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Köberl M, Erlacher A, Ramadan EM, El-Arabi TF, Müller H, Bragina A, Berg G. Comparisons of diazotrophic communities in native and agricultural desert ecosystems reveal plants as important drivers in diversity. FEMS Microbiol Ecol 2015; 92:fiv166. [PMID: 26705571 PMCID: PMC4730177 DOI: 10.1093/femsec/fiv166] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2015] [Indexed: 01/09/2023] Open
Abstract
Diazotrophs provide the only biological source of fixed atmospheric nitrogen in the biosphere. Although they are the key player for plant-available nitrogen, less is known about their diversity and potential importance in arid ecosystems. We investigated the nitrogenase gene diversity in native and agricultural desert soil as well as within root-associated microbiota of medicinal plants grown in Egypt through the combination of nifH-specific qPCR, fingerprints, amplicon pyrosequencing and fluorescence in situ hybridization–confocal laser scanning microscopy. Although the diazotrophic microbiota were characterized by generally high abundances and diversity, statistically significant differences were found between both soils, the different microhabitats, and between the investigated plants (Matricaria chamomilla L., Calendula officinalis L. and Solanum distichum Schumach. and Thonn.). We observed a considerable community shift from desert to agriculturally used soil that demonstrated a higher abundance and diversity in the agro-ecosystem. The endorhiza was characterized by lower abundances and only a subset of species when compared to the rhizosphere. While the microbiomes of the Asteraceae were similar and dominated by potential root-nodulating rhizobia acquired primarily from soil, the perennial S. distichum generally formed associations with free-living nitrogen fixers. These results underline the importance of diazotrophs in desert ecosystems and additionally identify plants as important drivers in functional gene pool diversity. The diazotrophic microbiome of desert ecosystems is characterized by a high diversity and abundance and specific for each plant rhizosphere.
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Affiliation(s)
- Martina Köberl
- Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | - Armin Erlacher
- Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | - Elshahat M Ramadan
- Faculty of Agriculture, Ain Shams University, 11566 Cairo, Egypt Biotechnology Laboratory, Heliopolis University, 11777 Cairo, Egypt
| | - Tarek F El-Arabi
- Faculty of Agriculture, Ain Shams University, 11566 Cairo, Egypt Biotechnology Laboratory, Heliopolis University, 11777 Cairo, Egypt
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | - Anastasia Bragina
- Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria
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102
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Wedin M, Maier S, Fernandez-Brime S, Cronholm B, Westberg M, Grube M. Microbiome change by symbiotic invasion in lichens. Environ Microbiol 2015; 18:1428-39. [PMID: 26310431 DOI: 10.1111/1462-2920.13032] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 08/17/2015] [Accepted: 08/17/2015] [Indexed: 12/01/2022]
Abstract
Lichens are obligate symbioses between fungi and green algae or cyanobacteria. Most lichens resynthesize their symbiotic thalli from propagules, but some develop within the structures of already existing lichen symbioses. Diploschistes muscorum starts as a parasite infecting the lichen Cladonia symphycarpa and gradually develops an independent Diploschistes lichen thallus. Here we studied how this process influences lichen-associated microbiomes and photobionts by sampling four transitional stages, at sites in Sweden and Germany, and characterizing their microbial communities using high-throughput 16S rRNA gene and photobiont-specific ITS rDNA sequencing, and fluorescence in situ hybridization. A gradual microbiome shift occurred during the transition, but fractions of Cladonia-associated bacteria were retained during the process of symbiotic reorganization. Consistent changes observed across sites included a notable decrease in the relative abundance of Alphaproteobacteria with a concomitant increase in Betaproteobacteria. Armatimonadia, Spartobacteria and Acidobacteria also decreased during the infection of Cladonia by Diploschistes. The lichens differed in photobiont specificity. Cladonia symphycarpa was associated with the same algal species at all sites, but Diploschistes muscorum had a flexible strategy with different photobiont combinations at each site. This symbiotic invasion system suggests that partners can be reorganized and selected for maintaining potential roles rather than depending on particular species.
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Affiliation(s)
- Mats Wedin
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, Stockholm, SE-104 05, Sweden
| | - Stefanie Maier
- Institute of Plant Sciences, University of Graz, Holteigasse 6, Graz, A-8010, Austria
| | - Samantha Fernandez-Brime
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, Stockholm, SE-104 05, Sweden
| | - Bodil Cronholm
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, Stockholm, SE-104 05, Sweden
| | - Martin Westberg
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, Stockholm, SE-104 05, Sweden
| | - Martin Grube
- Institute of Plant Sciences, University of Graz, Holteigasse 6, Graz, A-8010, Austria
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103
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Greshake B, Zehr S, Dal Grande F, Meiser A, Schmitt I, Ebersberger I. Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens. Mol Ecol Resour 2015; 16:511-23. [PMID: 26345272 DOI: 10.1111/1755-0998.12463] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/28/2015] [Accepted: 08/22/2015] [Indexed: 11/30/2022]
Abstract
Whole-genome shotgun sequencing of multispecies communities using only a single library layout is commonly used to assess taxonomic and functional diversity of microbial assemblages. Here, we investigate to what extent such metagenome skimming approaches are applicable for in-depth genomic characterizations of eukaryotic communities, for example lichens. We address how to best assemble a particular eukaryotic metagenome skimming data, what pitfalls can occur, and what genome quality can be expected from these data. To facilitate a project-specific benchmarking, we introduce the concept of twin sets, simulated data resembling the outcome of a particular metagenome sequencing study. We show that the quality of genome reconstructions depends essentially on assembler choice. Individual tools, including the metagenome assemblers Omega and MetaVelvet, are surprisingly sensitive to low and uneven coverages. In combination with the routine of assembly parameter choice to optimize the assembly N50 size, these tools can preclude an entire genome from the assembly. In contrast, MIRA, an all-purpose overlap assembler, and SPAdes, a multisized de Bruijn graph assembler, facilitate a comprehensive view on the individual genomes across a wide range of coverage ratios. Testing assemblers on a real-world metagenome skimming data from the lichen Lasallia pustulata demonstrates the applicability of twin sets for guiding method selection. Furthermore, it reveals that the assembly outcome for the photobiont Trebouxia sp. falls behind the a priori expectation given the simulations. Although the underlying reasons remain still unclear, this highlights that further studies on this organism require special attention during sequence data generation and downstream analysis.
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Affiliation(s)
- Bastian Greshake
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
| | - Simonida Zehr
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Anlage 25, D-60325, Frankfurt, Germany
| | - Anjuli Meiser
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberg Anlage 25, D-60325, Frankfurt, Germany.,Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
| | - Ingo Ebersberger
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue Str. 13, D-60438, Frankfurt, Germany
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104
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Cernava T, Müller H, Aschenbrenner IA, Grube M, Berg G. Analyzing the antagonistic potential of the lichen microbiome against pathogens by bridging metagenomic with culture studies. Front Microbiol 2015; 6:620. [PMID: 26157431 PMCID: PMC4476105 DOI: 10.3389/fmicb.2015.00620] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 06/08/2015] [Indexed: 02/01/2023] Open
Abstract
Naturally occurring antagonists toward pathogens play an important role to avoid pathogen outbreaks in ecosystems, and they can be applied as biocontrol agents for crops. Lichens present long-living symbiotic systems continuously exposed to pathogens. To analyze the antagonistic potential in lichens, we studied the bacterial community active against model bacteria and fungi by an integrative approach combining isolate screening, omics techniques, and high resolution mass spectrometry. The highly diverse microbiome of the lung lichen [Lobaria pulmonaria (L.) Hoffm.] included an abundant antagonistic community dominated by Stenotrophomonas, Pseudomonas, and Burkholderia. While antagonists represent 24.5% of the isolates, they were identified with only 7% in the metagenome; which means that they were overrepresented in the culturable fraction. Isolates of the dominant antagonistic genus Stenotrophomonas produced spermidine as main bioactive component. Moreover, spermidine-related genes, especially for the transport, were identified in the metagenome. The majority of hits identified belonged to Alphaproteobacteria, while Stenotrophomonas-specific spermidine synthases were not present in the dataset. Evidence for plant growth promoting effects was found for lichen-associated strains of Stenotrophomonas. Linking of metagenomic and culture data was possible but showed partly contradictory results, which required a comparative assessment. However, we have shown that lichens are important reservoirs for antagonistic bacteria, which open broad possibilities for biotechnological applications.
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Affiliation(s)
- Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology Graz, Austria
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology Graz, Austria
| | - Ines A Aschenbrenner
- Institute of Environmental Biotechnology, Graz University of Technology Graz, Austria ; Institute of Plant Sciences, University of Graz Graz, Austria
| | - Martin Grube
- Institute of Plant Sciences, University of Graz Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology Graz, Austria
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