Publications by authors named "Joseph Nesme"

25 Publications

  • Page 1 of 1

Kin discrimination promotes horizontal gene transfer between unrelated strains in Bacillus subtilis.

Nat Commun 2021 06 8;12(1):3457. Epub 2021 Jun 8.

Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.

Bacillus subtilis is a soil bacterium that is competent for natural transformation. Genetically distinct B. subtilis swarms form a boundary upon encounter, resulting in killing of one of the strains. This process is mediated by a fast-evolving kin discrimination (KD) system consisting of cellular attack and defence mechanisms. Here, we show that these swarm antagonisms promote transformation-mediated horizontal gene transfer between strains of low relatedness. Gene transfer between interacting non-kin strains is largely unidirectional, from killed cells of the donor strain to surviving cells of the recipient strain. It is associated with activation of a stress response mediated by sigma factor SigW in the donor cells, and induction of competence in the recipient strain. More closely related strains, which in theory would experience more efficient recombination due to increased sequence homology, do not upregulate transformation upon encounter. This result indicates that social interactions can override mechanistic barriers to horizontal gene transfer. We hypothesize that KD-mediated competence in response to the encounter of distinct neighbouring strains could maximize the probability of efficient incorporation of novel alleles and genes that have proved to function in a genomically and ecologically similar context.
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http://dx.doi.org/10.1038/s41467-021-23685-wDOI Listing
June 2021

Extended-Spectrum β-Lactamase and Carbapenemase Genes are Substantially and Sequentially Reduced during Conveyance and Treatment of Urban Sewage.

Environ Sci Technol 2021 05 22;55(9):5939-5949. Epub 2021 Apr 22.

Department of Environmental Engineering, Technical University of Denmark, Lyngby 2800, DK.

Urban wastewater systems (UWSs) are a main receptacle of excreted antibiotic resistance genes (ARGs) and their host microorganisms. However, we lack integrated and quantitative observations of the occurrence of ARGs in the UWS to characterize the sources and identify processes that contribute to their fate. We sampled the UWSs from three medium-size cities in Denmark, Spain, and the United Kingdom and quantified 70 clinically important extended-spectrum β-lactamase and carbapenemase genes along with the mobile genetic elements and microbial communities. Results from all three countries showed that sewage-especially from hospitals-carried substantial loads of ARGs (10-10 copies per person equivalent), but these loads progressively declined along sewers and through sewage treatment plants, resulting in minimal emissions (10-10 copies per person equivalent). Removal was primarily during sewage conveyance (65 ± 36%) rather than within sewage treatment (34 ± 23%). The extended-spectrum β-lactamase and carbapenemase genes were clustered in groups based on their persistence in the UWS compartments. The less-persistent groups were associated to putative host taxa (especially Enterobacteriaceae and Moraxellaceae), while the more persistent groups appeared horizontally transferred and correlated significantly with total cell numbers and mobile genetic elements. This documentation of a substantial ARG reduction during sewage conveyance provides opportunities for antibiotic resistance management and a caution for sewage-based antibiotic resistance surveillance.
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http://dx.doi.org/10.1021/acs.est.0c08548DOI Listing
May 2021

Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture.

Microorganisms 2021 Feb 19;9(2). Epub 2021 Feb 19.

Department for Sustainability, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, 00123 Rome, Italy.

A growing body of evidence demonstrates the potential of various microbes to enhance plant productivity in cropping systems although their successful field application may be impaired by several biotic and abiotic constraints. In the present work, we aimed at developing multifunctional synthetic microbial consortia to be used in combination with suitable bioactive compounds for improving crop yield and quality. Plant growth-promoting microorganisms (PGPMs) with different functional attributes were identified by a bottom-up approach. A comprehensive literature survey on PGPMs associated with maize, wheat, potato and tomato, and on commercial formulations, was conducted by examining peer-reviewed scientific publications and results from relevant European projects. Metagenome fragment recruitments on genomes of potential PGPMs represented in databases were also performed to help identify plant growth-promoting (PGP) strains. Following evidence of their ability to coexist, isolated PGPMs were synthetically assembled into three different microbial consortia. Additionally, the effects of bioactive compounds on the growth of individually PGPMs were tested in starvation conditions. The different combination products based on microbial and non-microbial biostimulants (BS) appear worth considering for greenhouse and open field trials to select those potentially adoptable in sustainable agriculture.
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http://dx.doi.org/10.3390/microorganisms9020426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7922931PMC
February 2021

Root exposure to apple replant disease soil triggers local defense response and rhizoplane microbiome dysbiosis.

FEMS Microbiol Ecol 2021 03;97(4)

Julius Kühn-Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany.

A soil column split-root experiment was designed to investigate the ability of apple replant disease (ARD)-causing agents to spread in soil. 'M26' apple rootstocks grew into a top layer of Control soil, followed by a barrier-free split-soil layer (Control soil/ARD soil). We observed a severely reduced root growth, concomitant with enhanced gene expression of phytoalexin biosynthetic genes and phytoalexin content in roots from ARD soil, indicating a pronounced local plant defense response. Amplicon sequencing (bacteria, archaea, fungi) revealed local shifts in diversity and composition of microorganisms in the rhizoplane of roots from ARD soil. An enrichment of operational taxonomic units affiliated to potential ARD fungal pathogens (Ilyonectria and Nectria sp.) and bacteria frequently associated with ARD (Streptomyces, Variovorax) was noted. In conclusion, our integrated study supports the idea of ARD being local and not spreading into surrounding soil, as only the roots in ARD soil were affected in terms of growth, phytoalexin biosynthetic gene expression, phytoalexin production and altered microbiome structure. This study further reinforces the microbiological nature of ARD, being likely triggered by a disturbed soil microbiome enriched with low mobility of the ARD-causing agents that induce a strong plant defense and rhizoplane microbiome dysbiosis, concurring with root damage.
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http://dx.doi.org/10.1093/femsec/fiab031DOI Listing
March 2021

Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories.

FEMS Microbiol Ecol 2021 03;97(4)

Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany.

A better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions in soils of a long-term field experiment with contrasting histories of tillage (mouldboard plough vs cultivator tillage), fertilization intensity (intensive standard nitrogen (N) + pesticides/growth regulators vs extensive reduced N without fungicides/growth regulators), and last standing field crop (rapeseed vs winter wheat). High-throughput sequencing of bacterial and archaeal 16S rRNA genes and fungal ITS2 regions amplified from total community DNA showed that these factors shaped the soil and rhizosphere microbiota of lettuce, however, to different extents among the microbial domains. Pseudomonas and Olpidium were identified as major indicators for agricultural management in the rhizosphere of lettuce. Long-term extensive fertilization history of soils resulted in higher lettuce growth and increased expression of genes involved in plant stress responses compared to intensive fertilization. Our work adds to the increasing knowledge on how soil microbiota can be manipulated by agricultural management practices which could be harnessed for sustainable crop production.
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http://dx.doi.org/10.1093/femsec/fiab027DOI Listing
March 2021

Reduced tillage, cover crops and organic amendments affect soil microbiota and improve soil health in Uruguayan vegetable farming systems.

FEMS Microbiol Ecol 2021 03;97(3)

Instituto Nacional de Investigación Agropecuaria (INIA), Programa de Producción y Sustentabilidad Ambiental, Estación Experimental INIA Las Brujas, Ruta 48 Km 10, 90200 Rincón del Colorado, Canelones, Uruguay.

Conventional tillage and mineral fertilization (CTMF) jeopardize soil health in conventional vegetable production systems. Using a field experiment established in Uruguay in 2012, we aimed to compare the soil restoration potential of organic fertilization (compost and poultry manure) combined with conventional tillage and cover crop incorporated into the soil (CTOF) or with reduced tillage and the use of cover crop as mulch (RTOF). In 2017, table beet was cultivated under CTMF, CTOF and RTOF, and yields, soil aggregate composition and nutrients, as well as soil and table beet rhizosphere microbiota (here: bacteria and archaea) were evaluated. Microbiota was studied by high-throughput sequencing of 16S rRNA gene fragments amplified from total community DNA. RTOF exhibited higher soil aggregation, soil organic C, nutrient availability and microbial alpha-diversity than CTMF, and became more similar to an adjacent natural undisturbed site. The soil microbiota was strongly shaped by the fertilization source which was conveyed to the rhizosphere and resulted in differentially abundant taxa. However, 229 amplicon sequencing variants were found to form the core table beet rhizosphere microbiota shared among managements. In conclusion, our study shows that after only 5 years of implementation, RTOF improves soil health under intensive vegetable farming systems.
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http://dx.doi.org/10.1093/femsec/fiab023DOI Listing
March 2021

Impact of Long-Term Organic and Mineral Fertilization on Rhizosphere Metabolites, Root-Microbial Interactions and Plant Health of Lettuce.

Front Microbiol 2020 13;11:597745. Epub 2021 Jan 13.

Department of Nutritional Crop Physiology, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany.

Fertilization management can affect plant performance and soil microbiota, involving still poorly understood rhizosphere interactions. We hypothesized that fertilization practice exerts specific effects on rhizodeposition with consequences for recruitment of rhizosphere microbiota and plant performance. To address this hypothesis, we conducted a minirhizotron experiment using lettuce as model plant and field soils with contrasting properties from two long-term field experiments (HUB-LTE: loamy sand, DOK-LTE: silty loam) with organic and mineral fertilization history. Increased relative abundance of plant-beneficial arbuscular mycorrhizal fungi and fungal pathotrophs were characteristic of the rhizospheres in the organically managed soils (HU-org; BIODYN2). Accordingly, defense-related genes were systemically expressed in shoot tissues of the respective plants. As a site-specific effect, high relative occurrence of the fungal lettuce pathogen sp. (76-90%) was recorded in the rhizosphere, both under long-term organic and mineral fertilization at the DOK-LTE site, likely supporting infection due to a lower water drainage potential compared to the sandy HUB-LTE soils. However, plant growth depressions and infection were exclusively recorded in the BIODYN2 soil with organic fertilization history. This was associated with a drastic (87-97%) reduction in rhizosphere abundance of potentially plant-beneficial microbiota (, ) and reduced concentrations of the antifungal root exudate benzoate, known to be increased in presence of spp. In contrast, high relative abundance of (Gammaproteobacteria) in the rhizosphere of plants grown in soils with long-term mineral fertilization (61-74%) coincided with high rhizosphere concentrations of chemotactic dicarboxylates (succinate, malate) and a high C (sugar)/N (amino acid) ratio, known to support the growth of Gammaproteobacteria. This was related with generally lower systemic expression of plant defense genes as compared with organic fertilization history. Our results suggest a complex network of belowground interactions among root exudates, site-specific factors and rhizosphere microbiota, modulating the impact of fertilization management with consequences for plant health and performance.
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http://dx.doi.org/10.3389/fmicb.2020.597745DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7838544PMC
January 2021

Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles.

ISME J 2021 04 6;15(4):1207-1221. Epub 2021 Jan 6.

Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.

Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.
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http://dx.doi.org/10.1038/s41396-020-00844-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8115648PMC
April 2021

Metagenomic analysis of a keratin-degrading bacterial consortium provides insight into the keratinolytic mechanisms.

Sci Total Environ 2021 Mar 29;761:143281. Epub 2020 Oct 29.

Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark. Electronic address:

Keratin is an insoluble fibrous protein from natural environments, which can be recycled to value-added products by keratinolytic microorganisms. A microbial consortium with efficient keratinolytic activity was previously enriched from soil, but the genetic basis behind its remarkable degradation properties was not investigated yet. To identify the metabolic pathways involved in keratinolysis and clarify the observed synergy among community members, shotgun metagenomic sequencing was performed to reconstruct metagenome-assembled genomes. More than 90% genera of the enriched bacterial consortium were affiliated to Chryseobacterium, Stenotrophomonas, and Pseudomonas. Metabolic potential and putative keratinases were predicted from the metagenomic annotation, providing the genetic basis of keratin degradation. Furthermore, metabolic pathways associated with keratinolytic processes such as amino acid metabolism, disulfide reduction and urea cycle were investigated from seven high-quality metagenome-assembled genomes, revealing the potential metabolic cooperation related to keratin degradation. This knowledge deepens the understanding of microbial keratinolytic mechanisms at play in a complex community, pinpointing the significance of synergistic interactions, which could be further used to optimize industrial keratin degradation processes.
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http://dx.doi.org/10.1016/j.scitotenv.2020.143281DOI Listing
March 2021

Comparison of antibiotic-resistant bacteria and antibiotic resistance genes abundance in hospital and community wastewater: A systematic review.

Sci Total Environ 2020 Nov 11;743:140804. Epub 2020 Jul 11.

Infectious Diseases Institute, Rambam Health Care Campus, Haifa, Israel, HaAliya HaShniya St 8, Haifa 3109601, Israel; The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Efron St 1, Haifa 3109601, Israel.

Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) are constantly shed into the aquatic environment, with hospital wastewater potentially acting as an important source for resistance spread into the environment. A systematic review was conducted aiming to investigate the role of hospital wastewater on dissemination of antimicrobial resistance in the aquatic environment. Studies included in the review compared the prevalence of ARB and/or ARGs in hospital versus community wastewater. Data were extracted on ARB and/or ARG prevalence. Data on sampling techniques, microbiological methodology and risk of bias of included studies were recorded. Thirty-seven studies were included. Higher frequencies of antibiotic resistance determinants were found in hospital wastewater compared to community sources in 30/37 (81%) of included studies. However, trends for specific multi-drug-resistant bacteria differed. Antibiotic-resistant Gram-negative were more prevalent in hospital compared to community wastewaters, with higher concentrations of extended-spectrum-beta-lactamase-producing pathogens and carbapenemase-producing Enterobacteriaceae in hospital sources in 9/9 studies and 6/7 studies, respectively. Hospitals did not contribute consistently to the abundance of vancomycin-resistant Enterococci (VRE); 5/10 studies found higher abundance of VRE in hospital compared to community wastewaters. Reporting on sampling methods, wastewater treatment processes and statistical analysis were at high risk of bias. Extreme heterogeneity in study methods and outcome reporting precluded meta-analysis. Current evidence concurs that hospital wastewater is an important source for antibiotic resistance in aquatic environments, mainly multidrug-resistant Gram-negative bacteria. Future research is needed to assess the effect of wastewater treatment processes on overall antibiotic resistance in the aquatic environment.
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http://dx.doi.org/10.1016/j.scitotenv.2020.140804DOI Listing
November 2020

Composted Sewage Sludge Influences the Microbiome and Persistence of Human Pathogens in Soil.

Microorganisms 2020 Jul 9;8(7). Epub 2020 Jul 9.

Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany.

Composted sewage sludge (CSS) gained attention as a potential fertilizer in agriculture. Application of CSS increases soil microbial activity and microbial biomass, however, it can also lead to increased chemical and microbiological risks. In this study, we performed microcosm experiments to assess how CSS reshapes the microbial community of diluvial sand (DS) soil. Further, we assessed the potential of CSS to increase the persistence of human pathogens in DS soil and the colonization of Chinese cabbage ( L. subsp (Lour.) Hanelt). The results revealed that CSS substantially altered the prokaryotic community composition. Moreover, addition of CSS increased the persistence of serovar Typhimurium strain 14028s and serovar Senftenberg in DS soil. However, the enhanced persistence in soil had no impact on the colonization rate of grown on soil inoculated with . We detected in leaves of 1.9% to 3.6% of plants. Addition of CSS had no impact on the plant colonization rate. The use of sewage sludge composts is an interesting option. However, safety measures should be applied in order to avoid contamination of crop plants by human pathogens.
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http://dx.doi.org/10.3390/microorganisms8071020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7409118PMC
July 2020

Metal-induced bacterial interactions promote diversity in river-sediment microbiomes.

FEMS Microbiol Ecol 2020 06;96(6)

Proteomics and Microbiology Laboratory, Research Institute for Biosciences, UMONS, 20 Place du Parc, 7000 Mons, Belgium.

Anthropogenic metal contamination results in long-term environmental selective pressure with unclear impacts on bacterial communities, which comprise key players in ecosystem functioning. Since metal contamination poses serious toxicity and bioaccumulation issues, assessing their impact on environmental microbiomes is important to respond to current environmental and health issues. Despite elevated metal concentrations, the river sedimentary microbiome near the MetalEurop foundry (France) shows unexpected higher diversity compared with the upstream control site. In this work, a follow-up of the microbial community assembly during a metal contamination event was performed in microcosms with periodic renewal of the supernatant river water. Sediments of the control site were gradually exposed to a mixture of metals (Cd, Cu, Pb and Zn) in order to reach similar concentrations to MetalEurop sediments. Illumina sequencing of 16S rRNA gene amplicons was performed. Metal-resistant genes, czcA and pbrA, as well as IncP plasmid content, were assessed by quantitative PCR. The outcomes of this study support previous in situ observations showing that metals act as community assembly managers, increasing diversity. This work revealed progressive adaptation of the sediment microbiome through the selection of different metal-resistant mechanisms and cross-species interactions involving public good-providing bacteria co-occurring with the rest of the community.
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http://dx.doi.org/10.1093/femsec/fiaa076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7781699PMC
June 2020

Salmonella persistence in soil depends on reciprocal interactions with indigenous microorganisms.

Environ Microbiol 2020 07 12;22(7):2639-2652. Epub 2020 Mar 12.

Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany.

Fresh fruits and vegetables have numerous benefits to human health. Unfortunately, their consumption is increasingly associated with food-borne diseases, Salmonella enterica being their most frequent cause in Europe. Agricultural soils were postulated as reservoir of human pathogens, contributing to the contamination of crops during the growing period. Since the competition with the indigenous soil microbiota for colonization sites plays a major role in the success of invading species, we hypothesized that reduced diversity will enhance the chance of Salmonella to successfully establish in agricultural environments. We demonstrated that the abundance of Salmonella drastically decreased in soil with highly diverse indigenous prokaryotic community, while in soil with reduced prokaryotic diversity, Salmonella persisted for a long period. Furthermore, in communities with low diversity, Salmonella had an impact on the abundance of other taxa. The high physiological plasticity allows Salmonella to use agricultural soils as alternative habitat which might provide a route of animal/human infections. In addition, adjusted transcriptional profile with amino acid biosynthesis and the glyoxylate cycle most prominently regulated, suggests an adaptation to the soil environment. Our results underline the importance of the maintenance of diverse soil microbiome as a part of strategy aiming at reduced risk of food-borne salmonellosis outbreaks.
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http://dx.doi.org/10.1111/1462-2920.14972DOI Listing
July 2020

Plasmids persist in a microbial community by providing fitness benefit to multiple phylotypes.

ISME J 2020 05 4;14(5):1170-1181. Epub 2020 Feb 4.

Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.

The current epidemic of antibiotic resistance has been facilitated by the wide and rapid horizontal dissemination of antibiotic resistance genes (ARGs) in microbial communities. Indeed, ARGs are often located on plasmids, which can efficiently shuttle genes across diverse taxa. While the existence conditions of plasmids have been extensively studied in a few model bacterial populations, their fate in complex bacterial communities is poorly understood. Here, we coupled plasmid transfer assays with serial growth experiments to investigate the persistence of the broad-host-range IncP-1 plasmid pKJK5 in microbial communities derived from a sewage treatment plant. The cultivation conditions combined different nutrient and oxygen levels, and were non-selective and non-conducive for liquid-phase conjugal transfer. Following initial transfer, the plasmid persisted in almost all conditions during a 10-day serial growth experiment (equivalent to 60 generations), with a transient transconjugant incidence up to 30%. By combining cell enumeration and sorting with amplicon sequencing, we mapped plasmid fitness effects across taxa of the microbial community. Unexpected plasmid fitness benefits were observed in multiple phylotypes of Aeromonas, Enterobacteriaceae, and Pseudomonas, which resulted in community-level plasmid persistence. We demonstrate, for the first time, that plasmid fitness effects across community members can be estimated in high-throughput without prior isolation. By gaining a fitness benefit when carrying plasmids, members within complex microbial communities might have a hitherto unrecognised potential to maintain plasmids for long-term community-wide access.
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http://dx.doi.org/10.1038/s41396-020-0596-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7174300PMC
May 2020

Construction of Simplified Microbial Consortia to Degrade Recalcitrant Materials Based on Enrichment and Dilution-to-Extinction Cultures.

Front Microbiol 2019 10;10:3010. Epub 2020 Jan 10.

Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.

The capacity of microbes to degrade recalcitrant materials has been extensively explored for environmental remediation and industrial production. Significant achievements have been made with single strains, but focus is now going toward the use of microbial consortia owning to their functional stability and efficiency. However, assembly of simplified microbial consortia (SMC) from complex environmental communities is still far from trivial due to large diversity and the effect of biotic interactions. Here we propose a strategy, based on enrichment and dilution-to-extinction cultures, to construct SMC with reduced diversity for degradation of keratinous materials. Serial dilutions were performed on a keratinolytic microbial consortium pre-enriched from a soil sample, monitoring the dilution effect on community growth and enzymatic activities. An appropriate dilution regime (10) was selected to construct a SMC library from the enriched microbial consortium. Further sequencing analysis and keratinolytic activity assays demonstrated that obtained SMC displayed actual reduced microbial diversity, together with various taxonomic composition, and biodegradation capabilities. More importantly, several SMC possessed equivalent levels of keratinolytic efficiency compared to the initial consortium, showing that simplification can be achieved without loss of function and efficiency. This methodology is also applicable to other types of recalcitrant material degradation involving microbial consortia, thus considerably broadening its application scope.
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http://dx.doi.org/10.3389/fmicb.2019.03010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6968696PMC
January 2020

Changes induced by heavy metals in the plant-associated microbiome of Miscanthus x giganteus.

Sci Total Environ 2020 Apr 13;711:134433. Epub 2019 Sep 13.

Helmholtz Zentrum München, Research Unit Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Technical University of Munich, Chair for Soil Ecology, Emil-Ramann-Straße 2, 85354 Freising, Germany. Electronic address:

Miscanthus x giganteus is a high biomass producing plant with tolerance to heavy metals. This makes Miscanthus interesting to be used for phytoremediation of heavy metal contaminated areas coupled with energy production. Since plant performance in metal polluted areas is impaired, their growth and phytoremediation effect can be improved with bacterial assistance. To identify positive and negative responders of M. x giganteus associated microbiome influenced by Cd, Pb and Zn stress compared to non-contaminated controls, we designed a greenhouse experiment. Structure of the bacterial community in three rhizocompartments, namely rhizosphere, rhizoplane and root endosphere was analysed using an isolation independent molecular approach based on 16S rRNA gene barcoding. Furthermore, quantitative PCR (qPCR) was used for bacterial biomass estimation. Our results indicated that biomass and total bacterial diversity in rhizosphere, rhizoplane and root endosphere did not significantly change despite of substantial root uptake of heavy metals. Overall, we detected 6621 OTUs, from which 171 were affected by metal addition. Whereas Streptomyces and Amycolatopsis taxa were negatively affected by the heavy metal treatment in endosphere, taxa assigned to Luteolibacter in rhizosphere and rhizoplane (log fold change 1.9-4.1) and Micromonospora in endosphere (log fold change 10.2) were found to be significantly enriched and highly abundant (0.1-3.7% relative abundance) under heavy metal stress. Those taxa might be of key importance for M. x giganteus performance under heavy metal pollution and might be interesting candidates for the development of new bioinocula in the future to promote plant growth and phytoremediation in heavy metal contaminated soils.
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http://dx.doi.org/10.1016/j.scitotenv.2019.134433DOI Listing
April 2020

Characterization of Extracellular Biosurfactants Expressed by a Pseudomonas putida Strain Isolated from the Interior of Healthy Roots from Sida hermaphrodita Grown in a Heavy Metal Contaminated Soil.

Curr Microbiol 2019 Nov 20;76(11):1320-1329. Epub 2019 Aug 20.

Institute for Ecology of Industrial Areas, Unit of Environmental Microbiology, Kossutha 6, 40-844, Katowice, Poland.

Pseudomonas putida E41 isolated from root interior of Sida hermaphrodita (grown on a field contaminated with heavy metals) showed high biosurfactant activity. In this paper, we describe data from mass spectrometry and genome analysis, to improve our understanding on the phenotypic properties of the strain. Supernatant derived from P. putida E41 liquid culture exhibited a strong decrease in the surface tension accompanied by the ability for emulsion stabilization. We identified extracellular lipopeptides, putisolvin I and II expression but did not detect rhamnolipids. Their presence was confirmed by matrix-assisted laser desorption and ionization (MALDI) TOF/TOF technique. Moreover, ten phospholipids (mainly phosphatidylethanolamines PE 33:1 and PE 32:1) which were excreted by vesicles were also detected. In contrast the bacterial cell pellet was dominated by phosphatidylglycerols (PGs), which were almost absent in the supernatant. It seems that the composition of extracellular (secreted to the environment) and cellular lipids in this strain differs. Long-read sequencing and complete genome reconstruction allowed the identification of a complete putisolvin biosynthesis pathway. In the genome of P. putida E41 were also found all genes involved in glycerophospholipid biosynthesis, and they are likely responsible for the production of detected phospholipids. Overall this is the first report describing the expression of extracellular lipopeptides (identified as putisolvins) and phospholipids by a P. putida strain, which might be explained by the need to adapt to the highly contaminated environment.
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http://dx.doi.org/10.1007/s00284-019-01757-xDOI Listing
November 2019

Improvement of pesticide removal in contaminated media using aqueous extracts from contaminated biopurification systems.

Sci Total Environ 2019 Nov 7;691:749-759. Epub 2019 Jul 7.

Department of Environmental Protection, Estación Experimental del Zaidín. Consejo Superior de Investigaciones Científicas (EEZ-CSIC), C/ Profesor Albareda 1, 18008 Granada, Spain. Electronic address:

Despite certain limitations, bioaugmentation enhances the efficiency of bioremediation systems. In this study, three aqueous extracts (APE, ACE and APE) from aged residual biomixtures in three biopurification systems (BPSs) exposed to pesticides at a pilot scale were found to improve pesticide removal. The addition of ACEs and AVEs to solutions containing the model compound diuron increased removal rates 6- and 17-fold, respectively, as compared to APEs. These extracts also increased the removal of the metabolite 3,4-dichloroaniline, while AVEs, in particular, were found to remove all pesticides within 9 days. Three metabolites less hazardous than 3,4-dichloroaniline were identified by SPME/GC/MS. AVEs, which also enhance linuron removal in liquid media, were found to increase diuron removal 6-fold in BPSs. We observed an increase in the relative abundance of taxa, such as Chloroflexi, Acidobacteria, Gemmatimonadetes, Firmicutes, Deinococcus-Thermus and especially Proteobacteria (10%), in AV biomixtures, as well as an enrichment of γ-proteobacteria and the actinobacterial genus Dokdonella in AVEs with respect to initial noncontaminated IV biomixture. We demonstrate that extracts containing a pollutant-acclimatized microbiome could be used as part of a bioaugmentation strategy to improve the functioning of on-farm BPSs and contaminated systems.
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http://dx.doi.org/10.1016/j.scitotenv.2019.07.087DOI Listing
November 2019

Fate of CMY-2-Encoding Plasmids Introduced into the Human Fecal Microbiota by Exogenous .

Antimicrob Agents Chemother 2019 05 25;63(5). Epub 2019 Apr 25.

Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, Hertfordshire, United Kingdom

The gut is a hot spot for transfer of antibiotic resistance genes from ingested exogenous bacteria to the indigenous microbiota. The objective of this study was to determine the fate of two nearly identical -harboring plasmids introduced into the human fecal microbiota by two strains isolated from a human and from poultry meat. The chromosome and the CMY-2-encoding plasmid of both strains were labeled with distinct fluorescent markers (mCherry and green fluorescent protein [GFP]), allowing fluorescence-activated cell sorting (FACS)-based tracking of the strain and the resident bacteria that have acquired its plasmid. Each strain was introduced into an established gut model (CoMiniGut) inoculated with individual feces from ten healthy volunteers. Fecal samples collected 2, 6, and 24 h after strain inoculation were analyzed by FACS and plate counts. Although the human strain survived better than the poultry meat strain, both strains transferred their plasmids to the fecal microbiota at concentrations as low as 10 CFU/ml. Strain survival and plasmid transfer varied significantly depending on inoculum concentration and individual fecal microbiota. Identification of transconjugants by 16S rRNA gene sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) revealed that the plasmids were predominantly acquired by species, such as and Our experimental data demonstrate that exogenous of human or animal origin can readily transfer CMY-2-encoding IncI1 plasmids to the human fecal microbiota. Small amounts of the exogenous strain are sufficient to ensure plasmid transfer if the strain is able to survive the gastric environment.
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http://dx.doi.org/10.1128/AAC.02528-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6496067PMC
May 2019

Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus.

Microbiome 2019 02 18;7(1):24. Epub 2019 Feb 18.

Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, 85764, Germany.

Background: Aquaculture is on the rise worldwide, and the use of antibiotics is fostering higher production intensity. However, recent findings suggest that the use of antibiotics comes at the price of increased antibiotic resistance. Yet, the effect of the oral administration of antibiotics on the mobility of microbial resistance genes in the fish gut is not well understood. In the present study, Piaractus mesopotamicus was used as a model to evaluate the effect of the antimicrobial florfenicol on the diversity of the gut microbiome as well as antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) using a metagenomic approach.

Results: The total relative abundance of ARGs and MGEs significantly increased during the antibiotic exposure. Additionally, phage integrases, transposases, and transposons flanking ARGs accumulated in the gut microbiome of P. mesopotamicus because of the antibiotic exposure. MGEs co-occurring with ARGs showed a significant positive correlation with the total ARGs found. Furthermore, shifts in the gut microbiome towards well-known putative pathogens such as Salmonella, Plesiomonas, and Citrobacter were observed following florfenicol treatment. Mainly Plesiomonas and Citrobacter harbored genes that code for multidrug and phenicol efflux pumps. Moreover, several genes related to RNA processing and modification, cell motility, SOS response, and extracellular structure were enriched due to the antibiotic application. The observed effects were visible during the complete application phase and disappeared at the post-exposure phase.

Conclusions: Our findings suggest that the oral administration of antibiotics increases the potential for MGE-mediated exchange of ARGs in the gut of fish and could contribute to the enrichment and dispersion of ARGs in aquaculture systems. Importantly, this increase in the potential for ARGs exchange could be an effect of changes in community structure and/or ARG mobilization.
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http://dx.doi.org/10.1186/s40168-019-0632-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6378726PMC
February 2019

Complete Genome Sequences of Two Plant-Associated Isolates with Increased Heavy-Metal Tolerance.

Genome Announc 2017 Nov 22;5(47). Epub 2017 Nov 22.

Research Unit for Comparative Microbiome Analysis, Department of Environmental Sciences, Helmholtz Zentrum München, Neuherberg, Germany.

We report here the complete genome sequences of two isolates recovered from surface-sterilized roots of The two isolates were characterized by an increased tolerance to zinc, cadmium, and lead. Furthermore, the strains showed typical plant growth-promoting properties, such as the production of indole acetic acid, cellulolytic enzymes, and siderophores.
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http://dx.doi.org/10.1128/genomeA.01330-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5701480PMC
November 2017

The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria.

Environ Microbiol 2015 Apr 17;17(4):913-30. Epub 2014 Dec 17.

Environmental Microbial Genomics, Bioengineering Departement, Laboratoire Ampère, CNRS UMR5005, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, Ecully, 69134, France.

Soil is a large reservoir of microbial diversity and the majority of antimicrobial compounds used today in human and veterinary health care have been isolated from soil microorganisms. The Darwinian hypothesis of an 'arms-shields race' between antibiotic producers and resistant strains is often cited to explain antibiotic resistance gene determinants (ARGD) origins and diversity. ARGD abundance and antibiotic molecule exposure are, however, not systematically linked, and many other factors can contribute to resistance gene emergence, selection and dissemination in the environment. Soil is a heterogeneous habitat and represents a broad spectrum of different ecological niches. Soil harbours a large genetic diversity at small spatial scale, favouring exchange of genetic materials by means of horizontal gene transfer (HGT) that will contribute to ARGD dissemination between bacteria and eventually acquisition by pathogen genomes, therefore threatening antibiotic therapies. Our current knowledge on the extent of the soil resistome abundance and diversity has been greatly enhanced since the metagenomic revolution and help of high-throughput sequencing technologies. Different ecological hypotheses explaining their high prevalence in soil and questioning their transfer rate to pathogens, in respect to these recent experimental results, will be discussed in the present review.
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http://dx.doi.org/10.1111/1462-2920.12631DOI Listing
April 2015

Large-scale metagenomic-based study of antibiotic resistance in the environment.

Curr Biol 2014 May 8;24(10):1096-100. Epub 2014 May 8.

Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France. Electronic address:

Antibiotic resistance, including multiresistance acquisition and dissemination by pathogens, is a critical healthcare issue threatening our management of infectious diseases [1-3]. Rapid accumulation of resistance phenotypes implies a reservoir of transferable antibiotic resistance gene determinants (ARGDs) selected in response to inhibition of antibiotic concentrations, as found in hospitals [1, 3-5]. Antibiotic resistance genes were found in environmental isolates, soil DNA [4-6], secluded caves [6, 7], and permafrost DNA [7, 8]. Antibiotics target essential and ubiquitous cell functions, and resistance is a common characteristic of environmental bacteria [8-11]. Environmental ARGDs are an abundant reservoir of potentially transferable resistance for pathogens [9-12]. Using metagenomic sequences, we show that ARGDs can be detected in all (n=71) environments analyzed. Soil metagenomes had the most diverse pool of ARGDs. The most common types of resistances found in environmental metagenomes were efflux pumps and genes conferring resistance to vancomycin, tetracycline, or β-lactam antibiotics used in veterinary and human healthcare. Our study describes the diverse and abundant antibiotic resistance genes in nonclinical environments and shows that these genes are not randomly distributed among different environments (e.g., soil, oceans or human feces).
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http://dx.doi.org/10.1016/j.cub.2014.03.036DOI Listing
May 2014

Fate of invading bacteria in soil and survival of transformants after simulated uptake of transgenes, as evaluated by a model system based on lindane degradation.

Res Microbiol 2012 Apr 10;163(3):200-10. Epub 2012 Feb 10.

Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Box 5003, N-1432 Ås, Norway.

Emergence of bacteria carrying new traits resulting from mutations, gene synthesis by gene-shuffling or acquisition of exogenous DNA underpins the need to better understand factors influencing their spread and establishment. Studies of soils may be difficult, since the gene of interest is often already present in high numbers. The gene linA, responsible for the first dechlorination steps during degradation of lindane (γ-hexachlorocyclohexane), has low background levels in soil and is simple to detect. Development of transgenic plants containing linA and newly proposed approaches to bioremediation by in situ electrotransformation after addition of a vector carrying this gene call for documentation on the fate of bacteria that incorporate it. We inserted linA into the broad-host-range conjugative RP4-plasmid and transferred it to different soil bacteria which were inoculated into soil microcosms in the presence/absence of lindane. Similar experiments were performed using Sphingobium francense Sp+, which carries all genes for complete lindane degradation. This strain increased in numbers during lindane mineralization, but other bacteria increased more, resulting in a modified bacterial community structure. The engineered strains decreased below the detection limit, but rose in numbers after nutrient addition, demonstrating that new invading bacteria may persist in soil in the form of small populations over extended time periods.
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http://dx.doi.org/10.1016/j.resmic.2012.01.007DOI Listing
April 2012