CO2 utilizing microbes — A comprehensive review

Biosynthesis of polyhydroxybutyrate from methane and carbon dioxide using type II methanotrophs

Methane (CH4) and carbon dioxide (CO2) are the dominant greenhouse gases (GHGs) that are increasing at an alarming rate. Methanotrophs have emerged as potential CH4 and CO2 biorefineries. This study demonstrated the synchronous incorporation of CH4 and CO2 into polyhydroxybutyrate (PHB) for the first time using 13C-labeling experiments in methanotrophs. By supplying substantial amounts of CO2, PHB content was enhanced in all investigated type II methanotrophic strains by 140 %, 146 %, and 162 %. The highest content of PHB from CH4 and CO2 in flask-scale cultivation reached 38 % dry cell weight in Methylocystis sp. MJC1, in which carbon percentage in PHB from CO2 was 45 %. Flux balance analysis predicted the critical roles of crotonyl-CoA carboxylase/reductase and phosphoenolpyruvate carboxylase in CO2 recycling. This study provided proof of the conversion of GHGs into a valuable and practical product using methanotrophic bacteria, contributing to addressing GHG emissions.

Biogeographic distribution of autotrophic bacteria was more affected by precipitation than by soil properties in an arid area

Introduction

Autotrophic bacteria play an important role in carbon dioxide fixation and are widespread in terrestrial ecosystems. However, the biogeographic patterns of autotrophic bacteria and the driving factors still remain poorly understood.

Methods

Herein, we conducted a 391-km north to south transect (mean annual precipitation <600 mm) survey in the Loess Plateau of China, to investigate the biogeographic distributions of autotrophic bacteria (RubisCO cbbL and cbbM genes) and the environmental drivers across different latitude sites with clear vegetational and climatic gradients.

Results and discussion

The soils in northern region with lower precipitation are dominated by grassland/forest, which is typically separated from the soils in southern region with higher precipitation. The community structure of autotrophic bacterial cbbL and cbbM genes generally differed between the soils in the southern and northern Loess Plateau, suggesting that precipitation and its related land use practices/ecosystem types, rather than local soil properties, are more important in shaping the soil autotrophic microorganisms. The cbbL-containing generalist OTUs were almost equally abundant across the northern and southern Loess Plateau, while the cbbM-containing bacterial taxa were more prevalent in the low precipitation northern region. Such differences indicate differentiate distribution patterns of cbbM- and cbbL-containing bacteria across the north to south transect. Our results suggest that the community composition and the differentiate distributions of soil cbbL- and cbbM-containing bacterial communities depend on precipitation and the related ecosystem types in the north to south transect in the Loess Plateau of China.

Genomic profiling and characteristics of a C1 degrading heterotrophic fresh-water bacterium Paracoccus sp. strain DMF

Paracoccus species are metabolically versatile gram-negative, aerobic facultative methylotrophic bacteria showing enormous promise for environmental and bioremediation studies. Here we report, the complete genome analysis of Paracoccus sp. strain DMF (P. DMF) that was isolated from a domestic wastewater treatment plant in Kanpur, India (26.4287 °N, 80.3891 °E) based on its ability to degrade a recalcitrant organic solvent N, N-dimethylformamide (DMF). The results reveal a genome size of 4,202,269 base pairs (bp) with a G + C content of 67.9%. The assembled genome comprises 4141 coding sequences (CDS), 46 RNA sequences, and 2 CRISPRs. Interestingly, catabolic operons related to the conventional marine-based methylated amines (MAs) degradation pathway were functionally annotated within the genome of an obligated aerobic heterotroph that is P. DMF. The genomic data-based characterization presented here for the novel heterotroph P. DMF aims to improve the understanding of the phenotypic gene products, enzymes, and pathways involved with greater emphasis on facultative methylotrophic motility-based latent pathogenicity.

Effects of adding corn steep liquor on bacterial community composition and carbon and nitrogen transformation during spent mushroom substrate composting

BACKGROUND

Carbon and nitrogen are essential energy and nutrient substances in the composting process. Corn steep liquor (CSL) is rich in soluble carbon and nitrogen nutrients and active substances and is widely used in the biological industry. Nonetheless, limited research has been done on the effect of CSL on composting. This work firstly reveals the effect of adding CSL to bacterial community composition and carbon and nitrogen conversion during composting. This study provides the choice of auxiliary materials for the spent mushroom substrate compost (SMS) and some novel knowledge about the effect of bacterial community on C and N cycling during composting of SMS and CSL. Two treatments were set up in the experiment: 100% spent mushroom substrate (SMS) as CK and SMS + 0.5% CSL (v/v) as CP.

RESULTS

The results showed that the addition of CSL enhanced the initial carbon and nitrogen content of the compost, altered the bacterial community structure, and increased the bacterial diversity and relative abundance, which might be beneficial to the conversion and retention of carbon and nitrogen in the composting process. In this paper, network analysis was used to screen the core bacteria involved in carbon and nitrogen conversion. In the CP network, the core bacteria were divided into two categories, synthesizing and degrading bacteria, and there were more synthesizing bacteria than degrading bacteria, so the degradation and synthesis of organic matter were carried out simultaneously, while only degrading bacteria were found in the CK network. Functional prediction by Faprotax identified 53 groups of functional bacteria, among which 20 (76.68% abundance) and 14 (13.15% abundance) groups of functional bacteria were related to carbon and nitrogen conversion, respectively. Adding CSL stimulated the compensatory effect of core and functional bacteria, enhanced the carbon and nitrogen transformation ability, stimulated the activity of low-abundance bacteria, and reduced the competitive relationship between the bacterial groups. This may be why the addition of CSL accelerated the organic matter degradation and increased carbon and nitrogen preservation.

CONCLUSIONS

These findings indicate that the addition of CSL promoted the cycling and preservation of carbon and nitrogen in the SMS composts, and the addition of CSL to the compost may be an effective way to dispose of agricultural waste.

Microbial electrosynthesis of acetate from CO2 under hypersaline conditions

Microbial electrosynthesis (MES) enables the bioproduction of multicarbon compounds from CO₂ using electricity as the driver. Although high salinity can improve the energetic performance of bioelectrochemical systems, acetogenic processes under elevated salinity are poorly known. Here MES under 35-60 g L^-1 salinity was evaluated. Acetate production in two-chamber MES systems at 35 g L^-1 salinity (seawater composition) gradually decreased within 60 days, both under -1.2 V cathode potential (vs. Ag/AgCl) and -1.56 A m^-2 reductive current. Carbonate precipitation on cathodes (mostly CaCO₃) likely declined the production through inhibiting CO₂ supply, the direct electrode contact for acetogens and H₂ production. Upon decreasing Ca²⁺ and Mg²⁺ levels in three-chamber reactors, acetate was stably produced over 137 days along with a low cathode apparent resistance at 1.9 ± 0.6 mΩ m² and an average production rate at 3.80 ± 0.21 g m^-2 d^-1. Increasing the salinity step-wise from 35 to 60 g L^-1 gave the most efficient acetate production at 40 g L^-1 salinity with average rates of acetate production and CO₂ consumption at 4.56 ± 3.09 and 7.02 ± 4.75 g m^-2 d^-1, respectively. The instantaneous coulombic efficiency for VFA averaged 55.1 ± 31.4%. Acetate production dropped at higher salinity likely due to the inhibited CO₂ dissolution and acetogenic metabolism. Acetobacterium up to 78% was enriched on cathodes as the main acetogen at 35 g L^-1. Under high-salinity selection, 96.5% Acetobacterium dominated on the cathode along with 34.0% Sphaerochaeta in catholyte. This research provides a first proof of concept that MES starting from CO₂ reduction can be achieved at elevated salinity.

Microbial autotrophy explains large-scale soil CO2 fixation

Microbial communities play critical roles in fixing carbon from the atmosphere and fixing it in the soils. However, the large-scale variations and drivers of these microbial communities remain poorly understood. Here, we conducted a large-scale survey across China and found that soil autotrophic organisms are critical for explaining CO₂ fluxes from the atmosphere to soils. In particular, we showed that large-scale variations in CO₂ fixation rates are highly correlated to those in autotrophic bacteria and phototrophic protists. Paddy soils, supporting a larger proportion of obligate bacterial and protist autotrophs, display four-fold of CO₂ fixation rates over upland and forest soils. Precipitation and pH, together with key ecological clusters of autotrophic microbes, also played important roles in controlling CO₂ fixation. Our work provides a novel quantification on the contribution of terrestrial autotrophic microbes to soil CO₂ fixation processes at a large scale, with implications for global carbon regulation under climate change.

Depth wide distribution and metabolic potential of chemolithoautotrophic microorganisms reactivated from deep continental granitic crust underneath the Deccan Traps at Koyna, India

Characterization of inorganic carbon (C) utilizing microorganisms from deep crystalline rocks is of major scientific interest owing to their crucial role in global carbon and other elemental cycles. In this study we investigate the microbial populations from the deep [up to 2,908 meters below surface (mbs)] granitic rocks within the Koyna seismogenic zone, reactivated (enriched) under anaerobic, high temperature (50°C), chemolithoautotrophic conditions. Subsurface rock samples from six different depths (1,679-2,908 mbs) are incubated (180 days) with CO₂ (+H₂) or HCO₃ ^- as the sole C source. Estimation of total protein, ATP, utilization of NO₃ ^- and SO₄ ^2- and 16S rRNA gene qPCR suggests considerable microbial growth within the chemolithotrophic conditions. We note a better response of rock hosted community towards CO₂ (+H₂) over HCO₃ ^-. 16S rRNA gene amplicon sequencing shows a depth-wide distribution of diverse chemolithotrophic (and a few fermentative) Bacteria and Archaea. Comamonas, Burkholderia-Caballeronia-Paraburkholderia, Ralstonia, Klebsiella, unclassified Burkholderiaceae and Enterobacteriaceae are reactivated as dominant organisms from the enrichments of the deeper rocks (2335-2,908 mbs) with both CO₂ and HCO₃ ^-. For the rock samples from shallower depths, organisms of varied taxa are enriched under CO₂ (+H₂) and HCO₃ ^-. Pseudomonas, Rhodanobacter, Methyloversatilis, and Thaumarchaeota are major CO₂ (+H₂) utilizers, while Nocardioides, Sphingomonas, Aeromonas, respond towards HCO₃ ^-. H₂ oxidizing Cupriavidus, Hydrogenophilus, Hydrogenophaga, CO₂ fixing Cyanobacteria Rhodobacter, Clostridium, Desulfovibrio and methanogenic archaea are also enriched. Enriched chemolithoautotrophic members show good correlation with CO₂, CH₄ and H₂ concentrations of the native rock environments, while the organisms from upper horizons correlate more to NO₃ ^-, SO₄ ^2- _, Fe and TIC levels of the rocks. Co-occurrence networks suggest close interaction between chemolithoautotrophic and chemoorganotrophic/fermentative organisms. Carbon fixing 3-HP and DC/HB cycles, hydrogen, sulfur oxidation, CH₄ and acetate metabolisms are predicted in the enriched communities. Our study elucidates the presence of live, C and H₂ utilizing Bacteria and Archaea in deep subsurface granitic rocks, which are enriched successfully. Significant impact of depth and geochemical controls on relative distribution of various chemolithotrophic species enriched and their C and H₂ metabolism are highlighted. These endolithic microorganisms show great potential for answering the fundamental questions of deep life and their exploitation in CO₂ capture and conversion to useful products.

A review of recent advances in engineering bacteria for enhanced CO2 capture and utilization

Carbon dioxide (CO₂) is emitted into the atmosphere due to some anthropogenic activities, such as the combustion of fossil fuels and industrial output. As a result, fears about catastrophic global warming and climate change have intensified. In the face of these challenges, conventional CO₂ capture technologies are typically ineffective, dangerous, and contribute to secondary pollution in the environment. Biological systems for CO₂ conversion, on the other hand, provide a potential path forward owing to its high application selectivity and adaptability. Moreover, many bacteria can use CO₂ as their only source of carbon and turn it into value-added products. The purpose of this review is to discuss recent significant breakthroughs in engineering bacteria to utilize CO₂ and other one-carbon compounds as substrate. In the same token, the paper also summarizes and presents aspects such as microbial CO₂ fixation pathways, engineered bacteria involved in CO₂ fixation, up-to-date genetic and metabolic engineering approaches for CO₂ fixation, and promising research directions for the production of value-added products from CO₂. This review's findings imply that using biological systems like modified bacteria to manage CO₂ has the added benefit of generating useful industrial byproducts like biofuels, pharmaceutical compounds, and bioplastics. The major downside, from an economic standpoint, thus far has been related to methods of cultivation. However, thanks to genetic engineering approaches, this can be addressed by large production yields. As a result, this review aids in the knowledge of various biological systems that can be used to construct a long-term CO₂ mitigation technology at an industrial scale, in this instance bacteria-based CO₂capture/utilization technology.

Carbon Materials Advancing Microorganisms in Driving Soil Organic Carbon Regulation

Carbon emission from soil is not only one of the major sources of greenhouse gases but also threatens biological diversity, agricultural productivity, and food security. Regulation and control of the soil carbon pool are political practices in many countries around the globe. Carbon pool management in engineering sense is much bigger and beyond laws and monitoring, as it has to contain proactive elements to restore active carbon. Biogeochemistry teaches us that soil microorganisms are crucial to manage the carbon content effectively. Adding carbon materials to soil is thereby not directly sequestration, as interaction of appropriately designed materials with the soil microbiome can result in both: metabolization and thereby nonsustainable use of the added carbon, or-more favorably-a biological amplification of human efforts and sequestration of extra CO₂ by microbial growth. We review here potential approaches to govern soil carbon, with a special focus set on the emerging practice of adding manufactured carbon materials to control soil carbon and its biological dynamics. Notably, research on so-called "biochar" is already relatively mature, while the role of artificial humic substance (A-HS) in microbial carbon sequestration is still in the developing stage. However, it is shown that the preparation and application of A-HS are large biological levers, as they directly interact with the environment and community building of the biological soil system. We believe that A-HS can play a central role in stabilizing carbon pools in soil.

Enhancement of algae ponds for rural domestic sewage treatment by prolonging daylight using artificial lamps

Algal ponds (APs) are widely used as treatment facilities for domestic sewage in sparsely populated rural areas. However, few AP studies have focused on daylight length to enhance pollutants removal. In this study, four algae ponds were set up, daylight was prolonged by 0, 2, 4, and 6 h with an illuminating intensity of 3000 lx. The highest removal efficiencies of total nitrogen, ammonium, and total phosphorus were 37.36%, 41.20%, and 21.56% due to the highest microbial abundance under optimum conditions (2 h PD), respectively. Excessive PD (4 h and 6 h) could inhibit the removal abilities. PD also increased the maximum relative electron transport rate of algae, leading to an increase in the photosynthetic capacity of APs. Meanwhile, the high microbial abundance indicates that chemoheterotrophic bacteria are the main influencing factor for the removal of nitrogen and phosphorus by the APs. Moreover, the system with PD using artificial lamps was proven to be feasible for engineering applications and potentially utilized in rural domestic wastewater treatment.

Bio-conversion of CO2 into biofuels and other value-added chemicals via metabolic engineering

Carbon dioxide (CO₂) occurs naturally in the atmosphere as a trace gas, which is produced naturally as well as by anthropogenic activities. CO₂ is a readily available source of carbon that in principle can be used as a raw material for the synthesis of valuable products. The autotrophic organisms are naturally equipped to convert CO₂ into biomass by obtaining energy from sunlight or inorganic electron donors. This autotrophic CO₂ fixation has been exploited in biotechnology, and microbial cell factories have been metabolically engineered to convert CO₂ into biofuels and other value-added bio-based chemicals. A variety of metabolic engineering efforts for CO₂ fixation ranging from basic copy, paste, and fine-tuning approaches to engineering and testing of novel synthetic CO₂ fixing pathways have been demonstrated. In this paper, we review the current advances and innovations in metabolic engineering for bio-conversion of CO₂ into bio biofuels and other value-added bio-based chemicals.

Acetate as a potential feedstock for the production of value-added chemicals: Metabolism and applications

Acetate is regarded as a promising carbon feedstock in biological production owing to its possible derivation from C₁ gases such as CO, CO₂ and methane. To best use of acetate, comprehensive understanding of acetate metabolisms from genes and enzymes to pathways and regulations is needed. This review aims to provide an overview on the potential of acetate as carbon feedstock for industrial biotechnology. Biochemical, microbial and biotechnological aspects of acetate metabolism are described. Especially, the current state-of-the art in the production of value-added chemicals from acetate is summarized. Challenges and future perspectives are also provided.

Long-term chemical fertilization-driving changes in soil autotrophic microbial community depresses soil CO2 fixation in a Mollisol

Soil is the largest C pool in the terrestrial ecosystem. Numerous studies have been devoted to the decomposition of soil organic C as influenced by agricultural management. However, little is known about the effect of fertilization on the microbial CO₂ fixation potential. Here, we examined the atmospheric CO₂ fixation rates and structure of autotrophic cbbL-containing bacterial communities and accA-containing archaeal communities in response to 38 years of chemical and/or organic fertilizer application in a Mollisol. The autotrophic microbial abundance and community composition were analyzed by quantitative polymerase chain reaction and high throughput sequencing, respectively. Our results showed that chemical fertilization additions significantly decreased CO₂ fixation rates by 57%, but organic manure use resulted in no notable differences compared to no fertilizer regimes (0.38 mg CO₂ kg^-1 soil d^-1) through stable isotope methods. The declining soil pH and increasing Olsen-phosphorus in soils with chemical fertilization dramatically reduced the cbbL gene diversity and accA gene abundances and altered both the autotrophic bacterial and archaeal community compositions. The changes in CO₂-fixation rate were more greatly attributed to the shifts in autotrophic bacterial community composition than to the diversity and abundance. The C fixation potentials were positively correlated with the relative abundances of Acidiphilium and Methylibium but were negatively related to those of Azospirillum and Nitrosospira. Both composition and abundance of the autotrophic archaeal community contributed together to the CO₂ fixation activities. Our finding suggests that long-term chemical fertilization has a strong impact on the soil microbial CO₂ fixation activity and autotrophic microorganisms in upland soils and highlight the important roles of the CO₂ fixing process in soil organic carbon sequestration.

Geothermal Gases Shape the Microbial Community of the Volcanic Soil of Pantelleria, Italy

Volcanic and geothermal environments are characterized by low pH, high temperatures, and gas emissions consisting of mainly CO₂ and varied CH₄, H₂S, and H₂ contents which allow the formation of chemolithoautotrophic microbial communities. To determine the link between the emitted gases and the microbial community composition, geochemical and metagenomic analysis were performed. Soil samples of the geothermic region Favara Grande (Pantelleria, Italy) were taken at various depths (1 to 50 cm). Analysis of the gas composition revealed that CH₄ and H₂ have the potential to serve as the driving forces for the microbial community. Our metagenomic analysis revealed a high relative abundance of Bacteria in the top layer (1 to 10 cm), but the relative abundance of Archaea increased with depth from 32% to 70%. In particular, a putative hydrogenotrophic methanogenic archaeon, related to Methanocella conradii, appeared to have a high relative abundance (63%) in deeper layers. A variety of [NiFe]-hydrogenase genes were detected, showing that H₂ was an important electron donor for microaerobic microorganisms in the upper layers. Furthermore, the bacterial population included verrucomicrobial and proteobacterial methanotrophs, the former showing an up to 7.8 times higher relative abundance. Analysis of the metabolic potential of this microbial community showed a clear capacity to oxidize CH₄ aerobically, as several genes for distinct particulate methane monooxygenases and lanthanide-dependent methanol dehydrogenases (XoxF-type) were retrieved. Analysis of the CO₂ fixation pathways showed the presence of the Calvin-Benson-Bassham cycle, the Wood-Ljungdahl pathway, and the (reverse) tricarboxylic acid (TCA) cycle, the latter being the most represented carbon fixation pathway. This study indicates that the methane emissions in the Favara Grande might be a combination of geothermal activity and biological processes and further provides insights into the diversity of the microbial population thriving on CH₄ and H₂ IMPORTANCE The Favara Grande nature reserve on the volcanic island of Pantelleria (Italy) is known for its geothermal gas emissions and high soil temperatures. These volcanic soil ecosystems represent "hot spots" of greenhouse gas emissions. The unique community might be shaped by the hostile conditions in the ecosystem, and it is involved in the cycling of elements such as carbon, hydrogen, sulfur, and nitrogen. Our metagenome study revealed that most of the microorganisms in this extreme environment are only distantly related to cultivated bacteria. The results obtained profoundly increased the understanding of these natural hot spots of greenhouse gas production/degradation and will help to enrich and isolate the microbial key players. After isolation, it will become possible to unravel the molecular mechanisms by which they adapt to extreme (thermo/acidophilic) conditions, and this may lead to new green enzymatic catalysts and technologies for industry.

Key internal factors leading to the variability in CO2 fixation efficiency of different sulfur-oxidizing bacteria during autotrophic cultivation

Variability in the apparent CO₂ fixation yield of four aerobic sulfur-oxidizing bacteria (Halothiobacillus neapolitanus DSM 15147, Thiobacillus thioparus DSM 505, Thiomonas intermedia DSM 18155, and Starkeya novella DSM 506) in autotrophic culturing was studied, and mutual effects of key intrinsic factors on CO₂ fixation were explored. DSM 15147 and DSM 505 exhibited much higher CO₂ fixation yields than DSM 18155 and DSM 506. The differences in CO₂ fixation yield were determined not only by cbb gene transcription, but also by cell synthesis rate, which was determined by rRNA gene copy number; the rRNA gene copy number had a more significant effect than cbb gene transcription on the apparent CO₂ fixation yield. Moreover, accumulation of EDOC was observed in all four strains during chemoautotrophic cultivation, and the proportion of EDOC accounting for total fixed organic carbon (TOC; EDOC/TOC ratio) was much higher in DSM 18155 and DSM 506 than in DSM 15147 and DSM 505. The accumulation of EDOC led to a significant decrease in the cbb gene transcription efficiency during cultivation, and a further feedback inhibitory effect on CO₂ fixation.

Use of acetate for the production of 3-hydroxypropionic acid by metabolically-engineered Pseudomonas denitrificans

The use of acetate as carbon feedstock can enhance sustainability and economics of the current bio-productions. This study explored the potential of acetate for the production of 3-hydroxypropionic acid by engineered Pseudomonas denitrificans. Heterologous mcr (encoding malonyl-CoA reductase) from Chloroflexus aurantiacus and endogenous accABCD (encoding acetyl-CoA carboxylase) were overexpressed in P. denitrificans. Carbon flux to 3-HP synthesis at the malonyl-CoA node was promoted by suppressing fatty acid synthesis through addition of cerulenin or deletion of fabF gene. In addition, stimulation of glyoxylate shunt and/or TCA cycle were attempted. Recombinant P. denitrificans overexpressing mcr and accABCD produced 19.3 mM 3-HP with cerulenin addition, and 14.2 mM with fabF deletion, respectively. Furthermore, the non-growing cells devoid of fabF could continuously produce 3-HP up to 40.4 mM without losing its production activity for 22 h. This study demonstrates that acetate is a good substrate for 3-HP production by recombinant P. denitrificans.

Dark microbial CO2 fixation in temperate forest soils increases with CO2 concentration

Dark, that is, nonphototrophic, microbial CO₂ fixation occurs in a large range of soils. However, it is still not known whether dark microbial CO₂ fixation substantially contributes to the C balance of soils and what factors control this process. Therefore, the objective of this study was to quantitate dark microbial CO₂ fixation in temperate forest soils, to determine the relationship between the soil CO₂ concentration and dark microbial CO₂ fixation, and to estimate the relative contribution of different microbial groups to dark CO₂ fixation. For this purpose, we conducted a ¹³ C-CO₂ labeling experiment. We found that the rates of dark microbial CO₂ fixation were positively correlated with the CO₂ concentration in all soils. Dark microbial CO₂ fixation amounted to up to 320 µg C kg^-1  soil day^-1 in the Ah horizon. The fixation rates were 2.8-8.9 times higher in the Ah horizon than in the Bw1 horizon. Although the rates of dark microbial fixation were small compared to the respiration rate (1.2%-3.9% of the respiration rate), our findings suggest that organic matter formed by microorganisms from CO₂ contributes to the soil organic matter pool, especially given that microbial detritus is more stable in soil than plant detritus. Phospholipid fatty acid analyses indicated that CO₂ was mostly fixed by gram-positive bacteria, and not by fungi. In conclusion, our study shows that the dark microbial CO₂ fixation rate in temperate forest soils increases in periods of high CO₂ concentrations, that dark microbial CO₂ fixation is mostly accomplished by gram-positive bacteria, and that dark microbial CO₂ fixation contributes to the formation of soil organic matter.

H2 Metabolism revealed by metagenomic analysis of subglacial sediment from East Antarctica

Subglacial ecosystems harbor diverse chemoautotrophic microbial communities in areas with limited organic carbon, and lithological H₂ produced during glacial erosion has been considered an important energy source in these ecosystems. To verify the H₂-utilizing potential there and to identify the related energy-converting metabolic mechanisms of these communities, we performed metagenomic analysis on subglacial sediment samples from East Antarctica with and without H₂ supplementation. Genes coding for several [NiFe]-hydrogenases were identified in raw sediment and were enriched after H₂ incubation. All genes in the dissimilatory nitrate reduction and denitrification pathways were detected in the subglacial community, and the genes coding for these pathways became enriched after H₂ was supplied. Similarly, genes transcribing key enzymes in the Calvin cycle were detected in raw sediment and were also enriched. Moreover, key genes involved in H₂ oxidization, nitrate reduction, oxidative phosphorylation, and the Calvin cycle were identified within one metagenome-assembled genome belonging to a Polaromonas sp. As suggested by our results, the microbial community in the subglacial environment we investigated consisted of chemoautotrophic populations supported by H₂ oxidation. These results further confirm the importance of H₂ in the cryosphere.

Cloning, Expression and Characterization of Two Beta Carbonic Anhydrases from a Newly Isolated CO2 Fixer, Serratia marcescens Wy064

Bacterial strains from karst landform soil were enriched via chemostat culture in the presence of sodium bicarbonate. Two chemolithotrophic strains were isolated and identified as Serratia marcescens Wy064 and Bacillus sp. Wy065. Both strains could grow using sodium bicarbonate as the sole carbon source. Furthermore, the supplement of the medium with three electron donors (Na₂S, NaNO₂, and Na₂S₂O₃) improved the growth of both strains. The activities of carbonic anhydrase (CA) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) could be detected in the crude enzyme of strain Wy064, implying that the strain Wy064 might employ Calvin cycle to fix CO₂. S. marcescens genome mining revealed four potential CA genes designated CA1-CA4. The proteins encoded by genes CA1-3 were cloned and expressed in Escherichia coli. The purified recombinant enzymes of CA1 and CA3 exhibited CO₂ hydration activities, whereas enzyme CA2 was expressed in inclusion bodies. A CO₂ hydration assay demonstrated that the specific activity of CA3 was significantly higher than that of CA1. The maximum CO₂ hydration activities for CA1 and CA3 were observed at pH 7.5 and 40 °C. The activities of CA1 and CA3 were significantly enhanced by several metal ions, especially Zn²⁺, which resulted in 21.1-fold and 26.1-fold increases of CO₂ hydration activities, respectively. The apparent K _m and V _max for CO₂ as substrate were 27 mM and 179 WAU/mg for CA1, and 14 mM and 247 WAU/mg for CA3, respectively. Structure modeling combined with sequence analysis indicated that CA1 and CA3 should belong to the Type II β-CA.

Carbon dioxide and organic waste valorization by microbial electrosynthesis and electro-fermentation

Carbon-rich waste materials (solid, liquid, or gaseous) are largely considered to be a burden on society due to the large capital and energy costs for their treatment and disposal. However, solid and liquid organic wastes have inherent energy and value, and similar as waste CO₂ gas they can be reused to produce value-added chemicals and materials. There has been a paradigm shift towards developing a closed loop, biorefinery approach for the valorization of these wastes into value-added products, and such an approach enables a more carbon-efficient and circular economy. This review quantitatively analyzes the state-of-the-art of the emerging microbial electrochemical technology (MET) platform and provides critical perspectives on research advancement and technology development. The review offers side-by-side comparison between microbial electrosynthesis (MES) and electro-fermentation (EF) processes in terms of principles, key performance metrics, data analysis, and microorganisms. The study also summarizes all the processes and products that have been developed using MES and EF to date for organic waste and CO₂ valorization. It finally identifies the technological and economic potentials and challenges on future system development.

Expanding the product spectrum of value added chemicals in microbial electrosynthesis through integrated process design-A review

Microbial electrosynthesis (MES) is a novel microbial electrochemical technology proposed for chemicals production with the storage of sustainable energy. However, the practical application of MES is currently restricted by the limited low market value of products in one-step conversion process, mostly acetate. A theme that is pervasive throughout this review is the challenges associated with the expanded product spectrum. Several recent research efforts to improve acetate production, using novel reactor configuration, renewable power supply, and various 3-D cathode are summarized. The importance of genetic modification, two-step hybrid process, as well as input substrates other than CO₂ are highlighted in this review as the future research paths for higher value chemicals production. At last, how to integrate MES with existing biochemicals processes is proposed. Definitely, more studies are encouraged to evaluate the overall performances and economic efficiency of these integrated process designs to make MES more competitive.

Engineering Microorganisms for Enhanced CO2 Sequestration

Microbial CO₂ sequestration not only provides a green and sustainable approach for ameliorating global warming but also simultaneously produces biofuels and chemicals. However, the efficiency of microbial CO₂ fixation is still very low. In addition, concomitant microbial CO₂ emission decreases the carbon yield of desired chemicals. To address these issues, strategies including engineering CO₂-fixing pathways and energy-harvesting systems have been developed to improve the efficiency of CO₂ fixation in autotrophic and heterotrophic microorganisms. Furthermore, metabolic pathways and energy metabolism can be rewired to reduce microbial CO₂ emissions and increase the carbon yield of value-added products. This review highlights the potential of biotechnology to promote microbial CO₂ sequestration and provides guidance for the broader use of microorganisms as attractive carbon sinks.

Inhibitory effect of self-generated extracellular dissolved organic carbon on carbon dioxide fixation in sulfur-oxidizing bacteria during a chemoautotrophic cultivation process and its elimination

The features of extracellular dissolved organic carbon (EDOC) generation in two typical aerobic sulfur-oxidizing bacteria (Thiobacillus thioparus DSM 505 and Halothiobacillus neapolitanus DSM 15147) and its impact on CO₂ fixation during chemoautotrophic cultivation process were investigated. The results showed that EDOC accumulated in both strains during CO₂ fixation process. Large molecular weight (MW) EDOC derived from cell lysis and decay was dominant during the entire process in DSM 505, whereas small MW EDOC accounted for a large proportion during initial and middle stages of DSM 15147 as its cytoskeleton synthesis rate did not keep up with CO₂ assimilation rate. The self-generated EDOC feedback repressed cbb gene transcription and thus decreased total bacterial cell number and CO₂ fixation yield in both strains, but DSM 505 was more sensitive to this inhibition effect. Moreover, the membrane bioreactor effectively decreased the EDOC/TOC ratio and improved carbon fixation yield of DSM 505.

High-value biomass from microalgae production platforms: strategies and progress based on carbon metabolism and energy conversion

Microalgae are capable of producing sustainable bioproducts and biofuels by using carbon dioxide or other carbon substances in various cultivation modes. It is of great significance to exploit microalgae for the economical viability of biofuels and the revenues from high-value bioproducts. However, the industrial performance of microalgae is still challenged with potential conflict between cost of microalgae cultivation and revenues from them, which is mainly ascribed to the lack of comprehensive understanding of carbon metabolism and energy conversion. In this review, we provide an overview of the recent advances in carbon and energy fluxes of light-dependent reaction, Calvin-Benson-Bassham cycle, tricarboxylic acid cycle, glycolysis pathway and processes of product biosynthesis in microalgae, with focus on the increased photosynthetic and carbon efficiencies. Recent strategies for the enhanced production of bioproducts and biofuels from microalgae are discussed in detail. Approaches to alter microbial physiology by controlling light, nutrient and other environmental conditions have the advantages of increasing biomass concentration and product yield through the efficient carbon conversion. Engineering strategies by regulating carbon partitioning and energy route are capable of improving the efficiencies of photosynthesis and carbon conversion, which consequently realize high-value biomass. The coordination of carbon and energy fluxes is emerging as the potential strategy to increase efficiency of carbon fixation and product biosynthesis. To achieve more desirable high-value products, coordination of multi-stage cultivation with engineering and stress-based strategies occupies significant positions in a long term.

Carbon dioxide capture, storage and production of biofuel and biomaterials by bacteria: A review

Due to industrialization and urbanization, as humans continue to rely on fossil fuels, carbon dioxide (CO₂) will inevitably be generated and result in an increase of Global Warming Gases (GWGs). However, their prospect is misted up because of the environmental and economic intimidation posed by probable climate shift, generally called it as the "green house effect". Among all GWGs, the major contributor in greenhouse effect is CO₂. Mitigation strategies that include capture and storage of CO₂ by biological means may reduce the impact of CO₂ emissions on environment. The biological CO₂ sequestration has significant advantage, since increasing atmospheric CO₂ level supports productivity and overall storage capacity of the natural system. This paper reviews CO₂ sequestration mechanism in bacteria and their pathways for production of value added products such as, biodiesel, bioplastics, extracellular polymeric substance (EPS), biosurfactants and other related biomaterials.

Complete genome sequence of the sulfur-oxidizing chemolithoautotrophic Sulfurovum lithotrophicum 42BKTT

A sulfur-oxidizing chemolithoautotrophic bacterium, Sulfurovum lithotrophicum 42BKT^T, isolated from hydrothermal sediments in Okinawa, Japan, has been used industrially for CO₂ bio-mitigation owing to its ability to convert CO₂ into C₅H₈NO₄⁻ at a high rate of specific mitigation (0.42 g CO₂/cell/h). The genome of S. lithotrophicum 42BKT^T comprised of a single chromosome of 2217,891 bp with 2217 genes, including 2146 protein-coding genes and 54 RNA genes. Here, we present its complete genome-sequence information, including information about the genes encoding enzymes involved in CO₂ fixation and sulfur oxidation.

Large perturbations in CO2 flux and subsequent chemosynthesis are induced in agricultural soil by the addition of elemental sulfur

The microbial contribution to soil organic matter has been shown to be much larger than previously thought and thus it plays a major role in carbon cycling. Among soil microorganisms, chemoautotrophs can fix CO₂ without sunlight and can glean energy through the oxidation of reduced elements such as sulfur. Here we show that the addition of sulfur to soil results in an initial surge in production of CO₂ through microbial respiration, followed by an order of magnitude increase in the capture of carbon from the atmosphere as elemental sulfur is oxidised to sulfate. Thiobacillus spp., take advantage of specific conditions to become the dominant chemoautotrophic group that consumes CO₂. We discern the direct incorporation of atmospheric carbon into soil carbohydrate, protein and aliphatic compounds and differentiate these from existing biomass. These results suggest that chemoautotrophs can play a large role in carbon cycling and that this carbon is heavily influenced by land management practises.

Genome Sequence of Carbon Dioxide-Sequestering Serratia sp. Strain ISTD04 Isolated from Marble Mining Rocks

The Serratia sp. strain ISTD04 has been identified as a carbon dioxide (CO₂)-sequestering bacterium isolated from marble mining rocks in the Umra area, Rajasthan, India. This strain grows chemolithotrophically on media that contain sodium bicarbonate (NaHCO₃) as the sole carbon source. Here, we report the genome sequence of 5.07 Mb Serratia sp. ISTD04.

Evaluation of 3-hydroxypropionate biosynthesis in vitro by partial introduction of the 3-hydroxypropionate/4-hydroxybutyrate cycle from Metallosphaera sedula

The chemical 3-hydroxypropionate (3HP) is an important starting reagent for the commercial synthesis of specialty chemicals. In this study, a part of the 3-hydroxypropionate/4-hydroxybutyrate cycle from Metallosphaera sedula was utilized for 3HP production. To study the basic biochemistry of this pathway, an in vitro-reconstituted system was established using acetyl-CoA as the substrate for the kinetic analysis of this system. The results indicated that 3HP formation was sensitive to acetyl-CoA carboxylase and malonyl-CoA reductase, but not malonate semialdehyde reductase. Also, the competition between 3HP formation and fatty acid production was analyzed both in vitro and in vivo. This study has highlighted how metabolic flux is controlled by different catalytic components. We believe that this reconstituted system would be valuable for understanding 3HP biosynthesis pathway and for future engineering studies to enhance 3HP production.

Production of 3-Hydroxypropionic Acid via the Propionyl-CoA Pathway Using Recombinant Escherichia coli Strains

Our study aimed to produce the commercially promising platform chemical 3-hydroxypropionic acid (3-HP) via the propionyl-CoA pathway in genetically engineered Escherichia coli. Recombinant E. coli Ec-P overexpressing propionyl-CoA dehydrogenase (PACD, encoded by the pacd gene from Candida rugosa) under the T7 promoter produced 1.33 mM of 3-HP in a shake flask culture supplemented with 0.5% propionate. When propionate CoA-transferase (PCT, encoded by the pct gene from Megasphaera elsdenii) and 3-hydroxypropionyl-CoA dehydratase (HPCD, encoded by the hpcd gene from Chloroflexus aurantiacus) were expressed along with PACD, the 3-HP titer of the resulting E. coli Ec-PPH strain was improved by 6-fold. The effect of the cultivation conditions on the 3-HP yield from propionate in the Ec-PPH strain was also investigated. When cultured at 30°C with 1% glucose in addition to propionate, 3-HP production by Ec-PPH increased 2-fold and 12-fold compared to the cultivation at 37°C (4.23 mM) or without glucose (0.68 mM). Deletion of the ygfH gene encoding propionyl-CoA: succinate CoA-transferase from Ec-PPH (resulting in the strain Ec-△Y-PPH) led to increase of 3-HP production in shake flask experiments (15.04 mM), whereas the strain Ec-△Y-PPH with deletion of the prpC gene (encoding methylcitrate synthase in the methylcitrate cycle) produced 17.76 mM of 3-HP. The strain Ec-△Y-△P-PPH with both ygfH and prpC genes deleted produced 24.14 mM of 3-HP, thus showing an 18-fold increase in the 3-HP titer in compare to the strain Ec-P.

Ecological restoration alters microbial communities in mine tailings profiles

Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0-30 cm soils and altered the bacterial communities at 0-20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30-60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0-20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.

Energetic assessment of fixation of CO2 and subsequent biofuel production using B. cereus SM1 isolated from sewage treatment plant

The ongoing work on global warming resulting from green house gases (GHGs) has led to explore the possibility of bacterial strains which can fix carbon dioxide (CO2) and can generate value-added products. The present work is an effort in this direction and has carried out an exhaustive batch experiments for the fixation of CO2 using B. Cereus SM1 isolated from sewage treatment plant (STP). The work has incorporated 5-day batch run for gaseous phase inlet CO2 concentration of 13 ± 1 % (%v/v). 84.6 (±5.76) % of CO2 removal was obtained in the gaseous phase at mentioned CO2 concentration (%v/v). Energetic requirement for CO2 fixation was assessed by varying Fe[II] ion concentration (0-200 ppm) on the per-day basis. The cell lysate obtained from CO2 fixation studies (Fe[II] ion = 100 ppm) was analyzed using Fourier transformation infrared spectroscopy (FTIR) and gas chromatography-mass spectroscopy (GC-MS). This analysis confirmed the presence of fatty acids and hydrocarbon as valuable products. The hydrocarbons were found in the range of C11-C22 which is equivalent to light oil. The obtained fatty acids were found in the range of C11-C19. The possibility of fatty acid conversion to biodiesel was explored by carrying out the transesterification reaction. The yield of biodiesel was obtained as 86.5 (±0.048) % under the transesterification reaction conditions. Results of this research work can provide the valuable information in the implementation of biomitigation of CO2 at real scenario.

Successful bi-enzyme stabilization for the biomimetic cascade transformation of carbon dioxide

In nature, carbon dioxide (CO₂) conversion to valuable chemicals occurs via several metabolic pathways through multi-enzymatic reactions.

Flux measurements and maintenance energy for carbon dioxide utilization by Methanococcus maripaludis

BACKGROUND

The rapidly growing mesophilic methanogen Methanococcus maripaludis S2 has a unique ability to consume both CO2 and N2, the main components of a flue gas, and produce methane with H2 as the electron donor. The existing literature lacks experimental measurements of CO2 and H2 uptake rates and CH4 production rates on M. maripaludis. Furthermore, it lacks estimates of maintenance energies for use with genome-scale models. In this paper, we performed batch culture experiments on M. maripaludis S2 using CO2 as the sole carbon substrate to quantify three key extracellular fluxes (CO2, H2, and CH4) along with specific growth rates. For precise computation of these fluxes from experimental measurements, we developed a systematic process simulation approach. Then, using an existing genome-scale model, we proposed an optimization procedure to estimate maintenance energy parameters: growth associated maintenance (GAM) and non-growth associated maintenance (NGAM).

RESULTS

The measured extracellular fluxes for M. maripaludis showed excellent agreement with in silico predictions from a validated genome-scale model (iMM518) for NGAM = 7.836 mmol/gDCW/h and GAM = 27.14 mmol/gDCW. M. maripaludis achieved a CO2 to CH4 conversion yield of 70-95 % and a growth yield of 3.549 ± 0.149 g DCW/mol CH4 during the exponential phase. The ATP gain of 0.35 molATP/molCH4 for M. maripaludis, computed using NGAM, is in the acceptable range of 0.3-0.7 mol ATP/molCH4 reported for methanogens. Interestingly, the uptake distribution of amino acids, quantified using iMM518, confirmed alanine to be the most preferred amino acids for growth and methanogenesis.

CONCLUSIONS

This is the first study to report experimental gas consumption and production rates for the growth of M. maripaludis on CO2 and H2 in minimal media. A systematic process simulation and optimization procedure was successfully developed to precisely quantify extracellular fluxes along with cell growth and maintenance energy parameters. Our growth yields, ATP gain, and energy parameters fall within acceptable ranges known in the literature for hydrogenotrophic methanogens.

Optimization of inorganic carbon sources to improve the carbon fixation efficiency of the non-photosynthetic microbial community with different electron donors

As the non-photosynthetic microbial community (NPMC) isolated from seawaters utilized inorganic carbon sources for carbon fixation, the concentrations and ratios of Na2CO3, NaHCO3, and CO2 were optimized by response surface methodology design. With H2 as the electron donor, the optimal carbon sources were 270 mg/L Na2CO3, 580 mg/L NaHCO3, and 120 mg/L CO2. The carbon fixation efficiency in response to total organic carbon (TOC) was up to 30.59 mg/L with optimal carbon sources, which was about 50% higher than that obtained with CO2 as the sole carbon source. The mixture of inorganic carbon sources developed a buffer system to prevent acidification or alkalization of the medium caused by CO2 or Na2CO3, respectively. Furthermore, CO2 and HCO3(-), the starting points of carbon fixation in the pathways of Calvin-Benson-Bassham and 3-hydroxypropionate cycles, were provided by the carbon source structure to facilitate carbon fixation by NPMC. However, in the presence of mixed electron donors composed of 1.25% Na2S, 0.50% Na2S2O3, and 0.457% NaNO2, the carbon source structure did not exhibit significant improvement in the carbon fixation efficiency, when compared with that achieved with CO2 as the sole carbon source. The positive effect of mixed electron donors on inorganic carbon fixation was much higher than that of the carbon source structure. Nevertheless, the carbon source structure could be used as an alternative to CO2 when using NPMC to fix carbon in industrial processes.

A genome-scale metabolic model of Methanococcus maripaludis S2 for CO2 capture and conversion to methane

Methane is a major energy source for heating and electricity. Its production by methanogenic bacteria is widely known in nature. M. maripaludis S2 is a fully sequenced hydrogenotrophic methanogen and an excellent laboratory strain with robust genetic tools. However, a quantitative systems biology model to complement these tools is absent in the literature. To understand and enhance its methanogenesis from CO2, this work presents the first constraint-based genome-scale metabolic model (iMM518). It comprises 570 reactions, 556 distinct metabolites, and 518 genes along with gene-protein-reaction (GPR) associations, and covers 30% of open reading frames (ORFs). The model was validated using biomass growth data and experimental phenotypic studies from the literature. Its comparison with the in silico models of Methanosarcina barkeri, Methanosarcina acetivorans, and Sulfolobus solfataricus P2 shows M. maripaludis S2 to be a better organism for producing methane. Using the model, genes essential for growth were identified, and the efficacies of alternative carbon, hydrogen and nitrogen sources were studied. The model can predict the effects of reengineering M. maripaludis S2 to guide or expedite experimental efforts.

Chemical and genomic evolution of enzyme-catalyzed reaction networks

There is a tendency that a unit of enzyme genes in an operon-like structure in the prokaryotic genome encodes enzymes that catalyze a series of consecutive reactions in a metabolic pathway. Our recent analysis shows that this and other genomic units correspond to chemical units reflecting chemical logic of organic reactions. From all known metabolic pathways in the KEGG database we identified chemical units, called reaction modules, as the conserved sequences of chemical structure transformation patterns of small molecules. The extracted patterns suggest co-evolution of genomic units and chemical units. While the core of the metabolic network may have evolved with mechanisms involving individual enzymes and reactions, its extension may have been driven by modular units of enzymes and reactions.

RubisCO-based CO2 fixation and C1 metabolism in the actinobacterium Pseudonocardia dioxanivorans CB1190

Pseudonocardia is an actinobacterial genus of interest due to its potential biotechnological, medical and environmental remediation applications, as well as for the ecologically relevant symbiotic relationships it forms with attine ants. Some Pseudonocardia spp. can grow autotrophically, but the genetic basis of this capability has not previously been reported. In this study, we examined autotrophy in Pseudonocardia dioxanivorans CB1190, which can grow using H2 and CO2, as well as heterotrophically. Genomic and transcriptomic analysis of CB1190 cells grown with H2/bicarbonate implicated the Calvin-Benson-Bassham (CBB) cycle in growth-supporting CO2 fixation, as well as a [NiFe] hydrogenase-encoding gene cluster in H2 oxidation. The CBB cycle genes are evolutionarily most related to actinobacterial homologues, although synteny has not been maintained. Ribulose-1,5-bisphosphate carboxylase activity was confirmed in H2/bicarbonate-grown CB1190 cells and was detected in cells grown with the C1 compounds formate, methanol and carbon monoxide. We also demonstrated the upregulation of CBB cycle genes upon exposure of CB1190 to these C1 substrates, and identified genes putatively involved in generating CO2 from the C1 substrates by using RT-qPCR. Finally, the potential for autotrophic growth of other Pseudonocardia spp. was explored, and the ecological implications of autotrophy in attine ant- and plant root-associated Pseudonocardia discussed.

Modeling phenotypic metabolic adaptations of Mycobacterium tuberculosis H37Rv under hypoxia

The ability to adapt to different conditions is key for Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), to successfully infect human hosts. Adaptations allow the organism to evade the host immune responses during acute infections and persist for an extended period of time during the latent infectious stage. In latently infected individuals, estimated to include one-third of the human population, the organism exists in a variety of metabolic states, which impedes the development of a simple strategy for controlling or eradicating this disease. Direct knowledge of the metabolic states of M. tuberculosis in patients would aid in the management of the disease as well as in forming the basis for developing new drugs and designing more efficacious drug cocktails. Here, we propose an in silico approach to create state-specific models based on readily available gene expression data. The coupling of differential gene expression data with a metabolic network model allowed us to characterize the metabolic adaptations of M. tuberculosis H37Rv to hypoxia. Given the microarray data for the alterations in gene expression, our model predicted reduced oxygen uptake, ATP production changes, and a global change from an oxidative to a reductive tricarboxylic acid (TCA) program. Alterations in the biomass composition indicated an increase in the cell wall metabolites required for cell-wall growth, as well as heightened accumulation of triacylglycerol in preparation for a low-nutrient, low metabolic activity life style. In contrast, the gene expression program in the deletion mutant of dosR, which encodes the immediate hypoxic response regulator, failed to adapt to low-oxygen stress. Our predictions were compatible with recent experimental observations of M. tuberculosis activity under hypoxic and anaerobic conditions. Importantly, alterations in the flow and accumulation of a particular metabolite were not necessarily directly linked to differential gene expression of the enzymes catalyzing the related metabolic reactions.

Mycobacterium tuberculosis latently infects one-third of the human population and is responsible for millions of deaths worldwide every year. The ability of the pathogen to persist in the human population stems from its capacity to adapt to host-induced stresses and adjust its metabolism to different host environments. We have developed a novel model to interpret M. tuberculosis H37Rv metabolic adjustment by combining gene transcription data with a genome-scale metabolic network model. Using our model, we were able to identify the changes in the metabolic program associated with hypoxia, predict phenotypic change, and determine the critical metabolic enzymes and pathways that are required for pathogen survival. In particular, we predicted the switch in the tricarboxylic acid cycle from an oxidative to a reductive path. The altered importance of different metabolites and pathways under hypoxic conditions may provide guidance for designing novel, adjuvant drug therapies for clearing persistent and latent infections.