Biodiversity and horizontal gene transfer in culturable bacteria isolated from activated sludge enriched in nonylphenol ethoxylates

Novel nonylphenol-degrading bacterial strains isolated from sewage sludge: Application in bioremediation of sludge

Nonylphenol (NP) is an anthropogenic pollutant frequently found in sewage sludge due to the insufficient degrading effectiveness of conventional WWTPs and has attracted attention as an endocrine disruptor. The aim of this study was to isolate specific NP-degrading bacteria from sewage sludge to be used in the degradation of this contaminant through bioaugmentation processes in aqueous solution and sewage sludge. Up to eight different bacterial strains were isolated, six of them not previously described as NP degraders. Bacillus safensis CN12 presented the best NP degradation in solution, and glucose used as an external carbon source increased its effect, reaching DT₅₀ degradation values (time to decline to half the initial concentration of the pollutant) of only 0.9 days and a complete degradation in <7 days. Four NP metabolites were identified throughout the biodegradation process, showing higher toxicity than the parent contaminant. In sewage sludge suspensions, the endogenous microbiota was capable of partially degrading NP, but a part remained adsorbed as bound residue. Bioaugmentation was used for the first time to remove NP from sewage sludge to obtain more environmentally friendly biosolids. However, B. safensis CN12 was not able to degrade NP due to its high adsorption on sludge, but the use of a cyclodextrin (HPBCD) as availability enhancer allowed us to extract NP and degrade it in solution. The addition of glucose as an external carbon source gave the best results since the metabolism of the sludge microbiota was activated, and HPBCD was able to remove NP from sewage sludge to the solution to be degraded by B. safensis CN12. These results indicate that B. safensis CN12 can be used to degrade NP in water and sewage sludge, but the method must be improved using consortia of B. safensis CN12 with other bacterial strains able to degrade the toxic metabolites produced.

Current Methods, Common Practices, and Perspectives in Tracking and Monitoring Bioinoculants in Soil

Microorganisms promised to lead the bio-based revolution for a more sustainable agriculture. Beneficial microorganisms could be a valid alternative to the use of chemical fertilizers or pesticides. However, the increasing use of microbial inoculants is also raising several questions about their efficacy and their effects on the autochthonous soil microorganisms. There are two major issues on the application of bioinoculants to soil: (i) their detection in soil, and the analysis of their persistence and fate; (ii) the monitoring of the impact of the introduced bioinoculant on native soil microbial communities. This review explores the strategies and methods that can be applied to the detection of microbial inoculants and to soil monitoring. The discussion includes a comprehensive critical assessment of the available tools, based on morpho-phenological, molecular, and microscopic analyses. The prospects for future development of protocols for regulatory or commercial purposes are also discussed, underlining the need for a multi-method (polyphasic) approach to ensure the necessary level of discrimination required to track and monitor bioinoculants in soil.

Mixed sulfur-iron particles packed reactor for simultaneous advanced removal of nitrogen and phosphorus from secondary effluent

A mixed sulfur-iron particles packed reactor (SFe reactor) was developed to simultaneously remove total nitrogen (TN) and total phosphorus (TP) of the secondary effluent from municipal wastewater treatment plants. Low effluent TN (<1.5 mg/L) and TP (<0.3 mg/L) concentrations were simultaneously obtained, and high TN removal rate [1.03 g N/(L·d)] and TP removal rate [0.29 g P/(L·d)] were achieved at the hydraulic retention time (HRT) of 0.13 h. Kinetic models describing denitrification were experimentally obtained, which predicted a higher denitrification rate [1.98 g N/(L·d)] of SFe reactor than that [1.58 g N/(L·d)] of sulfur alone packed reactor due to the mutual enhancement between sulfur-based autotrophic denitrification and iron-based chemical denitrification. A high TP removal obtained in SFe reactor was attributed to chemical precipitation of iron particles. Microbial community analysis based on 16S rRNA revealed that autotrophic denitrifying bacteria Thiobacillus and Sulfuricella were the dominant genus, indicating that autotrophic denitrification played important role in nitrate removal. These results indicate that sulfur and iron particles can be packed together in a single reactor to effectively remove nitrate and phosphorus.

Risk management tools and the case study Brassica napus: evaluating possible effects of genetically modified plants on soil microbial diversity

The cultivation of GMPs in Europe raises many questions about the environmental risks, in particular about their ecological impact on non-target organisms and on soil properties. The aim of a multidisciplinary group engaged in a LIFE+project (MAN-GMP-ITA) was to validate and improve an existing environmental risk assessment (ERA) methodology on GMPs within the European legislative framework on GMOs. Given the impossibility of evaluating GMO impact directly, as GMPs are banned in Italy, GMPs have not been used at any stage of the project. The project thus specifically focused on the conditions for the implementation of ERA in different areas of Italy, with an emphasis on some sensitive and protected areas located in the North, Centre, and South of the country, in order to lay the necessary baseline for evaluating the possible effects of a GMP on soil communities. Our sub-group carried out soil analyses in order to obtain soil health and fertility indicators to be used as baselines in the ERA model. Using various methods of chemical, biochemical, functional and genetic analysis, our study assessed the changes in diversity and functionality of bacterial populations, and arbuscular mycorrhizal fungi. The results show that plant identity and growth, soil characteristics, and field site climatic parameters are key factors in contributing to variation in microbial community structure and diversity, thus validating our methodological approach. Our project has come to the conclusion that the uneven composition and biological-agronomical quality of soils need to be taken into consideration in a risk analysis within the framework of ERA for the release of genetically modified plants.

Long-term effect of set potential on biocathodes in microbial fuel cells: electrochemical and phylogenetic characterization

The long-term effect of set potential on oxygen reducing biocathodes was investigated in terms of electrochemical and biological characteristics. Three biocathodes were poised at 200, 60 and -100 mV vs. saturated calomel electrode (SCE) for 110 days, including the first 17 days for startup. Electrochemical analyses showed that 60 mV was the optimum potential during long-term operation. The performance of all the biocathodes kept increasing after startup, suggesting a period longer than startup time needed to make potential regulation more effective. The inherent characteristics without oxygen transfer limitation were studied. Different from short-term regulation, the amounts of biomass were similar while the specific electrochemical activity was significantly influenced by potential. Moreover, potential showed a strong selection for cathode bacteria. Clones 98% similar with an uncultured Bacteroidetes bacterium clone CG84 accounted for 75% to 80% of the sequences on the biocathodes that showed higher electrochemical activity (60 and -100 mV).

Microbial community analysis in biocathode microbial fuel cells packed with different materials

Biocathode MFCs using microorganisms as catalysts have important advantages in lowering cost and improving sustainability. Electrode materials and microbial synergy determines biocathode MFCs performance. In this study, four materials, granular activated carbon (GAC), granular semicoke (GS), granular graphite (GG) and carbon felt cube (CFC) were used as packed cathodic materials. The microbial composition on each material and its correlation with the electricity generation performance of MFCs were investigated. Results showed that different biocathode materials had an important effect on the type of microbial species in biocathode MFCs. The microbes belonging to Bacteroidetes and Proteobacteria were the dominant phyla in the four materials packed biocathode MFCs. Comamonas of Betaproteobacteria might play significant roles in electron transfer process of GAC, GS and CFC packed biocathode MFCs, while in GG packed MFC Acidovorax may be correlated with power generation. The biocathode materials also had influence on the microbial diversity and evenness, but the differences in them were not positively related to the power production.

Electricity generation and microbial community changes in microbial fuel cells packed with different anodic materials

Four materials, carbon felt cube (CFC), granular graphite (GG), granular activated carbon (GAC) and granular semicoke (GS) were tested as packed anodic materials to seek a potentially practical material for microbial fuel cells (MFCs). The microbial community and its correlation with the electricity generation performance of MFCs were explored. The maximum power density was found in GAC, followed by CFC, GG and GS. In GAC and CFC packed MFCs, Geobacter was the dominating genus, while Azospira was the most populous group in GG. Results further indicated that GAC was the most favorable for Geobacter adherence and growth, and the maximum power densities had positive correlation with the total biomass and the relative abundance of Geobacter, but without apparent correlation with the microbial diversity. Due to the low content of Geobacter in GS, power generated in this system may be attributed to other microorganisms such as Synergistes, Bacteroidetes and Castellaniella.

Isolation from Tannery Wastewater and Characterization of Bacterial Strain Involved in Nonionic Surfactant Degradation

A bacterial strain OPQa3 capable of utilizing nonylphenol polyoxyethylene (NPnEO) as sole carbon source was isolated from water samples collected from tannery waste treatment plant suffered long-time application of NPnEO by enrichment method. It was preliminarily identified as Brevundimonas sp. (most similar to Brevundimonas diminuta (EU434566.1)), according to the observation of morphological characteristics, physiological-biochemical tests and the similarity analysis of its 16S rDNA gene sequence. Inoculated 2% of OPQa3 suspension, to give a final OD600of approximately 0.70, to inorganic salt medium in which the initial concentration of NPnEO was 746 mg•L-1, degradation test showed that, the degradation rate of strain OPQa3 was 84.5% within 120 hours, the optimum temperature was 30°C while the optimum pH value was about 7, and the growth period was of 24 hours.

Isolation of phylogenetically diverse nonylphenol ethoxylate-degrading bacteria and characterization of their corresponding biotransformation pathways

Most nonylphenol ethoxylate (NPEO)-degrading isolates have been assigned to gamma-Proteobacteria, which is different from the results acquired by using molecular ecological techniques. To better understand the environmental fate of NPEOs, bacterial isolation strategy characterized by the use of gellan gum as a gelling reagent and a low concentration of target carbon source were used to isolate phylogenetically diverse NPEO-degrading bacteria from activated sludge, and the biotransformation pathways of the isolates were investigated. Eight NPEO-degrading isolates with high diversity were acquired, which were distributed among seven different genera: Pseudomonas, Sphingomonas, Sphingobium, Cupriavidus, Ralstonia, Achromobacter and Staphylococcus. The latter five genera have never been reported to be able to degrade NPEOs. Three biotransformation pathways of NPEOs were observed in the eight stains. Six strains belonging to alpha, beta and gamma classes of Proteobacteria and Firmicutes phylum degraded NPEOs by initially shortening the EO chain and then oxidizing the terminal alcohol of the shortened NPEOs to the corresponding nonylphenoxy carboxylates (NPECs), which could explain most of the reported observations for the degradation of NPEOs in environment. An isolate (NP42a) belonging to the genus Sphingomonas degraded NPEOs through a non-oxidative pathway, with nonylphenol monoethoxylate (NP(1)EO) as the dominant product. Another isolate (NP47a) belonging to the genus Ralstonia degraded NPEOs by oxidizing the EO chain directly without the formation of short chain products.

Biodegradation of pharmaceutical and personal care products

Medical treatments and personal hygiene lead to the steady release of pharmaceutical and personal care products (PPCPs) into the environment. Some of these PPCPs have been shown to have detrimental environmental effects and could potentially impact human health. Understanding the biological transformation of PPCPs is essential for accurately determining their ultimate environmental fate, conducting accurate risk assessments, and improving PPCP removal. We summarize the current literature concerning the biological transformation of PPCPs in wastewater treatment plants, the environment, and by pure cultures of bacterial isolates. Although some PPCPs, such as ibuprofen, are readily degraded under most studied conditions, others, such as carbamazepine, tend to be recalcitrant. This variation in the biodegradability of PPCPs can be attributed to structural differences, because PPCPs are classified by application, not chemical structure. The degradation pathways of octylphenol by Sphingomonas sp. strain PWE1, ibuprofen by Sphingomonas sp. strain Ibu-2, and DEET by Pseudomonas putida DTB are discussed in more detail.

Biotransformation of nonylphenol ethoxylates during sewage treatment under anaerobic and aerobic conditions

Biotransformation of nonylphenol ethoxylates (NPEOs) during continuous anaerobic sewage treatment was compared with the aerobic treatment of sewage spiked with 23 micromol/L technical NPEOs over a period of 90 d. Immediate degradation of NPEOs was observed under both anaerobic and aerobic conditions, indicating that the enzymes and bacteria required for NPEO degradation existed abundantly in both aerobic and anaerobic sludge. Both treatments achieved high removal (> 92%) of the spiked NPEO9 mixture. Liquid chromatography-mass spectrometry (LC-MS) analysis showed that short-chain NPEOs (NPEO1-NPEO3) accumulated in anaerobic (2.01-2.56 micromol/L) and aerobic (1.62-2.03 micromol/L) effluents, with nonylphenol (NP) (0.24-0.31 micromol/L) as another group of metabolites in the anaerobic effluent, and nonylphenoxy carboxylates (NPECs) (2.79-3.30 micromol/L) in the aerobic effluent. Significant accumulation of NP in the anaerobic sludge and NPEO1-3 in the sludge of two reactors was observed. These results indicated that it was difficult to control these harmful metabolites in the conventional treatment processes. Denaturing gradient gel electrophoresis profiles of sludge samples support the speculation that the NPEO degradation bacteria might be the dominant indigenous species.

Study of 4-t-octylphenol degradation and microbial community in granular sludge

In this study, the authors have investigated the effects of various factors on both aerobic and anaerobic degradation of 4-t-octylphenol (4-t-OP) in granular sludge. In comparison, the aerobic degradation rate was much higher than that of anaerobic degradation. The optimal pH values for 4-t-OP degradation in granular sludge were 9 and 7 under aerobic and anaerobic conditions, respectively. And the degradation rate decreased with an increase in the initial 4-t-OP concentration. Addition of yeast extract or homologous compounds such as phenol also enhanced the 4-t-OP degradation, especially under the aerobic condition. To investigate the bacterial community in this study, the denaturing gradient gel electrophoresis (DGGE) method was applied, based on the primers, for the 16S rDNA V3 region of bacteria, gamma-proteobacteria and bacillus were identified as the major species of sludge.

Impact of non-ionic surfactant on the long-term development of lab-scale-activated sludge bacterial communities

The development of bacterial communities in replicate lab-scale-activated sludge reactors degrading a non-ionic surfactant was evaluated by statistical analysis of denaturing gradient gel electrophoresis (DGGE) fingerprints. Four sequential batch reactors were fed with synthetic sewage, two of which received, in addition, 0.01% of nonylphenol ethoxylates (NPE). The dynamic character of bacterial community structure was confirmed by the differences in species composition among replicate reactors. Measurement of similarities between reactors was obtained by pairwise similarity analysis using the Bray Curtis coefficient. The group of NPE-amended reactors exhibited the highest similarity values (Sjk=0.53+/-0.03), indicating that the bacterial community structure of NPE-amended reactors was better replicated than control reactors (Sjk=0.36+/-0.04). Replicate NPE-amended reactors taken at different times of operation clustered together, whereas analogous relations within the control reactor cluster were not observed. The DGGE pattern of isolates grown in conditioned media prepared with media taken at the end of the aeration cycle grouped separately from other conditioned and synthetic media regardless of the carbon source amendment, suggesting that NPE degradation residuals could have a role in the shaping of the community structure.

Selection and characterization of aerobic bacteria capable of degrading commercial mixtures of low-ethoxylated nonylphenols

AIMS

Isolation and characterization of new bacterial strains capable of degrading nonylphenol ethoxylates (NPnEO) with a low ethoxylation degree, which are particularly recalcitrant to biodegradation.

METHODS AND RESULTS

Seven aerobic bacterial strains were isolated from activated sludges derived from an Italian plant receiving NPnEO-contaminated wastewaters after enrichment with a low-ethoxylated NPnEO mixture. On the basis of 16S rDNA sequence, the strains were positioned into five genera: Ochrobactrum, Castellaniella, Variovorax, Pseudomonas and Psychrobacter. Their degradation capabilities have been evaluated on two commercial mixtures, i.e. Igepal CO-210 and Igepal CO-520, the former rich in low ethoxylated congeners and the latter containing a broader spectrum of NPnEO, and on 4-n-nonylphenol (NP). The strains degraded Igepal CO-210, Igepal CO-520 and 4-n-NP all applied at the initial concentration of 100 mg l(-1), by 35-75%, 35-90% and 15-25%, respectively, after 25 days of incubation.

CONCLUSIONS

Some of the isolated strains, in particular the Pseudomonas strains BCb12/1 and BCb12/3, showed interesting degradation capabilities towards low ethoxylated NPnEO congeners maintaining high cell vitality.

SIGNIFICANCE AND IMPACT OF THE STUDY

Increased knowledge of bacteria involved in NPnEO degradation and the possibility of using the isolated strains in tailored process for a tertiary biological treatment of effluents of wastewater treatment plants.

Development of biological process with pure bacterial cultures for effective bioconversion of sewage treatment plant sludge

Forty-six bacterial strains were isolated from nine different sources in four treatment plants namely Indah Water Konsortium (IWK) sewage treatment plant (STP), International Islamic University Malaysia (IIUM) wastewater treatment plant-1,-2 and -3 to evaluate the bioconversion process in terms of efficient biodegradation and bioseparation. The bacterial strains isolated were found to be 52.2% (24 isolates) and 47.8% (22 isolates) in the IWK and IIUM treatment plants, respectively. The results showed that higher microbial population (9-10 x 10(4) cfu/mL) was observed in the secondary clarifier of IWK treatment plant. Among the isolates, 23 isolates were gram-positive bacillus (GPB) and gram-positive cocci (GPC), 19 isolates were gram-negative bacillus (GNB) and gram-negative cocci (GNC), and the rest were undetermined. Gram-negative cocci (GNC) were not found in the isolates from IWK. A total of 15 bacterial strains were selected for effective and efficient sludge bioconversion. All the strains were tested against sludge (1% total suspended solids, TSS) to evaluate the biosolids production (TSS% content), chemical oxygen demand (COD) removal and filtration rate (filterability test). The strain S-1 (IWK1001) showed lower TSS content (0.8% TSS), maximum COD removal (84%) and increased filterability (1.1 min/10 mL of filtrate) of treated sludge followed by the strains S-11, S-14, S-2, S-15, S-13, S-7, S-8, S-4, S-3, S-6, S-12, S-16, S-17 and S-9. The pH values in the fermentation broth were affected by the bacterial cultures and recorded as well. Effective bioconversion was observed during the first three days of sludge treatment.

Replicability of dominant bacterial populations after long-term surfactant-enrichment in lab-scale activated sludge

Bacterial communities were examined in replicate lab-scale activated sludge reactors after a period of several months of enrichment with non-ionic nonylphenol ethoxylate (NPE) surfactants. Four sequential batch reactors were fed with synthetic sewage, two of which received additionally NPE. Small subunit rDNA-derived denaturing gel gradient electrophoresis (DGGE) profiles and 16S rDNA clone libraries were dominated by clones of Gammaproteobacteria class. Sequences of the other codominant rDNA phylotypes observed only in DGGE from NPE-amended reactors were, respectively, associated with the Group III of the Acidobacteria phylum. Intriguingly, 16S rRNA content from abundant Gammaproteobacteria cells was unexpectedly low. In addition to Acidobacteria, rRNA-derived DGGE profiles were dominated by members of the order Burkholderiales (of the Betaproteobacteria) and of the genus Sphingomonas (a member of the Alphaproteobacteria). Specific oligonucleotide probes for the selected ribotypes were designed and applied for quantitative real time polymerase chain reaction and fluorescence in situ hybridization, confirming their dominance in treated reactors. The parallel abundance of unique phylotypes in replicate reactors implies a distinctive selection of dominant organisms, which are better adapted to specialized niches in the highly selective environment.

Degradation of Low-Ethoxylated Nonylphenols by a Stenotrophomonas Strain and Development of New Phylogenetic Probes for Stenotrophomonas spp. Detection

An aerobic bacterium (BCc6), isolated from nonylphenol polyethoxylates (NPEOs)-contaminated sludge, was shown to be capable of degrading low-ethoxylated NPEO mixtures. Sequencing of 16S rRNA gene (rDNA) showed that it clustered with Stenotrophomonas nitritireducens. Fluorescent in situ hybridization (FISH), performed on BCc6 strain and on the previously isolated Stenotrophomonas BCaL2, also involved in NPEO degradation but clustering with S. maltophilia, showed that strain BCc6 did not hybridize with the S. maltophilia-specific probe, and neither of the two strains hybridized with probes targeted to the Gammaproteobacteria site, rDNA analyses performed on the two strains evidenced two new polymorphisms, the first one at the 23S rRNA Gammaproteobacteria site, characterizing the known members of the Stenotrophomonas genus, and the other one at the 16S rRNA level, characteristic of S. nitritireducens. Two new FISH probes were designed accordingly, tested on control bacterial cultures, and employed for in situ monitoring of Stenotrophomonas representatives.

Efficient Transformation of Cellulomonas flavigena by Electroporation and Conjugation with Bacillus thuringiensis

The conjugative self-transmissible plasmid pHT73, harbored in Bacillus thuringiensis var. kurstaki, was demonstrated to be transferred to Cellulomonas flavigena, a cellulolytic bacterium. Both conjugation and transformation procedures yielded resistant colonies; however, chromosomal integration was observed only when bacterial conjugation occurred. The efficiency of conjugation was 10% of recipient strain, which is considered a very efficient process. When the plasmid pHT73 was introduced by transformation, erythromycin-resistant cells contained the plasmid as an episome with no arrangements, as assayed by Southern blot analysis. In contrast, conjugated-resistant cells harbor the plasmid integrated into the chromosome. These data suggest a common mechanism of cell communication between nonrelated bacterial species with similar ecological habitats, and also that both electroporation and conjugation can be used to transform C. flavigena efficiently.

Aggregation-based cooperation during bacterial aerobic degradation of polyethoxylated nonylphenols

Three bacterial strains were isolated from activated sludge samples of two treatment plants receiving domestic and industrial wastewaters containing polyethoxylated nonylphenols. One strain (VA160) was isolated on rich medium, and the other two (BCaL1 and BCaL2) on mineral medium containing two industrial mixtures of nonylphenol ethoxylates as the sole carbon source. Strain VA160 was a Gram-positive, spore forming, filamentous bacterium, producing aggregates during growth in liquid medium. On the basis of phylogenetic analysis the strains were assigned to the Bacillus (VA160), Acinetobacter (BCaL1) and Stenothrophomonas (BCaL2) genera. High performance liquid chromatography analysis showed that only the Acinetobacter and Stenothrophomonas strains were involved in the degradation of polyethoxylated nonylphenols. Bacillus VA160, however, when co-cultured with the two degrading strains, induced the formation of cell aggregates and facilitated NPEO degradation. Fluorescent in situ hybridisation on the activated sludge sample from which Bacillus VA160 was isolated, using probes for Gram-positive bacteria with low G + C content, showed that bacteria belonging to this group specifically occurred inside the examined flocs. These observations suggest that the enhanced biodegradation of polyethoxylated nonylphenols in the three-membered co-culture is favoured by VA160-induced aggregation of BcaL1 and BcaL2 cells involved in the process.

Biodiversity of cultivable psychrotrophic marine bacteria isolated from Terra Nova Bay (Ross Sea, Antarctica)

A set of 146 Antarctic marine isolates from the Ross Sea was characterized by a combination of molecular techniques in order to determine the degree of inter- and intraspecific variability. Isolates were analyzed by amplified rDNA restriction analysis (ARDRA) using the tetrameric enzyme AluI, resulting in 52 different groups, corresponding to at least 52 different bacterial species, indicating a high degree of interspecific variability. The phylogenetic position of bacteria belonging to some ARDRA groups was obtained by sequencing of 16S rDNA. Random amplified polymorphic DNA (RAPD) analysis, carried out on the largest ARDRA groups, revealed a high intraspecific genetic variability, too. The analysis of plasmid content revealed the existence of horizontal gene transfer between strains belonging to the same and to different species. A comparison of the whole body of morphological, physiological and biochemical data was finally carried out.

Bacterial community shifts in nonylphenol polyethoxylates-enriched activated sludge

A molecular approach was used to evaluate the effect of nonylphenol ethoxylate surfactants on the bacterial diversity in lab-scale activated sludge reactors. Separate bench-scale units were fed synthetic wastewater with and without addition of branched nonylphenol ethoxylates (NPnEO). The performance of the reactors, in terms of carbonaceous removal was largely unaffected by the presence of NP10EO in the feeding solution. However, addition of NP10EO exerted a pronounced shift in bacterial community composition. In situ hybridization analyzing larger phylogenetic groups of bacteria with ribosomal RNA-targeted oligonucleotide probes revealed the dominance of clusters composed of Betaproteobacteria, accounting for up to one-third of 4',6-diamidino-2-phenylindol-dihydrochloride (DAPI)-stained cells in NP10EO amended reactors and only 5% of DAPI-stained cells in the controls. These shifts in populations of larger phylogenetic groups were confirmed by dot-blot analysis of rRNA. Members of gamma subclass of Proteobacteria were present in low numbers in all activated sludge samples examined, suggesting that only bacteria affiliated with the beta subclass of Proteobacteria may have a specific role in NP10EO degradation.

Fluctuation of bacteria isolated from elm tissues during different seasons and from different plant organs

In this work we isolated a culturable endophytic aerobic heterotrophic bacterial community from the stem and root tissues of elm trees (Ulmus spp.) and analyzed its fluctuations. A total of 724 bacterial isolates were collected at different times (April, June, September and December) from two elm trees, one infected with Elm Yellows phytoplasmas, and one which was healthy-looking. The isolates were grouped into 82 haplotypes, identified by means of amplified ribosomal DNA restriction analysis (ARDRA) using the restriction enzyme AluI, suggesting that the genetic diversity of the bacterial community was very high. The taxonomic position of the isolates belonging to the twelve main haplotypes, representing more than 72% of the total population, was determined by 16S rDNA sequencing. The main genera were Bacillus, Curtobacterium, Pseudomonas, Stenotrophomonas, Sphingomonas, Enterobacter, and Staphylococcus. The fluctuations in the bacterial community, determined by different parameters (seasonal changes, plant organ, presence of phytoplasmas) were studied, revealing that they were influenced both by variations in temperature (warm or cold according to the season) and by the organ examined (roots or stems). The role of the phytopathogenic status in these fluctuations was also discussed.

Detection of lateral gene transfer among microbial genomes

An increasingly comprehensive assessment is being developed of the extent and potential significance of lateral gene transfer among microbial genomes. Genomic sequences can be identified as being of putatively lateral origin by their unexpected phyletic distribution, atypical sequence composition, differential presence or absence in closely related genomes, or incongruent phylogenetic trees. These complementary approaches sometimes yield inconsistent results. Not only more data but also quantitative models and simulations are needed urgently.