1
|
Ikeda S, Okazaki K, Takahashi H, Tsurumaru H, Minamisawa K. Seasonal Shifts in Bacterial Community Structures in the Lateral Root of Sugar Beet Grown in an Andosol Field in Japan. Microbes Environ 2023; 38. [PMID: 36754423 PMCID: PMC10037095 DOI: 10.1264/jsme2.me22071] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
To investigate functional plant growth-promoting rhizobacteria in sugar beet, seasonal shifts in bacterial community structures in the lateral roots of sugar beet were examined using amplicon sequencing ana-lyses of the 16S rRNA gene. Shannon and Simpson indexes significantly increased between June and July, but did not significantly differ between July and subsequent months (August and September). A weighted UniFrac principal coordinate ana-lysis grouped bacterial samples into four clusters along with PC1 (43.8%), corresponding to the four sampling months in the order of sampling dates. Taxonomic ana-lyses revealed that bacterial diversity in the lateral roots was exclusively dominated by three phyla (Actinobacteria, Bacteroidetes, and Proteobacteria) in all samples examined. At the lower taxonomic levels, the dominant taxa were roughly classified into three groups. Therefore, the relative abundances of seven dominant genera (Janthinobacterium, Kribbella, Pedobacter, Rhodanobacter, Sphingobium, Sphingopyxis, and Streptomyces) were the highest in June and gradually decreased as sugar beet grew. The relative abundances of eight taxa (Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Novosphingobium, Phyllobacteriaceae, Pseudomonas, Rhizobiaceae, and Sphingomonas) were mainly high in July and/or August. The relative abundances of six taxa (unclassified Comamonadaceae, Cytophagaceae, unclassified Gammaproteobacteria, Haliangiaceae, unclassified Myxococcales, and Sinobacteraceae) were the highest in September. Among the dominant taxa, 12 genera (Amycolatopsis, Bradyrhizobium, Caulobacter, Devosia, Flavobacterium, Janthinobacterium, Kribbella, Kutzneria, Pedobacter, Rhizobium, Rhodanobacter, and Steroidobacter) were considered to be candidate groups of plant growth-promoting bacteria based on their previously reported beneficial traits as biopesticides and/or biofertilizers.
Collapse
Affiliation(s)
- Seishi Ikeda
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
| | - Kazuyuki Okazaki
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
| | - Hiroyuki Takahashi
- Memuro Research Station, Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
| | | | | |
Collapse
|
2
|
Wolfgang A, Temme N, Tilcher R, Berg G. Understanding the sugar beet holobiont for sustainable agriculture. Front Microbiol 2023; 14:1151052. [PMID: 37138624 PMCID: PMC10149816 DOI: 10.3389/fmicb.2023.1151052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
The importance of crop-associated microbiomes for the health and field performance of plants has been demonstrated in the last decades. Sugar beet is the most important source of sucrose in temperate climates, and-as a root crop-yield heavily depends on genetics as well as on the soil and rhizosphere microbiomes. Bacteria, fungi, and archaea are found in all organs and life stages of the plant, and research on sugar beet microbiomes contributed to our understanding of the plant microbiome in general, especially of microbiome-based control strategies against phytopathogens. Attempts to make sugar beet cultivation more sustainable are increasing, raising the interest in biocontrol of plant pathogens and pests, biofertilization and -stimulation as well as microbiome-assisted breeding. This review first summarizes already achieved results on sugar beet-associated microbiomes and their unique traits, correlating to their physical, chemical, and biological peculiarities. Temporal and spatial microbiome dynamics during sugar beet ontogenesis are discussed, emphasizing the rhizosphere formation and highlighting knowledge gaps. Secondly, potential or already tested biocontrol agents and application strategies are discussed, providing an overview of how microbiome-based sugar beet farming could be performed in the future. Thus, this review is intended as a reference and baseline for further sugar beet-microbiome research, aiming to promote investigations in rhizosphere modulation-based biocontrol options.
Collapse
Affiliation(s)
- Adrian Wolfgang
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Nora Temme
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Microbiome Biotechnology Department, Leibniz-Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- *Correspondence: Gabriele Berg
| |
Collapse
|
3
|
Safara S, Harighi B, Bahramnejad B, Ahmadi S. Antibacterial Activity of Endophytic Bacteria Against Sugar Beet Root Rot Agent by Volatile Organic Compound Production and Induction of Systemic Resistance. Front Microbiol 2022; 13:921762. [PMID: 35722285 PMCID: PMC9201493 DOI: 10.3389/fmicb.2022.921762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
The volatile organic compounds (VOCs) produced by endophytic bacteria have a significant role in the control of phytopathogens. In this research, the VOCs produced by the endophytic bacteria Streptomyces sp. B86, Pantoea sp. Dez632, Pseudomonas sp. Bt851, and Stenotrophomonas sp. Sh622 isolated from healthy sugar beet (Beta vulgaris) and sea beet (Beta maritima) were evaluated for their effects on the virulence traits of Bacillus pumilus Isf19, the causal agent of harvested sugar beet root rot disease. The gas chromatographymass spectrometry (GC-MS) analysis revealed that B86, Dez632, Bt851, and Sh622 produced 15, 28, 30, and 20 VOCs, respectively, with high quality. All antagonistic endophytic bacteria produced VOCs that significantly reduced soft root symptoms and inhibited the growth of B. pumilus Isf19 at different levels. The VOCs produced by endophytic bacteria significantly reduced swarming, swimming, and twitching motility by B. pumilus Isf19, which are important to pathogenicity. Our results revealed that VOCs produced by Sh622 and Bt851 significantly reduced attachment of B. pumilus Isf19 cells to sugar beetroots, and also all endophytic bacteria tested significantly reduced chemotaxis motility of the pathogen toward root extract. The VOCs produced by Dez632 and Bt851 significantly upregulated the expression levels of defense genes related to soft rot resistance. Induction of PR1 and NBS-LRR2 genes in sugar beetroot slices suggests the involvement of SA and JA pathways, respectively, in the induction of resistance against pathogen attack. Based on our results, the antibacterial VOCs produced by endophytic bacteria investigated in this study can reduce soft rot incidence.
Collapse
Affiliation(s)
- Somayeh Safara
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Behrouz Harighi
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Bahman Bahramnejad
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Slahadin Ahmadi
- Department of Medical Physiology and Pharmacology, School of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| |
Collapse
|
4
|
Spanner R, Neubauer J, Heick TM, Grusak MA, Hamilton O, Rivera-Varas V, de Jonge R, Pethybridge S, Webb KM, Leubner-Metzger G, Secor GA, Bolton MD. Seedborne Cercospora beticola Can Initiate Cercospora Leaf Spot from Sugar Beet ( Beta vulgaris) Fruit Tissue. PHYTOPATHOLOGY 2022; 112:1016-1028. [PMID: 34844416 DOI: 10.1094/phyto-03-21-0113-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cercospora leaf spot (CLS) is a globally important disease of sugar beet (Beta vulgaris) caused by the fungus Cercospora beticola. Long-distance movement of C. beticola has been indirectly evidenced in recent population genetic studies, suggesting potential dispersal via seed. Commercial sugar beet "seed" consists of the reproductive fruit (true seed surrounded by maternal pericarp tissue) coated in artificial pellet material. In this study, we confirmed the presence of viable C. beticola in sugar beet fruit for 10 of 37 tested seed lots. All isolates harbored the G143A mutation associated with quinone outside inhibitor resistance, and 32 of 38 isolates had reduced demethylation inhibitor sensitivity (EC50 > 1 µg/ml). Planting of commercial sugar beet seed demonstrated the ability of seedborne inoculum to initiate CLS in sugar beet. C. beticola DNA was detected in DNA isolated from xylem sap, suggesting the vascular system is used to systemically colonize the host. We established nuclear ribosomal internal transcribed spacer region amplicon sequencing using the MinION platform to detect fungi in sugar beet fruit. Fungal sequences from 19 different genera were identified from 11 different sugar beet seed lots, but Fusarium, Alternaria, and Cercospora were consistently the three most dominant taxa, comprising an average of 93% relative read abundance over 11 seed lots. We also present evidence that C. beticola resides in the pericarp of sugar beet fruit rather than the true seed. The presence of seedborne inoculum should be considered when implementing integrated disease management strategies for CLS of sugar beet in the future.
Collapse
Affiliation(s)
- Rebecca Spanner
- Edward T. Schafer Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service, Fargo, ND, U.S.A
- Department of Plant Pathology, North Dakota State University, Fargo, ND, U.S.A
| | - Jonathan Neubauer
- Edward T. Schafer Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service, Fargo, ND, U.S.A
| | - Thies M Heick
- Institute for Agroecology, Aarhus University, Slagelse, Denmark
| | - Michael A Grusak
- Edward T. Schafer Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service, Fargo, ND, U.S.A
| | - Olivia Hamilton
- Edward T. Schafer Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service, Fargo, ND, U.S.A
- Department of Plant Pathology, North Dakota State University, Fargo, ND, U.S.A
| | | | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Sarah Pethybridge
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, U.S.A
| | - Kimberley M Webb
- Soil Management and Sugar Beet Research Unit, United States Department of Agriculture-Agricultural Research Service, Fort Collins, CO, U.S.A
| | | | - Gary A Secor
- Department of Plant Pathology, North Dakota State University, Fargo, ND, U.S.A
| | - Melvin D Bolton
- Edward T. Schafer Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service, Fargo, ND, U.S.A
- Department of Plant Pathology, North Dakota State University, Fargo, ND, U.S.A
| |
Collapse
|
5
|
Oni FE, Esmaeel Q, Onyeka JT, Adeleke R, Jacquard C, Clement C, Gross H, Ait Barka E, Höfte M. Pseudomonas Lipopeptide-Mediated Biocontrol: Chemotaxonomy and Biological Activity. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27020372. [PMID: 35056688 PMCID: PMC8777863 DOI: 10.3390/molecules27020372] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/29/2021] [Accepted: 01/05/2022] [Indexed: 12/14/2022]
Abstract
Pseudomonas lipopeptides (Ps-LPs) play crucial roles in bacterial physiology, host–microbe interactions and plant disease control. Beneficial LP producers have mainly been isolated from the rhizosphere, phyllosphere and from bulk soils. Despite their wide geographic distribution and host range, emerging evidence suggests that LP-producing pseudomonads and their corresponding molecules display tight specificity and follow a phylogenetic distribution. About a decade ago, biocontrol LPs were mainly reported from the P. fluorescens group, but this has drastically advanced due to increased LP diversity research. On the one hand, the presence of a close-knit relationship between Pseudomonas taxonomy and the molecule produced may provide a startup toolbox for the delineation of unknown LPs into existing (or novel) LP groups. Furthermore, a taxonomy–molecule match may facilitate decisions regarding antimicrobial activity profiling and subsequent agricultural relevance of such LPs. In this review, we highlight and discuss the production of beneficial Ps-LPs by strains situated within unique taxonomic groups and the lineage-specificity and coevolution of this relationship. We also chronicle the antimicrobial activity demonstrated by these biomolecules in limited plant systems compared with multiple in vitro assays. Our review further stresses the need to systematically elucidate the roles of diverse Ps-LP groups in direct plant–pathogen interactions and in the enhancement of plant innate immunity.
Collapse
Affiliation(s)
- Feyisara Eyiwumi Oni
- Université de Reims Champagne Ardenne, Unité de Recherche RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Q.E.); (C.J.); (C.C.); (E.A.B.)
- Department of Biological Sciences, Faculty of Science, Anchor University, Ayobo P.M.B 00001, Lagos State, Nigeria
- Unit for Environmental Sciences and Management, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom 2520, South Africa;
- Correspondence:
| | - Qassim Esmaeel
- Université de Reims Champagne Ardenne, Unité de Recherche RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Q.E.); (C.J.); (C.C.); (E.A.B.)
| | - Joseph Tobias Onyeka
- Plant Pathology Unit, National Root Crops Research Institute (NRCRI), Umudike 440001, Abia State, Nigeria;
| | - Rasheed Adeleke
- Unit for Environmental Sciences and Management, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom 2520, South Africa;
| | - Cedric Jacquard
- Université de Reims Champagne Ardenne, Unité de Recherche RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Q.E.); (C.J.); (C.C.); (E.A.B.)
| | - Christophe Clement
- Université de Reims Champagne Ardenne, Unité de Recherche RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Q.E.); (C.J.); (C.C.); (E.A.B.)
| | - Harald Gross
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tubingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany;
| | - Essaid Ait Barka
- Université de Reims Champagne Ardenne, Unité de Recherche RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Q.E.); (C.J.); (C.C.); (E.A.B.)
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium;
| |
Collapse
|
6
|
Sneha GR, Swarnalakshmi K, Sharma M, Reddy K, Bhoumik A, Suman A, Kannepalli A. Soil type influence nutrient availability, microbial metabolic diversity, eubacterial and diazotroph abundance in chickpea rhizosphere. World J Microbiol Biotechnol 2021; 37:167. [PMID: 34468874 DOI: 10.1007/s11274-021-03132-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 08/18/2021] [Indexed: 11/30/2022]
Abstract
Rhizosphere microbial communities are dynamic and play a crucial role in diverse biochemical processes and nutrient cycling. Soil type and cultivar modulate the composition of rhizosphere microbial communities. Changes in the community composition significantly alter microbial function and ecological process. We examined the influence of soil type on eubacterial and diazotrophic community abundance and microbial metabolic potential in chickpea (cv. BG 372 and cv. BG 256) rhizosphere. The total eubacterial and diazotrophic community as estimated through 16 S rDNA and nifH gene copy numbers using qPCR showed the soil type influence with clear rhizosphere effect on gene abundance. PLFA study has shown the variation in microbial community structure with different soil types. Differential influence of soil types and cultivar on the ratio of Gram positive to Gram negative bacteria was observed with most rhizosphere soils corresponding to higher ratios than bulk soil. The rhizosphere microbial activities (urease, dehydrogenase, alkaline phosphatase and beta-glucosidase) were also assessed as an indicator of microbial metabolic diversity. Principal component analysis and K-means non-hierarchical cluster mapping grouped soils into three categories, each having different soil enzyme activity or edaphic drivers. Soil type and cultivar influence on average substrate utilization pattern analyzed through community level physiological profiling (CLPP) was higher for rhizosphere soils than bulk soils. The soil nutrient studies revealed that both soil type and cultivar influenced the available N, P, K and organic carbon content of rhizosphere soil. Our study signifies that soil type and cultivar jointly influenced soil microbial community abundance and their metabolic potential in chickpea rhizosphere.
Collapse
Affiliation(s)
- G R Sneha
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Meenakshi Sharma
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Kedharnath Reddy
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Arpan Bhoumik
- ICAR-IndianAgricultural Statistical Research Institute, New Delhi, 110012, India
| | - Archna Suman
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Annapurna Kannepalli
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| |
Collapse
|
7
|
Bacterial community analysis on Sclerotium-suppressive soil. Arch Microbiol 2021; 203:4539-4548. [PMID: 34152425 DOI: 10.1007/s00203-021-02426-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 10/21/2022]
Abstract
Difficulties in controlling the soil-borne plant pathogenic fungus Sclerotium rolfsii favoured the analysis of its suppressive soil for better understanding. In the present study, culture-independent molecular technique was used to analyse the bacterial communities of suppressive soil and conducive soil. Hence, metagenomic DNAs from both kinds of soils were directly extracted and their sequence polymorphism was analysed by targeting hypervariable domains, V4 + V5, of the 16S rRNA gene. The results of 16S rRNA gene-driven bacterial community diversity analysis along with soil physicochemical and biological properties clearly discriminated S. rolfsii suppressive soil from conducive soil. The dominant phylogenetic group of suppressive soil is Actinobacteria followed by Proteobacteria. The other groups include Acidobacteria, Firmicutes and Cyanobacteria. In contrast, conducive soil had very few Actinobacterial sequences and was dominated by Gamma- and Betaproteobacteria. Based on the relative proportion of different bacterial communities, their diversity and species richness were observed more in suppressive soil than in conducive soil. The present study identifies the dominant bacterial community which shares S. rolfsii suppressiveness.
Collapse
|
8
|
Leiva D, Fernández-Mendoza F, Acevedo J, Carú M, Grube M, Orlando J. The Bacterial Community of the Foliose Macro-lichen Peltigera frigida Is More than a Mere Extension of the Microbiota of the Subjacent Substrate. MICROBIAL ECOLOGY 2021; 81:965-976. [PMID: 33404820 DOI: 10.1007/s00248-020-01662-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Lichens host highly diverse microbial communities, with bacteria being one of the most explored groups in terms of their diversity and functioning. These bacteria could partly originate from symbiotic propagules developed by many lichens and, perhaps more commonly and depending on environmental conditions, from different sources of the surroundings. Using the narrowly distributed species Peltigera frigida as an object of study, we propose that bacterial communities in these lichens are different from those in their subjacent substrates, even if some taxa might be shared. Ten terricolous P. frigida lichens and their substrates were sampled from forested sites in the Coyhaique National Reserve, located in an understudied region in Chile. The mycobiont identity was confirmed using partial 28S and ITS sequences. Besides, 16S fragments revealed that mycobionts were associated with the same cyanobacterial haplotype. From both lichens and substrates, Illumina 16S amplicon sequencing was performed using primers that exclude cyanobacteria. In lichens, Proteobacteria was the most abundant phylum (37%), whereas soil substrates were dominated by Acidobacteriota (39%). At lower taxonomic levels, several bacterial groups differed in relative abundance among P. frigida lichens and their substrates, some of them being highly abundant in lichens but almost absent in substrates, like Sphingomonas (8% vs 0.2%), and others enriched in lichens, as an unassigned genus of Chitinophagaceae (10% vs 2%). These results reinforce the idea that lichens would carry some components of their microbiome when propagating, but they also could acquire part of their bacterial community from the substrates.
Collapse
Affiliation(s)
- Diego Leiva
- Faculty of Sciences, Department of Ecological Sciences, Universidad de Chile, Santiago, Chile
- Institute of Biology, University of Graz, Graz, Austria
| | | | - José Acevedo
- Faculty of Sciences, Department of Ecological Sciences, Universidad de Chile, Santiago, Chile
| | - Margarita Carú
- Faculty of Sciences, Department of Ecological Sciences, Universidad de Chile, Santiago, Chile
| | - Martin Grube
- Institute of Biology, University of Graz, Graz, Austria
| | - Julieta Orlando
- Faculty of Sciences, Department of Ecological Sciences, Universidad de Chile, Santiago, Chile.
| |
Collapse
|
9
|
Cerecetto V, Smalla K, Nesme J, Garaycochea S, Fresia P, Sørensen SJ, Babin D, Leoni C. Reduced tillage, cover crops and organic amendments affect soil microbiota and improve soil health in Uruguayan vegetable farming systems. FEMS Microbiol Ecol 2021; 97:6129805. [PMID: 33547893 DOI: 10.1093/femsec/fiab023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
Conventional tillage and mineral fertilization (CTMF) jeopardize soil health in conventional vegetable production systems. Using a field experiment established in Uruguay in 2012, we aimed to compare the soil restoration potential of organic fertilization (compost and poultry manure) combined with conventional tillage and cover crop incorporated into the soil (CTOF) or with reduced tillage and the use of cover crop as mulch (RTOF). In 2017, table beet was cultivated under CTMF, CTOF and RTOF, and yields, soil aggregate composition and nutrients, as well as soil and table beet rhizosphere microbiota (here: bacteria and archaea) were evaluated. Microbiota was studied by high-throughput sequencing of 16S rRNA gene fragments amplified from total community DNA. RTOF exhibited higher soil aggregation, soil organic C, nutrient availability and microbial alpha-diversity than CTMF, and became more similar to an adjacent natural undisturbed site. The soil microbiota was strongly shaped by the fertilization source which was conveyed to the rhizosphere and resulted in differentially abundant taxa. However, 229 amplicon sequencing variants were found to form the core table beet rhizosphere microbiota shared among managements. In conclusion, our study shows that after only 5 years of implementation, RTOF improves soil health under intensive vegetable farming systems.
Collapse
Affiliation(s)
- Victoria Cerecetto
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany.,Instituto Nacional de Investigación Agropecuaria (INIA), Programa de Producción y Sustentabilidad Ambiental, Estación Experimental INIA Las Brujas, Ruta 48 Km 10, 90200 Rincón del Colorado, Canelones, Uruguay
| | - Kornelia Smalla
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Joseph Nesme
- University of Copenhagen, Department of Biology, Section of Microbiology, Nørregade 10, 1165 Copenhagen, Denmark
| | - Silvia Garaycochea
- Instituto Nacional de Investigación Agropecuaria (INIA), Programa de Producción y Sustentabilidad Ambiental, Estación Experimental INIA Las Brujas, Ruta 48 Km 10, 90200 Rincón del Colorado, Canelones, Uruguay
| | - Pablo Fresia
- Unidad Mixta Institut Pasteur de Montevideo + Instituto Nacional de Investigación Agropecuaria INIA (UMPI), Mataojo 2020, 11400 Montevideo, Uruguay
| | - Søren Johannes Sørensen
- University of Copenhagen, Department of Biology, Section of Microbiology, Nørregade 10, 1165 Copenhagen, Denmark
| | - Doreen Babin
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Carolina Leoni
- Instituto Nacional de Investigación Agropecuaria (INIA), Programa de Producción y Sustentabilidad Ambiental, Estación Experimental INIA Las Brujas, Ruta 48 Km 10, 90200 Rincón del Colorado, Canelones, Uruguay
| |
Collapse
|
10
|
Sacristán-Pérez-Minayo G, López-Robles DJ, Rad C, Miranda-Barroso L. Microbial Inoculation for Productivity Improvements and Potential Biological Control in Sugar Beet Crops. FRONTIERS IN PLANT SCIENCE 2020; 11:604898. [PMID: 33414799 PMCID: PMC7783361 DOI: 10.3389/fpls.2020.604898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Used mainly for sucrose production, sugar beet is one of the most important crops in Castilla y León (Spain). Several studies have demonstrated the benefits of microorganisms in different crop management programs, among which Plant Growth Promoting Rhizobacteria (PGPR). This research aims to assess the beneficial effects of two PGPRs strains (Pseudomonas fluorescens Pf0-1 and Pseudomonas chlororaphis CECT 462) on sugar beet (Beta vulgaris) production. Three treatments: a PGPRs co-inoculation assay of untreated seeds without any chemical treatment (TB), a conventional treatment with commercial seeds and fungicide application (TT); and a control with seeds without protective coating, bacterial inoculation and chemical treatment (ST). The efficacy of PGPRs inoculation on sugar beet production was determined measuring periodically the photosynthetic status of plants, and the final yield and quality of tubers. Aerial and root plant biomass, maximum beet perimeter, polarization, and sugar values of the sugar beet plants inoculated with PGPRs showed higher values and significant differences to sugar beet subjected to other treatments. We could see that PGPRs inoculation (TB treatment) produced significant differences in the quantum yield of PSII (ΦPSII). TB showed the highest value for ΦPSII and the NPQ (non-photochemical quenching), the lowest value, even though the PSII (maximum quantum yield of photosystem II) was very similar in all treatments. The two assayed PGPR strains triggered a significant increase in sugar beet production yield and quality. PGPRs inoculation techniques could be used in different crops and they could be applied as biofertilizers, improving the agricultural production.
Collapse
Affiliation(s)
| | | | - Carlos Rad
- Edaphology and Agricultural Sciences Section, Faculty of Sciences, University of Burgos, Burgos, Spain
| | | |
Collapse
|
11
|
Kusstatscher P, Wicaksono WA, Bergna A, Cernava T, Bergau N, Tissier A, Hause B, Berg G. Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato. ENVIRONMENTAL MICROBIOME 2020; 15:17. [PMID: 33902724 PMCID: PMC8067393 DOI: 10.1186/s40793-020-00364-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/29/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND The plant phyllosphere is a well-studied habitat characterized by low nutrient availability and high community dynamics. In contrast, plant trichomes, known for their production of a large number of metabolites, are a yet unexplored habitat for microbes. We analyzed the phyllosphere as well as trichomes of two tomato genotypes (Solanum lycopersicum LA4024, S. habrochaites LA1777) by targeting bacterial 16S rRNA gene fragments. RESULTS Leaves, leaves without trichomes, and trichomes alone harbored similar abundances of bacteria (108-109 16S rRNA gene copy numbers per gram of sample). In contrast, bacterial diversity was found significantly increased in trichome samples (Shannon index: 4.4 vs. 2.5). Moreover, the community composition was significantly different when assessed with beta diversity analysis and corresponding statistical tests. At the bacterial class level, Alphaproteobacteria (23.6%) were significantly increased, whereas Bacilli (8.6%) were decreased in trichomes. The bacterial family Sphingomonadacea (8.4%) was identified as the most prominent, trichome-specific feature; Burkholderiaceae and Actinobacteriaceae showed similar patterns. Moreover, Sphingomonas was identified as a central element in the core microbiome of trichome samples, while distinct low-abundant bacterial families including Hymenobacteraceae and Alicyclobacillaceae were exclusively found in trichome samples. Niche preferences were statistically significant for both genotypes and genotype-specific enrichments were further observed. CONCLUSION Our results provide first evidence of a highly specific trichome microbiome in tomato and show the importance of micro-niches for the structure of bacterial communities on leaves. These findings provide further clues for breeding, plant pathology and protection as well as so far unexplored natural pathogen defense strategies.
Collapse
Affiliation(s)
- Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Alessandro Bergna
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Nick Bergau
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Bettina Hause
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| |
Collapse
|
12
|
Li M, Yang F, Wu X, Yan H, Liu Y. Effects of continuous cropping of sugar beet (Beta vulgaris L.) on its endophytic and soil bacterial community by high-throughput sequencing. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01583-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
As a major sugar crop, sugar beet (Beta vulgaris L.) plays an important role in both sugar industry and feed products. Soil, acts as the substrate for plant growth, provides not only nutrients to plants but also a habitat for soil microorganisms. High soil fertility and good micro-ecological environment are basic requirements for obtaining high-yield and high-sugar sugar beets. This study aimed at exploring the effects of continuous cropping of sugar beet on its endophytic, soil bacterial community structures, and diversity.
Methods
Using high-throughput sequencing technology which is based on Illumina Hiseq 2500 platform, the seeds of sugar beet (sample S), non-continuous cropping sugar beet (sample Bn) with its rhizosphere soil (sample Sr), and planting soil (sample Sn), continuous cropping sugar beet (sample Bc) with its planting soil (sample Sc), were collected as research materials.
Result
The results showed that the bacterial communities and diversity in each sample exhibited different OTU richness; 67.9% and 63.8% of total endophytic OTUs from samples Bc and Bn shared with their planting soil samples Sc and Sn, while sharing 36.4% and 31.8% of total OTUs with their seed sample S. Pseudarthrobacter and Bacillus as the two major groups coexisted among all samples, and other shared groups belonged to Achromobacter, Sphingomonas, Novosphingobium, Terribacillus, Planococcus, Paracoccus, Nesterenkonia, Halomonas, and Nocardioides. Genera, including Pantoea, Pseudomonas, Stenotrophomonas, Weissella, Leuconostoc, and Acinetobacter, were detected in each sugar beet sample but not in their corresponding soil sample. In this study, the bacterial community structures and soil compositions have significantly changed before and after continuous cropping; however, the effects of continuous cropping on endophytic bacteria of sugar beet were not statistically significant.
Conclusion
This study would provide a scientific basis and reference information for in-depth research on correlations between continuous cropping and micro-ecological environment of sugar beet plant.
Collapse
|
13
|
Wolfgang A, Zachow C, Müller H, Grand A, Temme N, Tilcher R, Berg G. Understanding the Impact of Cultivar, Seed Origin, and Substrate on Bacterial Diversity of the Sugar Beet Rhizosphere and Suppression of Soil-Borne Pathogens. FRONTIERS IN PLANT SCIENCE 2020; 11:560869. [PMID: 33101330 PMCID: PMC7554574 DOI: 10.3389/fpls.2020.560869] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/02/2020] [Indexed: 05/21/2023]
Abstract
The rhizosphere microbiome is crucial for plant health, especially for preventing roots from being infected by soil-borne pathogens. Microbiota-mediated pathogen response in the soil-root interface may hold the key for microbiome-based control strategies of phytopathogens. We studied the pathosystem sugar beet-late sugar beet root rot caused by Rhizoctonia solani in an integrative design of combining in vitro and in vivo (greenhouse and field) trials. We used five different cultivars originating from two propagation sites (France, Italy) with different degrees of susceptibility towards R. solani (two susceptible, one moderately tolerant and two cultivars with partial resistance). Analyzing bacterial communities in seeds and roots grown under different conditions by 16S rRNA amplicon sequencing, we found site-, cultivar-, and microhabitat-specific amplicon sequences variants (ASV) as well as a seed core microbiome shared between all sugar beet cultivars (121 ASVs representing 80%-91% relative abundance). In general, cultivar-specific differences in the bacterial communities were more pronounced in seeds than in roots. Seeds of Rhizoctonia-tolerant cultivars contain a higher relative abundance of the genera Paenibacillus, Kosakonia, and Enterobacter, while Gaiellales, Rhizobiales, and Kosakonia were enhanced in responsive rhizospheres. These results indicate a correlation between bacterial seed endophytes and Rhizoctonia-tolerant cultivars. Root communities are mainly substrate-derived but also comprise taxa exclusively derived from seeds. Interestingly, the signature of Pseudomonas poae Re*1-1-14, a well-studied sugar-beet specific biocontrol agent, was frequently found and in higher relative abundances in Rhizoctonia-tolerant than in susceptible cultivars. For microbiome management, we introduced microbial inoculants (consortia) and microbiome transplants (vermicompost) in greenhouse and field trials; both can modulate the rhizosphere and mediate tolerance towards late sugar beet root rot. Both, seeds and soil, provide specific beneficial bacteria for rhizosphere assembly and microbiota-mediated pathogen tolerance. This can be translated into microbiome management strategies for plant and ecosystem health.
Collapse
Affiliation(s)
- Adrian Wolfgang
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Graz, Austria
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Christin Zachow
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Graz, Austria
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- BioTenzz GmbH, Graz, Austria
| | | | - Nora Temme
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- *Correspondence: Gabriele Berg,
| |
Collapse
|
14
|
Kusstatscher P, Zachow C, Harms K, Maier J, Eigner H, Berg G, Cernava T. Microbiome-driven identification of microbial indicators for postharvest diseases of sugar beets. MICROBIOME 2019; 7:112. [PMID: 31391094 PMCID: PMC6686572 DOI: 10.1186/s40168-019-0728-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/31/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Sugar loss due to storage rot has a substantial economic impact on the sugar industry. The gradual spread of saprophytic fungi such as Fusarium and Penicillium spp. during storage in beet clamps is an ongoing challenge for postharvest processing. Early detection of shifts in microbial communities in beet clamps is a promising approach for the initiation of targeted countermeasures during developing storage rot. In a combined approach, high-throughput sequencing of bacterial and fungal genetic markers was complemented with cultivation-dependent methods and provided detailed insights into microbial communities colonizing stored roots. These data were used to develop a multi-target qPCR technique for early detection of postharvest diseases. RESULTS The comparison of beet microbiomes from six clamps in Austria and Germany highlighted regional differences; nevertheless, universal indicators of the health status were identified. Apart from a significant decrease in microbial diversity in decaying sugar beets (p ≤ 0.01), a distinctive shift in the taxonomic composition of the overall microbiome was found. Fungal taxa such as Candida and Penicillium together with the gram-positive Lactobacillus were the main disease indicators in the microbiome of decaying sugar beets. In contrast, the genera Plectosphaerella and Vishniacozyma as well as a higher microbial diversity in general were found to reflect the microbiome of healthy beets. Based on these findings, a qPCR-based early detection technique was developed and confirmed a twofold decrease of health indicators and an up to 10,000-fold increase of disease indicators in beet clamps. This was further verified with analyses of the sugar content in storage samples. CONCLUSION By conducting a detailed assessment of temporal microbiome changes during the storage of sugar beets, distinct indicator species were identified that reflect progressing rot and losses in sugar content. The insights generated in this study provide a novel basis to improve current or develop next-generation postharvest management techniques by tracking disease indicators during storage.
Collapse
Affiliation(s)
- Peter Kusstatscher
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Christin Zachow
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| | - Karsten Harms
- Südzucker AG, Maximilianstraße 10, 68165 Mannheim, Germany
| | - Johann Maier
- Südzucker AG, Maximilianstraße 10, 68165 Mannheim, Germany
| | - Herbert Eigner
- Agrana Research & Innovation Center, Josef-Reither-Straße 21 – 23, 3430 Tulln, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
- Roombiotic GmbH, c/o: SciencePark, Stremayrgasse 16/IV, 8010 Graz, Austria
| |
Collapse
|
15
|
Kusstatscher P, Cernava T, Liebminger S, Berg G. Replacing conventional decontamination of hatching eggs with a natural defense strategy based on antimicrobial, volatile pyrazines. Sci Rep 2017; 7:13253. [PMID: 29038499 PMCID: PMC5643471 DOI: 10.1038/s41598-017-13579-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/25/2017] [Indexed: 11/20/2022] Open
Abstract
The treatment of hatching eggs relies on classic yet environmentally harmful decontamination methods such as formaldehyde fumigation. We evaluated bacteria-derived volatiles as a replacement within a fundamentally novel approach based on volatile organic compounds (VOCs), which are naturally involved in microbial communication and antagonism due to their high antimicrobial efficiency. Pyrazine (5-isobutyl-2,3-dimethylpyrazine) was applied passively and actively in prototypes of a pre-industry-scale utilization. Altogether, pyrazine decontamination rates of up to 99.6% were observed, which is comparable to formaldehyde fumigation. While active evaporation was highly efficient in all experiments, passive treatment showed reducing effects in two of four tested groups only. These results were confirmed by visualization using LIVE/DEAD staining microscopy. The natural egg shell microbiome was characterized by an unexpected bacterial diversity of Pseudomonadales, Enterobacteriales, Sphingomonadales, Streptophyta, Burkholderiales, Actinomycetales, Xanthomonadales, Rhizobiales, Bacillales, Clostridiales, Lactobacillales, and Flavobacteriales members. Interestingly, we found that especially low pyrazine concentrations lead to a microbiome shift, which can be explained by varying antimicrobial effects on different microorganisms. Micrococcus spp., which are linked to embryonic death and reduced hatchability, was found to be highly sensitive to pyrazines. Taken together, pyrazine application was shown to be a promising, environmentally friendly alternative for fumigation treatments of hatchery eggs.
Collapse
Affiliation(s)
- Peter Kusstatscher
- ACIB GmbH, Petersgasse 14, 8010, Graz, Austria
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
| | - Tomislav Cernava
- ACIB GmbH, Petersgasse 14, 8010, Graz, Austria.
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria.
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
| |
Collapse
|
16
|
Hartman K, van der Heijden MG, Roussely-Provent V, Walser JC, Schlaeppi K. Deciphering composition and function of the root microbiome of a legume plant. MICROBIOME 2017; 5:2. [PMID: 28095877 PMCID: PMC5240445 DOI: 10.1186/s40168-016-0220-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/08/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND Diverse assemblages of microbes colonize plant roots and collectively function as a microbiome. Earlier work has characterized the root microbiomes of numerous plant species, but little information is available for legumes despite their key role in numerous ecosystems including agricultural systems. Legumes form a root nodule symbiosis with nitrogen-fixing Rhizobia bacteria and thereby account for large, natural nitrogen inputs into soils. Here, we describe the root bacteria microbiome of the legume Trifolium pratense combining culture-dependent and independent methods. For a functional understanding of individual microbiome members and their impact on plant growth, we began to inoculate root microbiome members alone or in combination to Trifolium roots. RESULTS At a whole-root scale, Rhizobia bacteria accounted for ~70% of the root microbiome. Other enriched members included bacteria from the genera Pantoea, Sphingomonas, Novosphingobium, and Pelomonas. We built a reference stock of 200 bacteria isolates, and we found that they corresponded to ~20% of the abundant root microbiome members. We developed a microcosm system to conduct simplified microbiota inoculation experiments with plants. We observed that while an abundant root microbiome member reduced plant growth when inoculated alone, this negative effect was alleviated if this Flavobacterium was co-inoculated with other root microbiome members. CONCLUSIONS The Trifolium root microbiome was dominated by nutrient-providing Rhizobia bacteria and enriched for bacteria from genera that may provide disease protection. First microbiota inoculation experiments indicated that individual community members can have plant growth compromising activities without being apparently pathogenic, and a more diverse root community can alleviate plant growth compromising activities of its individual members. A trait-based characterization of the reference stock bacteria will permit future microbiota manipulation experiments to decipher overall microbiome functioning and elucidate the biological mechanisms and interactions driving the observed effects. The presented reductionist experimental approach offers countless opportunities for future systematic and functional examinations of the plant root microbiome.
Collapse
Affiliation(s)
- Kyle Hartman
- Plant-Soil Interactions, Agroscope, Institute for Sustainability Sciences, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department for Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Marcel Ga van der Heijden
- Plant-Soil Interactions, Agroscope, Institute for Sustainability Sciences, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department for Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Plant-Microbe Interactions, Institute of Environmental Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | | | | | - Klaus Schlaeppi
- Plant-Soil Interactions, Agroscope, Institute for Sustainability Sciences, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland.
| |
Collapse
|
17
|
Müller CA, Obermeier MM, Berg G. Bioprospecting plant-associated microbiomes. J Biotechnol 2016; 235:171-80. [DOI: 10.1016/j.jbiotec.2016.03.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/17/2016] [Accepted: 03/21/2016] [Indexed: 10/22/2022]
|
18
|
van Overbeek LS, Saikkonen K. Impact of Bacterial-Fungal Interactions on the Colonization of the Endosphere. TRENDS IN PLANT SCIENCE 2016; 21:230-242. [PMID: 26821607 DOI: 10.1016/j.tplants.2016.01.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/15/2015] [Accepted: 01/04/2016] [Indexed: 06/05/2023]
Abstract
Research on different endophyte taxa and the related scientific disciplines have largely developed separately, and comprehensive community-level studies on bacterial and fungal interactions and their importance are lacking. Here, we discuss the transmission modes of bacteria and fungi and the nature of their interactions in the endosphere at both the molecular and physiological level. Mixed-community biofilms in the endosphere may have a role in protecting endophytes against encountered stresses, such as from plant defense systems. However, transmission from static (in biofilms) to free-living (planktonic) forms may be crucial for the exploration of new habitable spaces in plants. Important features previously recognized as plant-microbe interactions or antagonism in endophyte genomes and metagenomes are proposed to have essential roles in the modulation of endophyte communities.
Collapse
Affiliation(s)
- Leonard S van Overbeek
- Wageningen University and Research Centre, Droevendaalsesteeg 1, PO Box 16, 6700AA, Wageningen, The Netherlands.
| | - Kari Saikkonen
- Natural Resources Institute Finland (Luke), Management and Production of Renewable Resources, Itäinen Pitkäkatu 3, 20520 Turku, Finland.
| |
Collapse
|
19
|
Zachow C, Jahanshah G, de Bruijn I, Song C, Ianni F, Pataj Z, Gerhardt H, Pianet I, Lämmerhofer M, Berg G, Gross H, Raaijmakers JM. The Novel Lipopeptide Poaeamide of the Endophyte Pseudomonas poae RE*1-1-14 Is Involved in Pathogen Suppression and Root Colonization. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:800-10. [PMID: 25761208 DOI: 10.1094/mpmi-12-14-0406-r] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Endophytic Pseudomonas poae strain RE*1-1-14 was originally isolated from internal root tissue of sugar beet plants and shown to suppress growth of the fungal pathogen Rhizoctonia solani both in vitro and in the field. To identify genes involved in its biocontrol activity, RE*1-1-14 random mutagenesis and sequencing led to the identification of a nonribosomal peptide synthetase (NRPS) gene cluster predicted to encode a lipopeptide (LP) with a 10-amino-acid peptide moiety. The two unlinked gene clusters consisted of three NRPS genes, designated poaA (cluster 1) and poaB and poaC (cluster 2), spanning approximately 33.7 kb. In silico analysis followed by chemical analyses revealed that the encoded LP, designated poaeamide, is a structurally new member of the orfamide family. Poaeamide inhibited mycelial growth of R. solani and different oomycetes, including Phytophthora capsici, P. infestans, and Pythium ultimum. The novel LP was shown to be essential for swarming motility of strain RE*1-1-14 and had an impact on root colonization of sugar beet seedlings The poaeamide-deficient mutant colonized the rhizosphere and upper plant cortex at higher densities and with more scattered colonization patterns than the wild type. Collectively, these results indicate that Pseudomonas poae RE*1-1-14 produces a structurally new LP that is relevant for its antagonistic activity against soilborne plant pathogens and for colonization of sugar beet roots.
Collapse
Affiliation(s)
- Christin Zachow
- 1 Austrian Centre of Industrial Biotechnology (ACIB GmbH), 8010 Graz, Austria
| | - Ghazaleh Jahanshah
- 2 Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Irene de Bruijn
- 3 Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Chunxu Song
- 3 Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Federica Ianni
- 4 Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis, University of Tübingen
| | - Zoltán Pataj
- 4 Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis, University of Tübingen
| | - Heike Gerhardt
- 4 Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis, University of Tübingen
| | - Isabelle Pianet
- 5 CESAMO-ISM, UMR 5255, CNRS, Université Bordeaux I, 351 Cours de la Libération, F-33405 Talence, France
| | - Michael Lämmerhofer
- 4 Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis, University of Tübingen
| | - Gabriele Berg
- 6 Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria
| | - Harald Gross
- 2 Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Jos M Raaijmakers
- 3 Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Moissl-Eichinger C, Auerbach AK, Probst AJ, Mahnert A, Tom L, Piceno Y, Andersen GL, Venkateswaran K, Rettberg P, Barczyk S, Pukall R, Berg G. Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments. Sci Rep 2015; 5:9156. [PMID: 25778463 PMCID: PMC4361859 DOI: 10.1038/srep09156] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/11/2015] [Indexed: 01/06/2023] Open
Abstract
Space agencies maintain highly controlled cleanrooms to ensure the demands of planetary protection. To study potential effects of microbiome control, we analyzed microbial communities in two particulate-controlled cleanrooms (ISO 5 and ISO 8) and two vicinal uncontrolled areas (office, changing room) by cultivation and 16S rRNA gene amplicon analysis (cloning, pyrotagsequencing, and PhyloChip G3 analysis). Maintenance procedures affected the microbiome on total abundance and microbial community structure concerning richness, diversity and relative abundance of certain taxa. Cleanroom areas were found to be mainly predominated by potentially human-associated bacteria; archaeal signatures were detected in every area. Results indicate that microorganisms were mainly spread from the changing room (68%) into the cleanrooms, potentially carried along with human activity. The numbers of colony forming units were reduced by up to ~400 fold from the uncontrolled areas towards the ISO 5 cleanroom, accompanied with a reduction of the living portion of microorganisms from 45% (changing area) to 1% of total 16S rRNA gene signatures as revealed via propidium monoazide treatment of the samples. Our results demonstrate the strong effects of cleanroom maintenance on microbial communities in indoor environments and can be used to improve the design and operation of biologically controlled cleanrooms.
Collapse
Affiliation(s)
- Christine Moissl-Eichinger
- 1] Institute for Microbiology and Archaea Center, University of Regensburg, Universitaetsstrasse 31, 93053 Regensburg, Germany [2] Medical University Graz, Department of Internal Medicine, Auenbruggerplatz 15, 8036 Graz, Austria [3] BioTechMed Graz, Krenngasse 37, 8010 Graz, Austria
| | - Anna K Auerbach
- Institute for Microbiology and Archaea Center, University of Regensburg, Universitaetsstrasse 31, 93053 Regensburg, Germany
| | - Alexander J Probst
- Institute for Microbiology and Archaea Center, University of Regensburg, Universitaetsstrasse 31, 93053 Regensburg, Germany
| | - Alexander Mahnert
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Lauren Tom
- Lawrence Berkeley National Laboratory, Earth Sciences Division, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Yvette Piceno
- Lawrence Berkeley National Laboratory, Earth Sciences Division, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Gary L Andersen
- Lawrence Berkeley National Laboratory, Earth Sciences Division, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | | | - Petra Rettberg
- German Aerospace Center, Institute of Aerospace Medicine and Radiation Biology, Linder Höhe, 51147 Köln, Germany
| | - Simon Barczyk
- German Aerospace Center, Institute of Aerospace Medicine and Radiation Biology, Linder Höhe, 51147 Köln, Germany
| | - Rüdiger Pukall
- Leibniz Institute DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraβe 7 B, 38124 Braunschweig, Germany
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| |
Collapse
|
22
|
Zachow C, Müller H, Tilcher R, Berg G. Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima-ancestor of all beet crops-and modern sugar beets. Front Microbiol 2014; 5:415. [PMID: 25206350 PMCID: PMC4144093 DOI: 10.3389/fmicb.2014.00415] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 07/22/2014] [Indexed: 02/01/2023] Open
Abstract
The structure and function of the plant microbiome is driven by plant species and prevailing environmental conditions. Effectuated by breeding efforts, modern crops diverge genetically and phenotypically from their wild relatives but little is known about consequences for the associated microbiota. Therefore, we studied bacterial rhizosphere communities associated with the wild beet B. vulgaris ssp. maritima grown in their natural habitat soil from coastal drift lines (CS) and modern sugar beets (Beta vulgaris ssp. vulgaris) cultivated in CS and potting soil (PS) under greenhouse conditions. Analysis of 16S rRNA gene fingerprints and pyrosequencing-based amplicon libraries revealed plant genotype- and soil-specific microbiomes. Wild beet plants harbor distinct operational taxonomic units (OTUs) and a more diverse bacterial community than the domesticated sugar beet plants. Although the rhizospheres of both plant genotypes were dominated by Proteobacteria and Planctomycetes, 37.5% of dominant OTUs were additionally detected in the wild beet rhizosphere. Analysis of the cultivable fraction confirmed these plant genotype-specific differences at functional level. The proportion of isolates displayed in vitro activity against phytopathogens was lower for wild beet (≤45.8%) than for sugar beet (≤57.5%). Conversely, active isolates from the wild beet exhibited stronger ability to cope with abiotic stresses. From all samples, active isolates of Stenotrophomonas rhizophila were frequently identified. In addition, soil type-specific impacts on the composition of bacterial communities were found: Acidobacteria, Chloroflexi, and Planctomycetes were only detected in plants cultivated in CS; whereas Bacteroidetes and Proteobacteria dominated in PS. Overall, in comparison to modern sugar beets, wild beets were associated with taxonomically and functionally distinct microbiomes.
Collapse
Affiliation(s)
- Christin Zachow
- Austrian Center of Industrial Biotechnology (ACIB GmbH) Graz, Austria ; Institute of Environmental Biotechnology, Graz University of Technology Graz, Austria
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology Graz, Austria
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology Graz, Austria
| |
Collapse
|
23
|
Guida M, Cannavacciuolo PL, Cesarano M, Borra M, Biffali E, D’Alessandro R, De Felice B. Microbial diversity of landslide soils assessed by RFLP and SSCP fingerprints. J Appl Genet 2014; 55:403-15. [DOI: 10.1007/s13353-014-0208-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 03/10/2014] [Accepted: 03/24/2014] [Indexed: 11/27/2022]
|
24
|
Blagodatskaya E, Blagodatsky S, Anderson TH, Kuzyakov Y. Microbial growth and carbon use efficiency in the rhizosphere and root-free soil. PLoS One 2014; 9:e93282. [PMID: 24722409 PMCID: PMC3982954 DOI: 10.1371/journal.pone.0093282] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 03/03/2014] [Indexed: 11/18/2022] Open
Abstract
Plant-microbial interactions alter C and N balance in the rhizosphere and affect the microbial carbon use efficiency (CUE)–the fundamental characteristic of microbial metabolism. Estimation of CUE in microbial hotspots with high dynamics of activity and changes of microbial physiological state from dormancy to activity is a challenge in soil microbiology. We analyzed respiratory activity, microbial DNA content and CUE by manipulation the C and nutrients availability in the soil under Beta vulgaris. All measurements were done in root-free and rhizosphere soil under steady-state conditions and during microbial growth induced by addition of glucose. Microorganisms in the rhizosphere and root-free soil differed in their CUE dynamics due to varying time delays between respiration burst and DNA increase. Constant CUE in an exponentially-growing microbial community in rhizosphere demonstrated the balanced growth. In contrast, the CUE in the root-free soil increased more than three times at the end of exponential growth and was 1.5 times higher than in the rhizosphere. Plants alter the dynamics of microbial CUE by balancing the catabolic and anabolic processes, which were decoupled in the root-free soil. The effects of N and C availability on CUE in rhizosphere and root-free soil are discussed.
Collapse
Affiliation(s)
- Evgenia Blagodatskaya
- Soil Science of Temperate Ecosystems, Büsgen-Institute, University of Göttingen, Göttingen, Germany
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Russia
- Agricultural Soil Science, Büsgen-Institute, University of Göttingen, Göttingen, Germany
- * E-mail:
| | - Sergey Blagodatsky
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Russia
- Institute for Plant Production and Agroecology in the Tropics and Subtropics, University of Hohenheim, Stuttgart, Germany
| | | | - Yakov Kuzyakov
- Soil Science of Temperate Ecosystems, Büsgen-Institute, University of Göttingen, Göttingen, Germany
- Agricultural Soil Science, Büsgen-Institute, University of Göttingen, Göttingen, Germany
| |
Collapse
|
25
|
Schmidt R, Köberl M, Mostafa A, Ramadan EM, Monschein M, Jensen KB, Bauer R, Berg G. Effects of bacterial inoculants on the indigenous microbiome and secondary metabolites of chamomile plants. Front Microbiol 2014; 5:64. [PMID: 24600444 PMCID: PMC3928675 DOI: 10.3389/fmicb.2014.00064] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/01/2014] [Indexed: 12/04/2022] Open
Abstract
Plant-associated bacteria fulfill important functions for plant growth and health. However, our knowledge about the impact of bacterial treatments on the host's microbiome and physiology is limited. The present study was conducted to assess the impact of bacterial inoculants on the microbiome of chamomile plants Chamomilla recutita (L.) Rauschert grown in a field under organic management in Egypt. Chamomile seedlings were inoculated with three indigenous Gram-positive strains (Streptomyces subrutilus Wbn2-11, Bacillus subtilis Co1-6, Paenibacillus polymyxa Mc5Re-14) from Egypt and three European Gram-negative strains (Pseudomonas fluorescens L13-6-12, Stenotrophomonas rhizophila P69, Serratia plymuthica 3Re4-18) already known for their beneficial plant-microbe interaction. Molecular fingerprints of 16S rRNA gene as well as real-time PCR analyses did not show statistically significant differences for all applied bacterial antagonists compared to the control. In contrast, a pyrosequencing analysis of the 16S rRNA gene libraries revealed significant differences in the community structure of bacteria between the treatments. These differences could be clearly shown by a shift within the community structure and corresponding beta-diversity indices. Moreover, B. subtilis Co1-6 and P. polymyxa Mc5Re-14 showed an enhancement of the bioactive secondary metabolite apigenin-7-O-glucoside. This indicates a possible new function of bacterial inoculants: to interact with the plant microbiome as well as to influence the plant metabolome.
Collapse
Affiliation(s)
- Ruth Schmidt
- Institute for Environmental Biotechnology, Graz University of Technology Graz, Austria
| | - Martina Köberl
- Institute for Environmental Biotechnology, Graz University of Technology Graz, Austria
| | - Amr Mostafa
- Faculty of Agriculture, SEKEM, Heliopolis University, Ain Shams University Cairo, Egypt
| | - Elshahat M Ramadan
- Faculty of Agriculture, SEKEM, Heliopolis University, Ain Shams University Cairo, Egypt
| | - Marlene Monschein
- Department of Pharmacognosy, Institute of Pharmaceutical Sciences, University of Graz Graz, Austria
| | | | - Rudolf Bauer
- Department of Pharmacognosy, Institute of Pharmaceutical Sciences, University of Graz Graz, Austria
| | - Gabriele Berg
- Institute for Environmental Biotechnology, Graz University of Technology Graz, Austria
| |
Collapse
|
26
|
Köberl M, Schmidt R, Ramadan EM, Bauer R, Berg G. The microbiome of medicinal plants: diversity and importance for plant growth, quality and health. Front Microbiol 2013; 4:400. [PMID: 24391634 PMCID: PMC3868918 DOI: 10.3389/fmicb.2013.00400] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 12/05/2013] [Indexed: 01/22/2023] Open
Abstract
Past medicinal plant research primarily focused on bioactive phytochemicals, however, the focus is currently shifting due to the recognition that a significant number of phytotherapeutic compounds are actually produced by associated microbes or through interaction with their host. Medicinal plants provide an enormous bioresource of potential use in modern medicine and agriculture, yet their microbiome is largely unknown. The objective of this review is (i) to introduce novel insights into the plant microbiome with a focus on medicinal plants, (ii) to provide details about plant- and microbe-derived ingredients of medicinal plants, and (iii) to discuss possibilities for plant growth promotion and plant protection for commercial cultivation of medicinal plants. In addition, we also present a case study performed both to analyse the microbiome of three medicinal plants (Matricaria chamomilla L., Calendula officinalis L., and Solanum distichum Schumach. and Thonn.) cultivated on organically managed Egyptian desert farm and to develop biological control strategies. The soil microbiome of the desert ecosystem was comprised of a high abundance of Gram-positive bacteria of prime importance for pathogen suppression under arid soil conditions. For all three plants, we observed a clearly plant-specific selection of the microbes as well as highly specific diazotrophic communities that overall identify plant species as important drivers in structural and functional diversity. Lastly, native Bacillus spec. div. strains were able to promote plant growth and elevate the plants’ flavonoid production. These results underline the numerous links between the plant-associated microbiome and the plant metabolome.
Collapse
Affiliation(s)
- Martina Köberl
- Institute for Environmental Biotechnology, Graz University of Technology Graz, Austria
| | - Ruth Schmidt
- Institute for Environmental Biotechnology, Graz University of Technology Graz, Austria
| | - Elshahat M Ramadan
- Faculty of Agriculture, SEKEM, Heliopolis University, Ain Shams University Cairo, Egypt
| | - Rudolf Bauer
- Department of Pharmacognosy, Institute of Pharmaceutical Sciences, University of Graz Graz, Austria
| | - Gabriele Berg
- Institute for Environmental Biotechnology, Graz University of Technology Graz, Austria
| |
Collapse
|
27
|
Catch the Best: Novel Screening Strategy to Select Stress Protecting Agents for Crop Plants. AGRONOMY-BASEL 2013. [DOI: 10.3390/agronomy3040794] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
28
|
Oliveira V, Gomes NCM, Almeida A, Silva AMS, Simões MMQ, Smalla K, Cunha Â. Hydrocarbon contamination and plant species determine the phylogenetic and functional diversity of endophytic degrading bacteria. Mol Ecol 2013; 23:1392-1404. [DOI: 10.1111/mec.12559] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vanessa Oliveira
- Department of Biology & Center for Environmental and Marine Studies (CESAM); University of Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Newton C. M. Gomes
- Department of Biology & Center for Environmental and Marine Studies (CESAM); University of Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Adelaide Almeida
- Department of Biology & Center for Environmental and Marine Studies (CESAM); University of Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Artur M. S. Silva
- Department of Chemistry & QOPNA; University of Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Mário M. Q. Simões
- Department of Chemistry & QOPNA; University of Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
| | - Kornelia Smalla
- Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI); Department of Epidemiology and Pathogen Diagnostics; Messeweg 11-12 38104 Braunschweig Germany
| | - Ângela Cunha
- Department of Biology & Center for Environmental and Marine Studies (CESAM); University of Aveiro; Campus Universitário de Santiago 3810-193 Aveiro Portugal
| |
Collapse
|
29
|
Initial Steps towards Biocontrol in Hops: Successful Colonization and Plant Growth Promotion by Four Bacterial Biocontrol Agents. AGRONOMY-BASEL 2013. [DOI: 10.3390/agronomy3040583] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
30
|
Köberl M, Ramadan EM, Adam M, Cardinale M, Hallmann J, Heuer H, Smalla K, Berg G. BacillusandStreptomyceswere selected as broad-spectrum antagonists against soilborne pathogens from arid areas in Egypt. FEMS Microbiol Lett 2013; 342:168-78. [DOI: 10.1111/1574-6968.12089] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 01/17/2013] [Accepted: 01/21/2013] [Indexed: 01/22/2023] Open
Affiliation(s)
- Martina Köberl
- Institute for Environmental Biotechnology; Graz University of Technology; Graz; Austria
| | - Elshahat M. Ramadan
- Faculty of Agriculture; SEKEM, Heliopolis University, Ain Shams University; Cairo; Egypt
| | - Mohamed Adam
- Institute for Epidemiology and Pathogen Diagnostics; Julius Kühn-Institut - Federal Research Centre for Cultivated Plants; Braunschweig; Germany
| | | | - Johannes Hallmann
- Institute for Epidemiology and Pathogen Diagnostics; Julius Kühn-Institut - Federal Research Centre for Cultivated Plants; Braunschweig; Germany
| | - Holger Heuer
- Institute for Epidemiology and Pathogen Diagnostics; Julius Kühn-Institut - Federal Research Centre for Cultivated Plants; Braunschweig; Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics; Julius Kühn-Institut - Federal Research Centre for Cultivated Plants; Braunschweig; Germany
| | - Gabriele Berg
- Institute for Environmental Biotechnology; Graz University of Technology; Graz; Austria
| |
Collapse
|
31
|
Grube M, Köberl M, Lackner S, Berg C, Berg G. Host-parasite interaction and microbiome response: effects of fungal infections on the bacterial community of the Alpine lichen Solorina crocea. FEMS Microbiol Ecol 2012; 82:472-81. [PMID: 22671536 DOI: 10.1111/j.1574-6941.2012.01425.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 04/26/2012] [Accepted: 05/25/2012] [Indexed: 01/25/2023] Open
Abstract
The lichen symbiosis allows a self-sustained life under harsh environmental conditions, yet symbiotic integrity can be affected by fungal parasites. Nothing is known about the impact of these biologically diverse and often specific infections on the recently detected bacterial community in lichens. To address this question, we studied the arctic-alpine 'chocolate chip lichen' Solorina crocea, which is frequently infected by Rhagadostoma lichenicola. We sampled healthy and infected lichens at two different sites in the Eastern Alps. High abundances of Acidobacteria, Planctomycetes, and Proteobacteria were identified analyzing 16S rRNA gene regions obtained by barcoded pyrosequencing. At the phylum and genus level, no significant alterations were present among infected and healthy individuals. Yet, evidence for a differentiation of communities emerged, when data were analyzed at the strain level by detrended correspondence analysis. Further, a profile clustering network revealed strain-specific abundance shifts among Acidobacteria and other bacteria. Study of stability and change in host-associated bacterial communities requires a fine-grained analysis at strain level. No correlation with the infection was found by analysis of nifH genes responsible for nitrogen fixation.
Collapse
Affiliation(s)
- Martin Grube
- Institute of Plant Sciences, Karl-Franzens-University, Graz, Austria.
| | | | | | | | | |
Collapse
|
32
|
Banana-associated microbial communities in Uganda are highly diverse but dominated by Enterobacteriaceae. Appl Environ Microbiol 2012; 78:4933-41. [PMID: 22562988 DOI: 10.1128/aem.00772-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bananas are among the most widely consumed foods in the world. In Uganda, the country with the second largest banana production in the world, bananas are the most important staple food. The objective of this study was to analyze banana-associated microorganisms and to select efficient antagonists against fungal pathogens which are responsible for substantial yield losses. We studied the structure and function of microbial communities (endosphere, rhizosphere, and soil) obtained from three different traditional farms in Uganda by cultivation-independent (PCR-SSCP fingerprints of 16S rRNA/ITS genes, pyrosequencing of enterobacterial 16S rRNA gene fragments, quantitative PCR, fluorescence in situ hybridization coupled with confocal laser scanning microscopy, and PCR-based detection of broad-host-range plasmids and sulfonamide resistance genes) and cultivation-dependent methods. The results showed microhabitat-specific microbial communities that were significant across sites and treatments. Furthermore, all microhabitats contained a high number and broad spectrum of indigenous antagonists toward identified fungal pathogens. While bacterial antagonists were found to be enriched in banana plants, fungal antagonists were less abundant and mainly found in soil. The banana stem endosphere was the habitat with the highest bacterial counts (up to 10(9) gene copy numbers g(-1)). Here, enterics were found to be enhanced in abundance and diversity; they provided one-third of the bacteria and were identified by pyrosequencing with 14 genera, including not only potential human (Escherichia, Klebsiella, Salmonella, and Yersinia spp.) and plant (Pectobacterium spp.) pathogens but also disease-suppressive bacteria (Serratia spp.). The dominant role of enterics can be explained by the permanent nature and vegetative propagation of banana and the amendments of human, as well as animal, manure in these traditional cultivations.
Collapse
|
33
|
Bragina A, Maier S, Berg C, Müller H, Chobot V, Hadacek F, Berg G. Similar diversity of alphaproteobacteria and nitrogenase gene amplicons on two related sphagnum mosses. Front Microbiol 2012; 2:275. [PMID: 22294982 PMCID: PMC3261640 DOI: 10.3389/fmicb.2011.00275] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 12/22/2011] [Indexed: 11/13/2022] Open
Abstract
Sphagnum mosses represent a main vegetation component in ombrotrophic wetlands. They harbor a specific and diverse microbial community with essential functions for the host. To understand the extend of host specificity and impact of environment, Sphagnum fallax and Sphagnum angustifolium, two phylogenetically closely related species, which show distinct habitat preference with respect to the nutrient level, were analyzed by a multifaceted approach. Microbial fingerprints obtained by PCR-single-strand conformation polymorphism of 16S rRNA and nitrogenase-encoding (nifH) genes were highly similar for both Sphagnum species. Similarity was confirmed for colonization patterns obtained by fluorescence in situ hybridization (FISH) coupled with confocal laser scanning microscopy (CLSM): Alphaproteobacteria were the main colonizers inside the hyaline cells of Sphagnum leaves. A deeper survey of Alphaproteobacteria by 16S rRNA gene amplicon sequencing reveals a high diversity with Acidocella, Acidisphaera, Rhodopila, and Phenylobacterium as major genera for both mosses. Nitrogen fixation is an important function of Sphagnum-associated bacteria, which is fulfilled by microbial communities of Sphagna in a similar way. NifH libraries of Sphagnum-associated microbial communities were characterized by high diversity and abundance of Alphaproteobacteria but contained also diverse amplicons of other taxa, e.g., Cyanobacteria and Deltaproteobacteria. Statistically significant differences between the microbial communities of both Sphagnum species could not be discovered in any of the experimental approach. Our results show that the same close relationship, which exists between the physical, morphological, and chemical characteristics of Sphagnum mosses and the ecology and function of bog ecosystems, also connects moss plantlets with their associated bacterial communities.
Collapse
Affiliation(s)
- Anastasia Bragina
- Institute of Environmental Biotechnology, Graz University of Technology Graz, Austria
| | | | | | | | | | | | | |
Collapse
|
34
|
Köberl M, Müller H, Ramadan EM, Berg G. Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health. PLoS One 2011; 6:e24452. [PMID: 21912695 PMCID: PMC3166316 DOI: 10.1371/journal.pone.0024452] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 08/10/2011] [Indexed: 01/07/2023] Open
Abstract
Background To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known. Methodology/Principal Findings We studied the impact of long-term agriculture on desert soil in one of the most prominent examples for organic desert farming in Sekem (Egypt). Using a polyphasic methodological approach to analyse microbial communities in soil as well as associated with cultivated plants, drastic effects caused by 30 years of agriculture were detected. Analysing bacterial fingerprints, we found statistically significant differences between agricultural and native desert soil of about 60%. A pyrosequencing-based analysis of the 16S rRNA gene regions showed higher diversity in agricultural than in desert soil (Shannon diversity indices: 11.21/7.90), and displayed structural differences. The proportion of Firmicutes in field soil was significantly higher (37%) than in the desert (11%). Bacillus and Paenibacillus play the key role: they represented 96% of the antagonists towards phytopathogens, and identical 16S rRNA sequences in the amplicon library and for isolates were detected. The proportion of antagonistic strains was doubled in field in comparison to desert soil (21.6%/12.4%); disease-suppressive bacteria were especially enriched in plant roots. On the opposite, several extremophilic bacterial groups, e.g., Acidimicrobium, Rubellimicrobium and Deinococcus-Thermus, disappeared from soil after agricultural use. The N-fixing Herbaspirillum group only occurred in desert soil. Soil bacterial communities were strongly driven by the a-biotic factors water supply and pH. Conclusions/Significance After long-term farming, a drastic shift in the bacterial communities in desert soil was observed. Bacterial communities in agricultural soil showed a higher diversity and a better ecosystem function for plant health but a loss of extremophilic bacteria. Interestingly, we detected that indigenous desert microorganisms promoted plant health in desert agro-ecosystems.
Collapse
Affiliation(s)
- Martina Köberl
- Institute for Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Henry Müller
- Institute for Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Gabriele Berg
- Institute for Environmental Biotechnology, Graz University of Technology, Graz, Austria
- * E-mail:
| |
Collapse
|
35
|
Zachow C, Fatehi J, Cardinale M, Tilcher R, Berg G. Strain-specific colonization pattern of Rhizoctonia antagonists in the root system of sugar beet. FEMS Microbiol Ecol 2010; 74:124-35. [DOI: 10.1111/j.1574-6941.2010.00930.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
36
|
Gasser I, Müller H, Berg G. Ecology and characterization of polyhydroxyalkanoate-producing microorganisms on and in plants. FEMS Microbiol Ecol 2009; 70:142-50. [DOI: 10.1111/j.1574-6941.2009.00734.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
37
|
Berg G, Smalla K. Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 2009; 68:1-13. [DOI: 10.1111/j.1574-6941.2009.00654.x] [Citation(s) in RCA: 1474] [Impact Index Per Article: 98.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
38
|
Berg G, Smalla K. Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 2009. [DOI: 10.1111/j.1574-6941.2009.00654.x 1-13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
39
|
Plant host habitat and root exudates shape soil bacterial community structure. ISME JOURNAL 2008; 2:1221-30. [PMID: 18754043 DOI: 10.1038/ismej.2008.80] [Citation(s) in RCA: 470] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|