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Toriyama J.,Japan Forestry and Forest Products Research Institute | Kato T.,Chiyoda Corporation | Siregar C.A.,Forestry Research and Development Agency FORDA | Siringoringo H.H.,Forestry Research and Development Agency FORDA | And 2 more authors.
Forest Ecology and Management | Year: 2011

Soil carbon (C) stocks in forest ecosystems have been widely estimated to a fixed soil depth (i.e., 0-30. cm) to clarify temporal changes in the C pool. However, surface elevations change as a result of compaction or expansion of the soil under forest management and land use. On the other hand, the calculation of soil C stocks based on " equivalent soil mass" is not affected by compaction or expansion of forest soil. To contribute to the development of a forest C accounting methodology, we compared changes in soil C stocks over 4. years between depth- and mass-based approaches using original soil data collected at 0-30. cm depths in young plantations and secondary forests in West Java, Indonesia. Our methodology expanded on the mass-based approach; rather than using one representative value for the mass-based calculation of soil C stocks, we adjusted individual values, maintaining the coefficient of variance in soil mass. We also considered the effect of an increase or decrease in soil organic matter on equivalent soil mass. Both increasing and decreasing trends in soil C stocks became clearer when the mass-based approach was used rather than the depth-based approach. The trends in soil C stocks based on equivalent soil mass were particularly evident in the surface soil layers (0-5. cm) and in plantation sites, compared with those for soil profiles including subsurface soil layers (0-30. cm) and in secondary forests. These trends in soil C stocks corresponded with temporal trends in litter stocks. We suggest that equivalent mass-basis soil C stock for the upper 30. cm of soil be calculated based on multiple soil layers to reduce estimation errors. Changes in soil organic matter mass had little effect on the estimation of soil C stock on an equivalent mass basis. For the development of a forest C accounting system, the mass-based approach should be used to characterize temporal trends in soil C stocks and to improve C cycle models, rather than simpler methods of calculating soil C stocks. These improvements will help to increase the tier level of country-specific forest C accounting systems. © 2011 Elsevier B.V.


Sitepu I.R.,University of California at Davis | Sitepu I.R.,Forestry Research and Development Agency FORDA | Garay L.A.,University of California at Davis | Sestric R.,University of Manitoba | And 4 more authors.
Biotechnology Advances | Year: 2014

Production of biodiesel from edible plant oils is quickly expanding worldwide to fill a need for renewable, environmentally-friendly liquid transportation fuels. Due to concerns over use of edible commodities for fuels, production of biodiesel from non-edible oils including microbial oils is being developed. Microalgae biodiesel is approaching commercial viability, but has some inherent limitations such as requirements for sunlight. While yeast oils have been studied for decades, recent years have seen significant developments including discovery of new oleaginous yeast species and strains, greater understanding of the metabolic pathways that determine oleaginicity, optimization of cultivation processes for conversion of various types of waste plant biomass to oil using oleaginous yeasts, and development of strains with enhanced oil production. This review examines aspects of oleaginous yeasts not covered in depth in other recent reviews. Topics include the history of oleaginous yeast research, especially advances in the early 20th century; the phylogenetic diversity of oleaginous species, beyond the few species commonly studied; and physiological characteristics that should be considered when choosing yeast species and strains to be utilized for conversion of a given type of plant biomass to oleochemicals. Standardized terms are proposed for units that describe yeast cell mass and lipid production. © 2014.


Graham L.L.B.,University of Leicester | Turjaman M.,Forestry Research and Development Agency FORDA | Page S.E.,University of Leicester
Wetlands Ecology and Management | Year: 2013

Tropical peat swamp forests (TPSF) are being rapidly deforested, leading to disturbed hydrology, wildfires and carbon loss. Cost-effective methods are needed to increase the scale of restoration activities. One method is to inoculate seedlings with their corresponding mycorrhizae species, thereby increasing performance during nursery cultivation, although the benefits post-transplantation are less well understood. This study considered two TPSF tree species, Shorea balangeran and Dyera polyphylla (syn. Dyera lowii), and their mycorrhiza; Scleroderma columnare (S. balangeran) and Glomus clarum and Gigaspora decipiens (D. polyphylla). The performance of non-inoculated and inoculated seedlings was compared following transplantation into five forest zones, representing a gradient from intact to degraded TPSF. In the degraded area, both inoculated seedling species supported higher colonization levels compared to non-inoculated seedlings. Both tree species showed high survival rates in all forest zones, and survival, growth and biomass production were not affected by mycorrhizal treatment. Both species grew faster and accumulated greater biomass in the more degraded forest zones. Nitrogen and phosphorus content reduced for both tree species in the more degraded forest zones, however, inoculated D. polyphylla seedlings had higher nutrient content across all forest zones, as did S. balangeran though less uniformly. Both these tree species are therefore suitable for reforesting degraded TPSF and mycorrhizal inoculation is recommended given a) inoculated seedlings in the degraded area permitted a higher mycorrhizal colonization level, and b) mycorrhizae increased nutrient uptake in the transplanted seedlings, although in this short-term study survival or growth improvement in the inoculated seedlings was not apparent. © 2013 Springer Science+Business Media Dordrecht.


Kallio M.H.,Center for International Forestry Research | Kanninen M.,Center for International Forestry Research | Rohadi D.,Forestry Research and Development Agency FORDA
Forests Trees and Livelihoods | Year: 2011

The differences in socio-economic and perceptional characteristics between tree planting and nontree planting farmers were analysed in four case studies from three provinces in Indonesia. For each case study, the paper describes: a) the reasons for planting or not planting trees, b) how the income received from wood was used, c) the main disadvantages related to tree planting, and d) farmers willingness to continue tree planting under the current arrangements. The tree planters were mainly the farmers with more land; higher value of total assets; and with more active participation in farmer's groups or other social organizations. Long rotation length, lack of capital, low wood prices, and poor access to production inputs or markets affected farmers' willingness to plant trees in the future. Policies are needed that are conducive to the establishment of markets for fiber and timber with fair and reasonable pricing structures. © 2011 A B Academic Publishers-Printed in Great Britain.


Sitepu I.R.,University of California at Davis | Sitepu I.R.,Forestry Research and Development Agency FORDA | Jin M.,Michigan State University | Fernandez J.E.,University of California at Davis | And 3 more authors.
Applied Microbiology and Biotechnology | Year: 2014

Microbial oil is a potential alternative to food/plant-derived biodiesel fuel. Our previous screening studies identified a wide range of oleaginous yeast species, using a defined laboratory medium known to stimulate lipid accumulation. In this study, the ability of these yeasts to grow and accumulate lipids was further investigated in synthetic hydrolysate (SynH) and authentic ammonia fiber expansion (AFEX™)-pretreated corn stover hydrolysate (ACSH). Most yeast strains tested were able to accumulate lipids in SynH, but only a few were able to grow and accumulate lipids in ACSH medium. Cryptococcus humicola UCDFST 10-1004 was able to accumulate as high as 15.5 g/L lipids, out of a total of 36 g/L cellular biomass when grown in ACSH, with a cellular lipid content of 40 % of cell dry weight. This lipid production is among the highest reported values for oleaginous yeasts grown in authentic hydrolysate. Preculturing in SynH media with xylose as sole carbon source enabled yeasts to assimilate both glucose and xylose more efficiently in the subsequent hydrolysate medium. This study demonstrates that ACSH is a suitable medium for certain oleaginous yeasts to convert lignocellullosic sugars to triacylglycerols for production of biodiesel and other valuable oleochemicals. © 2014 Springer-Verlag.


Race D.,Australian National University | Sumirat B.,Forestry Research and Development Agency FORDA
International Journal of Sustainable Development | Year: 2015

Community forestry has been developed internationally as a policy response to reduce deforestation and to improve the livelihoods of forest-dependent communities. This article discusses the social dimension of community forestry, and uses the concept of social capital to analyse the implications of social inequalities in two community forestry initiatives in Indonesia. The article concludes with some revealing insights about the: 1) temporal nature of social capital in community forestry; 2) ways social capital can entrench inequalities; 3) role of 'outsiders' assisting the development of community forestry. Copyright © 2015 Inderscience Enterprises Ltd.


Sitepu I.,University of California at Davis | Sitepu I.,Forestry Research and Development Agency FORDA | Selby T.,University of California at Davis | Lin T.,University of California at Davis | And 2 more authors.
Journal of Industrial Microbiology and Biotechnology | Year: 2014

Conversion of lignocellulosic hydrolysates to lipids using oleaginous (high lipid) yeasts requires alignment of the hydrolysate composition with the characteristics of the yeast strain, including ability to utilize certain nutrients, ability to grow independently of costly nutrients such as vitamins, and ability to tolerate inhibitors. Some combination of these characteristics may be present in wild strains. In this study, 48 oleaginous yeast strains belonging to 45 species were tested for ability to utilize carbon sources associated with lignocellulosic hydrolysates, tolerate inhibitors, and grow in medium without supplemented vitamins. Some well-studied oleaginous yeast species, as well as some that have not been frequently utilized in research or industrial production, emerged as promising candidates for industrial use due to ability to utilize many carbon sources, including Cryptococcus aureus, Cryptococcus laurentii, Hannaella aff. zeae, Tremella encephala, and Trichosporon coremiiforme. Other species excelled in inhibitor tolerance, including Candida aff. tropicalis, Cyberlindnera jadinii, Metschnikowia pulcherrima, Schwanniomyces occidentalis and Wickerhamomyces ciferrii. No yeast tested could utilize all carbon sources and tolerate all inhibitors tested. These results indicate that yeast strains should be selected based on characteristics compatible with the composition of the targeted hydrolysate. Other factors to consider include the production of valuable co-products such as carotenoids, availability of genetic tools, biosafety level, and flocculation of the yeast strain. The data generated in this study will aid in aligning yeasts with compatible hydrolysates for conversion of carbohydrates to lipids to be used for biofuels and other oleochemicals. © 2014 Society for Industrial Microbiology and Biotechnology.


Sitepu I.R.,University of California at Davis | Sitepu I.R.,Forestry Research and Development Agency FORDA | Shi S.,University of California at Davis | Simmons B.A.,Joint BioEnergy Institute | And 6 more authors.
FEMS Yeast Research | Year: 2014

Lignocellulosic plant biomass is the target feedstock for production of second-generation biofuels. Ionic liquid (IL) pretreatment can enhance deconstruction of lignocellulosic biomass into sugars that can be fermented to ethanol. Although biomass is typically washed following IL pretreatment, small quantities of residual IL can inhibit fermentative microorganisms downstream, such as the widely used ethanologenic yeast, Saccharomyces cerevisiae. The aim of this study was to identify yeasts tolerant to the IL 1-ethyl-3-methylimidazolium acetate, one of the top performing ILs known for biomass pretreatment. One hundred and sixty eight strains spanning the Ascomycota and Basidiomycota phyla were selected for screening, with emphasis on yeasts within or closely related to the Saccharomyces genus and those tolerant to saline environments. Based on growth in media containing 1-ethyl-3-methylimidazolium acetate, tolerance to IL levels ranging 1-5% was observed for 80 strains. The effect of 1-ethyl-3-methylimidazolium acetate concentration on maximum cell density and growth rate was quantified to rank tolerance. The most tolerant yeasts included strains from the genera Clavispora, Debaryomyces, Galactomyces, Hyphopichia, Kazachstania, Meyerozyma, Naumovozyma, Wickerhamomyces, Yarrowia, and Zygoascus. These yeasts included species known to degrade plant cell wall polysaccharides and those capable of ethanol fermentation. These yeasts warrant further investigation for use in saccharification and fermentation of IL-pretreated lignocellulosic biomass to ethanol or other products. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.


Sitepu I.R.,University of California at Davis | Sitepu I.R.,Forestry Research and Development Agency FORDA | Ignatia L.,University of California at Davis | Franz A.K.,University of California at Davis | And 5 more authors.
Journal of Microbiological Methods | Year: 2012

A rapid and inexpensive method for estimating lipid content of yeasts is needed for screening large numbers of yeasts samples. Nile red is a fluorescent lipophilic dye used for detection and quantification of intracellular lipid droplets in various biological system including algae, yeasts and filamentous fungi. However, a published assay for yeast is affected by variable diffusion across the cell membrane, and variation in the time required to reach maximal fluorescence emission. In this study, parameters that may influence the emission were varied to determine optimal assay conditions. An improved assay with a high-throughput capability was developed that includes the addition of dimethyl sulfoxide (DMSO) solvent to improve cell permeability, elimination of the washing step, the reduction of Nile red concentration, kinetic readings rather than single time-point reading, and utilization of a black 96-well microplate. The improved method was validated by comparison to gravimetric determination of lipid content of a broad variety of ascomycete and basidiomycete yeast species. © 2012 Elsevier B.V.


Sitepu I.R.,University of California at Davis | Sitepu I.R.,Forestry Research and Development Agency FORDA | Sestric R.,University of Manitoba | Ignatia L.,University of California at Davis | And 5 more authors.
Bioresource Technology | Year: 2013

Oleaginous yeasts have been studied for oleochemical production for over 80. years. Only a few species have been studied intensely. To expand the diversity of oleaginous yeasts available for lipid research, we surveyed a broad diversity of yeasts with indicators of oleaginicity including known oleaginous clades, and buoyancy. Sixty-nine strains representing 17 genera and 50 species were screened for lipid production. Yeasts belonged to Ascomycota families, Basidiomycota orders, and the yeast-like algal genus Prototheca. Total intracellular lipids and fatty acid composition were determined under different incubation times and nitrogen availability. Thirteen new oleaginous yeast species were discovered, representing multiple ascomycete and basidiomycete clades. Nitrogen starvation generally increased intracellular lipid content. The fatty acid profiles varied with the growth conditions regardless of taxonomic affiliation. The dominant fatty acids were oleic acid, palmitic acid, linoleic acid, and stearic acid. Yeasts and culture conditions that produced fatty acids appropriate for biodiesel were identified. © 2013 Elsevier Ltd.

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