Pseudomonas is a large and diverse genus of Gammaproteobacteria. To provide a framework for discovery of evolutionary and taxonomic relationships of these bacteria, we compared the genomes of type strains of 163 species and 3 additional subspecies of Pseudomonas, including 118 genomes sequenced herein. A maximum likelihood phylogeny of the 166 type strains based on protein sequences of 100 single-copy orthologous genes revealed thirteen groups of Pseudomonas, composed of two to sixty three species each. Pairwise average nucleotide identities and alignment fractions were calculated for the data set of the 166 type strains and 1224 genomes of Pseudomonas available in public databases. Results revealed that 394 of the 1224 genomes were distinct from any type strain, suggesting that the type strains represent only a fraction of the genomic diversity of the genus. The core genome of Pseudomonas was determined to contain 794 genes conferring primarily housekeeping functions. The results of this study provide a phylogenetic framework for future studies aiming to resolve the classification and phylogenetic relationships, identify new gene functions and phenotypes, and explore the ecological and metabolic potential of the Pseudomonas spp.

Certain strains of fluorescent pseudomonads can effectively colonize plant roots and protect plants from diseases caused by a variety of root pathogens. Such beneficial or plant health-promoting strains are emerging as promising biocontrol agents. They are suited as soil inoculants either individually or in combination and may be compatible with current chemical pesticides (1, 2, 3, 4, 5, 6, 7, 8). In our biocontrol studies, we have focused on Pseudomonasfluorescens strain CHAO, an isolate from a suppressive soil in the western part of Switzerland (9). This strain was originally shown to colonize tobacco roots and to suppress black root rot, which is caused by the fungus Thielaviopsis basicola (9, 10). Subsequent work has established that disease suppression by strain CHAO displays little specificity with respect to the host plant and the pathogen. Protected plants include wheat, cucumber, sugar beet, cotton, flax, corn, and cress. Pathogenic action of at least the following fungal pathogens can be reduced by strain CHAO: Pythium ultimum, Gaeumannomyces graminis var. tritici (Ggt), Fusarium oxysporum f.s p. cucurbitaceae, Phomopsis sclerotioides, and Rhizoctonia solani (11, 12, 13, 14, 15; our unpublished data). Since the interactions between I! fluorescens, other organisms and the soil environment are extremely complex, it became important to develop reproducible methods that allow us to monitor the plant-beneficial effects of strain CHAO reliably and to analyze the traits that make it an effective biocontrol agent. In section 6.2 we will review some of our approaches to investigate the mechanisms by which strain CHAO achieves biological control.We are using strain CHAO as a model organism to study not only the mechanisms of disease suppression but also the ecological impact of introduced plant-beneficial bacteria (see section 6.3). In a parallel approach, we are investigating the potential applications of biological control agents to improve the yields of protected crops. We are testing a variety of strains, singly and in combination, for the development of greenhouse applications. A brief account of this work is presented in section 6.4. 68Disease Suppression by I! Fluorescens CHAO Mechanistic Studies on Biocontrol m i t s of Pseudomonas Fluorescens CHAO Chemical Identification of Extracellular MetabolitesMetabolites produced and excreted by I? fluorescens are assumed to be important biotic factors in the biological control of root diseases (2, 5, 16, 17, 18, 19, 20, 21). Until now, about a dozen low molecular weight compounds have been identified in culture supernatants of Rfluorescens CHAO ( Table 1). These products can be broadly classified into two groups: siderophores and secondary metabolites. The siderophores (e. g. , iron chelators) pyoverdine (pseudobactin), salicylate and pyochelin are all produced by I? fluorexens CHAO (22, 23 ; our unpublished results) and by other fluorescent pseudomonads when these bacteria are grown under ironlimiting conditions (24; reviewed by Loper & Buyer [20] and O'Sullivan...

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Although there are adequate DNA sequence differences among plant-associated and plant-pathogenic bacteria to facilitate molecular approaches for their identification, identification at a taxonomic level that is predictive of their phenotype is a challenge. The problem is the absence of a taxonomy that describes genetic variation at a biologically relevant resolution and of a database containing reference strains for comparison. Moreover, molecular evolution, population genetics, ecology, and epidemiology of many plant-pathogenic and plant-associated bacteria are still poorly understood. To address these challenges, a database with web interface was specifically designed for plant-associated and plant-pathogenic microorganisms. The Plant-Associated Microbes Database (PAMDB) comprises, thus far, data from multilocus sequence typing and analysis (MLST/MLSA) studies of Acidovorax citrulli, Pseudomonas syringae, Ralstonia solanacearum, and Xanthomonas spp. Using data deposited in PAMDB, a robust phylogeny of Xanthomonas axonopodis and related bacteria has been inferred, and the diversity existing in the Xanthomonas genus and in described Xanthomonas spp. has been compared with the diversity in P. syringae and R. solanacearum. Moreover, we show how PAMDB makes it easy to distinguish between different pathogens that cause almost identical diseases. The scalable design of PAMDB will make it easy to add more plant pathogens in the future.

Methyl bromide is a widely used fumigant for both pre‐plant and post‐harvest pest and pathogen control. The Montreal Protocol and the US Clean Air Act mandate a phase‐out of the import and manufacture of methyl bromide, beginning in 2001 and culminating with a complete ban, except for quarantine and certain pre‐shipment uses and exempted critical uses, in January 2005. In 1995, ARS built on its existing programs in soil‐borne plant pathology and post‐harvest entomology and plant pathology to initiate a national research program to develop alternatives to methyl bromide. The focus has been on strawberry, pepper, tomato, perennial and nursery cropping systems for pre‐plant methyl bromide use and fresh and durable commodities for post‐harvest use. Recently the program has been expanded to include research on alternatives for the ornamental and cut flower cropping systems. An overview of the national research program is presented. Results from four specific research trials are presented, ranging from organic to conventional systems. Good progress on short‐term alternatives is being made. These will be used as the foundation of integrated management systems which begin with pre‐plant management decisions and continue through post‐harvest processing. Published in 2003 for SCI by John Wiley & Sons, Ltd.

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Myxobacteria are soil dwelling gram-negative gliding bacteria that form fruiting bodies containing myxospores. Although myxobacteria produce a wide range of antibiotics and lytic enzymes that assist in their ability to prey on other microorganisms, their role in agriculture has received little attention. Myxococcus spp. were isolated from soils in organic and conventionally managed strawberry production and transplant fields in the absence of soil fumigation. Fumigation with methyl bromide and chloropicrin virtually eliminated these organisms from soil. However, soil fumigation had no effect on the frequency of isolation of Myxococcus spp. from strawberry roots. Six Myxococcus spp. were tested in vitro against eight soilborne plant pathogenic fungi (Cylindrocarpon spp., Fusarium oxysporum f. sp. apii, Phytophthora capsici, Pythium ultimum, Rhizoctonia spp., Sclerotinia minor, Verticillium albo-atrum, and V. dahliae) and against two fungal biological control agents (Gliocladium virens and Trichoderma viride). Phytophthora capsici, Pythium ultimum, Rhizoctonia spp., S. minor, and T. viride were completely inhibited by all of the Myxococcus spp. tested. F. oxysporum f. sp. apii was the least sensitive to the myxobacteria, and no inhibition occurred with some Myxococcus spp. Inhibition of the other fungi tested was variable. Myxococcus coralloides inhibited nearly all the fungi tested. The ability of bacterial biological control agents to produce antibiotics and other secondary metabolites determined whether or not they were lysed by myxobacteria. Secondary metabolite production regulated by gacS protected Pseudomonas fluorescens strain CHA0 from lysis by myxobacteria. More specifically, phenazine antibiotics produced by Pseudomonas aureofaciens strain 30–84 protected it from lysis.

Opinion 112 denies the request to place Seliberia Aristovskaya and Parinkina 1963 (Approved Lists 1980) on the list of rejected names because the information provided is insufficient. For the same reason, Opinion 113 denies the request to reject Shewanella irciniae Lee et al. 2006 and Opinion 114 denies the request to reject the name Enterobacter siamensis Khunthongpan et al. 2014. Opinion 115 rejects the epithet of Moorella thermoautotrophica (Wiegel et al. 1981) Collins et al. 1994, which is regarded as a nomen confusum. To assess the consequences of Rule 8, Opinion 116 revisits names of taxa above the rank of genus which should comprise the stem of the name of a nomenclatural type and a category-specific ending but fail to do so. Such names should be orthographically corrected if the sole error is the inadvertent usage of an incorrect stem or be regarded as illegitimate if otherwise. The necessary corrections are made for a number of names. In Opinion 117, the request to designate Methylothermus subterraneus Hirayama et al. 2011 as the type species of the genus Methylothermus is denied because an equivalent action compatible with the Code was already conducted. In Opinion 118, the possible orthographical correction of the name Flaviaesturariibacter is treated, as are the analogous cases of Fredinandcohnia and Hydrogeniiclostidium . The genus names are corrected to Flaviaestuariibacter, Ferdinandcohnia and Hydrogeniiclostridium , respectively. Opinion 119 concludes that assigning Actinomycetales Buchanan 1917 (Approved Lists 1980) as nomenclatural type of the class Actinobacteria Stackebrandt et al. 1997 would not render that name legitimate if Rule 8 remained retroactive. The request is granted but Actinomycetales is also assigned as type of Actinomycetes Krassilnikov 1949 (Approved Lists 1980). In Opinion 120, the possible orthographical correction of the name Amycolatopsis albidoflavus is treated. It is grammatically corrected to Amycolatopsis albidoflava. Six names which could according to Rule 61 be grammatically corrected by anyone are also corrected. Opinion 121 denies the request to revise Opinion 69 and notes that Opinion 69 does not have the undesirable consequences emphasized in the request. In Opinion 122, the request to reject various taxon names of Mollicutes proposed in 2018 is denied because it is based on misinterpretations of the Code, which are clarified. Alternative ways to solve the perceived problems are outlined. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.