Denis Faure

REVIEW: Predictive ecology in a changing world

1. In a rapidly changing world, ecology has the potential to move from empirical and conceptual stages to application and management issues. It is now possible to make large-scale predictions up to continental or global scales, ranging from the future distribution of biological diversity to changes in ecosystem functioning and services. With these recent developments, ecology has a historical opportunity to become a major actor in the development of a sustainable human society. With this opportunity, however, also comes an important responsibility in developing appropriate predictive models, correctly interpreting their outcomes and communicating their limitations. There is also a danger that predictions grow faster than our understanding of ecological systems, resulting in a gap between the scientists generating the predictions and stakeholders using them (conservation biologists, environmental managers, journalists, policymakers). n2. Here, we use the context provided by the current surge of ecological predictions on the future of biodiversity to clarify what prediction means, and to pinpoint the challenges that should be addressed in order to improve predictive ecological models and the way they are nunderstood and used. n3. Synthesis and applications. Ecologists face several challenges to ensure the healthy development of an operational predictive ecological science: (i) clarity on the distinction between explanatory and anticipatory predictions; (ii) developing new theories at the interface between nexplanatory and anticipatory predictions; (iii) open data to test and validate predictions; (iv) making predictions operational; and (v) developing a genuine ethics of prediction.

Next-generation sequencing as a powerful motor for advances in the biological and environmental sciences

AbstractNext-generation sequencing (NGS) provides unprecedented insight into (meta)genomes, (meta)transcriptomes (cDNA) and (meta)barcodes of individuals, populations and communities of Archaea, Bacteria and Eukarya, as well as viruses. This special issue combines reviews and original papers reporting technical and scientific advances in genomics and transcriptomics of non-model species, as well as quantification and functional analyses of biodiversity using NGS technologies of the second and third generations. In addition, certain papers also exemplify the transition from Sanger to NGS barcodes in molecular taxonomy.n

Environmental microbiology as a mosaic of explored ecosystems and issues

Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium’s efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.

Environmental microbiology reveals the Earth secret life

Environmental microbiology investigates the diversity, dynamics, evolution, functioning, and functions of the microbes in Earth ecosystems. Environmental microbiology is born as the meet of microbiology and environmental sciences. At the earliest times, the environmental microbiology was often associated to the applied microbiology, as attested by the existence of the reference journal Applied and Environmental Microbiology since 1952. In the 1990s, the interest of governments and scientists to the environmental sciences increased. This may be illustrated by the adoption of the United Nations Conference on Environment and Development (Rio de Janeiro, Brazil) in 1992 and the launch of the journal Environmental Science and Pollution Research in 1994. In parallel, milestones in technological advances and discoveries on microbes (diversity, functioning, and key role in ecosystem dynamics) accelerated the development of environmental microbiology as an emerging discipline (Fig. 1). Among the technologies which have reinforced the accessibility to microbes are the polymerase chain reaction (discovered by Kary Mullis in 1986, Nobel price in 1993) and, more recently, the next-generation sequencing in the 2000s (Fig. 1). Many other tools (transcriptomics, proteomics, metabolomics, imagery, isotopes...) and a tight interaction with environmental sciences also contributed to remarkable discoveries on microbes. The launch of the journal Environmental Microbiology in 1999 consecrated visibility of this discipline, which is reinforced in 2007 by the birth of The ISME journal. This journal rapidly became a flagship of the International Society of Microbial Ecology. In France, the environmental microbiology community of scientists was federated by the non-governmental BAssociation Francophone d’Ecologie Microbienne^ (http://mio.pytheas.univ-amu.fr/AFEM/), which was created in 2004 and organizes a biennial meeting, the next being in Anglet (Aquitaine, France) in November 2015. Since 2007, the national program BEcosphère Continentale et Côtière^ (EC2COhttp://www.insu.cnrs.fr/node/1497), which is coordinated by the CNRS (Centre National de la Recherche Scientifique), initiated a recurrent call for supporting researches in environmental microbiology. A launch funding was provided by the CNRS Mission for Interdisciplinary (http://www.cnrs.fr/mi/). From 2007 to 2015, eight annual calls allowed to supports around 120 2year starting projects (Fig. 2). Such a long-term action efficiently structures and boosts the environmental microbiology community and helps its members to access to more important national and international financial supports. This special issue is a collection of 15 key articles selected from environmental microbiology projects funded by CNRSINSU-EC2CO, which explore the secret life of microbes in Earth ecosystem. It combines reviews and original articles reporting technical and scientific advances from the EC2CO Environmental Microbiology community. The paper of Faure et al. (2015) illustrates the intense research devoted by the Microbial ecology EC2CO consortium to explore the biology, Responsible editor: Philippe Garrigues

11 – Modeling and Predicting Behaviors and Dynamics of Ecosystems

The functioning of ecosystems is nowadays understood as the result of interactions between various micro- and macroscopic organisms. These interactions, especially between microorganisms, have significant impacts on ecosystemic services (e.g. nutrient recycling, production of organic matter etc.). Although microbial abundance is a long-known fact, high-throughput genomic data have highlighted an amount of diversity that was unsuspected. These novel descriptions, however, remain one step towards the goal of elucidating, at the molecular level, the functioning of microbial ecosystems. To reach this goal, using dedicated models that mobilize the whole diversity of biotechnology resources is of fundamental importance.

The Omics of the Future

The diversity of scientific issues and methodologies described in the previous chapters clearly shows the dynamism of the international research community working on environmental genomics as well as its commitment to propel the environmental sciences into the integrative field of systems ecology. In this respect, omic technologies not only foster renewed scientific practices and questioning but also pave the way for a novel perspective on social and societal issues. The diversity of expertise in this domain calls for promoting initiatives to a systematically interdisciplinary approach of objects and issues dealing with environmental genomics. It also advocates to foster better sharing of data collection and valorization.

Functional Ecology and Population Genomics

The association of functional ecology and population genomics enables us to relate the knowledge we have of traits linked to essential functions of organisms to the novel knowledge we are acquiring about the structure and expression of genomes. The information collected by the various omics approaches (genomics, transcriptomics, proteomics, metabolomics, etc.) directly sheds light on the functional traits of populations, in tight relation with their interaction with the environment in its biotic and abiotic dimensions. NGS technologies are at the basis of the emergence of new analysis approaches called “ecogenomics” and “reverse ecology”. Beyond functional ecology, these fields of research are expected to propel advances in evolutionary biology, taxonomy, community ecology and chemical ecology, as well as in genomics, physiology, integrative biology, ecotoxicology and ecological engineering.

Technological Revolutions: Possibilities and Limitations

The 21st century has seen a revolution in DNA sequencing technologies. After decades devoted to improving the first-generation DNA sequencing methods, major technological revolution has enabled the emergence of second- and third-generation DNA sequencing methods, and they have quickly become prominent. These new technologies are still in their early stages when advances are expected as the quantity and accuracy of the produced DNA sequences still need improvement.

4 – Accuracy of NGS Data: From Sequence to Databases

Second-generation sequencing led to the production of DNA sequences with considerable throughput rates, but with reduced read lengths and varying error rates. This avalanche of sequences requires the development of new bio-computing tools to ensure that the information is optimally processed. Requirements for archive storage space and computing power are multiplied, which leads to the deployment of new computing infrastructures. The quality and accuracy of the data produced and the relevance of their analysis are now the challenges at stake for environmental genomics.

Evolution and Adaptation of Genes and Genomes

Fine-grained comprehension of the evolutionary history of phenotypic traits requires the identification of their genetic basis. The aim is to discover the genes or genomic structure involved in adaptive evolution, i.e. in response to natural selection. The panel of methodological tools that NGS provides enables the exploration and identification, in the whole genome, of important functional variants with their associated evolutionary or ecological changes, taking into account the confusing effects linked to the specific history of the studied populations.