Spatial Variation in Streptomyces Genetic Composition and Diversity in a Prairie Soil

Davelos, Anita L.; Xiao, Kun; Samac, Deborah A.; Martin, Andrew P.; Kinkel, Linda L.

doi:10.1007/s00248-004-0031-9

Cited by 43 publications

(33 citation statements)

References 71 publications

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“…Therefore, antibiotic activity is a practically and ecologically important trait of these microorganisms. In previous research, we have found the spatial localization of antibiotic inhibitory and resistance phenotypes between locations (Davelos et al , 2004a), as well as the spatial localization of genetic groups and variation in genetic diversity between locations (Davelos et al , 2004c).…”

Section: Introductionmentioning

confidence: 97%

Lack of correspondence between genetic and phenotypic groups amongst soil-borne streptomycetes

Baines

Xiao

Kinkel

2007

FEMS Microbiology Ecology

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Correspondence between two distinct genetic traits, 16S rRNA gene sequences and repetitive element-sequence-based BOX-PCR DNA fingerprints, and antibiotic inhibition and resistance phenotypes was explored for a spatially explicit sample of Streptomyces from a prairie soil. There was no correspondence between 16S rRNA gene sequence groups and antibiotic phenotypes. However, 16S rRNA gene sequence groups differed significantly in mean inhibition zone sizes. Specific antibiotic phenotypes may reflect local selection pressures, as suggested by the significant differences in mean inhibition zone sizes against specific test isolates by Streptomyces from the same 16S rRNA gene sequence group but from different locations in soil. Significant correlations between antibiotic phenotypes and BOX-PCR fingerprints were found, but were small (r=0.19-0.22). Although genetic characterizations alone were not predictive of specific antibiotic phenotypes, 16S rRNA gene sequence analyses may identify isolates that are most or least likely to possess substantial inhibitory potential, providing insight into the broad ecological strategy for individual isolates.

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Section: Introductionmentioning

confidence: 97%

Lack of correspondence between genetic and phenotypic groups amongst soil-borne streptomycetes

Baines

Xiao

Kinkel

2007

FEMS Microbiology Ecology

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“…Even in such cosmopolitan bacteria, there are local ecotypes that are unrelated to any other known strains (Gonzalez-Gonzalez et al, 2013; Avitia et al, 2014; Valdivia-Anistro et al, 2015). Streptomyces , a filament and spore producer, and the most extensively studied genera of Actinomycetes, has been studied and it had shown environmental gradients and regional endemism in some localities (Davelos et al, 2004; Antony-Babu, Stach & Goodfellow, 2008; Kinkel et al, 2014; Andam et al, 2016). …”

Section: Introductionmentioning

confidence: 99%

High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis

Arocha-Garza

Castillo

Eguiarte

et al. 2017

PeerJ

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The phylum Actinobacteria constitutes one of the largest and anciently divergent phyla within the Bacteria domain. Actinobacterial diversity has been thoroughly researched in various environments due to its unique biotechnological potential. Such studies have focused mostly on soil communities, but more recently marine and extreme environments have also been explored, finding rare taxa and demonstrating dispersal limitation and biogeographic patterns for Streptomyces. To test the distribution of Actinobacteria populations on a small scale, we chose the extremely oligotrophic and biodiverse Cuatro Cienegas Basin (CCB), an endangered oasis in the Chihuahuan desert to assess the diversity and uniqueness of Actinobacteria in the Churince System with a culture-dependent approach over a period of three years, using nine selective media. The 16S rDNA of putative Actinobacteria were sequenced using both bacteria universal and phylum-specific primer pairs. Phylogenetic reconstructions were performed to analyze OTUs clustering and taxonomic identification of the isolates in an evolutionary context, using validated type species of Streptomyces from previously phylogenies as a reference. Rarefaction analysis for total Actinobacteria and for Streptomyces isolates were performed to estimate species’ richness in the intermediate lagoon (IL) in the oligotrophic Churince system. A total of 350 morphologically and nutritionally diverse isolates were successfully cultured and characterized as members of the Phylum Actinobacteria. A total of 105 from the total isolates were successfully subcultured, processed for DNA extraction and 16S-rDNA sequenced. All strains belong to the order Actinomycetales, encompassing 11 genera of Actinobacteria; the genus Streptomyces was found to be the most abundant taxa in all the media tested throughout the 3-year sampling period. Phylogenetic analysis of our isolates and another 667 reference strains of the family Streptomycetaceae shows that our isolation effort produced 38 unique OTUs in six new monophyletic clades. This high biodiversity and uniqueness of Actinobacteria in an extreme oligotrophic environment, which has previously been reported for its diversity and endemicity, is a suggestive sign of microbial biogeography of Actinobacteria and it also represents an invaluable source of biological material for future ecological and bioprospecting studies.

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“…Recent evidence suggests that bacteria can exhibit patterns in taxonomic diversity and community composition similar to those of plants and animals (e.g., Horner-Devine et al 2003, 2004b. However, most of these studies have relied on measures of diversity that do not consider phylogenetic relatedness (Bohannan and Hughes 2003), and few studies have quantitatively examined bacterial communities within a phylogenetic context (Martin 2002, Davelos et al 2004.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic Clustering and Overdispersion in Bacterial Communities

Horner-Devine¹,

Bohannan²

2006

Ecology

312

264

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Abstract. Very little is known about the structure of microbial communities, despite their abundance and importance to ecosystem processes. Recent work suggests that bacterial biodiversity might exhibit patterns similar to those of plants and animals. However, relative to our knowledge about the diversity of macro-organisms, we know little about patterns of relatedness in free-living bacterial communities, and relatively few studies have quantitatively examined community structure in a phylogenetic framework. Here we apply phylogenetic tools to bacterial diversity data to determine whether bacterial communities are phylogenetically structured. We find that bacterial communities tend to contain lower taxonomic diversity and are more likely to be phylogenetically clustered than expected by chance. Such phylogenetic clustering may indicate the importance of habitat filtering (where a group of closely related species shares a trait, or suite of traits, that allow them to persist in a given habitat) in the assembly of bacterial communities. Microbial communities are especially accessible for phylogenetic analysis and thus have the potential to figure prominently in the integration of evolutionary biology and community ecology.

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Spatial Variation in Streptomyces Genetic Composition and Diversity in a Prairie Soil

Cited by 43 publications

References 71 publications

Lack of correspondence between genetic and phenotypic groups amongst soil-borne streptomycetes

Lack of correspondence between genetic and phenotypic groups amongst soil-borne streptomycetes

High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis

Phylogenetic Clustering and Overdispersion in Bacterial Communities

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