Active microbial ecosystem in glacier basal ice fuelled by iron and silicate comminution-derived hydrogen.

The basal zone of glaciers is characterized by physicochemical properties that are distinct from firnified ice due to strong interactions with underlying substrate and bedrock. Basal ice (BI) ecology and the roles that the microbiota play in biogeochemical cycling, weathering, and proglacial soil formation remain poorly described. We report on basal ice geochemistry, bacterial diversity (16S rRNA gene phylogeny), and inferred ecological roles at three temperate Icelandic glaciers. We sampled three physically distinct basal ice facies (stratified, dispersed, and debris bands) and found facies dependent on biological similarities and differences; basal ice character is therefore an important sampling consideration in future studies. Based on a high abundance of silicates and Fe-containing minerals and, compared to earlier BI literature, total C was detected that could sustain the basal ice ecosystem. It was hypothesized that C-fixing chemolithotrophic bacteria, especially Fe-oxidisers and hydrogenotrophs, mutualistically support associated heterotrophic communities. Basal ice-derived rRNA gene sequences corresponding to genera known to harbor hydrogenotrophic methanogens suggest that silicate comminution-derived hydrogen can also be utilized for methanogenesis. PICRUSt-predicted metabolism suggests that methane metabolism and C-fixation pathways could be highly relevant in BI, indicating the importance of these metabolic routes. The nutrients and microbial communities release from melting basal ice may play an important role in promoting pioneering communities establishment and soil development in deglaciating forelands.

Almacenamiento de carbono en sistemas agroforestales en los Llanos Orientales de Colombia / Carbon storage in agroforestry systems in Colombia's Eastern Plains

Introducción: Los cultivos de café, cacao y pasturas para la ganadería son actividades agropecuarias de interés económico en Colombia. Cuando estas actividades se desarrollan bajo sistemas agroforestales (SAF) promueven la conservación e incrementan la fijación de carbono y, por ende, la mitigación del cambio climático. Objetivo: El estudio estimó el almacenamiento de carbono en la biomasa aérea, necromasa y carbono orgánico del suelo bajo SAF con cacao (SAF cacao), SAF con café (café SAF), sistemas silvopastoriles (SSP) y bosque en el municipio de Mesetas, Meta (Colombia). Métodos: Se establecieron 44 parcelas de muestreo, en donde se tomaron medidas dasométricas a individuos con un diámetro del tronco a la altura del pecho (dap) ≥ 2.5 cm (latizales, fustales y fustales grandes), cuyos valores fueron transformados a carbono con modelos de biomasa y una fracción de carbono default. En los tres sistemas agropecuarios, se contó el número de árboles de cacao, café, plantas asociadas y se identificó el tipo de uso (maderable, alimento, combustión). Resultados: El almacenamiento de carbono presentó diferencias significativas (P < 0.0001) entre usos del suelo. La mayor acumulación se encontró en bosque, con 216.6 t C ha-1, superando en 59, 72 y 73 % a SAF cacao, SSP y SAF café, respectivamente. Fabaceae, Lauraceae y Primulaceae presentaron el mayor almacenamiento de carbono. En SAF cacao, la mayor acumulación de carbono fue encontrada en especies para alimento humano; en SAF café y SSP, el mayor almacenamiento fue presentado en las especies maderables. Conclusión: Estos resultados resaltan el potencial de almacenamiento de carbono en los sistemas productivos de mayor importancia en el departamento del Meta, lo cual es importante para el diseño de estrategias que permitan integrar acciones de mitigación de emisiones de gases de efecto invernadero y promover la economía campesina local.

Introduction: Coffee, cocoa crops and pastures for livestock are agricultural activities of economic interest in Colombia. When these activities are developed under agroforestry systems (AFS), they promote conservation and increase carbon fixation and, therefore, climate change mitigation. Objective: The study estimated carbon storage in aboveground biomass, necromass and soil organic carbon under SAF with cocoa (SAF cocoa), SAF with coffee (SAF coffee), silvopastoral systems (SPS) and forest in Mesetas, Meta (Colombia). Methods: Forty-four sampling plots were established, where dasometric measurements were taken from individuals with a trunk diameter at breast height (dbh) ≥ 2.5 cm (saplings, trees and large trees), whose values were transformed to carbon with biomass models and a default carbon fraction. In the three agricultural systems, the number of cocoa and coffee trees and associated plants was counted, and the type of use (timber, food, combustion) was identified. Results: Carbon storage showed significant differences (P < 0.0001) among land uses. The highest accumulation was found in forest, with 216.6 t C ha-1, exceeding in 59, 72 and 73 % to SAF cocoa, SSP and SAF coffee, respectively. The botanical families Fabaceae, Lauraceae and Primulaceae presented the greatest carbon storage. In SAF cocoa, the greatest accumulation of carbon was found in species for human food; in SAF coffee and SSP, the greatest storage was presented by timber species. Conclusion: These results highlight the potential for carbon storage in the most important productive systems in the Meta department, which is important for designing strategies that allow for integrating actions to mitigate greenhouse gas emissions and to promote the local peasant economy.

Optimal Ratio of Carbon Flux between Glycolysis and the Pentose Phosphate Pathway for Amino Acid Accumulation in Corynebacterium glutamicum.

Glucose is metabolized through central metabolic pathways such as glycolysis and the pentose phosphate pathway (PPP) to synthesize downstream metabolites including amino acids. However, how the split ratio of carbon flux between glycolysis and PPP specifically affects the formation of downstream metabolites remains largely unclear. Here, we conducted a comprehensive metabolomic analysis to investigate the effect of the split ratio between glycolysis and the PPP on the intracellular concentration of amino acids and their derivatives in Corynebacterium glutamicum. The split ratio was varied by exchanging the promoter of a gene encoding glucose 6-phosphate isomerase (PGI). The ratio was correlated with the pgi transcription level and the enzyme activity. Concentrations of threonine and lysine-derivative 1,5-diaminopentane increased with an increase of the split ratio into the PPP. In contrast, concentrations of alanine, leucine, and valine were increased with an increase of the split ratio into glycolysis. These results could provide a new engineering target for improving the production of the amino acids and the derivatives.

Steel slag amendment impacts on soil microbial communities and activities of rice (Oryza sativa L.).

With the increase in iron/steel production, the higher volume of by-products (slag) generated necessitates its efficient recycling. Because the Linz-Donawitz (LD) slag is rich in silicon (Si) and other fertilizer components, we aim to evaluate the impact of the LD slag amendment on soil quality (by measuring soil physicochemical and biological properties), plant nutrient uptake, and strengthens correlations between nutrient uptake and soil bacterial communities. We used 16 S rRNA illumine sequencing to study soil bacterial community and APIZYM assay to study soil enzymes involved in C, N, and P cycling. The LD slag was applied at 2 Mg ha-1 to Japonica and Indica rice cultivated under flooded conditions. The LD slag amendment significantly improved soil pH, plant photosynthesis, soil nutrient availability, and the crop yield, irrespective of cultivars. It significantly increased N, P, and Si uptake of rice straw. The slag amendment enhanced soil microbial biomass, soil enzyme activities and enriched certain bacterial taxa featuring copiotrophic lifestyles and having the potential role for ecosystem services provided to the benefit of the plant. The study evidenced that the short-term LD slag amendment in rice cropping systems is useful to improve soil physicochemical and biological status, and the crop yield.

Automatic Redirection of Carbon Flux between Glycolysis and Pentose Phosphate Pathway Using an Oxygen-Responsive Metabolic Switch in Corynebacterium glutamicum.

Controlling the carbon flux into a desired pathway is important for improving product yield in metabolic engineering. After entering a cell, glucose is channeled into glycolysis and the pentose phosphate pathway (PPP), which decreases the yield of target products whose synthesis relies on NADPH as a cofactor. Here, we demonstrate redirection of carbon flux into PPP under aerobic conditions in Corynebacterium glutamicum, achieved by replacing the promoter of glucose 6-phosphate isomerase gene (pgi) with an anaerobic-specific promoter of the lactate dehydrogenase gene (ldhA). The promoter replacement increased the split ratio of carbon flux into PPP from 39 to 83% under aerobic conditions. The titer, yield, and production rate of 1,5-diaminopentane, whose synthesis requires NADPH as a cofactor, were increased by 4.6-, 4.4-, and 2.6-fold, respectively. This is the largest improvement in the production of 1,5-diaminopentane or its precursor, lysine, reported to date. After aerobic cell growth, pgi expression was automatically induced under anaerobic conditions, altering the carbon flux from PPP to glycolysis, to produce succinate in a single metabolically engineered strain. Such an automatic redirection of metabolic pathway using an oxygen-responsive switch enables two-stage fermentation for efficient production of two different compounds by a single strain, potentially reducing the production costs and time for practical applications.

Carbon Flux as a Measure of Prostate Cancer Aggressiveness: [11C]-Acetate PET/CT.

Purpose: Dynamic [11C]-acetate positron emission tomography (PET) can be used to study tissue perfusion and carbon flux simultaneously. In this study, the feasibility of the quantification of prostate cancer aggressiveness using parametric methods assessing [11C]-acetate kinetics was investigated in prostate cancer subjects. The underlying uptake mechanism correlated with [11C]-acetate influx and efflux measured in real-time in vitro in cell culture. Methods: Twenty-one patients with newly diagnosed low-to-moderate risk prostate cancer underwent magnetic resonance imaging (MRI) and dynamic [11C]-acetate PET/CT examinations of the pelvis. Parametric images of K1 (extraction × perfusion), k2 (oxidative metabolism) and VT (=K1/k2, anabolic metabolism defined as carbon retention) were constructed using a one-tissue compartment model with an arterial input function derived from pelvic arteries. Regions of interest (ROIs) of the largest cancer lesion in each patient and normal prostate tissue were drawn using information from MRI (T2 and DWI images), biopsy results, and post-surgical histopathology of whole prostate sections (n=7). In vitro kinetics of [11C]-acetate were studied on DU145 and PC3 cell lines using LigandTracer® White equipment for the measurement of the radioactivity uptake in real-time at 37°C. Results: Mean prostate specific antigen (PSA) was 8.33±3.92 ng/mL and median Gleason Sum 6 (range 5-7). K1, VT and standardized uptake values (SUVs) were significantly higher in cancerous prostate tissues compared to normal ones for all patients (p<0.001), while k2 was not (p=0.26). PSA values correlated to early SUVs (r=0.50, p=0.02) and K1 (r=0.48, p=0.03). Early and late SUVs correlated to VT (r>0.76, p<0.001) and K1 (r>0.64, p<0.005). In vitro studies demonstrated higher extraction and retention (p<0.01) of [11C]-acetate in the more aggressive PC3 cells. Conclusion: Parametric images could be used to visualize the [11C]-acetate kinetics of the prostate cancer exhibiting elevated extraction associated with the cancer aggressiveness. The influx rate of [11C]-acetate studied in cell culture also showed dependence on the cancer aggressiveness associated with elevated lipogenesis. Dynamic [11C]-acetate/PET demonstrated potential for prostate cancer aggressiveness estimation using parametric-based K1 and VT values.

Micronutrients in support to the one carbon cycle for the modulation of blood fasting homocysteine in PCOS women.

PURPOSE: Fasting blood homocysteine is increased in PCOS women and is involved in several of its co-morbidities including cardiovascular disease and infertility. Corrective interventions based on the administration of supra-physiologic doses of folic acid work to a low extent. We aimed to test an alternative approach. METHODS: This was a prospective, randomized, parallel group, open label, controlled versus no treatment clinical study. PCOS women aged > 18, free from systemic diseases and from pharmacological treatments were randomized with a 2:1 ratio for treatment with activated micronutrients in support to the carbon cycle (Impryl, Parthenogen, Switzerland-n = 22) or no treatment (n = 10) and followed-up for 3 months. Fasting blood homocysteine, AMH, testosterone, SHBGs, and the resulting FTI were tested before and at the end of the follow-up. RESULTS: The mean baseline fasting blood homocysteine was above the normal limit of 12 µMol/L and inversely correlated with SHBG. AMH was also increased, whereas testosterone, SHBG, and FTI were within the normal limit. The treatment achieved a significant reduction of homocysteine, that did not change in the control group, independently of the starting value. The treatment also caused an increase of AMH and a decrease of SHBGs only in the subgroup with a normal homocysteine at baseline. CONCLUSIONS: In PCOS ladies, blood homocysteine is increased and inversely correlated with the SHBGs. Physiologic amounts of activated micronutrients in support to the carbon cycle achieve a reduction virtually in all exposed patients. Whether this is of clinical benefit remains to be established.

Hybrid Cyanobacterial-Tobacco Rubisco Supports Autotrophic Growth and Procarboxysomal Aggregation.

Much of the research aimed at improving photosynthesis and crop productivity attempts to overcome shortcomings of the primary CO2-fixing enzyme Rubisco. Cyanobacteria utilize a CO2-concentrating mechanism (CCM), which encapsulates Rubisco with poor specificity but a relatively fast catalytic rate within a carboxysome microcompartment. Alongside the active transport of bicarbonate into the cell and localization of carbonic anhydrase within the carboxysome shell with Rubisco, cyanobacteria are able to overcome the limitations of Rubisco via localization within a high-CO2 environment. As part of ongoing efforts to engineer a ß-cyanobacterial CCM into land plants, we investigated the potential for Rubisco large subunits (LSU) from the ß-cyanobacterium Synechococcus elongatus (Se) to form aggregated Rubisco complexes with the carboxysome linker protein CcmM35 within tobacco (Nicotiana tabacum) chloroplasts. Transplastomic plants were produced that lacked cognate Se Rubisco small subunits (SSU) and expressed the Se LSU in place of tobacco LSU, with and without CcmM35. Plants were able to form a hybrid enzyme utilizing tobacco SSU and the Se LSU, allowing slow autotrophic growth in high CO2 CcmM35 was able to form large Rubisco aggregates with the Se LSU, and these incorporated small amounts of native tobacco SSU. Plants lacking the Se SSU showed delayed growth, poor photosynthetic capacity, and significantly reduced Rubisco activity compared with both wild-type tobacco and lines expressing the Se SSU. These results demonstrate the ability of the Se LSU and CcmM35 to form large aggregates without the cognate Se SSU in planta, harboring active Rubisco that enables plant growth, albeit at a much slower pace than plants expressing the cognate Se SSU.

Pyrenoidal sequestration of cadmium impairs carbon dioxide fixation in a microalga.

Mixotrophic microorganisms are able to use organic carbon as well as inorganic carbon sources and thus, play an essential role in the biogeochemical carbon cycle. In aquatic ecosystems, the alteration of carbon dioxide (CO2 ) fixation by toxic metals such as cadmium - classified as a priority pollutant - could contribute to the unbalance of the carbon cycle. In consequence, the investigation of cadmium impact on carbon assimilation in mixotrophic microorganisms is of high interest. We exposed the mixotrophic microalga Chlamydomonas reinhardtii to cadmium in a growth medium containing both CO2 and labelled 13 C-[1,2] acetate as carbon sources. We showed that the accumulation of cadmium in the pyrenoid, where it was predominantly bound to sulphur ligands, impaired CO2 fixation to the benefit of acetate assimilation. Transmission electron microscopy (TEM)/X-ray energy dispersive spectroscopy (X-EDS) and micro X-ray fluorescence (µXRF)/micro X-ray absorption near-edge structure (µXANES) at Cd LIII- edge indicated the localization and the speciation of cadmium in the cellular structure. In addition, nanoscale secondary ion mass spectrometry (NanoSIMS) analysis of the 13 C/12 C ratio in pyrenoid and starch granules revealed the origin of carbon sources. The fraction of carbon in starch originating from CO2 decreased from 73 to 39% during cadmium stress. For the first time, the complementary use of high-resolution elemental and isotopic imaging techniques allowed relating the impact of cadmium at the subcellular level with carbon assimilation in a mixotrophic microalga.

Ex vivo and in vivo stable isotope labelling of central carbon metabolism and related pathways with analysis by LC-MS/MS.

Targeted tandem mass spectrometry (LC-MS/MS) has been extremely useful for profiling small molecules extracted from biological sources, such as cells, bodily fluids and tissues. Here, we present a protocol for analysing incorporation of the non-radioactive stable isotopes carbon-13 (13C) and nitrogen-15 (15N) into polar metabolites in central carbon metabolism and related pathways. Our platform utilizes selected reaction monitoring (SRM) with polarity switching and amide hydrophilic interaction liquid chromatography (HILIC) to capture transitions for carbon and nitrogen incorporation into selected metabolites using a hybrid triple quadrupole (QQQ) mass spectrometer. This protocol represents an extension of a previously published protocol for targeted metabolomics of unlabeled species and has been used extensively in tracing the metabolism of nutrients such as 13C-labeled glucose, 13C-glutamine and 15N-glutamine in a variety of biological settings (e.g., cell culture experiments and in vivo mouse labelling via i.p. injection). SRM signals are integrated to produce an array of peak areas for each labelling form that serve as the output for further analysis. The processed data are then used to obtain the degree and distribution of labelling of the targeted molecules (termed fluxomics). Each method can be customized on the basis of known unlabeled Q1/Q3 SRM transitions and adjusted to account for the corresponding 13C or 15N incorporation. The entire procedure takes ~6-7 h for a single sample from experimental labelling and metabolite extraction to peak integration.

Tracking acetate through a journey of living world: Evolution as alternative cellular fuel with potential for application in cancer therapeutics.

Acetate is a short chain fatty acid, comprising carbon, hydrogen and oxygen (C2H3O2-), which has emerged as a key alternative fuel for cellular metabolism. Beginning its voyage from the abiotic atmosphere, acetate has contributed to the physiology of both prokaryotes and eukaryotes. The main role of acetate includes its contribution to the global carbon cycle, bioenergetic and biosynthetic metabolic processes. Based on the ability to produce and consume acetate, organisms are categorized as acetogenic, acetate-consumers or both depending on their genetic make-up of the metabolizing enzymes' repertoire. The key molecules implicated in utilization and production of acetate include, but not limited to, monocarboxylate transporters, enzymes regulating acetate utilization like AMP-forming Acetyl CoA synthetase (ACS-AMP), Acyl-CoA short chain synthetase 1, 2 (ACSS1, 2), and production like Acetate kinase (ACK)/Phosphotransacetylase (PTA), ADP-forming acetyl CoA synthetase (ACS-ADP), Pyruvate:ferredoxin oxidoreductase, histone deacetylase and acetyl CoA hydrolase. These enzymes are utilized by the acetate homeostasis machinery in a variable manner. As malignant cells also display highly upregulated metabolic processes for rapid energy generation, they display an immense need for alternative carbon sources to fuel their metabolism. Tumor cells display over expression of transporters and enzymes implicated in their acetate utility machinery. This review also highlights mechanisms of the pro and antitumor potential of acetate depending on the genetic and metabolic makeup of neoplastic cells. The present review is a comprehensive compilation of the available literature with respect to the role of acetate in the biology of living organisms and its potential for being maneuvered in anticancer therapeutics.

Evolutionary convergence in lignin-degrading enzymes.

The resurrection of ancestral enzymes of now-extinct organisms (paleogenetics) is a developing field that allows the study of evolutionary hypotheses otherwise impossible to be tested. In the present study, we target fungal peroxidases that play a key role in lignin degradation, an essential process in the carbon cycle and often a limiting step in biobased industries. Ligninolytic peroxidases are secreted by wood-rotting fungi, the origin of which was recently established in the Carboniferous period associated with the appearance of these enzymes. These first peroxidases were not able to degrade lignin directly and used diffusible metal cations to attack its phenolic moiety. The phylogenetic analysis of the peroxidases of Polyporales, the order in which most extant wood-rotting fungi are included, suggests that later in evolution these enzymes would have acquired the ability to degrade nonphenolic lignin using a tryptophanyl radical interacting with the bulky polymer at the surface of the enzyme. Here, we track this powerful strategy for lignin degradation as a phenotypic trait in fungi and show that it is not an isolated event in the evolution of Polyporales. Using ancestral enzyme resurrection, we study the molecular changes that led to the appearance of the same surface oxidation site in two distant peroxidase lineages. By characterization of the resurrected enzymes, we demonstrate convergent evolution at the amino acid level during the evolution of these fungi and track the different changes leading to phylogenetically distant ligninolytic peroxidases from ancestors lacking the ability to degrade nonphenolic lignin.

One-carbon cycle support rescues sperm damage in experimentally induced varicocoele in rats.

OBJECTIVES: To investigate whether micronutrients in support of the one-carbon cycle and glutathione synthesis are effective in improving sperm damage after surgical varicocoele induction in rats and whether any effect is achieved without a rebound reductive stress as seen with oral antioxidants. MATERIALS AND METHODS: Surgical varicocoele was induced in adult male Wistar rats and resulted in significant damage to the testis and sperm cells measured at 2 and 4 months after surgery. At 2 months after surgery, rats received a 2-month oral supplementation in support of the one-carbon cycle containing B vitamins (B2, B3, B6, folic acid and B12), N-acetyl-cysteine, zinc, small amounts of vitamin E, and a natural source of betalains and quercetine (Condensyl® ; Parthenogen SAGL, Lugano, Switzerland and Nurilia SARL, Lyon, France). RESULTS: One-carbon cycle supplementation, compared to untreated controls, significantly improved the morphometric characteristics of testis (P < 0.05), sperm concentration, motility and abnormal morphology (P < 0.001), sperm chromatin condensation (aniline blue staining, P < 0.05), sperm DNA damage (acridine orange staining, P < 0.05) and sperm lipid peroxidation (BODIPY C11, P < 0.001). The improvement in both nuclear condensation and DNA damage and the lack of excessive inhibition of lipid peroxidation confirmed that no reductive stress had occurred. CONCLUSIONS: Micronutrients in support of the one-carbon cycle are effective in the treatment of surgically induced varicocoele in rats, probably by activating natural antioxidant defences and epigenetics. These results support the idea that essential micronutrients including B vitamins may also have a positive influence in clinical varicocoele, which should be tested in prospective clinical trials.

Maintenance of ATP Homeostasis Triggers Metabolic Shifts in Gas-Fermenting Acetogens.

Acetogens are promising cell factories for producing fuels and chemicals from waste feedstocks via gas fermentation, but quantitative characterization of carbon, energy, and redox metabolism is required to guide their rational metabolic engineering. Here, we explore acetogen gas fermentation using physiological, metabolomics, and transcriptomics data for Clostridium autoethanogenum steady-state chemostat cultures grown on syngas at various gas-liquid mass transfer rates. We observe that C. autoethanogenum shifts from acetate to ethanol production to maintain ATP homeostasis at higher biomass concentrations but reaches a limit at a molar acetate/ethanol ratio of ∼1. This regulatory mechanism eventually leads to depletion of the intracellular acetyl-CoA pool and collapse of metabolism. We accurately predict growth phenotypes using a genome-scale metabolic model. Modeling revealed that the methylene-THF reductase reaction was ferredoxin reducing. This work provides a reference dataset to advance the understanding and engineering of arguably the first carbon fixation pathway on Earth.

1-Carbon Cycle Metabolites Methylate Their Way to Fatty Liver.

Fatty liver is a complex disease often accompanying metabolic syndrome and Type 2 diabetes mellitus (T2DM). Hepatosteatosis may have roots in multiple metabolic abnormalities. However, metabolic dysfunction in the 1-carbon cycle (1CC), which produces the methyl donor S-adenosylmethionine (SAM) and phosphatidylcholine (PC), induces hepatic lipogenesis in model systems. Human diseases where 1CC or PC synthesis is disrupted, such as alcoholism, congenital lipodystrophy, or cystic fibrosis, often present with fatty liver. Given that the 1CC is clearly linked to this disease, it is critical to understand how the individual metabolites drive mechanisms increasing stored hepatic lipids. In this review, I summarize evidence that ties the 1CC to fatty liver disease along with data proposing mechanisms for increased lipogenesis or decreased lipid export by phosphatidylcholine.

Growth on ATP Elicits a P-Stress Response in the Picoeukaryote Micromonas pusilla.

The surface waters of oligotrophic oceans have chronically low phosphate (Pi) concentrations, which renders dissolved organic phosphorus (DOP) an important nutrient source. In the subtropical North Atlantic, cyanobacteria are often numerically dominant, but picoeukaryotes can dominate autotrophic biomass and productivity making them important contributors to the ocean carbon cycle. Despite their importance, little is known regarding the metabolic response of picoeukaryotes to changes in phosphorus (P) source and availability. To understand the molecular mechanisms that regulate P utilization in oligotrophic environments, we evaluated transcriptomes of the picoeukaryote Micromonas pusilla grown under Pi-replete and -deficient conditions, with an additional investigation of growth on DOP in replete conditions. Genes that function in sulfolipid substitution and Pi uptake increased in expression with Pi-deficiency, suggesting cells were reallocating cellular P and increasing P acquisition capabilities. Pi-deficient M. pusilla cells also increased alkaline phosphatase activity and reduced their cellular P content. Cells grown with DOP were able to maintain relatively high growth rates, however the transcriptomic response was more similar to the Pi-deficient response than that seen in cells grown under Pi-replete conditions. The results demonstrate that not all P sources are the same for growth; while M. pusilla, a model picoeukaryote, may grow well on DOP, the metabolic demand is greater than growth on Pi. These findings provide insight into the cellular strategies which may be used to support growth in a stratified future ocean predicted to favor picoeukaryotes.

Dissolved inorganic carbon uptake in Thiomicrospira crunogena XCL-2 is Δp- and ATP-sensitive and enhances RubisCO-mediated carbon fixation.

The gammaproteobacterium Thiomicrospira crunogena XCL-2 is an aerobic sulfur-oxidizing hydrothermal vent chemolithoautotroph that has a CO2 concentrating mechanism (CCM), which generates intracellular dissolved inorganic carbon (DIC) concentrations much higher than extracellular, thereby providing substrate for carbon fixation at sufficient rate. This CCM presumably requires at least one active DIC transporter to generate the elevated intracellular concentrations of DIC measured in this organism. In this study, the half-saturation constant (K CO2) for purified carboxysomal RubisCO was measured (276 ± 18 µM) which was much greater than the K CO2 of whole cells (1.03 µM), highlighting the degree to which the CCM facilitates CO2 fixation under low CO2 conditions. To clarify the bioenergetics powering active DIC uptake, cells were incubated in the presence of inhibitors targeting ATP synthesis (DCCD) or proton potential (CCCP). Incubations with each of these inhibitors resulted in diminished intracellular ATP, DIC, and fixed carbon, despite an absence of an inhibitory effect on proton potential in the DCCD-incubated cells. Electron transport complexes NADH dehydrogenase and the bc 1 complex were found to be insensitive to DCCD, suggesting that ATP synthase was the primary target of DCCD. Given the correlation of DIC uptake to the intracellular ATP concentration, the ABC transporter genes were targeted by qRT-PCR, but were not upregulated under low-DIC conditions. As the T. crunogena genome does not include orthologs of any genes encoding known DIC uptake systems, these data suggest that a novel, yet to be identified, ATP- and proton potential-dependent DIC transporter is active in this bacterium. This transporter serves to facilitate growth by T. crunogena and other Thiomicrospiras in the many habitats where they are found.

Interacting Effects of Light and Iron Availability on the Coupling of Photosynthetic Electron Transport and CO2-Assimilation in Marine Phytoplankton.

Iron availability directly affects photosynthesis and limits phytoplankton growth over vast oceanic regions. For this reason, the availability of iron is a crucial variable to consider in the development of active chlorophyll a fluorescence based estimates of phytoplankton primary productivity. These bio-optical approaches require a conversion factor to derive ecologically-relevant rates of CO2-assimilation from estimates of electron transport in photosystem II. The required conversion factor varies significantly across phytoplankton taxa and environmental conditions, but little information is available on its response to iron limitation. In this study, we examine the role of iron limitation, and the interacting effects of iron and light availability, on the coupling of photosynthetic electron transport and CO2-assimilation in marine phytoplankton. Our results show that excess irradiance causes increased decoupling of carbon fixation and electron transport, particularly under iron limiting conditions. We observed that reaction center II specific rates of electron transport (ETR(RCII), mol e- mol RCII(-1) s(-1)) increased under iron limitation, and we propose a simple conceptual model for this observation. We also observed a strong correlation between the derived conversion factor and the expression of non-photochemical quenching. Utilizing a dataset from in situ phytoplankton assemblages across a coastal--oceanic transect in the Northeast subarctic Pacific, this relationship was used to predict ETR(RCII): CO2-assimilation conversion factors and carbon-based primary productivity from FRRF data, without the need for any additional measurements.

Using a simple apparatus to measure direct and diffuse photosynthetically active radiation at remote locations.

Plant canopy interception of photosynthetically active radiation (PAR) drives carbon dioxide (CO2), water and energy cycling in the soil-plant-atmosphere system. Quantifying intercepted PAR requires accurate measurements of total incident PAR above canopies and direct beam and diffuse PAR components. While some regional data sets include these data, e.g. from Atmospheric Radiation Measurement (ARM) Program sites, they are not often applicable to local research sites because of the variable nature (spatial and temporal) of environmental variables that influence incoming PAR. Currently available instrumentation that measures diffuse and direct beam radiation separately can be cost prohibitive and require frequent adjustments. Alternatively, generalized empirical relationships that relate atmospheric variables and radiation components can be used but require assumptions that increase the potential for error. Our goal here was to construct and test a cheaper, highly portable instrument alternative that could be used at remote field sites to measure total, diffuse and direct beam PAR for extended time periods without supervision. The apparatus tested here uses a fabricated, solar powered rotating shadowband and other commercially available parts to collect continuous hourly PAR data. Measurements of total incident PAR had nearly a one-to-one relationship with total incident radiation measurements taken at the same research site by an unobstructed point quantum sensor. Additionally, measurements of diffuse PAR compared favorably with modeled estimates from previously published data, but displayed significant differences that were attributed to the important influence of rapidly changing local environmental conditions. The cost of the system is about 50% less than comparable commercially available systems that require periodic, but not continual adjustments. Overall, the data produced using this apparatus indicates that this instrumentation has the potential to support ecological research via a relatively inexpensive method to collect continuous measurements of total, direct beam and diffuse PAR in remote locations.

Impacts of diffuse radiation on light use efficiency across terrestrial ecosystems based on Eddy covariance observation in China.

Ecosystem light use efficiency (LUE) is a key factor of production models for gross primary production (GPP) predictions. Previous studies revealed that ecosystem LUE could be significantly enhanced by an increase on diffuse radiation. Under large spatial heterogeneity and increasing annual diffuse radiation in China, eddy covariance flux data at 6 sites across different ecosystems from 2003 to 2007 were used to investigate the impacts of diffuse radiation indicated by the cloudiness index (CI) on ecosystem LUE in grassland and forest ecosystems. Our results showed that the ecosystem LUE at the six sites was significantly correlated with the cloudiness variation (0.24 ≤ R(2) ≤ 0.85), especially at the Changbaishan temperate forest ecosystem (R(2) = 0.85). Meanwhile, the CI values appeared more frequently between 0.8 and 1.0 in two subtropical forest ecosystems (Qianyanzhou and Dinghushan) and were much larger than those in temperate ecosystems. Besides, cloudiness thresholds which were favorable for enhancing ecosystem carbon sequestration existed at the three forest sites, respectively. Our research confirmed that the ecosystem LUE at the six sites in China was positively responsive to the diffuse radiation, and the cloudiness index could be used as an environmental regulator for LUE modeling in regional GPP prediction.