1
|
Ishola OA, Kublik S, Durai Raj AC, Ohnmacht C, Schulz S, Foesel BU, Schloter M. Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models. Microorganisms 2024; 12:255. [PMID: 38399658 PMCID: PMC10892684 DOI: 10.3390/microorganisms12020255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Gnotobiotic murine models are important to understand microbiota-host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. Caudoviricetes (82.4%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class Caudoviricetes differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host's environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome "dark matter" and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome.
Collapse
Affiliation(s)
- Oluwaseun A. Ishola
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Abilash Chakravarthy Durai Raj
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Caspar Ohnmacht
- Mucosal Immunology Group, Center of Allery and Environment (ZAUM), Technical University of Munich, Helmholtz Zentrum München, 85764 München, Germany
| | - Stefanie Schulz
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Bärbel U. Foesel
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, 85764 Neuherberg, Germany; (O.A.I.)
- Chair for Environmental Microbiology, TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
- Central Institute for Nutrition and Health, Technical University of Munich, 85354 Freising, Germany
| |
Collapse
|
2
|
Bender SF, Schulz S, Martínez-Cuesta R, Laughlin RJ, Kublik S, Pfeiffer-Zakharova K, Vestergaard G, Hartman K, Parladé E, Römbke J, Watson CJ, Schloter M, van der Heijden MGA. Simplification of soil biota communities impairs nutrient recycling and enhances above- and belowground nitrogen losses. New Phytol 2023; 240:2020-2034. [PMID: 37700504 DOI: 10.1111/nph.19252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/18/2023] [Indexed: 09/14/2023]
Abstract
Agriculture is a major source of nutrient pollution, posing a threat to the earth system functioning. Factors determining the nutrient use efficiency of plant-soil systems need to be identified to develop strategies to reduce nutrient losses while ensuring crop productivity. The potential of soil biota to tighten nutrient cycles by improving plant nutrition and reducing soil nutrient losses is still poorly understood. We manipulated soil biota communities in outdoor lysimeters, planted maize, continuously collected leachates, and measured N2 O- and N2 -gas emissions after a fertilization pulse to test whether differences in soil biota communities affected nutrient recycling and N losses. Lysimeters with strongly simplified soil biota communities showed reduced crop N (-20%) and P (-58%) uptake, strongly increased N leaching losses (+65%), and gaseous emissions (+97%) of N2 O and N2 . Soil metagenomic analyses revealed differences in the abundance of genes responsible for nutrient uptake, nitrate reduction, and denitrification that helped explain the observed nutrient losses. Soil biota are major drivers of nutrient cycling and reductions in the diversity or abundance of certain groups (e.g. through land-use intensification) can disrupt nutrient cycling, reduce agricultural productivity and nutrient use efficiency, and exacerbate environmental pollution and global warming.
Collapse
Affiliation(s)
- S Franz Bender
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
| | - Stefanie Schulz
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Rubén Martínez-Cuesta
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
- Technical University of Munich, Chair for Environmental Microbiology, Emil-Ramann-Straße 2, D-85354, Freising, Germany
| | - Ronald J Laughlin
- Agri-Environment Branch, Agri-Food & Biosciences Institute, Belfast, BT9 5PX, UK
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Kristina Pfeiffer-Zakharova
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
| | - Gisle Vestergaard
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Kyle Hartman
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - Eloi Parladé
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Jörg Römbke
- ECT Ökotoxikologie GmbH, Böttgerstr. 2-14, D-65439, Flörsheim, Germany
| | - Catherine J Watson
- Agri-Environment Branch, Agri-Food & Biosciences Institute, Belfast, BT9 5PX, UK
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany
- Technical University of Munich, Chair for Environmental Microbiology, Emil-Ramann-Straße 2, D-85354, Freising, Germany
| | - Marcel G A van der Heijden
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
| |
Collapse
|
3
|
Shintani M, Vestergaard G, Milaković M, Kublik S, Smalla K, Schloter M, Udiković-Kolić N. Integrons, transposons and IS elements promote diversification of multidrug resistance plasmids and adaptation of their hosts to antibiotic pollutants from pharmaceutical companies. Environ Microbiol 2023; 25:3035-3051. [PMID: 37655671 DOI: 10.1111/1462-2920.16481] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/01/2023] [Indexed: 09/02/2023]
Abstract
Plasmids are important vehicles for the dissemination of antibiotic resistance genes (ARGs) among bacteria by conjugation. Here, we determined the complete nucleotide sequences of nine different plasmids previously obtained by exogenous plasmid isolation from river and creek sediments and wastewater from a pharmaceutical company. We identified six IncP/P-1ε plasmids and single members of IncL, IncN and IncFII-like plasmids. Genetic structures of the accessory regions of the IncP/P-1ε plasmids obtained implied that multiple insertions and deletions had occurred, mediated by different transposons and Class 1 integrons with various ARGs. Our study provides compelling evidence that Class 1 integrons, Tn402-like transposons, Tn3-like transposons and/or IS26 played important roles in the acquisition of ARGs across all investigated plasmids. Our plasmid sequencing data provide new insights into how these mobile genetic elements could mediate the acquisition and spread of ARGs in environmental bacteria.
Collapse
Affiliation(s)
- Masaki Shintani
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, Ibaraki, Japan
| | | | - Milena Milaković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Croatia
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Zagreb, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Zagreb, Germany
| | | |
Collapse
|
4
|
Staude B, Gschwendtner S, Frodermann T, Oehmke F, Kohl T, Kublik S, Schloter M, Ehrhardt H. Microbial signatures in amniotic fluid at preterm birth and association with bronchopulmonary dysplasia. Respir Res 2023; 24:248. [PMID: 37845700 PMCID: PMC10577941 DOI: 10.1186/s12931-023-02560-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/09/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Microbiome dysbiosis can have long-lasting effects on our health and induce the development of various diseases. Bronchopulmonary dysplasia (BPD) is a multifactorial disease with pre- and postnatal origins including intra-amniotic infection as main risk factor. Recently, postnatal pathologic lung microbiota colonization was associated with BPD. The objectives of this prospective observational cohort study were to describe differences in bacterial signatures in the amniotic fluid (AF) of intact pregnancies without clinical signs or risk of preterm delivery and AF samples obtained during preterm deliveries and their variations between different BPD disease severity stages. METHODS AF samples were collected under sterile conditions during fetal intervention from intact pregnancies (n = 17) or immediately before preterm delivery < 32 weeks (n = 126). Metabarcoding based approaches were used for the molecular assessment of bacterial 16S rRNA genes to describe bacterial community structure. RESULTS The absolute amount of 16S rRNA genes was significantly increased in AF of preterm deliveries and detailed profiling revealed a reduced alpha diversity and a significant change in beta diversity with a reduced relative abundance of 16S rRNA genes indicative for Lactobacillus and Acetobacter while Fusobacterium, Pseudomonas, Ureaplasma and Staphylococcus 16S rRNA gene prevailed. Although classification of BPD by disease severity revealed equivalent absolute 16S rRNA gene abundance and alpha and beta diversity in no, mild and moderate/severe BPD groups, for some 16S rRNA genes differences were observed in AF samples. Bacterial signatures of infants with moderate/severe BPD showed predominance of 16S rRNA genes belonging to the Escherichia-Shigella cluster while Ureaplasma and Enterococcus species were enriched in AF samples of infants with mild BPD. CONCLUSIONS Our study identified distinct and diverse intrauterine 16S rRNA gene patterns in preterm infants immediately before birth, differing from the 16S rRNA gene signature of intact pregnancies. The distinct 16S rRNA gene signatures at birth derive from bacteria with varying pathogenicity to the immature lung and are suited to identify preterm infants at risk. Our results emphasize the prenatal impact to the origins of BPD.
Collapse
Affiliation(s)
- Birte Staude
- Department of General Pediatrics and Neonatology, Justus Liebig University and Universities of Giessen and Marburg Lung Center, Giessen, Germany
- German Center for Lung Research (DZL), Giessen, Germany
| | - Silvia Gschwendtner
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Tina Frodermann
- Department of General Pediatrics and Neonatology, Justus Liebig University and Universities of Giessen and Marburg Lung Center, Giessen, Germany
| | - Frank Oehmke
- Department of Gynecology and Obstetrics, Justus Liebig University of Giessen, Giessen, Germany
| | - Thomas Kohl
- Department of Gynecology and Obstetrics, Justus Liebig University of Giessen, Giessen, Germany
- German Center for Fetal Surgery and Minimally Invasive Therapy (DZFT), University of Mannheim (UMM), Mannheim, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Harald Ehrhardt
- Department of General Pediatrics and Neonatology, Justus Liebig University and Universities of Giessen and Marburg Lung Center, Giessen, Germany
- German Center for Lung Research (DZL), Giessen, Germany
- Division of Neonatology and Pediatric Intensive Care Medicine, Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| |
Collapse
|
5
|
Amar Y, Rogner D, Silva RL, Foesel BU, Ud-Dean M, Lagkouvardos I, Steimle-Grauer SA, Niedermeier S, Kublik S, Jargosch M, Heinig M, Thomas J, Eyerich S, Wikström JD, Schloter M, Eyerich K, Biedermann T, Köberle M. Correction: Darier's disease exhibits a unique cutaneous microbial dysbiosis associated with inflammation and body malodour. Microbiome 2023; 11:206. [PMID: 37705089 PMCID: PMC10500857 DOI: 10.1186/s40168-023-01665-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Affiliation(s)
- Yacine Amar
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Danielle Rogner
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Rafaela L Silva
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Bärbel U Foesel
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Deutsches Forschungszentrum Für Gesundheit Und Umwelt (GmbH), 85764, Neuherberg, Germany
| | - Minhaz Ud-Dean
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Ilias Lagkouvardos
- Core Facility Microbiome, Technical University of Munich, 85354, Freising, Germany
| | - Susanne A Steimle-Grauer
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Sebastian Niedermeier
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Deutsches Forschungszentrum Für Gesundheit Und Umwelt (GmbH), 85764, Neuherberg, Germany
| | - Manja Jargosch
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Jenny Thomas
- Center of Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Zentrum München, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Stefanie Eyerich
- Center of Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Zentrum München, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Jakob D Wikström
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Dermato‑Venereology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Deutsches Forschungszentrum Für Gesundheit Und Umwelt (GmbH), 85764, Neuherberg, Germany
| | - Kilian Eyerich
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Dermatology and Venereology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Tilo Biedermann
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany.
| | - Martin Köberle
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| |
Collapse
|
6
|
Amar Y, Rogner D, Silva RL, Foesel BU, Ud-Dean M, Lagkouvardos I, Steimle-Grauer SA, Niedermeier S, Kublik S, Jargosch M, Heinig M, Thomas J, Eyerich S, Wikström JD, Schloter M, Eyerich K, Biedermann T, Köberle M. Darier's disease exhibits a unique cutaneous microbial dysbiosis associated with inflammation and body malodour. Microbiome 2023; 11:162. [PMID: 37496039 PMCID: PMC10369845 DOI: 10.1186/s40168-023-01587-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/01/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Darier's disease (DD) is a genodermatosis caused by mutations of the ATP2A2 gene leading to disrupted keratinocyte adhesion. Recurrent episodes of skin inflammation and infections with a typical malodour in DD indicate a role for microbial dysbiosis. Here, for the first time, we investigated the DD skin microbiome using a metabarcoding approach of 115 skin swabs from 14 patients and 14 healthy volunteers. Furthermore, we analyzed its changes in the context of DD malodour and the cutaneous DD transcriptome. RESULTS We identified a disease-specific cutaneous microbiome with a loss of microbial diversity and of potentially beneficial commensals. Expansion of inflammation-associated microbes such as Staphylococcus aureus and Staphylococcus warneri strongly correlated with disease severity. DD dysbiosis was further characterized by abundant species belonging to Corynebacteria, Staphylococci and Streptococci groups displaying strong associations with malodour intensity. Transcriptome analyses showed marked upregulation of epidermal repair, inflammatory and immune defence pathways reflecting epithelial and immune response mechanisms to DD dysbiotic microbiome. In contrast, barrier genes including claudin-4 and cadherin-4 were downregulated. CONCLUSIONS These findings allow a better understanding of Darier exacerbations, highlighting the role of cutaneous dysbiosis in DD inflammation and associated malodour. Our data also suggest potential biomarkers and targets of intervention for DD. Video Abstract.
Collapse
Affiliation(s)
- Yacine Amar
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Danielle Rogner
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Rafaela L Silva
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Bärbel U Foesel
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Deutsches Forschungszentrum Für Gesundheit Und Umwelt (GmbH), 85764, Neuherberg, Germany
| | - Minhaz Ud-Dean
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Ilias Lagkouvardos
- Core Facility Microbiome, Technical University of Munich, 85354, Freising, Germany
| | - Susanne A Steimle-Grauer
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Sebastian Niedermeier
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Deutsches Forschungszentrum Für Gesundheit Und Umwelt (GmbH), 85764, Neuherberg, Germany
| | - Manja Jargosch
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Jenny Thomas
- Center of Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Zentrum München, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Stefanie Eyerich
- Center of Allergy & Environment (ZAUM), Technical University of Munich (TUM) and Helmholtz Zentrum München, German Research Center for Environmental Health, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Jakob D Wikström
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Dermato-Venereology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Deutsches Forschungszentrum Für Gesundheit Und Umwelt (GmbH), 85764, Neuherberg, Germany
| | - Kilian Eyerich
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Dermatology and Venereology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Tilo Biedermann
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany.
| | - Martin Köberle
- Department of Dermatology and Allergy, Technical University of Munich, School of Medicine, Munich, Germany
| |
Collapse
|
7
|
Kurth JK, Albrecht M, Glaser K, Karsten U, Vestergaard G, Armbruster M, Kublik S, Schmid CAO, Schloter M, Schulz S. Biological soil crusts on agricultural soils of mesic regions promote microbial cross-kingdom co-occurrences and nutrient retention. Front Microbiol 2023; 14:1169958. [PMID: 37520365 PMCID: PMC10382179 DOI: 10.3389/fmicb.2023.1169958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/21/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Biological soil crusts (biocrusts) are known as biological hotspots on undisturbed, nutrient-poor bare soil surfaces and until now, are mostly observed in (semi-) arid regions but are currently poorly understood in agricultural systems. This is a crucial knowledge gap because managed sites of mesic regions can quickly cover large areas. Thus, we addressed the questions (i) if biocrusts from agricultural sites of mesic regions also increase nutrients and microbial biomass as their (semi-) arid counterparts, and (ii) how microbial community assemblage in those biocrusts is influenced by disturbances like different fertilization and tillage regimes. Methods We compared phototrophic biomass, nutrient concentrations as well as the abundance, diversity and co-occurrence of Archaea, Bacteria, and Fungi in biocrusts and bare soils at a site with low agricultural soil quality. Results and Discussion Biocrusts built up significant quantities of phototrophic and microbial biomass and stored more nutrients compared to bare soils independent of the fertilizer applied and the tillage management. Surprisingly, particularly low abundant Actinobacteria were highly connected in the networks of biocrusts. In contrast, Cyanobacteria were rarely connected, which indicates reduced importance within the microbial community of the biocrusts. However, in bare soil networks, Cyanobacteria were the most connected bacterial group and, hence, might play a role in early biocrust formation due to their ability to, e.g., fix nitrogen and thus induce hotspot-like properties. The microbial community composition differed and network complexity was reduced by conventional tillage. Mineral and organic fertilizers led to networks that are more complex with a higher percentage of positive correlations favoring microbe-microbe interactions. Our study demonstrates that biocrusts represent a microbial hotspot on soil surfaces under agricultural use, which may have important implications for sustainable management of such soils in the future.
Collapse
Affiliation(s)
- Julia Katharina Kurth
- Chair for Environmental Microbiology, TUM School of Life Science, Technical University Munich, Freising, Germany
- Environmental Health Centre, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Martin Albrecht
- Department of Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Karin Glaser
- Department of Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Ulf Karsten
- Department of Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Gisle Vestergaard
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Armbruster
- Agricultural Analytical and Research Institute Speyer (LUFA Speyer), Speyer, Germany
| | - Susanne Kublik
- Environmental Health Centre, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Christoph A. O. Schmid
- Environmental Health Centre, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Michael Schloter
- Chair for Environmental Microbiology, TUM School of Life Science, Technical University Munich, Freising, Germany
- Environmental Health Centre, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Stefanie Schulz
- Environmental Health Centre, Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| |
Collapse
|
8
|
Angstmann H, Pfeiffer S, Kublik S, Ehrhardt B, Uliczka K, Rabe KF, Roeder T, Wagner C, Schloter M, Krauss-Etschmann S. The microbial composition of larval airways from Drosophila melanogaster differ between specimens from laboratory and natural habitats. Environ Microbiome 2023; 18:55. [PMID: 37370177 DOI: 10.1186/s40793-023-00506-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/19/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND The fruit fly Drosophila melanogaster lives in natural habitats and has also long been used as a model organism in biological research. In this study, we used a molecular barcoding approach to analyse the airways microbiome of larvae of D. melanogaster, which were obtained from eggs of flies of the laboratory strain w1118 and from immune deficient flies (NF-kB-K), and from wild-caught flies. To assess intergenerational transmission of microbes, all eggs were incubated under the same semi-sterile conditions. RESULTS The airway microbiome of larvae from both lab-strains was dominated by the two families Acetobacteraceae and Lactobacillaceae, while larvae from wild-caught flies were dominated by Lactobacillaceae, Anaplasmataceae and Leuconostocaceae. Barcodes linked to Anaplasmataceae could be further assigned to Wolbachia sp., which is a widespread intracellular pathogen in arthropods. For Leuconostoceae, the most abundant reads were assigned to Weissella sp. Both Wolbachia and Weissella affect the development of the insects. Finally, a relative high abundance of Serratia sp. was found in larvae from immune deficient relish-/- compared to w1118 and wild-caught fly airways. CONCLUSIONS Our results show for the first time that larvae from D. melanogaster harbor an airway microbiome, which is of low complexity and strongly influenced by the environmental conditions and to a lesser extent by the immune status. Furthermore, our data indicate an intergenerational transmission of the microbiome as shaped by the environment.
Collapse
Affiliation(s)
- Hanna Angstmann
- Division of Experimental Asthma Research, Early Life Origins of Chronic Lung Disease, Research Center Borstel, German Center for Lung Research (DZL), Airway Research Center North (ARCN), Leibniz Lung Center, Borstel, Germany
| | - Stefan Pfeiffer
- ZIEL - Institute for Food and Health, Technical University of Munich, Freising, Germany
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Birte Ehrhardt
- Division of Experimental Asthma Research, Early Life Origins of Chronic Lung Disease, Research Center Borstel, German Center for Lung Research (DZL), Airway Research Center North (ARCN), Leibniz Lung Center, Borstel, Germany
| | - Karin Uliczka
- Division of Experimental Asthma Research, Early Life Origins of Chronic Lung Disease, Research Center Borstel, German Center for Lung Research (DZL), Airway Research Center North (ARCN), Leibniz Lung Center, Borstel, Germany
| | - Klaus F Rabe
- Department of Pneumology, Lungen Clinic, Grosshansdorf, Germany
- Department of Medicine, Christian Albrechts University, Germany Member of the German Center for Lung Research, Kiel, Germany
| | - Thomas Roeder
- Division of Molecular Physiology, Institute of Zoology, Christian-Albrechts University, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Kiel, Germany
| | - Christina Wagner
- Division of Experimental Asthma Research, Early Life Origins of Chronic Lung Disease, Research Center Borstel, German Center for Lung Research (DZL), Airway Research Center North (ARCN), Leibniz Lung Center, Borstel, Germany
| | - Michael Schloter
- ZIEL - Institute for Food and Health, Technical University of Munich, Freising, Germany
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Susanne Krauss-Etschmann
- Division of Experimental Asthma Research, Early Life Origins of Chronic Lung Disease, Research Center Borstel, German Center for Lung Research (DZL), Airway Research Center North (ARCN), Leibniz Lung Center, Borstel, Germany.
- Department of Medicine, Institute for Experimental Medicine, Christian Albrechts University, Kiel, Germany.
| |
Collapse
|
9
|
Khalaf DM, Cruzeiro C, Siani R, Kublik S, Schröder P. Resilience of barley (Hordeum vulgare) plants upon exposure to tramadol: Implication for the root-associated bacterial community and the antioxidative plant defence system. Sci Total Environ 2023:164260. [PMID: 37209727 DOI: 10.1016/j.scitotenv.2023.164260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/14/2023] [Accepted: 05/14/2023] [Indexed: 05/22/2023]
Abstract
Insufficiently treated reclaimed water can act as a source of contamination by introducing recalcitrant contaminants (e.g., pharmaceutical compounds) to various water bodies and/or agricultural soils after irrigation. Tramadol (TRD) is one of these pharmaceuticals that can be detected in influents and effluents of wastewater treatment plants, at discharge points as well as in surface waters in Europe. While the uptake of TRD by plants through irrigation water has been shown, plant responses towards this compound are still unclear. Therefore, this study aims to evaluate the effects of TRD on selected plant enzymes as well as on the root bacterial community structure. A hydroponic experiment was conducted to test the effects of TRD (100 μg L-1 TRD) on barley plants, at two harvesting time points after treatment. Accumulation of TRD in root tissues over time was observed reaching concentrations of 27.94 and 34.60 μg g-1 FW root after 12 and 24 days of exposure, respectively. Furthermore, noticeable inductions in guaiacol peroxidase (5.47-fold), catalase (1.83-fold) and glutathione S-transferase (3.23- and 2.09-fold) were recorded in roots of TRD-treated plants compared to controls after 24 days. A significant alteration in the beta diversity of root-associated bacteria due to TRD treatment was observed. Three amplicon sequence variants assigned to Hydrogenophaga, U. Xanthobacteraceae and Pseudacidovorax were differentially abundant in TRD-treated compared to control plants at both harvesting time points. This study reveals the resilience of plants through the induction of the antioxidative system and changes in the root-associated bacterial community to cope with the TRD metabolization/detoxification process.
Collapse
Affiliation(s)
- David Mamdouh Khalaf
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; Botany and Microbiology Department, Faculty of Science, Assiut University, 71516 Assiut, Egypt
| | - Catarina Cruzeiro
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
| | - Roberto Siani
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Peter Schröder
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| |
Collapse
|
10
|
Mahmoud FM, Kusari S, Kublik S, Benning S, Siani R, Zühlke S, Radl V, Mahnkopp-Dirks F, Schloter M. Draft Genome Sequence of the Bacterial Endophyte Priestia megaterium B1, Isolated from Roots of Apple ( Malus domestica). Microbiol Resour Announc 2023:e0117222. [PMID: 37199619 DOI: 10.1128/mra.01172-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023] Open
Abstract
Over the past years, a number of important traits supporting plant growth have been shown for different strains of Priestia megaterium (formerly known as Bacillus megaterium). Here, we report the draft genome sequence of the endophytic bacterial strain Priestia megaterium B1, which was isolated from surface-sterilized roots of apple plants.
Collapse
Affiliation(s)
- Fatma M Mahmoud
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Souvik Kusari
- Faculty of Chemistry and Chemical Biology, Center for Mass Spectrometry (CMS), TU Dortmund University, Dortmund, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sarah Benning
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Roberto Siani
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sebastian Zühlke
- Faculty of Chemistry and Chemical Biology, Center for Mass Spectrometry (CMS), TU Dortmund University, Dortmund, Germany
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Felix Mahnkopp-Dirks
- Institute of Horticultural Production Systems, Section Woody Plant and Propagation Physiology, Leibniz University Hannover, Hanover, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- Chair for Soil Science, Technical University of Munich, Freising, Germany
| |
Collapse
|
11
|
Kuhl-Nagel T, Rodriguez PA, Gantner I, Chowdhury SP, Schwehn P, Rosenkranz M, Weber B, Schnitzler JP, Kublik S, Schloter M, Rothballer M, Falter-Braun P. Novel Pseudomonas sp. SCA7 Promotes Plant Growth in Two Plant Families and Induces Systemic Resistance in Arabidopsis thaliana. Front Microbiol 2022; 13:923515. [PMID: 35875540 PMCID: PMC9297469 DOI: 10.3389/fmicb.2022.923515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas sp. SCA7, characterized in this study, was isolated from roots of the bread wheat Triticum aestivum. Sequencing and annotation of the complete SCA7 genome revealed that it represents a potential new Pseudomonas sp. with a remarkable repertoire of plant beneficial functions. In vitro and in planta experiments with the reference dicot plant A. thaliana and the original monocot host T. aestivum were conducted to identify the functional properties of SCA7. The isolate was able to colonize roots, modify root architecture, and promote growth in A. thaliana. Moreover, the isolate increased plant fresh weight in T. aestivum under unchallenged conditions. Gene expression analysis of SCA7-inoculated A. thaliana indicated a role of SCA7 in nutrient uptake and priming of plants. Moreover, confrontational assays of SCA7 with fungal and bacterial plant pathogens revealed growth restriction of the pathogens by SCA7 in direct as well as indirect contact. The latter indicated involvement of microbial volatile organic compounds (mVOCs) in this interaction. Gas chromatography-mass spectrometry (GC-MS) analyses revealed 1-undecene as the major mVOC, and octanal and 1,4-undecadiene as minor abundant compounds in the emission pattern of SCA7. Additionally, SCA7 enhanced resistance of A. thaliana against infection with the plant pathogen Pseudomonas syringae pv. tomato DC3000. In line with these results, SA- and JA/ET-related gene expression in A. thaliana during infection with Pst DC3000 was upregulated upon treatment with SCA7, indicating the ability of SCA7 to induce systemic resistance. The thorough characterization of the novel Pseudomonas sp. SCA7 showed a remarkable genomic and functional potential of plant beneficial traits, rendering it a promising candidate for application as a biocontrol or a biostimulation agent.
Collapse
Affiliation(s)
- Theresa Kuhl-Nagel
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Patricia Antonia Rodriguez
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Isabella Gantner
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Soumitra Paul Chowdhury
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Patrick Schwehn
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Maaria Rosenkranz
- Institute of Biochemical Plant Pathology, Research Unit Environmental Simulation, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Baris Weber
- Institute of Biochemical Plant Pathology, Research Unit Environmental Simulation, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Jörg-Peter Schnitzler
- Institute of Biochemical Plant Pathology, Research Unit Environmental Simulation, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Michael Rothballer
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Pascal Falter-Braun
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-University of Munich, Munich, Germany
| |
Collapse
|
12
|
Sachs C, Kanaparthi D, Kublik S, Szalay AR, Schloter M, Damgaard LR, Schramm A, Lueders T. Tracing long-distance electron transfer and cable bacteria in freshwater sediments by agar pillar gradient columns. FEMS Microbiol Ecol 2022; 98:6567839. [PMID: 35416241 DOI: 10.1093/femsec/fiac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/20/2022] [Accepted: 04/11/2022] [Indexed: 11/14/2022] Open
Abstract
Cable bacteria (CB) perform electrogenic sulphur oxidation (e-SOX) by spatially separating redox-half-reactions over cm-distances. For freshwater systems, the ecology of CB is not yet well understood, partly because they proved difficult to cultivate. This study introduces a new "agar pillar" approach to selectively enrich and investigate CB-populations. Within sediment columns, a central agar pillar is embedded, providing a sediment-free gradient-system in equilibrium with the surrounding sediment. We incubated freshwater sediments from a streambed, a sulfidic lake, and a hydrocarbon polluted aquifer in such agar pillar columns. Microprofiling revealed typical patterns of e-SOx, such as the development of a suboxic zone and the establishment of electric potentials. The bacterial communities in the sediments and agar pillars were analysed over depth by PacBio near-full-length 16S rRNA gene amplicon sequencing, allowing for a precise phylogenetic placement of taxa detected. The selective niche of the agar pillar was preferentially colonized by CB related to Candidatus Electronema for surface-water sediments, including several potentially novel species, but not for putative groundwater CB affiliated with Desulfurivibrio spp. The presence of CB was seemingly linked to co-enriched fermenters, hinting at a possible role of e-SOx-populations as an electron sink for heterotrophic microbes. These findings add to our current understanding of the diversity and ecology of CB in freshwater systems, and to a discrimination of CB from surface and groundwater sediments. The agar pillar approach provides a new strategy that may facilitate the cultivation of redox gradient-dependent microorganisms, including previously unrecognized CB populations.
Collapse
Affiliation(s)
- Corinna Sachs
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Germany.,Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Dheeraj Kanaparthi
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Germany.,Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Anna Roza Szalay
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München - German Research Center for Environmental Health, Germany
| | - Lars Riis Damgaard
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Denmark
| | - Andreas Schramm
- Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, Denmark
| | - Tillmann Lueders
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Germany
| |
Collapse
|
13
|
Mahnkopp-Dirks F, Radl V, Kublik S, Gschwendtner S, Schloter M, Winkelmann T. Dynamics of Bacterial Root Endophytes of Malus domestica Plants Grown in Field Soils Affected by Apple Replant Disease. Front Microbiol 2022; 13:841558. [PMID: 35401446 PMCID: PMC8993231 DOI: 10.3389/fmicb.2022.841558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/14/2022] [Indexed: 01/04/2023] Open
Abstract
Apple replant disease (ARD) is a worldwide problem for tree nurseries and orchards leading to reduced plant growth and fruit quality. The etiology of this complex phenomenon is poorly understood, but shifts of the bulk soil and rhizosphere microbiome seem to play an important role. Since roots are colonized by microbes from the rhizosphere, studies of the endophytic microbiome in relation to ARD are meaningful. In this study, culture-independent and culture-dependent approaches were used in order to unravel the endophytic root microbiome of apple plants 3, 7, and 12 months after planting in ARD-affected soil and ARD-unaffected control soil at two different field sites. Next to a high diversity of Pseudomonas in roots from all soils, molecular barcoding approaches revealed an increase in relative abundance of endophytic Actinobacteria over time in plants grown in ARD and control plots. Furthermore, several amplicon sequence variants (ASVs) linked to Streptomyces, which had been shown in a previous greenhouse ARD biotest to be negatively correlated to shoot length and fresh mass, were also detected in roots from both field sites. Especially in roots of apple plants from control soil, these Streptomyces ASVs increased in their relative abundance over time. The isolation of 150 bacterial strains in the culture-dependent approach revealed a high diversity of members of the genus Pseudomonas, confirming the data of the molecular barcoding approach. However, only partial overlaps were found between the two approaches, underlining the importance of combining these methods in order to better understand this complex disease and develop possible countermeasures. Overall, this study suggests a key role of Streptomyces in the etiology of ARD in the field.
Collapse
Affiliation(s)
- Felix Mahnkopp-Dirks
- Section Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hanover, Germany
| | - Viviane Radl
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Silvia Gschwendtner
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Traud Winkelmann
- Section Woody Plant and Propagation Physiology, Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hanover, Germany
| |
Collapse
|
14
|
Duffner C, Kublik S, Fösel B, Frostegård Å, Schloter M, Bakken L, Schulz S. Genotypic and phenotypic characterization of hydrogenotrophic denitrifiers. Environ Microbiol 2022; 24:1887-1901. [PMID: 35106904 DOI: 10.1111/1462-2920.15921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
Stimulating litho-autotrophic denitrification in aquifers with hydrogen is a promising strategy to remove excess NO3 - , but it often entails accumulation of the cytotoxic intermediate NO2 - and the greenhouse gas N2 O. To explore if these high NO2 - and N2 O concentrations are caused by differences in the genomic composition, the regulation of gene transcription or the kinetics of the reductases involved, we isolated hydrogenotrophic denitrifiers from a polluted aquifer, performed whole-genome sequencing and investigated their phenotypes. We therefore assessed the kinetics of NO2 - , NO, N2 O, N2 and O2 as they depleted O2 and transitioned to denitrification with NO3 - as the only electron acceptor and hydrogen as the electron donor. Isolates with a complete denitrification pathway, although differing intermediate accumulation, were closely related to Dechloromonas denitrificans, Ferribacterium limneticum or Hydrogenophaga taeniospiralis. High NO2 - accumulation was associated with the reductases' kinetics. While available, electrons only flowed towards NO3 - in the narG-containing H. taeniospiralis but flowed concurrently to all denitrification intermediates in the napA-containing D. denitrificans and F. limneticum. The denitrification regulator RegAB, present in the napA strains, may further secure low intermediate accumulation. High N2 O accumulation only occurred during the transition to denitrification and is thus likely caused by delayed N2 O reductase expression.
Collapse
Affiliation(s)
- Clara Duffner
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Bärbel Fösel
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Michael Schloter
- Chair of Soil Science, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Lars Bakken
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| |
Collapse
|
15
|
Amar Y, Lagkouvardos I, Silva RL, Ishola OA, Foesel BU, Kublik S, Schöler A, Niedermeier S, Bleuel R, Zink A, Neuhaus K, Schloter M, Biedermann T, Köberle M. Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA. Microbiome 2021; 9:123. [PMID: 34039428 PMCID: PMC8157445 DOI: 10.1186/s40168-021-01067-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/01/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND The identification of microbiota based on next-generation sequencing (NGS) of extracted DNA has drastically improved our understanding of the role of microbial communities in health and disease. However, DNA-based microbiome analysis cannot per se differentiate between living and dead microorganisms. In environments such as the skin, host defense mechanisms including antimicrobial peptides and low cutaneous pH result in a high microbial turnover, likely resulting in high numbers of dead cells present and releasing substantial amounts of microbial DNA. NGS analyses may thus lead to inaccurate estimations of microbiome structures and consequently functional capacities. RESULTS We investigated in this study the feasibility of a Benzonase-based approach (BDA) to pre-digest unprotected DNA, i.e., of dead microbial cells, as a method to overcome these limitations, thus offering a more accurate assessment of the living microbiome. A skin mock community as well as skin microbiome samples were analyzed using 16S rRNA gene sequencing and metagenomics sequencing after DNA extraction with and without a Benzonase digest to assess bacterial diversity patterns. The BDA method resulted in less reads from dead bacteria both in the skin mock community and skin swabs spiked with either heat-inactivated bacteria or bacterial-free DNA. This approach also efficiently depleted host DNA reads in samples with high human-to-microbial DNA ratios, with no obvious impact on the microbiome profile. We further observed that low biomass samples generate an α-diversity bias when the bacterial load is lower than 105 CFU and that Benzonase digest is not sufficient to overcome this bias. CONCLUSIONS The BDA approach enables both a better assessment of the living microbiota and depletion of host DNA reads. Video abstract.
Collapse
Affiliation(s)
- Yacine Amar
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Ilias Lagkouvardos
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), HCMR, Heraklion, Greece
- Core Facility Microbiome, Technische Universität München, 85354, Freising, Germany
| | - Rafaela L Silva
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Oluwaseun Ayodeji Ishola
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Bärbel U Foesel
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Anne Schöler
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
- DKFZ German Cancer Research Center, Berlin, Germany
| | - Sebastian Niedermeier
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Rachela Bleuel
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Alexander Zink
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, Technische Universität München, 85354, Freising, Germany
- ZIEL - Institute for Food & Health, Technische Universität München, 85354, Freising, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany
- ZIEL - Institute for Food & Health, Technische Universität München, 85354, Freising, Germany
| | - Tilo Biedermann
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany.
- Clinical Unit Allergology Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Helmholtz Zentrum München, 85764, Neuherberg, Germany.
| | - Martin Köberle
- Department of Dermatology and Allergology, Technical University of Munich, School of Medicine, Munich, Germany
| |
Collapse
|
16
|
Timsy, Spanner T, Ulrich A, Kublik S, Foesel BU, Kolb S, Horn MA, Behrendt U. Pseudomonas campi sp. nov., a nitrate-reducing bacterium isolated from grassland soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 34016249 DOI: 10.1099/ijsem.0.004799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain was isolated from grassland soil that has the potential to assimilate ammonium by the reduction of nitrate in the presence of oxygen. Whole genome sequence analysis revealed the presence of an assimilatory cytoplasmic nitrate reductase gene nasA and the assimilatory nitrite reductase genes nirBD which are involved in the sequential reduction of nitrate to nitrite and further to ammonium, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represents a member of the genus Pseudomonas. The closest phylogenetic neighbours based on 16S rRNA gene sequence analysis are the type strains of Pseudomonas peli (98.17%) and Pseudomonas guineae (98.03%). In contrast, phylogenomic analysis revealed a close relationship to Pseudomonas alcaligenes. Computation of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours of S1-A32-2T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. On the basis of these results, it was concluded that the soil isolate represents a novel species of the genus Pseudomonas, for which the name Pseudomonas campi sp. nov. (type strain S1-A32-2T=LMG 31521T=DSM 110222T) is proposed.
Collapse
Affiliation(s)
- Timsy
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Tobias Spanner
- Leibniz University Hannover, Institute of Microbiology, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Andreas Ulrich
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Susanne Kublik
- Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Bärbel U Foesel
- Helmholtz Center Munich, German Research Center for Environmental Health, Research Unit for Comparative Microbiome Analysis, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Steffen Kolb
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
| | - Marcus A Horn
- Leibniz University Hannover, Institute of Microbiology, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Undine Behrendt
- Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, D-15374 Müncheberg, Germany
| |
Collapse
|
17
|
Tanuwidjaja I, Vogel C, Pronk GJ, Schöler A, Kublik S, Vestergaard G, Kögel-Knabner I, Mrkonjic Fuka M, Schloter M, Schulz S. Microbial Key Players Involved in P Turnover Differ in Artificial Soil Mixtures Depending on Clay Mineral Composition. Microb Ecol 2021; 81:897-907. [PMID: 33161521 PMCID: PMC8062357 DOI: 10.1007/s00248-020-01635-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 10/27/2020] [Indexed: 05/24/2023]
Abstract
Nutrient turnover in soils is strongly driven by soil properties, including clay mineral composition. One main nutrient is phosphorus (P), which is known to be easily immobilized in soil. Therefore, the specific surface characteristics of clay minerals might substantially influence P availability in soil and thus the microbial strategies for accessing P pools. We used a metagenomic approach to analyze the microbial potential to access P after 842 days of incubation in artificial soils with a clay mineral composition of either non-expandable illite (IL) or expandable montmorillonite (MT), which differ in their surface characteristics like soil surface area and surface charge. Our data indicate that microorganisms of the two soils developed different strategies to overcome P depletion, resulting in similar total P concentrations. Genes predicted to encode inorganic pyrophosphatase (ppa), exopolyphosphatase (ppx), and the pstSCAB transport system were higher in MT, suggesting effective P uptake and the use of internal poly-P stores. Genes predicted to encode enzymes involved in organic P turnover like alkaline phosphatases (phoA, phoD) and glycerophosphoryl diester phosphodiesterase were detected in both soils in comparable numbers. In addition, Po concentrations did not differ significantly. Most identified genes were assigned to microbial lineages generally abundant in agricultural fields, but some were assigned to lineages known to include oligotrophic specialists, such as Bacillaceae and Microchaetaceae.
Collapse
Affiliation(s)
- Irina Tanuwidjaja
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
- Department of Microbiology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Cordula Vogel
- Lehrstuhl für Bodenkunde, Technische Universität München, Freising-Weihenstephan, Germany
- Institute of Soil Science and Site Ecology, Dresden University of Technology, Tharandt, Germany
| | - Geertje J Pronk
- Lehrstuhl für Bodenkunde, Technische Universität München, Freising-Weihenstephan, Germany
- Institute for Advanced Study, Technische Universität München, Garching, Germany
- KWR Watercycle Research Institute, Nieuwegein, Netherlands
| | - Anne Schöler
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ingrid Kögel-Knabner
- Lehrstuhl für Bodenkunde, Technische Universität München, Freising-Weihenstephan, Germany
- Institute for Advanced Study, Technische Universität München, Garching, Germany
| | - Mirna Mrkonjic Fuka
- Department of Microbiology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany
- Lehrstuhl für Bodenkunde, Technische Universität München, Freising-Weihenstephan, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Oberschleißheim, Germany.
| |
Collapse
|
18
|
Chiba A, Uchida Y, Kublik S, Vestergaard G, Buegger F, Schloter M, Schulz S. Soil Bacterial Diversity Is Positively Correlated with Decomposition Rates during Early Phases of Maize Litter Decomposition. Microorganisms 2021; 9:microorganisms9020357. [PMID: 33670245 PMCID: PMC7916959 DOI: 10.3390/microorganisms9020357] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
This study aimed to investigate the effects of different levels of soil- and plant-associated bacterial diversity on the rates of litter decomposition, and bacterial community dynamics during its early phases. We performed an incubation experiment where soil bacterial diversity (but not abundance) was manipulated by autoclaving and reinoculation. Natural or autoclaved maize leaves were applied to the soils and incubated for 6 weeks. Bacterial diversity was assessed before and during litter decomposition using 16S rRNA gene metabarcoding. We found a positive correlation between litter decomposition rates and soil bacterial diversity. The soil with the highest bacterial diversity was dominated by oligotrophic bacteria including Acidobacteria, Nitrospiraceae, and Gaiellaceae, and its community composition did not change during the incubation. In the less diverse soils, those taxa were absent but were replaced by copiotrophic bacteria, such as Caulobacteraceae and Beijerinckiaceae, until the end of the incubation period. SourceTracker analysis revealed that litter-associated bacteria, such as Beijerinckiaceae, only became part of the bacterial communities in the less diverse soils. This suggests a pivotal role of oligotrophic bacteria during the early phases of litter decomposition and the predominance of copiotrophic bacteria at low diversity.
Collapse
Affiliation(s)
- Akane Chiba
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (A.C.); (Y.U.)
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Crop Physiology, TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
| | - Yoshitaka Uchida
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (A.C.); (Y.U.)
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Section of Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Franz Buegger
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany;
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Correspondence: ; Tel.: +49-(0)89-3187-3054
| |
Collapse
|
19
|
Zhu B, Wang Z, Kanaparthi D, Kublik S, Ge T, Casper P, Schloter M, Lueders T. Long-Read Amplicon Sequencing of Nitric Oxide Dismutase (nod) Genes Reveal Diverse Oxygenic Denitrifiers in Agricultural Soils and Lake Sediments. Microb Ecol 2020; 80:243-247. [PMID: 31989236 PMCID: PMC7338807 DOI: 10.1007/s00248-020-01482-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
Microorganisms play an essential role in nitrogen cycling and greenhouse gas emissions in soils and sediments. The recently discovered oxygenic denitrifiers are proposed to reduce nitrate and nitrite via nitric oxide dismutation directly to N2 and O2. So far, the ecological role of these microbes is not well understood. The only available tool for a targeted study of oxygenic denitrifiers is their respective maker gene, nitric oxide dismutase (nod). Here, we established the use of PacBio long-read sequencing of nod gene amplicons to study the diversity and community structure of oxygenic denitrifiers. Two distinct sets of environmental samples, agricultural soil and lake sediment, were investigated as examples. The circular consensus sequences (ca 1.0 kb) obtained covered most substitution characteristic of NO dismutase and allowed for reliable classification of oxygenic denitrifiers. Distinct nod gene pools and community structure were revealed for the different habitats, with most sequence types affiliated to yet unidentified environmental nod lineages. The abundance of nod genes ranged 2.2 × 106-3.2 × 107 gene copies g-1 soil or sediment, accounting for up to 3% of total bacterial 16S rRNA gene counts. This study indicates that nod-gene-targeted long-read sequencing can be a powerful tool for studying the ecology of these novel microbes, and the results also suggest that oxygenic denitrifiers are prevalent and abundant in different terrestrial samples, where they could play an important, but yet overlooked role in nitrogen transformations.
Collapse
Affiliation(s)
- Baoli Zhu
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95440, Bayreuth, Germany.
| | - Zhe Wang
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95440, Bayreuth, Germany
| | - Dheeraj Kanaparthi
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95440, Bayreuth, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tida Ge
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Peter Casper
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tillmann Lueders
- Chair of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95440, Bayreuth, Germany.
| |
Collapse
|
20
|
Herpell JB, Schindler F, Bejtović M, Fragner L, Diallo B, Bellaire A, Kublik S, Foesel BU, Gschwendtner S, Kerou M, Schloter M, Weckwerth W. The Potato Yam Phyllosphere Ectosymbiont Paraburkholderia sp. Msb3 Is a Potent Growth Promotor in Tomato. Front Microbiol 2020; 11:581. [PMID: 32373084 PMCID: PMC7186400 DOI: 10.3389/fmicb.2020.00581] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/17/2020] [Indexed: 01/07/2023] Open
Abstract
The genus Paraburkholderia includes a variety of species with promising features for sustainable biotechnological solutions in agriculture through increasing crop productivity. Here, we present a novel Paraburkholderia isolate, a permanent and predominant member of the Dioscoreae bulbifera (yam family, Dioscoreaceae) phyllosphere, making up to 25% of the microbial community on leaf acumens. The 8.5 Mbp genome of isolate Msb3 encodes an unprecedented combination of features mediating a beneficial plant-associated lifestyle, including biological nitrogen fixation (BNF), plant hormone regulation, detoxification of various xenobiotics, degradation of aromatic compounds and multiple protein secretion systems including both T3SS and T6SS. The isolate exhibits significant growth promotion when applied to agriculturally important plants such as tomato, by increasing the total dry biomass by up to 40%. The open question about the “beneficial” nature of this strain led us to investigate ecological and generic boundaries in Burkholderia sensu lato. In a refined phylogeny including 279 Burkholderia sensu lato isolates strain Msb3 clusters within Clade I Paraburkholderia, which also includes few opportunistic strains that can potentially act as pathogens, as revealed by our ecological meta-data analysis. In fact, we demonstrate that all genera originating from the “plant beneficial and environmental” (PBE) Burkholderia species cluster include opportunists. This indicates that further functional examinations are needed before safe application of these strains in sustainable agricultural settings can be assured.
Collapse
Affiliation(s)
- Johannes B Herpell
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Florian Schindler
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Mersad Bejtović
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Lena Fragner
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Bocar Diallo
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Anke Bellaire
- Division of Structural and Functional Botany, Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany
| | - Bärbel U Foesel
- Research Unit for Comparative Microbiome Analysis, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany
| | - Silvia Gschwendtner
- Research Unit for Comparative Microbiome Analysis, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany
| | - Melina Kerou
- Archaea Biology and Ecogenomics Division, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| |
Collapse
|
21
|
Milaković M, Vestergaard G, González-Plaza JJ, Petrić I, Kosić-Vukšić J, Senta I, Kublik S, Schloter M, Udiković-Kolić N. Effects of industrial effluents containing moderate levels of antibiotic mixtures on the abundance of antibiotic resistance genes and bacterial community composition in exposed creek sediments. Sci Total Environ 2020; 706:136001. [PMID: 31855637 DOI: 10.1016/j.scitotenv.2019.136001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/21/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
Environmental discharges of very high (mg/L) antibiotic levels from pharmaceutical production contributed to the selection, spread and persistence of antibiotic resistance. However, the effects of less antibiotic-polluted effluents (μg/L) from drug-formulation on exposed aquatic microbial communities are still scarce. Here we analyzed formulation effluents and sediments from the receiving creek collected at the discharge site (DW0), upstream (UP) and 3000 m downstream of discharge (DW3000) during winter and summer season. Chemical analyses indicated the largest amounts of trimethoprim (up to 5.08 mg/kg) and azithromycin (up to 0.39 mg/kg) at DW0, but sulfonamides accumulated at DW3000 (total up to 1.17 mg/kg). Quantitative PCR revealed significantly increased relative abundance of various antibiotic resistance genes (ARGs) against β-lactams, macrolides, sulfonamides, trimethoprim and tetracyclines in sediments from DW0, despite relatively high background levels of some ARGs already at UP site. However, only sulfonamide (sul2) and macrolide ARG subtypes (mphG and msrE) were still elevated at DW3000 compared to UP. Sequencing of 16S rRNA genes revealed pronounced changes in the sediment bacterial community composition from both DW sites compared to UP site, regardless of the season. Numerous taxa with increased relative abundance at DW0 decreased to background levels at DW3000, suggesting die-off or lack of transport of effluent-originating bacteria. In contrast, various taxa that were more abundant in sediments than in effluents increased in relative abundance at DW3000 but not at DW0, possibly due to selection imposed by high sulfonamide levels. Network analysis revealed strong correlation between some clinically relevant ARGs (e.g. blaGES, blaOXA, ermB, tet39, sul2) and taxa with elevated abundance at DW sites, and known to harbour opportunistic pathogens, such as Acinetobacter, Arcobacter, Aeromonas and Shewanella. Our results demonstrate the necessity for improved management of pharmaceutical and rural waste disposal for mitigating the increasing problems with antibiotic resistance.
Collapse
Affiliation(s)
- Milena Milaković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Gisle Vestergaard
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany; Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Juan Jose González-Plaza
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ines Petrić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Josipa Kosić-Vukšić
- Andrija Štampar Teaching Institute of Public Health, Mirogojska cesta 16, 10 000 Zagreb, Croatia
| | - Ivan Senta
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Nikolina Udiković-Kolić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia.
| |
Collapse
|
22
|
Vuko M, Cania B, Vogel C, Kublik S, Schloter M, Schulz S. Shifts in reclamation management strategies shape the role of exopolysaccharide and lipopolysaccharide-producing bacteria during soil formation. Microb Biotechnol 2020; 13:584-598. [PMID: 31920012 PMCID: PMC7017822 DOI: 10.1111/1751-7915.13532] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/11/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022] Open
Abstract
Polymeric substances produced by microbes play a key role for the development of soil aggregates. Here, we investigated the dynamics of bacterial families contributing to the formation of exopolysaccharides and lipopolysaccharides, major constituents of polymeric substances, at a managed land reclamation site of a post-mining area. We collected soil samples from the initial and the agricultural management phase and expected a peak in the abundance of bacteria capable for exopolysaccharide and lipopolysaccharide production at the points of the biggest disturbances. We used shotgun metagenomic sequencing in combination with measurements of exopolysaccharide concentrations. Our results underline the importance of exopolysaccharide and lipopolysaccharide-producing bacteria after nutrient input combined with structural disturbance events, caused here by the initial planting of alfalfa and the introduction of a tillage regime together with organic fertilization in the agricultural management phase. Moreover, the changes in management caused a shift in the exopolysaccharide/lipopolysaccharide-producing community. The initial phase was dominated by typical colonizers of oligotrophic environments, specifically nitrogen fixers (Rhizobiaceae, Comamonadaceae, Hyphomicrobiaceae), while bacteria common in agricultural soils, such as Sphingomonadaceae, Oxalobacteraceae and Nitrospiraceae, prevailed in the agricultural management phase.
Collapse
Affiliation(s)
- Miljenka Vuko
- Research Unit Comparative Microbiome Analysis (COMI)Helmholtz Zentrum MünchenIngolstädter Landstr. 1DE‐85764NeuherbergGermany
- Chair of Soil ScienceTechnical University of MunichEmil‐Ramann‐Straße 2DE‐85354FreisingGermany
| | - Barbara Cania
- Research Unit Comparative Microbiome Analysis (COMI)Helmholtz Zentrum MünchenIngolstädter Landstr. 1DE‐85764NeuherbergGermany
| | - Cordula Vogel
- Institute of Soil Science and Site EcologyTechnical University of DresdenPienner Str. 19DE‐01737TharandtGermany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis (COMI)Helmholtz Zentrum MünchenIngolstädter Landstr. 1DE‐85764NeuherbergGermany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis (COMI)Helmholtz Zentrum MünchenIngolstädter Landstr. 1DE‐85764NeuherbergGermany
- Chair of Soil ScienceTechnical University of MunichEmil‐Ramann‐Straße 2DE‐85354FreisingGermany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis (COMI)Helmholtz Zentrum MünchenIngolstädter Landstr. 1DE‐85764NeuherbergGermany
| |
Collapse
|
23
|
Cania B, Vestergaard G, Kublik S, Köhne JM, Fischer T, Albert A, Winkler B, Schloter M, Schulz S. Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides. Microb Ecol 2020; 79:326-341. [PMID: 31372685 DOI: 10.1007/s00248-019-01415-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
Biological soil crusts (biocrusts) play an important role in improving soil stability and resistance to erosion by promoting aggregation of soil particles. During initial development, biocrusts are dominated by bacteria. Some bacterial members of the biocrusts can contribute to the formation of soil aggregates by producing exopolysaccharides and lipopolysaccharides that act as "glue" for soil particles. However, little is known about the dynamics of "soil glue" producers during the initial development of biocrusts. We hypothesized that different types of initial biocrusts harbor distinct producers of adhesive polysaccharides. To investigate this, we performed a microcosm experiment, cultivating biocrusts on two soil substrates. High-throughput shotgun sequencing was used to obtain metagenomic information on microbiomes of bulk soils from the beginning of the experiment, and biocrusts sampled after 4 and 10 months of incubation. We discovered that the relative abundance of genes involved in the biosynthesis of exopolysaccharides and lipopolysaccharides increased in biocrusts compared with bulk soils. At the same time, communities of potential "soil glue" producers that were highly similar in bulk soils underwent differentiation once biocrusts started to develop. In the bulk soils, the investigated genes were harbored mainly by Betaproteobacteria, whereas in the biocrusts, the major potential producers of adhesive polysaccharides were, aside from Alphaproteobacteria, either Cyanobacteria or Chloroflexi and Acidobacteria. Overall, our results indicate that the potential to form exopolysaccharides and lipopolysaccharides is an important bacterial trait for initial biocrusts and is maintained despite the shifts in bacterial community composition during biocrust development.
Collapse
Affiliation(s)
- Barbara Cania
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - John Maximilian Köhne
- Department of Soil System Science, Helmholtz Centre for Environmental Research (UFZ), Theodor-Lieser-Straße 4, 06120, Halle, Germany
| | - Thomas Fischer
- Central Analytical Laboratory, Brandenburg Technical University, Konrad-Wachsmann-Allee 6, 03046, Cottbus, Germany
| | - Andreas Albert
- Research Unit Environmental Simulation, Helmholtz Zentrum München Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Barbro Winkler
- Research Unit Environmental Simulation, Helmholtz Zentrum München Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- Chair for Soil Science, Technical University of Munich, Emil-Ramann-Straße 2, 85354, Freising, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
| |
Collapse
|
24
|
Mrkonjic Fuka M, Tanuwidjaja I, Zgomba Maksimovic A, Zunabovic-Pichler M, Kublik S, Hulak N, Domig KJ, Schloter M. Bacterial diversity of naturally fermented game meat sausages: Sources of new starter cultures. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2019.108782] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
25
|
Frank U, Kublik S, Mayer D, Engel M, Schloter M, Durner J, Gaupels F. A T-DNA mutant screen that combines high-throughput phenotyping with the efficient identification of mutated genes by targeted genome sequencing. BMC Plant Biol 2019; 19:539. [PMID: 31801481 PMCID: PMC6894221 DOI: 10.1186/s12870-019-2162-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Nitrogen dioxide (NO2) triggers hypersensitive response (HR)-like cell death in Arabidopsis thaliana. A high-throughput mutant screen was established to identify genes involved in this type of programmed cell death. RESULTS Altogether 14,282 lines of SALK T-DNA insertion mutants were screened. Growing 1000 pooled mutant lines per tray and simultaneous NO2 fumigation of 4 trays in parallel facilitated high-throughput screening. Candidate mutants were selected based on visible symptoms. Sensitive mutants showed lesions already after fumigation for 1 h with 10 ppm (ppm) NO2 whereas tolerant mutants were hardly damaged even after treatment with 30 ppm NO2. Identification of T-DNA insertion sites by adapter ligation-mediated PCR turned out to be successful but rather time consuming. Therefore, next generation sequencing after T-DNA-specific target enrichment was tested as an alternative screening method. The targeted genome sequencing was highly efficient due to (1.) combination of the pooled DNA from 124 candidate mutants in only two libraries, (2.) successful target enrichment using T-DNA border-specific 70mer probes, and (3.) stringent filtering of the sequencing reads. Seventy mutated genes were identified by at least 3 sequencing reads. Ten corresponding mutants were re-screened of which 8 mutants exhibited NO2-sensitivity or -tolerance confirming that the screen yielded reliable results. Identified candidate genes had published functions in HR, pathogen resistance, and stomata regulation. CONCLUSIONS The presented NO2 dead-or-alive screen combined with next-generation sequencing after T-DNA-specific target enrichment was highly efficient. Two researchers finished the screen within 3 months. Moreover, the target enrichment approach was cost-saving because of the limited number of DNA libraries and sequencing runs required. The experimental design can be easily adapted to other screening approaches e.g. involving high-throughput treatments with abiotic stressors or phytohormones.
Collapse
Affiliation(s)
- Ulrike Frank
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Dörte Mayer
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Marion Engel
- Scientific Computing Research Unit, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany
- Chair of Biochemical Plant Pathology, Technische Universität München, Freising, Germany
| | - Frank Gaupels
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, Neuherberg, Germany.
| |
Collapse
|
26
|
Radl V, Winkler JB, Kublik S, Yang L, Winkelmann T, Vestergaard G, Schröder P, Schloter M. Reduced microbial potential for the degradation of phenolic compounds in the rhizosphere of apple plantlets grown in soils affected by replant disease. Environ Microbiome 2019; 14:8. [PMID: 33902732 PMCID: PMC8204438 DOI: 10.1186/s40793-019-0346-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/07/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Apple replant disease (ARD) is a syndrome that occurs in areas where apple plants or closely related species have been previously cultivated. Even though ARD is a well-known phenomenon, which has been observed in different regions worldwide and occurs independent of the soil type, its causes still remain unclear. RESULTS As expected, the biomass of plants grown in replant soil was significantly lower compared to those grown in control (virgin) soil. A shotgun metagenome analysis showed a clear differentiation between the rhizosphere and bulk soil compartments independent from the soil used. However, significant differences associated with apple replant disease were only observed in the rhizosphere compartment, for which we detected changes in the abundance of major bacterial genera. Interestingly, reads assigned to Actinobacteria were significantly reduced in relative abundance in rhizosphere samples of the soil affected by replant disease. Even though reads assigned to pathogenic fungi were detected, their relative abundance was low and did not differ significantly between the two different soils. Differences in microbiome structure also resulted in shifts in functional pattern. We observed an increase in genes related to stress sensing in the rhizosphere of soils affected by replant disease, whereas genes linked to nutrient sensing and uptake dominated in control soils. Moreover, we observed a lower abundance of genes coding for enzymes which trigger the degradation of aromatic compounds in rhizosphere of soils affected by replant disease, which is probably connected with higher concentration of phenolic compounds, generally associated with disease progression. CONCLUSIONS Our study shows, for the first time, how apple replanting affects soil functioning by altering the soil microbiome. Particularly, the decrease in the abundance of genes which code for enzymes catalyzing the degradation of aromatic compounds, observed in the rhizosphere of plants grown in soil affected by apple replant disease, is of interest. Apple rootstocks are known to synthetize many phenolic compounds, including defense related phytoalexins, which have been considered for long to be connected with the emergence of replant disease. The knowledge gained in this study might help to develop targeted strategies to overcome or at least reduce the effects of ARD symptoms.
Collapse
Affiliation(s)
- Viviane Radl
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Jana Barbro Winkler
- Research Unit Environmental Simulations, Helmholtz Zentrum München, Munich, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Luhua Yang
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Traud Winkelmann
- Woody Plant and Propagation Physiology Section, Institute of Horticultural Production Systems, Leibniz Universität Hannover, Hanover, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Peter Schröder
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Munich, Germany
| |
Collapse
|
27
|
Hammerl V, Kastl EM, Schloter M, Kublik S, Schmidt H, Welzl G, Jentsch A, Beierkuhnlein C, Gschwendtner S. Influence of rewetting on microbial communities involved in nitrification and denitrification in a grassland soil after a prolonged drought period. Sci Rep 2019; 9:2280. [PMID: 30783152 PMCID: PMC6381133 DOI: 10.1038/s41598-018-38147-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 12/18/2018] [Indexed: 11/11/2022] Open
Abstract
The frequency of extreme drought and heavy rain events during the vegetation period will increase in Central Europe according to future climate change scenarios, which will affect the functioning of terrestrial ecosystems in multiple ways. In this study, we simulated an extreme drought event (40 days) at two different vegetation periods (spring and summer) to investigate season-related effects of drought and subsequent rewetting on nitrifiers and denitrifiers in a grassland soil. Abundance of the microbial groups of interest was assessed by quantification of functional genes (amoA, nirS/nirK and nosZ) via quantitative real-time PCR. Additionally, the diversity of ammonia-oxidizing archaea was determined based on fingerprinting of the archaeal amoA gene. Overall, the different time points of simulated drought and rewetting strongly influenced the obtained response pattern of microbial communities involved in N turnover as well as soil ammonium and nitrate dynamics. In spring, gene abundance of nirS was irreversible reduced after drought whereas nirK and nosZ remained unaffected. Furthermore, community composition of ammonia-oxidizing archaea was altered by subsequent rewetting although amoA gene abundance remained constant. In contrast, no drought/rewetting effects on functional gene abundance or diversity pattern of nitrifying archaea were observed in summer. Our results showed (I) high seasonal dependency of microbial community responses to extreme events, indicating a strong influence of plant-derived factors like vegetation stage and plant community composition and consequently close plant-microbe interactions and (II) remarkable resistance and/or resilience of functional microbial groups involved in nitrogen cycling to extreme weather events what might indicate that microbes in a silty soil are better adapted to stress situations as expected.
Collapse
Affiliation(s)
- Verena Hammerl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Chair for Soil Ecology - Technische Universität München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Eva-Maria Kastl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Holger Schmidt
- Institute of Natural Sciences - Universität Koblenz Landau, Campus Koblenz, Universitätsstraße 1, 56070, Koblenz, Germany
| | - Gerhard Welzl
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Anke Jentsch
- Disturbance Ecology - University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Carl Beierkuhnlein
- Chair of Biogeography - University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Silvia Gschwendtner
- Research Unit Comparative Microbiome Analysis - Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
| |
Collapse
|
28
|
Sáenz JS, Marques TV, Barone RSC, Cyrino JEP, Kublik S, Nesme J, Schloter M, Rath S, Vestergaard G. Oral administration of antibiotics increased the potential mobility of bacterial resistance genes in the gut of the fish Piaractus mesopotamicus. Microbiome 2019; 7:24. [PMID: 30773139 PMCID: PMC6378726 DOI: 10.1186/s40168-019-0632-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/21/2019] [Indexed: 05/29/2023]
Abstract
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.
Collapse
Affiliation(s)
- Johan S Sáenz
- Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, 85764, Germany
| | | | - Rafael Simões Coelho Barone
- Departamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz, University of São Paulo, Piracicaba, Brazil
| | - José Eurico Possebon Cyrino
- Departamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz, University of São Paulo, Piracicaba, Brazil
| | - Susanne Kublik
- Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, 85764, Germany
| | - Joseph Nesme
- Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, 85764, Germany
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Michael Schloter
- Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, 85764, Germany.
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354, Freising, Germany.
| | - Susanne Rath
- Institute of Chemistry, University of Campinas, Campinas, Brazil
| | - Gisle Vestergaard
- Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, 85764, Germany
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100, Copenhagen, Denmark
| |
Collapse
|
29
|
Milaković M, Vestergaard G, González-Plaza JJ, Petrić I, Šimatović A, Senta I, Kublik S, Schloter M, Smalla K, Udiković-Kolić N. Pollution from azithromycin-manufacturing promotes macrolide-resistance gene propagation and induces spatial and seasonal bacterial community shifts in receiving river sediments. Environ Int 2019; 123:501-511. [PMID: 30622075 DOI: 10.1016/j.envint.2018.12.050] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/05/2018] [Accepted: 12/22/2018] [Indexed: 06/09/2023]
Abstract
Effluents from antibiotic manufacturing may contain high concentrations of antibiotics, which are the main driving force behind the selection and spread of antibiotic resistance genes in the environment. However, our knowledge about the impact of such effluent discharges on the antibiotic resistome and bacterial communities is still limited. To gain insight into this impact, we collected effluents from an azithromycin-manufacturing industry discharge site as well as upstream and downstream sediments from the receiving Sava river during both winter and summer season. Chemical analyses of sediment and effluent samples indicated that the effluent discharge significantly increased the amount of macrolide antibiotics, heavy metals and nutrients in the receiving river sediments. Quantitative PCR revealed a significant increase of relative abundances of macrolide-resistance genes and class 1 integrons in effluent-impacted sediments. Amplicon sequencing of 16S rRNA genes showed spatial and seasonal bacterial community shifts in the receiving sediments. Redundancy analysis and Mantel test indicated that macrolides and copper together with nutrients significantly correlated with community shift close to the effluent discharge site. The number of taxa that were significantly increased in relative abundance at the discharge site decreased rapidly at the downstream sites, showing the resilience of the indigenous sediment bacterial community. Seasonal changes in the chemical properties of the sediment along with changes in effluent community composition could be responsible for sediment community shifts between winter and summer. Altogether, this study showed that the discharge of pharmaceutical effluents altered physicochemical characteristics and bacterial community of receiving river sediments, which contributed to the enrichment of macrolide-resistance genes and integrons.
Collapse
Affiliation(s)
- Milena Milaković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Juan J González-Plaza
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ines Petrić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ana Šimatović
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ivan Senta
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Kornelia Smalla
- Julius Kühn-Institut Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, D-38104 Braunschweig, Germany
| | - Nikolina Udiković-Kolić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia.
| |
Collapse
|
30
|
Grafe M, Goers M, von Tucher S, Baum C, Zimmer D, Leinweber P, Vestergaard G, Kublik S, Schloter M, Schulz S. Bacterial potentials for uptake, solubilization and mineralization of extracellular phosphorus in agricultural soils are highly stable under different fertilization regimes. Environ Microbiol Rep 2018; 10:320-327. [PMID: 29687664 DOI: 10.1111/1758-2229.12651] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 04/05/2018] [Accepted: 04/08/2018] [Indexed: 05/28/2023]
Abstract
Phosphorus is one of the most important macronutrient for plants. In agriculture, amending fertilizer with phosphorus (P) is common practice. However, natural phosphorus sources are finite, making research for more sustainable management practices necessary. We postulated that the addition of carbon (C) and nitrogen (N) would stimulate phosphorus mobilization by bacteria because of their desire to maintain a stable intracellular C:N:P stoichiometry. Therefore, we chose a metagenomic approach to investigate two agricultural soils, which only received mineral N fertilizer or mineral N and organic fertilizer for more than 20 years. The most abundant genes involved in the acquisition of external P sources in our study were those involved in solubilization and subsequent uptake of inorganic phosphorus. Independent of site and season, the relative abundance of genes involved in P turnover was not significantly affected by the addition of fertilizers. However, the type of fertilization had a significant impact on the diversity pattern of bacterial families harbouring genes coding for the different P transformation processes. This gives rise to the possibility that fertilizers can substantially change phosphorus turnover efficiency by favouring different families. Additionally, none of the families involved in phosphorus turnover covered all investigated processes. Therefore, promoting bacteria which play an essential role specifically in mobilization of hardly accessible phosphorus could help to secure the phosphorus supply of plants in soils with low P input.
Collapse
Affiliation(s)
- Martin Grafe
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg 85764, Germany
- Chair of Plant Nutrition, Technische Universität München Emil-Erlenmeyer-Forum 2, Freising 85354, Germany
| | - Manuela Goers
- Department of Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, Rostock 18051, Germany
| | - Sabine von Tucher
- Chair of Plant Nutrition, Technische Universität München Emil-Erlenmeyer-Forum 2, Freising 85354, Germany
| | - Christel Baum
- Department of Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, Rostock 18051, Germany
| | - Dana Zimmer
- Department of Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, Rostock 18051, Germany
| | - Peter Leinweber
- Department of Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, Rostock 18051, Germany
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg 85764, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg 85764, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg 85764, Germany
- Chair of Soil Science, Technische Universität München, Emil-Erlenmeyer-Forum 2, Freising 85354, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg 85764, Germany
| |
Collapse
|
31
|
Baraniya D, Nannipieri P, Kublik S, Vestergaard G, Schloter M, Schöler A. The Impact of the Diurnal Cycle on the Microbial Transcriptome in the Rhizosphere of Barley. Microb Ecol 2018; 75:830-833. [PMID: 29110064 DOI: 10.1007/s00248-017-1101-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 10/26/2017] [Indexed: 06/07/2023]
Abstract
While root exudation follows diurnal rhythms, little is known about the consequences for the microbiome of the rhizosphere. In this study, we used a metatranscriptomic approach to analyze the active microbial communities, before and after sunrise, in the rhizosphere of barley. We detected increased activities of many prokaryotic microbial taxa and functions at the pre-dawn stage, compared to post-dawn. Actinomycetales, Planctomycetales, Rhizobiales, and Burkholderiales were the most abundant and therefore the most active orders in the barley rhizosphere. The latter two, as well as Xanthomonadales, Sphingomonadales, and Caulobacterales showed a significantly higher abundance in pre-dawn samples compared to post-dawn samples. These changes in taxonomy coincide with functional changes as genes involved in both carbohydrate and amino acid metabolism were more abundant in pre-dawn samples compared to post-dawn samples. This study significantly enhances our present knowledge on how rhizospheric microbiota perceives and responds to changes in the soil during dark and light periods.
Collapse
Affiliation(s)
- Divyashri Baraniya
- Department of Agrifood Production and Environmental Sciences, University of Florence, Piazzale delle Cascine 28, 50144, Florence, Italy
| | - Paolo Nannipieri
- Department of Agrifood Production and Environmental Sciences, University of Florence, Piazzale delle Cascine 28, 50144, Florence, Italy
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Gisle Vestergaard
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
| | - Anne Schöler
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| |
Collapse
|
32
|
Šket R, Debevec T, Kublik S, Schloter M, Schoeller A, Murovec B, Vogel Mikuš K, Makuc D, Pečnik K, Plavec J, Mekjavić IB, Eiken O, Prevoršek Z, Stres B. Intestinal Metagenomes and Metabolomes in Healthy Young Males: Inactivity and Hypoxia Generated Negative Physiological Symptoms Precede Microbial Dysbiosis. Front Physiol 2018; 9:198. [PMID: 29593560 PMCID: PMC5859311 DOI: 10.3389/fphys.2018.00198] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/23/2018] [Indexed: 12/26/2022] Open
Abstract
We explored the metagenomic, metabolomic and trace metal makeup of intestinal microbiota and environment in healthy male participants during the run-in (5 day) and the following three 21-day interventions: normoxic bedrest (NBR), hypoxic bedrest (HBR) and hypoxic ambulation (HAmb) which were carried out within a controlled laboratory environment (circadian rhythm, fluid and dietary intakes, microbial bioburden, oxygen level, exercise). The fraction of inspired O2 (FiO2) and partial pressure of inspired O2 (PiO2) were 0.209 and 133.1 ± 0.3 mmHg for the NBR and 0.141 ± 0.004 and 90.0 ± 0.4 mmHg (~4,000 m simulated altitude) for HBR and HAmb interventions, respectively. Shotgun metagenomes were analyzed at various taxonomic and functional levels, 1H- and 13C -metabolomes were processed using standard quantitative and human expert approaches, whereas metals were assessed using X-ray fluorescence spectrometry. Inactivity and hypoxia resulted in a significant increase in the genus Bacteroides in HBR, in genes coding for proteins involved in iron acquisition and metabolism, cell wall, capsule, virulence, defense and mucin degradation, such as beta-galactosidase (EC3.2.1.23), α-L-fucosidase (EC3.2.1.51), Sialidase (EC3.2.1.18), and α-N-acetylglucosaminidase (EC3.2.1.50). In contrast, the microbial metabolomes, intestinal element and metal profiles, the diversity of bacterial, archaeal and fungal microbial communities were not significantly affected. The observed progressive decrease in defecation frequency and concomitant increase in the electrical conductivity (EC) preceded or took place in absence of significant changes at the taxonomic, functional gene, metabolome and intestinal metal profile levels. The fact that the genus Bacteroides and proteins involved in iron acquisition and metabolism, cell wall, capsule, virulence and mucin degradation were enriched at the end of HBR suggest that both constipation and EC decreased intestinal metal availability leading to modified expression of co-regulated genes in Bacteroides genomes. Bayesian network analysis was used to derive the first hierarchical model of initial inactivity mediated deconditioning steps over time. The PlanHab wash-out period corresponded to a profound life-style change (i.e., reintroduction of exercise) that resulted in stepwise amelioration of the negative physiological symptoms, indicating that exercise apparently prevented the crosstalk between the microbial physiology, mucin degradation and proinflammatory immune activities in the host.
Collapse
Affiliation(s)
- Robert Šket
- Group for Microbiology and Microbial Biotechnology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tadej Debevec
- Department of Automation, Biocybernetics and Robotics, Jozef Stefan Institute, Ljubljana, Slovenia.,Faculty of Sport, University of Ljubljana, Ljubljana, Slovenia
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Anne Schoeller
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Boštjan Murovec
- Machine Vision Laboratory, Faculty of Electrical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - Katarina Vogel Mikuš
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Damjan Makuc
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Klemen Pečnik
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Igor B Mekjavić
- Department of Automation, Biocybernetics and Robotics, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Ola Eiken
- Department of Environmental Physiology, Swedish Aerospace Physiology Centre, Royal Institute of Technology, Stockholm, Sweden
| | - Zala Prevoršek
- Group for Genetics, Animal Biotechnology and Immunology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Blaž Stres
- Group for Microbiology and Microbial Biotechnology, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,Center for Clinical Neurophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
33
|
Šket R, Treichel N, Kublik S, Debevec T, Eiken O, Mekjavić I, Schloter M, Vital M, Chandler J, Tiedje JM, Murovec B, Prevoršek Z, Likar M, Stres B. Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure: The PlanHab randomized trial pilot study. PLoS One 2017; 12:e0188556. [PMID: 29211803 PMCID: PMC5718606 DOI: 10.1371/journal.pone.0188556] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 11/07/2017] [Indexed: 12/27/2022] Open
Abstract
We explored the assembly of intestinal microbiota in healthy male participants during the randomized crossover design of run-in (5 day) and experimental phases (21-day normoxic bed rest (NBR), hypoxic bed rest (HBR) and hypoxic ambulation (HAmb) in a strictly controlled laboratory environment, with balanced fluid and dietary intakes, controlled circadian rhythm, microbial ambiental burden and 24/7 medical surveillance. The fraction of inspired O2 (FiO2) and partial pressure of inspired O2 (PiO2) were 0.209 and 133.1 ± 0.3 mmHg for NBR and 0.141 ± 0.004 and 90.0 ± 0.4 mmHg for both hypoxic variants (HBR and HAmb; ~4000 m simulated altitude), respectively. A number of parameters linked to intestinal environment such as defecation frequency, intestinal electrical conductivity (IEC), sterol and polyphenol content and diversity, indole, aromaticity and spectral characteristics of dissolved organic matter (DOM) were measured (64 variables). The structure and diversity of bacterial microbial community was assessed using 16S rRNA amplicon sequencing. Inactivity negatively affected frequency of defecation and in combination with hypoxia increased IEC (p < 0.05). In contrast, sterol and polyphenol diversity and content, various characteristics of DOM and aromatic compounds, the structure and diversity of bacterial microbial community were not significantly affected over time. A new in-house PlanHab database was established to integrate all measured variables on host physiology, diet, experiment, immune and metabolic markers (n = 231). The observed progressive decrease in defecation frequency and concomitant increase in IEC suggested that the transition from healthy physiological state towards the developed symptoms of low magnitude obesity-related syndromes was dose dependent on the extent of time spent in inactivity and preceded or took place in absence of significant rearrangements in bacterial microbial community. Species B. thetaiotamicron, B. fragilis, B. dorei and other Bacteroides with reported relevance for dysbiotic medical conditions were significantly enriched in HBR, characterized with most severe inflammation symptoms, indicating a shift towards host mucin degradation and proinflammatory immune crosstalk.
Collapse
Affiliation(s)
- Robert Šket
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nicole Treichel
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Tadej Debevec
- Department of Automation, Biocybernetics and Robotics, Jozef Stefan Institute, Ljubljana, Slovenia
- University of Ljubljana, Faculty of Sport, Ljubljana, Slovenia
| | - Ola Eiken
- Department of Environmental Physiology, Swedish Aerospace Physiology Centre, Royal Institute of Technology, Stockholm, Sweden
| | - Igor Mekjavić
- Department of Automation, Biocybernetics and Robotics, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Marius Vital
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jenna Chandler
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, United States of America
| | - Boštjan Murovec
- Laboratory for Artificial Sight and Automation, Faculty of Electrical Sciences, University of Ljubljana, Ljubljana, Slovenia
| | - Zala Prevoršek
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Matevž Likar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Blaž Stres
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Center for Clinical Neurophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- * E-mail:
| |
Collapse
|
34
|
Uksa M, Buegger F, Gschwendtner S, Lueders T, Kublik S, Kautz T, Athmann M, Köpke U, Munch JC, Schloter M, Fischer D. Bacteria utilizing plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil. Environ Microbiol Rep 2017; 9:729-741. [PMID: 28892269 DOI: 10.1111/1758-2229.12588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Root exudates shape microbial communities at the plant-soil interface. Here we compared bacterial communities that utilize plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a greenhouse using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant-derived carbon, 13 C-CO2 labelling of plants was performed for two weeks at the EC50 stage, followed by isopycnic density gradient centrifugation of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing. Our findings suggest substantially different bacterial key players and interaction mechanisms between plants and bacteria utilizing plant-derived carbon in the rhizosphere of subsoils and topsoil. Among the three soil depths, clear differences were found in 13 C enrichment pattern across abundant operational taxonomic units (OTUs). Whereas, OTUs linked to Proteobacteria were enriched in 13 C mainly in the topsoil, in both subsoil layers OTUs related to Cohnella, Paenibacillus, Flavobacterium showed a clear 13 C signal, indicating an important, so far overseen role of Firmicutes and Bacteriodetes in the subsoil rhizosphere.
Collapse
Affiliation(s)
- Marie Uksa
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
- Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, D-70599 Stuttgart, Germany
| | - Franz Buegger
- Institute of Biochemical Plant Pathology, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| | - Silvia Gschwendtner
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| | - Tillmann Lueders
- Institute for Groundwater Ecology, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| | - Timo Kautz
- Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
| | - Miriam Athmann
- Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
| | - Ulrich Köpke
- Institute of Organic Agriculture, University of Bonn, D-53115 Bonn, Germany
| | - Jean Charles Munch
- Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, D-70599 Stuttgart, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
- Chair for Soil Science, Research Department Ecology and Ecosystem Management, Technische Universität München, D-85350 Freising-Weihenstephan, Germany
| | - Doreen Fischer
- Research Unit for Comparative Microbiome Analysis, Department of Environmental Science, Helmholtz Zentrum München, D-85758 Oberschleissheim, Germany
| |
Collapse
|
35
|
Engel M, Endesfelder D, Schloter-Hai B, Kublik S, Granitsiotis MS, Boschetto P, Stendardo M, Barta I, Dome B, Deleuze JF, Boland A, Müller-Quernheim J, Prasse A, Welte T, Hohlfeld J, Subramanian D, Parr D, Gut IG, Greulich T, Koczulla AR, Nowinski A, Gorecka D, Singh D, Gupta S, Brightling CE, Hoffmann H, Frankenberger M, Hofer TP, Burggraf D, Heiss-Neumann M, Ziegler-Heitbrock L, Schloter M, zu Castell W. Influence of lung CT changes in chronic obstructive pulmonary disease (COPD) on the human lung microbiome. PLoS One 2017; 12:e0180859. [PMID: 28704452 PMCID: PMC5509234 DOI: 10.1371/journal.pone.0180859] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/22/2017] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Changes in microbial community composition in the lung of patients suffering from moderate to severe COPD have been well documented. However, knowledge about specific microbiome structures in the human lung associated with CT defined abnormalities is limited. METHODS Bacterial community composition derived from brush samples from lungs of 16 patients suffering from different CT defined subtypes of COPD and 9 healthy subjects was analyzed using a cultivation independent barcoding approach applying 454-pyrosequencing of 16S rRNA gene fragment amplicons. RESULTS We could show that bacterial community composition in patients with changes in CT (either airway or emphysema type changes, designated as severe subtypes) was different from community composition in lungs of patients without visible changes in CT as well as from healthy subjects (designated as mild COPD subtype and control group) (PC1, Padj = 0.002). Higher abundance of Prevotella in samples from patients with mild COPD subtype and from controls and of Streptococcus in the severe subtype cases mainly contributed to the separation of bacterial communities of subjects. No significant effects of treatment with inhaled glucocorticoids on bacterial community composition were detected within COPD cases with and without abnormalities in CT in PCoA. Co-occurrence analysis suggests the presence of networks of co-occurring bacteria. Four communities of positively correlated bacteria were revealed. The microbial communities can clearly be distinguished by their associations with the CT defined disease phenotype. CONCLUSION Our findings indicate that CT detectable structural changes in the lung of COPD patients, which we termed severe subtypes, are associated with alterations in bacterial communities, which may induce further changes in the interaction between microbes and host cells. This might result in a changed interplay with the host immune system.
Collapse
Affiliation(s)
- Marion Engel
- Scientific Computing Research Unit, Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - David Endesfelder
- Scientific Computing Research Unit, Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Brigitte Schloter-Hai
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael S. Granitsiotis
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Piera Boschetto
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | | | - Imre Barta
- Department of Pathophysiology, National Koranyi Institute for TB and Pulmonology, Budapest, Hungary
| | - Balazs Dome
- Department of Pathophysiology, National Koranyi Institute for TB and Pulmonology, Budapest, Hungary
| | | | - Anne Boland
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | | | - Antje Prasse
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
- Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Tobias Welte
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
- Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Jens Hohlfeld
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
- Member of the German Center for Lung Research (DZL), Giessen, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Deepak Subramanian
- Department of Respiratory Medicine, University Hospitals Coventry and Warwickshire NHS Trust, Coventry, United Kingdom
| | - David Parr
- Department of Respiratory Medicine, University Hospitals Coventry and Warwickshire NHS Trust, Coventry, United Kingdom
| | - Ivo Glynne Gut
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Timm Greulich
- Member of the German Center for Lung Research (DZL), Giessen, Germany
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Giessen and Marburg Philipps-University, Marburg, Germany
| | - Andreas Rembert Koczulla
- Member of the German Center for Lung Research (DZL), Giessen, Germany
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Giessen and Marburg Philipps-University, Marburg, Germany
| | - Adam Nowinski
- Second Department of Respiratory Medicine, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Dorota Gorecka
- Second Department of Respiratory Medicine, National Tuberculosis and Lung Diseases Research Institute, Warsaw, Poland
| | - Dave Singh
- University of Manchester, Medicines Evaluation Unit and University Hospital of South Manchester Foundation Trust, Manchester, United Kingdom
| | - Sumit Gupta
- Institute for Lung Health, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
| | - Christopher E. Brightling
- Institute for Lung Health, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
| | - Harald Hoffmann
- Institute of Microbiology and Laboratory Medicine, Synlab MVZ Gauting & IML red GmbH, Gauting, Germany
| | - Marion Frankenberger
- CPC Comprehensive Pneumology Center, Helmholtz Zentrum München, Ludwig-Maximilians Universität und Asklepios Klinik Gauting, Munich, Germany
| | - Thomas P. Hofer
- EvA Study Center, Helmholtz Zentrum Muenchen, Gauting, Germany
| | | | | | | | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Wolfgang zu Castell
- Scientific Computing Research Unit, Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Mathematics, Technische Universität München, Munich, Germany
| |
Collapse
|
36
|
Proença DN, Francisco R, Kublik S, Schöler A, Vestergaard G, Schloter M, Morais PV. The Microbiome of Endophytic, Wood Colonizing Bacteria from Pine Trees as Affected by Pine Wilt Disease. Sci Rep 2017. [PMID: 28646202 PMCID: PMC5482821 DOI: 10.1038/s41598-017-04141-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Pine wilt disease (PWD) is a devastating forest disease present worldwide. In this study we analyzed the effects of the invasion of the pinewood nematode Bursaphelenchus xylophilus, the major pathogen causing PWD, on the endophytic microbiome of adult P. pinaster trees. Wood samples from trees with different degrees of PWD disease were collected at two sites (A and M) in Portugal. Endophytic bacteria were characterized based on directly extracted DNA by fingerprinting and barcoding using the 16S rRNA gene as marker. Furthermore, cultivation-based approaches were used to obtain isolates of the major taxa to study their ecophysiology. The endophytic microbiome from P. pinaster trees differed significantly between the two sampling sites. Main bacterial OTUs belonged to the Proteobacteria (39% (site M) - 97% (site A)), and Firmicutes (0.70% (site A) - 44% (site M)). However, consequences of the invasion with the pathogen were comparable. Interestingly diversity of wood endophytic bacteria increased with the severity of the diseases, with highest diversity levels observed in in the most affected trees. Our results suggest that in the first stages of the disease, the defence mechanisms of plants are repressed by the pathogen, resulting in a colonization of the wood interior by soil microorganisms.
Collapse
Affiliation(s)
| | | | - Susanne Kublik
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Munich, Germany
| | - Anne Schöler
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Munich, Germany
| | - Gisle Vestergaard
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Munich, Germany
| | - Michael Schloter
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Munich, Germany.
| | - Paula V Morais
- CEMMPRE, University of Coimbra, Coimbra, Portugal.,Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| |
Collapse
|
37
|
Wasserstrom H, Kublik S, Wasserstrom R, Schulz S, Schloter M, Steinberger Y. Bacterial community composition in costal dunes of the Mediterranean along a gradient from the sea shore to the inland. Sci Rep 2017; 7:40266. [PMID: 28074923 PMCID: PMC5225477 DOI: 10.1038/srep40266] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/05/2016] [Indexed: 11/09/2022] Open
Abstract
Sand dunes are unique ecosystems with distinct features which limited the accumulation of biomass. The distance from seashore affects both the physical properties of the sand dunes and the biota living above- and below ground. The goal of the present study was to determine the effects of the distance from shore to inland on soil bacterial community composition during wet and dry season. We studied a chronosequence of sites close to the eastern Mediterranean coast. Bacterial diversity was assessed using directly extracted DNA from soil samples and 16 S ribosomal RNA gene fingerprinting. Our data indicates a significant influence of season and site on bacterial community structure. We showed that during the wet season soil organic matter, pH and salinity strongly influence bacterial community composition, whereas during the dry period bacterial diversity was mainly driven by the shortage of water at all sites. Consequently diversity was lowest during dry season at dunes close to the shore, whereas during the wet season the higher water content and the reduced salinity at the dunes which are more at the inland induced an increase in diversity, which illustrates the pronounced dynamics of microbial communities in soil over a season mainly at inland dunes.
Collapse
Affiliation(s)
- Haggai Wasserstrom
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Susanne Kublik
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Rachel Wasserstrom
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Stefanie Schulz
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Yosef Steinberger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| |
Collapse
|
38
|
Birzele LT, Depner M, Ege MJ, Engel M, Kublik S, Bernau C, Loss GJ, Genuneit J, Horak E, Schloter M, Braun-Fahrländer C, Danielewicz H, Heederik D, von Mutius E, Legatzki A. Environmental and mucosal microbiota and their role in childhood asthma. Allergy 2017; 72:109-119. [PMID: 27503830 DOI: 10.1111/all.13002] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2016] [Indexed: 12/27/2022]
Abstract
BACKGROUND High microbial diversity in the environment has been associated with lower asthma risk, particularly in children exposed to farming. It remains unclear whether this effect operates through an altered microbiome of the mucosal surfaces of the airways. METHODS DNA from mattress dust and nasal samples of 86 school age children was analyzed by 454 pyrosequencing of the 16S rRNA gene fragments. Based on operational taxonomic units (OTUs), bacterial diversity and composition were related to farm exposure and asthma status. RESULTS Farm exposure was positively associated with bacterial diversity in mattress dust samples as determined by richness (P = 8.1 × 10-6 ) and Shannon index (P = 1.3 × 10-5 ). Despite considerable agreement of richness between mattress and nasal samples, the association of richness with farming in nasal samples was restricted to a high gradient of farm exposure, that is, exposure to cows and straw vs no exposure at all. In mattress dust, the genera Clostridium, Facklamia, an unclassified genus within the family of Ruminococcaceae, and six OTUs were positively associated with farming. Asthma was inversely associated with richness [aOR = 0.48 (0.22-1.02)] and Shannon index [aOR = 0.41 (0.21-0.83)] in mattress dust and to a lower extent in nasal samples [richness aOR 0.63 = (0.38-1.06), Shannon index aOR = 0.66 (0.39-1.12)]. CONCLUSION The stronger inverse association of asthma with bacterial diversity in mattress dust as compared to nasal samples suggests microbial involvement beyond mere colonization of the upper airways. Whether inhalation of metabolites of environmental bacteria contributes to this phenomenon should be the focus of future research.
Collapse
Affiliation(s)
- L. T. Birzele
- Dr. von Hauner Children's Hospital; LMU Munich; Munich Germany
| | - M. Depner
- Dr. von Hauner Children's Hospital; LMU Munich; Munich Germany
| | - M. J. Ege
- Dr. von Hauner Children's Hospital; LMU Munich; Munich Germany
- Member of the German Center for Lung Research (DZL); Munich Germany
| | - M. Engel
- Research Unit Scientific Computing; Helmholtz Center Munich; Neuherberg Germany
- Research Unit for Environmental Genomics; Helmholtz Center Munich; Neuherberg Germany
| | - S. Kublik
- Research Unit for Environmental Genomics; Helmholtz Center Munich; Neuherberg Germany
| | - C. Bernau
- Leibniz Supercomputing Center of the Bavarian Academy of Sciences and Humanities; Garching Germany
| | - G. J. Loss
- Dr. von Hauner Children's Hospital; LMU Munich; Munich Germany
- Department of Pediatrics; School of Medicine; University of California; San Diego CA USA
| | - J. Genuneit
- Institute of Epidemiology and Medical Biometry; Ulm University; Ulm Germany
| | - E. Horak
- Division of Cardiology and Pulmonology; Department of Pediatrics and Adolescents; Innsbruck Medical University; Innsbruck Austria
| | - M. Schloter
- Research Unit for Environmental Genomics; Helmholtz Center Munich; Neuherberg Germany
| | - C. Braun-Fahrländer
- Swiss Tropical and Public Health Institute; Basel Switzerland
- Department of Epidemiology and Public Health; University of Basel; Basel Switzerland
| | - H. Danielewicz
- Department of Pediatrics, Allergology and Cardiology; Wroclaw Medical University; Wroclaw Poland
| | - D. Heederik
- Division of Environmental Epidemiology; Institute for Risk Assessment Sciences; University of Utrecht; Utrecht The Netherlands
| | - E. von Mutius
- Dr. von Hauner Children's Hospital; LMU Munich; Munich Germany
- Member of the German Center for Lung Research (DZL); Munich Germany
| | - A. Legatzki
- Dr. von Hauner Children's Hospital; LMU Munich; Munich Germany
| |
Collapse
|
39
|
Talk A, Kublik S, Uksa M, Engel M, Berghahn R, Welzl G, Schloter M, Mohr S. Effects of multiple but low pesticide loads on aquatic fungal communities colonizing leaf litter. J Environ Sci (China) 2016; 46:116-125. [PMID: 27521943 DOI: 10.1016/j.jes.2015.11.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 08/27/2015] [Accepted: 11/19/2015] [Indexed: 06/06/2023]
Abstract
In the first tier risk assessment (RA) of pesticides, risk for aquatic communities is estimated by using results from standard laboratory tests with algae, daphnids and fish for single pesticides such as herbicides, fungicides, and insecticides. However, fungi as key organisms for nutrient cycling in ecosystems as well as multiple pesticide applications are not considered in the RA. In this study, the effects of multiple low pesticide pulses using regulatory acceptable concentrations (RACs) on the dynamics of non-target aquatic fungi were investigated in a study using pond mesocosm. For that, fungi colonizing black alder (Alnus glutinosa) leaves were exposed to multiple, low pulses of 11 different pesticides over a period of 60days using a real farmer's pesticide application protocol for apple cropping. Four pond mesocosms served as treatments and 4 as controls. The composition of fungal communities colonizing the litter material was analyzed using a molecular fingerprinting approach based on the terminal Restriction Fragment Length Polymorphism (t-RFLP) of the fungal Internal Transcribed Spacer (ITS) region of the ribonucleic acid (RNA) gene(s). Our data indicated a clear fluctuation of fungal communities based on the degree of leaf litter degradation. However significant effects of the applied spraying sequence were not observed. Consequently also degradation rates of the litter material were not affected by the treatments. Our results indicate that the nutrient rich environment of the leaf litter material gave fungal communities the possibility to express genes that induce tolerance against the applied pesticides. Thus our data may not be transferred to other fresh water habitats with lower nutrient availability.
Collapse
Affiliation(s)
- Anne Talk
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
| | - Susanne Kublik
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Marie Uksa
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Marion Engel
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | | | - Gerhard Welzl
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Michael Schloter
- Research Unit Environmental Genomics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
| | - Silvia Mohr
- Umweltbundesamt, Schichauweg 58, 12307, Berlin, Germany
| |
Collapse
|
40
|
Gschwendtner S, Mansfeldt T, Kublik S, Touliari E, Buegger F, Schloter M. Long-term ferrocyanide application via deicing salts promotes the establishment of Actinomycetales assimilating ferrocyanide-derived carbon in soil. Microb Biotechnol 2016; 9:502-13. [PMID: 27194597 PMCID: PMC4919992 DOI: 10.1111/1751-7915.12362] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 03/18/2016] [Accepted: 03/28/2016] [Indexed: 11/28/2022] Open
Abstract
Cyanides are highly toxic and produced by various microorganisms as defence strategy or to increase their competitiveness. As degradation is the most efficient way of detoxification, some microbes developed the capability to use cyanides as carbon and nitrogen source. However, it is not clear if this potential also helps to lower cyanide concentrations in roadside soils where deicing salt application leads to significant inputs of ferrocyanide. The question remains if biodegradation in soils can occur without previous photolysis. By conducting a microcosm experiment using soils with/without pre-exposition to road salts spiked with (13) C-labelled ferrocyanide, we were able to confirm biodegradation and in parallel to identify bacteria using ferrocyanide as C source via DNA stable isotope probing (DNA-SIP), TRFLP fingerprinting and pyrosequencing. Bacteria assimilating (13) C were highly similar in the pre-exposed soils, belonging mostly to Actinomycetales (Kineosporia, Mycobacterium, Micromonosporaceae). In the soil without pre-exposition, bacteria belonging to Acidobacteria (Gp3, Gp4, Gp6), Gemmatimonadetes (Gemmatimonas) and Gammaproteobacteria (Thermomonas, Xanthomonadaceae) used ferrocyanide as C source but not the present Actinomycetales. This indicated that (i) various bacteria are able to assimilate ferrocyanide-derived C and (ii) long-term exposition to ferrocyanide applied with deicing salts leads to Actinomycetales outcompeting other microorganisms for the use of ferrocyanide as C source.
Collapse
Affiliation(s)
- Silvia Gschwendtner
- Research Unit Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Tim Mansfeldt
- Department Geowissenschaften, Bodengeographie/Bodenkunde, Universität zu Köln, Albertus-Magnus-Platz, Köln, 50923, Germany
| | - Susanne Kublik
- Research Unit Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Evangelia Touliari
- Research Unit Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Franz Buegger
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Michael Schloter
- Research Unit Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| |
Collapse
|
41
|
Gschwendtner S, Alatossava T, Kublik S, Fuka MM, Schloter M, Munsch-Alatossava P. N2 Gas Flushing Alleviates the Loss of Bacterial Diversity and Inhibits Psychrotrophic Pseudomonas during the Cold Storage of Bovine Raw Milk. PLoS One 2016; 11:e0146015. [PMID: 26730711 PMCID: PMC4701220 DOI: 10.1371/journal.pone.0146015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/12/2015] [Indexed: 01/28/2023] Open
Abstract
The quality and safety of raw milk still remains a worldwide challenge. Culture-dependent methods indicated that the continuous N2 gas-flushing of raw milk reduced the bacterial growth during cold storage by up to four orders of magnitude, compared to cold storage alone. This study investigated the influence of N2 gas-flushing on bacterial diversity in bovine raw-milk samples, that were either cold stored at 6°C or additionally flushed with pure N2 for up to one week. Next-generation sequencing (NGS) of the V1-V2 hypervariable regions of 16S rRNA genes, derived from amplified cDNA, which was obtained from RNA directly isolated from raw-milk samples, was performed. The reads, which were clustered into 2448 operational taxonomic units (OTUs), were phylogenetically classified. Our data revealed a drastic reduction in the diversity of OTUs in raw milk during cold storage at 6°C at 97% similarity level; but, the N2-flushing treatment alleviated this reduction and substantially limited the loss of bacterial diversity during the same cold-storage period. Compared to cold-stored milk, the initial raw-milk samples contained less Proteobacteria (mainly Pseudomonadaceae, Moraxellaceae and Enterobacteriaceae) but more Firmicutes (mainly Ruminococcaceaea, Lachnospiraceae and Oscillospiraceaea) and Bacteroidetes (mainly Bacteroidales). Significant differences between cold-stored and additionally N2-flushed milk were mainly related to higher levels of Pseudomononadaceae (including the genera Pseudomonas and Acinetobacter) in cold-stored milk samples; furthermore, rare taxa were better preserved by the N2 gas flushing compared to the cold storage alone. No major changes in bacterial composition with time were found regarding the distribution of the major 9 OTUs, that dominated the Pseudomonas genus in N2-flushed or non-flushed milk samples, other than an intriguing predominance of bacteria related to P. veronii. Overall, this study established that neither bacteria causing milk spoilage nor any well-known human pathogen or anaerobe benefited from the N2 gas flushing even though the N2-flushed and non-flushed cold-stored milk differed in bacterial counts by up to 104-fold.
Collapse
Affiliation(s)
- Silvia Gschwendtner
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tapani Alatossava
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Susanne Kublik
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Mirna Mrkonjić Fuka
- Department of Microbiology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Michael Schloter
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, Neuherberg, Germany
| | | |
Collapse
|
42
|
Leite J, Fischer D, Rouws LFM, Fernandes-Júnior PI, Hofmann A, Kublik S, Schloter M, Xavier GR, Radl V. Cowpea Nodules Harbor Non-rhizobial Bacterial Communities that Are Shaped by Soil Type Rather than Plant Genotype. Front Plant Sci 2016; 7:2064. [PMID: 28163711 PMCID: PMC5247471 DOI: 10.3389/fpls.2016.02064] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 12/26/2016] [Indexed: 05/04/2023]
Abstract
Many studies have been pointing to a high diversity of bacteria associated to legume root nodules. Even though most of these bacteria do not form nodules with legumes themselves, it was shown that they might enter infection threads when co-inoculated with rhizobial strains. The aim of this work was to describe the diversity of bacterial communities associated with cowpea (Vigna unguiculata L. Walp) root nodules using 16S rRNA gene amplicon sequencing, regarding the factors plant genotype and soil type. As expected, Bradyrhizobium was the most abundant genus of the detected genera. Furthermore, we found a high bacterial diversity associated to cowpea nodules; OTUs related to the genera Enterobacter, Chryseobacterium, Sphingobacterium, and unclassified Enterobacteriacea were the most abundant. The presence of these groups was significantly influenced by the soil type and, to a lesser extent, plant genotype. Interestingly, OTUs assigned to Chryseobacterium were highly abundant, particularly in samples obtained from an Ultisol soil. We confirmed their presence in root nodules and assessed their diversity using a target isolation approach. Though their functional role still needs to be addressed, we postulate that Chryseobacterium strains might help cowpea plant to cope with salt stress in semi-arid regions.
Collapse
Affiliation(s)
- Jakson Leite
- Soil Science Department, Universidade Federal Rural do Rio de JaneiroSeropédica, Brazil
| | - Doreen Fischer
- Embrapa AgrobiologiaSeropédica, Brazil
- Research Unit Environmental Genomics, Helmholtz Zentrum MünchenOberschleißheim, Germany
| | | | | | - Andreas Hofmann
- Embrapa AgrobiologiaSeropédica, Brazil
- Research Unit Environmental Genomics, Helmholtz Zentrum MünchenOberschleißheim, Germany
| | - Susanne Kublik
- Research Unit Environmental Genomics, Helmholtz Zentrum MünchenOberschleißheim, Germany
| | - Michael Schloter
- Research Unit Environmental Genomics, Helmholtz Zentrum MünchenOberschleißheim, Germany
| | | | - Viviane Radl
- Research Unit Environmental Genomics, Helmholtz Zentrum MünchenOberschleißheim, Germany
- *Correspondence: Viviane Radl,
| |
Collapse
|
43
|
Uksa M, Schloter M, Endesfelder D, Kublik S, Engel M, Kautz T, Köpke U, Fischer D. Prokaryotes in Subsoil-Evidence for a Strong Spatial Separation of Different Phyla by Analysing Co-occurrence Networks. Front Microbiol 2015; 6:1269. [PMID: 26635741 PMCID: PMC4649028 DOI: 10.3389/fmicb.2015.01269] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 10/30/2015] [Indexed: 02/03/2023] Open
Abstract
Microbial communities in soil provide a wide range of ecosystem services. On the small scale, nutrient rich hotspots in soil developed from the activities of animals or plants are important drivers for the composition of microbial communities and their functional patterns. However, in subsoil, the spatial heterogeneity of microbes with differing lifestyles has been rarely considered so far. In this study, the phylogenetic composition of the bacterial and archaeal microbiome based on 16S rRNA gene pyrosequencing was investigated in the soil compartments bulk soil, drilosphere, and rhizosphere in top- and in the subsoil of an agricultural field. With co-occurrence network analysis, the spatial separation of typically oligotrophic and copiotrophic microbes was assessed. Four bacterial clusters were identified and attributed to bulk topsoil, bulk subsoil, drilosphere, and rhizosphere. The bacterial phyla Proteobacteria and Bacteroidetes, representing mostly copiotrophic bacteria, were affiliated mainly to the rhizosphere and drilosphere—both in topsoil and subsoil. Acidobacteria, Actinobacteria, Gemmatimonadetes, Planctomycetes, and Verrucomicrobia, bacterial phyla which harbor many oligotrophic bacteria, were the most abundant groups in bulk subsoil. The bacterial core microbiome in this soil was estimated to cover 7.6% of the bacterial sequencing reads including both oligotrophic and copiotrophic bacteria. In contrast the archaeal core microbiome includes 56% of the overall archaeal diversity. Thus, the spatial variability of nutrient quality and quantity strongly shapes the bacterial community composition and their interaction in subsoil, whereas archaea build a stable backbone of the soil prokaryotes due to their low variability in the different soil compartments.
Collapse
Affiliation(s)
- Marie Uksa
- Research Unit Environmental Genomics, Department of Environmental Science, Helmholtz Zentrum München Oberschleissheim, Germany
| | - Michael Schloter
- Research Unit Environmental Genomics, Department of Environmental Science, Helmholtz Zentrum München Oberschleissheim, Germany
| | - David Endesfelder
- Scientific Computing Research Unit, Institute of Computational Biology, Helmholtz Zentrum München Oberschleissheim, Germany
| | - Susanne Kublik
- Research Unit Environmental Genomics, Department of Environmental Science, Helmholtz Zentrum München Oberschleissheim, Germany
| | - Marion Engel
- Scientific Computing Research Unit, Institute of Computational Biology, Helmholtz Zentrum München Oberschleissheim, Germany
| | - Timo Kautz
- Institute of Organic Agriculture, University of Bonn Bonn, Germany
| | - Ulrich Köpke
- Institute of Organic Agriculture, University of Bonn Bonn, Germany
| | - Doreen Fischer
- Research Unit Environmental Genomics, Department of Environmental Science, Helmholtz Zentrum München Oberschleissheim, Germany
| |
Collapse
|
44
|
Stempfhuber B, Engel M, Fischer D, Neskovic-Prit G, Wubet T, Schöning I, Gubry-Rangin C, Kublik S, Schloter-Hai B, Rattei T, Welzl G, Nicol GW, Schrumpf M, Buscot F, Prosser JI, Schloter M. pH as a Driver for Ammonia-Oxidizing Archaea in Forest Soils. Microb Ecol 2015; 69:879-883. [PMID: 25501889 DOI: 10.1007/s00248-014-0548-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/27/2014] [Indexed: 06/04/2023]
Abstract
In this study, we investigated the impact of soil pH on the diversity and abundance of archaeal ammonia oxidizers in 27 different forest soils across Germany. DNA was extracted from topsoil samples, the amoA gene, encoding ammonia monooxygenase, was amplified; and the amplicons were sequenced using a 454-based pyrosequencing approach. As expected, the ratio of archaeal (AOA) to bacterial (AOB) ammonia oxidizers' amoA genes increased sharply with decreasing soil pH. The diversity of AOA differed significantly between sites with ultra-acidic soil pH (<3.5) and sites with higher pH values. The major OTUs from soil samples with low pH could be detected at each site with a soil pH <3.5 but not at sites with pH >4.5, regardless of geographic position and vegetation. These OTUs could be related to the Nitrosotalea group 1.1 and the Nitrososphaera subcluster 7.2, respectively, and showed significant similarities to OTUs described from other acidic environments. Conversely, none of the major OTUs typical of sites with a soil pH >4.6 could be found in the ultra- and extreme acidic soils. Based on a comparison with the amoA gene sequence data from a previous study performed on agricultural soils, we could clearly show that the development of AOA communities in soils with ultra-acidic pH (<3.5) is mainly triggered by soil pH and is not influenced significantly by the type of land use, the soil type, or the geographic position of the site, which was observed for sites with acido-neutral soil pH.
Collapse
Affiliation(s)
- Barbara Stempfhuber
- Environmental Genomics, Helmholtz Zentrum München, German Research Centre for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Gschwendtner S, Leberecht M, Engel M, Kublik S, Dannenmann M, Polle A, Schloter M. Effects of Elevated Atmospheric CO2 on Microbial Community Structure at the Plant-Soil Interface of Young Beech Trees (Fagus sylvatica L.) Grown at Two Sites with Contrasting Climatic Conditions. Microb Ecol 2015; 69:867-878. [PMID: 25370887 DOI: 10.1007/s00248-014-0527-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 10/21/2014] [Indexed: 06/04/2023]
Abstract
Soil microbial community responses to elevated atmospheric CO2 concentrations (eCO2) occur mainly indirectly via CO2-induced plant growth stimulation leading to quantitative as well as qualitative changes in rhizodeposition and plant litter. In order to gain insight into short-term, site-specific effects of eCO2 on the microbial community structure at the plant-soil interface, young beech trees (Fagus sylvatica L.) from two opposing mountainous slopes with contrasting climatic conditions were incubated under ambient (360 ppm) CO2 concentrations in a greenhouse. One week before harvest, half of the trees were incubated for 2 days under eCO2 (1,100 ppm) conditions. Shifts in the microbial community structure in the adhering soil as well as in the root rhizosphere complex (RRC) were investigated via TRFLP and 454 pyrosequencing based on 16S ribosomal RNA (rRNA) genes. Multivariate analysis of the community profiles showed clear changes of microbial community structure between plants grown under ambient and elevated CO2 mainly in RRC. Both TRFLP and 454 pyrosequencing showed a significant decrease in the microbial diversity and evenness as a response of CO2 enrichment. While Alphaproteobacteria dominated by Rhizobiales decreased at eCO2, Betaproteobacteria, mainly Burkholderiales, remained unaffected. In contrast, Gammaproteobacteria and Deltaproteobacteria, predominated by Pseudomonadales and Myxococcales, respectively, increased at eCO2. Members of the order Actinomycetales increased, whereas within the phylum Acidobacteria subgroup Gp1 decreased, and the subgroups Gp4 and Gp6 increased under atmospheric CO2 enrichment. Moreover, Planctomycetes and Firmicutes, mainly members of Bacilli, increased under eCO2. Overall, the effect intensity of eCO2 on soil microbial communities was dependent on the distance to the roots. This effect was consistent for all trees under investigation; a site-specific effect of eCO2 in response to the origin of the trees was not observed.
Collapse
Affiliation(s)
- Silvia Gschwendtner
- Research Unit Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | | | | | | | | | | | | |
Collapse
|
46
|
Kleineidam K, Košmrlj K, Kublik S, Palmer I, Pfab H, Ruser R, Fiedler S, Schloter M. Influence of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on ammonia-oxidizing bacteria and archaea in rhizosphere and bulk soil. Chemosphere 2011; 84:182-6. [PMID: 21435682 DOI: 10.1016/j.chemosphere.2011.02.086] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 02/21/2011] [Accepted: 02/28/2011] [Indexed: 05/10/2023]
Abstract
In agricultural plant production nitrification inhibitors like 3,4-dimethylpyrazole phosphate (DMPP) are used to retard the microbial nitrification process of fertilized ammonium to enhance the nitrogen supply for cultivated crops and to reduce nitrogen losses from the production system. Besides the well-known ammonia-oxidizing bacteria (AOB) it is known for a few years that also ammonia-oxidizing archaea (AOA) are able to perform the first step in nitrification, hence being also a target for a nitrification inhibitor. However, so far no information are available concerning the effectiveness of DMPP and its extent towards AOB and AOA, neither in bulk soil nor in the root-rhizosphere complex. We investigated in a field experiment performed according to agricultural practice the effect of DMPP on the abundance of AOB and AOA two, four and eight weeks after fertilization. We observed impaired abundances of AOB but not of AOA in both soil compartments that were still visible eight weeks after application, possibly indicating a reduced effectiveness of the nitrification inhibitor in our study.
Collapse
Affiliation(s)
- Kristina Kleineidam
- Helmholtz Zentrum München, German Research Center for Environmental Health, Department of Terrestrial Ecogenetics, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
| | | | | | | | | | | | | | | |
Collapse
|