Characterization of a collection of plasmid-containing bacteria isolated from an on-farm biopurification system used for pesticide removal

Martini, María Carla; Albicoro, Francisco Javier; Nour, Eman; Schlüter, Andreas; Elsas, Jan Dirk van; Springael, Dirk; Smalla, K.; Pistorio, Mariano; Lagares, Antonio; Papa, María Florencia Del

doi:10.1016/j.plasmid.2015.05.001

Cited by 16 publications

(26 citation statements)

References 54 publications

(53 reference statements)

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“…Therefore, the broad-host-range property of plasmid-encoding conjugation systems can greatly contribute to the horizontal transfer of various genetic traits. Plasmids RP4, R388, and pKM101, which belong to the IncP-1, IncW, and IncN groups, respectively, are well-characterized and so-called broad-host-range plasmids because both their replication and conjugation systems can function in nearly all proteobacterial strains (30). The host ranges of these conjugation systems have been further shown to be broader than those of the replication systems; the former systems can deliver DNA into the bacterial recipient strains where the latter systems are not functional (31).…”

Section: Discussionmentioning

confidence: 99%

Host Range of the Conjugative Transfer System of IncP-9 Naphthalene-Catabolic Plasmid NAH7 and Characterization of Its oriT Region and Relaxase

Kishida

Irie

Ohtsubo

et al. 2017

Appl Environ Microbiol

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NAH7 and pWW0 from gammaproteobacterial Pseudomonas putida strains are IncP-9 conjugative plasmids that carry the genes for degradation of naphthalene and toluene, respectively. Although such genes on these plasmids are wellcharacterized, experimental investigation of their conjugation systems remains at a primitive level. To clarify these conjugation systems, in this study, we investigated the NAH7-encoded conjugation system by (i) analyzing the origin of its conjugative transfer (oriT)-containing region and its relaxase, which specifically nicks within the oriT region for initiation of transfer, and (ii) comparing the conjugation systems between NAH7 and pWW0. The NAH7 oriT (oriT N ) region was located within a 430-bp fragment, and the strand-specific nicking (nic) site and its upstream sequences that were important for efficient conjugation in the oriT N region were identified. Unlike many other relaxases, the NAH7 relaxase exhibited unique features in its ability to catalyze, in a conjugation-independent manner, the site-specific intramolecular recombination between two copies of the oriT N region, between two copies of the pWW0 oriT (oriT W ) region (which is clearly different from the oriT N region), and between the oriT N and oriT W regions. The pWW0 relaxase, which is also clearly different from the NAH7 relaxase, was strongly suggested to have the ability to conjugatively and efficiently mobilize the oriT Ncontaining plasmid. Such a plasmid was, in the presence of the NAH7Δnic derivative, conjugatively transferable to alphaproteobacterial and betaproteobacterial strains in which the NAH7 replication machinery is nonfunctional, indicating that the NAH7 conjugation system has a broader host range than its replication system. IMPORTANCE Various studies have strongly suggested an important contribution of conjugative transfer of catabolic plasmids to the rapid and wide dissemination of the plasmid-loaded degradation genes to microbial populations. Degradation genes on such plasmids are often loaded on transposons, which can be inserted into the genomes of the recipient bacterial strains where the transferred plasmids cannot replicate. The aim was to advance detailed molecular knowledge of the determinants of host range for plasmids. This aim is expected to be easily and comprehensively achieved using an experimental strategy in which the oriT region is connected with a plasmid that has a broad host range of replication. Using such a strategy in this study, we showed that (i) the NAH7 oriT-relaxase system has unique properties that are significantly different from other well-studied systems and (ii) the host range of the NAH7 conjugation system is broader than previously thought.KEYWORDS Pseudomonas, conjugation, oriT, plasmid, relaxase C onjugative transfer of plasmids that carry various genetic traits contributes greatly to the rapid adaptation and evolution of host bacteria (1). The conjugative transfer of plasmids in Gram-negative bacteria consists of DNA transfer and replication (Dtr) and

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Section: Discussionmentioning

confidence: 99%

Host Range of the Conjugative Transfer System of IncP-9 Naphthalene-Catabolic Plasmid NAH7 and Characterization of Its oriT Region and Relaxase

Kishida

Irie

Ohtsubo

et al. 2017

Appl Environ Microbiol

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“…Several toxic compounds (pesticides and other substances) from polluted wastewater sources generated in the farmyard can affect the associated microbiomes [34]. Martini et al [35] showed a high proportion of bacteria tolerant to antibiotics or heavy metals, isolated from on-farm biopurification systems (biofilters) used for pesticide removal from wastewater in intensive agricultural systems.…”

Section: The Mycobiome In Anthropogenic Soilsmentioning

confidence: 99%

Advances in Eco-Efficient Agriculture: The Plant-Soil Mycobiome

et al. 2017

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Abstract:In order to achieve a desirable ecological and sustainable agriculture a thorough understanding of the plant-soil mycobiome is imperative. Commercial industrial agriculture alters greenhouse gas emissions, promotes loss of plant and soil biodiversity, increases pollution by raising atmospheric CO 2 , and releases pesticides, thus affecting both terrestrial and aquatic ecosystems. Diversified farming systems, including perennial cultivated pastures, are among worldwide strategies that aim to reduce terrestrial greenhouse gas emissions and deal with threats to global sustainability. Additionally, stimulation of soil microbes and appropriate soil management can influence soil interactions as well as the rates of organic matter decomposition and the release of gases. Agricultural soil microbial communities play a central role in ecosystem processes and are affected by biocontrol agents, biofertilizers, and exposure to pesticides, the extent to which is yet to be fully elucidated. Intercropping different plant species is beneficial, as this can increase carbon fixation by plants, transferring carbon to the soil, especially via mycorrhizas, thus modifying interplant interactions. This review focuses on agro-ecosystems, showing the latest advances in the plant-soil interface (the mycobiome) for an eco-efficient agricultural production.

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“…In a previous report14 we showed that the isolates from the BPS collection were able to grow in the presence of different antibiotics and feature a great variability in their resistance levels. It was further demonstrated that different resistance genes are encoded on plasmids.…”

Section: Resultsmentioning

confidence: 94%

“…The sampled BPS was suggested to constitute a suitable source for the isolation of genes encoding novel catabolic enzymes and resistances to toxic elements/compounds based on the high abundance and diversity of MGEs detected in this habitat1516. In particular, the isolate collection characterized by Martini et al 14. harbors more than 50 HMW plasmids amounting to several megabases of sequence information.…”

mentioning

confidence: 99%

Genomics of high molecular weight plasmids isolated from an on-farm biopurification system

Martini

Wibberg

Lozano

et al. 2016

Sci Rep

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The use of biopurification systems (BPS) constitutes an efficient strategy to eliminate pesticides from polluted wastewaters from farm activities. BPS environments contain a high microbial density and diversity facilitating the exchange of information among bacteria, mediated by mobile genetic elements (MGEs), which play a key role in bacterial adaptation and evolution in such environments. Here we sequenced and characterized high-molecular-weight plasmids from a bacterial collection of an on-farm BPS. The high-throughput-sequencing of the plasmid pool yielded a total of several Mb sequence information. Assembly of the sequence data resulted in six complete replicons. Using in silico analyses we identified plasmid replication genes whose encoding proteins represent 13 different Pfam families, as well as proteins involved in plasmid conjugation, indicating a large diversity of plasmid replicons and suggesting the occurrence of horizontal gene transfer (HGT) events within the habitat analyzed. In addition, genes conferring resistance to 10 classes of antimicrobial compounds and those encoding enzymes potentially involved in pesticide and aromatic hydrocarbon degradation were found. Global analysis of the plasmid pool suggest that the analyzed BPS represents a key environment for further studies addressing the dissemination of MGEs carrying catabolic genes and pathway assembly regarding degradation capabilities.

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Characterization of a collection of plasmid-containing bacteria isolated from an on-farm biopurification system used for pesticide removal

Cited by 16 publications

References 54 publications

Host Range of the Conjugative Transfer System of IncP-9 Naphthalene-Catabolic Plasmid NAH7 and Characterization of Its oriT Region and Relaxase

Host Range of the Conjugative Transfer System of IncP-9 Naphthalene-Catabolic Plasmid NAH7 and Characterization of Its oriT Region and Relaxase

Advances in Eco-Efficient Agriculture: The Plant-Soil Mycobiome

Genomics of high molecular weight plasmids isolated from an on-farm biopurification system

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