Dominance of the genus Polaromonas in the microbial ecology of an Intermittently Aerated Sequencing Batch Reactor (IASBR) treating dairy processing wastewater under varying aeration rates.

In this Research Communication we investigate potential correlations between key bacterial groups and nutrient removal efficiency in an Intermittently Aerated Sequencing Batch Reactor (IASBR) treating synthetic dairy processing wastewater. Reactor aeration rates of 0·6 and 0·4 litre per minute (LPM) were applied to an 8 l laboratory scale system and the relative impacts on IASBR microbial community structure and orthophosphate (PO4-P) and ammonium (NH4-N) removal efficiencies compared. Aeration at 0·6 LPM over several sludge retention times (SRTs) resulted in approximately 92% removal efficiencies for both PO4-P and NH4-N. Biomass samples subjected to next-generation sequencing (NGS), 16S rRNA profiling revealed a concomitant enrichment of Polaromonas under 0·6 LPM conditions, up to ~50% relative abundance within the reactor biomass. The subsequent shift in reactor aeration to 0·4 LPM, over a period of 3 SRTs, resulted in markedly reduced nutrient removal efficiencies for PO4-P (50%) and NH4-N (45%). An 85·7% reduction in the genus level relative abundance of Polaromonas was observed under 0·4 LPM aeration conditions over the same period.

Functional characterization of a StyS sensor kinase reveals distinct domains associated with intracellular and extracellular sensing of styrene in P. putida CA-3.

Bacterial two-component systems (TCSs) are of vital importance in the translation of rapidly changing environmental conditions into appropriate cellular regulatory responses enabling adaptation, growth, and survival. The diverse range of environmental signals that TCSs can process, coupled with discrete modular domains within TCS proteins, offers considerable potential for the rational design of bio-sensor and/or bio-reporter strains. In this study we functionally characterize the multi-domain StyS sensor kinase associated with sensing of the aromatic pollutant styrene by Pseudomonas putida CA-3. Deletion analysis of discrete domains was performed and the ability of the truncated StyS sensor proteins to activate a cognate reporter system in an E. coli host assessed. The essential histidine kinase and PAS input domains were identified for StyS dependent activation of the reporter system. However, co-expression of an ABC-transporter protein StyE, previously linked to styrene transport in P. putida CA-3, enabled activation of the reporter system with a StyS construct containing a non-essential PAS input domain, suggesting a novel role for intracellular detection and/or activation. Site directed mutagenesis and amino acid deletions were employed to further characterize the PAS sensing domains of both input regions. The potential implications of these findings in the use of multi-domain sensor kinases in rational design strategies and the potential link between transport and intracellular sensing are discussed.

Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments.

Metagenomic based strategies have previously been successfully employed as powerful tools to isolate and identify enzymes with novel biocatalytic activities from the unculturable component of microbial communities from various terrestrial environmental niches. Both sequence based and function based screening approaches have been employed to identify genes encoding novel biocatalytic activities and metabolic pathways from metagenomic libraries. While much of the focus to date has centred on terrestrial based microbial ecosystems, it is clear that the marine environment has enormous microbial biodiversity that remains largely unstudied. Marine microbes are both extremely abundant and diverse; the environments they occupy likewise consist of very diverse niches. As culture-dependent methods have thus far resulted in the isolation of only a tiny percentage of the marine microbiota the application of metagenomic strategies holds great potential to study and exploit the enormous microbial biodiversity which is present within these marine environments.

Differential expression of genes involved in iron metabolism in Aspergillus fumigatus / Expresión diferencial de genes del metabolismo de hierro en Aspergillus fumigatus

The ability of fungi to survive in many environments is linked to their capacity to acquire essential nutrients. Iron is generally complexed and available in very limited amounts. Like bacteria, fungi have evolved highly specific systems for iron acquisition. Production and uptake of iron-chelating siderophores has been shown to be important for certain human bacterial pathogens, as well as in fungal pathogens such as Cryptococcus neoformans and Fusarium graminearum. This system also enables the opportunistic fungal pathogen Aspergillus fumigatus to infect and subsequently colonize the human lung. In this study, advantage was taken of genome sequence data available for both Aspergillus nidulans and A. fumigatus either to partially clone or to design PCR primers for 10 genes putatively involved in siderophore biosynthesis or uptake in A. fumigatus. The expression of these genes was then monitored by semi-quantitative and quantitative real-time PCR over a range of iron concentrations. As expected, the putative biosynthetic genes sidA, sidC and sidD were all strongly up-regulated under iron starvation conditions, although the variable degree of induction indicates complex regulation by a number of transcriptional factors, including the GATA family protein SreA. In contrast, the gene sidE shows no iron-regulation, suggesting that SidE may not be involved in siderophore biosynthesis. The characterisation of the expression patterns of this subset of genes in the iron regulon facilitates further studies into the importance of iron acquisition for pathogenesis of A. fumigatus (AU)

La capacidad de los hongos de sobrevivir en muchos ambientes está ligada a su capacidad de adquirir nutrientes esenciales. El hierro, por lo general, se encuentra unido a alguna molécula y disponible sólo en cantidades muy limitadas. Como las bacterias, los hongos han desarrollado un sistema muy específico para incorporar hierro. Se ha demostrado que la producción y la incorporación de sideróforos quelantes de hierro es importante para ciertas bacterias patógenas humanas, así como en los hongos patógenos Cryptococcus neoformans y Fusarium graminearum. Este sistema también permite al hongo patógeno oportunista Aspergillus fumigatus infectar y colonizar el pulmón humano. En este estudio se aprovechó la información disponible de la secuencia genómica de Aspergillus nidulans y A. fumigatus para clonar parcialmente o diseñar cebadores de PCR para 10 genes posiblemente implicados en la biosíntesis o incorporación de sideróforos en A. fumigatus. Se siguió la expresión de estos genes usando PCR semi-cuantitativa y cuantitativa en tiempo real en un intervalo dado de concentraciones de hierro. Tal como se esperaba, los genes putativos biosintéticos sidA, sidC y sidD estaban fuertemente regulados en condiciones de carencia de hierro, aunque el grado variable de inducción indica que existe una regulación compleja debida a varios factores de transcripción, como la proteína SreA de la familia GATA. En cambio, el gen sidE no muestra regulación por hierro, lo que sugiere que la proteína SidE quizá no intervenga en la biosíntesis de sideróforos. La caracterización de los patrones de expresión de este subconjunto de genes en el regulón del hierro facilita futuros estudios sobre la importancia de la incorporación de hierro para la patogénesis de A. fumigatus (AU)