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 Metagenome Assembled Genome of a Novel Verrucomicrobial Methanotroph From Pantelleria Island

2021 ◽  
Vol 12 ◽  
Author(s):  
Nunzia Picone ◽  
Pieter Blom ◽  
Carmen Hogendoorn ◽  
Jeroen Frank ◽  
Theo van Alen ◽  
...  
Keyword(s):  
Nitrate Reduction ◽  
Inorganic Carbon ◽  
Carbon Fixation ◽  
Hydrogen Oxidation ◽  
Aerobic Bacteria ◽  
Particulate Methane Monooxygenase ◽  
Coding Sequences ◽  
Extensive Analysis ◽  
Genes Encoding ◽  
Nitric Oxide Reduction

Verrucomicrobial methanotrophs are a group of aerobic bacteria isolated from volcanic environments. They are acidophiles, characterized by the presence of a particulate methane monooxygenase (pMMO) and a XoxF-type methanol dehydrogenase (MDH). Metagenomic analysis of DNA extracted from the soil of Favara Grande, a geothermal area on Pantelleria Island, Italy, revealed the presence of two verrucomicrobial Metagenome Assembled Genomes (MAGs). One of these MAGs did not phylogenetically classify within any existing genus. After extensive analysis of the MAG, we propose the name of “Candidatus Methylacidithermus pantelleriae” PQ17 gen. nov. sp. nov. The MAG consisted of 2,466,655 bp, 71 contigs and 3,127 predicted coding sequences. Completeness was found at 98.6% and contamination at 1.3%. Genes encoding the pMMO and XoxF-MDH were identified. Inorganic carbon fixation might use the Calvin-Benson-Bassham cycle since all genes were identified. The serine and ribulose monophosphate pathways were incomplete. The detoxification of formaldehyde could follow the tetrahydrofolate pathway. Furthermore, “Ca. Methylacidithermus pantelleriae” might be capable of nitric oxide reduction but genes for dissimilatory nitrate reduction and nitrogen fixation were not identified. Unlike other verrucomicrobial methanotrophs, genes encoding for enzymes involved in hydrogen oxidation could not be found. In conclusion, the discovery of this new MAG expands the diversity and metabolism of verrucomicrobial methanotrophs.

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.

scholarly journals Ubiquity and functional uniformity in CO2 concentrating mechanisms in multiple phyla of Bacteria is suggested by a diversity and prevalence of genes encoding candidate dissolved inorganic carbon transporters

2020 ◽  
Vol 367 (13) ◽  
Author(s):  
Kathleen M Scott ◽  
Tara L Harmer ◽  
Bradford J Gemmell ◽  
Andrew M Kramer ◽  
Markus Sutter ◽  
...  
Keyword(s):  
Inorganic Carbon ◽  
Dissolved Inorganic Carbon ◽  
Extreme Environments ◽  
Bacterial Genomes ◽  
Low Co2 ◽  
Transporter Family ◽  
Genes Encoding ◽  
Co2 Concentrating Mechanisms ◽  
Biological Component ◽  
Global Carbon

ABSTRACT Autotrophic microorganisms catalyze the entry of dissolved inorganic carbon (DIC; = CO2 + HCO3− + CO32−) into the biological component of the global carbon cycle, despite dramatic differences in DIC abundance and composition in their sometimes extreme environments. “Cyanobacteria” are known to have CO2 concentrating mechanisms (CCMs) to facilitate growth under low CO2 conditions. These CCMs consist of carboxysomes, containing enzymes ribulose 1,5-bisphosphate oxygenase and carbonic anhydrase, partnered to DIC transporters. CCMs and their DIC transporters have been studied in a handful of other prokaryotes, but it was not known how common CCMs were beyond “Cyanobacteria”. Since it had previously been noted that genes encoding potential transporters were found neighboring carboxysome loci, α-carboxysome loci were gathered from bacterial genomes, and potential transporter genes neighboring these loci are described here. Members of transporter families whose members all transport DIC (CHC, MDT and Sbt) were common in these neighborhoods, as were members of the SulP transporter family, many of which transport DIC. 109 of 115 taxa with carboxysome loci have some form of DIC transporter encoded in their genomes, suggesting that CCMs consisting of carboxysomes and DIC transporters are widespread not only among “Cyanobacteria”, but also among members of “Proteobacteria” and “Actinobacteria”.

scholarly journals Expression and Function of Four Carbonic Anhydrase Homologs in the Deep-Sea Chemolithoautotroph Thiomicrospira crunogena

2010 ◽  
Vol 76 (11) ◽  
pp. 3561-3567 ◽  
Author(s):  
Kimberly P. Dobrinski ◽  
Amanda J. Boller ◽  
Kathleen M. Scott
Keyword(s):  
Carbonic Anhydrase ◽  
Carbon Fixation ◽  
Dissolved Inorganic Carbon ◽  
Subcellular Location ◽  
Cell Extracts ◽  
Low Concentrations ◽  
Genes Encoding ◽  
A Minor ◽  
And Function ◽  
Thiomicrospira Crunogena

ABSTRACT The hydrothermal vent chemolithoautotroph Thiomicrospira crunogena grows rapidly in the presence of low concentrations of dissolved inorganic carbon (DIC) (= CO2 + HCO3 − + CO3 −2). Its genome encodes α-carbonic anhydrase (α-CA), β-CA, carboxysomal β-like CA (CsoSCA), and a protein distantly related to γ-CA. The purposes of this work were to characterize the gene products, determine whether they were differentially expressed, and identify those that are necessary for DIC uptake and fixation. When expressed in Escherichia coli, CA activity was detectable for α-CA, β-CA, and CsoSCA but not for the γ-CA-like protein. α-CA and CsoSCA but not β-CA were inhibited by sulfonamide inhibitors. CsoSCA was also inhibited by dithiothreitol. When grown under DIC limitation in chemostats, T. crunogena transcribed csoSCA more frequently than when ammonia limited, while genes encoding α-CA and β-CA were not differentially transcribed under these conditions. Cell extracts from T. crunogena grown under both DIC- and ammonia-limited conditions had CA activity that was strongly inhibited by sulfonamides, though extracts from nitrogen-limited cells had some CA activity that was resistant, perhaps due to a higher level of β-CA activity. Based on predictions from the SignalP software program, subcellular location when expressed in E. coli, and carbonic anhydrase assays conducted on intact T. crunogena cells, α-CA is located in the periplasm. However, inhibition of α-CA by acetazolamide had only a minor impact on rates of DIC uptake or fixation. Conversely, inhibition of CsoSCA with ethoxyzolamide inhibited carbon fixation but not DIC uptake, consistent with this enzyme functioning to facilitate DIC interconversion and fixation within carboxysomes.

scholarly journals Prediction of Genes That Function in Methanogenesis and CO2 Pathways in Extremophiles

2021 ◽  
Vol 9 (11) ◽  
pp. 2211
Author(s):  
Lulit Tilahun ◽  
Asfawossen Asrat ◽  
Gary M. Wessel ◽  
Addis Simachew
Keyword(s):  
Inorganic Carbon ◽  
Carbon Fixation ◽  
Underground Water ◽  
Specific Enzyme ◽  
Cooperative Interactions ◽  
Biological Source ◽  
Genes Encoding ◽  
Acetoclastic Methanogenesis ◽  
Ionic Components ◽  
Main Strategy

Gaet’ale (GAL) and Mud’ara (MUP) are two hypersaline ponds located in the Danakil Depression recharged by underground water from the surrounding highlands. These two ponds have different pH, salinity, and show variation in the concentration of many ionic components. Metagenomic analysis concludes that GAL is dominated by bacteria as in the case of the other hypersaline and acidic ponds in the Danakil Depression. However, Archaea dominated the ponds of MUP. In the current study, the application of SEED and KEGG helped to map the ordered steps of specific enzyme catalyzed reaction in converting CO2 into cell products. We predict that highly efficient and light-independent carbon fixation involving phosphoenolpyruvate carboxylase takes place in MUP. On the contrary, genes encoding enzymes involved in hydrogenotrophic and acetoclastic methanogenesis appeared solely in ponds of GAL, implying the biological source of the hazardous methane gas in that environment. Based on the investigation of the sources of the genes of interest, it is clear that cooperative interactions between members of the two communities and syntrophic metabolism is the main strategy adapted to utilize inorganic carbon as a carbon source in both MUP and GAL. This insight can be used to design biotechnological applications of microbial communities in production of methane biogas or to minimize CO2 emissions.

scholarly journals Nutrients recycle and the growth of Scenedesmus obliquus in synthetic wastewater under different sodium carbonate concentrations

2020 ◽  
Vol 7 (1) ◽  
pp. 191214 ◽  
Author(s):  
Yun Duan ◽  
Xin Guo ◽  
Jingjing Yang ◽  
Mingmei Zhang ◽  
Yangyang Li
Keyword(s):  
Sodium Carbonate ◽  
Inorganic Carbon ◽  
Carbon Fixation ◽  
Dissolved Inorganic Carbon ◽  
Scenedesmus Obliquus ◽  
Biomass Accumulation ◽  
Synthetic Wastewater ◽  
Nitrogen And Phosphorus ◽  
Fixation Rate ◽  
High Concentrations

This study illustrated the growth of Scenedesmus obliquus and recycle of nutrients in wastewater combined with inorganic carbon under autotrophic conditions. Scenedesmus obliquus was cultivated under different conditions by adding sodium carbonate (Na 2 CO 3 ) at 15–40 mg l −1 separately in wastewater containing high nitrogen and phosphorus content. The growth characteristics of S. obliquus , pH and dissolved inorganic carbon (DIC) changes of microalgae liquid, the recycle rate of ammonia and phosphorus and lipid content were determined. The changes of pH and DIC showed that S. obliquus could use Na 2 CO 3 to grow, with lipid contents of 18–25%. Among all Na 2 CO 3 concentrations, 20 mg l −1 was the optimum, of which S. obliquus had the highest NH 3 -N recycle of 52% and P O 4 3 – P recycle of 67%. By the 14th day, its biomass production also reaches the maximum of 0.21 g l −1 . However, inorganic carbon fixation rate was inversely proportional to its concentration. Moreover, the biomass was in positive correlation with the Na 2 CO 3 concentration except 20 mg l −1 , which provided a possibility that S. obliquus could be acclimatized to adjust to high concentrations of inorganic carbon to promote biomass accumulation and recycle of nutrients.

Bicarbonate uptake rates and diversity of RuBisCO genes in saline lake sediments

2021 ◽  
Vol 97 (4) ◽  
Author(s):  
Beichen Wang ◽  
Jianrong Huang ◽  
Jian Yang ◽  
Hongchen Jiang ◽  
Haiyi Xiao ◽  
...  
Keyword(s):  
Inorganic Carbon ◽  
Carbon Fixation ◽  
Dissolved Inorganic Carbon ◽  
Full Range ◽  
Microbial Populations ◽  
Fixation Rate ◽  
Organic Carbon Concentration ◽  
Uptake Rates ◽  
Bicarbonate Uptake ◽  
And Function

ABSTRACT There is limited knowledge of microbial carbon fixation rate, and carbon-fixing microbial abundance and diversity in saline lakes. In this study, the inorganic carbon uptake rates and carbon-fixing microbial populations were investigated in the surface sediments of lakes with a full range of salinity from freshwater to salt saturation. The results showed that in the studied lakes light-dependent bicarbonate uptake contributed substantially (>70%) to total bicarbonate uptake, while the contribution of dark bicarbonate uptake (1.35–25.17%) cannot be ignored. The light-dependent bicarbonate uptake rates were significantly correlated with pH and turbidity, while dark bicarbonate uptake rates were significantly influenced by dissolved inorganic carbon, pH, temperature and salinity. Carbon-fixing microbial populations using the Calvin-Benson-Bassham pathway were widespread in the studied lakes, and they were dominated by the cbbL and cbbM gene types affiliated with Cyanobacteria and Proteobacteria, respectively. The cbbL and cbbM gene abundance and population structures were significantly affected by different environmental variables, with the cbbL and cbbM genes being negatively correlated with salinity and organic carbon concentration, respectively. In summary, this study improves our knowledge of the abundance, diversity and function of carbon-fixing microbial populations in the lakes with a full range of salinity.

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