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- Environmental factors influencing molinate biodegradation by a two-member mixed culture in rice paddy field floodwaterPublication . Barreiros, Luisa; Peres, Joana; Azevedo, Nuno F.; Manaia, Célia M.; Nunes, Olga C.Bioaugmentation is reported as a feasible approach for the treatment of pesticide contaminated environments. Aiming the development and future implementation of a bioremediation process to treat natural waters polluted with molinate, a molinate-mineralizing culture, composed of Pseudomonas chlororaphis ON1 and Gulosibacter molinativorax ON4T (designated DC1), was assayed in paddy field floodwater microcosms. The influence of abiotic (temperature, presence of other herbicides) and biotic (floodwater autochthonous microbiota) factors on molinate mineralization by culture DC1 was assessed. In parallel, the proportion of the introduced strains in filter-sterilized floodwaters was monitored by fluorescent in situ hybridization (FISH). Molinate mineralization and growth of culture DC1 were observed under all tested conditions, although the kinetic parameters (maximum specific growth and degradation rates) were significantly affected by the environmental conditions and culture media used. Additionally, these two factors were observed to have a statistically significant interaction. The lowest values of both kinetic parameters were observed at 15 °C. The presence of the herbicides propanil, bentazone and MCPA, frequently applied in rice culture protection, did not affect the degrading capacity of culture DC1. Furthermore, it was possible to infer that the autochthonous microbiota does not retard or limit molinate biodegradation, given the growth and degradation rates by culture DC1 were higher in non-sterile microcosm assays. Although G. molinativorax ON4T is known to promote the initial breakdown of molinate, P. chlororaphis ON1 appeared to be responsible to pull up the process, since higher proportions of this organism were found at the exponential growth and molinate degradation phase. Culture DC1 is efficient, versatile and presents a promising potential to be applied as a bioaugmentation tool for the remediation of environmental waters contaminated with molinate.
- Applications of optical DNA mapping in microbiologyPublication . Bogas, Diana; Nyberg, Lena; Pacheco, Rui; Azevedo, Nuno F.; Beech, Jason P.; Gomila, Margarita; Lalucat, Jorge; Manaia, Célia M.; Nunes, Olga C.; Tegenfeldt, Jonas O.; Westerlund, FredrikOptical mapping (OM) has been used in microbiology for the past 20 years, initially as a technique to facilitate DNA sequence-based studies; however, with decreases in DNA sequencing costs and increases in sequence output from automated sequencing platforms, OM has grown into an important auxiliary tool for genome assembly and comparison. Currently, there are a number of new and exciting applications for OM in the field of microbiology, including investigation of disease outbreaks, identification of specific genes of clinical and/or epidemiological relevance, and the possibility of single-cell analysis when combined with cell-sorting approaches. In addition, designing lab-on-a-chip systems based on OM is now feasible and will allow the integrated and automated microbiological analysis of biological fluids. Here, we review the basic technology of OM, detail the current state of the art of the field, and look ahead to possible future developments in OM technology for microbiological applications.