Yeast diversity in relation to the production of fuels and chemicals

In addition to ethanol, yeasts have the potential to produce many other industrially-relevant chemicals from numerous different carbon sources. However there remains a paucity of information about overall capability across the yeast family tree. Here, 11 diverse species of yeasts with genetic backgrounds representative of different branches of the family tree were investigated. They were compared for their abilities to grow on a range of sugar carbon sources, to produce potential platform chemicals from such substrates and to ferment hydrothermally pretreated rice straw under simultaneous saccharification and fermentation conditions. The yeasts differed considerably in their metabolic capabilities and production of ethanol. A number could produce significant amounts of ethyl acetate, arabinitol, glycerol and acetate in addition to ethanol, including from hitherto unreported carbon sources. They also demonstrated widely differing efficiencies in the fermentation of sugars derived from pre-treated rice straw biomass and differential sensitivities to fermentation inhibitors. A new catabolic property of Rhodotorula mucilaginosa (NCYC 65) was discovered in which sugar substrate is cleaved but the products are not metabolised. We propose that engineering this and some of the other properties discovered in this study and transferring such properties to conventional industrial yeast strains could greatly expand their biotechnological utility

Multilocus Phylogenetic Study of the Scheffersomyces Yeast Clade and Characterization of the N-Terminal Region of Xylose Reductase Gene

Many of the known xylose-fermenting (X-F) yeasts are placed in the Scheffersomyces clade, a group of ascomycete yeasts that have been isolated from plant tissues and in association with lignicolous insects. We formally recognize fourteen species in this clade based on a maximum likelihood (ML) phylogenetic analysis using a multilocus dataset. This clade is divided into three subclades, each of which exhibits the biochemical ability to ferment cellobiose or xylose. New combinations are made for seven species of Candida in the clade, and three X-F taxa associated with rotted hardwood are described: Scheffersomyces illinoinensis (type strain NRRL Y-48827T  =  CBS 12624), Scheffersomyces quercinus (type strain NRRL Y-48825T  =  CBS 12625), and Scheffersomyces virginianus (type strain NRRL Y-48822T  =  CBS 12626). The new X-F species are distinctive based on their position in the multilocus phylogenetic analysis and biochemical and morphological characters. The molecular characterization of xylose reductase (XR) indicates that the regions surrounding the conserved domain contain mutations that may enhance the performance of the enzyme in X-F yeasts. The phylogenetic reconstruction using XYL1 or RPB1 was identical to the multilocus analysis, and these loci have potential for rapid identification of cryptic species in this clade

New methods for impact assessment of biotic-resource depletion in life cycle assessment of fisheries : theory and application

It is difficult to address all of the direct environmental impacts of fisheries using conventional methods of Life Cycle Assessment (LCA). A methodological framework was developed that calculates regionalised characterisation factors for biomass uptake by fishing activities to assess impacts of biotic-resource depletion at both species and ecosystem levels. These two levels were studied to include effects of catch on the collapse of a particular stock of a given species and on total biomass availability in oceans. Characterisation factors were calculated for 127 fish species and 88 marine provinces. The compatibility of this method with other frameworks is discussed, as well as the methodological limitations. The method was applied to two contrasting examples from fisheries (Northern Atlantic albacore tuna and Northern Argentine anchovy). The impacts of one tonne of tuna on biotic natural resources were 4 and 14 times as high as those of anchovy at the ecosystem and species levels, respectively. The application demonstrates that the method is relevant, as it addresses a topic of global interest and fills a gap in LCA impact assessment to contrast impacts of removals of different fish species in terms of biotic natural resource depletion

Sea-use impact category in life cycle assessment : state of the art and perspectives

The present study provides a review on sea-use impacts and how they are handled in life cycle assessments (LCA). It aims at defining the impact pathways for occupation and transformation impacts on marine ecosystems due to human activities (constructions, fishing, aquaculture, navigation). First, a review was performed on human interventions leading to environmental impacts in marine areas and on additional fishery-related impact categories used in LCA of seafood, in order to identify the main methodological deficiencies existing in LCA of seafood products. Second, the sea-use impact category has been defined, by detailing the human interventions leading to impacts on the marine environment and which should be accounted for in LCA. Subsequently, the identification and description of the possible impact pathways linking activities and interventions to impact categories are carried out at endpoint and midpoint levels. This assessment has been based on a review of existing methods of land use, and suggests the use of certain indicators, which could be available for different types of marine activities and ecosystems. This study highlights the needs to account for impacts of human activities due to sea use. Additional indicators have often been added in LCA of seafood, to assess the impacts of seafloor destruction and biomass removal. By extending the scope to other activities than fisheries, many interventions lead to impacts on marine ecosystems: biomass removal and benthic construction, invasive species release, shading, artificial habitat creation, noise, turbidity, and changes in original habitat availability. The impact pathway definition and the identification of the most relevant methods for sea use highlighted the need to assess impacts on ecosystem services (life support functions, global material cycling, and detoxification of pollutants) and on biodiversity as well as biotic resource depletion. A consensus for biotic resource depletion assessment still needs to be found despite recent innovative proposals. For the sea-use impact assessment, methods using species-area relationships, as well as methods focusing on ecosystem services, appear particularly relevant. In a context of strong marine resource overexploitation, and limited marine biodiversity data, the deficiencies in biomass production capability (provisioning services) could be the first stage of sea-use development

Sea use impact category in life cycle assessment : characterization factors for life support functions

The impact of human activities on marine environments is poorly addressed by the scope of life cycle impact assessment (LCIA). The aim of this study is to provide characterization factors to assess impacts of sea use such as fishing activities or seafloor destruction and transformation on the life support functions of marine ecosystems. The consensual framework of land use for ecosystem services damage potential assessment was applied, according to the recent United Nations Environment Programme-Society for Environmental Toxicology and Chemistry (UNEP-SETAC) guidelines, using the free net primary production as a quality index of life support functions. The impact of shading, biomass removal, seafloor destruction, and artificial habitat creation on the available quantity of organic biomass for the ecosystem functioning was quantified at the midpoint level with a common unit (kg of organic carbon equivalent). It included effects of human interventions on both the ecosystem production potential and the stock of biomass present within the ecosystem. Characterization factors (CF) for biomass removal vary from 0.1 kg(Ceq) kg(-1) for seaweed to 111.1 kg(Ceq) kg(-1) for tunas, bonitos, and billfishes. CF for seafloor destruction range from 0.164 kg(Ceq) m(-2) for a temperate seagrass ecosystem to 0.342 kg(Ceq) m(-2) for an intertidal tropical rocky habitat. This study provides an operational method in order to compute sea use impact assessment

Control of start-up and operation of anaerobic biofilm reactors: An overview of 15 years of research

International audienceAnaerobic biofilm reactors have to be operated in a way that optimizes on one hand the start-up period by a quick growth of an active biofilm, on the other hand the regular operation by an active control of the biofilm to avoid diffusion limitations and clogging. This article is an overview of the research carried out at INRA-LBE for the last 15 years. The start-up of anaerobic biofilm reactors may be considerably shortened by applying a short inoculation period (i.e. contact between the inoculum and the support media). Then, the increase of the organic loading rate should be operated at a short hydraulic retention time and low hydrodynamic constraints in order to favor biofilm growth. After the start-up period, biofilm growth should be controlled to maintain a high specific activity and prevent clogging. This can be done in particulate biofilm systems by using hydrodynamics to increase or decrease shear forces and attrition but is much more difficult in anaerobic fixed bed reactors

Encapsulation enhances protoplast fusant stability

A barrier to cost-efficient biomanufacturing is the instability of engineered genetic elements, such as plasmids. Instability can also manifest at the whole-genome level, when fungal dikaryons revert to parental species due to nuclear segregation during cell division. Here, we show that by encapsulating Saccharomyces cerevisiae-Pichia stipitis dikaryons in an alginate matrix, we can limit cell division and preserve their expanded metabolic capabilities. As a proxy to cellulosic ethanol production, we tested the capacity of such cells to carry out ethanologenic fermentation of glucose and xylose, examining substrate use, ploidy, and cell viability in relation to planktonic fusants, as well as in relation to planktonic and encapsulated cell cultures consisting of mixtures of these species. Glucose and xylose consumption and ethanol production by encapsulated dikaryons were greater than planktonic controls. Simultaneous co-fermentation did not occur; rather the order and kinetics of glucose and xylose catabolism by encapsulated dikaryons were similar to cultures where the two species were encapsulated together. Over repeated cycles of fed-batch culture, encapsulated S. cerevisiae-P. stipitis fusants exhibited a dramatic increase in genomic stability, relative to planktonic fusants. Encapsulation also increased the stability of antibiotic-resistance plasmids used to mark each species and preserved a fixed ratio of S. cerevisiae to P. stipitis cells in mixed cultures. Our data demonstrate how encapsulating cells in an extracellular matrix restricts cell division and, thereby, preserves the stability and biological activity of entities ranging from genomes to plasmids to mixed populations, each of which can be essential to cost-efficient biomanufacturing