The above-ground parts of plants are normally colonized by a variety of bacteria, yeasts, and fungi. While a few microbial species can be isolated from within plant tissues, many more are recovered from the surfaces of healthy plants. The aerial habitat colonized by these microbes is termed the

Microbiology of the Phyllosphere

Kloepper, J. W., Ryu, C.-M., and Zhang, S. 2004. Induced systemic resistance and promotion of plant growth by Bacillus spp. Phytopathology 94:1259-1266. Elicitation of induced systemic resistance (ISR) by plant-associated bacteria was initially demonstrated using Pseudomonas spp. and other gram-negative bacteria. Several reviews have summarized various aspects of the large volume of literature on Pseudomonas spp. as elicitors of ISR. Fewer published accounts of ISR by Bacillus spp. are available, and we review this literature for the first time. Published results are summarized showing that specific strains of the species B. amyloliquefaciens, B. subtilis, B. pasteurii, B. cereus, B. pumilus, B. mycoides, and B. sphaericus elicit significant reductions in the incidence or severity of various diseases on a diversity of hosts. Elicitation of ISR by these strains has been demonstrated in greenhouse or field trials on tomato, bell pepper, muskmelon, watermelon, sugar beet, tobacco, Arabidopsis sp., cucumber, loblolly pine, and two tropical crops (long cayenne pepper and green kuang futsoi). Protection resulting from ISR elicited by Bacillus spp. has been reported against leaf-spotting fungal and bacterial pathogens, systemic viruses, a crown-rotting fungal pathogen, root-knot nematodes, and a stem-blight fungal pathogen as well as damping-off, blue mold, and late blight diseases. Reductions in populations of three insect vectors have also been noted in the field: striped and spotted cucumber beetles that transmit cucurbit wilt disease and the silver leaf whitefly that transmits Tomato mottle virus. In most cases, Bacillus spp. that elicit ISR also elicit plant growth promotion. Studies on mechanisms indicate that elicitation of ISR by Bacillus spp. is associated with ultrastructural changes in plants during pathogen attack and with cytochemical alterations. Investigations into the signal transduction pathways of elicited plants suggest that Bacillus spp. activate some of the same pathways as Pseudomonas spp. and some additional pathways. For example, ISR elicited by several strains of Bacillus spp. is independent of salicylic acid but dependent on jasmonic acid, ethylene, and the regulatory gene NPR1—results that are in agreement with the model for ISR elicited by Pseudomonas spp. However, in other cases, ISR elicited by Bacillus spp. is dependent on salicylic acid and independent of jasmonic acid and NPR1. In addition, while ISR by Pseudomonas spp. does not lead to accumulation of the defense gene PR1 in plants, in some cases, ISR by Bacillus spp. does. Based on the strains and results summarized in this review, two products for commercial agriculture have been developed, one aimed mainly at plant growth promotion for transplanted vegetables and one, which has received registration from the U.S. Environmental Protection Agency, for disease protection on soybean. Plant growth-promoting rhizobacteria (PGPR) are among the various groups of plant-associated microorganisms that can elicit plant defenses (28). In concert with the terminology used by van Loon and Glick in their recent review of PGPR (28), we will use the term induced systemic resistance (ISR) for the process whereby treatment of plants with PGPR elicits host defense as indicated by reduction in the severity or incidence of diseases caused by pathogens that are spatially separated from the inducing agent. With each of the cases of ISR elicited by Bacillus spp. discussed in this review, spatial separation of the pathogen from the bacteria was confirmed in the cited manuscript or in a previous manuscript with the same bacterial strain. In the 1990s, several PGPR-based products became commercially available in the United States, and more are currently under development. Most of these products contain strains of Bacillus PGPR. Earlier attempts to commercialize products containing fluorescent pseudomonad strains of PGPR generally failed due to lack of long-term viability of these asporogenous bacteria. Although commercialization of PGPR is mainly proceeding with Bacillus spp. rather than pseudomonads, the preponderance of research on PGPR as elicitors of growth promotion or ISR employs PGPR strains that are fluorescent pseudomonads. In this review, we summarize research on Bacillus PGPR. Our main emphasis is on Bacillus spp., which elicit ISR; however, since most such Bacillus spp. also promote plant growth, this review summarizes work on both growth promotion and ISR. We concentrate the review on refereed journal articles with some inclusion of previously unpublished work. The results of new work are marked as such in the review. Greenhouse reports of systemic disease protection. Workers

https://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO.2004.94.11.1259

Induced Systemic Resistance and Promotion of Plant Growth by Bacillus spp.

Plant diseases need to be controlled to maintain the quality and abundance of food, feed, and fiber produced by growers around the world. Different approaches may be used to prevent, mitigate or control plant diseases. Beyond good agronomic and horticultural practices, growers often rely heavily on chemical fertilizers and pesticides. Such inputs to agriculture have contributed significantly to the spectacular improvements in crop productivity and quality over the past 100 years. However, the environmental pollution caused by excessive use and misuse of agrochemicals, as well as fear-mongering by some opponents of pesticides, has led to considerable changes in people’s attitudes towards the use of pesticides in agriculture. Today, there are strict regulations on chemical pesticide use, and there is political pressure to remove the most hazardous chemicals from the market. Additionally, the spread of plant diseases in natural ecosystems may preclude successful application of chemicals, because of the scale to which such applications might have to be applied. Consequently, some pest management researchers have focused their efforts on developing alternative inputs to synthetic chemicals for controlling pests and diseases. Among these alternatives are those referred to as biological controls.

/pdf/biological-control-of-plant-pathogens-2035vipjmu.pdf

Biological Control of Plant Pathogens

Although the number of biocontrol products is increasing, these products still represent only about 1% of agricultural chemical sales. Yet these are important contributions because biocontrol agents offer disease management alternatives with different mechanisms of action than chemical pesticides. Trends in research include the increased use of biorational screening processes to identify microorganisms with potential for biocontrol, increased testing under semicommercial and commercial production conditions, increased emphasis on combining biocontrol strains with each other and with other control methods, integrating biocontrol into an overall system.

Commercialization and Implementation of Biocontrol 1

Plant root secreted compounds alter the gene expression of associated microorganisms by acting as signal molecules that either stimulate or repel the interaction with beneficial or harmful species, respectively. However, it is still unclear whether two distinct groups of beneficial bacteria, non-plant-associated (soil) strains and plant-associated (endophytic) strains, respond uniformly or variably to the exposure with root exudates. Therefore, Bacillus mycoides, a potential biocontrol agent and plant growth-promoting bacterium, was isolated from the endosphere of potatoes and from soil of the same geographical region. Confocal fluorescence microscopy of plants inoculated with GFP-tagged B. mycoides strains showed that the endosphere isolate EC18 had a stronger plant colonization ability and competed more successfully for the colonization sites than the soil isolate SB8. To dissect these phenotypic differences, the genomes of the two strains were sequenced and the transcriptome response to potato root exudates was compared. The global transcriptome profiles evidenced that the endophytic isolate responded more pronounced than the soil-derived isolate and a higher number of significant differentially expressed genes were detected. Both isolates responded with the alteration of expression of an overlapping set of genes, which had previously been reported to be involved in plant-microbe interactions; including organic substance metabolism, oxidative reduction, and transmembrane transport. Notably, several genes were specifically upregulated in the endosphere isolate EC18, while being oppositely downregulated in the soil isolate SB8. These genes mainly encoded membrane proteins, transcriptional regulators or were involved in amino acid metabolism and biosynthesis. By contrast, several genes upregulated in the soil isolate SB8 and downregulated in the endosphere isolate EC18 were related to sugar transport, which might coincide with the different nutrient availability in the two environments. Altogether, the presented transcriptome profiles provide highly improved insights into the life strategies of plant-associated endophytes and soil isolates of B. mycoides.

/pdf/comparative-transcriptomics-of-bacillus-mycoides-strains-in-19apa035ph.pdf

Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates

Characterisation of systemic resistance in sugar beet elicited by a non-pathogenic, phyllosphere-colonizing Bacillus mycoides, biological control agent

Screening for the identification of potential biological control agents that induce systemic acquired resistance in sugar beet

Optimizing a Bacillus subtilis isolate for biological control of sugar beet cercospora leaf spot

Rhizoctonia crown and root rot, caused by the fungus Rhizoctonia solani AG 2-2, is one of the most damaging sugar beet diseases worldwide and causes significant economic losses in more than 25% of the sugar beet production area in the United States. We report on field trials in the years 1996 to 1999 testing both experimental fungicides and antagonistic Bacillus sp. for their potential to reduce disease severity and increase sugar yield in trials inoculated with R. solani AG 2-2. Fungicides were applied as in-furrow sprays at planting or as band sprays directed at the crown at the four-leaf stage, or four- plus eight-leaf stage, while bacteria were applied at the four-leaf stage only. The fungicides azoxystrobin and tebuconazole reduced crown and root rot disease by 50 to 90% over 3 years when used at rates of 76 to 304 g a.i./ha and 250 g a.i./ha, respectively. The disease index at harvest was reduced and the root and sugar yield increased with azoxystrobin compared with tebuconazole. The combination of azoxystrobin applied at 76 g a.i./ha and the Bacillus isolate MSU-127 resulted in best disease reduction and greatest root and sucrose yield increase.

https://apsjournals.apsnet.org/doi/pdfplus/10.1094/PDIS.2001.85.7.718

Integrated Control of Rhizoctonia Crown and Root Rot of Sugar Beet with Fungicides and Antagonistic Bacteria

Mycofumigation is the use of antimicrobial volatiles produced by fungi such as Muscodor albusitalic and M. roseus for the control of other organisms. Sugar beet (Beta vulgaris L.) stand establishment was increased and disease severity decreased by mycofumigation with M. roseus and M. albus in autoclaved soil infested with Rhizoctonia solani, Pythium ultimum, or Aphanomyces cochlioides. Eggplant seedlings (Solanum melongena L.) transplanted into autoclaved soil infested with Verticillium dahliae and mycofumigated with M. albus and M. roseus had significantly less disease (P < 0.05) after 4 and 5 weeks compared with nonmycofumigated Verticillium-infested soil. The effect of formulation on efficacy of mycofumigation with M. roseus was tested using potato dextrose agar strips, alginate capsules, ground barley, pesta granules, and stabileze granules. The stabileze and ground barley formulations of M. roseus resulted in the best control of P. ultimum damping-off. The best control of A. cochlioides damp...

Barry J. Jacobsen

Papers

Characterisation of systemic resistance in sugar beet elicited by a non-pathogenic, phyllosphere-colonizing Bacillus mycoides, biological control agent

Screening for the identification of potential biological control agents that induce systemic acquired resistance in sugar beet

Optimizing a Bacillus subtilis isolate for biological control of sugar beet cercospora leaf spot

Integrated Control of Rhizoctonia Crown and Root Rot of Sugar Beet with Fungicides and Antagonistic Bacteria

Mycofumigation with Muscodor albus and Muscodor roseus for Control of Seedling Diseases of Sugar Beet and Verticillium Wilt of Eggplant.