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Radjasa OK, Steven R, Humaira Z, Dwivany FM, Nugrahapraja H, Trinugroho JP, Kristianti T, Chahyadi A, Natanael Y, Priharto N, Kamarisima, Sembiring FAPB, Dwijayanti A, Kusmita L, Moeis MR, Suhardi VSH. Biosynthetic gene cluster profiling from North Java Sea Virgibacillus salarius reveals hidden potential metabolites. Sci Rep 2023; 13:19273. [PMID: 37935710 PMCID: PMC10630419 DOI: 10.1038/s41598-023-44603-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023] Open
Abstract
Virgibacillus salarius 19.PP.SC1.6 is a coral symbiont isolated from Indonesia's North Java Sea; it has the ability to produce secondary metabolites that provide survival advantages and biological functions, such as ectoine, which is synthesized by an ectoine gene cluster. Apart from being an osmoprotectant for bacteria, ectoine is also known as a chemical chaperone with numerous biological activities such as maintaining protein stability, which makes ectoine in high demand in the market industry and makes it beneficial to investigate V. salarius ectoine. However, there has been no research on genome-based secondary metabolite and ectoine gene cluster characterization from Indonesian marine V. salarius. In this study, we performed a genomic analysis and ectoine identification of V. salarius. A high-quality draft genome with total size of 4.45 Mb and 4426 coding sequence (CDS) was characterized and then mapped into the Cluster of Orthologous Groups (COG) category. The genus Virgibacillus has an "open" pangenome type with total of 18 genomic islands inside the V. salarius 19.PP.SC1.6 genome. There were seven clusters of secondary metabolite-producing genes found, with a total of 80 genes classified as NRPS, PKS (type III), terpenes, and ectoine biosynthetic related genes. The ectoine gene cluster forms one operon consists of ectABC gene with 2190 bp gene cluster length, and is successfully characterized. The presence of ectoine in V. salarius was confirmed using UPLC-MS/MS operated in Multiple Reaction Monitoring (MRM) mode, which indicates that V. salarius has an intact ectoine gene clusters and is capable of producing ectoine as compatible solutes.
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Affiliation(s)
- Ocky Karna Radjasa
- Research Center for Deep Sea, The Earth Sciences and Maritime Research Organization, National Research and Innovation Agency, Jakarta, 14430, Indonesia.
| | - Ray Steven
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Zalfa Humaira
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Fenny Martha Dwivany
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia.
| | - Husna Nugrahapraja
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Joko Pebrianto Trinugroho
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Tati Kristianti
- Institut Pendidikan Indonesia, Garut, West Java, 44151, Indonesia
| | - Agus Chahyadi
- University Center of Excellence for Nutraceuticals, Bioscience and Biotechnology Research Center, Bandung Institute of Technology, Bandung, West Java, Indonesia
| | - Yosua Natanael
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Neil Priharto
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | - Kamarisima
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
| | | | - Ari Dwijayanti
- CNRS@CREATE Ltd., 1 Create Way, #08-01 Create Tower, Singapore, 138602, Singapore
| | - Lia Kusmita
- STIFAR Yayasan Pharmasi Semarang, Semarang, Central Java, 50124, Indonesia
| | - Maelita R Moeis
- Department of Biotechnology, Faculty of Science and Technology, Universitas Muhammadiyah Bandung, Bandung, West Java, 40262, Indonesia
| | - V Sri Harjati Suhardi
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung, West Java, 40132, Indonesia
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2
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Lu J, Shu Y, Zhang H, Zhang S, Zhu C, Ding W, Zhang W. The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms. Int J Mol Sci 2023; 24:ijms24076491. [PMID: 37047466 PMCID: PMC10095273 DOI: 10.3390/ijms24076491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023] Open
Abstract
The development of metagenomics has opened up a new era in the study of marine microbiota, which play important roles in biogeochemical cycles. In recent years, the global ocean sampling expeditions have spurred this research field toward a deeper understanding of the microbial diversities and functions spanning various lifestyles, planktonic (free-living) or sessile (biofilm-associated). In this review, we deliver a comprehensive summary of marine microbiome datasets generated in global ocean expeditions conducted over the last 20 years, including the Sorcerer II GOS Expedition, the Tara Oceans project, the bioGEOTRACES project, the Micro B3 project, the Bio-GO-SHIP project, and the Marine Biofilms. These datasets have revealed unprecedented insights into the microscopic life in our oceans and led to the publication of world-leading research. We also note the progress of metatranscriptomics and metaproteomics, which are confined to local marine microbiota. Furthermore, approaches to transforming the global ocean microbiome datasets are highlighted, and the state-of-the-art techniques that can be combined with data analyses, which can present fresh perspectives on marine molecular ecology and microbiology, are proposed.
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Affiliation(s)
- Jie Lu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
| | - Yi Shu
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
| | - Heng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Shangxian Zhang
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Chengrui Zhu
- Haide College, Ocean University of China, Qingdao 266100, China
| | - Wei Ding
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao 266100, China;
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
- Correspondence: (W.D.); (W.Z.)
| | - Weipeng Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266100, China
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Haide College, Ocean University of China, Qingdao 266100, China
- Correspondence: (W.D.); (W.Z.)
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Garby TJ, Jordan M, Timms V, Walter MR, Neilan BA. 2-Methylhopanoids in geographically distinct, arid biological soil crusts are primarily cyanobacterial in origin. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:164-169. [PMID: 34898023 DOI: 10.1111/1758-2229.13037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/10/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Microbial palaeontology is largely reliant on the interpretation of geologically stable biomarkers or molecular fossils. Biomolecules that are both specific to particular groups of organisms and stable on a geological scale are invaluable for tracing the emergence and diversification of lifeforms, particularly in cases where mineral fossils are lacking. 2-Methylhopanoids and their diagenic product, 2-methylhopanes, are highly abundant bacterial membrane lipids, recoverable from samples in excess of a billion years old. In this work we used degenerate PCR, targeting 2-methylhopanoid biosynthesis genes, and sequencing to show that the ability to produce these molecules in arid biological soil crusts from deserts in diverse geographical locations (Utah, USA, and the Pilbara, Australia) is largely confined to cyanobacteria. These data suggest that 2-methylhopanes can be used as a proxy for cyanobacterial presence within these environments, contributing to our understanding of the emergence of terrestrial life on Earth.
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Affiliation(s)
- Tamsyn J Garby
- Australian Centre for Astrobiology, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Matthew Jordan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Verlaine Timms
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Malcolm R Walter
- Australian Centre for Astrobiology, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Brett A Neilan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
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4
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Matys ED, Mackey T, Grettenberger C, Mueller E, Jungblut A, Sumner DY, Hawes I, Summons RE. Environmental controls on bacteriohopanepolyol profiles of benthic microbial mats from Lake Fryxell, Antarctica. GEOBIOLOGY 2019; 17:551-563. [PMID: 31325234 DOI: 10.1111/gbi.12353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/20/2019] [Accepted: 05/04/2019] [Indexed: 06/10/2023]
Abstract
Bacteriohopanepolyols (BHPs) are pentacyclic triterpenoid lipids that contribute to the structural integrity and physiology of some bacteria. Because some BHPs originate from specific classes of bacteria, BHPs have potential as taxonomically and environmentally diagnostic biomarkers. For example, a stereoisomer of bacteriohopanetetrol (informally BHT II) has been associated with anaerobic ammonium oxidation (anammox) bacteria and suboxic to anoxic marine environments where anammox is active. As a result, the detection of BHT II in the sedimentary record and fluctuations in the relative abundance of BHT II may inform reconstructions of nitrogen cycling and ocean redox changes through the geological record. However, there are uncertainties concerning the sources of BHT II and whether or not BHT II is produced in abundance in non-marine environments, both of which are pertinent to interpretations of BHT II signatures in sediments. To address these questions, we investigate the BHP composition of benthic microbial mats from Lake Fryxell, Antarctica. Lake Fryxell is a perennially ice-covered lake with a sharp oxycline in a density-stabilized water column. We describe the diversity and abundance of BHPs in benthic microbial mats across a transect from oxic to anoxic conditions. Generally, BHP abundances and diversity vary with the morphologies of microbial mats, which were previously shown to reflect local environmental conditions, such as irradiance and oxygen and sulfide concentrations. BHT II was identified in mats that exist within oxic to anoxic portions of the lake. However, anammox bacteria have yet to be identified in Lake Fryxell. We examine our results in the context of BHPs as biomarkers in modern and ancient environments.
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Affiliation(s)
- Emily D Matys
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Tyler Mackey
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Elliott Mueller
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Anne Jungblut
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Dawn Y Sumner
- Department of Earth and Planetary Sciences, University of California, Davis, California
| | - Ian Hawes
- University of Waikato, Tauranga, New Zealand
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
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5
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Mangiarotti A, Galassi VV, Puentes EN, Oliveira RG, Del Pópolo MG, Wilke N. Hopanoids Like Sterols Form Compact but Fluid Films. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:9848-9857. [PMID: 31268719 DOI: 10.1021/acs.langmuir.9b01641] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Hopanoids are pentacyclic molecules present in membranes from some bacteria, recently proposed as sterol surrogates in these organisms. Diplopterol is an abundant hopanoid that, similar to sterols, does not self-aggregate in lamellar structures when pure, but forms monolayers at the air-water interface. Here, we analyze the interfacial behavior of pure diplopterol and compare it with sterols from different organisms: cholesterol from mammals, ergosterol from fungi, and stigmasterol from plants. We prepared Langmuir monolayers of the compounds and studied their surface properties using different experimental approaches and molecular dynamics simulations. Our results indicate that the films formed by diplopterol, despite being compact with low mean molecular areas, high surface potentials, and high refractive index, depict shear viscosity values similar to that for fluid films. Altogether, our results reveal that hopanoids have similar interfacial behavior than that of sterols, and thus they may have the capacity of modulating bacterial membrane properties in a similar way sterols do in eukaryotes.
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Affiliation(s)
| | - Vanesa V Galassi
- CONICET y Facultad de Ciencias Exactas y Naturales , Universidad Nacional de Cuyo , Padre Jorge Contreras 1300 , Parque General San Martín, M5502JMA Mendoza , Argentina
| | | | | | - Mario G Del Pópolo
- CONICET y Facultad de Ciencias Exactas y Naturales , Universidad Nacional de Cuyo , Padre Jorge Contreras 1300 , Parque General San Martín, M5502JMA Mendoza , Argentina
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Kharbush JJ, Thompson LR, Haroon MF, Knight R, Aluwihare LI. Hopanoid-producing bacteria in the Red Sea include the major marine nitrite oxidizers. FEMS Microbiol Ecol 2019; 94:4969676. [PMID: 29668882 DOI: 10.1093/femsec/fiy063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 01/26/2023] Open
Abstract
Hopanoids, including the extended side chain-containing bacteriohopanepolyols, are bacterial lipids found abundantly in the geological record and across Earth's surface environments. However, the physiological roles of this biomarker remain uncertain, limiting interpretation of their presence in current and past environments. Recent work investigating the diversity and distribution of hopanoid producers in the marine environment implicated low-oxygen regions as important loci of hopanoid production, and data from marine oxygen minimum zones suggested that the dominant hopanoid producers in these environments are nitrite-utilizing organisms, revealing a potential connection between hopanoid production and the marine nitrogen cycle. Here, we use metagenomic data from the Red Sea to investigate the ecology of hopanoid producers in an environmental setting that is biogeochemically distinct from those investigated previously. The distributions of hopanoid production and nitrite oxidation genes in the Red Sea are closely correlated, and the majority of hopanoid producers are taxonomically affiliated with the major marine nitrite oxidizers, Nitrospinae and Nitrospirae. These results suggest that the relationship between hopanoid production and nitrite oxidation is conserved across varying biogeochemical conditions in dark ocean microbial ecosystems.
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Affiliation(s)
- Jenan J Kharbush
- Department of Earth and Plantary Sciences, Harvard University, Cambridge, MA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Luke R Thompson
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | - Mohamed Fauzi Haroon
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Lihini I Aluwihare
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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7
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Ranjbar Jafarabadi A, Riyahi Bakhtiari A, Aliabadian M, Shadmehri Toosi A. Spatial distribution and composition of aliphatic hydrocarbons, polycyclic aromatic hydrocarbons and hopanes in superficial sediments of the coral reefs of the Persian Gulf, Iran. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 224:195-223. [PMID: 28216134 DOI: 10.1016/j.envpol.2017.01.080] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/16/2017] [Accepted: 01/31/2017] [Indexed: 06/06/2023]
Abstract
This study is the first quantitative report on petroleum biomarkers from the coral reefs systems of the Persian Gulf. 120 reef surface sediment samples from ten fragile coral reef ecosystems were collected and analyzed for grain size, biogenic elements, elemental ratios, and petroleum biomarkers (n-alkanes, PAHs1 and Hopanes) to assess the sources and early diagenesis of sedimentary organic matter. The mean grain size of the reef sediments ranged from 13.56 to 37.11% (Clay), 26.92 to 51.73% (Sand) and 35.97 to 43.85% (Silt). TOC2 (3.35-9.72 mg.g-1) and TON3 (0.4-1.10 mg.g-1) were identified as influencing factors on the accumulation of petroleum hydrocarbons, whilst BC4 (1.08-3.28 mg.g-1) and TIN5 (0.13-0.86) did not exhibit any determining effect. Although BC and TIN demonstrated heterogeneous spatial distribution, TOC and TON indicated homogenous distribution with continually upward trend in concentration from the east to west ward of the Gulf. The mean calculated TOC/TN ratios vacillated according to the stations (p < 0.05) from 2.96 at Shidvar Island to 8.64 at Hengam Island. The high TOC/TN ratios were observed in the Hengam (8.64), Kharg (8.04) and Siri (6.29), respectively, suggesting a predominant marine origin. The mean concentrations of ∑C11-35n-alkanes, ∑30 PAHs and ∑9Hopanes were found in the ranges of 385-937 μg.g-1dw, (overall mean:590 μg.g-1dw), 326-793 ng.g-1dw (499 ng.g-1dw), 88 to 568 ng.g-1 d (258 ng.g-1dw), respectively. Higher concentrations of detected petroleum biomarkers in reef sediments were chiefly distributed near main industrial areas, Kharg, Lavan and Siri, whilst the lower concentrations were in Hormoz and Qeshm. In addition, one-way ANOVA6 analysis demonstrated considerably significant differences (p < 0.05) among concentration of detected total petroleum hydrocarbons between most sampling locations. Some sampling sites especially Kharg, Lavan, Siri and Lark indicated higher concentration of n-alkanes due to the higher maintenance of organic matter by high clay content in the sediments. Furthermore, most sediment samples, except for Hormoz, Qeshm and Hengam showed an even carbon preference for n-alkanes which could be correlated to bacterial input. NPMDS7 analysis also demonstrated that among the congeners of petroleum biomarkers, n-C12,n-C14, n-C16,n-C18 and n-C20 for n-alkanes, Phe8 and Naph9 along with their Alkyl homologues for PAHs (2-3 rings accounted for 60%) and C30αβ and C29αβ for Hopanes were discriminated from their other congeners in the whole study area. Our results based on the PCA10 analysis and diagnostic indices of AHs11 and PAHs along with ring classification of PAHs, in addition, the ubiquitous presence of UCM,12 and Hopanes revealed that the main sources of the pollution were petroleum and petroleum combustion mainly from offshore oil exploration and extraction, discharge of pollutants from shipping activities.
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Affiliation(s)
- Ali Ranjbar Jafarabadi
- Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, TarbiatModares University(TMU), Noor, Mazandaran, Iran.
| | - Alireza Riyahi Bakhtiari
- Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, TarbiatModares University, Noor, Mazandaran, Iran.
| | - Mansour Aliabadian
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad (FUM), Mashhad, Khorasan Razavi, Iran
| | - Amirhossein Shadmehri Toosi
- Department of Civil & Environmental Engineering, Faculty of Engineering, Ferdowsi University of Mashhad (FUM), Mashhad, Khorasan Razavi, Iran
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8
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Ricci JN, Morton R, Kulkarni G, Summers ML, Newman DK. Hopanoids play a role in stress tolerance and nutrient storage in the cyanobacterium Nostoc punctiforme. GEOBIOLOGY 2017; 15:173-183. [PMID: 27527874 DOI: 10.1111/gbi.12204] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 07/15/2016] [Indexed: 06/06/2023]
Abstract
Hopanes are abundant in ancient sedimentary rocks at discrete intervals in Earth history, yet interpreting their significance in the geologic record is complicated by our incomplete knowledge of what their progenitors, hopanoids, do in modern cells. To date, few studies have addressed the breadth of diversity of physiological functions of these lipids and whether those functions are conserved across the hopanoid-producing bacterial phyla. Here, we generated mutants in the filamentous cyanobacterium, Nostoc punctiforme, that are unable to make all hopanoids (shc) or 2-methylhopanoids (hpnP). While the absence of hopanoids impedes growth of vegetative cells at high temperature, the shc mutant grows faster at low temperature. This finding is consistent with hopanoids acting as membrane rigidifiers, a function shared by other hopanoid-producing phyla. Apart from impacting fitness under temperature stress, hopanoids are dispensable for vegetative cells under other stress conditions. However, hopanoids are required for stress tolerance in akinetes, a resting survival cell type. While 2-methylated hopanoids do not appear to contribute to any stress phenotype, total hopanoids and to a lesser extent 2-methylhopanoids were found to promote the formation of cyanophycin granules in akinetes. Finally, although hopanoids support symbiotic interactions between Alphaproteobacteria and plants, they do not appear to facilitate symbiosis between N. punctiforme and the hornwort Anthoceros punctatus. Collectively, these findings support interpreting hopanes as general environmental stress biomarkers. If hopanoid-mediated enhancement of nitrogen-rich storage products turns out to be a conserved phenomenon in other organisms, a better understanding of this relationship may help us parse the enrichment of 2-methylhopanes in the rock record during episodes of disrupted nutrient cycling.
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Affiliation(s)
- J N Ricci
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - R Morton
- Department of Biology, California State University Northridge, Northridge, CA, USA
| | - G Kulkarni
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - M L Summers
- Department of Biology, California State University Northridge, Northridge, CA, USA
| | - D K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
- Howard Hughes Medical Institute, Pasadena, CA, USA
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9
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Talbot HM, Sidgwick FR, Bischoff J, Osborne KA, Rush D, Sherry A, Spencer-Jones CL. Analysis of non-derivatised bacteriohopanepolyols by ultrahigh-performance liquid chromatography/tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:2087-2098. [PMID: 27472174 DOI: 10.1002/rcm.7696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/18/2016] [Accepted: 07/20/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE Traditional investigation of bacteriohopanepolyols (BHPs) has relied on derivatisation by acetylation prior to gas chromatography/mass spectrometry (GC/MS) or liquid chromatography/MS (LC/MS) analysis. Here, modern chromatographic techniques (ultrahigh-performance liquid chromatography (UPLC)) and new column chemistries were tested to develop a method for BHP analysis without the need for derivatisation. METHODS Bacterial culture and sedimentary lipid extracts were analysed using a Waters Acquity Xevo TQ-S triple quadrupole mass spectrometer in positive ion atmospheric pressure chemical ionisation (APCI) mode. Waters BEH C18 and ACE Excel C18 were the central columns evaluated using a binary solvent gradient with 0.1% formic acid in the polar solvent phase in order to optimise performance and selectivity. RESULTS Non-amine BHPs and adenosylhopane showed similar performance on each C18 column; however, BHP-containing terminal amines were only identified eluting from the ultra-inert ACE Excel C18 column. APCI-MS/MS product ion scans revealed significant differences in fragmentation pathways from previous methods for acetylated compounds. The product ions used for targeted multiple reaction monitoring (MRM) are summarised. CONCLUSIONS UPLC/MS/MS analysis using an ACE Excel C18 column produced superior separation for amine-containing BHPs and reduced run times from 60 to 9 min compared with previous methods. Unexpected variations in fragmentation pathways between structural subgroups must be taken into account when optimising MRM transitions for future quantitative studies. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Helen M Talbot
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Frances R Sidgwick
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- Newcastle University Protein and Proteome Analysis (NUPPA), Devonshire Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Juliane Bischoff
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Kate A Osborne
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Darci Rush
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Angela Sherry
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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Tavares TCL, Normando LRO, de Vasconcelos ATR, Gerber AL, Agnez-Lima LF, Melo VMM. Metagenomic analysis of sediments under seaports influence in the Equatorial Atlantic Ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 557-558:888-900. [PMID: 27088626 DOI: 10.1016/j.scitotenv.2016.03.141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 03/18/2016] [Accepted: 03/19/2016] [Indexed: 06/05/2023]
Abstract
Maritime ports are anthropogenic interventions capable of causing serious alterations in coastal ecosystems. In this study, we examined the benthic microbial diversity and community structure under the influence of two maritime ports, Mucuripe (MUC) and Pecém (PEC), at Equatorial Atlantic Ocean in Northeast Brazil. Those seaports differ in architecture, time of functioning, cargo handling and contamination. The microbiomes from MUC and PEC were also compared in silico to 11 other globally distributed marine microbiomes. The comparative analysis of operational taxonomic units (OTUs) retrieved by PCR-DGGE showed that MUC presents greater richness and β diversity of Bacteria and Archaea than PEC. In line with these results, metagenomic analysis showed that MUC and PEC benthic microbial communities share the main common bacterial phyla found in coastal environments, although can be distinguish by greater abundance of Cyanobacteria in MUC and Deltaproteobacteria in PEC. Both ports differed in Archaea composition, being PEC port sediments dominated by Thaumarchaeota. The microbiomes showed little divergence in their potential metabolic pathways, although shifts on the microbial taxonomic signatures involved in nitrogen and sulphur metabolic pathways were observed. The comparative analysis of different benthic marine metagenomes from Brazil, Australia and Mexico grouped them by the geographic location rather than by the type of ecosystem, although at phylum level seaport sediments share a core microbiome constituted by Proteobacteria, Cyanobacteria, Actinobacteria, Tenericuteres, Firmicutes, Bacteriodetes and Euryarchaeota. Our results suggest that multiple physical and chemical factors acting on sediments as a result of at least 60years of port operation play a role in shaping the benthic microbial communities at taxonomic level, but not at functional level.
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Affiliation(s)
- Tallita Cruz Lopes Tavares
- Instituto de Ciências do Mar, Av. Abolição, 3207, 60170-151 Fortaleza, Ceará, Brazil; Laboratório de Ecologia Microbiana e Biotecnologia, Departamento de Biologia, Bloco 909, Centro de Ciências, Campus do Pici, Universidade Federal do Ceará, Av. Humberto Monte, 2775, 60440-554 Fortaleza, Ceará, Brazil
| | - Leonardo Ribeiro Oliveira Normando
- Laboratório de Ecologia Microbiana e Biotecnologia, Departamento de Biologia, Bloco 909, Centro de Ciências, Campus do Pici, Universidade Federal do Ceará, Av. Humberto Monte, 2775, 60440-554 Fortaleza, Ceará, Brazil
| | - Ana Tereza Ribeiro de Vasconcelos
- Laboratório de Bioinformática, Unidade de Genômica Computacional Darcy Fontoura de Almeida, Laboratório Nacional de Computação Científica, 25651-075, Petrópolis, Rio de Janeiro, Brazil
| | - Alexandra Lehmkuhl Gerber
- Laboratório de Bioinformática, Unidade de Genômica Computacional Darcy Fontoura de Almeida, Laboratório Nacional de Computação Científica, 25651-075, Petrópolis, Rio de Janeiro, Brazil
| | - Lucymara Fassarella Agnez-Lima
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, 59072-970 Natal, Rio Grande do Norte, Brazil
| | - Vânia Maria Maciel Melo
- Instituto de Ciências do Mar, Av. Abolição, 3207, 60170-151 Fortaleza, Ceará, Brazil; Laboratório de Ecologia Microbiana e Biotecnologia, Departamento de Biologia, Bloco 909, Centro de Ciências, Campus do Pici, Universidade Federal do Ceará, Av. Humberto Monte, 2775, 60440-554 Fortaleza, Ceará, Brazil.
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Kharbush JJ, Kejriwal K, Aluwihare LI. Distribution and Abundance of Hopanoid Producers in Low-Oxygen Environments of the Eastern Pacific Ocean. MICROBIAL ECOLOGY 2016; 71:401-408. [PMID: 26377203 DOI: 10.1007/s00248-015-0671-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 08/31/2015] [Indexed: 06/05/2023]
Abstract
Hopanoids are bacterial membrane lipid biomarker molecules that feature prominently in the molecular fossil record. In the modern marine water column, recent reports implicate bacteria inhabiting low-oxygen environments as important sources of hopanoids to marine sediments. However, the preliminary biogeography reported by recent studies and the environmental conditions governing such distributions can only be confirmed when the numerical abundance of these organisms is known with more certainty. In this study, we employ two different approaches to examine the quantitative significance of phylogenetically distinct hopanoid producers in low-oxygen environments. First, we develop a novel quantitative PCR (qPCR) assay for the squalene hopene cyclase (sqhC) gene, targeting a subset of hopanoid producers previously identified to be important in the eastern North Pacific Ocean. The results represent the first quantitative gene abundance data of any kind for hopanoid producers in the marine water column and show that these putative alphaproteobacterial hopanoid producers are rare, comprising at most 0.2 % of the total bacterial community in our samples. Second, a complementary analysis of existing low-oxygen metagenomic datasets further examined the generality of the qPCR observation. We find that the dominant sqhC sequences in these metagenomic datasets are associated with phyla such as Nitrospinae rather than Proteobacteria, consistent with the qPCR finding that alphaproteobacterial hopanoid producers are not very abundant in low-oxygen environments. In fact, positive correlations between sqhC gene abundance and environmental parameters in these samples identify nitrite availability as a potentially important factor in the ecology of hopanoid producers that dominate low-oxygen environments.
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Affiliation(s)
- Jenan J Kharbush
- Scripps Institution of Oceanography, UCSD, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Kanchi Kejriwal
- Scripps Institution of Oceanography, UCSD, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Lihini I Aluwihare
- Scripps Institution of Oceanography, UCSD, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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12
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Lopez D. Molecular composition of functional microdomains in bacterial membranes. Chem Phys Lipids 2015; 192:3-11. [PMID: 26320704 DOI: 10.1016/j.chemphyslip.2015.08.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 08/10/2015] [Accepted: 08/24/2015] [Indexed: 12/14/2022]
Abstract
Membranes of eukaryotic cells organize a number of proteins related to signal transduction and membrane trafficking into microdomains, which are enriched in particular lipids, like cholesterol and sphingolipids and are commonly referred as to lipid rafts or membrane rafts. The existence of this type of signaling platforms was traditionally associated with eukaryotic membranes because prokaryotic cells were considered too simple organisms to require a sophisticated organization of their signaling networks. However, the research that have been performed during last years have shown that bacteria organize many signaling transduction processes in Functional Membrane Microdomains (FMMs), which are similar to the lipid rafts that are found in eukaryotic cells. The current knowledge of the existence of FMMs in bacteria is described in this review and the specific structural and biological properties of these membrane microdomains are introduced. The organization of FMMs in bacterial membranes reveals an unexpected level of sophistication in signaling transduction and membrane organization that is unprecedented in bacteria, suggesting that bacteria as more complex organisms than previously considered.
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Affiliation(s)
- Daniel Lopez
- Research Center for Infectious Diseases (ZINF), Institute for Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider Strasse (2), 97080 Würzburg, Germany; Spanish National Center for Biotechnology (CNB), Campus de Cantoblanco, Darwin 3, 28049 Madrid, Spain.
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13
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Abstract
An interesting concept in the organization of cellular membranes is the proposed existence of lipid rafts. Membranes of eukaryotic cells organize signal transduction proteins into membrane rafts or lipid rafts that are enriched in particular lipids such as cholesterol and are important for the correct functionality of diverse cellular processes. The assembly of lipid rafts in eukaryotes has been considered a fundamental step during the evolution of cellular complexity, suggesting that bacteria and archaea were organisms too simple to require such a sophisticated organization of their cellular membranes. However, it was recently discovered that bacteria organize many signal transduction, protein secretion, and transport processes in functional membrane microdomains, which are equivalent to the lipid rafts of eukaryotic cells. This review contains the most significant advances during the last 4 years in understanding the structural and biological role of lipid rafts in bacteria. Furthermore, this review shows a detailed description of a number of molecular and genetic approaches related to the discovery of bacterial lipid rafts as well as an overview of the group of tentative lipid-protein and protein-protein interactions that give consistency to these sophisticated signaling platforms. Additional data suggesting that lipid rafts are widely distributed in bacteria are presented in this review. Therefore, we discuss the available techniques and optimized protocols for the purification and analysis of raft-associated proteins in various bacterial species to aid in the study of bacterial lipid rafts in other laboratories that could be interested in this topic. Overall, the discovery of lipid rafts in bacteria reveals a new level of sophistication in signal transduction and membrane organization that was unexpected for bacteria and shows that bacteria are more complex than previously appreciated.
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Affiliation(s)
- Marc Bramkamp
- Department of Biology I, University of Munich (LMU), Planegg/Martinsried, Germany
| | - Daniel Lopez
- Research Center for Infectious Diseases ZINF, University of Würzburg, Würzburg, Germany
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Englund E, Pattanaik B, Ubhayasekera SJK, Stensjö K, Bergquist J, Lindberg P. Production of squalene in Synechocystis sp. PCC 6803. PLoS One 2014; 9:e90270. [PMID: 24625633 PMCID: PMC3953072 DOI: 10.1371/journal.pone.0090270] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 01/26/2014] [Indexed: 12/22/2022] Open
Abstract
In recent years, there has been an increased interest in the research and development of sustainable alternatives to fossil fuels. Using photosynthetic microorganisms to produce such alternatives is advantageous, since they can achieve direct conversion of carbon dioxide from the atmosphere into the desired product, using sunlight as the energy source. Squalene is a naturally occurring 30-carbon isoprenoid, which has commercial use in cosmetics and in vaccines. If it could be produced sustainably on a large scale, it could also be used instead of petroleum as a raw material for fuels and as feedstock for the chemical industry. The unicellular cyanobacterium Synechocystis PCC 6803 possesses a gene, slr2089, predicted to encode squalene hopene cyclase (Shc), an enzyme converting squalene into hopene, the substrate for forming hopanoids. Through inactivation of slr2089 (shc), we explored the possibility to produce squalene using cyanobacteria. The inactivation led to accumulation of squalene, to a level over 70 times higher than in wild type cells, reaching 0.67 mg OD750−1 L−1. We did not observe any significant growth deficiency in the Δshc strain compared to the wild type Synechocystis, even at high light conditions, suggesting that the observed squalene accumulation was not detrimental to growth, and that formation of hopene by Shc is not crucial for growth under normal conditions, nor for high-light stress tolerance. Effects of different light intensities and growth stages on squalene accumulation in the Δshc strain were investigated. We also identified a gene, sll0513, as a putative squalene synthase in Synechocystis, and verified its function by inactivation. In this work, we show that it is possible to use the cyanobacterium Synechocystis to generate squalene, a hydrocarbon of commercial interest and a potential biofuel. We also report the first identification of a squalene hopene cyclase, and the second identification of squalene synthase, in cyanobacteria.
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Affiliation(s)
- Elias Englund
- Microbial Chemistry, Department of Chemistry, Ångström and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Bagmi Pattanaik
- Microbial Chemistry, Department of Chemistry, Ångström and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry, Ångström and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonas Bergquist
- Analytical Chemistry, Department of Chemistry, BMC and Science for Life Laboratory, Uppsala, Sweden
| | - Pia Lindberg
- Microbial Chemistry, Department of Chemistry, Ångström and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail:
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15
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Jahnke LL, Turk-Kubo KA, N Parenteau M, Green SJ, Kubo MDY, Vogel M, Summons RE, Des Marais DJ. Molecular and lipid biomarker analysis of a gypsum-hosted endoevaporitic microbial community. GEOBIOLOGY 2014; 12:62-82. [PMID: 24325308 DOI: 10.1111/gbi.12068] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 10/28/2013] [Indexed: 06/03/2023]
Abstract
Modern evaporitic microbial ecosystems are important analogs for understanding the record of earliest life on Earth. Although mineral-depositing shallow-marine environments were prevalent during the Precambrian, few such environments are now available today for study. We investigated the molecular and lipid biomarker composition of an endoevaporitic gypsarenite microbial mat community in Guerrero Negro, Mexico. The 16S ribosomal RNA gene-based phylogenetic analyses of this mat corroborate prior observations indicating that characteristic layered microbial communities colonize gypsum deposits world-wide despite considerable textural and morphological variability. Membrane fatty acid analysis of the surface tan/orange and lower green mat crust layers indicated cell densities of 1.6 × 10(9) and 4.2 × 10(9) cells cm(-3) , respectively. Several biomarker fatty acids, ∆7,10-hexadecadienoic, iso-heptadecenoic, 10-methylhexadecanoic, and a ∆12-methyloctadecenoic, correlated well with distributions of Euhalothece, Stenotrophomonas, Desulfohalobium, and Rhodobacterales, respectively, revealed by the phylogenetic analyses. Chlorophyll (Chl) a and cyanobacterial phylotypes were present at all depths in the mat. Bacteriochlorophyl (Bchl) a and Bchl c were first detected in the oxic-anoxic transition zone and increased with depth. A series of monomethylalkanes (MMA), 8-methylhexadecane, 8-methylheptadecane, and 9-methyloctadecane were present in the surface crust but increased in abundance in the lower anoxic layers. The MMA structures are similar to those identified previously in cultures of the marine Chloroflexus-like organism 'Candidatus Chlorothrix halophila' gen. nov., sp. nov., and may represent the Bchl c community. Novel 3-methylhopanoids were identified in cultures of marine purple non-sulfur bacteria and serve as a probable biomarker for this group in the lower anoxic purple and olive-black layers. Together microbial culture and environmental analyses support novel sources for lipid biomarkers in gypsum crust mats.
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Affiliation(s)
- L L Jahnke
- Exobiology Branch, NASA, Ames Research Center, Moffett Field, CA, USA
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Ricci JN, Coleman ML, Welander PV, Sessions AL, Summons RE, Spear JR, Newman DK. Diverse capacity for 2-methylhopanoid production correlates with a specific ecological niche. ISME JOURNAL 2013; 8:675-684. [PMID: 24152713 DOI: 10.1038/ismej.2013.191] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 09/04/2013] [Accepted: 09/22/2013] [Indexed: 12/20/2022]
Abstract
Molecular fossils of 2-methylhopanoids are prominent biomarkers in modern and ancient sediments that have been used as proxies for cyanobacteria and their main metabolism, oxygenic photosynthesis. However, substantial culture and genomic-based evidence now indicates that organisms other than cyanobacteria can make 2-methylhopanoids. Because few data directly address which organisms produce 2-methylhopanoids in the environment, we used metagenomic and clone library methods to determine the environmental diversity of hpnP, the gene encoding the C-2 hopanoid methylase. Here we show that hpnP copies from alphaproteobacteria and as yet uncultured organisms are found in diverse modern environments, including some modern habitats representative of those preserved in the rock record. In contrast, cyanobacterial hpnP genes are rarer and tend to be localized to specific habitats. To move beyond understanding the taxonomic distribution of environmental 2-methylhopanoid producers, we asked whether hpnP presence might track with particular variables. We found hpnP to be significantly correlated with organisms, metabolisms and environments known to support plant-microbe interactions (P-value<10(-6)); in addition, we observed diverse hpnP types in closely packed microbial communities from other environments, including stromatolites, hot springs and hypersaline microbial mats. The common features of these niches indicate that 2-methylhopanoids are enriched in sessile microbial communities inhabiting environments low in oxygen and fixed nitrogen with high osmolarity. Our results support the earlier conclusion that 2-methylhopanoids are not reliable biomarkers for cyanobacteria or any other taxonomic group, and raise the new hypothesis that, instead, they are indicators of a specific environmental niche.
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Affiliation(s)
- Jessica N Ricci
- Division of Biology, California Institute of Technology, MC156-29, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Maureen L Coleman
- Division of Biology, California Institute of Technology, MC156-29, 1200 E. California Boulevard, Pasadena, CA 91125, USA.,6Present address: Department of the Geophysical Sciences, University of Chicago, 5734 S. Ellis Avenue, Chicago, IL 60637
| | - Paula V Welander
- Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, E25-633, Cambridge, 02139, MA, USA.,7Present address: Department of Environmental Earth System Science, Stanford University, 473 Via Ortega Road, Rm 140, Stanford, CA 94305
| | - Alex L Sessions
- Division of Geological and Planetary Sciences, California Institute of Technology, MC100-23, 1200 E. California Boulevard, Pasadena, 91125, CA, USA
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, E25-633, Cambridge, 02139, MA, USA
| | - John R Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, 80401, CO, USA
| | - Dianne K Newman
- Division of Biology, California Institute of Technology, MC156-29, 1200 E. California Boulevard, Pasadena, CA 91125, USA, . .,Division of Geological and Planetary Sciences, California Institute of Technology, MC100-23, 1200 E. California Boulevard, Pasadena, 91125, CA, USA. .,Howard Hughes Medical Institute, MC156-29, 1200 E. California Boulevard, Pasadena, 91125, CA, USA.
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17
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Composite bacterial hopanoids and their microbial producers across oxygen gradients in the water column of the California Current. Appl Environ Microbiol 2013; 79:7491-501. [PMID: 24077702 DOI: 10.1128/aem.02367-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hopanoids are pentacyclic triterpenoid lipids produced by many prokaryotes as cell membrane components. The structural variations of composite hopanoids, or bacteriohopanepolyols (BHPs), produced by various bacterial genera make them potentially useful molecular biomarkers of bacterial communities and metabolic processes in both modern and ancient environments. Building on previous work suggesting that organisms in low-oxygen environments are important contributors to BHP production in the marine water column and that there may be physiological roles for BHPs specific to these environments, this study investigated the relationship between trends in BHP structural diversity and abundance and the genetic diversity of BHP producers for the first time in a low-oxygen environment of the Eastern Tropical North Pacific. Amplification of the hopanoid biosynthesis gene for squalene hopene cyclase (sqhC) indicated far greater genetic diversity than would be predicted by examining BHP structural diversity alone and that greater sqhC genetic diversity exists in the marine environment than is represented by cultured representatives and most marine metagenomes. In addition, the genetic relationships in this data set suggest microaerophilic environments as potential "hot spots" of BHP production. Finally, structural analysis of BHPs showed that an isomer of the commonly observed BHP bacteriohopanetetrol may be linked to a producer that is more abundant in low-oxygen environments. Results of this study increase the known diversity of BHP producers and provide a detailed phylogeny with implications for the role of hopanoids in modern bacteria, as well as the evolutionary history of hopanoid biosynthesis, both of which are important considerations for future interpretations of the marine sedimentary record.
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18
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Functional convergence of hopanoids and sterols in membrane ordering. Proc Natl Acad Sci U S A 2012; 109:14236-40. [PMID: 22893685 DOI: 10.1073/pnas.1212141109] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Liquid-ordered phases are one of two biochemically active membrane states, which until now were thought to be a unique consequence of the interactions between eukaryotic membrane lipids. The formation of a liquid-ordered phase depends crucially on the ordering properties of sterols. However, it is not known whether this capacity exists in organisms that lack sterols, such as bacteria. We show that diplopterol, the simplest bacterial hopanoid, has similar properties and that hopanoids are bacterial "sterol surrogates" with the ability to order saturated lipids and to form a liquid-ordered phase in model membranes. These observations suggest that the evolution of an ordered biochemically active liquid membrane could have evolved before the oxygenation of Earth's surface and the emergence of sterols.
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Sáenz JP, Waterbury JB, Eglinton TI, Summons RE. Hopanoids in marine cyanobacteria: probing their phylogenetic distribution and biological role. GEOBIOLOGY 2012; 10:311-319. [PMID: 22329628 DOI: 10.1111/j.1472-4669.2012.00318.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Cyanobacteria are key players in the global carbon and nitrogen cycles and are thought to have been responsible for the initial rise of atmospheric oxygen during the Neoarchean. There is evidence that a class of membrane lipids known as hopanoids serve as biomarkers for bacteria, including many cyanobacteria, in the environment and in the geologic record. However, the taxonomic distributions and physiological roles of hopanoids in marine cyanobacteria remain unclear. We examined the distribution of bacteriohopanepolyols (BHPs) in a collection of marine cyanobacterial enrichment and pure cultures and investigated the relationship between the cellular abundance of BHPs and nitrogen limitation in Crocosphaera watsonii, a globally significant nitrogen-fixing cyanobacterium. In pure culture, BHPs were only detected in species capable of nitrogen fixation, implicating hopanoids as potential markers for diazotrophy in the oceans. The enrichment cultures we examined exhibited a higher degree of BHP diversity, demonstrating that there are presently unaccounted for marine bacteria, possibly cyanobacteria, associated with the production of a range of BHP structures. Crocosphaera watsonii exhibited high membrane hopanoid content consistent with the idea that hopanoids have an important effect on the bulk physical properties of the membrane. However, the abundance of BHPs in C. watsonii did not vary considerably when grown under nitrogen-limiting and nitrogen-replete conditions, suggesting that the role of hopanoids in this organism is not directly related to the physiology of nitrogen fixation. Alternatively, we propose that high hopanoid content in C. watsonii may serve to reduce membrane permeability to antimicrobial toxins in the environment.
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Affiliation(s)
- J P Sáenz
- Joint Program in Chemical Oceanography, Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, Cambridge, MA, USA.
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Garby TJ, Walter MR, Larkum AWD, Neilan BA. Diversity of cyanobacterial biomarker genes from the stromatolites of Shark Bay, Western Australia. Environ Microbiol 2012; 15:1464-75. [PMID: 22712472 DOI: 10.1111/j.1462-2920.2012.02809.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Families of closely related chemical compounds, which are relatively resistant to degradation, are often used as biomarkers to help trace the evolutionary history of early groups of organisms and the environments in which they lived. Biomarkers derived from hopanoid variations are particularly useful in determining bacterial community compositions. 2-Methylhopananoids have been thought to be diagnostic for cyanobacteria, and 2-methylhopanes in the geological record are taken as evidence for the presence of cyanobacteria-containing communities at the time of sediment deposition. Recently, however, doubt has been cast on the validity of 2-methylhopanes as cyanobacterial biomarkers, since non-cyanobacterial species have been shown to produce significant amounts of 2-methylhopanoids. This study examines the diversity of hpnP, the hopanoid biosynthesis gene coding for the enzyme that methylates hopanoids at the C2 position. Genomic DNA isolated from stromatolite-associated pustular and smooth microbial mat samples from Shark Bay, Western Australia, was analysed for bacterial diversity, and used to construct an hpnP clone library. A total of 117 partial hpnP clones were sequenced, representing 12 operational taxonomic units (OTUs). Phylogenetic analysis showed that 11 of these OTUs, representing 115 sequences, cluster within the cyanobacterial clade. We conclude that the dominant types of microorganisms with the detected capability of producing 2-methylhopanoids within pustular and smooth microbial mats in Shark Bay are cyanobacteria.
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Affiliation(s)
- Tamsyn J Garby
- Australian Centre for Astrobiology and School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
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Abstract
Hopanoids and sterols are members of a large group of cyclic triterpenoic compounds that have important functions in many prokaryotic and eukaryotic organisms. They are biochemically synthesized from linear precursors (squalene, 2,3-oxidosqualene) in only one enzymatic step that is catalyzed by squalene-hopene cyclase (SHC) or oxidosqualene cyclase (OSC). SHCs and OSCs are related in amino acid sequences and probably are derived from a common ancestor. The SHC reaction requires the formation of five ring structures, 13 covalent bonds, and nine stereo centers and therefore is one of the most complex one-step enzymatic reactions. We summarize the knowledge of the properties of triterpene cyclases and details of the reaction mechanism of Alicyclobacillus acidocaldarius SHC. Properties of other SHCs are included.
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Affiliation(s)
| | - Dieter Jendrossek
- Institute for Microbiology, University of Stuttgart, Stuttgart, Germany
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22
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Zhang F, She Y, Zheng Y, Zhou Z, Kong S, Hou D. Molecular biologic techniques applied to the microbial prospecting of oil and gas in the Ban 876 gas and oil field in China. Appl Microbiol Biotechnol 2010; 86:1183-94. [PMID: 20107985 DOI: 10.1007/s00253-009-2426-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2009] [Revised: 12/14/2009] [Accepted: 12/24/2009] [Indexed: 11/26/2022]
Abstract
Currently, molecular biologic techniques achieve a great development in studies of soil samples. The objective of this research is to improve methods for microbial prospecting of oil and gas by applying culture-independent techniques to soil sampled from above a known oil and gas field. Firstly, the community structure of soil bacteria above the Ban 876 Gas and Oil Field was analyzed based on 16S rRNA gene clone libraries. The soil bacteria communities were consistently different along the depth; however, Chloroflexi and Gemmatimonadetes were predominant and methanotrophs were minor in both bacteria libraries (DGS1 and DGS2). Secondly, the numbers of methane-oxidizing bacteria, quantified using a culture-dependent procedure and culture-independent group-specific real-time PCR (RT-PCR), respectively, were inconsistent with a quantify variance of one or two orders of magnitude. Special emphasis was given to the counting advantages of RT-PCR based on the methanotrophic pmoA gene. Finally, the diversity and distribution of methanotrophic communities in the soil samples were analyzed by constructing clone libraries of functional gene. All 508-bp inserts in clones phylogenetically belonged to the methanotrophic pmoA gene with similarities from 83% to 100%. However, most of the similarities were below 96%. Five clone libraries of methanotrophs clearly showed that the anomalous methanotrophs (Methylosinus and Methylocystis) occupy the studied area.
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Affiliation(s)
- Fan Zhang
- The Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, Ministry of Education, Beijing, China
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23
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Pearson A, Leavitt WD, Sáenz JP, Summons RE, Tam MCM, Close HG. Diversity of hopanoids and squalene-hopene cyclases across a tropical land-sea gradient. Environ Microbiol 2009; 11:1208-23. [DOI: 10.1111/j.1462-2920.2008.01817.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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