High phylogenetic diversity of transconjugants carrying plasmid pJP4 in an activated sludge-derived microbial community

Arachis hypogaea PGPR isolated from Argentine soil modifies its lipids components in response to temperature and salinity

The aim of this work was to clarify the mechanism related to plant growth promoting of a bacterial strain (L115) isolated from Arachis hypogaea rhizospheres and the effects of high growth temperature and salinity on phospholipids and fatty acids composition. L115 was isolated from peanut rhizospheres and identified according to the sequence analysis of the 16S rRNA gene. Phenotypic, metabolic and plant growth promoting rhizobacteria (PGPR) characteristics of L115 were tested. Inoculation test in plant growth chamber was performed. In addition, L115 was exposed to a 37 °C and 300 mM NaCl and phospholipids and fatty acid composition were evaluated. L115 strain was identified as Ochrobactrum intermedium and was able to increase the peanut shoot and root length as well as dry weight, indicating a PGPR role by being able to produce indole acetic acid and siderophores and present ACC deaminase activity. In addition, L115 showed tolerance to both high growth temperature and 300 mM NaCl. The most striking change was a decreased percentage of 18:1 fatty acid and an increase in 16:0 and 18:0 fatty acids, under high growth temperature or a combination of increased temperature and salinity. The most important change in phospholipid levels was an increase in phosphatidylcholine biosynthesis in all growth conditions. L115 can promote the growth of peanut and can tolerate high growth temperature and salinity modifying the fatty acid unsaturation degree and increasing phosphatidylcholine levels. This work is the first to report the importance of the genus Ochrobactrum as PGPR on peanut growth as well as on the metabolic behaviour against abiotic stresses that occur in soil. This knowledge will be useful for developing strategies to improve the growth of this bacterium under stress and to enhance its bioprocess for the production of inoculants.

Horizontal transfer of PAH catabolism genes in Mycobacterium: evidence from comparative genomics and isolated pyrene-degrading bacteria

Biodegradation of high molecular weight polycyclic aromatic hydrocarbons (PAHs), such as pyrene and benzo[a]pyrene, has only been observed in a few genera, namely fast-growing Mycobacterium and Rhodococcus. In M. vanbaalenii PYR-1, multiple aromatic ring hydroxylating dioxygenase (ARHDOs) genes including pyrene dioxygenases nidAB and nidA3B3 are localized in one genomic region. Here we examine the homologous genomic regions in four other PAH-degrading Mycobacterium (strains JLS, KMS, and MCS, and M. gilvum PYR-GCK), presenting evidence for past horizontal gene transfer events. Seven distinct types of ARHDO genes are present in all five genomes, and display conserved syntenic architecture with respect to gene order, orientation, and association with other genes. Duplications and putative integrase and transposase genes suggest past gene shuffling. To corroborate these observations, pyrene-degrading strains were isolated from two PAH-contaminated sediments: Chattanooga Creek (Tennessee) and Lake Erie (western basin). Some were related to fast-growing Mycobacterium spp. and carried both nidA and nidA3 genes. Other isolates belonged to Microbacteriaceae and Intrasporangiaceae presenting the first evidence of pyrene degradation in these families. These isolates had nidA (and some, nidA3) genes that were homologous to Mycobacterial ARHDO genes, suggesting that horizontal gene transfer events have occurred.

Stenotrophomonas maltophilia: an emerging global opportunistic pathogen

Stenotrophomonas maltophilia is an emerging multidrug-resistant global opportunistic pathogen. The increasing incidence of nosocomial and community-acquired S. maltophilia infections is of particular concern for immunocompromised individuals, as this bacterial pathogen is associated with a significant fatality/case ratio. S. maltophilia is an environmental bacterium found in aqueous habitats, including plant rhizospheres, animals, foods, and water sources. Infections of S. maltophilia can occur in a range of organs and tissues; the organism is commonly found in respiratory tract infections. This review summarizes the current literature and presents S. maltophilia as an organism with various molecular mechanisms used for colonization and infection. S. maltophilia can be recovered from polymicrobial infections, most notably from the respiratory tract of cystic fibrosis patients, as a cocolonizer with Pseudomonas aeruginosa. Recent evidence of cell-cell communication between these pathogens has implications for the development of novel pharmacological therapies. Animal models of S. maltophilia infection have provided useful information about the type of host immune response induced by this opportunistic pathogen. Current and emerging treatments for patients infected with S. maltophilia are discussed.

The behavior and significance of degradative plasmids belonging to Inc groups in Pseudomonas within natural environments and microcosms

Over the past few decades, degradative plasmids have been isolated from bacteria capable of degrading a variety of both natural and man-made compounds. Degradative plasmids belonging to three incompatibility (Inc) groups in Pseudomonas (IncP-1, P-7, and P-9) have been well studied in terms of their replication, maintenance, and capacity for conjugative transfer. The host ranges of these plasmids are determined by replication or conjugative transfer systems. The host range of IncP-1 is broad, that of IncP-9 is intermediate, and that of IncP-7 is narrow. To understand the behavior of these plasmids and their hosts in various environments, the survivability of inocula, stability or transferability, and efficiency of biodegradation in environments and microcosms have been monitored. The biodegradation and plasmid transfer in various environments have been observed for all three groups, although the kinds of transconjugants differed with the Inc groups. In some cases, the deletion and amplification of catabolic genes acted to reduce the production of toxic catabolic intermediates, or to increase the activity on a particular catabolic pathway. The combination of degradative genes, the plasmid backbone of each Inc group, and the host of the plasmids is key to the degraders adapting to various hosts or to heterogeneous environments.

Differences in lateral gene transfer in hypersaline versus thermal environments

BACKGROUND

The role of lateral gene transfer (LGT) in the evolution of microorganisms is only beginning to be understood. While most LGT events occur between closely related individuals, inter-phylum and inter-domain LGT events are not uncommon. These distant transfer events offer potentially greater fitness advantages and it is for this reason that these "long distance" LGT events may have significantly impacted the evolution of microbes. One mechanism driving distant LGT events is microbial transformation. Theoretically, transformative events can occur between any two species provided that the DNA of one enters the habitat of the other. Two categories of microorganisms that are well-known for LGT are the thermophiles and halophiles.

RESULTS

We identified potential inter-class LGT events into both a thermophilic class of Archaea (Thermoprotei) and a halophilic class of Archaea (Halobacteria). We then categorized these LGT genes as originating in thermophiles and halophiles respectively. While more than 68% of transfer events into Thermoprotei taxa originated in other thermophiles, less than 11% of transfer events into Halobacteria taxa originated in other halophiles.

CONCLUSIONS

Our results suggest that there is a fundamental difference between LGT in thermophiles and halophiles. We theorize that the difference lies in the different natures of the environments. While DNA degrades rapidly in thermal environments due to temperature-driven denaturization, hypersaline environments are adept at preserving DNA. Furthermore, most hypersaline environments, as topographical minima, are natural collectors of cellular debris. Thus halophiles would in theory be exposed to a greater diversity and quantity of extracellular DNA than thermophiles.

Effects of gene augmentation on the removal of 2,4-dichlorophenoxyacetic acid in a biofilm reactor under different scales and substrate conditions

With a conjugative plasmid pJP4 carrying strain as the donor, two bioaugmentation experiments were conducted in a microcosm biofilm reactor with 2,4-D as the sole carbon source operated in fed-batch mode, and an enlarged lab-scale sequence batch biofilm reactor with mixed carbon sources of 2,4-D and other easily biodegradable compounds, respectively. In the microcosm study under sole carbon source condition, bioaugmentation led to a persistently increased 2,4-D degradation rate in the five operation cycles with enhancement of 13-64%. For the enlarged lab-scale bioaugmentation experiment under mixed carbon source conditions, no enhancement in 2,4-D removal could be observed during start-up period. After a period of operation, biofilm samples from the bioaugmented reactor demonstrated a stronger degradation capacity than the control and showed the presence of a large number of transconjugants. This study indicates that bioaugmentation based on plasmid horizontal transfer is a feasible strategy to establish functional microbial community in a biofilm reactor, and the strong selective pressure of 2,4-D existing alone and persistently was more favorable for the success of gene augmentation.

Role of a serine-type D-alanyl-D-alanine carboxypeptidase on the survival of Ochrobactrum sp. 11a under ionic and hyperosmotic stress

The plant growth-promoting rhizobacterium, Ochrobactrum sp. 11a displays a high intrinsic salinity tolerance and has been used in this work to study the molecular basis of bacterial responses to high concentrations of NaCl. A collection of Ochrobactrum sp. 11a mutants was generated by Tn5-B21 mutagenesis and screened for sensitivity to salinity. One clone, designated PBP and unable to grow on glutamate mannitol salt agar medium supplemented with 300 mM NaCl was selected and further characterized. The PBP mutant carries a single transposon insertion in a gene showing a high degree of identity to the serine-type d-alanyl-d-alanine carboxypeptidase gene of Ochrobactrum anthropi. Interestingly, the expression of this gene was shown to be upregulated by salt in the PBP mutant. Moreover, evidence is presented for the requirement of the gene product for adaptation to high-salt conditions as well as to overcome the toxicity of LiCl, KCl, sucrose, polyethylene glycol (PEG), AlCl(3), CuSO(4), and ZnSO(4). In addition to the altered tolerance to both ionic and osmotic stresses, the PBP mutant exhibited changes in colony and cell morphology, exopolysaccharide production, and an increased sensitivity to detergents.

A novel nicotine catabolic plasmid pMH1 in Pseudomonas sp. strain HF-1

Attempts were made to acquire a plasmid-loss mutant via various methods (spontaneous mutation, SDS, and mitomycin C), among which the method involving mitomycin C (10 µg/mL) has been proven successful. Concomitant with the loss of the plasmid in Pseudomonas sp. strain HF-1, the cured derivative was identified as having a nicotine-negative (Nic–) phenotype, named mutant strain 6-13 (Nic–). After plasmids were transferred from strain HF-1 (named plasmid pMH1) to the mutant strain 6-13, the mutant strain acquired nicotine-degrading ability, called 6-13 transformant (Nic+). There were no differences in growth or nicotine-degrading efficiency between strain HF-1 (wild-type strain) and strain 6-13 transformant. After pMH1 was transferred to Escherichia coli strain Top10 (Nic–), a distant relative of Pseudomonas, it also gained nicotine-degrading ability, showing the highest nicotine degradation efficiency at pH 7.0, the optimal pH for growth of E. coli. The hsp gene, which encodes 6-hydroxy-3-succinoylpyridine hydroxylase, is involved in nicotine degradation in Pseudomonas putida strain S16 and was present in pMH1 but not in pAO1, the well-known nicotine degradation plasmid in Arthrobacter nicotinovorans . It was demonstrated that plasmid pMH1 is a novel nicotine-degrading plasmid.

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.

TOL plasmid transfer during bacterial conjugation in vitro and rhizoremediation of oil compounds in vivo

Molecular profiling methods for horizontal transfer of aromatics-degrading plasmids were developed and applied during rhizoremediation in vivo and conjugations in vitro. pWW0 was conjugated from Pseudomonas to Rhizobium. The xylE gene was detected both in Rhizobium galegae bv. officinalis and bv. orientalis, but it was neither stably maintained in orientalis nor functional in officinalis. TOL plasmids were a major group of catabolic plasmids among the bacterial strains isolated from the oil-contaminated rhizosphere of Galega orientalis. A new finding was that some Pseudomonas migulae and Pseudomonas oryzihabitans strains harbored a TOL plasmid with both pWW0- and pDK1-type xylE gene. P. oryzihabitans 29 had received the archetypal TOL plasmid pWW0 from Pseudomonas putida PaW85. As an application for environmental biotechnology, the biodegradation potential of oil-polluted soil and the success of bioremediation could be estimated by monitoring changes not only in the type and amount but also in transfer of degradation plasmids.

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.

Comparative sequence analysis of the internal transcribed spacer 1 of Ochrobactrum species

The internal 16S/23S rDNA (rrs/rrl) internal spacer region 1 (ITS1) of 54 Ochrobactrum strains and close relatives was analysed. Separation of ITS1 containing PCR products by gel-electrophoresis, DGGE, cloning and sequencing revealed ITS1 length and sequence heterogeneity. We found up to 5 different allelic ITS1 stretches within a single strain (Ochrobactrum intermedium LMG 3301T), and 2-3 different ITS1 alleles in O. tritici. Within ITS1, ITS1c, being part of the conserved double-stranded rrn processing stem dsPS1, produced the most reliable segment tree. The overall ITS1, ITS1c and rrs phylogenetic tree topologies were generally consistent, but there was evidence for horizontal rrn (segment) transfer in O. tritici LMG 2134 (formerly O. anthropi). Good correlations were found between ITS1, ITS1c and rrs sequence similarity and DNA-DNA hybridization values indicating that phylogenetic analysis of ITS1 and ITS1c both can be used to preliminarily deduce the phylogenetic affiliation if HGT was excluded. Strains sharing > 96.19% ITS1c (> 95.11% ITS1) similarity fell within a species, and < or = 68.42% ITS1c (< or = 70.33% ITS1) similarity outside a genus. Both ITS1 and ITS1c analysis resolved microdiversity more profoundly than rrs analysis and revealed clades (genomovars) within O. anthropi that were also produced in rep cluster analysis. There was no evidence for habitat-specific ITS1 genomovars within Ochrobactrum species. Diversity of Ochrobactrum was higher in soil than at the rhizoplane below and at the species level. Isolates from soil contained only 1 rrn type whereas isolates from human clinical, animal and rhizoplane specimens could contain more.

Potential of predominant activated sludge bacteria as recipients in conjugative plasmid transfer

We investigated the possibility of conjugative plasmid transfer to the predominant bacteria in activated sludge and the factors influencing the transfer frequency in the activated sludge process. We performed conjugative transfers of a self-transmissible, broad-host-range plasmid RP4 from Escherichia coli C600 to activated sludge bacteria by broth mating. Most of the activated sludge bacteria tested could acquire plasmid RP4, although the transfer frequencies varied from 8.8 x 10(-7) to 1.3 x 10(-2) transconjugants per recipient. The transfer frequencies in several strains were similar to, or higher than, that in intraspecific transfer to E. coli HB101. Matings under various environmental conditions showed that factors relevant to physiological activity, such as temperature and nutrient conditions, seemed to affect the transfer frequency. In addition, conjugative transfer was detected even in filtered raw and treated wastewaters. Thus, the predominant activated sludge bacteria seem to have sufficient potential as recipients in conjugative plasmid transfer under the conditions likely to occur in the activated sludge process. Transfer frequency was reduced by agitation in the presence of suspended solid. This may suggest that conjugative plasmid transfer is physically inhibited in aeration tanks.

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.

A soil-based microbial biofilm exposed to 2,4-D: bacterial community development and establishment of conjugative plasmid pJP4

A soil suspension was used as a source to initiate the development of microbial communities in flow cells irrigated with 2,4-dichlorophenoxyacetic acid (2,4-D) (25 microg ml(-1)). Culturable bacterial members of the community were identified by 16S rRNA gene sequencing and found to be members of the genera Pseudomonas, Burkholderia, Collimonas and Rhodococcus. A 2,4-D degrading donor strain, Pseudomonas putida SM1443 (pJP4::gfp), was inoculated into flow cell chambers containing 2-day old biofilm communities. Transfer of pJP4::gfp from the donor to the bacterial community was detectable as GFP fluorescing cells and images were captured using confocal scanning laser microscopy (GFP fluorescence was repressed in the donor due to the presence of a chromosomally located lacI(q) repressor gene). Approximately 5-10 transconjugant microcolonies, 20-40 microm in diameter, could be seen to develop in each chamber. A 2,4-D degrading transconjugant strain was isolated from the flow cell system belonging to the genus Burkholderia.

Microbial population dynamics at effluent treatment plants

The requirements for treated wastewater are becoming increasingly more stringent, and therefore the improved efficiency of biological treatment processes is indispensable at industrial effluent treatment plants (ETPs). Microorganisms such as bacteria play an important role in the natural cycling of materials and particularly in the decomposition of organic wastes. The knowledge of the interactions among these microbial populations needs to be harnessed for optimum evaluation and functioning of effluent treatment plants. Modern molecular techniques have revolutionized the methods of assessing these microbial populations. The combination of the results of these microbial assessments along with the on-site parameters at ETPs would favor an efficient treatment. In this review, the various approaches and importance of correlating the microbial population dynamics and treatment of wastewater at industrial ETPs has been elaborated.