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The fruit microbiome: A new frontier for postharvest biocontrol and postharvest biology
Postharvest Biology and Technology 140 (2018) 107–112
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The fruit microbiome: A new frontier for postharvest biocontrol and postharvest biology ⁎
Samir Drobya, , Michael Wisniewskib, a b
T
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Dept. Postharvest Science, Institute of Postharvest and Food Sciences, ARO, the Volcani Center, P.O. 15159, Rishon LeZion, 7505101, Israel USDA-ARS, Appalachian Fruit Research Station, Kearneysville, WV, 25430, USA
A R T I C LE I N FO
A B S T R A C T
Keywords: Biological control Postharvest diseases Synthetic microbial communities Fruit endopytes Fruit epiphytes Stem-end rots Microbial networks
Microorganisms are an integral part of the composition of fruits and vegetables and are found as epiphytes on the surface or as endophytes within tissues. The realization that fruit surfaces harbor beneficial microorganisms fostered the field of biological control using epiphytic microorganisms which led to the development of several commercial biocontrol products. Advances in DNA sequencing and “omics” technologies have enhanced our ability to characterize the diversity and function of microbial communities (microbiome) present in and on plant tissues. Microbiome studies have the potential of providing knowledge that will lead to a fundamental paradigm shift in the way we think about biocontrol strategies, biocontrol products, and postharvest biology, as well as the health attributes of fruits and vegetables. Fruit microbiome research will enhance our understanding of harvested commodities as an ecosystem in which the microbiome plays an essential role in the health and physiology of fruit after it is harvested. Meta-omic (metagenomics, metatranscriptomics, metaproteomics, and metametabolomics) technologies are only beginning to be applied to postharvest studies and will revolutionize our understanding of postharvest biocontrol systems, foodborne pathogens, and postharvest physiology. The role of the microbiome in plant health, productivity, and cultivar development should be considered as much as the plant itself. Plant breeding or genetic modification of plants could be used to intentionally modulate the composition of the microbiome and its function, recruiting disease antagonists and plant-growth promoters that enhance plant health and the quality of the harvested products. Increased knowledge of microbial community systems will lead to the development of natural or synthetic consortia that can be used to prevent postharvest diseases and mitigate physiological disorders in harvested commodities.
1. Introduction Microorganisms are an integral part of the composition of fruits and vegetables and are found as epiphytes on the surface or as endophytes within tissues. The majority of these microorganisms are not pathogenic, however, their role and function in fruit health, quality, and disease resistance before and after harvest is largely unknown. Information about their ecology, colonization, survival, and growth on and in harvested commodities is also lacking. The realization that fruit surfaces harbor beneficial microorganisms fostered the field of biological control using epiphytic microorganisms and led to the development of several commercial biocontrol products, and numerous scientific publications (Droby et al., 2016). Rapid developments in exploring and understanding the microbiome, now offer the opportunity to develop new approaches to postharvest biocontrol that are more effective. It is our opinion that studies of the microbiome in and on fruit offer a
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new frontier that will greatly change our understanding of postharvest biocontrol and postharvest biology. Droby et al. (2009) reviewed twenty-years of postharvest biocontrol research, providing a brief history, and their ideas about the concepts underlying the science of postharvest biocontrol and the limitations experienced by postharvest biocontrol products in the marketplace. They suggested that it was time to develop new paradigms about the biology and functional application of biocontrol agents if biocontrol was going to reach its’ full potential. They emphasized the need to view the postharvest biocontrol as a system as an integrated whole, composed of the biocontrol agent, the pathogen, the host, and the environment. While such an approach represented distinct challenges, they indicated that it was necessary if problems related to the efficacy and consistent performance of biocontrol products were to be overcome. The role of fruit microbiome in the biocontrol system, however, was not raised at that time since the technologies to study the
Corresponding author. Corresponding author. E-mail addresses: [email protected] (S. Droby), [email protected] (M. Wisniewski).
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https://doi.org/10.1016/j.postharvbio.2018.03.004 Received 13 January 2018; Received in revised form 28 February 2018; Accepted 7 March 2018 0925-5214/ © 2018 Elsevier B.V. All rights reserved.
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microbiome were not yet readily available. In 2016, two articles in a Special Issue of Postharvest Biology and Technology were devoted to reviewing alternative approaches in general and biocontrol in particular (Wisniewski et al., 2016; Droby et al., 2016). Advances in the science and development of biocontrol agents were described, especially in regard to our understanding of the interaction between microbial antagonists and their hosts, target pathogens, and the resident microflora. Wisniewski et al. (2016) and Droby et al. (2016) noted that the interest in biological approaches to postharvest disease control, and biologically-based products in general, continues to grow and discussed the drivers underlying the sustained interest in biocontrol products. Droby, et al. (2016) noted that the approach utilized to identify and select postharvest biocontrol agents had not changed much since the original approach was discussed by Wilson and Wisniewski (1989) and a selection method was described by Wilson et al. (1993). The commonly-used approach involves the identification of a single antagonist possessing properties that allow it to develop rapidly in wounded fruit tissue, thus preventing pathogens from becoming established. This approach, however, neglects the fact that the introduced antagonist is not the only player in the system, and in general neglects the interactions antagonists experience as part of a microbial network and as a component of a biological system (Droby et al., 2016). One aspect of microbial ecology that has the potential to revolutionize our understanding of plant pathology and biology is the technological advances that have been made in the use of next-generation-sequencing (NGS) and meta-omic technologies to characterize the diversity and function of the microbial communities present in and on host tissues (Abdelfattah et al., 2017). NGS technologies are opening a new frontier in exploring the role of microbes in our environment and their interaction with various hosts (Berg et al., 2016). It is our opinion that microbiome studies will provide information that will result in a fundamental paradigm shift in the way we think about biocontrol strategies, biocontrol products, and postharvest biology, as well as the health attributes of fruits and vegetables. Investigations of the fruit microbiome will enhance our understanding of harvested commodities as an ecosystem in which the microbiome plays an essential role in the health and physiology of fruit before and after it is harvested. The current contribution, rather than serving as a comprehensive review, discusses various aspects of microbiome research and highlights how they can serve as a foundation for studies on postharvest biocontrol and biology. A comprehensive review of the application and the tools used for microbiome research on biocontrol of plant diseases was recently provided by Massarat et al. (2015) and Abdelfattah et al. (2017).
however, the role of the microbiota in postharvest pathology and physiology is poorly understood, and how the resident microflora impacts biocontrol efficacy is simply not known. Meta-omic (metagenomics, metranscriptomics, metaproteomics, and metametabolomics) technologies are only beginning to be applied to postharvest studies. Microbiome theory suggests that species, due to their close relationship and interaction with microbial assemblages, should be viewed as metaorganisms, defined as an organism plus its associated microbiome. The “holobiont” theory further suggests that microbial assemblages and their associated hosts have co-evolved and resulted in stable microbiome-organism relationships (Zilber-Rosenberg and Rosenberg, 2008). Berg et al., (2016) have indicated that it is critical to consider the role of the microbiome in experimental botany and breeding strategies. How the concept of the metaorganism relates to postharvest biocontrol systems and postharvest biology, in general, remains to be determined. Importantly, Douglas and Werren (2016) have suggested that the holobiont or hologenome concept is too rigid and will need to be adjusted as more data on the relationship between hosts and their associated microbiota become available. 3. The fruit microbiome An increasing number of studies have documented the microbial diversity present on a variety of fruit species (Abdelfattah et al., 2017). These studies have examined the impact of management practices on the composition of the microflora, temporal changes in the microbiome over the course of a growing season, and the composition of the microbiota after harvesting, processing, shipping, and distribution to a local supermarket. Studies documenting the effect of the application of biocontrol agents on the resident microflora have been comprehensively reviewed by Massart et al. (2015), however, most of the reported studies were not postharvest studies. Abdelfattah et al. (2016) demonstrated that the alpha and beta diversity of the fungal microflora of harvested apples differed significantly between fruit parts (Fig. 1). PCoA analysis indicated that the microbiota of samples clustered distinctly based on the part of the fruit from which they were obtained, such as peel, wound, calyx-end, or stem-end tissues. This strongly indicates that the microflora associated with different portions of the apple fruit need to be considered when designing biocontrol systems for the management of postharvest diseases. Significantly different populations of fungi were present on fruit obtained from organic vs. conventional orchards, and the presence of several unique taxa in the organically-produced fruit may have been related to the management practice used to grow the fruit. In their study, Penicillium was dominate in peel samples, while Alternaria was dominant in the calyx- and stem-end samples. Ascomycota accounted for over 90% of the observed species, followed by Basidiomycota (8%), and Chytridiomycota (0.1%). No significant temporal changes in the microbiome were observed over a two-week storage period at room temperature. Additional studies are presently being conducted to determine the impact of waxing and storage on the resident microbiome of harvested apples, and the impact of waxing on the specific survival of the foodborne pathogen, Listeria monocytogenes. Temporal changes in the wound-related microbiome of apple and citrus fruit and their effect on biocontrol agents in the wound are also being investigated. Preliminary findings indicate the presence of a wide spectrum of bacteria in wounds and that their presence and abundance is influenced by inoculation of the wound with a pathogen or the application of a biocontrol agent (unpublished data). The effect of wound-colonizing endophytic bacteria on infection and the development of decay, as well as the efficacy of biocontrol agents are still largely unknown. A major question that needs to be resolved is how unique and stable is the core microbiome (as defined by taxa) of fruit across different climates, growing regions, and cultivars. While one would predict a stable, predictable microbiome based on the holobiont theory, previous research in grape has indicated
2. Microbiome theory and concepts Microbial communities have an essential role in ecosystem processes, including nutrient cycling, primary production, litter decomposition, and disease resistance (Delgado-Baquerizo et al., 2015). Unfortunately, a complete description of the microbial diversity present in an ecosystem cannot be obtained by standard culturing methods alone. This is also true for identifying the diversity of microbes that inhabit the internal and external portions of an organism. Regarding postharvest diseases, biocontrol of postharvest diseases, and postharvest biology in general, this shortcoming has greatly limited our understanding of the impact that whole microbial communities and their genetic material (the microbiome) potentially play in the physiology of a plant and its interactions with the environment and other organisms (Berg et al., 2016; Abdelfattah et al., 2017). The use of amplicon sequencing and metagenomics (shotgun sequencing), have provided a fundamental breakthrough in our ability to describe, compare, and discover new microbial communities (Ursell et al., 2012). Various studies have demonstrated that the composition of the microbiota inhabiting an organism (both endo- and epiphytically) can have a profound effect on the physiology of their hosts, including disease resistance responses (Hardoim et al., 2015). In general, 108
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Fig. 1. abundance of fungal genera in peel (PE), surface wounds (W), calyx end (CE), and stem end (SE). Adopted from Abdelfattah et al. (2016).
metagenomics and metatranscriptomics. The microbiota recruited by a given plant genotype in different environments seems to share greater functional similarity than taxonomic similarity (Lemanceau and Moënne-Loccoz, 2017). Information about the genes that are actively expressed in these communities, however, is lacking and how members of the communities interact with each other, and how these activities and relationships are influenced by various environmental and agricultural practices is also presently unknown. Descriptive studies can't provide definitive information on which microbial functional traits are changing in response to external stimuli and/or internal metabolic and physiological changes taking place in plant tissue. Functional metaomics approaches, including metatranscriptomics, metametabolomics, and metaproteomics, provide detailed functional information that can better reflect host-microbiome interactions and provide valuable information on the active and non-active microbial populations and their relationship to plant health and disease, as well as quality and health benefits to humans. Rhizosphere microbiome research indicates that microbes can influence nearly every functional plant trait (Friesen et al., 2011). The effect of the microbiome (epiphytic and endophytic) of harvested fruits on fruit physiology and its susceptibility to pathogen attack remains to be explored. Plant associated microorganisms have been reported to produce various phytohormones such as auxins, cytokinins, and ethylene (Spaepen, 2015). Production of plant hormones such as indole-3acetic acid (IAA) is widespread among plant-associated bacteria, particularly rhizobia (Ghosh et al., 2011), and some Bacillus spp. can produce gibberellins (Gutierrez-Manero et al., 2001). Pseudomonas syringae produces hormone analogs that interfere with jasmonate and ethylene signaling (Melotto et al., 2006). Degradation of hormones or hormone precursors by bacteria has also been documented (Glick, 2005). Microorganisms also have the potential to produce secondary metabolites capable of directly or indirectly affect fruit physiology. Thus, there is a critical need to understand the function of the carposphere microbiome, including aspects of metabolism and physiology, such as their contribution to hormonal signaling pathways that are linked to fruit ripening and senescence. Lemanceau and Moënne-Loccoz (2017) stated that the core
that the soil serves as a key source of vine-associated bacteria and that edaphic factors and vineyard-specific properties can influence the native preharvest grapevine microbiome (Zarraonaindia et al., 2015). In this regard, an international collaboration is in progress to document the microbiome of a specific cultivar of apple at harvest grown in different regions of the USA, Israel, Spain, Italy, Turkey, and Switzerland. Such foundational knowledge is imperative for determining the ability to utilize ubiquitous biocontrol agents on an international scale. Many factors are likely to be involved in determining the species composition of bacterial and fungal communities in different parts of plants. The availability of immigrant inoculum (Kinkel et al., 1987; Lindemann and Upper, 1985), host plant phenology (Blakeman, 1985; Martins et al., 2012), physico-chemical conditions (O’Brien and Lindow, 1989; Berg and Smalla, 2009), and nutritional characteristics of the phyllosphere or carposphere (Marschner et al., 2004; Compant et al., 2005). Martins et al. (2013) studied the diversity of epiphytic bacteria on grape berries and other plant parts, including leaves and bark tissues. They suggested that variability in nutrient supply between these niches might explain the observed differences in bacterial community structure, as well as the diversity of culturable genera among the different plant parts. Fruit undergo dramatic physiological (internal and external) changes during ripening and senescence that have a significant impact on their susceptibility to infection and decay. How these changes and postharvest treatments and handling processes influence the composition of the fruit microbiome and its susceptibility to pathogens is still not understood. It would be of great interest to determine if it is possible to define a unique microbiota to a specific physiological change or disorder or a specific level of host susceptibility or resistance to various pathogens. 4. Diversity and function of the fruit microbiome: a new frontier Microbiome studies are now shifting from studying just the taxonomic composition of the plant microbiome, using 16S and ITS rRNA sequence information, to a broader investigation of the functional potential of the microbiota. This has been made possible using shotgun 109
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computational simulations allow one to address the influence of dynamics in the environmental inputs (e.g., secreted metabolome) or the functional repertoire of the community (genomic composition of the sample) on network structure. Iterative simulations can be applied for delineating the functional division between community members – e.g., co-dependencies on specific nutrients and hierarchical cross-feeding interactions. These approaches can be used to achieve an understanding of the processes shaping the causal microbiology of post-harvest diseases and the mechanisms behind pathogen-resistant vs. susceptible communities, as well as the potential impact of specific microbiomes on the quality attributes of harvested commodities.
microbiome should be based not only on the composition of the taxa but by its function as well. Function at an individual microbe level will depend on the genes that are being expressed, while at a community level, function will depend on the interactions that occur between members of that community. Boon et al. (2014) argued that treating genes as ecological agents can help determine if shifts in the taxa present in an assemblage will impact the function of that community. If different taxa possess genes that serve a similar function than one would not expect the introduction or loss of a specific microbe to impact community function. Microbiome studies and meta-omics offer the opportunity to explore a new frontier that can have a major impact on the development of biocontrol agents. Recently, Poudel et al. (2016) described how an understanding of microbiome networks can serve as a systems framework for identifying microbial assemblages for disease management. As stated by Boon et al. (2014), “a deeper understanding of microbial communities will allow a shift from observation-based questions of ‘Who is there?’ and ‘What are they doing?’ to mechanisticdriven questions of ‘How will they respond?”
6. Managing the fruit microbiome for postharvest biocontrol and stress tolerance – is it feasible? Studies on ways to manipulate the microbiota of the rhizosphere to benefit plants in agricultural and horticultural systems has become a major area of research (Colla et al., 2017) and a recent report by Mazzola and Freilich (2017) have highlighted the potential of manipulating the soil microbiome using natural and synthetic microbial consortia to promote suppression of soil-borne diseases. Mazzola and Freilich (2017) stressed that a greater knowledge of the functional aspects of microbial community as a system through meta-omic studies will be needed to realize this potential. Colla et al. (2017) note that in contrast to the rhizosphere, the phyllosphere (and by extension the carposphere) has received much less attention and questions about the role of the surface and endophytic microbiome are just beginning to be addressed. Although a great deal of fundamental knowledge needs to be acquired, empirical investigations can also be pursued, keeping the “whole” system in mind when interpreting the impact of various experiments (Fig. 2). In this regard, Colla et al. (2017) noted the critical role that amino acids play in determining the composition of a microbiome and suggested that the utilization of protein hydrolysates have potential to be used as biostimulants to promote a microbial composition that favors species that suppress disease and enhance growth. In a study of four biostimulants, Tejada et al. (2011) found that the amendment derived from rice bran contained the highest level of protein and had the greatest impact on the soil microflora. Colla et al. (2017) also reviewed a study by Luziatelli et al. (2016) in which the plant-derived products, Trainer® and Auxym®, containing protein hydrolysates altered the microbial community of lettuce and increased growth and chlorophyll content. Interestingly, many of the microbial genera obtained from the treated leaves, especially Pantoea, Micrococcus, and Acinetobacter, had the ability to solubilize phosphorus and synthesize IAA. Isolates of Bacillus with strong inhibitory activity against plant pathogens were also obtained. Based on the available evidence, Colla et al. (2017) hypothesized that products containing protein hydrolysates and select microbes could be formulated to specifically support beneficial plant-microbial relationships and enhance
5. The role of endophytes in biocontrol systems and fruit biology The existence of endophytic microorganisms in plant tissues and their role in increasing biotic and abiotic stress tolerance in their hosts, as well as in improving nutrient acquisition and plant growth promotion, is well documented in the literature (reviewed by Kaul et al., 2016). The effect of the interactions of endophytic groups with the host plant and other microbial consortia on the physiology of the plant, however, are still poorly understood. The existence and function of endophytic microorganisms within host plants has not widely studied in harvested commodities. Diskin et al (2017) provided insights on the taxonomic diversity of endophytic fungal and bacterial families and their dynamics in the stems of mango fruit during storage and ripening. They documented the presence of several stem-end pathogens, such as Alternaria, Colletotrichum, and Lasiodiplodia, along with other diverse endophytic fungal and bacterial species. The abundance of the different members of the stem-end microbiota was influenced by fruit ripening and by the applied postharvest treatment. It was also shown that stem-ends that did not develop disease had more diverse microbial communities relative to stemends that were diseased. These findings suggest the existence of a natural mechanism of biocontrol in which pathogens have a silent endophytic stage and become active and cause disease when the composition of the microbiota changes in response to host physiological changes and postharvest treatments. This knowledge may influence the way we look at biocontrol and the possible use of endophytes in biocontrol systems. Although not directly related to harvested commodities and postharvest biocontrol, Liu et al. (2018) examined the influence of apple rootstocks on the composition of the endophyte community in different scion cultivars. A distinct genotype effect of the scion on the composition of the fungal endophytic community was observed, suggesting that different cultivars may harbor their own distinct microbiome. A similar effect of genotype on the foliar microbiome was reported for different poplar genotypes planted in a common garden (Bálint et al., 2013). Such studies lend support to the holobiont concept of co-evolution. How the potential for different endophytic microbiota being present in different apple cultivars would affect postharvest biocontrol systems and fruit physiology remains to be determined. Beyond the characterization of community structure, metagenomic surveys have allowed the construction of catalogues of gene/functions in specific samples (Bulgarelli et al., 2015; Ofek-Lalzar et al., 2014). Like genomic approaches, where species-specific metabolic networks are constructed based on the presence of enzyme coding genes, community networks can be constructed based on the functional annotations of metagenomic data (Abubucker et al., 2012; Zelezniak et al., 2015). Beyond the static representation of data as a network,
Fig. 2. Interactions of different components of the postharvest system.
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plant productivity. Mendes et al. (2011) showed that when soils suppressive to Rhizoctonia solani, the causal agent of damping-off and other economically important plant diseases, are added to disease conducive soils at a 1:9 ratio (w/w), R. solani infection in sugar beet is successfully suppressed. Metagenomic analysis of the soils revealed the consistent presence of 17 bacterial communities belonging to Proteobacteria, Firmicutes, and Actinobacteria and considered as a core-microbiome in disease suppression. Mazzola et al. (2015) demonstrated the ability of seed meal amendments derived from Brassica juncea/Sinapsis alba to suppress apple replant disease. In contrast to chemically fumigated soils where apple root pathogens became prevalent one year after fumigation, the seed meal treated soils prevented re-infestation after two years. Mazzola and Freilich (2017) noted the shortcomings of the single antagonist model when developing soil-based biocontrol products. The same case may be said for the study of postharvest biocontrol and the development of postharvest biocontrol products. Truly, this represents a new paradigm and a new frontier for postharvest biocontrol research.
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7. Conclusions Specific taxa of microbes can assemble into plant-associated communities that influence the fitness of both the hosts they inhabit and the microbes themselves (Lebeis et al., 2015; Berg et al., 2014). The assembled community is truly greater than the sum of its parts (Lebeis et al., 2015). Understanding the functioning of epiphytic, endophytic, and rhizosphere communities and their influence on host physiology and disease resistance is a new frontier that will modify many of the existing paradigms that exist about biocontrol systems, stress tolerance, and plant growth and development. It is understood that properties of the rhizosphere microbiome do not necessarily extend to the phyllosphere (Colla et al., 2017). The rhizosphere is nutrient-rich and able to host a high level of microbial diversity in comparison to the phyllosphere, which is considered nutrient poor. The carposphere, however, represents a unique environment and it is unclear if findings reported for either the rhizosphere or the phyllosphere can be extrapolated to conditions present on and in fruit, where nutrient levels may vary with age and a host of unique volatiles may be emitted. While the challenges posed by this new frontier are many, the opportunities for addressing many agricultural problems are great, including the development of function-based biocontrol systems and biological-based strategies for addressing postharvest physiological disorders. As indicated by Wisniewski et al. (2016), we are truly moving from an age of chemistry to an age of biology. Regarding postharvest disease and biocontrol systems, significant foundational questions regarding the characterization of core microbiomes on different commodities, and the impact of management, harvesting, processing, and storage systems on the functioning of native microbial communities, still need to be addressed. The role of the microbiome and its relationship to plant health, productivity, and plant breeding should be considered as much as the plant itself. Plant breeding or genetic modification of plants could be used to intentionally modulate the composition of the microbiome and its function, recruiting disease antagonists and plant-growth promoters that enhance plant health and the quality of harvested products. We predict that increased knowledge of microbial community systems will lead to the development of synthetic consortia that can be used to prevent postharvest diseases and mitigate physiological disorders in harvested commodities. Droby et al. (2009) asked the question, ‘Are new paradigms needed to advance the development of postharvest biocontrol systems?’ It is our belief that the rapidly evolving field of microbiome studies will be the source of developing these new paradigms in the coming years. References Abdelfattah, A., Malacrino, A., Wisniewski, M., Cacciola, S.O., Schena, L., 2017.
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Poudel, R., Jumpponen, A., Schlatter, D.C., Paulitz, T.C., McSpadden Gardener, B.B., Kinkel, L.L., Garrett, K.A., 2016. Microbiome networks: a systems framework for identifying candidate microbial assemblages for disease management. Phytopathol. 106, 1083–1096. Spaepen, S., 2015. Plant hormones produced by microbes. In: Lugtenberg, B. (Ed.), Principles of Plant-Microbe Interactions. Springer, Cham. Ursell, L.K., Metcalf, J.L., Parfrey, L.W., Knight, R., 2012. Defining the human microbiome. Nat. Rev. 70 (Suppl. 1), S38–S44. http://dx.doi.org/10.1111/j.1753-4887. 2012.00493.x. Wilson, C.L., Wisniewski, M., 1989. Biological control of postharvest diseases of fruits and vegetables: an emerging technology. Ann. Rev. Phytopathol. 27, 425–441. Wilson, C.L., Wisniewski, M., Droby, S., Chalutz, E., 1993. A selection strategy for microbial antagonist to control postharvest diseases of fruits and vegetables. Sci. Hortic. 53, 183–189. Wisniewski, M., Droby, S., Norelli, J., Liu, J., Schena, L., 2016. Alternative management technologies for postharvest disease control: The journey from simplicity to complexity. Postharvest Biol. Technol. 122, 3–10. Zarraonaindia, I., Owens, S.M., Weisenhorn, P., West, K., Hampton-Marcell, J., Lax, S., Bokulich, N.A., Mills, D.A., Martin, G., Taghavi, S., van der Lelie, D., Gilbert, J.A., 2015. The soil microbiome influences grapevine-associated microbiota. mBio 6 (2), e02527–14. http://dx.doi.org/10.1128/mBio.02527-14. Zelezniak, A., Andrejev, S., Ponomarova, O., Mende, D.R., Bork, P., Patil, K.R., 2015. Metabolic dependencies drive species co-occurrence in diverse microbial communities. Proc. Natl. Acad. Sci. U. S. A. 112, 6449–6454. http://dx.doi.org/10.1073/ pnas.1421834112. Zilber-Rosenberg, I., Rosenberg, E., 2008. Role of microorganisms in The evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol. Rev. 32 (5), 723–735. http://dx.doi.org/10.1111/j.1574-6976.2008.00123.x.
bacterial communities in relation to plant species, nutrition and soil type. Plant Soil 261, 199–208. Martins, G., Miot-Sertier, C., Lauga, B., Claisse, O., Lonvaud-Funel, A., Soulas, G., Masneuf-Pomarède, I., 2012. Grape berry bacterial microbiota: Impact of the ripening process and the farming system. Int. J. Food Microbiol. 158, 93–100. Martins, G., Lauga, B., Miot-Sertier, C., Mercier, A., Lonvaud, A., Soulas, M.L., Soulas, G., Masneuf-Pomare, I., 2013. Characterization of epiphytic bacterial communities from grapes, leaves, bark and soil of grapevine plants grown, and their relations. PLoS One 8 (8), e73013. http://dx.doi.org/10.1371/journal.pone.0073013. Melotto, M., Underwood, W., Koczan, J., Nomura, K., He, S.Y., 2006. Plant stomata function in innate immunity against bacterial invasion. Cell 126, 969–980. Mendes, R., Kruijt, K., de Bruijn, I., Dekkers, E., van der Voort, M., Schneider, J.H., Piceno, Y.M., DeSantis, T.Z., Andersen, G.L., Bakker, P.A., Raaijmakers, J.M., 2011. Deciphering the rhizosphere microbiome for diseasesuppressive bacteria. Science 332, 1097–1100. http://dx.doi.org/10.1126/science.1203980. Massart, S., Perazzolli, M., Höfte, M., Pertot, I., Jijakli, M.H., 2015. Impact of the omic technologies for understanding the modes of action of biological control agents against plant pathogens. BioControl. http://dx.doi.org/10.1007/s10526-015-9686-z. Mazzola, M., Hewavitharana, S.S., Strauss, S.L., 2015. Brassica seed meal soil amendments transform the rhizosphere microbiome and improve apple production though resistance to pathogen re-infestation. Phytopathology 105, 460–469. Mazzola, M., Freilich, S., 2017. Prospects for biological soil-borne disease control: application of indigenous versus synthetic microbiomes. Phytopathology 107, 256–263. O’Brien, R.D., Lindow, S.E., 1989. Effect of plant species and environmental conditions on epiphytic population sizes of pseudomonas syringae and other bacteria. Phytopathology 79, 619–627. Ofek-Lalzar, M., Sela, N., Goldman-Voronov, M., Green, S.J., Hadar, Y., Minz, D., 2014. Niche and host-associated functional signatures of the root surface microbiome. Nat. Commun. 5, 4950. http://dx.doi.org/10.1038/ncomms5950.
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Contents lists available at ScienceDirect
Postharvest Biology and Technology journal homepage: www.elsevier.com/locate/postharvbio
The fruit microbiome: A new frontier for postharvest biocontrol and postharvest biology ⁎
Samir Drobya, , Michael Wisniewskib, a b
T
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Dept. Postharvest Science, Institute of Postharvest and Food Sciences, ARO, the Volcani Center, P.O. 15159, Rishon LeZion, 7505101, Israel USDA-ARS, Appalachian Fruit Research Station, Kearneysville, WV, 25430, USA
A R T I C LE I N FO
A B S T R A C T
Keywords: Biological control Postharvest diseases Synthetic microbial communities Fruit endopytes Fruit epiphytes Stem-end rots Microbial networks
Microorganisms are an integral part of the composition of fruits and vegetables and are found as epiphytes on the surface or as endophytes within tissues. The realization that fruit surfaces harbor beneficial microorganisms fostered the field of biological control using epiphytic microorganisms which led to the development of several commercial biocontrol products. Advances in DNA sequencing and “omics” technologies have enhanced our ability to characterize the diversity and function of microbial communities (microbiome) present in and on plant tissues. Microbiome studies have the potential of providing knowledge that will lead to a fundamental paradigm shift in the way we think about biocontrol strategies, biocontrol products, and postharvest biology, as well as the health attributes of fruits and vegetables. Fruit microbiome research will enhance our understanding of harvested commodities as an ecosystem in which the microbiome plays an essential role in the health and physiology of fruit after it is harvested. Meta-omic (metagenomics, metatranscriptomics, metaproteomics, and metametabolomics) technologies are only beginning to be applied to postharvest studies and will revolutionize our understanding of postharvest biocontrol systems, foodborne pathogens, and postharvest physiology. The role of the microbiome in plant health, productivity, and cultivar development should be considered as much as the plant itself. Plant breeding or genetic modification of plants could be used to intentionally modulate the composition of the microbiome and its function, recruiting disease antagonists and plant-growth promoters that enhance plant health and the quality of the harvested products. Increased knowledge of microbial community systems will lead to the development of natural or synthetic consortia that can be used to prevent postharvest diseases and mitigate physiological disorders in harvested commodities.
1. Introduction Microorganisms are an integral part of the composition of fruits and vegetables and are found as epiphytes on the surface or as endophytes within tissues. The majority of these microorganisms are not pathogenic, however, their role and function in fruit health, quality, and disease resistance before and after harvest is largely unknown. Information about their ecology, colonization, survival, and growth on and in harvested commodities is also lacking. The realization that fruit surfaces harbor beneficial microorganisms fostered the field of biological control using epiphytic microorganisms and led to the development of several commercial biocontrol products, and numerous scientific publications (Droby et al., 2016). Rapid developments in exploring and understanding the microbiome, now offer the opportunity to develop new approaches to postharvest biocontrol that are more effective. It is our opinion that studies of the microbiome in and on fruit offer a
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new frontier that will greatly change our understanding of postharvest biocontrol and postharvest biology. Droby et al. (2009) reviewed twenty-years of postharvest biocontrol research, providing a brief history, and their ideas about the concepts underlying the science of postharvest biocontrol and the limitations experienced by postharvest biocontrol products in the marketplace. They suggested that it was time to develop new paradigms about the biology and functional application of biocontrol agents if biocontrol was going to reach its’ full potential. They emphasized the need to view the postharvest biocontrol as a system as an integrated whole, composed of the biocontrol agent, the pathogen, the host, and the environment. While such an approach represented distinct challenges, they indicated that it was necessary if problems related to the efficacy and consistent performance of biocontrol products were to be overcome. The role of fruit microbiome in the biocontrol system, however, was not raised at that time since the technologies to study the
Corresponding author. Corresponding author. E-mail addresses: [email protected] (S. Droby), [email protected] (M. Wisniewski).
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https://doi.org/10.1016/j.postharvbio.2018.03.004 Received 13 January 2018; Received in revised form 28 February 2018; Accepted 7 March 2018 0925-5214/ © 2018 Elsevier B.V. All rights reserved.
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microbiome were not yet readily available. In 2016, two articles in a Special Issue of Postharvest Biology and Technology were devoted to reviewing alternative approaches in general and biocontrol in particular (Wisniewski et al., 2016; Droby et al., 2016). Advances in the science and development of biocontrol agents were described, especially in regard to our understanding of the interaction between microbial antagonists and their hosts, target pathogens, and the resident microflora. Wisniewski et al. (2016) and Droby et al. (2016) noted that the interest in biological approaches to postharvest disease control, and biologically-based products in general, continues to grow and discussed the drivers underlying the sustained interest in biocontrol products. Droby, et al. (2016) noted that the approach utilized to identify and select postharvest biocontrol agents had not changed much since the original approach was discussed by Wilson and Wisniewski (1989) and a selection method was described by Wilson et al. (1993). The commonly-used approach involves the identification of a single antagonist possessing properties that allow it to develop rapidly in wounded fruit tissue, thus preventing pathogens from becoming established. This approach, however, neglects the fact that the introduced antagonist is not the only player in the system, and in general neglects the interactions antagonists experience as part of a microbial network and as a component of a biological system (Droby et al., 2016). One aspect of microbial ecology that has the potential to revolutionize our understanding of plant pathology and biology is the technological advances that have been made in the use of next-generation-sequencing (NGS) and meta-omic technologies to characterize the diversity and function of the microbial communities present in and on host tissues (Abdelfattah et al., 2017). NGS technologies are opening a new frontier in exploring the role of microbes in our environment and their interaction with various hosts (Berg et al., 2016). It is our opinion that microbiome studies will provide information that will result in a fundamental paradigm shift in the way we think about biocontrol strategies, biocontrol products, and postharvest biology, as well as the health attributes of fruits and vegetables. Investigations of the fruit microbiome will enhance our understanding of harvested commodities as an ecosystem in which the microbiome plays an essential role in the health and physiology of fruit before and after it is harvested. The current contribution, rather than serving as a comprehensive review, discusses various aspects of microbiome research and highlights how they can serve as a foundation for studies on postharvest biocontrol and biology. A comprehensive review of the application and the tools used for microbiome research on biocontrol of plant diseases was recently provided by Massarat et al. (2015) and Abdelfattah et al. (2017).
however, the role of the microbiota in postharvest pathology and physiology is poorly understood, and how the resident microflora impacts biocontrol efficacy is simply not known. Meta-omic (metagenomics, metranscriptomics, metaproteomics, and metametabolomics) technologies are only beginning to be applied to postharvest studies. Microbiome theory suggests that species, due to their close relationship and interaction with microbial assemblages, should be viewed as metaorganisms, defined as an organism plus its associated microbiome. The “holobiont” theory further suggests that microbial assemblages and their associated hosts have co-evolved and resulted in stable microbiome-organism relationships (Zilber-Rosenberg and Rosenberg, 2008). Berg et al., (2016) have indicated that it is critical to consider the role of the microbiome in experimental botany and breeding strategies. How the concept of the metaorganism relates to postharvest biocontrol systems and postharvest biology, in general, remains to be determined. Importantly, Douglas and Werren (2016) have suggested that the holobiont or hologenome concept is too rigid and will need to be adjusted as more data on the relationship between hosts and their associated microbiota become available. 3. The fruit microbiome An increasing number of studies have documented the microbial diversity present on a variety of fruit species (Abdelfattah et al., 2017). These studies have examined the impact of management practices on the composition of the microflora, temporal changes in the microbiome over the course of a growing season, and the composition of the microbiota after harvesting, processing, shipping, and distribution to a local supermarket. Studies documenting the effect of the application of biocontrol agents on the resident microflora have been comprehensively reviewed by Massart et al. (2015), however, most of the reported studies were not postharvest studies. Abdelfattah et al. (2016) demonstrated that the alpha and beta diversity of the fungal microflora of harvested apples differed significantly between fruit parts (Fig. 1). PCoA analysis indicated that the microbiota of samples clustered distinctly based on the part of the fruit from which they were obtained, such as peel, wound, calyx-end, or stem-end tissues. This strongly indicates that the microflora associated with different portions of the apple fruit need to be considered when designing biocontrol systems for the management of postharvest diseases. Significantly different populations of fungi were present on fruit obtained from organic vs. conventional orchards, and the presence of several unique taxa in the organically-produced fruit may have been related to the management practice used to grow the fruit. In their study, Penicillium was dominate in peel samples, while Alternaria was dominant in the calyx- and stem-end samples. Ascomycota accounted for over 90% of the observed species, followed by Basidiomycota (8%), and Chytridiomycota (0.1%). No significant temporal changes in the microbiome were observed over a two-week storage period at room temperature. Additional studies are presently being conducted to determine the impact of waxing and storage on the resident microbiome of harvested apples, and the impact of waxing on the specific survival of the foodborne pathogen, Listeria monocytogenes. Temporal changes in the wound-related microbiome of apple and citrus fruit and their effect on biocontrol agents in the wound are also being investigated. Preliminary findings indicate the presence of a wide spectrum of bacteria in wounds and that their presence and abundance is influenced by inoculation of the wound with a pathogen or the application of a biocontrol agent (unpublished data). The effect of wound-colonizing endophytic bacteria on infection and the development of decay, as well as the efficacy of biocontrol agents are still largely unknown. A major question that needs to be resolved is how unique and stable is the core microbiome (as defined by taxa) of fruit across different climates, growing regions, and cultivars. While one would predict a stable, predictable microbiome based on the holobiont theory, previous research in grape has indicated
2. Microbiome theory and concepts Microbial communities have an essential role in ecosystem processes, including nutrient cycling, primary production, litter decomposition, and disease resistance (Delgado-Baquerizo et al., 2015). Unfortunately, a complete description of the microbial diversity present in an ecosystem cannot be obtained by standard culturing methods alone. This is also true for identifying the diversity of microbes that inhabit the internal and external portions of an organism. Regarding postharvest diseases, biocontrol of postharvest diseases, and postharvest biology in general, this shortcoming has greatly limited our understanding of the impact that whole microbial communities and their genetic material (the microbiome) potentially play in the physiology of a plant and its interactions with the environment and other organisms (Berg et al., 2016; Abdelfattah et al., 2017). The use of amplicon sequencing and metagenomics (shotgun sequencing), have provided a fundamental breakthrough in our ability to describe, compare, and discover new microbial communities (Ursell et al., 2012). Various studies have demonstrated that the composition of the microbiota inhabiting an organism (both endo- and epiphytically) can have a profound effect on the physiology of their hosts, including disease resistance responses (Hardoim et al., 2015). In general, 108
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Fig. 1. abundance of fungal genera in peel (PE), surface wounds (W), calyx end (CE), and stem end (SE). Adopted from Abdelfattah et al. (2016).
metagenomics and metatranscriptomics. The microbiota recruited by a given plant genotype in different environments seems to share greater functional similarity than taxonomic similarity (Lemanceau and Moënne-Loccoz, 2017). Information about the genes that are actively expressed in these communities, however, is lacking and how members of the communities interact with each other, and how these activities and relationships are influenced by various environmental and agricultural practices is also presently unknown. Descriptive studies can't provide definitive information on which microbial functional traits are changing in response to external stimuli and/or internal metabolic and physiological changes taking place in plant tissue. Functional metaomics approaches, including metatranscriptomics, metametabolomics, and metaproteomics, provide detailed functional information that can better reflect host-microbiome interactions and provide valuable information on the active and non-active microbial populations and their relationship to plant health and disease, as well as quality and health benefits to humans. Rhizosphere microbiome research indicates that microbes can influence nearly every functional plant trait (Friesen et al., 2011). The effect of the microbiome (epiphytic and endophytic) of harvested fruits on fruit physiology and its susceptibility to pathogen attack remains to be explored. Plant associated microorganisms have been reported to produce various phytohormones such as auxins, cytokinins, and ethylene (Spaepen, 2015). Production of plant hormones such as indole-3acetic acid (IAA) is widespread among plant-associated bacteria, particularly rhizobia (Ghosh et al., 2011), and some Bacillus spp. can produce gibberellins (Gutierrez-Manero et al., 2001). Pseudomonas syringae produces hormone analogs that interfere with jasmonate and ethylene signaling (Melotto et al., 2006). Degradation of hormones or hormone precursors by bacteria has also been documented (Glick, 2005). Microorganisms also have the potential to produce secondary metabolites capable of directly or indirectly affect fruit physiology. Thus, there is a critical need to understand the function of the carposphere microbiome, including aspects of metabolism and physiology, such as their contribution to hormonal signaling pathways that are linked to fruit ripening and senescence. Lemanceau and Moënne-Loccoz (2017) stated that the core
that the soil serves as a key source of vine-associated bacteria and that edaphic factors and vineyard-specific properties can influence the native preharvest grapevine microbiome (Zarraonaindia et al., 2015). In this regard, an international collaboration is in progress to document the microbiome of a specific cultivar of apple at harvest grown in different regions of the USA, Israel, Spain, Italy, Turkey, and Switzerland. Such foundational knowledge is imperative for determining the ability to utilize ubiquitous biocontrol agents on an international scale. Many factors are likely to be involved in determining the species composition of bacterial and fungal communities in different parts of plants. The availability of immigrant inoculum (Kinkel et al., 1987; Lindemann and Upper, 1985), host plant phenology (Blakeman, 1985; Martins et al., 2012), physico-chemical conditions (O’Brien and Lindow, 1989; Berg and Smalla, 2009), and nutritional characteristics of the phyllosphere or carposphere (Marschner et al., 2004; Compant et al., 2005). Martins et al. (2013) studied the diversity of epiphytic bacteria on grape berries and other plant parts, including leaves and bark tissues. They suggested that variability in nutrient supply between these niches might explain the observed differences in bacterial community structure, as well as the diversity of culturable genera among the different plant parts. Fruit undergo dramatic physiological (internal and external) changes during ripening and senescence that have a significant impact on their susceptibility to infection and decay. How these changes and postharvest treatments and handling processes influence the composition of the fruit microbiome and its susceptibility to pathogens is still not understood. It would be of great interest to determine if it is possible to define a unique microbiota to a specific physiological change or disorder or a specific level of host susceptibility or resistance to various pathogens. 4. Diversity and function of the fruit microbiome: a new frontier Microbiome studies are now shifting from studying just the taxonomic composition of the plant microbiome, using 16S and ITS rRNA sequence information, to a broader investigation of the functional potential of the microbiota. This has been made possible using shotgun 109
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computational simulations allow one to address the influence of dynamics in the environmental inputs (e.g., secreted metabolome) or the functional repertoire of the community (genomic composition of the sample) on network structure. Iterative simulations can be applied for delineating the functional division between community members – e.g., co-dependencies on specific nutrients and hierarchical cross-feeding interactions. These approaches can be used to achieve an understanding of the processes shaping the causal microbiology of post-harvest diseases and the mechanisms behind pathogen-resistant vs. susceptible communities, as well as the potential impact of specific microbiomes on the quality attributes of harvested commodities.
microbiome should be based not only on the composition of the taxa but by its function as well. Function at an individual microbe level will depend on the genes that are being expressed, while at a community level, function will depend on the interactions that occur between members of that community. Boon et al. (2014) argued that treating genes as ecological agents can help determine if shifts in the taxa present in an assemblage will impact the function of that community. If different taxa possess genes that serve a similar function than one would not expect the introduction or loss of a specific microbe to impact community function. Microbiome studies and meta-omics offer the opportunity to explore a new frontier that can have a major impact on the development of biocontrol agents. Recently, Poudel et al. (2016) described how an understanding of microbiome networks can serve as a systems framework for identifying microbial assemblages for disease management. As stated by Boon et al. (2014), “a deeper understanding of microbial communities will allow a shift from observation-based questions of ‘Who is there?’ and ‘What are they doing?’ to mechanisticdriven questions of ‘How will they respond?”
6. Managing the fruit microbiome for postharvest biocontrol and stress tolerance – is it feasible? Studies on ways to manipulate the microbiota of the rhizosphere to benefit plants in agricultural and horticultural systems has become a major area of research (Colla et al., 2017) and a recent report by Mazzola and Freilich (2017) have highlighted the potential of manipulating the soil microbiome using natural and synthetic microbial consortia to promote suppression of soil-borne diseases. Mazzola and Freilich (2017) stressed that a greater knowledge of the functional aspects of microbial community as a system through meta-omic studies will be needed to realize this potential. Colla et al. (2017) note that in contrast to the rhizosphere, the phyllosphere (and by extension the carposphere) has received much less attention and questions about the role of the surface and endophytic microbiome are just beginning to be addressed. Although a great deal of fundamental knowledge needs to be acquired, empirical investigations can also be pursued, keeping the “whole” system in mind when interpreting the impact of various experiments (Fig. 2). In this regard, Colla et al. (2017) noted the critical role that amino acids play in determining the composition of a microbiome and suggested that the utilization of protein hydrolysates have potential to be used as biostimulants to promote a microbial composition that favors species that suppress disease and enhance growth. In a study of four biostimulants, Tejada et al. (2011) found that the amendment derived from rice bran contained the highest level of protein and had the greatest impact on the soil microflora. Colla et al. (2017) also reviewed a study by Luziatelli et al. (2016) in which the plant-derived products, Trainer® and Auxym®, containing protein hydrolysates altered the microbial community of lettuce and increased growth and chlorophyll content. Interestingly, many of the microbial genera obtained from the treated leaves, especially Pantoea, Micrococcus, and Acinetobacter, had the ability to solubilize phosphorus and synthesize IAA. Isolates of Bacillus with strong inhibitory activity against plant pathogens were also obtained. Based on the available evidence, Colla et al. (2017) hypothesized that products containing protein hydrolysates and select microbes could be formulated to specifically support beneficial plant-microbial relationships and enhance
5. The role of endophytes in biocontrol systems and fruit biology The existence of endophytic microorganisms in plant tissues and their role in increasing biotic and abiotic stress tolerance in their hosts, as well as in improving nutrient acquisition and plant growth promotion, is well documented in the literature (reviewed by Kaul et al., 2016). The effect of the interactions of endophytic groups with the host plant and other microbial consortia on the physiology of the plant, however, are still poorly understood. The existence and function of endophytic microorganisms within host plants has not widely studied in harvested commodities. Diskin et al (2017) provided insights on the taxonomic diversity of endophytic fungal and bacterial families and their dynamics in the stems of mango fruit during storage and ripening. They documented the presence of several stem-end pathogens, such as Alternaria, Colletotrichum, and Lasiodiplodia, along with other diverse endophytic fungal and bacterial species. The abundance of the different members of the stem-end microbiota was influenced by fruit ripening and by the applied postharvest treatment. It was also shown that stem-ends that did not develop disease had more diverse microbial communities relative to stemends that were diseased. These findings suggest the existence of a natural mechanism of biocontrol in which pathogens have a silent endophytic stage and become active and cause disease when the composition of the microbiota changes in response to host physiological changes and postharvest treatments. This knowledge may influence the way we look at biocontrol and the possible use of endophytes in biocontrol systems. Although not directly related to harvested commodities and postharvest biocontrol, Liu et al. (2018) examined the influence of apple rootstocks on the composition of the endophyte community in different scion cultivars. A distinct genotype effect of the scion on the composition of the fungal endophytic community was observed, suggesting that different cultivars may harbor their own distinct microbiome. A similar effect of genotype on the foliar microbiome was reported for different poplar genotypes planted in a common garden (Bálint et al., 2013). Such studies lend support to the holobiont concept of co-evolution. How the potential for different endophytic microbiota being present in different apple cultivars would affect postharvest biocontrol systems and fruit physiology remains to be determined. Beyond the characterization of community structure, metagenomic surveys have allowed the construction of catalogues of gene/functions in specific samples (Bulgarelli et al., 2015; Ofek-Lalzar et al., 2014). Like genomic approaches, where species-specific metabolic networks are constructed based on the presence of enzyme coding genes, community networks can be constructed based on the functional annotations of metagenomic data (Abubucker et al., 2012; Zelezniak et al., 2015). Beyond the static representation of data as a network,
Fig. 2. Interactions of different components of the postharvest system.
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plant productivity. Mendes et al. (2011) showed that when soils suppressive to Rhizoctonia solani, the causal agent of damping-off and other economically important plant diseases, are added to disease conducive soils at a 1:9 ratio (w/w), R. solani infection in sugar beet is successfully suppressed. Metagenomic analysis of the soils revealed the consistent presence of 17 bacterial communities belonging to Proteobacteria, Firmicutes, and Actinobacteria and considered as a core-microbiome in disease suppression. Mazzola et al. (2015) demonstrated the ability of seed meal amendments derived from Brassica juncea/Sinapsis alba to suppress apple replant disease. In contrast to chemically fumigated soils where apple root pathogens became prevalent one year after fumigation, the seed meal treated soils prevented re-infestation after two years. Mazzola and Freilich (2017) noted the shortcomings of the single antagonist model when developing soil-based biocontrol products. The same case may be said for the study of postharvest biocontrol and the development of postharvest biocontrol products. Truly, this represents a new paradigm and a new frontier for postharvest biocontrol research.
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7. Conclusions Specific taxa of microbes can assemble into plant-associated communities that influence the fitness of both the hosts they inhabit and the microbes themselves (Lebeis et al., 2015; Berg et al., 2014). The assembled community is truly greater than the sum of its parts (Lebeis et al., 2015). Understanding the functioning of epiphytic, endophytic, and rhizosphere communities and their influence on host physiology and disease resistance is a new frontier that will modify many of the existing paradigms that exist about biocontrol systems, stress tolerance, and plant growth and development. It is understood that properties of the rhizosphere microbiome do not necessarily extend to the phyllosphere (Colla et al., 2017). The rhizosphere is nutrient-rich and able to host a high level of microbial diversity in comparison to the phyllosphere, which is considered nutrient poor. The carposphere, however, represents a unique environment and it is unclear if findings reported for either the rhizosphere or the phyllosphere can be extrapolated to conditions present on and in fruit, where nutrient levels may vary with age and a host of unique volatiles may be emitted. While the challenges posed by this new frontier are many, the opportunities for addressing many agricultural problems are great, including the development of function-based biocontrol systems and biological-based strategies for addressing postharvest physiological disorders. As indicated by Wisniewski et al. (2016), we are truly moving from an age of chemistry to an age of biology. Regarding postharvest disease and biocontrol systems, significant foundational questions regarding the characterization of core microbiomes on different commodities, and the impact of management, harvesting, processing, and storage systems on the functioning of native microbial communities, still need to be addressed. The role of the microbiome and its relationship to plant health, productivity, and plant breeding should be considered as much as the plant itself. Plant breeding or genetic modification of plants could be used to intentionally modulate the composition of the microbiome and its function, recruiting disease antagonists and plant-growth promoters that enhance plant health and the quality of harvested products. We predict that increased knowledge of microbial community systems will lead to the development of synthetic consortia that can be used to prevent postharvest diseases and mitigate physiological disorders in harvested commodities. Droby et al. (2009) asked the question, ‘Are new paradigms needed to advance the development of postharvest biocontrol systems?’ It is our belief that the rapidly evolving field of microbiome studies will be the source of developing these new paradigms in the coming years. References Abdelfattah, A., Malacrino, A., Wisniewski, M., Cacciola, S.O., Schena, L., 2017.
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