INTRODUCTION . EVOLUTION OF TAXONOMIC CONCEPTS . Early Work ..... . ..... . . . . . . . . . . . . . ..... . . . . ..... . . . . . . . . . . . . . . . .... . . . . . . . . . . . . Modern Work .... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . MOLECULAR TAXONOMY . DNA Composition and Genome Size . . . . . . . . . . . . . . . . . . . . . . . . . . ... . . . . . . . . . . . . . . . . . . . . . . . . . . Polynucleotide Sequence Relatedness . . . . . . . . . . ...... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Electrophoretic Comparison of Iso-Functional Enzymes . Immunologic Cross-Reactions Between Iso-Functional Enzymes . Physical Properties and Regulation of Enzymes . . . . . . . . . . ... . . . . . . . . . . . . . ... . . . . . . . . . . . . .

The Genus Serratia

Fresh fruits and vegetables can harbor large and diverse populations of bacteria. However, most of the work on produce-associated bacteria has focused on a relatively small number of pathogenic bacteria and, as a result, we know far less about the overall diversity and composition of those bacterial communities found on produce and how the structure of these communities varies across produce types. Moreover, we lack a comprehensive view of the potential effects of differing farming practices on the bacterial communities to which consumers are exposed. We addressed these knowledge gaps by assessing bacterial community structure on conventional and organic analogs of eleven store-bought produce types using a culture-independent approach, 16 S rRNA gene pyrosequencing. Our results demonstrated that the fruits and vegetables harbored diverse bacterial communities, and the communities on each produce type were significantly distinct from one another. However, certain produce types (i.e., sprouts, spinach, lettuce, tomatoes, peppers, and strawberries) tended to share more similar communities as they all had high relative abundances of taxa belonging to the family Enterobacteriaceae when compared to the other produce types (i.e., apples, peaches, grapes, and mushrooms) which were dominated by taxa belonging to the Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria phyla. Although potentially driven by factors other than farming practice, we also observed significant differences in community composition between conventional and organic analogs within produce types. These differences were often attributable to distinctions in the relative abundances of Enterobacteriaceae taxa, which were generally less abundant in organically-grown produce. Taken together, our results suggest that humans are exposed to substantially different bacteria depending on the types of fresh produce they consume with differences between conventionally and organically farmed varieties contributing to this variation.

http://fiererlab.org/wp-content/uploads/2014/09/LeffFierer_2013_produce.pdf

Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables

Bacteria associated with plants have been observed frequently to form assemblages referred to as aggregates, microcolonies, symplasmata, or biofilms on leaves and on root surfaces and within intercellular spaces of plant tissues. In a wide range of habitats, biofilms are purported to be microniches of conditions markedly different from those of the ambient environment and drive microbial cells to effect functions not possible alone or outside of biofilms. This review constructs a portrait of how biofilms associated with leaves, roots and within intercellular spaces influence the ecology of the bacteria they harbor and the relationship of bacteria with plants. We also consider how biofilms may enhance airborne dissemination, ubiquity and diversification of plant-associated bacteria and may influence strategies for biological control of plant disease and for assuring food safety. Trapped by a nexus, coordinates uncertain Ever expanding or contracting Cannibalistic and scavenging sorties Excavations through signs of past alliances Consensus signals sound revelry Then time warped by viscosity Genomes showing codependence A virtual microbial beach party With no curfew and no time-out A few estranged cells seeking exit options, Looking for another menagerie. David Sands, Montana State University, Bozeman, February 2003

The ecological significance of biofilm formation by plant-associated bacteria.

The genus Klebsiella is seemingly ubiquitous in terms of its habitat associations. Klebsiella is a common opportunistic pathogen for humans and other animals, as well as being resident or transient flora (particularly in the gastrointestinal tract). Other habitats include sewage, drinking water, soils, surface waters, industrial effluents, and vegetation. Until recently, almost all these Klebsiella have been identified as one species, ie, K. pneumoniae. However, phenotypic and genotypic studies have shown that “K. pneumoniae” actually consists of at least four species, all with distinct characteristics and habitats. General habitat associations of Klebsiella species are as follows: K. pneumoniae—humans, animals, sewage, and polluted waters and soils; K. oxytoca—frequent association with most habitats; K. terrigena— unpolluted surface waters and soils, drinking water, and vegetation; K. planticola—sewage, polluted surface waters, soils, and vegetation; and K. ozaenae/K. rhinoscleromatis—infrequently detected (primarily with humans).

Habitat association of Klebsiella species.

Infections due to gram-negative bacilli result in significant morbidity and mortality, and the incidence of such infections has been increasing in hospitals [1-3]. Klebsiella has been prominent among the gram-negative bacilli causing these hospital-associated infections. This organism usually has been reviewed as a gram-negative bacillus or has been considered together with Enterobacter and Serratia species as a member of the tribe Klebsielleae. There is evidence, however, that Klebsiella has characteristic clinical, pathological, and epidemiologic behaviors that warrant a separate review of this genus [4]. A review of the epidemiology of Klebsiella has been difficult because of variations in the taxonomy that defines these organisms. Kauffman [5], Edwards and Fife [6], and others have clarified the taxonomy, and problems of nomenclature have been reviewed by others [7, 8]. Organisms of the genus Klebsiella are now recognized as gram-negative bacilli that are capsulated, form mucous colonies, and are nonmotile. Other criteria that were frequently used to identify Klebsiella in earlier studies were positive VogesProskauer and citrate reactions in conjunction with a negative result in the methyl red test. Most earlier studies did not use the biochemical reactions described by Edwards and Ewing [9] as criteria for classification as Klebsiella. In the present review, the following organisms are considered members of the genus Klebsiella: Klebsiella pneumoniae, Klebsiella aerogenes, Klebsiella ozaenae, Klebsiella rhinoscleromatis, Friedlander's bacillus, and Bacillus mucosus capsulatum. Aerobacter aerogenes has been excluded since this group includes both motile and nonmotile strains [10, 11]. An understanding of the epidemiology of Klebsiella has largely been dependent on the development of the quellung reaction, which provides a means for serotyping by measuring capsular swelling. In 1926 Julianelle described three capsular

Epidemiology of Klebsiella and Hospital-Associated Infections

Klebsiella, Enterobacter, and Serratia were recovered frequently in high counts from vegetable salads. Pseudomonas aeruginosa, although isolated frequently, was in lower counts.

Enterobacteriaceae and Pseudomonas aeruginosa recovered from vegetable salads.

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Enterobacteriaceae and Pseudomonas aeruginosa recovered from vegetable salads.