Publications by authors named "Dana Elhottová"

24 Publications

  • Page 1 of 1

Native soil microorganisms hinder the soil enrichment with antibiotic resistance genes following manure applications.

Sci Rep 2019 05 1;9(1):6760. Epub 2019 May 1.

Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.

Bacterial genes responsible for resistance to antibiotic agents (ARG) are spread from livestock to soil through application of manure, threatening environmental and human health. We investigated the mechanisms of ARG dissemination and persistence to disentangle i) the influence of nutrients and microorganisms on the soil tetracycline (TET) resistome, and ii) the role of indigenous soil microbiota in preventing ARG spread. We analysed short-term (7 days) and persistent (84 days) effects of manure on the resistome of three antibiotic-free pasture soils. Four microcosm treatments were evaluated: control, mineral nutrient fertilization, and deposition of a layer of fresh manure onto soil or γ-irradiated soil. We quantified five TET-resistance genes, isolated 135 TET-resistant bacteria and sequenced both culturable TET-resistant and whole bacterial communities. Manure amendments, but not nutrient addition, increased the abundance of TET-r genes such as tet(Y). Such changes persisted with time, in contrast with the TET-resistant bacterial composition, which partially recovered after manure amendments. Manured γ-irradiated soils showed significantly lower nutrient content and higher TET-r gene abundance than non-irradiated soils, suggesting that native soil bacteria are essential for the fertilization effect of manure on soil as well as control the dissemination of potentially risky TET-r genes.
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http://dx.doi.org/10.1038/s41598-019-42734-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6494816PMC
May 2019

Functioning grouped soil microbial communities according to ecosystem type, based on comparison of fallows and meadows in the same region.

Sci Total Environ 2017 Dec 11;599-600:981-991. Epub 2017 May 11.

Institute of Botany, Jagiellonian University, Kopernika 27, 31-501 Kraków, Poland.

Predicting the composition and function of microbial communities at a bio-geographical scale, across ecosystems, is challenging. We compared six abandoned fields to six meadows to see whether soil microbial community structure and activity are more similar within the ecosystem type than between the types. We implemented bacteria and fungi phylogenetic markers profiling, phospholipids analysis, fluorescence counts of total bacteria and algae and microscopy of arbuscular mycorrhizal fungi (AMF). The functional performance of microbial communities was assessed using enzymes activity measurements as well as culturing and incubation experiments. The studied fallows and meadows had similar biomass and general structure of soil microbial communities. However, the AMF root colonization frequency was higher in the meadows than in the fallows. The AMF colonization was promoted in meadows characterised by lower availability of NO, P and K as well as higher soil pH, which additionally hampered plant acquisition of P at the P-limited ecosystem. Fallow and meadow microbial communities showed characteristic functional traits. Meadow soils exhibited higher basal respiration rate, while cellulose decomposition and nitrogen mineralization were faster in fallows. Even when no major differences in community structure could have been detected soil microbial communities adapted to local and/or instantaneous environmental conditions and formed functionally-specific ecotypes. This work points out the relevance of preserving meadows as reservoirs of plant diversity, which cope excellent in nutrient depleted conditions and in mountain regions thanks to microbial components of ecosystem.
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http://dx.doi.org/10.1016/j.scitotenv.2017.04.220DOI Listing
December 2017

Characterization of tet(Y)-carrying LowGC plasmids exogenously captured from cow manure at a conventional dairy farm.

FEMS Microbiol Ecol 2016 Jun 15;92(6):fiw075. Epub 2016 Apr 15.

Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology, Na Sádkách 7, 370 05 České Budějovice, Czech Republic.

Manure from dairy farms has been shown to contain diverse tetracycline resistance genes that are transferable to soil. Here, we focus on conjugative plasmids that may spread tetracycline resistance at a conventional dairy farm. We performed exogenous plasmid isolation from cattle feces using chlortetracycline for transconjugant selection. The transconjugants obtained harbored LowGC-type plasmids and tet(Y). A representative plasmid (pFK2-7) was fully sequenced and this was compared with previously described LowGC plasmids from piggery manure-treated soil and a GenBank record from Acinetobacter nosocomialis that we also identified as a LowGC plasmid. The pFK2-7 plasmid had the conservative backbone typical of LowGC plasmids, though this region was interrupted with an insert containing the tet(Y)-tet(R) tetracycline resistance genes and the strA-strB streptomycin resistance genes. Despite Acinetobacter populations being considered natural hosts of LowGC plasmids, these plasmids were not found in three Acinetobacter isolates from the study farm. The isolates harbored tet(Y)-tet(R) genes in identical genetic surroundings as pFK2-7, however, suggesting genetic exchange between Acinetobacter and LowGC plasmids. Abundance of LowGC plasmids and tet(Y) was correlated in manure and soil samples from the farm, indicating that LowGC plasmids may be involved in the spread of tet(Y) in the environment.
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http://dx.doi.org/10.1093/femsec/fiw075DOI Listing
June 2016

Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering.

PLoS One 2015 14;10(8):e0135627. Epub 2015 Aug 14.

Helmholtz Zentrum München, Research Unit for Environmental Genomics, Ingolstädter Landstraße 1, Neuherberg, Germany.

Archaea and bacteria are important drivers for nutrient transformations in soils and catalyse the production and consumption of important greenhouse gases. In this study, we investigate changes in archaeal and bacterial communities of four Czech grassland soils affected by outdoor cattle husbandry. Two show short-term (3 years; STI) and long-term impact (17 years; LTI), one is regenerating from cattle impact (REG) and a control is unaffected by cattle (CON). Cattle manure (CMN), the source of allochthonous microbes, was collected from the same area. We used pyrosequencing of 16S rRNA genes to assess the composition of archaeal and bacterial communities in each soil type and CMN. Both short- and long- term cattle impact negatively altered archaeal and bacterial diversity, leading to increase of homogenization of microbial communities in overwintering soils over time. Moreover, strong shifts in the prokaryotic communities were observed in response to cattle overwintering, with the greatest impact on archaea. Oligotrophic and acidophilic microorganisms (e.g. Thaumarchaeota, Acidobacteria, and α-Proteobacteria) dominated in CON and expressed strong negative response to increased pH, total C and N. Whereas copiotrophic and alkalophilic microbes (e.g. methanogenic Euryarchaeota, Firmicutes, Chloroflexi, Actinobacteria, and Bacteroidetes) were common in LTI showing opposite trends. Crenarchaeota were also found in LTI, though their trophic interactions remain cryptic. Firmicutes, Bacteroidetes, Methanobacteriaceae, and Methanomicrobiaceae indicated the introduction and establishment of faecal microbes into the impacted soils, while Chloroflexi and Methanosarcinaceae suggested increased abundance of soil-borne microbes under altered environmental conditions. The observed changes in prokaryotic community composition may have driven corresponding changes in soil functioning.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135627PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537298PMC
May 2016

Spread of tetracycline resistance genes at a conventional dairy farm.

Front Microbiol 2015 29;6:536. Epub 2015 May 29.

Institute of Soil Biology, Biology Centre of the Czech Academy of Sciences České Budějovice, Czech Republic.

The use of antibiotics in animal husbandry contributes to the worldwide problem of increasing antibiotic resistance in animal and human pathogens. Intensive animal production is considered an important source of antibiotic resistance genes released to the environment, while the contribution of smaller farms remains to be evaluated. Here we monitor the spread of tetracycline resistance (TC-r) genes at a middle-size conventional dairy farm, where chlortetracycline (CTC, as intrauterine suppository) is prophylactically used after each calving. Our study has shown that animals at the farm acquired the TC-r genes in their early age (1-2 weeks), likely due to colonization with TC-resistant bacteria from their mothers and/or the farm environment. The relative abundance of the TC-r genes tet(W), tet(Q), and tet(M) in fresh excrements of calves was about 1-2 orders of magnitude higher compared to heifers and dairy cows, possibly due to the presence of antibiotic residues in milk fed to calves. The occurrence and abundance of TC-r genes in fresh excrements of heifers and adult cows remained unaffected by intrauterine CTC applications, with tet(O), tet(Q), and tet(W) representing a "core TC-resistome" of the farm, and tet(A), tet(M), tet(Y), and tet(X) occurring occasionally. The genes tet(A), tet(M), tet(Y), and tet(X) were shown to be respectively harbored by Shigella, Lactobacillus and Clostridium, Acinetobacter, and Wautersiella. Soil in the farm proximity, as well as field soil to which manure from the farm was applied, was contaminated with TC-r genes occurring in the farm, and some of the TC-r genes persisted in the field over 3 months following the manure application. Concluding, our study shows that antibiotic resistance genes may be a stable part of the intestinal metagenome of cattle even if antibiotics are not used for growth stimulation, and that smaller dairy farms may also contribute to environmental pollution with antibiotic resistance genes.
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http://dx.doi.org/10.3389/fmicb.2015.00536DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4448040PMC
June 2015

Quantitative analysis of volatile metabolites released in vitro by bacteria of the genus Stenotrophomonas for identification of breath biomarkers of respiratory infection in cystic fibrosis.

J Breath Res 2015 Apr 1;9(2):027104. Epub 2015 Apr 1.

J Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 18223 Prague 8, Czech Republic.

The aim of the present study was to characterize the volatile metabolites produced by genotypically diverse strains of the Stenotrophomonas genus in order to evaluate their potential as biomarkers of lung infection by non-invasive breath analysis. Volatile organic compounds (VOCs) emitted from 15 clinical and five environmental strains belonging to different genogroups of Stenotrophomonas maltophilia (n = 18) and Stenotrophomonas rhizophila (n = 2) cultured in Mueller-Hinton Broth (MHB) liquid media were analysed by gas chromatography mass spectrometry (GC-MS) and selected ion flow tube mass spectrometry (SIFT-MS). Several VOCs were detected in high concentration, including ammonia, propanol, dimethyl disulphide propanol and dimethyl disulphide. The GC-MS measurements showed that all 15 clinical strains produced similar headspace VOCs compositions, and SIFT-MS quantification showed that the rates of production of the VOCs by the genotypically distinct strains were very similar. All in vitro cultures of both the Stenotrophomonas species were characterised by efficient production of two isomers of methyl butanol, which can be described by known biochemical pathways and which is absent in other pathogens, including Pseudomonas aeruginosa. These in-vitro data indicate that methyl butanol isomers may be exhaled breath biomarkers of S. maltophilia lung infection in patients with cystic fibrosis.
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http://dx.doi.org/10.1088/1752-7155/9/2/027104DOI Listing
April 2015

The effect of dibenzo-p-dioxin- and dibenzofuran-contaminated soil on the earthworm Eisenia andrei.

Environ Pollut 2014 Oct 1;193:22-28. Epub 2014 Jul 1.

Department of Immunology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, v. v. i., Vídeňská 1083, 142 20, Praha 4, Czech Republic. Electronic address:

Polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) belong to the group of persistent organic pollutants, highly toxic environmental pollutants that include hydrophobic compounds with the tendency to bioaccumulate. Earthworms (Eisenia andrei) were exposed to PCDD/Fs-contaminated soil, and changes in their lipophilic structures and the gene expression of their defense molecules were followed. Damage to the intestinal wall and adjacent chloragogenous tissue was observed. Further, the up-regulation of the expression of several genes was detected. On the basis of these results, the mechanism of the impact of PCDD/Fs on earthworms has been proposed. Dioxins that accumulate in the lipophilic structures cause an increase in reactive oxidative species that triggers oxidative stress followed by the gene expression of two molecules that play a role in protection against oxidant toxicity, calreticulin (CRT) and Hsp70. Moreover, the effect of microbial biomass on the expression of coelomic cytolytic factor (CCF), a pattern recognition receptor, was also observed.
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http://dx.doi.org/10.1016/j.envpol.2014.05.026DOI Listing
October 2014

Draft Genome Sequence of Stenotrophomonas maltophilia Strain 5BA-I-2, a Soil Isolate and a Member of a Phylogenetically Basal Lineage.

Genome Announc 2014 Mar 6;2(2). Epub 2014 Mar 6.

Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic.

Stenotrophomonas maltophilia is an omnipresent environmental bacterium emerging as an opportunistic human pathogen and exhibiting multidrug resistance. Here, we report the draft genome sequence of S. maltophilia strain 5BA-I-2, a soil isolate and a member of a phylogenetically basal lineage.
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http://dx.doi.org/10.1128/genomeA.00134-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3945504PMC
March 2014

Microbial environment affects innate immunity in two closely related earthworm species Eisenia andrei and Eisenia fetida.

PLoS One 2013 1;8(11):e79257. Epub 2013 Nov 1.

Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, v. v. i., Prague, Czech Republic.

Survival of earthworms in the environment depends on their ability to recognize and eliminate potential pathogens. This work is aimed to compare the innate defense mechanisms of two closely related earthworm species, Eisenia andrei and Eisenia fetida, that inhabit substantially different ecological niches. While E. andrei lives in a compost and manure, E. fetida can be found in the litter layer in forests. Therefore, the influence of environment-specific microbiota on the immune response of both species was followed. Firstly, a reliable method to discern between E. andrei and E. fetida based on species-specific primers for cytochrome c oxidase I (COI) and stringent PCR conditions was developed. Secondly, to analyze the immunological profile in both earthworm species, the activity and expression of lysozyme, pattern recognition protein CCF, and antimicrobial proteins with hemolytic function, fetidin and lysenins, have been assessed. Whereas, CCF and lysozyme showed only slight differences in the expression and activity, fetidin/lysenins expression as well as the hemolytic activity was considerably higher in E. andrei as compared to E. fetida. The expression of fetidin/lysenins in E. fetida was not affected upon the challenge with compost microbiota, suggesting more substantial changes in the regulation of the gene expression. Genomic DNA analyses revealed significantly higher level of fetidin/lysenins (determined using universal primer pairs) in E. andrei compared to E. fetida. It can be hypothesized that E. andrei colonizing compost as a new habitat acquired an evolutionary selection advantage resulting in a higher expression of antimicrobial proteins.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0079257PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815151PMC
August 2014

Cow excrements enhance the occurrence of tetracycline resistance genes in soil regardless of their oxytetracycline content.

Chemosphere 2013 Nov 18;93(10):2413-8. Epub 2013 Sep 18.

Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Soil Biology, 370 05 České Budějovice, Czech Republic. Electronic address:

Fertilizing soils with animal excrements from farms with common antibiotic use represents a risk of disseminating antibiotic resistance genes into the environment. In the case of tetracycline antibiotics, it is not clear, however, whether the presence of antibiotic residues further enhances the gene occurrence in manured soils. We established a microcosm experiment in which 3 farm soils that had no recent history of fertilization with animal excrements were amended on a weekly basis (9 times) with excrements from either an oxytetracycline-treated or an untreated cow. Throughout the study, the concentration of oxytetracycline in excrements from the treated cow was above 500 μg g(-1)dw, whereas no oxytetracycline was detected in excrements from the healthy cow. Both excrements contained tetracycline resistance (TC-r) genes tet(L), tet(M), tet(V), tet(Z), tet(Q) and tet(W). The excrements from the treated cow also contained the tet(B) gene, and a higher abundance of tet(Z), tet(Q) and tet(W). Three weeks after the last excrement addition, the individual TC-r genes differed in their persistence in soil: tet(Q) and tet(B) were not detectable while tet(L), tet(M), tet(Z) and tet(W) were found in all 3 soils. There were, however, no significant differences in the total number, nor in the abundance, of TC-r genes between soil samples amended with each excrement type. The oxytetracycline-rich and the oxytetracycline-free excrement therefore contributed equally to the increase of tetracycline resistome in soil. Our results indicate that other mechanisms than OTC-selection pressure may be involved in the maintenance of TC-r genes in manured soils.
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http://dx.doi.org/10.1016/j.chemosphere.2013.08.058DOI Listing
November 2013

The microbial communities and potential greenhouse gas production in boreal acid sulphate, non-acid sulphate, and reedy sulphidic soils.

Sci Total Environ 2014 Jan 19;466-467:663-72. Epub 2013 Aug 19.

Biology Centre AS CR, v. v. i., Institute of Soil Biology, 370 05 České Budějovice, Czech Republic; University of South Bohemia, Faculty of Science, 370 05 České Budějovice, Czech Republic. Electronic address:

Acid sulphate (AS) soils along the Baltic coasts contain significant amounts of organic carbon and nitrogen in their subsoils. The abundance, composition, and activity of microbial communities throughout the AS soil profile were analysed. The data from a drained AS soil were compared with those from a drained non-AS soil and a pristine wetland soil from the same region. Moreover, the potential production of methane, carbon dioxide, and nitrous oxide from the soils was determined under laboratory conditions. Direct microscopic counting, glucose-induced respiration (GIR), whole cell hybridisation, and extended phospholipid fatty acid (PLFA) analysis confirmed the presence of abundant microbial communities in the topsoil and also in the deepest Cg2 horizon of the AS soil. The patterns of microbial counts, biomass and activity in the profile of the AS soil and partly also in the non-AS soil therefore differed from the general tendency of gradual decreases in soil profiles. High respiration in the deepest Cg2 horizon of the AS soil (5.66 μg Cg(-1)h(-1), as compared to 2.71 μg Cg(-1)h(-1) in a top Ap horizon) is unusual but reasonable given the large amount of organic carbon in this horizon. Nitrous oxide production peaked in the BCgc horizon of the AS and in the BC horizon of the non-AS soil, but the peak value was ten-fold higher in the AS soil than in the non-AS soil (82.3 vs. 8.6 ng Ng(-1)d(-1)). The data suggest that boreal AS soils on the Baltic coast contain high microbial abundance and activity. This, together with the abundant carbon and total and mineral nitrogen in the deep layers of AS soils, may result in substantial gas production. Consequently, high GHG emissions could occur, for example, when the generally high water table is lowered because of arable farming.
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http://dx.doi.org/10.1016/j.scitotenv.2013.07.083DOI Listing
January 2014

The new species Enterobacter oryziphilus sp. nov. and Enterobacter oryzendophyticus sp. nov. are key inhabitants of the endosphere of rice.

BMC Microbiol 2013 Jul 16;13:164. Epub 2013 Jul 16.

Department of Microbial Ecology, University of Groningen, Centre for Ecological and Evolutionary Studies, Nijenborgh 7, Groningen 9747AG, The Netherlands.

Background: Six independent Gram-negative, facultatively anaerobic, non-spore-forming, nitrogen-fixing rod-shaped isolates were obtained from the root endosphere of rice grown at the International Rice Research Institute (IRRI) and investigated in a polyphasic taxonomic study.

Results: The strains produced fatty acid patterns typical for members of the family Enterobacteriaceae. Comparative sequence analyses of the 16S rRNA as well as rpoB genes allocated the strains to two well-defined groups within the genus Enterobacter, family Enterobacteriaceae. The analyses indicated Enterobacter radicincitans, Enterobacter arachidis and Enterobacter oryzae to be the closest related species. An RpoB (translated) protein comparison supported the placement in the genus Enterobacter and the relatedness of our isolates to the aforementioned species. Genomic DNA:DNA hybridization analyses and biochemical analyses provided further evidence that the novel strains belong to two new species within the genus Enterobacter. The two species can be differentiated from each other and from existing enteric species by acid production from L-rhamnose and D-melibiose, decarboxylation of ornithine and utilization of D-alanine, D-raffinose L-proline and L-aspartic acid, among other characteristics. Members of both species revealed capacities to colonise rice roots, including plant-growth-promoting capabilities such as an active supply of fixed nitrogen to the plant and solubilisation of inorganic phosphorus, next to traits allowing adaptation to the plant.

Conclusions: Two novel proposed enterobacterial species, denominated Enterobacter oryziphilus sp. nov. (type strain REICA_142(T)=LMG 26429(T)=NCCB 100393(T)) and Enterobacter oryzendophyticus sp. nov. (type strain REICA_082(T)=LMG 26432(T) =NCCB 100390(T)) were isolated from rice roots. Both species are capable of promoting rice growth by supplying nitrogen and phosphorus.
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http://dx.doi.org/10.1186/1471-2180-13-164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728145PMC
July 2013

Fungal contribution to nitrous oxide emissions from cattle impacted soils.

Chemosphere 2013 Jan 13;90(2):565-72. Epub 2012 Sep 13.

Biology Centre AS CR, v.v.i., Institute of Soil Biology, Na Sádkách 7, CZ 37005 České Budějovice, Czech Republic.

Microscopic soil fungi isolated from arable, grassland and forest soils have been suggested as producers of nitrous oxide (N(2)O). The aim of this work was to screen the capabilities for N(2)O production of microscopic fungi originating in the pasture soils of a cattle overwintering area with three levels of cattle impact intensity. In total, 36 fungal species from 11 genera were isolated during a 2-year study, and production of N(2)O under laboratory conditions was confirmed in 23 species (64%). Species belonging to the genera Fusarium, Penicillium, Monographella, Acremonium, Gibberella, Eurotium, and Pseudallescheria were found to be the most potent N(2)O-producers. Different N(2)O production patterns and wide variations in production rates, ranging from 1 to 150 μg N(2)O-Nd(-1), were observed, resulting in the transformation of 0.2-18.4% of the initial NO(2)(-)-N present in the cultivation medium. The data revealed distinct soil fungal communities in the different sections of the cattle overwintering area, and indicate a significant effect of cattle overwintering on the composition of soil fungal consortia. These observations confirm the importance of soil fungi in total N(2)O fluxes from grazed grassland ecosystems.
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http://dx.doi.org/10.1016/j.chemosphere.2012.08.031DOI Listing
January 2013

Tetracycline resistance and presence of tetracycline resistance determinants tet(V) and tap in rapidly growing mycobacteria from agricultural soils and clinical isolates.

Microbes Environ 2012 17;27(4):413-22. Epub 2012 May 17.

Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Soil Biology, České Budějovice, Czech Republic.

Rapidly growing mycobacteria (RGM) inhabit soil and water but certain strains represent a health risk for human and animals. Both clinical and soil RGM may be under selection pressure for resistance to tetracycline (TET) antibiotics, since tetracyclines are administrated to humans and farm animals, and TET residues enter soil through manuring; however, resistance to TET and the presence of TET-resistance genes have been assessed only in clinical isolates. We were therefore interested in comparing soil and clinical RGM in terms of TET resistance and the presence of TET-resistance genes. We used 44 RGM from grasslands with different exposure to animal manure, and 38 clinical RGM from Czech hospitals. There was no difference between the clinical and soil isolates in TET resistance, with >50% resistant isolates in both groups. otr(A), otr(B), tet(K), tet(L) or tet(M) were not detected in any soil or clinical isolate. In contrast, most isolates harbored tet(V) and tap, both encoding mycobacterial efflux pumps, including species where these genes have never been evidenced before. The phylogeny of tet(V) correlated with isolates' BOX-PCR profiles, suggesting that this gene evolved along with mycobacterial genomes as a part of the intrinsic resistome. In certain cases, tet(V) and/or tap were found in TET-sensitive isolates, or inversely, were not found in resistant strains. Concluding, intrinsic efflux pumps may be more important for TET resistance than horizontally transferred genes in both soil and clinical RGM. Their simple presence, however, does not attest to resistance, and therefore their diversity, function and expression merit further research.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103549PMC
http://dx.doi.org/10.1264/jsme2.me12028DOI Listing
June 2013

Microbial diversity determines the invasion of soil by a bacterial pathogen.

Proc Natl Acad Sci U S A 2012 Jan 9;109(4):1159-64. Epub 2012 Jan 9.

Department of Microbial Ecology, Center for Evolutionary and Ecological Studies, University of Groningen, 9700 CC, Groningen, The Netherlands.

Natural ecosystems show variable resistance to invasion by alien species, and this resistance can relate to the species diversity in the system. In soil, microorganisms are key components that determine life support functions, but the functional redundancy in the microbiota of most soils has long been thought to overwhelm microbial diversity-function relationships. We here show an inverse relationship between soil microbial diversity and survival of the invading species Escherichia coli O157:H7, assessed by using the marked derivative strain T. The invader's fate in soil was determined in the presence of (i) differentially constructed culturable bacterial communities, and (ii) microbial communities established using a dilution-to-extinction approach. Both approaches revealed a negative correlation between the diversity of the soil microbiota and survival of the invader. The relationship could be explained by a decrease in the competitive ability of the invader in species-rich vs. species-poor bacterial communities, reflected in the amount of resources used and the rate of their consumption. Soil microbial diversity is a key factor that controls the extent to which bacterial invaders can establish.
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http://dx.doi.org/10.1073/pnas.1109326109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268289PMC
January 2012

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

Differences in cold adaptation of Bacillus subtilis under anaerobic and aerobic conditions.

J Bacteriol 2010 Aug 25;192(16):4164-71. Epub 2010 Jun 25.

Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague, Czech Republic.

Bacillus subtilis, which grows under aerobic conditions, employs fatty acid desaturase (Des) to fluidize its membrane when subjected to temperature downshift. Des requires molecular oxygen for its activity, and its expression is regulated by DesK-DesR, a two-component system. Transcription of des is induced by the temperature downshift and is decreased when membrane fluidity is restored. B. subtilis is also capable of anaerobic growth by nitrate or nitrite respiration. We studied the mechanism of cold adaptation in B. subtilis under anaerobic conditions that were predicted to inhibit Des activity. We found that in anaerobiosis, in contrast to aerobic growth, the induction of des expression after temperature downshift (from 37 degrees C to 25 degrees C) was not downregulated. However, the transfer from anaerobic to aerobic conditions rapidly restored the downregulation. Under both aerobic and anaerobic conditions, the induction of des expression was substantially reduced by the addition of external fluidizing oleic acid and was fully dependent on the DesK-DesR two-component regulatory system. Fatty acid analysis proved that there was no desaturation after des induction under anaerobic conditions despite the presence of high levels of the des protein product, which was shown by immunoblot analysis. The cold adaptation of B. subtilis in anaerobiosis is therefore mediated exclusively by the increased anteiso/iso ratio of branched-chain fatty acids and not by the temporarily increased level of unsaturated fatty acids that is typical under aerobic conditions. The degrees of membrane fluidization, as measured by diphenylhexatriene fluorescence anisotropy, were found to be similar under both aerobic and anaerobic conditions.
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http://dx.doi.org/10.1128/JB.00384-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2916416PMC
August 2010

Biodiversity of streptomycetes isolated from a succession sequence at a post-mining site and their evidence in Miocene lacustrine sediment.

Microbiol Res 2010 Sep 16;165(7):594-608. Epub 2009 Dec 16.

Biology Centre of the Academy of Sciences of the Czech Republic, V. V. I.-Institute of Soil Biology, Na Sádkách 7, 37005 Ceské Budejovice, Czech Republic.

The genetic diversity of streptomycetes in colliery spoil heaps (Sokolov, Czech Republic) was investigated by restriction pattern analysis of 16S-internal transcribed spacer rDNA and 16S sequences. We sampled freshly excavated Miocene sediment (17-19-million-year-old) and four sites of primary succession (initial, early, middle, and late stages; aged 1-44 years) on the same sediment. Active bacteria were present even in fresh Miocene sediment, and the relative proportion of actinomycetes among total bacterial and their genetic diversity increased significantly with the age of the sampling site. The replacement of pioneer species by late succession species during succession was observed. Plate assays of Streptomyces strains revealed 27% antibiotic-producing strains. Screening for nonribosomal peptide synthases and type I polyketide synthases systems suggested that 90% and 55% streptomycetes, respectively, are putative producers of biologically active compounds. The frequencies of tetracycline-, amoxicillin-, and chloramphenicol-resistant streptomycetes were 6%, 9%, and 15%, respectively. These findings document the occurrence of genetic elements encoding antibiotic resistance genes and the production of antibiotics by streptomycetes located in pristine environments. Our results indicate key roles for ancient streptomycetes related to S. microflavus, S. spororaveus, and S. flavofuscus in pioneering community development in freshly excavated substrates.
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http://dx.doi.org/10.1016/j.micres.2009.10.002DOI Listing
September 2010

Fungal bioremediation of the creosote-contaminated soil: influence of Pleurotus ostreatus and Irpex lacteus on polycyclic aromatic hydrocarbons removal and soil microbial community composition in the laboratory-scale study.

Chemosphere 2008 Nov 7;73(9):1518-23. Epub 2008 Sep 7.

Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic.

The aim of this study was to determine the efficacy of selected basidiomycetes in the removing of polycyclic aromatic hydrocarbons (PAH) from the creosote-contaminated soil. Fungi Pleurotus ostreatus and Irpex lacteus were supplemented with creosote-contaminated (50-200 mg kg(-1) PAH) soil originating from a wood-preserving plant and incubated at 15 °C for 120 d. Either fungus degraded PAH with 4-6 aromatic rings more efficiently than the microbial community present initially in the soil. PAH removal was higher in P. ostreatus treatments (55-67%) than in I. lacteus treatments (27-36%) in general. P. ostreatus (respectively, I. lacteus) removed 86-96% (47-59%) of 2-rings PAH, 63-72% (33-45%) of 3-rings PAH, 32-49% (9-14%) of 4-rings PAH and 31-38% (11-13%) of 5-6-rings PAH. MIS (Microbial Identification System) Sherlock analysis of the bacterial community determined the presence of dominant Gram-negative bacteria (G-) Pseudomonas in the inoculated soil before the application of fungi. Complex soil microbial community was characterized by phospholipid fatty acids analysis followed by GC-MS/MS. Either fungus induced the decrease of bacterial biomass (G- bacteria in particular), but the soil microbial community was influenced by P. ostreatus in a different way than by I. lacteus. The bacterial community was stressed more by the presence of I. lacteus than P. ostreatus (as proved by the ratio of the fungal/bacterial markers and by the ratio of trans/cis mono-unsaturated fatty acids). Moreover, P. ostreatus stimulated the growth of Gram-positive bacteria (G+), especially actinobacteria and these results indicate the potential of the positive synergistic interaction of this fungus and actinobacteria in creosote biodegradation.
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http://dx.doi.org/10.1016/j.chemosphere.2008.07.030DOI Listing
November 2008

Metabolic control of the membrane fluidity in Bacillus subtilis during cold adaptation.

Biochim Biophys Acta 2008 Feb 4;1778(2):445-53. Epub 2007 Dec 4.

Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicná 5, 128 44 Praha 2, Czech Republic.

Membrane fluidity adaptation to the low growth temperature in Bacillus subtilis involves two distinct mechanisms: (1) long-term adaptation accomplished by increasing the ratio of anteiso- to iso-branched fatty acids and (2) rapid desaturation of fatty acid chains in existing phospholipids by induction of fatty acid desaturase after cold shock. In this work we studied the effect of medium composition on cold adaptation of membrane fluidity. Bacillus subtilis was cultivated at optimum (40 degrees C) and low (20 degrees C) temperatures in complex medium with glucose or in mineral medium with either glucose or glycerol. Cold adaptation was characterized by fatty acid analysis and by measuring the midpoint of phospholipid phase transition T(m) (differential scanning calorimetry) and membrane fluidity (DPH fluorescence polarization). Cells cultured and measured at 40 degrees C displayed the same membrane fluidity in all three media despite a markedly different fatty acid composition. The T(m) was surprisingly the highest in the case of a culture grown in complex medium. On the contrary, cultivation at 20 degrees C in the complex medium gave rise to the highest membrane fluidity with concomitant decrease of T(m) by 10.5 degrees C. In mineral media at 20 degrees C the corresponding changes of T(m) were almost negligible. After a temperature shift from 40 to 20 degrees C, the cultures from all three media displayed the same adaptive induction of fatty acid desaturase despite their different membrane fluidity values immediately after cold shock.
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http://dx.doi.org/10.1016/j.bbamem.2007.11.012DOI Listing
February 2008

Effects of cattle husbandry on abundance and activity of methanogenic archaea in upland soils.

ISME J 2007 Sep 19;1(5):443-52. Epub 2007 Jul 19.

Chair of Soil Ecology, Technical University of Munich, Oberschleissheim, Munich, Germany.

In the present study, we tested the hypothesis that animal treading associated with a high input of organic matter would favour methanogenesis in soils used as overwintering pasture. Hence, methane emissions and methanogen populations were examined at sections with different degree of cattle impact in a Farm in South Bohemia, Czech Republic. In spring, methane emission positively corresponded to the gradient of animal impact. Applying phospholipid etherlipid analysis, the highest archaeal biomass was found in section severe impact (SI), followed by moderate impact (MI) and no impact. The same trend was observed for the methanogens as showed by real-time quantitative PCR analyses of methyl coenzyme M reductase (mcrA) genes. The detection of monounsaturated isoprenoid side chain hydrocarbons (i20:1) indicated the presence of acetoclastic methanogens in the cattle-impacted sites. This result was corroborated by the phylogenetic analysis of mcrA gene sequences obtained from section SI, which showed that 33% of the analysed clones belonged to the genus Methanosarcina. The majority of the sequenced clones (41%) showed close affiliations with uncultured rumen archaeons. This leads to the assumption that a substantial part of the methanogenic community in plot SI derived from the grazing cattle itself. Compared to the spring sampling, in autumn, a significant reduction in archaeal biomass and number of copies of mcrA genes was observed mainly for section MI. It can be concluded that after 5 months without cattle impact, the severely impact section maintained its methane production potential, whereas the methane production potential under moderate impact returned to background values.
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http://dx.doi.org/10.1038/ismej.2007.60DOI Listing
September 2007

Survival of genetically marked Escherichia coli O157:H7 in soil as affected by soil microbial community shifts.

ISME J 2007 Jul 31;1(3):204-14. Epub 2007 May 31.

Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Haren, The Netherlands.

A loamy sand soil sampled from a species-rich permanent grassland at a long-term experimental site (Wildekamp, Bennekom, The Netherlands) was used to construct soil microcosms in which the microbial community compositions had been modified by fumigation at different intensities (depths). As expected, increasing depth of fumigation was shown to result in progressively increasing effects on the microbiological soil parameters, as determined by cultivation-based as well as cultivation-independent (PCR-DGGE, PLFA) methods. Both at 7 and at 60 days after fumigation, shifts in the bacterial, fungal and protozoan communities were noted, indicating that altered community compositions had emerged following a transition phase. At the level of bacteria culturable on plates, an increase of the prevalence of bacterial r-strategists was noted at 7 days followed by a decline at 60 days, which also hinted at the effectiveness of the fumigation treatments. The survival of a non-toxigenic Escherichia coli O157:H7 derivative, strain T, was then assessed over 60 days in these microcosms, using detection via colony forming units counts as well as via PCR-DGGE. Both data sets were consistent with each other. Thus, a clear effect of fumigation depth on the survival of the invading strain T was noted, as a progressive increase of depth coincided with a progressively enhanced inoculant survival rate. As fumigation depth was presumably inversely related to community complexity, this was consistent with the hypothesis that soil systems with reduced biological complexity offer enhanced opportunities for invading microbial species to establish and persist. The significance of this finding is discussed in the light of the ongoing discussion about the complexity-invasiveness relationship within microbial communities, in particular regarding the opportunities of pathogens to persist.
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http://dx.doi.org/10.1038/ismej.2007.21DOI Listing
July 2007

Screening for microbial markers in Miocene sediment exposed during open-cast brown coal mining.

Antonie Van Leeuwenhoek 2006 Apr-May;89(3-4):459-63. Epub 2006 Apr 19.

Institute of Soil Biology, Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, Ceské Budejovice, Czech Republic.

Viable microorganisms were found in Miocene lacustrine clays of the cypris formation excavated from 200-m below the surface as spoil during open-cast brown coal mining (Sokolov Brown Coal Basin, North-Western Bohemia, Czech Republic). Both saprotrophic microfungi of the genera Penicillium, Verticillium, Cladosporium and Aspergillus as well as heterotrophic bacteria were isolated from an intact sediment cores. Heterotrophic bacteria were classified by the MIS Sherlock System as representatives of genera Nocardiopsis, Arthrobacter, Micrococcus, Kocuria, Rothia, Clavibacter, Bacillus, Paenibacillus, Brevibacillus, Microbacterium, Acinetobacter and Pseudomonas. A bacterium found among the strains had an atypical fatty acids profile enriched by branched fatty acids and polyunsaturated fatty acid (18:3 omega 6) and gave no MIS Sherlock match. Phospholipid fatty acids analysis indicates a relatively high (535 pmol g(-1)) but inhomogeneously distributed viable microbial biomass. Fatty acids analyses of non-fractioned lipids (representing viable, storage and dead biomass; 8390 pmol g(-1)) detected rich and homogenous profiles with fungal, bacterial and actinomycetal markers but no protozoan and algal fatty acids markers.
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http://dx.doi.org/10.1007/s10482-005-9044-8DOI Listing
August 2006