Monitoring the spread of broad host and narrow host range plasmids in soil microcosms

Promotion of plasmid maintenance by heterogeneous partitioning of microbial communities

Transferable plasmids play a critical role in shaping the functions of microbial communities. Previous studies suggested multiple mechanisms underlying plasmid persistence and abundance. Here, we focus on the interplay between heterogeneous community partitioning and plasmid fates. Natural microbiomes often experience partitioning that creates heterogeneous local communities with reduced population sizes and biodiversity. Little is known about how population partitioning affects the plasmid fate through the modulation of community structure. By modeling and experiments, we show that heterogeneous community partitioning can paradoxically promote the persistence of a plasmid that would otherwise not persist in a global community. Among the local communities created by partitioning, a minority will primarily consist of members able to transfer the plasmid fast enough to support its maintenance by serving as a local plasmid haven. Our results provide insights into plasmid maintenance and suggest a generalizable approach to modulate plasmid persistence for engineering and medical applications.

Genomic diversity across the Rickettsia and 'Candidatus Megaira' genera and proposal of genus status for the Torix group

Members of the bacterial genus Rickettsia were originally identified as causative agents of vector-borne diseases in mammals. However, many Rickettsia species are arthropod symbionts and close relatives of ‘Candidatus Megaira’, which are symbiotic associates of microeukaryotes. Here, we clarify the evolutionary relationships between these organisms by assembling 26 genomes of Rickettsia species from understudied groups, including the Torix group, and two genomes of ‘Ca. Megaira’ from various insects and microeukaryotes. Our analyses of the new genomes, in comparison with previously described ones, indicate that the accessory genome diversity and broad host range of Torix Rickettsia are comparable to those of all other Rickettsia combined. Therefore, the Torix clade may play unrecognized roles in invertebrate biology and physiology. We argue this clade should be given its own genus status, for which we propose the name ‘Candidatus Tisiphia’.

The bacterial genus Rickettsia includes vector-borne pathogens and arthropod symbionts that are close relatives of symbionts of microeukaryotes classified under the genus ‘Candidatus Megaira’. Here, Davison et al. clarify the evolutionary relationships between these organisms by assembling 28 genomes of understudied species, and propose that a distinct clade known as Torix Rickettsia should be considered a separate genus.

Species- and site-specific genome editing in complex bacterial communities

Understanding microbial gene functions relies on the application of experimental genetics in cultured microorganisms. However, the vast majority of bacteria and archaea remain uncultured, precluding the application of traditional genetic methods to these organisms and their interactions. Here, we characterize and validate a generalizable strategy for editing the genomes of specific organisms in microbial communities. We apply environmental transformation sequencing (ET-seq), in which nontargeted transposon insertions are mapped and quantified following delivery to a microbial community, to identify genetically tractable constituents. Next, DNA-editing all-in-one RNA-guided CRISPR-Cas transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-seq are used to enable organism- and locus-specific genetic manipulation in a community context. Using a combination of ET-seq and DART in soil and infant gut microbiota, we conduct species- and site-specific edits in several bacteria, measure gene fitness in a nonmodel bacterium and enrich targeted species. These tools enable editing of microbial communities for understanding and control.

The spread of the plasmid RP4 in a synthetic bacterial community is dependent on the particular donor strain

The rapid spread of antibiotic resistance challenges modern medicine. So far, mechanistic and quantitative knowledge concerning the spread of resistance genes mainly relies on laboratory experiments with simplified setups, e.g. two strain communities. Thus, the transferability of the obtained process rates might be limited. To investigate the role of a diverse community concerning the dissemination of the multidrug resistance plasmid RP4, an Escherichia coli harboring RP4 invaded a microbial community consisting of 21 species. Changes in the community composition as well as plasmid uptake by community members were monitored for 22 days. Special focus was laid on the question of whether the observed changes were dependent on the actual invading donor isolate and the ambient antibiotic concentration. In our microcosm experiment, the community composition was primarily influenced by the given environmental variables and only secondarily by the particular invader E. coli. The establishment of resistance within the community, however, was directly dependent on the donor identity. The extent to which ambient conditions influence the spread of RP4 depended on the E. coli donor strain. These results emphasize that even within one species there are great differences in the ability to conquer an ecological niche and to spread antibiotic resistance.

Successful Dissemination of Plasmid-Mediated Extended-Spectrum β-Lactamases in Enterobacterales over Humans to Wild Fauna

Background: The emergence of multidrug-resistant bacteria remains poorly understood in the wild ecosystem and at the interface of habitats. Here, we explored the spread of Escherichia coli containing IncI1-ST3 plasmid encoding resistance gene cefotaximase-Munich-1 (bla_CTX-M-1) in human-influenced habitats and wild fauna using a genomic approach. Methods. Multilocus sequence typing (MLST), single-nucleotide polymorphism comparison, synteny-based analysis and data mining approaches were used to analyse a dataset of genomes and circularised plasmids. Results. CTX-M-1 E. coli sequence types (STs) were preferentially associated with ecosystems. Few STs were shared by distinct habitats. IncI1-ST3-bla_CTX-M-1 plasmids are disseminated among all E. coli phylogroups. The main divergences in plasmids were located in a shuffling zone including bla_CTX-M-1 inserted in a conserved site. This insertion hot spot exhibited diverse positions and orientations in a zone-modulating conjugation, and the resulting synteny was associated with geographic and biological sources. Conclusions. The ecological success of IncI1-ST3-bla_CTX-M-1 appears less linked to the spread of their bacterial recipients than to their ability to transfer in a broad spectrum of bacterial lineages. This feature is associated with the diversity of their shuffling conjugation region that contain bla_CTX-M-1. These might be involved in the resistance to antimicrobials, but also in their spread.

The equine hindgut as a reservoir of mobile genetic elements and antimicrobial resistance genes

Antibiotic resistance in bacterial pathogens is a growing problem for both human and veterinary medicine. Mobile genetic elements (MGEs) such as plasmids, transposons, and integrons enable the spread of antibiotic resistance genes (ARGs) among bacteria, and the overuse of antibiotics drives this process by providing the selection pressure for resistance genes to establish and persist in bacterial populations. Because bacteria, MGEs, and resistance genes can readily spread between different ecological compartments (e.g. soil, plants, animals, humans, wastewater), a "One Health" approach is needed to combat this problem. The equine hindgut is an understudied but potentially significant reservoir of ARGs and MGEs, since horses have close contact with humans, their manure is used in agriculture, they have a dense microbiome of both bacteria and fungi, and many antimicrobials used for equine treatment are also used in human medicine. Here, we collate information to date about resistance genes, plasmids, and class 1 integrons from equine-derived bacteria, we discuss why the equine hindgut deserves increased attention as a potential reservoir of ARGs, and we suggest ways to minimize the selection for ARGs in horses, in order to prevent their spread to the wider community.

The proficiency of the original host species determines community-level plasmid dynamics

Plasmids are common in natural bacterial communities, facilitating bacterial evolution via horizontal gene transfer. Bacterial species vary in their proficiency to host plasmids: whereas plasmids are stably maintained in some species regardless of selection for plasmid-encoded genes, in other species, even beneficial plasmids are rapidly lost. It is, however, unclear how this variation in host proficiency affects plasmid persistence in communities. Here, we test this using multispecies bacterial soil communities comprising species varying in their proficiency to host a large conjugative mercury resistance plasmid, pQBR103. The plasmid reached higher community-level abundance where beneficial and when introduced to the community in a more proficient host species. Proficient plasmid host species were also better able to disseminate the plasmid to a wider diversity of host species. These findings suggest that the dynamics of plasmids in natural bacterial communities depend not only upon the plasmid's attributes and the selective environment but also upon the proficiency of their host species.

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

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

Diversity of CTX-M-1-producing E. coli from German food samples and genetic diversity of the blaCTX-M-1 region on IncI1 ST3 plasmids

Antimicrobial resistance to cephalosporins is commonly mediated by extended-spectrum β-lactamases (ESBL) or plasmidic AmpC β-lactamases (pAmpC). In livestock bla_CTX-M-1 is the most frequently detected ESBL-encoding gene. As transmission to consumers through contaminated food is often proposed, this study characterized ESBL/pAmpC-producing E. coli collected from food samples. Therefore, samples from food products of animal origin and vegetables were screened for phenotypically resistant E. coli by selective cultivation. The ESBL genotype was confirmed for 404 isolates with the majority of them (n = 212) harboring the bla_CTX-M-1 gene. PFGE and MLST analyses as well as plasmid characterization were carried out for 89 isolates, selected under epidemiological aspects. In addition, 44 isolates were investigated by whole genome sequencing and/or sequencing of their plasmids on an Illumina Miseq platform. MLST and PFGE indicated a diverse population of CTX-M-1-producing E. coli in German food samples with no spread of single clonal lineages. The majority of the isolates harbored the bla_CTX-M-1 gene on IncI1 plasmids. Frequently, the gene was associated with the ISEcp1 element and located on a ∼100 kb IncI1 plasmid depicting the plasmid multilocus sequence type (ST) 3. The bla_CTX-M-1 gene and its flanking sequences were located within the shufflon of the type IV pilus region in diverse orientations. In conclusion, dissemination of the CTX-M-1 β-lactamase within food samples of animal origin is driven by the transmission of a ∼100 kb large IncI1 ST3 plasmid. Apart from conjugal transfer of IncI1 ST3 plasmids the transmission of the bla_CTX-M-1 gene might be further promoted through mobilization due to its location within a recombination hot-spot of IncI1 plasmids.

Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization

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.

Plasmid Detection, Characterization, and Ecology

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.

Autoclave treatment of pig manure does not reduce the risk of transmission and transfer of tetracycline resistance genes in soil: successive determinations with soil column experiments

The increasing use of antibiotics, especially tetracycline, in livestock feed adversely affects animal health and ecological integrity. Therefore, approaches to decrease this risk are urgently needed. High temperatures facilitate antibiotic degradation; whether this reduces transmission risk and transfer of tetracycline-resistant bacteria (TRBs) and tetracycline resistance genes (TRGs) in soil remains unknown. Successive experiments with soil columns evaluated the effects of autoclaving pig manure (APM) on soil TRB populations and TRGs over time at different soil depths. The data showed sharp increases in TRB populations and TRGs in each subsoil layer of PM (non-APM) and APM treatments within 30 days, indicating that TRBs and TRGs transferred rapidly. The level of TRBs in the upper soil layers was approximately 15-fold higher than in subsoils. TRBs were not dependent on PM and APM levels, especially in the late phase. Nevertheless, higher levels of APM led to rapid expansion of TRBs as compared to PM. Moreover, temporal changes in TRB frequencies in total culturable bacteria (TCBs) were similar to TRBs, indicating that the impact of PM or APM on TRBs was more obvious than for TCBs. TRBs were hypothesized to depend on the numbers of TRGs and indigenous recipient bacteria. In the plough layer, five TRGs (tetB, tetG, tetM, tetW, and tetB/P) existed in each treatment within 150 days. Selective pressure of TC may not be a necessary condition for the transfer and persistence of TRGs in soil. High temperatures might reduce TRBs in PM, which had minimal impact on the transmission and transfer of TRGs in soil. Identifying alternatives to decrease TRG transmission remains a major challenge.

Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

Conjugal plasmids can provide microbes with full complements of new genes and constitute potent vehicles for horizontal gene transfer. Conjugal plasmid transfer is deemed responsible for the rapid spread of antibiotic resistance among microbes. While broad host range plasmids are known to transfer to diverse hosts in pure culture, the extent of their ability to transfer in the complex bacterial communities present in most habitats has not been comprehensively studied. Here, we isolated and characterized transconjugants with a degree of sensitivity not previously realized to investigate the transfer range of IncP- and IncPromA-type broad host range plasmids from three proteobacterial donors to a soil bacterial community. We identified transfer to many different recipients belonging to 11 different bacterial phyla. The prevalence of transconjugants belonging to diverse Gram-positive Firmicutes and Actinobacteria suggests that inter-Gram plasmid transfer of IncP-1 and IncPromA-type plasmids is a frequent phenomenon. While the plasmid receiving fractions of the community were both plasmid- and donor- dependent, we identified a core super-permissive fraction that could take up different plasmids from diverse donor strains. This fraction, comprising 80% of the identified transconjugants, thus has the potential to dominate IncP- and IncPromA-type plasmid transfer in soil. Our results demonstrate that these broad host range plasmids have a hitherto unrecognized potential to transfer readily to very diverse bacteria and can, therefore, directly connect large proportions of the soil bacterial gene pool. This finding reinforces the evolutionary and medical significances of these plasmids.

Transferable antibiotic resistance plasmids from biogas plant digestates often belong to the IncP-1ε subgroup

Manure is known to contain residues of antibiotics administered to farm animals as well as bacteria carrying antibiotic resistance genes (ARGs). These genes are often located on mobile genetic elements. In biogas plants (BGPs), organic substrates such as manure and plant material are mixed and fermented in order to provide energy, and resulting digestates are used for soil fertilization. The fate of plasmid carrying bacteria from manure during the fermentation process is unknown. The present study focused on transferable antibiotic resistance plasmids from digestates of seven BGPs, using manure as a co-substrate, and their phenotypic and genotypic characterization. Plasmids conferring resistance to either tetracycline or sulfadiazine were captured by means of exogenous plasmid isolation from digestates into Pseudomonas putida KT2442 and Escherichia coli CV601 recipients, at transfer frequencies ranging from 10(-5) to 10(-7). Transconjugants (n = 101) were screened by PCR-Southern blot hybridization and real-time PCR for the presence of IncP-1, IncP-1ε, IncW, IncN, IncP-7, IncP-9, LowGC, and IncQ plasmids. While 61 plasmids remained unassigned, 40 plasmids belonged to the IncP-1ε subgroup. All these IncP-1ε plasmids were shown to harbor the genes tet(A), sul1, qacEΔ1, intI1, and integron gene cassette amplicons of different size. Further analysis of 16 representative IncP-1ε plasmids showed that they conferred six different multiple antibiotic resistance patterns and their diversity seemed to be driven by the gene cassette arrays. IncP-1ε plasmids displaying similar restriction and antibiotic resistance patterns were captured from different BGPs, suggesting that they may be typical of this environment. Our study showed that BGP digestates are a potential source of transferable antibiotic resistance plasmids, and in particular the broad host range IncP-1ε plasmids might contribute to the spread of ARGs when digestates are used as fertilizer.

Does a drop in the bucket make a splash? Assessing the impact of antibiotic use on plants

Antibiotics are applied to plants to prevent bacterial diseases, although the diversity of antibiotics and total amounts used are dwarfed by antibiotic use in animal agriculture. Nevertheless, the release of antibiotics into the open environment during crop treatment draws scrutiny for its potential impact on the global pool of resistance genes. The main use of antibiotics on plants is application of streptomycin to prevent fire blight, a serious disease of apple and pear trees. A series of recent studies identified and quantified antibiotic resistance genes and profiled bacterial communities in apple orchard plots that were or were not sprayed with streptomycin. While the specific objectives and methods varied, the results of these studies suggest that streptomycin application for fire blight control does not influence bacterial community structure or increase the abundance of resistance genes in orchards.

The arable ecosystem as battleground for emergence of new human pathogens

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.

Effect of streptomycin treatment on bacterial community structure in the apple phyllosphere

We studied the effect of many years of streptomycin use in apple orchards on the proportion of phyllosphere bacteria resistant to streptomycin and bacterial community structure. Leaf samples were collected during early July through early September from four orchards that had been sprayed with streptomycin during spring of most years for at least 10 years and four orchards that had not been sprayed. The percentage of cultured phyllosphere bacteria resistant to streptomycin at non-sprayed orchards (mean of 65%) was greater than at sprayed orchards (mean of 50%) (P = 0.0271). For each orchard, a 16S rRNA gene clone library was constructed from leaf samples. Proteobacteria dominated the bacterial communities at all orchards, accounting for 71 of 104 OTUs (determined at 97% sequence similarity) and 93% of all sequences. The genera Massilia, Methylobacterium, Pantoea, Pseudomonas, and Sphingomonas were shared across all sites. Shannon and Simpson's diversity indices and Pielou's evenness index were similar among orchards regardless of streptomycin use. Analysis of Similarity (ANOSIM) indicated that long-term streptomycin treatment did not account for the observed variability in community structure among orchards (R = -0.104, P = 0.655). Other variables, including time of summer, temperature and time at sampling, and relative distance of the orchards from each other, also had no significant effect on bacterial community structure. We conclude that factors other than streptomycin exposure drive both the proportion of streptomycin-resistant bacteria and phylogenetic makeup of bacterial communities in the apple phyllosphere in middle to late summer.

Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome

Numerous mobile genetic elements (MGE) are associated with the human gut microbiota and collectively referred to as the gut mobile metagenome. The role of this flexible gene pool in development and functioning of the gut microbial community remains largely unexplored, yet recent evidence suggests that at least some MGE comprising this fraction of the gut microbiome reflect the co-evolution of host and microbe in the gastro-intestinal tract. In conjunction, the high level of novel gene content typical of MGE coupled with their predicted high diversity, suggests that the mobile metagenome constitutes an immense and largely unexplored gene-space likely to encode many novel activities with potential biotechnological or pharmaceutical value, as well as being important to the development and functioning of the gut microbiota. Of the various types of MGE that comprise the gut mobile metagenome, plasmids are of particular importance since these elements are often capable of autonomous transfer between disparate bacterial species, and are known to encode accessory functions that increase bacterial fitness in a given environment facilitating bacterial adaptation. In this article current knowledge regarding plasmids resident in the human gut mobile metagenome is reviewed, and available strategies to access and characterize this portion of the gut microbiome are described. The relative merits of these methods and their present as well as prospective impact on our understanding of the human gut microbiota is discussed.

Association of antibiotic resistance in agricultural Escherichia coli isolates with attachment to quartz

Surface water can be contaminated by bacteria from various sources, including manure from agricultural facilities. Attachment of these bacteria to soil and organic particles contributes to their transport through the environment, though the mechanism of attachment is unknown. As bacterial attachment to human tissues is known to be correlated with antibiotic resistance, we have investigated here the relationship between bacterial attachment to environmental particles and antibiotic resistance in agricultural isolates. We evaluated 203 Escherichia coli isolates collected from swine facilities for attachment to quartz, resistance to 13 antibiotics, and the presence of genes encoding 13 attachment factors. The genes encoding type I, EcpA, P pili, and Ag43 were detected, though none was significantly related to attachment. Quartz attachment was positively and significantly (P < 0.0038) related to combined resistance to amoxicillin/streptomycin/tetracycline/sulfamethazine/tylosin/chlortetracycline and negatively and significantly (P < 0.0038) related to combined resistance to nalidixic acid/kanamycin/neomycin. These results provide clear evidence for a link between antibiotic resistance and attachment to quartz in agricultural isolates. We propose that this may be due to encoding by the responsible genes on a mobile genetic element. Further exploration of the relationship between antibiotic resistance and attachment to environmental particles will improve the understanding and modeling of environmental transport processes, with the goal of preventing human exposure to antibiotic-resistant or virulent microorganisms.

Characterization of the metabolically modified heavy metal-resistant Cupriavidus metallidurans strain MSR33 generated for mercury bioremediation

Background

Mercury-polluted environments are often contaminated with other heavy metals. Therefore, bacteria with resistance to several heavy metals may be useful for bioremediation. Cupriavidus metallidurans CH34 is a model heavy metal-resistant bacterium, but possesses a low resistance to mercury compounds.

Methodology/Principal Findings

To improve inorganic and organic mercury resistance of strain CH34, the IncP-1β plasmid pTP6 that provides novel merB, merG genes and additional other mer genes was introduced into the bacterium by biparental mating. The transconjugant Cupriavidus metallidurans strain MSR33 was genetically and biochemically characterized. Strain MSR33 maintained stably the plasmid pTP6 over 70 generations under non-selective conditions. The organomercurial lyase protein MerB and the mercuric reductase MerA of strain MSR33 were synthesized in presence of Hg²⁺. The minimum inhibitory concentrations (mM) for strain MSR33 were: Hg²⁺, 0.12 and CH₃Hg⁺, 0.08. The addition of Hg²⁺ (0.04 mM) at exponential phase had not an effect on the growth rate of strain MSR33. In contrast, after Hg²⁺ addition at exponential phase the parental strain CH34 showed an immediate cessation of cell growth. During exposure to Hg²⁺ no effects in the morphology of MSR33 cells were observed, whereas CH34 cells exposed to Hg²⁺ showed a fuzzy outer membrane. Bioremediation with strain MSR33 of two mercury-contaminated aqueous solutions was evaluated. Hg²⁺ (0.10 and 0.15 mM) was completely volatilized by strain MSR33 from the polluted waters in presence of thioglycolate (5 mM) after 2 h.

Conclusions/Significance

A broad-spectrum mercury-resistant strain MSR33 was generated by incorporation of plasmid pTP6 that was directly isolated from the environment into C. metallidurans CH34. Strain MSR33 is capable to remove mercury from polluted waters. This is the first study to use an IncP-1β plasmid directly isolated from the environment, to generate a novel and stable bacterial strain useful for mercury bioremediation.

Phylogenetic and functional diversity of alkane degrading bacteria associated with Italian ryegrass (Lolium multiflorum) and Birdsfoot trefoil (Lotus corniculatus) in a petroleum oil-contaminated environment

Twenty-six different plant species were analyzed regarding their performance in soil contaminated with petroleum oil. Two well-performing species, Italian ryegrass (Lolium multiflorum var. Taurus), Birdsfoot trefoil (Lotus corniculatus var. Leo) and the combination of these two plants were selected to study the ecology of plant-associated, culturable alkane-degrading bacteria. Hydrocarbon degrading bacteria were isolated from the rhizosphere, root interior and shoot interior and subjected to the analysis of 16S rRNA gene, the 16S and 23S rRNA intergenic spacer region and alkane hydroxylase genes. Furthermore, we investigated whether alkane hydroxylase genes are plasmid located. Higher numbers of culturable, alkane-degrading bacteria were associated with Italian ryegrass, which were also characterized by a higher diversity, particularly in the plant interior. Only half of the isolated bacteria hosted known alkane hydroxylase genes (alkB and cytochrome P153-like). Degradation genes were found both on plasmids as well as in the chromosome. In regard to application of plants for rhizodegradation, where support of numerous degrading bacteria is essential for efficient break-down of pollutants, Italian ryegrass seems to be more appropriate than Birdsfoot trefoil.

Broad-host-range plasmids in treated wastewater effluent and receiving streams

The occurrence of broad-host-range (BHR) plasmid amplicons belonging to incompatibility (Inc) groups IncA/C, IncN, IncP, and IncW in two wastewater treatment plant (WWTP) effluents and effluent-receiving streams in Northwest Arkansas, Mud Creek and Spring Creek, was determined. Community DNA captured on filter membranes and plasmid DNA extracted from antibiotic-resistant Escherichia coli isolated from Mud Creek was used for polymerase chain reaction at amplification of partial gene sequences specific to BHR plasmids. IncP plasmid amplicons were detected in effluent and downstream sites in both streams, while IncN and IncW plasmid amplicons were detected in Spring Creek in effluent and downstream but not upstream. IncA/C plasmid amplicons, in contrast, were detected at all sites, including upstream in most samples in Spring Creek and in one sample from Mud Creek. One IncP and two IncN were the only BHR plasmid amplicons found in 85 screened antibiotic-resistant E. coli isolates, and were detected only in isolates from effluent and downstream samples. Broad-host-range plasmids frequently carry antibiotic-resistance genes and can facilitate horizontal transfer of those genes. While BHR plasmids have been detected in WWTPs, WWTPs do not target these genetic elements for destruction. This study indicates that BHR plasmids are in WWTP effluent and are introducing BHR plasmids into streams. Additionally, species other than E. coli may be better targets as indicator bacteria for future studies of the impact of treated effluent on environmental dissemination of BHR plasmids.

Predicting plasmid promiscuity based on genomic signature

Despite the important contribution of self-transmissible plasmids to bacterial evolution, little is understood about the range of hosts in which these plasmids have evolved. Our goal was to infer this so-called evolutionary host range. The nucleotide composition, or genomic signature, of plasmids is often similar to that of the chromosome of their current host, suggesting that plasmids acquire their hosts' signature over time. Therefore, we examined whether the evolutionary host range of plasmids could be inferred by comparing their trinucleotide composition to that of all completely sequenced bacterial chromosomes. The diversity of candidate hosts was determined using taxonomic classification and genetic distance. The method was first tested using plasmids from six incompatibility (Inc) groups whose host ranges are generally thought to be narrow (IncF, IncH, and IncI) or broad (IncN, IncP, and IncW) and then applied to other plasmid groups. The evolutionary host range was found to be broad for IncP plasmids, narrow for IncF and IncI plasmids, and intermediate for IncH and IncN plasmids, which corresponds with their known host range. The IncW plasmids as well as several plasmids from the IncA/C, IncP, IncQ, IncU, and PromA groups have signatures that were not similar to any of the chromosomal signatures, raising the hypothesis that these plasmids have not been ameliorated in any host due to their promiscuous nature. The inferred evolutionary host range of IncA/C, IncP-9, and IncL/M plasmids requires further investigation. In this era of high-throughput sequencing, this genomic signature method is a useful tool for predicting the host range of novel mobile elements.

Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia

In this study, the combination of culture enrichments and molecular tools was used to identify bacterial guilds, plasmids and functional genes potentially important in the process of petroleum hydrocarbon (PH) decontamination in mangrove microniches (rhizospheres and bulk sediment). In addition, we aimed to recover PH-degrading consortia (PHDC) for future use in remediation strategies. The PHDC were enriched with petroleum from rhizosphere and bulk sediment samples taken from a mangrove chronically polluted with oil hydrocarbons. Southern blot hybridization (SBH) assays of PCR amplicons from environmental DNA before enrichments resulted in weak positive signals for the functional gene types targeted, suggesting that PH-degrading genotypes and plasmids were in low abundance in the rhizosphere and bulk sediments. However, after enrichment, these genes were detected and strong microniche-dependent differences in the abundance and composition of hydrocarbonoclastic bacterial populations, plasmids (IncP-1α, IncP-1β, IncP-7 and IncP-9) and functional genes (naphthalene, extradiol and intradiol dioxygenases) were revealed by in-depth molecular analyses [PCR-denaturing gradient gel electrophoresis and hybridization (SBH and microarray)]. Our results suggest that, despite the low abundance of PH-degrading genes and plasmids in the environmental samples, the original bacterial composition of the mangrove microniches determined the structural and functional diversity of the PHDC enriched.

Novel assay to assess permissiveness of a soil microbial community toward receipt of mobile genetic elements

There is a wealth of evidence indicating that mobile genetic elements can spread in natural microbial communities. However, little is known regarding the fraction of the community that actually engages in this behavior. Here we report on a new approach to quantify the fraction of a bacterial community that is able to receive and maintain an exogenous conjugal plasmid termed community permissiveness. Conjugal transfer of a broad-host-range plasmid labeled with a zygotically inducible green fluorescent protein (RP4::gfp) from a donor strain (Pseudomonas putida) to a soil bacterial suspension was examined. The mixture of cells was incubated on membrane filters supported by different solid media. Plasmid transfer was scored by in situ visualization of green fluorescent transconjugant microcolonies, and host range was determined by traditional plating or microcolony isolation by using a micromanipulator. Among the conditions tested, the highest plasmid transfer incidence (approximately 1 transfer per 10(4) soil bacteria) was measured after 48 h of incubation on either a 10% soil extract or a 10-fold diluted R2A medium. Stereomicroscopy combined with image analysis allowed easy examination and enumeration of green fluorescent microcolonies. In all experiments, however, stereomicroscopy consistently underestimated the number of conjugation events (approximately 10-fold) in comparison to confocal laser scanning microscopy. The plasmid host range was broad and included bacteria belonging to the Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria classes of proteobacteria. The isolation of transconjugant microcolonies by micromanipulation greatly extended the estimated plasmid host range among soil bacteria. The new approach can be applied to examine the permissiveness of various communities toward receipt of different mobile elements.

Short-term effects of amoxicillin on bacterial communities in manured soil

Antibiotic-resistant bacteria, nutrients and antibiotics that enter the soil by means of manure may enhance the proportion of bacteria displaying antibiotic resistance among soil bacteria and may affect bacterial community structure and function. To investigate the effect of manure and amoxicillin added to manure on soil bacterial communities, microcosm experiments were performed with two soil types and the following treatments: (1) nontreated, (2) manure-treated, (3) treated with manure supplemented with 10 mg amoxicillin kg(-1) soil and (4) treated with manure supplemented with 100 mg amoxicillin kg(-1) soil, with four replicates per treatment. Manure significantly increased the total CFU count and the amoxicillin-resistant CFU count of both soil types. However, only the soil with a history of manure treatment showed a significant increase in the relative number of amoxicillin-resistant bacteria as a result of amoxicillin amendment. The majority of plasmids exogenously isolated from soil originated from soil treated with amoxicillin-supplemented manure. All 16 characterized plasmids carried the bla-TEM gene, and 10 of them belonged to the IncN group. The bla-TEM gene was detected in DNA directly extracted from soil by dot-blot hybridization of PCR amplicons and showed an increased abundance in soil samples treated with manure. Molecular fingerprint analysis of 16S rRNA gene fragments amplified from soil DNA revealed significant effects of manure and amoxicillin on the bacterial community of both soils.

Long-term dynamics of catabolic plasmids introduced to a microbial community in a polluted environment: a mathematical model

The long-term dynamics of mobile plasmids in natural environments are unclear. This is the first study of the long-term dynamics of introduced plasmids with xenobiotic degradation abilities using a mathematical model that describes the horizontal gene transfer (HGT) of plasmids into indigenous bacteria via conjugation. We focussed on negative feedback between the spread of plasmids and their selective advantage, i.e. the severe competition between plasmid-bearing and plasmid-free bacteria resulting from a decrease in xenobiotic concentration caused by the gene expression of plasmids, favoring plasmid-free bacteria. Two types of HGT enhanced the persistence of plasmids and the degradation of the xenobiotic in different conditions: a relatively low rate of 'intergeneric HGT' from introduced to indigenous bacteria and a high rate of 'intraindigenous HGT' from indigenous to indigenous bacteria. In addition, when the indigenous resource supply rate was high and when the cost of bearing plasmids was low, both types of HGT made large contributions to xenobiotic degradation compared to the contribution of vertical transfer via plasmid replication within the introduced host population. Initial conditions were also important; a higher initial density of introduced plasmid-bearing bacteria led to a lower degradation rate over a long time scale.

Manure and sulfadiazine synergistically increased bacterial antibiotic resistance in soil over at least two months

Manuring of arable soils may stimulate the spread of resistance genes by introduction of resistant populations and antibiotics. We investigated effects of pig manure and sulfadiazine (SDZ) on bacterial communities in soil microcosms. A silt loam and a loamy sand were mixed with manure containing SDZ (10 or 100 mg per kilogram of soil), and compared with untreated soil and manured soil without SDZ over a 2-month period. In both soils, manure and SDZ positively affected the quotients of total and SDZ-resistant culturable bacteria [most probable number (MPN)], and transfer frequencies of plasmids conferring SDZ resistance in filter matings of soil bacteria and an Escherichia coli recipient. Detection of sulfonamide resistance genes sul1, sul2 and sul3 in community DNA by polymerase chain reaction (PCR) and hybridization revealed a high prevalence of sul1 in manure and manured soils, while sul2 was mainly found in the loamy sand treated with manure and high SDZ amounts, and sul3 was not detected. By PCR quantification of sul1 and bacterial rrn genes, a transient effect of manure alone and a long-term effect of SDZ plus manure on absolute and relative sul1 abundance in soil was shown. The dynamics in soil of class 1 integrons, which are typically associated with sul1, was analysed by amplification of the gene cassette region. Integrons introduced by manure established in both soils. Soil type and SDZ affected the composition of integrons. The synergistic effects of manure and SDZ were still detectable after 2 months. The results suggest that manure from treated pigs enhances spread of antibiotic resistances in soil bacterial communities.

Effects of stress and other environmental factors on horizontal plasmid transfer assessed by direct quantification of discrete transfer events

Selection pressure may affect the horizontal transfer of plasmids. The inability to distinguish between gene transfer and the growth of transconjugants complicates testing. We have developed a method that enables the quantification of discrete transfer events. It uses large numbers of replicate matings (192 or 384) in microtiter wells and the counting of transfer-positive and transfer-negative wells. We applied the method to study the transfer of the IncP1 plasmid pRO103 between Escherichia coli and Pseudomonas putida strains. pRO103 encodes resistance to mercury and tetracycline and partial degradation of 2,4-dichlorophenoxyacetic acid (2,4-D). The results showed positive correlation between transfer and donor metabolic activity, and an optimal temperature for transfer of 29 degrees C. On stimulation of donor activity, the optimal temperature was decreased to 24.5 degrees C. HgCl(2) above 1.0 microg L(-1) negatively affected transfer, whereas 2,4-D up to 0.3 mM had no effect. The negative effect of mercury was shown to be a result of stressing of the recipient. No effects of mercury on transfer could be detected by traditional filter mating. Thus, the method is superior to filter mating and, as the experimental design allows the manipulation of individual parameters, it is ideal for the assessment and comparison of effects of environmental factors on plasmid transfer.

Plasmids from freshwater environments capable of IncQ retrotransfer are diverse and include pQKH54, a new IncP-1 subgroup archetype

Nine mercury-resistance plasmids isolated from river epilithon were assessed for their ability to retrotransfer the non-conjugative IncQ plasmid, R300B, derivatives of which have commercial uses that may result in accidental or deliberate release into the environment. Retrotransfer frequencies ranging from 2.1 x 10(-4) to 1.75 x 10(-5) were obtained for five of the nine plasmids--the remaining plasmids showed low or undetectable retrotransfer ability. The majority of the retrotransfer-proficient plasmids could not be classified by the tests used. Classical incompatibility testing with RP4 identified pQKH6, pQKH54 and pQM719 as IncP-1. Hybridization to replicon probes confirmed this for pQKH6 and pQM719 and added pQKH33. PCR with primers designed to amplify trfA and korA regions of IncP-1 plasmids did not identify any other plasmids. Plasmids pQKH6 and pQM719 but not pQKH54 produced similar SphI restriction profiles to the IncP-1beta subgroup. The complete nucleotide sequence of pQKH54 was determined, revealing it to have a complete IncP-1 backbone but belonging to a new distinct subgroup which was designated IncP-1gamma. The results emphasize the ubiquity and diversity of IncP-1 plasmids in the environment but demonstrate that plasmids of as yet unknown groups are also able to retrotransfer IncQ plasmids efficiently.

Increased abundance of IncP-1beta plasmids and mercury resistance genes in mercury-polluted river sediments: first discovery of IncP-1beta plasmids with a complex mer transposon as the sole accessory element

Although it is generally assumed that mobile genetic elements facilitate the adaptation of microbial communities to environmental stresses, environmental data supporting this assumption are rare. In this study, river sediment samples taken from two mercury-polluted (A and B) and two nonpolluted or less-polluted (C and D) areas of the river Nura (Kazakhstan) were analyzed by PCR for the presence and abundance of mercury resistance genes and of broad-host-range plasmids. PCR-based detection revealed that mercury pollution corresponded to an increased abundance of mercury resistance genes and of IncP-1beta replicon-specific sequences detected in total community DNA. The isolation of IncP-1beta plasmids from contaminated sediments was attempted in order to determine whether they carry mercury resistance genes and thus contribute to an adaptation of bacterial populations to Hg pollution. We failed to detect IncP-1beta plasmids in the genomic DNA of the cultured Hg-resistant bacterial isolates. However, without selection for mercury resistance, three different IncP-1beta plasmids (pTP6, pTP7, and pTP8) were captured directly from contaminated sediment slurry in Cupriavidus necator JMP228 based on their ability to mobilize the IncQ plasmid pIE723. These plasmids hybridized with the merRTDeltaP probe and conferred Hg resistance to their host. A broad host range and high stability under conditions of nonselective growth were observed for pTP6 and pTP7. The full sequence of plasmid pTP6 was determined and revealed a backbone almost identical to that of the IncP-1beta plasmids R751 and pB8. However, this is the first example of an IncP-1beta plasmid which had acquired only a mercury resistance transposon but no antibiotic resistance or biodegradation genes. This transposon carries a rather complex set of mer genes and is inserted between Tra1 and Tra2.

Evolutionary algorithms and flow cytometry to examine the parameters influencing transconjugant formation

An evolutionary algorithm was used to determine the optimal combination of parameters for transconjugant formation. As a model system, a gfp tagged TOL plasmid pWW0 was chosen to examine transfer from Pseudomonas putida to Escherichia coli. A comparison of flow cytometry results with plating and microscopy showed that the majority of transconjugants were not culturable. The transconjugant ratio therefore was determined by flow cytometry. The evolutionary algorithm showed that the optimal conditions were obtained at 28 degrees C and at the highest nutrient concentrations. This work demonstrates that evolutionary algorithms can be used to find optimal parameter interactions in environmental microbiology.

Plasmid donor affects host range of promiscuous IncP-1beta plasmid pB10 in an activated-sludge microbial community

Horizontal transfer of multiresistance plasmids in the environment contributes to the growing problem of drug-resistant pathogens. Even though the plasmid host cell is the primary environment in which the plasmid functions, possible effects of the plasmid donor on the range of bacteria to which plasmids spread in microbial communities have not been investigated. In this study we show that the host range of a broad-host-range plasmid within an activated-sludge microbial community was influenced by the donor strain and that various mating conditions and isolation strategies increased the diversity of transconjugants detected. To detect transconjugants, the plasmid pB10 was marked with lacp-rfp, while rfp expression was repressed in the donors by chromosomal lacI(q). The phylogeny of 306 transconjugants obtained was determined by analysis of partial 16S rRNA gene sequences. The transconjugants belonged to 15 genera of the alpha- and gamma-Proteobacteria. The phylogenetic diversity of transconjugants obtained in separate matings with donors Pseudomonas putida SM1443, Ralstonia eutropha JMP228, and Sinorhizobium meliloti RM1021 was significantly different. For example, the transconjugants obtained after matings in sludge with S. meliloti RM1021 included eight genera that were not represented among the transconjugants obtained with the other two donors. Our results indicate that the spectrum of hosts to which a promiscuous plasmid transfers in a microbial community can be strongly influenced by the donor from which it transfers.

Horizontal gene transfer in the phytosphere

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.

Functional and mutational analysis of conjugative transfer region 2 (Tra2) from the IncHI1 plasmid R27

The transfer 2 region (Tra2) of the conjugative plasmid drR27 (derepressed R27) was analyzed by PSI-BLAST, insertional mutagenesis, genetic complementation, and an H-pilus assay. Tra2 contains 11 mating-pair formation (Mpf) genes that are essential for conjugative transfer, 9 of which are essential for H-pilus production (trhA, -L, -E, -K, -B, -V, -C, -P, and -W). TrhK has similarity to secretin proteins, suggesting a mechanism by which DNA could traverse the outer membrane of donors. The remaining two Mpf genes, trhU and trhN, play an auxiliary role in H-pilus synthesis and are proposed to be involved in DNA transfer and mating-pair stabilization, respectively. Conjugative transfer abilities were restored for each mutant when complemented with the corresponding transfer gene. In addition to the essential Mpf genes, three genes, trhO, trhZ, and htdA, modulate R27 transfer frequency. Disruption of trhO and trhZ severely reduced the transfer frequencies of drR27, whereas disruption of htdA greatly increased the transfer frequency of wild-type R27 to drR27 levels. A comparison of the essential transfer genes encoded by the Tra2 and Tra1 (T. D. Lawley, M. W. Gilmour, J. E. Gunton, L. J. Standeven, and D. E. Taylor, J. Bacteriol. 184:2173-2183, 2002) of R27 to other transfer systems illustrates that the R27 conjugative transfer system is a chimera composed of IncF-like and IncP-like transfer systems. Furthermore, the Mpf/type IV secretion systems encoded by IncH and IncF transfer systems are distinct from that of the IncP transfer system. The phenotypic and ecological significance of these observations is discussed.

The complete nucleotide sequence and environmental distribution of the cryptic, conjugative, broad-host-range plasmid pIPO2 isolated from bacteria of the wheat rhizosphere

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.

Map of the IncP1beta plasmid pTSA encoding the widespread genes (tsa) for p-toluenesulfonate degradation in Comamonas testosteroni T-2

The catabolic IncP1beta plasmid pTSA from Comamonas testosteroni T-2 was mapped by subtractive analysis of restriction digests, by sequencing outwards from the tsa operon (toluenesulfonate degradation), and by generating overlapping, long-distance-PCR amplification products. The plasmid was estimated to comprise 72 +/- 4 kb. The tsa region was found to be a composite transposon flanked by two IS1071 elements. A cryptic tsa operon was also present in the tsa transposon. Those backbone genes and regions which we sequenced were in the same order as the corresponding genes in resistance plasmid R751, and identities of about 99% were observed. Enrichment cultures with samples from four continents were done to obtain organisms able to utilize p-toluenesulfonate as the sole source of carbon and energy for aerobic growth. Most (15) of the 16 cultures (13 of them isolates) were obtained from contaminated sites and were attributed to three metabolic groups, depending on their metabolism of p-toluenesulfonate. The largest group contained the tsa transposon, usually (six of seven isolates) with negligible differences in sequence from strain T-2.

Naphthalene and donor cell density influence field conjugation of naphthalene catabolism plasmids

We examined transfer of naphthalene-catabolic genes from donor microorganisms native to a contaminated site to site-derived, rifampin-resistant recipient bacteria unable to grow on naphthalene. Horizontal gene transfer (HGT) was demonstrated in filter matings using groundwater microorganisms as donors. Two distinct but similar plasmid types, closely related to pDTG1, were retrieved. In laboratory-incubated sediment matings, the addition of naphthalene stimulated HGT. However, recipient bacteria deployed in recoverable vessels in the field site (in situ) did not retrieve plasmids from native donors. Only when plasmid-containing donor cells and naphthalene were added to the in situ mating experiments did HGT occur.