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J.Miguel Barea - La era de la biotecnología microbiana en la agricultura


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Los días 20 y 21 de mayo de 2014, la Fundación Ramón Areces organizó el Simposio Internacional 'Microorganismos beneficiosos para la agricultura y la protección de la biosfera' dentro de su programa de Ciencias de la Vida y de la Materia.

Published in: Science, Technology

J.Miguel Barea - La era de la biotecnología microbiana en la agricultura

  1. 1. Thanks !!! Beneficial Microbes for Agriculture and Biosphere Protection B A B A B José-Miguel Barea
  2. 2. Estación Experimental del Zaidín (CSIC), Granada, Spain Dpto. Soil Microbiology and Symbiotic Systems The Mycorrhiza Group
  3. 3. Closing notes: The era of Microbial Biotechnology in Agriculture and Biosphere Protection José-Miguel Barea
  4. 4. 1. Problematic and Challenges 2. Research Approaches and Achievements 3. The Future: Challenges and Opportunities Presentation content:
  5. 5. 1. Problematic and Challenges
  6. 6. The problem: more people to feed !!! The challenge: to produce more foods while preserving the biosphere !!!
  7. 7. An intensive agricultural production is essentially necessary to satisfy food requirements for the growing world population, thus modern agriculture is nowadays being implemented at a global scale
  8. 8. A tremendous problem: intensive agriculture is associated to the mass consumption of:  Energy  Fossil fuel  Water  Forested areas  Topsoil  Rock phosphate reserves ...and with the emission of greenhouse gases generating global (climate) changes
  9. 9. Human population (increase in resource use) Human activities (Industry, Energy, Mining, Agriculture, Leisure, etc) Land transformations Changes in the biota (invassions, hanting, fishing) Biogeochemical cycles (C, N, P…) Climatic change (Global warming) Biodiversity losses (species extintion, ecosystem degradation) At a glance, the causes and consequencies Global Change: F. Sapiña, adapted from Vitousek et al. Science, 1977
  10. 10. G l o b a l c h a n g e s S u s t a i n a b l e s y s t e m s Population dinamics Biodiversity Landscape dinamics Ecosystem functioning AnthropicactivityInteractions: Biodiversity - Ecosystems functioning – Global change - (Kennedy & Smith, 1995)
  11. 11. Fertile soil Degradaded agrosystem Economic development Intensive Agriculture: Induces perturbations and unbalances, which give way to a spiral of stress situations for the agro-systems A human activity which generates Global change and degraded the agro-systems
  12. 12. As a consecuency of Intensive Agriculture, diverse types of stress situations are generated, all of then impacting on agro-ecosystems functionallity/ productivity: Salinity, Drought, Contamination Diseases, Pest Plant invassions Soil erosion Nutrient deficit Intensive Agriculture Global change Climatic change Stress factors Agrochemicals are used to control disease and pests and to provide plant with available nutrients, but this is not ecologically acceptable
  13. 13.  Agricultural and forestal productivity losses  Soil erosion  Biodiversity losses  Ecosystem degradation  Landscape fragmentation In summary: intensive agriculture, environmental contamination and deforestation cause an increase in the production of “greenhouse gases”, thereby increasing Earth´s temperature, known as the anthropogenic global warming, impacting on biosphere stability Consequently, a number of ecological constraits impacts on agro-ecosystems causing:
  14. 14. We need to produce more food, feed, fibre and bio-energy at low environmental costs, for the increasing world population, but preserving the biosphere, thus the challenge is to envisage sustainable alternatives and research approaches to meet these aims Unless the effects of agriculture are carefully managed through sustainable development, both agricultural systems and remaining natural ecosystems, will suffer degradation, increasing the lost of diversity and further limiting the ecosystem services they are capable of providing The triangle of sustainability Zancarini et al., 2013
  15. 15. 2. Research Approaches and Achievements
  16. 16. Different research approaches are being undertaken addressed to meet environmental and economical sustainability issues, trying to save at most as possible usage of non-renewable natural resources, but without compromising on yields New crops and cropping systems are needed, but production methods need to focus on efficient recycling of nutrients and effective control of pests and pathogens Soil is a non-renewable resource that perform key environmental, social, and cultural functions which are vital to human life and for the sustainability of global ecosystems, defined as ecosystem services. These, in part, result from soil microorganisms
  17. 17. A feasible and effective approach toward developing sustainable practices in modern agriculture is that based on exploiting the interactions between rhizosphere microbial communities and crops Most studies on rhizosphere microbial communities focuss on bacteria and fungi, either beneficial or pathogens Angus & Hirsch, 2013 Paungfoo et al, 2013
  18. 18. Many belowground interactions are known to affect plant health and productivity Zolla et al., 2013 Understanding root-microbiome interactions Environmental characteristics impacting plant performance are shown in the central triangle Root exudates potentially play major roles in attracting and maintaining beneficial soil communities The environmental quality of plant life is defined by interacting factors, including, soil, microbial activity, and outcomes of the plant´s own activity 109 cells,106 taxa, per g of soil, most of them are “unculturable”
  19. 19. Stimulation of seed germination and rooting Increasing soil nutrient availability Biocontrol of diseases and pests Plant protection against abiotic stresses Improvement of soil structure  Microorganisms carry out well-known activities able to improve plant growth and health, and soil quality  They can be manipulated as crops inoculants  Were crucial for plants to evolve on Earth  Beneficial services afforded by the soil microbiome Barea et al., 2013 Soil microbes can be threfore considered as “anti-stress” agents
  20. 20. Microorganisms played a fundamental role to facilitate plant origin, terrestrialization and evolution on Earth It is a fascinant history which demonstrates that microbes were crucial to help plants to thrive in a hostile and extremely stressed environment Microorganisms have to do the same now … and we have to increse our knowledge to exploit the ad hoc opportunities in manipulating their capabilities
  21. 21. Fossil and extant: Unicellular Green Fossil Extant Fossil Extant Cyanobacteria were found integrating stromatolites dated to be 3 300 M years old, the oldest living entity… … being able to fix atmospheric N and C Stromatolites: only 4 places in the world have fossilised representatives: Shark Bay, Australia AlgaeCyanobacteria Salar Llamara, Chile 2.000 M years old Lessons from fossils !!!
  22. 22. Earth formation Life origin ARCHAEAN PROTEROZOIC FANEROZOICPRECAMBRIAN Years (x106) Time/ Era Period Cyanobacteria Fungi Scale of the Geological Time 4500 4000 3500 3000 2500 2000 1500 1000 500 0 PHOTOSYNTHESIS NITROGENASE Biological C Fixation Biological N Fixation Unicellular Algae Plants “soil” appear Green Algae A mechanism for P supply was needed … … but we have evidences to think in AM for that !!!
  23. 23. Fossil AM fungal spores in the Rhynie Chert (about 410 M year-old) Dotzler et al, Mycol Progress, 2009 Fossil spores in a dolomite rock in Wisconsin (Ordivician, 460 MY) Redecker, Science (2000) Extant Arbuscules in early Devonian bryophyte–like plants (liverworts) and in early vascular plants (Rhyniophyta) Taylor, 2004 Smith & Read, 2008 Fossil like-AM fungal structures in early liverworts (Ordovician) Extant More than 450 MY of a common history of plants and their mycorrhiza Presence of AM structures in earlier “plants” suggests AM as a mechanism for P supply
  24. 24. Equisetes Licopodia “Rhynie” Liverworts Arbuscules in the stems Arbuscules is rhizomes Ferns AM in root, similar to those extant Cycadins AM extant Ginkgoals AM Araucariaceae AM Conifers N hemipher AM/ECM Cesalpinoideae Mimosaceae Salicaceae ECM y AM Ericals Ericoid Orquids Orquidoid Angiosperms ECMPinaceae ECM o AM Fagals ECM (+ AM) AM a key tool for plant origin and evolution
  25. 25. Conclusions: AM fungi and other microorganisms helped plant to thrive (terrestrialization) in a very hostile environment They co-evolved with the plant and are currently continuing playing such a role in environments suffering from any type of stress As stress situations impact negatively both on crops and plant communities, and on their associated root-microbiome, we need to restore beneficial microorganisms by means of microbial inoculation or by harnessing the remaining microbiome to improve plant nutrition and health
  26. 26. Possible effects of disrupting plant-microbiome adaptation on sensitivity to subsequent disease outbreaks Bakker et al. Plant Soil 360:1-13 (2012) Longstanding and specific relationships between microbes and plants appear to have led to a co-evolution between the two
  27. 27. Sustainable quality production/ Ecological revegetation To maximize the benefical role of rhizosphere microbes Modern agriculture/ Ecosystem restoration Microbial inoculum application or transplanting of microbized plants GLOMYGEL®
  28. 28. Sapropytes N2–fixing and others bacteria Rhizobacteria Rhizofungi (Trichoderma) Endophytic symbionts Mycorrhizal and other fungi Beneficial microorganisms used as crop inoculants Endo- Ectendo- Ecto- Seedling establishment Nutrient cycling Plant protection Bioremediation Soil conservation Plant succession Mycoparasitism, Antibiotic production, Induced Resistance
  29. 29. Plant protection against osmotic stress: drought, salinity etc. Quorum sensing Rhizobacteria (PGPR): benefiting plant growth and health, and improving soil quality Biocontrol of plant pathogens Plant growth promotion Antibiosis Antagonism Antioxidants Induced resistance Siderophores Plant hormones N2-fixation P-solubilization ACC deaminase Siderophores Improvement of soil quality: soil structure, organic matter cycling and fitoremediation Biodiversity regulation and eco-dynamics of microbial populations Barea, Azcón, Pozo & Azcón-Aguilar, 2013
  30. 30. Rhizosphere Roots * Plant establishment and development (Phytostimulation) * Nutrient cycling and supply (Biofertilization) * Plant protection, Induced resistance (Biocontrol) * Phytoremediation (Bioremediation) * Soil conservation (Agro-ecosystems restoration) Tailored Mycorrhizosphere Co-inoculation with target bacteria Microbe-Microbe interactions Mycorrhiza Mycorrhizosphere Mycorrhizosphere tailoring to improve plant fitness and soil quality through key ecological processes Barea, Azcón, Pozo & Azcón-Aguilar, 2013 MHB
  31. 31. Defense A B C D EA B Synergistic interactions among antagonistic microorganisms and mycorrhiza for the biological control of plant pathogens: A model including plant roots, mycorrhizas, bacteria, fungi, nematodes, etc. Antagonistic bacteria on the root surface (A) or associated to spores or mycelia (B) from mycorrhizal plants (C) and Trichoderma spp, a mycoparasitic fungus (D). These microorganisms synergistically interact and protect the plant against pathogens (E) through the combination of different mechanisms Barea, Azcón, Pozo & Azcón-Aguilar, 2013
  32. 32. 3. The Future: Challenges and Opportunities
  33. 33. The future The present Beneficial Microbes for Agriculture and Biosphere Protection  Establishing action/concepts & scenarios for the application of beneficial microbes through implementing the production of high quality microbial inoculants  Understanding root-microbiome interactions based on using the already available culture-independent molecular techniques  Engineering the rhizosphere to optimize their role in nutrient supply and plant protection: the “biased rhizosphere” concept/action Challenges and opportunities in the nearest future The past
  34. 34.  Agroecology  Sustainable agriculture  Inducing resistance to environmental stresses  Improvement of the quality of agro-derived foods  Ecosystem restoration (& recovery of endangered flora)  Enhancing resilience of plant communities  Adaptive strategies for biodiversity conservation Action/concepts & scenarios for applying eneficial microbes to increase stability/productivity of agro-ecosystems while preserving the biosphere (in the current scenario of climatic change)
  35. 35. Agroecology: a basis for sustainability A target scenario to manage the soil microbiome Sustainability Agroecology EnvironmentSociety Economy Life standard Environmental awareness Sustainable development
  36. 36. Sustinable productivity Resource conservation Environmentally-acceptable Safe and healthy Reduction of chemical inputs Residue management Uses renewable energy sources Biotechnology (nitrogenase, legumes, cereals) Crop rotation Water and soil conservation Integrated control of pest and diseases Use of microbes to improve nutrient availability Sustainable Agriculture Biodiversity conservative
  37. 37. What do we need to implement? - To increase the scientific/technological bases of inoculum production and application - Generation of specific normatives for each inoculant type and its application, either on the seeds or on the soil, or to the plant,to be transplanted already microbized - Quality control protocols - Minimize the variability of the field results - Implementation of knowledge dissemination approaches: advantages & limitations, and benefits for Society/Science Microbial inoculants in Agriculture By courtesy of Juan Sanjuan Taking advantage from co-inoculation
  38. 38. Yoav Bashan, Luz E. de Bashan, S. R. Prabhu, J. P. Hernandez Plant and Soil 378:1-33 (2014) Procedures for developing bacterial inoculants
  39. 39. Yoav Bashan, Luz E. de Bashan, S. R. Prabhu, J. P. Hernandez Plant and Soil 378:1-33 (2014) Advances in plant growth-promoting bacterial inoculant technology: formulations and practical perspectives Formulations of inoculants for agricultural and environmental uses
  40. 40. Visualization of root-establishment of inoculated microorganisms Inoculated biocontrol Pseudomonas form biofilms covered by a mucoid layer (f), which created an ideal condition for QS and the related synthesis of antibiotic & enzymes (Lugtenberg et al., 2013) Endophytic bacteria (FISH) Malfanova et al., 2013 Mercado-Blanco & Prieto, 2013 Endophytic Pseudomonas
  41. 41. Developing strategies for using microbes and plant in cutting-edge application areas such as sustainable agriculture and phytoremediation • Using a plethora of culture-independent molecular techniques, including genomic sequencing and metagenomics • How signaling between plants and microorganisms promotes plant growth and development as well as nitrogen fixation and mycorrhization • Biocontrol and disease-suppression approaches • Properties of bacterial endophytes leading to maximized host fitness • Applications and implications for ecological studies, decontamination of heavy metals, and food production in the era of climate change • How plants structure microbial communities in the rhizosphere to encourage beneficial organisms and ward off pathogens • Engineering the rhizosphere: The biased rhizosphere concept de Bruijn, F.J. (Ed.) Molecular Microbial Ecology of the Rhizosphere (2013)
  42. 42. System-based approaches to study the plant-microbial interactions Omics-driven microbial ecology: the tools are available Barret et al., 2013 . Pyrosequencing . 3rd generation sequencing Comparative genomic information on plant-associated bacteria
  43. 43. Rhizosphere metatranscriptomics, although currently challenging, is providing microbial activity profiles in the form of expressed functional genes that play important roles during these and other yet unknown interactions Carvalhais et al., 2013 Research scenarios for dissecting root-microbe relationships Rhizosphere metatranscriptomics: challenges and opportunities
  44. 44. PGPR, through impacting on plant hormone status, modify root architecture to capture existing soil resources, including nutrients (N, P, Fe) and enhance water acquisition Ortiz-Castro & López-Bucio, 2013 Transkingdon communications Small molecule signals that regulate plant architecture, including the six classic phytohormones and novel plant signal (alkamides) bacterially- produced AHLs and diketopiperacines Fundamental for understanding root-microbiome interactions
  45. 45. Transkingdon communications Major signaling events occurring between plant roots and PGPR or between PGPR themselves Drogue et al., 2013 Plants and microbes use chemical signals to communicate and this determines which microbes associate with the plant
  46. 46. Jayaraman et al 2012 Signaling in key processes involved in nutrient supply and plant protection follows similar pathways PAMP = Pathogen-Associated Molecular Partners Effectors are strain specific and contribute to pathogen virulence How signaling between plants and microorganisms promotes plant growth and development as well as nitrogen fixation and mycorrhization
  47. 47. Different root-associated microbes elicit induced systemic resistance (ISR) via jasmonic acid- (JA), ethylene- (ET,) salicylic acid- (SA) or abscisic acid- (ABA) signaling pathways. Root-associated microbes are also known to induce plant growth promotion via auxin- (AUX), cytokinin- (CK), brassinosteroid- (BR) and gibberellin- (GA) signaling pathways. JA is considered the main hormone regulating the switch from growth to defense through positive and negative crosstalk with other plant hormones. Model of interactions between plant hormones regulating plant defense and development in microbe–plant–insect interactions Pangesti, N., Pineda, A., Pieterse, C. Dicke, M., and Van Loon, J. Frontiers in Plant-Microbe Interaction|2013
  48. 48. Mycorrhiza Induced Systemic Resistance (MIR) aginst plant pathogens Priming (JA regulated) of plant defenses: a key for MIR” AM formation reduced release of strigolactones (SLs), which minimizes the risk of infection by root parasitic plants The primed plant defense restrict the development of necrotrophic pathogens and the performance of phytophagous insects in the abovegrown plant parts. Indirect defenses, such as the release of volatiles, are boosted and parasitoids are efficiently attracted Priming (JA regulated) of plant defenses by AM leads to a general reduction of the incidence and/or damage caused by soil- borne pathogens, nematodes, and chewing insects Pozo, M.J., Jung, S.C., Martínez-Medina, A., López-Ráez, J.A., Azcón-Aguilar, C., Barea, J.M. 2013. In: Symbiotic Endophytes (Ed: R. Aroca). Springer-Verlag
  49. 49. Schematic overview showing the different types of plant-endophyte interactions leading to the synthesis of metabolites Metabolic potential of endophytic bacteria Current Opinion in Biotechnology 27 (2014) 30 - 37 Brader, G ., Compant, S., Mitter, B., Trognitz F, Sessitsch, A.
  50. 50. Improving phytoremediation by rhizosphere microbes • Extracellular chelation/precipitation • Trapping the metal by cell wall components • Intracelullar chelation • Intracellular storage Mechanisms involved in HM tolerance in AM fungi Several studieshave demonstrated that: AM fungi can play a key role in phytoremediation of HM-contaminated soils because they improve plant establishment and development, and reduce HM translocation to the shoot, therefore, AM-PLANTS RESULT MORE TOLERANT TO HM The molecular mechanisms involved are being studied N. Ferrol et al. EEZ Germaine et al.,2013 Afzal et al.,2013 Plants can transform alkanes but only rhizobacteria and endophytes can completely degrade them
  51. 51. Schlaeppi et al.,2013 Achouak and Haichar, 2013 Plants select their own microbiome Philippot et al.,2013 Zolla et al.,2013 Shaping microbial communities in the rhizosphere as a new opportunity for linking structure and function of the root-microbiome to increase nutrient supply and plant protection: Plants having different life-forms have the capacity to promote diverse AMF communities based of their functional characteristics López-García, Barea & Azcón-Aguilar, 2014 Which are the biotic and abiotic factors that shape the rhizosphere microbiome ? Which are the factors that regulate the expression of plant-beneficial microbial traits ?
  52. 52.  Plants select their associated microbiome, a selection which is depending on the age of the plant  Belowgrown microbiome by changing plants´ physiological and metabolical response, facilitates ISR and predation strategies above-grown  The impact of root-associated microbiome on plant fitness changes with plant age Spence & Bais (2013) Temporal dynamics of AMF colonizing roots of representative shrub species in a semi-arid Mediterranean ecosystem Sánchez-Castro, Ferrol, Cornejo & Barea, 2012 Microbial diversity in the rhizosphere may change with age and season in both agrosystem and natural ecosystem A key protagonist is rhizodeposition
  53. 53. Hirsch et al., 2013 The possibilities for manipulating plant-driven regulation for intended agricultural, environmental, ecological, and food safety outcomes are now becoming apparent The rhizodeposits influence soil microbial community structure associated to a target plant Now is becoming feasible that the pattern of plant host exudation can be bred or engineered to establish biased rhizospheres with bacteria that can naturally, or by engineering, to use metabolic resources produced by the host plant Origing of the various rhizodeposit pools
  54. 54. Alternate paths to realizing the goal of using plants to enrich beneficial microbial functions: targetting particular microbial taxa or services (left side), or a broad microbiome characteristics that may promote plant performance (right side) Bakker et al. Plant Soil 360:1-13 (2012) Harnessing the rhizosphere microbiome through plant breeding and agricultural management Strategies for more effectively exploiting beneficial microbial services on agricultural systems
  55. 55. Bakker et al. Plant Soil 360:1-13 (2012) Harnessing the rhizosphere microbiome through plant breeding and agricultural management A variety of strategies could be used to promote beneficial services provided by soil microbial communities, with the aim of reducing chemical inputs while sustaining or improving crop yields Manipulating plant traits that are related to interactions with microbes (left side), or manipulating soil microbial communities directly (right side),could improve conditions for plant productivity (center mechanisms) Strategies for more effectively exploiting beneficial microbial services on agricultural systems
  56. 56. Priorities for future research to advance the goal of more fully exploiting beneficial microbial functions in agriculture (I) • Make positive interactions with the rhizosphere microbiome an explicit goal of plant breeding, and expand understanding of the mechanistic basis for the interactions. • Understand the impacts of plant genotype on the rhizosphere microbiome and on the ability of plants to interact with beneficial microbes. • Develop strategies to selectively enrich for indigenous microbes performing beneficial functions. • Identify root exudate components that have the largest/most consistent effects on shaping microbial communities. • Clarify the relative importance of exudate identity, quantity, and diversity. Bakker et al (2012)
  57. 57. • Clarify the importance of chemical signaling (vs. resource provision) in plant-driven structuring of the rhizosphere microbiome. • Expand study of mechanisms and extent of plant impacts on the bulk soil microbiome. • Understand the extent and significance of microbial adaptation to host plants. • Expand study of naturally occurring positive plant-soil feedbacks to draw new insights for agriculture. • Investigate the importance of broad microbiome characteristics (such as richness and evenness) in promoting plant health. Priorities for future research to advance the goal of more fully exploiting beneficial microbial functions in agriculture (II) Bakker et al (2012)
  58. 58. Feed-back loop in plant–microbe interactions in the rhizosphere that links plant genotype/functioning and microbial communities Zancarini et al., 2013 Combining molecular microbial ecology with ecophysiology and plant genetic for a better understanding of plant-microbiome interactions in the rhizosphere Exploiting plant genotypic influence to manipulate the functional capabilities of rhizosphere microbiome, or “direct” plant-soil-microbes interactions to benefit nutrient supply and plant protection: a key tool for future sustainable agriculture
  59. 59. Impact of stress on plant – microbiome interactions in the rhizosphere Zolla et al., 2013 • Plant stresses alter plant-microbe interactions in the rhizosphere through a combination of altered root exudation and shared experience of stress by soil microbes. • Plants may direct interactions with microbes to encourage microbial activities that alleviate plant stress. • Plant changes in morphology, stress physiology, and transporter activity result in changed a root exudate profile The cross talk involved in plant-microbiome interactions in the rhizosphere is altered under stress conditions, and may be used by plants to recruit microbes with stress-alleviating functions. Improved and emerging technologies will allow for more complete characterization of the rhizosphere microbiome and root exudation Harnessing beneficial microbial functions to enhance plant performance under stress will complement ongoing improvements through conventional plant breeding and genetic engineering
  60. 60. Thanks for your attention !!!