DOCSLIB.ORG

Horizontal Acquisition of a Patchwork Calvin Cycle by Symbiotic and Free-Living Campylobacterota (Formerly Epsilonproteobacteria)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Horizontal Acquisition of a Patchwork Calvin Cycle by Symbiotic and Free-Living Campylobacterota (Formerly Epsilonproteobacteria) The ISME Journal (2020) 14:104–122 https://doi.org/10.1038/s41396-019-0508-7 ARTICLE Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria) 1,9 1 1,10 1 1,2 Adrien Assié ● Nikolaus Leisch ● Dimitri V. Meier ● Harald Gruber-Vodicka ● Halina E. Tegetmeyer ● 1 3,4 3,5,6 7 7,11 Anke Meyerdierks ● Manuel Kleiner ● Tjorven Hinzke ● Samantha Joye ● Matthew Saxton ● 1,8 1,10 Nicole Dubilier ● Jillian M. Petersen Received: 7 April 2019 / Revised: 6 August 2019 / Accepted: 15 August 2019 / Published online: 27 September 2019 © The Author(s) 2019. This article is published with open access Abstract Most autotrophs use the Calvin–Benson–Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts (“Candidatus Thiobarba”) of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB cycle genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely 1234567890();,: 1234567890();,: related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that “Ca. Thiobarba” switched from the rTCA cycle to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated “Ca. Thiobarba”. Direct stable isotope fingerprinting showed that “Ca. Thiobarba” has typical CBB signatures, suggesting that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment. Introduction These authors contributed equally: Adrien Assié, Nikolaus Leisch All life on Earth is based on carbon fixation, and its Supplementary information The online version of this article (https:// molecular machinery is increasingly becoming a focus of doi.org/10.1038/s41396-019-0508-7) contains supplementary biotechnology and geo-engineering efforts due to its material, which is available to authorized users. * Adrien Assié 5 Department of Pharmaceutical Biotechnology, University of [email protected] Greifswald, Institute of Pharmacy, D-17489 Greifswald, Germany * Nicole Dubilier 6 [email protected] Institute of Marine Biotechnology, D-17489 Greifswald, Germany 7 * Jillian M. Petersen Department of Marine Sciences, The University of Georgia, Room [email protected] 159, Marine Sciences Bldg, Athens, GA 30602-3636, USA 8 MARUM—Zentrum für Marine Umweltwissenschaften, 1 Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, University of Bremen, Leobener Str. 2, 28359 Bremen, Germany D-28359 Bremen, Germany 9 Present address: Baylor College of Medicine, One Baylor Plaza, 2 Center for Biotechnology, Bielefeld University, Houston, TX 77030, USA Universitaetsstrasse 27, 33615 Bielefeld, Germany 10 Present address: Centre for Microbiology and Environmental 3 Department of Geoscience, University of Calgary, 2500 University Systems Science, Division of Microbial Ecology, University of Drive Northwest, Alberta, Calgary, AB T2N 1N4, Canada Vienna, Althanstrasse 14, 1090 Vienna, Austria 11 4 Department of Plant and Microbial Biology, North Carolina State Present address: Department of Biological Sciences, Miami University, Raleigh, NC 27695, USA University, 4200N University Blvd, Middletown, OH 45042, USA Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota. 105 potential to improve crop yields and sequester carbon endosymbionts, which they rely on for most of their nutri- dioxide from the atmosphere [1]. Seven carbon fixation tion [27, 28]. Some vent and seep invertebrates associate pathways have evolved in nature, and one purely synthetic with both gammaproteobacterial and campylobacterotal pathwayrunsinvitro[2–4]. Of the seven natural path- symbionts simultaneously, which raises the question of how ways, the Calvin–Benson–Bassham (CBB) cycle was the these co-occurring symbionts with differing habitat pre- first discovered, and is believed to be the most widespread ferences can both be provided with suitable conditions [5–7]. The CBB cycle is used by a diverse array of [27, 29, 30]. organisms throughout the tree of life, including plants and Bathymodiolin mussels, a subfamily of mytilid bivalves, algae, cyanobacteria, and autotrophic members of the are found worldwide at hydrothermal vents and cold seeps Alpha-, Beta-, and Gammaproteobacteria. Its key enzyme, [31]. They have evolved symbiotic relationships with che- the ribulose 1,5-bisphosphate carboxylase/oxygenase mosynthetic bacteria, allowing them to colonize these (RuBisCO) is thought to be the most abundant, as well as extreme environments. Inside their gills, they host intra- one of the most ancient enzymes on Earth [8, 9]. cellular gammaproteobacterial endosymbionts in epithelial The reductive tricarboxylic acid (rTCA) cycle was the cells called bacteriocytes. The dominant endosymbionts are second described carbon fixation pathway [10]. In short, it sulfur- and methane-oxidizing bacteria, often co-occurring is a reversal of the energy-generating oxidative TCA cycle. in the same mussel species. Some sulfur-oxidizing sym- Instead of oxidizing acetyl-CoA and generating ATP and bionts also use hydrogen as an energy source, and some reducing equivalents, it reduces CO2 at the expense of ATP mussel species host additional symbionts that gain energy and reducing equivalents [2, 7, 10]. Most of the enzymes from short-chain alkanes [32, 33]. In addition to these are shared with the TCA cycle, except for those that cata- dominant endosymbionts, Assié et al. recently discovered lyze irreversible reactions in the TCA, such as citrate syn- epibionts that colonize bathymodiolin mussels from around thase, which is catalyzed by ATP citrate lyase in the the world [34]. In contrast to the gammaproteobacterial rTCA cycle. However, given sufficiently high reactant to endosymbionts of bathymodiolins, these epibionts belong to product ratios and enzyme concentrations, the citrate syn- the Campylobacterota. They are filamentous and colonize thase reaction can be reversed to run the TCA cycle the surfaces of the gill epithelia in dense patches in the reductively, without any additional enzymes [11, 12]. The extracellular spaces between the gill filaments, through rTCA pathway is widely distributed in nature, and has which the mussel pumps the inflow of oxygenated seawater been described in diverse lineages of anaerobes and (Fig. S1). The nature of the association between the epi- microaerobes, such as the Chlorobi, Aquificae, Nitrospirae, biotic Campylobacterota and their mussel hosts is not clear. and is also commonly observed among the Proteobacteria, Similar associations in other deep-sea invertebrates, such as including the Deltaproteobacteria and the Campylobacter- Kiwa crabs [35], gastropods [36], and shallow-water ota, (formerly Epsilonproteobacteria) [13, 14]. It is parti- nematodes [37] are thought to be beneficial or commensal. cularly prominent in the Campylobacterota, as all In this study, we used a multi-omics approach to inves- previously described autotrophic members of this class use tigate the metabolism of the Campylobacterota epibionts in the rTCA pathway for CO2 fixation [2, 13]. two bathymodiolin mussels species, “Bathymodiolus” Carbon fixation by chemoautotrophic microorganisms childressi from cold seeps in the Gulf of Mexico, which forms the basis of entire ecosystems at deep-sea hydro- have only methane oxidizers as their dominant endo- thermal vents and cold seeps [15, 16]. Most of this carbon is symbiont, and Bathymodiolus azoricus from the Mid- fixed either via the CBB cycle, used by many gammapro- Atlantic Ridge, which host both a sulfur- and a methane- teobacterial autotrophs, or the rTCA cycle, used by cam- oxidizing endosymbiont [27]. Unexpectedly, the epibionts pylobacterotal autotrophs. This difference is reflected by the had, and expressed, all genes required for the CBB cycle but different niches colonized by these organisms at hydro- appeared to lack key genes of the rTCA cycle. These CBB thermal vents and seeps, with Gammaproteobacteria typi- cycle genes were most likely acquired by horizontal gene cally dominating habitats with higher oxygen and lower transfer (HGT) from diverse sources. With a recently sulfide concentrations where the CBB cycle would be more developed, highly sensitive, direct stable isotope finger- efficient, and Campylobacterota typically thriving at lower printing technique [38], we show that the proteins of these oxygen and higher sulfide concentrations where the rTCA epibionts had an isotopic signature typical of the CBB cycle could provide a selective advantage [17–23]. cycle, further demonstrating its importance for the meta- Experimental studies have linked substrate preferences in bolism of these epibionts. The discovery of Campylo- cultured Gammaproteobacteria and Campylobacterota to bacterota that use
Load more

Recommended publications
  • Lecture 29 Spring 2007
    Geol. 656 Isotope Geochemistry Lecture 29 Spring 2007 ISOTOPE FRACTIONATION IN THE BIOSPHERE INTRODUCTION As we noted, biological processes often involve large isotopic fractionations. Indeed, biological proc- esses are the most important cause of variations in the isotope composition of carbon, nitrogen, and sul- fur. For the most part, the largest fractionations occur during the initial production of organic matter by the so-called primary producers, or autotrophs. These include all plants and many kinds of bacteria. The most important means of production of organic matter is photosynthesis, but organic matter may also be produced by chemosynthesis, for example at mid-ocean ridge hydrothermal vents. Large frac- tions of both carbon and nitrogen occur during primary production. Additional fractionations also oc- cur in subsequent reactions and up through the food chain as hetrotrophs consume primary producers, but these are generally smaller. CARBON ISOTOPE FRACTIONATION DURING PHOTOSYNTHESIS The most important of process producing isotopic fractionation of carbon is photosynthesis. As we earlier noted, photosynthetic fractionation of carbon isotopes is primarily kinetic. The early work of Park and Epstein (1960) suggested fractionation occurred in several steps. Subsequent work has eluci- dated the fractionations involved in these steps, which we will consider in more detail here. For terrestrial plants (those utilizing atmospheric CO2), the first step is diffusion of CO2 into the boundary layer surrounding the leaf, through the stomata, and internally in the leaf. The average δ13C of various species of plants has been correlated with the stomatal conductance (Delucia et al., 1988), in- dicating that diffusion into the plant is indeed important in fractionating carbon isotopes.
    [Show full text]
  • Lecture 7 - the Calvin Cycle and the Pentose Phosphate Pathway
    Lecture 7 - The Calvin Cycle and the Pentose Phosphate Pathway Chem 454: Regulatory Mechanisms in Biochemistry University of Wisconsin-Eau Claire 1 Introduction The Calvin cycle Text The dark reactions of photosynthesis in green plants Reduces carbon from CO2 to hexose (C6H12O6) Requires ATP for free energy and NADPH as a reducing agent. 2 2 Introduction NADH versus Text NADPH 3 3 Introduction The Pentose Phosphate Pathway Used in all organisms Glucose is oxidized and decarboxylated to produce reduced NADPH Used for the synthesis and degradation of pentoses Shares reactions with the Calvin cycle 4 4 1. The Calvin Cycle Source of carbon is CO2 Text Takes place in the stroma of the chloroplasts Comprises three stages Fixation of CO2 by ribulose 1,5-bisphosphate to form two 3-phosphoglycerate molecules Reduction of 3-phosphoglycerate to produce hexose sugars Regeneration of ribulose 1,5-bisphosphate 5 5 1. Calvin Cycle Three stages 6 6 1.1 Stage I: Fixation Incorporation of CO2 into 3-phosphoglycerate 7 7 1.1 Stage I: Fixation Rubisco: Ribulose 1,5- bisphosphate carboxylase/ oxygenase 8 8 1.1 Stage I: Fixation Active site contains a divalent metal ion 9 9 1.2 Rubisco Oxygenase Activity Rubisco also catalyzes a wasteful oxygenase reaction: 10 10 1.3 State II: Formation of Hexoses Reactions similar to those of gluconeogenesis But they take place in the chloroplasts And use NADPH instead of NADH 11 11 1.3 State III: Regeneration of Ribulose 1,5-Bisphosphosphate Involves a sequence of transketolase and aldolase reactions. 12 12 1.3 State III:
    [Show full text]
  • Cyanobacterial Evolution During the Precambrian
    International Journal of Astrobiology 15 (3): 187–204 (2016) doi:10.1017/S1473550415000579 © Cambridge University Press 2016 This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited. Cyanobacterial evolution during the Precambrian Bettina E. Schirrmeister1, Patricia Sanchez-Baracaldo2 and David Wacey1,3 1School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen’s Road, Bristol BS8 1RJ, UK e-mail: [email protected] 2School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK 3Centre for Microscopy, Characterisation and Analysis, and ARC Centre of Excellence for Core to Crust Fluid Systems, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia Abstract: Life on Earth has existed for at least 3.5 billion years. Yet, relatively little is known of its evolution during the first two billion years, due to the scarceness and generally poor preservation of fossilized biological material. Cyanobacteria, formerly known as blue green algae were among the first crown Eubacteria to evolve and for more than 2.5 billion years they have strongly influenced Earth’s biosphere. Being the only organism where oxygenic photosynthesis has originated, they have oxygenated Earth’s atmosphere and hydrosphere, triggered the evolution of plants –being ancestral to chloroplasts– and enabled the evolution of complex life based on aerobic respiration. Having such a strong impact on early life, one might expect that the evolutionary success of this group may also have triggered further biosphere changes during early Earth history.
    [Show full text]
  • Thiomargarita Namibiensis Cells by Using Microelectrodes Heide N
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Nov. 2002, p. 5746–5749 Vol. 68, No. 11 0099-2240/02/$04.00ϩ0 DOI: 10.1128/AEM.68.11.5746–5749.2002 Copyright © 2002, American Society for Microbiology. All Rights Reserved. Uptake Rates of Oxygen and Sulfide Measured with Individual Thiomargarita namibiensis Cells by Using Microelectrodes Heide N. Schulz1,2* and Dirk de Beer1 Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany,1 and Section of Microbiology, University of California, Davis, Davis, California 956162 Received 25 March 2002/Accepted 31 July 2002 Gradients of oxygen and sulfide measured towards individual cells of the large nitrate-storing sulfur bacterium Thiomargarita namibiensis showed that in addition to nitrate oxygen is used for oxidation of sulfide. Stable gradients around the cells were found only if acetate was added to the medium at low concentrations. The sulfur bacterium Thiomargarita namibiensis is a close conclusions about their physiology by observing chemotactic relative of the filamentous sulfur bacteria of the genera Beg- behavior, as has been done successfully with Beggiatoa and giatoa and Thioploca. It was only recently discovered off the Thioploca filaments (5, 10). However, because of the large size Namibian coast in fluid sediments rich in organic matter and of Thiomargarita cells, they develop, around individual cells, sulfide (15). The large, spherical cells of Thiomargarita (diam- measurable gradients of oxygen and sulfide that can be used eter, 100 to 300 ␮m) are held together in a chain by mucus that for calculating uptake rates of oxygen and sulfide. Thus, the surrounds each cell (Fig. 1). Most of the cell volume is taken physiological reactions of individual cells to changes in oxygen up by a central vacuole in which nitrate is stored at concen- and sulfide concentrations can be directly observed by observ- trations of up to 800 mM.
    [Show full text]
  • BIOLOGICAL SCIENCE FIFTH EDITION Freeman Quillin Allison 10
    BIOLOGICAL SCIENCE FIFTH EDITION Freeman Quillin Allison 10 Lecture Presentation by Cindy S. Malone, PhD, California State University Northridge © 2014 Pearson Education, Inc. Roadmap 10 In this chapter you will learn how Photosynthesis links life to the power of the Sun by previewing by examining Conversion of light How photosynthetic pigments energy into chemical capture light energy 10.2 energy 10.1 then looking closer at Energy flow and ATP Photosystem II production10.3 Photosystem I and exploring CO2 fixation and reduction to The Calvin cycle form sugars 10.4 © 2014 Pearson Education, Inc. ▪ Photosynthesis – Is the process of using sunlight to produce carbohydrate – Requires sunlight, carbon dioxide, and water – Produces oxygen as a by-product ▪ The overall reaction when glucose is the carbohydrate: 6 CO2 6 H2O light energy C6H12O6 6 O2 © 2014 Pearson Education, Inc. ▪ Photosynthesis contrasts with cellular respiration – Photosynthesis is endergonic – Reduces CO2 to sugar – Cellular respiration is exergonic – Oxidizes sugar to CO2 Electrons are Electrons are pulled __________; pulled _______________; C is _________ O is _________ Potential energy increases 6 CO2 6 H2O Input of 6 O2 (carbon dioxide) (water) energy Glucose (oxygen) © 2014 Pearson Education, Inc. ▪ Light-dependent reactions – Produce O2 from H2O ▪ Calvin cycle reactions – Produce sugar from CO2 ▪ The reactions are linked by electrons – Released in the light-dependent reactions – When water is split to form oxygen gas – Then transferred to the electron carrier NADP+, forming NADPH © 2014 Pearson Education, Inc. ▪ The Calvin cycle Figure 10.2 then uses Sunlight (Light – These electrons energy) – The potential Light- energy in ATP capturing reactions – To reduce CO2 to (Chemical make sugars energy) Calvin cycle (Chemical energy) © 2014 Pearson Education, Inc.
    [Show full text]
  • AP Biology-00001310.Cdr
    ® INTERNATIONAL ACADEMY OF SCIENCE Acellus AP Biology AP Biology Course Curriculum Unit 1 - Evolution Drives the Diversity and Unity of Life 46 Photosystems 1 Intro to AP Biology 47 Photophosphorylation 2 Nature of Science 48 Carbon Fixation (or Calvin Cycle) 3 Evidence for Evolution 49 Putting It Together - Photosynthesis and Respiration 4 Natural Selection - Descent with Modification 50 Feedback Mechanisms 5 Hardy - Weinberg Theorem 51 Cell Communication 6 Hardy - Weinberg Equilibrium Unit 6 - The Cell Cycle 7 Biological Evolution 52 Why Do Cells Divide? 8 Phylogeny - Evolutionary History 53 Origin of the Cell Cycle 9 Modern Synthesis Theory of Evolution 54 Chromosome Structure Unit 2 - Water Potential 55 Phases of the Cycle 10 Abiogenesis 56 Lab: Cell Division - Part I 11 Properties of Water 57 Lab: Cell Division - Part II 12 Organic Molecules 58 Variances in the Cell Cycle 13 Origin of Cells 59 Control of the Cell Cycle 14 Endosymbiosis 60 Uncontrolled Cell Cycle 15 Characteristics of Life 61 Lab: Cell Division - Part III 16 Cell Membranes - Structure Unit 7 - Mitosis and Meiosis 17 Selective Permeability 62 Two Types of Cell Reproduction 18 Diffusion and Cell Size 63 Meiosis Overview 19 Water Potential - Concentration Gradient 64 The Phases of Meiosis 20 Lab: Water Potential 65 Meiosis and Genetic Variation Unit 3 - Cell Structure 66 Lab: Cell Division - Part IV 21 Basic Cell Structure 67 Lab: Cell Division - Part V 22 Prokaryotes 68 Meiosis and Gamete Formation 23 Eukaryotes Unit 8 - History of Genetics 24 Mitochondria and Chloroplasts
    [Show full text]
  • Photorespiration
    Arjun Adhikari, Asst. Prof. M.C. College, Barpeta Photorespiration Photorespiration is a wasteful pathway that competes with the Calvin cycle. It begins when rubisco acts on oxygen instead of carbon dioxide. RuBP oxygenase-carboxylase (rubisco ), a key enzyme in photosynthesis. In the process of carbon fixation , rubisco incorporates carbon dioxide into an organic molecule during the first stage of the Calvin cycle . Rubisco is so important to plants that it makes upto 30% percent or more of the soluble protein in a typical plant leaf. But rubisco also has a major flaw: instead of always using CO 2 as a substrate, it sometimes picks up O2 instead. This side reaction initiates a pathway called photorespiration , which, rather than fixing carbon, actually leads to the loss of already -fixed carbon as CO 2. Photorespiration wastes energy and decreases sugar synthesis, so when rubisco initiates this pathway, it's committing a serious molecular mess. Rubisco binds to either CO 2 or O2 As we know , the enzyme rubisco can use either CO 2 or O2 as a substrate. Rubisco adds whichever molecule it binds to a five -carbon compound called ribulose -1,5-bisphosphate (RuBP). The reaction that uses CO 2 is the first step of the Calvin cycle and leads to the production of sugar. The reaction that uses O2 is the first step o f the photorespiration pathway, which wastes energy and "undoes" the work of the Calvin cycle . When a plant has its stomata, or leaf pores, open CO 2 diffuses in, O2 and water vapor diffuse out, and photorespiration is minimized.
    [Show full text]
  • History of Microbiology: Spontaneous Generation Theory
    HISTORY OF MICROBIOLOGY: SPONTANEOUS GENERATION THEORY Microbiology often has been defined as the study of organisms and agents too small to be seen clearly by the unaided eye—that is, the study of microorganisms. Because objects less than about one millimeter in diameter cannot be seen clearly and must be examined with a microscope, microbiology is concerned primarily with organisms and agents this small and smaller. Microbial World Microorganisms are everywhere. Almost every natural surface is colonized by microbes (including our skin). Some microorganisms can live quite happily in boiling hot springs, whereas others form complex microbial communities in frozen sea ice. Most microorganisms are harmless to humans. You swallow millions of microbes every day with no ill effects. In fact, we are dependent on microbes to help us digest our food and to protect our bodies from pathogens. Microbes also keep the biosphere running by carrying out essential functions such as decomposition of dead animals and plants. Microbes are the dominant form of life on planet Earth. More than half the biomass on Earth consists of microorganisms, whereas animals constitute only 15% of the mass of living organisms on Earth. This Microbiology course deals with • How and where they live • Their structure • How they derive food and energy • Functions of soil micro flora • Role in nutrient transformation • Relation with plant • Importance in Industries The microorganisms can be divided into two distinct groups based on the nucleus structure: Prokaryotes – The organism lacking true nucleus (membrane enclosed chromosome and nucleolus) and other organelles like mitochondria, golgi body, entoplasmic reticulum etc. are referred as Prokaryotes.
    [Show full text]
  • Chemosynthetic Symbiont with a Drastically Reduced Genome Serves As Primary Energy Storage in the Marine Flatworm Paracatenula
    Chemosynthetic symbiont with a drastically reduced genome serves as primary energy storage in the marine flatworm Paracatenula Oliver Jäcklea, Brandon K. B. Seaha, Målin Tietjena, Nikolaus Leischa, Manuel Liebekea, Manuel Kleinerb,c, Jasmine S. Berga,d, and Harald R. Gruber-Vodickaa,1 aMax Planck Institute for Marine Microbiology, 28359 Bremen, Germany; bDepartment of Geoscience, University of Calgary, AB T2N 1N4, Canada; cDepartment of Plant & Microbial Biology, North Carolina State University, Raleigh, NC 27695; and dInstitut de Minéralogie, Physique des Matériaux et Cosmochimie, Université Pierre et Marie Curie, 75252 Paris Cedex 05, France Edited by Margaret J. McFall-Ngai, University of Hawaii at Manoa, Honolulu, HI, and approved March 1, 2019 (received for review November 7, 2018) Hosts of chemoautotrophic bacteria typically have much higher thrive in both free-living environmental and symbiotic states, it is biomass than their symbionts and consume symbiont cells for difficult to attribute their genomic features to either functions nutrition. In contrast to this, chemoautotrophic Candidatus Riegeria they provide to their host, or traits that are necessary for envi- symbionts in mouthless Paracatenula flatworms comprise up to ronmental survival or to both. half of the biomass of the consortium. Each species of Paracate- The smallest genomes of chemoautotrophic symbionts have nula harbors a specific Ca. Riegeria, and the endosymbionts have been observed for the gammaproteobacterial symbionts of ves- been vertically transmitted for at least 500 million years. Such icomyid clams that are directly transmitted between host genera- prolonged strict vertical transmission leads to streamlining of sym- tions (13, 14). Such strict vertical transmission leads to substantial biont genomes, and the retained physiological capacities reveal and ongoing genome reduction.
    [Show full text]
  • Microbial Ecology of Biofiltration Units Used for the Desulfurization of Biogas
    chemengineering Review Microbial Ecology of Biofiltration Units Used for the Desulfurization of Biogas Sylvie Le Borgne 1,* and Guillermo Baquerizo 2,3 1 Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana- Unidad Cuajimalpa, 05348 Ciudad de México, Mexico 2 Irstea, UR REVERSAAL, F-69626 Villeurbanne CEDEX, France 3 Departamento de Ingeniería Química, Alimentos y Ambiental, Universidad de las Américas Puebla, 72810 San Andrés Cholula, Puebla, Mexico * Correspondence: [email protected]; Tel.: +52–555–146–500 (ext. 3877) Received: 1 May 2019; Accepted: 28 June 2019; Published: 7 August 2019 Abstract: Bacterial communities’ composition, activity and robustness determines the effectiveness of biofiltration units for the desulfurization of biogas. It is therefore important to get a better understanding of the bacterial communities that coexist in biofiltration units under different operational conditions for the removal of H2S, the main reduced sulfur compound to eliminate in biogas. This review presents the main characteristics of sulfur-oxidizing chemotrophic bacteria that are the base of the biological transformation of H2S to innocuous products in biofilters. A survey of the existing biofiltration technologies in relation to H2S elimination is then presented followed by a review of the microbial ecology studies performed to date on biotrickling filter units for the treatment of H2S in biogas under aerobic and anoxic conditions. Keywords: biogas; desulfurization; hydrogen sulfide; sulfur-oxidizing bacteria; biofiltration; biotrickling filters; anoxic biofiltration; autotrophic denitrification; microbial ecology; molecular techniques 1. Introduction Biogas is a promising renewable energy source that could contribute to regional economic growth due to its indigenous local-based production together with reduced greenhouse gas emissions [1].
    [Show full text]
  • A. Calvin Cycle Discussion on Biology-Online.Org's Forum
    Cordova's Finding: Affirming NSF's Definition of Francis K. Fong's Discovery of Margerum's Work of Fiction that Begot the Calvin Cycle and its Z scheme A. Calvin Cycle Discussion on Biology-Online.Org's Forum This post complements NSFfunding.com's Website on Calvin cycle, the dark reactions in photosynthesis. There is an interesting discussion on biology-online.org/biology-forum under the title, "the Calvin cycle???help please." First, the universally accepted interpretation of the Calvin cycle is described: "NADPH is actually electron provided and made blablabla, not hydrogen. And last, but not least this triose called glyceraldehyde phosphate is primarily recycled, that's why is it called 'The Calvin CYCLE,' and why it can work all the time - Just a minor part is transformed to hexose (primarily fructose), the rest has nothing to do with the Calvin cycle." Then, Biology-Online.Org's discussion departs from the accepted interpretation, in that Melvin Calvin, to whom is attributed the Calvin cycle, or the dark reactions in photosynthesis, had nothing to do with the Calvin cycle. The reason is because Calvin and his group at Berkeley published, in their original papers, findings from their C-14 tracer experiments that the "triose called glyceraldehyde phosphate is NOT recycled." Calvin et al reported a carboxylation reaction in photosynthesis which is neither dark nor cyclic, but a photoreductive reaction. The CO2 assimilated from the air by the RuBP (ribulose bisphosphate) results in reductive splitting of the 6-C intermediate into one molecule of PGA (phosphoglycerate) and the other a triose, glyceraldehyde phosphate, which condenses to make glucose and, then, starch.
    [Show full text]
  • Photorespiration Pathways in a Chemolithoautotroph
    bioRxiv preprint doi: https://doi.org/10.1101/2020.05.08.083683; this version posted May 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Photorespiration pathways in a chemolithoautotroph Nico J. Claassens*1, Giovanni Scarinci*1, Axel Fischer1, Avi I. Flamholz2, William Newell1, Stefan Frielingsdorf3, Oliver Lenz3, Arren Bar-Even†1 1Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany 2Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States. 3Institut für Chemie, Physikalische Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany †corresponding author; phone: +49 331 567-8910; Email: [email protected] *contributed equally Key words: CO2 fixation; hydrogen-oxidizing bacteria; glyoxylate shunt; malate synthase; oxalate metabolism 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.08.083683; this version posted May 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Abstract Carbon fixation via the Calvin cycle is constrained by the side activity of Rubisco with dioxygen, generating 2-phosphoglycolate. The metabolic recycling of 2-phosphoglycolate, an essential process termed photorespiration, was extensively studied in photoautotrophic organisms, including plants, algae, and cyanobacteria, but remains uncharacterized in chemolithoautotrophic bacteria.
    [Show full text]