By placing the anode of a sediment microbial fuel cell (SMFC) in the rhizosphere of a rice plant, rootexcreted rhizodeposits can be microbially oxidized with concomitant current generation. Here, various molecular techniques were used to characterize the composition of bacterial and archaeal communities on such anodes, as influenced by electrical circuitry, sediment matrix, and the presence of plants. Closed-circuit anodes in potting soil were enriched with Desulfobulbus-like species, members of the family Geobacteraceae, and as yet uncultured representatives of the domain Archaea.Living plants release substantial amounts of carbon in the soil as rhizodeposits, which are to a large extent transformed into the greenhouse gas methane in wetlands (21). It was recently demonstrated (8, 33) that the rhizodeposits can be harvested by plant microbial fuel cells (plant MFCs) and transformed into electricity. In its most straightforward form, a plant MFC is an adaptation of a sediment MFC (SMFC), which has an anode buried in (planted) sediment, allowing (microbial) oxidation of reduced compounds, and a cathode in the overlying water.The roots and surrounding rhizosphere in a plant SMFC add an extra parameter to the as yet multifaceted SMFC system. In the present study, two molecular profiling techniques (denaturing gradient gel electrophoresis [DGGE] and terminal restriction fragment length polymorphism [T-RFLP]) will be applied to evaluate the effect of plant presence, support material, operation of the electrical circuit, and anode depth on the bacterial and archaeal communities associated with rice SMFC anodes. Phylogenetic analysis will give further insight in their composition.Experimental setup and operation. Several groups of SMFCs planted with rice were set up, operated, and electrochemically evaluated as previously described (8). Two series (A and B) of SMFCs were installed during subsequent summers as replication in time. Both series consisted of one group of reactors filled with vermiculite (exfoliated vermiculite; Sibli SA, Andenne, Belgium) and one group of reactors filled with potting soil (structural professional type 1; M. Snebbout N.V., Kaprijke, Belgium) as support for plant growth. The potting soil was based on NPK-enriched peat (peat enriched with nitrogen, phosphorus, and potassium) with a mean of 150 mg SO 4 2Ϫ liter Ϫ1 and 20% organic substances. In the reactors of series A, two anodic carbon felts were placed at 6 and 14 cm (depth indicated as H for high and L for low, respectively) below the support surface (one anode at 6 cm in open-circuit reactors). For the more-extensive series B, three anodic carbon felts were placed at 5-, 11-, and 17-cm depths (H, M for medium, and L, respectively). The reactors were inoculated with effluent from an acetate-fed MFC (series A and B) and with a methanogenic culture (presettler of constructed wetland, Wontergem, Belgium) (only series A). At the end of the reactor runs, the pH was 6.2 Ϯ 0.6 for reactors with soil and 7.0 Ϯ 0.5 for those with vermiculite.

Rare members of environmental microbial communities are often overlooked and unexplored, primarily due to the lack of techniques capable of acquiring their genomes. Chloroflexi belong to one of the most understudied phyla, even though many of its members are ubiquitous in the environment and some play important roles in biochemical cycles or biotechnological applications. We here used a targeted cellsorting approach, which enables the selection of specific taxa by fluorescent labeling and is compatible with subsequent single-cell genomics, to enrich for rare Chloroflexi species from a wastewater-treatment plant and obtain their genomes. The combined workflow was able to retrieve a substantially higher number of novel Chloroflexi draft genomes with much greater phylogenetical diversity when compared to a metagenomics approach from the same sample. The method offers an opportunity to access genetic information from rare biosphere members which would have otherwise stayed hidden as microbial dark matter and can therefore serve as an essential complement to cultivation-based, metagenomics, and microbial community-focused research approaches.

In the anaerobic ammonium oxidation (anammox) process, ammonia is oxidized with nitrite as primary electron acceptor under strictly anoxic conditions. The reaction is catalysed by a specialized group of planctomycete-like bacteria. These anammox bacteria use a complex reaction mechanism involving hydrazine as an intermediate. The reactions are assumed to be carried out in a unique prokaryotic organelle, the anammoxosome. This organelle is surrounded by ladderane lipids, which make the organelle nearly impermeable to hydrazine and protons. The localization of the major anammox protein, hydrazine oxidoreductase, was determined via immunogold labelling to be inside the anammoxosome. The anammox bacteria have been detected in many marine and freshwater ecosystems and were estimated to contribute up to 50% of oceanic nitrogen loss. Furthermore, the anammox process is currently implemented in water treatment for the low-cost removal of ammonia from high-strength waste streams. Recent findings suggested that the anammox bacteria may also use organic acids to convert nitrate and nitrite into dinitrogen gas when ammonia is in short supply.

Anaerobic digestion is used with success for the treatment of solid waste, urban and industrial effluents with a concomitant energy production. The process is robust and stable, but the complexity of the microbial community involved in the process is not yet fully comprehensive. Nowadays, the study of this complex ecosystem is facilitated by the availability of different molecular tools, but it is very important to choose the adequate tool to answer specific questions. The aim of this review is to describe different molecular techniques, indicate the questions that can be addressed by each technique, enumerate their limitations and give practical advices for their use. Examples of how the molecular tools have been used to address various questions in anaerobic digestion are presented. The key point now is to apply all this information to improve anaerobic digestion. The integration of concepts of microbial-ecology, environmental-engineering, modeling and bioinformatics is currently necessary.