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Production of common bean (Phaseolus vulgaris) is limited by the occurrence of damping off (rhizoctoniosis), which is caused by the fungus Rhizoctonia solani. However, the co-inoculation of plant growth-promoting rhizobacteria (PGPR) involved in biological control along with diatomic nitrogen (N2)-fixing rhizobia can enhance N nutrition and increase production. In this context, finding microorganisms with synergistic effects that perform these two roles is of fundamental importance to ensure adequate yield levels. The aim of this study was to evaluate the effects of co-inoculation of nodule endophytic strains of the genera Bacillus, Paenibacillus, Burkholderia, and Pseudomonas with Rhizobium tropici CIAT 899, an N2-fixing rhizobial strain, on the biocontrol of damping off and growth promotion in common bean plants. Greenhouse experiments were conducted under axenic conditions using the common bean cultivar Perola. The first experiment evaluated the potential of the 14 rhizobacterial strains, which were inoculated alone or in combination with CIAT 899, for the control of R. solani. The second experiment evaluated the ability of these 14 rhizobacterial strains to promote plant growth with three manners of N supply: co-inoculation with CIAT 899 at low mineral N supply (5.25 mg N mL−1), low mineral N supply (5.25 mg N mL−1), and high mineral N supply (52.5 mg N mL−1). The use of rhizobacteria combined with rhizobia contributed in a synergistic manner to the promotion of growth and the control of damping off in the common bean. Co-inoculation of the strains UFLA 02-281/03-18 (Pseudomonas sp.), UFLA 02-286 (Bacillus sp.), and UFLA 04-227 (Burkholderia fungorum) together with CIAT 899 effectively controlled damping off. For the common bean, mineral N supply can be replaced by the co-inoculation of CIAT 899 with plant growth-promoting strains UFLA 02-281/02-286/02-290/02-293. Nodule endophytes UFLA 02-281/02-286 are promising for co-inoculation with CIAT 899 in the common bean, promoting synergy with rhizobial inoculation and protection against disease.

The novel bacterial strains Burkholderia fungorum T3A13001 and Caulobacter sp T2A12002, which were previously isolated from oil-contaminated sites and identified via 16S RNA sequences, were tested for their hydrocarbon degrading efficiency. Media spiked with 100 ppm pyrene were incubated at 25 °C and 37 °C. The bacterial isolates' pyrene-degrading capability was assessed in acidic (pH 5.0) and alkaline (pH 9.0) media. Caulobacter sp degraded 21% and 24% of the pyrene at pH 9.0 and 5.0, respectively; thus, the strain was more active at pH 5.0 than pH 9.0. B. fungorum was active in a wide range of pH values, because it biodegraded 59%–62% of the provided pyrene in acidic and alkaline media. Caulobacter sp degraded 35%–36% of the provided pyrene in cultures at 37 °C and 25 °C. B. fungorum degraded 56% and 59% of the provided pyrene at 37 °C and 25 °C, respectively. Given that B. fungorum biodegraded over the half-life of the initial 100 ppm pyrene in the cultures, the strain may be suitable for bioremediation of high molecular weight PAHs. The study provides important insight into possible PAH biodegradation and bioremediation of hydrocarbon-polluted sites using novel bacterial strains.

Multispecies biofilms are the dominant form of biofilms found in Nature. The application of fluorescence in situ hybridization (FISH)-based techniques to the discrimination of biofilm populations might contribute to the understanding of microorganism interactions in these structures, and might allow the development of efficient strategies to prevent or minimize biofilm-associated diseases. This work presents the first study that develops, optimizes and validates a multiplex FISH procedure using locked nucleic acid (LNA) and 2-O-methyl RNA (2OMe) oligonucleotides probes for the in vitro discrimination within mixed populations. As a case study, Escherichia coli, the major cause of urinary tract infections (UTIs), and three other atypical colonizers of urinary catheters (Delftia tsuruhatensis, Achromobacter xylosoxidans and Burkholderia fungorum) with unproven pathogenic potential, were selected. Specific probes for these species were designed and optimized for specific hybridization in multiplex experiments. Results showed that the LNA/2OMe-FISH method performed well in multiplex experiments and presented a good correlation with total and cultivability counts, regardless of the cells physiological state. In fact, the method was also able to report variations of viable but non-cultivable populations. Further analysis of mixed biofilm structures by confocal laser scanning microscopy provided a clear discrimination in three dimensions between the location of the different populations., This work was funded by FEDER funds through the Operational Programme for Competitiveness Factors - COMPETE, ON.2 - O Novo Norte -North Portugal Regional Operational Programme and National Funds through FCT - Foundation for Science and Technology under the projects: PEst-C/EQB/UI0511, NORTE-07-0124-FEDER-000025 - RL2_ Environment & Health and Project "DNA mimics" PIC/IC/82815/2007; PhD Fellowship [SFRH/BD/82663/2011]; and Postdoctoral Fellowship [SFRH/BPD/74480/2010]. The authors would like to thank to M. Fenice and A. Steinbuchel for kindly providing the D. tsuruhatensis BM90 and A. xylosoxidans B3 strains, respectively.

Microorganisms play an important role in the transformation of material within the earth’s crust. The storage of CO2 could affect the composition of inorganic and organic components in the reservoir, consequently influencing microbial activities. To study the microbial induced processes together with geochemical, petrophysical and mineralogical changes, occurring during CO2 storage, long-term laboratory experiments under simulated reservoir P-T conditions were carried out. Clean inner core sections, obtained from the reservoir region at the CO2 storage site in Ketzin (Germany) from a depth of about 650 m, were incubated in high pressure vessels together with sterile synthetic formation brine under in situ P-T conditions of 5.5 MPa and 40 °C. A 16S rDNA based fingerprinting method was used to identify the dominant species in DNA extracts of pristine sandstone samples. Members of the α - and β -subdivisions of Proteobacteria and the Actinobacteria were identified. So far sequences belonging to facultative anaerobic, chemoheterotrophic bacteria (Burkholderia fungorum, Agrobacterium tumefaciens) gaining their energy from the oxidation of organic molecules and a genus also capable of chemolithoautotrophic growth (Hydrogenophaga) was identified. During CO2 incubation minor changes in the microbial community composition were observed. The majority of microbes were able to adapt to the changed conditions. During CO2 exposure increased concentrations of Ca2+, K+, Mg2+ and SO42− were observed. Partially, concentration rises are (i) due to equilibration between rock pore water and synthetic brine, and (ii) between rock and brine, and are thus independent on CO2 exposure. However, observed concentrations of Ca2+, K+, Mg2+ are even higher than in the original reservoir fluid and therefore indicate mineral dissolution due to CO2 exposure.