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Managing and manipulating the rhizosphere microbiome for plant health: A systems approach
Author’s Accepted Manuscript Managing and manipulating the rhizosphere microbiome for plant health: A systems approach Matthew D. Wallenstein
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PII: DOI: Reference:
S2452-2198(17)30044-7 http://dx.doi.org/10.1016/j.rhisph.2017.04.004 RHISPH48
To appear in: Rhizosphere Received date: 24 February 2017 Revised date: 6 April 2017 Accepted date: 6 April 2017 Cite this article as: Matthew D. Wallenstein, Managing and manipulating the rhizosphere microbiome for plant health: A systems approach, Rhizosphere, http://dx.doi.org/10.1016/j.rhisph.2017.04.004 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Managing and manipulating the rhizosphere microbiome for plant health: A systems approach Matthew D. Wallensteina,b1 a
Department of Ecosystem Science and Sustainability, Colorado State University Natural Resource Ecology Laboratory, Colorado State University
b
[email protected] Abstract Plants co-evolved with microbes, and plant genotypes that supported microbiomes that increased their own health likely had a fitness advantage under natural selection. Plant domestication and crop breeding under fertilization have largely decoupled the rhizosphere microbiome from plant selection. If important interactions have been lost as a result, there is an exciting opportunity to re-engineer characteristics of beneficial rhizosphere microbiomes back into agricultural cropping systems. New tools will allow us to engineer the rhizosphere with increasing sophistication in the future, but must recognize that the rhizosphere is a highly connected and interactive system. Plant-microbe rhizosphere interactions: Evolution of the holobiont Plants evolved into a microbial world. When the earliest plants extended their roots into primordial soil, they encountered a habitat already teeming with bacterial and fungal life (Heckman et al. 2001). From day one, plants likely started to influence the rhizosphere microbiome. Their roots altered the physical structure of soils. They extracted nutrients from the soil, competing with microbes. They extracted water from the soil, altering the soil moisture regime encountered by microbes. Their detritus led to the accumulation of organic carbon which was then processed by heterotrophic microbes, leading to the formation of soil organic matter (SOM) (Cotrufo et al. 2013, Lehmann and Kleber 2015). As they began leaking carbon-rich substrates through their roots, those labile substrates likely favored microbes that could quickly assimilate them (Doornbos et al. 2012). By altering the physical and chemical environment in the rhizosphere, plants affected the fitness of different microbial groups, interactions among microbes, and spurred evolution of new microbes better suited to life in the rhizosphere (Lambers et al. 2009). There is now overwhelming evidence that plants engineer the rhizosphere microbiome (Chaparro et al. 2014). Even the most ancient lineages of plants show a strong ability to alter the relative abundance of microbial groups in the soils surrounding the rhizosphere (Valverde et al. 2016). Different plant species support unique microbiomes (Gertsson and Alsanius 2001). These contrasting microbiomes have been attributed to differences in root exudate chemistry (Bais et al. 2006, Rasmann and Turlings 2016) and in plant nutrient uptake rates (Bell et al. 2015). Given that plants can affect the rhizosphere microbiome through numerous mechanisms and that the microbiome can affect plant health (Berendsen et al. 2012, Mueller and Sachs 2015), a reasonable hypothesis emerges: Genotypic and phenotypic variations in plant traits that support microbiomes that increase plant nutrient availability, prevent pathogens or otherwise enhance plant health, growth and performance incur a fitness advantage. Thus, the ability of a plant to support a beneficial microbiome is a plant trait under selection. The fitness advantage incurred by the microbiome must outweigh the cost to the plant in diverted C and energy. The close symbiosis of plants and microbes can be viewed as an 1
Campus Delivery 1499, Fort Collins, CO 80523, USA. 970-556-2591
integrated ecological unit known as a holobiont (Vandenkoornhuyse et al. 2015). For hundreds of millions of years, the holobiont may have been the unit under selection, guiding evolution towards plant traits that supported beneficial microbiomes. Plant domestication and crop breeding: Decoupling the holobiont As humans began to domesticate plants and develop cropping systems, farmers began to artificially select crops based on traits other than reproductive fitness, diverging from natural selection. As humans began to select for large seed size, reduced bitterness–a key defense mechanism– and other traits, we inadvertently changed plant traits that regulate the microbiome. Recent evidence suggests that domestication has altered the microbiomes recruited by plants (Leff et al. 2016, Perez-Jaramillo et al. 2016), though the functional consequences are unknown. Some of these plant traits under breeding selection may be linked to the microbiome. For example, plant phenology has been shown to be influenced by the soil microbiome (Wagner et al. 2014, Panke-Buisse et al. 2015). In early agriculture, plants that supported beneficial microbiomes may still have been selected, as they may have exhibited favorable traits such as more rapid growth and production and better disease resistance. The greatest divergence from natural selection likely occurred with the advent of Haber-Bosch fertilizer. From that point on, we partly obviated the need for one of the key microbial functions- nutrient cycling. No longer was crop yield directly linked to a plants’ ability to support microbial nutrient cycling. In fact, N fertilization reduces microbial biomass and diversity (Treseder 2008, Ramirez et al. 2010), promoting copiotrophs over oligotrophs (Fierer et al. 2012). The selection of plants under high fertilization regimes likely accelerated the decoupling of the soil microbiome from plant fitness. Since we began breeding plants under high fertilization regimes, we may have been selecting against genotypes that support microbial N mineralization (Schmidt et al. 2016), as there must be important trade-offs. As a result, modern varieties may have lost their ability to support microbiomes that degrade organic nitrogen and solubilize mineral nutrients like phosphorus (Figure 1). Rhizosphere Engineering: A systems perspective Imagine if we had the tools to engineer the ideal rhizosphere. What characteristics would we engineer for? How would it function? Certainly, we would want to optimize water holding capacity, nutrient cycling rates, and pathogen resistance. Given the key roles of microbes in soil organic matter formation, nutrient mineralization and solubilization and pathogen pressure, approaches and tools that allow us to manipulate the microbiome would be key to rhizosphere engineering. Currently, our ability to manage and manipulate the rhizosphere microbiome is limited. The most direct way to alter the microbiome is through inoculation. Products containing one or several species of bacteria or fungi have been commercially available for decades (Calvo et al. 2014). However, most of these species were isolated under traditional culturing conditions that do not emulate the soil chemical environment. Inoculants often show promising results under controlled lab and greenhouse conditions which are not consistently reproducible under natural field conditions but there is only limited evidence that these inoculated microbes establish, compete, and function in agricultural soils (Verbruggen et al. 2013). In part, this is due to the broad range of conditions experienced by microbes in the field. Not only do key attributes like pH, nutrient stoichiometry and texture differ among soils, but the climate regime experienced by microbes in the field spans a broad range. The conditions must overlap with the multidimensional niche of the inoculated microbes for them to have a chance to survive, reproduce and function. But, they also must integrate themselves not only with the native microbiome, but with the food web (Morrien 2016). Many inoculants may fail under field conditions simply because they are quickly consumed by predators or outcompeted for resources by native microbes. In nature, healthy plants recruit microbes from highly diverse, but weakly connected bulk soils, and favor rhizosphere microbiomes that
are less diverse but highly structured into modules of highly interactive microbes and soil fauna (Figure 1; DeVries and Wallenstein, in press). Effective inoculants must form associations with the rest of the microbiome, emulating the strongly structured networks in native rhizosphere soils (Figure 1; DeVries and Wallenstein in press, Shi et al. 2016). Other approaches add organic materials with rich but undefined and unknown mixtures of microbes to soils (Scheuerell and Mahaffee 2002, Naidu et al. 2010), with the idea that adding diversity should lead to improved function and pathogen resistance (Jousset et al. 2011, van Elsas et al. 2012). If true, diversity could also decrease the ability of beneficial inoculants to proliferate. But, evidence for a strong positive relationship between microbial -diversity and function is weak in all but the most barren soils (Griffiths and Philippot 2013). Furthermore, resource pulses can temporarily alleviate competition, which could lead to pathogen invasion (Mallon et al. 2015). This approach is likely to have more success in highly degraded soils with low diversity and weak food web interactions.
While nature has already offered an incredible diversity of microbes that vary in traits and function, new gene editing and synthetic biology tools offer another path to engineer microbes with targeted functions (Hutchison et al. 2016). While these techniques are powerful, they raise concerns related to novel gene release and face negative consumer attitudes towards gene modifications (Leak 2010). A systems perspective suggests that they are unlikely to function under field conditions unless their interactions with the environment and the soil food web are considered in their design–a complex challenge. Another pathway to engineering the rhizosphere is through breeding or engineering plant traits (Nogales et al. 2015). As we identify specific root exudates, root architecture, or other plant traits that support beneficial microbiomes, we will be able to engineer those traits into crops through CRISPR and other gene editing tools. This approach seems promising as it emulates the interactions that support beneficial microbes in natural systems and which were selected through evolution of the holobiont. Since the microbiome is strongly influenced by the quantity and quality of SOM, management practices that aim to enhance these soil attributes should benefit the microbiome. In addition to management practices like no-till and cover crops, we can directly increase soil organic matter through additions of organic materials. For example, small additions of compost can have lasting benefits (Ryals et al. 2014). Yet, millions of tons of food-related waste are sent to landfills each year (Parfitt et al. 2010). There is a tremendous opportunity to process this organic waste and return it back to the farm. If these resource pulses coincide with beneficial inoculants, the temporary decrease in competition by native microbes could enhance their success. In the coming decades, we will be purposefully engineering the rhizosphere with increasing sophistication. The rhizosphere is a complex adaptive system of closely interacting biological, chemical, and physical components. Successful rhizosphere engineering will require a systems perspective (Figure 1). As we learn how to engineer the interactive rhizosphere, we can enhance the efficiency and sustainability of crop production only by emulating the symbiotic interactions between plants, soils, and microbes that evolved over millions of years in nature.
Figure 1. Hypothesized conceptual models of rhizosphere systems in (A) natural ecosystems, (B) degraded systems such as those under intensive management and high fertilization and (C) rhizospheres that have been engineered through inoculants that form connections with the native microbiome or soil amendments that stimulate microbial activity. Natural rhizospheres are characterized by highly structured and interactive microbiomes and food webs because plants co-evolved with their microbiomes and support them through root exudation. As crops were selected under intensive management, these connections likely decreased. In the future, a systems approach to rhizosphere engineering could restore some features of natural rhizospheres through soil amendments, inoculants and plant traits that support beneficial microbiomes. References Bais, H. P., T. L. Weir, L. G. Perry, S. Gilroy, and J. M. Vivanco. 2006. The role of root exudates in rhizosphere interactions with plants and other organisms. Annual review of plant biology 57:233– 66. Bell, C. W., S. Asao, F. Calderon, B. Wolk, and M. D. Wallenstein. 2015. Plant nitrogen uptake drives rhizosphere bacterial community assembly during plant growth. Soil Biology and Biochemistry 85:170–182. Berendsen, R. L., C. M. J. Pieterse, and P. A. H. M. Bakker. 2012. The rhizosphere microbiome and plant health. Trends in Plant Science 17:478–486. Calvo, P., L. Nelson, and J. W. Kloepper. 2014. Agricultural uses of plant biostimulants. Plant and Soil 383:3–41. Chaparro, J. M., D. V Badri, and J. M. Vivanco. 2014. Rhizosphere microbiome assemblage is affected by plant development. The ISME journal 8:790–803. Cotrufo, M. F., M. D. Wallenstein, C. M. Boot, K. Denef, and E. Paul. 2013. The Microbial EfficiencyMatrix Stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization: Do labile plant inputs form stable soil organic matter? Global Change Biology 19:988–995. DeVries, F., and M. D. Wallenstein. (n.d.). Belowground connections underlying aboveground food production: a framework for optimising ecological connections in the rhizosphere. Journal of Ecology. Doornbos, R. F., L. C. Van Loon, and P. A. H. M. Bakker. 2012. Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. A review. Agronomy for Sustainable Development 32:227–243.
van Elsas, J. D., M. Chiurazzi, C. A. Mallon, D. Elhottova, V. Kristufek, and J. F. Salles. 2012. Microbial diversity determines the invasion of soil by a bacterial pathogen. Proceedings of the National Academy of Sciences of the United States of America 109:1159–64. Fierer, N., C. L. Lauber, K. S. Ramirez, J. Zaneveld, M. A. Bradford, and R. Knight. 2012. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. The ISME Journal 6:1007–17. Gertsson, U. E., and B. W. Alsanius. 2001. Plant Response of Hydroponically Grown Tomato to Bacterization. International Symposium on Growing Media and Hydroponics 644:583–588. Griffiths, B. S., and L. Philippot. 2013. Insights into the resistance and resilience of the soil microbial community. FEMS Microbiology Reviews 37:112–129. Heckman, D. S., D. M. Geiser, B. R. Eidell, R. L. Stauffer, N. L. Kardos, and S. B. Hedges. 2001. Molecular Evidence for the Early Colonization of Land by Fungi and Plants. Science 293. Hutchison, C. A., R.-Y. Chuang, V. N. Noskov, N. Assad-Garcia, T. J. Deerinck, M. H. Ellisman, J. Gill, K. Kannan, B. J. Karas, L. Ma, J. F. Pelletier, Z.-Q. Qi, R. A. Richter, E. A. Strychalski, L. Sun, Y. Suzuki, B. Tsvetanova, K. S. Wise, H. O. Smith, J. I. Glass, C. Merryman, D. G. Gibson, and J. C. Venter. 2016. Design and synthesis of a minimal bacterial genome. Science 351. Jousset, A., W. Schulz, S. Scheu, and N. Eisenhauer. 2011. Intraspecific genotypic richness and relatedness predict the invasibility of microbial communities. The ISME Journal 5:1108–1114. Lambers, H., C. Mougel, B. Jaillard, and P. Hinsinger. 2009. Plant-microbe-soil interactions in the rhizosphere: an evolutionary perspective. Plant and Soil 321:83–115. Leak, D. 2010. “Venter creates synthetic life” - should we be scared? Chemistry & Industry:16–16. Leff, J. W., R. C. Lynch, N. C. Kane, and N. Fierer. 2016. Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus. New Phytologist 214:412–423. Lehmann, J., and M. Kleber. 2015. The contentious nature of soil organic matter. Nature 528:60–8. Mallon, C. A., F. Poly, X. Le Roux, I. Marring, J. D. Van Elsas, and J. F. Salles. 2015. Resource pulses can alleviate the biodiversity-invasion relationship in soil microbial communities. Ecology 96:915– 926. Morrien, E. 2016. Understanding soil food web dynamics, how close do we get? Soil Biology and Biochemistry 102:10–13. Mueller, U. G., and J. L. Sachs. 2015. Engineering Microbiomes to Improve Plant and Animal Health. Trends in Microbiology xx:1–12. Naidu, Y., S. Meon, J. Kadir, and Y. Siddiqui. 2010. Microbial starter for the enhancement of biological activity of compost tea. International Journal of Agriculture and Biology 12:51–56. Nogales, A., V. Valadas, C. Ragonezi, A. Polidoros, and B. Arnholdt-schmitt. 2015. Can functional hologenomics aid tackling current challenges in plant breeding ?1–10. Panke-Buisse, K., A. C. Poole, J. K. Goodrich, R. E. Ley, and J. Kao-Kniffin. 2015. Selection on soil microbiomes reveals reproducible impacts on plant function. The ISME journal 9:980–9. Parfitt, J., M. Barthel, and S. Macnaughton. 2010. Food waste within food supply chains : quantification and potential for change to 2050:3065–3081. Perez-Jaramillo, J. E., R. Mendes, and J. M. Raaijmakers. 2016. Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Molecular Biology 90:635–644. Ramirez, K. S., C. L. Lauber, R. Knight, M. A. Bradford, and N. Fierer. 2010. Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems. Ecology 91:3463–3470. Rasmann, S., and T. C. J. Turlings. 2016. Root signals that mediate mutualistic interactions in the rhizosphere. Ryals, R., M. Kaiser, M. S. Torn, A. Asefaw, and W. L. Silver. 2014. Soil Biology & Biochemistry Impacts of organic matter amendments on carbon and nitrogen dynamics in grassland soils. Soil Biology and Biochemistry 68:52–61. Scheuerell, S., and W. Mahaffee. 2002. Compost tea: Principles and prospects for plant disease control. Compost Science & Utilization 10:313–338.
Schmidt, J. E., T. M. Bowles, and A. C. M. Gaudin. 2016. Using Ancient Traits to Convert Soil Health into Crop Yield: Impact of Selection on Maize Root and Rhizosphere Function. Frontiers in plant science 7:373. Shi, S., E. E. Nuccio, Z. J. Shi, Z. He, J. Zhou, M. K. Firestone, and N. Johnson. 2016. The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages. Treseder, K. K. 2008. Nitrogen additions and microbial biomass: A meta-analysis of ecosystem studies. Ecology Letters 11:1111–1120. Valverde, A., P. De Maayer, T. Oberholster, J. Henschel, M. K. Louw, and D. Cowan. 2016. Specific Microbial Communities Associate with the Rhizosphere of Welwitschia mirabilis, a Living Fossil. PLOS ONE 11:e0153353. Vandenkoornhuyse, P., A. Quaiser, M. Duhamel, A. Le Van, and A. Dufresne. 2015. The importance of the microbiome of the plant holobiont. New Phytologist 206:1196–1206. Verbruggen, E., M. G. A. van der Heijden, M. C. Rillig, and E. T. Kiers. 2013. Mycorrhizal fungal establishment in agricultural soils: factors determining inoculation success. New Phytologist 197:1104–1109. Wagner, M. R., D. S. Lundberg, D. Coleman-Derr, S. G. Tringe, J. L. Dangl, and T. Mitchell-Olds. 2014. Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecology Letters 17:717–726.
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PII: DOI: Reference:
S2452-2198(17)30044-7 http://dx.doi.org/10.1016/j.rhisph.2017.04.004 RHISPH48
To appear in: Rhizosphere Received date: 24 February 2017 Revised date: 6 April 2017 Accepted date: 6 April 2017 Cite this article as: Matthew D. Wallenstein, Managing and manipulating the rhizosphere microbiome for plant health: A systems approach, Rhizosphere, http://dx.doi.org/10.1016/j.rhisph.2017.04.004 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Managing and manipulating the rhizosphere microbiome for plant health: A systems approach Matthew D. Wallensteina,b1 a
Department of Ecosystem Science and Sustainability, Colorado State University Natural Resource Ecology Laboratory, Colorado State University
b
[email protected] Abstract Plants co-evolved with microbes, and plant genotypes that supported microbiomes that increased their own health likely had a fitness advantage under natural selection. Plant domestication and crop breeding under fertilization have largely decoupled the rhizosphere microbiome from plant selection. If important interactions have been lost as a result, there is an exciting opportunity to re-engineer characteristics of beneficial rhizosphere microbiomes back into agricultural cropping systems. New tools will allow us to engineer the rhizosphere with increasing sophistication in the future, but must recognize that the rhizosphere is a highly connected and interactive system. Plant-microbe rhizosphere interactions: Evolution of the holobiont Plants evolved into a microbial world. When the earliest plants extended their roots into primordial soil, they encountered a habitat already teeming with bacterial and fungal life (Heckman et al. 2001). From day one, plants likely started to influence the rhizosphere microbiome. Their roots altered the physical structure of soils. They extracted nutrients from the soil, competing with microbes. They extracted water from the soil, altering the soil moisture regime encountered by microbes. Their detritus led to the accumulation of organic carbon which was then processed by heterotrophic microbes, leading to the formation of soil organic matter (SOM) (Cotrufo et al. 2013, Lehmann and Kleber 2015). As they began leaking carbon-rich substrates through their roots, those labile substrates likely favored microbes that could quickly assimilate them (Doornbos et al. 2012). By altering the physical and chemical environment in the rhizosphere, plants affected the fitness of different microbial groups, interactions among microbes, and spurred evolution of new microbes better suited to life in the rhizosphere (Lambers et al. 2009). There is now overwhelming evidence that plants engineer the rhizosphere microbiome (Chaparro et al. 2014). Even the most ancient lineages of plants show a strong ability to alter the relative abundance of microbial groups in the soils surrounding the rhizosphere (Valverde et al. 2016). Different plant species support unique microbiomes (Gertsson and Alsanius 2001). These contrasting microbiomes have been attributed to differences in root exudate chemistry (Bais et al. 2006, Rasmann and Turlings 2016) and in plant nutrient uptake rates (Bell et al. 2015). Given that plants can affect the rhizosphere microbiome through numerous mechanisms and that the microbiome can affect plant health (Berendsen et al. 2012, Mueller and Sachs 2015), a reasonable hypothesis emerges: Genotypic and phenotypic variations in plant traits that support microbiomes that increase plant nutrient availability, prevent pathogens or otherwise enhance plant health, growth and performance incur a fitness advantage. Thus, the ability of a plant to support a beneficial microbiome is a plant trait under selection. The fitness advantage incurred by the microbiome must outweigh the cost to the plant in diverted C and energy. The close symbiosis of plants and microbes can be viewed as an 1
Campus Delivery 1499, Fort Collins, CO 80523, USA. 970-556-2591
integrated ecological unit known as a holobiont (Vandenkoornhuyse et al. 2015). For hundreds of millions of years, the holobiont may have been the unit under selection, guiding evolution towards plant traits that supported beneficial microbiomes. Plant domestication and crop breeding: Decoupling the holobiont As humans began to domesticate plants and develop cropping systems, farmers began to artificially select crops based on traits other than reproductive fitness, diverging from natural selection. As humans began to select for large seed size, reduced bitterness–a key defense mechanism– and other traits, we inadvertently changed plant traits that regulate the microbiome. Recent evidence suggests that domestication has altered the microbiomes recruited by plants (Leff et al. 2016, Perez-Jaramillo et al. 2016), though the functional consequences are unknown. Some of these plant traits under breeding selection may be linked to the microbiome. For example, plant phenology has been shown to be influenced by the soil microbiome (Wagner et al. 2014, Panke-Buisse et al. 2015). In early agriculture, plants that supported beneficial microbiomes may still have been selected, as they may have exhibited favorable traits such as more rapid growth and production and better disease resistance. The greatest divergence from natural selection likely occurred with the advent of Haber-Bosch fertilizer. From that point on, we partly obviated the need for one of the key microbial functions- nutrient cycling. No longer was crop yield directly linked to a plants’ ability to support microbial nutrient cycling. In fact, N fertilization reduces microbial biomass and diversity (Treseder 2008, Ramirez et al. 2010), promoting copiotrophs over oligotrophs (Fierer et al. 2012). The selection of plants under high fertilization regimes likely accelerated the decoupling of the soil microbiome from plant fitness. Since we began breeding plants under high fertilization regimes, we may have been selecting against genotypes that support microbial N mineralization (Schmidt et al. 2016), as there must be important trade-offs. As a result, modern varieties may have lost their ability to support microbiomes that degrade organic nitrogen and solubilize mineral nutrients like phosphorus (Figure 1). Rhizosphere Engineering: A systems perspective Imagine if we had the tools to engineer the ideal rhizosphere. What characteristics would we engineer for? How would it function? Certainly, we would want to optimize water holding capacity, nutrient cycling rates, and pathogen resistance. Given the key roles of microbes in soil organic matter formation, nutrient mineralization and solubilization and pathogen pressure, approaches and tools that allow us to manipulate the microbiome would be key to rhizosphere engineering. Currently, our ability to manage and manipulate the rhizosphere microbiome is limited. The most direct way to alter the microbiome is through inoculation. Products containing one or several species of bacteria or fungi have been commercially available for decades (Calvo et al. 2014). However, most of these species were isolated under traditional culturing conditions that do not emulate the soil chemical environment. Inoculants often show promising results under controlled lab and greenhouse conditions which are not consistently reproducible under natural field conditions but there is only limited evidence that these inoculated microbes establish, compete, and function in agricultural soils (Verbruggen et al. 2013). In part, this is due to the broad range of conditions experienced by microbes in the field. Not only do key attributes like pH, nutrient stoichiometry and texture differ among soils, but the climate regime experienced by microbes in the field spans a broad range. The conditions must overlap with the multidimensional niche of the inoculated microbes for them to have a chance to survive, reproduce and function. But, they also must integrate themselves not only with the native microbiome, but with the food web (Morrien 2016). Many inoculants may fail under field conditions simply because they are quickly consumed by predators or outcompeted for resources by native microbes. In nature, healthy plants recruit microbes from highly diverse, but weakly connected bulk soils, and favor rhizosphere microbiomes that
are less diverse but highly structured into modules of highly interactive microbes and soil fauna (Figure 1; DeVries and Wallenstein, in press). Effective inoculants must form associations with the rest of the microbiome, emulating the strongly structured networks in native rhizosphere soils (Figure 1; DeVries and Wallenstein in press, Shi et al. 2016). Other approaches add organic materials with rich but undefined and unknown mixtures of microbes to soils (Scheuerell and Mahaffee 2002, Naidu et al. 2010), with the idea that adding diversity should lead to improved function and pathogen resistance (Jousset et al. 2011, van Elsas et al. 2012). If true, diversity could also decrease the ability of beneficial inoculants to proliferate. But, evidence for a strong positive relationship between microbial -diversity and function is weak in all but the most barren soils (Griffiths and Philippot 2013). Furthermore, resource pulses can temporarily alleviate competition, which could lead to pathogen invasion (Mallon et al. 2015). This approach is likely to have more success in highly degraded soils with low diversity and weak food web interactions.
While nature has already offered an incredible diversity of microbes that vary in traits and function, new gene editing and synthetic biology tools offer another path to engineer microbes with targeted functions (Hutchison et al. 2016). While these techniques are powerful, they raise concerns related to novel gene release and face negative consumer attitudes towards gene modifications (Leak 2010). A systems perspective suggests that they are unlikely to function under field conditions unless their interactions with the environment and the soil food web are considered in their design–a complex challenge. Another pathway to engineering the rhizosphere is through breeding or engineering plant traits (Nogales et al. 2015). As we identify specific root exudates, root architecture, or other plant traits that support beneficial microbiomes, we will be able to engineer those traits into crops through CRISPR and other gene editing tools. This approach seems promising as it emulates the interactions that support beneficial microbes in natural systems and which were selected through evolution of the holobiont. Since the microbiome is strongly influenced by the quantity and quality of SOM, management practices that aim to enhance these soil attributes should benefit the microbiome. In addition to management practices like no-till and cover crops, we can directly increase soil organic matter through additions of organic materials. For example, small additions of compost can have lasting benefits (Ryals et al. 2014). Yet, millions of tons of food-related waste are sent to landfills each year (Parfitt et al. 2010). There is a tremendous opportunity to process this organic waste and return it back to the farm. If these resource pulses coincide with beneficial inoculants, the temporary decrease in competition by native microbes could enhance their success. In the coming decades, we will be purposefully engineering the rhizosphere with increasing sophistication. The rhizosphere is a complex adaptive system of closely interacting biological, chemical, and physical components. Successful rhizosphere engineering will require a systems perspective (Figure 1). As we learn how to engineer the interactive rhizosphere, we can enhance the efficiency and sustainability of crop production only by emulating the symbiotic interactions between plants, soils, and microbes that evolved over millions of years in nature.
Figure 1. Hypothesized conceptual models of rhizosphere systems in (A) natural ecosystems, (B) degraded systems such as those under intensive management and high fertilization and (C) rhizospheres that have been engineered through inoculants that form connections with the native microbiome or soil amendments that stimulate microbial activity. Natural rhizospheres are characterized by highly structured and interactive microbiomes and food webs because plants co-evolved with their microbiomes and support them through root exudation. As crops were selected under intensive management, these connections likely decreased. In the future, a systems approach to rhizosphere engineering could restore some features of natural rhizospheres through soil amendments, inoculants and plant traits that support beneficial microbiomes. References Bais, H. P., T. L. Weir, L. G. Perry, S. Gilroy, and J. M. Vivanco. 2006. The role of root exudates in rhizosphere interactions with plants and other organisms. Annual review of plant biology 57:233– 66. Bell, C. W., S. Asao, F. Calderon, B. Wolk, and M. D. Wallenstein. 2015. Plant nitrogen uptake drives rhizosphere bacterial community assembly during plant growth. Soil Biology and Biochemistry 85:170–182. Berendsen, R. L., C. M. J. Pieterse, and P. A. H. M. Bakker. 2012. The rhizosphere microbiome and plant health. Trends in Plant Science 17:478–486. Calvo, P., L. Nelson, and J. W. Kloepper. 2014. Agricultural uses of plant biostimulants. Plant and Soil 383:3–41. Chaparro, J. M., D. V Badri, and J. M. Vivanco. 2014. Rhizosphere microbiome assemblage is affected by plant development. The ISME journal 8:790–803. Cotrufo, M. F., M. D. Wallenstein, C. M. Boot, K. Denef, and E. Paul. 2013. The Microbial EfficiencyMatrix Stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization: Do labile plant inputs form stable soil organic matter? Global Change Biology 19:988–995. DeVries, F., and M. D. Wallenstein. (n.d.). Belowground connections underlying aboveground food production: a framework for optimising ecological connections in the rhizosphere. Journal of Ecology. Doornbos, R. F., L. C. Van Loon, and P. A. H. M. Bakker. 2012. Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. A review. Agronomy for Sustainable Development 32:227–243.
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