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Angenent, L. T.

Publications and source records attributed to Angenent, L. T..

34 records · Page 2Linked to original sources

Power-to-Vitamins: Producing Folate (Vitamin B9) from Renewable Electric Power and CO2 with a Microbial Protein System

Meeting a surging demand for superior micronutrient-rich protein sources and finding production practices that are less detrimental to the climate will be critical challenges of the 21st century. New technologies are needed to decouple food production from land use. Our group previously proposed a two-stage Power-to-Protein technology to produce microbial protein from renewable electric power and CO2. Two stages were operated in series: (1) Clostridium ljungdahlii in Stage A to utilize H2 to reduce CO2 into acetate; and (2) Saccharomyces cerevisiae in Stage B to utilize O2 and produce microbial protein from acetate. Renewable energy would power water electrolysis to produce H2 and O2. A disadvantage of C. ljungdahlii in Stage A is the need to continuously feed vitamins to sustain growth and acid production. Changing to the more robust thermophilic acetogen Thermoanaerobacter kivui avoids providing any vitamins. Additionally, S. cerevisiae produces folate when grown with acetate as a sole carbon source under aerobic conditions. A total folate concentration of 6.7 mg per 100 g biomass with an average biomass concentration of 3 g L-1 in Stage B is achieved. The developed Power-to-Vitamin system enables folate production from renewable power and CO2 with zero or negative net-carbon emissions.

microbiology↗

Exclusive D-lactate-isomer production during a reactor-microbiome conversion of lactose-rich waste by controlling pH and temperature

Lactate is among the top-ten-biobased products. It occurs naturally as D- or L-isomer and as a racemic mixture (DL-lactate). Generally, lactate with a high optical purity is more valuable. In searching for suitable renewable feedstocks for lactate production, unutilized organic waste streams are increasingly coming into focus. Here, we investigated acid whey, which is a lactose-rich byproduct of yogurt production, that represents a considerable environmental footprint for the dairy industry. We investigated the steering of the lactate-isomer composition in a continuous and open culture system (HRT = 0.6 d) at different pH values (pH 5.0 vs. pH 6.5) and process temperatures (38{degrees}C to 50{degrees}C). The process startup was achieved by autoinoculation. At a pH of 5.0 and a temperature of 47{degrees}C-50{degrees}C, exclusive D-lactate production occurred because of the dominance of Lactobacillus spp. (> 95% of relative abundance). The highest volumetric D-lactate production rate of 722 {+/-} 94.6 mmol C L-1 d-1 (0.90 {+/-} 0.12 g L-1 h-1), yielding 0.93 {+/-} 0.15 mmol C mmol C-1, was achieved at a pH of 5.0 and a temperature of 44{degrees}C (n = 18). At a pH of 6.5 and a temperature of 44{degrees}C, we found a mixture of DL-lactate (average D-to-L-lactate production rate ratio of 1.69 {+/-} 0.90), which correlated with a high abundance of Streptococcus spp. and Enterococcus spp. However, exclusive L-lactate production could not be achieved. Our results show that for the continuous conversion of lactose-rich dairy waste streams, the pH was a critical process parameter to control the yield of lactate isomers by influencing the composition of the microbiota. In contrast, temperature adjustments allowed the improvement of bioprocess kinetics.

bioengineering↗

An integrated systems-biology platform for power-to-gas technology

Methanogenesis allows methanogenic archaea (methanogens) to generate cellular energy for their growth while producing methane. Hydrogenotrophic methanogens thrive on carbon dioxide and molecular hydrogen as sole carbon and energy sources. Thermophilic and hydrogenotrophic Methanothermobacter spp. have been recognized as robust biocatalysts for a circular carbon economy and are now applied in power-to-gas technology. Here, we generated the first manually curated genome-scale metabolic reconstruction for three Methanothermobacter spp.. We investigated differences in the growth performance of three wild-type strains and one genetically engineered strain in two independent chemostat bioreactor experiments. In the first experiment, with molecular hydrogen and carbon dioxide, we found the highest methane production rate for Methanothermobacter thermautotrophicus {Delta}H, while Methanothermobacter marburgensis Marburg reached the highest biomass growth rate. Systems biology investigations, including implementing a pan-model that contains combined reactions from all three microbes, allowed us to perform an interspecies comparison. This comparison enabled us to identify crucial differences in formate anabolism. In the second experiment, with sodium formate, we found stable growth with an M. thermautotrophicus {Delta}H plasmid-carrying strain with similar performance parameters compared to wild-type Methanothermobacter thermautotrophicus Z-245. Our findings reveal that formate anabolism influences the diversion of carbon to biomass and methane with implications for biotechnological applications of Methanothermobacter spp. in power-to-gas technology and for chemical production. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/522236v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1d468aeorg.highwire.dtl.DTLVardef@24a595org.highwire.dtl.DTLVardef@1f2dd60org.highwire.dtl.DTLVardef@1a3d8fc_HPS_FORMAT_FIGEXP M_FIG C_FIG Broader contextRenewable energy sources (e.g., wind and solar) provide carbon-free electric power. However, their intermittency and offset between peak production and demand generate the need to store this electric power. Furthermore, these technologies alone do not satisfy the demand for carbon-based commodities. Power-to-gas technology provides a means to store intermittent renewable electric power with concomitant carbon dioxide recycling into a chemical energy carrier, such as methane, on a centralized and decentralized scale. This is particularly important to establish equitable energy strategies for all countries, as is highlighted by the United Nations Sustainable Development Goals. With this work, we provide an integrated systems-biology platform for Methanothermobacter spp. to optimize biological power-to-gas technology and formulate strategies to produce other value-added products besides methane.

microbiology↗

Carbon oxidation with sacrificial anodes to inhibit O2 evolution in membrane-less bioelectrochemical systems for microbial electrosynthesis

Microbial electrosynthesis is an emerging biosynthesis technology that produces value-added chemicals and fuels and, at the same time, reduces the environmental carbon footprint. However, constraints, such as low current densities and high inner resistance, disfavor this technology for industrial-scale purposes. The cathode performance has been strongly improved in recent years, while the anode performance has not been given enough attention despite its importance in closing the electric circuit. For traditional water electrolysis, O2 is produced at the anode, which is toxic to the anaerobic autotrophs that engage in microbial electrosynthesis. To overcome O2 toxicity in conventional microbial electrosynthesis, the anode and the cathode chamber have been separated by an ion-exchange membrane to avoid contact between the microbes and O2. However, ion-exchange membranes increase the maintenance costs and compromise the production efficiency by introducing an additional internal resistance. Furthermore, O2 is inevitably transferred to the catholyte due to diffusion and electro-osmotic fluxes that occur within the membrane. Here, we proved the concept of integrating carbon oxidation with sacrificial anodes and microbes to simultaneously inhibit the O2 evolution reaction (OER) and circumvent membrane application, which allows microbial electrosynthesis to proceed in a single chamber. The carbon-based anodes performed carbon oxidation as the alternative reaction to the OER. This enables microbial electrosynthesis to be performed with cell voltages as low as 1.8-2.1 V at 10 A{middle dot}m-2. We utilized Methanothermobacter thermautotrophicus {Delta}H in a single-chamber Bioelectrochemical system (BES) with the best performing carbon-based anode (i.e., activated-carbon anode with soluble iron) to achieve a maximum cathode-geometric CH4 production rate of 27.3 L{middle dot}m-2{middle dot}d-1, which is equal to a volumetric methane production rate of 0.11 L{middle dot}L-1{middle dot}d-1 in our BES, at a coulombic efficiency of 99.4%. In this study, Methanothermobacter thermautotrophicus {Delta}H was majorly limited by sulfur that inhibited electromethanogenesis. However, this proof-of-concept study allows microbial electrosynthesis to be performed more energy-efficiently and can be immediately utilized for research purposes in microbial electrosynthesis.

bioengineering↗

The targeted deletion of genes responsible for expression of the Mth60 fimbriae leads to loss of cell-cell connections in M. thermautotrophicus ΔH

This study was continued by the Environmental Biotechnology Group of the University of Tubingen in memoriam to Reinhard Wirth, who initiated the work on Mth60 fimbriae at the University of Regensburg. Growth in biofilms or biofilm-like structures is the prevailing lifestyle for most microbes in nature. The first step to initiate biofilms is the adherence of microbes to biotic and abiotic surfaces. Therefore, it is important to elucidate the initial step of biofilm formation, which is generally established through cell-surface structures (i.e., cell appendages), such as fimbriae or pili, that adhere to surfaces. The Mth60 fimbriae of Methanothermobacter thermautotrophicus {Delta}H are one of only few known archaeal cell appendages that do not assemble via the type-IV assembly mechanism. Here, we report the constitutive expression of Mth60 fimbriae-encoding genes from a shuttle-vector construct, as well as the deletion of the Mth60 fimbriae-encoding genes from the genomic DNA of M. thermautotrophicus {Delta}H. We expanded our system for genetic modification of M. thermautotrophicus {Delta}H by an allelic-exchange method. While overexpression of the respective genes resulted in an increase of the Mth60 fimbriae, deletion of the Mth60 fimbriae-encoding genes led to a loss of Mth60 fimbriae in planktonic cells of M. thermautotrophicus {Delta}H. This either increased or decreased number of Mth60 fimbriae correlated with a significant increase or decrease of biotic cell-cell connections in the respective M. thermautotrophicus {Delta}H strains compared to the wild-type strain. Originality-Significance StatementMethanothermobacter spp. have been studied for the biochemistry of hydrogenotrophic methanogenesis for many years. However, due to the lack of genetic tools, the detailed investigation of certain aspects, such as regulatory processes, was not possible. Here, we amend our genetic toolbox for M. thermautotrophicus {Delta}H with an allelic exchange method. We report the deletion of genes that encode for the Mth60 fimbriae. Our findings provide a first insight into the regulation of the expression of these genes and reveal a role of the Mth60 fimbriae in the formation of cell-cell connections of M. thermautotrophicus {Delta}H.

microbiology↗

Near-neutral pH increased n-caprylate production in a microbiome with product inhibition of methanogenesis

The pH is a critical parameter in chain-elongating bioreactors, affecting: (1) the concentration of inhibitory undissociated carboxylic acids, which in turn affects the efficiency of product extraction; (2) the thermodynamics; and (3) the kinetics. Here, we examined the effect of five different pH levels (5.5 to 7.0) on n-caprylate (C8) production using an anaerobic sequencing batch reactor (ASBR) with continuous membrane-based liquid-liquid extraction (pertraction). We found that the product spectrum was directed by pH: mildly acidic pH (5-6) led to n-caproate (C6) production, while near-neutral and neutral pH (6.75-7) favored n-caprylate production. In particular, the pH of 6.75 led to the maximum values of volumetric n-caprylate production rate (75.6 {+/-} 0.6 mmol C L-1 d-1; 0.06 g L-1 d-1) and n-caprylate concentration in the fermentation broth (420 mM C; 7.57 g L-1). Given that methane production remained low at near-neutral and neutral pH, we theorized that the high concentration of undissociated n-caprylic acid (5.71 mM C) inhibited methanogenesis. We then demonstrated such an inhibitory effect at neutral pH in: (1) microcosm experiments; and (2) the continuous bioreactor by adding methanogenic sludge. Furthermore, 16S rRNA gene sequencing analysis revealed that near-neutral and neutral pH led to more diverse microbial communities than at mildly-acidic pH. For the first time, we report predominant n-caprylate production in a microbiome at near-neutral and neutral pH conditions where methanogenesis was controlled by the inhibitory effects of undissociated n-caprylic acid. At the same time, extraction of this species occurred even at near-neutral and neutral pH.

bioengineering↗

Genetic evidence reveals the indispensable role of the rseC gene for autotrophy and the importance of a functional electron balance for nitrate reduction in Clostridium ljungdahlii

For Clostridium ljungdahlii, the RNF complex plays a key role for energy conversion from gaseous substrates such as hydrogen and carbon dioxide. In a previous study, a disruption of RNF-complex genes led to the loss of autotrophy, while heterotrophy was still possible via glycolysis. Furthermore, it was shown that the energy limitation during autotrophy could be lifted by nitrate supplementation, which resulted in an elevated cellular growth and ATP yield. Here, we used CRISPR-Cas12a to delete: 1) the RNF complex-encoding gene cluster rnfCDGEAB; 2) the putative RNF regulator gene rseC; and 3) a gene cluster that encodes for a putative nitrate reductase. The deletion of either rnfCDGEAB or rseC resulted in a complete loss of autotrophy, which could be restored by plasmid-based complementation of the deleted genes. We observed a transcriptional repression of the RNF-gene cluster in the rseC-deletion strain during autotrophy and investigated the distribution of the rseC gene among acetogenic bacteria. To examine nitrate reduction and its connection to the RNF complex, we compared autotrophic and heterotrophic growth of our three deletion strains with either ammonium or nitrate. The rnfCDGEAB- and rseC-deletion strains failed to reduce nitrate as a metabolic activity in non-growing cultures during autotrophy but not during heterotrophy. In contrast, the nitrate reductase deletion strain was able to grow in all tested conditions but lost the ability to reduce nitrate. Our findings highlight the important role of the rseC gene for autotrophy and contribute to understand the connection of nitrate reduction to energy metabolism. Significance StatementAcetogenic bacteria are widely known for their ability to convert gaseous substrates, such as hydrogen, carbon dioxide, and carbon monoxide, into short-chain fatty acids and alcohols, which can be utilized as sustainable platform chemicals and fuels. However, acetogenic bacteria conserve energy at the thermodynamic limit of life during autotrophy, and thus the production of more complex and energy-dense chemicals is limited due to low ATP yields. Therefore, it is key to decipher the interplay of the electron balancing reactions to understand and optimize the acetogenic metabolism. Recent findings with alternative electron acceptors that accelerated the cellular growth and ATP yield during autotrophy, such as nitrate, provide an opportunity to overcome energetic barriers in the acetogenic metabolism. The interrogation of the nitrate metabolism and the interplay between nitrate reduction and energy conservation in C. ljungdahlii, will contribute to fine-tuning of the acetogenic metabolism for biotechnological applications.

microbiology↗

A shuttle-vector system allows heterologous gene expression in the thermophilic methanogen Methanothermobacter thermautotrophicus ΔH

Thermophilic Methanothermobacter spp. are used as model microbes to study the physiology and biochemistry of the conversion of hydrogen and carbon dioxide into methane (i.e., hydrogenotrophic methanogenesis), because of their short doubling times and robust growth with high growth yields. Yet, a genetic system for these model microbes was missing despite intense work for four decades. Here, we report the establishment of tools for genetic modification of M. thermautotrophicus. We developed the modular Methanothermobacter vector system, which provided shuttle-vector plasmids (pMVS) with exchangeable selectable markers and replicons for both Escherichia coli and M. thermautotrophicus. For M. thermautotrophicus, a thermostable neomycin-resistance cassette served as the selectable marker for positive selection with neomycin, and the cryptic plasmid pME2001 from Methanothermobacter marburgensis served as the replicon. The pMVS-plasmid DNA was transferred from E. coli into M. thermautotrophicus via interdomain conjugation. After the successful validation of DNA transfer and positive selection in M. thermautotrophicus, we demonstrated heterologous gene expression of a thermostable {beta}-galactosidase-encoding gene (bgaB) from Geobacillus stearothermophilus under the expression control of four distinct synthetic and native promoters. In quantitative in-vitro enzyme activity assays, we found significantly different {beta}-galactosidase activity with these distinct promoters. With a formate dehydrogenase operon-encoding shuttle vector, we allowed growth of M. thermautotrophicus on formate as the sole growth substrate, while this was not possible for the empty vector control. These genetic tools provide the basis to investigate hypotheses from four decades of research on the physiology and biochemistry of Methanothermobacter spp. on a genetic level. Significance StatementThe world economies are facing permanently increasing energy demands. At the same time, carbon emissions from fossil sources need to be circumvented to minimize harmful effects from climate change. The power-to-gas platform is utilized to store renewable electric power and decarbonize the natural gas grid. The microbe Methanothermobacter thermautotrophicus is already applied as the industrial biocatalyst for the biological methanation step in large-scale power-to-gas processes. To improve the biocatalyst in a targeted fashion, genetic engineering is required. With our shuttle-vector system for heterologous gene expression in M. thermautotrophicus, we set the cornerstone to engineer the microbe for optimized methane production, but also for production of high-value platform chemicals in power-to-x processes.

microbiology↗

Direct medium-chain carboxylic-acid oil separation from a bioreactor by an electrodialysis/phase separation cell

Medium-chain carboxylic acids (MCCAs) are valuable platform chemicals with numerous industrial-scale applications. These MCCAs can be produced from waste biomass sources or syngas fermentation effluent through an anaerobic fermentation process called chain elongation. We have previously demonstrated successful approaches to separate >90%-purity oil with several MCCAs by integrating the anaerobic bioprocess with membrane-based liquid-liquid extraction (pertraction) and membrane electrolysis. However, membrane electrolysis without pertraction was not able to separate MCCA oil. Therefore, we developed an electrodialysis/phase separation cell (ED/PS) and evaluated whether it can function as a stand-alone extraction and separation unit. First, we tested an ED/PS cell, which, when evaluated in series with pertraction, achieved a maximum MCCA-oil flux of 1,665 g d-1 per projected area (m2) (19.3 mL oil d-1) and a MCCA-oil transfer efficiency [100%*moles MCCA-oil moles electrons-1] of 74% at 15 A m-2. This extraction system demonstrated a [~]10 times lower electric-power consumption of 1.05 kWh kg-1 MCCA oil when compared to membrane electrolysis in series with pertration (11.1 kWh kg-1 MCCA oil) at 15 A m-2. Second, we evaluated our ED/PS as a stand-alone unit when integrated with the anaerobic bioprocess (without pertraction), and demonstrated that we can selectively extract and separate MCCA oil directly from chain-elongating bioreactor broth with just an abiotic electrochemical cell. We assumed that such a stand-alone unit would reduce capital and operating costs, but electric-power consumption increased considerably due to the lower MCCA concentrations in the bioreactor broth compared to the pertraction broth. Only a full techno-economic analysis will be able to determine whether the use of the ED/PS cell should be as a stand-alone unit or after pertraction.

bioengineering↗

The isolate Caproiciproducens sp. 7D4C2 produces n-caproate at mildly acidic conditions from hexoses: genome and rBOX comparison with related strains and chain-elongating bacteria

BackgroundBulk production of medium-chain carboxylates (MCCs) with 6-12 carbon atoms is of great interest to biotechnology. Open cultures (e.g., reactor microbiomes) have been utilized to generate MCCs in bioreactors. When in-line MCC extraction and prevention of product inhibition is required, the bioreactors have been operated at mildly acidic pH (5.0-5.5). However, model chain-elongating bacteria grow optimally at neutral pH values. Here, we isolated a chain-elongating bacterium (strain 7D4C2) that thrives at mildly acidic pH. We studied its metabolism and compared its whole genome and the reverse {beta}-oxidation (rBOX) genes to other bacteria. ResultsStrain 7D4C2 produces lactate, acetate, n-butyrate, n-caproate, biomass, and H2/CO2 from hexoses. With only fructose as substrate (pH 5.5), the maximum n-caproate specificity (i.e., products per other carboxylates produced) was 60.9 {+/-} 1.5%. However, this was considerably higher at 83.1 {+/-} 0.44% when both fructose and n-butyrate (electron acceptor) were combined as a substrate. A comparison of serum bottles with fructose and n-butyrate with an increasing pH value from 4.5 to 9.0 showed a decreasing n-caproate specificity from [~]92% at mildly acidic pH (pH 4.5-5.0) to [~]24% at alkaline pH (pH 9.0). Moreover, when carboxylates were extracted from the broth (undissociated n-caproic acid was [~]0.3 mM), the n-caproate selectivity (i.e., product per substrate fed) was 42.6 {+/-} 19.0% higher compared to serum bottles without extraction. Based on the 16S rRNA gene sequence, strain 7D4C2 is most closely related to the isolates Caproicibacter fermentans (99.5%) and Caproiciproducens galactitolivorans (94.7%), which are chain-elongating bacteria that are also capable of lactate production. Whole-genome analyses indicate that strain 7D4C2, C. fermentans, and C. galactitolivorans belong to the same genus of Caproiciproducens. Their rBOX genes are conserved and located next to each other, forming a gene cluster, which is different than for other chain-elongating bacteria such as Megasphaera spp. ConclusionsCaproiciproducens spp., comprising strain 7D4C2, C. fermentans, C. galactitolivorans, and several unclassified strains, are chain-elongating bacteria that encode a highly conserved rBOX gene cluster. Caproiciproducens sp. 7D4C2 (DSM 110548) was studied here to understand n-caproate production better at mildly acidic pH within microbiomes and has the additional potential as a pure-culture production strain to convert sugars into n-caproate.

microbiology↗

Food waste as a resource: grinding, dilution, and storage as a pretreatment strategy to produce fermentation intermediates

In several states of the U.S., one measure to mitigate greenhouse-gas emissions has been to ban food wastes from landfills. As a result, U.S.-based companies are now providing decentralized food-waste management systems for supermarkets and restaurants, which include storage as a slurry. It is unclear, however, which storage conditions (factors) would affect the spontaneous microbial activity, resulting in a different fermentation product spectra, and how this would affect further post-treatment. Here, we performed two experiments to mimic: 1) storage and 2) subsequent anaerobic digestion. For the food-waste storage system, we designed a mixed-level fractional factorial analysis with 12 experimental combinations, including separating food waste into: carbohydrate-rich, lipid-rich, and protein-rich food waste. We found that all factors that we tested correlated with the fermentation product spectra, but that especially the factors: i) storage temperature; ii) food-waste composition; and iii) storage time affected the fermentation outcome. We observed that relatively low pH levels of 3-4, which were achieved due to rapid lactic acid accumulation by microbial activity during storage, coincided with greater lactate production at a maximum chemical oxygen demand (COD) selectivity of 90%. This provides an opportunity to optimize lactate production, which is ideal for subsequent methane or chemical production. TOC/Abstract graphic O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

bioengineering↗

Reprogramming acetogenic bacteria with CRISPR-targeted base editing via deamination

Acetogenic bacteria are rising in popularity as chassis microbes in biotechnology due to their capability of converting inorganic one-carbon (C1) gases to organic chemicals. To fully uncover the potential of acetogenic bacteria, synthetic-biology tools are imperative to either engineer designed functions or to interrogate the physiology. Here, we report a genome-editing tool at a one-nucleotide resolution, namely base editing, for acetogenic bacteria based on CRISPR-targeted deamination. This tool combines nuclease deactivated Cas9 with activation-induced cytidine deaminase to enable cytosine-to-thymine substitution without DNA cleavage, homology-directed repair, and donor DNA, which are generally the bottlenecks for applying conventional CRISPR-Cas systems in bacteria. We designed and validated a modularized base-editing tool in the model acetogenic bacterium Clostridium ljungdahlii. The editing principles were investigated, and an in-silico analysis revealed the capability of base editing across the genome. Moreover, genes related to acetate and ethanol production were disrupted individually by installing premature STOP codons to reprogram carbon flux towards improved acetate production. This resulted in engineered C. ljungdahlii strains with the desired phenotypes and stable genotypes. Our base-editing tool promotes the application and research in acetogenic bacteria and provides a blueprint to upgrade CRISPR-Cas-based genome editing in bacteria in general. SignificanceAcetogenic bacteria metabolize one-carbon (C1) gases, such as industrial waste gases, to produce fuels and commodity chemicals. However, the lack of efficient gene-manipulation approaches hampers faster progress in the application of acetogenic bacteria in biotechnology. We developed a CRISPR-targeted base-editing tool at a one-nucleotide resolution for acetogenic bacteria. Our tool illustrates great potential in engineering other A-T-rich bacteria and links designed single-nucleotide variations with biotechnology. It provides unique advantages for engineering industrially relevant bacteria without creating genetically modified organisms (GMOs) under the legislation of many countries. This base-editing tool provides an example for adapting CRISPR-Cas systems in bacteria, especially those that are highly sensitive to heterologously expressed Cas proteins and have limited ability of receiving foreign DNA.

synthetic biology↗

The short-term effect of residential home energy retrofits on indoor air quality and microbial exposure: a case-control study

Weatherization of residential homes is a popular retrofit procedure to improve the energy efficiency of older homes by reducing building leakage. It is a vital tool in the fight against climate change. Several studies have evaluated the effect of weatherization on indoor pollutants such as formaldehyde and radon, but few studies have evaluated the effect of weatherization on indoor particulates and microbial exposure. In this study, we compared the effect of change in building leakage on indoor pollutants and bacterial communities in weatherized compared to non-weatherized single-family residential homes in New York State. Nine weatherized and eleven non-weatherized single-family homes in Tompkins County, New York were sampled twice: before and after the weatherization procedures for case homes, and at least 3 months apart for control homes that were not weatherized. We found a significant increase in both indoor-outdoor temperature ratio and living-area- and basement-radon levels of weatherized homes compared to control homes. The indoor-outdoor relative humidity ratio significantly decreased in weatherized compared to control homes. The indoor microbiome also became less similar to the outdoor community after weatherization. Compared to the changes in ventilation rate, temperature, relative humidity, and occupancy, the change in season was a more predictive measure of indoor bacterial concentration. Ventilation rate reduction from weatherization procedures led to an increase in indoor radon levels, as well as a warmer and less humid indoor environment. However, it did not affect indoor particulate mass concentration or indoor airborne bacteria load, and did only marginally affect the microbiome composition of residential homes. Finally, we found that changes in airborne bacterial load are more sensitive to shifts in season, whereas radon levels are more sensitive to ventilation rate.

microbiology↗

Suppressing peatland methane production by electron snorkeling through pyrogenic carbon

Northern peatlands are experiencing more frequent fire events as a result of changing climate conditions. Forest fires naturally result in a direct and negative climate impact by emitting large amounts of carbon into the atmosphere. Recent studies show that this extensive emission may shift the soil carbon regime from a sink to a source. However, the fires also convert parts of the burnt biomass into pyrogenic carbon. Here, we show an indirect, but positive, climate impact induced by fire-derived pyrogenic carbon. We found that the accumulation of pyrogenic carbon reduced post-fire methane production from peatland soils by 13-24%. The conductive, capacitive, and redox-cycling electron transfer mechanisms enabled pyrogenic carbon to function as an electron snorkel, which redirected soil electron fluxes to facilitate alternative microbial respiration and reduced the rate of methane production by 50%. Given the fact that methane has a 34-fold greater warming potential than carbon dioxide, we estimate that global greenhouse gas emissions are reduced by 35 Tg CO2e annually through the electron snorkeling of pyrogenic carbon in peatlands. Our results highlight an important, but overlooked, function of pyrogenic carbon in neutralizing forest fire emissions and call for its consideration in the global carbon budget estimation.

microbiology↗

An open-source multiple-bioreactor system for replicable gas-fermentation experiments: Nitrate feed results in stochastic inhibition events, but improves ethanol production of Clostridium ljungdahlii with CO2 and H2

The pH-value in fermentation broth has a large impact on the metabolic flux and growth behavior of acetogens. A decreasing pH level throughout time due to undissociated acetic acid accumulation is anticipated under uncontrolled pH conditions such as in bottle experiment. As a result, the impact of changes in the metabolism (e.g., due to a genetic modification) might remain unclear or even unrevealed. In contrast, pH-controlled conditions can be easily achieved in commercially available bioreactors. However, their acquisition is costly and their operation is time consuming, and therefore the experiment is often limited to a single bioreactor run. Here, we present a self-built, relatively cheap, and easy to handle open-source multiple-bioreactor system (MBS) consisting of six pH-controlled bioreactors at a 1-L scale. The functionality of the MBS was tested in three experiments by cultivating the acetogen Clostridium ljungdahlii with CO2 and H2 at steady-state conditions (=chemostat). The experiments were addressing the questions: (1) does the MBS provide replicable data for gas-fermentation experiments?; (2) does feeding acetate alter the production rate of ethanol; and (3) does feeding nitrate influence the product spectrum under controlled pH conditions with CO2 and H2? We applied four different periods in each experiment ranging from pH 6.0 to pH 4.5. Our data show high reproducibility for gas-fermentation experiments with C. ljungdahlii, using the MBS. We found that feeding acetate did not improve ethanol production, but rather impaired growth and reduced acetate production. Using nitrate as sole N-source, on the other hand, enhanced biomass production even at a low pH. However, we observed differences in growth, acetate, and ethanol production rates between triplicate bioreactors (n=3). We explained the different performances because of stochastic inhibition events, which we observed through the accumulation of nitrite, and which led to complete crashes at different operating times. One of these bioreactors recovered after the crash and showed enhanced ethanol production rates while simultaneously producing less acetate. The MBS offers a great opportunity to perform bench-scale bioreactor experiments at steady-state conditions with replicates, which is especially attractive for academia.

microbiology↗

Syntrophy via interspecies H2 transfer between Christensenella and Methanobrevibacter underlies their global co-occurrence in the human gut

Across human populations, 16S rRNA gene-based surveys of gut microbiomes have revealed that the bacterial family Christensenellaceae and the archaeal family Methanobacteriaceae co-occur and are enriched in individuals with a lean, compared to an obese, BMI. Whether these association patterns reflect interactions between metabolic partners remains to be ascertained, as well as whether these associations play a role in the lean host phenotype with which they associate. Here, we validated previously reported co-occurrence patterns of the two families, and their association with a lean BMI, with a meta-analysis of 1,821 metagenomes derived from 10 independent studies. Furthermore, we report positive associations at the genus and species level between Christensenella spp. and Methanobrevibacter smithii, the most abundant methanogen of the human gut. By co-culturing three Christensenella spp. With M. smithii, we show that Christensenella spp. efficiently support the of M. smithii via H2 production, far better than Bacteroides thetaiotaomicron. C. minuta forms flocs colonized by M. smithii even when H2 is in excess. In culture with C. minuta, H2 consumption by M. smithii shifts the metabolic output of C. minutas fermentation towards acetate rather than butyrate. Together, these results indicate that the widespread co-occurrence of these microbiota is underpinned by both physical and metabolic interactions. Their combined metabolic activity may provide insights into their association with a lean host BMI. ImportanceThe human gut microbiome is made of trillions of microbial cells, most of which are Bacteria, with a subset of Archaea. The bacterial family Christensenellaceae and the archaeal family Methanobacteriaceae are widespread in human guts. They correlate with each other and with a lean body type. Whether species of these two families interact, and how they affect the body type, are unanswered questions. Here, we showed that species within these families correlate with each other across people. We also demonstrated that particular species of these two families grow together in dense flocs, wherein the bacteria provide hydrogen gas to the archaea, which then make methane. When the archaea are present, the ratio of bacterial products (which are nutrients for humans) is changed. These observations indicate when these species grow together, their products have the potential to affect the physiology of their human host.

microbiology↗