Study of performances, stability and microbial characterization of a Sequencing Batch Biofilter Granular Reactor working at low recirculation flow

probeBase is a curated database of annotated rRNA-targeted oligonucleotide probes and supporting information. Rapid access to probe, microarray and reference data is achieved by powerful search tools and via different lists that are based on selected categories such as functional or taxonomic properties of the target organism(s) or the hybridization format (fluorescence in situ hybridization or microarray) in which the probes were applied. Additional information on probe coverage and specificity is available through direct submissions of probe sequences from probeBase to RDP-II and Greengenes, two major rRNA sequence databases. A freely editable user comments field for each probe entry allows any user to add, modify or remove information or to report errors in real-time. probeBase entries increased from 700 to more than 1200 during the past three years. Several options for submission of single probes or entire probe sets, even prior to publication of newly developed probes, should further contribute to keeping probeBase an up-to-date and useful resource. probeBase is freely accessible at . Email correspondence can be addressed to probebase@microbial-ecology.net.

Although the aceticlastic methanoarchaea Methanosarcina and Methanosaeta employ different enzymes to catalyze the first step of aceticlastic methanogenesis, it has long been assumed that the remainder of the pathway was the same. Analysis of the recently completed genome sequence of Methanosaeta thermophila confirms that the majority of core steps of the pathway are similar in both genera, but striking differences have been discovered in electron transfer and energy conservation. In addition, the presence of genes encoding enzymes for the CO(2) reduction pathway in the Msa. thermophila genome suggests the possibility that Methanosaeta might be more metabolically diverse than previously thought. Thus, genome analysis of Msa. thermophila presents new research avenues for this forgotten methanogen and reminds us of the questions that still remain unanswered about aceticlastic methanogenesis in both Methanosaeta and Methanosarcina.

The abundance of potential denitrifiers in full-scale wastewater treatment plants with biological nitrogen and phosphorus removal was investigated by FISH and various oligonucleotide probes. The potential denitrifiers were characterized as probe-defined populations that were able to consume radiolabelled substrate with oxygen, nitrate and nitrite as electron acceptor as determined by microautoradiography. The most abundant potential denitrifiers were related to the genera Aquaspirillum, Azoarcus, Thauera and Rhodocyclus, all within the Betaproteobacteria. They made up 20-49% of all bacteria in most of the 17 nitrogen removal plants investigated and were hardly present in four plants without denitrification. The ecophysiology of Aquaspirillum, Azoarcus and Thauera-related bacteria was consistent within each probe-defined group in the plants investigated. These three groups showed distinct physiological differences, with the Aquaspirillum-related bacteria appearing as the most specialized one, consuming only amino acids among the substrates tested, and Thauera as the most versatile consuming some volatile fatty acids, ethanol and amino acids. The coexistence of Aquaspirillum, Azoarcus and Thauera-related bacteria in a range of treatment plants with differences in wastewater, design and operation suggest that the populations ensure a functional stability of the plants by occupying different ecological niches related to the carbon transformation.