Carbon Flow Research Articles

The Carbon Flow Shifts from Primary to Secondary Metabolism during Xylem Vessel Cell Differentiation inArabidopsis thaliana.

Xylem vessel cell differentiation is characterized by the deposition of a secondary cell wall (SCW) containing cellulose, hemicellulose and lignin. VASCULAR-RELATED NAC-DOMAIN7 (VND7), a plant-specific NAC (NAM, ATAF1/2, and CUC2) transcription factor, is a master regulator of xylem vessel cell differentiation in Arabidopsis (Arabidopsis thaliana). Previous metabolome analysis using the VND7-inducible system in tobacco BY-2 cells successfully revealed significant quantitative changes in primary metabolites during xylem vessel cell differentiation. However, the flow of primary metabolites is not yet well understood. Here, we performed a metabolomic analysis of VND7-inducible Arabidopsis T87 suspension cells. Capillary electrophoresis-time-of-flight mass spectrometry quantified 57 metabolites, and subsequent data analysis highlighted active changes in the levels of UDP-glucose and phenylalanine, which are building blocks of cellulose and lignin, respectively. In a metabolic flow analysis using stable carbon 13 (13C) isotope, the 13C-labeling ratio specifically increased in 3-phosphoglycerate after 12 h of VND7 induction, followed by an increase in shikimate after 24 h of induction, while the inflow of 13C into lactate from pyruvate was significantly inhibited, indicating an active shift of carbon flow from glycolysis to the shikimate pathway during xylem vessel cell differentiation. In support of this notion, most glycolytic genes involved in the downstream of glyceraldehyde 3-phosphate were downregulated following the induction of xylem vessel cell differentiation, whereas genes for the shikimate pathway and phenylalanine biosynthesis were upregulated. These findings provide evidence for the active shift of carbon flow from primary metabolic pathways to the SCW polymer biosynthetic pathway at specific points during xylem vessel cell differentiation.

Regulatory NADH dehydrogenase-like complex optimizes C4 photosynthetic carbon flow and cellular redox in maize.

C4 plants typically operate a CO2 concentration mechanism from mesophyll (M) cells into bundle sheath (BS) cells. NADH dehydrogenase-like (NDH) complex is enriched in the BS cells of many NADP-malic enzyme (ME) type C4 plants and is more abundant in C4 than in C3 plants, but to what extent it is involved in the CO2 concentration mechanism remains to be experimentally investigated. We created maize and rice mutants deficient in NDH function and then used a combination of transcriptomic, proteomic, and metabolomic approaches for comparative analysis. Considerable decreases in growth, photosynthetic activities, and levels of key photosynthetic proteins were observed in maize but not rice mutants. However, transcript abundance for many cyclic electron transport (CET) and Calvin-Benson cycle components, as well as BS-specific C4 enzymes, was increased in maize mutants. Metabolite analysis of the maize ndh mutants revealed an increased NADPH : NADP ratio, as well as malate, ribulose 1,5-bisphosphate (RuBP), fructose 1,6-bisphosphate (FBP), and photorespiration intermediates. We suggest that by optimizing NADPH and malate levels and adjusting NADP-ME activity, NDH functions to balance metabolic and redox states in the BS cells of maize (in addition to ATP supply), coordinating photosynthetic transcript abundance and protein content, thus directly regulating the carbon flow in the two-celled C4 system of maize.

Spatiotemporal variations of water, land, and carbon footprints of pig production in China

Pig production not only consumes large water and land, but also emits substantial greenhouse gases. Scholars have used environmental footprint, including water, land, and carbon footprints, to assess the environmental impacts of pig production. However, there is a lack of simultaneous analysis of water, land, and carbon footprints for pig production, particularly in China, the leading pig breeding and consumption country in the world. In this study, we used environmental footprint analysis to develop a water-land-carbon footprint model for pig production system from the life cycle perspective. We also examined virtual water, land and carbon flows embedded in trade. The life cycle of pig production mainly involves feed crop cultivation, feed production, and pig breeding. Then we analyzed the water, land, and carbon footprints of the pig production in China from 1990 to 2018. The findings indicated that both the total water footprint and the total land footprint increased, whereas the total carbon footprints fluctuated over the years. All the unit footprints generally decreased. Feed crop cultivation had a significant impact on the footprints. Regarding the spatial characteristics in China, all the three total footprints were generally higher in the southeast compared to the northwest. While the unit footprints in different provinces exhibited spatial heterogeneity, primarily attributed to the different feed consumptions. Overall, the trade of feed crop shifted virtual water, land and carbon flows from the north to the south, reducing the three total footprints on the whole. To achieve a resource-saving and eco-friendly pig production in China, we proposed some potential recommendations, including improving feed crop cultivation techniques, reducing feed conversion ratio, implementing precision feeding, and managing manure. We hope not only mitigate the environmental impacts of China’s pig production, but also provide references for achieving agricultural sustainability in other regions of the world.

Biomass chemical looping: Advancements and strategies with the moving bed reactor for gasification and hydrogen generation

This work presents advances in OSU's BTS technology, targeted explicitly toward hydrogen production from experimental and process simulation results. Two experimental parameters: residence time and enhancer steam flowrate, are explored. A volume reduction of ∼67 % can be achieved in Reducer while ensuring high char conversion. The steam injection enhances char gasification and H2 content; however, it may lead to increased tar content due to decreased gas residence time. The steam injection of ∼5 % of the inlet carbon flow rate can be adequate for efficient biomass gasification and injecting additional steam downstream into the WGS unit is optimal for H2 generation. Two cases that implement modularization for tighter process integration are compared with the conventional BTS and BDCL processes for H2 generation. The application of modularization eliminates the energy-intensive AGR unit and increases ETE by ∼17 % over the BTS process. Modularization offers product flexibility and increased control with lower operational risks over the BDCL process but at 7 % lower ETE, which can be attributed to the high amounts of oxygen present in the biomass, leading to decreased syngas purity. H2 yield can be further increased by co-injection of low oxygen feedstocks such as plastics, which can increase H2 yield by ∼12 %.

Evaluating nutrient limitation in co-culture of Chlorella pyrenoidosa and Rhodobacter sphaeroides

The influence of nitrogen deficiency on microalgae-bacteria co-culture has been studied mostly with nitrogen-fixing bacteria. Photosynthetic bacteria (PSB), which are non-nitrogen-fixing bacteria, the impact of N deficiency on its co-culture with microalgae is unknown. In this study, Chlorella pyrenoidosa and Rhodobacter sphaeroides co-culture was cultivated photoheterotrophically with acetate. The impact of N starvation and different P supply levels on oil production were examined. When phosphorus was sufficient, N starvation increased the fatty acid methyl ester (FAME) content from 21.7 % to 28.2 %, and also increased the FAME yield (g CODFAME/g CODAcetate) from 0.17 to 0.22. However, the biomass and FAME productivities decreased. Sufficient phosphorus was also essential for a high growth rate and FAME productivity. Deficiencies in either N or P led to a decrease in the proportion of unsaturated FAMEs. iTRAQ analysis indicated N starvation promoted oil accumulation by driving the carbon flow to fatty acid synthesis in microalgae from co-culture. This study improves the understanding of biomass and lipid production via microalgae-PSB co-culture in photoheterotrophic cultivation. The mechanism of interaction between microalgae and bacteria needs further study.

Mapping CO2 spatiotemporal transfers embodied in China's trade using a global dynamic network model endogenizing fixed capital

A systematic approach that accurately assesses carbon emissions is essential to design climate policies. To fully consider the impacts of the intertemporal dynamics of using the past-formed capital for future production, endogenizing capital as an input into carbon accounting system has been proposed, and lead to the reallocation of emissions. However, little is known about how this reallocation occur, i.e., how carbon flows from the past-formed capital to the products it is used to produce and to the consumers who purchase these products. Here, enabled by a global CO2 transfer network model with capital endogenization, we take China as an example to trace the full process of CO2 spatiotemporal transfer and re-assess CO2 footprints. China contributed more than 40% of the global capital-related CO2 emissions with only 14% of global capital consumption. China drove domestic and foreign CO2 emissions mainly through purchasing service products, while foreign regions outsourced an order of magnitude higher emissions to China by importing products such as electricity, machinery and equipment. Along temporal horizons, CO2 emitted in historical years contributed 87% of the total emissions embodied in China's capital consumption, while new-formed capital contained 5.50 Gt CO2 emissions, which will be attributed to the future. Based on this, China's dynamic CO2 footprint was re-assessed as 4.65 Gt, an increase of more than 1/4 over the traditional results. This increase comes mainly from service products directly consuming building structure, especially real estate and public administration services. This study provided new understanding of CO2 accounting and identified new hotspots for differentiated climate policies.

Proteome efficiency of metabolic pathways in Escherichia coli increases along the nutrient flow.

Understanding the allocation of the cellular proteome to different cellular processes is central to unraveling the organizing principles of bacterial physiology. Proteome allocation to protein translation itself is maximally efficient, i.e., it represents the minimal allocation of dry mass able to sustain the observed protein production rate. In contrast, recent studies on bacteria have demonstrated that the concentrations of many proteins exceed the minimal level required to support the observed growth rate, indicating some heterogeneity across pathways in their proteome efficiency. Here, we systematically analyze the proteome efficiency of metabolic pathways, which together account for more than half of the Escherichia coli proteome during exponential growth. Comparing the predicted minimal and the observed proteome allocation to different metabolic pathways across growth conditions, we find that the protein abundance in the most costly biosynthesis pathways-those for amino acid biosynthesis and cofactor biosynthesis-is regulated for near-optimal efficiency. Overall, proteome efficiency increases along the carbon flow through the metabolic network; proteins involved in pathways of nutrient uptake and central metabolism tend to be highly over-abundant, while proteins involved in anabolic pathways and in protein translation are much closer to the expected minimal abundance across conditions. Our work thus provides a bird's-eye view of metabolic pathway efficiency, demonstrating systematic deviations from optimal cellular efficiency at the network level. IMPORTANCE Protein translation is the most expensive cellular process in fast-growing bacteria, and efficient proteome usage should thus be under strong natural selection. However, recent studies show that a considerable part of the proteome is unneeded for instantaneous cell growth in Escherichia coli. We still lack a systematic understanding of how this excess proteome is distributed across different pathways as a function of the growth conditions. We estimated the minimal required proteome across growth conditions in E. coli and compared the predictions with experimental data. We found that the proteome allocated to the most expensive internal pathways, including translation and the synthesis of amino acids and cofactors, is near the minimally required levels. In contrast, transporters and central carbon metabolism show much higher proteome levels than the predicted minimal abundance. Our analyses show that the proteome fraction unneeded for instantaneous cell growth decreases along the nutrient flow in E. coli.

Transcriptional profile reveals the physiological responses to prey availability in the mixotrophic chrysophyte Poterioochromonas malhamensis.

Mixotrophic flagellates, which have diverse nutritional modes and play important roles in connecting the microbial loop with the classical food chain, are ideal models to study the mechanisms of adaptation between different nutritional modes in protists. In their natural ecosystems, mixotrophic flagellates may encounter microalgal prey of different digestibility, which may affect the carbon flow. To date, a molecular biological view of the metabolic processes in the mixotrophic flagellate Poterioochromonas malhamensis during nutritional adaptation and feeding on microalgal prey of different digestibility is still lacking. Accordingly, this study focused on the gene expression differences in P. malhamensis under autotrophy, being fed by the digestible microalga Chlorella sorokiniana GT-1, and being fed by the indigestible microalga C. sorokiniana CMBB-146. Results showed that the growth rate of P. malhamensis under autotrophy was much lower than that when fed by digestible microalgae. Addition of C. sorokiniana CMBB-146 could only increase the growth rate of P. malhamensis in the first 3 days, but the cell concentration of P. malhamensis started to decrease gradually after 4 days. Compared to autotrophic P. malhamensis, total 6,583 and 3,510 genes were significantly and differentially expressed in P. malhamensis fed by digestible microalgae and indigestible microalgae, respectively. Compared to autotrophic cells, genes related to the ribosome, lysosome, glycolysis, gluconeogenesis, TCA cycle, β-oxidation, duplication, and β-1,3-glucan in P. malhamensis grazing on digestible prey were up-regulated, while genes related to light harvesting and key enzymes referring to chlorophyll were down-regulated. Genes related to apoptosis and necrosis in P. malhamensis were up-regulated after grazing on indigestible microalgae compared to the autotrophic group, which we suggest is associated with the up-regulation of genes related to lysosome enzymes. This study provides abundant information on the potential intracellular physiological responses of P. malhamensis during the process of nutritional adaptation.

Source‐sink patterns on coffee trees related to annual climate variability: An approach through stable isotopes analysis

AbstractStable isotopic determination constitutes a useful tool to identify the processes that control the dynamics of the carbon and nitrogen flow in plants, unravelling the mechanisms of their differential investment under different environments. This work aimed to evaluate the spatiotemporal variation of source‐sink patterns of coffee trees under field conditions in response to climatic conditions through the assessment of stable isotopes. For this purpose, stems, leaves, and fruit samples from coffee trees were collected following a temporal pattern based on the region's climatic characteristics and the plant's phenology and a spatial pattern considering different parts of the canopy. The carbon and nitrogen percentage content, the C/N ratio, and the carbon and nitrogen isotopic compositions (δ13C and δ15N) were determined for all samples. The basal portion of the orthotropic branch was also considered for the isotopic analysis of the tree's growth rings. The results obtained were correlated with the climatic variables of the region through a Pearson correlation analysis (p < .05). Coffee plants showed traditional δ13C values of C3 plants. Temporal δ13C variation was associated with the different growth rates between phenological stages and the use of substrates produced at different times under different environmental conditions leading to differences in photosynthetic discrimination. Spatial δ13C variation was observed with heterotrophic tissues isotopically heavier than leaves, with a significant decrease trend in δ13C values from the top (upper third) to the bottom (lower third), associated with ecophysiological differences between the canopy, isotopic fractionation processes downstream of photosynthetic carbon discrimination, and the fixation of C from other pools. Temporal δ15N variation was associated with the precipitation rates in the region and the fertilization distribution across the tree, while the spatial variation was with the plant's nitrogen assimilation and translocation patterns. The tree growth rings isotopic analyses showed isotopic differences between growth rings of the same plant addressed by the climatic conditions, with precipitation being the primary climatic determinant influencing the fixation and discrimination against 13C. Our results highlight the importance of using stable isotope analysis as a reference point for coffee ecophysiological studies to characterize how the temporal and spatial patterns of δ13C and δ15N emerge and signal the influence of climate on the source‐sink relationship of coffee trees under field conditions.

Enrichment potential of carbon and metals through biogeochemical pools of particulate matter and organisms of the coastal and continental margin

Loads of trace metals and organic materials on the coastal and shelf waters of the Sunda Shelf from vast terrestrial input will affect the flux dynamic, especially through biogeochemical pools. The Sunda Shelf’s biogeochemical pools (i.e., the reservoirs or storage spaces for materials such as carbon and trace metals) vary from coastal to pelagic systems. In this context, such pools can represent suspended particulate matter, sediment, water column, and trophic levels or communities of organisms. We hypothesized that the enrichment of carbon and trace metals would follow the nitrogen stable isotope enrichment. Based on the hypothesis, this study has the following purposes: 1) to assess whether trace metals and δ13C enrichment follows the increase in trophic level; 2) to assess the correlation between trace metals and carbon or nitrogen stable isotope (δ13C or δ15N) enrichment; and 3) to elucidate the potential of carbon and metals flow through the biogeochemical pools. We analyzed the isotope and trace metals properties of the biogeochemical pool of seagrass, suspended particulate matter (SPM), mollusk, and fish. We compared the trophic level value of each pool, its carbon isotope, and metal concentration. The result shows that the sources of carbon for consumers (i.e., mollusks and fish) are seagrass, particulate organic matter (POM), and SPM. SPM presents a plausible reservoir of carbon and nitrogen that can be utilized by mollusks. In addition, the potential sources of carbon and nitrogen for fish could be seagrass, POM, epiphytes, SPM, or even mollusks. Carbon enrichment occurred from the primary producers to the higher trophic levels. Nonetheless, solely cadmium (Cd) and iron (Fe) demonstrated a notable adverse association with δ13C and δ15N, correspondingly. This result suggests that the dispersion of these trace metals likely aligns with the trophic level.

The Muschelkalk aquifer of the Molasse basin in SW-Germany: implications on the origin and development of highly saline lithium-rich brines in calcareous hydrothermal reservoirs

Highly saline lithium-rich hydrothermal fluids (measured chloride concentration up to 44 g kg−1, lithium concentration up to 162 mg kg−1) occur in the deep calcareous Muschelkalk aquifer beneath the northern Alpine foreland (Molasse) basin. We have combined geologic, hydraulic, hydrochemical, and stress field data of the Triassic Muschelkalk aquifer beneath younger sediments of Triassic–Jurassic successions and the Cenozoic Molasse basin of SW-Germany for a synthesis to constrain the origin and development of these brines. In contrast to the regional southeast plunge of Jurassic and Cenozoic strata, low-gradient groundwater flow in the Upper Muschelkalk aquifer is to the north, induced by regional recharge from west, south, and east. The investigated area is seismically active and north trending maximum horizontal stress likely fosters development of necessary fracture permeability for northward flow in the competent carbonates of the Upper Muschelkalk aquifer. The highest lithium concentrations and total dissolved solids (TDS) can be found in the southern parts of the Muschelkalk aquifer. Here, the Muschelkalk Group overlays directly a crystalline basement swell separating two ENE-trending Permocarboniferous troughs. We argue that the highly saline lithium-rich fluids originate from fluid–rock interaction of meteoric water with Variscan crystalline basement rocks and entered the Muschelkalk aquifer on top of the basement swell by permeable faults and fractures. The marginal calcareous sand-rich facies of the Muschelkalk enables the inflow of brines from crystalline basement faults and fractures into the aquifer. We thus argue for an external origin of these brines into the aquifer and further intra-reservoir development by dilution with meteoric water.

Carbon feasibility of terminating plastic waste leakage by landfill mining: A case study based on practical projects in China

Over 900 million tons (Mt) of plastic waste (PW) are disposed in Chinese landfills, posing a permanent risk of migration through environmental media. Landfill mining has emerged as a promising solution to this problem but requires incineration and a substantial energy supply for the excavation, sorting and recycling processes, which themselves exert environmental impacts, particularly on climate change. Based on the life cycle assessment of pilot-scale demonstration projects, this study investigates the carbon feasibility of landfill mining followed by several PW treatments to quantify whether terminating PW leakage from landfills will produce unaffordable greenhouse gas emissions in the drive towards carbon neutrality. The changing trend of the carbon feasibility was deduced considering the decarbonization scenarios of electricity sector and petrochemical industries. When all the sorted PW is treated by incineration with power generation, the climate-change impact of mining is 134.10 kg CO2-eq per ton of aged refuse, projected to increase by 100.47 % in 2050. To completely eliminate the PW in Chinese landfills, the incineration pathway would generate a minimum of 2457.66 Mt CO2-eq emissions, equivalent to 17.69 % of the 2020 emissions in China by carbon flow analysis. In all scenarios, the most carbon-feasible solution was mechanical recycling of high-quality PW combined with chemical recycling of low-quality PW, although the industrial application of chemical recycling technologies remains uncertain. This study provides stakeholders with systematic guidance for balancing the trade-off between PW management and climate action.

The presence of benzene ring activating CoA ligases for aromatics degradation in the ANaerobic MEthanotrophic (ANME) archaea.

Petroleum-source and black carbon-source aromatic compounds are present in the cold seep environments, where ANaerobic MEthanotrophic (ANME) archaea as the dominant microbial community mediates the anaerobic oxidation of methane to produce inorganic and organic carbon. Here, by predicting the aromatics catabolic pathways in ANME metagenome-assembled genomes, we provide genomic and biochemical evidences that ANME have the potential of metabolizing aromatics via the strategy of CoA activation of the benzene ring using phenylacetic acid and benzoate as the substrates. Two ring-activating enzymes phenylacetate-CoA ligase (PaaKANME) and benzoate-CoA ligase (BadAANME) are able to convert phenylacetate to phenylacetyl-CoA and benzoate to benzoyl-CoA in vitro, respectively. They are mesophilic, alkali resistance, and with broad substrate spectra showing different affinity with various substrates. An exploration of the relative gene abundance in ANME genomes and cold seep environments indicates that about 50% of ANME genomes contain PCL genes, and various bacteria and archaea contain PCL and BCL genes. The results provide evidences for the capability of heterotrophic metabolism of aromatic compounds by ANME. This has not only enhanced our understanding of the nutrient range of ANME but also helped to explore the additional ecological and biogeochemical significance of this ubiquitous sedimentary archaea in the carbon flow in the cold seep environments. IMPORTANCE ANaerobic MEthanotrophic (ANME) archaea is the dominant microbial community mediating the anaerobic oxidation of methane in the cold seep environments, where aromatic compounds are present. Then it is hypothesized that ANME may be involved in the metabolism of aromatics. Here, we provide genomic and biochemical evidences for the heterotrophic metabolism of aromatic compounds by ANME, enhancing our understanding of their nutrient range and also shedding light on the ecological and biogeochemical significance of these ubiquitous sedimentary archaea in carbon flow within cold seep environments. Overall, this study offers valuable insights into the metabolic capabilities of ANME and their potential contributions to the global carbon cycle.

Artificial switches induce the bespoke production of functional compounds in marine microalgae Chlorella by neutralizing CO2

To improve the CO2 tolerance of a marine microalga Chlorella sp. of which the production capacity has been demonstrated industrially, a mutant library was created and a strain hct53 was screened. Compared to the parental strain, hct53 shows a high CO2 capture capacity, while starch biosynthesis is compromised, with increases in health beneficial metabolites and antioxidant capacity. Global gene expression and genome-wide mutation distribution revealed that transcript choreography was concomitant with more active CO2 sequestration, an increase in the lipid synthesis, and a decrease in the starch and protein synthesis. These results suggest that artificial trait improvement via mutagenesis, couple with multiomics analysis, helps discover genetic switches that induce the bespoke conversion of carbon flow from “redundant metabolites” to valuable ones for functional food.

The Four-Dimensional Carbon Cycle of the Southern Ocean.

The Southern Ocean plays a fundamental role in the global carbon cycle, dominating the oceanic uptake of heat and carbon added by anthropogenic activities and modulating atmospheric carbon concentrations in past, present, and future climates. However, the remote and extreme conditions found there make the Southern Ocean perpetually one of the most difficult places on the planet to observe and to model, resulting in significant and persistent uncertainties in our knowledge of the oceanic carbon cycle there. The flow of carbon in the Southern Ocean is traditionally understood using a zonal mean framework, in which the meridional overturning circulation drives the latitudinal variability observed in both air-sea flux and interior ocean carbon concentration. However, recent advances, based largely on expanded observation and modeling capabilities in the region, reveal the importance of processes acting at smaller scales, including basin-scale zonal asymmetries in mixed-layer depth, mesoscale eddies, and high-frequency atmospheric variability. Assessing the current state of knowledge and remaining gaps emphasizes the need to move beyond the zonal mean picture and embrace a four-dimensional understanding of the carbon cycle in the Southern Ocean.

Two-tiered mutualism improves survival and competitiveness of cross-feeding soil bacteria

Metabolic cross-feeding is a pervasive microbial interaction type that affects community stability and functioning and directs carbon and energy flows. The mechanisms that underlie these interactions and their association with metal/metalloid biogeochemistry, however, remain poorly understood. Here, we identified two soil bacteria, Bacillus sp. BP-3 and Delftia sp. DT-2, that engage in a two-tiered mutualism. Strain BP-3 has low utilization ability of pyruvic acid while strain DT-2 lacks hexokinase, lacks a phosphotransferase system, and is defective in glucose utilization. When strain BP-3 is grown in isolation with glucose, it releases pyruvic acid to the environment resulting in acidification and eventual self-killing. However, when strain BP-3 is grown together with strain DT-2, strain DT-2 utilizes the released pyruvic acid to meet its energy requirements, consequently rescuing strain BP-3 from pyruvic acid-induced growth inhibition. The two bacteria further enhance their collective competitiveness against other microbes by using arsenic as a weapon. Strain DT-2 reduces relatively non-toxic methylarsenate [MAs(V)] to highly toxic methylarsenite [MAs(III)], which kills or suppresses competitors, while strain BP-3 detoxifies MAs(III) by methylation to non-toxic dimethylarsenate [DMAs(V)]. These two arsenic transformations are enhanced when strains DT-2 and BP-3 are grown together. The two strains, along with their close relatives, widely co-occur in soils and their abundances increase with the soil arsenic concentration. Our results reveal that these bacterial types employ a two-tiered mutualism to ensure their collective metabolic activity and maintain their ecological competitive against other soil microbes. These findings shed light on the intricateness of bacterial interactions and their roles in ecosystem functioning.

Carbon Flow Analysis of Hunan Province from 2012 to 2020 Based on Material Flow Analysis

Carbon Flow Analysis of Hunan Province from 2012 to 2020 Based on Material Flow Analysis

Optimal energy and redox metabolism in the cyanobacterium Synechocystis sp. PCC 6803

Understanding energy and redox homeostasis and carbon partitioning is crucial for systems metabolic engineering of cell factories. Carbon metabolism alone cannot achieve maximal accumulation of metabolites in production hosts, since an efficient production of target molecules requires energy and redox balance, in addition to carbon flow. The interplay between cofactor regeneration and heterologous production in photosynthetic microorganisms is not fully explored. To investigate the optimality of energy and redox metabolism, while overproducing alkenes—isobutene, isoprene, ethylene and 1-undecene, in the cyanobacterium Synechocystis sp. PCC 6803, we applied stoichiometric metabolic modelling. Our network-wide analysis indicates that the rate of NAD(P)H regeneration, rather than of ATP, controls ATP/NADPH ratio, and thereby bioproduction. The simulation also implies that energy and redox balance is interconnected with carbon and nitrogen metabolism. Furthermore, we show that an auxiliary pathway, composed of serine, one-carbon and glycine metabolism, supports cellular redox homeostasis and ATP cycling. The study revealed non-intuitive metabolic pathways required to enhance alkene production, which are mainly driven by a few key reactions carrying a high flux. We envision that the presented comparative in-silico metabolic analysis will guide the rational design of Synechocystis as a photobiological production platform of target chemicals.

Cover crops in pear (Pyrus communis) orchards: effects on soil nematode assemblage

Long-term vegetation cover can affect soil organic carbon content and carbon flow within the soil food web. Nematode trophic structure and soil properties were evaluated in pear rows (intra) maintained without weeds applying herbicide and in the inter-rows (between rows) covered with: Medicago+grasses (MG), fescue or spontaneous vegetation. Soil samples were taken at 0-20 and 20-40 cm depths from 2012 to 2014. Nematode assemblage was different in each inter-row and row, mainly in the topsoil. The inter-rows were reservoirs of omnivores-predators. The MG inter-row promoted the highest accumulation of organic carbon, total N and exchangeable K in the soil. The enrichment index was related to the quantity of dry matter produced by cover crops with the highest index observed in MG. Nematode biomass showed a positive correlation with intra and inter-rows soil organic carbon. Carbon flow through bacterivores prevailed in intra-rows, while bacterivores or herbivores canalized the inter-rows. Highlights: Each cover crop (Medicago+grasses, spontaneous vegetation and fescue) was associated with a different nematode assemblage, mainly in the topsoil. Omnivores-predators were higher in the inter-row than its associated row. Nematode Biomass showed a positive correlation with the content of SOC in the row and in the inter-row. Soil energy channels revealed higher carbon flow within the soil food web under Medicago+grasses and spontaneous vegetation than under fescue.

An optimal control problem for resource utilisation by microorganisms

Decomposition of organic matter controls the flow of carbon and nutrients in terrestrial and aquatic ecosystems. Several kinetic laws have been proposed to describe decomposition rates, but they neglect adaptation of the microbial decomposer to environmental conditions. Here we formalise decomposition as an optimal control problem by assuming that microorganisms regulate the uptake rate of a substrate to maximise their growth over the period of decomposition. The result is an optimal control problem consisting of two differential equations and auxiliary conditions that determine the optimal value of the control variable (the uptake rate), the remaining substrate at any given time, and the optimal completion time. This problem serves as a case study to illustrate the solution of differential equations and optimal control problems for students in undergraduate courses. The mathematical analysis of the problem requires rewriting the differential equations in reverse time along with the solution of a nonhomogeneous linear first order differential equation. We then return to modelling with some biologically motivated questions about how the parameters of the model representing environmental conditions and microbial functional traits affect the outcome. Finally, we discuss alternative ways to use the material with students.