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Wolters B, Hauschild K, Blau K, Mulder I, Heyde BJ, Sørensen SJ, Siemens J, Jechalke S, Smalla K, Nesme J. Biosolids for safe land application: does wastewater treatment plant size matters when considering antibiotics, pollutants, microbiome, mobile genetic elements and associated resistance genes? Environ Microbiol 2022; 24:1573-1589. [PMID: 35192222 PMCID: PMC9306954 DOI: 10.1111/1462-2920.15938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/04/2022] [Accepted: 02/11/2022] [Indexed: 01/04/2023]
Abstract
Soil fertilization with wastewater treatment plant (WWTP) biosolids is associated with the introduction of resistance genes (RGs), mobile genetic elements (MGEs) and potentially selective pollutants (antibiotics, heavy metals, disinfectants) into soil. Not much data are available on the parallel analysis of biosolid pollutant contents, RG/MGE abundances and microbial community composition. In the present study, DNA extracted from biosolids taken at 12 WWTPs (two large-scale, six middle-scale and four small-scale plants) was used to determine the abundance of RGs and MGEs via quantitative real-time PCR and the bacterial and archaeal community composition was assessed by 16S rRNA gene amplicon sequencing. Concentrations of heavy metals, antibiotics, the biocides triclosan, triclocarban and quaternary ammonium compounds (QACs) were measured. Strong and significant correlations were revealed between several target genes and concentrations of Cu, Zn, triclosan, several antibiotics and QACs. Interestingly, the size of the sewage treatment plant (inhabitant equivalents) was negatively correlated with antibiotic concentrations, RGs and MGEs abundances and had little influence on the load of metals and QACs or the microbial community composition. Biosolids from WWTPs with anaerobic treatment and hospitals in their catchment area were associated with a higher abundance of potential opportunistic pathogens and higher concentrations of QACs.
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Affiliation(s)
- Birgit Wolters
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Kristin Hauschild
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Khald Blau
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Ines Mulder
- Justus Liebig University Giessen, Institute of Soil Science and Soil Conservation, iFZ Research Centre for Biosystems, Land Use and Nutrition, Giessen, Germany
| | - Benjamin Justus Heyde
- Justus Liebig University Giessen, Institute of Soil Science and Soil Conservation, iFZ Research Centre for Biosystems, Land Use and Nutrition, Giessen, Germany
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jan Siemens
- Justus Liebig University Giessen, Institute of Soil Science and Soil Conservation, iFZ Research Centre for Biosystems, Land Use and Nutrition, Giessen, Germany
| | - Sven Jechalke
- Justus Liebig University Giessen, Institute of Phytopathology, iFZ Research Centre for Biosystems, Land Use and Nutrition, Giessen, Germany
| | - Kornelia Smalla
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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2
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Balthazar C, Joly DL, Filion M. Exploiting Beneficial Pseudomonas spp. for Cannabis Production. Front Microbiol 2022; 12:833172. [PMID: 35095829 PMCID: PMC8795690 DOI: 10.3389/fmicb.2021.833172] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022] Open
Abstract
Among the oldest domesticated crops, cannabis plants (Cannabis sativa L., marijuana and hemp) have been used to produce food, fiber, and drugs for thousands of years. With the ongoing legalization of cannabis in several jurisdictions worldwide, a new high-value market is emerging for the supply of marijuana and hemp products. This creates unprecedented challenges to achieve better yields and environmental sustainability, while lowering production costs. In this review, we discuss the opportunities and challenges pertaining to the use of beneficial Pseudomonas spp. bacteria as crop inoculants to improve productivity. The prevalence and diversity of naturally occurring Pseudomonas strains within the cannabis microbiome is overviewed, followed by their potential mechanisms involved in plant growth promotion and tolerance to abiotic and biotic stresses. Emphasis is placed on specific aspects relevant for hemp and marijuana crops in various production systems. Finally, factors likely to influence inoculant efficacy are provided, along with strategies to identify promising strains, overcome commercialization bottlenecks, and design adapted formulations. This work aims at supporting the development of the cannabis industry in a sustainable way, by exploiting the many beneficial attributes of Pseudomonas spp.
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Affiliation(s)
- Carole Balthazar
- Department of Biology, Faculty of Sciences, Université de Moncton, Moncton, NB, Canada
| | - David L. Joly
- Department of Biology, Faculty of Sciences, Université de Moncton, Moncton, NB, Canada
| | - Martin Filion
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada
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3
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Law A, Solano O, Brown CJ, Hunter SS, Fagnan M, Top EM, Stalder T. Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria. Front Microbiol 2021; 12:606409. [PMID: 33967971 PMCID: PMC8098119 DOI: 10.3389/fmicb.2021.606409] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/09/2021] [Indexed: 12/05/2022] Open
Abstract
Antibiotic resistance (AR) is a threat to modern medicine, and plasmids are driving the global spread of AR by horizontal gene transfer across microbiomes and environments. Determining the mobile resistome responsible for this spread of AR among environments is essential in our efforts to attenuate the current crisis. Biosolids are a wastewater treatment plant (WWTP) byproduct used globally as fertilizer in agriculture. Here, we investigated the mobile resistome of biosolids that are used as fertilizer. This was done by capturing resistance plasmids that can transfer to human pathogens and commensal bacteria. We used a higher-throughput version of the exogenous plasmid isolation approach by mixing several ESKAPE pathogens and a commensal Escherichia coli with biosolids and screening for newly acquired resistance to about 10 antibiotics in these strains. Six unique resistance plasmids transferred to Salmonella typhimurium, Klebsiella aerogenes, and E. coli. All the plasmids were self-transferable and carried 3-6 antibiotic resistance genes (ARG) conferring resistance to 2-4 antibiotic classes. These plasmids-borne resistance genes were further embedded in genetic elements promoting intracellular recombination (i.e., transposons or class 1 integrons). The plasmids belonged to the broad-host-range plasmid (BHR) groups IncP-1 or PromA. Several of them were persistent in their new hosts when grown in the absence of antibiotics, suggesting that the newly acquired drug resistance traits would be sustained over time. This study highlights the role of BHRs in the spread of ARG between environmental bacteria and human pathogens and commensals, where they may persist. The work further emphasizes biosolids as potential vehicles of highly mobile plasmid-borne antibiotic resistance genes.
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Affiliation(s)
- Aaron Law
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Olubunmi Solano
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Celeste J. Brown
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Samuel S. Hunter
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
- UC-Davis Genome Center, Davis, CA, United States
| | - Matt Fagnan
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Eva M. Top
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
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4
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Pratama AA, van Elsas JD. Gene mobility in microbiomes of the mycosphere and mycorrhizosphere -role of plasmids and bacteriophages. FEMS Microbiol Ecol 2020; 95:5454738. [PMID: 30980672 DOI: 10.1093/femsec/fiz053] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/12/2019] [Indexed: 12/22/2022] Open
Abstract
Microbial activity in soil, including horizontal gene transfer (HGT), occurs in soil hot spots and at "hot moments". Given their capacities to explore soil for nutrients, soil fungi (associated or not with plant roots) can act as (1) selectors of myco(rrhizo)sphere-adapted organisms and (2) accelerators of HGT processes across the cell populations that are locally present. This minireview critically examines our current understanding of the drivers of gene mobility in the myco(rrhizo)sphere. We place a special focus on the role of two major groups of gene mobility agents, i.e. plasmids and bacteriophages. With respect to plasmids, there is mounting evidence that broad-host-range (IncP-1β and PromA group) plasmids are prominent drivers of gene mobility across mycosphere inhabitants. A role of IncP-1β plasmids in Fe uptake processes has been revealed. Moreover, a screening of typical mycosphere-inhabiting Paraburkholderia spp. revealed carriage of integrated plasmids, next to prophages, that presumably confer fitness enhancements. In particular, functions involved in biofilm formation and nutrient uptake were thus identified. The potential of the respective gene mobility agents to promote the movement of such genes is critically examined.
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Affiliation(s)
- Akbar Adjie Pratama
- Department of Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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5
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Lu W, Wang M, Wu J, Jiang Q, Jin J, Jin Q, Yang W, Chen J, Wang Y, Xiao M. Spread of chloramphenicol and tetracycline resistance genes by plasmid mobilization in agricultural soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 260:113998. [PMID: 31991360 DOI: 10.1016/j.envpol.2020.113998] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 01/14/2020] [Accepted: 01/14/2020] [Indexed: 06/10/2023]
Abstract
Spread of antibiotic resistance genes (ARGs) poses a worldwide threat to public health and food safety. However, ARG spread by plasmid mobilization, a broad host range transfer system, in agricultural soil has received little attention. Here, we investigated the spread of chloramphenicol resistance gene (CRG) and tetracycline resistance gene (TRG) in agricultural soil by mobilization of pSUP106 under different conditions, including different concentrations of nutrients, temperatures, soil depths, rhizosphere soils, and soil types. The number of resistant bacteria isolated in non-sterilized soil from the experiments was approximately 104 to 107 per gram of soil, belonging to 5-10 species from four genera, including nonpathogen, opportunistic pathogen, pathogen bacteria, and gram-positive and gram-negative bacteria, depending on the experiment conditions. In sterilized soil, higher levels of nutrients and higher temperatures promoted plasmid mobilization and ARG expression. Topsoil and deep soil might not support the spread of antibiotic resistance, while ARG dissemination by plasmid mobilization was better supported by maize rhizosphere and loam soils. All these factors might change bacterial growth and the activity of bacteria and lead to the above influence. Introduction of only the donor and helper, or the donor alone also resulted in the transfer of ARGs and large numbers of antibiotic resistant bacteria (ARB), indicating that some indigenous bacteria contain the elements necessary for plasmid mobilization. Our results showed that plasmid mobilization facilitated dissemination of ARGs and ARB in soil, which led to the disturbance of indigenous bacterial communities. It is important to clear ARG dissemination routes and inhibit the spread of ARGs.
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Affiliation(s)
- Wenwei Lu
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Min Wang
- Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Jianqiang Wu
- Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Qiuyan Jiang
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jieren Jin
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Qing Jin
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Wenwu Yang
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jun Chen
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yujing Wang
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Ming Xiao
- Development Center of Plant Germplasm, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Key Laboratory of Urban Agriculture, Ministry of Agriculture, Shanghai, 200240, China.
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6
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Dias ACF, Cotta SR, Andreote FD, van Elsas JD. The parA Region of Broad-Host-Range PromA Plasmids Is a Carrier of Mobile Genes. MICROBIAL ECOLOGY 2018; 75:479-486. [PMID: 28875307 DOI: 10.1007/s00248-017-1059-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
The ecological competences in microbiomes are driven by the adaptive capabilities present within microbiome members. Horizontal gene transfer (HGT) promoted by plasmids provides a rapid adaptive strategy to microbiomes, an interesting feature considering the constantly changing conditions in most environments. This study examined the parA locus, found in the highly promiscuous PromA class of plasmids, as the insertion site for incoming genes. A novel PCR system was designed that enabled examining insertions into this locus. Microbiomes of mangrove sediments, salt marsh, mycosphere, and bulk soil revealed habitat-specific sets of insertions in this plasmid region. Furthermore, such habitats could be differentiated based on patterns of parA-inserted genes, and the genes carried by these plasmids. Thus, a suite of dioxygenase-related genes and transposase elements were found in oil-affected mangroves, whereas genes involved in nitrogen and carbon cycling were detected in salt marsh and soils. All genes detected could be associated with capabilities of members of the microbiome to adapt to and survive in each habitat. The methodology developed in this work was effective, sensitive, and practical, allowing detection of mobilized genes between microorganisms.
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Affiliation(s)
- Armando Cavalcante Franco Dias
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Av Padua Dias, 11, Piracicaba, SP, 13418-900, Brazil.
- Microbial Ecology Group, Genomic Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), Groningen, Netherlands.
| | - Simone Raposo Cotta
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Av Padua Dias, 11, Piracicaba, SP, 13418-900, Brazil
- Microbial Ecology Group, Genomic Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), Groningen, Netherlands
| | - Fernando Dini Andreote
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Av Padua Dias, 11, Piracicaba, SP, 13418-900, Brazil
| | - Jan Dirk van Elsas
- Microbial Ecology Group, Genomic Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), Groningen, Netherlands
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7
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Exploring the Influence of Environmental Factors on Bacterial Communities within the Rhizosphere of the Cu-tolerant plant, Elsholtzia splendens. Sci Rep 2016; 6:36302. [PMID: 27782202 PMCID: PMC5080579 DOI: 10.1038/srep36302] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/10/2016] [Indexed: 12/11/2022] Open
Abstract
Bacterial communities of rhizospheric soils play an important role in the tolerance and uptake of metal-tolerant/hyperaccumulating plants to metals, e.g. the Cu-tolerant Elsholtzia splendens native to China. In this work, pyrosequencing of the bacterial 16S rRNA gene was firstly applied to investigate the rhizospheric bacterial community of E. splendens grown at Cu contaminated sites. The 47 phyla including 11 dominant phyla (>1%) in E. splendens rhizosphere were presented. The effects of Cu and other environmental factors (total organic carbon, total nitrogen and pH) on the rhizospheric bacterial community were studied comprehensively. The phyla abundances were affected by the environmental factors to different extent, and we found pH, instead of Cu concentration, influenced UniFrac distance significantly and was identified as the most important environmental factor affecting bacterial community. In addition, the influence of environmental factors on gene profiles was explored according to the predicted metagenomes obtained by PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states). Our study illustrates a view about Cu-tolerant E. splendens rhizospheric bacterial communities (composition, diversity and gene profiles) and their influencing factors, giving a hand for the understanding on bacterial community is formed and affected in rhizosphere.
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8
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Lopes LD, Pereira E Silva MDC, Andreote FD. Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization. Front Microbiol 2016; 7:1341. [PMID: 27610108 PMCID: PMC4997060 DOI: 10.3389/fmicb.2016.01341] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/15/2016] [Indexed: 11/13/2022] Open
Abstract
The rhizosphere harbors one of the most complex, diverse, and active plant-associated microbial communities. This community can be recruited by the plant host to either supply it with nutrients or to help in the survival under stressful conditions. Although selection for the rhizosphere community is evident, the specific bacterial traits that make them able to colonize this environment are still poorly understood. Thus, here we used a combination of community level physiological profile (CLPP) analysis and 16S rRNA gene quantification and sequencing (coupled with in silico analysis and metagenome prediction), to get insights on bacterial features and processes involved in rhizosphere colonization of sugarcane. CLPP revealed a higher metabolic activity in the rhizosphere compared to bulk soil, and suggested that D-galacturonic acid plays a role in bacterial selection by the plant roots (supported by results of metagenome prediction). Quantification of the 16S rRNA gene confirmed the higher abundance of bacteria in the rhizosphere. Sequence analysis showed that of the 252 classified families sampled, 24 were significantly more abundant in the bulk soil and 29 were more abundant in the rhizosphere. Furthermore, metagenomes predicted from the 16S rRNA gene sequences revealed a significant higher abundance of predicted genes associated with biofilm formation and with horizontal gene transfer (HGT) processes. In sum, this study identified major bacterial groups and their potential abilities to occupy the sugarcane rhizosphere, and indicated that polygalacturonase activity and HGT events may be important features for rhizosphere colonization.
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Affiliation(s)
- Lucas D Lopes
- Soil Microbiology Lab, Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo Piracicaba, Brazil
| | - Michele de Cássia Pereira E Silva
- Soil Microbiology Lab, Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo Piracicaba, Brazil
| | - Fernando D Andreote
- Soil Microbiology Lab, Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo Piracicaba, Brazil
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9
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Abstract
Plasmids are important vehicles for rapid adaptation of bacterial populations to changing environmental conditions. It is thought that to reduce the cost of plasmid carriage, only a fraction of a local population carries plasmids or is permissive to plasmid uptake. Plasmids provide various accessory traits which might be beneficial under particular conditions. The genetic variation generated by plasmid carriage within populations ensures the robustness toward environmental changes. Plasmid-mediated gene transfer plays an important role not only in the mobilization and dissemination of antibiotic resistance genes but also in the spread of degradative pathways and pathogenicity determinants of pathogens. Here we summarize the state-of-the-art methods to study the occurrence, abundance, and diversity of plasmids in environmental bacteria. Increasingly, cultivation-independent total-community DNA-based methods are being used to characterize and quantify the diversity and abundance of plasmids in relation to various biotic and abiotic factors. An improved understanding of the ecology of plasmids and their hosts is crucial in the development of intervention strategies for antibiotic-resistance-gene spread. We discuss the potentials and limitations of methods used to determine the host range of plasmids, as the ecology of plasmids is tightly linked to their hosts. The recent advances in sequencing technologies provide an enormous potential for plasmid classification, diversity, and evolution studies, but numerous challenges still exist.
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10
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Conjugative transfer of broad host range plasmids to an acidobacterial strain, Edaphobacter aggregans. J Biotechnol 2016; 221:107-13. [DOI: 10.1016/j.jbiotec.2016.01.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 01/18/2016] [Accepted: 01/20/2016] [Indexed: 01/19/2023]
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11
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Li X, Wang Y, Brown CJ, Yao F, Jiang Y, Top EM, Li H. Diversification of broad host range plasmids correlates with the presence of antibiotic resistance genes. FEMS Microbiol Ecol 2015; 92:fiv151. [PMID: 26635412 DOI: 10.1093/femsec/fiv151] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2015] [Indexed: 11/13/2022] Open
Abstract
The IncP-1ε subgroup is a recently identified phylogenetic clade within IncP-1 plasmids, which plays an important role in the spread of antibiotic resistance and degradation of xenobiotic pollutants. Here, four IncP-1ε plasmids were exogenously captured from a petroleum-contaminated habitat in China and compared phylogenetically and genomically with previously reported IncP-1ε and other IncP-1 plasmids. The IncP-1ε plasmids can be clearly subdivided into two subclades, designated as ε-I and ε-II, based on phylogenetic analysis of backbone proteins TraI and TrfA. This was further supported by comparison of concatenated backbone genes. Moreover, the two subclades differed in the transposon types, phenotypes and insertion locations of the accessory elements. The accessory genes on ε-I plasmids were inserted between parA and traC, and harbored ISPa17 and Tn402-like transposon modules, typically carrying antibiotic resistance genes. In contrast, the accessory elements on ε-II plasmids were typically located between trfA and oriV, and contained IS1071, which was commonly inserted within the Tn501-like transposon, typically harboring a cluster of genes encoding mercury resistance and/or catabolic pathways. Our study is one of the first to compare IncP-1 plasmid genomes from China, expands the available collection of IncP-1ε plasmids and enhances our understanding of their diversity, biogeography and evolutionary history.
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Affiliation(s)
- Xiaobin Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yafei Wang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
| | - Celeste J Brown
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844-3051, USA
| | - Fei Yao
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Jiang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
| | - Eva M Top
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, ID 83844-3051, USA
| | - Hui Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
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12
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Ulrich A, Becker R, Ulrich K, Ewald D. Conjugative transfer of a derivative of the IncP-1α plasmid RP4 and establishment of transconjugants in the indigenous bacterial community of poplar plants. FEMS Microbiol Lett 2015; 362:fnv201. [PMID: 26490946 PMCID: PMC4643746 DOI: 10.1093/femsle/fnv201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/09/2015] [Accepted: 10/16/2015] [Indexed: 12/14/2022] Open
Abstract
The persistence of traits introduced into the indigenous bacterial community of poplar plants was investigated using bioluminescence mediated by the luc gene. Three endophytic bacterial strains provided with the IncP-1α plasmid RP4-Tn-luc were used to inoculate poplar cuttings at different phenological stages. Screening of isolates by bioluminescence and real-time PCR detection of the luc gene revealed stable persistence for at least 10 weeks. Although the inoculated strains became established with a high population density after inoculation at leaf development (April) and senescence (October), the strains were suppressed by the indigenous bacteria at stem elongation (June). Transconjugants could be detected only at this phenological stage. Indigenous bacteria harbouring RP4-Tn-luc became established with densities ranging from 2 × 10(5) to 9 × 10(6) CFU g(-1) fresh weight 3 and 10 weeks after inoculation. The increased colonization of the cuttings by indigenous bacteria at stem elongation seemed to strongly compete with the introduced strains. Otherwise, the phenological stage of the plants as well as the density of the indigenous recipients could serve as the driver for a more frequent conjugative plasmid transfer. A phylogenetic assignment of transconjugants indicated the transfer of RP4-Tn-luc into six genera of Proteobacteria, mainly Sphingomonas, Stenotrophomonas and Xanthomonas.
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Affiliation(s)
- Andreas Ulrich
- Leibniz Centre for Agricultural Landscape Research (ZALF), Institute for Landscape Biogeochemistry, D-15374 Müncheberg, Germany
| | - Regina Becker
- Leibniz Centre for Agricultural Landscape Research (ZALF), Institute for Landscape Biogeochemistry, D-15374 Müncheberg, Germany
| | - Kristina Ulrich
- Johann Heinrich von Thünen-Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Institute of Forest Genetics, Waldsieversdorf D-15377, Germany
| | - Dietrich Ewald
- Johann Heinrich von Thünen-Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Institute of Forest Genetics, Waldsieversdorf D-15377, Germany
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13
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Monsieurs P, Hobman J, Vandenbussche G, Mergeay M, Van Houdt R. Response of Cupriavidus metallidurans CH34 to Metals. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-3-319-20594-6_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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14
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Zhang M, Visser S, Pereira e Silva MC, van Elsas JD. IncP-1 and PromA group plasmids are major providers of horizontal gene transfer capacities across bacteria in the mycosphere of different soil fungi. MICROBIAL ECOLOGY 2015; 69:169-179. [PMID: 25149284 DOI: 10.1007/s00248-014-0482-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 08/08/2014] [Indexed: 06/03/2023]
Abstract
Plasmids of the IncP-1β group have been found to be important carriers of accessory genes that enhance the ecological fitness of bacteria, whereas plasmids of the PromA group are key agents of horizontal gene transfer in particular soil settings. However, there is still a paucity of knowledge with respect to the diversity, abundance, and involvement in horizontal gene transfer of plasmids of both groups in the mycosphere. Using triparental exogenous isolation based on the IncQ tracer plasmid pSUP104 as well as direct molecular detection, we analyzed the pool of mobilizer and self-transferable plasmids in mycosphere soil. Replicate mushroom types that were related to Russula, Inocybe, Ampulloclitocybe, and Galerina spp. were sampled from a forest soil area, and bulk soil was used as the control. The data showed that the levels of IncP-1β plasmids are significantly raised across several of the mycospheres analyzed, whereas those of PromA group plasmids were similar across the mycospheres and corresponding bulk soil. Moreover, the frequencies of triparental exogenous isolation of mobilizer plasmids into a Pseudomonas fluorescens recipient strain were significantly elevated in communities from several mycospheres as compared with those from bulk soil. Molecular analysis of selected transconjugants, as well as from directly isolated strains, revealed the presence of plasmids of three size groups, i.e., (1) 40-45, (2) 50-60, and (3) ≥60 kb, across all isolations. Replicon typing using IncN, IncW and IncA/C proxies revealed no positive signals. In contrast, a suite of plasmids produced signals with IncP-1β as well as PromA type replicon typing systems. Moreover, a selected subset of plasmids, obtained from the Inocybe and Galerina isolates, was transferred out further, revealing their capacities to transfer and mobilize across a broad host range.
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Affiliation(s)
- Miaozhi Zhang
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
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Klümper U, Droumpali A, Dechesne A, Smets BF. Novel assay to measure the plasmid mobilizing potential of mixed microbial communities. Front Microbiol 2014; 5:730. [PMID: 25566238 PMCID: PMC4273639 DOI: 10.3389/fmicb.2014.00730] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/04/2014] [Indexed: 01/21/2023] Open
Abstract
Mobilizable plasmids lack necessary genes for complete conjugation and are therefore non-self-transmissible. Instead, they rely on the conjugation system of conjugal plasmids to be horizontally transferred to new recipients. While community permissiveness, the fraction of a mixed microbial community that can receive self-transmissible conjugal plasmids, has been studied, the intrinsic ability of a community to mobilize plasmids that lack conjugation systems is unexplored. Here, we present a novel framework and experimental method to estimate the mobilization potential of mixed communities. We compare the transfer frequency of a mobilizable plasmid to that of a mobilizing and conjugal plasmid measured for a model strain and for the assayed community. With Pseudomonas putida carrying the gfp-tagged mobilizable IncQ plasmid RSF1010 as donor strain, we conducted solid surface mating experiments with either a P. putida strain carrying the mobilizing IncP-1α plasmid RP4 or a model bacterial community that was extracted from the inner walls of a domestic shower conduit. Additionally, we estimated the permissiveness of the same community for RP4 using P. putida as donor strain. The permissiveness of the model community for RP4 [at 1.16 × 10-4 transconjugants per recipient (T/R)] was similar to that previously measured for soil microbial communities. RSF1010 was mobilized by the model community at a frequency of 1.16 × 10-5 T/R, only one order of magnitude lower than its permissiveness to RP4. This mobilization frequency is unexpectedly high considering that (i) mobilization requires the presence of mobilizing conjugal plasmids within the permissive fraction of the recipients; (ii) in pure culture experiments with P. putida retromobilization of RSF1010 through RP4 only took place in approximately half of the donors receiving the conjugal plasmid in the first step. Further work is needed to establish how plasmid mobilization potential varies within and across microbial communities. This method has the potential to provide such insights; in addition it allows for the direct isolation of in situ mobilizing plasmids together with their endogenous hosts.
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Affiliation(s)
- Uli Klümper
- Department of Environmental Engineering, Technical University of Denmark Kongens Lyngby, Denmark
| | - Ariadni Droumpali
- Department of Environmental Engineering, Technical University of Denmark Kongens Lyngby, Denmark
| | - Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark Kongens Lyngby, Denmark
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark Kongens Lyngby, Denmark
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Haq IU, Zhang M, Yang P, van Elsas JD. The interactions of bacteria with fungi in soil: emerging concepts. ADVANCES IN APPLIED MICROBIOLOGY 2014; 89:185-215. [PMID: 25131403 DOI: 10.1016/b978-0-12-800259-9.00005-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this chapter, we review the existing literature on bacterial-fungal interactions in soil, exploring the role fungi may play for soil bacteria as providers of hospitable niches. A focus is placed on the mycosphere, i.e., the narrow zone of influence of fungal hyphae on the external soil milieu, in which hypha-associated bacterial cells dwell. Evidence is brought forward for the contention that the hyphae of both mycorrhizal and saprotrophic fungi serve as providers of ecological opportunities in a grossly carbon-limited soil, as a result of their release of carbonaceous compounds next to the provision of a colonizable surface. Soil bacteria of particular nature are postulated to have adapted to such selection pressures, evolving to the extent that they acquired capabilities that allow them to thrive in the novel habitat created by the emerging fungal hyphae. The mechanisms involved in the interactions and the modes of genetic adaptation of the mycosphere dwellers are discussed, with an emphasis on one key mycosphere-adapted bacterium, Burkholderia terrae BS001. In this discussion, we interrogate the positive interactions between soil fungi and bacteria, and refrain from considering negative interactions.
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Affiliation(s)
- Irshad Ul Haq
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen, Groningen, The Netherlands
| | - Miaozhi Zhang
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen, Groningen, The Netherlands
| | - Pu Yang
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen, Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen, Groningen, The Netherlands.
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Zhang M, Pereira e Silva MDC, Chaib De Mares M, van Elsas JD. The mycosphere constitutes an arena for horizontal gene transfer with strong evolutionary implications for bacterial-fungal interactions. FEMS Microbiol Ecol 2014; 89:516-26. [DOI: 10.1111/1574-6941.12350] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 04/24/2014] [Accepted: 04/25/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- MiaoZhi Zhang
- Department of Microbial Ecology; Centre for Life Sciences; University of Groningen; Groningen The Netherlands
| | | | - Maryam Chaib De Mares
- Department of Microbial Ecology; Centre for Life Sciences; University of Groningen; Groningen The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology; Centre for Life Sciences; University of Groningen; Groningen The Netherlands
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Herrick J, Haynes R, Heringa S, Brooks J, Sobota L. Coselection for resistance to multiple late-generation human therapeutic antibiotics encoded on tetracycline resistance plasmids captured from uncultivated stream and soil bacteria. J Appl Microbiol 2014; 117:380-9. [DOI: 10.1111/jam.12538] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 04/04/2014] [Accepted: 04/23/2014] [Indexed: 11/30/2022]
Affiliation(s)
- J.B. Herrick
- Department of Biology; James Madison University; Harrisonburg VA USA
| | - R. Haynes
- Department of Biology; James Madison University; Harrisonburg VA USA
| | - S. Heringa
- Department of Biology; James Madison University; Harrisonburg VA USA
| | - J.M. Brooks
- Department of Biology; James Madison University; Harrisonburg VA USA
| | - L.T. Sobota
- Department of Biology; James Madison University; Harrisonburg VA USA
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Musovic S, Klümper U, Dechesne A, Magid J, Smets BF. Long-term manure exposure increases soil bacterial community potential for plasmid uptake. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:125-30. [PMID: 24596284 DOI: 10.1111/1758-2229.12138] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/21/2013] [Accepted: 11/05/2013] [Indexed: 05/26/2023]
Abstract
Microbial communities derived from soils subject to different agronomic treatments were challenged with three broad host range plasmids, RP4, pIPO2tet and pRO101, via solid surface filter matings to assess their permissiveness. Approximately 1 in 10 000 soil bacterial cells could receive and maintain the plasmids. The community permissiveness increased up to 100% in communities derived from manured soil. While the plasmid transfer frequency was significantly influenced by both the type of plasmid and the agronomic treatment, the diversity of the transconjugal pools was purely plasmid dependent and was dominated by β- and γ-Proteobacteria.
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Affiliation(s)
- Sanin Musovic
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
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20
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van Overbeek LS, van Doorn J, Wichers JH, van Amerongen A, van Roermund HJW, Willemsen PTJ. The arable ecosystem as battleground for emergence of new human pathogens. Front Microbiol 2014; 5:104. [PMID: 24688484 PMCID: PMC3960585 DOI: 10.3389/fmicb.2014.00104] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 02/27/2014] [Indexed: 01/10/2023] Open
Abstract
Disease incidences related to Escherichia coli and Salmonella enterica infections by consumption of (fresh) vegetables, sprouts, and occasionally fruits made clear that these pathogens are not only transmitted to humans via the "classical" routes of meat, eggs, and dairy products, but also can be transmitted to humans via plants or products derived from plants. Nowadays, it is of major concern that these human pathogens, especially the ones belonging to the taxonomical family of Enterobacteriaceae, become adapted to environmental habitats without losing their virulence to humans. Adaptation to the plant environment would lead to longer persistence in plants, increasing their chances on transmission to humans via consumption of plant-derived food. One of the mechanisms of adaptation to the plant environment in human pathogens, proposed in this paper, is horizontal transfer of genes from different microbial communities present in the arable ecosystem, like the ones originating from soil, animal digestive track systems (manure), water and plants themselves. Genes that would confer better adaptation to the phytosphere might be genes involved in plant colonization, stress resistance and nutrient acquisition and utilization. Because human pathogenic enterics often were prone to genetic exchanges via phages and conjugative plasmids, it was postulated that these genetic elements may be hold key responsible for horizontal gene transfers between human pathogens and indigenous microbes in agroproduction systems. In analogy to zoonosis, we coin the term phytonosis for a human pathogen that is transmitted via plants and not exclusively via animals.
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Affiliation(s)
- Leonard S van Overbeek
- Plant Research International, Wageningen University and Research Centre Wageningen, Netherlands
| | - Joop van Doorn
- Applied Plant Research, Wageningen University and Research Centre Lisse, Netherlands
| | - Jan H Wichers
- Food and Biobased Research, Wageningen University and Research Centre Wageningen, Netherlands
| | - Aart van Amerongen
- Food and Biobased Research, Wageningen University and Research Centre Wageningen, Netherlands
| | - Herman J W van Roermund
- Central Veterinary Institute, Wageningen University and Research Centre Lelystad, Netherlands
| | - Peter T J Willemsen
- Central Veterinary Institute, Wageningen University and Research Centre Lelystad, Netherlands
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Norberg P, Bergström M, Hermansson M. Complete nucleotide sequence and analysis of two conjugative broad host range plasmids from a marine microbial biofilm. PLoS One 2014; 9:e92321. [PMID: 24647540 PMCID: PMC3960245 DOI: 10.1371/journal.pone.0092321] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 02/20/2014] [Indexed: 11/26/2022] Open
Abstract
The complete nucleotide sequence of plasmids pMCBF1 and pMCBF6 was determined and analyzed. pMCBF1 and pMCBF6 form a novel clade within the IncP-1 plasmid family designated IncP-1 ς. The plasmids were exogenously isolated earlier from a marine biofilm. pMCBF1 (62 689 base pairs; bp) and pMCBF6 (66 729 bp) have identical backbones, but differ in their mercury resistance transposons. pMCBF1 carries Tn5053 and pMCBF6 carries Tn5058. Both are flanked by 5 bp direct repeats, typical of replicative transposition. Both insertions are in the vicinity of a resolvase gene in the backbone, supporting the idea that both transposons are “res-site hunters” that preferably insert close to and use external resolvase functions. The similarity of the backbones indicates recent insertion of the two transposons and the ongoing dynamics of plasmid evolution in marine biofilms. Both plasmids also carry the insertion sequence ISPst1, albeit without flanking repeats. ISPs1is located in an unusual site within the control region of the plasmid. In contrast to most known IncP-1 plasmids the pMCBF1/pMCBF6 backbone has no insert between the replication initiation gene (trfA) and the vegetative replication origin (oriV). One pMCBF1/pMCBF6 block of about 2.5 kilo bases (kb) has no similarity with known sequences in the databases. Furthermore, insertion of three genes with similarity to the multidrug efflux pump operon mexEF and a gene from the NodT family of the tripartite multi-drug resistance-nodulation-division (RND) system in Pseudomonas aeruginosa was found. They do not seem to confer antibiotic resistance to the hosts of pMCBF1/pMCBF6, but the presence of RND on promiscuous plasmids may have serious implications for the spread of antibiotic multi-resistance.
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Affiliation(s)
- Peter Norberg
- Department of Infectious Diseases, University of Gothenburg, Göteborg, Sweden
| | - Maria Bergström
- Department of Chemistry and Molecular Biology, Microbiology, University of Gothenburg, Göteborg, Sweden
| | - Malte Hermansson
- Department of Chemistry and Molecular Biology, Microbiology, University of Gothenburg, Göteborg, Sweden
- * E-mail:
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Diverse broad-host-range plasmids from freshwater carry few accessory genes. Appl Environ Microbiol 2013; 79:7684-95. [PMID: 24096417 DOI: 10.1128/aem.02252-13] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Broad-host-range self-transferable plasmids are known to facilitate bacterial adaptation by spreading genes between phylogenetically distinct hosts. These plasmids typically have a conserved backbone region and a variable accessory region that encodes host-beneficial traits. We do not know, however, how well plasmids that do not encode accessory functions can survive in nature. The goal of this study was to characterize the backbone and accessory gene content of plasmids that were captured from freshwater sources without selecting for a particular phenotype or cultivating their host. To do this, triparental matings were used such that the only required phenotype was the plasmid's ability to mobilize a nonconjugative plasmid. Based on complete genome sequences of 10 plasmids, only 5 carried identifiable accessory gene regions, and none carried antibiotic resistance genes. The plasmids belong to four known incompatibility groups (IncN, IncP-1, IncU, and IncW) and two potentially new groups. Eight of the plasmids were shown to have a broad host range, being able to transfer into alpha-, beta-, and gammaproteobacteria. Because of the absence of antibiotic resistance genes, we resampled one of the sites and compared the proportion of captured plasmids that conferred antibiotic resistance to their hosts with the proportion of such plasmids captured from the effluent of a local wastewater treatment plant. Few of the captured plasmids from either site encoded antibiotic resistance. A high diversity of plasmids that encode no or unknown accessory functions is thus readily found in freshwater habitats. The question remains how the plasmids persist in these microbial communities.
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Heuer H, Smalla K. Plasmids foster diversification and adaptation of bacterial populations in soil. FEMS Microbiol Rev 2012; 36:1083-104. [DOI: 10.1111/j.1574-6976.2012.00337.x] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 10/15/2011] [Accepted: 02/24/2012] [Indexed: 11/26/2022] Open
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Alvarado A, Garcillán-Barcia MP, de la Cruz F. A degenerate primer MOB typing (DPMT) method to classify gamma-proteobacterial plasmids in clinical and environmental settings. PLoS One 2012; 7:e40438. [PMID: 22792321 PMCID: PMC3394729 DOI: 10.1371/journal.pone.0040438] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 06/07/2012] [Indexed: 11/18/2022] Open
Abstract
Transmissible plasmids are responsible for the spread of genetic determinants, such as antibiotic resistance or virulence traits, causing a large ecological and epidemiological impact. Transmissible plasmids, either conjugative or mobilizable, have in common the presence of a relaxase gene. Relaxases were previously classified in six protein families according to their phylogeny. Degenerate primers hybridizing to coding sequences of conserved amino acid motifs were designed to amplify related relaxase genes from γ-Proteobacterial plasmids. Specificity and sensitivity of a selected set of 19 primer pairs were first tested using a collection of 33 reference relaxases, representing the diversity of γ-Proteobacterial plasmids. The validated set was then applied to the analysis of two plasmid collections obtained from clinical isolates. The relaxase screening method, which we call “Degenerate Primer MOB Typing” or DPMT, detected not only most known Inc/Rep groups, but also a plethora of plasmids not previously assigned to any Inc group or Rep-type.
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Affiliation(s)
- Andrés Alvarado
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN, Santander, Spain
| | - M. Pilar Garcillán-Barcia
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN, Santander, Spain
| | - Fernando de la Cruz
- Departamento de Biología Molecular e Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas-SODERCAN, Santander, Spain
- * E-mail:
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Janssen PJ, Van Houdt R, Moors H, Monsieurs P, Morin N, Michaux A, Benotmane MA, Leys N, Vallaeys T, Lapidus A, Monchy S, Médigue C, Taghavi S, McCorkle S, Dunn J, van der Lelie D, Mergeay M. The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS One 2010; 5:e10433. [PMID: 20463976 PMCID: PMC2864759 DOI: 10.1371/journal.pone.0010433] [Citation(s) in RCA: 199] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Accepted: 03/29/2010] [Indexed: 11/21/2022] Open
Abstract
Many bacteria in the environment have adapted to the presence of toxic heavy metals. Over the last 30 years, this heavy metal tolerance was the subject of extensive research. The bacterium Cupriavidus metallidurans strain CH34, originally isolated by us in 1976 from a metal processing factory, is considered a major model organism in this field because it withstands milli-molar range concentrations of over 20 different heavy metal ions. This tolerance is mostly achieved by rapid ion efflux but also by metal-complexation and -reduction. We present here the full genome sequence of strain CH34 and the manual annotation of all its genes. The genome of C. metallidurans CH34 is composed of two large circular chromosomes CHR1 and CHR2 of, respectively, 3,928,089 bp and 2,580,084 bp, and two megaplasmids pMOL28 and pMOL30 of, respectively, 171,459 bp and 233,720 bp in size. At least 25 loci for heavy-metal resistance (HMR) are distributed over the four replicons. Approximately 67% of the 6,717 coding sequences (CDSs) present in the CH34 genome could be assigned a putative function, and 9.1% (611 genes) appear to be unique to this strain. One out of five proteins is associated with either transport or transcription while the relay of environmental stimuli is governed by more than 600 signal transduction systems. The CH34 genome is most similar to the genomes of other Cupriavidus strains by correspondence between the respective CHR1 replicons but also displays similarity to the genomes of more distantly related species as a result of gene transfer and through the presence of large genomic islands. The presence of at least 57 IS elements and 19 transposons and the ability to take in and express foreign genes indicates a very dynamic and complex genome shaped by evolutionary forces. The genome data show that C. metallidurans CH34 is particularly well equipped to live in extreme conditions and anthropogenic environments that are rich in metals.
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Affiliation(s)
- Paul J Janssen
- Molecular and Cellular Biology, Belgian Nuclear Research Center SCK*CEN, Mol, Belgium.
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Nazir R, Warmink JA, Boersma H, van Elsas JD. Mechanisms that promote bacterial fitness in fungal-affected soil microhabitats. FEMS Microbiol Ecol 2010; 71:169-85. [DOI: 10.1111/j.1574-6941.2009.00807.x] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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27
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Weyens N, Taghavi S, Barac T, van der Lelie D, Boulet J, Artois T, Carleer R, Vangronsveld J. Bacteria associated with oak and ash on a TCE-contaminated site: characterization of isolates with potential to avoid evapotranspiration of TCE. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2009; 16:830-843. [PMID: 19401827 DOI: 10.1007/s11356-009-0154-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 04/26/2009] [Indexed: 05/26/2023]
Abstract
BACKGROUND, AIM, AND SCOPE Along transects under a mixed woodland of English Oak (Quercus robur) and Common Ash (Fraxinus excelsior) growing on a trichloroethylene (TCE)-contaminated groundwater plume, sharp decreases in TCE concentrations were observed, while transects outside the planted area did not show this remarkable decrease. This suggested a possibly active role of the trees and their associated bacteria in the remediation process. Therefore, the cultivable bacterial communities associated with both tree species growing on this TCE-contaminated groundwater plume were investigated in order to assess the possibilities and practical aspects of using these common native tree species and their associated bacteria for phytoremediation. In this study, only the cultivable bacteria were characterized because the final aim was to isolate TCE-degrading, heavy metal resistant bacteria that might be used as traceable inocula to enhance bioremediation. MATERIALS AND METHODS Cultivable bacteria isolated from bulk soil, rhizosphere, root, stem, and leaf were genotypically characterized by amplified rDNA restriction analysis (ARDRA) of their 16S rRNA gene and identified by 16S rRNA gene sequencing. Bacteria that displayed distinct ARDRA patterns were screened for heavy metal resistance, as well as TCE tolerance and degradation, as preparation for possible future in situ inoculation experiments. Furthermore, in situ evapotranspiration measurements were performed to investigate if the degradation capacity of the associated bacteria is enough to prevent TCE evapotranspiration to the air. RESULTS AND DISCUSSION Between both tree species, the associated populations of cultivable bacteria clearly differed in composition. In English Oak, more species-specific, most likely obligate endophytes were found. The majority of the isolated bacteria showed increased tolerance to TCE, and TCE degradation capacity was observed in some of the strains. However, in situ evapotranspiration measurements revealed that a significant amount of TCE and its metabolites was evaporating through the leaves to the atmosphere. CONCLUSIONS AND PERSPECTIVES The characterization of the isolates obtained in this study shows that the bacterial community associated with Oak and Ash on a TCE-contaminated site, was strongly enriched with TCE-tolerant strains. However, this was not sufficient to degrade all TCE before it reaches the leaves. A possible strategy to overcome this evapotranspiration to the atmosphere is to enrich the plant-associated TCE-degrading bacteria by in situ inoculation with endophytic strains capable of degrading TCE.
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Affiliation(s)
- Nele Weyens
- Environmental Biology, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
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28
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Coombs JM. Potential for horizontal gene transfer in microbial communities of the terrestrial subsurface. Methods Mol Biol 2009; 532:413-33. [PMID: 19271199 DOI: 10.1007/978-1-60327-853-9_24] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The deep terrestrial subsurface is a vast, largely unexplored environment that is oligotrophic, highly heterogeneous, and may contain extremes of both physical and chemical factors. In spite of harsh conditions, subsurface studies at several widely distributed geographic sites have revealed diverse communities of viable organisms, which have provided evidence of low but detectable metabolic activity. Although much of the terrestrial subsurface may be considered to be distant and isolated, the concept of horizontal gene transfer (HGT) in this environment has far-reaching implications for bioremediation efforts and groundwater quality, industrial harvesting of subsurface natural resources such as petroleum, and accurate assessment of the risks associated with DNA release and transport from genetically modified organisms. This chapter will explore what is known about some of the major mechanisms of HGT, and how the information gained from surface organisms might apply to conditions in the terrestrial subsurface. Evidence for the presence of mobile elements in subsurface bacteria and limited retrospective studies examining genetic signatures of potential past gene transfer events will be discussed.
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Affiliation(s)
- Jonna M Coombs
- Department of Biology, Adelphi University, Garden City, NY, USA
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Chee-Sanford JC, Mackie RI, Koike S, Krapac IG, Lin YF, Yannarell AC, Maxwell S, Aminov RI. Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure waste. JOURNAL OF ENVIRONMENTAL QUALITY 2009; 38:1086-108. [PMID: 19398507 DOI: 10.2134/jeq2008.0128] [Citation(s) in RCA: 472] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Antibiotics are used in animal livestock production for therapeutic treatment of disease and at subtherapeutic levels for growth promotion and improvement of feed efficiency. It is estimated that approximately 75% of antibiotics are not absorbed by animals and are excreted in waste. Antibiotic resistance selection occurs among gastrointestinal bacteria, which are also excreted in manure and stored in waste holding systems. Land application of animal waste is a common disposal method used in the United States and is a means for environmental entry of both antibiotics and genetic resistance determinants. Concerns for bacterial resistance gene selection and dissemination of resistance genes have prompted interest about the concentrations and biological activity of drug residues and break-down metabolites, and their fate and transport. Fecal bacteria can survive for weeks to months in the environment, depending on species and temperature, however, genetic elements can persist regardless of cell viability. Phylogenetic analyses indicate antibiotic resistance genes have evolved, although some genes have been maintained in bacteria before the modern antibiotic era. Quantitative measurements of drug residues and levels of resistance genes are needed, in addition to understanding the environmental mechanisms of genetic selection, gene acquisition, and the spatiotemporal dynamics of these resistance genes and their bacterial hosts. This review article discusses an accumulation of findings that address aspects of the fate, transport, and persistence of antibiotics and antibiotic resistance genes in natural environments, with emphasis on mechanisms pertaining to soil environments following land application of animal waste effluent.
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Van der Auwera GA, Król JE, Suzuki H, Foster B, Van Houdt R, Brown CJ, Mergeay M, Top EM. Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids. Antonie van Leeuwenhoek 2009; 96:193-204. [PMID: 19259779 DOI: 10.1007/s10482-009-9316-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 02/08/2009] [Indexed: 11/29/2022]
Abstract
The self-transmissible, broad-host-range (BHR) plasmid pMOL98 was previously isolated from polluted soil using a triparental plasmid capture approach and shown to possess a replicon similar to that of the BHR plasmids pSB102 and pIPO2. Here, complete sequence analysis and comparative genomics reveal that the 55.5 kb nucleotide sequence of pMOL98 shows extensive sequence similarity and synteny with the BHR plasmid family that now includes pIPO2, pSB102, pTER331, and pMRAD02. They share a plasmid backbone comprising replication, partitioning and conjugative transfer functions. Comparison of the variable accessory regions of these plasmids shows that the majority of natural transposons, as well as the mini-transposon used to mark the plasmids, are inserted in the parA locus. The transposon unique to pMOL98 appears to have inserted from the chromosome of the recipient strain used in the plasmid capture procedure. This demonstrates the necessity for careful screening of plasmids and host chromosomes to avoid mis-interpretation of plasmid genome content. The presence of very similar BHR plasmids with different accessory genes in geographically distinct locations suggests an important role in horizontal gene exchange and bacterial adaptation for this recently defined plasmid group, which we propose to name "PromA".
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Khan SJ, Roser DJ, Davies CM, Peters GM, Stuetz RM, Tucker R, Ashbolt NJ. Chemical contaminants in feedlot wastes: concentrations, effects and attenuation. ENVIRONMENT INTERNATIONAL 2008; 34:839-859. [PMID: 18055014 DOI: 10.1016/j.envint.2007.10.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Revised: 10/28/2007] [Accepted: 10/29/2007] [Indexed: 05/25/2023]
Abstract
Commercial feedlots for beef cattle finishing are potential sources of a range of trace chemicals which have human health or environmental significance. To ensure adequate protection of human and environmental health from exposure to these chemicals, the application of effective manure and effluent management practices is warranted. The Australian meat and livestock industry has adopted a proactive approach to the identification of best management practices. Accordingly, this review was undertaken to identify key chemical species that may require consideration in the development of guidelines for feedlot manure and effluent management practices in Australia. Important classes of trace chemicals identified include steroidal hormones, antibiotics, ectoparasiticides, mycotoxins, heavy metals and dioxins. These are described in terms of their likely sources, expected concentrations and public health or environmental significance based on international data and research. Androgenic hormones such as testosterone and trenbolone are significantly active in feedlot wastes, but they are poorly understood in terms of fate and environmental implications. The careful management of residues of antibiotics including virginiamycin, tylosin and oxytetracycline appears prudent in terms of minimising the risk of potential public health impacts from resistant strains of bacteria. Good management of ectoparasiticides including synthetic pyrethroids, macrocyclic lactones, fluazuron, and amitraz is important for the prevention of potential ecological implications, particularly towards dung beetles. Very few of these individual chemical contaminants have been thoroughly investigated in terms of concentrations, effects and attenuation in Australian feedlot wastes.
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Affiliation(s)
- S J Khan
- Centre for Water and Waste Technology, School of Civil and Environmental Engineering, University of New South Wales, NSW 2054, Australia.
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Binh CTT, Heuer H, Kaupenjohann M, Smalla K. Piggery manure used for soil fertilization is a reservoir for transferable antibiotic resistance plasmids. FEMS Microbiol Ecol 2008; 66:25-37. [PMID: 18557938 DOI: 10.1111/j.1574-6941.2008.00526.x] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
In this study, the prevalence and types of transferable antibiotic resistance plasmids in piggery manure were investigated. Samples from manure storage tanks of 15 farms in Germany were analysed, representing diverse sizes of herds, meat or piglet production. Antibiotic resistance plasmids from manure bacteria were captured in gfp-tagged rifampicin-resistant Escherichia coli and characterized. The occurrence of plasmid types was also detected in total community DNA by PCR and hybridization. A total of 228 transconjugants were captured from 15 manures using selective media supplemented with amoxicillin, sulfadiazine or tetracycline. The restriction patterns of 81 plasmids representing different antibiotic resistance patterns or different samples clustered into seven groups. Replicon probing revealed that 28 of the plasmids belonged to IncN, one to IncW, 13 to IncP-1 and 19 to the recently discovered pHHV216-like plasmids. The amoxicillin resistance gene bla-TEM was detected on 44 plasmids, and sulphonamide resistance genes sul1, sul2 and/or sul3 on 68 plasmids. Hybridization of replicon-specific sequences amplified from community DNA revealed that IncP-1 and pHHV216-like plasmids were detected in all manures, while IncN and IncW ones were less frequent. This study showed that 'field-scale' piggery manure is a reservoir of broad-host range plasmids conferring multiple antibiotic resistance genes.
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Affiliation(s)
- Chu Thi Thanh Binh
- Julius Kühn-Institute, Federal Research Centre for Cultivated Crops, Braunschweig, Germany
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33
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Mela F, Fritsche K, Boersma H, van Elsas JD, Bartels D, Meyer F, de Boer W, van Veen JA, Leveau JHJ. Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331. FEMS Microbiol Ecol 2008; 66:45-62. [PMID: 18355297 DOI: 10.1111/j.1574-6941.2008.00472.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Plasmid pTer331 from the bacterium Collimonas fungivorans Ter331 is a new member of the pIPO2/pSB102 family of environmental plasmids. The 40 457-bp sequence of pTer331 codes for 44 putative ORFs, most of which represent genes involved in replication, partitioning and transfer of the plasmid. We confirmed that pTer331 is stably maintained in its native host. Deletion analysis identified a mini-replicon capable of replicating autonomously in Escherichia coli and Pseudomonas putida. Furthermore, plasmid pTer331 was able to mobilize and retromobilize IncQ plasmid pSM1890 at typical rates of 10(-4) and 10(-8), respectively. Analysis of the 91% DNA sequence identity between pTer331 and pIPO2 revealed functional conservation of coding sequences, the deletion of DNA fragments flanked by short direct repeats (DR), and sequence preservation of long DRs. In addition, we experimentally established that pTer331 has no obvious contribution in several of the phenotypes that are characteristic of its host C. fungivorans Ter331, including the ability to efficiently colonize plant roots. Based on our findings, we hypothesize that cryptic plasmids such as pTer331 and pIPO2 might not confer an individual advantage to bacteria, but, due to their broad-host-range and ability to retromobilize, benefit bacterial populations by accelerating the intracommunal dissemination of the mobile gene pool.
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Affiliation(s)
- Francesca Mela
- Centre for Terrestrial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, Heteren, The Netherlands
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Schlüter A, Szczepanowski R, Pühler A, Top EM. Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool. FEMS Microbiol Rev 2007; 31:449-77. [PMID: 17553065 DOI: 10.1111/j.1574-6976.2007.00074.x] [Citation(s) in RCA: 286] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The dramatic spread of antibiotic resistance is a crisis in the treatment of infectious diseases that affect humans. Several studies suggest that wastewater treatment plants (WWTP) are reservoirs for diverse mobile antibiotic resistance elements. This review summarizes findings derived from genomic analysis of IncP-1 resistance plasmids isolated from WWTP bacteria. Plasmids that belong to the IncP-1 group are self-transmissible, and transfer to and replicate in a wide range of hosts. Their backbone functions are described with respect to their impact on vegetative replication, stable maintenance and inheritance, mobility and plasmid control. Accessory genetic modules, mainly representing mobile genetic elements, are integrated in-between functional plasmid backbone modules. These elements carry determinants conferring resistance to nearly all clinically relevant antimicrobial drug classes, to heavy metals, and quaternary ammonium compounds used as disinfectants. All plasmids analysed here contain integrons that potentially facilitate integration, exchange and dissemination of resistance gene cassettes. Comparative genomics of accessory modules located on plasmids from WWTP and corresponding modules previously identified in other bacterial genomes revealed that animal, human and plant pathogens and other bacteria isolated from different habitats share a common pool of resistance determinants.
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Affiliation(s)
- Andreas Schlüter
- Fakultät für Biologie, Lehrstuhl für Genetik, Universität Bielefeld, Bielefeld, Germany
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El Yacoubi B, Brunings AM, Yuan Q, Shankar S, Gabriel DW. In planta horizontal transfer of a major pathogenicity effector gene. Appl Environ Microbiol 2007; 73:1612-21. [PMID: 17220258 PMCID: PMC1828793 DOI: 10.1128/aem.00261-06] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xanthomonas citri pv. citri is a clonal group of strains that causes citrus canker disease and appears to have originated in Asia. A phylogenetically distinct clonal group that causes identical disease symptoms on susceptible citrus, X. citri pv. aurantifolii, arose more recently in South America. Genomes of X. citri pv. aurantifolii strains carry two DNA fragments that hybridize to pthA, an X. citri pv. citri gene which encodes a major type III pathogenicity effector protein that is absolutely required to cause citrus canker. Marker interruption mutagenesis and complementation revealed that X. citri pv. aurantifolii strain B69 carried one functional pthA homolog, designated pthB, that was required to cause cankers on citrus. Gene pthB was found among 38 open reading frames on a 37,106-bp plasmid, designated pXcB, which was sequenced and annotated. No additional pathogenicity effectors were found on pXcB, but 11 out of 38 open reading frames appeared to encode a type IV transfer system. pXcB transferred horizontally in planta, without added selection, from B69 to a nonpathogenic X. citri pv. citri (pthA::Tn5) mutant strain, fully restoring canker. In planta transfer efficiencies were very high (>0.1%/recipient) and equivalent to those observed for agar medium with antibiotic selection, indicating that pthB conferred a strong selective advantage to the recipient strain. A single pathogenicity effector that can confer a distinct selective advantage in planta may both facilitate plasmid survival following horizontal gene transfer and account for the origination of phylogenetically distinct groups of strains causing identical disease symptoms.
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Affiliation(s)
- B El Yacoubi
- Plant Molecular and Cell Biology Program and Department of Plant Pathology, University of Florida, Gainesville, FL 32611-0680, USA
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Unno Y, Okubo K, Wasaki J, Shinano T, Osaki M. Plant growth promotion abilities and microscale bacterial dynamics in the rhizosphere of Lupin analysed by phytate utilization ability. Environ Microbiol 2005; 7:396-404. [PMID: 15683400 DOI: 10.1111/j.1462-2920.2004.00701.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the rhizosphere, phosphorus (P) levels are low because of P uptake into the roots. Rhizobacteria live on carbon (C) exuded from roots, and may contribute to plant nutrition by liberating P from organic compounds such as phytates. We isolated over 300 phytate (Na-inositol hexa-phosphate; Na-IHP)-utilizing bacterial strains from the rhizosheath and the rhizoplane of Lupinus albus (L.). Almost all of the isolates were classified as Burkholderia based on 16S rDNA sequence analysis. Rhizosheath isolates cultured with Na-IHP as the only source of C and P showed lower P uptake at the same extracellular phytase activity than rhizoplane strains, suggesting that bacteria from the rhizosheath utilized phytate as a C source. Many isolates also utilized insoluble phytate (Al-IHP and/or Fe-IHP). In co-culture with Lotus japonicus seedlings, some isolates promoted plant growth significantly.
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Affiliation(s)
- Yusuke Unno
- Graduate School of Agriculture, Hokkaido University, N9W9, Kita-ku, Sapporo 060-8589, Japan
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Lilley AK, Bailey MJ, Barr M, Kilshaw K, Timms-Wilson TM, Day MJ, Norris SJ, Jones TH, Godfray HCJ. Population dynamics and gene transfer in genetically modified bacteria in a model microcosm. Mol Ecol 2004; 12:3097-107. [PMID: 14629389 DOI: 10.1046/j.1365-294x.2003.01960.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The horizontal transfer and effects on host fitness of a neutral gene cassette inserted into three different genomic loci of a plant-colonizing pseudomonad was assessed in a model ecosystem. The KX reporter cassette (kanamycin resistance, aph, and catechol 2, 3, dioxygenase, xylE) was introduced on the disarmed transposon mini-Tn5 into: (I) the chromosome of a spontaneous rifampicin resistant mutant Pseudomonas fluorescens SBW25R; (II) the chromosome of SBW25R in the presence of a naturally occurring lysogenic-phage (phage Phi101); and (III) a naturally occurring plasmid pQBR11 (330 kbp, tra+, Hgr) introduced into SBW25R. These bacteria were applied to Stellaria media (chickweed) plants as seed dressings [c. 5 x 104 colony-forming units (cfu)/seed] and the seedlings planted in 16 microcosm chambers containing model plant and animal communities. Gene transfer to pseudomonads in the phyllosphere and rhizosphere was found only in the plasmid treatment (III). Bacteria in the phage treatment (II) initially declined in density and free phage was detected, but populations partly recovered as the plants matured. Surprisingly, bacteria in the chromosome insertion treatment (I) consistently achieved higher population densities than the unmanipulated control and other treatments. Plasmids were acquired from indigenous bacterial populations in the control and chromosome insertion treatments. Plasmid acquisition, plasmid transfer from inocula and selection for plasmid carrying inocula coincided with plant maturation.
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Affiliation(s)
- A K Lilley
- Molecular Microbial Ecology Group, Centre for Ecology and Hydrology, Mansfield Road, Oxford OX1 3SR, UK
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40
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Van Elsas JD, Turner S, Bailey MJ. Horizontal gene transfer in the phytosphere. THE NEW PHYTOLOGIST 2003; 157:525-537. [PMID: 33873398 DOI: 10.1046/j.1469-8137.2003.00697.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Here, the ecological aspects of gene transfer processes between bacteria in the phytosphere are examined in the context of emerging evidence for the dominant role that horizontal gene transfer (HGT) has played in the evolutionary shaping of bacterial communities. Moreover, the impact of the putative capture of genetic material by bacteria from plants is discussed. Examples are provided that illustrate how mobile genetic elements (MGEs) influence the behaviour of bacteria in their natural habitat, especially in structured communities such as biofilms on plant surfaces. This community behaviour is used as a framework to pose questions on the evolutionary role and significance of gene transfer processes in plant-associated habitats. Selection within the highly structured phytosphere is likely to represent a dominant force shaping the genetic make-up of plant-associated bacterial communities. Current understanding of the triggering and impact of horizontal gene transfer, however, remains limited by our lack of understanding of the nature of the selective forces that act on bacteria in situ. The individual, colony, population and community level selection benefits imposed by the ability to use specific carbon sources or survive selective compounds are clear, but it is not always possible to assess what drives gene transfer and persistence. The role of HGT in the adaptation of host bacteria to their environmental niche is still not fully understood.
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Affiliation(s)
- Jan Dirk Van Elsas
- Plant Research International, PO Box 16, 6700 AA Wageningen, The Netherlands
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Haagensen JA, Hansen S, Johansen T, Molin S. In situ detection of horizontal transfer of mobile genetic elements. FEMS Microbiol Ecol 2002; 42:261-8. [DOI: 10.1111/j.1574-6941.2002.tb01016.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Abstract
To better understand prokaryotic gene flux in marine ecosystems and to determine whether or not environmental parameters can effect the composition and structure of plasmid populations in marine bacterial communities, information on the distribution, diversity, and ecological traits of marine plasmids is necessary. This mini-review highlights recent insights gained into the molecular diversity and ecology of plasmids occurring in marine microbial communities.
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Affiliation(s)
- Patricia A Sobecky
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, USA.
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Smalla K, Sobecky PA. The prevalence and diversity of mobile genetic elements in bacterial communities of different environmental habitats: insights gained from different methodological approaches. FEMS Microbiol Ecol 2002; 42:165-75. [DOI: 10.1111/j.1574-6941.2002.tb01006.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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45
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Heuer H, Krögerrecklenfort E, Wellington EMH, Egan S, van Elsas JD, van Overbeek L, Collard JM, Guillaume G, Karagouni AD, Nikolakopoulou TL, Smalla K. Gentamicin resistance genes in environmental bacteria: prevalence and transfer. FEMS Microbiol Ecol 2002; 42:289-302. [PMID: 19709289 DOI: 10.1111/j.1574-6941.2002.tb01019.x] [Citation(s) in RCA: 166] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- H Heuer
- Federal Biological Research Centre for Agriculture and Forestry, Institute for Plant Virology, Microbiology and Biosafety, Messeweg 11/12, D-38104 Braunschweig, Germany
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Tauch A, Schneiker S, Selbitschka W, Pühler A, van Overbeek LS, Smalla K, Thomas CM, Bailey MJ, Forney LJ, Weightman A, Ceglowski P, Pembroke T, Tietze E, Schröder G, Lanka E, van Elsas JD. The complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 isolated from bacteria of the wheat rhizosphere. MICROBIOLOGY (READING, ENGLAND) 2002; 148:1637-1653. [PMID: 12055285 DOI: 10.1099/00221287-148-6-1637] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Plasmid pIPO2 is a cryptic, conjugative, broad-host-range plasmid isolated from the wheat rhizosphere. It efficiently self-transfers between alpha, beta and gamma Proteobacteria and has a mobilizing/retromobilizing capacity for IncQ plasmids. The complete nucleotide sequence of pIPO2 is presented on the basis of its mini-Tn5::luxABtet-tagged derivative, pIPO2T. The pIPO2 sequence is 39815 bp long and contains at least 43 complete ORFs. Apart from a suite of ORFs with unknown function, all of the genes carried on pIPO2 are predicted to be involved in plasmid replication, maintenance and conjugative transfer. The overall organization of these genes is different from previously described plasmids, but is similar to the genetic organization seen in pSB102, a conjugative plasmid recently isolated from the bacterial community of the alfalfa rhizosphere. The putative conjugative transfer region of pIPO2 covers 23 kb and contains the genes required for DNA processing (Dtr) and mating pair formation (Mpf). The organization of these transfer genes in pIPO2 is highly similar to the genetic organization seen in the environmental plasmid pSB102 and in pXF51 from the plant pathogen Xylella fastidiosa. Plasmids pSB102 and pXF51 have recently been proposed to form a new family of environmental broad-host-range plasmids. Here it is suggested that pIPO2 is a new member of this family. The proposed Mpf system of pIPO2 shares high amino acid sequence similarity with equivalent VirB proteins from the type IV secretion system of Brucella spp. Sequence information was used to design primers specific for the detection of pIPO2. Environmental DNA from a range of diverse habitats was screened by PCR with these primers. Consistently positive signals for the presence of pIPO2 were obtained from a range of soil-related habitats, including the rhizospheres of young wheat plants, of field-grown oats and of grass (all gramineous plants), as well as from the rhizosphere of tomato plants. These data add to the growing evidence that plasmids carry advantageous genes with as yet undefined functions in plant-associated communities.
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Affiliation(s)
- Andreas Tauch
- Zentrum für Genomforschung, Universität Bielefeld, D-33615 Bielefeld, Germany1
| | - Susanne Schneiker
- Lehrstuhl für Genetik, Universität Bielefeld, D-33615 Bielefeld, Germany2
| | - Werner Selbitschka
- Lehrstuhl für Genetik, Universität Bielefeld, D-33615 Bielefeld, Germany2
| | - Alfred Pühler
- Lehrstuhl für Genetik, Universität Bielefeld, D-33615 Bielefeld, Germany2
| | | | - Kornelia Smalla
- Biologische Bundesanstalt für Land-und Forstwirtschaft, D-38104 Braunschweig, Germany4
| | - Christopher M Thomas
- School for Biological Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK5
| | - Mark J Bailey
- NERC Institute of Virology and Environmental Microbiology, Oxford OX1 3SR, UK6
| | - Larry J Forney
- Department of Biology, University of Idaho, Moscow, ID 83844, USA7
| | - Andrew Weightman
- Cardiff School of Biosciences, University of Wales, Cardiff CF10 3TL, UK8
| | - Piotr Ceglowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland9
| | - Tony Pembroke
- Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland10
| | - Erhard Tietze
- Robert Koch-Institut, Bereich Wernigerode, D-38855 Wernigerode, Germany11
| | - Gunnar Schröder
- Max-Planck-Institut für Molekulare Genetik, Dahlem, D-14195 Berlin, Germany12
| | - Erich Lanka
- Max-Planck-Institut für Molekulare Genetik, Dahlem, D-14195 Berlin, Germany12
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Beeson KE, Erdner DL, Bagwell CE, Lovell CR, Sobecky PA. Differentiation of plasmids in marine diazotroph assemblages determined by randomly amplified polymorphic DNA analysis. MICROBIOLOGY (READING, ENGLAND) 2002; 148:179-189. [PMID: 11782510 DOI: 10.1099/00221287-148-1-179] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Nitrogen fixation by diazotrophic bacteria is a significant source of new nitrogen in salt marsh ecosystems. Recent studies have characterized the physiological and phylogenetic diversity of oxygen-utilizing diazotrophs isolated from the rhizoplanes of spatially separated intertidal macrophyte habitats. However, there is a paucity of information regarding the traits encoded by and the diversity of plasmids occurring in this key ecological functional group. Five-hundred and twenty-one isolates cultivated from the rhizoplanes of Juncus roemarianus, Spartina patens and different growth forms (short-form and tall-form) of Spartina alterniflora were screened for the presence of plasmids. One-hundred and thirty-four diazotrophs carrying plasmids that ranged in size from 2 to >100 kbp were identified. The majority of the marine bacteria contained one plasmid. Diazotrophs from the short-form S. alterniflora rhizoplane contained significantly fewer plasmids relative to isolates from tall-form S. alterniflora, J. roemarianus and S. patens. Although some plasmids exhibited homology to a nifH gene probe, the majority of the plasmids were classified as cryptic. Two oligonucleotide primers were developed to facilitate genotypic typing of the endogenously isolated marine plasmids by the randomly amplified polymorphic DNA (RAPD)-PCR technique. These primers proved to be more effective than 21 commercially available primers tested to generate RAPD-PCR patterns. Analysis of the RAPD-PCR patterns indicated as many as 71 different plasmid genotypes occurring in diazotroph bacterial assemblages within and between the four different salt marsh grass rhizoplane habitats investigated in this study.
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Affiliation(s)
- Keri E Beeson
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, USA1
| | - Deana L Erdner
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, USA1
| | - Christopher E Bagwell
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA2
| | - Charles R Lovell
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA2
| | - Patricia A Sobecky
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, USA1
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Schmidt-Eisenlohr H, Rittig M, Preithner S, Baron C. Biomonitoring of pJP4-carrying Pseudomonas chlororaphis with Trb protein-specific antisera. Environ Microbiol 2001; 3:720-30. [PMID: 11846762 DOI: 10.1046/j.1462-2920.2001.00244.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The transfer of catabolic genes on conjugative plasmids to indigenous organisms from which they may spread further into the community allows the introduction of new biodegradative pathways for metabolic conversion of pollutants to the community. Biomonitoring of IncP plasmid pJP4-carrying Pseudomonas chlororaphis from the rhizosphere of Arabidopsis thaliana was achieved using antisera specific for proteins from the plasmid transfer machinery. Antisera were generated that recognized TrbC and TrbF, the putative major and minor components of pJP4-determined pili, respectively, and the putative lipoprotein TrbH. Cell fractionation studies showed association of TrbC, TrbF and TrbH with the cells and suggested that TrbC and TrbF are part of extracellular pJP4-determined pili. TrbF and TrbH antisera allowed specific detection of IncP compared with IncN or IncW plasmid-carrying cells and even permitted differentiation between bacteria carrying IncPalpha plasmid RP4 and IncPbeta plasmid pJP4. Immunofluorescence microscopy was applied to detect TrbF and TrbH signal at the cell periphery, allowing distinction from autofluorescing cells and soil debris. In situ experiments showed specific recognition of pJP4-carrying cells from laboratory cultures, as well as from the rhizosphere of A. thaliana grown in natural soil. After co-inoculation of donor P. chlororaphis pJP4 and recipient Ralstonia eutropha, a combination of immunofluorescence and oligonucleotide hybridization techniques permitted the detection of plasmid transfer between both organisms in the A. thaliana rhizosphere. This strategy may be generally applicable for the analysis of plasmid transfer in natural ecosystems.
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Affiliation(s)
- H Schmidt-Eisenlohr
- Institut für Genetik und Mikrobiologie der Universität München, Lehrstuhl für Mikrobiologie, Maria-Ward-Str. 1a, D-80638 München, Germany
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50
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Cook MA, Osborn AM, Bettandorff J, Sobecky PA. Endogenous isolation of replicon probes for assessing plasmid ecology of marine sediment microbial communities. MICROBIOLOGY (READING, ENGLAND) 2001; 147:2089-2101. [PMID: 11495987 DOI: 10.1099/00221287-147-8-2089] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Six functional replication origins (repGA14, repGA33, repGA70, repSD41, repSD164 and repSD172), obtained from endogenously isolated, broad-host-range (BHR) marine plasmids ranging in size from 5 to 60 kb, were used to determine plasmid occurrence in three coastal marine sediment sites (in California, Georgia and South Carolina, USA). The plasmid-specific replicons were isolated from plasmid-bearing marine sediment bacteria belonging to the alpha and gamma subclasses of the Proteobacteria. The plasmid sources of the endogenous replicons were considered to be cryptic due to a lack of identifiable phenotypic traits. The putative Rep proteins from a number of these replicons showed similarity to replicons of two recognized families: RCR group III (repSD164) and the FIA family of theta group A (repSD41, repSD121, repGA33 and repGA14). Plasmids isolated from marine bacteria belonging to the genera Pseudoalteromonas, Shewanella and Vibrio cultivated from geographically different coastal sites exhibited homology to two of the marine plasmid replicons, repSD41 and repGA70, obtained from a Vibrio sp. The repGA33 plasmid origin, obtained from a Shewanella sp. isolated from coastal Georgia, was detected in 7% of the Georgia marine sediment Shewanella sp. isolates. Microbial community DNA extracted from marine sediments was also screened for the presence of the plasmid replication sequences. Community DNA samples amplified by PCR yielded a positive signal for the repSD172 and repGA14 replication sequences. The replication origin of BHR plasmid RK2 (IncP) was also detected in marine Vibrio sp. and microbial community DNA extracted from the three coastal sites. These findings provide molecular evidence that marine sediment bacteria harbour an untapped population of BHR plasmids.
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Affiliation(s)
- Marisa A Cook
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, USA1
| | - A Mark Osborn
- Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK2
| | - Juli Bettandorff
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, USA1
| | - Patricia A Sobecky
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta, GA 30332-0230, USA1
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