Recovering complete and draft population genomes from metagenome datasets.

Assembly of metagenomic sequence data into microbial genomes is of fundamental value to improving our understanding of microbial ecology and metabolism by elucidating the functional potential of hard-to-culture microorganisms. Here, we provide a synthesis of available methods to bin metagenomic contigs into species-level groups and highlight how genetic diversity, sequencing depth, and coverage influence binning success. Despite the computational cost on application to deeply sequenced complex metagenomes (e.g., soil), covarying patterns of contig coverage across multiple datasets significantly improves the binning process. We also discuss and compare current genome validation methods and reveal how these methods tackle the problem of chimeric genome bins i.e., sequences from multiple species. Finally, we explore how population genome assembly can be used to uncover biogeographic trends and to characterize the effect of in situ functional constraints on the genome-wide evolution

Proceedings of the ECCS 2005 satellite workshop: embracing complexity in design - Paris 17 November 2005

Embracing complexity in design is one of the critical issues and challenges of the 21st century. As the realization grows that design activities and artefacts display properties associated with complex adaptive systems, so grows the need to use complexity concepts and methods to understand these properties and inform the design of better artifacts. It is a great challenge because complexity science represents an epistemological and methodological swift that promises a holistic approach in the understanding and operational support of design. But design is also a major contributor in complexity research. Design science is concerned with problems that are fundamental in the sciences in general and complexity sciences in particular. For instance, design has been perceived and studied as a ubiquitous activity inherent in every human activity, as the art of generating hypotheses, as a type of experiment, or as a creative co-evolutionary process. Design science and its established approaches and practices can be a great source for advancement and innovation in complexity science. These proceedings are the result of a workshop organized as part of the activities of a UK government AHRB/EPSRC funded research cluster called Embracing Complexity in Design (www.complexityanddesign.net) and the European Conference in Complex Systems (complexsystems.lri.fr). Embracing complexity in design is one of the critical issues and challenges of the 21st century. As the realization grows that design activities and artefacts display properties associated with complex adaptive systems, so grows the need to use complexity concepts and methods to understand these properties and inform the design of better artifacts. It is a great challenge because complexity science represents an epistemological and methodological swift that promises a holistic approach in the understanding and operational support of design. But design is also a major contributor in complexity research. Design science is concerned with problems that are fundamental in the sciences in general and complexity sciences in particular. For instance, design has been perceived and studied as a ubiquitous activity inherent in every human activity, as the art of generating hypotheses, as a type of experiment, or as a creative co-evolutionary process. Design science and its established approaches and practices can be a great source for advancement and innovation in complexity science. These proceedings are the result of a workshop organized as part of the activities of a UK government AHRB/EPSRC funded research cluster called Embracing Complexity in Design (www.complexityanddesign.net) and the European Conference in Complex Systems (complexsystems.lri.fr)

Lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome

Cinnamoyl-CoA reductase (CCR), an enzyme central to the lignin bio-synthetic pathway, represents a promising biotechnological target to reduce lignin levels and to improve the commercial viability of lignocellulosic biomass. However, silencing of the CCR gene results in considerable flux changes of the general and monolignol-specific lignin pathways, ultimately leading to the accumulation of various extractable phenolic compounds in the xylem. Here, we evaluated host genotype-dependent effects of field-grown, CCR-down-regulated poplar trees (Populus tremula x Populus alba) on the bacterial rhizosphere microbiome and the endosphere microbiome, namely the microbiota present in roots, stems, and leaves. Plant-associated bacteria were isolated from all plant compartments by selective isolation and enrichment techniques with specific phenolic carbon sources (such as ferulic acid) that are up-regulated in CCR-deficient poplar trees. The bacterial microbiomes present in the endosphere were highly responsive to the CCR-deficient poplar genotype with remarkably different metabolic capacities and associated community structures compared with the WT trees. In contrast, the rhizosphere microbiome of CCR-deficient and WT poplar trees featured highly overlapping bacterial community structures and metabolic capacities. We demonstrate the host genotype modulation of the plant microbiome by minute genetic variations in the plant genome. Hence, these interactions need to be taken into consideration to understand the full consequences of plant metabolic pathway engineering and its relation with the environment and the intended genetic improvement