: 12/21/2022] Open
Abstract
A better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions in soils of a long-term field experiment with contrasting histories of tillage (mouldboard plough vs cultivator tillage), fertilization intensity (intensive standard nitrogen (N) + pesticides/growth regulators vs extensive reduced N without fungicides/growth regulators), and last standing field crop (rapeseed vs winter wheat). High-throughput sequencing of bacterial and archaeal 16S rRNA genes and fungal ITS2 regions amplified from total community DNA showed that these factors shaped the soil and rhizosphere microbiota of lettuce, however, to different extents among the microbial domains. Pseudomonas and Olpidium were identified as major indicators for agricultural management in the rhizosphere of lettuce. Long-term extensive fertilization history of soils resulted in higher lettuce growth and increased expression of genes involved in plant stress responses compared to intensive fertilization. Our work adds to the increasing knowledge on how soil microbiota can be manipulated by agricultural management practices which could be harnessed for sustainable crop production.
Collapse
Affiliation(s)
- Doreen Babin
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Loreen Sommermann
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Institute of Bioanalytical Sciences (IBAS), Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Soumitra Paul Chowdhury
- Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Jan H Behr
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Martin Sandmann
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Günter Neumann
- University of Hohenheim, Institute of Crop Science, Department of Nutritional Crop Physiology, Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Joseph Nesme
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Ingo Schellenberg
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Institute of Bioanalytical Sciences (IBAS), Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Michael Rothballer
- Institute of Network Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Joerg Geistlinger
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Institute of Bioanalytical Sciences (IBAS), Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| |
Collapse
|
20
|
De Tender C, Vandecasteele B, Verstraeten B, Ommeslag S, De Meyer T, De Visscher J, Dawyndt P, Clement L, Kyndt T, Debode J. Chitin in Strawberry Cultivation: Foliar Growth and Defense Response Promotion, but Reduced Fruit Yield and Disease Resistance by Nutrient Imbalances. Mol Plant Microbe Interact 2021; 34:227-239. [PMID: 33135964 DOI: 10.1094/mpmi-08-20-0223-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Strawberry cultivation is associated with high mineral fertilizer doses and extensive use of chemical plant protection products. Based on previous research, we expected that chitin application to peat substrate would increase the nutrient availability and activate the plant systemic defense response, resulting in higher strawberry yields and fewer disease symptoms. We set up two experiments in which the temporal variability and differences in initial nutrient concentrations of the growing media were taken into account. Chitin treatment resulted in the attraction of plant growth-promoting fungi toward the plant root, such as species from genera Mortierella and Umbelopsis. In addition, by the end of the experiments 87 mg of mineral nitrogen (N) per liter of substrate was mineralized, which can be related to the observed increase in plant shoot biomass. This, however, led to nutrient imbalances in plant shoots and fruit; N concentration in the leaves increased over 30%, exceeding the optimal range, while phosphorous (P) and potassium (K) deficiencies occurred, with concentrations lower than 50% of the optimal range. This may explain the decreased fruit yield and disease resistance of the fruit toward Botrytis cinerea. In contrast, chitin caused a clear defense priming effect in the strawberry leaves, with a strong induction of the jasmonic acid response, resulting in fewer foliar disease symptoms. Chitin causes positive effects on shoot growth and foliar disease resistance, but caution needs to be taken for nutrient imbalances leading to negative influences on root growth, fruit production, and disease susceptibility toward B. cinerea.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- C De Tender
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 S9, 9000 Ghent, Belgium
| | - B Vandecasteele
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
| | - B Verstraeten
- Epigenetics & Defence Research Group, Department Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - S Ommeslag
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
| | - T De Meyer
- Department of Data Analysis & Mathematical Modelling, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent From Nucleotides to Networks, Ghent University, 9000 Ghent, Belgium
| | - J De Visscher
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
- Epigenetics & Defence Research Group, Department Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - P Dawyndt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 S9, 9000 Ghent, Belgium
| | - L Clement
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan 281 S9, 9000 Ghent, Belgium
- Bioinformatics Institute Ghent From Nucleotides to Networks, Ghent University, 9000 Ghent, Belgium
| | - T Kyndt
- Epigenetics & Defence Research Group, Department Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - J Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
| |
Collapse
|
21
|
Mathew GM, Mathew DC, Sukumaran RK, Sindhu R, Huang CC, Binod P, Sirohi R, Kim SH, Pandey A. Sustainable and eco-friendly strategies for shrimp shell valorization. Environ Pollut 2020; 267:115656. [PMID: 33254615 DOI: 10.1016/j.envpol.2020.115656] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 07/09/2020] [Revised: 08/31/2020] [Accepted: 09/12/2020] [Indexed: 06/12/2023]
Abstract
Among the seafood used globally, shellfish consumption is in great demand. The utilization of these shellfish such as prawn/shrimp has opened a new market for the utilization of the shellfish wastes. Considering the trends on the production of wealth from wastes, shrimp shell wastes seem an important resource for the generation of high value products when processed on the principles of a biorefinery. In recent years, various chemical strategies have been tried to valorize the shrimp shell wastes, which required harsh chemicals such as HCl and NaOH for demineralization (DM) and deproteination (DP) of the shrimp wastes. Disposal of chemicals by the chitin and chitosan industries into the aquatic bodies pose harm to the aquatic flora and fauna. Thus, there has been intensive efforts to develop safe and sustainable technologies for the management of shrimp shell wastes. This review provides an insight about environmentally-friendly methods along with biological methods to valorize the shrimp waste compared to the strategies employing concentrated chemicals. The main objective of this review article is to explain the utilization shrimp shell wastes in a productive manner such that it would be offer environment and economic sustainability. The application of valorized by-products developed from the shrimp shell wastes and physical methods to improve the pretreatment process of shellfish wastes for valorization are also highlighted in this paper.
Collapse
Affiliation(s)
- Gincy Marina Mathew
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Dony Chacko Mathew
- Department of Cosmeceutics, College of Biopharmaceutical and Food Sciences, China Medical University, Taichung, 40402, Taiwan
| | - Rajeev Kumar Sukumaran
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, No. 145, Xingda Road, South District, Taichung City, 402, Taiwan
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum, 695 019, India
| | - Ranjna Sirohi
- Department of Post Harvest Process and Food Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, 263 145, India
| | - Sang-Hyoun Kim
- Department of Chemical and Environmental Engineering, Yonsei University, Seoul, South Korea
| | - Ashok Pandey
- Center for Innovation and Translational Research, CSIR- Indian Institute of Toxicology Research, Lucknow, 226 001, India; Frontier Research Lab, Yonsei University, Seoul, South Korea.
| |
Collapse
|
22
|
Gärttling D, Kirchner SM, Schulz H. Assessment of the N- and P-Fertilization Effect of Black Soldier Fly (Diptera: Stratiomyidae) By-Products on Maize. J Insect Sci 2020; 20:5910012. [PMID: 32960967 PMCID: PMC7508297 DOI: 10.1093/jisesa/ieaa089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 05/06/2020] [Indexed: 05/20/2023]
Abstract
To meet the growing demand for an alternative animal protein source, the Black Soldier Fly (BSF) (Hermetia illucens) industry is expanding. Thus, the valuation of its byproducts, foremost BSF frass, is getting more economic and ecological weight. Three different residues, BSF frass, larval skins, and dead adult flies, were compared with a mineral and an organic commercial fertilizer in a pot trial with maize (Zea mays L., [Poales: Poaceae]). byproducts were applied in three nutrient-based application rates (180; 215 kg N/ha; 75 kg P2O5/ha), and plant nutrients, physiological and yield parameters were measured at harvest date. Ground flies had the highest N-fertilizing effect of all byproducts, similar to commercial mineral and organic fertilizers used as controls, whereas its proportion of the BSF production systems' output is low. Frass as the abundant byproduct showed comparably low N-fertilization effects. Its low N availability was attributed to volatilization losses, mainly driven by high pH and ammonium contents. BSF frass as the main byproduct output is more suited as a basic fertilizer or potting substrate amendment than as a short-term organic fertilizer. Postprocessing of frass seems reasonable. For a profound assessment of frass as fertilizer, several aspects (e.g., the overall impact of postprocessing, plant strengthening and plant protection potential, effects on microbial processes) must be clarified.
Collapse
Affiliation(s)
- Daniel Gärttling
- Organic Farming and Cropping Systems, University of Kassel, Witzenhausen, Germany
- Corresponding author, e-mail:
| | - Sascha M Kirchner
- Section of Agricultural and Biosystems Engineering, University of Kassel, Witzenhausen, Germany
| | - Hannes Schulz
- Kuratorium für Technik und Bauwesen in der Landwirtschaft e.V. (KTBL), Darmstadt, Germany
| |
Collapse
|
23
|
Barragán-Fonseca KY, Barragán-Fonseca KB, Verschoor G, van Loon JJ, Dicke M. Insects for peace. Curr Opin Insect Sci 2020; 40:85-93. [PMID: 32622192 DOI: 10.1016/j.cois.2020.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
Insects such as the black soldier fly (BSF) are a nutritious feed component for livestock with high protein levels. BSF can be reared on a wide range of organic residual streams. This allows for local production within a circular agriculture, decoupling livestock production from import of expensive feed components, such as fishmeal or soymeal. Rearing of BSF can be done by smallholder farmers, thus contributing to their livelihood, economic sustainability and social status. Smallholder farmers contribute importantly to food security, which is a prerequisite for a stable society. In armed conflicts, smallholder farmers are usually the first to suffer. In countries recovering from conflict, agricultural development should focus on restoring food production by smallholder farmers, improving their socio-economic position, thereby contributing to sustainable development goals 2 (zero hunger) and 16 (peace and justice). Here, we focus on these SDGs with an example of reintegration of ex-combatants as smallholder insect producers in post-conflict Colombia.
Collapse
Affiliation(s)
| | - Karol B Barragán-Fonseca
- Departamento de Producción Animal, Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, 111321, Bogotá, Colombia
| | - Gerard Verschoor
- Sociology of Development and Change Group, Wageningen University, PO Box 8130, 6700 EW Wageningen, The Netherlands
| | - Joop Ja van Loon
- Laboratory of Entomology, Wageningen University, PO Box 16, 6700 AA Wageningen, The Netherlands
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University, PO Box 16, 6700 AA Wageningen, The Netherlands.
| |
Collapse
|
24
|
Yergaliyev TM, Alexander-Shani R, Dimerets H, Pivonia S, Bird DM, Rachmilevitch S, Szitenberg A. Bacterial Community Structure Dynamics in Meloidogyne incognita-Infected Roots and Its Role in Worm-Microbiome Interactions. mSphere 2020; 5:e00306-20. [PMID: 32669465 DOI: 10.1128/mSphere.00306-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Plant parasitic nematodes such as Meloidogyne incognita have a complex life cycle, occurring sequentially in various niches of the root and rhizosphere. They are known to form a range of interactions with bacteria and other microorganisms that can affect their densities and virulence. High-throughput sequencing can reveal these interactions in high temporal and geographic resolutions, although thus far we have only scratched the surface. In this study, we have carried out a longitudinal sampling scheme, repeatedly collecting rhizosphere soil, roots, galls, and second-stage juveniles from 20 plants to provide a high-resolution view of bacterial succession in these niches, using 16S rRNA metabarcoding. Our findings indicate that a structured community develops in the root, in which gall communities diverge from root segments lacking a gall, and that this structure is maintained throughout the crop season. We describe the successional process leading toward this structure, which is driven by interactions with the nematode and later by an increase in bacteria often found in hypoxic and anaerobic environments. We present evidence that this structure may play a role in the nematode's chemotaxis toward uninfected root segments. Finally, we describe the J2 epibiotic microenvironment as ecologically deterministic, in part, due to the active bacterial attraction of second-stage juveniles.IMPORTANCE The study of high-resolution successional processes within tightly linked microniches is rare. Using the power and relatively low cost of metabarcoding, we describe the bacterial succession and community structure in roots infected with root-knot nematodes and in the nematodes themselves. We reveal separate successional processes in galls and adjacent non-gall root sections, which are driven by the nematode's life cycle and the progression of the crop season. With their relatively low genetic diversity, large geographic range, spatially complex life cycle, and the simplified agricultural ecosystems they occupy, root-knot nematodes can serve as a model organism for terrestrial holobiont ecology. This perspective can improve our understanding of the temporal and spatial aspects of biological control efficacy.
Collapse
|
25
|
Venneman J, De Tender C, Debode J, Audenaert K, Baert G, Vermeir P, Cremelie P, Bekaert B, Landschoot S, Thienpondt B, Djailo BD, Vereecke D, Haesaert G. Sebacinoids within rhizospheric fungal communities associated with subsistence farming in the Congo Basin: a needle in each haystack. FEMS Microbiol Ecol 2020; 95:5524361. [PMID: 31247636 DOI: 10.1093/femsec/fiz101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/25/2019] [Indexed: 12/15/2022] Open
Abstract
The unique ecosystem of the Congolese rainforest has only scarcely been explored for its plant-fungal interactions. Here, we characterized the root fungal communities of field-grown maize and of Panicum from adjacent borders in the Congo Basin and assessed parameters that could shape them. The soil properties indicated that comparable poor soil conditions prevailed in fields and borders, illustrating the low input character of local subsistence farming. The rhizosphere fungal communities, dominated by ascomycetous members, were structured by plant species, slash-and-burn practices and soil P, pH and C/N ratio. Examining fungi with potential plant growth-promoting abilities, the glomeromycotan communities appeared to be affected by the same parameters, whereas the inconspicuous symbionts of the order Sebacinales seemed less susceptible to environmental and anthropogenic factors. Notwithstanding the low abundances at which they were detected, sebacinoids occurred in 87% of the field samples, implying that they represent a consistent taxon within indigenous fungal populations across smallholder farm sites. Pending further insight into their ecosystem functionality, these data suggest that Sebacinales are robust root inhabitants that might be relevant for on-farm inoculum development within sustainable soil fertility management in the Sub-Saharan region.
Collapse
Affiliation(s)
- Jolien Venneman
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Caroline De Tender
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96, BE-9820, Merelbeke, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Krijgslaan 281, S9, BE-9000, Ghent, Belgium
| | - Jane Debode
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96, BE-9820, Merelbeke, Belgium
| | - Kris Audenaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Geert Baert
- Department of Environment, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Pieter Vermeir
- Department of Green Chemistry and Technology, Laboratory of Chemical Analysis (LCA), Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Pieter Cremelie
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96, BE-9820, Merelbeke, Belgium
| | - Boris Bekaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Sofie Landschoot
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Bert Thienpondt
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Benoît Dhed'a Djailo
- Faculty of Science and Agriculture, Kisangani University, B.P. 2012, Kisangani, Democratic Republic of Congo
| | - Danny Vereecke
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Geert Haesaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| |
Collapse
|
26
|
Randall TE, Fernandez-Bayo JD, Harrold DR, Achmon Y, Hestmark KV, Gordon TR, Stapleton JJ, Simmons CW, VanderGheynst JS. Changes of Fusarium oxysporum f.sp. lactucae levels and soil microbial community during soil biosolarization using chitin as soil amendment. PLoS One 2020; 15:e0232662. [PMID: 32369503 PMCID: PMC7199936 DOI: 10.1371/journal.pone.0232662] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/20/2020] [Indexed: 11/18/2022] Open
Abstract
Regulatory pressure along with environmental and human health concerns drive the development of soil fumigation alternatives such as soil biosolarization (SBS). SBS involves tarping soil that is at field capacity with a transparent film following amendment with certain organic materials. Heating via the greenhouse effect results in an increase of the soil temperature. The organic amendments can promote microbial activity that can enhance pest inactivation by depleting oxygen, producing biopesticidal fermentation products, and competing with pests. The properties of the organic amendments can heavily influence the type and magnitude of these effects. This study evaluated the viability of chitin as a novel SBS soil amendment to influence soil fungal and bacterial microbial communities, including control of the plant pathogen Fusarium oxysporum f.sp. lactucae (FOL). Changes to FOL and the broader soil microbiota were monitored in response to biosolarization using 0.1% (by dry weight) amendment with chitin (Rootguard). FOL suppression was only observed in chitin amended soils that were incubated at room temperature, not under solarized conditions. Conversely, it decreased solarization efficacy in the upper (0–10 cm) soil layer. The presence of chitin also showed increase in FOL under anaerobic and fluctuating temperature regime conditions. Biosolarization with chitin amendment did exhibit an impact on the overall soil microbial community. The fungal genus Mortierella and the bacterial family Chitinophagaceae were consistently enriched in biosolarized soils with chitin amendment. This study showed low potential FOL suppression due chitin amendment at the studied levels. However, chitin amendment showed a higher impact on the fungal community than the bacterial community. The impact of these microbial changes on crop protection and yields need to be studied in the long-term.
Collapse
Affiliation(s)
- Tara E. Randall
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, United States of America
| | - Jesus D. Fernandez-Bayo
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, United States of America
- Department of Food Science and Technology, University of California, Davis, CA, United States of America
- * E-mail:
| | - Duff R. Harrold
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, United States of America
| | - Yigal Achmon
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, United States of America
- Department of Food Science and Technology, University of California, Davis, CA, United States of America
| | - Kelley V. Hestmark
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, United States of America
| | - Thomas R. Gordon
- Department of Plant Pathology, University of California, Davis, CA, United States of America
| | - James J. Stapleton
- Statewide Integrated Pest Management Program, University of California, Kearney Agricultural Research and Extension Center, Parlier, CA, United States of America
| | - Christopher W. Simmons
- Department of Food Science and Technology, University of California, Davis, CA, United States of America
| | - Jean S. VanderGheynst
- Department of Biological and Agricultural Engineering, University of California, Davis, CA, United States of America
- Department of Bioengineering, University of Massachusetts, Dartmouth, MA, United States of America
| |
Collapse
|
27
|
Schönbichler A, Díaz-Moreno SM, Srivastava V, McKee LS. Exploring the Potential for Fungal Antagonism and Cell Wall Attack by Bacillus subtilis natto. Front Microbiol 2020; 11:521. [PMID: 32296406 PMCID: PMC7136451 DOI: 10.3389/fmicb.2020.00521] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 01/16/2020] [Accepted: 03/10/2020] [Indexed: 12/18/2022] Open
Abstract
To develop more ecologically sustainable agricultural practices requires that we reduce our reliance on synthetic chemical pesticides for crop protection. This will likely involve optimized biocontrol approaches - the use of beneficial soil microbes to attack potential plant pathogens to protect plants from diseases. Many bacterial species, including strains of Bacillus subtilis, have been explored for their biocontrol properties, as they can control the growth of harmful fungi, often by disrupting the fungal cell wall. A strain that is not often considered for this particular application is Bacillus subtilis natto, primarily known for fermenting soybeans via cell wall degradation in the Japanese probiotic dish "natto." Because deconstruction of the fungal cell wall is considered an important biocontrol trait, we were motivated to explore the possible anti-fungal properties of the B. subtilis natto strain. We show that B. subtilis natto can use complex fungal material as a carbon source for growth, and can effectively deconstruct fungal cell walls. We found degradation of fungal cell wall proteins, and showed that growth on a mix of peptides was very strong. We also found that intact fungal cell walls can induce the secretion of chitinases and proteases. Surprisingly, we could show that chitin, the bulk component of the fungal cell wall, does not permit successful growth of the natto strain or induce the secretion of chitinolytic enzymes, although these were produced during exposure to proteins or to complex fungal material. We have further shown that protease secretion is likely a constitutively enabled mechanism for nutrient scavenging by B. subtilis natto, as well as a potent tool for the degradation of fungal cell walls. Overall, our data highlight B. subtilis natto as a promising candidate for biocontrol products, with relevant behaviors that can be optimized by altering growth conditions. Whereas it is common for bacterial biocontrol products to be supplied with chitin or chitosan as a priming polysaccharide, our data indicate that this is not a useful approach with this particular bacterium, which should instead be supplied with either glucose or attenuated fungal material.
Collapse
Affiliation(s)
- Anna Schönbichler
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Sara M Díaz-Moreno
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden
| | - Lauren Sara McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.,Wallenberg Wood Science Center, Stockholm, Sweden
| |
Collapse
|
28
|
Shen Y, Nie J, Kuang L, Zhang J, Li H. DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables. Microb Biotechnol 2020; 14:323-362. [PMID: 32207561 PMCID: PMC7936329 DOI: 10.1111/1751-7915.13560] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/20/2022] Open
Abstract
The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.
Collapse
Affiliation(s)
- Youming Shen
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jiyun Nie
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China.,College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lixue Kuang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jianyi Zhang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Haifei Li
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| |
Collapse
|
29
|
De Tender C, Mesuere B, Van der Jeugt F, Haegeman A, Ruttink T, Vandecasteele B, Dawyndt P, Debode J, Kuramae EE. Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome. Sci Rep 2019; 9:9890. [PMID: 31289280 PMCID: PMC6617458 DOI: 10.1038/s41598-019-46106-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/19/2019] [Indexed: 11/09/2022] Open
Abstract
Chitin is a valuable peat substrate amendment by increasing lettuce growth and reducing the survival of the zoonotic pathogen Salmonella enterica on lettuce leaves. The production of chitin-catabolic enzymes (chitinases) play a crucial role and are mediated through the microbial community. A higher abundance of plant-growth promoting microorganisms and genera involved in N and chitin metabolism are present in a chitin-enriched substrate. In this study, we hypothesize that chitin addition to peat substrate stimulates the microbial chitinase production. The degradation of chitin leads to nutrient release and the production of small chitin oligomers that are related to plant growth promotion and activation of the plant's defense response. First a shotgun metagenomics approach was used to decipher the potential rhizosphere microbial functions then the nutritional content of the peat substrate was measured. Our results show that chitin addition increases chitin-catabolic enzymes, bacterial ammonium oxidizing and siderophore genes. Lettuce growth promotion can be explained by a cascade degradation of chitin to N-acetylglucosamine and eventually ammonium. The occurrence of increased ammonium oxidizing bacteria, Nitrosospira, and amoA genes results in an elevated concentration of plant-available nitrate. In addition, the increase in chitinase and siderophore genes may have stimulated the plant's systemic resistance.
Collapse
Affiliation(s)
- C De Tender
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium.
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281 S9, 9000, Ghent, Belgium.
| | - B Mesuere
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281 S9, 9000, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, B-9000, Ghent, Belgium
| | - F Van der Jeugt
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281 S9, 9000, Ghent, Belgium
| | - A Haegeman
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - T Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - B Vandecasteele
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - P Dawyndt
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, Krijgslaan 281 S9, 9000, Ghent, Belgium
| | - J Debode
- Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burgemeester Van Gansberghelaan 92, 9820, Merelbeke, Belgium
| | - E E Kuramae
- Netherlands Institute of Ecology, department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| |
Collapse
|
30
|
Zegeye EK, Brislawn CJ, Farris Y, Fansler SJ, Hofmockel KS, Jansson JK, Wright AT, Graham EB, Naylor D, McClure RS, Bernstein HC. Selection, Succession, and Stabilization of Soil Microbial Consortia. mSystems 2019; 4:e00055-19. [PMID: 31098394 DOI: 10.1128/mSystems.00055-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/24/2019] [Indexed: 12/25/2022] Open
Abstract
Soil microorganisms play fundamental roles in cycling of soil carbon, nitrogen, and other nutrients, yet we have a poor understanding of how soil microbiomes are shaped by their nutritional and physical environment. In this study, we investigated the successional dynamics of a soil microbiome during 21 weeks of enrichment on chitin and its monomer, N-acetylglucosamine. We examined succession of the soil communities in a physically heterogeneous soil matrix as well as a homogeneous liquid medium. The guiding hypothesis was that the initial species richness would influence the tendency for the selected consortia to stabilize and maintain a relatively constant community structure over time. We also hypothesized that long-term, substrate-driven growth would result in consortia with reduced species richness compared to the parent microbiome and that this process would be deterministic with relatively little variation between replicates. We found that the initial species richness does influence the long-term community stability in both liquid media and soil and that lower initial richness results in a more rapid convergence to stability. Despite use of the same soil inoculum and access to the same major substrate, the resulting community composition differed greatly in soil from that in liquid medium. Hence, distinct selective pressures in soils relative to homogenous liquid media exist and can control community succession dynamics. This difference is likely related to the fact that soil microbiomes are more likely to thrive, with fewer compositional changes, in a soil matrix than in liquid environments. IMPORTANCE The soil microbiome carries out important ecosystem functions, but interactions between soil microbial communities have been difficult to study due to the high microbial diversity and complexity of the soil habitat. In this study, we successfully obtained stable consortia with reduced complexity that contained species found in the original source soil. These consortia and the methods used to obtain them can be a valuable resource for exploration of specific mechanisms underlying soil microbial community ecology. The results of this study also provide new experimental context to better inform how soil microbial communities are shaped by new environments and how a combination of initial taxonomic structure and physical environment influences stability.
Collapse
|
31
|
Egusa M, Parada R, Aklog YF, Ifuku S, Kaminaka H. Nanofibrillation enhances the protective effect of crab shells against Fusarium wilt disease in tomato. Int J Biol Macromol 2019; 128:22-27. [PMID: 30682468 DOI: 10.1016/j.ijbiomac.2019.01.088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/20/2018] [Accepted: 01/17/2019] [Indexed: 12/20/2022]
Abstract
Chitin, a polymer of N‑acetyl‑d‑glucosamine, is a beneficial material for agriculture because it enhances plant growth and disease control. Although chitin utilization is limited by handling difficulties, chitin nanofiber (CNF) can be more feasibly used since it behaves as a water-soluble material. To broaden the utilization of chitin, protein/CaCO3/chitin nanofiber (P/Ca/CNF) and protein/chitin nanofiber (P/CNF) complexes were prepared from crab shells without using environmentally hazardous chemical in chitin purification processes. Chitin was disintegrated into nanofibers by grinder pretreatment and the subsequent use of a high-pressure water jet system. The nanofibrillation degree depended on the number of mechanical treatments applied. The addition of CNFs to soil slightly enhanced tomato growth relative to that of CNF-untreated or crushed crab shell-treated plants. Furthermore, CNFs treatment reduced the incidence of Fusarium wilt disease in tomato plants. Disease inhibition by P/Ca/CNF and P/CNF was more effective than that by crushed crab shells, and comparable to that by pure CNF. There was no significant relationship between disease reduction level and nanofibrillation degree. In conclusion, P/Ca/CNF prepared with the minimal number of steps was sufficiently able to inhibit Fusarium wilt disease in tomato, and could thus be an eco-friendly material to control plant diseases in sustainable agriculture.
Collapse
Affiliation(s)
- Mayumi Egusa
- Faculty of Agriculture, Tottori University, 4-101 Koyama-Minami, Tottori 680-8553, Japan
| | - RoxanaYanira Parada
- Faculty of Agriculture, Tottori University, 4-101 Koyama-Minami, Tottori 680-8553, Japan
| | - Yihun Fantahun Aklog
- Department of Engineering, Graduate School of Sustainability Science, 680-8552, Japan
| | - Shinsuke Ifuku
- Department of Engineering, Graduate School of Sustainability Science, 680-8552, Japan
| | - Hironori Kaminaka
- Faculty of Agriculture, Tottori University, 4-101 Koyama-Minami, Tottori 680-8553, Japan.
| |
Collapse
|
32
|
Lacombe-Harvey MÈ, Brzezinski R, Beaulieu C. Chitinolytic functions in actinobacteria: ecology, enzymes, and evolution. Appl Microbiol Biotechnol 2018; 102:7219-7230. [PMID: 29931600 PMCID: PMC6097792 DOI: 10.1007/s00253-018-9149-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 12/20/2022]
Abstract
Actinobacteria, a large group of Gram-positive bacteria, secrete a wide range of extracellular enzymes involved in the degradation of organic compounds and biopolymers including the ubiquitous aminopolysaccharides chitin and chitosan. While chitinolytic enzymes are distributed in all kingdoms of life, actinobacteria are recognized as particularly good decomposers of chitinous material and several members of this taxon carry impressive sets of genes dedicated to chitin and chitosan degradation. Degradation of these polymers in actinobacteria is dependent on endo- and exo-acting hydrolases as well as lytic polysaccharide monooxygenases. Actinobacterial chitinases and chitosanases belong to nine major families of glycosyl hydrolases that share no sequence similarity. In this paper, the distribution of chitinolytic actinobacteria within different ecosystems is examined and their chitinolytic machinery is described and compared to those of other chitinolytic organisms.
Collapse
Affiliation(s)
| | - Ryszard Brzezinski
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Carole Beaulieu
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada.
| |
Collapse
|
33
|
Al-Maliki S, Al-Masoudi M. Interactions between Mycorrhizal Fungi, Tea Wastes, and Algal Biomass Affecting the Microbial Community, Soil Structure, and Alleviating of Salinity Stress in Corn Yield ( Zeamays L.). Plants (Basel) 2018; 7:plants7030063. [PMID: 30096837 PMCID: PMC6161139 DOI: 10.3390/plants7030063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/27/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
Soil salinity has an adverse impact on soil biological properties and growth of corn plant, majorly in arid and semi-arid lands. A mesocosm experiment was conducted to investigate the effect of mycorrhizal fungi (M) (Glomus mosseae), tea wastes (T), algal dried biomass (A), and their combinations on soil respiration, total bacteria, total fungi, soil mean weight diameter (MWD), and corn yield (Zeamays L.). under saline and non-saline soils. Results showed that M, T, and A treatments increased significantly CO₂ release compared to the control. Whereas, M significantly decreased CO₂ release compared to T and A treatments. In non-saline soil, M increased greatly MWD, bacterial and fungal counts, and infection rate. Whereas, the opposite was true in the saline soil; neither M nor T improved bacterial communities and MWD. However, in the saline soil, M + T was highly efficient in improving MWD, SOC, bacterial and fungal counts, infection rate, and corn grain yield. It can be suggested that the inoculation of mycorrhizal fungi with tea wastes in saline soils considered an important strategy that increases the toleration of the corn plant to salinity by improving soil microbial activity, MWD, SOC, infection rate, and total grain yield.
Collapse
Affiliation(s)
- Salwan Al-Maliki
- Soil and Water Science Department, College of Agriculture, Al-Qasim Green University, Al Qasim 13239, Iraq.
| | - Mugtaba Al-Masoudi
- Soil and Water Science Department, College of Agriculture, Al-Qasim Green University, Al Qasim 13239, Iraq.
| |
Collapse
|
34
|
Mercado-Blanco J, Abrantes I, Barra Caracciolo A, Bevivino A, Ciancio A, Grenni P, Hrynkiewicz K, Kredics L, Proença DN. Belowground Microbiota and the Health of Tree Crops. Front Microbiol 2018; 9:1006. [PMID: 29922245 PMCID: PMC5996133 DOI: 10.3389/fmicb.2018.01006] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [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: 01/02/2018] [Accepted: 04/30/2018] [Indexed: 11/13/2022] Open
Abstract
Trees are crucial for sustaining life on our planet. Forests and land devoted to tree crops do not only supply essential edible products to humans and animals, but also additional goods such as paper or wood. They also prevent soil erosion, support microbial, animal, and plant biodiversity, play key roles in nutrient and water cycling processes, and mitigate the effects of climate change acting as carbon dioxide sinks. Hence, the health of forests and tree cropping systems is of particular significance. In particular, soil/rhizosphere/root-associated microbial communities (known as microbiota) are decisive to sustain the fitness, development, and productivity of trees. These benefits rely on processes aiming to enhance nutrient assimilation efficiency (plant growth promotion) and/or to protect against a number of (a)biotic constraints. Moreover, specific members of the microbial communities associated with perennial tree crops interact with soil invertebrate food webs, underpinning many density regulation mechanisms. This review discusses belowground microbiota interactions influencing the growth of tree crops. The study of tree-(micro)organism interactions taking place at the belowground level is crucial to understand how they contribute to processes like carbon sequestration, regulation of ecosystem functioning, and nutrient cycling. A comprehensive understanding of the relationship between roots and their associate microbiota can also facilitate the design of novel sustainable approaches for the benefit of these relevant agro-ecosystems. Here, we summarize the methodological approaches to unravel the composition and function of belowground microbiota, the factors influencing their interaction with tree crops, their benefits and harms, with a focus on representative examples of Biological Control Agents (BCA) used against relevant biotic constraints of tree crops. Finally, we add some concluding remarks and suggest future perspectives concerning the microbiota-assisted management strategies to sustain tree crops.
Collapse
Affiliation(s)
- Jesús Mercado-Blanco
- Department of Crop Protection, Agencia Estatal Consejo Superior de Investigaciones Científicas, Institute for Sustainable Agriculture, Córdoba, Spain
| | - Isabel Abrantes
- Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
| | | | - Annamaria Bevivino
- Department for Sustainability of Production and Territorial Systems, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Rome, Italy
| | - Aurelio Ciancio
- Institute for Sustainable Plant Protection, National Research Council, Bari, Italy
| | - Paola Grenni
- Water Research Institute (CNR-IRSA), National Research Council, Rome, Italy
| | - Katarzyna Hrynkiewicz
- Department of Microbiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Toruń, Poland
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Diogo N. Proença
- Centre for Mechanical Engineering, Materials and Processes (CEMMPRE) and Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| |
Collapse
|
35
|
Desirò A, Hao Z, Liber JA, Benucci GMN, Lowry D, Roberson R, Bonito G. Mycoplasma-related endobacteria within Mortierellomycotina fungi: diversity, distribution and functional insights into their lifestyle. ISME J 2018; 12:1743-1757. [PMID: 29476142 DOI: 10.1038/s41396-018-0053-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 12/22/2017] [Accepted: 01/10/2018] [Indexed: 11/09/2022]
Abstract
Bacterial interactions with animals and plants have been examined for over a century; by contrast, the study of bacterial-fungal interactions has received less attention. Bacteria interact with fungi in diverse ways, and endobacteria that reside inside fungal cells represent the most intimate interaction. The most significant bacterial endosymbionts that have been studied are associated with Mucoromycota and include two main groups: Burkholderia-related and Mycoplasma-related endobacteria (MRE). Examples of Burkholderia-related endobacteria have been reported in the three Mucoromycota subphyla. By contrast, MRE have only been identified in Glomeromycotina and Mucoromycotina. This study aims to understand whether MRE dwell in Mortierellomycotina and, if so, to determine their impact on the fungal host. We carried out a large-scale screening of 394 Mortierellomycotina strains and employed a combination of microscopy, molecular phylogeny, next-generation sequencing and qPCR. We detected MRE in 12 strains. These endosymbionts represent novel bacterial phylotypes and show evidence of recombination. Their presence in Mortierellomycotina demonstrates that MRE occur within fungi across Mucoromycota and they may have lived in their common ancestor. We cured the fungus of its endosymbionts with antibiotics and observed improved biomass production in isogenic lines lacking MRE, demonstrating that these endobacteria impose some fitness costs to their fungal host. Here we provided the first functional insights into the lifestyle of MRE. Our findings indicate that MRE may be antagonistic to their fungal hosts, and adapted to a non-lethal parasitic lifestyle in the mycelium of Mucoromycota. However, context-dependent adaptive benefits to their host at minimal cost cannot not be excluded. Finally, we conclude that Mortierellomycotina represent attractive model organisms for exploring interactions between MRE and fungi.
Collapse
Affiliation(s)
- Alessandro Desirò
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
| | - Zhen Hao
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Julian A Liber
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | | | - David Lowry
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Robert Roberson
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| |
Collapse
|
36
|
Debode J, De Tender C, Cremelie P, Lee AS, Kyndt T, Muylle H, De Swaef T, Vandecasteele B. Trichoderma-Inoculated Miscanthus Straw Can Replace Peat in Strawberry Cultivation, with Beneficial Effects on Disease Control. Front Plant Sci 2018; 9:213. [PMID: 29515613 PMCID: PMC5826379 DOI: 10.3389/fpls.2018.00213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/05/2018] [Indexed: 05/30/2023]
Abstract
Peat based growing media are not ecologically sustainable and often fail to support biological control. Miscanthus straw was (1) tested to partially replace peat; and (2) pre-colonized with a Trichoderma strain to increase the biological control capacity of the growing media. In two strawberry pot trials (denoted as experiment I & II), extruded and non-extruded miscanthus straw, with or without pre-colonization with T. harzianum T22, was used to partially (20% v/v) replace peat. We tested the performance of each mixture by monitoring strawberry plant development, nutrient content in the leaves and growing media, sensitivity of the fruit to the fungal pathogen Botrytis cinerea, rhizosphere community and strawberry defense responses. N immobilization by miscanthus straw reduced strawberry growth and yield in experiment II but not in I. The pre-colonization of the straw with Trichoderma increased the post-harvest disease suppressiveness against B. cinerea and changed the rhizosphere fungal microbiome in both experiments. In addition, defense-related genes were induced in experiment II. The use of miscanthus straw in growing media will reduce the demand for peat and close resource loops. Successful pre-colonization of this straw with biological control fungi will optimize crop cultivation, requiring fewer pesticide applications, which will benefit the environment and human health.
Collapse
Affiliation(s)
- Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Caroline De Tender
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Pieter Cremelie
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Ana S. Lee
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
- Epigenetics & Defence Research Group, Department Molecular Biotechnology, Ghent University, Ghent, Belgium
| | - Tina Kyndt
- Epigenetics & Defence Research Group, Department Molecular Biotechnology, Ghent University, Ghent, Belgium
| | - Hilde Muylle
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Tom De Swaef
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| | - Bart Vandecasteele
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, Belgium
| |
Collapse
|
37
|
Sieber V, Hofer M, Brück WM, Garbe D, Brück T, Lynch CA. ChiBio: An Integrated Bio-refinery for Processing Chitin-Rich Bio-waste to Specialty Chemicals. Grand Challenges in Marine Biotechnology 2018. [DOI: 10.1007/978-3-319-69075-9_14] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
38
|
Inderbitzin P, Ward J, Barbella A, Solares N, Izyumin D, Burman P, Chellemi DO, Subbarao KV. Soil Microbiomes Associated with Verticillium Wilt-Suppressive Broccoli and Chitin Amendments are Enriched with Potential Biocontrol Agents. Phytopathology 2018; 108:31-43. [PMID: 28876209 DOI: 10.1094/phyto-07-17-0242-r] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Two naturally infested Verticillium wilt-conducive soils from the Salinas Valley of coastal California were amended with disease-suppressive broccoli residue or crab meal amendments, and changes to the soil prokaryote community were monitored using Illumina sequencing of a 16S ribosomal RNA gene library generated from 160 bulk soil samples. The experiment was run in a greenhouse, twice, with eggplant as the Verticillium wilt-susceptible host. Disease suppression, plant height, soil microsclerotia density, and soil chitinase activity were assessed at the conclusion of each experiment. In soil with high microsclerotia density, all amendments significantly reduced Verticillium wilt severity and microsclerotia density, and increased soil chitinase activity. Plant height was increased only in the broccoli-containing treatments. In total, 8,790 error-corrected sequence variants representing 1,917,893 different sequences were included in the analyses. The treatments had a significant impact on the soil microbiome community structure but measures of α diversity did not vary between treatments. Community structure correlated with disease score, plant height, microsclerotia density, and soil chitinase activity, suggesting that the prokaryote community may affect the disease-related response variables or vice versa. Similarly, the abundance of 107 sequence variants correlated with disease-related response variables, which included variants from genera with known antagonists of filamentous fungal plant pathogens, such as Pseudomonas and Streptomyces. Overall, genera with antifungal antagonists were more abundant in amended soils than unamended soils, and constituted up to 8.9% of all sequences in broccoli+crabmeal-amended soil. This study demonstrates that substrate-mediated shifts in soil prokaryote communities are associated with the transition of Verticillium wilt-conducive soils to Verticillium wilt-suppressive soils, and suggests that soils likely harbor numerous additional antagonists of fungal plant pathogens that contribute to the biological suppression of plant disease.
Collapse
Affiliation(s)
- Patrik Inderbitzin
- First and eighth authors: Department of Plant Pathology, and fifth and sixth authors: Department of Statistics, University of California, Davis; and second, third, fourth, and seventh authors: Driscoll's Strawberry Associates, Watsonville, CA
| | - Judson Ward
- First and eighth authors: Department of Plant Pathology, and fifth and sixth authors: Department of Statistics, University of California, Davis; and second, third, fourth, and seventh authors: Driscoll's Strawberry Associates, Watsonville, CA
| | - Alexandra Barbella
- First and eighth authors: Department of Plant Pathology, and fifth and sixth authors: Department of Statistics, University of California, Davis; and second, third, fourth, and seventh authors: Driscoll's Strawberry Associates, Watsonville, CA
| | - Natalie Solares
- First and eighth authors: Department of Plant Pathology, and fifth and sixth authors: Department of Statistics, University of California, Davis; and second, third, fourth, and seventh authors: Driscoll's Strawberry Associates, Watsonville, CA
| | - Dmitriy Izyumin
- First and eighth authors: Department of Plant Pathology, and fifth and sixth authors: Department of Statistics, University of California, Davis; and second, third, fourth, and seventh authors: Driscoll's Strawberry Associates, Watsonville, CA
| | - Prabir Burman
- First and eighth authors: Department of Plant Pathology, and fifth and sixth authors: Department of Statistics, University of California, Davis; and second, third, fourth, and seventh authors: Driscoll's Strawberry Associates, Watsonville, CA
| | - Dan O Chellemi
- First and eighth authors: Department of Plant Pathology, and fifth and sixth authors: Department of Statistics, University of California, Davis; and second, third, fourth, and seventh authors: Driscoll's Strawberry Associates, Watsonville, CA
| | - Krishna V Subbarao
- First and eighth authors: Department of Plant Pathology, and fifth and sixth authors: Department of Statistics, University of California, Davis; and second, third, fourth, and seventh authors: Driscoll's Strawberry Associates, Watsonville, CA
| |
Collapse
|
39
|
De Tender C, Devriese LI, Haegeman A, Maes S, Vangeyte J, Cattrijsse A, Dawyndt P, Ruttink T. Temporal Dynamics of Bacterial and Fungal Colonization on Plastic Debris in the North Sea. Environ Sci Technol 2017; 51:7350-7360. [PMID: 28562015 DOI: 10.1021/acs.est.7b00697] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Despite growing evidence that biofilm formation on plastic debris in the marine environment may be essential for its biodegradation, the underlying processes have yet to be fully understood. Thus, far, bacterial biofilm formation had only been studied after short-term exposure or on floating plastic, yet a prominent share of plastic litter accumulates on the seafloor. In this study, we explored the taxonomic composition of bacterial and fungal communities on polyethylene plastic sheets and dolly ropes during long-term exposure on the seafloor, both at a harbor and an offshore location in the Belgian part of the North Sea. We reconstructed the sequence of events during biofilm formation on plastic in the harbor environment and identified a core bacteriome and subsets of bacterial indicator species for early, intermediate, and late stages of biofilm formation. Additionally, by implementing ITS2 metabarcoding on plastic debris, we identified and characterized for the first time fungal genera on plastic debris. Surprisingly, none of the plastics exposed to offshore conditions displayed the typical signature of a late stage biofilm, suggesting that biofilm formation is severely hampered in the natural environment where most plastic debris accumulates.
Collapse
Affiliation(s)
- Caroline De Tender
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
- Ghent University , Department of Applied Mathematics, Computer Sciences and Statistics, Krijgslaan 281 S9, 9000 Ghent, Belgium
| | - Lisa I Devriese
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
- Department of Environment and Health, Vrije Universiteit Amsterdam , De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
| | - Annelies Haegeman
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
| | - Sara Maes
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
| | - Jürgen Vangeyte
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
| | - André Cattrijsse
- Flanders Marine Institute , InnovOcean site, Wandelaarkaai 7, 8400 Oostende, Belgium
| | - Peter Dawyndt
- Ghent University , Department of Applied Mathematics, Computer Sciences and Statistics, Krijgslaan 281 S9, 9000 Ghent, Belgium
| | - Tom Ruttink
- Institute of Agricultural, Fisheries and Food Research (ILVO) , Burgemeester Van Gansberghelaan 92, 9820 Merelbeke, Belgium
| |
Collapse
|
40
|
Ji R, Dong G, Shi W, Min J. Effects of Liquid Organic Fertilizers on Plant Growth and Rhizosphere Soil Characteristics of Chrysanthemum. Sustainability 2017; 9:841. [DOI: 10.3390/su9050841] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
41
|
De Tender C, Haegeman A, Vandecasteele B, Clement L, Cremelie P, Dawyndt P, Maes M, Debode J. Dynamics in the Strawberry Rhizosphere Microbiome in Response to Biochar and Botrytis cinerea Leaf Infection. Front Microbiol 2016; 7:2062. [PMID: 28066380 PMCID: PMC5177642 DOI: 10.3389/fmicb.2016.02062] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 12/07/2016] [Indexed: 01/18/2023] Open
Abstract
Adding biochar, the solid coproduct of biofuel production, to peat can enhance strawberry growth, and disease resistance against the airborne fungal pathogen Botrytis cinerea. Additionally, biochar can induce shifts in the strawberry rhizosphere microbiome. However, the moment that this biochar-mediated shift occurs in the rhizosphere is not known. Further, the effect of an above-ground infection on the strawberry rhizosphere microbiome is unknown. In the present study we established two experiments in which strawberry transplants (cv. Elsanta) were planted either in peat or in peat amended with 3% biochar. First, we established a time course experiment to measure the effect of biochar on the rhizosphere bacterial and fungal communities over time. In a second experiment, we inoculated the strawberry leaves with B. cinerea, and studied the impact of the infection on the rhizosphere bacterial community. The fungal rhizosphere community was stabilized after 1 week, except for the upcoming Auriculariales, whereas the bacterial community shifted till 6 weeks. An effect of the addition of biochar to the peat on the rhizosphere microbiome was solely measured for the bacterial community from week 6 of plant growth onwards. When scoring the plant development, biochar addition was associated with enhanced root formation, fruit production, and postharvest resistance of the fruits against B. cinerea. We hypothesize that the bacterial rhizosphere microbiome, but also biochar-mediated changes in chemical substrate composition could be involved in these events. Infection of the strawberry leaves with B. cinerea induced shifts in the bacterial rhizosphere community, with an increased bacterial richness. This disease-induced effect was not observed in the rhizospheres of the B. cinerea-infected plants grown in the biochar-amended peat. The results show that an above-ground infection has its effect on the strawberry rhizosphere microbiome, changing the bacterial interactions in the root-substrate interface. This infection effect on the bacterial rhizosphere microbiome seems to be comparable to, but less pronounced than the effect of biochar-addition to the peat. The biological meaning of these observations needs further research, but this study indicates that biochar and an above-ground pathogen attack help the plant to recruit rhizosphere microbes that may aid them in their plant growth and health.
Collapse
Affiliation(s)
- Caroline De Tender
- Plant Sciences Unit, Crop Protection, Institute of Agricultural and Fisheries ResearchMerelbeke, Belgium; Department of Applied Mathematics Computer Sciences and Statistics, Ghent UniversityGhent, Belgium
| | - Annelies Haegeman
- Plant Sciences Unit, Crop Protection, Institute of Agricultural and Fisheries Research Merelbeke, Belgium
| | - Bart Vandecasteele
- Plant Sciences Unit, Crop Husbandry and Environment, Institute of Agricultural and Fisheries Research Merelbeke, Belgium
| | - Lieven Clement
- Department of Applied Mathematics Computer Sciences and Statistics, Ghent UniversityGhent, Belgium; Bioinformatics Institute Ghent From Nucleotides to Networks, Ghent UniversityGhent, Belgium
| | - Pieter Cremelie
- Plant Sciences Unit, Crop Protection, Institute of Agricultural and Fisheries ResearchMerelbeke, Belgium; Plant Sciences Unit, Crop Husbandry and Environment, Institute of Agricultural and Fisheries ResearchMerelbeke, Belgium
| | - Peter Dawyndt
- Department of Applied Mathematics Computer Sciences and Statistics, Ghent University Ghent, Belgium
| | - Martine Maes
- Plant Sciences Unit, Crop Protection, Institute of Agricultural and Fisheries Research Merelbeke, Belgium
| | - Jane Debode
- Plant Sciences Unit, Crop Protection, Institute of Agricultural and Fisheries Research Merelbeke, Belgium
| |
Collapse
|