Ferric Iron Reduction in Extreme Acidophiles

Biochemical processes are a key element of natural cycles occurring in the environment and enabling life on earth. With regard to microbially catalyzed iron transformation, research predominantly has focused on iron oxidation in acidophiles, whereas iron reduction played a minor role. Microbial conversion of ferric to ferrous iron has however become more relevant in recent years. While there are several reviews on neutrophilic iron reducers, this article summarizes the research on extreme acidophilic iron reducers. After the first reports of dissimilatory iron reduction by acidophilic, chemolithoautotrophic Acidithiobacillus strains and heterotrophic Acidiphilium species, many other prokaryotes were shown to reduce iron as part of their metabolism. Still, little is known about the exact mechanisms of iron reduction in extreme acidophiles. Initially, hypotheses and postulations for the occurring mechanisms relied on observations of growth behavior or predictions based on the genome. By comparing genomes of well-studied neutrophilic with acidophilic iron reducers (e.g., Ferroglobus placidus and Sulfolobus spp.), it became clear that the electron transport for iron reduction proceeds differently in acidophiles. Moreover, transcriptomic investigations indicated an enzymatically-mediated process in Acidithiobacillus ferrooxidans using respiratory chain components of the iron oxidation in reverse. Depending on the strain of At. ferrooxidans, further mechanisms were postulated, e.g., indirect iron reduction by hydrogen sulfide, which may form by disproportionation of elemental sulfur. Alternative scenarios include Hip, a high potential iron-sulfur protein, and further cytochromes. Apart from the anaerobic iron reduction mechanisms, sulfur-oxidizing acidithiobacilli have been shown to mediate iron reduction at low pH (< 1.3) under aerobic conditions. This presumably non-enzymatic process may be attributed to intermediates formed during sulfur/tetrathionate and/or hydrogen oxidation and has already been successfully applied for the reductive bioleaching of laterites. The aim of this review is to provide an up-to-date overview on ferric iron reduction by acidophiles. The importance of this process in anaerobic habitats will be demonstrated as well as its potential for application.

Functional roles of multiple Ton complex genes in a Sphingobium degrader of lignin-derived aromatic compounds

TonB-dependent transporters (TBDTs) mediate outer membrane transport of nutrients using the energy derived from proton motive force transmitted from the TonB–ExbB–ExbD complex localized in the inner membrane. Recently, we discovered ddvT encoding a TBDT responsible for the uptake of a 5,5-type lignin-derived dimer in Sphingobium sp. strain SYK-6. Furthermore, overexpression of ddvT in an SYK-6-derivative strain enhanced its uptake capacity, improving the rate of platform chemical production. Thus, understanding the uptake system of lignin-derived aromatics is fundamental for microbial conversion-based lignin valorization. Here we examined whether multiple tonB-, exbB-, and exbD-like genes in SYK-6 contribute to the outer membrane transport of lignin-derived aromatics. The disruption of tonB2–6 and exbB3 did not reduce the capacity of SYK-6 to convert or grow on lignin-derived aromatics. In contrast, the introduction of the tonB1–exbB1–exbD1–exbD2 operon genes into SYK-6, which could not be disrupted, promoted the conversion of β-O-4-, β-5-, β-1-, β-β-, and 5,5-type dimers and monomers, such as ferulate, vanillate, syringate, and protocatechuate. These results suggest that TonB-dependent uptake involving the tonB1 operon genes is responsible for the outer membrane transport of the above aromatics. Additionally, exbB2/tolQ and exbD3/tolR were suggested to constitute the Tol-Pal system that maintains the outer membrane integrity.

Strain evolution and novel downstream processing with integrated catalysis enable highly efficient co-production of 1,3-Propanediol and organic acid esters from crude glycerol

Bioconversion process with a single target product often lacks economic competitiveness owing to incomplete use of raw material and high costs of downstream processing (DSP). Here, we show with the microbial conversion of crude glycerol that an integrated strain engineering and catalytic conversion of the so-called byproducts can greatly improve DSP and the process economy. Specifically, Clostridium pasteurianum was first adapted to increased concentration of crude glycerol in a novel automatic laboratory evolution system. At m3 scale bioreactor the strain achieved a simultaneous production of 1,3-propanediol (PDO), acetic and butyric acids at 81.21, 18.72 and 11.09 g/L within only 19 h, respectively, representing the most efficient fermentation of crude glycerol to targeted products. A heterogeneous catalytic step was developed and integrated into the DSP process to obtain high-value methyl esters from acetic and butyric acids at high yields. The co-production of the esters also greatly simplified the recovery of PDO. For example, a cosmetic grade PDO (96% PDO) was easily obtained by a simple single-stage distillation process (with an overall yield more than 77%). This integrated approach provides an industrially attractive route for a complete use of the raw material with the simultaneous production of three appealing products which greatly improve the process economy and ecology.

Higher Long-Term Soil Moisture Increases Organic Carbon Accrual Through Microbial Conversion of Organic Inputs

High long-term soil moisture may either stimulate or inhibit soil organic carbon (SOC) losses through changes to mineral and chemical composition, and resultant organo-mineral interactions. Yet, the trade-off between mineralization and accrual of SOC under long-term variation in unsaturated soil moisture remains an uncertainty. In this study, we tested the underexplored relationships between long-term soil moisture and organo-mineral chemical composition, and its implications for SOC persistence. The results provide new insights into SOC accrual mechanisms under different long-term moisture levels commonly observed in well-drained soils. Differences in long-term mean volumetric water content ranging from 0.4 - 0.63 (v/v) on fallow plots in an experimental field in New York, USA, were positively correlated with SOC contents (R2 = 0.228; P = 0.019, n = 20), mineral-associated organic matter (MAOM) (R2 = 0.442; P = 0.001; n = 20) and occluded particulate organic matter (oPOM) contents (R2 = 0.178; P = 0.033; n = 20). Higher long-term soil moisture decreased the relative content of sodium pyrophosphate extractable Fe (R2 = 0.33; P < 0.005; n = 20), increased that of sodium dithionite extractable Fe (R2 = 0.443; P < 0.001; n = 20), and increased the overall importance of non-crystalline Al pools (extracted with sodium pyrophosphate and hydroxylamine extractable) for SOC retention. Higher long-term soil moisture supported up to a four-fold increase in microbial biomass (per unit SOC), and lower C:N ratios in MAOM fractions of high-moisture soils (from C:N 9.5 to 9, R2 = 0.267, P = 0.011, n =20). This was reflected by a 15% and 10% greater proportion of oxidized carboxylic-C to aromatic-C and O-alkyl C, respectively, as measured with 13C-NMR, and a more pronounced FTIR signature of N-containing proteinaceous compounds in high-moisture MAOM fractions, reflective of microbial metabolites. SOC accrual increased with increasing soil moisture (P = 0.019), exchangeable Ca2+ (P = 0.013), and pyrophosphate-extractable Al content (P = 0.0001) and Al/Fe ratio (P = 0.017). Taken together, our results show that high long-term soil moisture resulted in SOC accrual by enhancing microbial conversion of plant inputs to metabolites that interact with reactive minerals.

Higher Long-Term Soil Moisture Increases Organic Carbon Accrual Through Microbial Conversion of Organic Inputs

High long-term soil moisture may either stimulate or inhibit soil organic carbon (SOC) losses through changes to mineral and chemical composition, and resultant organo-mineral interactions. Yet, the trade-off between mineralization and accrual of SOC under long-term variation in unsaturated soil moisture remains an uncertainty. In this study, we tested the underexplored relationships between long-term soil moisture and organo-mineral chemical composition, and its implications for SOC persistence. The results provide new insights into SOC accrual mechanisms under different long-term moisture levels commonly observed in well-drained soils. Differences in long-term mean volumetric water content ranging from 0.4 - 0.63 (v/v) on fallow plots in an experimental field in New York, USA, were positively correlated with SOC contents (R2 = 0.228; P = 0.019, n = 20), mineral-associated organic matter (MAOM) (R2 = 0.442; P = 0.001; n = 20) and occluded particulate organic matter (oPOM) contents (R2 = 0.178; P = 0.033; n = 20). Higher long-term soil moisture decreased the relative content of sodium pyrophosphate extractable Fe (R2 = 0.33; P < 0.005; n = 20), increased that of sodium dithionite extractable Fe (R2 = 0.443; P < 0.001; n = 20), and increased the overall importance of non-crystalline Al pools (extracted with sodium pyrophosphate and hydroxylamine extractable) for SOC retention. Higher long-term soil moisture supported up to a four-fold increase in microbial biomass (per unit SOC), and lower C:N ratios in MAOM fractions of high-moisture soils (from C:N 9.5 to 9, R2 = 0.267, P = 0.011, n =20). This was reflected by a 15% and 10% greater proportion of oxidized carboxylic-C to aromatic-C and O-alkyl C, respectively, as measured with 13C-NMR, and a more pronounced FTIR signature of N-containing proteinaceous compounds in high-moisture MAOM fractions, reflective of microbial metabolites. SOC accrual increased with increasing soil moisture (P = 0.019), exchangeable Ca2+ (P = 0.013), and pyrophosphate-extractable Al content (P = 0.0001) and Al/Fe ratio (P = 0.017). Taken together, our results show that high long-term soil moisture resulted in SOC accrual by enhancing microbial conversion of plant inputs to metabolites that interact with reactive minerals.

MIXed plastics biodegradation and UPcycling using microbial communities: EU Horizon 2020 project MIX-UP started January 2020

This article introduces the EU Horizon 2020 research project MIX-UP, "Mixed plastics biodegradation and upcycling using microbial communities". The project focuses on changing the traditional linear value chain of plastics to a sustainable, biodegradable based one. Plastic mixtures contain five of the top six fossil-based recalcitrant plastics [polyethylene (PE), polyurethane (PUR), polypropylene (PP), polyethylene terephthalate (PET), polystyrene (PS)], along with upcoming bioplastics polyhydroxyalkanoate (PHA) and polylactate (PLA) will be used as feedstock for microbial transformations. Consecutive controlled enzymatic and microbial degradation of mechanically pre-treated plastics wastes combined with subsequent microbial conversion to polymers and value-added chemicals by mixed cultures. Known plastic-degrading enzymes will be optimised by integrated protein engineering to achieve high specific binding capacities, stability, and catalytic efficacy towards a broad spectrum of plastic polymers under high salt and temperature conditions. Another focus lies in the search and isolation of novel enzymes active on recalcitrant polymers. MIX-UP will formulate enzyme cocktails tailored to specific waste streams and strives to enhance enzyme production significantly. In vivo and in vitro application of these cocktails enable stable, self-sustaining microbiomes to convert the released plastic monomers selectively into value-added products, key building blocks, and biomass. Any remaining material recalcitrant to the enzymatic activities will be recirculated into the process by physicochemical treatment. The Chinese–European MIX-UP consortium is multidisciplinary and industry-participating to address the market need for novel sustainable routes to valorise plastic waste streams. The project's new workflow realises a circular (bio)plastic economy and adds value to present poorly recycled plastic wastes where mechanical and chemical plastic recycling show limits.

Clostridium thermocellum as a Promising Source of Genetic Material for Designer Cellulosomes: An Overview

Plant biomass-based biofuels have gradually substituted for conventional energy sources thanks to their obvious advantages, such as renewability, huge quantity, wide availability, economic feasibility, and sustainability. However, to make use of the large amount of carbon sources stored in the plant cell wall, robust cellulolytic microorganisms are highly demanded to efficiently disintegrate the recalcitrant intertwined cellulose fibers to release fermentable sugars for microbial conversion. The Gram-positive, thermophilic, cellulolytic bacterium Clostridium thermocellum possesses a cellulolytic multienzyme complex termed the cellulosome, which has been widely considered to be nature’s finest cellulolytic machinery, fascinating scientists as an auspicious source of saccharolytic enzymes for biomass-based biofuel production. Owing to the supra-modular characteristics of the C. thermocellum cellulosome architecture, the cellulosomal components, including cohesin, dockerin, scaffoldin protein, and the plentiful cellulolytic and hemicellulolytic enzymes have been widely used for constructing artificial cellulosomes for basic studies and industrial applications. In addition, as the well-known microbial workhorses are naïve to biomass deconstruction, several research groups have sought to transform them from non-cellulolytic microbes into consolidated bioprocessing-enabling microbes. This review aims to update and discuss the current progress in these mentioned issues, point out their limitations, and suggest some future directions.