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.

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.

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).

The Structure of Ecological Networks Across Levels of Organization

2020 ◽  
Vol 51 (1) ◽  
pp. 433-460 ◽  
Author(s):  
Paulo R. Guimarães
Keyword(s):  
Food Webs ◽  
Ecological Systems ◽  
Ecological Networks ◽  
Ecological Communities ◽  
Ecological Interactions ◽  
Biological Organization ◽  
Architectural Patterns ◽  
Fundamental Challenge ◽  
Spatiotemporal Scales ◽  
Multiple Levels

Interactions connect the units of ecological systems, forming networks. Individual-based networks characterize variation in niches among individuals within populations. These individual-based networks merge with each other, forming species-based networks and food webs that describe the architecture of ecological communities. Networks at broader spatiotemporal scales portray the structure of ecological interactions across landscapes and over macroevolutionary time. Here, I review the patterns observed in ecological networks across multiple levels of biological organization. A fundamental challenge is to understand the amount of interdependence as we move from individual-based networks to species-based networks and beyond. Despite the uneven distribution of studies, regularities in network structure emerge across scales due to the fundamental architectural patterns shared by complex networks and the interplay between traits and numerical effects. I illustrate the integration of these organizational scales by exploring the consequences of the emergence of highly connected species for network structures across scales.

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 Trophic redundancy reduces vulnerability to extinction cascades

2018 ◽  
Vol 115 (10) ◽  
pp. 2419-2424 ◽  
Author(s):  
Dirk Sanders ◽  
Elisa Thébault ◽  
Rachel Kehoe ◽  
F. J. Frank van Veen
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Parasitoid Wasp ◽  
Biodiversity Loss ◽  
Species Loss ◽  
Ecological Interactions ◽  
Insect Communities ◽  
Extinction Rates ◽  
Trophic Links ◽  
Current Species

Current species extinction rates are at unprecedentedly high levels. While human activities can be the direct cause of some extinctions, it is becoming increasingly clear that species extinctions themselves can be the cause of further extinctions, since species affect each other through the network of ecological interactions among them. There is concern that the simplification of ecosystems, due to the loss of species and ecological interactions, increases their vulnerability to such secondary extinctions. It is predicted that more complex food webs will be less vulnerable to secondary extinctions due to greater trophic redundancy that can buffer against the effects of species loss. Here, we demonstrate in a field experiment with replicated plant-insect communities, that the probability of secondary extinctions is indeed smaller in food webs that include trophic redundancy. Harvesting one species of parasitoid wasp led to secondary extinctions of other, indirectly linked, species at the same trophic level. This effect was markedly stronger in simple communities than for the same species within a more complex food web. We show that this is due to functional redundancy in the more complex food webs and confirm this mechanism with a food web simulation model by highlighting the importance of the presence and strength of trophic links providing redundancy to those links that were lost. Our results demonstrate that biodiversity loss, leading to a reduction in redundant interactions, can increase the vulnerability of ecosystems to secondary extinctions, which, when they occur, can then lead to further simplification and run-away extinction cascades.

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 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 Systems-informed genome mining for electroautotrophic microbial production

2020 ◽  
Author(s):  
Anthony J. Abel ◽  
Jacob M. Hilzinger ◽  
Adam P. Arkin ◽  
Douglas S. Clark
Keyword(s):  
Carbon Fixation ◽  
Microbial Respiration ◽  
Tricarboxylic Acid Cycle ◽  
Genome Mining ◽  
Tricarboxylic Acid ◽  
Nitrate Respiration ◽  
Fixation Rate ◽  
Acid Cycle ◽  
Carbon Molecules ◽  
Reductive Tricarboxylic Acid Cycle

AbstractMicrobial electrosynthesis (MES) systems can store renewable energy and CO2 in many-carbon molecules inaccessible to abiotic electrochemistry. Here, we develop a multiphysics model to investigate the fundamental and practical limits of MES enabled by direct electron uptake and we identify organisms in which this biotechnological CO2-fixation strategy can be realized. Systematic model comparisons of microbial respiration and carbon fixation strategies revealed that, under aerobic conditions, the CO2 fixation rate is limited to <6 μmol/cm2/hr by O2 mass transport despite efficient electron utilization. In contrast, anaerobic nitrate respiration enables CO2 fixation rates >50 μmol/cm2/hr for microbes using the reductive tricarboxylic acid cycle. Phylogenetic analysis, validated by recapitulating experimental demonstrations of electroautotrophy, uncovered multiple probable electroautotrophic organisms and a significant number of genetically tractable strains that require heterologous expression of <5 proteins to gain electroautotrophic function. The model and analysis presented here will guide microbial engineering and reactor design for practical MES systems.

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