At two intertidal sites (one sandy and one silty, in the Scheldt estuary, The Netherlands), the fate of microphytobenthos was studied through an in situ 13 C pulse-chase experiment. Label was added at the beginning of low tide, and uptake of 13 C by algae was linear during the whole period of tidal exposure (about 27 mg m Ϫ2 h Ϫ1 in the top millimeter at both sites). The 13 C fixed by microphytobenthos was rapidly displaced toward deeper sediment layers (down to 6 cm), in particular at the dynamic, sandy site. The residence times of microphytobenthos with respect to external losses (resuspension and respiration) were about 2.4 and 5.6 d at the sandy and silty stations, respectively. The transfer of carbon from microphytobenthos to benthic consumers was estimated from the appearance of 13 C in bacterial biomarkers, handpicked nematodes, and macrofauna. The incorporation of 13 C into bacterial biomass was quantified by carbon isotope analysis of polar lipid derived fatty acids specific for bacteria. The bacterial polar lipidderived fatty acids (i14:0, i15:0, a15:0, i16:0, and 18:17c) showed rapid, significant transfer from benthic algae to bacteria with maximum labeling after 1 d. Nematodes became enriched after 1 h, and 13 C assimilation increased until day 3. Microphytobenthos carbon entered all heterotrophic components in proportion to heterotrophic biomass distribution (bacteria Ͼ macrofauna Ͼ meiofauna). Our results indicate a central role for microphytobenthos in moderating carbon flow in coastal sediments.

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The use of biomarkers in combination with stable isotope analysis is a new approach in microbial ecology and a number of papers on a variety of subjects have appeared. We will first discuss the techniques for analysing stable isotopes in biomarkers, primarily gas chromatography-combustion-isotope ratio mass spectrometry, and then describe a number of applications in microbial ecology based on 13C. Natural abundance isotope ratios of biomarkers can be used to study organic matter sources utilised by microorganisms in complex ecosystems and for identifying specific groups of bacteria like methanotrophs. Addition of labelled substrates in combination with biomarker analysis enables direct identification of microbes involved in specific processes and also allows for the incorporation of bacteria into food web studies. We believe that the full potential of the technique in microbial ecology has just started to be exploited.

Rising atmospheric CO 2 levels are predicted to have major consequences on carbon cycling and the functioning of terrestrial ecosystems. Increased photosynthetic activity is expected, especially for C-3 plants, thereby influencing vegetation dynamics; however, little is known about the path of fixed carbon into soil-borne communities and resulting feedbacks on ecosystem function. Here, we examine how arbuscular mycorrhizal fungi (AMF) act as a major conduit in the transfer of carbon between plants and soil and how elevated atmospheric CO 2 modulates the belowground translocation pathway of plant-fixed carbon. Shifts in active AMF species under elevated atmospheric CO 2 conditions are coupled to changes within active rhizosphere bacterial and fungal communities. Thus, as opposed to simply increasing the activity of soil-borne microbes through enhanced rhizodeposition, elevated atmospheric CO 2 clearly evokes the emergence of distinct opportunistic plantassociated microbial communities. Analyses involving RNA-based stable isotope probing, neutral/phosphate lipid fatty acids stable isotope probing, community fingerprinting, and real-time PCR allowed us to trace plant-fixed carbon to the affected soil-borne microorganisms. Based on our data, we present a conceptual model in which plant-assimilated carbon is rapidly transferred to AMF, followed by a slower release from AMF to the bacterial and fungal populations well-adapted to the prevailing (myco-)rhizosphere conditions. This model provides a general framework for reappraising carbon-flow paths in soils, facilitating predictions of future interactions between rising atmospheric CO 2 concentrations and terrestrial ecosystems. 13C | arbuscular mycorrhizal | climate change | RNA-based stable isotope probing | rhizosphere

Stable carbon isotope ratios of bacterial biomarkers were determined to infer sources of organic carbon used by bacteria in the sediments of three salt marshes. Biomarkers studied were polar lipid-derived fatty acids (PLFA), mainly bacteria-specific, methyl-branched i15 : 0 and a15 : 0. Experiments showed that isotopic fractionation between substrate and biomarkers was relatively constant (Ϫ4 to Ϫ6‰, on average) compared to the wide range in 13 C/ 12 C ratios of carbon sources found in the studied marshes. At the Spartina site of the Waarde Marsh (The Netherlands), biomarker 13 C/ 12 C ratios were depleted by approximately 6‰ more than expected for bacteria growing on Spartina litter and were similar to an unvegetated control sediment. This pattern suggested that local macrophyte production was of little importance and that other material (probably of algal origin) was the dominant carbon source for bacterial growth. Spartina contributed about half of the carbon in bacterial PLFA at the Kattendijke Marsh (The Netherlands) and dominated at the Great Marshes (U.S.). The variation in bacterial carbon sources in these marshes was probably related to estimated inputs of nonmacrophyte organic matter to the sediment. At the Waarde Marsh, a clear plant species effect was found as coupling between plant and bacteria was more important in Scirpus maritimus than in Spartina anglica. The contribution of local plant production to bacterial biomass in salt-marsh sediments is highly variable between marshes and depends on the input of nonmacrophyte material by sedimentation in comparison to local plant input, which in turn may differ among plant species.

Recently, a novel mode of sulphur oxidation was described in marine sediments, in which sulphide oxidation in deeper anoxic layers was electrically coupled to oxygen reduction at the sediment surface. Subsequent experimental evidence identified that long filamentous bacteria belonging to the family Desulfobulbaceae likely mediated the electron transport across the centimetre-scale distances. Such long-range electron transfer challenges some long-held views in microbial ecology and could have profound implications for sulphur cycling in marine sediments. But, so far, this process of electrogenic sulphur oxidation has been documented only in laboratory experiments and so its imprint on the seafloor remains unknown. Here we show that the geochemical signature of electrogenic sulphur oxidation occurs in a variety of coastal sediment environments, including a salt marsh, a seasonally hypoxic basin, and a subtidal coastal mud plain. In all cases, electrogenic sulphur oxidation was detected together with an abundance of Desulfobulbaceae filaments. Complementary laboratory experiments in intertidal sands demonstrated that mechanical disturbance by bioturbating fauna destroys the electrogenic sulphur oxidation signal. A survey of published geochemical data and 16S rRNA gene sequences identified that electrogenic sulphide oxidation is likely present in a variety of marine sediments with high sulphide generation and restricted bioturbation, such as mangrove swamps, aquaculture areas, seasonally hypoxic basins, cold sulphide seeps and possibly hydrothermal vent environments. This study shows for the first time that electrogenic sulphur oxidation occurs in a wide range of marine sediments and that bioturbation may exert a dominant control on its natural distribution.

The unusually harsh environmental conditions of terrestrial Antarctic habitats result in ecosystems with simplified trophic structures, where microbial processes are especially dominant as drivers of soil-borne nutrient cycling. We examined soil-borne Antarctic communities (bacteria, fungi and nematodes) at five locations along a southern latitudinal gradient from the Falkland Islands (51 degrees S) to the base of the Antarctic Peninsula (72 degrees S), and compared principally vegetated vs. fell-field locations at three of these sites. Results of molecular (denaturing gradient gel electrophoresis, real-time PCR), biochemical (ergosterol, phospholipid fatty acids) and traditional microbiological (temperature- and medium-related CFU) analyses were related to key soil and environmental properties. Microbial abundance generally showed a significant positive relationship with vegetation and vegetation-associated soil factors (e.g. water content, organic C, total N). Microbial community structure was mainly related to latitude or location and latitude-dependent factors (e.g. mean temperature, NO3, pH). Furthermore, strong interactions between vegetation cover and location were observed, with the effects of vegetation cover being most pronounced in more extreme sites. These results provide insight into the main drivers of microbial community size and structure across a range of terrestrial Antarctic and sub-Antarctic habitats, potentially serving as a useful baseline to study the impact of predicted global warming on these unique and pristine ecosystems.

Biphytanyl membrane lipids and 16S rRNA sequences derived from marine Crenarchaeota were detected in shallow North Sea surface water in February 2002. To investigate the carbon fixation mechanism of these uncultivated archaea in situ (13)C bicarbonate tracer experiments were performed with this water in the absence of light. About 70% of the detected (13)C incorporation into lipids (including fatty acids and sterols) is accounted for by the crenarchaeotal biphytanyl membrane lipids. This finding indicates that marine Crenarchaeota can utilize bicarbonate or CO(2) derived thereof in the absence of light and are chemoautotrophic organisms.