Publications by authors named "Markéta Ságová-Marečková"

19 Publications

  • Page 1 of 1

gen. nov., sp. nov., an acidophilic actinobacterium, and proposal of the new actinobacterial family fam. nov.

Int J Syst Evol Microbiol 2020 Sep;70(9):5106-5114

Epidemiology and Ecology of Microorganisms, Crop Research Institute, Drnovska 507, Prague 6, Czechia.

A novel actinobacterial strain, designated 15TR583, was isolated from a waterlogged acidic soil collected near the town of Trebon, Czech Republic, and was subjected to a polyphasic taxonomic characterization. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences revealed that the organism forms an individual line of descent related to the order , class . The strain shared highest 16S rRNA gene sequence similarity, yet of only 92.8%, with IFO 14752. The strain grew in white colonies of aerobic, Gram-stain-positive, unbranching substrate mycelium bearing single spores at hyphae tips. The major fatty acids (>10%) were iso-C, C, isoCω9 and 10-methyl-C. The fatty acid pattern differed from all patterns currently described for actinobacterial genera. The organism contained as major menaquinones MK9(H) and MK9(H), which differentiated it from other actinobacterial families. Polar lipids were composed of six unidentified glycolipids, an unidentified phosphoglycolipid, two unidentified phospholipids and two unidentified aminolipids. Whole-cell sugars contained galactose, xylose and arabinose as major components. The peptidoglycan type was A1γ -diaminopimelic acid. The genomic DNA G+C content was 69.7 mol%. The distinct phylogenetic position and unusual combination of chemotaxonomic characteristics justify the proposal of gen. nov., with the type species sp. nov. (type strain 15TR583=CCM 8942=DSM 109105), within fam. nov.
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http://dx.doi.org/10.1099/ijsem.0.004388DOI Listing
September 2020

Bacterial, archaeal and micro-eukaryotic communities characterize a disease-suppressive or conducive soil and a cultivar resistant or susceptible to common scab.

Sci Rep 2019 10 16;9(1):14883. Epub 2019 Oct 16.

Crop Research Institute, Epidemiology and Ecology of Microorganisms, Drnovská 509, 161 06, Prague 6, Czech Republic.

Control of common scab disease can be reached by resistant cultivars or suppressive soils. Both mechanisms are likely to translate into particular potato microbiome profiles, but the relative importance of each is not known. Here, microbiomes of bulk and tuberosphere soil and of potato periderm were studied in one resistant and one susceptible cultivar grown in a conducive and a suppressive field. Disease severity was suppressed similarly by both means yet, the copy numbers of txtB gene (coding for a pathogenicity determinant) were similar in both soils but higher in periderms of the susceptible cultivar from conducive soil. Illumina sequencing of 16S rRNA genes for bacteria (completed by 16S rRNA microarray approach) and archaea, and of 18S rRNA genes for micro-eukarytes showed that in bacteria, the more important was the effect of cultivar and diversity decreased from resistant cultivar to bulk soil to susceptible cultivar. The major changes occurred in proportions of Actinobacteria, Chloroflexi, and Proteobacteria. In archaea and micro-eukaryotes, differences were primarily due to the suppressive and conducive soil. The effect of soil suppressiveness × cultivar resistance depended on the microbial community considered, but differed also with respect to soil and plant nutrient contents particularly in N, S and Fe.
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http://dx.doi.org/10.1038/s41598-019-51570-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796001PMC
October 2019

A Short-Term Response of Soil Microbial Communities to Cadmium and Organic Substrate Amendment in Long-Term Contaminated Soil by Toxic Elements.

Front Microbiol 2018 20;9:2807. Epub 2018 Nov 20.

Department of Epidemiology and Ecology of Microorganisms, Crop Research Institute, Prague, Czechia.

Two long-term contaminated soils differing in contents of Pb, Zn, As, Cd were compared in a microcosm experiment for changes in microbial community structure and respiration after various treatments. We observed that the extent of long-term contamination (over 200 years) by toxic elements did not change the total numbers and diversity of bacteria but influenced their community composition. Namely, numbers of determined by phylum specific qPCR increased and also the proportion of and increased in Illumina sequence libraries in the more contaminated soil. In the experiment, secondary disturbance by supplemented cadmium (doses from double to 100-fold the concentration in the original soil) and organic substrates (cellobiose or straw) increased bacterial diversity in the less contaminated soil and decreased it in the more contaminated soil. Respiration in the experiment was higher in the more contaminated soil in all treatments and correlated with bacterial numbers. Considering the most significant changes in bacterial community, it seemed that particularly withstand contamination by toxic elements. The results proved higher resistance to secondary disturbance in terms of both, respiration and bacterial community structure in the less contaminated soil.
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http://dx.doi.org/10.3389/fmicb.2018.02807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6256134PMC
November 2018

The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems.

Sci Total Environ 2018 Oct 22;637-638:1295-1310. Epub 2018 May 22.

Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany.

The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.
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http://dx.doi.org/10.1016/j.scitotenv.2018.05.002DOI Listing
October 2018

The effect of peat and iron supplements on the severity of potato common scab and bacterial community in tuberosphere soil.

FEMS Microbiol Ecol 2017 01 8;93(1). Epub 2016 Oct 8.

Department of Epidemiology and Ecology of Microorganisms, Crop Research Institute, 16106 Prague, Czech Republic.

The control of common scab (CS) of potatoes includes resistant cultivars, specific fertilization, increase of soil moisture and chemical treatments. Yet, these management practices do not have common or reproducible results at differing sites. In order to determine the effects of soil organic matter, iron and pH on CS development, peat and DTPA-chelated iron were supplemented to pots filled with soil conducive for CS. All results were compared with the same data obtained for a suppressive soil, which has naturally low severity of CS and occurs nearby. Bacteria, Actinobacteria and the txtB genes from the biosynthetic cluster of thaxtomin, which is responsible for the disease development, were quantified by qPCR in tuberosphere soil and potato periderm. Illumina amplicon sequencing of bacterial 16S rRNA genes was performed for tuberosphere soils. Both peat and iron supplements controlled potato scab, and the combination of the two supplements reduced CS most effectively. The bacterial community was modified by all treatments but the highest number of operational taxonomic units (OTUs) changed towards the suppressive soil after the combined peat and iron treatment. It seemed that iron supplement supported plant defense while both iron and peat additions changed the bacterial community in favor of CS suppression.
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http://dx.doi.org/10.1093/femsec/fiw206DOI Listing
January 2017

Assessment of Bacterial Communities in Thirteen Species of Laboratory-Cultured Domestic Mites (Acari: Acaridida).

J Econ Entomol 2016 08 27;109(4):1887-96. Epub 2016 Apr 27.

Crop Research Institute, Prague, Czechia

House dust mites (HDMs) and stored-product mites (SPMs) of various species inhabit human homes and stored agricultural products. These mites are carriers and hosts of microorganisms that enable their survival. The bacteriome from 13 species of SPMs and HDMs was analyzed and compared by 454 pyrosequencing of partial 16S rRNA gene amplicons. Altogether 128,052 sequences were obtained and assigned to 71 operational taxonomic units (OTUs) at the 97% identity level. The number of sequences in the OTUs between species of mites ranged from 6 to 31 in the individual mite species. We did not find any significant effect of diet or evolutionary origin of mites or their interaction on the composition of the mite bacteriome. In mite species with low bacterial diversity, the bacterial communities were dominated by potential symbiotic or parasitic bacteria, i.e., Cardinium in Dermatophagoides farinae (Hughes, 1961) and Aeroglyphus robustus (Banks 1906) and the enteric bacteria Erwinia in Blomia tropicalis Van Bronswijk, de Cock & Oshima, 1974 and Xenorhabdus in Tyroborus lini (Oudemans, 1924). Among the bacterial species identified, Staphylococcus, Bacillus, Kocuria, Brevibacterium, Corynebacterium, and Brachybacterium likely serve as food sources for the mites. The domestic acaridid mites carried high numbers of various bacteria that are potential threats to human health. These results contribute to the general understanding of the ecology of mite adaptation to human-made habitats.
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http://dx.doi.org/10.1093/jee/tow089DOI Listing
August 2016

Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria.

BMC Microbiol 2015 Apr 1;15:81. Epub 2015 Apr 1.

Epidemiology and Ecology of Microorganisms, Crop Research Institute, Prague, Czech Republic.

Background: Distribution and evolutionary history of resistance genes in environmental actinobacteria provide information on intensity of antibiosis and evolution of specific secondary metabolic pathways at a given site. To this day, actinobacteria producing biologically active compounds were isolated mostly from soil but only a limited range of soil environments were commonly sampled. Consequently, soil remains an unexplored environment in search for novel producers and related evolutionary questions.

Results: Ninety actinobacteria strains isolated at contrasting soil sites were characterized phylogenetically by 16S rRNA gene, for presence of erm and ABC transporter resistance genes and antibiotic production. An analogous analysis was performed in silico with 246 and 31 strains from Integrated Microbial Genomes (JGI_IMG) database selected by the presence of ABC transporter genes and erm genes, respectively. In the isolates, distances of erm gene sequences were significantly correlated to phylogenetic distances based on 16S rRNA genes, while ABC transporter gene distances were not. The phylogenetic distance of isolates was significantly correlated to soil pH and organic matter content of isolation sites. In the analysis of JGI_IMG datasets the correlation between phylogeny of resistance genes and the strain phylogeny based on 16S rRNA genes or five housekeeping genes was observed for both the erm genes and ABC transporter genes in both actinobacteria and streptomycetes. However, in the analysis of sequences from genomes where both resistance genes occurred together the correlation was observed for both ABC transporter and erm genes in actinobacteria but in streptomycetes only in the erm gene.

Conclusions: The type of erm resistance gene sequences was influenced by linkage to 16S rRNA gene sequences and site characteristics. The phylogeny of ABC transporter gene was correlated to 16S rRNA genes mainly above the genus level. The results support the concept of new specific secondary metabolite scaffolds occurring more likely in taxonomically distant producers but suggest that the antibiotic selection of gene pools is also influenced by site conditions.
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http://dx.doi.org/10.1186/s12866-015-0416-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391685PMC
April 2015

Experimental assessment of the water quality influence on the phosphorus uptake of an invasive aquatic plant: biological responses throughout its phenological stage.

PLoS One 2015 18;10(3):e0118844. Epub 2015 Mar 18.

Laboratoire d'Hydrologie et de Géochimie de Strasbourg (LHyGeS UMR 7517 UdS / CNRS), Institut de Botanique, 28 rue Goethe, F-67083, Strasbourg Cedex, France.

Understanding how an invasive plant can colonize a large range of environments is still a great challenge in freshwater ecology. For the first time, we assessed the relative importance of four factors on the phosphorus uptake and growth of an invasive macrophyte Elodea nuttallii (Planch.) St. John. This study provided data on its phenotypic plasticity, which is frequently suggested as an important mechanism but remains poorly investigated. The phosphorus uptake of two Elodea nuttallii subpopulations was experimentally studied under contrasting environmental conditions. Plants were sampled in the Rhine floodplain and in the Northern Vosges mountains, and then maintained in aquaria in hard (Rhine) or soft (Vosges) water. Under these conditions, we tested the influence of two trophic states (eutrophic state, 100 μg x l(-1) P-PO4(3-) and hypertrophic state, 300 μg x l(-1) P-PO4(3-)) on the P metabolism of plant subpopulations collected at three seasons (winter, spring and summer). Elodea nuttallii was able to absorb high levels of phosphorus through its shoots and enhance its phosphorus uptake, continually, after an increase of the resource availability (hypertrophic > eutrophic). The lowest efficiency in nutrient use was observed in winter, whereas the highest was recorded in spring, what revealed thus a storage strategy which can be beneficial to new shoots. This experiment provided evidence that generally, the water trophic state is the main factor governing P uptake, and the mineral status (softwater > hardwater) of the stream water is the second main factor. The phenological stage appeared to be a confounding factor to P level in water. Nonetheless, phenology played a role in P turnover in the plant. Finally, phenotypic plasticity allows both subpopulations to adapt to a changing environment.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118844PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364775PMC
February 2016

Determination of factors associated with natural soil suppressivity to potato common scab.

PLoS One 2015 22;10(1):e0116291. Epub 2015 Jan 22.

Crop Research Institute, Dept. Epidemiology and Ecology of Microorganisms, Prague, Czech Republic.

Common scab of potatoes is a disease, which is difficult to manage due to complex interactions of the pathogenic bacteria (Streptomyces spp.) with soil, microbial community and potato plants. In Bohemian-Moravian Highlands in the Czech Republic two sites (Vyklantice and Zdirec) were selected for a study of common scab disease suppressivity. At both sites, a field with low disease severity occurs next to one with high severity and the situation was regularly observed over four decades although all four fields undergo a crop rotation. In the four fields, quantities of bacteria, actinobacteria and the gene txtB from the biosynthetic gene cluster of thaxtomin, the main pathogenicity factor of common scab, were analyzed by real-time PCR. Microbial community structure was compared by terminal fragment length polymorphism analysis. Soil and potato periderm were characterized by contents of carbon, nitrogen, phosphorus, sulphur, calcium, magnesium, and iron. Quality of organic matter was assessed by high performance liquid chromatography of soil extracts. The study demonstrated that the suppressive character of the fields is locally specific. At Zdirec, the suppressivity was associated with low txtB gene copies in bulk soil, while at Vyklantice site it was associated with low txtB gene copies in the tuberosphere. The differences were discussed with respect to the effect of abiotic conditions at Zdirec and interaction between potato plant and soil microbial community at Vyklantice. Soil pH, Ca soil content or cation concentrations, although different were not in the range to predict the disease severity. Low severity of common scab was associated with low content of soil C, N, C/N, Ca and Fe suggesting that oligotrophic conditions may be favorable to common scab suppression.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0116291PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4303419PMC
September 2015

Evaluation of rhizobacterial indicators of tobacco black root rot suppressiveness in farmers' fields.

Environ Microbiol Rep 2014 Aug 8;6(4):346-53. Epub 2014 Jan 8.

Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, Ecologie Microbienne, UMR5557, Villeurbanne, France; Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Soil Biology, České Budějovice, Czech Republic.

Very few soil quality indicators include disease-suppressiveness criteria. We assessed whether 64 16S rRNA microarray probes whose signals correlated with tobacco black root rot suppressiveness in greenhouse analysis could also discriminate suppressive from conducive soils under field conditions. Rhizobacterial communities of tobacco and wheat sampled in 2 years from four farmers' fields of contrasted suppressiveness status were compared. The 64 previously identified indicator probes correctly classified 72% of 29 field samples, with nine probes for Azospirillum, Gluconacetobacter, Sphingomonadaceae, Planctomycetes, Mycoplasma, Lactobacillus crispatus and Thermodesulforhabdus providing the best prediction. The whole probe set (1033 probes) revealed strong effects of plant, field location and year on rhizobacterial community composition, and a smaller (7% variance) but significant effect of soil suppressiveness status. Seventeen additional probes correlating with suppressiveness status in the field (noticeably for Agrobacterium, Methylobacterium, Ochrobactrum) were selected, and combined with the nine others, they improved correct sample classification from 72% to 79% (100% tobacco and 63% wheat samples). Pseudomonas probes were not informative in the field, even those targeting biocontrol pseudomonads producing 2,4-diacetylphloroglucinol, nor was quantitative polymerase chain reaction for 2,4-diacetylphloroglucinol-synthesis gene phlD. This study shows that a subset of 16S rRNA probes targeting diverse rhizobacteria can be useful as suppressiveness indicators under field conditions.
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http://dx.doi.org/10.1111/1758-2229.12131DOI Listing
August 2014

Shift of bacterial community in synanthropic mite Tyrophagus putrescentiae induced by Fusarium fungal diet.

PLoS One 2012 31;7(10):e48429. Epub 2012 Oct 31.

Department of Pest Control of Stored Products and Food Safety, Crop Research Institute, Prague, Czech Republic.

Background: Tyrophagus putrescentiae (Acari: Astigmata) and Fusarium sp. co-occur in poorly managed grain. In a laboratory experiment, mite grazing resulted in significant reduction of fungal mycelium on cultivation plates. The destruction of mycelium appeared to be a result of an interaction between the mites, fungi and associated bacteria.

Methodology And Principal Findings: A laboratory experiment was performed to simulate a situation of grain multiinfested by mites and Fusarium fungi. Changes of mite-associated bacterial community in T. putrescentiae were described in 3 habitats: (i) T. putrescentiae mites from a rearing diet prior to their transfer to fungal diet; (ii) fungal mycelium before mite introduction; (iii) mites after 7 day diet of each Fusarium avenaceum, F. culmorum, F. poae and F. verticillioides. Bacterial communities were characterized by 16 S rRNA gene sequencing. In total, 157 nearly full-length 16 S rRNA gene sequences from 9 samples representing selected habitats were analyzed. In the mites, the shift from rearing to fungal diet caused changes in mite associated bacterial community. A diverse bacterial community was associated with mites feeding on F. avenaceum, while feeding on the other three Fusarium spp. led to selection of a community dominated by Bacillaceae.

Conclusions/significance: The work demonstrated changes of bacterial community associated with T. putrescentiae after shift to fungal diets suggesting selection for Bacillaceae species known as chitinase producers, which might participate in the fungal mycelium hydrolysis.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048429PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3485207PMC
April 2013

Actinobacterial community dominated by a distinct clade in acidic soil of a waterlogged deciduous forest.

FEMS Microbiol Ecol 2011 Nov 9;78(2):386-94. Epub 2011 Aug 9.

Crop Research Institute, Prague, Czech Republic.

Members of the Actinobacteria are among the most important litter decomposers in soil. The site of a waterlogged deciduous forest with acidic soil was explored for actinobacteria because seasonality of litter inputs, temperature, and precipitation provided contrasting environmental conditions, particularly variation of organic matter quantity and quality. We hypothesized that these factors, which are known to influence decomposition, were also likely to affect actinobacterial community composition. The relationship between the actinobacterial community, soil moisture and organic matter content was assessed in two soil horizons in the summer and winter seasons using a 16S rRNA taxonomic microarray and cloning-sequencing of 16S rRNA genes. Both approaches showed that the community differed significantly between horizons and seasons, paralleling the changes in soil moisture and organic matter content. The microarray analysis further indicated that the actinobacterial community of the upper horizon was characterized by high incidence of the genus Mycobacterium. In both horizons and seasons, the actinobacterial clone libraries were dominated (by 80%) by sequences of a separate clade sharing an ancestral node with Streptosporangineae. This relatedness is supported also by some common adaptations, for example, to soil acidity and periodic oxygen deprivation or dryness.
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http://dx.doi.org/10.1111/j.1574-6941.2011.01173.xDOI Listing
November 2011

Detection and identification of species-specific bacteria associated with synanthropic mites.

Microb Ecol 2012 May 5;63(4):919-28. Epub 2011 Nov 5.

Crop Research Institute, Drnovská 507, Praha 6-Ruzyně, Czech Republic.

Internal bacterial communities of synanthropic mites Acarus siro, Dermatophagoides farinae, Lepidoglyphus destructor, and Tyrophagus putrescentiae (Acari: Astigmata) were analyzed by culturing and culture-independent approaches from specimens obtained from laboratory colonies. Homogenates of surface-sterilized mites were used for cultivation on non-selective agar and DNA extraction. Isolated bacteria were identified by sequencing of the 16S rRNA gene. PCR amplified 16S rRNA genes were analyzed by terminal restriction fragment length polymorphism analysis (T-RFLP) and cloning sequencing. Fluorescence in situ hybridization using universal bacterial probes was used for direct bacterial localization. T-RFLP analysis of 16S rRNA gene revealed distinct species-specific bacterial communities. The results were further confirmed by cloning and sequencing (284 clones). L. destructor and D. farinae showed more diverse communities then A. siro and T. putrescentiae. In the cultivated part of the community, the mean CFUs from four mite species ranged from 5.2 × 10(2) to 1.4 × 10(3) per mite. D. farinae had significantly higher CFUs than the other species. Bacteria were located in the digestive and reproductive tract, parenchymatical tissue, and in bacteriocytes. Among the clones, Bartonella-like bacteria occurring in A. siro and T. putresecentiae represented a distinct group related to Bartonellaceae and to Bartonella-like symbionts of ants. The clones of high similarity to Xenorhabdus cabanillasii were found in L. destructor and D. farinae, and one clone related to Photorhabdus temperata in A. siro. Members of Sphingobacteriales cloned from D. farinae and A. siro clustered with the sequences of "Candidatus Cardinium hertigii" and as a separate novel cluster.
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http://dx.doi.org/10.1007/s00248-011-9969-6DOI Listing
May 2012

Microbial communities show parallels at sites with distinct litter and soil characteristics.

Appl Environ Microbiol 2011 Nov 16;77(21):7560-7. Epub 2011 Sep 16.

Laboratory for Diagnostics and Epidemiology of Microorganisms, Crop Research Institute, Drnovska 507, 16106 Prague 6, Czech Republic.

Plant and microbial community composition in connection with soil chemistry determines soil nutrient cycling. The study aimed at demonstrating links between plant and microbial communities and soil chemistry occurring among and within four sites: two pine forests with contrasting soil pH and two grasslands of dissimilar soil chemistry and vegetation. Soil was characterized by C and N content, particle size, and profiles of low-molecular-weight compounds determined by high-performance liquid chromatography (HPLC) of soil extracts. Bacterial and actinobacterial community composition was assessed by terminal restriction fragment length polymorphism (T-RFLP) and cloning followed by sequencing. Abundances of bacteria, fungi, and actinobacteria were determined by quantitative PCR. In addition, a pool of secondary metabolites was estimated by erm resistance genes coding for rRNA methyltransferases. The sites were characterized by a stable proportion of C/N within each site, while on a larger scale, the grasslands had a significantly lower C/N ratio than the forests. A Spearman's test showed that soil pH was correlated with bacterial community composition not only among sites but also within each site. Bacterial, actinobacterial, and fungal abundances were related to carbon sources while T-RFLP-assessed microbial community composition was correlated with the chemical environment represented by HPLC profiles. Actinobacteria community composition was the only studied microbial characteristic correlated to all measured factors. It was concluded that the microbial communities of our sites were influenced primarily not only by soil abiotic characteristics but also by dominant litter quality, particularly, by percentage of recalcitrant compounds.
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http://dx.doi.org/10.1128/AEM.00527-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3209186PMC
November 2011

Development of bacterial community during spontaneous succession on spoil heaps after brown coal mining.

FEMS Microbiol Ecol 2011 Oct 21;78(1):59-69. Epub 2011 Jul 21.

Laboratory of Environmental Microbiology, Institute of Microbiology of the ASCR, Praha, Czech Republic.

Changes in the abundance of bacteria and fungi and in the composition of bacterial communities during primary succession were investigated in a brown coal mine deposit area near Sokolov, the Czech Republic, using phospholipid fatty acids analysis, microarray and 16S rRNA gene sequencing. The study considered a chronosequence of sites undergoing spontaneous succession: 6-, 12-, 21- and 45-year-old and a 21-year-old site revegetated with Alnus glutinosa. During succession, organic carbon and the total nitrogen content increased while the pH and the C/N ratio decreased. Microbial biomass and bacterial diversity increased until 21 years and decreased later; bacteria dominated over fungi in the initial and late phases of succession. Bacterial community composition of the 6-year-old site with no vegetation cover largely differed from the older sites, especially by a higher content of Gammaproteobacteria, Cyanobacteria and some Alphaproteobacteria. Bacteria belonging to the genera Acidithiobacillus, Thiobacillus and related taxa, the CO(2) and N(2) fixers, dominated the community at this site. In the later phases, bacterial community development seemed to reflect more the changes in soil nutrient content and pH than vegetation with a decrease of Actinobacteria and an increase of Acidobacteria. The site revegetated with A. glutinosa resembled the 45-year-old primary succession site and exhibited an even lower pH and C/N ratio, indicating that recultivation is able to accelerate soil development.
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http://dx.doi.org/10.1111/j.1574-6941.2011.01164.xDOI Listing
October 2011

Subunit-subunit interactions are weakened in mutant forms of acetohydroxy acid synthase insensitive to valine inhibition.

Arch Microbiol 2010 Mar 28;192(3):195-200. Epub 2010 Jan 28.

Laboratory for Biology of Secondary Metabolism, Institute of Microbiology of the ASCR, vvi Vídenská 1083, CZ-14220 Prague 4, Czech Republic.

In acetohydroxy acid synthase from Streptomyces cinnamonensis mutants affected in valine regulation, the impact of mutations on interactions between the catalytic and the regulatory subunits was examined using yeast two-hybrid system. Mutations in the catalytic and the regulatory subunits were projected into homology models of the respective proteins. Two changes in the catalytic subunit, E139A (alpha domain) and DeltaQ217 (beta domain), both located on the surface of the catalytic subunit dimer, lowered the interaction with the regulatory subunit. Three consecutive changes in the N-terminal part of the regulatory subunit were examined. Changes G16D and V17D in a loop and adjacent alpha-helix of ACT domain affected the interaction considerably, indicating that this region might be in contact with the catalytic subunit during allosteric regulation. In contrast, the adjacent mutation L18F did not influence the interaction at all. Thus, L18 might participate in valine binding or conformational change transfer within the regulatory subunits. Shortening of the regulatory subunit to 107 residues reduced the interaction essentially, suggesting that the C-terminal part of the regulatory subunit is also important for the catalytic subunit binding.
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http://dx.doi.org/10.1007/s00203-010-0545-0DOI Listing
March 2010

Comparison of rhizobacterial community composition in soil suppressive or conducive to tobacco black root rot disease.

ISME J 2009 Oct 25;3(10):1127-38. Epub 2009 Jun 25.

Université de Lyon, Lyon, France.

Work on soils suppressive to Thielaviopsis basicola-mediated tobacco black root rot has focused on antagonistic pseudomonads to date. The role of non-Pseudomonas rhizosphere populations has been neglected, and whether they differ in black root rot-suppressive versus -conducive soils is unknown. To assess this possibility, tobacco was grown in a suppressive and a conducive soil of similar physicochemical properties, and rhizobacterial community composition was compared using a 16S rRNA taxonomic microarray. The microarray contains 1033 probes and targets 19 bacterial phyla. Among them, 398 probes were designed for Proteobacteria, Firmicutes, Actinomycetes, Cyanobacteria and Bacteroidetes genera/species known to include strains relevant for plant protection or plant growth promotion. Hierarchical clustering as well as principal component analysis of microarray data discriminated clearly between black root rot-suppressive and -conducive soils. In contrast, T. basicola inoculation had no impact on rhizobacterial community composition. In addition to fluorescent Pseudomonas, the taxa Azospirillum, Gluconacetobacter, Burkholderia, Comamonas and Sphingomonadaceae, which are known to comprise strains with plant-beneficial properties, were more prevalent in the suppressive soil. Mycobacterium, Bradyrhizobium, Rhodobacteraceae, Rhodospirillum and others were more prevalent in the conducive soil. For selected taxa, microarray results were largely corroborated by quantitative PCR and cloning/sequencing. In conclusion, this work identified novel bacterial taxa that could serve as indicators of disease suppressiveness in soil-quality assessments, and it extends the range of bacterial taxa hypothesized to participate in black root rot suppression.
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http://dx.doi.org/10.1038/ismej.2009.61DOI Listing
October 2009

Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera.

Antonie Van Leeuwenhoek 2008 Oct 4;94(3):439-53. Epub 2008 Jul 4.

Université de Lyon, Lyon, France.

Actinomycetes are known for their secondary metabolites, which have been successfully used as drugs in human and veterinary medicines. However, information on the distribution of this group of Gram-positive bacteria in diverse ecosystems and a comprehension of their activities in ecosystem processes are still scarce. We have developed a 16S rRNA-based taxonomic microarray that targets key actinomycetes at the genus level. In total, 113 actinomycete 16S rRNA probes, corresponding to 55 of the 202 described genera, were designed. The microarray accuracy was evaluated by comparing signal intensities with probe/target-weighted mismatch values and the Gibbs energy of the probe/target duplex formation by hybridizing 17 non-actinomycete and 29 actinomycete strains/clones with the probe set. The validation proved that the probe set was specific, with only 1.3% of false results. The incomplete coverage of actinomycetes by a genus-specific probe was caused by the limited number of 16S rRNA gene sequences in databases or insufficient 16S rRNA gene polymorphism. The microarray enabled discrimination between actinomycete communities from three forest soil samples collected at one site. Cloning and sequencing of 16S rRNA genes from one of the soil samples confirmed the microarray results. We propose that this newly constructed microarray will be a valuable tool for genus-level comparisons of actinomycete communities in various ecological conditions.
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http://dx.doi.org/10.1007/s10482-008-9261-zDOI Listing
October 2008

Innovative methods for soil DNA purification tested in soils with widely differing characteristics.

Appl Environ Microbiol 2008 May 14;74(9):2902-7. Epub 2008 Mar 14.

Crop Research Institute v.v.i., Drnovska 507, CZ-161 06 Prague 6, Czech Republic.

Seven methods of soil DNA extraction and purification were tested in a set of 14 soils differing in bedrock, texture, pH, salinity, moisture, organic matter content, and vegetation cover. The methods introduced in this study included pretreatment of soil with CaCO(3) or purification of extracted DNA by CaCl(2). The performance of innovated methods was compared to that of the commercial kit Mo Bio PowerSoil and the phenol-chloroform-based method of D. N. Miller, J. E. Bryant, E. L. Madsen, and W. C. Ghiorse (Appl. Environ. Microbiol. 65:4715-4724, 1999). This study demonstrated significant differences between the tested methods in terms of DNA yield, PCR performance, and recovered bacterial diversity. The differences in DNA yields were correlated to vegetation cover, soil pH, and clay content. The differences in PCR performances were correlated to vegetation cover and soil pH. The innovative methods improved PCR performance in our set of soils, in particular for forest acidic soils. PCR was successful in 95% of cases by the method using CaCl(2) purification and in 93% of cases by the method based on CaCO(3) pretreatment, but only in 79% by Mo Bio PowerSoil, for our range of soils. Also, the innovative methods recovered a higher percentage of actinomycete diversity from a subset of three soils. Recommendations include the assessment of soil characteristics prior to selecting the optimal protocol for soil DNA extraction and purification.
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http://dx.doi.org/10.1128/AEM.02161-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2394906PMC
May 2008