Project description:Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics.
Project description:Although N2 fixation can occur in free-living cyanobacteria, the unicellular endosymbiotic cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is considered to be a dominant N2-fixing species in marine ecosystems. Four UCYN-A sublineages are known from partial nitrogenase (nifH) gene sequences. However, few studies have investigated their habitat preferences and regulation by their respective hosts in open-ocean versus coastal environments. Here, we compared UCYN-A transcriptomes from oligotrophic open-ocean versus nutrient-rich coastal waters. UCYN-A1 metabolism was more impacted by habitat changes than UCYN-A2. However, across habitats and sublineages genes for nitrogen fixation and energy production were highly transcribed. Curiously these genes, critical to the symbiosis for the exchange of fixed nitrogen for fixed carbon, maintained the same schedule of diel expression across habitats and UCYN-A sublineages, including UCYN-A3 in the open-ocean transcriptomes. Our results undersore the importance of nitrogen fixation in UCYN-A symbioses across habitats, with consequences for community interaction and global biogeochemical cycles.
Project description:Ponds are often identified by their small size and shallow depths, but the lack of a universal evidence-based definition hampers science and weakens legal protection. Here, we compile existing pond definitions, compare ecosystem metrics (e.g., metabolism, nutrient concentrations, and gas fluxes) among ponds, wetlands, and lakes, and propose an evidence-based pond definition. Compiled definitions often mentioned surface area and depth, but were largely qualitative and variable. Government legislation rarely defined ponds, despite commonly using the term. Ponds, as defined in published studies, varied in origin and hydroperiod and were often distinct from lakes and wetlands in water chemistry. We also compared how ecosystem metrics related to three variables often seen in waterbody definitions: waterbody size, maximum depth, and emergent vegetation cover. Most ecosystem metrics (e.g., water chemistry, gas fluxes, and metabolism) exhibited nonlinear relationships with these variables, with average threshold changes at 3.7 ± 1.8 ha (median: 1.5 ha) in surface area, 5.8 ± 2.5 m (median: 5.2 m) in depth, and 13.4 ± 6.3% (median: 8.2%) emergent vegetation cover. We use this evidence and prior definitions to define ponds as waterbodies that are small (< 5 ha), shallow (< 5 m), with < 30% emergent vegetation and we highlight areas for further study near these boundaries. This definition will inform the science, policy, and management of globally abundant and ecologically significant pond ecosystems.
Project description:The availability of organic carbon represents a major bottleneck for the development of soil microbial communities and the regulation of microbially-mediated ecosystem processes. However, there is still a lack of knowledge on how the lifestyle and population abundances are physiologically regulated by the availability of energy and organic carbon in soil ecosystems. To date, functional insights into the lifestyles of microbial populations have been limited by the lack of straightforward approaches to the tracking of the active microbial populations. Here, by the use of an comprehensiv metaproteomics and genomics, we reveal that C-availability modulates the lifestyles of bacterial and fungal populations in drylands and determines the compartmentalization of functional niches. This study highlights that the active diversity (evaluated by metaproteomics) but not the diversity of the whole microbial community (estimated by genome profiling) is modulated by the availability of carbon and is connected to the ecosystem functionality in drylands.
Project description:Marine cyanobacteria are thought to be the most sensitive of the phytoplankton groups to copper toxicity, yet little is known of the transcriptional response of marine Synechococcus to copper shock. Global transcriptional response to two levels of copper shock was assayed in both a coastal and an open ocean strain of marine Synechococcus using whole genome expression microarrays. Both strains showed an osmoregulatory-like response, perhaps as a result of increasing membrane permeability. This could have implications for marine carbon cycling if copper shock leads to dissolved organic carbon leakage in Synechococcus. The two strains additionally showed a reduction in photosynthetic gene transcripts. Contrastingly, the open ocean strain showed a typical stress response whereas the coastal strain exhibited a more specific oxidative or heavy metal type response. In addition, the coastal strain activated more regulatory elements and transporters, many of which are not conserved in other marine Synechococcus strains and may have been acquired by horizontal gene transfer. Thus, tolerance to copper shock in some marine Synechococcus may in part be a result of an increased ability to sense and respond in a more specialized manner.