scholarly journals Pronounced uptake and metabolism of organic substrates by diatoms revealed by pulse-labeling metabolomics

2021 ◽  
Author(s):  
Nils Meyer ◽  
Aljoscha Rydzyk ◽  
Georg Pohnert
Keyword(s):  
Organic Material ◽  
Carbon Fixation ◽  
Organic Substrates ◽  
Dominant Group ◽  
Pulse Label ◽  
Organic Resources ◽  
Global Carbon ◽  
Uptake And Metabolism ◽  
General Scope ◽  
Material Fluxes

Diatoms contribute as a dominant group of microalgae to approximately 20 per cent of the global carbon fixation. In the plankton, these photosynthetic algae are exposed to a plethora of metabolites, especially when competing algae are lysed. It is well established that diatoms can take up specific metabolites, such as vitamins, amino acids as nitrogen source, or dimethylsulfoniopropoionate to compensate for changes in water salinity. It is, however, unclear to which extent diatoms take up other organic resources and if these are incorporated into the cells metabolism. Here, we ask about the general scope of uptake of metabolites from competitors. Using labeled metabolites released during lysis of algae grown under a 13CO2 atmosphere, we show that the cosmopolitan diatom Chaetoceros didymus takes up organic substrates with little bias and remarkable efficiency. The newly developed pulse label/ mass spectrometry metabolomics approach reveals that polarity and molecular weight has no detectable influence on uptake efficiency. We also reveal that the taken-up pool of metabolites is partly maintained unaltered within the cells but is also subject to catabolic and anabolic transformation. One of the most dominant phytoplankton groups is thus substantially competing with other heterotrophs for organic material, suggesting that the observed absorbotrophy may substantially impact organic material fluxes in the oceans. Our findings call for the refinement of our understanding of competition in the plankton.

scholarly journals High Rates of Ecosytem Metabolism in Five Western Rivers

2011 ◽  
Vol 33 ◽  
pp. 115-118
Author(s):  
Robert Hall ◽  
Jennifer Tank ◽  
Michelle Baker ◽  
Emma Rosi-Marshall ◽  
Michael Grace ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Primary Production ◽  
Carbon Cycling ◽  
Carbon Balance ◽  
Carbon Fixation ◽  
Higher Plants ◽  
Ecosystem Respiration ◽  
Gross Primary Production ◽  
Total Rate ◽  
Global Carbon

Primary production and respiration are core functions of river ecosystems that in part determine the carbon balance. Gross primary production (GPP) is the total rate of carbon fixation by autotrophs such as algae and higher plants and is equivalent to photosynthesis. Ecosystem respiration (ER) measures rate at which organic carbon is mineralized to CO2 by all organisms in an ecosystem. Together these fluxes can indicate the base of the food web to support animal production (Marcarelli et al. 2011), can predict the cycling of other elements (Hall and Tank 2003), and can link ecosystems to global carbon cycling (Cole et al. 2007).

scholarly journals Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens

2019 ◽  
Vol 116 (11) ◽  
pp. 5037-5044 ◽  
Author(s):  
Bojk A. Berghuis ◽  
Feiqiao Brian Yu ◽  
Frederik Schulz ◽  
Paul C. Blainey ◽  
Tanja Woyke ◽  
...  
Keyword(s):  
Paradigm Shift ◽  
Carbon Fixation ◽  
Methanogenic Archaea ◽  
Global Carbon Cycle ◽  
Hydrogenotrophic Methanogenesis ◽  
Shared Ancestry ◽  
Hydrogenotrophic Methanogens ◽  
Methyl Coenzyme M Reductase ◽  
Global Carbon ◽  
Insight Into

Methanogenic archaea are major contributors to the global carbon cycle and were long thought to belong exclusively to the euryarchaeal phylum. Discovery of the methanogenesis gene cluster methyl-coenzyme M reductase (Mcr) in the Bathyarchaeota, and thereafter the Verstraetearchaeota, led to a paradigm shift, pushing back the evolutionary origin of methanogenesis to predate that of the Euryarchaeota. The methylotrophic methanogenesis found in the non-Euryarchaota distinguished itself from the predominantly hydrogenotrophic methanogens found in euryarchaeal orders as the former do not couple methanogenesis to carbon fixation through the reductive acetyl-CoA [Wood–Ljungdahl pathway (WLP)], which was interpreted as evidence for independent evolution of the two methanogenesis pathways. Here, we report the discovery of a complete and divergent hydrogenotrophic methanogenesis pathway in a thermophilic order of the Verstraetearchaeota, which we have named Candidatus Methanohydrogenales, as well as the presence of the WLP in the crenarchaeal order Desulfurococcales. Our findings support the ancient origin of hydrogenotrophic methanogenesis, suggest that methylotrophic methanogenesis might be a later adaptation of specific orders, and provide insight into how the transition from hydrogenotrophic to methylotrophic methanogenesis might have occurred.

scholarly journals The PduL Phosphotransacylase Is Used To Recycle Coenzyme A within the Pdu Microcompartment

2015 ◽  
Vol 197 (14) ◽  
pp. 2392-2399 ◽  
Author(s):  
Yu Liu ◽  
Julien Jorda ◽  
Todd O. Yeates ◽  
Thomas A. Bobik
Keyword(s):  
Carbon Fixation ◽  
Coenzyme A ◽  
Fluorescent Protein ◽  
Heterologous Proteins ◽  
Content Type ◽  
Bacterial Microcompartment ◽  
Green Fluorescent ◽  
Necessary And Sufficient ◽  
Global Carbon ◽  
Bioinformatic Approach

ABSTRACTInSalmonella enterica, 1,2-propanediol (1,2-PD) utilization (Pdu) is mediated by a bacterial microcompartment (MCP). The Pdu MCP consists of a multiprotein shell that encapsulates enzymes and cofactors for 1,2-PD catabolism, and its role is to sequester a reactive intermediate (propionaldehyde) to minimize cellular toxicity and DNA damage. For the Pdu MCP to function, the enzymes encapsulated within must be provided with a steady supply of substrates and cofactors. In the present study, Western blotting assays were used to demonstrate that the PduL phosphotransacylase is a component of the Pdu MCP. We also show that the N-terminal 20-residue-long peptide of PduL is necessary and sufficient for targeting PduL and enhanced green fluorescent protein (eGFP) to the lumen of the Pdu MCP. We present the results of genetic tests that indicate that PduL plays a role in the recycling of coenzyme A internally within the Pdu MCP. However, the results indicate that some coenzyme A recycling occurs externally to the Pdu MCP. Hence, our results support a model in which a steady supply of coenzyme A is provided to MCP lumen enzymes by internal recycling by PduL as well as by the movement of coenzyme A across the shell by an unknown mechanism. These studies expand our understanding of the Pdu MCP, which has been linked to enteric pathogenesis and which provides a possible basis for the development of intracellular bioreactors for use in biotechnology.IMPORTANCEBacterial MCPs are widespread organelles that play important roles in pathogenesis and global carbon fixation. Here we show that the PduL phosphotransacylase is a component of the Pdu MCP. We also show that PduL plays a key role in cofactor homeostasis by recycling coenzyme A internally within the Pdu MCP. Further, we identify a potential N-terminal targeting sequence using a bioinformatic approach and show that this short sequence extension is necessary and sufficient for directing PduL as well as heterologous proteins to the lumen of the Pdu MCP. These findings expand our general understanding of bacterial MCP assembly and cofactor homeostasis.

scholarly journals A polyyne toxin produced by an antagonistic bacterium blinds and lyses a Chlamydomonad alga

2021 ◽  
Vol 118 (33) ◽  
pp. e2107695118
Author(s):  
Vivien Hotter ◽  
David Zopf ◽  
Hak Joong Kim ◽  
Anja Silge ◽  
Michael Schmitt ◽  
...  
Keyword(s):  
Visual System ◽  
Food Webs ◽  
Carbon Fixation ◽  
Mutational Analysis ◽  
Genome Mining ◽  
Ecological Interactions ◽  
Unicellular Alga ◽  
Phototactic Behavior ◽  
Cyclic Lipopeptide ◽  
Global Carbon

Algae are key contributors to global carbon fixation and form the basis of many food webs. In nature, their growth is often supported or suppressed by microorganisms. The bacterium Pseudomonas protegens Pf-5 arrests the growth of the green unicellular alga Chlamydomonas reinhardtii, deflagellates the alga by the cyclic lipopeptide orfamide A, and alters its morphology [P. Aiyar et al., Nat. Commun. 8, 1756 (2017)]. Using a combination of Raman microspectroscopy, genome mining, and mutational analysis, we discovered a polyyne toxin, protegencin, which is secreted by P. protegens, penetrates the algal cells, and causes destruction of the carotenoids of their primitive visual system, the eyespot. Together with secreted orfamide A, protegencin thus prevents the phototactic behavior of C. reinhardtii. A mutant of P. protegens deficient in protegencin production does not affect growth or eyespot carotenoids of C. reinhardtii. Protegencin acts in a direct and destructive way by lysing and killing the algal cells. The toxic effect of protegencin is also observed in an eyeless mutant and with the colony-forming Chlorophyte alga Gonium pectorale. These data reveal a two-pronged molecular strategy involving a cyclic lipopeptide and a conjugated tetrayne used by bacteria to attack select Chlamydomonad algae. In conjunction with the bloom-forming activity of several chlorophytes and the presence of the protegencin gene cluster in over 50 different Pseudomonas genomes [A. J. Mullins et al., bioRxiv [Preprint] (2021). https://www.biorxiv.org/content/10.1101/2021.03.05.433886v1 (Accessed 17 April 2021)], these data are highly relevant to ecological interactions between Chlorophyte algae and Pseudomonadales bacteria.

Uptake and metabolism of organic compounds by Chlorobium phaeobacteroides isolated from Lake Kinneret

1981 ◽  
Vol 27 (10) ◽  
pp. 1087-1091 ◽  
Author(s):  
T. Bergstein ◽  
Y. Henis ◽  
B. Z. Cavari
Keyword(s):  
Organic Compounds ◽  
Photosynthetic Activity ◽  
Glyoxylic Acid ◽  
The Other ◽  
Organic Substrates ◽  
Acid Cycle ◽  
Acetate Concentration ◽  
Chlorobium Phaeobacteroides ◽  
Cell Fractions ◽  
Uptake And Metabolism

Organic substrates have an important role in Chlorobium phaeobacteroides nutrition, especially under suboptimal light intensities for photosynthetic activity. In addition, increasing acetate concentration in the medium caused a decrease in photosynthetic activity. Approximately 50% of the acetate carbon was retained in the cells, while the other 50% was released as CO2. Acetate carbon and CO2 carbon were assimilated into the same cell fractions. Two key enzymes of the glyoxylic acid cycle were found in Chlorobium cells, indicating that acetate is incorporated via this pathway.

High primary productivity under submerged soil raises the net ecosystem productivity of a secondary mangrove forest in eastern Thailand

2012 ◽  
Vol 28 (3) ◽  
pp. 303-306 ◽  
Author(s):  
Sasitorn Poungparn ◽  
Akira Komiyama ◽  
Tanuwong Sangteian ◽  
Chatree Maknual ◽  
Pipat Patanaponpaiboon ◽  
...  
Keyword(s):  
Primary Productivity ◽  
Mangrove Forest ◽  
Carbon Fixation ◽  
Distribution Area ◽  
Net Ecosystem Productivity ◽  
Mangrove Forests ◽  
Coastal Zones ◽  
Ecosystem Productivity ◽  
Submerged Soil ◽  
Global Carbon

The distribution of mangrove forests is limited to the coastal zones of tropical and subtropical regions, and their total area is far smaller than that of upland forests (Spalding et al. 2010). Mangrove forests often show unique patterns of biomass allocation and carbon dynamics because they are periodically submerged by tides (Komiyama et al. 2008). Therefore, the contribution of mangrove forests to the global carbon fixation process should be carefully evaluated even though their distribution area is limited.

scholarly journals Anticyclonic eddies are more productive than cyclonic eddies in subtropical gyres because of winter mixing

2016 ◽  
Vol 2 (5) ◽  
pp. e1600282 ◽  
Author(s):  
François Dufois ◽  
Nick J. Hardman-Mountford ◽  
Jim Greenwood ◽  
Anthony J. Richardson ◽  
Ming Feng ◽  
...  
Keyword(s):  
Ocean Circulation ◽  
Carbon Fixation ◽  
Phytoplankton Production ◽  
Biogeochemical Model ◽  
Substantial Portion ◽  
New Paradigm ◽  
Carbon Pump ◽  
Anticyclonic Eddies ◽  
Global Carbon ◽  
Biological Carbon Pump

Mesoscale eddies are ubiquitous features of ocean circulation that modulate the supply of nutrients to the upper sunlit ocean, influencing the rates of carbon fixation and export. The popular eddy-pumping paradigm implies that nutrient fluxes are enhanced in cyclonic eddies because of upwelling inside the eddy, leading to higher phytoplankton production. We show that this view does not hold for a substantial portion of eddies within oceanic subtropical gyres, the largest ecosystems in the ocean. Using space-based measurements and a global biogeochemical model, we demonstrate that during winter when subtropical eddies are most productive, there is increased chlorophyll in anticyclones compared with cyclones in all subtropical gyres (by 3.6 to 16.7% for the five basins). The model suggests that this is a consequence of the modulation of winter mixing by eddies. These results establish a new paradigm for anticyclonic eddies in subtropical gyres and could have important implications for the biological carbon pump and the global carbon cycle.

scholarly journals Draft genome of a novel methanotrophic Methylobacter sp. from the volcanic soils of Pantelleria Island

2021 ◽  
Vol 114 (3) ◽  
pp. 313-324
Author(s):  
Carmen Hogendoorn ◽  
Nunzia Picone ◽  
Femke van Hout ◽  
Sophie Vijverberg ◽  
Lianna Poghosyan ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Draft Genome ◽  
Ph Homeostasis ◽  
Dominant Group ◽  
Metabolic Potential ◽  
Gene Encoding ◽  
Protein Coding ◽  
Methane Oxidizing Bacteria ◽  
Phylogenetic Affiliation ◽  
Geothermal Soils

AbstractThe genus Methylobacter is considered an important and often dominant group of aerobic methane-oxidizing bacteria in many oxic ecosystems, where members of this genus contribute to the reduction of CH4 emissions. Metagenomic studies of the upper oxic layers of geothermal soils of the Favara Grande, Pantelleria, Italy, revealed the presence of various methane-oxidizing bacteria, and resulted in a near complete metagenome assembled genome (MAG) of an aerobic methanotroph, which was classified as a Methylobacter species. In this study, the Methylobacter sp. B2 MAG was used to investigate its metabolic potential and phylogenetic affiliation. The MAG has a size of 4,086,539 bp, consists of 134 contigs and 3955 genes were found, of which 3902 were protein coding genes. All genes for CH4 oxidation to CO2 were detected, including pmoCAB encoding particulate methane monooxygenase (pMMO) and xoxF encoding a methanol dehydrogenase. No gene encoding a formaldehyde dehydrogenase was present and the formaldehyde to formate conversion follows the tetrahydromethanopterin (H4MPT) pathway. “Ca. Methylobacter favarea” B2 uses the Ribulose-Mono-Phosphate (RuMP) pathway for carbon fixation. Analysis of the MAG indicates that Na+/H+ antiporters and the urease system might be important in the maintenance of pH homeostasis of this strain to cope with acidic conditions. So far, thermoacidophilic Methylobacter species have not been isolated, however this study indicates that members of the genus Methylobacter can be found in distinct ecosystems and their presence is not restricted to freshwater or marine sediments.

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 A polyyne toxin produced by an antagonistic bacterium blinds and lyses a green microalga

2021 ◽  
Author(s):  
Vivien Hotter ◽  
David Zopf ◽  
Hak Joong Kim ◽  
Anja Silge ◽  
Michael Schmitt ◽  
...  
Keyword(s):  
Visual System ◽  
Food Webs ◽  
Carbon Fixation ◽  
Mutational Analysis ◽  
Genome Mining ◽  
Algicidal Bacteria ◽  
Phototactic Behavior ◽  
Cyclic Lipopeptide ◽  
Green Microalga ◽  
Global Carbon

Microalgae are key contributors to global carbon fixation and the basis of many food webs. In nature, their growth is often supported or suppressed by other microorganisms. The bacterium Pseudomonas protegens Pf-5 arrests the growth of the green alga Chlamydomonas reinhardtii, deflagellates the alga by the cyclic lipopeptide orfamide A, and alters its morphology. Using a combination of Raman microspectroscopy, genome mining and mutational analysis, we discovered a novel polyyne toxin we name protegencin that is secreted by P. protegens and penetrates algal cells to destroy their primitive visual system, the eyespot. Together with secreted orfamide A, protegencin prevents the phototactic behavior of C. reinhardtii needed to perform optimal photosynthesis. A protegencin-deficient biosynthetic mutant of P. protegens does not affect growth or eyespot carotenoids of C. reinhardtii. Thus, protegencin acts in a direct and destructive way, and reveals at least a two-pronged molecular strategy used by algicidal bacteria.

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