scholarly journals Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow)

2021 ◽  
Vol 9 (7) ◽  
pp. 1368
Author(s):  
Qianqian Li ◽  
Rebecca E. Cooper ◽  
Carl-Eric Wegner ◽  
Martin Taubert ◽  
Nico Jehmlich ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Co2 Fixation ◽  
Carbon Fixation ◽  
Stable Isotope Probing ◽  
Acidic Lake ◽  
General Role ◽  
Polysaccharide Biosynthesis ◽  
Iron Oxidizers ◽  
Metabolic Activities ◽  
Chemolithoautotrophic Bacteria

Pelagic aggregates function as biological carbon pumps for transporting fixed organic carbon to sediments. In iron-rich (ferruginous) lakes, photoferrotrophic and chemolithoautotrophic bacteria contribute to CO2 fixation by oxidizing reduced iron, leading to the formation of iron-rich pelagic aggregates (iron snow). The significance of iron oxidizers in carbon fixation, their general role in iron snow functioning and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis of iron snow collected from an acidic lake with protein-based stable isotope probing to determine general metabolic activities and to trace 13CO2 incorporation in iron snow over time under oxic and anoxic conditions. mRNA-derived metatranscriptome of iron snow identified four key players (Leptospirillum, Ferrovum, Acidithrix, Acidiphilium) with relative abundances (59.6–85.7%) encoding ecologically relevant pathways, including carbon fixation and polysaccharide biosynthesis. No transcriptional activity for carbon fixation from archaea or eukaryotes was detected. 13CO2 incorporation studies identified active chemolithoautotroph Ferrovum under both conditions. Only 1.0–5.3% relative 13C abundances were found in heterotrophic Acidiphilium and Acidocella under oxic conditions. These data show that iron oxidizers play an important role in CO2 fixation, but the majority of fixed C will be directly transported to the sediment without feeding heterotrophs in the water column in acidic ferruginous lakes.

scholarly journals The carbon fixation efficiency in biomass of Cylindrotheca closterium (Ehrenberg) Reimann & J. C. Lewin (Bacillariophyceae) under the conditions of cumulative cultivation

2020 ◽  
Vol 5 (1) ◽  
pp. 12-19
Author(s):  
R. G. Gevorgiz ◽  
S. N. Zheleznova
Keyword(s):  
Co2 Fixation ◽  
Carbon Fixation ◽  
Utilization Efficiency ◽  
Chlorella Protothecoides ◽  
Carbonic Anhydrases ◽  
Low Carbon ◽  
Carbon Utilization ◽  
Porphyridium Purpureum ◽  
Cylindrotheca Closterium ◽  
Dry Biomass

The carbon utilization efficiency is an important characteristic of the cultivated object. Diatom Cylindrotheca closterium (Ehrenberg) Reimann & J. C. Lewin is known to use carbon from aquatic environment quite effectively, as it has many unique carbonic anhydrases and carbon transporters. However, the carbon fixation efficiency for many types of diatoms in culture is still unknown. When calculating the carbon fixation efficiency, researchers use different terminology and methods, and it leads to significant difficulties when comparing the carbon fixation efficiency in the biomass of various types of microalgae. The aims of this study are: 1) to update terms and definitions used in literature on the basis of modern concepts of carbon fixation in microalgae biomass, as well as absorption of inorganic carbon by microalgae culture; 2) to evaluate the carbon fixation efficiency in the biomass of C. closterium diatom under conditions of cumulative cultivation. C. closterium was grown at a temperature of +20 °C on a nutrient medium RS. During the cultivation, the culture was bubbled with air (1.1 L of air per 1 L of culture per minute). The air temperature at the outlet of the suspension was of +19 °C; the maximum productivity of the culture was of 1.254 g·L−1·day−1. According to the results of the CHN analysis, the proportion of carbon in C. closterium dry biomass was of 23 %. Under the conditions of cumulative cultivation in C. closterium, the carbon fixation efficiency in biomass was of 90 %. Compared with other algae species, C. closterium is characterized by a rather high CO2 fixation efficiency. For example, in green microalga Chlorella protothecoides and Ch. vulgaris, the CO2 fixation efficiency was of 20 % and 55.3 %, respectively; in cyanobacteria Spirulina sp. – of 38 %; in red microalgae Porphyridium purpureum – of 69 %. It was observed that to ensure an increase of 1 g of C. closterium dry biomass per day at a temperature of +19 °C, a minimum of 0.46 L of CO2, or 1132 L of air, should be consumed. Possibly, it is high carbon fixation efficiency, as well as low carbon fraction in C. closterium biomass, that explains the high production indices of this species. Under equal conditions of cultivation in terms of light and carbon availability, the productivity of C. closterium can exceed the productivity of other types of microalgae by 5–10 times. So, while Spirulina sp. productivity reaches 0.2 g·L−1·day−1, C. closterium productivity is of 1.254 g·L−1·day−1.

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.

scholarly journals AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Abhijeet Singh ◽  
Bettina Müller ◽  
Hans-Henrik Fuxelius ◽  
Anna Schnürer
Keyword(s):  
Carbon Fixation ◽  
Sequence Data ◽  
Gene Encoding ◽  
Formyltetrahydrofolate Synthetase ◽  
Protein Levels ◽  
Acetogenic Bacteria ◽  
Blast Database ◽  
Key Enzyme ◽  
Chemolithoautotrophic Bacteria ◽  
Taxonomic Studies

Abstract Acetogenic bacteria are imperative to environmental carbon cycling and diverse biotechnological applications, but their extensive physiological and taxonomical diversity is an impediment to systematic taxonomic studies. Acetogens are chemolithoautotrophic bacteria that perform reductive carbon fixation under anaerobic conditions through the Wood–Ljungdahl pathway (WLP)/acetyl-coenzyme A pathway. The gene-encoding formyltetrahydrofolate synthetase (FTHFS), a key enzyme of this pathway, is highly conserved and can be used as a molecular marker to probe acetogenic communities. However, there is a lack of systematic collection of FTHFS sequence data at nucleotide and protein levels. In an attempt to streamline investigations on acetogens, we developed AcetoBase - a repository and database for systematically collecting and organizing information related to FTHFS sequences. AcetoBase also provides an opportunity to submit data and obtain accession numbers, perform homology searches for sequence identification and access a customized blast database of submitted sequences. AcetoBase provides the prospect to identify potential acetogenic bacteria, based on metadata information related to genome content and the WLP, supplemented with FTHFS sequence accessions, and can be an important tool in the study of acetogenic communities. AcetoBase can be publicly accessed at https://acetobase.molbio.slu.se.

scholarly journals Systems analysis of the CO2 concentrating mechanism in cyanobacteria

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Niall M Mangan ◽  
Michael P Brenner
Keyword(s):  
Systems Analysis ◽  
Photosynthetic Bacteria ◽  
Spatial Organization ◽  
Co2 Fixation ◽  
Carbon Fixation ◽  
Co2 Uptake ◽  
Co2 Concentrating Mechanism ◽  
Concentrating Mechanism ◽  
Molecular Components ◽  
External Ph

Cyanobacteria are photosynthetic bacteria with a unique CO2 concentrating mechanism (CCM), enhancing carbon fixation. Understanding the CCM requires a systems level perspective of how molecular components work together to enhance CO2 fixation. We present a mathematical model of the cyanobacterial CCM, giving the parameter regime (expression levels, catalytic rates, permeability of carboxysome shell) for efficient carbon fixation. Efficiency requires saturating the RuBisCO reaction, staying below saturation for carbonic anhydrase, and avoiding wasteful oxygenation reactions. We find selectivity at the carboxysome shell is not necessary; there is an optimal non-specific carboxysome shell permeability. We compare the efficacy of facilitated CO2 uptake, CO2 scavenging, and HCO3− transport with varying external pH. At the optimal carboxysome permeability, contributions from CO2 scavenging at the cell membrane are small. We examine the cumulative benefits of CCM spatial organization strategies: enzyme co-localization and compartmentalization.

Bacteria Responsible for Nitrate-dependent Antimonite Oxidation in Antimony-contaminated Paddy Soil Revealed by the Combination of DNA-SIP and Metagenomics

2020 ◽  
Author(s):  
Miaomiao Zhang ◽  
Zhe Li ◽  
Max M. Häggblom ◽  
Lily Young ◽  
Fangbai Li ◽  
...  
Keyword(s):  
Paddy Soil ◽  
Carbon Fixation ◽  
Current Knowledge ◽  
Stable Isotope Probing ◽  
Metagenomic Sequencing ◽  
Proof Of Concept ◽  
Ecological Role ◽  
Shotgun Metagenomic Sequencing ◽  
Anoxic Environments ◽  
Contaminated Paddy Soil

Abstract Background: Antimonite (Sb(III)) oxidation (SbO) can decrease the toxicity of antimony (Sb) and its uptake into plants (e.g., rice), thus serving an ecological role in bioremediation of Sb contamination. In some anoxic environments, Sb(III) can be oxidized coupled with nitrate as the electron acceptor. Here we investigate the potential for nitrate-dependent SbO in Sb contaminated rice paddies and identify nitrate-dependent Sb(III)-oxidizing bacteria (SbOB) using stable isotope probing (SIP) coupled with amplicon and shotgun metagenomic sequencing.Results: Anaerobic SbO was exclusively observed in the paddy soil amended with both Sb(III) and NO3-, whereas no apparent SbO was detected in the soil amended with Sb(III) only. The increasing abundance of the arsenite oxidase (aioA) gene suggests that nitrate-dependent SbO was catalysed by microorganisms harbouring the aioA gene. After 60-day DNA-SIP incubation, obvious shift in the aioA gene to heavy DNA fractions only in the treatment amended with 13C-NaHCO3, Sb(III) and NO3- suggested the incorporation of 13C by nitrate-dependent SbOB. Accordingly, DNA-SIP identified a number of putative nitrate-dependent SbOB in the paddy soil, including Azoarcus, Azospira and Chelativorans. Metagenomic analysis further revealed that they contained aioA gene and genes involved in denitrification and carbon fixation, supporting their capability for nitrate-dependent SbO.Conclusions: These observations in this study suggested the occurrence of nitrate-dependent SbO in paddy soils. A number of putative nitrate-dependent SbOB (i.e., Azoarcus, Azospira and Chelativorans) were reported here, which expands our current knowledge regarding the diversity of nitrate-dependent SbOB. In addition, this study provides a proof of concept using DNA-SIP to identify nitrate-dependent SbOB.

CO2(aq) concentration–dependent CO2 fixation via carboxylation by decarboxylase

2021 ◽  
Author(s):  
Yan Fan ◽  
Jianqiang Feng ◽  
miao yang ◽  
xin Tan ◽  
Hongjun Fan ◽  
...  
Keyword(s):  
Co2 Sequestration ◽  
Co2 Fixation ◽  
Carbon Fixation ◽  
Decarboxylation Reaction

Enzymatic carbon fixation is one of the most interesting processes in CO2 sequestration. A number of decarboxylases can catalyze the reversible decarboxylation reaction in vivo, while can strengthen the carboxylation...

scholarly journals Geochemical Rate-RNA Integration Study: Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Gene Transcription and Photosynthetic Capacity of Planktonic Photoautotrophs

2004 ◽  
Vol 70 (9) ◽  
pp. 5459-5468 ◽  
Author(s):  
Jorge E. Corredor ◽  
Boris Wawrik ◽  
John H. Paul ◽  
Hiep Tran ◽  
Lee Kerkhof ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Carbon Fixation ◽  
Photosynthetic Capacity ◽  
Large Subunit ◽  
Mrna Levels ◽  
Bisphosphate Carboxylase ◽  
Pigment Analysis ◽  
Reverse Transcription Pcr ◽  
The Relationship ◽  
Rrna Sequences

ABSTRACT A pilot field experiment to assess the relationship between traditional biogeochemical rate measurements and transcriptional activity of microbial populations was carried out at the LEO 15 site off Tuckerton, N.J. Here, we report the relationship between photosynthetic capacity of autotrophic plankton and transcriptional activity of the large subunit gene (rbcL) for ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), the enzyme responsible for primary carbon fixation during photosynthesis. Similar diel patterns of carbon fixation and rbcL gene expression were observed in three of four time series, with maxima for photosynthetic capacity (P max) and rbcL mRNA occurring between 10 a.m. and 1 p.m.. The lowest P max and rbcL levels were detected between 6 p.m. and 10:30 p.m.. A significant correlation was found between P max and form ID rbcL mRNA (R 2 = 0.56) and forms IA and IB (R 2 = 0.41 and 0.47, respectively). The correlation between the abundance of “diatom” rbcL and P max mRNA was modest (R 2 = 0.49; n = 12) but improved dramatically (R 2 = 0.97; n = 10) upon removal of two outliers which represented afternoon samples with high P max but lower mRNA levels. Clone libraries from reverse transcription-PCR-amplified rbcL mRNA indicated the presence of several chromophytic algae (diatoms, prymnesiophytes, and chrysophytes) and some eukaryotic green flagellates. Analogous results were obtained from amplified small rRNA sequences and secondary pigment analysis. These results suggest that diatoms were a major contributor to carbon fixation at LEO 15 at the time of sampling and that photosynthetic carbon fixation was partially controlled by transcriptional regulation of the RubisCO gene.

scholarly journals Small phytoplankton contribute greatly to CO2-fixation after the diatom bloom in the Southern Ocean

2021 ◽  
Author(s):  
Solène Irion ◽  
Urania Christaki ◽  
Hugo Berthelot ◽  
Stéphane L’Helguen ◽  
Ludwig Jardillier
Keyword(s):  
Southern Ocean ◽  
Co2 Fixation ◽  
Carbon Fixation ◽  
Deep Ocean ◽  
Small Cells ◽  
Cell Level ◽  
Carbon Pump ◽  
Small Phytoplankton ◽  
Important Pathway

AbstractPhytoplankton is composed of a broad-sized spectrum of phylogenetically diverse microorganisms. Assessing CO2-fixation intra- and inter-group variability is crucial in understanding how the carbon pump functions, as each group of phytoplankton may be characterized by diverse efficiencies in carbon fixation and export to the deep ocean. We measured the CO2-fixation of different groups of phytoplankton at the single-cell level around the naturally iron-fertilized Kerguelen plateau (Southern Ocean), known for intense diatoms blooms suspected to enhance CO2 sequestration. After the bloom, small cells (<20 µm) composed of phylogenetically distant taxa (prymnesiophytes, prasinophytes, and small diatoms) were growing faster (0.37 ± 0.13 and 0.22 ± 0.09 division d−1 on- and off-plateau, respectively) than larger diatoms (0.11 ± 0.14 and 0.09 ± 0.11 division d−1 on- and off-plateau, respectively), which showed heterogeneous growth and a large proportion of inactive cells (19 ± 13%). As a result, small phytoplankton contributed to a large proportion of the CO2 fixation (41–70%). The analysis of pigment vertical distribution indicated that grazing may be an important pathway of small phytoplankton export. Overall, this study highlights the need to further explore the role of small cells in CO2-fixation and export in the Southern Ocean.

scholarly journals Reviews and syntheses: Heterotrophic fixation of inorganic carbon – significant but invisible flux in global carbon cycling

2020 ◽  
Author(s):  
Alexander Braun ◽  
Marina Spona-Friedl ◽  
Maria Avramov ◽  
Martin Elsner ◽  
Federico Baltar ◽  
...  
Keyword(s):  
Co2 Fixation ◽  
Inorganic Carbon ◽  
Carbon Fixation ◽  
Standing Stock ◽  
Co2 Flux ◽  
Global Carbon Cycle ◽  
Autotrophic Co2 Fixation ◽  
Global Carbon ◽  
Heterotrophic Biomass ◽  
Heterotrophic Production

Abstract. Heterotrophic CO2 fixation is a significant, yet underappreciated CO2 flux in the global carbon cycle. In contrast to photosynthesis and chemolithoautotrophy – the main recognized autotrophic CO2 fixation pathways – the importance of heterotrophic CO2 fixation remains enigmatic. All heterotrophs – from microorganisms to humans – take up CO2 and incorporate it into their biomass. Depending on the available growth substrates, heterotrophic CO2 fixation contributes at least 2–8 % and in the case of methanotrophs up to 50 % of the carbon building up their biomass. Assuming a standing stock of global heterotrophic biomass of 47–85 Pg C, we estimate that up to 7 Pg C have been derived from heterotrophic CO2 fixation and up to 20 Pg C yr−1 originating from heterotrophic CO2 fixation are funneled into the global annual heterotrophic production of 34–245 Pg C yr−1. These first estimates on the importance of heterotrophic fixation of inorganic carbon indicate that this carbon fixation pathway should be included in present and future global carbon budgets.

scholarly journals Lokiarchaeon exhibits homoacetogenesis

2019 ◽  
Author(s):  
William D. Orsi ◽  
Aurèle Vuillemin ◽  
Paula Rodriguez ◽  
Ömer K. Coskun ◽  
Gonzalo V. Gomez-Saez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Host Cell ◽  
Extracellular Polymeric Substances ◽  
Carbon Fixation ◽  
Carbon Sources ◽  
Stable Isotope Probing ◽  
Organic Substrates ◽  
Sugar Fermentation ◽  
Expression Of Genes ◽  
Wide Range

AbstractThe proposed Asgard superphylum of Archaea comprises the closest archaeal relatives of eukaryotes, whose genomes hold clues pertaining to the nature host cell that acquired the mitochondrion at the origin of eukaryotes1-4. Genomes of the Asgard candidate Phylum ‘Candidatus Lokiarchaeota’ [Lokiarchaeon] suggest an acetogenic H2 –dependent lifestyle5 and mixotrophic capabilities6. However, data on the activity of Lokiarchaeon are currently lacking, and the ecology of the host cell that acquired the mitochondrion is debated4,7. Here, we show that in anoxic marine sediments underlying highly productive waters on the Namibian continental shelf Lokiarchaeon gene expression increases with depth below the seafloor, and was significantly different across a redox gradient spanning hypoxic to sulfidic conditions. Notably, Lokiarchaeon increased expression of genes involved in growth, carbohydrate metabolism, and the H2-dependent Wood-Ljungdahl (WLP) carbon fixation pathway under the most reducing (sulfidic) conditions. Quantitative stable isotope probing experiments revealed multiple populations of Lokiarchaeota utilizing both CO2 and diatomaceous extracellular polymeric substances (dEPS) as carbon sources over a 10-day incubation under anoxic conditions. This apparent anaerobic mixotrophic metabolism was consistent with the expression of Lokiarchaeon genes involved in transport and fermentation of sugars and amino acids. Remarkably, several Asgard populations were more enriched with 13C-dEPS compared to the community average, indicating a preference for dEPS as a growth substrate. The qSIP and gene expression data indicate a metabolism of “Candidatus Lokiarchaeota” similar to that of sugar fermenting homoacetogenic bacteria8, namely that Lokiarchaeon can couple fermentative H2 production from organic substrates with electron bifurcation and the autotrophic and H2-dependent WLP. Homoacetogenesis allows to access a wide range of substrates and relatively high ATP gain during acetogenic sugar fermentation8 thereby providing an ecological advantage for Lokiarchaeon in anoxic, energy limited settings.

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