The Black Sea, with its highly sulfidic water column, is the largest anoxic basin in the world. Within its sediments, the mineralization of organic matter occurs essentially through sulfate reduction and methanogenesis. In this study, the sulfate-reducing community was investigated in order to understand how these microorganisms are distributed relative to the chemical zonation: in the upper sulfate zone, at the sulfate-methane transition zone, and deeply within the methane zone. Total bacteria were quantified by real-time PCR of 16S rRNA genes whereas sulfate-reducing microorganisms (SRM) were quantified by targeting their metabolic key gene, the dissimilatory (bi)sulfite reductase (dsrA). Sulfate-reducing microorganisms were predominant in the sulfate zone but occurred also in the methane zone, relative proportion was maximal around the sulfate-methane transition, c. 30%, and equally high in the sulfate and methane zones, 5-10%. The dsrAB clone library from the sulfate-methane transition zone, showed mostly sequences affiliated with the Desulfobacteraceae. While, the dsrAB clone libraries from the upper, sulfate-rich zone and the deep, sulfate-poor zone were dominated by similar, novel deeply branching sequences which might represent Gram-positive spore-forming sulfate- and/or sulfite-reducing microorganisms. We thus hypothesize that terminal carbon mineralization in surface sediments of the Black Sea is largely due to the sulfate reduction activity of previously hidden SRM. Although these novel SRM were also abundant in sulfate-poor, methanogenic areas of the Black Sea sediment, their activities and possibly very versatile metabolic capabilities remain subject of further study.

The factors and processes driving cyanobacterial blooms in eutrophic freshwater ecosystems have been extensively studied in the past decade. A growing number of these studies concern the direct or indirect interactions between cyanobacteria and heterotrophic bacteria. The presence of bacteria that are directly attached or immediately adjacent to cyanobacterial cells suggests that intense nutrient exchanges occur between these microorganisms. In order to determine if there is a specific association between cyanobacteria and bacteria, we compared the bacterial community composition during two cyanobacteria blooms of Anabaena (filamentous and N2-fixing) and Microcystis (colonial and non-N2 fixing) that occurred successively within the same lake. Using high-throughput sequencing, we revealed a clear distinction between associated and free-living communities and between cyanobacterial genera. The interactions between cyanobacteria and bacteria appeared to be based on dissolved organic matter degradation and on N recycling, both for N2-fixing and non N2-fixing cyanobacteria. Thus, the genus and potentially the species of cyanobacteria and its metabolic capacities appeared to select for the bacterial community in the phycosphere.

In order to better understand the main factors that influence the distribution of sulfate-reducing bacteria (SRB), their population size and their metabolic activity in high- and low-sulfate zones, we studied the SRB diversity in 3- to 5-m-deep sediment cores, which comprised the entire sulfate reduction zone and the upper methanogenic zone. By combining EMA (ethidium monoazide that can only enter damaged/dead cells and may also bind to free DNA) treatment with real-time PCR, we determined the distributions of total intact bacteria (16S rDNA genes) and intact SRB (dsrAB gene), their relative population sizes, and the proportion of dead cells or free DNA with depth. The abundance of SRB corresponded in average to 13% of the total bacterial community in the sulfate zone, 22% in the sulfate-methane transition zone and 8% in the methane zone. Compared with the total bacterial community, there were relatively less dead/damaged cells and free DNA present than among the SRB and this fraction did not change systematically with depth. By DGGE analysis, based on the amplification of the dsrA gene (400 bp), we found that the richness of SRB did not change with depth through the geochemical zones; but the clustering was related to the chemical zonation. A full-length clone library of the dsrAB gene (1900 bp) was constructed from four different depths (20, 110, 280 and 500 cm), and showed that the dsrAB genes in the near-surface sediment (20 cm) was mainly composed of sequences close to the Desulfobacteraceae, including marine complete and incomplete oxidizers such as Desulfosarcina, Desulfobacterium and Desulfococcus. The three other libraries were predominantly composed of Gram-positive SRB.

The diversity of sulfate-reducing microorganisms was investigated in two contrasting mudflats of the Seine estuary, by PCR amplification, cloning and sequencing of the genes coding for parts of the alpha and beta subunits of dissimilatory sulfite reductase (dsrAB). One site is located in the mixing-zone and shows marine characteristics, with high salinity and sulfate concentration, whereas the other site shows freshwater characteristics, with low salinity and sulfate concentration. Diversity and abundance of dsrAB genes differed between the two sites. In the mixing-zone sediments, most of the dsrAB sequences were affiliated to those of marine Gram-negative bacteria belonging to the order of Desulfobacterales, whereas in the freshwater sediments, a majority of dsrAB sequences was related to those of the Gram-positive bacteria belonging to the genus Desulfotomaculum. It is speculated that this is related to the salinity and the sulfate concentration in the two mudflats.

No abstract

Summary1. Declines in availability of plant resources to pollinators are a major cause of pollinator loss. The management of plant communities to enhance floral resources is often proposed as a way to sustain pollinator populations. Nectar, the main energetic resource for pollinators, plays a central role in behaviour and composition of pollinator communities. Abiotic and biotic factors are known to influence nectar traits at both the species and community levels, but the impact of plant community composition itself has never been investigated. 2. Below-ground interactions in plant communities can induce changes in plant development through (i) plant-derived litter amendment of the soil and (ii) competition for soil resources between plants. We tested how plant below-ground interactions affect above-ground nectar traits involved in plant attractiveness to pollinators. 3. A short-term pot experiment was carried out with three temperate grassland species Mimulus guttatus, Lamium amplexicaule, and Medicago sativa, showing distinct litter stoichiometry and competitive abilities for soil resources. Litter amendment (none, mono and tri-specific litter) and plant interaction treatments (monocultures, two-and three-species mixtures) were crossed in a factorial design. 4. Litter amendment to the soil led to an increase in total nectar sugar content in L. amplexicaule plants but not in the two other species. We also found that the presence of M. guttatus, a competitive species, reduced the total nectar sugar content in L. amplexicaule through a concomitant decrease in nectar volume per flower and in floral display size, but not in other species. Species-specific responses of nectar traits to variation in soil nitrogen availability were thus observed, suggesting consequences for plant species and community attractiveness to pollinators. However, we did not find evidence that the legume M. sativa affected nectar traits of any neighbouring plants. 5. Synthesis. Our results demonstrate that litter inputs and competition between plants for soil resources can alter nectar traits linked to plant attractiveness to pollinators. This supports the idea that below-ground plant-plant interactions for soil resources can influence above-ground plantplant interactions for pollination services. This offers promising perspectives in studying the role of below-ground-above-ground interactions on higher trophic levels.

An underlying assumption of most soil carbon (C) dynamics models is that soil microbial communities are functionally similar; in other words, that microbial activity under given conditions is not dependent on the composition or diversity of the communities. Although a number of studies have indicated that microbial communities are not intrinsically functionally similar, most soil C dynamics models can adequately describe C dynamics without explicitly describing microbial functioning. Here, we provide a mechanistic basis for reconciling this apparent discrepancy. In a reciprocal transplant experiment, we show that the environmental context (soil and pore-network properties) of microbial communities can constrain the activity of functionally different communities to such an extent that their activities are indistinguishable. The data also suggest that when microbial activity is less constrained, the intrinsic functional differences among communities can be expressed. We conclude that soil C dynamics may depend on microbial community structure or diversity in environments where their activity is less constrained, such as the rhizosphere or the litter layer, but not in oligotrophic environments such as the mineral layers of soil.

In this study, we describe a competitive polymerase chain reaction (PCR) for the quantification of the sequences of dsrAB in sulfatereducing microorganisms. We used the dsr1F/dsr4R set of primers, previously designed by Wagner et al. (1998), and a competitor sequence was constructed from the dsrAB genes of Desulfovibrio vulgaris. The detection limit of competitive PCR corresponded to 45 copies of the dsrAB genes per ng of extracted DNA, and most of the dsrAB sequences amplified and cloned from DNA extracted from Seine estuary sediments were amplified with a similar efficiency. Competitive PCR was then used to assess the abundance of dsrAB genes in the total DNA extracted from the sediment of the Seine estuary mudflats. We observed that the abundance of dsrAB coincided with the variation in the sulfate reduction rate with the depth of the sample, confirming the importance of 'dsrAB' sulfate-reducing microorganisms in sulfidogenesis in anoxic environments. We obtained values ranging from 0.045U10 3 to 6.63U10 3 copies of dsrAB per ng of extracted DNA, and values of the sulfate reduction rate ranging from 35 to 158 nmol cm 33 day 31 . These results are similar to those obtained in other studies using molecular biology techniques.