Omics Approaches for Designing Biofuel Producing Cocultures for Enhanced Microbial Conversion of Lignocellulosic Substrates

Levin, David B.; Verbeke, Tobin J.; Munir, Riffat; Islam, Rumana; Ramachandran, Umesh; Lal, Sadhana; Schellenberg, John; Sparling, Richard

doi:10.1016/b978-0-444-59592-8.00017-8

Cited by 15 publications

(9 citation statements)

References 93 publications

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“…Within the family Lachnospiraceae, the lower GI tract of Abert's squirrels had higher abundance and diversity within the genus Marvinbryantia , with four ASVs represented in the lower core microbiome (compared to one in fox squirrels), all of which were in higher abundance in Abert's squirrels relative to fox squirrels. The one currently described species in this genus, Marvinbryantia formatexigens , is known to have cellulolytic capabilities (Levin et al, ). Thus, the presence of several undescribed representatives of this genus in the lower GI tract of Abert's squirrels highlights potential involvement in facilitating digestion of the high‐fiber diet of Abert's squirrels.…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species (Sciurus aberti and S. niger) living in sympatry

Reed

Pigage

et al. 2019

Ecology and Evolution

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Microbiota inhabiting the gastrointestinal (GI) tract of animals has important impacts on many host physiological processes. Although host diet is a major factor influencing the composition of the gut micro‐organismal community, few comparative studies have considered how differences in diet influence community composition across the length of the GI tract. We used 16S sequencing to compare the microbiota along the length of the GI tract in Abert's (Sciurus aberti) and fox squirrels (S. niger) living in the same habitat. While fox squirrels are generalist omnivores, the diet of Abert's squirrels is unusually high in plant fiber, particularly in winter when they extensively consume fiber‐rich inner bark of ponderosa pine (Pinus ponderosa). Consistent with previous studies, microbiota of the upper GI tract of both species consisted primarily of facultative anaerobes and was less diverse than that of the lower GI tract, which included mainly obligate anaerobes. While we found relatively little differentiation between the species in the microbiota of the upper GI tract, the community composition of the lower GI tract was clearly delineated. Notably, the Abert's squirrel lower GI community was more stable in composition and enriched for microbes that play a role in the degradation of plant fiber. In contrast, overall microbial diversity was higher in fox squirrels. We hypothesize that these disparities reflect differences in diet quality and diet breadth between the species.

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Section: Discussionmentioning

confidence: 99%

Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species (Sciurus aberti and S. niger) living in sympatry

Reed

Pigage

et al. 2019

Ecology and Evolution

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“…Another highly transcribed Ruminococcus -related PG (SC.Bin1) in the early growth phase in the SWH-C-35 culture was phylogenetic closely related to Eubacterium siraeum V10Sc8a, Ruminococcus flavefaciens FD1 and Ruminococcus sp. 18P13, all of which have been reported to have potential cellulolytic functions [ 68 , 69 ], and close relatives of which have been detected in cellulolytic biogas reactors [ 70 ]. However, no cellulosome-related transcripts were detected in the SC.Bin1 transcriptome (Additional file 6 ), although R. flavefaciens has been reported to use cellulosomes to degrade cellulose in cow rumens [ 69 ], indicating phylogenetically close populations might still adopt different cellulose hydrolysis mechanisms.…”

Section: Discussionmentioning

confidence: 99%

Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion

Jia

et al. 2018

Biotechnol Biofuels

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BackgroundAlthough anaerobic digestion for biogas production is used worldwide in treatment processes to recover energy from carbon-rich waste such as cellulosic biomass, the activities and interactions among the microbial populations that perform anaerobic digestion deserve further investigations, especially at the population genome level. To understand the cellulosic biomass-degrading potentials in two full-scale digesters, this study examined five methanogenic enrichment cultures derived from the digesters that anaerobically digested cellulose or xylan for more than 2 years under 35 or 55 °C conditions.ResultsMetagenomics and metatranscriptomics were used to capture the active microbial populations in each enrichment culture and reconstruct their meta-metabolic network and ecological roles. 107 population genomes were reconstructed from the five enrichment cultures using a differential coverage binning approach, of which only a subset was highly transcribed in the metatranscriptomes. Phylogenetic and functional convergence of communities by enrichment condition and phase of fermentation was observed for the highly transcribed populations in the metatranscriptomes. In the 35 °C cultures grown on cellulose, Clostridium cellulolyticum-related and Ruminococcus-related bacteria were identified as major hydrolyzers and primary fermenters in the early growth phase, while Clostridium leptum-related bacteria were major secondary fermenters and potential fatty acid scavengers in the late growth phase. While the meta-metabolism and trophic roles of the cultures were similar, the bacterial populations performing each function were distinct between the enrichment conditions.ConclusionsOverall, a population genome-centric view of the meta-metabolism and functional roles of key active players in anaerobic digestion of cellulosic biomass was obtained. This study represents a major step forward towards understanding the microbial functions and interactions at population genome level during the microbial conversion of lignocellulosic biomass to methane. The knowledge of this study can facilitate development of potential biomarkers and rational design of the microbiome in anaerobic digesters.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1121-0) contains supplementary material, which is available to authorized users.

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“…CBP is a promising alternative approach, in which cellulase production, enzymatic saccharification and microbial fermentation are consolidated in a single unit operation (consolidated bioprocess, Figure 4) (Minty and Lin, 2015). Such approaches could improve the economic feasibility of jet biofuel synthesis through reduced feedstock processing complexity, lower energy requirements and increased conversion efficiency compared to multiple units (Levin et al, 2015). FIGURE 4 | Bioprocessing methods for the conversion of lignocellulosic biomass to advanced jet fuel feedstocks.…”

Section: Bioprocessing Strategies For Biojet Fuel Production From Ligmentioning

confidence: 99%

Sustainable Production of Microbial Isoprenoid Derived Advanced Biojet Fuels Using Different Generation Feedstocks: A Review

Walls

Rios‐Solis

2020

Front. Bioeng. Biotechnol.

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As the fastest mode of transport, the aircraft is a major driver for globalization and economic growth. The development of alternative advanced liquid fuels is critical to sustainable development within the sector. Such fuels should be compatible with existing infrastructure and derived from second generation feedstocks to avoid competition with food markets. With properties similar to petroleum based fuels, isoprenoid derived compounds such as limonene, bisabolane, farnesane, and pinene dimers are of increasing interest as "drop-in" replacement jet fuels. In this review potential isoprenoid derived jet fuels and progress toward their microbial production was discussed in detail. Although substantial advancements have been achieved, the use of first generation feedstocks remains ubiquitous. Lignocellulosic biomass is the most abundant raw material available for biofuel production, however, technological constraints associated with its pretreatment and saccharification hinder its economic feasibility for low-value commodity production. Non-conventional microbes with novel characteristics including cellulolytic bacteria and fungi capable of highly efficient lignocellulose degradation and xylose fermenting oleaginous yeast with enhanced ligninassociated inhibitor tolerance were investigated as alternatives to traditional model hosts. Finally, innovative bioprocessing methods including consolidated bioprocessing and sequential bioreactor approaches, with potential to capitalize on such unique natural capabilities were considered.

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Omics Approaches for Designing Biofuel Producing Cocultures for Enhanced Microbial Conversion of Lignocellulosic Substrates

Cited by 15 publications

References 93 publications

Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species (Sciurus aberti and S. niger) living in sympatry

Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species (Sciurus aberti and S. niger) living in sympatry

Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion

Sustainable Production of Microbial Isoprenoid Derived Advanced Biojet Fuels Using Different Generation Feedstocks: A Review

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