SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created Aug. 22, 2019, is named 51215-002003_Sequence_Listing_08.22.19_ST25 and is 227,509 bytes in size.

BACKGROUND

Certain invertebrates, such as nematodes and arthropods (e.g., insects, e.g., European honey bees (Apis melliferia) or silkworms (Bombyx mori)), are utilized in agriculture for pollination efforts and pest control as well as in commerce for the production of commercial products, such as honey or silk. To cultivate beneficial nematodes and arthropods for use in agricultural or commercial industries, there is a need in the art for ways to promote the growth and fitness of beneficial invertebrates.

SUMMARY OF THE INVENTION

Disclosed herein are compositions and methods for modulating the fitness of invertebrates for agriculture or commerce. The composition includes an agent that alters a level, activity, or metabolism of one or more microorganisms resident in a host, the alteration resulting in a modulation in the host's fitness.

In one aspect, provided herein is a method for increasing the fitness of a honeybee, the method including administering to the honeybee a composition including an effective amount of an organophosphorus insecticide-metabolizing bacteria formulated with an insect comestible carrier.

In some embodiments, the administration involves delivering the composition to a honeybee hive or at least one habitat where the honeybee grows, lives, reproduces, or feeds.

In some embodiments, the composition may be a liquid, a solid, an aerosol, a paste, a gel, or a gas.

In some embodiments, the organophosphorus insecticide may be fenitrothion.

In some embodiments, the carrier may be a seed coating.

In some embodiments, the honeybee may be in a honeybee colony.

In another aspect, provided herein is a composition including an effective amount of an organophosphorus insecticide-metabolizing bacteria formulated with an insect comestible carrier as a liquid, a solid, an aerosol, a paste, a gel, or a gas.

In some embodiments of the second aspect, the organophosphorus insecticide-metabolizing bacteria metabolize fenitrothion.

In some embodiments of the second aspect, the carrier is a seed coating.

In some embodiments of the second aspect, the organophosphorus insecticide-metabolizing bacteria are at a concentration of at least 100,000 cells/ml (e.g., at least about 100,000 cells/ml, at least about 150,000 cells/ml, at least about 200,000 cells/ml, at least about 250,000 cells/ml, at least about 300,000 cells/ml, at least about 350,000 cells/ml, at least about 400,000 cells/ml, at least about 450,000 cells/ml, or at least about 500,000 cells/ml).

In yet another aspect, the composition includes an agent that alters a level, activity, or metabolism of one or more microorganisms resident in an insect host, the alteration resulting in an increase in the insect host's fitness.

In another instance, the composition includes an agent that alters a level, activity, or metabolism of one or more microorganisms resident in a nematode host, the alteration resulting in an increase in the nematode host's fitness.

In some embodiments of any of the above compositions, the one or more microorganisms may be a bacterium or fungus resident in the host. In some embodiments, the bacterium resident in the host is at least one selected from the group consisting ofCandidatusspp,Bucheneraspp,Blattabacteriumspp,Baumaniaspp,Wigglesworthiaspp,Wolbachiaspp,Rickettsiaspp,Orientiaspp,Sodalisspp,Burkholderiaspp,Cupriavidusspp,Frankiaspp,Snirhizobiumspp,Streptococcusspp,Wolinellaspp,Xylellaspp,Erwiniaspp,Agrobacteriumspp,Bacillusspp,Paenibacillusspp,Streptomycesspp,Micrococcusspp,Corynebacteriumspp,Acetobacterspp,Cyanobacteriaspp,Salmonellaspp,Rhodococcusspp,Pseudomonasspp,Lactobacillusspp,Enterococcusspp,Alcaligenesspp,Klebsiellaspp,Paenibacillusspp,Arthrobacterspp,Corynebacteriumspp,Brevibacteriumspp,Thermusspp,Pseudomonasspp,Clostridiumspp, andEscherichiaspp. In some embodiments, the fungus resident in the host is at least one selected from the group consisting ofCandida, Metschnikowia, Debaromyces, Starmerella, Pichia, Cryptococcus, Pseudozyma, Symbiotaphrina bucneri, Symbiotaphrina Scheffersomyces shehatae, Scheffersomyces stipites, Cryptococcus, Trichosporon, Amylostereum areolatum, Epichloespp,Pichia pinus, Hansenula capsulate, Daldinia decipien, Ceratocytisspp,Ophiostomaspp, andAttamyces bromatificus.

In any of the above compositions, the agent, which hereinafter may also be referred to as a modulating agent, may alter the growth, division, viability, metabolism, and/or longevity of the microorganism resident in the host. In any of the above embodiments, the modulating agent may decrease the viability of the one or more microorganisms resident in the host. In some embodiments, the modulating agent increases growth or viability of the one or more microorganisms resident in the host.

In any of the above embodiments, the modulating agent is a phage, a polypeptide, a small molecule, an antibiotic, a bacterium, or any combination thereof.

In some embodiments, the phage binds a cell surface protein on a bacterium resident in the host. In some embodiments, the phage is virulent to a bacterium resident in the host. In some embodiments, the phage is at least one selected from the group consisting of Myoviridae, Siphoviridae, Podoviridae, Lipothrixviridae, Rudiviridae, Ampullaviridae, Bicaudaviridae, Clavaviridae, Corticoviridae, Cystoviridae, Fuselloviridae, Gluboloviridae, Guttaviridae, Inoviridae, Leviviridae, Microviridae, Plasmaviridae, and Tectiviridae.

In some embodiments, the polypeptide is at least one of a bacteriocin, R-type bacteriocin, nodule C-rich peptide, antimicrobial peptide, lysin, or bacteriocyte regulatory peptide.

In some embodiments, the small molecule is a metabolite.

In some embodiments, the antibiotic is a broad-spectrum antibiotic.

In some embodiments, the modulating agent is a naturally occurring bacteria. In some embodiments, the bacteria is at least one selected from the group consisting ofBartonella apis, Parasaccharibacter apium, Frischella perrara, Snodgrassella alvi, Gilliamela apicola, Bifidobacteriumspp, andLactobacillusspp. In some embodiments, the bacterium is at least one selected from the group consisting ofCandidatusspp,Bucheneraspp,Blattabacteriumspp,Baumaniaspp,Wigglesworthiaspp,Wolbachiaspp,Rickettsiaspp,Orientiaspp,Sodalisspp,Burkholderiaspp,Cupriavidusspp,Frankiaspp,Snirhizobiumspp,Streptococcusspp,Wolinellaspp,Xylellaspp,Erwiniaspp,Agrobacteriumspp,Bacillusspp,Paenibacillusspp,Streptomycesspp,Micrococcusspp,Corynebacteriumspp,Acetobacterspp,Cyanobacteriaspp,Salmonellaspp,Rhodococcusspp,Pseudomonasspp,Lactobacillusspp,Enterococcusspp,Alcaligenesspp,Klebsiellaspp,Paenibacillusspp,Arthrobacterspp,Corynebacteriumspp,Brevibacteriumspp,Thermusspp,Pseudomonasspp,Clostridiumspp, andEscherichiaspp. In certain instances, the bacterium is a naturally occurring bacterium that is capable of degrading pesticides such as organophosphorus insecticides (e.g., phosphorothioate, e.g., fenitrothion).

In any of the above compositions, host fitness may be measured by survival, reproduction, or metabolism of the host. In some embodiments, the modulating agent modulates the host's fitness by decreasing pesticidal susceptibility of the host (e.g., susceptibility to a pesticide listed in Table 12). In some embodiments, the pesticidal susceptibility is bactericidal or fungicidal susceptibility. In some embodiments, the pesticidal susceptibility is insecticidal or nematicidal susceptibility.

In any of the above compositions, the composition may include a plurality of different modulating agents. In some embodiments, the composition includes a modulating agent and a pesticidal agent (e.g., a pesticide listed in Table 12). In some embodiments, the pesticidal agent is a bactericidal or fungicidal agent. In some embodiments, the pesticidal agent is an insecticidal or nematicidal agent.

In any of the above compositions, the composition may include a modulating agent and an agent that increases crop growth.

In any of the above compositions, modulating agent may be linked to a second moiety. In some embodiments, the second moiety is a modulating agent.

In any of the above compositions, the modulating agent may be linked to a targeting domain. In some embodiments, the targeting domain targets the modulating agent to a target site in the host. In some embodiments, the targeting domain targets the modulating agent to the one or more microorganisms resident in the host.

In any of the above compositions, the modulating agent may include an inactivating pre- or pro-sequence, thereby forming a precursor modulating agent. In some embodiments, the precursor modulating agent is converted to an active form in the host.

In any of the above compositions, the modulating agent may include a linker. In some embodiments, the linker is a cleavable linker.

In any of the above compositions, the composition may further include a carrier. In some instances, the carrier may be an agriculturally acceptable carrier.

In any of the above compositions, the composition may further include a host bait, a sticky agent, or a combination thereof. In some embodiments, the host bait is a comestible agent and/or a chemoattractant.

In any of the above compositions, the composition may be at a dose effective to modulate host fitness.

In any of the above compositions, the composition may be formulated for delivery to a microorganism inhabiting the gut of the host.

In any of the above compositions, the composition may be formulated for delivery to a microorganism inhabiting a bacteriocyte of the host and/or the gut of the host. In some embodiments, the composition may be formulated for delivery to a plant. In some embodiments, the composition may be formulated for use in a host feeding station.

In any of the above compositions, the composition may be formulated as a liquid, a powder, granules, or nanoparticles. In some embodiments, the composition is formulated as one selected from the group consisting of a liposome, polymer, bacteria secreting peptide, and synthetic nanocapsule. In some embodiments, the synthetic nanocapsule delivers the composition to a target site in the host. In some embodiments, the target site is the gut of the host. In some embodiments, the target site is a bacteriocyte in the host.

In a further aspect, also provided herein are hosts that include any of the above compositions. In some embodiments, the host is an insect. In some embodiments, the insect aids in pest control, pollination, generation of a commercial product, or a combination thereof. In some embodiments, the insect is a species belonging toCoccinellidae, Carabidae, Mantidae,Syrphidae, Lampyridae, Myrmeliontidase, Chrysopidae, Hemerobiidae, Brachonidae, Ichneumonidae, orOdonata. In some embodiments, the insect is a species belonging to Andrenidae, Apidae, Colletidae, Halicitdae, or Megahlidae. In some embodiments, the insect is a species belonging to Bombycidae or Saturniidae. In certain embodiments, the insect is a honey bee or silkworm.

In some embodiments, the host is a nematode. In some embodiments, the nematode is a species belonging to Heterorhabditis or Steinernema.

In yet a further aspect, also provided herein is a system for modulating a host's fitness comprising a modulating agent that targets a microorganism that is required for a host's fitness, wherein the system is effective to modulate the host's fitness, and wherein the host is an insect or nematode. The modulating agent may include any of the compositions described herein. In some embodiments, the modulating agent is formulated as a powder. In some embodiments, the modulating agent is formulated as a solvent. In some embodiments, the modulating agent is formulated as a concentrate. In some embodiments, the modulating agent is formulated as a diluent. In some embodiments, the modulating agent is prepared for delivery by combining any of the previous compositions with a carrier.

In another aspect, also provided herein are methods for modulating the fitness of an insect or nematode using any of the compositions described herein. In one instance, the method of modulating the fitness of an insect or nematode host includes delivering the composition of any one of the previous claims to the host, wherein the modulating agent targets the one or more microorganisms resident in the host, and thereby modulates the host's fitness. In another instance, the method of modulating microbial diversity in an insect or nematode host includes delivering the composition of any one of the previous claims to the host, wherein the modulating agent targets the one or more microorganisms resident in the host, and thereby modulates microbial diversity in the host.

In some embodiments of any of the above methods, the modulating agent may alter the levels of the one or more microorganisms resident in the host. In some embodiments of any of the above methods, the modulating agent may alter the function of the one or more microorganisms resident in the host. In some embodiments, the one or more microorganisms may be a bacterium and/or fungus. In some embodiments, the one or more microorganisms are required for host fitness. In some embodiments, the one or more microorganisms are required for host survival.

In some embodiments of any of the above methods, the delivering step may include providing the modulating agent at a dose and time sufficient to effect the one or more microorganisms, thereby modulating microbial diversity in the host. In some embodiments, the delivering step includes topical application of any of the previous compositions to a plant. In some embodiments, the delivering step includes providing the modulating agent through a genetically engineered plant. In some embodiments, the delivering step includes providing the modulating agent to the host as a comestible. In some embodiments, the delivering step includes providing a host carrying the modulating agent. In some embodiments the host carrying the modulating agent can transmit the modulating agent to one or more additional hosts.

In some embodiments of any of the above methods, the composition is effective to increase health and/or survival of the host. In some embodiments, the composition is effective to increase host fitness, increase host lifespan, increase effective pollination, increase generation of a host product, increase host reproduction, or a combination thereof. In some embodiments, the composition is effective to decrease the host's sensitivity to a pesticidal agent (e.g., a pesticide listed in Table 12). In certain embodiments, the pesticidal agent is a neonicotinoid (e.g., imidacloprid). In certain embodiments, the pesticidal agent is an organophosphorus insecticide (e.g., a phosphorothioate, e.g., fenitrothion). In some embodiments, the composition is effective to increase the host's resistance to an allelochemical agent produced by a plant. In some embodiments, the allelochemical agent is toxic to the host prior to delivery of the composition. In some embodiments, the allelochemical agent is caffeine, soyacystatin N, monoterpenes, diterpene acids, or phenolic compounds.

In some embodiments of any of the above methods, the host is an insect. In some embodiments, the insect aids in pest control, pollination, generation of a commercial product, waste degradation, or a combination thereof. In some embodiments, the insect is a species belonging toCoccinellidae, Carabidae, Mantidae,Syrphidae, Lampyridae, Myrmeliontidase, Chrysopidae, Hemerobiidae, Brachonidae, Ichneumonidae, orOdonata. In some embodiments, the insect is a species belonging to Andrenidae, Apidae, Colletidae, Halicitdae, or Megahlidae. In some embodiments, the insect is a species belonging to Bombycidae or Saturniidae. In certain embodiments, the insect is a honey bee or silkworm.

In some embodiments, the host is a nematode. In some embodiments, the nematode is a species belonging to Heterorhabditis or Steinernema.

In some embodiments of any of the above methods, the delivering step includes delivering any of the previous compositions to a plant. In some embodiments, the plant is an agricultural crop. In some embodiments, the crop is an unharvested crop at the time of delivery. In some embodiments, the crop is a harvested crop at the time of delivery. The some embodiments, the crop comprises harvested fruits or vegetables. In some embodiments, the composition is delivered in an amount and for a duration effective to increase growth of the crop. In some embodiments, the crop includes corn, soybean, or wheat plants.

In another aspect, also provided herein are screening assays to identify modulating agent that modulate the fitness of a host. In one instance, the screening assay to identify a modulating agent that modulates the fitness of a host, includes the steps of (a) exposing a microorganism that can be resident in the host to one or more candidate modulating agents and (b) identifying a modulating agent that increases the fitness of the host.

In some embodiments of the screening assay, the modulating agent is a microorganism resident in the host. In some embodiments, the microorganism is a bacterium. In some embodiments, the bacterium, when resident in the host, increases host fitness. In some embodiments, the bacterium degrades a pesticide (e.g., a pesticide listed in Table 12). In certain embodiments, the pesticide is a neonicotinoid (e.g., imidacloprid) or an organophosphorus insecticide (e.g., a phosphorothioate, e.g., fenitrothion). In some embodiments, the bacterium secretes an amino acid. In certain embodiments, wherein the amino acid is methionine.

In some embodiments of the screening assay, the modulating agent affects an allelochemical-degrading microorganism. In some embodiments, the modulating agent is a phage, an antibiotic, or a test compound. In certain embodiments, the antibiotic is timentin or azithromycin.

In some embodiments of the screening assay, the host may be an invertebrate. In some embodiments, the invertebrate is an insect or a nematode. In certain embodiments, the insect is a honey bee. In other particular embodiments, the insect is a silkworm.

In any of the above embodiments of the screening assay, host fitness may be modulated by altering the host microbiota.

Definitions

As used herein, the term “bacteriocin” refers to a peptide or polypeptide that possesses anti-microbial properties. Naturally occurring bacteriocins are produced by certain prokaryotes and act against organisms related to the producer strain, but not against the producer strain itself. Bacteriocins contemplated herein include, but are not limited to, naturally occurring bacteriocins, such as bacteriocins produced by bacteria, or derivatives thereof, such as engineered bacteriocins, recombinantly expressed bacteriocins, or chemically synthesized bacteriocins. In some instances, the bacteriocin is a functionally active variant of the bacteriocins described herein. In some instances, the variant of the bacteriocin has at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity, e.g., over a specified region or over the entire sequence, to a sequence of a bacteriocin described herein or a naturally occurring bacteriocin.

As used herein, the term “bacteriocyte” refers to a specialized cell found in certain insects where intracellular bacteria reside with symbiotic bacterial properties.

As used herein, the term “effective amount” refers to an amount of a modulating agent (e.g., a phage, lysin, bacteriocin, small molecule, or antibiotic) or composition including said agent sufficient to effect the recited result, e.g., to increase or promote the fitness of a host organism (e.g., insect); to reach a target level (e.g., a predetermined or threshold level) of a modulating agent concentration inside a target host; to reach a target level (e.g., a predetermined or threshold level) of a modulating agent concentration inside a target host gut; to reach a target level (e.g., a predetermined or threshold level) of a modulating agent concentration inside a target host bacteriocyte; to modulate the level, or an activity, of one or more microorganism (e.g., endosymbiont) in the target host.

As used herein, the term “fitness” refers to the ability of a host organism to survive, grow, and/or to produce surviving offspring. Fitness of an organism may be measured by one or more parameters, including, but not limited to, life span, reproductive rate, mobility, body weight, and/or metabolic rate. Fitness may additionally be measured based on measures of activity (e.g., pollination) or product output (e.g., honey or silk).

As used herein, the term “gut” refers to any portion of a host's gut, including, the foregut, midgut, or hindgut of the host.

As used herein, the term “host” refers to an organism (e.g., insect) carrying resident microorganisms (e.g., endogenous microorganisms, endosymbiotic microorganisms (e.g., primary or secondary endosymbionts), commensal organisms, and/or pathogenic microorganisms).

As used herein “increasing host fitness” or “promoting host fitness” refers to any favorable alteration in host physiology, or any activity carried out by said host, as a consequence of administration of a modulating agent, including, but not limited to, any one or more of the following desired effects: (1) increasing a population of a host by about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, 100% or more; (2) increasing the reproductive rate of a host (e.g., insect, e.g., bee or silkworm) by about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, 100% or more; (3) increasing the mobility of a host (e.g., insect, e.g., bee or silkworm) by about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, 100% or more; (4) increasing the body weight of a host (e.g., insect, e.g., bee or silkworm) by about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, 100% or more; (5) increasing the metabolic rate or activity of a host (e.g., insect, e.g., bee or silkworm) by about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, 100% or more; (6) increasing pollination (e.g., number of plants pollinated in a given amount of time) by a host (e.g., insect, e.g., bee or silkworm) by about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, 100% or more; (7) increasing production of host (e.g., insect, e.g., bee or silkworm) byproducts (e.g., honey from a honeybee or silk from a silkworm) by about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, 100% or more; (8) increasing nutrient content of the host (e.g., insect) (e.g., protein, fatty acids, or amino acids) by about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, 100% or more; or (9) increasing host resistance to pesticides (e.g., a neonicotinoid (e.g., imidacloprid) or an organophosphorus insecticide (e.g., a phosphorothioate, e.g., fenitrothion)) by about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, 100% or more. An increase in host fitness can be determined in comparison to a host organism to which the modulating agent has not been administered.

The term “insect” includes any organism belonging to the phylumArthropodaand to the classInsectaor the class Arachnida, in any stage of development, i.e., immature or adult insects.

As used herein, “lysin” also known as endolysin, autolysin, murein hydrolase, peptidoglycan hydrolase, or cell wall hydrolase refers to a hydrolytic enzyme that can lyse a bacterium by cleaving peptidoglycan in the cell wall of the bacterium. Lysins contemplated herein include, but are not limited to, naturally occurring lysins, such as lysins produced by phages, lysins produced by bacteria, or derivatives thereof, such as engineered lysins, recombinantly expressed lysins, or chemically synthesized lysins. A functionally active variant of the bacteriocin may have at least 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity, e.g., over a specified region or over the entire sequence, to a sequence of a synthetic, recombinant, or naturally derived bacteriocin, including any described herein.

As used herein, the term “microorganism” refers to bacteria or fungi. Microorganisms may refer to microorganisms resident in a host organism (e.g., endogenous microorganisms, endosymbiotic microorganisms (e.g., primary or secondary endosymbionts)) or microorganisms exogenous to the host, including those that may act as modulating agents. As used herein, the term “target microorganism” refers to a microorganism that is resident in the host and impacted by a modulating agent, either directly or indirectly.

As used herein, the term “agent” or “modulating agent” refers to an agent that is capable of altering the levels and/or functioning of microorganisms resident in a host organism (e.g., insect), and thereby modulate (e.g., increase) the fitness of the host organism (e.g., insect).

As used herein, the term “pesticide” or “pesticidal agent” refers to a substance that can be used in the control of agricultural, environmental, or domestic/household pests, such as insects, fungi, bacteria, or viruses. The term “pesticide” is understood to encompass naturally occurring or synthetic insecticides (larvicides or adulticides), insect growth regulators, acaricides (miticides), nematicides, ectoparasiticides, bactericides, fungicides, or herbicides (substance which can be used in agriculture to control or modify plant growth). Further examples of pesticides or pesticidal agents are listed in Table 12. In some instances, the pesticide is an allelochemical. As used herein, “allelochemical” or “allelochemical agent” is a substance produced by an organism that can effect a physiological function (e.g., the germination, growth, survival, or reproduction) of another organism (e.g., a host insect or nematode).

As used herein, the term “peptide,” “protein,” or “polypeptide” encompasses any chain of naturally or non-naturally occurring amino acids (either D- or L-amino acids), regardless of length (e.g., at least 2, 3, 4, 5, 6, 7, 10, 12, 14, 16, 18, 20, 25, 30, 40, 50, 100, or more amino acids), the presence or absence of post-translational modifications (e.g., glycosylation or phosphorylation), or the presence of, e.g., one or more non-amino acyl groups (for example, sugar, lipid, etc.) covalently linked to the peptide, and includes, for example, natural proteins, synthetic, or recombinant polypeptides and peptides, hybrid molecules, peptoids, or peptidomimetics.

As used herein, “percent identity” between two sequences is determined by the BLAST 2.0 algorithm, which is described in Altschul et al. (J. Mol. Biol.215:403-410, 1990). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information.

As used herein, the term “phage” or “bacteriophage” refers to a virus that infects and replicates in bacteria. Bacteriophages replicate within bacteria following the injection of their genome into the cytoplasm and do so using either a lytic cycle, which results in bacterial cell lysis, or a lysogenic (non-lytic) cycle, which leaves the bacterial cell intact. The phage may be a naturally occurring phage isolate, or an engineered phage, including vectors, or nucleic acids that encode either a partial phage genome (e.g., including at least all essential genes necessary to carry out the life cycle of the phage inside a host bacterium) or the full phage genome.

As used herein, the term “plant” refers to whole plants, plant organs, plant tissues, seeds, plant cells, seeds, and progeny of the same. Plant cells include, without limitation, cells from seeds, suspension cultures, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen, or microspores. Plant parts include differentiated or undifferentiated tissues including, but not limited to the following: roots, stems, shoots, leaves, pollen, seeds, tumor tissue, and various forms of cells and culture (e.g., single cells, protoplasts, embryos, or callus tissue). The plant tissue may be in a plant or in a plant organ, tissue, or cell culture. In addition, a plant may be genetically engineered to produce a heterologous protein or RNA, for example, of any of the modulating agents in the methods or compositions described herein.

The terms “obtainable by”, “producible by” or the like are used to indicate that a claim or embodiment refers to compound, composition, product, etc. per se, i.e. that the compound, composition, product, etc. can be obtained or produced by a method which is described for manufacture of the compound, composition, product, etc., but that the compound, composition, product, etc. may be obtained or produced by other methods than the described one as well. The terms “obtained by,” “produced by,” or the like indicate that the compound, composition, product, is obtained or produced by a recited specific method. It is to be understood that the terms “obtainable by,” “producible by” and the like also disclose the terms “obtained by”, “produced by” and the like as a preferred embodiment of “obtainable by”, “producible by” and the like.

Other features and advantages of the invention will be apparent from the following Detailed Description and the Claims.

