Deep-sea hydrothermal ecosystems are considered oases of life in oceans. Since the discovery of these ecosystems in the late 1970s, many endemic species of Bacteria, Archaea, and other organisms, such as annelids and crabs, have been described. Considerable knowledge has been acquired about the diversity of (micro)organisms in these ecosystems, but the diversity of fungi has not been studied to date. These organisms are considered key organisms in terrestrial ecosystems because of their ecological functions and especially their ability to degrade organic matter. The lack of knowledge about them in the sea reflects the widely held belief that fungi are terrestrial organisms. The first inventory of such organisms in deep-sea hydrothermal environments was obtained in this study. Fungal diversity was investigated by analyzing the small-subunit rRNA gene sequences amplified by culture-independent PCR using DNA extracts from hydrothermal samples and from a culture collection that was established. Our work revealed an unsuspected diversity of species in three of the five fungal phyla. We found a new branch of Chytridiomycota forming an ancient evolutionary lineage. Many of the species identified are unknown, even at higher taxonomic levels in the Chytridiomycota, Ascomycota, and Basidiomycota. This work opens the way to new studies of the diversity, ecology, and physiology of fungi in oceans and might stimulate new prospecting for biomolecules. From an evolutionary point of view, the diversification of fungi in the oceans can no longer be ignored.Since the discovery of hydrothermal vent ecosystems 30 years ago, unexpected species diversity has been revealed that has shed light on the functional coupling between the geosphere and the biosphere. When submersibles dive to the seafloor, they bring numerous organisms back to the surface, and this has resulted in the description of nearly two new species per month (10). Deep-sea hydrothermal ecosystems are considered hotspots of microbial diversity on the seafloor. Indeed, they are ecosystems that produce biomass using the wide range of chemical compounds released by the polymetallic sulfite chimneys or "black smokers" that represent the huge quantity of chemical energy that is available (26). The vent fluid, having been heated close to a magma chamber, can have a temperature of 400°C when it is emitted. It is also characterized by a lack of dissolved oxygen, strong acidity (pH 2 to 3), a high concentration of electron donors (i.e., reduced compounds such as methane and hydrogen sulfide), and the presence of heavy metals (36). Continual mixing with the cold ocean water (2 to 4°C) that is rich in electron acceptors creates a dynamic chemical disequilibrium that is a source of energy for microorganisms that control the rates of redox reactions (16).Each ridge displays varied geochemistry, and the vent fluids differ, even at scales as small as the fractures, pipes, and porosities in the black smokers, creating diverse microhabitats for biota (10,

Plant roots harbor a large diversity of microorganisms that have an essential role in ecosystem functioning. To better understand the level of intimacy of root-inhabiting microbes such as arbuscular mycorrhizal fungi and bacteria, we provided 13 CO2 to plants at atmospheric concentration during a 5-h pulse. We expected microbes dependent on a carbon flux from their host plant to become rapidly labeled. We showed that a wide variety of microbes occurred in roots, mostly previously unknown. Strikingly, the greatest part of this unsuspected diversity corresponded to active primary consumers. We found 17 bacterial phylotypes co-occurring within roots of a single plant, including five potentially new phylotypes. Fourteen phylotypes were heavily labeled with the 13 C. Eight were phylogenetically close to Burkholderiales, which encompass known symbionts; the others were potentially new bacterial root symbionts. By analyzing unlabeled and 13 C-enriched RNAs, we demonstrated differential activity in C consumption among these root-inhabiting microbes. Arbuscular mycorrhizal fungal RNAs were heavily labeled, confirming the high carbon flux from the plant to the fungal compartment, but some of the fungi present appeared to be much more active than others. The results presented here reveal the possibility of uncharacterized root symbioses.ribosomal RNA ͉ stable isotope probing ͉ symbiosis ͉ arbuscular mycorrhiza ͉ endophytes P lants are the dominant primary producers in most terrestrial ecosystems. In the soil, they are escorted by a myriad of microorganisms living freely or in intimate interaction with their roots (1, 2). These microorganisms can be pathogenic, parasitic, saprotrophic, or mutualistic. Among the root symbionts, arbuscular mycorrhizal (AM) fungi are well known and have been observed colonizing the roots of most plant species in many ecosystems (3). Recent studies show that high diversity is the norm even where plant diversity is low (4-6). These AM fungi are biotrophs, unable to grow in the absence of a living plant, and often display a broad host range although there is growing evidence for differences in host preference (5-8). They have been demonstrated to improve plant mineral nutrition (3) and stress resistance (3). AM fungi are important for the global carbon cycle because up to 20% of photoassimilates can be translocated to them (9). We also know that the diversity of AM fungi can determine plant community structure and ecosystem productivity (10). The plant-bacteria symbioses are variably documented. The best studied symbiosis is the rhizobiumlegume interaction, but a single plant root can harbor a large variety of fungi (1) and bacteria (2), as well as several different archaea (2). So far we have no information about the functions of most of these root-living microbes. The strategy chosen herein, stable isotope probing (SIP)-RNA analysis, enabled us to highlight an unsuspected diversity of microbes living in roots. We identified microbes that are active and direct utilizers of photosynthetic carbon ...

BackgroundIn environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylogenetic analyses and the adoption of the phylogenetic species concept.Such analysis requires that the reference sequences are well identified and deposited in public-access databases. However, many entries in the public sequence databases are problematic in terms of quality and reliability and these data require screening to ensure correct phylogenetic interpretation.Methods and Principal FindingsTo facilitate phylogenetic inferences and phylogenetic assignment, we introduce a fungal sequence database. The database PHYMYCO-DB comprises fungal sequences from GenBank that have been filtered to satisfy stringent sequence quality criteria. For the first release, two widely used molecular taxonomic markers were chosen: the nuclear SSU rRNA and EF1-α gene sequences. Following the automatic extraction and filtration, a manual curation is performed to remove problematic sequences while preserving relevant sequences useful for phylogenetic studies. As a result of curation, ∼20% of the automatically filtered sequences have been removed from the database. To demonstrate how PHYMYCO-DB can be employed, we test a set of environmental Chytridiomycota sequences obtained from deep sea samples.ConclusionPHYMYCO-DB offers the tools necessary to: (i) extract high quality fungal sequences for each of the 5 fungal phyla, at all taxonomic levels, (ii) extract already performed alignments, to act as ‘reference alignments’, (iii) launch alignments of personal sequences along with stored data. A total of 9120 SSU rRNA and 672 EF1-α high-quality fungal sequences are now available.The PHYMYCO-DB is accessible through the URL http://phymycodb.genouest.org/.

Environmental genomics and genome-wide expression approaches deal with large-scale sequence-based information obtained from environmental samples, at organismal, population or community levels. To date, environmental genomics, transcriptomics and proteomics are arguably the most powerful approaches to discover completely novel ecological functions and to link organismal capabilities, organism–environment interactions, functional diversity, ecosystem processes, evolution and Earth history. Thus, environmental genomics is not merely a toolbox of new technologies but also a source of novel ecological concepts and hypotheses. By removing previous dichotomies between ecophysiology, population ecology, community ecology and ecosystem functioning, environmental genomics enables the integration of sequence-based information into higher ecological and evolutionary levels. However, environmental genomics, along with transcriptomics and proteomics, must involve pluridisciplinary research, such as new developments in bioinformatics, in order to integrate high-throughput molecular biology techniques into ecology. In this review, the validity of environmental genomics and post-genomics for studying ecosystem functioning is discussed in terms of major advances and expectations, as well as in terms of potential hurdles and limitations. Novel avenues for improving the use of these approaches to test theory-driven ecological hypotheses are also explored.

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The field of geotechnics is moving fast towards benefiting from new methods and tools to improve the understanding of couplings among complex transport, chemical and biological phenomena. Calcite bio-mineralization, result of bio-grouting, stands out as such a problem where solute and solid transport phenomena, cell attachment, and cell/crystal growth mechanisms hold the key towards the formation of new, improved geo-materials. In the present study, focus is put on the real-time monitoring of the critical evolution of calcite precipitation within long trajectories in microfluidic chips. The total transport path, across which these phenomena are captured and interpreted, ranges between 1 and 1.5 meters to evaluate at which extend calcite crystal growth and deposition varies along the infiltrated porous chips. Results reveal varying number and sizes of crystals which precipitate across the flow path while qualitative characteristics are also discussed. Overall, the study aims to shed light into the previously underexplored, activation of the bio-cementation reaction, which governs nucleation, transport, and growth of calcite mineral binders and, therefore, influences the mechanical response of geo-materials subjected to bio-grouting applications.