Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions

Impacts of sample handling and storage conditions on archiving physiologically active soil microbial communities

Soil microbial communities are fundamental to ecosystem processes and plant growth, yet community composition is seasonally and successionally dynamic, which interferes with long-term iterative experimentation of plant-microbe interactions. We explore how soil sample handling (e.g. filtering) and sample storage conditions impact the ability to revive the original, physiologically active, soil microbial community. We obtained soil from agricultural fields in Montana and Oklahoma, USA and samples were sieved to 2 mm or filtered to 45 µm. Sieved and filtered soil samples were archived at -20°C or -80°C for 50 days and revived for 2 or 7 days. We extracted DNA and the more transient RNA pools from control and treatment samples and characterized microbial communities using 16S amplicon sequencing. Filtration and storage treatments significantly altered soil microbial communities, impacting both species richness and community composition. Storing sieved soil at -20°C did not alter species richness and resulted in the least disruption to the microbial community composition in comparison to nonarchived controls as characterized by RNA pools from soils of both sites. Filtration significantly altered composition but not species richness. Archiving sieved soil at -20°C could allow for long-term and repeated experimentation on preserved physiologically active microbial communities.

Bacterial diversity dynamics in microbial consortia selected for lignin utilization

Lignin is nature's largest source of phenolic compounds. Its recalcitrance to enzymatic conversion is still a limiting step to increase the value of lignin. Although bacteria are able to degrade lignin in nature, most studies have focused on lignin degradation by fungi. To understand which bacteria are able to use lignin as the sole carbon source, natural selection over time was used to obtain enriched microbial consortia over a 12-week period. The source of microorganisms to establish these microbial consortia were commercial and backyard compost soils. Cultivation occurred at two different temperatures, 30°C and 37°C, in defined culture media containing either Kraft lignin or alkaline-extracted lignin as carbon source. iTag DNA sequencing of bacterial 16S rDNA gene was performed for each of the consortia at six timepoints (passages). The initial bacterial richness and diversity of backyard compost soil consortia was greater than that of commercial soil consortia, and both parameters decreased after the enrichment protocol, corroborating that selection was occurring. Bacterial consortia composition tended to stabilize from the fourth passage on. After the enrichment protocol, Firmicutes phylum bacteria were predominant when lignin extracted by alkaline method was used as a carbon source, whereas Proteobacteria were predominant when Kraft lignin was used. Bray-Curtis dissimilarity calculations at genus level, visualized using NMDS plots, showed that the type of lignin used as a carbon source contributed more to differentiate the bacterial consortia than the variable temperature. The main known bacterial genera selected to use lignin as a carbon source were Altererythrobacter, Aminobacter, Bacillus, Burkholderia, Lysinibacillus, Microvirga, Mycobacterium, Ochrobactrum, Paenibacillus, Pseudomonas, Pseudoxanthomonas, Rhizobiales and Sphingobium. These selected bacterial genera can be of particular interest for studying lignin degradation and utilization, as well as for lignin-related biotechnology applications.

Functional characterization of thermotolerant microbial consortium for lignocellulolytic enzymes with central role of Firmicutes in rice straw depolymerization

Rice (Oryza sativa L.) straw, an agricultural waste of high yield, is a sustainable source of fermentable sugars for biofuel and other chemicals. However, it shows recalcitrance to microbial catalysed depolymerization. We herein describe development of thermotolerant microbial consortium (RSV) from vermicompost with ability to degrade rice straw and analysis of its metagenome for bacterial diversity, and lignocellulolytic carbohydrate active enzymes (CAZymes) and their phylogenetic affiliations. RSV secretome exhibited cellulases and hemicellulases with higher activity at 60 °C. It catalysed depolymerization of chemical pretreated rice straw as revealed by scanning electron microscopy and saccharification yield of 460 mg g^-1 rice straw. Microbial diversity of RSV was distinct from other compost habitats, with predominance of members of phyla Firmicutes, Proteobacteria and Bacteroidetes; and Pseudoclostridium, Thermoanaerobacterium, Chelatococcus and Algoriphagus being most abundant genera. RSV harboured 1389 CAZyme encoding ORFs of glycoside hydrolase, carbohydrate esterase, glycosyl transferase, carbohydrate binding module and auxiliary activity functions. Microorganisms of Firmicutes showed central role in lignocellulose deconstruction with importance in hemicellulose degradation; whereas representatives of Proteobacteria and Bacteroidetes contributed to cellulose and lignin degradation, respectively. RSV consortium could be a resource for mining thermotolerant cellulolytic bacteria or enzymes and studying their synergism in deconstruction of chemically pretreated rice straw.

A Recent Overview of Microbes and Microbiome Preservation

Microbes are mediators in almost all ecosystem processes and act as a pivotal game changer in various ecological activities, globally. Therefore, understanding of microbial community structure and related functions in different environmental and micro-environmental niches is not only critical, but also a matter of greatest importance. Due to our inability to cultivate and preserve all sorts of microorganisms, we are losing some ecologically and industrially relevant components of microbial community, due to extinction caused by environmental and climatic variations with time. Intact sample and microbiome preservation are crucial for future cultivation as well as to study the effects of ecological and climatic variations on community functionality and shift with time, using OMICS. Although, methods for pure culture preservation are almost optimized, the techniques of microbiome preservation still remain as an unsolved challenge for microbiologists due to technical and physiological constraints. Present article discusses, recent approaches of microbial preservation with special reference to intact sample, mixed culture and microbiome preservation. It also incorporates recent practices used to achieve the highest viability and metabolic activities in long-term preserved microbiome.

Interactions of Glycerol, Diglycerol, and Water Studied Using Attenuated Total Reflection Infrared Spectroscopy

In order to examine the mixing properties of glycerol-water and diglycerol-water solutions, these solutions were measured using attenuated total reflection infrared spectroscopy. The absorbance spectra corrected for 1 µm thickness were subtracted by pure polyols for obtaining water spectra, and by pure water for polyol spectra. Both asymmetric and symmetric CH₂ stretching vibration bands (around 2940, 2885 cm^-1) shifted about 10 cm^-1 to lower wavenumber side (redshifts) with increasing polyol concentrations, especially at higher concentrations. Redshifts of C-O-H rocking bands (around 1335 cm^-1) with increasing polyol concentrations are slightly larger for diglycerol-water (10 > 6 cm^-1) than glycerol-water solutions. C-O stretching bands of CHOH groups (1125 and 1112 cm^-1) shift slightly but in opposite sides for glycerol and diglycerol at highest polyol concentrations (90-100 wt%). These shifts of CH₂ stretching, COH rocking, and CO stretching of CHOH at higher polyol concentrations suggest interactions of outer CH₂ with inner CHOH groups of surrounding polyols. The normalized band area changes with polyol concentrations could be fitted by quadratic polynomials possibly due to mixtures of different interactions between water-water, polyol-water, and polyol-polyol molecules. The OH stretching band for diglycerol 90 wt% shows three humps indicating at least three OH components: long, medium, and short H bond water molecules. Short H bond water molecules are the major component possibly between inner CHOH and outer side CH₂OH groups, while the long H component might loosely bind to outer CH₂OH groups.

Cryopreservation and fast recovery of enriched syngas-converting microbial communities

Over the last decades, the use of mixed microbial communities has attracted increasing scientific attention due to their potential biotechnological applications in several emerging technological platforms such as the carboxylate, bioplastic, syngas and bio-electrochemical synthesis platforms. However, this increasing interest has not been accompanied by a parallel development of suitable cryopreservation techniques for microbial communities. While cryopreservation methods for the long-term storage of axenic cultures are well established, their effectiveness in preserving the microbial diversity and functionality of microbial communities has rarely been studied. In this study, the effect of the addition of different cryopreservation agents on the long-term storage of microbial communities at -80 °C was studied using a stable enrichment culture converting syngas into acetate and ethanol. The cryopreservation agents considered in the study were glycerol, dimethylsulfoxide, polyvinylpyrrolidone, Tween 80 and yeast extract, as well as with no addition of cryopreservation agent. Their effectiveness was evaluated based on the microbial activity recovery and the maintenance of the microbial diversity and community structure upon revival of the microbial community. The results showed that the commonly used glycerol and no addition of cryopreservation agent were the least recommendable methods for the long-term frozen storage of microbial communities, while Tween 80 and polyvinylpyrrolidone were overall the most effective. Among the cryoprotectants studied, polyvinylpyrrolidone and especially Tween 80 were the only ones assuring reproducible results in terms of microbial activity recovery and microbial community structure preservation.

Techno-economic assessment of non-sterile batch and continuous production of lactic acid from food waste

Non-sterile lactic acid (LA) fermentation of highly viscous food waste was demonstrated in batch and continuous flow fermentations. With Streptococcus sp., an indigenous consortium, and/or applied glucoamylase, food waste was fermented without addition of external carbon or nitrogen sources. Experimental results were used for economic and energy evaluations under consideration of different catchment area sizes from 50,000 to 1,000,000 inhabitants. During batch mode, addition of glucoamylase resulted in a titer (after 24 h), yield, and productivity of 50 g L^-1, 63%, and 2.93 g L^-1h^-1, respectively. While titer and yield were enhanced, productivity was lower during continuous operation and 69 g L^-1, 86%, and 1.27 g L^-1h^-1 were obtained at a dilution rate of 0.44 d^-1 when glucoamylase was added. Both batch and continuous flow fermentations were found economically profitable with food waste from 200,000 or more inhabitants.

Effect of spatial origin and hydrocarbon composition on bacterial consortia community structure and hydrocarbon biodegradation rates

Oil reserves in deep-sea sediments are currently subject to intense exploration, with associated risks of oil spills. Previous research suggests that microbial communities from deep-sea sediment (>1000m) can degrade hydrocarbons (HCs), but have a lower degradation ability than shallow (<200m) communities, probably due to in situ temperature. This study aimed to assess the effect of marine origin on microbial HC degradation potential while separating the influence of temperature, and to characterise associated HC-degrading bacterial communities. Microbial communities from 135 and 1000 m deep sediments were selectively enriched on crude oil at in situ temperatures and both consortia were subsequently incubated for 42 days at 20°C with two HC mixtures: diesel fuel or model oil. Significant HC biodegradation occurred rapidly in the presence of both consortia, especially of low molecular weight HCs and was concomitant with microbial community changes. Further, oil degradation was higher with the shallow consortium than with the deep one. Dominant HC-degrading bacteria differed based on both spatial origin of the consortia and supplemented HC types. This study provides evidence for influence of sediment spatial origin and HC composition on the selection and activity of marine HC-degrading bacterial communities and is relevant for future bioremediationdevelopments.

Hydrocarbon-degrading bacteria in deep-water subarctic sediments (Faroe-Shetland Channel)

AIMS

The aim of this study was the baseline description of oil-degrading sediment bacteria along a depth transect in the Faroe-Shetland Channel (FSC) and the identification of biomarker taxa for the detection of oil contamination in FSC sediments.

METHODS AND RESULTS

Oil-degrading sediment bacteria from 135, 500 and 1000 m were enriched in cultures with crude oil as the sole carbon source (at 12, 5 and 0°C respectively). The enriched communities were studied using culture-dependent and culture-independent (clone libraries) techniques. Isolated bacterial strains were tested for hydrocarbon degradation capability. Bacterial isolates included well-known oil-degrading taxa and several that are reported in that capacity for the first time (Sulfitobacter, Ahrensia, Belliella, Chryseobacterium). The orders Oceanospirillales and Alteromonadales dominated clone libraries in all stations but significant differences occurred at genus level particularly between the shallow and the deep, cold-water stations. Alcanivorax constituted 64% of clones at FSC135 but was absent at deeper stations. Pseudoalteromonas and Oleispira dominated the bacterial community at 500 and 1000 m.

CONCLUSIONS

The genus Oleispira emerged as a major player in the early stages of crude oil degradation in deep-sea sediments of the FSC particularly at subzero temperatures. This finding is offering a direction for future research into biomonitoring tools for the detection of low levels of crude oil contamination in the deep FSC, and possibly high latitude cold waters in general.

SIGNIFICANCE AND IMPACT OF THE STUDY

Oil and gas exploration in the FSC occurs at depths >1000 m but baseline environmental data necessary for the assessment of ecosystem recovery to prespill conditions in the event of an oil spill are lacking. This study will contribute to our ability to assess the impact of oil release in the FSC and guide the direction of bioremediation strategies tailored to the area.

Treatment of Ammonium-Rich Digestate from Methane Fermentation Using Aerobic Granular Sludge

Digestate produced by cofermentation of agricultural waste and manure can be difficult to dispose of because its high ammonium content impedes its use in agriculture due to generation of odor and overfertilization. This study investigated the possibility of treating such nitrogen-rich digestate with aerobic granular sludge depending on the nitrogen load in the reactor. At nitrogen loading rate of 1.0 g TN/(L·day), the nitrogen removal efficiency was high (64.9 ± 9.8%), ammonium nitrogen was completely oxidized, and nitrate was the main nitrification product. At nitrogen loading rate of 3.4 g TN/(L·day), ammonium oxidization was still good (93.6 ± 2.0%), but the percentage of partial nitrification was high (over 68%) and nitrogen removal efficiency worsened to 30.2 ± 2.6%. Despite this, the overall amount of nitrogen removed was 0.86 g TN/(L·day) and was over nearly two times higher than at the lower nitrogen loading rate. At both nitrogen loading rates, in the effluent nitrogen in a form of suspended solids predominated. To diminish the overall N loading in the effluent, treatment is therefore recommended enabling removal of solids, e.g., microfiltration, should be applied, or the digestate should be separated into solid and liquid phases, and only the liquid fraction should be subjected to biological treatment. At high N load in aerobic granules, a very versatile community of N-metabolizing microorganisms was present. More than 50% of all bacteria in aerobic granules were able to metabolize nitrogen, and the predominant genera (35%) was Thauera, which indicated that stable ammonium removal was achieved mostly as a result of heterotrophic nitrification.

Microbial diversity of thermophiles with biomass deconstruction potential in a foliage-rich hot spring

The ability of thermophilic microorganisms and their enzymes to decompose biomass have attracted attention due to their quick reaction time, thermostability, and decreased risk of contamination. Exploitation of efficient thermostable glycoside hydrolases (GHs) could accelerate the industrialization of biofuels and biochemicals. However, the full spectrum of thermophiles and their enzymes that are important for biomass degradation at high temperatures have not yet been thoroughly studied. We examined a Malaysian Y-shaped Sungai Klah hot spring located within a wooded area. The fallen foliage that formed a thick layer of biomass bed under the heated water of the Y-shaped Sungai Klah hot spring was an ideal environment for the discovery and analysis of microbial biomass decay communities. We sequenced the hypervariable regions of bacterial and archaeal 16S rRNA genes using total community DNA extracted from the hot spring. Data suggested that 25 phyla, 58 classes, 110 orders, 171 families, and 328 genera inhabited this hot spring. Among the detected genera, members of Acidimicrobium, Aeropyrum, Caldilinea, Caldisphaera, Chloracidobacterium, Chloroflexus, Desulfurobacterium, Fervidobacterium, Geobacillus, Meiothermus, Melioribacter, Methanothermococcus, Methanotorris, Roseiflexus, Thermoanaerobacter, Thermoanaerobacterium, Thermoanaerobaculum, and Thermosipho were the main thermophiles containing various GHs that play an important role in cellulose and hemicellulose breakdown. Collectively, the results suggest that the microbial community in this hot spring represents a good source for isolating efficient biomass degrading thermophiles and thermozymes.

Ionic Liquids Impact the Bioenergy Feedstock-Degrading Microbiome and Transcription of Enzymes Relevant to Polysaccharide Hydrolysis

Pretreatment using ionic liquids (IL) is a promising approach for the conversion of lignocellulose to biofuels. Because IL can be inhibitory to enzymes and microorganisms involved in downstream hydrolysis and fermentation steps, discovery of IL-tolerant organisms and enzymes is critical for advancing this technology. Employing metatranscriptomics in the analysis of IL-enriched cultures facilitated tracking of dynamic changes in a complex microbial community at the level of gene transcription and doing so with genome resolution. Specific organisms were discovered that could simultaneously tolerate a moderate IL concentration and transcribe a diverse array of cellulolytic enzymes. Gene sequences of cellulolytic enzymes and efflux pumps from those same organisms were also identified, providing important resources for future research on engineering IL-tolerant organisms and enzymes.

Ionic liquid (IL) pretreatment is a promising approach for the conversion of lignocellulose to biofuels. The toxicity of residual IL, however, negatively impacts the performance of industrial enzymes and microorganisms in hydrolysis and fermentation. In this study, a thermophilic microbial community was cultured on switchgrass amended with various levels of the ionic liquid 1-ethyl-3-methylimidazolium acetate. Changes in the microbial community composition and transcription of genes relevant to IL tolerance and lignocellulose hydrolysis were quantified. Increasing the level of IL to 0.1% (wt) led to increased levels of relative abundance and transcription in organisms of the phylum Firmicutes. Interestingly, IL concentrations of up to 1% (wt) also resulted in greater xylanase transcription and enzyme activity as well as increased transcription of endoglucanase, beta-glucosidase, and IL tolerance genes compared to communities without IL. IL levels above 1% (wt) resulted in decreased enzyme activity and transcription of genes involved in lignocellulose hydrolysis. The results indicate that moderate levels of IL select for thermophilic microorganisms that not only tolerate IL but also effectively hydrolyze lignocellulose from switchgrass. Discovery of IL-tolerant organisms and enzymes is critical for the development of biological processes that convert IL-pretreated biomass to biofuels and chemicals. Employing metatranscriptomic analysis of enrichment cultures can facilitate the discovery of microorganisms and enzymes that may be active in the presence of toxic compounds such as ionic liquids.

IMPORTANCE Pretreatment using ionic liquids (IL) is a promising approach for the conversion of lignocellulose to biofuels. Because IL can be inhibitory to enzymes and microorganisms involved in downstream hydrolysis and fermentation steps, discovery of IL-tolerant organisms and enzymes is critical for advancing this technology. Employing metatranscriptomics in the analysis of IL-enriched cultures facilitated tracking of dynamic changes in a complex microbial community at the level of gene transcription and doing so with genome resolution. Specific organisms were discovered that could simultaneously tolerate a moderate IL concentration and transcribe a diverse array of cellulolytic enzymes. Gene sequences of cellulolytic enzymes and efflux pumps from those same organisms were also identified, providing important resources for future research on engineering IL-tolerant organisms and enzymes.

Ionic liquid-tolerant microorganisms and microbial communities for lignocellulose conversion to bioproducts

Chemical and physical pretreatment of biomass is a critical step in the conversion of lignocellulose to biofuels and bioproducts. Ionic liquid (IL) pretreatment has attracted significant attention due to the unique ability of certain ILs to solubilize some or all components of the plant cell wall. However, these ILs inhibit not only the enzyme activities but also the growth and productivity of microorganisms used in downstream hydrolysis and fermentation processes. While pretreated biomass can be washed to remove residual IL and reduce inhibition, extensive washing is costly and not feasible in large-scale processes. IL-tolerant microorganisms and microbial communities have been discovered from environmental samples and studies begun to elucidate mechanisms of IL tolerance. The discovery of IL tolerance in environmental microbial communities and individual microbes has lead to the proposal of molecular mechanisms of resistance. In this article, we review recent progress on discovering IL-tolerant microorganisms, identifying metabolic pathways and mechanisms of tolerance, and engineering microorganisms for IL tolerance. Research in these areas will yield new approaches to overcome inhibition in lignocellulosic biomass bioconversion processes and increase opportunities for the use of ILs in biomass pretreatment.