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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2024; 44:1164-1182. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/22/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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2
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Martinez I Quer A, Arias CA, Ellegaard-Jensen L, Johansen A, Paulsen ML, Pastor A, Carvalho PN. Saturated constructed wetlands for the remediation of cylindrospermopsin and microcystin-LR: Plants, microbes, and biodegradation pathways. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174745. [PMID: 39032754 DOI: 10.1016/j.scitotenv.2024.174745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 06/16/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024]
Abstract
Harmful cyanobacterial blooms will be more intense and frequent in the future, contaminating surface waters with cyanotoxins and posing a threat to communities heavily reliant on surface water usage for crop irrigation. Constructed wetlands (CWs) are proposed to ensure safe crop irrigation, but more research is needed before implementation. The present study operated 28 mesocosms in continuous mode mimicking horizontal sub-surface flow CWs. Mesocosms were fed with synthetic lake water and spiked periodically with two cyanotoxins, microcystin-LR (MC-LR) and cylindrospermopsin (CYN), at environmentally relevant cyanotoxins concentrations (10 μg L-1). The influence of various design factors, including plant species, porous media, and seasonality, was explored. The mesocosms achieved maximum MC-LR and CYN mass removal rates of 95 % and 98 %, respectively. CYN removal is reported for the first time in CWs mimicking horizontal sub-surface flow CWs. Planted mesocosms consistently outperformed unplanted mesocosms, with Phragmites australis exhibiting superior cyanotoxin mass removal compared to Juncus effusus. Considering evapotranspiration, J. effusus yielded the least cyanotoxin-concentrated effluent due to the lower water losses in comparison with P. australis. Using the P-kC* model, different scaling-up scenarios for future piloting were calculated and discussed. Additionally, bacterial community structure was analyzed through correlation matrices and differential taxa analyses, offering valuable insights into their removal of cyanotoxins. Nevertheless, attempts to validate microcystin-LR biotransformation via the known mlrA gene degradation pathway were unfruitful, indicating alternative enzymatic degradation pathways occurring in such complex CW systems. Further investigation into the precise molecular mechanisms of removal and the identification of transformation products is needed for the comprehensive understanding of cyanotoxin mitigation in CW. This study points towards the feasibility of horizontal sub-surface flow CWs to be employed to control cyanotoxins in irrigation or recreational waters.
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Affiliation(s)
- Alba Martinez I Quer
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Carlos Alberto Arias
- Department of Biology, Aarhus University, Ole Worms Allé 1, 8000 Aarhus, C, Denmark; WATEC, Centre for Water Technology, Aarhus University, Ny Munkegade 120, 8000 Aarhus, C, Denmark
| | - Lea Ellegaard-Jensen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark; WATEC, Centre for Water Technology, Aarhus University, Ny Munkegade 120, 8000 Aarhus, C, Denmark
| | - Anders Johansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark; WATEC, Centre for Water Technology, Aarhus University, Ny Munkegade 120, 8000 Aarhus, C, Denmark
| | - Maria Lund Paulsen
- Arctic Research Centre, Department of Biology, Ole Worms Allé 1, 8000, Aarhus, C, Denmark; Marine Microbiology, Bergen University, Thormøhlens gate, 53, Bergen, Norway
| | - Ada Pastor
- Department of Biology, Aarhus University, Ole Worms Allé 1, 8000 Aarhus, C, Denmark; Group of Continental Aquatic Ecology Research (GRECO), Institute of Aquatic Ecology, University of Girona, Campus Montilivi, 17003 Girona, Spain
| | - Pedro N Carvalho
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark; WATEC, Centre for Water Technology, Aarhus University, Ny Munkegade 120, 8000 Aarhus, C, Denmark.
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3
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Thyssen LA, Martinez I Quer A, Arias CA, Ellegaard-Jensen L, Carvalho PN, Johansen A. Constructed wetland mesocosms improve the biodegradation of microcystin-LR and cylindrospermopsin by indigenous bacterial consortia. HARMFUL ALGAE 2024; 131:102549. [PMID: 38212082 DOI: 10.1016/j.hal.2023.102549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 01/13/2024]
Abstract
Cyanobacterial blooms releasing harmful cyanotoxins, such as microcystin (MC) and cylindrospermopsin (CYN), are prominent threats to human and animal health. Constructed wetlands (CW) may be a nature-based solution for bioremediation of lake surface water containing cyanotoxins, due to its low-cost requirement of infrastructure and environmentally friendly operation. There is recent evidence that microcystin-LR (MC-LR) can efficiently be removed in CW microcosms where CYN degradation in CW is unknown. Likewise, the mechanistic background regarding cyanotoxins transformation in CW is not yet elucidated. In the present study, the objective was to compare MC-LR and CYN degradation efficiencies by two similar microbial communities obtained from CW mesocosms, by two different experiments setup: 1) in vitro batch experiment in serum bottles with an introduced CW community, and 2) degradation in CW mesocosms. In experiment 1) MC-LR and CYN were spiked at 100 µg L-1 and in experiment 2) 200 µg L-1 were spiked. Results showed that MC-LR was degraded to ≤1 µg L-1 within seven days in both experiments. However, with a markedly higher degradation rate constant in the CW mesocosms (0.18 day-1 and 0.75 day-1, respectively). No CYN removal was detected in the in vitro incubations, whereas around 50 % of the spiked CYN was removed in the CW mesocosms. The microbial community responded markedly to the cyanotoxin treatment, with the most prominent increase of bacteria affiliated with Methylophilaceae (order: Methylophilales, phylum: Proteobacteria). The results strongly indicate that CWs can develop an active microbial community capable of efficient removal of MC-LR and CYN. However, the CW operational conditions need to be optimized to achieve a full CYN degradation. To the best of our knowledge, this study is the first to report the ability of CW mesocosms to degrade CYN.
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Affiliation(s)
- Lasse Ahrenkiel Thyssen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Alba Martinez I Quer
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Carlos Alberto Arias
- Department of Biology, Aarhus University, Ole Worms Allé 1, 8000 Aarhus C, Denmark; WATEC, Centre for Water Technology, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark
| | - Lea Ellegaard-Jensen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark; WATEC, Centre for Water Technology, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark
| | - Pedro N Carvalho
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark; WATEC, Centre for Water Technology, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark.
| | - Anders Johansen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark; WATEC, Centre for Water Technology, Aarhus University, Ny Munkegade 120, 8000 Aarhus C, Denmark
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Bou Orm E, Sauvagère S, Rocher J, Benezet JC, Bayle S, Siatka C, Bergeret A, Malhautier L. Estimating the bias related to DNA recovery from hemp stems for retting microbial community investigation. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12582-5. [PMID: 37227475 DOI: 10.1007/s00253-023-12582-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 05/26/2023]
Abstract
The industrial hemp plant Cannabis sativa is a source of vegetable fiber for both textiles and biocomposite applications. After harvesting, the plant stems are laid out on the ground and colonized by microorganisms (bacteria and fungi) naturally present in the soil and on the stems. By producing hydrolytic enzymes that degrade the plant wall polymers, the natural cement that binds the fiber bundles together is removed, thus facilitating their dissociation (retting process) which is required for producing high-performant fibers. To investigate temporal dynamics of retting microbial communities (density levels, diversity, and structure), a reliable protocol for extracting genomic DNA from stems is mandatory. However, very little attention has been paid to the methodological aspects of nucleic acid extraction, although they are crucial for the significance of the final result. Three protocols were selected and tested: a commercial kit (FastDNA™ Spin Kit for soil), the Gns-GII procedure, and a custom procedure from the Genosol platform. A comparative analysis was carried out on soil and two different varieties of hemp stem. The efficiency of each method was measured by evaluating both the quantity and quality of the extracted DNA and the abundance and taxonomy of bacterial and fungal populations. The Genosol protocol provides interesting yields in terms of quantity and quality of genomic DNA compared to the other two protocols. However, no major difference was observed in microbial diversity between the two extraction procedures (FastDNA™ SPIN Kit and Genosol protocol). Based on these results, the FastDNA™ SPIN kit or the Genosol procedure seems to be suitable for studying bacterial and fungal communities of the retting process. It should be noted that this work has demonstrated the importance of evaluating biases associated with DNA recovery from hemp stems. KEY POINTS: • Metagenomic DNA was successfully extracted from hemp stem samples using three different protocols. • Further evaluation was performed in terms of DNA yield and purity, abundance level, and microbial community structure. • This work exhibited the crucial importance of DNA recovery bias evaluation.
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Affiliation(s)
- Eliane Bou Orm
- Polymers, Composites and Hybrids (PCH), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Stéphane Sauvagère
- École de l'ADN, Université de Nîmes, 19 Grand Rue BP 81295, 30015, Nîmes cedex 1, France
| | - Janick Rocher
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Jean-Charles Benezet
- Polymers, Composites and Hybrids (PCH), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Sandrine Bayle
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Christian Siatka
- UPR CHROME, Université de Nîmes, Place Gabriel Péri, 30000, Nîmes cedex 1, France
| | - Anne Bergeret
- Polymers, Composites and Hybrids (PCH), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France
| | - Luc Malhautier
- Laboratoire des Sciences des Risques (LSR), IMT Mines Alès, 6 avenue de Clavières, 30319, Alès Cedex, France.
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Del Frari G, Aggerbeck MR, Gobbi A, Ingrà C, Volpi L, Nascimento T, Ferrandino A, Hansen LH, Ferreira RB. Pruning Wound Protection Products Induce Alterations in the Wood Mycobiome Profile of Grapevines. J Fungi (Basel) 2023; 9:jof9040488. [PMID: 37108942 PMCID: PMC10141712 DOI: 10.3390/jof9040488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/13/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Fungal pathogens involved in grapevine trunk diseases (GTDs) may infect grapevines throughout their lifetime, from nursery to vineyard, via open wounds in stems, canes or roots. In vineyards, pruning wound protection products (PWPPs) offer the best means to reduce the chance of infection by GTD fungi. However, PWPPs may affect non-target microorganisms that comprise the natural endophytic mycobiome residing in treated canes, disrupting microbial homeostasis and indirectly influencing grapevine health. Using DNA metabarcoding, we characterized the endophytic mycobiome of one-year-old canes of cultivars Cabernet Sauvignon and Syrah in two vineyards in Portugal and Italy and assessed the impact of established and novel PWPPs on the fungal communities of treated canes. Our results reveal a large fungal diversity (176 taxa), and we report multiple genera never detected before in grapevine wood (e.g., Symmetrospora and Akenomyces). We found differences in mycobiome beta diversity when comparing vineyards (p = 0.01) but not cultivars (p > 0.05). When examining PWPP-treated canes, we detected cultivar- and vineyard-dependent alterations in both alpha and beta diversity. In addition, numerous fungal taxa were over- or under-represented when compared to control canes. Among them, Epicoccum sp., a beneficial genus with biological control potential, was negatively affected by selected PWPPs. This study demonstrates that PWPPs induce alterations in the fungal communities of grapevines, requiring an urgent evaluation of their direct and indirect effects on plants health with consideration of factors such as climatic conditions and yearly variations, in order to better advise viticulturists and policy makers.
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Affiliation(s)
- Giovanni Del Frari
- LEAF-Linking Landscape, Environment, Agriculture and Food-Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | | | - Alex Gobbi
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Chiara Ingrà
- Department of Agricultural, Forestry, Food Sciences (DISAFA), University of Turin, Largo P. Braccini, 2, Grugliasco, 10095 Torino, Italy
| | - Lorenzo Volpi
- LEAF-Linking Landscape, Environment, Agriculture and Food-Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Teresa Nascimento
- LEAF-Linking Landscape, Environment, Agriculture and Food-Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Alessandra Ferrandino
- Department of Agricultural, Forestry, Food Sciences (DISAFA), University of Turin, Largo P. Braccini, 2, Grugliasco, 10095 Torino, Italy
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Ricardo Boavida Ferreira
- LEAF-Linking Landscape, Environment, Agriculture and Food-Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
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Grinding Beads Influence Microbial DNA Extraction from Organic-Rich Sub-Seafloor Sediment. Microorganisms 2022; 10:microorganisms10122505. [PMID: 36557758 PMCID: PMC9784657 DOI: 10.3390/microorganisms10122505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Sub-seafloor sediment is the largest microbial habitat on Earth. The study of microbes in sub-seafloor sediment is largely limited by the technical challenge of acquiring ambient microbial DNA because of sediment heterogeneity. Changes in the extraction method, even just by one step, can affect the extraction yields for complicated sediment samples. In this work, sub-seafloor sediment samples from the Baltic Sea with high organic carbon content were used to evaluate the influence of different grinding beads on DNA extraction. We found that the grinding beads can affect the DNA extraction from the organic-matter- and biosiliceous-clay-rich samples. A mixture of 0.5-mm and 0.1-mm grinding beads exhibited higher DNA yields and recovered more unique taxa than other bead combinations, such as Stenotrophomonas from Gammaproteobacteria and Leptotrichia from Fusobacteria; therefore, these beads are more suitable than the others for DNA extraction from the samples used in this study. This advantage might be magnified in samples with high biomass. On the contrary, the use of only small beads might lead to underestimation for certain Gram-positive strains. Overall, the discovery of abundant widespread deep biosphere clades in our samples indicated that our optimized DNA extraction method successfully recovered the in situ microbial community.
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Martín L, García-García B, Alguacil MDM. Interactions of the Fungal Community in the Complex Patho-System of Esca, a Grapevine Trunk Disease. Int J Mol Sci 2022; 23:14726. [PMID: 36499052 PMCID: PMC9736784 DOI: 10.3390/ijms232314726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/19/2022] [Accepted: 11/23/2022] [Indexed: 11/26/2022] Open
Abstract
Worldwide, Esca is a complex and devastating Grapevine Trunk Disease (GTD), characterized by inconstant foliar symptoms and internal wood degradation. A large range of fungal taxa have been reported as causal agents. We applied both culture-dependent and culture-independent methods (Illumina Technology and q-PCR) to investigate this concerning disease. Woods from vines with asymptomatic leaves and vines with leaf Esca symptoms were compared. Internally, different types of wood were found, from healthy wood with black necrosis to wood with white rot. A combination of leaf and wood Esca symptoms resulted in four experimental categories. Although there was no relation with symptoms, culture-independent mycobiome composition revealed Phaeomoniella chlamydospora, a GTD pathogen, as the most abundant species (detected in 85.4% of wood samples, with 14.8% relative abundance). Using TaqMan q-PCR, P. chlamydospora DNA was detected in 60.4% of samples (far from the 18.8% of positive results in the culture-dependent approach). There was a predominance of saprotrophs, even if their abundance was not affected by Esca symptoms. Concerning pathotrophs, the white rot development within grapevines was linked to the abundance of fungi belonging to the Hymenochaetaceae family. The Botryosphaeriaceae family was identified as an indicator for expression of Esca foliar symptoms. Lastly, the Aureobasidiaceae family was found to be a potential biocontrol agent for Esca, since it was most abundant in the control asymptomatic plants.
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Affiliation(s)
- Laura Martín
- Plant Protection Department, Scientific and Technological Research Centre of Extremadura (CICYTEX), 06187 Guadajira, Spain
| | - Blanca García-García
- Plant Protection Department, Scientific and Technological Research Centre of Extremadura (CICYTEX), 06187 Guadajira, Spain
| | - María del Mar Alguacil
- CSIC-Centro de Edafología y Biología Aplicada del Segura, Department of Soil and Water Conservation, Campus de Espinardo, 164, 30100 Murcia, Spain
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Cardoza RE, Mayo-Prieto S, Martínez-Reyes N, McCormick SP, Carro-Huerga G, Campelo MP, Rodríguez-González Á, Lorenzana A, Proctor RH, Casquero PA, Gutiérrez S. Effects of trichothecene production by Trichoderma arundinaceum isolates from bean-field soils on the defense response, growth and development of bean plants ( Phaseolus vulgaris). FRONTIERS IN PLANT SCIENCE 2022; 13:1005906. [PMID: 36452093 PMCID: PMC9702529 DOI: 10.3389/fpls.2022.1005906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/18/2022] [Indexed: 06/17/2023]
Abstract
The trichothecene toxin-producing fungus Trichoderma arundinaceum has potential as a biological control agent. However, most biocontrol studies have focused only on one strain, IBT 40837. In the current study, three Trichoderma isolates recovered from bean-field soils produced the trichothecene harzianum A (HA) and trichodermol, the latter being an intermediate in the HA biosynthesis. Based on phylogenetic analysis, the three isolates were assigned to the species T. arundinaceum. Their genome sequences had a high degree of similarity to the reference IBT 40837 strain, in terms of total genome size, number of predicted genes, and diversity of putative secondary metabolite biosynthetic gene clusters. HA production by these bean-field isolates conferred significant in vitro antifungal activity against Rhizoctonia solani and Sclerotinia sclerotiorum, which are some of the most important bean pathogens. Furthermore, the bean-field isolates stimulated germination of bean seeds and subsequent growth of above ground parts of the bean plant. Transcriptomic analysis of bean plants inoculated with these T. arundinaceum bean-field soil isolates indicated that HA production significantly affected expression of plant defense-related genes; this effect was particularly significant in the expression of chitinase-encoding genes. Together, these results indicate that Trichoderma species producing non-phytotoxic trichothecenes can induce defenses in plants without negatively affecting germination and development.
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Affiliation(s)
- Rosa E. Cardoza
- University Group for Research in Engineering and Sustainable Agriculture (GUIIAS), Area of Microbiology, Universidad de León, Ponferrada, Spain
| | - Sara Mayo-Prieto
- University Group for Research in Engineering and Sustainable Agriculture (GUIIAS), Area of Crop Production, Universidad de León, León, Spain
| | - Natalia Martínez-Reyes
- University Group for Research in Engineering and Sustainable Agriculture (GUIIAS), Area of Microbiology, Universidad de León, Ponferrada, Spain
| | - Susan P. McCormick
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utiization Research, Agriculture Research Service, U.S. Department of Agriculture, Peoria, IL, United States
| | - Guzmán Carro-Huerga
- University Group for Research in Engineering and Sustainable Agriculture (GUIIAS), Area of Crop Production, Universidad de León, León, Spain
| | - M. Piedad Campelo
- University Group for Research in Engineering and Sustainable Agriculture (GUIIAS), Area of Crop Production, Universidad de León, León, Spain
| | - Álvaro Rodríguez-González
- University Group for Research in Engineering and Sustainable Agriculture (GUIIAS), Area of Crop Production, Universidad de León, León, Spain
| | - Alicia Lorenzana
- University Group for Research in Engineering and Sustainable Agriculture (GUIIAS), Area of Crop Production, Universidad de León, León, Spain
| | - Robert H. Proctor
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utiization Research, Agriculture Research Service, U.S. Department of Agriculture, Peoria, IL, United States
| | - Pedro A. Casquero
- University Group for Research in Engineering and Sustainable Agriculture (GUIIAS), Area of Crop Production, Universidad de León, León, Spain
| | - Santiago Gutiérrez
- University Group for Research in Engineering and Sustainable Agriculture (GUIIAS), Area of Microbiology, Universidad de León, Ponferrada, Spain
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Schostag MD, Gobbi A, Fini MN, Ellegaard-Jensen L, Aamand J, Hansen LH, Muff J, Albers CN. Combining reverse osmosis and microbial degradation for remediation of drinking water contaminated with recalcitrant pesticide residue. WATER RESEARCH 2022; 216:118352. [PMID: 35358881 DOI: 10.1016/j.watres.2022.118352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Groundwater contamination by recalcitrant organic micropollutants such as pesticide residues poses a great threat to the quality of drinking water. One way to remediate drinking water containing micropollutants is to bioaugment with specific pollutant degrading bacteria. Previous attempts to augment sand filters with the 2,6-dichlorobenzamide (BAM) degrading bacterium Aminobacter niigataensis MSH1 to remediate BAM-polluted drinking water initially worked well, but the efficiency rapidly decreased due to loss of degrader bacteria. Here, we use pilot-scale augmented sand filters to treat retentate of reverse osmosis treatment, thus increasing residence time in the biofilters and potentially nutrient availability. In a first pilot-scale experiment, BAM and most of the measured nutrients were concentrated 5-10 times in the retentate. This did not adversely affect the abundances of inoculated bacteria and the general prokaryotic community of the sand filter presented only minor differences. On the other hand, the high degradation activity was not prolonged compared to the filter receiving non-concentrated water at the same residence time. Using laboratory columns, it was shown that efficient BAM degradation could be achieved for >100 days by increasing the residence time in the sand filter. A slower flow may have practical implications for the treatment of large volumes of water, however this can be circumvented when treating only the retentate water equalling 10-15% of the volume of inlet water. We therefore conducted a second pilot-scale experiment with two inoculated sand filters receiving membrane retentate operated with different residence times (22 versus 133 min) for 65 days. While the number of MSH1 in the biofilters was not affected, the effect on degradation was significant. In the filter with short residence time, BAM degradation decreased from 86% to a stable level of 10-30% degradation within the first two weeks. The filter with the long residence time initially showed >97% BAM degradation, which only slightly decreased with time (88% at day 65). Our study demonstrates the advantage of combining membrane filtration with bioaugmented filters in cases where flow rate is of high importance.
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Affiliation(s)
- Morten D Schostag
- Department of Geochemistry, Geological Survey of Denmark & Greenland (GEUS), Copenhagen, Denmark
| | - Alex Gobbi
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Mahdi Nikbakht Fini
- Center for Membrane Technology, Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | | | - Jens Aamand
- Department of Geochemistry, Geological Survey of Denmark & Greenland (GEUS), Copenhagen, Denmark
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jens Muff
- Center for Membrane Technology, Department of Chemistry and Bioscience, Aalborg University, Esbjerg, Denmark
| | - Christian N Albers
- Department of Geochemistry, Geological Survey of Denmark & Greenland (GEUS), Copenhagen, Denmark.
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10
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Gobbi A, Acedo A, Imam N, Santini RG, Ortiz-Álvarez R, Ellegaard-Jensen L, Belda I, Hansen LH. A global microbiome survey of vineyard soils highlights the microbial dimension of viticultural terroirs. Commun Biol 2022; 5:241. [PMID: 35304890 PMCID: PMC8933554 DOI: 10.1038/s42003-022-03202-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/24/2022] [Indexed: 02/01/2023] Open
Abstract
The microbial biodiversity found in different vitivinicultural regions is an important determinant of wine terroir. It should be studied and preserved, although it may, in the future, be subjected to manipulation by precision agriculture and oenology. Here, we conducted a global survey of vineyards' soil microbial communities. We analysed soil samples from 200 vineyards on four continents to establish the basis for the development of a vineyard soil microbiome's map, representing microbial biogeographical patterns on a global scale. This study describes vineyard microbial communities worldwide and establishes links between vineyard locations and microbial biodiversity on different scales: between continents, countries, and between different regions within the same country. Climate data correlates with fungal alpha diversity but not with prokaryotes alpha diversity, while spatial distance, on a global and national scale, is the main variable explaining beta-diversity in fungal and prokaryotes communities. Proteobacteria, Actinobacteria and Acidobacteria phyla, and Archaea genus Nitrososphaera dominate prokaryotic communities in soil samples while the overall fungal community is dominated by the genera Solicoccozyma, Mortierella and Alternaria. Finally, we used microbiome data to develop a predictive model based on random forest analyses to discriminate between microbial patterns and to predict the geographical source of the samples with reasonable precision.
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Affiliation(s)
- Alex Gobbi
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | | | - Nabeel Imam
- Biome Makers Inc., 95605, West Sacramento, CA, USA
| | - Rui G Santini
- Natural History Museum, Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Ignacio Belda
- Biome Makers Inc., 95605, West Sacramento, CA, USA.
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, 28040, Madrid, Spain.
| | - Lars H Hansen
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
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11
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Caron K, Craw P, Richardson MB, Bodrossy L, Voelcker NH, Thissen H, Sutherland TD. The Requirement of Genetic Diagnostic Technologies for Environmental Surveillance of Antimicrobial Resistance. SENSORS 2021; 21:s21196625. [PMID: 34640944 PMCID: PMC8513014 DOI: 10.3390/s21196625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 12/11/2022]
Abstract
Antimicrobial resistance (AMR) is threatening modern medicine. While the primary cost of AMR is paid in the healthcare domain, the agricultural and environmental domains are also reservoirs of resistant microorganisms and hence perpetual sources of AMR infections in humans. Consequently, the World Health Organisation and other international agencies are calling for surveillance of AMR in all three domains to guide intervention and risk reduction strategies. Technologies for detecting AMR that have been developed for healthcare settings are not immediately transferable to environmental and agricultural settings, and limited dialogue between the domains has hampered opportunities for cross-fertilisation to develop modified or new technologies. In this feature, we discuss the limitations of currently available AMR sensing technologies used in the clinic for sensing in other environments, and what is required to overcome these limitations.
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Affiliation(s)
- Karine Caron
- CSIRO Health & Biosecurity, Canberra, ACT 2602, Australia;
| | - Pascal Craw
- CSIRO Oceans & Atmosphere, Hobart, TAS 7004, Australia; (P.C.); (L.B.)
| | - Mark B. Richardson
- CSIRO Manufacturing, Clayton, VIC 3168, Australia; (M.B.R.); (N.H.V.); (H.T.)
| | - Levente Bodrossy
- CSIRO Oceans & Atmosphere, Hobart, TAS 7004, Australia; (P.C.); (L.B.)
| | - Nicolas H. Voelcker
- CSIRO Manufacturing, Clayton, VIC 3168, Australia; (M.B.R.); (N.H.V.); (H.T.)
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, VIC 3168, Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Helmut Thissen
- CSIRO Manufacturing, Clayton, VIC 3168, Australia; (M.B.R.); (N.H.V.); (H.T.)
| | - Tara D. Sutherland
- CSIRO Health & Biosecurity, Canberra, ACT 2602, Australia;
- Correspondence:
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12
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Rivera-Urbalejo AP, Vázquez D, Fernández Vázquez JL, Rosete Enríquez M, Cesa-Luna C, Morales-García YE, Muñoz Rojas J, Quintero Hernández V. APORTES Y DIFICULTADES DE LA METAGENÓMICA DE SUELOS Y SU IMPACTO EN LA AGRICULTURA. ACTA BIOLÓGICA COLOMBIANA 2021. [DOI: 10.15446/abc.v26n3.85760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Los microorganismos son de gran interés porque colonizan todo tipo de ambiente, sin embargo, uno de los problemas al que nos enfrentamos para conocer su diversidad biológica es que no todos los microorganismos son cultivables. El desarrollo de nuevas tecnologías como la generación de vectores de clonación aunado al desarrollo de técnicas de secuenciación de alto rendimiento ha favorecido el surgimiento de una nueva herramienta llamada metagenómica, la cual nos permite estudiar genomas de comunidades enteras de microorganismos. Debido a que ningún ambiente es idéntico a otro, es importante mencionar que dependiendo del tipo de muestra a analizar será el tipo de reto al cual nos enfrentaremos al trabajar con metagenómica, en el caso específico del suelo existen diversas variantes como la contaminación del suelo con metales pesados o diversos compuestos químicos que podrían limitar los estudios. Sin embargo, pese a las limitaciones que el mismo ambiente presenta, la metagenómica ha permitido tanto el descubrimiento de nuevos genes como la caracterización de las comunidades microbianas que influyen positivamente en el desarrollo de plantas, lo cual en un futuro podría generar un gran impacto en la agricultura. En este artículo se realizó una revisión de diversas investigaciones que han empleado metagenómica, reportadas en las bases de datos de PudMed y Google Schoolar, con el objetivo de examinar los beneficios y limitaciones de las diversas metodologías empleadas en el tratamiento del ADN metagenómico de suelo y el impacto de la metagenómica en la agricultura.
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13
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Oyuela Aguilar M, Gobbi A, Browne PD, Ellegaard-Jensen L, Hansen LH, Semorile L, Pistorio M. Influence of vintage, geographic location and cultivar on the structure of microbial communities associated with the grapevine rhizosphere in vineyards of San Juan Province, Argentina. PLoS One 2020; 15:e0243848. [PMID: 33315910 PMCID: PMC7735631 DOI: 10.1371/journal.pone.0243848] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/29/2020] [Indexed: 12/02/2022] Open
Abstract
Soil microbiomes, as a primary reservoir for plant colonizing fungi and bacteria, play a major role in determining plant productivity and preventing invasion by pathogenic microorganisms. The use of 16S rRNA and ITS high-throughput amplicon sequencing for analysis of complex microbial communities have increased dramatically in recent years, establishing links between wine specificity and, environmental and viticultural factors, which are framed into the elusive terroir concept. Given the diverse and complex role these factors play on microbial soil structuring of agricultural crops, the main aim of this study is to evaluate how external factors, such as vintage, vineyard location, cultivar and soil characteristics, may affect the diversity of the microbial communities present. Additionally, we aim to compare the influence these factors have on the structuring of bacterial and fungal populations associated with Malbec grapevine rhizosphere with that of the more widespread Cabernet Sauvignon grapevine cultivar. Samples were taken from Malbec and Cabernet Sauvignon cultivars from two different vineyards in the San Juan Province of Argentina. Total DNA extracts from the rhizosphere soil samples were sequenced using Illumina’s Miseq technology, targeting the V3-V4 hypervariable 16S rRNA region in prokaryotes and the ITS1 region in yeasts. The major bacterial taxa identified were Proteobacteria, Bacteroidetes and Firmicutes, while the major fungal taxa were Ascomycetes, Basidiomycetes, Mortierellomycetes and a low percentage of Glomeromycetes. Significant differences in microbial community composition were found between vintages and vineyard locations, whose soils showed variances in pH, organic matter, and content of carbon, nitrogen, and absorbable phosphorus.
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Affiliation(s)
- Mónica Oyuela Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Dto de Cs. Biológicas, Fac. Cs. Exactas, UNLP, La Plata, Argentina
| | - Alex Gobbi
- Section of Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Patrick D. Browne
- Section of Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Lars Hestbjerg Hansen
- Section of Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Liliana Semorile
- Laboratorio de Microbiología Molecular, Departamento de Ciencia y Tecnología, Instituto de Microbiología Básica y Aplicada, Universidad de Nacional de Quilmes (UNQ), Bernal, Buenos Aires, Argentina
| | - Mariano Pistorio
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET, Dto de Cs. Biológicas, Fac. Cs. Exactas, UNLP, La Plata, Argentina
- * E-mail:
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14
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Garcia-Lemos AM, Gobbi A, Nicolaisen MH, Hansen LH, Roitsch T, Veierskov B, Nybroe O. Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development. Front Microbiol 2020; 11:198. [PMID: 32194515 PMCID: PMC7064441 DOI: 10.3389/fmicb.2020.00198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/28/2020] [Indexed: 01/01/2023] Open
Abstract
Abies nordmanniana is an economically important tree crop widely used for Christmas tree production. After initial growth in nurseries, seedlings are transplanted to the field. Rhizosphere bacterial communities generally impact the growth and health of the host plant. However, the dynamics of these communities during A. nordmanniana growth in nurseries, and during transplanting, has not previously been addressed. By a 16S rRNA gene amplicon sequencing approach, we characterized the composition and dynamics of bacterial communities in the rhizosphere during early plant growth in field and greenhouse nurseries and for plants transplanted from the greenhouse to the field. Moreover, the N-cycling potential of rhizosphere bacteria across plant age was addressed in both nurseries. Overall, a rhizosphere core microbiome of A. nordmanniana, comprising 19.9% of the taxa at genus level, was maintained across plant age, nursery production systems, and even during the transplantation of plants from the greenhouse to the field. The core microbiome included the bacterial genera Bradyrhizobium, Burkholderia, Flavobacterium, Pseudomonas, Rhizobium, Rhodanobacter, and Sphingomonas, which harbor several N-fixing and plant growth–promoting taxa. Nevertheless, both plant age and production system caused significant changes in the rhizosphere bacterial communities. Concerning community composition, the relative abundance of Rhizobiales (genera Rhizobium, Bradyrhizobium, and Devosia) was higher in the rhizosphere of field-grown A. nordmanniana, whereas the relative abundance of Enterobacteriales and Pseudomonadales (genus Pseudomonas) was higher in the greenhouse. Analysis of community dynamics across plant age showed that in the field nursery, the most abundant bacterial orders showed more dynamic changes in their relative abundance in the rhizosphere than in the bulk soil. In the greenhouse, age-dependent dynamics even occurred but affected different taxa than for the field-grown plants. The N-cycling potential of rhizosphere bacterial communities showed an increase of the relative abundance of genes involved in nitrogen fixation and denitrification by plant age. Similarly, the relative abundance of reported nitrogen-fixing or denitrifying bacteria increased by plant age. However, different community structures seemed to lead to an increased potential for nitrogen fixation and denitrification in the field versus greenhouse nurseries.
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Affiliation(s)
- Adriana M Garcia-Lemos
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Alex Gobbi
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Mette Haubjerg Nicolaisen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark.,Department of Adaptive Biotechnologies, Global Change Research Institute, CAS, Brno, Czechia
| | - Bjarke Veierskov
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Ole Nybroe
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
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15
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Gobbi A, Kyrkou I, Filippi E, Ellegaard-Jensen L, Hansen LH. Seasonal epiphytic microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments. Sci Rep 2020; 10:681. [PMID: 31959791 PMCID: PMC6971271 DOI: 10.1038/s41598-019-56741-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/10/2019] [Indexed: 02/01/2023] Open
Abstract
Winemakers have long used copper as a conventional fungicide treatment on grapevine and only recently, the use of biocontrol agents depicted a promising alternative. Most of the studies that investigate the impact of fungicide treatments, focus on specific pathogenic microbes. In the present work instead, a field experiment conducted in South Africa shows the seasonal microbial change occurring on grapevine leaves, periodically treated with two different fungicide treatments: copper sulphate and Lactobacillus plantarum MW-1. In this work, NGS data were combined with strain-specific and community qPCRs to reveal the shift of the microbial communities throughout the growing season and highlight the impact of fungicides on the microbiota. Only the family of Lactobacillaceae systematically changed between treatments, while the bacterial community remained relatively stable over time. MW-1 was exclusively detected on biocontrol-sprayed leaves. Conversely, the fungal community was largely shaped by sampling time, underlining the succession of different dominant taxa over the months. Between treatments, only a few fungal taxa appeared to change significantly and the fungal load was also comparable. Monitoring the dynamics of the microbial community under different fungicide treatments may advise the best timing to apply treatments to the plants, toward the realization of more sustainable agricultural practices.
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Affiliation(s)
- Alex Gobbi
- Environmental Microbial Genomics (EMG), Plant and Environmental Microbiology, Copenhagen University, Copenhagen, DK, Denmark
- Aarhus University, Department of Environmental Science, Roskilde, DK, Denmark
| | - Ifigeneia Kyrkou
- Aarhus University, Department of Environmental Science, Roskilde, DK, Denmark
| | - Elisa Filippi
- Aarhus University, Department of Environmental Science, Roskilde, DK, Denmark
| | | | - Lars Hestbjerg Hansen
- Environmental Microbial Genomics (EMG), Plant and Environmental Microbiology, Copenhagen University, Copenhagen, DK, Denmark.
- Aarhus University, Department of Environmental Science, Roskilde, DK, Denmark.
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16
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Del Frari G, Gobbi A, Aggerbeck MR, Oliveira H, Hansen LH, Ferreira RB. Characterization of the Wood Mycobiome of Vitis vinifera in a Vineyard Affected by Esca. Spatial Distribution of Fungal Communities and Their Putative Relation With Leaf Symptoms. FRONTIERS IN PLANT SCIENCE 2019; 10:910. [PMID: 31354777 PMCID: PMC6640213 DOI: 10.3389/fpls.2019.00910] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/26/2019] [Indexed: 05/12/2023]
Abstract
Esca is a disease complex belonging to the grapevine trunk diseases cluster. It comprises five syndromes, three main fungal pathogenic agents and several symptoms, both internal (i.e., affecting woody tissue) and external (e.g., affecting leaves and bunches). The etiology and epidemiology of this disease complex remain, in part, unclear. Some of the points that are still under discussion concern the sudden rise in disease incidence, the simultaneous presence of multiple wood pathogens in affected grapevines, the causal agents and the discontinuity in time of leaf symptoms manifestation. The standard approach to the study of esca has been mostly through culture-dependent studies, yet, leaving many questions unanswered. In this study, we used Illumina® next-generation amplicon sequencing to investigate the mycobiome of grapevines wood in a vineyard with history of esca. We characterized the wood mycobiome composition, investigated the spatial dynamics of the fungal communities in different areas of the stem and in canes, and assessed the putative link between mycobiome and leaf symptoms. An unprecedented diversity of fungi is presented (289 taxa), including five genera reported for the first time in association with grapevines wood (Debaryomyces, Trematosphaeria, Biatriospora, Lopadostoma, and Malassezia) and numerous hitherto unreported species. Esca-associated fungi Phaeomoniella chlamydospora and Fomitiporia sp. dominate the fungal community, and numerous other fungi associated with wood syndromes are also encountered (e.g., Eutypa spp., Inonotus hispidus). The spatial analysis revealed differences in diversity, evenness and taxa abundances, the unique presence of certain fungi in specific areas of the plants, and tissue specificity. Lastly, the mycobiome composition of the woody tissue in proximity to leaves manifesting 'tiger stripes' symptoms of esca, as well as in leaf-symptomatic canes, was highly similar to that of plants not exhibiting any leaf symptomatology. This observation supports the current understanding that leaf symptoms are not directly linked with the fungal communities in the wood. This work builds to the understanding of the microbial ecology of the grapevines wood, offering insights and a critical view on the current knowledge of the etiology of esca.
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Affiliation(s)
- Giovanni Del Frari
- LEAF – Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal
- *Correspondence: Giovanni Del Frari,
| | - Alex Gobbi
- Environmental Microbial Genomics Group, Section for Environmental Microbiology and Biotechnology, Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Marie Rønne Aggerbeck
- Environmental Microbial Genomics Group, Section for Environmental Microbiology and Biotechnology, Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Helena Oliveira
- LEAF – Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal
| | - Lars Hestbjerg Hansen
- Environmental Microbial Genomics Group, Section for Environmental Microbiology and Biotechnology, Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Ricardo Boavida Ferreira
- LEAF – Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal
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17
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Del Frari G, Gobbi A, Aggerbeck MR, Oliveira H, Hansen LH, Ferreira RB. Fungicides and the Grapevine Wood Mycobiome: A Case Study on Tracheomycotic Ascomycete Phaeomoniella chlamydospora Reveals Potential for Two Novel Control Strategies. FRONTIERS IN PLANT SCIENCE 2019; 10:1405. [PMID: 31737020 PMCID: PMC6836639 DOI: 10.3389/fpls.2019.01405] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 10/10/2019] [Indexed: 05/09/2023]
Abstract
Phaeomoniella chlamydospora is a tracheomycotic fungus that colonizes the xylem of grapevines (Vitis vinifera L.), causing wood discoloration, brown wood streaking, gummosis, and wood necrosis, which negatively affect the overall health, productivity, and life span of vines. Current control strategies to prevent or cope with P. chlamydospora infections are frequently ineffective. Moreover, it is unclear how fungicides commonly applied in vineyards against downy and powdery mildew agents affect the wood mycobiome, including wood pathogens such as P. chlamydospora. In this study, we used next-generation sequencing to assess the effects of foliar spray of grapevines with inorganic (copper oxychloride and sulfur), synthetic (penconazole and fosetyl-aluminum), and natural (Blad) fungicides currently used against the downy and powdery mildews. The subjects of our investigation were (i) the resident wood mycobiome, (ii) the early colonization by a consortium of fungal wood endophytes (ACEA1), (iii) the wood colonization success of P. chlamydospora, and (iv) the in planta interaction between P. chlamydospora and ACEA1, under greenhouse conditions, in rooted grapevine cuttings of cv. Cabernet Sauvignon. The data obtained suggest that the resident mycobiome is affected by different fungicide treatments. In addition, the early colonization success of the endophytes composing ACEA1 varied in response to fungicides, with relative abundances of some taxa being overrepresented or underrepresented when compared with the control. The wood colonization by P. chlamydospora comported significant changes in the mycobiome composition, and in addition, it was greatly affected by the foliar spray with Blad, which decreased the relative abundance of this pathogen 12-fold (4.9%) when compared with the control (60.7%) and other treatments. The presence of the pathogen also decreased considerably when co-inoculated into the plant with ACEA1, reaching relative abundances between 13.9% and 2.0%, depending on the fungicide treatment applied. This study shows that fungicides sprayed to prevent infections of powdery and downy mildews have an effect on non-target fungi that colonize the endosphere of grapevines. We suggest two potential control strategies to fight P. chlamydospora, namely, the foliar spray with Blad and the use of ACEA1. Further studies to confirm these results are required.
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Affiliation(s)
- Giovanni Del Frari
- LEAF—Linking Landscape Environment Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal
- *Correspondence: Giovanni Del Frari,
| | - Alex Gobbi
- Department of Environmental Science, Section for Environmental Microbiology and Biotechnology, Environmental Microbial Genomics Group (EMG), Aarhus University, Roskilde, Denmark
| | - Marie Rønne Aggerbeck
- Department of Environmental Science, Section for Environmental Microbiology and Biotechnology, Environmental Microbial Genomics Group (EMG), Aarhus University, Roskilde, Denmark
| | - Helena Oliveira
- LEAF—Linking Landscape Environment Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal
| | - Lars Hestbjerg Hansen
- Department of Environmental Science, Section for Environmental Microbiology and Biotechnology, Environmental Microbial Genomics Group (EMG), Aarhus University, Roskilde, Denmark
| | - Ricardo Boavida Ferreira
- LEAF—Linking Landscape Environment Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal
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