Publications by authors named "Kornelia Smalla"

182 Publications

Editorial to the Thematic Topic "Towards a more sustainable agriculture through managing soil microbiomes".

FEMS Microbiol Ecol 2021 07;97(8)

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

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http://dx.doi.org/10.1093/femsec/fiab094DOI Listing
July 2021

Microbiome Modulation-Toward a Better Understanding of Plant Microbiome Response to Microbial Inoculants.

Front Microbiol 2021 8;12:650610. Epub 2021 Apr 8.

Julius Kühn Institute (JKI) Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany.

Plant-associated microorganisms are involved in important functions related to growth, performance and health of their hosts. Understanding their modes of action is important for the design of promising microbial inoculants for sustainable agriculture. Plant-associated microorganisms are able to interact with their hosts and often exert specific functions toward potential pathogens; the underlying interactions are well studied. In contrast, effects of inoculants, and especially their impact on the plant indigenous microbiome was mostly neglected so far. Recently, microbiome research has revolutionized our understanding of plants as coevolved holobionts but also of indigenous microbiome-inoculant interactions. Here we disentangle the effects of microbial inoculants on the indigenous plant microbiome and point out the following types of plant microbiome modulations: (i) transient microbiome shifts, (ii) stabilization or increase of microbial diversity, (iii) stabilization or increase of plant microbiome evenness, (iv) restoration of a dysbiosis/compensation or reduction of a pathogen-induced shift, (v) targeted shifts toward plant beneficial members of the indigenous microbiota, and (vi) suppression of potential pathogens. Therefore, we suggest microbiome modulations as novel and efficient mode of action for microbial inoculants that can also be mediated the plant.
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http://dx.doi.org/10.3389/fmicb.2021.650610DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8060476PMC
April 2021

Potato plant spheres and to a lesser extent the soil type influence the proportion and diversity of bacterial isolates with in vitro antagonistic activity towards Ralstonia solanacearum.

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.

Ralstonia solanacearum biovar2-race3 (Rs r3b2) is an epidemic soil-borne bacterial phytopathogen causing brown rot disease in potato. In this study, we assessed how three soil types stored at the same field site influenced the proportion and diversity of bacterial isolates with in vitro antagonistic activity towards Rs in bulk soil and different potato plant spheres (rhizosphere, endorhiza and endocaulosphere; ecto- and endosphere of seed and yield tubers). In general, the plate counts observed for each sample type were not significantly different. A total of 96 colonies per sample type was picked and screened for in vitro antagonistic activity against Rs. Antagonists were obtained from all bulk soils and plant spheres with the highest proportion obtained from the endorhiza and endocaulosphere of potato plants. BOX-PCR fingerprints of antagonists showed that some were specific for particular plant spheres independent of the soil type, while others originated from different plant spheres of a particular soil type. The majority of antagonists belonged to Pseudomonas. A high proportion of antagonists produced siderophores, and interestingly antagonists from potato tubers frequently carried multiple antibiotic production genes. Our data showed an enrichment of bacteria with genes or traits potentially involved in biocontrol in the rhizosphere and in endophytic compartments. We report that the proportion and diversity of in vitro antagonists towards Rs isolated from bulk soil and different spheres of potato plants grown under field conditions in three different soil types was mainly shaped by the plant sphere and to a lesser extent by the soil type. Bacteria with antagonistic activity towards Ralstonia solanacearum were isolated from all plant spheres and bulk soils but their proportion was highest in endophytic compartments.
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http://dx.doi.org/10.1093/femsec/fiab038DOI Listing
March 2021

Soil Texture, Sampling Depth and Root Hairs Shape the Structure of ACC Deaminase Bacterial Community Composition in Maize Rhizosphere.

Front Microbiol 2021 4;12:616828. Epub 2021 Feb 4.

Helmholtz Centre for Environmental Research, Halle, Germany.

Preservation of the phytostimulatory functions of plant growth-promoting bacteria relies on the adaptation of their community to the rhizosphere environment. Here, an amplicon sequencing approach was implemented to specifically target microorganisms with 1-aminocyclopropane-1-carboxylate deaminase activity, carrying the gene. We stated the hypothesis that the relative phylogenetic distribution of carrying microorganisms is affected by the presence or absence of root hairs, soil type, and depth. To this end, a standardized soil column experiment was conducted with maize wild type and root hair defective mutant in the substrates loam and sand, and harvest was implemented from three depths. Most sequences (99%) were affiliated to Actinobacteria and Proteobacteria, and the strongest influence on the relative abundances of sequences were exerted by the substrate. , and sequences dominated in loam, whereas and were more abundant in sand. Soil depth caused strong variations in sequence distribution, with differential levels in the relative abundances of sequences affiliated to , and in loam, but , , and in sand. Maize genotype influenced the distribution of sequences mainly in loam and only in the uppermost depth. Variovorax sequences were more abundant in WT, but , and in rhizosphere. Substrate and soil depth were strong and plant genotype a further significant single and interacting drivers of carrying microbial community composition in the rhizosphere of maize. This suggests that maize rhizosphere carrying bacterial community establishes according to the environmental constraints, and that root hairs possess a minor but significant impact on carrying bacterial populations.
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http://dx.doi.org/10.3389/fmicb.2021.616828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7891401PMC
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

Impacts of switching tillage to no-tillage and vice versa on soil structure, enzyme activities and prokaryotic community profiles in Argentinean semi-arid soils.

FEMS Microbiol Ecol 2021 03;97(4)

Laboratorio de Bioquímica y Microbiología de Suelo, Centro de Bioquímica y Microbiología de Suelos, Universidad Nacional de Quilmes, B1876BXD Bernal, Buenos Aires, Argentina.

The effects of tillage on soil structure, physiology and microbiota structure were studied in a long-term field experiment, with side-to-side plots, established to compare effects of conventional tillage (CT) vs no-till (NT) agriculture. After 27 years, part of the field under CT was switched to NT and vice versa. Soil texture, soil enzymatic profiles and the prokaryotic community structure (16S rRNA genes amplicon sequencing) were analyzed at two soil depths (0-5 and 5-10 cm) in samples taken 6, 18 and 30 months after switching tillage practices. Soil enzymatic activities were higher in NT than CT, and enzymatic profiles responded to the changes much earlier than the overall prokaryotic community structure. Beta diversity measurements of the prokaryotic community indicated that the levels of stratification observed in long-term NT soils were already recovered in the new NT soils 30 months after switching from CT to NT. Bacteria and Archaea OTUs that responded to NT were associated with coarse soil fraction, soil organic carbon and C cycle enzymes, while CT responders were related to fine soil fractions and S cycle enzymes. This study showed the potential of managing the soil prokaryotic community and soil health through changes in agricultural management practices.
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http://dx.doi.org/10.1093/femsec/fiab025DOI 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

Tillage shapes the soil and rhizosphere microbiome of barley-but not its susceptibility towards Blumeria graminis f. sp. hordei.

FEMS Microbiol Ecol 2021 03;97(3)

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

Long-term agricultural practices are assumed to shape the rhizosphere microbiome of crops with implications for plant health. In a long-term field experiment, we investigated the effect of different tillage and fertilization practices on soil and barley rhizosphere microbial communities by means of amplicon sequencing of 16S rRNA gene fragments from total community DNA. Differences in the microbial community composition depending on the tillage practice, but not the fertilization intensity were revealed. To examine whether these soil and rhizosphere microbiome differences influence the plant defense response, barley (cultivar Golden Promise) was grown in field or standard potting soil under greenhouse conditions and challenged with Blumeria graminis f. sp. hordei (Bgh). Amplicon sequence analysis showed that preceding tillage practice, but also aboveground Bgh challenge significantly influenced the microbial community composition. Expression of plant defense-related genes PR1b and PR17b was higher in challenged compared to unchallenged plants. The Bgh infection rates were strikingly lower for barley grown in field soil compared to potting soil. Although previous agricultural management shaped the rhizosphere microbiome, no differences in plant health were observed. We propose therefore that the management-independent higher microbial diversity of field soils compared to potting soils contributed to the low infection rates of barley.
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http://dx.doi.org/10.1093/femsec/fiab018DOI 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

Microbial community analysis of soils under different soybean cropping regimes in the Argentinean south-eastern Humid Pampas.

FEMS Microbiol Ecol 2021 03;97(3)

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

Soil microbial communities are key players of ecosystem processes and important for crop and soil health. The Humid Pampas region in Argentina concentrates 75% of the national soybean production, which is based on intensive use of agrochemicals, monocropping and no-till. A long-term field experiment under no-till management in the southeast of the Argentinean Pampas provides a unique opportunity to compare soybean under monocropping with cultivation including alternating cover crops or in a three-phase rotation. We hypothesized that cropping regimes and season affect soil microbial community composition and diversity. Amplicon sequencing of 16S rRNA genes and internal transcribed spacer fragments showed a stronger microbial seasonal dynamic in conservation regimes compared to monocropping. In addition, several bacterial (e.g. Catenulispora, Streptomyces and Bacillus) and fungal genera (e.g. Exophiala) with cropping regime-dependent differential relative abundances were identified. Despite a temporal shift in microbial and chemical parameters, this study shows that long-term cropping regimes shaped the soil microbiota. This might have important implications for soil quality and soybean performance and should therefore be considered in the development of sustainable agricultural managements.
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http://dx.doi.org/10.1093/femsec/fiab007DOI Listing
March 2021

pv. pv. nov., a clonal pathogen causing an emerging, devastating disease of the ornamental plant spp.

Phytopathology 2021 Jan 11. Epub 2021 Jan 11.

University of Malaga, 16752, Área de Genética, Facultad de Ciencias, Malaga, Spain.

Commercial production of the ornamental plant dipladenia ( spp.) is threatened by dipladenia leaf and stem spot disease, caused by the bacterium . includes four pathovars of woody hosts differentiated by a characteristic host range in olive, oleander, ash and broom plants. However, isolates from dipladenia have not been ascribed to any particular lineage or pathovar. Here we report that isolates from dipladenia represent a distinct, clonal lineage. First, dipladenia isolates display very similar plasmid profiles, including a plasmid encoding the gene for biosynthesis of indole-3-acetic acid. Second, multilocus sequence analysis and core-genome single-nucleotide-polymorphisms phylogenies showed a monophyletic origin for dipladenia isolates, which cluster with isolates from oleander (pathovar ) in a distinct clade well separated from other strains. Metabolic profiling and cross-pathogenicity tests in olive, oleander, ash, broom and dipladenia clearly distinguished dipladenia isolates from the four . pathovars. Comparative genomics of the draft genome sequence of the dipladenia strain Ph3 with the other four pathovars showed that Ph3 encodes very few strain-specific genes, and a similar set of virulence genes to pv. , including its repertoire of type III secretion system effectors. However, hierarchical clustering based on the catalogue of effectors and their allelic variants clearly separated Ph3 from pv. strains. Based on their distinctive pathogenicity profile, we propose a pathovar for isolates from dipladenia, pv. pv. nov., for which strain Ph3 (CFBP 8832) has been designated as the pathotype strain.
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http://dx.doi.org/10.1094/PHYTO-11-20-0526-RDOI Listing
January 2021

Plant Species-Dependent Increased Abundance and Diversity of IncP-1 Plasmids in the Rhizosphere: New Insights Into Their Role and Ecology.

Front Microbiol 2020 27;11:590776. Epub 2020 Nov 27.

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

IncP-1 plasmids, first isolated from clinical specimens (R751, RP4), are recognized as important vectors spreading antibiotic resistance genes. The abundance of IncP-1 plasmids in the environment, previously reported, suggested a correlation with anthropogenic pollution. Unexpectedly, qPCR-based detection of IncP-1 plasmids revealed also an increased relative abundance of IncP-1 plasmids in total community DNA from the rhizosphere of lettuce and tomato plants grown in non-polluted soil along with plant age. Here we report the successful isolation of IncP-1 plasmids by exploiting their ability to mobilize plasmid pSM1890. IncP-1 plasmids were captured from the rhizosphere but not from bulk soil, and a high diversity was revealed by sequencing 14 different plasmids that were assigned to IncP-1β, δ, and ε subgroups. Although backbone genes were highly conserved and mobile elements or remnants as Tn, IS, Tn, or class 1 integron were carried by 13 of the sequenced IncP-1 plasmids, no antibiotic resistance genes were found. Instead, seven plasmids had a operon with Tn-like transposon and five plasmids contained putative metabolic gene clusters linked to these mobile elements. In-depth sequence comparisons with previously known plasmids indicate that the IncP-1 plasmids captured from the rhizosphere are archetypes of those found in clinical isolates. Our findings that IncP-1 plasmids do not always carry accessory genes in unpolluted rhizospheres are important to understand the ecology and role of the IncP-1 plasmids in the natural environment.
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http://dx.doi.org/10.3389/fmicb.2020.590776DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7728920PMC
November 2020

Colistin-Resistant Isolated From Process Waters and Wastewater From German Poultry and Pig Slaughterhouses.

Front Microbiol 2020 30;11:575391. Epub 2020 Oct 30.

Institute of Animal Sciences, University of Bonn, Bonn, Germany.

Due to the high prevalence of colistin-resistant in poultry and pigs, process waters and wastewater from slaughterhouses were considered as a hotspot for isolates carrying plasmid-encoded, mobilizable colistin resistances ( genes). Thus, questions on the effectiveness of wastewater treatment in in-house and municipal wastewater treatment plants (WWTPs) as well as on the diversity of the prevailing isolates, plasmid types, and their transmissibility arise. Process waters and wastewater accruing in the delivery and unclean areas of two poultry and two pig slaughterhouses were screened for the presence of target colistin-resistant bacteria (i.e., , spp., complex). In-house and municipal WWTPs (mWWTPs) including receiving waterbodies were investigated as well. Samples taken in the poultry slaughterhouses yielded the highest occurrence of target colistin-resistant (40.2%, 33/82), followed by mWWTPs (25.0%, 9/36) and pig slaughterhouses (14.9%, 10/67). Recovered isolates exhibited various resistance patterns. The resistance rates using epidemiological cut-off values were higher in comparison to those obtained with clinical breakpoints. Noteworthy, MCR-1-producing and were detected in scalding waters and preflooders of mWWTPs. A total of 70.8% (46/65) of and 20.6% (7/34) of isolates carried on a variety of transferable plasmids with incompatibility groups IncI1, IncHI2, IncX4, IncF, and IncI2 ranging between 30 and 360 kb. The analyzed isolates carrying on transferable plasmids ( = 53) exhibited a broad diversity, as they were assigned to 25 different I profiles. Interestingly, in the majority of colistin-resistant -negative and isolates non-synonymous polymorphisms in were detected. Our findings demonstrated high occurrence of colistin-resistant and carrying on transferrable plasmids in poultry and pig slaughterhouses and indicate their dissemination into surface water.
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http://dx.doi.org/10.3389/fmicb.2020.575391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7661462PMC
October 2020

Exploring microbial determinants of apple replant disease (ARD): a microhabitat approach under split-root design.

FEMS Microbiol Ecol 2020 12;96(12)

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

Apple replant disease (ARD) occurs worldwide in apple orchards and nurseries and leads to a severe growth and productivity decline. Despite research on the topic, its causality remains unclear. In a split-root experiment, we grew ARD-susceptible 'M26' apple rootstocks in different substrate combinations (+ARD: ARD soil; -ARD: gamma-irradiated ARD soil; and Control: soil with no apple history). We investigated the microbial community composition by 16S rRNA gene amplicon sequencing (bacteria and archaea) along the soil-root continuum (bulk soil, rhizosphere and rhizoplane). Significant differences in microbial community composition and structure were found between +ARD and -ARD or +ARD and Control along the soil-root continuum, even for plants exposed simultaneously to two different substrates (-ARD/+ARD and Control/+ARD). The substrates in the respective split-root compartment defined the assembly of root-associated microbial communities, being hardly influenced by the type of substrate in the respective neighbor compartment. Root-associated representatives from Actinobacteria were the most dynamic taxa in response to the treatments, suggesting a pivotal role in ARD. Altogether, we evidenced an altered state of the microbial community in the +ARD soil, displaying altered alpha- and beta-diversity, which in turn will also impact the normal development of apple rhizosphere and rhizoplane microbiota (dysbiosis), concurring with symptom appearance.
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http://dx.doi.org/10.1093/femsec/fiaa211DOI Listing
December 2020

Editorial: The Environmental Dimension of Antibiotic Resistance.

FEMS Microbiol Ecol 2020 08;96(8)

Department of Infectious Disease, Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden.

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http://dx.doi.org/10.1093/femsec/fiaa130DOI Listing
August 2020

Transferable Extended-Spectrum β-Lactamase (ESBL) Plasmids in from Irrigation Water.

Microorganisms 2020 Jun 30;8(7). Epub 2020 Jun 30.

Department of Life Sciences, Albstadt-Sigmaringen University, 72488 Sigmaringen, Germany.

Extended-spectrum β-lactamase (ESBL)-producing are classified as serious threats to human health by the U.S. Centers for Disease Control and Prevention. Water used for irrigation of fresh produce can transmit such resistant bacteria directly to edible plant parts. We screened ESBL-producing , , and isolated from irrigation water for their potential to transmit resistance to antibiotic-susceptible . All strains were genome-sequenced and tested in vitro for transmission of resistance to third-generation cephalosporins on solid agar as well as in liquid culture. Of the 19 screened isolates, five ESBL-producing were able to transfer resistance with different efficiency to susceptible recipient . Transconjugant strains were sequenced for detection of transferred antibiotic resistance genes (ARGs) and compared to the known ARG pattern of their respective donors. Additionally, phenotypic resistance patterns were obtained for both transconjugant and corresponding donor strains, confirming ESBL-producing phenotypes of all obtained transconjugants.
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http://dx.doi.org/10.3390/microorganisms8070978DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7409067PMC
June 2020

Compatibility of X-ray computed tomography with plant gene expression, rhizosphere bacterial communities and enzyme activities.

J Exp Bot 2020 09;71(18):5603-5614

Helmholtz Centre for Environmental Research, Halle, Germany.

Non-invasive X-ray computed tomography (XRCT) is increasingly used in rhizosphere research to visualize development of soil-root interfaces in situ. However, exposing living systems to X-rays can potentially impact their processes and metabolites. In order to evaluate these effects, we assessed the responses of rhizosphere processes 1 and 24 h after a low X-ray exposure (0.81 Gy). Changes in root gene expression patterns occurred 1 h after exposure with down-regulation of cell wall-, lipid metabolism-, and cell stress-related genes, but no differences remained after 24 h. At either time point, XRCT did not affect either root antioxidative enzyme activities or the composition of the rhizosphere bacterial microbiome and microbial growth parameters. The potential activities of leucine aminopeptidase and phosphomonoesterase were lower at 1 h, but did not differ from the control 24 h after exposure. A time delay of 24 h after a low X-ray exposure (0.81 Gy) was sufficient to reverse any effects on the observed rhizosphere systems. Our data suggest that before implementing novel experimental designs involving XRCT, a study on its impact on the investigated processes should be conducted.
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http://dx.doi.org/10.1093/jxb/eraa262DOI Listing
September 2020

PromA Plasmids Are Instrumental in the Dissemination of Linuron Catabolic Genes Between Different Genera.

Front Microbiol 2020 18;11:149. Epub 2020 Feb 18.

Division of Soil and Water Management, KU Leuven, Leuven, Belgium.

PromA plasmids are broad host range (BHR) plasmids, which are often cryptic and hence have an uncertain ecological role. We present three novel PromA γ plasmids which carry genes associated with degradation of the phenylurea herbicide linuron, two of which originated from unrelated hosts isolated from different environments (pPBL-H3-2 and pBPS33-2), and one (pEN1) which was exogenously captured from an on-farm biopurification system (BPS). sp. plasmid pBPS33-2 carries all three necessary gene clusters () determining the three main steps for conversion of linuron to Krebs cycle intermediates, while pEN1 only determines the initial linuron hydrolysis step. sp. plasmid pPBL-H3-2 exists as two variants, both containing but with the and gene modules interchanged between each other at exactly the same location. Linuron catabolic gene clusters that determine the same step were identical on all plasmids, encompassed in differently arranged constellations and characterized by the presence of multiple IS elements. In all plasmids except pEN1, the insertion spot of the catabolic genes in the PromA γ plasmids was the same. Highly similar PromA plasmids carrying the linuron degrading gene cargo at the same insertion spot were previously identified in linuron degrading sp. Interestingly, in both populations not every PromA plasmid copy carries catabolic genes. The results indicate that PromA plasmids are important vehicles of linuron catabolic gene dissemination, rather than being cryptic and only important for the mobilization of other plasmids.
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http://dx.doi.org/10.3389/fmicb.2020.00149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7039861PMC
February 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

Whole Genome Sequencing of From Store-Bought Produce.

Front Microbiol 2019 29;10:3050. Epub 2020 Jan 29.

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

The role of agriculture in the transfer of drug resistant pathogens to humans is widely debated and poorly understood. is a valuable indicator organism for contamination and carriage of antimicrobial resistance (AMR) in foods. Whilst whole genome sequences for from animals and associated meats are common, sequences from produce are scarce. Produce may acquire drug resistant from animal manure fertilizers, contaminated irrigation water and wildlife, particularly birds. Whole genome sequencing was used to characterize 120 tetracycline (TET) resistant from store-bought, ready-to-eat cilantro, arugula and mixed salad from two German cities. were recovered on the day of purchase and after 7 days of refrigeration. Cilantro was far more frequently contaminated with TET-resistant providing 102 (85%) sequenced strains. Phylogroup B1 dominated the collection ( = 84, 70%) with multi-locus sequence types B1-ST6186 ( = 37, 31%), C-ST165 ( = 17, 14%), B1-ST58 ( = 14, 12%), B1-ST641 ( = 8, 7%), and C-ST88 ( = 5, 4%) frequently identified. Notably, seven strains of diverse sequence type (ST) carried genetic indicators of ColV virulence plasmid carriage. A number of previously identified and novel integrons associated with insertion elements including IS were also identified. Storage may affect the lineages of isolated, however further studies are needed. Our study indicates produce predominantly carry with a commensal phylogroup and a variety of AMR and virulence-associated traits. Genomic surveillance of bacteria that contaminate produce should be a matter of public health importance in order to develop a holistic understanding of the environmental dimensions of AMR.
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http://dx.doi.org/10.3389/fmicb.2019.03050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7000624PMC
January 2020

Biocontrol of Bacterial Wilt Disease Through Complex Interaction Between Tomato Plant, Antagonists, the Indigenous Rhizosphere Microbiota, and .

Front Microbiol 2019 10;10:2835. Epub 2020 Jan 10.

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

(biovar2, race3) is the causal agent of bacterial wilt and this quarantine phytopathogen is responsible for massive losses in several commercially important crops. Biological control of this pathogen might become a suitable plant protection measure in areas where is endemic. Two bacterial strains, (B63) and (P142) with antagonistic activity toward (B3B) were tested for rhizosphere competence, efficient biological control of wilt symptoms on greenhouse-grown tomato, and effects on the indigenous rhizosphere prokaryotic communities. The population densities of B3B and the antagonists were estimated in rhizosphere community DNA by selective plating, real-time quantitative PCR, and -specific PCR-Southern blot hybridization. Moreover, we investigated how the pathogen and/or the antagonists altered the composition of the tomato rhizosphere prokaryotic community by 16S rRNA gene amplicon sequencing. (B63) and (P142)-inoculated plants showed drastically reduced wilt disease symptoms, accompanied by significantly lower abundance of the B3B population compared to the non-inoculated pathogen control. Pronounced shifts in prokaryotic community compositions were observed in response to the inoculation of B63 or P142 in the presence or absence of the pathogen B3B and numerous dynamic taxa were identified. Confocal laser scanning microscopy (CLSM) visualization of the -tagged antagonist P142 revealed heterogeneous colonization patterns and P142 was detected in lateral roots, root hairs, epidermal cells, and within xylem vessels. Although competitive niche exclusion cannot be excluded, it is more likely that the inoculation of P142 or B63 and the corresponding microbiome shifts primed the plant defense against the pathogen B3B. Both inoculants are promising biological agents for efficient control of under field conditions.
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http://dx.doi.org/10.3389/fmicb.2019.02835DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6967407PMC
January 2020

Suppression treatment differentially influences the microbial community and the occurrence of broad host range plasmids in the rhizosphere of the model cover crop Avena sativa L.

PLoS One 2019 9;14(10):e0223600. Epub 2019 Oct 9.

Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina.

Cover crop suppression with glyphosate-based herbicides (GBHs) represents a common agricultural practice. The objective of this study was to compare rhizospheric microbial communities of A. sativa plants treated with a GBH relative to the mechanical suppression (mowing) in order to assess their differences and the potential implications for soil processes. Samples were obtained at 4, 10, 17 and 26 days post-suppression. Soil catabolic profiling and DNA-based methods were applied. At 26 days, higher respiration responses and functional diversity indices (Shannon index and catabolic evenness) were observed under glyphosate suppression and a neat separation of catabolic profiles was detected in multivariate analysis. Sarcosine and Tween 20 showed the highest contribution to this separation. Metabarcoding revealed a non-significant effect of suppression method on either alpha-diversity metrics or beta-diversity. Conversely, differences were detected in the relative abundance of specific bacterial taxa. Mesorhizobium sequences were detected in higher relative abundance in glyphosate-treated plants at the end of the experiment while the opposite trend was observed for Gaiella. Quantitative PCR of amoA gene from ammonia-oxidizing archaea showed a lower abundance under GBH suppression again at 26 days, while ammonia-oxidizing bacteria remained lower at all sampling times. Broad host range plasmids IncP-1β and IncP-1ε were exclusively detected in the rhizosphere of glyphosate-treated plants at 10 days and at 26 days, respectively. Overall, our study demonstrates differential effects of suppression methods on the abundance of specific bacterial taxa, on the physiology and mobile genetic elements of microbial communities while no differences were detected in taxonomic diversity.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223600PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6785065PMC
March 2020

Detection, Isolation, and Characterization of Plasmids in the Environment.

Methods Mol Biol 2020 ;2075:39-60

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

Plasmids play a major role in the bacterial adaptation to changing and stressful environmental conditions caused by antibiotics, heavy metals, and disinfectants. However, the investigation of the ecology and diversity of environmental plasmids is challenging due to their typically low abundance in soil bacterial communities and the low cultivability of their hosts. Here we discuss the potentials and limitations of cultivation-dependent and cultivation-independent approaches for detecting and quantifying plasmids in total community DNA from environmental samples. Protocols for PCR-based detection of plasmid-specific sequences in total community DNA are presented. Furthermore, protocols to obtain and characterize plasmids either from isolates (endogenous plasmid isolation) or by capturing into a recipient strain by biparental and triparental mating will be provided.
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http://dx.doi.org/10.1007/978-1-4939-9877-7_3DOI Listing
January 2021

Enhanced tomato plant growth in soil under reduced P supply through microbial inoculants and microbiome shifts.

FEMS Microbiol Ecol 2019 09;95(9)

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

Soil microbial communities interact with roots, affecting plant growth and nutrient acquisition. In the present study, we aimed to decipher the effects of the inoculants Trichoderma harzianum T-22, Pseudomonas sp. DSMZ 13134, Bacillus amyloliquefaciens FZB42 or Pseudomonas sp. RU47 on the rhizosphere microbial community and their beneficial effects on tomato plants grown in moderately low phosphorous soil under greenhouse conditions. We analyzed the plant mass, inoculant colony forming units and rhizosphere communities on 15, 22, 29 and 43 days after sowing. Selective plating showed that the bacterial inoculants had a good rhizocompetence and accelerated shoot and root growth and nutrient accumulation. 16S rRNA gene fingerprints indicated changes in the rhizosphere bacterial community composition. Amplicon sequencing revealed that rhizosphere bacterial communities from plants treated with bacterial inoculants were more similar to each other and distinct from those of the control and the Trichoderma inoculated plants at harvest time, and numerous dynamic taxa were identified. In conclusion, likely both, inoculants and the rhizosphere microbiome shifts, stimulated early plant growth mainly by improved spatial acquisition of available nutrients via root growth promotion. At harvest, all tomato plants were P-deficient, suggesting a limited contribution of inoculants and the microbiome shifts to the solubilization of sparingly soluble soil P.
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http://dx.doi.org/10.1093/femsec/fiz124DOI Listing
September 2019

A Novel Group of -Like Agrobacteria Associated with Crown Gall Disease of Rhododendron and Blueberry.

Phytopathology 2019 Nov 2;109(11):1840-1848. Epub 2019 Oct 2.

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

Crown gall is an economically important and widespread plant disease caused by tumorigenic bacteria that are commonly affiliated within the genera , and . Although crown gall disease was reported to occur on rhododendron, literature data regarding this disease are limited. In this study, an atypical group of tumorigenic agrobacteria belonging to the genus was identified as a causative agent of crown gall on rhododendron. Genome analysis suggested that tumorigenic bacteria isolated from rhododendron tumors are most closely related to , a new tumorigenic bacterium discovered recently on blackberry in Serbia. However, and novel rhododendron strains belong to separate species and form a homogenous clade within the genus , which we named the "tumorigenes" clade. Moreover, tumorigenic bacteria isolated from rhododendron seem to carry a distinct tumor-inducing (Ti) plasmid, compared with those carried by strains and Ti plasmids described thus far. To facilitate rapid identification of bacteria belonging to the "tumorigenes" clade, regardless of whether they are pathogenic or not, a conventional PCR method targeting putative chromosomal gene-encoding flagellin protein FlaA was developed in this study. Finally, our results suggested that this novel group of tumorigenic agrobacteria occurs on blueberry but it cannot be excluded that it is distributed more widely.
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http://dx.doi.org/10.1094/PHYTO-05-19-0167-RDOI Listing
November 2019

Contrasting microbial community responses to salinization and straw amendment in a semiarid bare soil and its wheat rhizosphere.

Sci Rep 2019 07 5;9(1):9795. Epub 2019 Jul 5.

Thünen Institute of Biodiversity, Braunschweig, Germany.

Soil salinization is a major constraint of agriculture in semiarid ecosystems. In this study soil microcosms were applied to evaluate the impact of a lower- and higher-level salinization treatment of a pristine scrubland soil on the abundance of Bacteria, Archaea, and Fungi, and on prokaryotic diversity in bare soil and the rhizosphere of wheat assessed by qPCR and high-throughput sequencing of 16S rRNA gene amplicons. Furthermore, the impact of soil straw amendment as a salt-stress alleviation strategy was studied. While the low-level salinity stimulated plant growth, the seedlings did not survive under the higher-level salinity unless the soil was amended with straw. Without the straw amendment, salinization had only minor effects on the microbial community in bare soil. On the other hand, it decreased prokaryotic diversity in the rhizosphere of wheat, but the straw amendment was effective in mitigating this effect. The straw however, was not a significant nutrient source for the rhizosphere microbiota but more likely acted indirectly by ameliorating the salinity stress on the plant. Members of Proteobacteria, Actinobacteria, and Firmicutes were abundant among the bacteria that reacted to soil salinization and the straw amendment but showed inconsistent responses indicating the large physiological diversity within these phyla.
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http://dx.doi.org/10.1038/s41598-019-46070-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6611862PMC
July 2019

Antibiotic-manufacturing sites are hot-spots for the release and spread of antibiotic resistance genes and mobile genetic elements in receiving aquatic environments.

Environ Int 2019 09 28;130:104735. Epub 2019 Jun 28.

Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia. Electronic address:

High antibiotic releases from manufacturing facilities have been identified as a risk factor for antibiotic resistance development in bacterial pathogens. However, the role of antibiotic pollution in selection and transferability of antibiotic resistance genes (ARGs) is still limited. In this study, we analyzed effluents from azithromycin-synthesis and veterinary-drug formulation facilities as well as sediments from receiving river and creek taken at the effluent discharge sites, upstream and downstream of discharge. Culturing showed that the effluent discharge significantly increased the proportion of antibiotic resistant bacteria in exposed sediments compared to the upstream ones. Quantitative real-time PCR revealed that effluents from both industries contained high and similar relative abundances of resistance genes [sul1, sul2, qacE/qacEΔ1, tet(A)], class 1 integrons (intI1) and IncP-1 plasmids (korB). Consequently, these genes significantly increased in relative abundances in receiving sediments, with more pronounced effects being observed for river than for creek sediments due to lower background levels of the investigated genes in the river. In addition, effluent discharge considerably increased transfer frequencies of captured ARGs from exposed sediments into Escherichia coli CV601 recipient as shown by biparental mating experiments. Most plasmids exogenously captured from effluent and polluted sediments belonged to the broad host range IncP-1ε plasmid group, conferred multiple antibiotic resistance and harbored class 1 integrons. Discharge of pharmaceutical waste from antibiotic manufacturing sites thus poses a risk for development and dissemination of multi-resistant bacteria, including pathogens.
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http://dx.doi.org/10.1016/j.envint.2019.04.007DOI Listing
September 2019

Establishment in Agricultural Soil and Colonization of Crop Plants Depend on Soil Type and Plant Species.

Front Microbiol 2019 15;10:967. Epub 2019 May 15.

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

Human pathogenic bacteria, such as , are able to colonize crop plants. So far, not much is known about biotic and abiotic factors influencing this colonization in field soil. This understanding, however, is imperative for the provision of safe fresh produce to the consumer. In this study, we investigated the effects of soil type, organic fertilization, plant species and the way of entry into the plant production system, on the survival of in soil as well as the colonization of plants. The selected serovar Typhimurium strain 14028s, Typhimurium strain LT2 and Senftenberg were able to persist in soil for several weeks. persistence in soil was prolonged in loamy, if compared to sandy soil, and when applied together with organic fertilizer. The leaves of lettuce and corn salad were colonized by providing evidence for internalization from the soil the root. Colonization rates were affected by soil type, plant species and strain. Overall, was detected in leaves of 0.5-0.9% of the plants, while lettuce was more frequently colonized than corn salad. Plants grown in sandy soil were more often colonized than plants grown in loamy soil. After spray inoculation, could be detected on and in leaves for several weeks by cultivation-depending methods, confirmed by confocal microscopy using GFP-labeled Typhimurium 14028s. On the one hand, transcriptome data from Typhimurium 14028s assessed in response to lettuce medium or lettuce root exudates showed an upregulation of genes associated with biofilm formation and virulence. On the other hand, lettuce inoculated with Typhimurium 14028s showed a strong upregulation of genes associated with plant immune response and genes related to stress response. In summary, these results showed that organic fertilizers can increase the persistence of in soil and that soil type and plant species play a crucial role in the interactions between human pathogens and crop plants. This understanding is therefore a starting point for new strategies to provide safe food for the consumer.
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http://dx.doi.org/10.3389/fmicb.2019.00967DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6529577PMC
May 2019

Manure and Doxycycline Affect the Bacterial Community and Its Resistome in Lettuce Rhizosphere and Bulk Soil.

Front Microbiol 2019 16;10:725. Epub 2019 Apr 16.

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

Manure application to agricultural soil introduces antibiotic residues and increases the abundance of antibiotic-resistant bacteria (ARB) carrying antibiotic resistance genes (ARGs), often located on mobile genetic elements (MGEs). The rhizosphere is regarded as a hotspot of microbial activity and gene transfer, which can alter and prolong the effects of organic fertilizers containing antibiotics. However, not much is known about the influence of plants on the effects of doxycycline applied to soil via manure. In this study, the effects of manure spiked with or without doxycycline on the prokaryotic community composition as well as on the relative abundance of ARGs and MGEs in lettuce rhizosphere and bulk soil were investigated by means of a polyphasic cultivation-independent approach. Samples were taken 42 days after manure application, and total community DNA was extracted. Besides a pronounced manure effect, doxycycline spiking caused an additional enrichment of ARGs and MGEs. High-throughput quantitative PCR revealed an increase in tetracycline, aminoglycoside, and macrolide-lincosamide-streptogramin B (MLSB) resistance genes associated with the application of manure spiked with doxycycline. This effect was unexpectedly lower in the rhizosphere than in bulk soil, suggesting a faster dissipation of the antibiotic and a more resilient prokaryotic community in the rhizosphere. Interestingly, the tetracycline resistance gene (P) was highly enriched in manure-treated bulk soil and rhizosphere, with highest values observed in doxycycline-treated bulk soil, concurring with an enrichment of Clostridia. Thus, the gene (P) might be a suitable marker of soil contamination by ARB, ARGs, and antibiotics of manure origin. These findings illustrate that the effects of manure and doxycycline on ARGs and MGEs differ between rhizosphere and bulk soil, which needs to be considered when assessing risks for human health connected to the spread of ARGs in the environment.
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http://dx.doi.org/10.3389/fmicb.2019.00725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6477490PMC
April 2019