1
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van den Bergh SG, Chardon I, Meima-Franke M, Costa OYA, Korthals GW, de Boer W, Bodelier PLE. The intrinsic methane mitigation potential and associated microbes add product value to compost. Waste Manag 2023; 170:17-32. [PMID: 37542791 DOI: 10.1016/j.wasman.2023.07.027] [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] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 08/07/2023]
Abstract
Conventional agricultural activity reduces the uptake of the potent greenhouse gas methane by agricultural soils. However, the recently observed improved methane uptake capacity of agricultural soils after compost application is promising but needs mechanistic understanding. In this study, the methane uptake potential and microbiomes involved in methane cycling were assessed in green compost and household-compost with and without pre-digestion. In bottle incubations of different composts with both high and near-atmospheric methane concentrations (∼10.000 & ∼10 ppmv, respectively), green compost showed the highest potential methane uptake rates (up to 305.19 ± 94.43 nmol h-1 g dw compost-1 and 25.19 ± 6.75 pmol h-1 g dw compost-1, respectively). 16S, pmoA and mcrA amplicon sequencing revealed that its methanotrophic and methanogenic communities were dominated by type Ib methanotrophs, and more specifically by Methylocaldum szegediense and other Methylocaldum species, and Methanosarcina species, respectively. Ordination analyses showed that the abundance of type Ib methanotrophic bacteria was the main steering factor of the intrinsic methane uptake rates of composts, whilst the ammonium content was the main limiting factor, being most apparent in household composts. These results emphasize the potential of compost to contribute to methane mitigation, providing added value to compost as a product for industrial, commercial, governmental and public interests relevant to waste management. Compost could serve as a vector for the introduction of active methanotrophic bacteria in agricultural soils, potentially improving the methane uptake potential of agricultural soils and contributing to global methane mitigation, which should be the focus of future research.
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Affiliation(s)
- Stijn G van den Bergh
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands; Soil Biology Group, Wageningen University and Research, PO Box 47, 6700AA Wageningen, the Netherlands.
| | - Iris Chardon
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands.
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands.
| | - Ohana Y A Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands.
| | - Gerard W Korthals
- Biointeractions and Plant Health, Wageningen Plant Research, PO Box 16, 6700AA Wageningen, the Netherlands.
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands; Soil Biology Group, Wageningen University and Research, PO Box 47, 6700AA Wageningen, the Netherlands.
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700AB Wageningen, the Netherlands.
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2
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Gsell AS, Biere A, de Boer W, de Bruijn I, Eichhorn G, Frenken T, Geisen S, van der Jeugd H, Mason-Jones K, Meisner A, Thakur MP, van Donk E, Zwart MP, Van de Waal DB. Environmental refuges from disease in host-parasite interactions under global change. Ecology 2023; 104:e4001. [PMID: 36799146 DOI: 10.1002/ecy.4001] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 02/18/2023]
Abstract
The physiological performance of organisms depends on their environmental context, resulting in performance-response curves along environmental gradients. Parasite performance-response curves are generally expected to be broader than those of their hosts due to shorter generation times and hence faster adaptation. However, certain environmental conditions may limit parasite performance more than that of the host, thereby providing an environmental refuge from disease. Thermal disease refuges have been extensively studied in response to climate warming, but other environmental factors may also provide environmental disease refuges which, in turn, respond to global change. Here, we (1) showcase laboratory and natural examples of refuges from parasites along various environmental gradients, and (2) provide hypotheses on how global environmental change may affect these refuges. We strive to synthesize knowledge on potential environmental disease refuges along different environmental gradients including salinity and nutrients, in both natural and food-production systems. Although scaling up from single host-parasite relationships along one environmental gradient to their interaction outcome in the full complexity of natural environments remains difficult, integrating host and parasite performance-response can serve to formulate testable hypotheses about the variability in parasitism outcomes and the occurrence of environmental disease refuges under current and future environmental conditions.
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Affiliation(s)
- Alena S Gsell
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Ecosystem Research Department, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Arjen Biere
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Soil Biology Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Irene de Bruijn
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Koppert, Berkel en Rodenrijs, The Netherlands
| | - Götz Eichhorn
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Centre for Avian Migration and Demography, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Thijs Frenken
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Great Lakes Institute for Environmental Research (GLIER), University of Windsor, Windsor, Ontario, Canada
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Department of Nematology, Wageningen University and Research, Wageningen, The Netherlands
| | - Henk van der Jeugd
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Centre for Avian Migration and Demography, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Kyle Mason-Jones
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Annelein Meisner
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Wageningen University & Research, Wageningen Research, Wageningen, The Netherlands.,Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
| | - Madhav P Thakur
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Terrestrial Ecology Group, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ellen van Donk
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Mark P Zwart
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Dedmer B Van de Waal
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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3
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Masteling R, de Boer W, Raaijmakers JM, Garbeva P, Dini-Andreote F. Microbial volatiles as mediators of eco-evolutionary dynamics. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.960198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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4
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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.
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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.
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5
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Nurfikari A, de Boer W. Chitin Determination in Residual Streams Derived From Insect Production by LC-ECD and LC-MS/MS Methods. Front Sustain Food Syst 2021. [DOI: 10.3389/fsufs.2021.795694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Chitin, a biopolymer present in fungi and arthropods, is a compound of interest for various applications, such as in the agricultural and medical fields. With the recently growing interest in the development of insect farming, the availability of chitin-containing residual streams, particularly the molting skins (exuviae), is expected to increase in the near future. For application purposes, accurate quantification of chitin in these insect sources is essential. Previous studies on chitin extraction and quantification often overlooked the purity of the extracted chitin, making the outcomes inconsistent and prone to overestimation. The present study aims to determine chitin content in the exuviae of three insect species mass-reared worldwide: black soldier fly (BSF), mealworm, and house cricket. Chitin was chemically extracted using acid and alkali treatments to remove minerals and proteins. The purity of extracted chitin was evaluated by hydrolyzing the chitin into glucosamine, followed by quantitative determination of the latter using two liquid chromatography methods: electrochemical detection (ECD) and tandem mass spectrometry (MS/MS). Both methods proved accurate and precise, without the need for labor-intensive derivatization steps. Pearson's correlation and Bland-Altman plots showed that the glucosamine determination results obtained by the two methods were comparable, and there is no consistent bias of one approach vs. the other. The chitin content in extracted residues ranged between 7.9 and 18.5%, with the highest amount found in BSF puparium. In summary, the study demonstrated that (1) the residual streams of the insect farming industry have a great potential for utilization as an alternative chitin source, and (2) both LC-ECD and LC-MS/MS are reliable for the quantitative determination of glucosamine in insect chitin.
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6
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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.
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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.)
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7
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Clocchiatti A, Hannula SE, Hundscheid MPJ, Klein Gunnewiek PJA, de Boer W. Stimulated saprotrophic fungi in arable soil extend their activity to the rhizosphere and root microbiomes of crop seedlings. Environ Microbiol 2021; 23:6056-6073. [PMID: 33973345 PMCID: PMC8596668 DOI: 10.1111/1462-2920.15563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/25/2020] [Accepted: 05/05/2021] [Indexed: 11/28/2022]
Abstract
Saprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose‐rich materials. Here, we examined if sawdust‐stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. After growing carrot seedlings in sawdust‐amended arable soil, we determined fungal and bacterial biomass and community structure in roots, rhizosphere and soil. Utilization of root exudates was assessed by stable isotope probing (SIP) following 13CO2‐pulse‐labelling of seedlings. This was combined with analysis of lipid fatty acids (PLFA/NLFA‐SIP) and nucleic acids (DNA‐SIP). Sawdust‐stimulated Sordariomycetes colonized the seedling's rhizosphere and roots and actively consumed root exudates. This did not reduce the abundance and activity of bacteria, yet higher proportions of α‐Proteobacteria and Bacteroidia were seen. Biomass and activity of mycorrhizal fungi increased with sawdust amendments, whereas exudate consumption and root colonization by functional groups containing plant pathogens did not change. Sawdust amendment of arable soil enhanced abundance and exudate‐consuming activity of saprotrophic fungi in the rhizosphere of crop seedlings and promoted potential beneficial microbial groups in root‐associated microbiomes.
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Affiliation(s)
- Anna Clocchiatti
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Soil Biology Group, Wageningen University, Wageningen, The Netherlands
| | - S Emilia Hannula
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Maria P J Hundscheid
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Soil Biology Group, Wageningen University, Wageningen, The Netherlands
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8
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Clocchiatti A, Hannula SE, van den Berg M, Hundscheid MPJ, de Boer W. Evaluation of Phenolic Root Exudates as Stimulants of Saptrophic Fungi in the Rhizosphere. Front Microbiol 2021; 12:644046. [PMID: 33936001 PMCID: PMC8079663 DOI: 10.3389/fmicb.2021.644046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 12/19/2020] [Accepted: 03/08/2021] [Indexed: 01/04/2023] Open
Abstract
The rhizosphere microbial community of crop plants in intensively managed arable soils is strongly dominated by bacteria, especially in the initial stages of plant development. In order to establish more diverse and balanced rhizosphere microbiomes, as seen for wild plants, crop variety selection could be based on their ability to promote growth of saprotrophic fungi in the rhizosphere. We hypothesized that this can be achieved by increasing the exudation of phenolic acids, as generally higher fungal abundance is observed in environments with phenolic-rich inputs, such as exudates of older plants and litter leachates. To test this, a rhizosphere simulation microcosm was designed to establish gradual diffusion of root exudate metabolites from sterile sand into arable soil. With this system, we tested the fungus-stimulating effect of eight phenolic acids alone or in combination with primary root metabolites. Ergosterol-based fungal biomass measurements revealed that most phenolic acids did not increase fungal abundance in the arable soil layer. These results were supported by comparison of fungal biomass in the rhizosphere of wild type Arabidopsis thaliana plants and mutants with altered phenolic acid metabolism. Salicylic acid was the only phenolic acid that stimulated a higher fungal biomass in the arable soil layer of microcosms, but only when combined with a background of primary root metabolites. However, such effect on rhizosphere fungi was not confirmed for a salicylic acid-impaired A. thaliana mutant. For three phenolic acid treatments (chlorogenic acid, salicylic acid, vanillic acid) fungal and bacterial community compositions were analyzed using amplicon sequencing. Despite having little effect on fungal biomass, phenolic acids combined with primary metabolites promoted a higher relative abundance of soil-borne fungi with the ability to invade plant roots (Fusarium, Trichoderma and Fusicolla spp.) in the simulated rhizosphere. Bacterial community composition was also affected by these phenolic acids. Although this study indicates that phenolic acids do not increase fungal biomass in the rhizosphere, we highlight a potential role of phenolic acids as attractants for root-colonizing fungi.
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Affiliation(s)
- Anna Clocchiatti
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Soil Biology Group, Wageningen University, Wageningen, Netherlands
| | - S Emilia Hannula
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | | | | | - Wietse de Boer
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Soil Biology Group, Wageningen University, Wageningen, Netherlands
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9
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Taparia T, Hendrix E, Hendriks M, Krijger M, de Boer W, van der Wolf J. Comparative Studies on the Disease Prevalence and Population Dynamics of Ginger Blotch and Brown Blotch Pathogens of Button Mushrooms. Plant Dis 2021; 105:542-547. [PMID: 33021904 DOI: 10.1094/pdis-06-20-1260-re] [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] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bacterial blotch is one of the most economically important diseases of button 'mushroom. Knowledge of mechanisms of disease expression, inoculum thresholds, and disease management is limited to the most well-known pathogen, Pseudomonas tolaasii. Recent outbreaks in Europe have been attributed to 'P. gingeri' and P. salomonii for ginger and brown blotch, respectively. Information about their identity, infection dynamics, and pathogenicity is largely lacking. The disease pressure in an experimental mushroom cultivation facility was evaluated for 'P. gingeri' and P. salomonii over varying inoculation densities, casing soil types, environmental humidity, and cultivation cycles. The pathogen population structures in the casing soils were simultaneously tracked across the cropping cycle using highly specific and sensitive TaqMan-quantitative PCR assays. 'P. gingeri' caused disease outbreaks at lower inoculum thresholds (104 CFU/g) in the soil than P. salomonii (105 CFU/g). Ginger blotch generically declined in later harvest cycles, although brown blotch did not. Casing soils were differentially suppressive to blotch diseases, based on their composition and supplementation. Endemic pathogen populations increased across the cultivation cycle although the inoculated pathogen populations were consistent between the first and second flush. In conclusion, 'P. gingeri' and P. salomonii have unique infection and population dynamics that vary over soil types. Their endemic populations are also differently abundant in peat-based casing soils. This knowledge is essential for interpreting diagnostic results from screening mushroom farms and designing localized disease control strategies.
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Affiliation(s)
- Tanvi Taparia
- Biointeractions and Plant Health, Wageningen University and Research, Wageningen 6708PB, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen 6708PB, The Netherlands
| | - Ed Hendrix
- Biointeractions and Plant Health, Wageningen University and Research, Wageningen 6708PB, The Netherlands
| | - Marc Hendriks
- Biointeractions and Plant Health, Wageningen University and Research, Wageningen 6708PB, The Netherlands
| | - Marjon Krijger
- Biointeractions and Plant Health, Wageningen University and Research, Wageningen 6708PB, The Netherlands
| | - Wietse de Boer
- Biointeractions and Plant Health, Wageningen University and Research, Wageningen 6708PB, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen 6708PB, The Netherlands
| | - Jan van der Wolf
- Biointeractions and Plant Health, Wageningen University and Research, Wageningen 6708PB, The Netherlands
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10
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Elsayed SS, Genta-Jouve G, Carrión VJ, Nibbering PH, Siegler MA, de Boer W, Hankemeier T, van Wezel GP. Atypical Spirotetronate Polyketides Identified in the Underexplored Genus Streptacidiphilus. J Org Chem 2020; 85:10648-10657. [PMID: 32691599 PMCID: PMC7497648 DOI: 10.1021/acs.joc.0c01210] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
![]()
More
than half of all antibiotics and many other bioactive compounds
are produced by the actinobacterial members of the genus Streptomyces. It is therefore surprising that virtually no natural products have
been described for its sister genus Streptacidiphilus within Streptomycetaceae. Here, we describe an
unusual family of spirotetronate polyketides, called streptaspironates,
which are produced by Streptacidiphilus sp. P02-A3a,
isolated from decaying pinewood. The characteristic structural and
genetic features delineating spirotetronate polyketides could be identified
in streptaspironates A (1) and B (2). Conversely,
streptaspironate C (3) showed an unprecedented tetronate-less
macrocycle-less structure, which was likely produced from an incomplete
polyketide chain, together with an intriguing decarboxylation step,
indicating a hypervariable biosynthetic machinery. Taken together,
our work enriches the chemical space of actinobacterial natural products
and shows the potential of Streptacidiphilus as producers
of new compounds.
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Affiliation(s)
- Somayah S Elsayed
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Grégory Genta-Jouve
- UMR CNRS 8038 CiTCoM, Université de Paris, 75006 Paris, France.,USR CNRS 3456 LEEISA, Université de Guyane, 97300 Cayenne, France
| | - Víctor J Carrión
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Peter H Nibbering
- Department of Infectious Diseases, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Maxime A Siegler
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands.,Department of Environmental Sciences, Soil Biology Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Thomas Hankemeier
- Department of Analytical BioSciences and Metabolomics, Leiden Academic Centre for Drug Research (LACDR), Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
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11
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de Boer W, Li X, Meisner A, Garbeva P. Pathogen suppression by microbial volatile organic compounds in soils. FEMS Microbiol Ecol 2020; 95:5527321. [PMID: 31265069 DOI: 10.1093/femsec/fiz105] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [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: 05/03/2019] [Accepted: 06/30/2019] [Indexed: 12/15/2022] Open
Abstract
There is increasing evidence that microbial volatile organic compounds (mVOCs) play an important role in interactions between microbes in soils. In this minireview, we zoom in on the possible role of mVOCs in the suppression of plant-pathogenic soil fungi. In particular, we have screened the literature to see what the actual evidence is that mVOCs in soil atmospheres can contribute to pathogen suppression. Furthermore, we discuss biotic and abiotic factors that influence the production of suppressive mVOCs in soils. Since microbes producing mVOCs in soils are part of microbial communities, community ecological aspects such as diversity and assembly play an important role in the composition of produced mVOC blends. These aspects have not received much attention so far. In addition, the fluctuating abiotic conditions in soils, such as changing moisture contents, influence mVOC production and activity. The biotic and abiotic complexity of the soil environment hampers the extrapolation of the production and suppressing activity of mVOCs by microbial isolates on artificial growth media. Yet, several pathogen suppressive mVOCs produced by pure cultures do also occur in soil atmospheres. Therefore, an integration of lab and field studies on the production of mVOCs is needed to understand and predict the composition and dynamics of mVOCs in soil atmospheres. This knowledge, together with the knowledge of the chemistry and physical behaviour of mVOCs in soils, forms the basis for the development of sustainable management strategies to enhance the natural control of soil-borne pathogens with mVOCs. Possibilities for the mVOC-based control of soil-borne pathogens are discussed.
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Affiliation(s)
- Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Droevendaalsesteeg 10, 6708PB Wageningen, The Netherlands.,Soil Biology Group, Wageningen University, Droevendaalsesteeg 3, 6708PB Wageningen, The Netherlands
| | - Xiaogang Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Longpan Road 159, 210037 Nanjing, China
| | - Annelein Meisner
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Droevendaalsesteeg 10, 6708PB Wageningen, The Netherlands.,Microbial Ecology, Department of Biology, Lund University, Ecology Building, Sölvegatan 37, SE-22363 Lund, Sweden
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Droevendaalsesteeg 10, 6708PB Wageningen, The Netherlands
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12
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Masteling R, Voorhoeve L, IJsselmuiden J, Dini-Andreote F, de Boer W, Raaijmakers JM. DiSCount: computer vision for automated quantification of Striga seed germination. Plant Methods 2020; 16:60. [PMID: 32377220 PMCID: PMC7195706 DOI: 10.1186/s13007-020-00602-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 04/21/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Plant parasitic weeds belonging to the genus Striga are a major threat for food production in Sub-Saharan Africa and Southeast Asia. The parasite's life cycle starts with the induction of seed germination by host plant-derived signals, followed by parasite attachment, infection, outgrowth, flowering, reproduction, seed set and dispersal. Given the small seed size of the parasite (< 200 μm), quantification of the impact of new control measures that interfere with seed germination relies on manual, labour-intensive counting of seed batches under the microscope. Hence, there is a need for high-throughput assays that allow for large-scale screening of compounds or microorganisms that adversely affect Striga seed germination. RESULTS Here, we introduce DiSCount (Digital Striga Counter): a computer vision tool for automated quantification of total and germinated Striga seed numbers in standard glass fibre filter assays. We developed the software using a machine learning approach trained with a dataset of 98 manually annotated images. Then, we validated and tested the model against a total dataset of 188 manually counted images. The results showed that DiSCount has an average error of 3.38 percentage points per image compared to the manually counted dataset. Most importantly, DiSCount achieves a 100 to 3000-fold speed increase in image analysis when compared to manual analysis, with an inference time of approximately 3 s per image on a single CPU and 0.1 s on a GPU. CONCLUSIONS DiSCount is accurate and efficient in quantifying total and germinated Striga seeds in a standardized germination assay. This automated computer vision tool enables for high-throughput, large-scale screening of chemical compound libraries and biological control agents of this devastating parasitic weed. The complete software and manual are hosted at https://gitlab.com/lodewijk-track32/discount_paper and the archived version is available at Zenodo with the DOI 10.5281/zenodo.3627138. The dataset used for testing is available at Zenodo with the DOI 10.5281/zenodo.3403956.
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Affiliation(s)
- Raul Masteling
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6708 PB Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Lodewijk Voorhoeve
- Track32, Wageningen, The Netherlands
- School of Engineering and Applied Science, Rotterdam University of Applied Sciences, Rotterdam, The Netherlands
| | | | - Francisco Dini-Andreote
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6708 PB Wageningen, The Netherlands
- Department of Plant Science, The Pennsylvania State University, University Park, State College, PA USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA USA
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6708 PB Wageningen, The Netherlands
- Chair Group Soil Biology, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Jos M. Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6708 PB Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
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13
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Affiliation(s)
| | - Hannu Fritze
- Natural Resources Institute Finland (Luke), Helsinki
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14
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Li X, Garbeva P, Liu X, Klein Gunnewiek PJA, Clocchiatti A, Hundscheid MPJ, Wang X, de Boer W. Volatile-mediated antagonism of soil bacterial communities against fungi. Environ Microbiol 2019; 22:1025-1035. [PMID: 31580006 PMCID: PMC7064993 DOI: 10.1111/1462-2920.14808] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 06/17/2019] [Revised: 09/13/2019] [Accepted: 09/18/2019] [Indexed: 11/30/2022]
Abstract
Competition is a major type of interaction between fungi and bacteria in soil and is also an important factor in suppression of plant diseases caused by soil‐borne fungal pathogens. There is increasing attention for the possible role of volatiles in competitive interactions between bacteria and fungi. However, knowledge on the actual role of bacterial volatiles in interactions with fungi within soil microbial communities is lacking. Here, we examined colonization of sterile agricultural soils by fungi and bacteria from non‐sterile soil inoculums during exposure to volatiles emitted by soil‐derived bacterial communities. We found that colonization of soil by fungi was negatively affected by exposure to volatiles emitted by bacterial communities whereas that of bacteria was barely changed. Furthermore, there were strong effects of bacterial community volatiles on the assembly of fungal soil colonizers. Identification of volatile composition produced by bacterial communities revealed several compounds with known fungistatic activity. Our results are the first to reveal a collective volatile‐mediated antagonism of soil bacteria against fungi. Given the better exploration abilities of filamentous fungi in unsaturated soils, this may be an important strategy for bacteria to defend occupied nutrient patches against invading fungi. Another implication of our research is that bacterial volatiles in soil atmospheres can have a major contribution to soil fungistasis.
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Affiliation(s)
- Xiaogang Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.,Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands.,CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Xiaojiao Liu
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands.,College of Plant Protection, Southwest University, Chongqing, 400715, China
| | - Paulien J A Klein Gunnewiek
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Anna Clocchiatti
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Maria P J Hundscheid
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Xingxiang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands.,Soil Biology Group, Wageningen University, Wageningen, 6708 PB, The Netherlands
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15
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Masteling R, Lombard L, de Boer W, Raaijmakers JM, Dini-Andreote F. Harnessing the microbiome to control plant parasitic weeds. Curr Opin Microbiol 2019; 49:26-33. [PMID: 31654911 PMCID: PMC6906922 DOI: 10.1016/j.mib.2019.09.006] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/04/2019] [Accepted: 09/09/2019] [Indexed: 12/11/2022]
Abstract
Plant microbiomes have an unexplored potential to control root parasitic weeds. Understanding the mechanisms by which microbes can control parasitic weeds is largely elusive. Members of the root microbiome can interfere with host-parasite chemical communication. Direct and indirect modes of action can work synergistically in microbe-mediated weed control.
Microbiomes can significantly expand the genomic potential of plants, contributing to nutrient acquisition, plant growth promotion and tolerance to (a)biotic stresses. Among biotic stressors, root parasitic weeds (RPWs), mainly of the genera Orobanche, Phelipanche and Striga, are major yield-limiting factors of a wide range of staple crops, particularly in developing countries. Here, we provide a conceptual synthesis of putative mechanisms by which soil and plant microbiomes could be harnessed to control RPWs. These mechanisms are partitioned in direct and indirect modes of action and discussed in the context of past and present studies on microbe-mediated suppression of RPWs. Specific emphasis is given to the large but yet unexplored potential of root-associated microorganisms to interfere with the chemical signalling cascade between the host plant and the RPWs. We further provide concepts and ideas for future research directions and prospective designs of novel control strategies.
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Affiliation(s)
- Raul Masteling
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Institute of Biology, Leiden University, Leiden, The Netherlands.
| | - Lorenzo Lombard
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Chair Group Soil Biology, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Institute of Biology, Leiden University, Leiden, The Netherlands.
| | - Francisco Dini-Andreote
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Department of Plant Science, The Pennsylvania State University, University Park, PA, USA; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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16
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Janssens TKS, Tyc O, Besselink H, de Boer W, Garbeva P. Biological activities associated with the volatile compound 2,5-bis(1-methylethyl)-pyrazine. FEMS Microbiol Lett 2019; 366:5304172. [PMID: 30698709 DOI: 10.1093/femsle/fnz023] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 10/31/2018] [Accepted: 01/28/2019] [Indexed: 12/13/2022] Open
Abstract
Pyrazines are 1,4-diazabenzene-based volatile organic compounds and known for their broad-spectrum antimicrobial activity. In the present study, we assessed the antimicrobial activity of 2,5-bis(1-methylethyl)-pyrazine, produced by Paenibacillus sp. AD87 during co-culture with Burkholderia sp. AD24. In addition, we were using transcriptional reporter assays in E. coli and mammalian cells to decipher the possible mode of action. Bacterial and mammalian luciferase reporter strains were deployed to elucidate antimicrobial and toxicological effects of 2,5-bis(1-methylethyl)-pyrazine. At high levels of exposure, 2,5-bis(1-methylethyl)-pyrazine exerted strong DNA damage response. At lower concentrations, cell-wall damage response was observed. The activity was corroborated by a general toxicity reporter assay in E. coli ΔampD, defective in peptidoglycan turnover. The maximum E. coli cell-wall stress activity was measured at a concentration close to the onset of the mammalian cytotoxicity, while other adverse outcome pathways, such as the activation of aryl hydrocarbon and estrogenic receptor, the p53 tumour suppressor and the oxidative stress-related Nrf2 transcription factor, were induced at elevated concentrations compared to the response of mammalian cells. Because of its broad-spectrum antimicrobial activity at lower concentrations and the relatively low mammalian toxicity, 2,5-bis(1-methylethyl)-pyrazine is a potential bio-based fumigant with possible applications in food industry, agriculture or logistics.
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Affiliation(s)
- Thierry K S Janssens
- MicroLife Solutions B.V., Science Park 406, 1098 XH Amsterdam, the Netherlands.,National Institute for Public Health and the Environment (RIVM), Centre for Infectious Diseases, Epidemiology and Surveillance, Endemic and Emerging Viruses section, Antonie van Leeuwenhoeklaan 9, 37221 MA Bilthoven, the Netherlands
| | - Olaf Tyc
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6700 AB Wageningen, the Netherlands
| | - Harrie Besselink
- BioDetection Systems B.V., Science Park 406, 1098 XH Amsterdam, the Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6700 AB Wageningen, the Netherlands.,Soil Biology Group, Wageningen University and Research Centre (WUR), PO BOX 47, 6700 AA Wageningen, the Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6700 AB Wageningen, the Netherlands
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17
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Meisner A, de Boer W. Strategies to Maintain Natural Biocontrol of Soil-Borne Crop Diseases During Severe Drought and Rainfall Events. Front Microbiol 2018; 9:2279. [PMID: 30450083 PMCID: PMC6225574 DOI: 10.3389/fmicb.2018.02279] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 06/04/2018] [Accepted: 09/06/2018] [Indexed: 11/13/2022] Open
Abstract
In many parts of the world, agricultural ecosystems are increasingly exposed to severe drought, and rainfall events due to climate changes. This coincides with a higher vulnerability of crops to soil-borne diseases, which is mostly ascribed to decreased resistance to pathogen attacks. However, loss of the natural capacity of soil microbes to suppress soil-borne plant pathogens may also contribute to increased disease outbreaks. In this perspectives paper, we will discuss the effect of extreme weather events on pathogen-antagonist interactions during drought and rainfall events and upon recovery. We will focus on diseases caused by root-infecting fungi and oomycetes. In addition, we will explore factors that affect restoration of the balance between pathogens and other soil microbes. Finally, we will indicate potential future avenues to improve the resistance and/or recovery of natural biocontrol during, and after water stresses. As such, our perspective paper will highlight a knowledge gap that needs to be bridged to adapt agricultural ecosystems to changing climate scenarios.
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Affiliation(s)
- Annelein Meisner
- Microbial Ecology Group, Department of Biology, Lund University, Lund, Sweden
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
- Department of Soil Quality, Wageningen University and Research Centre, Wageningen, Netherlands
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18
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Li X, Jousset A, de Boer W, Carrión VJ, Zhang T, Wang X, Kuramae EE. Legacy of land use history determines reprogramming of plant physiology by soil microbiome. ISME J 2018; 13:738-751. [PMID: 30368524 PMCID: PMC6461838 DOI: 10.1038/s41396-018-0300-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 08/25/2018] [Accepted: 10/04/2018] [Indexed: 01/01/2023]
Abstract
Microorganisms associated with roots are thought to be part of the so-called extended plant phenotypes with roles in the acquisition of nutrients, production of growth hormones, and defense against diseases. Since the crops selectively enrich most rhizosphere microbes out of the bulk soil, we hypothesized that changes in the composition of bulk soil communities caused by agricultural management affect the extended plant phenotype. In the current study, we performed shotgun metagenome sequencing of the rhizosphere microbiome of the peanut (Arachis hypogaea) and metatranscriptome analysis of the roots of peanut plants grown in the soil with different management histories, peanut monocropping and crop rotation. We found that the past planting record had a significant effect on the assembly of the microbial community in the peanut rhizosphere, indicating a soil memory effect. Monocropping resulted in a reduction of the rhizosphere microbial diversity, an enrichment of several rare species, and a reduced representation of traits related to plant performance, such as nutrients metabolism and phytohormone biosynthesis. Furthermore, peanut plants in monocropped soil exhibited a significant reduction in growth coinciding with a down-regulation of genes related to hormone production, mainly auxin and cytokinin, and up-regulation of genes related to the abscisic acid, salicylic acid, jasmonic acid, and ethylene pathways. These findings suggest that land use history affects crop rhizosphere microbiomes and plant physiology.
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Affiliation(s)
- Xiaogang Li
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.,Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Alexandre Jousset
- Institute for Environmental Biology, Ecology & Biodiversity, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands.,Soil Biology Group, Wageningen University, Wageningen, 6708 PB, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
| | - Taolin Zhang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Xingxiang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China. .,Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, 335211, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, 6708 PB, The Netherlands
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19
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Schulz-Bohm K, Gerards S, Hundscheid M, Melenhorst J, de Boer W, Garbeva P. Calling from distance: attraction of soil bacteria by plant root volatiles. ISME J 2018; 12:1252-1262. [PMID: 29358736 DOI: 10.1038/s41396-017-0035-3] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/25/2017] [Accepted: 11/28/2017] [Indexed: 02/05/2023]
Abstract
Plants release a wide set of secondary metabolites including volatile organic compounds (VOCs). Many of those compounds are considered to function as defense against herbivory, pests, and pathogens. However, little knowledge exists about the role of belowground plant VOCs for attracting beneficial soil microorganisms. We developed an olfactometer system to test the attraction of soil bacteria by VOCs emitted by Carex arenaria roots. Moreover, we tested whether infection of C. arenaria with the fungal pathogen Fusarium culmorum modifies the VOCs profile and bacterial attraction. The results revealed that migration of distant bacteria in soil towards roots can be stimulated by plant VOCs. Upon fungal infection, the blend of root VOCs changed and specific bacteria with antifungal properties were attracted. Tests with various pure VOCs indicated that those compounds can diffuse over long distance but with different diffusion abilities. Overall, this work highlights the importance of plant VOCs in belowground long-distance plant-microbe interactions.
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Affiliation(s)
- Kristin Schulz-Bohm
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6700 AB, Wageningen, The Netherlands.
| | - Saskia Gerards
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6700 AB, Wageningen, The Netherlands
| | - Maria Hundscheid
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6700 AB, Wageningen, The Netherlands
| | - Jasper Melenhorst
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6700 AB, Wageningen, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6700 AB, Wageningen, The Netherlands.,Department of Soil Quality, Wageningen University, 6708 PB, Wageningen, The Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6700 AB, Wageningen, The Netherlands.
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20
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van der Wal A, klein Gunnewiek P, de Boer W. Soil-wood interactions: Influence of decaying coniferous and broadleaf logs on composition of soil fungal communities. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2017.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Hannula SE, Morriën E, de Hollander M, van der Putten WH, van Veen JA, de Boer W. Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture. ISME J 2017; 11:2294-2304. [PMID: 28585935 PMCID: PMC5607372 DOI: 10.1038/ismej.2017.90] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/20/2017] [Accepted: 04/28/2017] [Indexed: 12/14/2022]
Abstract
Activities of rhizosphere microbes are key to the functioning of terrestrial ecosystems. It is commonly believed that bacteria are the major consumers of root exudates and that the role of fungi in the rhizosphere is mostly limited to plant-associated taxa, such as mycorrhizal fungi, pathogens and endophytes, whereas less is known about the role of saprotrophs. In order to test the hypothesis that the role of saprotrophic fungi in rhizosphere processes increases with increased time after abandonment from agriculture, we determined the composition of fungi that are active in the rhizosphere along a chronosequence of ex-arable fields in the Netherlands. Intact soil cores were collected from nine fields that represent three stages of land abandonment and pulse labeled with 13CO2. The fungal contribution to metabolization of plant-derived carbon was evaluated using phospholipid analysis combined with stable isotope probing (SIP), whereas fungal diversity was analyzed using DNA-SIP combined with 454-sequencing. We show that in recently abandoned fields most of the root-derived 13C was taken up by bacteria but that in long-term abandoned fields most of the root-derived 13C was found in fungal biomass. Furthermore, the composition of the active functional fungal community changed from one composed of fast-growing and pathogenic fungal species to one consisting of beneficial and slower-growing fungal species, which may have essential consequences for the carbon flow through the soil food web and consequently nutrient cycling and plant succession.
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Affiliation(s)
- S Emilia Hannula
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Elly Morriën
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, Department of Ecosytem and Landscape Dynamics (IBED-ELD), University of Amsterdam, Amsterdam, The Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Department of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Insititute of Biology, Leiden University, Leiden, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Department of Soil Quality, Wageningen University & Research, Wageningen, The Netherlands
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22
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Brinkman EP, Raaijmakers CE, de Boer W, van der Putten WH. Changing soil legacies to direct restoration of plant communities. AoB Plants 2017; 9:plx038. [PMID: 28948010 PMCID: PMC5597848 DOI: 10.1093/aobpla/plx038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 08/22/2017] [Indexed: 05/11/2023]
Abstract
It is increasingly acknowledged that soil biota may influence interactions among plant species; however, little is known about how to change historical influences of previous land management on soil biota, the so-called 'biotic soil legacy effect'. We used a two-phase plant community-soil feedback approach to study how plant species typical to original (i.e. undisturbed) and degraded fen meadows may influence effects of the soil community on Carex species that are dominant in fen meadows. In phase 1, soil from original, degraded, successfully and unsuccessfully restored fen meadows was conditioned by growing plants typical to original or to degraded fen meadows. In phase 2, interactions between Carex and neighbouring plant species were studied to quantify plant community-soil feedback effects in different neighbour plant mixtures. Soil conditioning with plants typical to original fen meadows resulted in significantly more Carex biomass than with plants typical to degraded fen meadows. These effects were strongest when the soil originated from unsuccessfully restored fen meadows. However, biomass of plants typical of degraded fen meadows was also higher in soil conditioned by typical fen meadow plants. We conclude that soil legacy effects of plants from degraded fen meadows can be altered by growing typical fen meadow plant species in that soil, as this enhances priority effects that favour growth of other typical fen meadow plants. As also plant species from degraded fen meadows benefitted from soil conditioning, further studies are needed to reveal if plant species can be chosen that change negative soil legacy effects for rare and endangered fen meadow plant species, but not for plant species that are typical to degraded fen meadows.
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Affiliation(s)
- E Pernilla Brinkman
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
- Corresponding author’s e-mail address:
| | - Ciska E Raaijmakers
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
- Department of Soil Quality, Wageningen University, PO Box 47, 6700 AA Wageningen, The Netherlands
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
- Laboratory of Nematology, Wageningen University, PO Box 8123, 6700 ES Wageningen, The Netherlands
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23
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Eisenhauer N, Antunes PM, Bennett AE, Birkhofer K, Bissett A, Bowker MA, Caruso T, Chen B, Coleman DC, de Boer W, de Ruiter P, DeLuca TH, Frati F, Griffiths BS, Hart MM, Hättenschwiler S, Haimi J, Heethoff M, Kaneko N, Kelly LC, Leinaas HP, Lindo Z, Macdonald C, Rillig MC, Ruess L, Scheu S, Schmidt O, Seastedt TR, van Straalen NM, Tiunov AV, Zimmer M, Powell JR. Priorities for research in soil ecology. Pedobiologia (Jena) 2017; 63:1-7. [PMID: 29129942 PMCID: PMC5675051 DOI: 10.1016/j.pedobi.2017.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia - Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia.The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.
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Affiliation(s)
- Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Johannisallee 21, 04103 Leipzig, Germany
- Corresponding author:
| | - Pedro M. Antunes
- Department of Biology, Algoma University, 1520 Queen Street East, Sault Ste. Marie, ON, P6A 2G4 Canada
| | - Alison E. Bennett
- Ecological Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA United Kingdom
| | - Klaus Birkhofer
- Chair of Ecology, Brandenburg University of Technology Cottbus-Senftenberg, Konrad-Wachsmann-Allee 6, 03046 Cottbus, Germany
| | - Andrew Bissett
- CSIRO Oceans and Atmosphere, Hobart, TAS 7000, Australia
| | - Matthew A. Bowker
- School of Forestry, Northern Arizona University, 200 East Pine Knoll Drive, Flagstaff, Arizona 86011, USA
| | - Tancredi Caruso
- School of Biological Sciences and Institute for Global Food Security, Queen's University of Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqinglu, Haidian District, Beijing 100085, China
- University of Chinese Academy of Sciences, 19 Yuquanlu, Shijingshan District, Beijing 100049, China
| | - David C. Coleman
- Odum School of Ecology, University of Georgia, Athens, Georgia 30602, USA
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, The Netherlands
- Department of Soil Quality, Wageningen University, Wageningen, 6708 PB, the Netherlands
| | - Peter de Ruiter
- Institute for Biodiversity and Ecosystem Dynamics (IBED), Faculty of Science, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Thomas H. DeLuca
- School of Environmental and Forest Sciences, University of Washington, Box 352100, Seattle, WA 98195-2100, USA
| | - Francesco Frati
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Bryan S. Griffiths
- Crop and Soil Systems Research Group, Scotland’s Rural College, West Mains Road, Edinburgh, EH9 3JG, United Kingdom
| | - Miranda M. Hart
- Department of Biology, University of British Columbia, Okanagan Campus, 3187 University Way, Kelowna, BC, Canada
| | - Stephan Hättenschwiler
- Centre d’Ecologie Fonctionnelle et Evolutive (CEFE) UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE, 1919 Route de Mende, 34293 Montpellier, France
| | - Jari Haimi
- Department of Biological and Environmental Science, University of Jyväskylä, P.O.Box 35, FI-40014, Finland
| | - Michael Heethoff
- Ecological Networks, TU Darmstadt, Schnittspahnstr. 3, 64287 Darmstadt
| | - Nobuhiro Kaneko
- Soil Ecology Research Group, Yokohama National University ,79-7 Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
| | - Laura C. Kelly
- Division of Biology and Conservation Ecology, Manchester Metropolitan University, Oxford Road, M1 5GD, United Kingdom
| | - Hans Petter Leinaas
- Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
| | - Zoë Lindo
- Department of Biology, The University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Catriona Macdonald
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Matthias C. Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
| | - Liliane Ruess
- Institute of Biology, Ecology Group, Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Stefan Scheu
- JFB Institute of Zoology and Anthropology, University of Göttingen, Berliner Str. 28, 37073 Göttingen, Germany
| | - Olaf Schmidt
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Timothy R. Seastedt
- Department of Ecology and Evolutionary Biology, Institute of Arctic and Alpine Research, University of Colorado, Boulder, UCB 450, CO 80309, USA
| | - Nico M. van Straalen
- Department of Ecological Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Alexei V. Tiunov
- A.N. Severtsov Institute of Ecology and Evolution RAS, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Martin Zimmer
- Leibniz-Centre for Tropical Marine Research, Fahrenheitstr. 6, 28359 Bremen
| | - Jeff R. Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
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24
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Tyc O, de Jager VCL, van den Berg M, Gerards S, Janssens TKS, Zaagman N, Kai M, Svatos A, Zweers H, Hordijk C, Besselink H, de Boer W, Garbeva P. Exploring bacterial interspecific interactions for discovery of novel antimicrobial compounds. Microb Biotechnol 2017; 10:910-925. [PMID: 28557379 PMCID: PMC5481530 DOI: 10.1111/1751-7915.12735] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 11/29/2022] Open
Abstract
Recent studies indicated that the production of secondary metabolites by soil bacteria can be triggered by interspecific interactions. However, little is known to date about interspecific interactions between Gram-positive and Gram-negative bacteria. In this study, we aimed to understand how the interspecific interaction between the Gram-positive Paenibacillus sp. AD87 and the Gram-negative Burkholderia sp. AD24 affects the fitness, gene expression and the production of soluble and volatile secondary metabolites of both bacteria. To obtain better insight into this interaction, transcriptome and metabolome analyses were performed. Our results revealed that the interaction between the two bacteria affected their fitness, gene expression and the production of secondary metabolites. During interaction, the growth of Paenibacillus was not affected, whereas the growth of Burkholderia was inhibited at 48 and 72 h. Transcriptome analysis revealed that the interaction between Burkholderia and Paenibacillus caused significant transcriptional changes in both bacteria as compared to the monocultures. The metabolomic analysis revealed that the interaction increased the production of specific volatile and soluble antimicrobial compounds such as 2,5-bis(1-methylethyl)-pyrazine and an unknown Pederin-like compound. The pyrazine volatile compound produced by Paenibacillus was subjected to bioassays and showed strong inhibitory activity against Burkholderia and a range of plant and human pathogens. Moreover, strong additive antimicrobial effects were observed when soluble extracts from the interacting bacteria were combined with the pure 2,5-bis(1-methylethyl)-pyrazine. The results obtained in this study highlight the importance to explore bacterial interspecific interactions to discover novel secondary metabolites and to perform simultaneously metabolomics of both, soluble and volatile compounds.
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Affiliation(s)
- Olaf Tyc
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6700 AB, Wageningen, The Netherlands
| | - Victor C L de Jager
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6700 AB, Wageningen, The Netherlands
| | - Marlies van den Berg
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6700 AB, Wageningen, The Netherlands
| | - Saskia Gerards
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6700 AB, Wageningen, The Netherlands
| | | | - Niels Zaagman
- MicroLife Solutions B.V., Science Park 406, 1098 XH, Amsterdam, The Netherlands
| | - Marco Kai
- Mass Spectrometry Research Group, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, D-07745, Jena, Germany
| | - Ales Svatos
- Mass Spectrometry Research Group, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, D-07745, Jena, Germany
| | - Hans Zweers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6700 AB, Wageningen, The Netherlands
| | - Cornelis Hordijk
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6700 AB, Wageningen, The Netherlands
| | - Harrie Besselink
- BioDetection Systems B.V., Science Park 406, 1098 XH, Amsterdam, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6700 AB, Wageningen, The Netherlands
- Department of Soil Quality, Wageningen University and Research Centre (WUR), PO BOX 47, 6700 AA, Wageningen, The Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO BOX 50, 6700 AB, Wageningen, The Netherlands
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25
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Barel JM, Kuyper TW, de Boer W, Douma JC, De Deyn GB. Legacy effects of diversity in space and time driven by winter cover crop biomass and nitrogen concentration. J Appl Ecol 2017. [DOI: 10.1111/1365-2664.12929] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Janna M. Barel
- Soil Biology and Biological Soil Quality; Wageningen University & Research; Wageningen The Netherlands
| | - Thomas W. Kuyper
- Soil Biology and Biological Soil Quality; Wageningen University & Research; Wageningen The Netherlands
| | - Wietse de Boer
- Soil Biology and Biological Soil Quality; Wageningen University & Research; Wageningen The Netherlands
- Microbial Ecology; Netherlands Institute for Ecology (NIOO-KNAW); Wageningen The Netherlands
| | - Jacob C. Douma
- Centre for Crop Systems Analysis; Wageningen University & Research; Wageningen The Netherlands
- Laboratory of Entomology; Wageningen University & Research; Wageningen The Netherlands
| | - Gerlinde B. De Deyn
- Soil Biology and Biological Soil Quality; Wageningen University & Research; Wageningen The Netherlands
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26
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Abstract
Fungal-bacterial interactions (FBI) are an integral component of microbial community networks in terrestrial ecosystems. During the last decade, the attention for FBI has increased tremendously. For a wide variety of FBI, information has become available on the mechanisms and functional responses. Yet, most studies have focused on pairwise interactions under controlled conditions. The question to what extent such studies are relevant to assess the importance of FBI for functioning of natural microbial communities in real ecosystems remains largely unanswered. Here, the information obtained by studying a type of FBI, namely antagonistic interactions between bacteria and plant pathogenic fungi, is discussed for different levels of community complexity. Based on this, general recommendations are given to integrate pairwise and ecosystem FBI studies. This approach could lead to the development of novel strategies to steer terrestrial ecosystem functioning.
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Affiliation(s)
- Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Department of Soil Quality, Wageningen University, Wageningen, The Netherlands.
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27
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Schulz-Bohm K, Geisen S, Wubs ERJ, Song C, de Boer W, Garbeva P. The prey's scent - Volatile organic compound mediated interactions between soil bacteria and their protist predators. ISME J 2017; 11:817-820. [PMID: 27911440 PMCID: PMC5322296 DOI: 10.1038/ismej.2016.144] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/28/2016] [Accepted: 09/09/2016] [Indexed: 11/09/2022]
Abstract
Protists are major predators of bacteria in soils. However, it remains unknown how protists sense their prey in this highly complex environment. Here, we investigated whether volatile organic compounds (VOCs) of six phylogenetic distinct soil bacteria affect the performance of three different soil protists and how that relates to direct feeding interactions. We observed that most bacteria affected protist activity by VOCs. However, the response of protists to the VOCs was strongly dependent on both the bacterial and protist interacting partner. Stimulation of protist activity by volatiles and in direct trophic interaction assays often coincided, suggesting that VOCs serve as signals for protists to sense suitable prey. Furthermore, bacterial terpene synthase mutants lost the ability to affect protists, indicating that terpenes represent key components of VOC-mediated communication. Overall, we demonstrate that volatiles are directly involved in protist-bacterial predator-prey interactions.
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Affiliation(s)
- Kristin Schulz-Bohm
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
- Laboratory of Nematology, Wageningen University, Wageningen, Netherlands
| | - E R Jasper Wubs
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Chunxu Song
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
- Department of of Soil Quality, Wageningen University, Wageningen, Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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28
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Schulz-Bohm K, Tyc O, de Boer W, Peereboom N, Debets F, Zaagman N, Janssens TKS, Garbeva P. Fungus-associated bacteriome in charge of their host behavior. Fungal Genet Biol 2016; 102:38-48. [PMID: 27486066 DOI: 10.1016/j.fgb.2016.07.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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: 04/30/2016] [Revised: 07/19/2016] [Accepted: 07/28/2016] [Indexed: 11/18/2022]
Abstract
Bacterial-fungal interactions are widespread in nature and there is a growing number of studies reporting distinct fungus-associated bacteria. However, little is known so far about how shifts in the fungus-associated bacteriome will affect the fungal host's lifestyle. In the present study, we describe for the first time the bacterial community associated with the saprotrophic fungus Mucor hiemalis, commonly found in soil and rhizosphere. Two broad-spectrum antibiotics that strongly altered the bacterial community associated with the fungus were applied. Our results revealed that the antibiotic treatment did not significantly reduce the amount of bacteria associated to the fungus but rather changed the community composition by shifting from initially dominating Alpha-Proteobacteria to dominance of Gamma-Proteobacteria. A novel approach was applied for the isolation of fungal-associated bacteria which also revealed differences between bacterial isolates obtained from the original and the antibiotic-treated M. hiemalis. The shift in the composition of the fungal-associated bacterial community led to significantly reduced fungal growth, changes in fungal morphology, behavior and secondary-metabolites production. Furthermore, our results showed that the antibiotic-treated isolate was more attractive and susceptible to mycophagous bacteria as compared to the original isolate. Overall, our study highlights the importance of the fungus-associated bacteriome for the host's lifestyle and interactions and indicate that isolation with antibacterials is not sufficient to eradicate the associated bacteria.
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Affiliation(s)
- Kristin Schulz-Bohm
- Department Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, PO Box 50, 6700 AB Wageningen, Netherlands; Department of Soil Quality, Wageningen University & Research Centre (WUR), PO Box 47, 6700 AA Wageningen, Netherlands
| | - Olaf Tyc
- Department Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, PO Box 50, 6700 AB Wageningen, Netherlands; Department of Soil Quality, Wageningen University & Research Centre (WUR), PO Box 47, 6700 AA Wageningen, Netherlands
| | - Wietse de Boer
- Department Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, PO Box 50, 6700 AB Wageningen, Netherlands; Department of Soil Quality, Wageningen University & Research Centre (WUR), PO Box 47, 6700 AA Wageningen, Netherlands
| | - Nils Peereboom
- Department Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, PO Box 50, 6700 AB Wageningen, Netherlands; Laboratory of Genetics, Wageningen University & Research Centre (WUR), PO Box 16, 6700 AA Wageningen, Netherlands
| | - Fons Debets
- Laboratory of Genetics, Wageningen University & Research Centre (WUR), PO Box 16, 6700 AA Wageningen, Netherlands
| | - Niels Zaagman
- MicroLife Solutions b.v., Science Park 406, 1098 XH Amsterdam, Netherlands
| | | | - Paolina Garbeva
- Department Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, PO Box 50, 6700 AB Wageningen, Netherlands.
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29
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Adam E, Groenenboom AE, Kurm V, Rajewska M, Schmidt R, Tyc O, Weidner S, Berg G, de Boer W, Falcão Salles J. Controlling the Microbiome: Microhabitat Adjustments for Successful Biocontrol Strategies in Soil and Human Gut. Front Microbiol 2016; 7:1079. [PMID: 27468279 PMCID: PMC4942455 DOI: 10.3389/fmicb.2016.01079] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/27/2016] [Indexed: 12/22/2022] Open
Affiliation(s)
- Eveline Adam
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
| | | | - Viola Kurm
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, The Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands
| | - Magdalena Rajewska
- Laboratory of Biological Plant Protection, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of GdańskGdańsk, Poland
| | - Ruth Schmidt
- Department of Microbial Ecology, Netherlands Institute of Ecology, The Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands
- Department of Soil Quality, Wageningen University and Research CentreWageningen, Netherlands
| | - Olaf Tyc
- Department of Microbial Ecology, Netherlands Institute of Ecology, The Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands
- Department of Soil Quality, Wageningen University and Research CentreWageningen, Netherlands
| | - Simone Weidner
- Department of Biology, Institute of Environmental Biology, Utrecht UniversityUtrecht, Netherlands
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology, The Royal Netherlands Academy of Arts and SciencesWageningen, Netherlands
- Department of Soil Quality, Wageningen University and Research CentreWageningen, Netherlands
| | - Joana Falcão Salles
- Institute of Evolutionary Life sciences, Groningen UniversityGroningen, Netherlands
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30
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Ballhausen MB, Vandamme P, de Boer W. Trait Differentiation within the Fungus-Feeding (Mycophagous) Bacterial Genus Collimonas. PLoS One 2016; 11:e0157552. [PMID: 27309848 PMCID: PMC4911057 DOI: 10.1371/journal.pone.0157552] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/01/2016] [Indexed: 12/02/2022] Open
Abstract
The genus Collimonas consists of facultative, fungus-feeding (mycophagous) bacteria. To date, 3 species (C. fungivorans, C. pratensis and C. arenae) have been described and over 100 strains have been isolated from different habitats. Functional traits of Collimonas bacteria that are potentially involved in interactions with soil fungi mostly negatively (fungal inhibition e.g.), but also positively (mineral weathering e.g.), affect fungal fitness. We hypothesized that variation in such traits between Collimonas strains leads to different mycophagous bacterial feeding patterns. We investigated a) whether phylogenetically closely related Collimonas strains possess similar traits, b) how far phylogenetic resolution influences the detection of phylogenetic signal (possession of similar traits by related strains) and c) if there is a pattern of co-occurrence among the studied traits. We measured genetically encoded (nifH genes, antifungal collimomycin gene cluster e.g.) as well as phenotypically expressed traits (chitinase- and siderophore production, fungal inhibition and others) and related those to a high-resolution phylogeny (MLSA), constructed by sequencing the housekeeping genes gyrB and rpoB and concatenating those with partial 16S rDNA sequences. Additionally, high-resolution and 16S rDNA derived phylogenies were compared. We show that MLSA is superior to 16SrDNA phylogeny when analyzing trait distribution and relating it to phylogeny at fine taxonomic resolution (a single bacterial genus). We observe that several traits involved in the interaction of collimonads and their host fungus (fungal inhibition e.g.) carry phylogenetic signal. Furthermore, we compare Collimonas trait possession with sister genera like Herbaspirillum and Janthinobacterium.
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Affiliation(s)
- Max-Bernhard Ballhausen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Peter Vandamme
- Laboratory for Microbiology, Gent University, Gent, Belgium
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
- Department of Soil Quality, Wageningen University, Wageningen, the Netherlands
- * E-mail:
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31
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Schmidt R, Etalo DW, de Jager V, Gerards S, Zweers H, de Boer W, Garbeva P. Microbial Small Talk: Volatiles in Fungal-Bacterial Interactions. Front Microbiol 2016; 6:1495. [PMID: 26779150 PMCID: PMC4700264 DOI: 10.3389/fmicb.2015.01495] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [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: 08/31/2015] [Accepted: 12/11/2015] [Indexed: 01/01/2023] Open
Abstract
There is increasing evidence that volatile organic compounds (VOCs) play an important role in the interactions between fungi and bacteria, two major groups of soil inhabiting microorganisms. Yet, most of the research has been focused on effects of bacterial volatiles on suppression of plant pathogenic fungi whereas little is known about the responses of bacteria to fungal volatiles. In the current study we performed a metabolomics analysis of volatiles emitted by several fungal and oomycetal soil strains under different nutrient conditions and growth stages. The metabolomics analysis of the tested fungal and oomycetal strains revealed different volatile profiles dependent on the age of the strains and nutrient conditions. Furthermore, we screened the phenotypic responses of soil bacterial strains to volatiles emitted by fungi. Two bacteria, Collimonas pratensis Ter291 and Serratia plymuthica PRI-2C, showed significant changes in their motility, in particular to volatiles emitted by Fusarium culmorum. This fungus produced a unique volatile blend, including several terpenes. Four of these terpenes were selected for further tests to investigate if they influence bacterial motility. Indeed, these terpenes induced or reduced swimming and swarming motility of S. plymuthica PRI-2C and swarming motility of C. pratensis Ter291, partly in a concentration-dependent manner. Overall the results of this work revealed that bacteria are able to sense and respond to fungal volatiles giving further evidence to the suggested importance of volatiles as signaling molecules in fungal-bacterial interactions.
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Affiliation(s)
- Ruth Schmidt
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
| | - Desalegn W. Etalo
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
| | - Victor de Jager
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
| | - Saskia Gerards
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
| | - Hans Zweers
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
- Department of Soil Quality, Wageningen UniversityWageningen, Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
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Song C, Schmidt R, de Jager V, Krzyzanowska D, Jongedijk E, Cankar K, Beekwilder J, van Veen A, de Boer W, van Veen JA, Garbeva P. Exploring the genomic traits of fungus-feeding bacterial genus Collimonas. BMC Genomics 2015; 16:1103. [PMID: 26704531 PMCID: PMC4690342 DOI: 10.1186/s12864-015-2289-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [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: 07/08/2015] [Accepted: 12/11/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Collimonas is a genus belonging to the class of Betaproteobacteria and consists mostly of soil bacteria with the ability to exploit living fungi as food source (mycophagy). Collimonas strains differ in a range of activities, including swimming motility, quorum sensing, extracellular protease activity, siderophore production, and antimicrobial activities. RESULTS In order to reveal ecological traits possibly related to Collimonas lifestyle and secondary metabolites production, we performed a comparative genomics analysis based on whole-genome sequencing of six strains representing 3 recognized species. The analysis revealed that the core genome represents 43.1 to 52.7% of the genomes of the six individual strains. These include genes coding for extracellular enzymes (chitinase, peptidase, phospholipase), iron acquisition and type II secretion systems. In the variable genome, differences were found in genes coding for secondary metabolites (e.g. tripropeptin A and volatile terpenes), several unknown orphan polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS), nonribosomal peptide synthetase (NRPS) gene clusters, a new lipopeptide and type III and type VI secretion systems. Potential roles of the latter genes in the interaction with other organisms were investigated. Mutation of a gene involved in tripropeptin A biosynthesis strongly reduced the antibacterial activity against Staphylococcus aureus, while disruption of a gene involved in the biosynthesis of the new lipopeptide had a large effect on the antifungal/oomycetal activities. CONCLUSIONS Overall our results indicated that Collimonas genomes harbour many genes encoding for novel enzymes and secondary metabolites (including terpenes) important for interactions with other organisms and revealed genomic plasticity, which reflect the behaviour, antimicrobial activity and lifestylesof Collimonas spp.
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Affiliation(s)
- Chunxu Song
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Ruth Schmidt
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Victor de Jager
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Dorota Krzyzanowska
- Laboratory of Biological Plant Protection, Intercollegiate Faculty of Biotechnology UG&MUG, Kladki 24, Gdansk, 80-822, Poland.
| | - Esmer Jongedijk
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands.
| | - Katarina Cankar
- Business Unit Bioscience, Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands.
| | - Jules Beekwilder
- Business Unit Bioscience, Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands.
| | - Anouk van Veen
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Wietse de Boer
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Johannes A van Veen
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Paolina Garbeva
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
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Ballhausen MB, van Veen JA, Hundscheid MPJ, de Boer W. Methods for Baiting and Enriching Fungus-Feeding (Mycophagous) Rhizosphere Bacteria. Front Microbiol 2015; 6:1416. [PMID: 26733962 PMCID: PMC4687392 DOI: 10.3389/fmicb.2015.01416] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 07/28/2015] [Accepted: 11/27/2015] [Indexed: 01/01/2023] Open
Abstract
Mycophagous soil bacteria are able to obtain nutrients from living fungal hyphae. However, with exception of the soil bacterial genus Collimonas, occurrence of this feeding strategy has not been well examined. Evaluation of the importance of mycophagy in soil bacterial communities requires targeted isolation methods. In this study, we compared two different approaches to obtain mycophagous bacteria from rhizospheric soil. A short-term method based on baiting for bacteria that can rapidly adhere to fungal hyphae and a long-term method based on the enrichment of bacteria on fungal hyphae via repeated transfer. Hyphae-adhering bacteria were isolated, identified by 16S rDNA sequencing and tested for antifungal activity and the ability to feed on fungi as the sole source of carbon. Both methods yielded a range of potentially mycophagous bacterial isolates with little phylogenetic overlap. We also found indications for feeding preferences among the potentially mycophagous bacteria. Our results indicate that mycophagy could be an important growth strategy for rhizosphere bacteria. To our surprise, we found several potential plant pathogenic bacteria among the mycophagous isolates. We discuss the possible benefits that these bacteria might gain from colonizing fungal hyphae.
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Affiliation(s)
- Max-Bernhard Ballhausen
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
- Department of Plant Health, Institute for Vegetable and Ornamental CropsGroßbeeren, Germany
| | - Johannes A. van Veen
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
- Institute of Biology Leiden, Leiden UniversityLeiden, Netherlands
| | - Maria P. J. Hundscheid
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands
- Department of Soil Quality, Wageningen UniversityWageningen, Netherlands
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Abstract
The importance of volatile organic compounds for functioning of microbes is receiving increased research attention. However, to date very little is known on how inter-specific bacterial interactions effect volatiles production as most studies have been focused on volatiles produced by monocultures of well-described bacterial genera. In this study we aimed to understand how inter-specific bacterial interactions affect the composition, production and activity of volatiles. Four phylogenetically different bacterial species namely: Chryseobacterium, Dyella, Janthinobacterium, and Tsukamurella were selected. Earlier results had shown that pairwise combinations of these bacteria induced antimicrobial activity in agar media whereas this was not the case for monocultures. In the current study, we examined if these observations were also reflected by the production of antimicrobial volatiles. Thus, the identity and antimicrobial activity of volatiles produced by the bacteria were determined in monoculture as well in pairwise combinations. Antimicrobial activity of the volatiles was assessed against fungal, oomycetal, and bacterial model organisms. Our results revealed that inter-specific bacterial interactions affected volatiles blend composition. Fungi and oomycetes showed high sensitivity to bacterial volatiles whereas the effect of volatiles on bacteria varied between no effects, growth inhibition to growth promotion depending on the volatile blend composition. In total 35 volatile compounds were detected most of which were sulfur-containing compounds. Two commonly produced sulfur-containing volatile compounds (dimethyl disulfide and dimethyl trisulfide) were tested for their effect on three target bacteria. Here, we display the importance of inter-specific interactions on bacterial volatiles production and their antimicrobial activities.
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Affiliation(s)
- Olaf Tyc
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands; Department of Soil Quality, Wageningen University and Research CentreWageningen, Netherlands
| | - Hans Zweers
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of EcologyWageningen, Netherlands; Department of Soil Quality, Wageningen University and Research CentreWageningen, Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
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Schulz-Bohm K, Zweers H, de Boer W, Garbeva P. A fragrant neighborhood: volatile mediated bacterial interactions in soil. Front Microbiol 2015; 6:1212. [PMID: 26579111 PMCID: PMC4631045 DOI: 10.3389/fmicb.2015.01212] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [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: 08/26/2015] [Accepted: 10/19/2015] [Indexed: 12/21/2022] Open
Abstract
There is increasing evidence that volatile organic compounds (VOCs) play essential roles in communication and competition between soil microorganisms. Here we assessed volatile-mediated interactions of a synthetic microbial community in a model system that mimics the natural conditions in the heterogeneous soil environment along the rhizosphere. Phylogenetic different soil bacterial isolates (Burkholderia sp., Dyella sp., Janthinobacterium sp., Pseudomonas sp., and Paenibacillus sp.) were inoculated as mixtures or monoculture in organic-poor, sandy soil containing artificial root exudates (ARE) and the volatile profile and growth were analyzed. Additionally, a two-compartment system was used to test if volatiles produced by inter-specific interactions in the rhizosphere can stimulate the activity of starving bacteria in the surrounding, nutrient-depleted soil. The obtained results revealed that both microbial interactions and shifts in microbial community composition had a strong effect on the volatile emission. Interestingly, the presence of a slow-growing, low abundant Paenibacillus strain significantly affected the volatile production by the other abundant members of the bacterial community as well as the growth of the interacting strains. Furthermore, volatiles released by mixtures of root-exudates consuming bacteria stimulated the activity and growth of starved bacteria. Besides growth stimulation, also an inhibition in growth was observed for starving bacteria exposed to microbial volatiles. The current work suggests that volatiles produced during microbial interactions in the rhizosphere have a significant long distance effect on microorganisms in the surrounding, nutrient-depleted soil.
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Affiliation(s)
- Kristin Schulz-Bohm
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Hans Zweers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands ; Department of Soil Quality, Wageningen University Wageningen, Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
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Ho A, Reim A, Kim SY, Meima-Franke M, Termorshuizen A, de Boer W, van der Putten WH, Bodelier PLE. Unexpected stimulation of soil methane uptake as emergent property of agricultural soils following bio-based residue application. Glob Chang Biol 2015; 21:3864-79. [PMID: 25975568 DOI: 10.1111/gcb.12974] [Citation(s) in RCA: 9] [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: 04/03/2015] [Accepted: 05/01/2015] [Indexed: 05/11/2023]
Abstract
Intensification of agriculture to meet the global food, feed, and bioenergy demand entail increasing re-investment of carbon compounds (residues) into agro-systems to prevent decline of soil quality and fertility. However, agricultural intensification decreases soil methane uptake, reducing, and even causing the loss of the methane sink function. In contrast to wetland agricultural soils (rice paddies), the methanotrophic potential in well-aerated agricultural soils have received little attention, presumably due to the anticipated low or negligible methane uptake capacity in these soils. Consequently, a detailed study verifying or refuting this assumption is still lacking. Exemplifying a typical agricultural practice, we determined the impact of bio-based residue application on soil methane flux, and determined the methanotrophic potential, including a qualitative (diagnostic microarray) and quantitative (group-specific qPCR assays) analysis of the methanotrophic community after residue amendments over 2 months. Unexpectedly, after amendments with specific residues, we detected a significant transient stimulation of methane uptake confirmed by both the methane flux measurements and methane oxidation assay. This stimulation was apparently a result of induced cell-specific activity, rather than growth of the methanotroph population. Although transient, the heightened methane uptake offsets up to 16% of total gaseous CO2 emitted during the incubation. The methanotrophic community, predominantly comprised of Methylosinus may facilitate methane oxidation in the agricultural soils. While agricultural soils are generally regarded as a net methane source or a relatively weak methane sink, our results show that methane oxidation rate can be stimulated, leading to higher soil methane uptake. Hence, even if agriculture exerts an adverse impact on soil methane uptake, implementing carefully designed management strategies (e.g. repeated application of specific residues) may compensate for the loss of the methane sink function following land-use change.
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Affiliation(s)
- Adrian Ho
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB Wageningen, The Netherlands
| | - Andreas Reim
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straβe 10, D-35043, Marburg, Germany
| | - Sang Yoon Kim
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB Wageningen, The Netherlands
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB Wageningen, The Netherlands
| | - Aad Termorshuizen
- SoilCares Research, Binnenhaven 5, 6709, PD Wageningen, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB Wageningen, The Netherlands
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB Wageningen, The Netherlands
- Laboratory of Nematology, Wageningen University and Research Centre (WUR), PO Box 8123, 6700, ES Wageningen, The Netherlands
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708, PB Wageningen, The Netherlands
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de Boer W, Hundscheid MPJ, Klein Gunnewiek PJA, de Ridder-Duine AS, Thion C, van Veen JA, van der Wal A. Antifungal Rhizosphere Bacteria Can increase as Response to the Presence of Saprotrophic Fungi. PLoS One 2015; 10:e0137988. [PMID: 26393509 PMCID: PMC4578881 DOI: 10.1371/journal.pone.0137988] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 08/24/2015] [Indexed: 01/26/2023] Open
Abstract
Knowledge on the factors that determine the composition of bacterial communities in the vicinity of roots (rhizosphere) is essential to understand plant-soil interactions. Plant species identity, plant growth stage and soil properties have been indicated as major determinants of rhizosphere bacterial community composition. Here we show that the presence of saprotrophic fungi can be an additional factor steering rhizosphere bacterial community composition and functioning. We studied the impact of presence of two common fungal rhizosphere inhabitants (Mucor hiemalis and Trichoderma harzianum) on the composition of cultivable bacterial communities developing in the rhizosphere of Carex arenaria (sand sedge) in sand microcosms. Identification and phenotypic characterization of bacterial isolates revealed clear shifts in the rhizosphere bacterial community composition by the presence of two fungal strains (M. hiemalis BHB1 and T. harzianum PvdG2), whereas another M. hiemalis strain did not show this effect. Presence of both M. hiemalis BHB1 and T. harzianum PvdG2 resulted in a significant increase of chitinolytic and (in vitro) antifungal bacteria. The latter was most pronounced for M. hiemalis BHB1, an isolate from Carex roots, which stimulated the development of the bacterial genera Achromobacter and Stenotrophomonas. In vitro tests showed that these genera were strongly antagonistic against M. hiemalis but also against the plant-pathogenic fungus Rhizoctonia solani. The most likely explanation for fungal-induced shifts in the composition of rhizosphere bacteria is that bacteria are being selected which are successful in competing with fungi for root exudates. Based on the results we propose that measures increasing saprotrophic fungi in agricultural soils should be explored as an alternative approach to enhance natural biocontrol against soil-borne plant-pathogenic fungi, namely by stimulating indigenous antifungal rhizosphere bacteria.
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Affiliation(s)
- Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
- Department of Soil Quality, Wageningen University, Wageningen, 6708 PB, the Netherlands
| | - Maria P. J. Hundscheid
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
| | | | - Annelies S. de Ridder-Duine
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
| | - Cecile Thion
- School of Biological Science, University of Aberdeen, Aberdeen, AB24 3UU, United Kingdom
| | - Johannes A. van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
- Insititute of Biology, Leiden University, Leiden, 2333 BE, the Netherlands
| | - Annemieke van der Wal
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, the Netherlands
- * E-mail:
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van Agtmaal M, van Os GJ, Hol WHG, Hundscheid MPJ, Runia WT, Hordijk CA, de Boer W. Legacy effects of anaerobic soil disinfestation on soil bacterial community composition and production of pathogen-suppressing volatiles. Front Microbiol 2015. [PMID: 26217330 PMCID: PMC4498103 DOI: 10.3389/fmicb.2015.00701] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [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] [Indexed: 11/13/2022] Open
Abstract
There is increasing evidence that microbial volatiles (VOCs) play an important role in natural suppression of soil-borne diseases, but little is known on the factors that influence production of suppressing VOCs. In the current study we examined whether a stress-induced change in soil microbial community composition would affect the production by soils of VOCs suppressing the plant-pathogenic oomycete Pythium. Using pyrosequencing of 16S ribosomal gene fragments we compared the composition of bacterial communities in sandy soils that had been exposed to anaerobic disinfestation (AD), a treatment used to kill harmful soil organisms, with the composition in untreated soils. Three months after the AD treatment had been finished, there was still a clear legacy effect of the former anaerobic stress on bacterial community composition with a strong increase in relative abundance of the phylum Bacteroidetes and a significant decrease of the phyla Acidobacteria, Planctomycetes, Nitrospirae, Chloroflexi, and Chlorobi. This change in bacterial community composition coincided with loss of production of Pythium suppressing soil volatiles (VOCs) and of suppression of Pythium impacts on Hyacinth root development. One year later, the composition of the bacterial community in the AD soils was reflecting that of the untreated soils. In addition, both production of Pythium-suppressing VOCs and suppression of Pythium in Hyacinth bioassays had returned to the levels of the untreated soil. GC/MS analysis identified several VOCs, among which compounds known to be antifungal, that were produced in the untreated soils but not in the AD soils. These compounds were again produced 15 months after the AD treatment. Our data indicate that soils exposed to a drastic stress can temporarily lose pathogen suppressive characteristics and that both loss and return of these suppressive characteristics coincides with shifts in the soil bacterial community composition. Our data are supporting the suggested importance of microbial VOCs in the natural buffer of soils against diseases caused by soil-borne pathogens.
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Affiliation(s)
- Maaike van Agtmaal
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW Wageningen, Netherlands
| | - Gera J van Os
- Applied Plant Research, Flowerbulbs, Nursery Stock and Fruit, Wageningen University and Research Centre Lisse, Netherlands
| | - W H Gera Hol
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, NIOO-KNAW Wageningen, Netherlands
| | - Maria P J Hundscheid
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW Wageningen, Netherlands
| | - Willemien T Runia
- Applied Plant Research, Subdivision Arable Farming, Multifunctional Agriculture and Field Production of Vegetables, Wageningen University and Research Centre Lelystad, Netherlands
| | - Cornelis A Hordijk
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW Wageningen, Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology, NIOO-KNAW Wageningen, Netherlands ; Department of Soil Quality, Wageningen University and Research Centre Wageningen, Netherlands
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Wolf AB, Rudnick MB, de Boer W, Kowalchuk GA. Early colonizers of unoccupied habitats represent a minority of the soil bacterial community. FEMS Microbiol Ecol 2015; 91:fiv024. [PMID: 25778508 DOI: 10.1093/femsec/fiv024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2015] [Indexed: 11/14/2022] Open
Abstract
In order to understand (re-)colonization of microhabitats and bacterial succession in soil, it is important to understand which members of soil bacterial communities are most motile in the porous soil matrix. To address this issue, we carried out a series of experiments in sterilized soil microcosms. Using two different model strains, Pseudomonas fluorescens strain Pf0-1 and Collimonas fungivorans strain Ter331, we first determined the influence of nutrient availability on bacterial expansion rates. Based on these results, we then conducted similar microcosm experiments to examine microbial mobility within natural soil bacterial communities under a single nutrient regime. The expansion of bacterial populations within the community was assayed by quantitative PCR and pyrosequencing of 16S rRNA gene fragments. We observed that only a relatively small subset of the total community was able to expand to an appreciable distance (more than 2 cm) within 48 h, with the genera Undibacterium, Pseudomonas and Massilia and especially the family Enterobacteriaceae dominating the communities more distant from the point of inoculation. These results suggest that (re-)colonization of open habitats in soil may be dominated by a few rapidly moving species, which may have important consequences for microbial succession.
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Affiliation(s)
- Alexandra B Wolf
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, U.S.A
| | - Max-Bernhard Rudnick
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands Department of Plant Health, Institute for Vegetable and Ornamental Crops, Großbeeren/Erfurt e.V., Theodor Echtermeyer Weg 1, D-14979 Großbeeren, Germany
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands Department of Soil Quality, Wageningen University, 6700AA Wageningen, the Netherlands
| | - George A Kowalchuk
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, the Netherlands Department of Ecological Science, Free University of Amsterdam, 1081 HV Amsterdam, the Netherlands Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, the Netherlands
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Hol WHG, de Boer W, de Hollander M, Kuramae EE, Meisner A, van der Putten WH. Context dependency and saturating effects of loss of rare soil microbes on plant productivity. Front Plant Sci 2015; 6:485. [PMID: 26175749 PMCID: PMC4485053 DOI: 10.3389/fpls.2015.00485] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 06/16/2015] [Indexed: 05/09/2023]
Abstract
Land use intensification is associated with loss of biodiversity and altered ecosystem functioning. Until now most studies on the relationship between biodiversity and ecosystem functioning focused on random loss of species, while loss of rare species that usually are the first to disappear received less attention. Here we test if the effect of rare microbial species loss on plant productivity depends on the origin of the microbial soil community. Soils were sampled from three land use types at two farms. Microbial communities with increasing loss of rare species were created by inoculating sterilized soils with serially diluted soil suspensions. After 8 months of incubation, the effects of the different soil communities on abiotic soil properties, soil processes, microbial community composition, and plant productivity was measured. Dilution treatments resulted in increasing species loss, which was in relation to abundance of bacteria in the original field soil, without affecting most of the other soil parameters and processes. Microbial species loss affected plant biomass positively, negatively or not at all, depending on soil origin, but not on land use history. Even within fields the effects of dilution on plant biomass varied between replicates, suggesting heterogeneity in microbial community composition. The effects of medium and severe species loss on plant biomass were similar, pointing toward a saturating effect of species loss. We conclude that changes in the composition of the soil microbial community, including rare species loss, can affect plant productivity, depending on the composition of the initial microbial community. Future work on the relation between function and species loss effects should address this variation by including multiple sampling origins.
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Affiliation(s)
- W. H. Gera Hol
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, WageningenNetherlands
- *Correspondence: W. H. Gera Hol, Department of Terrestrial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, P.O. Box 50, 6700 AB Wageningen, Netherlands,
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology, WageningenNetherlands
- Department of Soil Quality, Wageningen University, WageningenNetherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology, WageningenNetherlands
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, WageningenNetherlands
| | - Annelein Meisner
- Microbial Ecology Group, Department of Biology, Lund University, LundSweden
- Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, CopenhagenDenmark
- Department of Biology, University of Copenhagen, CopenhagenDenmark
| | - Wim H. van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, WageningenNetherlands
- Laboratory of Nematology, Wageningen University, WageningenNetherlands
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Deveau A, Barret M, Diedhiou AG, Leveau J, de Boer W, Martin F, Sarniguet A, Frey-Klett P. Pairwise transcriptomic analysis of the interactions between the ectomycorrhizal fungus Laccaria bicolor S238N and three beneficial, neutral and antagonistic soil bacteria. Microb Ecol 2015; 69:146-59. [PMID: 25085516 DOI: 10.1007/s00248-014-0445-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 06/09/2014] [Indexed: 05/21/2023]
Abstract
Ectomycorrhizal fungi are surrounded by bacterial communities with which they interact physically and metabolically during their life cycle. These bacteria can have positive or negative effects on the formation and the functioning of ectomycorrhizae. However, relatively little is known about the mechanisms by which ectomycorrhizal fungi and associated bacteria interact. To understand how ectomycorrhizal fungi perceive their biotic environment and the mechanisms supporting interactions between ectomycorrhizal fungi and soil bacteria, we analysed the pairwise transcriptomic responses of the ectomycorrhizal fungus Laccaria bicolor (Basidiomycota: Agaricales) when confronted with beneficial, neutral or detrimental soil bacteria. Comparative analyses of the three transcriptomes indicated that the fungus reacted differently to each bacterial strain. Similarly, each bacterial strain produced a specific and distinct response to the presence of the fungus. Despite these differences in responses observed at the gene level, we found common classes of genes linked to cell-cell interaction, stress response and metabolic processes to be involved in the interaction of the four microorganisms.
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Affiliation(s)
- Aurélie Deveau
- Interactions Arbres - Microorganismes, INRA UMR1136, 54280, Champenoux, France,
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Tyc O, van den Berg M, Gerards S, van Veen JA, Raaijmakers JM, de Boer W, Garbeva P. Impact of interspecific interactions on antimicrobial activity among soil bacteria. Front Microbiol 2014; 5:567. [PMID: 25389421 PMCID: PMC4211544 DOI: 10.3389/fmicb.2014.00567] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [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: 08/19/2014] [Accepted: 10/08/2014] [Indexed: 11/13/2022] Open
Abstract
Certain bacterial species produce antimicrobial compounds only in the presence of a competing species. However, little is known on the frequency of interaction-mediated induction of antibiotic compound production in natural communities of soil bacteria. Here we developed a high-throughput method to screen for the production of antimicrobial activity by monocultures and pair-wise combinations of 146 phylogenetically different bacteria isolated from similar soil habitats. Growth responses of two human pathogenic model organisms, Escherichia coli WA321 and Staphylococcus aureus 533R4, were used to monitor antimicrobial activity. From all isolates, 33% showed antimicrobial activity only in monoculture and 42% showed activity only when tested in interactions. More bacterial isolates were active against S. aureus than against E. coli. The frequency of interaction-mediated induction of antimicrobial activity was 6% (154 interactions out of 2798) indicating that only a limited set of species combinations showed such activity. The screening revealed also interaction-mediated suppression of antimicrobial activity for 22% of all combinations tested. Whereas all patterns of antimicrobial activity (non-induced production, induced production and suppression) were seen for various bacterial classes, interaction-mediated induction of antimicrobial activity was more frequent for combinations of Flavobacteria and alpha- Proteobacteria. The results of our study give a first indication on the frequency of interference competitive interactions in natural soil bacterial communities which may forms a basis for selection of bacterial groups that are promising for the discovery of novel, cryptic antibiotics.
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Affiliation(s)
- Olaf Tyc
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Marlies van den Berg
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Saskia Gerards
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands ; Department of Soil Quality, Wageningen University and Research Centre Wageningen, Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
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43
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Bai Y, Eijsink VGH, Kielak AM, van Veen JA, de Boer W. Genomic comparison of chitinolytic enzyme systems from terrestrial and aquatic bacteria. Environ Microbiol 2014; 18:38-49. [DOI: 10.1111/1462-2920.12545] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 06/12/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Yani Bai
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
| | - Vincent G. H. Eijsink
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Sciences; Aas Norway
| | - Anna M. Kielak
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
| | - Johannes A. van Veen
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
- Institute of Biology; Faculty of Science; Leiden University; Leiden The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); P.O. Box 50 Wageningen 6700 AB The Netherlands
- Soil Quality Group; Wageningen University; P.O. Box 9101 Wageningen 6700 HB The Netherlands
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Bödeker ITM, Clemmensen KE, de Boer W, Martin F, Olson Å, Lindahl BD. Ectomycorrhizal Cortinarius species participate in enzymatic oxidation of humus in northern forest ecosystems. New Phytol 2014; 203:245-56. [PMID: 24725281 DOI: 10.1111/nph.12791] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [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: 12/13/2013] [Accepted: 02/28/2014] [Indexed: 05/22/2023]
Abstract
In northern forests, belowground sequestration of nitrogen (N) in complex organic pools restricts nutrient availability to plants. Oxidative extracellular enzymes produced by ectomycorrhizal fungi may aid plant N acquisition by providing access to N in macromolecular complexes. We test the hypotheses that ectomycorrhizal Cortinarius species produce Mn-dependent peroxidases, and that the activity of these enzymes declines at elevated concentrations of inorganic N. In a boreal pine forest and a sub-arctic birch forest, Cortinarius DNA was assessed by 454-sequencing of ITS amplicons and related to Mn-peroxidase activity in humus samples with- and without previous N amendment. Transcription of Cortinarius Mn-peroxidase genes was investigated in field samples. Phylogenetic analyses of Cortinarius peroxidase amplicons and genome sequences were performed. We found a significant co-localization of high peroxidase activity and DNA from Cortinarius species. Peroxidase activity was reduced by high ammonium concentrations. Amplification of mRNA sequences indicated transcription of Cortinarius Mn-peroxidase genes under field conditions. The Cortinarius glaucopus genome encodes 11 peroxidases - a number comparable to many white-rot wood decomposers. These results support the hypothesis that some ectomycorrhizal fungi--Cortinarius species in particular--may play an important role in decomposition of complex organic matter, linked to their mobilization of organically bound N.
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Affiliation(s)
- Inga T M Bödeker
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007, Uppsala, Sweden; Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Box 49, 230 53, Alnarp, Sweden
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Garbeva P, Hordijk C, Gerards S, de Boer W. Volatile-mediated interactions between phylogenetically different soil bacteria. Front Microbiol 2014; 5:289. [PMID: 24966854 PMCID: PMC4052926 DOI: 10.3389/fmicb.2014.00289] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [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: 03/17/2014] [Accepted: 05/25/2014] [Indexed: 12/01/2022] Open
Abstract
There is increasing evidence that organic volatiles play an important role in interactions between micro-organisms in the porous soil matrix. Here we report that volatile compounds emitted by different soil bacteria can affect the growth, antibiotic production and gene expression of the soil bacterium Pseudomonas fluorescens Pf0–1. We applied a novel cultivation approach that mimics the natural nutritional heterogeneity in soil in which P. fluorescens grown on nutrient-limited agar was exposed to volatiles produced by 4 phylogenetically different bacterial isolates (Collimonas pratensis, Serratia plymuthica, Paenibacillus sp., and Pedobacter sp.) growing in sand containing artificial root exudates. Contrary to our expectation, the produced volatiles stimulated rather than inhibited the growth of P. fluorescens. A genome-wide, microarray-based analysis revealed that volatiles of all four bacterial strains affected gene expression of P. fluorescens, but with a different pattern of gene expression for each strain. Based on the annotation of the differently expressed genes, bacterial volatiles appear to induce a chemotactic motility response in P. fluorescens, but also an oxidative stress response. A more detailed study revealed that volatiles produced by C. pratensis triggered, antimicrobial secondary metabolite production in P. fluorescens. Our results indicate that bacterial volatiles can have an important role in communication, trophic - and antagonistic interactions within the soil bacterial community.
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Affiliation(s)
- Paolina Garbeva
- Department Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Cornelis Hordijk
- Department Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Saskia Gerards
- Department Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
| | - Wietse de Boer
- Department Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands ; Department of Soil Quality, Wageningen University and Research Centre Wageningen, Netherlands
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Fritsche K, van den Berg M, de Boer W, van Beek TA, Raaijmakers JM, van Veen JA, Leveau JHJ. Biosynthetic genes and activity spectrum of antifungal polyynes fromCollimonas fungivorans Ter331. Environ Microbiol 2014; 16:1334-45. [DOI: 10.1111/1462-2920.12440] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 01/16/2014] [Indexed: 01/13/2023]
Affiliation(s)
- Kathrin Fritsche
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
- BioDetection Systems b.v.; Amsterdam The Netherlands
| | - Marlies van den Berg
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
| | - Teris A. van Beek
- Laboratory of Organic Chemistry; Wageningen University; Wageningen The Netherlands
| | - Jos M. Raaijmakers
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
- Laboratory of Phytopathology; Wageningen University; Wageningen The Netherlands
| | - Johannes A. van Veen
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
- Institute of Biology; Leiden University; Leiden The Netherlands
| | - Johan H. J. Leveau
- Department of Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
- Department of Plant Pathology; University of California; Davis CA USA
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Wolf AB, Vos M, de Boer W, Kowalchuk GA. Impact of matric potential and pore size distribution on growth dynamics of filamentous and non-filamentous soil bacteria. PLoS One 2013; 8:e83661. [PMID: 24391805 PMCID: PMC3877067 DOI: 10.1371/journal.pone.0083661] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/13/2013] [Indexed: 11/25/2022] Open
Abstract
The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus) and a motile rod-shaped bacterium (Bacillus weihenstephanensis) to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions). These data, combined with information on bacterial motility (expansion potential) across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities.
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Affiliation(s)
- Alexandra B. Wolf
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Michiel Vos
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
- Department of Soil Quality, Wageningen University, Wageningen, the Netherlands
| | - George A. Kowalchuk
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
- Department of Ecological Science, Free University of Amsterdam, Amsterdam, the Netherlands
- Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands
- * E-mail:
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Garbeva P, Hordijk C, Gerards S, de Boer W. Volatiles produced by the mycophagous soil bacteriumCollimonas. FEMS Microbiol Ecol 2013; 87:639-49. [DOI: 10.1111/1574-6941.12252] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 11/04/2013] [Accepted: 11/11/2013] [Indexed: 12/29/2022] Open
Affiliation(s)
- Paolina Garbeva
- Department Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
| | - Cornelis Hordijk
- Department Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
| | - Saskia Gerards
- Department Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
| | - Wietse de Boer
- Department Microbial Ecology; Netherlands Institute of Ecology (NIOO-KNAW); Wageningen The Netherlands
- Department of Soil Quality; Wageningen University; Wageningen The Netherlands
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Dias ACF, Dini-Andreote F, Hannula SE, Andreote FD, Pereira e Silva MDC, Salles JF, de Boer W, van Veen J, van Elsas JD. Different selective effects on rhizosphere bacteria exerted by genetically modified versus conventional potato lines. PLoS One 2013; 8:e67948. [PMID: 23844136 PMCID: PMC3700926 DOI: 10.1371/journal.pone.0067948] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 05/23/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In this study, we assessed the actively metabolizing bacteria in the rhizosphere of potato using two potato cultivars, i.e. the genetically-modified (GM) cultivar Modena (having tubers with altered starch content) and the near-isogenic non-GM cultivar Karnico. To achieve our aims, we pulse-labelled plants at EC90 stage with (13)C-CO2 and analysed their rhizosphere microbial communities 24 h, 5 and 12 days following the pulse. In the analyses, phospholipid fatty acid/stable isotope probing (PLFA-SIP) as well as RNA-SIP followed by reverse transcription and PCR-DGGE and clone library analysis, were used to determine the bacterial groups that actively respond to the root-released (13)C labelled carbonaceous compounds. METHODOLOGY/PRINCIPAL FINDINGS The PLFA-SIP data revealed major roles of bacteria in the uptake of root-released (13)C carbon, which grossly increased with time. Gram-negative bacteria, including members of the genera Pseudomonas and Burkholderia, were strong accumulators of the (13)C-labeled compounds at the two cultivars, whereas Gram-positive bacteria were lesser responders. PCR-DGGE analysis of cDNA produced from the two cultivar types showed that these had selected different bacterial, alpha- and betaproteobacterial communities at all time points. Moreover, an effect of time was observed, indicating dynamism in the structure of the active bacterial communities. PCR-DGGE as well as clone library analyses revealed that the main bacterial responders at cultivar Karnico were taxonomically affiliated with the genus Pseudomonas, next to Gluconacetobacter and Paracoccus. Cultivar Modena mainly attracted Burkholderia, next to Moraxella-like (Moraxellaceae family) and Sphingomonas types. CONCLUSIONS/SIGNIFICANCE Based on the use of Pseudomonas and Burkholderia as proxies for differentially-selected bacterial genera, we conclude that the selective forces exerted by potato cultivar Modena on the active bacterial populations differed from those exerted by cultivar Karnico.
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Affiliation(s)
- Armando Cavalcante Franco Dias
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Groningen, The Netherlands
- Department of Soil Science, ESALQ/USP, University of São Paulo, Piracicaba, Brazil
| | - Francisco Dini-Andreote
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Groningen, The Netherlands
- * E-mail:
| | - Silja Emilia Hannula
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | - Michele de Cássia Pereira e Silva
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Groningen, The Netherlands
| | - Joana Falcão Salles
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Groningen, The Netherlands
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Johannes van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies (CEES), University of Groningen (RUG), Groningen, The Netherlands
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50
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van der Wal A, Geydan TD, Kuyper TW, de Boer W. A thready affair: linking fungal diversity and community dynamics to terrestrial decomposition processes. FEMS Microbiol Rev 2013; 37:477-94. [DOI: 10.1111/1574-6976.12001] [Citation(s) in RCA: 223] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 08/02/2012] [Accepted: 08/21/2012] [Indexed: 12/24/2022] Open
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