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Hopmans EC, Grossi V, Sahonero-Canavesi DX, Bale NJ, Cravo-Laureau C, Sinninghe Damsté JS. Mono- to tetra-alkyl ether cardiolipins in a mesophilic, sulfate-reducing bacterium identified by UHPLC-HRMS n: a novel class of membrane lipids. Front Microbiol 2024; 15:1404328. [PMID: 38841066 PMCID: PMC11150832 DOI: 10.3389/fmicb.2024.1404328] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/06/2024] [Indexed: 06/07/2024] Open
Abstract
The composition of membrane lipids varies in a number of ways as adjustment to growth conditions. Variations in head group composition and carbon skeleton and degree of unsaturation of glycerol-bound acyl or alkyl chains results in a high structural complexity of the lipidome of bacterial cells. We studied the lipidome of the mesophilic, sulfate-reducing bacterium, Desulfatibacillum alkenivorans strain PF2803T by ultra-high-pressure liquid chromatography coupled with high-resolution tandem mass spectrometry (UHPLC-HRMSn). This anaerobic bacterium has been previously shown to produce high amounts of mono-and di-alkyl glycerol ethers as core membrane lipids. Our analyses revealed that these core lipids occur with phosphatidylethanomamine (PE) and phosphatidylglycerol (PG) head groups, representing each approximately one third of the phospholipids. The third class was a novel group of phospholipids, i.e., cardiolipins (CDLs) containing one (monoether/triester) to four (tetraether) ether-linked saturated straight-chain or methyl-branched alkyl chains. Tetraether CDLs have been shown to occur in archaea (with isoprenoid alkyl chains) but have not been previously reported in the bacterial Domain. Structurally related CDLs with one or two alkyl/acyl chains missing, so-called monolyso-and dilyso-CDLs, were also observed. The potential biosynthetic pathway of these novel CDLs was investigated by examining the genome of D. alkenivorans. Three CDL synthases were identified; one catalyzes the condensation of two PGs, the other two are probably involved in the condensation of a PE with a PG. A heterologous gene expression experiment showed the in vivo production of dialkylglycerols upon anaerobic expression of the glycerol ester reductase enzyme of D. alkenivorans in E. coli. Reduction of the ester bonds probably occurs first at the sn-1 and subsequently at the sn-2 position after the formation of PEs and PGs.
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Affiliation(s)
- Ellen C. Hopmans
- Department of Marine Microbiology and Biogeochemistry, NIOZ Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Vincent Grossi
- Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement (LGL-TPE, UMR CNRS 5276), Univ Lyon, UCBL, Villeurbanne, France
| | - Diana X. Sahonero-Canavesi
- Department of Marine Microbiology and Biogeochemistry, NIOZ Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Netherlands Institute for Sea Research, Den Burg, Netherlands
| | | | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Netherlands Institute for Sea Research, Den Burg, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
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2
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Dedysh SN. Describing difficult-to-culture bacteria: Taking a shortcut or investing time to discover something new? Syst Appl Microbiol 2023; 46:126439. [PMID: 37413783 DOI: 10.1016/j.syapm.2023.126439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/17/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Despite the growing interest in isolating representatives of poorly studied and as-yet-uncultivated bacterial phylogenetic groups, these microorganisms remain difficult objects for taxonomic studies. The time required for describing one of these fastidious bacteria is commonly measured in several years. What is even more problematic, many routine laboratory tests, which were originally developed for fast-growing and fast-responding microorganisms, are not fully suitable for many environmentally relevant, slow-growing bacteria. Standard techniques used in chemotaxonomic analyses do not identify unique lipids produced by these bacteria. A common practice of preparing taxonomic descriptions that report a minimal set of features to name a newly isolated organism deepens a gap between microbial ecologists and taxonomists. By contrast, investing time in detailed analysis of cell biology and experimental verification of genome-encoded capabilities of newly isolated microorganisms opens a window for novel, unexpected findings, which may shape our ideas about the functional role of these microbes in the environment.
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Affiliation(s)
- Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
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3
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López-García P, Moreira D. The symbiotic origin of the eukaryotic cell. C R Biol 2023; 346:55-73. [PMID: 37254790 DOI: 10.5802/crbiol.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 06/01/2023]
Abstract
Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.
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Sinninghe Damsté JS, Rijpstra WIC, Huber KJ, Albuquerque L, Egas C, Bale NJ. Dominance of mixed ether/ester, intact polar membrane lipids in five species of the order Rubrobacterales: Another group of bacteria not obeying the "lipid divide". Syst Appl Microbiol 2023; 46:126404. [PMID: 36868099 DOI: 10.1016/j.syapm.2023.126404] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/26/2023] [Accepted: 02/20/2023] [Indexed: 02/26/2023]
Abstract
The composition of the core lipids and intact polar lipids (IPLs) of five Rubrobacter species was examined. Methylated (ω-4) fatty acids (FAs) characterized the core lipids of Rubrobacter radiotolerans, R. xylanophilus and R. bracarensis. In contrast, R. calidifluminis and R. naiadicus lacked ω-4 methyl FAs but instead contained abundant (i.e., 34-41 % of the core lipids) ω-cyclohexyl FAs not reported before in the order Rubrobacterales. Their genomes contained an almost complete operon encoding proteins enabling production of cyclohexane carboxylic acid CoA thioester, which acts as a building block for ω-cyclohexyl FAs in other bacteria. Hence, the most plausible explanation for the biosynthesis of these cyclic FAs in R. calidifluminis and R. naiadicus is a recent acquisition of this operon. All strains contained 1-O-alkyl glycerol ether lipids in abundance (up to 46 % of the core lipids), in line with the dominance (>90 %) of mixed ether/ester IPLs with a variety of polar headgroups. The IPL head group distribution of R. calidifluminis and R. naiadicus differed, e.g. they lacked a novel IPL tentatively assigned as phosphothreoninol. The genomes of all five Rubrobacter species contained a putative operon encoding the synthesis of the 1-O-alkyl glycerol phosphate, the presumed building block of mixed ether/ester IPLs, which shows some resemblance with an operon enabling ether lipid production in various other aerobic bacteria but requires more study. The uncommon dominance of mixed ether/ester IPLs in Rubrobacter species exemplifies our recent growing awareness that the lipid divide between archaea and bacteria/eukaryotes is not as clear cut as previously thought.
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Affiliation(s)
- Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, the Netherlands; Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, the Netherlands.
| | - W Irene C Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, the Netherlands
| | - Katharina J Huber
- Department of Microorganisms, Leibniz-Institute DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, D-38124 Braunschweig, Germany
| | - Luciana Albuquerque
- CNC - Center for Neuroscience and Cell Biology, UC-Biotech, Biocant Park, 3060-197, Cantanhede, Portugal
| | - Conceição Egas
- CNC - Center for Neuroscience and Cell Biology, UC-Biotech, Biocant Park, 3060-197, Cantanhede, Portugal; BIOCANT - Transfer Technology Association, Biocant Park, 3060-197 Cantanhede, Portugal
| | - Nicole J Bale
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, the Netherlands
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5
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Halamka TA, Raberg JH, McFarlin JM, Younkin AD, Mulligan C, Liu X, Kopf SH. Production of diverse brGDGTs by Acidobacterium Solibacter usitatus in response to temperature, pH, and O 2 provides a culturing perspective on brGDGT proxies and biosynthesis. GEOBIOLOGY 2023; 21:102-118. [PMID: 36150122 PMCID: PMC10087280 DOI: 10.1111/gbi.12525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/08/2022] [Accepted: 08/24/2022] [Indexed: 05/04/2023]
Abstract
Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are bacterial membrane lipids that are frequently employed as paleoenvironmental proxies because of the strong empirical correlations between their relative abundances and environmental temperature and pH. Despite the ubiquity of brGDGTs in modern and paleoenvironments, the source organisms of these enigmatic compounds have remained elusive, requiring paleoenvironmental applications to rely solely on observed environmental correlations. Previous laboratory and environmental studies have suggested that the globally abundant bacterial phylum of the Acidobacteria may be an important brGDGT producer in nature. Here, we report on experiments with a cultured Acidobacterium, Solibacter usitatus, that makes a large portion of its cellular membrane (24 ± 9% across all experiments) out of a structurally diverse set of tetraethers including the common brGDGTs Ia, IIa, IIIa, Ib, and IIb. Solibacter usitatus was grown across a range of conditions including temperatures from 15 to 30°C, pH from 5.0 to 6.5, and O2 from 1% to 21%, and demonstrated pronounced shifts in the degree of brGDGT methylation across these growth conditions. The temperature response in culture was in close agreement with trends observed in published environmental datasets, supporting a physiological basis for the empirical relationship between brGDGT methylation number and temperature. However, brGDGT methylation at lower temperatures (15 and 20°C) was modulated by culture pH with higher pH systematically increasing the degree of methylation. In contrast, pH had little effect on brGDGT cyclization, supporting the hypothesis that changes in bacterial community composition may underlie the link between cyclization number and pH observed in environmental samples. Oxygen concentration likewise affected brGDGT methylation highlighting the potential for this environmental parameter to impact paleotemperature reconstruction. Low O2 culture conditions further resulted in the production of uncommon brGDGT isomers that could be indicators of O2 limitation. Finally, the production of brGTGTs (trialkyl tetraethers) in addition to the previously discovered iso-C15-based mono- and diethers in S. usitatus suggests a potential biosynthetic pathway for brGDGTs that uses homologs of the archaeal tetraether synthase (Tes) enzyme for tetraether synthesis from diethers.
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Affiliation(s)
- Toby A. Halamka
- Department of Geological SciencesUniversity of Colorado BoulderDenverCOUSA
| | - Jonathan H. Raberg
- Department of Geological SciencesUniversity of Colorado BoulderDenverCOUSA
- Faculty of Earth SciencesUniversity of IcelandReykjavikIceland
| | - Jamie M. McFarlin
- Department of Geological SciencesUniversity of Colorado BoulderDenverCOUSA
| | - Adam D. Younkin
- Department of Geological SciencesUniversity of Colorado BoulderDenverCOUSA
| | | | - Xiao‐Lei Liu
- School of GeosciencesUniversity of OklahomaNormanOklahomaUSA
| | - Sebastian H. Kopf
- Department of Geological SciencesUniversity of Colorado BoulderDenverCOUSA
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6
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de Kok NAW, Driessen AJM. The catalytic and structural basis of archaeal glycerophospholipid biosynthesis. Extremophiles 2022; 26:29. [PMID: 35976526 PMCID: PMC9385802 DOI: 10.1007/s00792-022-01277-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022]
Abstract
Archaeal glycerophospholipids are the main constituents of the cytoplasmic membrane in the archaeal domain of life and fundamentally differ in chemical composition compared to bacterial phospholipids. They consist of isoprenyl chains ether-bonded to glycerol-1-phosphate. In contrast, bacterial glycerophospholipids are composed of fatty acyl chains ester-bonded to glycerol-3-phosphate. This largely domain-distinguishing feature has been termed the “lipid-divide”. The chemical composition of archaeal membranes contributes to the ability of archaea to survive and thrive in extreme environments. However, ether-bonded glycerophospholipids are not only limited to extremophiles and found also in mesophilic archaea. Resolving the structural basis of glycerophospholipid biosynthesis is a key objective to provide insights in the early evolution of membrane formation and to deepen our understanding of the molecular basis of extremophilicity. Many of the glycerophospholipid enzymes are either integral membrane proteins or membrane-associated, and hence are intrinsically difficult to study structurally. However, in recent years, the crystal structures of several key enzymes have been solved, while unresolved enzymatic steps in the archaeal glycerophospholipid biosynthetic pathway have been clarified providing further insights in the lipid-divide and the evolution of early life.
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Affiliation(s)
- Niels A W de Kok
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands.
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7
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Wörmer L, Gajendra N, Schubotz F, Matys ED, Evans TW, Summons RE, Hinrichs KU. A micrometer-scale snapshot on phototroph spatial distributions: mass spectrometry imaging of microbial mats in Octopus Spring, Yellowstone National Park. GEOBIOLOGY 2020; 18:742-759. [PMID: 32936514 DOI: 10.1111/gbi.12411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 07/10/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Microbial mats from alkaline hot springs in the Yellowstone National Park are ideal natural laboratories to study photosynthetic life under extreme conditions, as well as the nuanced interactions of oxygenic and anoxygenic phototrophs. They represent distinctive examples of chlorophototroph (i.e., chlorophyll or bacteriochlorophyll-based phototroph) diversity, and several novel phototrophs have been first described in these systems, all confined in space, coexisting and competing for niches defined by parameters such as light, oxygen, or temperature. In a novel approach, we employed mass spectrometry imaging of chloropigments, quinones, and intact polar lipids (IPLs) to describe the spatial distribution of different groups of chlorophototrophs along the ~ 1 cm thick microbial mat at 75 µm resolution and in the top ~ 1.5 mm green part of the mat at 25 µm resolution. We observed a fine-tuned sequence of oxygenic and anoxygenic chlorophototrophs with distinctive biomarker signatures populating the microbial mat. The transition of oxic to anoxic conditions is characterized by an accumulation of biomarkers indicative of anoxygenic phototrophy. It is also identified as a clear boundary for different species and ecotypes, which adjust their biomarker inventory, particularly the interplay of quinones and chloropigments, to prevailing conditions. Colocalization of the different biomarker groups led to the identification of characteristic IPL signatures and indicates that glycosidic diether glycerolipids are diagnostic for anoxygenic phototrophs in this mat system. The zoom-in into the upper green part further reveals how oxygenic and anoxygenic phototrophs share this microenvironment and informs on subtle, microscale adjustments in lipid composition of Synechococcus spp.
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Affiliation(s)
- Lars Wörmer
- MARUM - Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Niroshan Gajendra
- MARUM - Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Florence Schubotz
- MARUM - Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Emily D Matys
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas W Evans
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kai-Uwe Hinrichs
- MARUM - Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany
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8
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Chaves Torres L, Kaur G, Melbourne LA, Pancost RD. Selective chemical degradation of silica sinters of the Taupo Volcanic Zone (New Zealand). Implications for early Earth and Astrobiology. GEOBIOLOGY 2019; 17:449-464. [PMID: 31020785 DOI: 10.1111/gbi.12340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 02/26/2019] [Accepted: 03/21/2019] [Indexed: 06/09/2023]
Abstract
Most organic matter (OM) on Earth occurs as kerogen-like materials, that is naturally formed macromolecules insoluble with standard organic solvents. The formation of this insoluble organic matter (IOM) is a topic of much interest, especially when it limits the detection of compounds of geomicrobiological interest. For example, studies that search for biomarker evidence of life on early Earth or other planets usually use solvent-based extractions. This leaves behind a pool of OM as unexplored post-extraction residues, potentially containing diagnostic biomarkers. Since the IOM has an enhanced potential for preservation compared to soluble OM, analysing IOM-released biomarkers can also provide even deeper insights into the ecology of ancient settings, with implications for early Earth and Astrobiology investigations. Here, we analyse the prokaryotic lipid biosignature within soluble and IOM of the Taupo Volcanic Zone (TVZ) silica sinters, which are key analogues in the search for life. We apply sequential solvent extractions and a selective chemical degradation upon the post-solvent extraction residue. Moreover, we compare the IOM from TVZ sinters to analogous studies on peat and marine sediments to assess patterns in OM insolubilisation across the geosphere. Consistent with previous work, we find significant but variable proportions-1%-45% of the total prokaryotic lipids recovered-associated with IOM fractions. This occurs even in recently formed silica sinters, likely indicating inherent cell insolubility. Moreover, archaeal lipids seem more prone to insolubilisation as compared to the bacterial analogues, which might enhance their preservation and also bias overall biomarkers interpretation. These observations are similar to those observed in other settings, confirming that even in a setting where the OM derives predominantly from prokaryotic sources, patterns of IOM formation/occurrence are conserved. Differences with other settings, however, such as the occurrence of archaeol in IOM fractions, could be indicative of different mechanisms for IOM formation that merit further exploration.
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Affiliation(s)
- Lidia Chaves Torres
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
- Cabot Institute, University of Bristol, Bristol, UK
| | - Gurpreet Kaur
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
- Cabot Institute, University of Bristol, Bristol, UK
| | - Leanne A Melbourne
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
- Cabot Institute, University of Bristol, Bristol, UK
| | - Richard D Pancost
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
- Cabot Institute, University of Bristol, Bristol, UK
- School of Earth Sciences, University of Bristol, Bristol, UK
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9
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Dedysh SN, Yilmaz P. Refining the taxonomic structure of the phylum Acidobacteria. Int J Syst Evol Microbiol 2018; 68:3796-3806. [DOI: 10.1099/ijsem.0.003062] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Svetlana N. Dedysh
- 1Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Pelin Yilmaz
- 2Microbial Physiology Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
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Vinçon-Laugier A, Cravo-Laureau C, Mitteau I, Grossi V. Temperature-Dependent Alkyl Glycerol Ether Lipid Composition of Mesophilic and Thermophilic Sulfate-Reducing Bacteria. Front Microbiol 2017; 8:1532. [PMID: 28848536 PMCID: PMC5552659 DOI: 10.3389/fmicb.2017.01532] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/28/2017] [Indexed: 11/13/2022] Open
Abstract
The occurrence of non-isoprenoid alkyl glycerol ether lipids in Bacteria and natural environments is increasingly being reported and the specificity and diagenetic stability of these lipids make them powerful biomarkers for biogeochemical and environmental studies. Yet the environmental controls on the biosynthesis of these peculiar membrane lipids remain poorly documented. Here, the lipid content of two mesophilic (Desulfatibacillum aliphaticivorans and Desulfatibacillum alkenivorans) and one thermophilic (Thermodesulfobacterium commune) sulfate-reducing bacteria-whose membranes are mostly composed of ether lipids-was investigated as a function of growth temperature (20-40°C and 54-84°C, respectively). For all strains, the cellular lipid content was lower at sub- or supra-optimal growth temperature, but the relative proportions of dialkyl glycerols, monoalkyl glycerols and fatty acids remained remarkably stable whatever the growth temperature. Rather than changing the proportions of the different lipid classes, the three strains responded to temperature changes by modifying the average structural composition of the alkyl and acyl chains constitutive of their membrane lipids. Major adaptive mechanisms concerned modifications of the level of branching and of the proportions of the different methyl branched lipids. Specifically, an increase in temperature induced mesophilic strains to produce less dimethyl branched dialkyl glycerols and 10-methyl branched lipids relative to linear structures, and the thermophilic strain to decrease the proportion of anteiso relative to iso methyl branched compounds. These modifications were in agreement with a regulation of the membrane fluidity. In one mesophilic and the thermophilic strains, a modification of the growth temperature further induced changes in the relative proportions of sn-2 vs sn-1 monoalkyl glycerols, suggesting an unprecedented mechanism of homeoviscous adaptation in Bacteria. Strong linear correlations observed between different ratios of alkyl glycerols and temperature allow to hypothesize the use of these specific lipids as indicators of temperature changes in the environment.
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Affiliation(s)
| | - Cristiana Cravo-Laureau
- Equipe Environnement et Microbiologie, UMR CNRS 5254, Université de Pau et des Pays de l'Adour, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les MatériauxPau, France
| | - Isabelle Mitteau
- Equipe Environnement et Microbiologie, UMR CNRS 5254, Université de Pau et des Pays de l'Adour, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les MatériauxPau, France
| | - Vincent Grossi
- Laboratoire de Géologie de Lyon, UMR CNRS 5276, Université Lyon 1Villeurbanne, France
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11
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Damsté JSS, Rijpstra WIC, Dedysh SN, Foesel BU, Villanueva L. Pheno- and Genotyping of Hopanoid Production in Acidobacteria. Front Microbiol 2017; 8:968. [PMID: 28642737 PMCID: PMC5462960 DOI: 10.3389/fmicb.2017.00968] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/15/2017] [Indexed: 11/28/2022] Open
Abstract
Hopanoids are pentacyclic triterpenoid lipids synthesized by different bacterial groups. Methylated hopanoids were believed to be exclusively synthesized by cyanobacteria and aerobic methanotrophs until the genes encoding for the methylation at the C-2 and C-3 position (hpnP and hpnR) were found to be widespread in the bacterial domain, invalidating their use as specific biomarkers. These genes have been detected in the genome of the Acidobacterium "Ca. Koribacter versatilis," but our knowledge of the synthesis of hopanoids and the presence of genes of their biosynthetic pathway in other member of the Acidobacteria is limited. We analyzed 38 different strains of seven Acidobacteria subdivisions (SDs 1, 3, 4, 6, 8, 10, and 23) for the presence of C30 hopenes and C30+ bacteriohopane polyols (BHPs) using the Rohmer reaction. BHPs and/or C30 hopenes were detected in all strains of SD1 and SD3 but not in SD4 (excepting Chloracidobacterium thermophilum), 6, 8, 10, and 23. This is in good agreement with the presence of genes required for hopanoid biosynthesis in the 31 available whole genomes of cultivated Acidobacteria. All genomes encode the enzymes involved in the non-mevalonate pathway ultimately leading to farnesyl diphosphate but only SD1 and 3 Acidobacteria and C. thermophilum encode all three enzymes required for the synthesis of squalene, its cyclization (shc), and addition and modification of the extended side chain (hpnG, hpnH, hpnI, hpnJ, hpnO). In almost all strains, only tetrafunctionalized BHPs were detected; three strains contained variable relative abundances (up to 45%) of pentafunctionalized BHPs. Only "Ca. K. versatilis" contained methylated hopanoids (i.e., 2,3-dimethyl bishomohopanol), although in low (<10%) amounts. These genes are not present in any other Acidobacterium, consistent with the absence of methylated BHPs in the other examined strains. These data are in agreement with the scattered occurrence of methylated BHPs in other bacterial phyla such as the Alpha-, Beta-, and Gammaproteobacteria and the Cyanobacteria, limiting their biomarker potential. Metagenomes of Acidobacteria were also examined for the presence of genes required for hopanoid biosynthesis. The complete pathway for BHP biosynthesis was evident in SD2 Acidobacteria and a group phylogenetically related to SD1 and SD3, in line with the limited occurrence of BHPs in acidobacterial cultures.
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Affiliation(s)
- Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands
- Department of Earth Sciences, Geochemistry, Faculty of Geosciences, Utrecht UniversityUtrecht, Netherlands
| | - W. Irene C. Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands
| | - Svetlana N. Dedysh
- S. N. Winogradsky Institute of Microbiology, Research Center of Biotechnology of Russian Academy of SciencesMoscow, Russia
| | - Bärbel U. Foesel
- Department of Microbial Ecology and Diversity Research, German Collection of Microorganisms and Cell Cultures (LG)Braunschweig, Germany
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands
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12
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Gocke MI, Huguet A, Derenne S, Kolb S, Dippold MA, Wiesenberg GLB. Disentangling interactions between microbial communities and roots in deep subsoil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 575:135-145. [PMID: 27744199 DOI: 10.1016/j.scitotenv.2016.09.184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/19/2016] [Accepted: 09/22/2016] [Indexed: 06/06/2023]
Abstract
Soils, paleosols and terrestrial sediments serve as archives for studying climate change, and represent important terrestrial carbon pools. Archive functioning relies on the chronological integrity of the respective units. Incorporation of younger organic matter (OM) e.g. by plant roots and associated microorganisms into deep subsoil and underlying soil parent material may reduce reliability of paleoenvironmental records and stability of buried OM. Long-term effects of sedimentary characteristics and deep rooting on deep subsoil microbial communities remain largely unknown. We characterized fossil and living microbial communities based on molecular markers in a Central European Late Pleistocene loess-paleosol sequence containing recent and ancient roots with ages of several millenia. The molecular approach, comprising free and phospholipid fatty acids (FAs), core and intact polar glycerol dialkyl glycerol tetraethers (GDGTs), as well as 16S rRNA genes from bacterial DNA, revealed the presence of living microorganisms along the sequence, with bacterial community composition comparable to that of modern topsoils. Up to 88% redundancy between bacterial genetic fingerprint and molecular signature of fossil microorganisms suggested a time-integrated signal of the molecular markers accumulated over a time span potentially lasting from sedimentation over one or more rooting phases until today. Free FAs, core GDGTs and DNA, considered as remains of fossil microorganisms, corresponded with ancient and recent root quantities, whereas phospholipid FAs and intact polar GDGTs, presumably derived from living microorganisms, correlated only with living roots. The biogeochemical and ecological disequilibrium induced by postsedimentary rooting may entail long-term microbial processes like OM mineralization, which may continue even millenia after the lifetime of the root. Deep roots and their fossil remains have been observed in various terrestrial settings, and roots as well as associated microorganisms cause both, OM incorporation and mineralization. Therefore, these findings are crucial for improved understanding of OM dynamics and carbon sequestration potential in deep subsoils.
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Affiliation(s)
- Martina I Gocke
- Department of Geography, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Arnaud Huguet
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7619, METIS, 75005 Paris, France.
| | - Sylvie Derenne
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7619, METIS, 75005 Paris, France.
| | - Steffen Kolb
- Leibniz Center for Agricultural Landscape Research, Landscape Biogeochemistry, Eberswalder Straße 84, 15374 Müncheberg, Germany.
| | - Michaela A Dippold
- Department of Agricultural Soil Science, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany.
| | - Guido L B Wiesenberg
- Department of Geography, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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13
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Villanueva L, Schouten S, Damsté JSS. Phylogenomic analysis of lipid biosynthetic genes of Archaea shed light on the ‘lipid divide’. Environ Microbiol 2016; 19:54-69. [DOI: 10.1111/1462-2920.13361] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/22/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryNIOZ, Royal Netherlands Institute for Sea Research, and Utrecht UniversityP.O. Box 591790AB Den Burg Texel The Netherlands
| | - Stefan Schouten
- Department of Marine Microbiology and BiogeochemistryNIOZ, Royal Netherlands Institute for Sea Research, and Utrecht UniversityP.O. Box 591790AB Den Burg Texel The Netherlands
- Faculty of GeosciencesUtrecht UniversityP.O. Box 80.021Utrecht3508 TA The Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryNIOZ, Royal Netherlands Institute for Sea Research, and Utrecht UniversityP.O. Box 591790AB Den Burg Texel The Netherlands
- Faculty of GeosciencesUtrecht UniversityP.O. Box 80.021Utrecht3508 TA The Netherlands
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14
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Wüst PK, Foesel BU, Geppert A, Huber KJ, Luckner M, Wanner G, Overmann J. Brevitalea aridisoli, B. deliciosa and Arenimicrobium luteum, three novel species of Acidobacteria subdivision 4 (class Blastocatellia) isolated from savanna soil and description of the novel family Pyrinomonadaceae. Int J Syst Evol Microbiol 2016; 66:3355-3366. [PMID: 27255677 DOI: 10.1099/ijsem.0.001199] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three novel strains of the phylum Acidobacteria (Ac_11_E3T, Ac_12_G8T and Ac_16_C4T) were isolated from Namibian semiarid savanna soils by a high-throughput cultivation approach using low-nutrient growth media. 16S rRNA gene sequence analysis placed all three strains in the order Blastocatellales of the class Blastocatellia (Acidobacteria subdivision 4). However, 16S rRNA gene sequence similarities to their closest relative Pyrinomonas methylaliphatogenes K22T were ≤90 %. Cells of strains Ac_11_E3T, Ac_12_G8T and Ac_16_C4T were Gram-staining-negative and non-motile and divided by binary fission. Ac_11_E3T and Ac_16_C4T formed white colonies, while those of Ac_12_G8T were orange-yellowish. All three strains were aerobic chemoorganoheterotrophic mesophiles with a broad pH range for growth. All strains used a very limited spectrum of carbon and energy sources for growth, with a preference for complex proteinaceous substrates. The major respiratory quinone was MK-8. The major shared fatty acid was iso-C15 : 0. The DNA G+C contents of strains Ac_11_E3T, Ac_12_G8T and Ac_16_C4T were 55.9 mol%, 66.9 mol% and 54.7 mol%, respectively. Based on these characteristics, the two novel genera Brevitaleagen. nov. and Arenimicrobiumgen. nov. are proposed, harboring the novel species Brevitaleaaridisoli sp. nov. (Ac_11_E3T=DSM 27934T=LMG 28618T), Brevitalea deliciosa sp. nov. (Ac_16_C4T=DSM 29892T=LMG 28995T) and Arenimicrobium luteum sp. nov. (Ac_12_G8T=DSM 26556T=LMG 29166T), respectively. Since these novel genera are only distantly related to established families, we propose the novel family Pyrinomonadaceaefam. nov. that accommodates the proposed genera and the genus Pyrinomonas(Crowe et al., 2014).
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Affiliation(s)
- Pia K Wüst
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Bärbel U Foesel
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Alicia Geppert
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Katharina J Huber
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Manja Luckner
- Department of Biology I, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Gerhard Wanner
- Department of Biology I, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.,Technische Universität Braunschweig, Braunschweig, Germany
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15
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Huber KJ, Geppert AM, Wanner G, Fösel BU, Wüst PK, Overmann J. The first representative of the globally widespread subdivision 6 Acidobacteria,Vicinamibacter silvestris gen. nov., sp. nov., isolated from subtropical savannah soil. Int J Syst Evol Microbiol 2016; 66:2971-2979. [PMID: 27150379 DOI: 10.1099/ijsem.0.001131] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Members of the phylum Acidobacteria are abundant in a wide variety of soil environments. Despite this, previous cultivation attempts have frequently failed to retrieve representative phylotypes of Acidobacteria, which have, therefore, been discovered by culture-independent methods (13175 acidobacterial sequences in the SILVA database version 123; NR99) and only 47 species have been described so far. Strain Ac_5_C6T represents the first isolate of the globally widespread and abundant subdivision 6 Acidobacteria and is described in the present study. Cells of strain Ac_5_C6T were Gram-stain-negative, immotile rods that divided by binary fission. They formed yellow, extremely cohesive colonies and stable aggregates even in rapidly shaken liquid cultures. Ac_5_C6T was tolerant of a wide range of temperatures (12-40 °C) and pH values (4.7-9.0). It grew chemoorganoheterotrophically on a broad range of substrates including different sugars, organic acids, nucleic acids and complex proteinaceous compounds. The major fatty acids of Ac_5_C6T were iso-C17 : 1 ω9c, C18 : 1 ω7c and iso-C15 : 0. Summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), iso-C17 : 0 and C16 : 0 were also detected. Phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid were identified as polar lipids. The major quinone was MK-8. The DNA G+C content of Ac_5_C6T was 65.9 mol%. With 16S rRNA gene sequence similarities of 83-84 %, the closest described relatives were Acidicapsa borealis KA1T, Acidobacterium capsulatum 161T, Granulicella pectinovorans TPB6011T, Occallatibacter riparius 277T and Paludibaculum fermentans P105T. According to the morphological, physiological and molecular characteristics, the novel genus Vicinamibacter gen. nov., and the novel species, Vicinamibacter silvestris sp. nov. (type strain Ac_5_C6T = DSM 29464T = LMG 29035T) are proposed.
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Affiliation(s)
- Katharina J Huber
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alicia M Geppert
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Gerhard Wanner
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Bärbel U Fösel
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Pia K Wüst
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Technical University Braunschweig, Braunschweig, Germany
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16
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Hynönen U, Rasinkangas P, Satokari R, Paulin L, de Vos WM, Pietilä TE, Kant R, Palva A. Isolation and whole genome sequencing of a Ruminococcus-like bacterium, associated with irritable bowel syndrome. Anaerobe 2016; 39:60-7. [PMID: 26946362 DOI: 10.1016/j.anaerobe.2016.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/23/2016] [Accepted: 03/01/2016] [Indexed: 12/11/2022]
Abstract
In our previous studies on the intestinal microbiota in irritable bowel syndrome (IBS), we identified a bacterial phylotype with higher abundance in patients suffering from diarrhea than in healthy controls. In the present work, we have isolated in pure culture strain RT94, belonging to this phylotype, determined its whole genome sequence and performed an extensive genomic analysis and phenotypical testing. This revealed strain RT94 to be a strict anaerobe apparently belonging to a novel species with only 94% similarity in the 16S rRNA gene sequence to the closest relatives Ruminococcus torques and Ruminococcus lactaris. The G + C content of strain RT94 is 45.2 mol% and the major long-chain cellular fatty acids are C16:0, C18:0 and C14:0. The isolate is metabolically versatile but not a mucus or cellulose utilizer. It produces acetate, ethanol, succinate, lactate and formate, but very little butyrate, as end products of glucose metabolism. The mechanisms underlying the association of strain RT94 with diarrhea-type IBS are discussed.
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Affiliation(s)
- Ulla Hynönen
- Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland.
| | - Pia Rasinkangas
- Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland.
| | - Reetta Satokari
- Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland.
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland.
| | - Willem M de Vos
- Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland.
| | - Taija E Pietilä
- Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland.
| | - Ravi Kant
- Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland.
| | - Airi Palva
- Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland.
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17
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Novel isolates double the number of chemotrophic species and allow the first description of higher taxa in Acidobacteria subdivision 4. Syst Appl Microbiol 2015; 38:534-44. [DOI: 10.1016/j.syapm.2015.08.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 08/10/2015] [Accepted: 08/17/2015] [Indexed: 01/15/2023]
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18
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Lee KCY, Morgan XC, Power JF, Dunfield PF, Huttenhower C, Stott MB. Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22(T). Stand Genomic Sci 2015; 10:101. [PMID: 26568784 PMCID: PMC4644332 DOI: 10.1186/s40793-015-0099-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 11/10/2015] [Indexed: 11/10/2022] Open
Abstract
Strain K22(T) is the type species of the recently- described genus Pyrinomonas, in subdivision 4 of the phylum Acidobacteria (Int J Syst Evol Micr. 2014; 64(1):220-7). It was isolated from geothermally-heated soil from Mt. Ngauruhoe, New Zealand, using low-nutrient medium. P. methylaliphatogenes K22(T) has a chemoheterotrophic metabolism; it can hydrolyze a limited range of simple carbohydrates and polypeptides. Its cell membrane is dominated by iso-branching fatty acids, and up to 40 % of its lipid content is membrane-spanning and ether lipids. It is obligately aerobic, thermophilic, moderately acidophilic, and non-spore-forming. The 3,788,560 bp genome of P. methylaliphatogenes K22(T) has a G + C content of 59.36 % and contains 3,189 protein-encoding and 55 non-coding RNA genes. Genomic analysis was consistent with nutritional requirements; in particular, the identified transporter classes reflect the oligotrophic nature of this strain.
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Affiliation(s)
- Kevin C Y Lee
- GNS Science, Extremophiles Research Group, Taupō, New Zealand
| | - Xochitl C Morgan
- Department of Biostatistics, Harvard School of Public Health, Boston, MA USA ; Broad Institute of Harvard and MIT, Cambridge, MA USA
| | - Jean F Power
- GNS Science, Extremophiles Research Group, Taupō, New Zealand
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, Boston, MA USA ; Broad Institute of Harvard and MIT, Cambridge, MA USA
| | - Matthew B Stott
- GNS Science, Extremophiles Research Group, Taupō, New Zealand
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19
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Moore EK, Villanueva L, Hopmans EC, Rijpstra WIC, Mets A, Dedysh SN, Sinninghe Damsté JS. Abundant Trimethylornithine Lipids and Specific Gene Sequences Are Indicative of Planctomycete Importance at the Oxic/Anoxic Interface in Sphagnum-Dominated Northern Wetlands. Appl Environ Microbiol 2015; 81:6333-44. [PMID: 26150465 PMCID: PMC4542221 DOI: 10.1128/aem.00324-15] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 06/30/2015] [Indexed: 12/19/2022] Open
Abstract
Northern wetlands make up a substantial terrestrial carbon sink and are often dominated by decay-resistant Sphagnum mosses. Recent studies have shown that planctomycetes appear to be involved in degradation of Sphagnum-derived debris. Novel trimethylornithine (TMO) lipids have recently been characterized as abundant lipids in various Sphagnum wetland planctomycete isolates, but their occurrence in the environment has not yet been confirmed. We applied a combined intact polar lipid (IPL) and molecular analysis of peat cores collected from two northern wetlands (Saxnäs Mosse [Sweden] and Obukhovskoye [Russia]) in order to investigate the preferred niche and abundance of TMO-producing planctomycetes. TMOs were present throughout the profiles of Sphagnum bogs, but their concentration peaked at the oxic/anoxic interface, which coincided with a maximum abundance of planctomycete-specific 16S rRNA gene sequences. The sequences detected at the oxic/anoxic interface were affiliated with the Isosphaera group, while sequences present in the anoxic peat layers were related to an uncultured planctomycete group. Pyrosequencing-based analysis identified Planctomycetes as the major bacterial group at the oxic/anoxic interface at the Obukhovskoye peat (54% of total 16S rRNA gene sequence reads), followed by Acidobacteria (19% reads), while in the Saxnäs Mosse peat, Acidobacteria were dominant (46%), and Planctomycetes contributed to 6% of the total reads. The detection of abundant TMO lipids in planctomycetes isolated from peat bogs and the lack of TMO production by cultures of acidobacteria suggest that planctomycetes are the producers of TMOs in peat bogs. The higher accumulation of TMOs at the oxic/anoxic interface and the change in the planctomycete community with depth suggest that these IPLs could be synthesized as a response to changing redox conditions at the oxic/anoxic interface.
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Affiliation(s)
- Eli K Moore
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, Texel, The Netherlands
| | - Laura Villanueva
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, Texel, The Netherlands
| | - Ellen C Hopmans
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, Texel, The Netherlands
| | - W Irene C Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, Texel, The Netherlands
| | - Anchelique Mets
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, Texel, The Netherlands
| | - Svetlana N Dedysh
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Organic Biogeochemistry, Texel, The Netherlands Utrecht University, Faculty of Geosciences, Utrecht, The Netherlands
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20
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Tank M, Bryant DA. Chloracidobacterium thermophilum gen. nov., sp. nov.: an anoxygenic microaerophilic chlorophotoheterotrophic acidobacterium. Int J Syst Evol Microbiol 2015; 65:1426-1430. [DOI: 10.1099/ijs.0.000113] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel anoxygenic photoheterotrophic member of the phylum
Acidobacteria
, Chloracidobacterium thermophilum strain B sp. nov., was isolated from a cyanobacterial enrichment culture derived from microbial mats associated with Octopus Spring, Yellowstone National Park, WY. C. thermophilum sp. nov. was a Gram-stain-negative rod (diameter, approximately 0.8–1.0 µm; variable length, approximately 2.5 µm), which formed greenish-brown liquid suspension cultures. It was a moderately thermophilic microaerophile and grew in a defined medium at 51 °C (Topt; range 44 to 58 °C) and in the pH range 5.5 to 9.5 (pHopt = ~7.0). The DNA G+C content was 61.3 mol%, and phylogenetic analysis, based on the 16S rRNA sequence, showed that C. thermophilum sp. nov. belongs to subdivision 4 (
Acidobacteriaceae
) of the
Acidobacteria
. C. thermophilum sp. nov. was unable to synthesize branched-chain amino acids, l-lysine, and vitamin B12, which were required for growth. Although the organism lacked genes/enzymes for autotrophic carbon fixation, bicarbonate was required. Growth was stimulated by other amino acids and 2-oxoglutarate. Cells produced chlorosomes containing a diverse mixture of bacteriochlorophyll (BChl) c derivatives, and additionally, synthesized BChl a
P, Chl a
PD, and Zn-BChl a′P, which occurred in type-1 homodimeric reaction centres. The carotenoids included echinenone, canthaxanthin, lycopene, γ-carotene and β-carotene. C. thermophilum sp. nov. produced iso-diabolic acid as its major fatty acid and synthesized three hopanoids (diploptene, bacteriohopanetetrol and bacteriohopanetetrol cyclitol ether). Based upon its phenotypic and genotypic properties, the name Chloracidobacterium thermophilum gen. nov., sp. nov. is proposed for this isolate; the type strain is C. thermophilum strain BT (ATCC BAA-2647 = JCM 30199).
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Affiliation(s)
- Marcus Tank
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802 USA
| | - Donald A. Bryant
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717 USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802 USA
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21
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Mono- and dialkyl glycerol ether lipids in anaerobic bacteria: biosynthetic insights from the mesophilic sulfate reducer Desulfatibacillum alkenivorans PF2803T. Appl Environ Microbiol 2015; 81:3157-68. [PMID: 25724965 DOI: 10.1128/aem.03794-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 02/22/2015] [Indexed: 11/20/2022] Open
Abstract
Bacterial glycerol ether lipids (alkylglycerols) have received increasing attention during the last decades, notably due to their potential role in cell resistance or adaptation to adverse environmental conditions. Major uncertainties remain, however, regarding the origin, biosynthesis, and modes of formation of these uncommon bacterial lipids. We report here the preponderance of monoalkyl- and dialkylglycerols (1-O-alkyl-, 2-O-alkyl-, and 1,2-O-dialkylglycerols) among the hydrolyzed lipids of the marine mesophilic sulfate-reducing proteobacterium Desulfatibacillum alkenivorans PF2803T grown on n-alkenes (pentadec-1-ene or hexadec-1-ene) as the sole carbon and energy source. Alkylglycerols account for one-third to two-thirds of the total cellular lipids (alkylglycerols plus acylglycerols), depending on the growth substrate, with dialkylglycerols contributing to one-fifth to two-fifths of the total ether lipids. The carbon chain distribution of the lipids of D. alkenivorans also depends on that of the substrate, but the chain length and methyl-branching patterns of fatty acids and monoalkyl- and dialkylglycerols are systematically congruent, supporting the idea of a biosynthetic link between the three classes of compounds. Vinyl ethers (1-alken-1'-yl-glycerols, known as plasmalogens) are not detected among the lipids of strain PF2803T. Cultures grown on different (per)deuterated n-alkene, n-alkanol, and n-fatty acid substrates further demonstrate that saturated alkylglycerols are not formed via the reduction of hypothetic alken-1'-yl intermediates. Our results support an unprecedented biosynthetic pathway to monoalkyl/monoacyl- and dialkylglycerols in anaerobic bacteria and suggest that n-alkyl compounds present in the environment can serve as the substrates for supplying the building blocks of ether phospholipids of heterotrophic bacteria.
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