Microbial Inorganic Carbon Fixation

2010 ◽  
Author(s):  
Takaaki Sato ◽  
Haruyuki Atomi
Keyword(s):  
Inorganic Carbon ◽  
Carbon Fixation

scholarly journals Insights into Biodegradation Related Metabolism in an Abnormally Low Dissolved Inorganic Carbon (DIC) Petroleum-Contaminated Aquifer by Metagenomics Analysis

2019 ◽  
Vol 7 (10) ◽  
pp. 412 ◽  
Author(s):  
Pingping Cai ◽  
Zhuo Ning ◽  
Ningning Zhang ◽  
Min Zhang ◽  
Caijuan Guo ◽  
...  
Keyword(s):  
Nitrate Reduction ◽  
Inorganic Carbon ◽  
Carbon Fixation ◽  
Dissolved Inorganic Carbon ◽  
Contaminated Aquifer ◽  
Genes Encoding ◽  
New Finding ◽  
Key Genes ◽  
Contaminated Aquifers ◽  
Metagenomics Analysis

In petroleum-contaminated aquifers, biodegradation is always associated with various types of microbial metabolism. It can be classified as autotrophic (such as methanogenic and other carbon fixation) and heterotrophic (such as nitrate/sulfate reduction and hydrocarbon consumption) metabolism. For each metabolic type, there are several key genes encoding the reaction enzymes, which can be identified by metagenomics analysis. Based on this principle, in an abnormally low dissolved inorganic carbon (DIC) petroleum-contaminated aquifer in North China, nine groundwater samples were collected along the groundwater flow, and metagenomics analysis was used to discover biodegradation related metabolism by key genes. The major new finding is that autotrophic metabolism was revealed, and, more usefully, we attempt to explain the reasons for abnormally low DIC. The results show that the methanogenesis gene, Mcr, was undetected but more carbon fixation genes than nitrate reduction and sulfate genes were found. This suggests that there may be a considerable number of autotrophic microorganisms that cause the phenomenon of low concentration of dissolved inorganic carbon in contaminated areas. The metagenomics data also revealed that most heterotrophic, sulfate, and nitrate reduction genes in the aquifer were assimilatory sulfate and dissimilatory nitrate reduction genes. Although there was limited dissolved oxygen, aerobic degrading genes AlkB and Cdo were more abundant than anaerobic degrading genes AssA and BssA. The metagenomics information can enrich our microorganic knowledge about petroleum-contaminated aquifers and provide basic data for further bioremediation.

scholarly journals Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat

2020 ◽  
Vol 86 (7) ◽  
Author(s):  
Laurey Steinke ◽  
Gordon W. Slysz ◽  
Mary S. Lipton ◽  
Christian Klatt ◽  
James J. Moran ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Inorganic Carbon ◽  
Microbial Mats ◽  
Carbon Fixation ◽  
Hot Springs ◽  
Hot Spring ◽  
Stable Isotope Probing ◽  
Short Term ◽  
Low Light ◽  
Assembly Sequences

ABSTRACT The upper green layer of the chlorophototrophic microbial mats associated with the alkaline siliceous hot springs of Yellowstone National Park consists of oxygenic cyanobacteria (Synechococcus spp.), anoxygenic Roseiflexus spp., and several other anoxygenic chlorophototrophs. Synechococcus spp. are believed to be the main fixers of inorganic carbon (Ci), but some evidence suggests that Roseiflexus spp. also contribute to inorganic carbon fixation during low-light, anoxic morning periods. Contributions of other phototrophic taxa have not been investigated. In order to follow the pathway of Ci incorporation into different taxa, mat samples were incubated with [13C]bicarbonate for 3 h during the early-morning, low-light anoxic period. Extracted proteins were treated with trypsin and analyzed by mass spectrometry, leading to peptide identifications and peptide isotopic profile signatures containing evidence of 13C label incorporation. A total of 25,483 peptides, corresponding to 7,221 proteins, were identified from spectral features and associated with mat taxa by comparison to metagenomic assembly sequences. A total of 1,417 peptides, derived from 720 proteins, were detectably labeled with 13C. Most 13C-labeled peptides were derived from proteins of Synechococcus spp. and Roseiflexus spp. Chaperones and proteins of carbohydrate metabolism were most abundantly labeled. Proteins involved in photosynthesis, Ci fixation, and N2 fixation were also labeled in Synechococcus spp. Importantly, most proteins of the 3-hydroxypropionate bi-cycle for Ci fixation in Roseiflexus spp. were labeled, establishing that members of this taxocene contribute to Ci fixation. Other taxa showed much lower [13C]bicarbonate incorporation. IMPORTANCE Yellowstone hot spring mats have been studied as natural models for understanding microbial community ecology and as modern analogs of stromatolites, the earliest community fossils on Earth. Stable-isotope probing of proteins (Pro-SIP) permitted short-term interrogation of the taxa that are involved in the important process of light-driven Ci fixation in this highly active community and will be useful in linking other metabolic processes to mat taxa. Here, evidence is presented that Roseiflexus spp., which use the 3-hydroxypropionate bi-cycle, are active in Ci fixation. Because this pathway imparts a lower degree of selection of isotopically heavy Ci than does the Calvin-Benson-Bassham cycle, the results suggest a mechanism to explain why the natural abundance of 13C in mat biomass is greater than expected if only the latter pathway were involved. Understanding how mat community members influence the 13C/12C ratios of mat biomass will help geochemists interpret the 13C/12C ratios of organic carbon in the fossil record.

Inorganic carbon fixation in ice-covered lakes of the McMurdo Dry Valleys

2019 ◽  
Vol 31 (3) ◽  
pp. 123-132 ◽  
Author(s):  
Trista J. Vick-Majors ◽  
John C. Priscu
Keyword(s):  
Aquatic Ecosystems ◽  
Inorganic Carbon ◽  
Carbon Fixation ◽  
Dry Valleys ◽  
Ammonia Oxidizers ◽  
Fixed Carbon ◽  
Carbon Supply ◽  
Gain Energy ◽  
Photosynthetic Microorganisms ◽  
Dark Carbon Fixation

AbstractInorganic carbon fixation, usually mediated by photosynthetic microorganisms, is considered to form the base of the food chain in aquatic ecosystems. In high-latitude lakes, lack of sunlight owing to seasonal solar radiation limits the activity of photosynthetic plankton during the polar winter, causing respiration-driven demand for carbon to exceed supply. Here, we show that inorganic carbon fixation in the dark, driven by organisms that gain energy from chemical reactions rather than sunlight (chemolithoautotrophs), provides a significant influx of fixed carbon to two permanently ice-covered lakes (Fryxell and East Bonney). Fryxell, which has higher biomass per unit volume of water, had higher rates of inorganic dark carbon fixation by chemolithoautotrophs than East Bonney (trophogenic zone average 1.0 µg C l−1 d−1vs 0.08 µg C l−1 d−1, respectively). This contribution from dark carbon fixation was partly due to the activity of ammonia oxidizers, which are present in both lakes. Despite the potential importance of new carbon input by chemolithoautotrophic activity, both lakes remain net heterotrophic, with respiratory demand for carbon exceeding supply. Dark carbon fixation increased the ratio of new carbon supply to respiratory demand from 0.16 to 0.47 in Fryxell, and from 0.14 to 0.22 in East Bonney.

Differential visible spectral influence on carbon metabolism in heterotrophic marine flavobacteria

2020 ◽  
Vol 96 (3) ◽  
Author(s):  
Asif Hameed ◽  
Wei-An Lai ◽  
Mariyam Shahina ◽  
Paul Stothard ◽  
Li-Sen Young ◽  
...  
Keyword(s):  
Carbon Sequestration ◽  
Organic Carbon ◽  
Visible Light ◽  
Blue Light ◽  
Carbon Metabolism ◽  
Inorganic Carbon ◽  
Carbon Fixation ◽  
Heterotrophic Bacteria ◽  
Hydrolytic Enzymes ◽  
Full Spectrum

ABSTRACT The visible spectrum of solar radiation is known to stimulate photoheterotrophic bacterial carbon metabolism. However, its impact on ‘strictly’ heterotrophic bacteria remains less explored. Here, we show that heterotrophic flavobacteria exhibit enhanced uptake and mineralization of dissolved organic carbon with increasing wavelengths of visible light, without employing any ‘known’ light-harvesting mechanisms. RNA sequencing identified blue light as a major constraint in the extracellular enzymatic hydrolysis of polymeric carbohydrates and acquisition of sugars, despite acting as a stimulus for inorganic carbon sequestration. In contrast, green–red and continuous full-spectrum lights activated diverse hydrolytic enzymes and sugar transporters, but obstructed inorganic carbon fixation. This ‘metabolic switching’ was apparent through limited nutrient uptake, suppressed light-sensitivity, oxidative stress response and promotion of inorganic carbon sequestration pathways under blue light. The visible light impact on metabolism may be of significant ecological relevance as it appears to promote cell-mediated mineralization of organic carbon in ‘green-colored’ chlorophyll-rich copiotrophic coastal seawater and inorganic carbon sequestration in ‘blue-colored’ oligotrophic open ocean. Thus, a novel regulatory role played by light on heterotrophic metabolism and a hidden potential of flavobacteria to sense and respond differentially to monochromatic lights influencing marine carbon cycling were unraveled.

scholarly journals CO2 Uptake and Fixation by Endosymbiotic Chemoautotrophs from the Bivalve Solemya velum

2006 ◽  
Vol 73 (4) ◽  
pp. 1174-1179 ◽  
Author(s):  
Kathleen M. Scott ◽  
Colleen M. Cavanaugh
Keyword(s):  
Inorganic Carbon ◽  
Carbon Fixation ◽  
Dissolved Inorganic Carbon ◽  
Co2 Uptake ◽  
Maximal Velocity ◽  
Marine Habitats ◽  
Half Saturation Constant ◽  
Oxygen Conditions ◽  
Solemya Velum ◽  
Influence Of Ph

ABSTRACT Chemoautotrophic symbioses, in which endosymbiotic bacteria are the major source of organic carbon for the host, are found in marine habitats where sulfide and oxygen coexist. The purpose of this study was to determine the influence of pH, alternate sulfur sources, and electron acceptors on carbon fixation and to investigate which form(s) of inorganic carbon is taken up and fixed by the gamma-proteobacterial endosymbionts of the protobranch bivalve Solemya velum. Symbiont-enriched suspensions were generated by homogenization of S. velum gills, followed by velocity centrifugation to pellet the symbiont cells. Carbon fixation was measured by incubating the cells with 14C-labeled dissolved inorganic carbon. When oxygen was present, both sulfide and thiosulfate stimulated carbon fixation; however, elevated levels of either sulfide (>0.5 mM) or oxygen (1 mM) were inhibitory. In the absence of oxygen, nitrate did not enhance carbon fixation rates when sulfide was present. Symbionts fixed carbon most rapidly between pH 7.5 and 8.5. Under optimal pH, sulfide, and oxygen conditions, symbiont carbon fixation rates correlated with the concentrations of extracellular CO2 and not with HCO3 − concentrations. The half-saturation constant for carbon fixation with respect to extracellular dissolved CO2 was 28 � 3 μM, and the average maximal velocity was 50.8 � 7.1 μmol min−1 g of protein−1. The reliance of S. velum symbionts on extracellular CO2 is consistent with their intracellular lifestyle, since HCO3 − utilization would require protein-mediated transport across the bacteriocyte membrane, perisymbiont vacuole membrane, and symbiont outer and inner membranes. The use of CO2 may be a general trait shared with many symbioses with an intracellular chemoautotrophic partner.

Photosynthesis in the Aquatic Macrophyte Egeria densa. II. Effects of Inorganic Carbon Conditions on 14C Fixation

1979 ◽  
Vol 6 (1) ◽  
pp. 1 ◽  
Author(s):  
JA Browse ◽  
JMA Brown ◽  
FI Dromgoole
Keyword(s):  
Inorganic Carbon ◽  
Carbon Fixation ◽  
Aquatic Macrophyte ◽  
Calvin Cycle ◽  
Total Carbon ◽  
Absolute Amount ◽  
Ambient Conditions ◽  
Fixation Rate ◽  
Rate Of Photosynthesis ◽  
Time Courses

In short-term labelling experiments, tripling the concentration of total inorganic carbon (TIC) did not significantly increase the high rates of 14C fixation reported in an earlier paper [19.0 μmol C (g dry wt)-1 min-1 at pH 6.8, [TIC] = 1 mM]. However, either decreasing [TIC] or increasing the pH caused the fixation rate to fall markedly. Thus at pH 6.8, [TIC] = 38 μM and pH 10.2, [TIC] = 1.0 mM, photosynthesis was 2.3 and 1.3 μmol g-1 min-1, respectively. Time courses of the distribution of photosynthetic intermediates indicated that the Calvin cycle remained the predominant pathway of carbon fixation, irrespective of the ambient conditions of TIC and pH. When the rate of photosynthesis was reduced by decreasing [TIC] or increasing pH, the proportion (but not the absolute amount) of label found in malate increased. At pH 6.8, [TIC] = 2.9 mM, μ-carboxylation accounted for only 2.7% of the total carbon fixed, compared with 9% at air levels of CO2 (pH 4.5, [TIC] = 13 μM). Egeria does not appear to exhibit C4 photosynthesis under any of the conditions studied, but malate may be a significant product of photosynthesis whenever the fixation rate is reduced by carbon availability.

scholarly journals The evolution of photosynthesis…again?

2008 ◽  
Vol 363 (1504) ◽  
pp. 2787-2801 ◽  
Author(s):  
Lynn J Rothschild
Keyword(s):  
Organic Carbon ◽  
Life Form ◽  
Inorganic Carbon ◽  
Carbon Fixation ◽  
Light Harvesting ◽  
Oxygenic Photosynthesis ◽  
Early Earth ◽  
Carboxylating Enzymes ◽  
Evolution Of Photosynthesis ◽  
Carbon Based

‘Replaying the tape’ is an intriguing ‘would it happen again?’ exercise. With respect to broad evolutionary innovations, such as photosynthesis, the answers are central to our search for life elsewhere. Photosynthesis permits a large planetary biomass on Earth. Specifically, oxygenic photosynthesis has allowed an oxygenated atmosphere and the evolution of large metabolically demanding creatures, including ourselves. There are at least six prerequisites for the evolution of biological carbon fixation: a carbon-based life form; the presence of inorganic carbon; the availability of reductants; the presence of light; a light-harvesting mechanism to convert the light energy into chemical energy; and carboxylating enzymes. All were present on the early Earth. To provide the evolutionary pressure, organic carbon must be a scarce resource in contrast to inorganic carbon. The probability of evolving a carboxylase is approached by creating an inventory of carbon-fixation enzymes and comparing them, leading to the conclusion that carbon fixation in general is basic to life and has arisen multiple times. Certainly, the evolutionary pressure to evolve new pathways for carbon fixation would have been present early in evolution. From knowledge about planetary systems and extraterrestrial chemistry, if organic carbon-based life occurs elsewhere, photosynthesis—although perhaps not oxygenic photosynthesis—would also have evolved.

scholarly journals Stable Carbon Isotopic Fractionations Associated with Inorganic Carbon Fixation by Anaerobic Ammonium-Oxidizing Bacteria

2004 ◽  
Vol 70 (6) ◽  
pp. 3785-3788 ◽  
Author(s):  
Stefan Schouten ◽  
Marc Strous ◽  
Marcel M. M. Kuypers ◽  
W. Irene C. Rijpstra ◽  
Marianne Baas ◽  
...  
Keyword(s):  
Inorganic Carbon ◽  
Carbon Fixation ◽  
Calvin Cycle ◽  
The Black Sea ◽  
Anammox Bacteria ◽  
Anammox Bacterium ◽  
Stable Carbon ◽  
Acetyl Coenzyme A ◽  
Carbon Isotopic ◽  
Isotopic Analyses

ABSTRACT Isotopic analyses of Candidatus “Brocadia anammoxidans,” a chemolithoautotrophic bacterium that anaerobically oxidizes ammonium (anammox), show that it strongly fractionates against 13C; i.e., lipids are depleted by up to 47‰ versus CO2. Similar results were obtained for the anammox bacterium Candidatus “Scalindua sorokinii,” which thrives in the anoxic water column of the Black Sea, suggesting that different anammox bacteria use identical carbon fixation pathways, which may be either the Calvin cycle or the acetyl coenzyme A pathway.

Evidence for bicarbonate accumulation by Anacystis nidulans

1984 ◽  
Vol 62 (7) ◽  
pp. 1398-1403 ◽  
Author(s):  
Barry J. Shelp ◽  
David T. Canvin
Keyword(s):  
Inorganic Carbon ◽  
Carbon Fixation ◽  
External Medium ◽  
Anacystis Nidulans ◽  
Carbon Pool ◽  
Carbon Accumulation ◽  
Total Carbon ◽  
Apparent Affinity ◽  
Photosynthetic Carbon Fixation ◽  
Photosynthetic Carbon

Kinetic studies of photosynthetic O2 evolution as a function of pH were conducted to investigate the nature of the inorganic carbon used during photosynthesis by Anacystis nidulans. At pH 5, the apparent affinity for carbon during photosynthesis was similar in air-grown and high CO2 grown cells, but at alkaline pH, the apparent affinity was much greater in air-grown cells. The substrate concentration for half-maximum rates of photosynthesis in air-grown cells remained constant as a function of pH when the substrate was expressed as total carbon, suggesting that these cells were capable of using varying proportions of CO2 and [Formula: see text]. Photosynthesis in high CO2 grown algae appeared to be more dependent on CO2 over the pH range, indicating that CO2 was the predominant carbon species used, but [Formula: see text] uptake was also indicated. Internal inorganic carbon and photosynthetic carbon fixation in air-grown cells were determined at pH 8.5, using silicone oil centrifugation. Anacystis accumulated inorganic carbon in large excess of that in the external medium by a mechanism which is sensitive to inhibitors of energy metabolism and independent of concurrent carbon fixation; light was required to accumulate and maintain the internal carbon pool. The degree of accumulation was a function of the carbon concentration in the external medium; at 12 μM external carbon, the accumulation ratio was in excess of 100-fold, whereas at 4.76 mM, the ratio was only 5-fold. The rates of carbon transport were always sufficient to maintain photosynthesis. Carbon efflux rates approaching 40% of the influx rate were found at equilibrium internal carbon concentrations. Kinetic parameters of photosynthesis are discussed with reference to the known properties of algal ribulose bisphosphate (RuBP) carboxylase–oxygenase. It is concluded that the internal inorganic carbon pool serves as an intermediate for photosynthetic carbon fixation and that, if CO2 and [Formula: see text] are in equilibrium, the carbon accumulation at ambient CO2 and O2 is sufficient to suppress RuBP oxygenase activity.

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