Rapid and effective oxidative pretreatment of woody biomass at mild reaction conditions and low oxidant loadings

BACKGROUND: One route for producing cellulosic biofuels is by the fermentation of lignocellulose-derived sugars generated from a pretreatment that can be effectively coupled with an enzymatic hydrolysis of the plant cell wall. While woody biomass exhibits a number of positive agronomic and logistical attributes, these feedstocks are significantly more recalcitrant to chemical pretreatments than herbaceous feedstocks, requiring higher chemical and energy inputs to achieve high sugar yields from enzymatic hydrolysis. We previously discovered that alkaline hydrogen peroxide (AHP) pretreatment catalyzed by copper(II) 2,2΄-bipyridine complexes significantly improves subsequent enzymatic glucose and xylose release from hybrid poplar heartwood and sapwood relative to uncatalyzed AHP pretreatment at modest reaction conditions (room temperature and atmospheric pressure). In the present work, the reaction conditions for this catalyzed AHP pretreatment were investigated in more detail with the aim of better characterizing the relationship between pretreatment conditions and subsequent enzymatic sugar release. RESULTS: We found that for a wide range of pretreatment conditions, the catalyzed pretreatment resulted in significantly higher glucose and xylose enzymatic hydrolysis yields (as high as 80% for both glucose and xylose) relative to uncatalyzed pretreatment (up to 40% for glucose and 50% for xylose). We identified that the extent of improvement in glucan and xylan yield using this catalyzed pretreatment approach was a function of pretreatment conditions that included H(2)O(2) loading on biomass, catalyst concentration, solids concentration, and pretreatment duration. Based on these results, several important improvements in pretreatment and hydrolysis conditions were identified that may have a positive economic impact for a process employing a catalyzed oxidative pretreatment. These improvements include identifying that: (1) substantially lower H(2)O(2) loadings can be used that may result in up to a 50-65% decrease in H(2)O(2) application (from 100 mg H(2)O(2)/g biomass to 35–50 mg/g) with only minor losses in glucose and xylose yield, (2) a 60% decrease in the catalyst concentration from 5.0 mM to 2.0 mM (corresponding to a catalyst loading of 25 μmol/g biomass to 10 μmol/g biomass) can be achieved without a subsequent loss in glucose yield, (3) an order of magnitude improvement in the time required for pretreatment (minutes versus hours or days) can be realized using the catalyzed pretreatment approach, and (4) enzyme dosage can be reduced to less than 30 mg protein/g glucan and potentially further with only minor losses in glucose and xylose yields. In addition, we established that the reaction rate is improved in both catalyzed and uncatalyzed AHP pretreatment by increased solids concentrations. CONCLUSIONS: This work explored the relationship between reaction conditions impacting a catalyzed oxidative pretreatment of woody biomass and identified that significant decreases in the H(2)O(2), catalyst, and enzyme loading on the biomass as well as decreases in the pretreatment time could be realized with only minor losses in the subsequent sugar released enzymatically. Together these changes would have positive implications for the economics of a process based on this pretreatment approach

Why Orange Guaymas Basin Beggiatoa spp. Are Orange: Single-Filament-Genome-Enabled Identification of an Abundant Octaheme Cytochrome with Hydroxylamine Oxidase, Hydrazine Oxidase, and Nitrite Reductase Activities

ABSTRACT Orange, white, and yellow vacuolated Beggiatoaceae filaments are visually dominant members of microbial mats found near sea floor hydrothermal vents and cold seeps, with orange filaments typically concentrated toward the mat centers. No marine vacuolate Beggiatoaceae are yet in pure culture, but evidence to date suggests they are nitrate-reducing, sulfide-oxidizing bacteria. The nearly complete genome sequence of a single orange Beggiatoa (“ Candidatus Maribeggiatoa”) filament from a microbial mat sample collected in 2008 at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) was recently obtained. From this sequence, the gene encoding an abundant soluble orange-pigmented protein in Guaymas Basin mat samples (collected in 2009) was identified by microcapillary reverse-phase high-performance liquid chromatography (HPLC) nano-electrospray tandem mass spectrometry (μLC–MS-MS) of a pigmented band excised from a denaturing polyacrylamide gel. The predicted protein sequence is related to a large group of octaheme cytochromes whose few characterized representatives are hydroxylamine or hydrazine oxidases. The protein was partially purified and shown by in vitro assays to have hydroxylamine oxidase, hydrazine oxidase, and nitrite reductase activities. From what is known of Beggiatoaceae physiology, nitrite reduction is the most likely in vivo role of the octaheme protein, but future experiments are required to confirm this tentative conclusion. Thus, while present-day genomic and proteomic techniques have allowed precise identification of an abundant mat protein, and its potential activities could be assayed, proof of its physiological role remains elusive in the absence of a pure culture that can be genetically manipulated

Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga \u3ci\u3eNannochloropsis oceanica\u3c/i\u3e CCMP1779

Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high-value lipid products. First success in applying reverse genetics by targeted gene replacement makes Nannochloropsis oceanica an attractive model to investigate the cell and molecular biology and biochemistry of this fascinating organism group. Here we present the assembly of the 28.7 Mb genome of N. oceanica CCMP1779. RNA sequencing data from nitrogen-replete and nitrogendepleted growth conditions support a total of 11,973 genes, of which in addition to automatic annotation some were manually inspected to predict the biochemical repertoire for this organism. Among others, more than 100 genes putatively related to lipid metabolism, 114 predicted transcription factors, and 109 transcriptional regulators were annotated. Comparison of the N. oceanica CCMP1779 gene repertoire with the recently published N. gaditana genome identified 2,649 genes likely specific to N. oceanica CCMP1779. Many of these N. oceanica–specific genes have putative orthologs in other species or are supported by transcriptional evidence. However, because similarity-based annotations are limited, functions of most of these species-specific genes remain unknown. Aside from the genome sequence and its analysis, protocols for the transformation of N. oceanica CCMP1779 are provided. The availability of genomic and transcriptomic data for Nannochloropsis oceanica CCMP1779, along with efficient transformation protocols, provides a blueprint for future detailed gene functional analysis and genetic engineering of Nannochloropsis species by a growing academic community focused on this genus