51
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Jaroszuk-Ściseł J, Tyśkiewicz R, Nowak A, Ozimek E, Majewska M, Hanaka A, Tyśkiewicz K, Pawlik A, Janusz G. Phytohormones (Auxin, Gibberellin) and ACC Deaminase In Vitro Synthesized by the Mycoparasitic Trichoderma DEMTkZ3A0 Strain and Changes in the Level of Auxin and Plant Resistance Markers in Wheat Seedlings Inoculated with this Strain Conidia. Int J Mol Sci 2019; 20:E4923. [PMID: 31590281 PMCID: PMC6801869 DOI: 10.3390/ijms20194923] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 11/17/2022] Open
Abstract
Both hormonal balance and plant growth may be shaped by microorganisms synthesizing phytohormones, regulating its synthesis in the plant and inducing plant resistance by releasing elicitors from cell walls (CW) by degrading enzymes (CWDE). It was shown that the Trichoderma DEMTkZ3A0 strain, isolated from a healthy rye rhizosphere, colonized the rhizoplane of wheat seedlings and root border cells (RBC) and caused approximately 40% increase of stem weight. The strain inhibited (in over 90%) the growth of polyphagous Fusarium spp. (F. culmorum, F. oxysporum, F. graminearum) phytopathogens through a mechanism of mycoparasitism. Chitinolytic and glucanolytic activity, strongly stimulated by CW of F. culmorum in the DEMTkZ3A0 liquid culture, is most likely responsible for the lysis of hyphae and macroconidia of phytopathogenic Fusarium spp. as well as the release of plant resistance elicitors. In DEMTkZ3A0 inoculated plants, an increase in the activity of the six tested plant resistance markers and a decrease in the concentration of indoleacetic acid (IAA) auxin were noted. IAA and gibberellic acid (GA) but also the 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase (ACCD) enzyme regulating ethylene production by plant were synthesized by DEMTkZ3A0 in the liquid culture. IAA synthesis was dependent on tryptophan and negatively correlated with temperature, whereas GA synthesis was positively correlated with the biomass and temperature.
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Affiliation(s)
- Jolanta Jaroszuk-Ściseł
- Department of Environmental Microbiology, Maria Curie-Sklodowska University, Akademicka St. 19, 20-033 Lublin, Poland.
| | - Renata Tyśkiewicz
- Department of Environmental Microbiology, Maria Curie-Sklodowska University, Akademicka St. 19, 20-033 Lublin, Poland.
- Military Institute of Hygiene and Epidemiology, Lubelska St. 2, 24-100 Puławy, Poland.
| | - Artur Nowak
- Department of Environmental Microbiology, Maria Curie-Sklodowska University, Akademicka St. 19, 20-033 Lublin, Poland.
| | - Ewa Ozimek
- Department of Environmental Microbiology, Maria Curie-Sklodowska University, Akademicka St. 19, 20-033 Lublin, Poland.
| | - Małgorzata Majewska
- Department of Environmental Microbiology, Maria Curie-Sklodowska University, Akademicka St. 19, 20-033 Lublin, Poland.
| | - Agnieszka Hanaka
- Department of Plant Physiology, Maria Curie-Sklodowska University, Akademicka St. 19, 20-033 Lublin, Poland.
| | - Katarzyna Tyśkiewicz
- ŁUKASIEWICZ Research Network-New Chemical Syntheses Institute, Tysiąclecia Państwa Polskiego Ave. 13a, 24-110 Puławy, Poland.
| | - Anna Pawlik
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka St. 19, 20-033 Lublin, Poland.
| | - Grzegorz Janusz
- Department of Biochemistry, Maria Curie-Sklodowska University, Akademicka St. 19, 20-033 Lublin, Poland.
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52
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Essarioui A, LeBlanc N, Otto-Hanson L, Schlatter DC, Kistler HC, Kinkel LL. Inhibitory and nutrient use phenotypes among coexisting Fusarium and Streptomyces populations suggest local coevolutionary interactions in soil. Environ Microbiol 2019; 22:976-985. [PMID: 31424591 DOI: 10.1111/1462-2920.14782] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 06/22/2019] [Accepted: 08/14/2019] [Indexed: 11/29/2022]
Abstract
Bacteria and fungi are key components of virtually all natural habitats, yet the significance of fungal-bacterial inhibitory interactions for the ecological and evolutionary dynamics of specific bacterial and fungal populations in natural habitats have been overlooked. More specifically, despite the broad consensus that antibiotics play a key role in providing a fitness advantage to competing microbes, the significance of antibiotic production in mediating cross-kingdom coevolutionary interactions has received relatively little attention. Here, we characterize reciprocal inhibition among Streptomyces and Fusarium populations from prairie soil, and explore antibiotic inhibition in relation to niche overlap among sympatric and allopatric populations. We found evidence for local adaptation between Fusarium and Streptomyces populations as indicated by significantly greater inhibition among sympatric than allopatric populations. Additionally, for both taxa, there was a significant positive correlation between the strength of inhibition against the other taxon and the intensity of resource competition from that taxon among sympatric but not allopatric populations. These data suggest that coevolutionary antagonistic interactions between Fusarium and Streptomyces are driven by resource competition, and support the hypothesis that antibiotics act as weapons in mediating bacterial-fungal interactions in soil.
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Affiliation(s)
- Adil Essarioui
- National Institute of Agronomic Research, Regional Center of Errachidia, Errachidia, Morocco.,Department of plant pathology, University of Minnesota, Minneapolis, MN, USA
| | - Nicholas LeBlanc
- Department of plant pathology, University of Minnesota, Minneapolis, MN, USA
| | - Lindsey Otto-Hanson
- Department of plant pathology, University of Minnesota, Minneapolis, MN, USA
| | | | - Harold Corby Kistler
- USDA-ARS Cereal Disease Laboratory, Department of Plant Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Linda L Kinkel
- Department of plant pathology, University of Minnesota, Minneapolis, MN, USA
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53
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van Bruggen AHC, Goss EM, Havelaar A, van Diepeningen AD, Finckh MR, Morris JG. One Health - Cycling of diverse microbial communities as a connecting force for soil, plant, animal, human and ecosystem health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 664:927-937. [PMID: 30769316 DOI: 10.1016/j.scitotenv.2019.02.091] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 05/06/2023]
Abstract
The One Health concept proposes that there is a connection between human, animal and environmental health. Plants and their health are not explicitly included. In this review, we broaden the One Health concept to include soil, plant, animal and ecosystem health. We argue that the health conditions of all organisms in an ecosystem are interconnected through the cycling of subsets of microbial communities from the environment (in particular the soil) to plants, animals and humans, and back into the environment. After an introduction on health concepts, we present examples of community stability and resilience, diversity and interconnectedness as affected by pollutants, and integrity of nutrient cycles and energy flows. Next, we explain our concept of microbial cycling in relation to ecosystem health, and end with examples of plant and animal disease outbreaks in relation to microbial community composition and diversity. We conclude that we need a better understanding of the role of interconnected microbiomes in promoting plant and animal health and possible ways to stimulate a healthy, diverse microbiome throughout human-dominated ecosystems. We suggest that it is essential to maintain ecosystem and soil health through diversification of plant communities and oligotrophication of managed ecosystems.
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Affiliation(s)
- Ariena H C van Bruggen
- Department of Plant Pathology, University of Florida, Gainesville FL32611, USA; Emerging Pathogens Institute, University of Florida, Gainesville FL32611, USA.
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville FL32611, USA; Emerging Pathogens Institute, University of Florida, Gainesville FL32611, USA
| | - Arie Havelaar
- Emerging Pathogens Institute, University of Florida, Gainesville FL32611, USA; Department of Animal Science, University of Florida, Gainesville FL32611, USA
| | - Anne D van Diepeningen
- Business Unit Biointeractions and Plant Health, Wageningen UR, 6708 PB Wageningen, the Netherlands
| | - Maria R Finckh
- Faculty of Organic Agricultural Sciences, Ecological Plant Protection, University of Kassel, 37213 Witzenhausen, Germany
| | - J Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville FL32611, USA; Department of Medicine, School of Medicine, University of Florida, Gainesville FL32611, USA
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54
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Matthews A, Pierce S, Hipperson H, Raymond B. Rhizobacterial Community Assembly Patterns Vary Between Crop Species. Front Microbiol 2019; 10:581. [PMID: 31019492 PMCID: PMC6458290 DOI: 10.3389/fmicb.2019.00581] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/06/2019] [Indexed: 02/01/2023] Open
Abstract
Currently our limited understanding of crop rhizosphere community assembly hinders attempts to manipulate it beneficially. Variation in root communities has been attributed to plant host effects, soil type, and plant condition, but it is hard to disentangle the relative importance of soil and host without experimental manipulation. To examine the effects of soil origin and host plant on root associated bacterial communities we experimentally manipulated four crop species in split-plot mesocosms and surveyed variation in bacterial diversity by Illumina amplicon sequencing. Overall, plant species had a greater impact than soil type on community composition. While plant species associated with different Operational Taxonomic Units (OTUs) in different soils, plants tended to recruit bacteria from similar, higher order, taxonomic groups in different soils. However, the effect of soil on root-associated communities varied between crop species: Onion had a relatively invariant bacterial community while other species (maize and pea) had a more variable community structure. Dynamic communities could result from environment specific recruitment, differential bacterial colonization or reflect broader symbiont host range; while invariant community assembly implies tighter evolutionary or ecological interactions between plants and root-associated bacteria. Irrespective of mechanism, it appears both communities and community assembly rules vary between crop species.
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Affiliation(s)
- Andrew Matthews
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Sarah Pierce
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom.,School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Helen Hipperson
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom.,Department of Animal and Plant Sciences, P3 Institute for Plant and Soil Biology, The University of Sheffield, Sheffield, United Kingdom
| | - Ben Raymond
- College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
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55
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Cardinale M, Suarez C, Steffens D, Ratering S, Schnell S. Effect of Different Soil Phosphate Sources on the Active Bacterial Microbiota Is Greater in the Rhizosphere than in the Endorhiza of Barley (Hordeum vulgare L.). MICROBIAL ECOLOGY 2019; 77:689-700. [PMID: 30259168 DOI: 10.1007/s00248-018-1264-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 09/16/2018] [Indexed: 06/08/2023]
Abstract
Phosphate is a macronutrient and often the limiting growing factor of many ecosystems. The aim of this work was to assess the effect of various phosphate sources on the active bacterial microbiota of barley rhizosphere and endorhiza. Barley was grown on poor soil supplemented with either Ca(H2PO4)2 (CaP), Gafsa rock phosphate (Gafsa), sodium hexaphytate (NaHex), or not amended (P0). RNA was extracted and cDNA synthesized via reverse transcription from both rhizosphere and endorhiza of barley roots; the obtained 16S rRNA cDNA was sequenced by Ion Torrent and analyzed with QIIME and co-occurrence network analysis. Phosphatase activity was measured in the rhizosphere. The phosphate source significantly affected alpha- and beta-diversities of the active microbiota, especially in the rhizosphere. CaP enriched the relative abundance of a broad range of taxa, while NaHex and Gafsa specifically enriched one dominant Massilia-related OTU. Co-occurrence network analysis showed that the most abundant OTUs were affected by phosphate source and, at the same time, were low connected to other OTUs (thus they were relatively "independent" from other bacteria); this indicates a successful adaptation to the specific abiotic conditions. In the rhizosphere, the phosphatase activities were correlated to several OTUs. Moreover, the phosphodiesterase/alk. phosphomonoesterase ratio was highly correlated to the dominance index of the microbiota and to the relative abundance of the dominant Massilia OTU. This study shows the differential response of the rhizosphere- and endorhiza bacterial microbiota of barley to various phosphate sources in soil, thus providing insights onto this largely unknown aspect of the soil microbiome ecology and plant-microbe interactions.
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Affiliation(s)
- Massimiliano Cardinale
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Christian Suarez
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Diedrich Steffens
- Institute of Plant Nutrition, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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56
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Safronova V, Belimov A, Sazanova A, Chirak E, Kuznetsova I, Andronov E, Pinaev A, Tsyganova A, Seliverstova E, Kitaeva A, Tsyganov V, Tikhonovich I. Two Broad Host Range Rhizobial Strains Isolated From Relict Legumes Have Various Complementary Effects on Symbiotic Parameters of Co-inoculated Plants. Front Microbiol 2019; 10:514. [PMID: 30930885 PMCID: PMC6428766 DOI: 10.3389/fmicb.2019.00514] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 02/28/2019] [Indexed: 11/23/2022] Open
Abstract
Two bacterial strains Ach-343 and Opo-235 were isolated, respectively from nodules of Miocene-Pliocene relict legumes Astragalus chorinensis Bunge and Oxytropis popoviana Peschkova originated from Buryatia (Baikal Lake region, Russia). For identification of these strains the sequencing of 16S rRNA (rrs) gene was used. Strain Opo-235 belonged to the species Mesorhizobium japonicum, while the strain Ach-343 was identified as M. kowhaii (100 and 99.9% rrs similarity with the type strains MAFF 303099T and ICMP 19512T, respectively). Symbiotic genes of these strains as well as some genes that promote plant growth (acdS, gibberellin- and auxin-synthesis related genes) were searched throughout the whole genome sequences. The sets of plant growth-promoting genes found were almost identical in both strains, whereas the sets of symbiotic genes were different and complemented each other with several nod, nif, and fix genes. Effects of mono- and co-inoculation of Astragalus sericeocanus, Oxytropis caespitosa, Glycyrrhiza uralensis, Medicago sativa, and Trifolium pratense plants with the strains M. kowhaii Ach-343 and M. japonicum Opo-235 expressing fluorescent proteins mCherry (red) and EGFP (green) were studied in the gnotobiotic plant nodulation assay. It was shown that both strains had a wide range of host specificity, including species of different legume genera from two tribes (Galegeae and Trifolieae). The effects of co-microsymbionts on plants depended on the plant species and varied from decrease, no effect, to increase in the number of nodules, nitrogen-fixing activity and plant biomass. One of the reasons for this phenomenon may be the discovered complementarity in co-microsymbionts of symbiotic genes responsible for the specific modification of Nod-factors and nitrogenase activity. Localization and co-localization of the strains in nodules was confirmed by the confocal microscopy. Analysis of histological and ultrastructural organization of A. chorinensis and O. popoviana root nodules was performed. It can be concluded that the strains M. kowhaii Ach-343 and M. japonicum Opo-235 demonstrate lack of high symbiotic specificity that is characteristic for primitive legume-rhizobia systems. Further study of the root nodule bacteria having complementary sets of symbiotic genes will contribute to clarify the evolutionary paths of legume-rhizobia relationships and the mechanisms of effective integration between partners.
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Affiliation(s)
- Vera Safronova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Andrey Belimov
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center, Russian Academy of Sciences, Kazan, Russia
| | - Anna Sazanova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Elizaveta Chirak
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Irina Kuznetsova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Evgeny Andronov
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Alexander Pinaev
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Anna Tsyganova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Elena Seliverstova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Saint Petersburg, Russia
| | - Anna Kitaeva
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Viktor Tsyganov
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
- Department of Genetics and Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
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57
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Whitaker BK, Reynolds HL, Clay K. Foliar fungal endophyte communities are structured by environment but not host ecotype in Panicum virgatum (switchgrass). Ecology 2018; 99:2703-2711. [PMID: 30367461 DOI: 10.1002/ecy.2543] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/06/2018] [Accepted: 10/02/2018] [Indexed: 11/06/2022]
Abstract
Experimental tests of community assembly mechanisms for host-associated microbiomes in nature are lacking. Asymptomatic foliar fungal endophytes are a major component of the plant microbiome and are increasingly recognized for their impacts on plant performance, including pathogen defense, hormonal manipulation, and drought tolerance. However, it remains unclear whether fungal endophytes preferentially colonize certain host ecotypes or genotypes, reflecting some degree of biotic adaptation in the symbioses, or whether colonization is simply a function of spore type and abundance within the local environment. Whether host ecotype, local environment, or some combination of both controls the pattern of microbiome formation across hosts represents a new dimension to the age-old debate of nature versus nurture. Here, we used a reciprocal transplant design to explore the extent of host specificity and biotic adaptation in the plant microbiome, as evidenced by differential colonization of host genetic types by endophytes. Specifically, replicate plants from three locally-adapted ecotypes of the native grass Panicum virgatum (switchgrass) were transplanted at three geographically distinct field sites (one home and two away) in the Midwestern US. At the end of the growing season, plant leaves were harvested and the fungal microbiome characterized using culture-dependent sequencing techniques. Our results demonstrated that fungal endophyte community structure was determined by local environment (i.e., site), but not by host ecotype. Fungal richness and diversity also strongly differed by site, with lower fungal diversity at a riparian field site, whereas host ecotype had no effect. By contrast, there were significant differences in plant phenotypes across all ecotypes and sites, indicating ecotypic differentiation of host phenotype. Overall, our results indicate that environmental factors are the primary drivers of community structure in the switchgrass fungal microbiome.
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Affiliation(s)
- Briana K Whitaker
- Department of Biology, Indiana University, 1001 East 3rd St., Bloomington, Indiana, 47401, USA.,Department of Plant & Microbial Biology, North Carolina State University, Box 7612, Raleigh, North Carolina, 27695-7612, USA
| | - Heather L Reynolds
- Department of Biology, Indiana University, 1001 East 3rd St., Bloomington, Indiana, 47401, USA
| | - Keith Clay
- Department of Biology, Indiana University, 1001 East 3rd St., Bloomington, Indiana, 47401, USA.,Department of Ecology & Evolutionary Biology, Tulane University, 6823 St,. Charles Ave., New Orleans, Louisiana, 70118, USA
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58
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Garrett KA, Alcalá-Briseño RI, Andersen KF, Buddenhagen CE, Choudhury RA, Fulton JC, Hernandez Nopsa JF, Poudel R, Xing Y. Network Analysis: A Systems Framework to Address Grand Challenges in Plant Pathology. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:559-580. [PMID: 29979928 DOI: 10.1146/annurev-phyto-080516-035326] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plant pathology must address a number of challenges, most of which are characterized by complexity. Network analysis offers useful tools for addressing complex systems and an opportunity for synthesis within plant pathology and between it and relevant disciplines such as in the social sciences. We discuss applications of network analysis, which ultimately may be integrated together into more synthetic analyses of how to optimize plant disease management systems. The analysis of microbiome networks and tripartite phytobiome networks of host-vector-pathogen interactions offers promise for identifying biocontrol strategies and anticipating disease emergence. Linking epidemic network analysis with social network analysis will support strategies for sustainable agricultural development and for scaling up solutions for disease management. Statistical tools for evaluating networks, such as Bayesian network analysis and exponential random graph models, have been underused in plant pathology and are promising for informing strategies. We conclude with research priorities for network analysis applications in plant pathology.
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Affiliation(s)
- K A Garrett
- Plant Pathology Department, University of Florida, Gainesville, Florida 32611, USA;
- Institute for Sustainable Food Systems, University of Florida, Gainesville, Florida 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32611, USA
| | - R I Alcalá-Briseño
- Plant Pathology Department, University of Florida, Gainesville, Florida 32611, USA;
- Institute for Sustainable Food Systems, University of Florida, Gainesville, Florida 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32611, USA
| | - K F Andersen
- Plant Pathology Department, University of Florida, Gainesville, Florida 32611, USA;
- Institute for Sustainable Food Systems, University of Florida, Gainesville, Florida 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32611, USA
| | - C E Buddenhagen
- Plant Pathology Department, University of Florida, Gainesville, Florida 32611, USA;
- Institute for Sustainable Food Systems, University of Florida, Gainesville, Florida 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32611, USA
- Current address: AgResearch, Hamilton, New Zealand 3240
| | - R A Choudhury
- Plant Pathology Department, University of Florida, Gainesville, Florida 32611, USA;
- Institute for Sustainable Food Systems, University of Florida, Gainesville, Florida 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32611, USA
| | - J C Fulton
- Plant Pathology Department, University of Florida, Gainesville, Florida 32611, USA;
- Institute for Sustainable Food Systems, University of Florida, Gainesville, Florida 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32611, USA
| | - J F Hernandez Nopsa
- Plant Pathology Department, University of Florida, Gainesville, Florida 32611, USA;
- Institute for Sustainable Food Systems, University of Florida, Gainesville, Florida 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32611, USA
- Current address: Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Departamento de Semillas, Mosquera-Bogotá, Colombia 344300
| | - R Poudel
- Plant Pathology Department, University of Florida, Gainesville, Florida 32611, USA;
- Institute for Sustainable Food Systems, University of Florida, Gainesville, Florida 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Y Xing
- Plant Pathology Department, University of Florida, Gainesville, Florida 32611, USA;
- Institute for Sustainable Food Systems, University of Florida, Gainesville, Florida 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32611, USA
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59
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Abdullah AS, Turo C, Moffat CS, Lopez-Ruiz FJ, Gibberd MR, Hamblin J, Zerihun A. Real-Time PCR for Diagnosing and Quantifying Co-infection by Two Globally Distributed Fungal Pathogens of Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1086. [PMID: 30140271 PMCID: PMC6095046 DOI: 10.3389/fpls.2018.01086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/05/2018] [Indexed: 06/01/2023]
Abstract
Co-infections - invasions of a host-plant by multiple pathogen species or strains - are common, and are thought to have consequences for pathogen ecology and evolution. Despite their apparent significance, co-infections have received limited attention; in part due to lack of suitable quantitative tools for monitoring of co-infecting pathogens. Here, we report on a duplex real-time PCR assay that simultaneously distinguishes and quantifies co-infections by two globally important fungal pathogens of wheat: Pyrenophora tritici-repentis and Parastagonospora nodorum. These fungi share common characteristics and host species, creating a challenge for conventional disease diagnosis and subsequent management strategies. The assay uses uniquely assigned fluorogenic probes to quantify fungal biomass as nucleic acid equivalents. The probes provide highly specific target quantification with accurate discrimination against non-target closely related fungal species and host genes. Quantification of the fungal targets is linear over a wide range (5000-0.5 pg DNA μl-1) with high reproducibility (RSD ≤ 10%). In the presence of host DNA in the assay matrix, fungal biomass can be quantified up to a fungal to wheat DNA ratio of 1 to 200. The utility of the method was demonstrated using field samples of a cultivar sensitive to both pathogens. While visual and culture diagnosis suggested the presence of only one of the pathogen species, the assay revealed not only presence of both co-infecting pathogens (hence enabling asymptomatic detection) but also allowed quantification of relative abundances of the pathogens as a function of disease severity. Thus, the assay provides for accurate diagnosis; it is suitable for high-throughput screening of co-infections in epidemiological studies, and for exploring pathogen-pathogen interactions and dynamics, none of which would be possible with conventional approaches.
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Affiliation(s)
- Araz S. Abdullah
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Chala Turo
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Caroline S. Moffat
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Francisco J. Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Mark R. Gibberd
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - John Hamblin
- Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Ayalsew Zerihun
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
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60
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Anderson AJ, McLean JE, Jacobson AR, Britt DW. CuO and ZnO Nanoparticles Modify Interkingdom Cell Signaling Processes Relevant to Crop Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:6513-6524. [PMID: 28481096 DOI: 10.1021/acs.jafc.7b01302] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
As the world population increases, strategies for sustainable agriculture are needed to fulfill the global need for plants for food and other commercial products. Nanoparticle formulations are likely to be part of the developing strategies. CuO and ZnO nanoparticles (NPs) offer potential as fertilizers, as they provide bioavailable essential metals, and as pesticides, because of dose-dependent toxicity. Effects of these metal oxide NPs on rhizosphere functions are the focus of this review. These NPs at doses of ≥10 mg metal/kg change the production of key metabolites involved in plant protection in a root-associated microbe, Pseudomonas chlororaphis O6. Altered synthesis occurs in the microbe for phenazines, which function in plant resistance to pathogens, the pyoverdine-like siderophore that enhances Fe bioavailability in the rhizosphere and indole-3-acetic acid affecting plant growth. In wheat seedlings, reprogramming of root morphology involves increases in root hair proliferation (CuO NPs) and lateral root formation (ZnO NPs). Systemic changes in wheat shoot gene expression point to altered regulation for metal stress resilience as well as the potential for enhanced survival under stress commonly encountered in the field. These responses to the NPs cross kingdoms involving the bacteria, fungi, and plants in the rhizosphere. Our challenge is to learn how to understand the value of these potential changes and successfully formulate the NPs for optimal activity in the rhizosphere of crop plants. These formulations may be integrated into developing practices to ensure the sustainability of crop production.
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Affiliation(s)
- Anne J Anderson
- Department of Biology , Utah State University , Logan , Utah 84322-5305 , United States
| | - Joan E McLean
- Department of Civil and Environmental Engineering, Utah Water Research Laboratory , Utah State University , Logan , Utah 84322-8200 , United States
| | - Astrid R Jacobson
- Department of Plants, Soils and Climate , Utah State University , Logan , Utah 84322-4820 , United States
| | - David W Britt
- Department of Bioengineering , Utah State University , Logan , Utah 84322-4105 , United States
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61
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Flandroy L, Poutahidis T, Berg G, Clarke G, Dao MC, Decaestecker E, Furman E, Haahtela T, Massart S, Plovier H, Sanz Y, Rook G. The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:1018-1038. [PMID: 29426121 DOI: 10.1016/j.scitotenv.2018.01.288] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/28/2018] [Accepted: 01/28/2018] [Indexed: 05/03/2023]
Abstract
Plants, animals and humans, are colonized by microorganisms (microbiota) and transiently exposed to countless others. The microbiota affects the development and function of essentially all organ systems, and contributes to adaptation and evolution, while protecting against pathogenic microorganisms and toxins. Genetics and lifestyle factors, including diet, antibiotics and other drugs, and exposure to the natural environment, affect the composition of the microbiota, which influences host health through modulation of interrelated physiological systems. These include immune system development and regulation, metabolic and endocrine pathways, brain function and epigenetic modification of the genome. Importantly, parental microbiotas have transgenerational impacts on the health of progeny. Humans, animals and plants share similar relationships with microbes. Research paradigms from humans and other mammals, amphibians, insects, planktonic crustaceans and plants demonstrate the influence of environmental microbial ecosystems on the microbiota and health of organisms, and indicate links between environmental and internal microbial diversity and good health. Therefore, overlapping compositions, and interconnected roles of microbes in human, animal and plant health should be considered within the broader context of terrestrial and aquatic microbial ecosystems that are challenged by the human lifestyle and by agricultural and industrial activities. Here, we propose research priorities and organizational, educational and administrative measures that will help to identify safe microbe-associated health-promoting modalities and practices. In the spirit of an expanding version of "One health" that includes environmental health and its relation to human cultures and habits (EcoHealth), we urge that the lifestyle-microbiota-human health nexus be taken into account in societal decision making.
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Affiliation(s)
- Lucette Flandroy
- Federal Public Service Health, Food Chain Safety and Environment, Belgium
| | - Theofilos Poutahidis
- Laboratory of Pathology, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Gabriele Berg
- Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioural Science, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Maria-Carlota Dao
- ICAN, Institute of Cardiometabolism and Nutrition, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris, France; INSERM, UMRS U1166 (Eq 6) Nutriomics, Paris 6, France; UPMC, Sorbonne University, Pierre et Marie Curie-Paris 6, France
| | - Ellen Decaestecker
- Aquatic Biology, Department Biology, Science, Engineering & Technology Group, KU Leuven, Campus Kortrijk. E. Sabbelaan 53, B-8500 Kortrijk, Belgium
| | - Eeva Furman
- Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Tari Haahtela
- Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Finland
| | - Sébastien Massart
- Laboratory of Integrated and Urban Phytopathology, TERRA, Gembloux Agro-Bio Tech, University of Liège, Passage des deportes, 2, 5030 Gembloux, Belgium
| | - Hubert Plovier
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Yolanda Sanz
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Graham Rook
- Centre for Clinical Microbiology, Department of Infection, UCL (University College London), London, UK.
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62
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Schlatter DC, Burke I, Paulitz TC. Succession of Fungal and Oomycete Communities in Glyphosate-Killed Wheat Roots. PHYTOPATHOLOGY 2018; 108:582-594. [PMID: 29256828 DOI: 10.1094/phyto-06-17-0212-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The successional dynamics of root-colonizing microbes are hypothesized to be critical to displacing fungal pathogens that can proliferate after the use of some herbicides. Applications of glyphosate in particular, which compromises the plant defense system by interfering with the production of aromatic amino acids, are thought to promote a buildup of root pathogens and can result in a "greenbridge" between weeds or volunteers and crop hosts. By planting 2 to 3 weeks after spraying, growers can avoid most negative impacts of the greenbridge by allowing pathogen populations to decline, but with the added cost of delayed planting dates. However, the specific changes in microbial communities during this period of root death and the microbial taxa likely to be involved in displacing pathogens are poorly characterized. Using high-throughput sequencing, we characterized fungal and oomycete communities in roots after applications of herbicides with different modes of action (glyphosate or clethodim) and tracked their dynamics over 3 weeks in both naturally infested soil and soil inoculated with Rhizoctonia solani AG-8. We found that many unexpected taxa were present at high relative abundance (e.g., Pythium volutum and Myrmecridium species) in live and dying wheat roots and may play an under-recognized role in greenbridge dynamics. Moreover, communities were highly dynamic over time and had herbicide-specific successional patterns, but became relatively stable by 2 weeks after herbicide application. Network analysis of communities over time revealed patterns of interactions among taxa that were both common and unique to each herbicide treatment and identified two primary groups of taxa with many positive associations within-groups but negative associations between-groups, suggesting that these groups are antagonistic to one another in dying roots and may play a role in displacing pathogen populations during greenbridge dynamics.
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Affiliation(s)
- Daniel C Schlatter
- First and third authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics and Quality Research Unit, Washington State University, Pullman 99164-6430; and second author: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420
| | - Ian Burke
- First and third authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics and Quality Research Unit, Washington State University, Pullman 99164-6430; and second author: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420
| | - Timothy C Paulitz
- First and third authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics and Quality Research Unit, Washington State University, Pullman 99164-6430; and second author: Department of Crop and Soil Sciences, Washington State University, Pullman 99164-6420
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63
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Erlandson S, Wei X, Savage J, Cavender-Bares J, Peay K. Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure. Mol Ecol 2018; 27:2007-2024. [PMID: 29603835 DOI: 10.1111/mec.14576] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 03/21/2018] [Indexed: 01/03/2023]
Abstract
Predicting the outcome of interspecific interactions is a central goal in ecology. The diverse soil microbes that interact with plants are shaped by different aspects of plant identity, such as phylogenetic history and functional group. Species interactions may also be strongly shaped by abiotic environment, but there is mixed evidence on the relative importance of environment, plant identity and their interactions in shaping soil microbial communities. Using a multifactor, split-plot field experiment, we tested how hydrologic context, and three facets of Salicaceae plant identity-habitat specialization, phylogenetic distance and species identity-influence soil microbial community structure. Analysis of microbial community sequencing data with generalized dissimilarity models showed that abiotic environment explained up to 25% of variation in community composition of soil bacteria, fungi and archaea, while Salicaceae identity influenced <1% of the variation in community composition of soil microbial taxa. Multivariate linear models indicated that the influence of Salicaceae identity was small, but did contribute to differentiation of soil microbes within treatments. Moreover, results from a microbial niche breadth analysis show that soil microbes in wetlands have more specialized host associations than soil microbes in drier environments-showing that abiotic environment changed how plant identity correlated with soil microbial communities. This study demonstrates the predominance of major abiotic factors in shaping soil microbial community structure; the significance of abiotic context to biotic influence on soil microbes; and the utility of field experiments to disentangling the abiotic and biotic factors that are thought to be most essential for soil microbial communities.
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Affiliation(s)
- Sonya Erlandson
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Xiaojing Wei
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA
| | - Jessica Savage
- Department of Biology, University of Minnesota, Duluth, MN, USA
| | | | - Kabir Peay
- Department of Biology, Stanford University, Stanford, CA, USA
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64
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Chignell JF, Park S, Lacerda CMR, De Long SK, Reardon KF. Label-Free Proteomics of a Defined, Binary Co-culture Reveals Diversity of Competitive Responses Between Members of a Model Soil Microbial System. MICROBIAL ECOLOGY 2018; 75:701-719. [PMID: 28975425 DOI: 10.1007/s00248-017-1072-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/08/2017] [Indexed: 06/07/2023]
Abstract
Interactions among members of microbial consortia drive the complex dynamics in soil, gut, and biotechnology microbiomes. Proteomic analysis of defined co-cultures of well-characterized species provides valuable information about microbial interactions. We used a label-free approach to quantify the responses to co-culture of two model bacterial species relevant to soil and rhizosphere ecology, Bacillus atrophaeus and Pseudomonas putida. Experiments determined the ratio of species in co-culture that would result in the greatest number of high-confidence protein identifications for both species. The 281 and 256 proteins with significant shifts in abundance for B. atrophaeus and P. putida, respectively, indicated responses to co-culture in overall metabolism, cell motility, and response to antagonistic compounds. Proteins associated with a virulent phenotype during surface-associated growth were significantly more abundant for P. putida in co-culture. Co-culture on agar plates triggered a filamentous phenotype in P. putida and avoidance of P. putida by B. atrophaeus colonies, corroborating antagonistic interactions between these species. Additional experiments showing increased relative abundance of P. putida under conditions of iron or zinc limitation and increased relative abundance of B. atrophaeus under magnesium limitation were consistent with patterns of changes in abundance of metal-binding proteins during co-culture. These results provide details on the nature of interactions between two species with antagonistic capabilities. Significant challenges remaining for the development of proteomics as a tool in microbial ecology include accurate quantification of low-abundance peptides, especially from rare species present at low relative abundance in a consortium.
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Affiliation(s)
- J F Chignell
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | - S Park
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
| | - C M R Lacerda
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX, USA
| | - S K De Long
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, USA
| | - K F Reardon
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA.
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, USA.
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65
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Hassani MA, Durán P, Hacquard S. Microbial interactions within the plant holobiont. MICROBIOME 2018; 6:58. [PMID: 29587885 PMCID: PMC5870681 DOI: 10.1186/s40168-018-0445-0] [Citation(s) in RCA: 516] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/13/2018] [Indexed: 05/09/2023]
Abstract
Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.
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Affiliation(s)
- M Amine Hassani
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Paloma Durán
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
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66
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Wu SH, Huang BH, Huang CL, Li G, Liao PC. The Aboveground Vegetation Type and Underground Soil Property Mediate the Divergence of Soil Microbiomes and the Biological Interactions. MICROBIAL ECOLOGY 2018; 75:434-446. [PMID: 28765980 DOI: 10.1007/s00248-017-1050-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 07/24/2017] [Indexed: 06/07/2023]
Abstract
The composition of the soil microbiome is influenced by environmental (abiotic) variables and biological interactions (biotic factors). To determine whether the aboveground vegetation and soil physicochemical properties were the main determinant of beta-diversity and biological interaction of soil microbial community, we sampled soils from the temperate coniferous forest and grassland. Clustering of operational taxonomic units was conducted using 16S rRNA gene. We found that the microbial composition of the rhizospheres, in which root exudates influence the microbial environment, show lower alpha-diversity than that of nonroot soils. The nonsignificant rhizosphere effect suggested other undetermined factors or stochastic processes accounted for microbial diversity in the rhizosphere. More significant microbe-microbe interactions were observed in forest and rhizosphere soils relative to the grassland soils. The elevated number of positive correlations for relative abundances in forest soil implied beneficial associations being common among bacteria, in particular within the rhizosphere environment. The particular soil properties generated by root exudates also alter the physicochemical properties of soil such as K and pH value, and might in turn favor the adoption of teamwork-cooperation strategies for microbe-microbe interactions, represented as large clusters of positive associations among bacterial taxa. Specific biological interactions differentiated the microbiomes within forest soils. Thus, the environmental selection pressure of aboveground vegetation accounts for differences between soil microbiomes while biotic factors are responsible for fine-scale differences of the microbial community in forest soils.
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Affiliation(s)
- Shu-Hong Wu
- School of Nature Conservation, Beijing Forestry University, No.35 Tsinghua East Road, Haidian District, Beijing, 100083, China
| | - Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, Taiwan
| | - Chia-Lung Huang
- Department of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, Taiwan
| | - Gang Li
- School of Nature Conservation, Beijing Forestry University, No.35 Tsinghua East Road, Haidian District, Beijing, 100083, China
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, No. 88 Ting-Chow Rd., Sec. 4, Taipei, Taiwan.
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67
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Matilla MA, Krell T. Plant Growth Promotion and Biocontrol Mediated by Plant-Associated Bacteria. PLANT MICROBIOME: STRESS RESPONSE 2018. [DOI: 10.1007/978-981-10-5514-0_3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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68
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Sergaki C, Lagunas B, Lidbury I, Gifford ML, Schäfer P. Challenges and Approaches in Microbiome Research: From Fundamental to Applied. FRONTIERS IN PLANT SCIENCE 2018; 9:1205. [PMID: 30174681 PMCID: PMC6107787 DOI: 10.3389/fpls.2018.01205] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/26/2018] [Indexed: 05/07/2023]
Abstract
We face major agricultural challenges that remain a threat for global food security. Soil microbes harbor enormous potentials to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and, hence, crop productivity. In this review we give an overview regarding the current state-of-the-art of microbiome research by discussing new technologies and approaches. We also provide insights into fundamental microbiome research that aim to provide a deeper understanding of the dynamics within microbial communities, as well as their interactions with different plant hosts and the environment. We aim to connect all these approaches with potential applications and reflect how we can use microbial communities in modern agricultural systems to realize a more customized and sustainable use of valuable resources (e.g., soil).
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Affiliation(s)
- Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- *Correspondence: Chrysi Sergaki,
| | - Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ian Lidbury
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Miriam L. Gifford
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, United Kingdom
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69
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Hortal S, Lozano YM, Bastida F, Armas C, Moreno JL, Garcia C, Pugnaire FI. Plant-plant competition outcomes are modulated by plant effects on the soil bacterial community. Sci Rep 2017; 7:17756. [PMID: 29259319 PMCID: PMC5736699 DOI: 10.1038/s41598-017-18103-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 12/05/2017] [Indexed: 11/23/2022] Open
Abstract
Competition is a key process that determines plant community structure and dynamics, often mediated by nutrients and water availability. However, the role of soil microorganisms on plant competition, and the links between above- and belowground processes, are not well understood. Here we show that the effects of interspecific plant competition on plant performance are mediated by feedbacks between plants and soil bacterial communities. Each plant species selects a singular community of soil microorganisms in its rhizosphere with a specific species composition, abundance and activity. When two plant species interact, the resulting soil bacterial community matches that of the most competitive plant species, suggesting strong competitive interactions between soil bacterial communities as well. We propose a novel mechanism by which changes in belowground bacterial communities promoted by the most competitive plant species influence plant performance and competition outcome. These findings emphasise the strong links between plant and soil communities, paving the way to a better understanding of plant community dynamics and the effects of soil bacterial communities on ecosystem functioning and services.
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Affiliation(s)
- S Hortal
- Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas (EEZA-CSIC), Carretera de Sacramento s/n, E-04120, La Cañada de San Urbano, Almería, Spain. .,Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Y M Lozano
- Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas (EEZA-CSIC), Carretera de Sacramento s/n, E-04120, La Cañada de San Urbano, Almería, Spain.,Freie Universität Berlin, Institut für Biologie, Plant Ecology, D-14195, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), D-14195, Berlin, Germany
| | - F Bastida
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), Campus Universitario de Espinardo, P.O. Box 164, E-30100, Murcia, Spain
| | - C Armas
- Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas (EEZA-CSIC), Carretera de Sacramento s/n, E-04120, La Cañada de San Urbano, Almería, Spain
| | - J L Moreno
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), Campus Universitario de Espinardo, P.O. Box 164, E-30100, Murcia, Spain
| | - C Garcia
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), Campus Universitario de Espinardo, P.O. Box 164, E-30100, Murcia, Spain
| | - F I Pugnaire
- Estación Experimental de Zonas Áridas, Consejo Superior de Investigaciones Científicas (EEZA-CSIC), Carretera de Sacramento s/n, E-04120, La Cañada de San Urbano, Almería, Spain
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70
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McHugh TA, Morrissey EM, Mueller RC, Gallegos-Graves LV, Kuske CR, Reed SC. Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland. Environ Microbiol 2017; 19:1600-1611. [DOI: 10.1111/1462-2920.13678] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 12/22/2016] [Accepted: 12/27/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Theresa A. McHugh
- U.S. Geological Survey; Southwest Biological Science Center; Moab UT USA
- Department of Biological Sciences; Colorado Mesa University; Grand Junction CO USA
| | - Ember M. Morrissey
- Division of Plant and Soil Sciences; West Virginia University; Morgantown WV USA
| | | | | | - Cheryl R. Kuske
- Bioscience Division; Los Alamos National Laboratory; Los Alamos NM USA
| | - Sasha C. Reed
- U.S. Geological Survey; Southwest Biological Science Center; Moab UT USA
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71
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Toju H, Kishida O, Katayama N, Takagi K. Networks Depicting the Fine-Scale Co-Occurrences of Fungi in Soil Horizons. PLoS One 2016; 11:e0165987. [PMID: 27861486 PMCID: PMC5115672 DOI: 10.1371/journal.pone.0165987] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/20/2016] [Indexed: 01/29/2023] Open
Abstract
Fungi in soil play pivotal roles in nutrient cycling, pest controls, and plant community succession in terrestrial ecosystems. Despite the ecosystem functions provided by soil fungi, our knowledge of the assembly processes of belowground fungi has been limited. In particular, we still have limited knowledge of how diverse functional groups of fungi interact with each other in facilitative and competitive ways in soil. Based on the high-throughput sequencing data of fungi in a cool-temperate forest in northern Japan, we analyzed how taxonomically and functionally diverse fungi showed correlated fine-scale distributions in soil. By uncovering pairs of fungi that frequently co-occurred in the same soil samples, networks depicting fine-scale co-occurrences of fungi were inferred at the O (organic matter) and A (surface soil) horizons. The results then led to the working hypothesis that mycorrhizal, endophytic, saprotrophic, and pathogenic fungi could form compartmentalized (modular) networks of facilitative, antagonistic, and/or competitive interactions in belowground ecosystems. Overall, this study provides a research basis for further understanding how interspecific interactions, along with sharing of niches among fungi, drive the dynamics of poorly explored biospheres in soil.
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Affiliation(s)
- Hirokazu Toju
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto, Japan
| | - Osamu Kishida
- Tomakomai Experimental Forest, Field Science Center for Northern Biosphere, Hokkaido University, Aza-Takaoka, Tomakomai, Hokkaido, Japan
| | - Noboru Katayama
- Center for Ecological Research, Kyoto University, 2-chome, Hirano, Otsu, Shiga, Japan
| | - Kentaro Takagi
- Teshio Experimental Forest, Field Science Center for Northern Biosphere, Hokkaido University, Aza-Toikanbetsu 131, Horonobe-cho, Teshio-gun, Hokkaido, Japan
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72
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Poudel R, Jumpponen A, Schlatter DC, Paulitz TC, Gardener BBM, Kinkel LL, Garrett KA. Microbiome Networks: A Systems Framework for Identifying Candidate Microbial Assemblages for Disease Management. PHYTOPATHOLOGY 2016; 106:1083-1096. [PMID: 27482625 DOI: 10.1094/phyto-02-16-0058-fi] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Network models of soil and plant microbiomes provide new opportunities for enhancing disease management, but also challenges for interpretation. We present a framework for interpreting microbiome networks, illustrating how observed network structures can be used to generate testable hypotheses about candidate microbes affecting plant health. The framework includes four types of network analyses. "General network analysis" identifies candidate taxa for maintaining an existing microbial community. "Host-focused analysis" includes a node representing a plant response such as yield, identifying taxa with direct or indirect associations with that node. "Pathogen-focused analysis" identifies taxa with direct or indirect associations with taxa known a priori as pathogens. "Disease-focused analysis" identifies taxa associated with disease. Positive direct or indirect associations with desirable outcomes, or negative associations with undesirable outcomes, indicate candidate taxa. Network analysis provides characterization not only of taxa with direct associations with important outcomes such as disease suppression, biofertilization, or expression of plant host resistance, but also taxa with indirect associations via their association with other key taxa. We illustrate the interpretation of network structure with analyses of microbiomes in the oak phyllosphere, and in wheat rhizosphere and bulk soil associated with the presence or absence of infection by Rhizoctonia solani.
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Affiliation(s)
- R Poudel
- First and seventh authors: Plant Pathology Department, Institute for Sustainable Food Systems, and Emerging Pathogens Institute, University of Florida, Gainesville 32611-0680; second author: Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan 66506; third and fourth authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman, WA 99164; fifth author: Department of Plant Pathology, The Ohio State University-OARDC, Wooster 44691; and sixth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108
| | - A Jumpponen
- First and seventh authors: Plant Pathology Department, Institute for Sustainable Food Systems, and Emerging Pathogens Institute, University of Florida, Gainesville 32611-0680; second author: Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan 66506; third and fourth authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman, WA 99164; fifth author: Department of Plant Pathology, The Ohio State University-OARDC, Wooster 44691; and sixth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108
| | - D C Schlatter
- First and seventh authors: Plant Pathology Department, Institute for Sustainable Food Systems, and Emerging Pathogens Institute, University of Florida, Gainesville 32611-0680; second author: Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan 66506; third and fourth authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman, WA 99164; fifth author: Department of Plant Pathology, The Ohio State University-OARDC, Wooster 44691; and sixth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108
| | - T C Paulitz
- First and seventh authors: Plant Pathology Department, Institute for Sustainable Food Systems, and Emerging Pathogens Institute, University of Florida, Gainesville 32611-0680; second author: Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan 66506; third and fourth authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman, WA 99164; fifth author: Department of Plant Pathology, The Ohio State University-OARDC, Wooster 44691; and sixth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108
| | - B B McSpadden Gardener
- First and seventh authors: Plant Pathology Department, Institute for Sustainable Food Systems, and Emerging Pathogens Institute, University of Florida, Gainesville 32611-0680; second author: Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan 66506; third and fourth authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman, WA 99164; fifth author: Department of Plant Pathology, The Ohio State University-OARDC, Wooster 44691; and sixth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108
| | - L L Kinkel
- First and seventh authors: Plant Pathology Department, Institute for Sustainable Food Systems, and Emerging Pathogens Institute, University of Florida, Gainesville 32611-0680; second author: Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan 66506; third and fourth authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman, WA 99164; fifth author: Department of Plant Pathology, The Ohio State University-OARDC, Wooster 44691; and sixth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108
| | - K A Garrett
- First and seventh authors: Plant Pathology Department, Institute for Sustainable Food Systems, and Emerging Pathogens Institute, University of Florida, Gainesville 32611-0680; second author: Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan 66506; third and fourth authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Health, Genetics, and Quality Research Unit, Washington State University, Pullman, WA 99164; fifth author: Department of Plant Pathology, The Ohio State University-OARDC, Wooster 44691; and sixth author: Department of Plant Pathology, University of Minnesota, St. Paul 55108
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73
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Tree species effects on pathogen-suppressive capacities of soil bacteria across two tropical dry forests in Costa Rica. Oecologia 2016; 182:789-802. [PMID: 27573616 DOI: 10.1007/s00442-016-3702-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/08/2016] [Indexed: 10/21/2022]
Abstract
Antibiotic-producing bacteria in the genus Streptomyces can inhibit soil-borne plant pathogens, and have the potential to mediate the impacts of disease on plant communities. Little is known about how antibiotic production varies among soil communities in tropical forests, despite a long history of interest in the role of soil-borne pathogens in these ecosystems. Our objective was to determine how tree species and soils influence variation in antibiotic-mediated pathogen suppression among Streptomyces communities in two tropical dry forest sites (Santa Rosa and Palo Verde). We targeted tree species that co-occur in both sites and used a culture-based functional assay to quantify pathogen-suppressive capacities of Streptomyces communities beneath 50 focal trees. We also measured host-associated litter and soil element concentrations as potential mechanisms by which trees may influence soil microbes. Pathogen-suppressive capacities of Streptomyces communities varied within and among tree species, and inhibitory phenotypes were significantly related to soil and litter element concentrations. Average proportions of inhibitory Streptomyces in soils from the same tree species varied between 1.6 and 3.3-fold between sites. Densities and proportions of pathogen-suppressive bacteria were always higher in Santa Rosa than Palo Verde. Our results suggest that spatial heterogeneity in the potential for antibiotic-mediated disease suppression is shaped by tree species, site, and soil characteristics, which could have significant implications for understanding plant community composition and diversity in tropical dry forests.
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Niu G, Chater KF, Tian Y, Zhang J, Tan H. Specialised metabolites regulating antibiotic biosynthesis in Streptomyces spp. FEMS Microbiol Rev 2016; 40:554-73. [PMID: 27288284 DOI: 10.1093/femsre/fuw012] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2016] [Indexed: 12/11/2022] Open
Abstract
Streptomyces bacteria are the major source of antibiotics and other secondary metabolites. Various environmental and physiological conditions affect the onset and level of production of each antibiotic by influencing concentrations of the ligands for conserved global regulatory proteins. In addition, as reviewed here, well-known autoregulators such as γ-butyrolactones, themselves products of secondary metabolism, accumulate late in growth to concentrations allowing their effective interaction with cognate binding proteins, in a necessary prelude to antibiotic biosynthesis. Most autoregulator binding proteins target the conserved global regulatory gene adpA, and/or regulatory genes for 'cluster-situated regulators' (CSRs) linked to antibiotic biosynthetic gene clusters. It now appears that some CSRs bind intermediates and end products of antibiotic biosynthesis, with regulatory effects interwoven with those of autoregulators. These ligands can exert cross-pathway effects within producers of more than one antibiotic, and when excreted into the extracellular environment may have population-wide effects on production, and mediate interactions with neighbouring microorganisms in natural communities, influencing speciation. Greater understanding of these autoregulatory and cross-regulatory activities may aid the discovery of new signalling molecules and their use in activating cryptic antibiotic biosynthetic pathways.
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Affiliation(s)
- Guoqing Niu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Keith F Chater
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Yuqing Tian
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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75
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Cardona C, Weisenhorn P, Henry C, Gilbert JA. Network-based metabolic analysis and microbial community modeling. Curr Opin Microbiol 2016; 31:124-131. [PMID: 27060776 DOI: 10.1016/j.mib.2016.03.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 03/17/2016] [Accepted: 03/20/2016] [Indexed: 01/08/2023]
Abstract
Network inference is being applied to studies of microbial ecology to visualize and characterize microbial communities. Network representations can allow examination of the underlying organizational structure of a microbial community, and identification of key players or environmental conditions that influence community assembly and stability. Microbial co-association networks provide information on the dynamics of community structure as a function of time or other external variables. Community metabolic networks can provide a mechanistic link between species through identification of metabolite exchanges and species specific resource requirements. When used together, co-association networks and metabolic networks can provide a more in-depth view of the hidden rules that govern the stability and dynamics of microbial communities.
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Affiliation(s)
- Cesar Cardona
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, United States; Department of Surgery, University of Chicago, Chicago, IL 60637, United States
| | - Pamela Weisenhorn
- Department of Surgery, University of Chicago, Chicago, IL 60637, United States; Division of Biosciences, Argonne National Laboratory, Lemont, IL 60439, United States
| | - Chris Henry
- Division of Mathematics and Computer Science, Argonne National Laboratory, Lemont, IL 60439, United States
| | - Jack A Gilbert
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, United States; Department of Surgery, University of Chicago, Chicago, IL 60637, United States; Division of Biosciences, Argonne National Laboratory, Lemont, IL 60439, United States.
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76
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Toju H, Yamamoto S, Tanabe AS, Hayakawa T, Ishii HS. Network modules and hubs in plant-root fungal biomes. J R Soc Interface 2016; 13:20151097. [PMID: 26962029 PMCID: PMC4843674 DOI: 10.1098/rsif.2015.1097] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/15/2016] [Indexed: 01/31/2023] Open
Abstract
Terrestrial plants host phylogenetically and functionally diverse groups of below-ground microbes, whose community structure controls plant growth/survival in both natural and agricultural ecosystems. Therefore, understanding the processes by which whole root-associated microbiomes are organized is one of the major challenges in ecology and plant science. We here report that diverse root-associated fungi can form highly compartmentalized networks of coexistence within host roots and that the structure of the fungal symbiont communities can be partitioned into semi-discrete types even within a single host plant population. Illumina sequencing of root-associated fungi in a monodominant south beech forest revealed that the network representing symbiont-symbiont co-occurrence patterns was compartmentalized into clear modules, which consisted of diverse functional groups of mycorrhizal and endophytic fungi. Consequently, terminal roots of the plant were colonized by either of the two largest fungal species sets (represented by Oidiodendron or Cenococcum). Thus, species-rich root microbiomes can have alternative community structures, as recently shown in the relationships between human gut microbiome type (i.e., 'enterotype') and host individual health. This study also shows an analytical framework for pinpointing network hubs in symbiont-symbiont networks, leading to the working hypothesis that a small number of microbial species organize the overall root-microbiome dynamics.
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Affiliation(s)
- Hirokazu Toju
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Satoshi Yamamoto
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan
| | - Akifumi S Tanabe
- National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Takashi Hayakawa
- Department of Wildlife Science (Nagoya Railroad Co., Ltd.), Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan Japan Monkey Centre, Inuyama, Aichi 484-0081, Japan
| | - Hiroshi S Ishii
- Department of Environmental Biology and Chemistry, Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
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77
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An assessment of US microbiome research. Nat Microbiol 2016; 1:15015. [PMID: 27571759 DOI: 10.1038/nmicrobiol.2015.15] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/09/2015] [Indexed: 12/19/2022]
Abstract
Genome-enabled technologies have supported a dramatic increase in our ability to study microbial communities in environments and hosts. Taking stock of previously funded microbiome research can help to identify common themes, under-represented areas and research priorities to consider moving forward. To assess the status of US microbiome research, a team of government scientists conducted an analysis of federally funded microbiome research. Microbiomes were defined as host-, ecosystem- or habitat-associated communities of microorganisms, and microbiome research was defined as those studies that emphasize community-level analyses using 'omics technologies. Single pathogen, single strain and culture-based studies were not included, except symbiosis studies that served as models for more complex communities. Fourteen governmental organizations participated in the data call. The analysis examined three broad research themes, eight environments and eight microbial categories. Human microbiome research was larger than any other environment studied, and the basic biology research theme accounted for half of the total research activities. Computational biology and bioinformatics, reference databases and biorepositories, standardized protocols and high-throughput tools were commonly identified needs. Longitudinal and functional studies and interdisciplinary research were also identified as needs. This study has implications for the funding of future microbiome research, not only in the United States but beyond.
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78
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Cha JY, Han S, Hong HJ, Cho H, Kim D, Kwon Y, Kwon SK, Crüsemann M, Bok Lee Y, Kim JF, Giaever G, Nislow C, Moore BS, Thomashow LS, Weller DM, Kwak YS. Microbial and biochemical basis of a Fusarium wilt-suppressive soil. THE ISME JOURNAL 2016; 10:119-29. [PMID: 26057845 PMCID: PMC4681868 DOI: 10.1038/ismej.2015.95] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 04/26/2015] [Accepted: 05/03/2015] [Indexed: 01/21/2023]
Abstract
Crops lack genetic resistance to most necrotrophic pathogens. To compensate for this disadvantage, plants recruit antagonistic members of the soil microbiome to defend their roots against pathogens and other pests. The best examples of this microbially based defense of roots are observed in disease-suppressive soils in which suppressiveness is induced by continuously growing crops that are susceptible to a pathogen, but the molecular basis of most is poorly understood. Here we report the microbial characterization of a Korean soil with specific suppressiveness to Fusarium wilt of strawberry. In this soil, an attack on strawberry roots by Fusarium oxysporum results in a response by microbial defenders, of which members of the Actinobacteria appear to have a key role. We also identify Streptomyces genes responsible for the ribosomal synthesis of a novel heat-stable antifungal thiopeptide antibiotic inhibitory to F. oxysporum and the antibiotic's mode of action against fungal cell wall biosynthesis. Both classical- and community-oriented approaches were required to dissect this suppressive soil from the field to the molecular level, and the results highlight the role of natural antibiotics as weapons in the microbial warfare in the rhizosphere that is integral to plant health, vigor and development.
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Affiliation(s)
- Jae-Yul Cha
- IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Sangjo Han
- Bioinformatics Tech Lab, SK Telecom, Sungnam, Republic of Korea
| | - Hee-Jeon Hong
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Hyunji Cho
- RILS and Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Daran Kim
- IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Youngho Kwon
- IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Soon-Kyeong Kwon
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul, Republic of Korea
| | - Max Crüsemann
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Yong Bok Lee
- RILS and Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul, Republic of Korea
| | - Guri Giaever
- Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Corey Nislow
- Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Linda S Thomashow
- US Department of Agriculture, Agricultural Research Service, Root Disease and Biological Control Research Unit, Pullman, WA, USA
| | - David M Weller
- US Department of Agriculture, Agricultural Research Service, Root Disease and Biological Control Research Unit, Pullman, WA, USA
| | - Youn-Sig Kwak
- IALS and Department of Plant Medicine, Gyeongsang National University, Jinju, Republic of Korea
- RILS and Division of Applied Life Science, Gyeongsang National University, Jinju, Republic of Korea
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79
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Trujillo ME, Riesco R, Benito P, Carro L. Endophytic Actinobacteria and the Interaction of Micromonospora and Nitrogen Fixing Plants. Front Microbiol 2015; 6:1341. [PMID: 26648923 PMCID: PMC4664631 DOI: 10.3389/fmicb.2015.01341] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/16/2015] [Indexed: 01/07/2023] Open
Abstract
For a long time, it was believed that a healthy plant did not harbor any microorganisms within its tissues, as these were often considered detrimental for the plant. In the last three decades, the numbers of studies on plant microbe-interactions has led to a change in our view and we now know that many of these invisible partners are essential for the overall welfare of the plant. The application of Next Generation Sequencing techniques is a powerful tool that has permitted the detection and identification of microbial communities in healthy plants. Among the new plant microbe interactions recently reported several actinobacteria such as Micromonospora are included. Micromonospora is a Gram-positive bacterium with a wide geographical distribution; it can be found in the soil, mangrove sediments, and freshwater and marine ecosistems. In the last years our group has focused on the isolation of Micromonospora strains from nitrogen fixing nodules of both leguminous and actinorhizal plants and reported for the first time its wide distribution in nitrogen fixing nodules of both types of plants. These studies have shown how this microoganism had been largely overlooked in this niche due to its slow growth. Surprisingly, the genetic diversity of Micromonospora strains isolated from nodules is very high and several new species have been described. The current data indicate that Micromonospora saelicesensis is the most frequently isolated species from the nodular tissues of both leguminous and actinorhizal plants. Further studies have also been carried out to confirm the presence of Micromonospora inside the nodule tissues, mainly by specific in situ hybridization. The information derived from the genome of the model strain, Micromonospora lupini, Lupac 08, has provided useful information as to how this bacterium may relate with its host plant. Several strategies potentially necessary for Micromonospora to thrive in the soil, a highly competitive, and rough environment, and as an endophytic bacterium with the capacity to colonize the internal plant tissues which are protected from the invasion of other soil microbes were identified. The genome data also revealed the potential of M. lupini Lupac 08 as a plant growth promoting bacterium. Several loci involved in plant growth promotion features such as the production of siderophores, phytohormones, and the degradation of chitin (biocontrol) were also located on the genome and the functionality of these genes was confirmed in the laboratory. In addition, when several host plants species were inoculated with Micromonospora strains, the plant growth enhancing effect was evident under greenhouse conditions. Unexpectedly, a high number of plant-cell wall degrading enzymes were also detected, a trait usually found only in pathogenic bacteria. Thus, Micromonospora can be added to the list of new plant-microbe interactions. The current data indicate that this microorganism may have an important application in agriculture and other biotechnological processes. The available information is promising but limited, much research is still needed to determine which is the ecological function of Micromonospora in interaction with nitrogen fixing plants.
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Affiliation(s)
- Martha E Trujillo
- Departamento de Microbiología y Genética, Universidad de Salamanca Salamanca, Spain
| | - Raúl Riesco
- Departamento de Microbiología y Genética, Universidad de Salamanca Salamanca, Spain
| | - Patricia Benito
- Departamento de Microbiología y Genética, Universidad de Salamanca Salamanca, Spain
| | - Lorena Carro
- Departamento de Microbiología y Genética, Universidad de Salamanca Salamanca, Spain
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80
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Goldmann K, Schöning I, Buscot F, Wubet T. Forest Management Type Influences Diversity and Community Composition of Soil Fungi across Temperate Forest Ecosystems. Front Microbiol 2015; 6:1300. [PMID: 26635766 PMCID: PMC4656839 DOI: 10.3389/fmicb.2015.01300] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/06/2015] [Indexed: 11/18/2022] Open
Abstract
Fungal communities have been shown to be highly sensitive toward shifts in plant diversity and species composition in forest ecosystems. However, little is known about the impact of forest management on fungal diversity and community composition of geographically separated sites. This study examined the effects of four different forest management types on soil fungal communities. These forest management types include age class forests of young managed beech (Fagus sylvatica L.), with beech stands age of approximately 30 years, age class beech stands with an age of approximately 70 years, unmanaged beech stands, and coniferous stands dominated by either pine (Pinus sylvestris L.) or spruce (Picea abies Karst.) which are located in three study sites across Germany. Soil were sampled from 48 study plots and we employed fungal ITS rDNA pyrotag sequencing to assess the soil fungal diversity and community structure. We found that forest management type significantly affects the Shannon diversity of soil fungi and a significant interaction effect of study site and forest management on the fungal operational taxonomic units richness. Consequently distinct fungal communities were detected in the three study sites and within the four forest management types, which were mainly related to the main tree species. Further analysis of the contribution of soil properties revealed that C/N ratio being the most important factor in all the three study sites whereas soil pH was significantly related to the fungal community in two study sites. Functional assignment of the fungal communities indicated that 38% of the observed communities were Ectomycorrhizal fungi (ECM) and their distribution is significantly influenced by the forest management. Soil pH and C/N ratio were found to be the main drivers of the ECM fungal community composition. Additional fungal community similarity analysis revealed the presence of study site and management type specific ECM genera. This study extends our knowledge on the impact of forest management type on general and ectomycorrhizal fungal diversity and community structure in temperate forests. High plasticity across management types but also study site specific spatial distribution revealed new insights in the ECM fungal distribution patterns.
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Affiliation(s)
- Kezia Goldmann
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZHalle, Germany
- Department of Biology II, University of LeipzigLeipzig, Germany
| | - Ingo Schöning
- Max Planck Institute for BiogeochemistryJena, Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZHalle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZHalle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
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81
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Mueller U, Sachs J. Engineering Microbiomes to Improve Plant and Animal Health. Trends Microbiol 2015; 23:606-617. [DOI: 10.1016/j.tim.2015.07.009] [Citation(s) in RCA: 252] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/08/2015] [Accepted: 07/22/2015] [Indexed: 12/22/2022]
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82
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Sloan SS, Lebeis SL. Exercising influence: distinct biotic interactions shape root microbiomes. CURRENT OPINION IN PLANT BIOLOGY 2015; 26:32-36. [PMID: 26116973 DOI: 10.1016/j.pbi.2015.05.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/20/2015] [Accepted: 05/21/2015] [Indexed: 06/04/2023]
Abstract
Root microbiomes are formed from diverse microbial soil settings with extraordinary consistency, suggesting both defined mechanisms of assembly and specific microbial activity. Recent improvements in sequencing technologies, data analysis techniques, and study design, allow definition of the microbiota within these intimate and important relationships with increasing accuracy. Comparing datasets provides powerful insights into the overlap of plant microbiomes, as well as the impacts of surrounding plants and microbes on root microbiomes and long-term soil conditioning. Here we address how recent studies tease apart the impact of various biotic interactions, including: plant-plant, plant-microbe, and microbe-microbe on root microbiome composition.
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Affiliation(s)
- Sarah Stuart Sloan
- Department of Microbiology, University of Tennessee, Knoxville, United States
| | - Sarah L Lebeis
- Department of Microbiology, University of Tennessee, Knoxville, United States.
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83
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Vandenkoornhuyse P, Quaiser A, Duhamel M, Le Van A, Dufresne A. The importance of the microbiome of the plant holobiont. THE NEW PHYTOLOGIST 2015; 206:1196-206. [PMID: 25655016 DOI: 10.1111/nph.13312] [Citation(s) in RCA: 894] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/05/2015] [Indexed: 05/18/2023]
Abstract
Plants can no longer be considered as standalone entities and a more holistic perception is needed. Indeed, plants harbor a wide diversity of microorganisms both inside and outside their tissues, in the endosphere and ectosphere, respectively. These microorganisms, which mostly belong to Bacteria and Fungi, are involved in major functions such as plant nutrition and plant resistance to biotic and abiotic stresses. Hence, the microbiota impact plant growth and survival, two key components of fitness. Plant fitness is therefore a consequence of the plant per se and its microbiota, which collectively form a holobiont. Complementary to the reductionist perception of evolutionary pressures acting on plant or symbiotic compartments, the plant holobiont concept requires a novel perception of evolution. The interlinkages between the plant holobiont components are explored here in the light of current ecological and evolutionary theories. Microbiome complexity and the rules of microbiotic community assemblage are not yet fully understood. It is suggested that the plant can modulate its microbiota to dynamically adjust to its environment. To better understand the level of plant dependence on the microbiotic components, the core microbiota need to be determined at different hierarchical scales of ecology while pan-microbiome analyses would improve characterization of the functions displayed.
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Affiliation(s)
| | - Achim Quaiser
- CNRS, UMR 6553 Ecobio, Université de Rennes 1, Campus Beaulieu, 35000, Rennes, France
| | - Marie Duhamel
- CNRS, UMR 6553 Ecobio, Université de Rennes 1, Campus Beaulieu, 35000, Rennes, France
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Amandine Le Van
- CNRS, UMR 6553 Ecobio, Université de Rennes 1, Campus Beaulieu, 35000, Rennes, France
| | - Alexis Dufresne
- CNRS, UMR 6553 Ecobio, Université de Rennes 1, Campus Beaulieu, 35000, Rennes, France
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84
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Lebeis SL. Greater than the sum of their parts: characterizing plant microbiomes at the community-level. CURRENT OPINION IN PLANT BIOLOGY 2015; 24:82-6. [PMID: 25710740 DOI: 10.1016/j.pbi.2015.02.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 05/25/2023]
Abstract
Specific subsets of microbes are capable of assembly into plant-associated communities that influence the fitness of both the host and the microbes. While there is a large spectrum of plant phenotypes cause by microbes, the microbial community members benefit from living in protected and nutrient rich plant-associated environments. Recent advances in '-omics' technologies have provided researchers with the ability to identify and assign functions to even unculturable microbes inhabiting both above-ground and below-ground plant tissues. Thus, we are beginning to unravel the molecular mechanisms of microbiome assembly and activities that contribute to overall plant health, not only for individuals, but also at the community-level.
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Affiliation(s)
- Sarah L Lebeis
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States.
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85
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Schlatter DC, Bakker MG, Bradeen JM, Kinkel LL. Plant community richness and microbial interactions structure bacterial communities in soil. Ecology 2015; 96:134-42. [DOI: 10.1890/13-1648.1] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Daniel C. Schlatter
- Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, Minnesota 55108 USA
| | - Matthew G. Bakker
- Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, Minnesota 55108 USA
| | - James M. Bradeen
- Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, Minnesota 55108 USA
| | - Linda L. Kinkel
- Department of Plant Pathology, University of Minnesota, 1991 Upper Buford Circle, Saint Paul, Minnesota 55108 USA
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86
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Rieseberg L, Vines T, Gow J, Geraldes A. Editorial 2015. Mol Ecol 2015; 24:1-17. [DOI: 10.1111/mec.12997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 11/10/2014] [Indexed: 11/30/2022]
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Brown P, Saa S. Biostimulants in agriculture. FRONTIERS IN PLANT SCIENCE 2015; 6:671. [PMID: 26379695 PMCID: PMC4550782 DOI: 10.3389/fpls.2015.00671] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/13/2015] [Indexed: 05/02/2023]
Affiliation(s)
- Patrick Brown
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
- *Correspondence: Patrick Brown, Department of Plant Sciences, University of California, Davis, MS#2, One Shields Avenue, Davis, CA 95616, USA
| | - Sebastian Saa
- Escuela de Agronomía, Pontificia Universidad Católica de ValparaísoQuillota, Chile
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88
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Becklund KK, Kinkel LL, Powers JS. Landscape-scale Variation in Pathogen-suppressive Bacteria in Tropical Dry Forest Soils of Costa Rica. Biotropica 2014. [DOI: 10.1111/btp.12155] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Kristen K. Becklund
- Department of Ecology, Evolution and Behavior; University of Minnesota; 100 Ecology Building 1987 Upper Buford Circle St. Paul MN 55108 U.S.A
| | - Linda L. Kinkel
- Department of Plant Pathology; University of Minnesota; St. Paul MN 55108 U.S.A
| | - Jennifer S. Powers
- Department of Ecology, Evolution and Behavior; University of Minnesota; 100 Ecology Building 1987 Upper Buford Circle St. Paul MN 55108 U.S.A
- Department of Plant Biology; University of Minnesota; St. Paul MN 55108 U.S.A
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89
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Russell JA, Dubilier N, Rudgers JA. Nature's microbiome: introduction. Mol Ecol 2014; 23:1225-1237. [PMID: 24628935 DOI: 10.1111/mec.12676] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 01/18/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Jacob A Russell
- Department of Biology, Drexel University, Philadelphia, PA, 19104, USA
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