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WO 2015/100431 A2 July 2015 (02.07.2015) W P O P C T (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2015/100431 A2 July 2015 (02.07.2015) W P O P C T (51) International Patent Classification: c/o Symbiota. Inc., 1 Memorial Drive, 7th Floor, Cam A 63/02 (2006.01) bridge, MA 02421 (US). MARQUEZ, Luis, Miguel; c/o Symbiota, Inc., 1 Memorial Drive, 7th Floor, Cambridge, (21) International Application Number: MA 02421 (US). JOHNSTON, David, Morris; c/o Sym PCT/US2014/072399 biota, Inc., 1 Memorial Drive, 7th Floor, Cambridge, MA (22) International Filing Date: 02421 (US). MILLET, Yves, Alain; c/o Symbiota, Inc., 1 24 December 2014 (24. 12.2014) Memorial Drive, 7th Floor, Cambridge, MA 02421 (US). LYFORD, Jeffrey; c/o Symbiota, Inc., 1 Memorial Drive, (25) Filing Language: English 7th Floor, Cambridge, MA 02421 (US). LEFF, Jonathan, (26) Publication Language: English W.; c/o Symbiota, Inc., 1 Memorial Drive, 7th Floor, Cam bridge, MA 02421 (US). SAMAYOA, Philip; c/o Symbi (30) Priority Data: ota, Inc., 1 Memorial Drive, 7th Floor, Cambridge, MA 61/920,557 24 December 201 3 (24. 12.2013) US 02421 (US). SADOWSKI, Craig; c/o Symbiota, Inc., 1 61/920,529 24 December 201 3 (24. 12.2013) US Memorial Drive, 7th Floor, Cambridge, MA 02421 (US). 61/920,5 17 24 December 201 3 (24. 12.2013) us 61/920,616 24 December 201 3 (24. 12.2013) us (74) Agents: SHUSTER, Michael J. et al; Fenwick & West 61/920,638 24 December 201 3 (24. 12.2013) us LLP, Silicon Valley Center, 801 California Street, Moun 61/920,659 24 December 201 3 (24. 12.2013) us tain View, CA 94041 (US). 61/920,554 24 December 201 3 (24. 12.2013) us (81) Designated States (unless otherwise indicated, for every (71) Applicants: SYMBIOTA, INC. [US/US]; 1 Memorial kind of national protection available): AE, AG, AL, AM, Drive, 7th Floor, Cambridge, MA 02421 (US). AIT AUS¬ AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, TRIAN INSTITUTE OF TECHNOLOGY GMBH BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, [AT/AT]; Tech Gate Wien Wissensch. U. Tech. Park, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, Doanu-City-Str 1, A-1220 Vienna (AT). HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, (72) Inventors: MITTER, Birgit; c/o Ait Austrian Institute Of MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, Technology Gmbh, Tech Gate Wien Wissensch. U. Tech., PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, Park Donau-city-str 1, A-1220 Vienna (AT). NAVEED, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, Muhammad; c/o Ait Austrian Institute Of Technology TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. Gmbh, Tech Gate Wien Wissensch. U. Tech., Park Donau- city-str 1, A-1220 Vienna (AT). BERNINGER, Teresa; (84) Designated States (unless otherwise indicated, for every c/o Ait Austrian Institute Of Technology Gmbh, Tech Gate kind of regional protection available): ARIPO (BW, GH, Wien Wissensch. U. Tech., Park Donau-city-str 1, A-1220 GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, Vienna (AT). COMPANT, Stephane; c/o Ait Austrian In TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, stitute Of Technology Gmbh, Tech Gate Wien Wissensch. TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, U. Tech., Park Donau-city-str 1, A-1220 Vienna (AT). DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, SESSITSCH, Angela; c/o Ait Austrian Institute Of Tech LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, nology Gmbh, Tech Gate Wien Wissensch. U. Tech., Park SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, Donau-city-str 1, A-1220 Vienna (AT). VON GW, KM, ML, MR, NE, SN, TD, TG). MALTZAHN, Geoffrey; c/o Symbiota, Inc., 1 Memorial Published: Drive, 7th Floor, Cambridge, MA 02421 (US). FLAV- ELL, Rihard, Bailey; c/o Symbiota, Inc., 1 Memorial — without international search report and to be republished Drive, 7th Floor, Cambridge, MA 02421 (US). TOLEDO, upon receipt of that report (Rule 48.2(g)) Gerardo, V.; C/o Symbiota, Inc., 1 Memorial Drive, 7th Floor, Cambridge, MA 02421 (US). DJONOVIC, Slavica; (54) Title: PLANTS CONTAINING BENEFICIAL ENDOPHYTES (57) Abstract: This application relates to methods and materials for providing a benefit to a seed, seedling or plant by producing seeds that are internally colonized with endophytes. Beneficial endophytes with particular characteristics are provided. These may be used in the methods described to provide a benefit to a seed, seedling or plant. PLANTS CONTAINING BENEFICIAL ENDOPHYTES SEQUENCE LISTING The instant application contains a Sequence Listing which has been filed electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on December 24, 2014, is named 28273PCT_CRF_sequencelisting.txt and is 1,164,153 bytes in size. TECHNICAL FIELD This application relates to methods and materials for providing a benefit to a seed or seedling of an agricultural plant, or an agricultural plant derived from the seed or seedling. For example, this application provides purified microbial populations that include microbial endophytes, and synthetic combinations of seeds and/or seedlings with seed-derived microbial endophytes such as heterologous seed-derived microbial endophytes. Such seed microbial endophytes can provide beneficial properties to the seed, seedling, or the agricultural plant derived from the seed or seedling, including beneficial properties related to metabolic, transcriptional, or proteome alterations, morphology, and the resilience to a variety of environmental stresses, and combination of such properties. BACKGROUND The present invention relates to the methods of producing plant seeds comprising microbes, as well as compositions of plants and seed comprising microbes. Agriculture faces numerous challenges that are making it increasingly difficult to provide food, materials, and fuels to the world's population. Population growth and changes in diet associated with rising incomes are increasing global food demand, while many key resources for agriculture are becoming increasingly scarce. By 2050, the FAO projects that total food production must increase by 70% to meet the needs of the growing population, a challenge that is exacerbated by numerous factors, including diminishing freshwater resources, increasing competition for arable land, rising energy prices, increasing input costs, and the likely need for crops to adapt to the pressures of a more extreme global climate. The need to grow nearly twice as much food in more uncertain climates is driving a critical need for new innovations. Today, crop performance is optimized via of technologies directed towards the interplay between crop genotype (e.g., plant breeding, genetically-modified (GM) crops) and its surrounding environment (e.g., fertilizer, synthetic herbicides, pesticides). While these paradigms have assisted in doubling global food production in the past fifty years, yield growth rates have stalled in many major crops and shifts in the climate have been linked to production declines in important crops such as wheat. In addition to their long development and regulatory timelines, public fears of GM-crops and synthetic chemicals has challenged their use in many key crops and countries, resulting in a complete lack of acceptance for GM traits in wheat and the exclusion of GM crops and many synthetic chemistries from European markets. Thus, there is a significant need for innovative, effective, and publically-acceptable approaches to improving the intrinsic yield and resilience of crops to severe stresses. Like humans, which benefit from a complement of beneficial microbial symbionts, plants have been purported to benefit somewhat from the vast array of bacteria and fungi that live both within and around their tissues to support their health and growth. Endophytes are fungal or bacterial organisms that live within plants. Bacterial and fungal endophytes appear to inhabit various host plant tissues and have been isolated from plant leaves, stems, or roots. There is an increasing appreciation of the roles played by microbes, including endophytic bacteria, in improving plant growth, health and productivity. For example, association with certain microbes can promote plant growth using an array of mechanisms, including playing an essential role in biological nitrogen fixation (BNF), the synthesis of phytohormones and vitamins, increasing the host plant's tolerance to numerous environmental stresses (including both biotic and abiotic stresses), alteration of hormone production, as well as increasing the bioavailability to the plant of macro- and micronutrients such as phosphorus and iron. Endophytic organisms associated with plants occupy a relatively privileged niche within a plant and contribute to plant health or growth. Endophytes have been targeted as valuable sources of new bioactive compounds. Endophytes inhabit plant tissues, particularly the so-called intercellular space. Endophytic microorganisms have been found in virtually every plant studied, where they colonize the internal tissues of their host plant and can form a range of different relationships including symbiotic, mutualistic, commensalistic and trophobiotic. Most endophytes appear to originate from the rhizosphere or phyllosphere; however, some may be transmitted through the seed. Endophytic microorganisms can promote plant growth and yield and can act as biocontrol agents. Endophytes can also be beneficial to their host by producing natural products that are beneficial to the plant and could also be harnessed for potential use in medicine, agriculture or industry. In addition, it has been shown that they have the potential to remove soil contaminants by enhancing phytoremediation and may play a role in soil fertility through phosphate solubilization and nitrogen fixation.
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