The use of endophytic microbes is increasing in commercial agriculture. This review will begin with a strain selection. Most strains will not function well, so only a few provide adequate performance. It will also describe the endophyte–plant relationship and the fungi and bacteria involved. Their abilities to alleviate biotic (diseases and pests) and abiotic stresses (drought, salt, and flooding) to remediate pollution and increase photosynthetic capabilities will be described. Their mechanisms of action will be elucidated. These frequently result in increased plant yields. Finally, methods and practices for formulation and commercial use will be described.

Growing populations and their greater longevity continue to increase the demand for both more food and fresh water. The phyllospheres and endospheres of plants can be considered as extensions of soil systems because they are inhabited by organisms for which the soil is also a habitat. The diverse populations of microbes that live in the phyllosphere – bacteria, fungi, yeasts, and others – provide the plant with various nutritional services and support its development in exchange for the water and energy that they receive from the plant. The structure of phyllosphere communities reflects the migration, survival, and growth of microbial colonizers, influenced by multiple environmental factors, by physical and chemical properties of the leaf, as well as by the relative fitness of the different species for living in these situations. Arbuscular mycorrhizal fungi are obligate plant symbionts, i.e., they cannot complete their life cycle when not resident in plant roots where they live as endophytes.

A common view of microbes is that they are a nuisance – pernicious pathogens that constrain agricultural crop production. This chapter discusses the contributions of fungi with a focus on the fungus Trichoderma, which lives ubiquitously within soil systems. Fungi live ubiquitously within the soil and elsewhere, with some of them living also within plants as symbiotic endophytes. Fungi live also in many other environments aboveground, but they cannot survive where there is no oxygen because, as aerobic organisms, they require oxygen for their metabolism. Trichoderma fungi live and thrive in a wide variety of different ecological niches. Trichoderma strongly interact with other organisms in the soil and elsewhere via their parasitic attacks on other fungi. In the past, such attacks were considered to be the principal mechanism by which Trichoderma could control fungal plant pathogens.

This chapter discusses on the concept and practices of inoculation because it is more connected to the functioning of microbiomes than is the broader category of biofertilization. Generally, inoculation introduces its active, biological components to or through plant roots. Fertilization in general refers to adding inorganic materials to the soil, usually some form of nitrogen or a phosphate such as zinc phosphate. The distinction between the two terms is somewhat hazy. The host and its associated microorganisms function in many ways as a unit which is referred to as a holobiont now that the myriad relationships among plants, microbes, and their soil environment are becoming better understood. The modifications in plant gene expression associated with the introduced microbes include changes in mRNA that regulate production of phytohormones, photosynthesis efficiency, carbohydrate metabolism, and cell division and expansion. The myriad connections within a holobiont are becoming more decipherable at the molecular level with state-of-the-art analytical methods.

Most of the bacteria and fungi that inhabit the roots and aboveground organs of plants reside in the surrounding soil for some part of their lives, providing a dynamic linkage between plants and soil. Plant and soil scientists have found it helpful to think and write in terms of three respective domains – around, on, and inside plants – where diverse populations of microbes reside and interact among themselves and with plant organs. Microbiomes and plants depend upon each other in part because the microbes that inhabit plants and their surroundings contain some portion of the host plants' secondary genome. The microbiomes for both plants and animals are not amorphous aggregations of microbes. Some of the most important processes in the life of plants occur within the plant rhizosphere. Plant roots function somewhat like the intestines of mammals, absorbing nutrients and water, while acting also something like mammals' lungs.

Regulatory concerns for Trichoderma are similar to any other biological organism. This review will use regulations in place in the USA. In this country, there are both federal regulations and regulations in each of the 50 states. There are also organic regulations, both from federal agencies.

Microorganisms have been known for more than a century to provide multiple benefits to plants. A key to understanding the benefits imparted is knowledge of the specific kinds of interactions that occur continuously between plants and microorganisms. This chapter reviews how knowledge of these has evolved over time, what the resulting benefits are, and how microorganisms can be used to benefit plant agriculture and the natural environment.

Plants exist in close association with uncountable numbers of microorganisms around, on, and within them. Some of these endophytically colonize plant roots. The colonization of roots by certain symbiotic strains of plant-associated bacteria and fungi results in these plants performing better than plants whose roots are colonized by only the wild populations of microbes. We consider here crop plants whose roots are inhabited by introduced organisms, referring to them as Enhanced Plant Holobionts (EPHs). EPHs frequently exhibit resistance to specific plant diseases and pests (biotic stresses); resistance to abiotic stresses such as drought, cold, salinity, and flooding; enhanced nutrient acquisition and nutrient use efficiency; increased photosynthetic capability; and enhanced ability to maintain efficient internal cellular functioning. The microbes described here generate effects in part through their production of Symbiont-Associated Molecular Patterns (SAMPs) that interact with receptors in plant cell membranes. Such interaction results in the transduction of systemic signals that cause plant-wide changes in the plants’ gene expression and physiology. EPH effects arise not only from plant-microbe interactions, but also from microbe-microbe interactions like competition, mycoparasitism, and antibiotic production. When root and shoot growth are enhanced as a consequence of these root endophytes, this increases the yield from EPH plants. An additional benefit from growing larger root systems and having greater photosynthetic capability is greater sequestration of atmospheric CO 2 . This is transferred to roots where sequestered C, through exudation or root decomposition, becomes part of the total soil carbon, which reduces global warming potential in the atmosphere. Forming EPHs requires selection and introduction of appropriate strains of microorganisms, with EPH performance affected also by the delivery and management practices.

Abstract Bacteria and fungi are both used in biological seed treatments. While all have potential uses, some organisms are more widely and successfully used than others. Shelf life is an important consideration. For this reason, organisms that lack cell walls are more difficult to use than ones with long-lasting spores. Bacillus and Trichoderma are both widely effective, have good shelf life, and are frequently used. However, Rhizobiacae lack cell walls, which is a limitation; they are widely used because their symbiosis with legumes facilitates nitrogen fixation which is an important factor that provides economic, agricultural and environmental sustainability. For all organisms, proper formulation is critical for success; this is especially true for Rhizobiacae and other gram-negative bacteria. There are several specialized processes to deliver microbial agents or to enhance their biological activity, such as solid matrix priming and hydroseeding. Biorational chemicals derived from microorganisms are also frequently used. Both living organisms and biorationals provide benefits to plant agriculture. They can control diseases and increase resistance to abiotic stresses such as drought, temperature, salt, and flooding. They also can enhance mineral nutrition and photosynthesis. For these applications, the most effective ones colonize roots internally and provide season-long benefits. These endophytes induce systemic changes in plants’ gene expression and encoding of proteins.

Plants should not be regarded as entities unto themselves, but as the visible part of plant-microbe complexes which are best understood as "holobiomes." Some microorganisms when given the opportunity to inhabit plant roots become root symbionts. Such root colonization by symbiotic microbes can raise crop yields by promoting the growth of both shoots and roots, by enhancing uptake, fixation, and/or more efficient use of nutrients, by improving plants' resistance to pests, diseases, and abiotic stresses that include drought, salt, and other environmental conditions, and by enhancing plants' capacity for photosynthesis. We refer plant-microbe associations with these capabilities that have been purposefully established as enhanced plant holobiomes (EPHs). Here, we consider four groups of phylogenetically distinct and distant symbiotic endophytes: (1) Rhizobiaceae bacteria; (2) plant-obligate arbuscular mycorrhizal fungi (AMF); (3) selected endophytic strains of fungi in the genus Trichoderma; and (4) fungi in the Sebicales order, specifically Piriformospora indica. Although these exhibit quite different "lifestyles" when inhabiting plants, all induce beneficial systemic changes in plants' gene expression that are surprisingly similar. For example, all induce gene expression that produces proteins which detoxify reactive oxygen species (ROS). ROS are increased by environmental stresses on plants or by overexcitation of photosynthetic pigments. Gene overexpression results in a cellular environment where ROS levels are controlled and made more compatible with plants' metabolic processes. EPHs also frequently exhibit increased rates of photosynthesis that contribute to greater plant growth and other capabilities. Soil organic matter (SOM) is augmented when plant root growth is increased and roots remain in the soil. The combination of enhanced photosynthesis, increasing sequestration of CO2 from the air, and elevation of SOM removes C from the atmosphere and stores it in the soil. Reductions in global greenhouse gas levels can be accelerated by incentives for carbon farming and carbon cap-and-trade programs that reward such climate-friendly agriculture. The development and spread of EPHs as part of such initiatives has potential both to enhance farm productivity and incomes and to decelerate global warming.

The world faces two enormous challenges that can be met, at least in part and at low cost, by making certain changes in agricultural practices. There is need to produce enough food and fibre for a growing population in the face of adverse climatic trends, and to remove greenhouse gases to avert the worst consequences of global climate change. Improving photosynthetic efficiency of crop plants can help meet both challenges. Fortuitously, when crop plants' roots are colonized by certain root endophytic fungi in the genus Trichoderma, this induces up-regulation of genes and pigments that improve the plants' photosynthesis. Plants under physiological or environmental stress suffer losses in their photosynthetic capability through damage to photosystems and other cellular processes caused by reactive oxygen species (ROS). But certain Trichoderma strains activate biochemical pathways that reduce ROS to less harmful molecules. This and other mechanisms described here make plants more resistant to biotic and abiotic stresses. The net effect of these fungi's residence in plants is to induce greater shoot and root growth, increasing crop yields, which will raise future food production. Furthermore, if photosynthesis rates are increased, more CO2 will be extracted from the atmosphere, and enhanced plant root growth means that more sequestered C will be transferred to roots and stored in the soil. Reductions in global greenhouse gas levels can be accelerated by giving incentives for climate-friendly carbon farming and carbon cap-and-trade programmes that reward practices transferring carbon from the atmosphere into the soil, also enhancing soil fertility and agricultural production.

N.Y. Stasz et al., 1987, Phytopathology 77(12):1771. 73 Assignee: Cornell Research Foundation, Inc., Ogawa et al., 1987, Enzyme Microb. Technol. 9: Ithaca, N.Y. 229-231. Bojnanska et al., 1980, Asta Microbiol. Acad. Sci. 21 Appl. No.: 597,119 Hung, 27: 305-307. 22 Filed: Oct. 16, 1990 Picataggio et al., 1983, Eur. J. Appl. Microbiol. Bi otechnol. 17: 12-128. Related U.S. Application Data Gracheck, Abstract of Ph.D. Thesis, May 1984, Univer sity of Arkansas. I63) Continuation of Ser. No. 244444, Sep. 14, 1988, abanHong et al. (1985) J. Nat. Acad. Sci. Repub. Korea Nat. doned, which is a continuation-in-part of Ser. No. Sci. Ser. 24(0): 53-90 (abstract cited). 34,304, Apr. 3, 1987, abandoned. Toyama et al. (1984) Appl. Environ. Microbiol. 47(2): 51 Int. Cl. ....................... C12N 1/14; C12N 15/00; 363-8. A01C 1/06; A01N 63/00 P. Examiner-David T. F 52 U.S. C. .............................. A.C. Primary Examiner-David T. Fox 435/945; 47/57.6; 424/930, 935/96, 935/97 (57) ABSTRACT 58 Field of Search ..................... 435/172.2, 254,945; Fused strains of Trichoderma spp described herein are 935/97, 96; 47/57.6, 58, 57.604; 424/93, 93 Q useful as biocontrol agents to protect seeds, especially (56) References Cited when used in conjunction with solid matrix priming or osmoconditioning. U.S. PATENT DOCUMENTS

This chapter examines events leading to loss of seed quality, and considers how seed quality influences the activity of both beneficial and harmful soil-inhabiting microorganisms. Seed deterioration ultimately leads to seed death. As seeds deteriorate, vigor is lost much more quickly than viability. The chapter uses lowered seed vigor as the best index of seed deterioration. In soils, nutrient availability is the limiting factor determining microbial growth. Among the plethora of microorganisms in soil, a few fungi have been extensively studied because of their ability to colonize and/or rot seeds. The chapter describes some of the complex microbial interactions that occur within a short time after seeds are planted in soil. Major components of the soil microflora become intensely active after seeds are planted. Seeds efficiently overcome effects of soil fungistasis. Depending on the organisms involved and the intensity of their activity, the probability of good stand is increased or decreased.

Fusarium head blight (FHB), caused by Gibberella zeae (anamorph: Fusarium graminearum), is a destructive disease of cereals. Previous studies demonstrated that Clonostachys rosea strain ACM941 is an antagonist of G. zeae that parasitizes the pathogen and reduces FHB severity in wheat. The objective of this research was to evaluate the efficacy of CLO-1, a formulated product of ACM941, for reducing perithecial production on various crop residues in comparison with the registered fungicide Folicur (tebuconazole) under field conditions. When applied on G. zeae inoculated corn, soybean and wheat residues in the spring of 2009 and 2010, CLO-1 significantly inhibited perithecial production on all crop residue types, reducing daily perithecial production (DPP) by 93.1% on corn residue, 94.4% on soybean residue and 84.0% on wheat residue, compared with the untreated control. When applied on naturally infected wheat residues in the autumn of 2009 and 2010, CLO-1 significantly reduced DPP in the following growing season by 72.3% on peduncles, 51.0% on spikelets and 57.2% on stems. These effects were numerically better but not significantly different from those achieved by Folicur fungicide used as a positive control in the same experiments. Results from this study suggest that CLO-1 is a promising biofungicide against G. zeae and may be used as a control measure to reduce the initial inoculum of FHB in an integrated FHB management programme.

•CLO-1 (Clonostachys rosea strain ACM941) controls Fusarium head blight in wheat.•CLO-1 biofungicide was to large extent as effective as conventional fungicides.•CLO-1 biofungicide was most effective on moderately resistant cultivars.