Effects of grazing, phosphorus and light on the growth rates of major bacterioplankton taxa in the coastal NW Mediterranean.

Estimation of growth rates is crucial to understand the ecological role of prokaryotes and their contribution to marine biogeochemical cycling. However, there are only a few estimates for individual taxa. Two top-down (grazing) and bottom-up (phosphorus (P) availability) manipulation experiments were conducted under different light regimes in the NW Mediterranean Sea. Growth rate of different phylogenetic groups, including the Bacteroidetes, Rhodobacteraceae, SAR11, Gammaproteobacteria and its subgroups Alteromonadaceae and the NOR5/OM60 clade, were estimated from changes in cell numbers. Maximal growth rates were achieved in the P-amended treatments but when comparing values between treatments (response ratios), the response to predation removal was in general larger than to P-amendment. The Alteromonadaceae displayed the highest rates in both experiments followed by the Rhodobacteraceae, but all groups largely responded to filtration and P-amendment, even the SAR11 which presented low growth rates. Comparing light and dark treatments, growth rates were on average equal or higher in the dark than in the light for all groups, except for the Rhodobacteraceae and particularly the NOR5 clade, groups that contain photoheterotrophic species. These results are useful to evaluate the potential contributions of different bacterial types to biogeochemical processes under changing environmental conditions.

Insights into microbial diversity in wastewater treatment systems: How far have we come?

Biological wastewater treatment processes are based on the exploitation of the concerted activity of microorganisms. Knowledge on the microbial community structure and the links to the changing environmental conditions is therefore crucial for the development and optimization of biological systems by engineers. The advent of molecular techniques occurred in the last decades quickly showed the inadequacy of culture-dependent methodologies to unveil the great level of diversity present in sludge samples. Initially, culture-independent technologies and more recently the application of -omics in wastewater microbiology, have drawn a new view of microbial diversity and function of wastewater treatment systems. This article reviews the current knowledge on the topic placing emphasis on crucial microbial processes carried out in biological wastewater treatment systems driven by specific groups of microbes, such as nitrogen and phosphorus removal bacteria, filamentous and electrogenic microorganisms, as well as Archaea. Despite the recent -omics has offered substantial insights into the diversity and ecophysiology of these bacteria never envisioned before by providing millions of sequence reads at an unprecedented scale, studies based on high-throughput sequencing are still scarce. In order to obtain significant gains in the analysis of structure-function relationships, a greater sequencing investment is needed, particularly to uncover gene expression patterns of functionally relevant genes.

Presence of opportunistic oil-degrading microorganisms operating at the initial steps of oil extraction and handling.

Hydrocarbon-degrading microorganisms from natural environments have been isolated and identified using culture-dependent or molecular techniques. However, there has been little research into the occurrence of microorganisms incorporated into crude oil in the initial steps of extraction and handling, which can reduce the quality of stored petroleum. In the present study, a packed-column reactor filled with autoclaved perlite soaked with crude oil was subjected to a continuous flow of sterile medium in order to determine the presence of potential hydrocarbon degraders. Microorganisms developed on the surface of the perlite within a period of 73 days. DNA was extracted from the biofilm and then PCR-amplified using 16S rRNA bacterial and archaeal primers and 18S rRNA eukaryotic primers. No amplification was obtained using archaeal primers. However, denaturing gradient gel electrophoresis (DGGE) revealed the presence of unique bands indicating bacterial and eukaryotic amplification. Excision of these bands, sequencing, and subsequent BLAST search showed that they corresponded to Bacillus sp. and Aspergillus versicolor. The fungus was later isolated from intact perlite in agar plates. A bacterial clone library was used to confirm the presence in the biofilm of a unique hydrocarbon-degrading bacterium closely related to Bacillus sp. Analysis of the petroleum components by gas chromatography showed that there n-alkanes, aromatic hydrocarbons, and carbazoles were degraded.