Culture-dependent and culture-independent assessment of bacteria in the apple phyllosphere

Yashiro, Erika; Spear, R. N.; McManus, Patricia S.

doi:10.1111/j.1365-2672.2011.04975.x

Cited by 102 publications

(85 citation statements)

References 62 publications

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“…Although likely an underestimate of the total diversity in these samples (Experimental Procedures), ∼2,400 observed OTUs represent four-to fivefold fewer than that observed in bulk soil samples and comparable to the levels that are observed in specialized niches like the rhizosphere (18,19). The specificity of the bacterial genera observed is supported by previous studies of analyses of fruit surfaces (20) (especially the apple phyllosphere) (21) and also microbiome studies of other fruit-associated animals like Drosophila (22,23). Particular bacterial phylotypes were identified from quite disparate habitats (e.g., a snail, a rotting apple, and a rotting orange), which could indicate their close association with C. elegans animals, but further studies of more habitats and C. elegans populations are needed to test this link.…”

Section: Resultssupporting

confidence: 80%

Caenorhabditis elegans responses to bacteria from its natural habitats

Samuel

Rowedder

Braendle

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

343

479

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Most Caenorhabditis elegans studies have used laboratory Escherichia coli as diet and microbial environment. Here we characterize bacteria of C. elegans' natural habitats of rotting fruits and vegetation to provide greater context for its physiological responses. By the use of 16S ribosomal DNA (rDNA)-based sequencing, we identified a large variety of bacteria in C. elegans habitats, with phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria being most abundant. From laboratory assays using isolated natural bacteria, C. elegans is able to forage on most bacteria (robust growth on ∼80% of >550 isolates), although ∼20% also impaired growth and arrested and/or stressed animals. Bacterial community composition can predict wild C. elegans population states in both rotting apples and reconstructed microbiomes: alpha-Proteobacteria-rich communities promote proliferation, whereas Bacteroidetes or pathogens correlate with nonproliferating dauers. Combinatorial mixtures of detrimental and beneficial bacteria indicate that bacterial influence is not simply nutritional. Together, these studies provide a foundation for interrogating how bacteria naturally influence C. elegans physiology.Caenorhabditis elegans | host-microbe interactions | ecology B iological organisms constantly live in contact with other organisms in a complex web of ecological interactions, which include prey-predator, host-parasite, competitive, or positive symbiotic relationships. Bacteria are now considered key players in multiple aspects of the biology of multicellular organisms (1-3). The richness and importance of these interactions were so far neglected because laboratory biology had succeeded in simplifying and standardizing the environment of the model organisms, providing in most cases a single microbe as a food source, and not necessarily even a naturally encountered one. The many aspects of organismal biology that were shaped by evolution in natural environments are thus undetectable in the artificial laboratory environment and can only be revealed in the presence of other interacting species. Examples include feeding behavior, metabolism of diverse natural food sources, interactions with natural pathogens that have shaped the organism's immune system, behavioral traits, and regulation of development and reproduction. At the genomic level, many individual genes may not be required in a standard laboratory environment but their role may be revealed by using more diverse and relevant environments (4, 5).The nematode Caenorhabditis elegans is a typical example of a model organism that has been disconnected from its natural ecology: although the species has been studied intensively in the laboratory for half a century, its habitat and natural ecology-what it naturally feeds on, its natural predators and pathogens,

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Section: Resultssupporting

confidence: 80%

Caenorhabditis elegans responses to bacteria from its natural habitats

Samuel

Rowedder

Braendle

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

343

479

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“…Sphingomonas bacteria were identified in all our samples, in contrast to previous investigations of the leafy-green phyllosphere (14). However, Sphingomonas bacteria have been reported to be prevalent in other studies of the leaf microbiota on other plants (31,37) and are known to contribute to plant health (30). A comprehensive knowledge of the drivers of bacterial community structure in the phyllosphere is of the utmost importance in developing new strategies for plant protection.…”

Section: Discussioncontrasting

confidence: 81%

Bacterial Communities Associated with Surfaces of Leafy Greens: Shift in Composition and Decrease in Richness over Time

Dees

Lysøe

Nordskog

et al. 2015

Appl Environ Microbiol

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The phyllosphere is colonized by a wide variety of bacteria and fungi; it harbors epiphytes, as well as plant-pathogenic bacteria and even human pathogens. However, little is known about how the bacterial community composition on leafy greens develops over time. The bacterial community of the leafy-green phyllosphere obtained from two plantings of rocket salad (Diplotaxis tenuifolia) and three plantings of lettuce (Lactuca sativa) at two farms in Norway were profiled by an Illumina MiSeq-based approach. We found that the bacterial richness of the L. sativa samples was significantly greater shortly (3 weeks) after planting than at harvest (5 to 7 weeks after planting) for plantings 1 and 3 at both farms. For the second planting, the bacterial diversity remained consistent at the two sites. This suggests that the effect on bacterial colonization of leaves, at least in part must, be seasonally driven rather than driven solely by leaf maturity. The distribution of phyllosphere communities varied between D. tenuifolia and L. sativa at harvest. The variability between these species at the same location suggests that the leaf-dwelling bacteria are not only passive inhabitants but interact with the host, which shapes niches favoring the growth of particular taxa. This work contributes to our understanding of host plant-specific microbial community structures and shows how these communities change throughout plant development.T he phyllosphere is a habitat on the surface of plant leaves colonized by a variety of bacteria, yeasts, and fungi (1). It harbors epiphytes, as well as plant-pathogenic bacteria and even human pathogens. Microbial populations on leaf surfaces are highly influenced by rapid fluctuations in UV radiation, temperature, and humidity and are restricted by limited access to nutrients (1, 2). Resident bacteria on leaves can have neutral, negative, or positive influences on their host plants by serving as pathogens, preventing leaf colonization by pathogens, or acting as growth promoters (3). Traditionally, phyllosphere bacteria have been characterized by using culture-based approaches and much of the work on produce-associated bacteria has focused on a small number of pathogenic species. Culture-based methods will not include bacteria that are not able to grow on standard artificial media or are slow growing. This limits our understanding of the phyllosphere microbial community's ecology, genetics, and physiology (4). Bacterial communities associated with leafy greens have already been described by several culture-independent studies. "First-generation" molecular techniques have been used to describe variation in community structure in the context of leaf surface properties and microbial interactions (5), seasonal variation in the community structure (6), and monitoring of bacterial communities in the food chain (7). The introduction of culture-independent methods, in particular, microbial profiling using high-throughput sequencing to study microorganisms, has revealed more complexity and diversity of the...

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“…This work is part of a larger study to understand the impact of streptomycin on microbial communities in apple orchards. We previously reported that streptomycin had no measured effect on microbial communities associated with apple leaves, twigs (52,53), or flowers (54). In a related study describing orchard soil microbial metagenomes, we detected strA and strB, the genes from the transposon Tn5393 that confer streptomycin resistance (55).…”

Section: Discussionmentioning

confidence: 82%

Streptomycin Application Has No Detectable Effect on Bacterial Community Structure in Apple Orchard Soil

Shade

Klimowicz

Spear

et al. 2013

Appl Environ Microbiol

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Streptomycin is commonly used to control fire blight disease on apple trees. Although the practice has incited controversy, little is known about its nontarget effects in the environment. We investigated the impact of aerial application of streptomycin on nontarget bacterial communities in soil beneath streptomycin-treated and untreated trees in a commercial apple orchard. Soil samples were collected in two consecutive years at 4 or 10 days before spraying streptomycin and 8 or 9 days after the final spray. Three sources of microbial DNA were profiled using tag-pyrosequencing of 16S rRNA genes: uncultured bacteria from the soil (culture independent) and bacteria cultured on unamended or streptomycin-amended (15 g/ml) media. Multivariate tests for differences in community structure, Shannon diversity, and Pielou's evenness test results showed no evidence of community response to streptomycin. The results indicate that use of streptomycin for disease management has minimal, if any, immediate effect on apple orchard soil bacterial communities. This study contributes to the profile of an agroecosystem in which antibiotic use for disease prevention appears to have minimal consequences for nontarget bacteria.

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Culture-dependent and culture-independent assessment of bacteria in the apple phyllosphere

Cited by 102 publications

References 62 publications

Caenorhabditis elegans responses to bacteria from its natural habitats

Caenorhabditis elegans responses to bacteria from its natural habitats

Bacterial Communities Associated with Surfaces of Leafy Greens: Shift in Composition and Decrease in Richness over Time

Streptomycin Application Has No Detectable Effect on Bacterial Community Structure in Apple Orchard Soil

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