Use of randomly amplified polymorphic DNA as a means of developing genus- and strain-specific Streptomyces DNA probes

Effects of ultrasound treatments on wine microorganisms

Ultrasound is one of the most promising non-thermal an emerging technique in food technology. The objective of the present work was to evaluate the effect of different ultrasonic treatments on the most important wine microbiota (Saccharomyces and non-Saccharomyces yeasts and lactic acid bacteria). Two stages were carried out: the assessment step, where six different ultrasonic treatments (with varying power, time, and pulses) were used on Saccharomyces cerevisiae, Brettanomyces spp., and Lactiplantibacillus plantarum; and the validation step, where two chosen ultrasonic treatments were used on Zigosaccharomyces bailli, Brettanomyces spp., Saccharomyces cerevisiae, Saccharomyces bayanus, Pichia membranifaciens, Schizosaccharomyces pombe, and Hanseniaspora osmophila. The most sensitive microorganism was Brettanomyces spp., and the most resistant was Lactiplantibacillus plantarum. Ultrasonic treatments had varying effects on vitality (delay of growth or maximum OD reduction) and on viability (reduction of microbial growth).

Phenotypic and molecular analysis of dominant occurring antibiotic active-producing Streptomyces soil flora in Northern Jordan

This investigation aimed to determine the relatedness of dominant occurring soil Streptomyces spp. in Northern Jordan based on their RAPD-PCR fingerprints, and to compare RAPD technique with the conventional phenotypic characterization of Streptomyces isolates. Fifty-eight white and gray color-bearing aerial mycelia antibiotic active-producing Streptomyces soil isolates along with three reference strains were genetically analyzed by RAPD-PCR. Polymorphisms between the isolates showed 1 to 10 bands per isolate and ranged from 200 to 3200 bp in size. Results revealed one common band of ~600 bp shared by ~85% of the isolates, and the observation of bands specific to some reference strains and some soil isolates. When RAPD patterns were analyzed with the UPGMA, results revealed clustering the tested isolates into two equal main super clusters (50% each). Super cluster I appeared to be homogenous and include the three reference strains. However, super cluster II was heterogeneous and but not including any of the reference strains. The association of the antibiotic activity of the dominant white and gray aerial mycelium-bearing Streptomyces isolates to RAPD clustering is reported for the first time, and the RAPD-PCR fingerprints generated here deserve to be cloned, characterized and sequenced in future as Streptomyces species-specific DNA markers. The more random primers used in the analysis may add to RAPD technique a cost-effective, fast, precise result, and less labor work solution for analyzing the similarities and differences among the Streptomyces isolates.

Streptomyces sp. strain SK68, isolated from peanut rhizosphere, promotes growth and alleviates salt stress in tomato (Solanum lycopersicum cv. Micro-Tom)

A novel actinobacterium, strain SK68, was isolated from the rhizosphere of peanut plant and its salinity stress alleviation ability was studied using tomato (Solanum lycopersicum cv. Micro-Tom) plants. Based on 16S rDNA based phylogenetic analysis, strain SK68 has been identified as a Streptomyces sp. Strain SK68 had branched substrate mycelium bearing smooth surfaced spores and the spore colour is brownish grey on ISP4 medium. It exhibited enzyme activities such as xylanase, cellulase, amylase, and pectinase and degraded hypoxanthine, casein, and L-tyrosine. The strain SK68 differed in its banding pattern in BOX-PCR and RAPD fingerprinting compared to the closely matching type strains Streptomyces erythrochromogenes NBRC 3304^T (AB184746), S. flavotricini NBRC 12770^T (AB184132), S. racemochromogenes NBRC 12906^T (AB184235), and S. polychromogenes NBRC 13072^T (NR041109). Strain SK68 was evaluated for its salinity stress-alleviating activity in tomato plants with 180 mmol/L NaCl under gnotobiotic condition. A significant increase in plant biomass was observed in strain SK68-inoculated tomato plants under salt stress compared to control and salt-stressed non-inoculated plants.

Phylogenetic conservatism of thermal traits explains dispersal limitation and genomic differentiation of Streptomyces sister-taxa

The latitudinal diversity gradient is a pattern of biogeography observed broadly in plants and animals but largely undocumented in terrestrial microbial systems. Although patterns of microbial biogeography across broad taxonomic scales have been described in a range of contexts, the mechanisms that generate biogeographic patterns between closely related taxa remain incompletely characterized. Adaptive processes are a major driver of microbial biogeography, but there is less understanding of how microbial biogeography and diversification are shaped by dispersal limitation and drift. We recently described a latitudinal diversity gradient of species richness and intraspecific genetic diversity in Streptomyces by using a geographically explicit culture collection. Within this geographically explicit culture collection, we have identified Streptomyces sister-taxa whose geographic distribution is delimited by latitude. These sister-taxa differ in geographic distribution, genomic diversity, and ecological traits despite having nearly identical SSU rRNA gene sequences. Comparative genomic analysis reveals genomic differentiation of these sister-taxa consistent with restricted gene flow across latitude. Furthermore, we show phylogenetic conservatism of thermal traits between the sister-taxa suggesting that thermal trait adaptation limits dispersal and gene flow across climate regimes as defined by latitude. Such phylogenetic conservatism of thermal traits is commonly associated with latitudinal diversity gradients for plants and animals. These data provide further support for the hypothesis that the Streptomyces latitudinal diversity gradient was formed as a result of historical demographic processes defined by dispersal limitation and driven by paleoclimate dynamics.

Streptomyces euryhalinus sp. nov., a new actinomycete isolated from a mangrove forest

A Gram-positive, aerobic, non-motile actinomycete (strain MS 3/20^T) was isolated from the sediment of the Sundarbans mangrove forest in India. On International Streptomyces Project (ISP) medium 2, the isolate produced yellowish brown to red aerial hyphae that carried spiny-surfaced spores in a retinaculum-apertum arrangement. Whole-cell hydrolysate of the strain contained LL-diaminopimelic acid and galactose. Predominant menaquinones were MK-9(H₈) and MK-9(H₆). Diagnostic polar lipids were glycolipid, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, unidentified phospholipid and unidentified amino lipid. The major fatty acids were anteiso-C_15:0 (17.53%), iso-C_16:0 (23.89%) and anteiso-C_17:0 (10.29%). The strain showed 100% 16S ribosomal RNA (rRNA) gene sequence similarity with Streptomyces variabilis NBRC 12825^T, Streptomyces erythrogriseus LMG 19406^T, Streptomyces griseoincarnatus LMG 19316^T and Streptomyces labedae NBRC 15864^T. However, strain MS 3/20^T could be distinguished from these and seven other closely related species based on low levels of DNA-DNA relatedness (27.2-53.8%), supported by the unique banding pattern obtained from random amplified polymorphic DNA-PCR amplification and the distinctive matrix-assisted laser desorption/ionization-time-of-flight/mass spectrometry (MALDI-TOF/MS) profile of whole-cell proteins acquired for strain MS 3/20^T in comparison with its phylogenetic relatives. Disparate morphological, physiological and chemotaxonomic features, principally growth in NaCl, further corroborated the distinction of strain MS 3/20^T from other phylogenetic relatives. Strain MS 3/20^T is therefore suggested to be a novel species of the genus Streptomyces, for which the name Streptomyces euryhalinus sp. nov. is proposed. The type strain is MS 3/20^T (=CICC 11032^T=DSM 103378^T).

Latitude delineates patterns of biogeography in terrestrial Streptomyces

The biogeography of Streptomyces was examined at regional spatial scales to identify factors that govern patterns of microbial diversity. Streptomyces are spore forming filamentous bacteria which are widespread in soil. Streptomyces strains were isolated from perennial grass habitats sampled across a spatial scale of more than 6000 km. Previous analysis of this geographically explicit culture collection provided evidence for a latitudinal diversity gradient in Streptomyces species. Here the hypothesis that this latitudinal diversity gradient is a result of evolutionary dynamics associated with historical demographic processes was evaluated. Historical demographic phenomena have genetic consequences that can be evaluated through analysis of population genetics. Population genetic approaches were applied to analyze population structure in six of the most numerically abundant and geographically widespread Streptomyces phylogroups from our culture collection. Streptomyces population structure varied at regional spatial scales, and allelic diversity correlated with geographic distance. In addition, allelic diversity and gene flow are partitioned by latitude. Finally, it was found that nucleotide diversity within phylogroups was negatively correlated with latitude. These results indicate that phylogroup diversification is constrained by dispersal limitation at regional spatial scales, and they are consistent with the hypothesis that historical demographic processes have influenced the contemporary biogeography of Streptomyces.

A Latitudinal Diversity Gradient in Terrestrial Bacteria of the Genus Streptomyces

We show that Streptomyces biogeography in soils across North America is influenced by the regional diversification of microorganisms due to dispersal limitation and genetic drift. Streptomyces spp. form desiccation-resistant spores, which can be dispersed on the wind, allowing for a strong test of whether dispersal limitation governs patterns of terrestrial microbial diversity. We employed an approach that has high sensitivity for determining the effects of genetic drift. Specifically, we examined the genetic diversity and phylogeography of physiologically similar Streptomyces strains isolated from geographically distributed yet ecologically similar habitats. We found that Streptomyces beta diversity scales with geographic distance and both beta diversity and phylogenetic diversity manifest in a latitudinal diversity gradient. This pattern of Streptomyces biogeography resembles patterns seen for diverse species of plants and animals, and we therefore evaluated these data in the context of ecological and evolutionary hypotheses proposed to explain latitudinal diversity gradients. The data are consistent with the hypothesis that niche conservatism limits dispersal, and historical patterns of glaciation have limited the time for speciation in higher-latitude sites. Most notably, higher-latitude sites have lower phylogenetic diversity, higher phylogenetic clustering, and evidence of range expansion from lower latitudes. In addition, patterns of beta diversity partition with respect to the glacial history of sites. Hence, the data support the hypothesis that extant patterns of Streptomyces biogeography have been driven by historical patterns of glaciation and are the result of demographic range expansion, dispersal limitation, and regional diversification due to drift.

Biogeographic patterns provide insight into the evolutionary and ecological processes that govern biodiversity. However, the evolutionary and ecological processes that govern terrestrial microbial diversity remain poorly characterized. We evaluated the biogeography of the genus Streptomyces to show that the diversity of terrestrial bacteria is governed by many of the same processes that govern the diversity of many plant and animal species. While bacteria of the genus Streptomyces are a preeminent source of antibiotics, their evolutionary history, biogeography, and biodiversity remain poorly characterized. The observations we describe provide insight into the drivers of Streptomyces biodiversity and the processes that underlie microbial diversification in terrestrial habitats.

Reporter systems for in vivo tracking of lactic acid bacteria in animal model studies

Bioluminescence (BLI) and fluorescence imaging (FI) allow for non-invasive detection of viable microorganisms from within living tissue and are thus ideally suited for in vivo probiotic studies. Highly sensitive optical imaging techniques detect signals from the excitation of fluorescent proteins, or luciferase-catalyzed oxidation reactions. The excellent relation between microbial numbers and photon emission allow for quantification of tagged bacteria in vivo with extreme accuracy. More information is gained over a shorter period compared to traditional pre-clinical animal studies. The review summarizes the latest advances in in vivo bioluminescence and fluorescence imaging and points out the advantages and limitations of different techniques. The practical application of BLI and FI in the tracking of lactic acid bacteria in animal models is addressed.

Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds

Marine microorganisms continue to be a source of structurally and biologically novel compounds with potential use in the biotechnology industry. The unique physiochemical properties of the marine environment (such as pH, pressure, temperature, osmolarity) and uncommon functional groups (such as isonitrile, dichloroimine, isocyanate, and halogenated functional groups) are frequently found in marine metabolites. These facts have resulted in the production of bioactive substances with different properties than those found in terrestrial habitats. In fact, the marine environment contains a relatively untapped reservoir of bioactivity. Recent advances in genomics, metagenomics, proteomics, combinatorial biosynthesis, synthetic biology, screening methods, expression systems, bioinformatics, and the ever increasing availability of sequenced genomes provides us with more opportunities than ever in the discovery of novel bioactive compounds and biocatalysts. The combination of these advanced techniques with traditional techniques, together with the use of dereplication strategies to eliminate known compounds, provides a powerful tool in the discovery of novel marine bioactive compounds. This review outlines and discusses the emerging strategies for the biodiscovery of these bioactive compounds.

Mutation of a degS homologue in Enterobacter cloacae decreases colonization and biological control of damping-off on cucumber

We have been using mutagenesis to determine how biocontrol bacteria such as Enterobacter cloacae 501R3 deal with complex nutritional environments found in association with plants. E. cloacae C10, a mutant of 501R3 with a transposon insertion in degS, was diminished in growth on synthetic cucumber root exudate (SRE), colonization of cucumber seed and roots, and control of damping-off of cucumber caused by Pythium ultimum. DegS, a periplasmic serine protease in the closely related bacterium Escherichia coli K12, is required for the RpoE-mediated stress response. C10 containing wild-type degS from 501R3 or from E. coli K12 on pBeloBAC11 was significantly increased in growth on SRE, colonization of cucumber roots, and control of P. ultimum relative to C10 containing pBeloBAC11 alone. C10 and 501R3 were similar in sensitivity to acidic conditions, plant-derived phenolic compounds, oxidative stress caused by hydrogen peroxide, dessication, and high osmoticum; stress conditions potentially associated with plants. This study demonstrates a role for degS in the spermosphere and rhizosphere during colonization and disease control by Enterobacter cloacae. This study implicates, for the first time, the involvement of DegS and, by extension, the RpoE-mediated stress response, in reducing stress on E. cloacae resulting from the complex nutritional environments in the spermosphere and rhizosphere.

Molecular phylogeny of methylotrophs in a deep-sea sediment from a tropical west Pacific Warm Pool

The presence and phylogeny of methylotrophs, including methanotrophs, in a deep-sea sediment of a tropical west Pacific Warm Pool site WP was investigated by molecular marker-based analysis of mxaF, pmoA and archaeal 16S rRNA genes. MxaF amino acid sequence analysis revealed that microbes belonging to the alpha-Proteobacteria and most related to Hyphomicrobium and Methylobacterium were the dominant aerobic methylotrophs in this deep-sea sediment; also, a small percentage of type II methanotrophs, closely related to Methylocystis and Methylosinus, were detected in this environment. On the other hand, the use of a pmoA gene marker could not demonstrate the presence of any methanotrophs in this environment, suggesting that the mxaF gene probe is a more suitable marker in this deep-sea sediment for the detection of methylotrophs (including methanotrophs). mxaF quantitative polymerase chain reaction results showed that the west Pacific WP sediment contained approximately 3x10(4-5) methylotrophs per gram sediment, 10-100 times more than the samples collected from several other deep-sea Pacific sediments, but, on the other hand, about 10 times less than the amounts present in samples collected from rice and flower garden soil. Archaeal diversity as analyzed by 16S rRNA gene sequences indicated that a non-thermophilic marine group I crenarchaeote was the major archaeal group present in the west Pacific WP.

Streptomyces koyangensis sp. nov., a novel actinomycete that produces 4-phenyl-3-butenoic acid

A 4-phenyl-3-butenoic acid-producing actinomycete, designated strain VK-A60T, was isolated from a soil sample collected from Koyang, Korea. Morphological and chemical characteristics of the strain were consistent with those of the genus Streptomyces. The cell wall of the strain contains LL-diaminopimelic acid. The predominant fatty acids are anteiso-C(15 : 0), iso-C(16 : 0) and C(16 : 0). The strain formed a distinct monophyletic line within the 16S rRNA gene sequence phylogenetic tree. Analyses of its morphological, physiological and biochemical characteristics, together with random amplified polymorphic DNA and DNA-DNA relatedness data, confirmed that strain VK-A60T represents a novel Streptomyces taxon that is distinguishable from closely related reference strains. Strain VK-A60T (=KCCM 10555T=NBRC 100598T) is proposed as the type strain of a novel species, for which the name Streptomyces koyangensis sp. nov. is proposed.

Microbial dynamics and interactions in the spermosphere

The spermosphere represents a short-lived, rapidly changing, and microbiologically dynamic zone of soil surrounding a germinating seed. It is analogous to the rhizosphere, being established largely by the carbon compounds released into the soil once the seed begins to hydrate. These seed exudations drive the microbial activities that take place in the spermosphere, many of which can have long-lasting impacts on plant growth and development as well as on plant health. In this review, I discuss the nature of the spermosphere habitat and the factors that give rise to its character, with emphasis on the types of microbial activities in the spermosphere that have important implications for disease development and biological disease control. This review, which represents the first comprehensive synthesis of the literature on spermosphere biology, is meant to illustrate the unique nature of the spermosphere and how studies of interactions in this habitat may serve as useful experimental models for testing hypotheses about plant-microbe associations and microbial ecology.

Interactions Between Strains of 2,4-Diacetylphloroglucinol-Producing Pseudomonas fluorescens in the Rhizosphere of Wheat

ABSTRACT Strains of fluorescent Pseudomonas spp. that produce the antibiotic 2,4-diacetylphoroglucinol (2,4-DAPG) are among the most effective rhizobacteria controlling diseases caused by soilborne pathogens. The genotypic diversity that exists among 2,4-DAPG producers can be exploited to improve rhizosphere competence and biocontrol activity. Knowing that D-genotype 2,4-DAPG-producing strains are enriched in some take-all decline soils and that P. fluorescens Q8r1-96, a representative D-genotype strain, as defined by whole-cell repetitive sequence-based polymerase chain reaction (rep-PCR) with the BOXA1R primer, is a superior colonizer of wheat roots, we analyzed whether the exceptional rhizosphere competence of strain Q8r1-96 on wheat is characteristic of other D-genotype isolates. The rhizosphere population densities of four D-genotype strains and a K-genotype strain introduced individually into the soil were significantly greater than the densities of four strains belonging to other genotypes (A, B, and L) and remained above log 6.8 CFU/g of root over a 30-week cycling experiment in which wheat was grown for 10 successive cycles of 3 weeks each. We also explored the competitive interactions between strains of different genotypes inhabiting the same soil or rhizosphere when coinoculated into the soil. Strain Q8r1-96 became dominant in the rhizosphere and in nonrhizosphere soil during a 15-week cycling experiment when mixed in a 1:1 ratio with either strain Pf-5 (A genotype), Q2-87 (B genotype), or 1M1-96 (L genotype). Furthermore, the use of the de Wit replacement series demonstrated a competitive disadvantage for strain Q2-87 or strong antagonism by strain Q8r1-96 against Q2-87 in the wheat rhizosphere. Amplified rDNA restriction analysis and sequence analysis of 16S rDNA showed that species of Arthrobacter, Chryseobacterium, Flavobacterium, Massilia, Microbacterium, and Ralstonia also were enriched in culturable populations from the rhizosphere of wheat at the end of a 30-week cycling experiment in the presence of 2,4-DAPG producers. Identifying the interactions among 2,4-DAPG producers and with other indigenous bacteria in the wheat rhizosphere will help to elucidate the variability in biocontrol efficacy of introduced 2,4-DAPG producers and fluctuations in the robustness of take-all suppressive soils.

Mutation of rpiA in Enterobacter cloacae decreases seed and root colonization and biocontrol of damping-off caused by Pythium ultimum on cucumber

Strains of Enterobacter cloacae show promise as biocontrol agents for Pythium ultimum-induced damping-off on cucumber and other crops. E. cloacae A145 is a mini-Tn5 Km transposon mutant of strain 501R3 that was significantly reduced in suppression of damping-off on cucumber caused by P. ultimum. Strain A145 was deficient in colonization of cucumber, sunflower, and wheat seeds and significantly reduced in colonization of corn and cowpea seeds relative to strain 501R3. Populations of strain A145 were also significantly lower than those of strain 501R3 at all sampling times in cucumber, wheat, and sunflower rhizosphere. Populations of strain A145 were not detectable in any rhizosphere after 42 days, while populations of strain 501R3 remained at substantial levels throughout all experiments. Molecular characterization of strain A145 indicated mini-Tn5 Km was inserted in a region of the E. cloacae genome with a high degree of DNA and amino acid sequence similarity to rpiA, which encodes ribose-5-phosphate isomerase. In Escherichia coli, RpiA catalyzes the interconversion of ribose-5-phosphate and ribulose-5-phosphate and is a key enzyme in the pentose phosphate pathway. Ribose-5-phosphate isomerase activity in cell lysates from strain A145 was approximately 3.5% of that from strain 501R3. In addition, strain A145 was a ribose auxotroph, as expected for an rpiA mutant. Introduction of a 1.0-kb DNA fragment containing only the rpiA homologue into strain A145 restored ribose phosphate isomerase activity, prototrophy, seedling colonization, and disease suppression to levels similar to those associated with strain 501R3. Experiments reported here indicate a key role for rpiA and possibly the pentose phosphate pathway in suppression of damping-off and colonization of subterranean portions of plants by E. cloacae.

Differentiation of plasmids in marine diazotroph assemblages determined by randomly amplified polymorphic DNA analysis

Nitrogen fixation by diazotrophic bacteria is a significant source of new nitrogen in salt marsh ecosystems. Recent studies have characterized the physiological and phylogenetic diversity of oxygen-utilizing diazotrophs isolated from the rhizoplanes of spatially separated intertidal macrophyte habitats. However, there is a paucity of information regarding the traits encoded by and the diversity of plasmids occurring in this key ecological functional group. Five-hundred and twenty-one isolates cultivated from the rhizoplanes of Juncus roemarianus, Spartina patens and different growth forms (short-form and tall-form) of Spartina alterniflora were screened for the presence of plasmids. One-hundred and thirty-four diazotrophs carrying plasmids that ranged in size from 2 to >100 kbp were identified. The majority of the marine bacteria contained one plasmid. Diazotrophs from the short-form S. alterniflora rhizoplane contained significantly fewer plasmids relative to isolates from tall-form S. alterniflora, J. roemarianus and S. patens. Although some plasmids exhibited homology to a nifH gene probe, the majority of the plasmids were classified as cryptic. Two oligonucleotide primers were developed to facilitate genotypic typing of the endogenously isolated marine plasmids by the randomly amplified polymorphic DNA (RAPD)-PCR technique. These primers proved to be more effective than 21 commercially available primers tested to generate RAPD-PCR patterns. Analysis of the RAPD-PCR patterns indicated as many as 71 different plasmid genotypes occurring in diazotroph bacterial assemblages within and between the four different salt marsh grass rhizoplane habitats investigated in this study.

PCR primers targeting the 16S rRNA gene for the specific detection of streptomycetes

Streptomycetes are filamentous actinobacteria commonly found in soil and biotechnically important, but they also have adverse effects on human health. In this work, two primer pairs, StrepB/StrepE and StrepB/StrepF combined with Bst YI restriction endonuclease digestion, targeting the 16S rRNA gene of streptomycetes were designed. The specificity of the primers was determined by polymerase chain reaction (PCR) amplification from Streptomyces strains and near relatives. All streptomycetes tested positive and non-streptomycetes were not amplified except three strains that, however, gave Bst YI restriction endonuclease digestion results distinct from streptomycetes. Moreover, both primer pairs gave an amplification product of the expected size only when Streptomyces VTT E-99-1334 DNA was present in the template DNA mixture isolated from six bacterial and three fungal strains. The primers were further successfully used to amplify from DNA isolated from two soil and two building material samples. The 40 sequenced amplification products obtained with the primer pair StrepB/StrepE showed greater than 96.1% similarity to streptomycete 16S rRNA sequences. Seventy PCR amplification products obtained with the primers StrepB/StrepF were analysed by sequencing and restriction analysis. All 54 PCR products having >95.7% similarity to streptomycete sequences were cleaved with Bst YI. No false-positive results were achieved. Both primer sets proved to be specific for streptomycetes, and applicable for the detection of streptomycetes in environmental samples.