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Dove A, Charters MD, Campbell MJ, Blake H, Menon M, Sarasan V. Fungal Community Composition at the Last Remaining Wild Site of Yellow Early Marsh Orchid ( Dactylorhiza incarnata ssp. ochroleuca). Microorganisms 2023; 11:2124. [PMID: 37630684 PMCID: PMC10459220 DOI: 10.3390/microorganisms11082124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
The yellow early marsh orchid (Dactylorhiza incarnata ssp. ochroleuca) is a critically endangered terrestrial orchid in Britain. Previous attempts to translocate symbiotic seedlings to a site near the last remaining wild site demonstrated some success, with a 10% survival rate despite adverse weather conditions over a two-year period. However, to facilitate future reintroduction efforts or conservation translocations, a more comprehensive understanding of the fungal microbiome and abiotic soil characteristics at the final remaining wild site is required. Obtaining comprehensive information on both the fungal community and soil nutrient composition from wild sites has significant benefits and may prove critical for the success of future conservation translocations involving threatened orchids. This preliminary study, conducted at the last remaining wild site, revealed a significant correlation between the relative abundance of the orchid mycorrhizal fungal order Cantharellales and the concentrations of nitrate and phosphate in the soil. Another orchid mycorrhizal fungal group, Sebacinales, was found to be distributed extensively throughout the site. The composition of fungal communities across the entire site, orchid-hosting and non-orchid-hosting soils is discussed in relation to reinforcing the current population and preventing the extinction of this orchid.
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Affiliation(s)
- Andrea Dove
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
| | | | | | - Hanna Blake
- Department of Geography, University of Sheffield, Sheffield S10 2TN, UK; (H.B.)
| | - Manoj Menon
- Department of Geography, University of Sheffield, Sheffield S10 2TN, UK; (H.B.)
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Rasa K, Pennanen T, Peltoniemi K, Velmala S, Fritze H, Kaseva J, Joona J, Uusitalo R. Pulp and paper mill sludges decrease soil erodibility. JOURNAL OF ENVIRONMENTAL QUALITY 2021; 50:172-184. [PMID: 33084047 PMCID: PMC7898543 DOI: 10.1002/jeq2.20170] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/23/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
Declining carbon (C) content in agricultural soils threatens soil fertility and makes soil prone to erosion, which could be rectified with organic soil amendments. In a 4-yr field trial, we made a single application of three different organic sludges from the pulp and paper industry and studied their effects on cereal yield, soil C content, and fungal and bacterial composition. In laboratory rainfall simulations, we also studied the effects of the soil amendments on susceptibility to erosion and nutrient mobilization of a clay-textured soil by measuring the quality of percolation water passing through 40-cm intact soil monoliths during 2-d rainfall simulations over four consecutive years after application. A nutrient-poor fiber sludge reduced wheat yield in the first growing season, but there were no other significant effects on cereal yield or grain quality. An input of ∼8 Mg ha-1 C with the soil amendments had only minor effects on soil C content after 4 yr, likely because of fast microbe-mediated turnover. The amendments clearly changed the fungal and bacterial community composition. All amendments significantly reduced suspended solids (SS) and total phosphorus (TP) concentrations in percolation water. The effect declined with time, but the reduction in SS and TP was still >25% 4 yr after application. We attributed the lower tendency for particle detachment in rain simulations to direct interactions of soil minerals with the added particulate organic matter and microbe-derived compounds that stabilize soil aggregates. In soils with low organic matter content, pulp and paper industry by-products can be a viable measure for erosion mitigation.
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Affiliation(s)
- Kimmo Rasa
- Natural Resources Institute FinlandTietotie 4JokioinenFI‐31600Finland
| | - Taina Pennanen
- Natural Resources Institute FinlandLatokartanonkaari 9HelsinkiFI‐00790Finland
| | - Krista Peltoniemi
- Natural Resources Institute FinlandLatokartanonkaari 9HelsinkiFI‐00790Finland
| | - Sannakajsa Velmala
- Natural Resources Institute FinlandLatokartanonkaari 9HelsinkiFI‐00790Finland
| | - Hannu Fritze
- Natural Resources Institute FinlandLatokartanonkaari 9HelsinkiFI‐00790Finland
| | - Janne Kaseva
- Natural Resources Institute FinlandTietotie 4JokioinenFI‐31600Finland
| | - Juuso Joona
- Soilfood OyViikinkaari 6HelsinkiFI‐00790Finland
| | - Risto Uusitalo
- Natural Resources Institute FinlandTietotie 4JokioinenFI‐31600Finland
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Garnica S, Rosenstein R, Schön ME. Belowground fungal community diversity, composition and ecological functionality associated with winter wheat in conventional and organic agricultural systems. PeerJ 2020; 8:e9732. [PMID: 33083101 PMCID: PMC7566770 DOI: 10.7717/peerj.9732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/24/2020] [Indexed: 11/20/2022] Open
Abstract
Understanding the impacts of agricultural practices on belowground fungal communities is crucial in order to preserve biological diversity in agricultural soils and enhance their role in agroecosystem functioning. Although fungal communities are widely distributed, relatively few studies have correlated agricultural production practices. We investigated the diversity, composition and ecological functionality of fungal communities in roots of winter wheat (Triticum aestivum) growing in conventional and organic farming systems. Direct and nested polymerase chain reaction (PCR) amplifications spanning the internal transcribed spacer (ITS) region of the rDNA from pooled fine root samples were performed with two different sets of fungal specific primers. Fungal identification was carried out through similarity searches against validated reference sequences (RefSeq). The R package ‘picante’ and FUNGuild were used to analyse fungal community composition and trophic mode, respectively. Either by direct or cloning sequencing, 130 complete ITS sequences were clustered into 39 operational taxonomic units (OTUs) (25 singletons), belonging to the Ascomycota (24), the Basidiomycota (14) and to the Glomeromycota (1). Fungal communities from conventional farming sites are phylogenetically more related than expected by chance. Constrained ordination analysis identified total N, total S and Pcal that had a significant effect on the OTU’s abundance and distribution, and a further correlation with the diversity of the co-occurring vegetation could be hypothesised. The functional predictions based on FUNGuild suggested that conventional farming increased the presence of plant pathogenic fungi compared with organic farming. Based on diversity, OTU distribution, nutrition mode and the significant phylogenetic clustering of fungal communities, this study shows that fungal communities differ across sampling sites, depending on agricultural practices. Although it is not fully clear which factors determine the fungal communities, our findings suggest that organic farming systems have a positive effect on fungal communities in winter wheat crops.
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Affiliation(s)
- Sigisfredo Garnica
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Isla Teja, Chile
| | - Ronja Rosenstein
- Institute of Evolution and Ecology, Plant Evolutionary Ecology, University of Tuebingen, Tuebingen, Germany
| | - Max Emil Schön
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Vogt-Schilb H, Těšitelová T, Kotilínek M, Sucháček P, Kohout P, Jersáková J. Altered rhizoctonia assemblages in grasslands on ex-arable land support germination of mycorrhizal generalist, not specialist orchids. THE NEW PHYTOLOGIST 2020; 227:1200-1212. [PMID: 32285948 DOI: 10.1111/nph.16604] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/01/2020] [Indexed: 05/03/2023]
Abstract
Species-rich seminatural grasslands in Central Europe have suffered a dramatic loss of biodiversity due to conversion to arable land, but vast areas are being restored. Population recovery of orchids, which depend on mycorrhizal fungi for germination, is however limited. We hypothesised that ploughing and fertilisation caused shifts in orchid mycorrhizal communities in soil and restricted orchid germination. We examined edaphic conditions in 60 restored and seminatural grasslands, and germination success in 10 restored grasslands. Using a newly designed primer, we screened the composition of rhizoctonias in soil, seedlings and roots of seven orchid species. Seminatural and restored grasslands differed significantly in nutrient amounts and rhizoctonia assemblages in soil. While Serendipitaceae prevailed in seminatural grasslands with a higher organic matter content, Ceratobasidiaceae were more frequent in phosphorus-rich restored grasslands with increased abundance on younger restored sites. Tulasnellaceae displayed no preference. Germination success in restored grasslands differed significantly between orchid species; two mycorrhizal generalist species germinated with a broad range of rhizoctonias at most restored grasslands, while germination success of specialists was low. Past agricultural practices have a long-lasting effect on soil conditions and orchid mycorrhizal communities. Altered mycorrhizal availability may be the main reason for low germination success of specialist orchid species.
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Affiliation(s)
- Hélène Vogt-Schilb
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, České Budějovice, Czech Republic
- CEFE, CNRS, EPHE, IRD, Université de Montpellier, Université Paul-Valéry Montpellier, 1919 Route de Mende, 34293, Montpellier, France
| | - Tamara Těšitelová
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, České Budějovice, Czech Republic
| | - Milan Kotilínek
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, České Budějovice, Czech Republic
| | - Pavel Sucháček
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, České Budějovice, Czech Republic
| | - Petr Kohout
- Institute of Microbiology ASCR, Vídeňská 1083, 142 20, Prague 4 - Krč, Czech Republic
- Faculty of Science, Charles University, CZ-128 44, Prague 2, Czech Republic
| | - Jana Jersáková
- Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, České Budějovice, Czech Republic
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Evaluation of genome size and quantitative features of the dolipore septum as taxonomic predictors for the Serendipita 'williamsii' species complex. Fungal Biol 2020; 124:781-800. [PMID: 32883429 DOI: 10.1016/j.funbio.2020.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 05/23/2020] [Accepted: 06/10/2020] [Indexed: 11/21/2022]
Abstract
Despite multiple taxonomic revisions, several uncertainties at the genus and species level remain to be resolved within the Serendipitaceae family (Sebacinales). This volatile classification is attributed to the limited number of available axenic cultures and the scarcity of useful morphological traits. In the current study, we attempted to discover alternative taxonomic markers not relying on DNA sequences to differentiate among the closely related members of our Congolese Serendipita isolate collection and the reference strains S. indica (syn. Piriformospora indica) and S. williamsii (syn. P. williamsii). We demonstrated that nuclear distribution across hyphal cells and genome size (determined by flow cytometry) did not have enough resolving power, but quantitative and qualitative variations in the ultrastructure of the dolipore septa investigated by transmission electron microscopy did provide useful markers. Multivariate analysis revealed that subtle differences in ultrastructural characteristics of the parenthesome and the attached endoplasmic reticulum are most relevant when studying this fungal group. Moreover, the observed clustering pattern showed that there might be more diversity amongst the Congolese isolates within the S. 'williamsii' species complex than previously anticipated based on molecular data. Altogether, our results provide novel perspectives on the use of integrative approaches to support sebacinoid and Serendipitaceae taxonomy.
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Venneman J, De Tender C, Debode J, Audenaert K, Baert G, Vermeir P, Cremelie P, Bekaert B, Landschoot S, Thienpondt B, Djailo BD, Vereecke D, Haesaert G. Sebacinoids within rhizospheric fungal communities associated with subsistence farming in the Congo Basin: a needle in each haystack. FEMS Microbiol Ecol 2020; 95:5524361. [PMID: 31247636 DOI: 10.1093/femsec/fiz101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/25/2019] [Indexed: 12/15/2022] Open
Abstract
The unique ecosystem of the Congolese rainforest has only scarcely been explored for its plant-fungal interactions. Here, we characterized the root fungal communities of field-grown maize and of Panicum from adjacent borders in the Congo Basin and assessed parameters that could shape them. The soil properties indicated that comparable poor soil conditions prevailed in fields and borders, illustrating the low input character of local subsistence farming. The rhizosphere fungal communities, dominated by ascomycetous members, were structured by plant species, slash-and-burn practices and soil P, pH and C/N ratio. Examining fungi with potential plant growth-promoting abilities, the glomeromycotan communities appeared to be affected by the same parameters, whereas the inconspicuous symbionts of the order Sebacinales seemed less susceptible to environmental and anthropogenic factors. Notwithstanding the low abundances at which they were detected, sebacinoids occurred in 87% of the field samples, implying that they represent a consistent taxon within indigenous fungal populations across smallholder farm sites. Pending further insight into their ecosystem functionality, these data suggest that Sebacinales are robust root inhabitants that might be relevant for on-farm inoculum development within sustainable soil fertility management in the Sub-Saharan region.
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Affiliation(s)
- Jolien Venneman
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Caroline De Tender
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96, BE-9820, Merelbeke, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Krijgslaan 281, S9, BE-9000, Ghent, Belgium
| | - Jane Debode
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96, BE-9820, Merelbeke, Belgium
| | - Kris Audenaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Geert Baert
- Department of Environment, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Pieter Vermeir
- Department of Green Chemistry and Technology, Laboratory of Chemical Analysis (LCA), Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Pieter Cremelie
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Burg. Van Gansberghelaan 96, BE-9820, Merelbeke, Belgium
| | - Boris Bekaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Sofie Landschoot
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Bert Thienpondt
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Benoît Dhed'a Djailo
- Faculty of Science and Agriculture, Kisangani University, B.P. 2012, Kisangani, Democratic Republic of Congo
| | - Danny Vereecke
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
| | - Geert Haesaert
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium
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Deyett E, Rolshausen PE. Endophytic microbial assemblage in grapevine. FEMS Microbiol Ecol 2020; 96:5810658. [DOI: 10.1093/femsec/fiaa053] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/19/2020] [Indexed: 12/16/2022] Open
Abstract
ABSTRACT
The plant vascular system has remained an underexplored niche despite its potential for hosting beneficial microbes. The aim of this work was to determine the origin of the microbial endophytes inhabiting grapevine. We focused on a single commercial vineyard in California over a two-year period and used an amplicon metagenomics approach to profile the bacterial (16S–V4) and fungal (ITS) communities of the microbiome across a continuum of six grapevine compartments: bulk soil, rhizosphere, root, cordon, cane and sap. Our data supported that roots are a bottleneck to microbial richness and that they are mostly colonized with soilborne microbes, including plant growth-promoting bacteria recruited by the host, but also saprophytic and pathogenic fungal invaders. A core group of taxa was identified throughout the vine; however, there was clear partitioning of the microbiome with niche adaptation of distinct taxonomic groups. Above- and belowground plant tissues displayed distinct microbial fingerprints and were intermixed in a limited capacity mostly by way of the plant sap. We discuss how cultural practices and human contact may shape the endosphere microbiome and identify potential channels for transmission of its residents.
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Affiliation(s)
- E Deyett
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - P E Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
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Coller E, Cestaro A, Zanzotti R, Bertoldi D, Pindo M, Larger S, Albanese D, Mescalchin E, Donati C. Microbiome of vineyard soils is shaped by geography and management. MICROBIOME 2019; 7:140. [PMID: 31699155 PMCID: PMC6839268 DOI: 10.1186/s40168-019-0758-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/09/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Despite their importance as a reservoir of biodiversity, the factors shaping soil microbial communities and the extent by which these are impacted by cultivation are still poorly understood. Using 16S rRNA gene and ITS sequencing, we characterized the soil microbiota of vineyards and of neighboring permanent grassland soils in the Italian province of Trentino, and correlated their structure and composition to location, chemical properties of the soil, and land management. RESULTS Bacterial communities had a core of conserved taxa accounting for more than 60% of the reads of each sample, that was influenced both by geography and cultivation. The core fungal microbiota was much smaller and dominated by geography alone. Cultivation altered the structure and composition of the soil microbiota both for bacteria and fungi, with site-specific effects on their diversity. The diversity of bacterial and fungal communities was generally inversely correlated across locations. We identified several taxa that were impacted by the chemical properties and texture of the soil. CONCLUSIONS Our results highlight the different responses of bacterial and fungal communities to environmental factors and highlight the need to characterize both components of the soil microbiota to fully understand the factors that drive their variability.
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Affiliation(s)
- Emanuela Coller
- Faculty of Science and Technology, Free University of Bozen, P.za Università 1, 39100 Bolzano, Italy
| | - Alessandro Cestaro
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige, Italy
| | - Roberto Zanzotti
- Technology Transfer Center, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige, Italy
| | - Daniela Bertoldi
- Technology Transfer Center, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige, Italy
| | - Massimo Pindo
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige, Italy
| | - Simone Larger
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige, Italy
| | - Davide Albanese
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige, Italy
| | - Enzo Mescalchin
- Technology Transfer Center, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige, Italy
| | - Claudio Donati
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 38010 San Michele all’Adige, Italy
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Sefloo NG, Wieczorek K, Steinkellner S, Hage-Ahmed K. Serendipita Species Trigger Cultivar-Specific Responses to Fusarium Wilt in Tomato. AGRONOMY-BASEL 2019; 9:595. [PMID: 31857912 PMCID: PMC6923139 DOI: 10.3390/agronomy9100595] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The endophytic fungi Serendipita indica and S. vermifera have recently gained increasing attention due to their beneficial effects on plant growth and plant health. Little is known about other species, such as S. williamsii and S. herbamans. To test their biocontrol and growth-promoting potential, susceptible and tolerant tomato cultivars (Kremser Perle and Micro-Tom, respectively) were inoculated with S. williamsii, S. herbamans, S. indica, or S. vermifera and challenged with the soilborne pathogen Fusarium oxysporum f. sp. lycopersici (Fol) in greenhouse experiments. Furthermore, in vitro assays on the direct inhibitory effects of Serendipita spp. against Fol were performed. Negative effects of Fol on phenological growth in the susceptible cultivar were alleviated by all four applied Serendipita spp. Apart from these similar effects on biometric parameters, disease incidence was only reduced by S. herbamans and S. vermifera. In the tolerant cultivar, disease parameters remained unaffected although shoot dry mass was negatively affected by S. vermifera. Direct effects of Serendipita spp. against Fol were not evident in the in vitro assays indicating an indirect effect via the host plant. Our results highlight the importance of identifying cultivar-specific effects in pathogen–endophyte–plant interactions to determine the most beneficial combinations.
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Banerjee S, Walder F, Büchi L, Meyer M, Held AY, Gattinger A, Keller T, Charles R, van der Heijden MGA. Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. THE ISME JOURNAL 2019; 13:1722-1736. [PMID: 30850707 PMCID: PMC6591126 DOI: 10.1038/s41396-019-0383-2] [Citation(s) in RCA: 398] [Impact Index Per Article: 79.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/04/2019] [Accepted: 02/17/2019] [Indexed: 01/28/2023]
Abstract
Root-associated microbes play a key role in plant performance and productivity, making them important players in agroecosystems. So far, very few studies have assessed the impact of different farming systems on the root microbiota and it is still unclear whether agricultural intensification influences the structure and complexity of microbial communities. We investigated the impact of conventional, no-till, and organic farming on wheat root fungal communities using PacBio SMRT sequencing on samples collected from 60 farmlands in Switzerland. Organic farming harbored a much more complex fungal network with significantly higher connectivity than conventional and no-till farming systems. The abundance of keystone taxa was the highest under organic farming where agricultural intensification was the lowest. We also found a strong negative association (R2 = 0.366; P < 0.0001) between agricultural intensification and root fungal network connectivity. The occurrence of keystone taxa was best explained by soil phosphorus levels, bulk density, pH, and mycorrhizal colonization. The majority of keystone taxa are known to form arbuscular mycorrhizal associations with plants and belong to the orders Glomerales, Paraglomerales, and Diversisporales. Supporting this, the abundance of mycorrhizal fungi in roots and soils was also significantly higher under organic farming. To our knowledge, this is the first study to report mycorrhizal keystone taxa for agroecosystems, and we demonstrate that agricultural intensification reduces network complexity and the abundance of keystone taxa in the root microbiome.
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Affiliation(s)
- Samiran Banerjee
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland.
| | - Florian Walder
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland.
| | - Lucie Büchi
- Agroscope, Plant Production Systems, Route de Duillier 50, 1260, Nyon, Switzerland
- Natural Resources Institute, University of Greenwich, London, UK
| | - Marcel Meyer
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
| | - Alain Y Held
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
| | - Andreas Gattinger
- Research Institute of Organic Agriculture FiBL, 5070, Frick, Switzerland
- Justus-Liebig University Giessen, Organic Farming with focus on Sustainable Soil Use, Karl-Glöckner-Str. 21C, 35394, Giessen, Germany
| | - Thomas Keller
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Swedish University of Agricultural Sciences, Department of Soil & Environment, Box 7014, 75007, Uppsala, Sweden
| | - Raphael Charles
- Agroscope, Plant Production Systems, Route de Duillier 50, 1260, Nyon, Switzerland
- Research Institute of Organic Agriculture FiBL, Jordils 3, 1001, Lausanne, Switzerland
| | - Marcel G A van der Heijden
- Agroscope, Department of Agroecology & Environment, Reckenholzstrasse 191, 8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, 8008, Zürich, Switzerland
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Fesel PH, Zuccaro A. Dissecting endophytic lifestyle along the parasitism/mutualism continuum in Arabidopsis. Curr Opin Microbiol 2016; 32:103-112. [DOI: 10.1016/j.mib.2016.05.008] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 11/17/2022]
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12
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Weiß M, Waller F, Zuccaro A, Selosse MA. Sebacinales - one thousand and one interactions with land plants. THE NEW PHYTOLOGIST 2016; 211:20-40. [PMID: 27193559 DOI: 10.1111/nph.13977] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/05/2016] [Indexed: 05/20/2023]
Abstract
20 I 21 II 21 III 23 IV 29 V 33 VI 35 36 36 References 36 SUMMARY: Root endophytism and mycorrhizal associations are complex derived traits in fungi that shape plant physiology. Sebacinales (Agaricomycetes, Basidiomycota) display highly diverse interactions with plants. Although early-diverging Sebacinales lineages are root endophytes and/or have saprotrophic abilities, several more derived clades harbour obligate biotrophs forming mycorrhizal associations. Sebacinales thus display transitions from saprotrophy to endophytism and to mycorrhizal nutrition within one fungal order. This review discusses the genomic traits possibly associated with these transitions. We also show how molecular ecology revealed the hyperdiversity of Sebacinales and their evolutionary diversification into two sister families: Sebacinaceae encompasses mainly ectomycorrhizal and early-diverging saprotrophic species; the second family includes endophytes and lineages that repeatedly evolved ericoid, orchid and ectomycorrhizal abilities. We propose the name Serendipitaceae for this family and, within it, we transfer to the genus Serendipita the endophytic cultivable species Piriformospora indica and P. williamsii. Such cultivable Serendipitaceae species provide excellent models for root endophytism, especially because of available genomes, genetic tractability, and broad host plant range including important crop plants and the model plant Arabidopsis thaliana. We review insights gained with endophytic Serendipitaceae species into the molecular mechanisms of endophytism and of beneficial effects on host plants, including enhanced resistance to abiotic and pathogen stress.
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Affiliation(s)
- Michael Weiß
- Steinbeis-Innovationszentrum Organismische Mykologie und Mikrobiologie, Vor dem Kreuzberg 17, 72070, Tübingen, Germany
- Department of Biology, University of Tübingen, Auf der Morgenstelle 1, 72076, Tübingen, Germany
| | - Frank Waller
- Pharmaceutical Biology, Julius von Sachs Institute for Biosciences, Biocenter, Würzburg University, Julius-von-Sachs Platz 2, 97082, Würzburg, Germany
| | - Alga Zuccaro
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), BioCenter, University of Cologne, 50674, Cologne, Germany
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Marc-André Selosse
- Département Systématique et Evolution (UMR 7205 ISYEB), Muséum national d'Histoire naturelle, CP 50, 45 rue Buffon, 75005, Paris, France
- Department of Plant Taxonomy and Nature Conservation, University of Gdansk, Gdansk, Poland
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13
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López-García Á, Horn S, Rillig MC, Hempel S. Spatial and niche-based ecological processes drive the distribution of endophytic Sebacinales in soil and root of grassland communities. FEMS Microbiol Ecol 2016; 92:fiw079. [PMID: 27090761 DOI: 10.1093/femsec/fiw079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2016] [Indexed: 11/13/2022] Open
Abstract
The interest in endophytic sebacinalean communities has been increasing during the last decade due to the increased knowledge about their symbiotic life style and potential role for ecosystem functioning. Although they are present in many ecosystems, their abundance in individual plant roots is very limited. This fact affects their study: they are difficult to isolate and to detect in root DNA samples. To advance knowledge of the forces that shape their distribution, we approached the parallel study of sebacinalean communities in roots and soil of grassland. Using a small-scale spatially explicit sampling design, we analysed the contribution of spatial position, soil properties, plant community and phylogenetic components to the variation of sebacinalean communities. The results revealed the presence of 11 operational taxonomic units (OTUs) and a high coincidence between root and soil communities: on an average a single-OTU per sample was recorded for both sample types. Spatial distance was found to mainly drive the distribution of Sebacinales in soil, whereas phylogenetic plus environmental signatures mainly drove their presence in roots. Independently of the sample type, we found clear evidence of environmental filtering caused by soil pH which, furthermore, seemed to control the presence of a specialized sebacinalean OTU.
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Affiliation(s)
- Álvaro López-García
- Department of Plant Ecology, Institut für Biologie, Freie Universität Berlin, D-14195 Berlin, Germany Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
| | - Sebastian Horn
- Department of Soil Biology and Genomics, Hawkesbury Institute for the Environment, University of Western Sydney, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Matthias C Rillig
- Department of Plant Ecology, Institut für Biologie, Freie Universität Berlin, D-14195 Berlin, Germany Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
| | - Stefan Hempel
- Department of Plant Ecology, Institut für Biologie, Freie Universität Berlin, D-14195 Berlin, Germany Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
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14
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Veresoglou SD, Halley JM, Rillig MC. Extinction risk of soil biota. Nat Commun 2015; 6:8862. [PMID: 26593272 PMCID: PMC4673489 DOI: 10.1038/ncomms9862] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 10/09/2015] [Indexed: 01/01/2023] Open
Abstract
No species lives on earth forever. Knowing when and why species go extinct is crucial for a complete understanding of the consequences of anthropogenic activity, and its impact on ecosystem functioning. Even though soil biota play a key role in maintaining the functioning of ecosystems, the vast majority of existing studies focus on aboveground organisms. Many questions about the fate of belowground organisms remain open, so the combined effort of theorists and applied ecologists is needed in the ongoing development of soil extinction ecology.
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Affiliation(s)
- Stavros D. Veresoglou
- Freie Universität Berlin, Institut für Biologie, Plant Ecology, Altensteinstrasse 6, D-14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
| | - John M. Halley
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece
| | - Matthias C. Rillig
- Freie Universität Berlin, Institut für Biologie, Plant Ecology, Altensteinstrasse 6, D-14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195 Berlin, Germany
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