Bacterial Diversity in Tree Canopies of the Atlantic Forest

Lambais, Márcio Rodrigues; Crowley, David E.; Cury, José; Büll, R. C.; Rodrigues, Ricardo Ribeiro

doi:10.1126/science.1124696

Cited by 218 publications

(164 citation statements)

References 6 publications

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“…Recent culture-independent community analyses have confirmed the apparent selectivity of leaf surfaces, finding that leaf surfaces harbor less diverse communities than other environments, such as the immediate subtending soil (3,4). Furthermore, plant species identity also appears to be a factor that can influence the composition of associated phyllosphere bacterial communities (5)(6)(7)(8)(9). While epiphytes are apparently distinct in their ability to grow and survive on leaves, their adaptations needed to thrive in this habitat remain largely unknown.…”

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confidence: 84%

High-Level Culturability of Epiphytic Bacteria and Frequency of Biosurfactant Producers on Leaves

Burch

Paulina

Sbodio

et al. 2016

Appl Environ Microbiol

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To better characterize the bacterial community members capable of biosurfactant production on leaves, we distinguished culturable biosurfactant-producing bacteria from nonproducers and used community sequencing to compare the composition of these distinct cultured populations with that from DNA directly recovered from leaves. Communities on spinach, romaine, and head lettuce leaves were compared with communities from adjacent samples of soil and irrigation source water. Soil communities were poorly described by culturing, with recovery of cultured representatives from only 21% of the prevalent operational taxonomic units (OTUs) (>0.2% reads) identified. The dominant biosurfactant producers cultured from soil included bacilli and pseudomonads. In contrast, the cultured communities from leaves are highly representative of the culture-independent communities, with over 85% of the prevalent OTUs recovered. The dominant taxa of surfactant producers from leaves were pseudomonads as well as members of the infrequently studied genus Chryseobacterium. The proportions of bacteria cultured from head lettuce and romaine leaves that produce biosurfactants were directly correlated with the culture-independent proportion of pseudomonads in a given sample, whereas spinach harbored a wider diversity of biosurfactant producers. A subset of the culturable bacteria in irrigation water also became enriched on romaine leaves that were irrigated overhead. Although our study was designed to identify surfactant producers on plants, we also provide evidence that most bacteria in some habitats, such as agronomic plant surfaces, are culturable, and these communities can be readily investigated and described by more classical culturing methods. IMPORTANCEThe importance of biosurfactant production to the bacteria that live on waxy leaf surfaces as well as their ability to be accurately assessed using culture-based methodologies was determined by interrogating epiphytic populations by both culture-dependent and culture-independent methods. Biosurfactant production was much more frequently observed in cultured communities on leaves than in other nearby habitats, such as soil and water, suggesting that this trait is important to life on a leaf by altering either the leaf itself or the interaction of bacteria with water. While pseudomonads were the most common biosurfactant producers isolated, this habitat also selects for taxa, such as Chryseobacterium, for which this trait was previously unrecognized. The finding that most epiphytic bacterial taxa were culturable validates strategies using more classical culturing methodologies for their study in this habitat. The phyllosphere is recognized to be a selective habitat in which epiphytic bacteria must be able to access limited and spatially heterogeneous nutrient supplies and endure frequent fluctuations in moisture availability on a water-repellent surface (1, 2). Recent culture-independent community analyses have confirmed the apparent selectivity of leaf surfaces, finding that leaf sur...

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mentioning

confidence: 84%

High-Level Culturability of Epiphytic Bacteria and Frequency of Biosurfactant Producers on Leaves

Burch

Paulina

Sbodio

et al. 2016

Appl Environ Microbiol

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“…botrytis) [18]. Similarly, the diversity and structure of the bacterial community in the phyllosphere of a number of tree species has been described [19][20][21][22]. More than basic descriptions of community structure, 16S rRNA techniques have also been used to examine how the phyllosphere community is influenced by environmental factors, such as ultraviolet light [15] and rainfall [23], as well as pesticide [24,25] or biological control agent [16,26] application.…”

Section: General Characteristics Of Phyllosphere Bacterial Communitiesmentioning

confidence: 99%

Emerging Perspectives on the Natural Microbiome of Fresh Produce Vegetables

2015

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Plants harbor a diverse microbiome existing as bacterial populations on the leaf surface (the phyllosphere) and within plant tissues (endophytes). The composition of this microbiome has been largely unexplored in fresh produce vegetables, where studies have tended to focus on pathogen detection and survival. However, the application of next-generation 16S rRNA gene sequencing approaches is beginning to reveal the diversity of this produce-associated bacterial community. In this article we review what is known about the composition of the microbiome of fresh produce vegetables, placing it in the context of general phyllosphere research. We also demonstrate how next-generation sequencing can be used to assess the bacterial assemblages present on fresh produce, using fresh herbs as an example. That data shows how the use of such culture-independent approaches can detect groups of taxa (anaerobes, psychrophiles) that may be missed by traditional culture-based techniques. Other issues discussed include questions as to whether to determine the microbiome during plant growth or at point of purchase or consumption, and the potential role of the natural bacterial community in mitigating pathogen survival.

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“…The global number of plant species is estimated at ϳ300,000 (1), and they encompass a wide range of morphologies, leaf surface chemistries, and ecological ranges. Sympatric plant species may harbor different microbial communities (2,3), and microbial communities in the phyllosphere of conspecific plants differ across habitat (4) and time (5). Within a single plant, the microbial communities can differ between leaves (6) or even between different parts of the same leaf (7).…”

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confidence: 99%

Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree

Finkel

Delmont

Post

et al. 2016

Appl Environ Microbiol

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The leaves of Tamarix aphylla, a globally distributed, salt-secreting desert tree, are dotted with alkaline droplets of high salinity. To successfully inhabit these organic carbon-rich droplets, bacteria need to be adapted to multiple stress factors, including high salinity, high alkalinity, high UV radiation, and periodic desiccation. To identify genes that are important for survival in this harsh habitat, microbial community DNA was extracted from the leaf surfaces of 10 Tamarix aphylla trees along a 350-km longitudinal gradient. Shotgun metagenomic sequencing, contig assembly, and binning yielded 17 genome bins, six of which were >80% complete. These genomic bins, representing three phyla (Proteobacteria, Bacteroidetes, and Firmicutes), were closely related to halophilic and alkaliphilic taxa isolated from aquatic and soil environments. Comparison of these genomic bins to the genomes of their closest relatives revealed functional traits characteristic of bacterial populations inhabiting the Tamarix phyllosphere, independent of their taxonomic affiliation. These functions, most notably light-sensing genes, are postulated to represent important adaptations toward colonization of this habitat. IMPORTANCEPlant leaves are an extensive and diverse microbial habitat, forming the main interface between solar energy and the terrestrial biosphere. There are hundreds of thousands of plant species in the world, exhibiting a wide range of morphologies, leaf surface chemistries, and ecological ranges. In order to understand the core adaptations of microorganisms to this habitat, it is important to diversify the type of leaves that are studied. This study provides an analysis of the genomic content of the most abundant bacterial inhabitants of the globally distributed, salt-secreting desert tree Tamarix aphylla. Draft genomes of these bacteria were assembled, using the culture-independent technique of assembly and binning of metagenomic data. Analysis of the genomes reveals traits that are important for survival in this habitat, most notably, light-sensing and light utilization genes.

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Bacterial Diversity in Tree Canopies of the Atlantic Forest

Cited by 218 publications

References 6 publications

High-Level Culturability of Epiphytic Bacteria and Frequency of Biosurfactant Producers on Leaves

High-Level Culturability of Epiphytic Bacteria and Frequency of Biosurfactant Producers on Leaves

Emerging Perspectives on the Natural Microbiome of Fresh Produce Vegetables

Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree

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