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WO 2016/200987 Al 15 December 2016 (15.12.2016) P O P C T

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WO 2016/200987 Al 15 December 2016 (15.12.2016) 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 2016/200987 Al 15 December 2016 (15.12.2016) P O P C T (51) International Patent Classification: Trudi, A.; Indigo Agriculture, Inc., 500 Rutherford Aven A01N 63/02 (2006.01) A01C 1/00 (2006.01) ue, North Building, Boston, MA 02129 (US). A01N 63/00 (2006.01) A01C 1/06 (2006.01) (74) Agents: HUBL, Susan, T. et al; Fenwick & West LLP, (21) International Application Number: Silicon Valley Center, 801 California Street, Mountain PCT/US20 16/036504 View, CA 94041 (US). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 8 June 2016 (08.06.2016) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (25) Filing Language: English BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (26) Publication Language: English DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, N , IR, IS, JP, KE, KG, KN, KP, KR, (30) Priority Data: KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, 62/172,748 8 June 2015 (08.06.2015) US MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, 62/172,750 8 June 2015 (08.06.2015) US PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, 62/172,755 8 June 2015 (08.06.2015) us SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 62/3 16,386 31 March 2016 (3 1.03.2016) us TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (71) Applicant: INDIGO AGRICULTURE, INC. [US/US]; (84) Designated States (unless otherwise indicated, for every 500 Rutherford Avenue, North Building, Boston, MA kind of regional protection available): ARIPO (BW, GH, 02129 (US). GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, (72) Inventors: DJONOVIC, Slavica; Indigo Agriculture, Inc., TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, 500 Rutherford Avenue, North Building, Boston, MA TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, 02129 (US). MCKENZIE, Elizabeth, Alexa; Indigo Agri DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, culture, Inc., 500 Rutherford Avenue, North Building, Bo LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, ston, MA 02129 (US). TOLEDO, Gerardo, V.; Indigo SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, Agriculture, Inc., 500 Rutherford Avenue, North Building, GW, KM, ML, MR, NE, SN, TD, TG). Boston, MA 02129 (US). SADOWSKI, Craig; Indigo A g Declarations under Rule 4.17 : riculture, Inc., 500 Rutherford Avenue, North Building, Boston, MA 02129 (US). VON MALTZAHN, Geoffrey; — of inventorship (Rule 4.17(iv)) Indigo Agriculture, Inc., 500 Rutherford Avenue, North Published: Building, Boston, MA 02129 (US). AMBROSE, Karen, — with international search report (Art. 21(3)) V.; Indigo Agriculture, Inc., 500 Rutherford Avenue, North Building, Boston, MA 02129 (US). ZHANG, Xuecheng; — before the expiration of the time limit for amending the Indigo Agriculture, Inc., 500 Rutherford Avenue, North claims and to be republished in the event of receipt of Building, Boston, MA 02129 (US). JOHNSTON, David, amendments (Rule 48.2(h)) Morris; Indigo Agriculture, Inc., 500 Rutherford Avenue, — with sequence listing part of description (Rule 5.2(a)) North Building, Boston, MA 02129 (US). GULICK, 00 o© (54) Title: STREPTOMYCES ENDOPHYTE COMPOSITIONS AND METHODS FOR IMPROVED AGRONOMIC TRAITS IN v PLANTS o (57) Abstract: This invention relates to methods and compositions for providing a benefit to a plant by associating the plant with a beneficial endophyte of the genus Streptomyces, including benefits to a plant derived from a seed or other plant element treated with said endophyte. For example, this invention provides purified endophytes, synthetic combinations comprising endophytes, and meth o ods of making and using the same. In particular, this invention relates to compositions and methods of improving soybean and maize plants. STREPTOMYCES ENDOPHYTE COMPOSITIONS AND METHODS FOR IMPROVED AGRONOMIC TRAITS IN PLANTS CROSS REFERENCE TO RELATED APPLICATIONS [0001] This application claims the benefit of U.S. Provisional Application No. 62/172,748 filed 08 June 2015, and of U.S. Provisional No. 62/172,750 filed on 08 June 2015, and of U.S. Provisional Application No. 62/172,755 filed on 08 June 2015, and of U.S. Provisional Application No. 62/316,386 filed on 3 1 March 2016, all of which are hereby incorporated by reference in their entireties. SEQUENCE LISTING [0002] The instant application includes a Sequence Listing with 4779 sequences which has been submitted via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on June 8, 2016, is named 33897PCT_sequencelisting.txt, and is 8.83 MB in size. FIELD OF THE INVENTION [0003] This invention relates to compositions and methods for improving the cultivation of plants, particularly agricultural plants, such as soybeans and maize. For example, this invention describes bacteria, such as strains of the genus Streptomyces, that are capable of living in or otherwise associated with a plant, which may be used to impart improved agronomic traits to plants. The disclosed invention also describes methods of improving plant characteristics by introducing bacteria to those plants. Further, this invention also provides methods of treating seeds and other plant elements with Streptomyces bacteria that are capable of living within or otherwise associated with a plant, to impart improved agronomic characteristics to plants, particularly agricultural plants, for example soybeans or maize. BACKGROUND OF THE INVENTION [0004] According the United Nations Food and Agricultural Organization (UN FAO), the world's population will exceed 9.6 billion people by the year 2050, which will require significant improvements in agricultural to meet growing food demands. At the same time, conservation of resources (such as water, land), reduction of inputs (such as fertilizer, pesticides, herbicides), environmental sustainability, and climate change are increasingly important factors in how food is grown. There is a need for improved agricultural plants and farming practices that will enable the need for a nearly doubled food production with fewer resources, more environmentally sustainable inputs, and with plants with improved responses to various biotic and abiotic stresses (such as pests, drought, disease). [0005] Today, crop performance is optimized primarily via 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 instability and declines in important crops, driving an urgent need for novel solutions to crop yield improvement. In addition to their long development and regulatory timelines, public fears of GM-crops and synthetic chemicals have challenged their use in many key crops and countries, resulting in a lack of acceptance for many GM traits and the exclusion of GM crops and many synthetic chemistries from some global markets. Thus, there is a significant need for innovative, effective, environmentally-sustainable, and publically-acceptable approaches to improving the yield and resilience of crops to stresses. [0006] Improvement of crop resilience to biotic and abiotic stresses has proven challenging for conventional genetic and chemical paradigms for crop improvement. This challenge is in part due to the complex, network-level changes that arise during exposure to these stresses. [0007] Like humans, who utilize a complement of beneficial microbial symbionts, plants have been purported to derive a benefit from the vast array of bacteria and fungi that live both within and around their tissues in order to support the plant's health and growth. Endophytes are symbiotic organisms (typically bacteria or fungi) that live within plants, and inhabit various plant tissues, often colonizing the intercellular spaces of host leaves, stems, flowers, fruits, seeds, or roots. To date, a small number of symbiotic endophyte-host relationships have been analyzed in limited studies to provide fitness benefits to model host plants within controlled laboratory settings, such as enhancement of biomass production (i.e., yield) and nutrition, increased tolerance to stress such as drought and pests. There is still a need to develop better plant-endophyte systems to confer benefits to a variety of agriculturally- important plants such as soybean and maize, for example to provide improved yield and tolerance to the environmental stresses present in many agricultural situations for such agricultural plants. [0008] Thus, there is a need for compositions and methods of providing agricultural plants with improved yield and tolerance to various biotic and abiotic stresses. Provided herein are novel compositions including bacteria that are capable of living within a plant, formulations comprising these compositions for treatment of plants and plant elements, and methods of use for the same, created based on the analysis of the key properties that enhance the utility and commercialization of an endophyte composition. SUMMARY OF THE INVENTION [0009] In an aspect, the invention provides a method for preparing a plant reproductive element composition, comprising contacting the surface of a plant reproductive element of a plant with a formulation comprising a purified microbial population that comprises a Streptomyces endophyte that is heterologous to the plant reproductive element and comprises a 16S nucleic acid sequence that is at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, or at least 99% identical over at least 600 nucleotides to a nucleic acid sequence selected from SEQ ID NO: 2 through SEQ ID NO: 18.
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