Do diet and taxonomy influence insect gut bacterial communities?

Many insects contain diverse gut microbial communities. While several studies have focused on a single or small group of species, comparative studies of phylogenetically diverse hosts can illuminate general patterns of host–microbiota associations. In this study, we tested the hypotheses that (i) host diet and (ii) host taxonomy structure intestinal bacterial community composition among insects. We used published 16S rRNA gene sequence data for 58 insect species in addition to four beetle species sampled from the Sevilleta National Wildlife Refuge to test these hypotheses. Overall, gut bacterial species richness in these insects was low. Decaying wood xylophagous insects harboured the richest bacterial gut flora (102.8 species level operational taxonomic units (OTUs)/sample ± 71.7, 11.8 ± 5.9 phylogenetic diversity (PD)/sample), while bees and wasps harboured the least rich bacterial communities (11.0 species level OTUs/sample ± 5.4, 2.6 ± 0.8 PD/sample). We found evidence to support our hypotheses that host diet and taxonomy structure insect gut bacterial communities (P < 0.001 for both). However, while host taxonomy was important in hymenopteran and termite gut community structure, diet was an important community structuring factor particularly for insect hosts that ingest lignocellulose‐derived substances. Our analysis provides a baseline comparison of insect gut bacterial communities from which to test further hypotheses concerning proximate and ultimate causes of these associations.     

Culture-Independent Phylogenetic Analysis of the Microbial Community in Industrial Sugarcane Bagasse Feedstock Piles

Sugarcane bagasse is an important lignocellulosic by-product with potential for conversion to biofuels and chemicals in biorefinery. As a step towards an understanding of microbial diversity and the processes existing in bagasse collection sites, the microbial community in industrial bagasse feedstock piles was investigated. Molecular biodiversity analysis of 16S rDNA sequences revealed the presence of a complex bacterial community. A diverse group of mainly aerobic and facultative anaerobic bacteria was identified reflecting the aerobic and high temperature microenvironmental conditions under the pile surface. The major bacterial taxa present were identified as Firmicutes, Alpha- and Gammaproteobacteria, Acidobacteria, Bacteroidetes, and Actinobacteria. Analysis of the eukaryotic microbial assemblage based on an internal transcribed spacer revealed the predominance of diverse cellulolytic and hemicellulolytic ascomycota. A microbial interaction model is proposed, focusing on lignocellulose degradation and methane metabolism. The insights into the microbial community in this study provide a basis for efficient utilization of bagasse in lignocellulosic biomass-based industries.     

Techno‐economic analysis for incorporating a liquid–liquid extraction system to remove acetic acid into a proposed commercial scale biorefinery

Mitigating the effect of fermentation inhibitors in bioethanol plants can have a great positive impact on the economy of this industry. Liquid–liquid extraction (LLE) using ethyl acetate is able to remove fermentation inhibitors—chiefly, acetic acid—from an aqueous solution used to produce bioethanol. The fermentation broth resulting from LLE has higher performance for ethanol yield and its production rate. Previous techno‐economic analyses focused on second‐generation biofuel production did not address the impact of removing the fermentation inhibitors on the economic performance of the biorefinery. A comprehensive analysis of applying a separation system to mitigate the fermentation inhibition effect and to provide an analysis on the economic impact of removal of acetic acid from corn stover hydrolysate on the overall revenue of the biorefinery is necessary. This study examines the pros and cons associated with implementing LLE column along with the solvent recovery system into a commercial scale bioethanol plant. Using details from the NREL‐developed model of corn stover biorefinery, the capital costs associated with the equipment and the operating cost for the use of solvent were estimated and the results were compared with the profit gain due to higher ethanol production. Results indicate that the additional capital will add 1% to the total capital and manufacturing cost will increase by 5.9%. The benefit arises from the higher ethanol production rate and yield as a consequence of inhibitor extraction and results in a $0.35 per gallon reduction in the minimum ethanol selling price (MESP). © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:971–977, 2016     

Environmental and economic analysis of the fully integrated biorefinery

Cellulosic biofuel systems have the potential to significantly reduce the environmental impact of the world's transportation energy requirements. However, realizing this potential will require systems level thinking and scale integration. Until now, we have lacked modeling tools for studying the behavior of integrated cellulosic biofuel systems. In this paper, we describe a new research tool, the Biorefinery and Farm Integration Tool (BFIT) in which the production of fuel ethanol from cellulosic biomass is integrated with crop and animal (agricultural) production models. Uniting these three subsystems in a single combined model has allowed, for the first time, basic environmental and economic analysis of biomass production, possible secondary products, fertilizer production, and bioenergy production across various regions of the United States. Using BFIT, we simulate cellulosic ethanol production embedded in realistic agricultural landscapes in nine locations under a collection of farm management scenarios. This combined modeling approach permits analysis of economic profitability and highlights key areas for environmental improvement. These results show the advantages of introducing integrated biorefinery systems within agricultural landscapes. This is particularly true in the Midwest, which our results suggest is a good setting for the cellulosic ethanol industry. Specifically, results show that inclusion of cellulosic biofuel systems into existing agriculture enhances farm economics and reduces total landscape emissions. Model results also indicate a limited ethanol price effect from increased biomass transportation distance. Sensitivity analysis using BFIT revealed those variables having the strongest effects on the overall system performance, namely: biorefinery size, switchgrass yield, and biomass farm gate price.     

Integrated biorefineries with engineered microbes and high-value co-products for profitable biofuels production

Corn-based fuel ethanol production processes provide several advantages which could be synergistically applied to overcome limitations of biofuel processes based on lignocellulose. These include resources such as equipment, manpower, nutrients, water, and heat. The fact that several demonstration-scale biomass ethanol processes are using corn as a platform supports this viewpoint. This report summarizes the advantages of first-generation corn-based biofuel processes and then describes the technologies, advantages, and limitations of second-generation lignocellulose-based biofuel systems. This is followed by a discussion of the potential benefit of fully integrating first- and second-generation processes. We conclude with an overview of the technology improvements that are needed to enhance the profitability of biofuel production through development of an integrated biorefinery. A key requirement is creation of industrially robust, multifunctional ethanologens that are engineered for maximum ethanol production from mixed sugars. In addition to ethanol, combined biorefineries could also be the source of valuable co-products, such as chemicals and plastics. However, this will require expression systems that produce high-value co-products. Advantages of this approach are that (1) such strains could be used for bioconversion in any part of the combined biorefinery and (2) using one recombinant organism with many additions should simplify the process of obtaining necessary FDA approval for feed products produced by or containing recombinant organisms.     

Critical applications of Mucor circinelloides within a biorefinery context

The establishment of an efficient and feasible biorefinery model depends on, among other factors, particularly the selection of the most appropriate microorganism. Mucor circinelloides is a dimorphic fungus species able to produce a wide variety of hydrolytic enzymes, lipids prone to biodiesel production, carotenoids, ethanol, and biomass with significant nutritional value. M. circinelloides also has been selected as a model species for genetic modification by being the first filamentous oleaginous species to have its genome fully characterized, as well as being a species characterized as a potential bioremediation agent. Considering the potential of replacing several nonrenewable feedstocks is widely dependent on fossil fuels, the exploitation of microbial processes and products is a desirable solution for promoting a green and sustainable future. Here, we introduce and thoroughly describe the recent and critical applications of this remarkable fungus within the context of developing a fungal-based biorefinery.     

Implications of Three Biofuel Crops for Beneficial Arthropods in Agricultural Landscapes

Production of biofuel feedstocks in agricultural landscapes will result in land use changes that may have major implications for arthropod-mediated ecosystem services such as pollination and pest suppression. By comparing the abundance and diversity of insect pollinators and generalist natural enemies in three model biofuel crops: corn, switchgrass, and mixed prairie, we tested the hypothesis that biofuel crops comprised of more diverse plant communities would support increased levels of beneficial insects. These three biofuel crops contained a diverse bee community comprised of 75 species. Overall, bees were three to four times more abundant in switchgrass and prairie than in corn, with members of the sweat bee (Halictidae) and small carpenter bee (Ceratina spp.) groups the most abundant. Switchgrass and prairie had significantly greater bee species richness than corn during the July sampling period. The natural enemy community at these sites was dominated by lady beetles (Coccinellidae), long-legged flies (Dolichopodidae), and hover flies (Syrphidae) which varied in their response to crop type. Coccinellids were generally most abundant in prairie and switchgrass, with the exception of the pollen feeding Coleomegilla maculata that was most abundant in corn. Several rare or declining coccinellid species were detected in prairie and switchgrass sites. Dolichopodidae were more abundant in prairie and switchgrass while Syrphidae showed no significant response to crop type. Our results indicate that beneficial insects generally responded positively to the increased vegetational diversity of prairie and switchgrass sites; however, when managed as a dedicated biofuel crop, plant and arthropod diversity in switchgrass may decrease. Our findings support the hypothesis that vegetationally diverse biofuel crops support higher abundance and diversity of beneficial insects. Future policy regarding the production of biofuel feedstocks should consider the ecosystem services that different biofuel crops may support in agricultural landscapes.     

Culture-independent phylogenetic analysis of the microbial community in industrial sugarcane bagasse feedstock piles

Sugarcane bagasse is an important lignocellulosic by-product with potential for conversion to biofuels and chemicals in biorefinery. As a step towards an understanding of microbial diversity and the processes existing in bagasse collection sites, the microbial community in industrial bagasse feedstock piles was investigated. Molecular biodiversity analysis of 16S rDNA sequences revealed the presence of a complex bacterial community. A diverse group of mainly aerobic and facultative anaerobic bacteria was identified reflecting the aerobic and high temperature microenvironmental conditions under the pile surface. The major bacterial taxa present were identified as Firmicutes, Alpha- and Gammaproteobacteria, Acidobacteria, Bacteroidetes, and Actinobacteria. Analysis of the eukaryotic microbial assemblage based on an internal transcribed spacer revealed the predominance of diverse cellulolytic and hemicellulolytic ascomycota. A microbial interaction model is proposed, focusing on lignocellulose degradation and methane metabolism. The insights into the microbial community in this study provide a basis for efficient utilization of bagasse in lignocellulosic biomass-based industries.     

Analysis of cellulolytic and hemicellulolytic enzyme activity within the Tipula abdominalis (Diptera: Tipulidae) larval gut and characterization of Crocebacterium ilecola gen. nov., sp. nov., isolated from the Tipula abdominalis larval hindgut

Abstract In forested stream ecosystems of the north and eastern United States, larvae of the aquatic crane fly Tipula abdominalis are important shredders of leaf litter detritus. T. abdominalis larvae harbor a dense and diverse microbial community in their hindgut that may aide in the degradation of lignocellulose. In this study, the activities of cellulolytic and hemicellulolytic enzymes were demonstrated from hindgut extracts and from bacterial isolates using model sugar substrates. One of the bacterial isolates was further characterized as a member of the family Microbacteriaceae. Taxonomic position of the isolate within this family was determined by a polyphasic approach, as is commonly employed for the separation of genera within the family Microbacteriaceae. The bacterial isolate is Gram-type positive, motile, non-sporulating, and rod-shaped. The G + C content of the DNA is 64.9 mol%. The cell wall contains B2γ type peptidoglycan, D- and L-diaminobutyric acid as the diamino acid, and rhamnose as the predominant sugar. The predominant fatty acids are 12-methyltetradecanoic acid (ai-C_15:0) and 14-methylhexadecanoic acid (ai-C_17:0). The isolate forms a distinct lineage within the family Microbacteriaceae, as determined by 16S rRNA sequence analysis. We propose the name Crocebacterium ilecola gen. nov., sp. nov., to accommodate this bacterial isolate. The type species is T202^T (ATCC BAA-1359; GenBank Accession DQ826511).     

Does host‐feeding on GNA‐intoxicated aphids by Aphelinus abdominalis affect their longevity and/or fecundity?

Transgenic potatoes have been transformed with a gene coding the snowdrop lectin Galanthus nivalis agglutinin (GNA) and they have been shown to be partially resistant to aphids. GNA binds to insect gut cells, including those of aphids, consequently inducing disruption of nutrient assimilation. Aphid parasitoids are important natural biocontrol agents of aphids and some species such as Aphelinus abdominalis are commercially available. Aphid parasitoids are endoparasitoids during their larval stages and free-living insects as adults. They could be directly or indirectly affected by GNA during both these stages. In this work, we present data on the potential direct and indirect effects of GNA on adult A. abdominalis. Aphelinus abdominalis is a synovigenic species (eggs are matured throughout the adult life) which needs a diet relatively rich in proteins and amino-acids to produce anhydropic eggs (large, yolk-rich eggs that do not expand in the host during embryonic stages). Adult A. abdominalis females feed on aphid haemolymph and they may be directly exposed to the entomotoxin or indirectly affected by a change in aphid haemolymph quality due to intoxication by GNA. We conducted a first tier experiment to investigate this potential risk. A. abdominalis females were offered either aphids reared on control diet or aphids reared on GNA 0.1% diet as hosts (i.e., as food and oviposition sites). No trace of GNA was found in females fed with GNA-aphids but no GNA could be detected in the haemolymph of aphids fed a 0.1% GNA diet. Longevity and fecundity were not affected suggesting that the quality of the haemolymph necessary for A. abdominalis egg maturation and production was not significantly altered.     

Multiscale dynamic modeling and simulation of a biorefinery

A biorefinery comprises a variety of process steps to synthesize products from sustainable natural resources. Dynamic plant-wide simulation enhances the process understanding, leads to improved cost efficiency and enables model-based operation and control. It is thereby important for an increased competitiveness to conventional processes. To this end, we developed a Modelica library with replaceable building blocks that allow dynamic modeling of an entire biorefinery. For the microbial conversion step, we built on the dynamic flux balance analysis (DFBA) approach to formulate process models for the simulation of cellular metabolism under changing environmental conditions. The resulting system of differential-algebraic equations with embedded optimization criteria (DAEO) is solved by a tailor-made toolbox. In summary, our modeling framework comprises three major pillars: A Modelica library of dynamic unit operations, an easy-to-use interface to formulate DFBA process models and a DAEO toolbox that allows simulation with standard environments based on the Modelica modeling language. A biorefinery model for dynamic simulation of the OrganoCat pretreatment process and microbial conversion of the resulting feedstock by Corynebacterium glutamicum serves as case study to demonstrate its practical relevance.     

A Cross-Taxon Analysis of Insect-Associated Bacterial Diversity

Although it is well known that plants and animals harbor microbial symbionts that can influence host traits, the factors regulating the structure of these microbial communities often remain largely undetermined. This is particularly true for insect-associated microbial communities, as few cross-taxon comparisons have been conducted to date. To address this knowledge gap and determine how host phylogeny and ecology affect insect-associated microbial communities, we collected 137 insect specimens representing 39 species, 28 families, and 8 orders, and characterized the bacterial communities associated with each specimen via 16S rRNA gene sequencing. Bacterial taxa within the phylum Proteobacteria were dominant in nearly all insects sampled. On average, the insect-associated bacterial communities were not very diverse, with individuals typically harboring fewer than 8 bacterial phylotypes. Bacterial communities also tended to be dominated by a single phylotype; on average, the most abundant phylotype represented 54.7% of community membership. Bacterial communities were significantly more similar among closely related insects than among less-related insects, a pattern driven by within-species community similarity but detected at every level of insect taxonomy tested. Diet was a poor predictor of bacterial community composition. Individual insect species harbored remarkably unique communities: the distribution of 69.0% of bacterial phylotypes was limited to unique insect species, whereas only 5.7% of phylotypes were detected in more than five insect species. Together these results suggest that host characteristics strongly regulate the colonization and assembly of bacterial communities across insect lineages, patterns that are driven either by co-evolution between insects and their symbionts or by closely related insects sharing conserved traits that directly select for similar bacterial communities.     

Integration in a depot‐based decentralized biorefinery system: Corn stover‐based cellulosic biofuel

The current or “conventional” paradigm for producing process energy in a biorefinery processing cellulosic biomass is on‐site energy recovery through combustion of residual solids and biogas generated by the process. Excess electricity is then exported, resulting in large greenhouse gas (GHG) credits. However, this approach will cause lifecycle GHG emissions of biofuels to increase as more renewable energy sources (wind, solar, etc.) participate in grid‐electricity generation, and the GHG credits from displacing fossil fuel decrease. To overcome this drawback, a decentralized (depot‐based) biorefinery can be integrated with a coal‐fired power plant near a large urban area. In an integrated, decentralized, depot‐based biorefinery (IDB), the residual solids are co‐fired with coal either in the adjacent power plant or in coal‐fired boilers elsewhere to displace coal. An IDB system does not rely on indirect GHG credits through grid‐electricity displacement. In an IDB system, biogas from the wastewater treatment facility is also upgraded to biomethane and used as a transportation biofuel. The GHG savings per unit of cropland in the IDB systems (2.7–2.9 MgCO₂/ha) are 1.5–1.6 fold greater than those in a conventional centralized system (1.7–1.8 MgCO₂/ha). Importantly, the biofuel selling price in the IDBs is lower by 28–30 cents per gasoline‐equivalent liter than in the conventional centralized system. Furthermore, the total capital investment per annual biofuel volume in the IDB is much lower (by ~80%) than that in the conventional centralized system. Therefore, utilization of biomethane and residual solids in the IDB systems leads to much lower biofuel selling prices and significantly greater GHG savings per unit of cropland participating in the biorefinery system compared to the conventional centralized biorefineries.     

The Enteric Two‐Step: nutritional strategies of bacterial pathogens within the gut

The gut microbiota is a dense and diverse microbial community governed by dynamic microbe–microbe and microbe–host interactions, the status of which influences whether enteric pathogens can cause disease. Here we review recent insights into the key roles that nutrients play in bacterial pathogen exploitation of the gut microbial ecosystem. We synthesize recent findings to support a five‐stage model describing the transition between a healthy microbiota and one dominated by a pathogen and disease. Within this five‐stage model, two stages are critical to the pathogen: (i) an initial expansion phase that must occur in the absence of pathogen‐induced inflammation, followed by (ii) pathogen‐promoting physiological changes such as inflammation and diarrhoea. We discuss how this emerging paradigm of pathogen life within the lumen of the gut is giving rise to novel therapeutic strategies.     

Plant biotechnology for lignocellulosic biofuel production

Lignocelluloses from plant cell walls are attractive resources for sustainable biofuel production. However, conversion of lignocellulose to biofuel is more expensive than other current technologies, due to the costs of chemical pretreatment and enzyme hydrolysis for cell wall deconstruction. Recalcitrance of cell walls to deconstruction has been reduced in many plant species by modifying plant cell walls through biotechnology. These results have been achieved by reducing lignin content and altering its composition and structure. Reduction of recalcitrance has also been achieved by manipulating hemicellulose biosynthesis and by overexpression of bacterial enzymes in plants to disrupt linkages in the lignin–carbohydrate complexes. These modified plants often have improved saccharification yield and higher ethanol production. Cell wall‐degrading (CWD) enzymes from bacteria and fungi have been expressed at high levels in plants to increase the efficiency of saccharification compared with exogenous addition of cellulolytic enzymes. In planta expression of heat‐stable CWD enzymes from bacterial thermophiles has made autohydrolysis possible. Transgenic plants can be engineered to reduce recalcitrance without any yield penalty, indicating that successful cell wall modification can be achieved without impacting cell wall integrity or plant development. A more complete understanding of cell wall formation and structure should greatly improve lignocellulosic feedstocks and reduce the cost of biofuel production.     

昆虫与生物质能源利用:一个新的交叉学科前沿

昆虫与生物质能源利用密切相关。这些昆虫包括白蚁类、甲虫类、树蜂类、食叶类水生昆虫、衣鱼类、大蚊类等。它们能在树木、枯枝以及落叶上生活,并具有了相当可观的降解和转化木质纤维素的能力,是自然界中协助进行碳循环的一类重要节肢动物。近几年来,这些昆虫独特的肠道消化能力以及它们的生物质催化转化系统已引起了科学家和研究人员的极大兴趣,希望能通过发现新的降解木质纤维素的酶及酶系统、掌握相关的这些酶的表达和其功能控制基因、并能解开昆虫肠道的消化及其相关机制的谜;更高效的降解和转化植物细胞壁中的碳水化合物并用来生产不同种类的生物能源或生物基材料。目前,对这类昆虫高效降解木质纤维素能力的认识和相关降解机制的研究已发展成为一个与生物质能源应用密切相关的新兴研究领域,成为新的交叉学科前沿。本文将简要讨论这类昆虫消化木质纤维素的几种不同作用机制、共生微生物与昆虫所产生的不同木质纤维素酶以及相互间的协同作用的基础上,还探讨了当前第二代生物质能源研究与开发中所面临的主要挑战、消化木质纤维素类昆虫,特别是白蚁所处的独特地位、潜在的科学和应用价值,以及今后的主要研究方向。     

Isolation of Polymer-Degrading Bacteria and Characterization of the Hindgut Bacterial Community from the Detritus-Feeding Larvae of Tipula abdominalis (Diptera: Tipulidae)

The Tipula abdominalis larval hindgut microbial community presumably facilitates digestion of the lignocellulosic diet. The microbial community was investigated through characterization of bacterial isolates and analysis of 16S rRNA gene clone libraries. This initial study revealed novel bacteria and provides a framework for future studies of this symbiosis.     

The Sphagnum microbiome supports bog ecosystem functioning under extreme conditions

Sphagnum‐dominated bogs represent a unique yet widely distributed type of terrestrial ecosystem and strongly contribute to global biosphere functioning. Sphagnum is colonized by highly diverse microbial communities, but less is known about their function. We identified a high functional diversity within the Sphagnum microbiome applying an Illumina‐based metagenomic approach followed by de novo assembly and MG‐RAST annotation. An interenvironmental comparison revealed that the Sphagnum microbiome harbours specific genetic features that distinguish it significantly from microbiomes of higher plants and peat soils. The differential traits especially support ecosystem functioning by a symbiotic lifestyle under poikilohydric and ombrotrophic conditions. To realise a plasticity–stability balance, we found abundant subsystems responsible to cope with oxidative and drought stresses, to exchange (mobile) genetic elements, and genes that encode for resistance to detrimental environmental factors, repair and self‐controlling mechanisms. Multiple microbe–microbe and plant–microbe interactions were also found to play a crucial role as indicated by diverse genes necessary for biofilm formation, interaction via quorum sensing and nutrient exchange. A high proportion of genes involved in nitrogen cycle and recycling of organic material supported the role of bacteria for nutrient supply. 16S rDNA analysis indicated a higher structural diversity than that which had been previously detected using PCR‐dependent techniques. Altogether, the diverse Sphagnum microbiome has the ability to support the life of the host plant and the entire ecosystem under changing environmental conditions. Beyond this, the moss microbiome presents a promising bio‐resource for environmental biotechnology – with respect to novel enzymes or stress‐protecting bacteria.     

Diversity and resilience of the wood‐feeding higher termite Mironasutitermes shangchengensis gut microbiota in response to temporal and diet variations

Termites are considered among the most efficient bioreactors, with high capacities for lignocellulose degradation and utilization. Recently, several studies have characterized the gut microbiota of diverse termites. However, the temporal dynamics of the gut microbiota within a given termite with dietary diversity are poorly understood. Here, we employed 16S rDNA barcoded pyrosequencing analysis to investigate temporal changes in bacterial diversity and richness of the gut microbiota of wood‐feeding higher termite Mironasutitermes shangchengensis under three lignocellulose content‐based diets that feature wood, corn stalks, and filter paper. Compositions of the predominant termite gut residents were largely constant among the gut microbiomes under different diets, but each diet caused specific changes in the bacterial composition over time. Notably, microbial communities exhibited an unexpectedly strong resilience during continuous feeding on both corn stalks and filter paper. Members of five bacterial phyla, that is, Spirochaetes, Firmicutes, Actinobacteria, Tenericutes, and Acidobacteria, were strongly associated with the resilience. These findings provide insights into the stability of the gut microbiota in higher termites and have important implications for the future design of robust bioreactors for lignocellulose degradation and utilization.