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Bourhane Z, Cagnon C, Castañeda C, Rodríguez-Ochoa R, Álvaro-Fuentes J, Cravo-Laureau C, Duran R. Vertical organization of microbial communities in Salineta hypersaline wetland, Spain. Front Microbiol 2023; 14:869907. [PMID: 36778872 PMCID: PMC9911865 DOI: 10.3389/fmicb.2023.869907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 01/03/2023] [Indexed: 01/28/2023] Open
Abstract
Microbial communities inhabiting hypersaline wetlands, well adapted to the environmental fluctuations due to flooding and desiccation events, play a key role in the biogeochemical cycles, ensuring ecosystem service. To better understand the ecosystem functioning, we studied soil microbial communities of Salineta wetland (NE Spain) in dry and wet seasons in three different landscape stations representing situations characteristic of ephemeral saline lakes: S1 soil usually submerged, S2 soil intermittently flooded, and S3 soil with halophytes. Microbial community composition was determined according to different redox layers by 16S rRNA gene barcoding. We observed reversed redox gradient, negative at the surface and positive in depth, which was identified by PERMANOVA as the main factor explaining microbial distribution. The Pseudomonadota, Gemmatimonadota, Bacteroidota, Desulfobacterota, and Halobacteriota phyla were dominant in all stations. Linear discriminant analysis effect size (LEfSe) revealed that the upper soil surface layer was characterized by the predominance of operational taxonomic units (OTUs) affiliated to strictly or facultative anaerobic halophilic bacteria and archaea while the subsurface soil layer was dominated by an OTU affiliated to Roseibaca, an aerobic alkali-tolerant bacterium. In addition, the potential functional capabilities, inferred by PICRUSt2 analysis, involved in carbon, nitrogen, and sulfur cycles were similar in all samples, irrespective of the redox stratification, suggesting functional redundancy. Our findings show microbial community changes according to water flooding conditions, which represent useful information for biomonitoring and management of these wetlands whose extreme aridity and salinity conditions are exposed to irreversible changes due to human activities.
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Affiliation(s)
- Zeina Bourhane
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Christine Cagnon
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Rafael Rodríguez-Ochoa
- Departamento de Medio Ambiente y Ciencias del Suelo, Universidad de Lleida, Lleida, Spain
| | | | | | - Robert Duran
- Université de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, Pau, France
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Antiscalants Used in Seawater Desalination: Biodegradability and Effects on Microbial Diversity. Microorganisms 2022; 10:microorganisms10081580. [PMID: 36013998 PMCID: PMC9414044 DOI: 10.3390/microorganisms10081580] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2022] Open
Abstract
Antiscalants are organic polymers widely used for scale inhibition in seawater desalination. While they are susceptible to biodegradation, they provide nutrients for bacterial cell growth and energy for the microbes that assimilate and degrade them. This paper shows the biodegradability of three commercial antiscalants (polyacrylate—CA, polyphosphonate—PP, and carboxylated dendrimers—DN) applied in seawater reverse osmosis desalination (SWRO) as well as analyzing the antiscalant’s effects on microbial diversity using microbial cultures grown in seawater, under semi-continuous batch conditions. Nutritional uptake and contribution of the antiscalants to microbial growth were investigated by measuring DOC, TDN, NO3−, NO2−, PO4−, NH4+, and TP of the filtered samples of the incubated batch, twice a month, for twelve months. The microbial community was estimated by 16S rRNA sequencing. The main changes in the microbial communities were determined by the incubation period. However, bacterial orders of the antiscalant treatments differed significantly from the control treatment, namely Planctomycetales, Clostridiales, Sphingobacteriales, Rhodobacterales, and Flavobacteriales, and other unclassified bacterial orders, which were found in various relative abundances dependent on incubation times. The results showed the PP antiscalant to be the least biodegradable and to have the least effect on the bacterial community composition compared to the control. This result emphasizes the need to reassess the suitability criteria of antiscalants, and to further monitor their long-term environmental effects.
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3
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Wiegand S, Rast P, Kallscheuer N, Jogler M, Heuer A, Boedeker C, Jeske O, Kohn T, Vollmers J, Kaster AK, Quast C, Glöckner FO, Rohde M, Jogler C. Analysis of Bacterial Communities on North Sea Macroalgae and Characterization of the Isolated Planctomycetes Adhaeretor mobilis gen. nov., sp. nov., Roseimaritima multifibrata sp. nov., Rosistilla ulvae sp. nov. and Rubripirellula lacrimiformis sp. nov. Microorganisms 2021; 9:microorganisms9071494. [PMID: 34361930 PMCID: PMC8303584 DOI: 10.3390/microorganisms9071494] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 12/31/2022] Open
Abstract
Planctomycetes are bacteria that were long thought to be unculturable, of low abundance, and therefore neglectable in the environment. This view changed in recent years, after it was shown that members of the phylum Planctomycetes can be abundant in many aquatic environments, e.g., in the epiphytic communities on macroalgae surfaces. Here, we analyzed three different macroalgae from the North Sea and show that Planctomycetes is the most abundant bacterial phylum on the alga Fucus sp., while it represents a minor fraction of the surface-associated bacterial community of Ulva sp. and Laminaria sp. Especially dominant within the phylum Planctomycetes were Blastopirellula sp., followed by Rhodopirellula sp., Rubripirellula sp., as well as other Pirellulaceae and Lacipirellulaceae, but also members of the OM190 lineage. Motivated by the observed abundance, we isolated four novel planctomycetal strains to expand the collection of species available as axenic cultures since access to different strains is a prerequisite to investigate the success of planctomycetes in marine environments. The isolated strains constitute four novel species belonging to one novel and three previously described genera in the order Pirellulales, class Planctomycetia, phylum Planctomycetes.
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Affiliation(s)
- Sandra Wiegand
- Department of Microbiology, Radboud University, 6525 AJ Nijmegen, The Netherlands; (S.W.); (N.K.); (T.K.)
- Institute for Biological Interfaces 5 (IBG-5), Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (J.V.); (A.-K.K.)
| | - Patrick Rast
- Leibniz Institute DSMZ, 38124 Braunschweig, Germany; (P.R.); (A.H.); (C.B.); (O.J.)
| | - Nicolai Kallscheuer
- Department of Microbiology, Radboud University, 6525 AJ Nijmegen, The Netherlands; (S.W.); (N.K.); (T.K.)
- Institute of Bio- and Geosciences, Biotechnology (IBG-1), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Mareike Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich-Schiller University, 07743 Jena, Germany;
| | - Anja Heuer
- Leibniz Institute DSMZ, 38124 Braunschweig, Germany; (P.R.); (A.H.); (C.B.); (O.J.)
| | - Christian Boedeker
- Leibniz Institute DSMZ, 38124 Braunschweig, Germany; (P.R.); (A.H.); (C.B.); (O.J.)
| | - Olga Jeske
- Leibniz Institute DSMZ, 38124 Braunschweig, Germany; (P.R.); (A.H.); (C.B.); (O.J.)
| | - Timo Kohn
- Department of Microbiology, Radboud University, 6525 AJ Nijmegen, The Netherlands; (S.W.); (N.K.); (T.K.)
| | - John Vollmers
- Institute for Biological Interfaces 5 (IBG-5), Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (J.V.); (A.-K.K.)
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5 (IBG-5), Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany; (J.V.); (A.-K.K.)
| | - Christian Quast
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany;
| | - Frank Oliver Glöckner
- Alfred Wegener Institute Bremerhaven, MARUM, University of Bremen, 28359 Bremen, Germany;
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
| | - Christian Jogler
- Department of Microbiology, Radboud University, 6525 AJ Nijmegen, The Netherlands; (S.W.); (N.K.); (T.K.)
- Department of Microbial Interactions, Institute of Microbiology, Friedrich-Schiller University, 07743 Jena, Germany;
- Correspondence: ; Tel.: +49-364-194-9301
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Rivas-Marin E, Wiegand S, Kallscheuer N, Jogler M, Peeters SH, Heuer A, Jetten MSM, Boedeker C, Rohde M, Devos DP, Jogler C. Thalassoglobus polymorphus sp. nov., a novel Planctomycete isolated close to a public beach of Mallorca Island. Antonie Van Leeuwenhoek 2020; 113:1915-1926. [PMID: 32583191 PMCID: PMC7716918 DOI: 10.1007/s10482-020-01437-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023]
Abstract
Access to axenic cultures is crucial to extend the knowledge of the biology, lifestyle or metabolic capabilities of bacteria from different phyla. The phylum Planctomycetes is an excellent example since its members display an unusual cell biology and complex lifestyles. As a contribution to the current collection of axenic planctomycete cultures, here we describe strain Mal48T isolated from phytoplankton material sampled at the coast of S'Arenal close to Palma de Mallorca (Spain). The isolated strain shows optimal growth at pH 7.0-7.5 and 30 °C and exhibits typical features of Planctomycetes. Cells of the strain are spherical to pear-shaped, divide by polar budding with daughter cells showing the same shape as the mother cell, tend to aggregate, display a stalk and produce matrix or fimbriae. Strain Mal48T showed 95.8% 16S rRNA gene sequence similarity with the recently described Thalassoglobus neptunius KOR42T. The genome sequence of the novel isolate has a size of 6,357,355 bp with a G+C content of 50.3%. A total of 4874 protein-coding genes, 41 tRNA genes and 2 copies of the 16S rRNA gene are encoded in the genome. Based on phylogenetic, morphological and physiological analyses, we conclude that strain Mal48T (= DSM 100737T = LMG 29019T) should be classified as the type strain of a new species in the genus Thalassoglobus, for which the name Thalassoglobus polymorphus sp. nov. is proposed.
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Affiliation(s)
- Elena Rivas-Marin
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Seville, Spain
| | - Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | - Mareike Jogler
- Department of Microbial Interactions, Friedrich-Schiller University, Jena, Germany
| | - Stijn H Peeters
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Seville, Spain
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Friedrich-Schiller University, Jena, Germany.
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Wu S, Liu Y, Lei L, Zhang H. Endogenous antisense walR RNA modulates biofilm organization and pathogenicity of Enterococcus faecalis. Exp Ther Med 2020; 21:69. [PMID: 33365069 PMCID: PMC7716642 DOI: 10.3892/etm.2020.9501] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 06/10/2020] [Indexed: 02/05/2023] Open
Abstract
Enterococcus faecalis (E. faecalis) is regarded as the major pathogen for persistent periapical periodontitis. The aim of the present study was to investigate the role of antisense walR RNA in the regulation of adjacent downstream genes. Reverse transcription-PCR assays were performed to validate walR. Adjacent downstream genes walK, EF1195, EF1196, and EF1197 were co-transcribed and detect antisense walR RNA. Northern blotting and 5'-rapid amplification of cDNA ends (5'-RACE) assays were conducted to detect and confirm a novel walR antisense (ASwalR) RNA. ASwalR overexpression mutants were constructed, and the biofilm biomass was determined using a crystal violet microtiter assay. The present study detected and confirmed a 550-bp noncoding antisense RNA with the potential to attenuate the activities of the essential response regulator WalR. The levels of antisense walR RNA transcripts were inversely associated with the production of WalR protein. It was showed that overexpression of ASwalR leads to reduced biofilm formation and exopolysaccharide synthesis. Furthermore, the pathogenicity of E. faecalis was markedly decreased by ASwalR overexpression in an in vivo periapical periodontitis model. In summary, the present study detected a novel antisense walR RNA that leads to a reduction in biofilm formation and the pathogenicity of E. faecalis. Collectively, the data suggest a role for ASwalR as a post-transcriptional modulator of the WalR regulator in E. faecalis.
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Affiliation(s)
- Shizhou Wu
- Department of Orthopedics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China.,State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, P.R. China.,Department of Advanced Oral Sciences and Therapeutics, University of Maryland School of Dentistry, Baltimore, MD 21201, USA
| | - Yunjie Liu
- West China School of Public Health, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Lei Lei
- State Key Laboratory of Oral Diseases, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Hui Zhang
- Department of Orthopedics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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Stieleria varia sp. nov., isolated from wood particles in the Baltic Sea, constitutes a novel species in the family Pirellulaceae within the phylum Planctomycetes. Antonie van Leeuwenhoek 2020; 113:1953-1963. [PMID: 32797359 PMCID: PMC7717043 DOI: 10.1007/s10482-020-01456-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023]
Abstract
Species belonging to the bacterial phylum Planctomycetes are ubiquitous members of the microbial communities in aquatic environments and are frequently isolated from various biotic and abiotic surfaces in marine and limnic water bodies. Planctomycetes have large genomes of up to 12.4 Mb, follow complex lifestyles and display an uncommon cell biology; features which motivate the investigation of members of this phylum in greater detail. As a contribution to the current collection of axenic cultures of Planctomycetes, we here describe strain Pla52T isolated from wood particles in the Baltic Sea. Phylogenetic analysis places the strain in the family Pirellulaceae and suggests two species of the recently described genus Stieleria as current closest neighbours. Strain Pla52nT shows typical features of members of the class Planctomycetia, including division by polar budding and the presence of crateriform structures. Colonies of strain Pla52nT have a light orange colour, which is an unusual pigmentation compared to the majority of members in the phylum, which show either a pink to red pigmentation or entirely lack pigmentation. Optimal growth of strain Pla52nT at 33 °C and pH 7.5 indicates a mesophilic (i.e. with optimal growth between 20 and 45 °C) and neutrophilic growth profile. The strain is an aerobic heterotroph with motile daughter cells. Its genome has a size of 9.6 Mb and a G + C content of 56.0%. Polyphasic analyses justify delineation of the strain from described species within the genus Stieleria. Therefore, we conclude that strain Pla52nT = LMG 29463T = VKM B-3447T should be classified as the type strain of a novel species, for which we propose the name Stieleria varia sp. nov.
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7
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Yang Y, Yang Y, Fan Q, Huang Z, Li J, Wu Q, Tang X, Ding J, Han N, Xu B. Molecular and Biochemical Characterization of Salt-Tolerant Trehalose-6-Phosphate Hydrolases Identified by Screening and Sequencing Salt-Tolerant Clones From the Metagenomic Library of the Gastrointestinal Tract. Front Microbiol 2020; 11:1466. [PMID: 32733411 PMCID: PMC7358406 DOI: 10.3389/fmicb.2020.01466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/04/2020] [Indexed: 11/13/2022] Open
Abstract
The exploration and utilization of microbial salt-tolerant enzymatic and genetic resources are of great significance in the field of biotechnology and for the research of the adaptation of microorganisms to extreme environments. The presence of new salt-tolerant genes and enzymes in the microbial metagenomic library of the gastrointestinal tract has been confirmed through metagenomic technology. This paper aimed to identify and characterize enzymes that confer salt tolerance in the gastrointestinal tract microbe. By screening the fecal metagenomic library, 48 salt-tolerant clones were detected, of which 10 salt-tolerant clones exhibited stronger tolerance to 7% (wt/vol) NaCl and stability in different concentrations of NaCl [5%-9% (wt/vol)]. High-throughput sequencing and biological information analysis showed that 91 potential genes encoded proteins and enzymes that were widely involved in salt tolerance. Furthermore, two trehalose-6-phosphate hydrolase genes, namely, tre_P2 and tre_P3, were successfully cloned and expressed in Escherichia coli BL21 (DE3). By virtue of the substrate of p-nitrophenyl-α-D-glucopyranoside (pNPG) which can be specifically hydrolyzed by trehalose-6-phosphate hydrolase to produce glucose and p-nitrophenol, the two enzymes can act optimally at pH 7.5 and 30°C. Steady-state kinetics with pNPG showed that the K M and K cat values were 15.63 mM and 10.04 s-1 for rTRE_P2 and 12.51 mM and 10.71 s-1 for rTRE_P3, respectively. Characterization of enzymatic properties demonstrated that rTRE_P2 and rTRE_P3 were salt-tolerant. The enzymatic activity increased with increasing NaCl concentration, and the maximum activities of rTRE_P2 and rTRE_P3 were obtained at 4 and 3 M NaCl, respectively. The activities of rTRE_P2 increased by approximately 43-fold even after 24 h of incubation with 5 M NaCl. This study is the first to report the identification as well as molecular and biochemical characterization of salt-tolerant trehalose-6-phosphate hydrolase from the metagenomic library of the gastrointestinal tract. Results indicate the existence of numerous salt-tolerant genes and enzymes in gastrointestinal microbes and provide new insights into the salt-tolerant mechanisms in the gastrointestinal environment.
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Affiliation(s)
- Yanxia Yang
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Yunjuan Yang
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Qin Fan
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Zunxi Huang
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Junjun Li
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Qian Wu
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Xianghua Tang
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Junmei Ding
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Nanyu Han
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Bo Xu
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
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Frank H, Fussmann KE, Rahav E, Bar Zeev E. Chronic effects of brine discharge form large-scale seawater reverse osmosis desalination facilities on benthic bacteria. WATER RESEARCH 2019; 151:478-487. [PMID: 30641463 DOI: 10.1016/j.watres.2018.12.046] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/15/2018] [Accepted: 12/08/2018] [Indexed: 06/09/2023]
Abstract
Seawater desalination facilities continuously discharge hyper-saline brine into the coastal environment which often flows as a concentrated plume over the seafloor, hence possibly impacting benthic microorganisms. Yet, the effects of brine discharge from desalination plants on benthic bacteria, key players in biodegradation of organic material and nutrient recycling is unknown. In this study, we tested the chronic (years) effects of brine discharge from three large-scale desalination facilities on the abundance, metabolic activity and community composition of benthic bacteria. To this end, four sampling campaigns were carried at the outfall areas of the Ashkelon, Sorek and Hadera desalination facilities. The effects of the brine were compared to corresponding reference stations which were not influenced by the brine (i.e., water temperature and salinity). Our sampling data indicate that bacterial abundance and activity that includes bacterial growth efficiency were 1.3-2.6-fold higher at the outfall area than the reference station. Concomitant analysis pointed out that the bacterial community structure at the brine discharge area was also different than the reference station, yet varied between each desalination facility. Our results demonstrate that the impact of brine effluent from desalination facilities on benthic bacteria are site-specific and localized (<1.4 Km2) around the discharge point. Namely, that the effects on benthic bacteria are prominent at the brine mixing zone and change according to the discharge method used to disperse the brine as well as local stressors (e.g., eutrophication and elevated water temperature). Our results contribute new insights on the effects of desalination-brine to benthic microbes, while providing scientifically-based aspects on the ecological impacts of brine dispersion for decision makers.
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Affiliation(s)
- Hila Frank
- Zuckerberg Institute for Water Research (ZIWR), The Jacob Blaustein Institutes for Desert Research (BIDR) Ben-Gurion University of the Negev, 84990, Israel; Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, 8030, Israel
| | - Katarina E Fussmann
- Zuckerberg Institute for Water Research (ZIWR), The Jacob Blaustein Institutes for Desert Research (BIDR) Ben-Gurion University of the Negev, 84990, Israel; Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, 8030, Israel
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, 8030, Israel.
| | - Edo Bar Zeev
- Zuckerberg Institute for Water Research (ZIWR), The Jacob Blaustein Institutes for Desert Research (BIDR) Ben-Gurion University of the Negev, 84990, Israel.
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9
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Guo M, Yang R, Huang C, Liao Q, Fan G, Sun C, Lee SMY. Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae. BMC Microbiol 2017; 17:86. [PMID: 28376722 PMCID: PMC5381049 DOI: 10.1186/s12866-017-0981-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 03/11/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nuclear envelope is considered a key classification marker that distinguishes prokaryotes from eukaryotes. However, this marker does not apply to the family Planctomycetaceae, which has intracellular spaces divided by lipidic intracytoplasmic membranes (ICMs). Nuclear localization signal (NLS), a short stretch of amino acid sequence, destines to transport proteins from cytoplasm into nucleus, and is also associated with the development of nuclear envelope. We attempted to investigate the NLS motifs in Planctomycetaceae genomes to demonstrate the potential molecular transition in the development of intracellular membrane system. RESULTS In this study, we identified NLS-like motifs that have the same amino acid compositions as experimentally identified NLSs in genomes of 11 representative species of family Planctomycetaceae. A total of 15 NLS types and 170 NLS-bearing proteins were detected in the 11 strains. To determine the molecular transformation, we compared NLS-bearing protein abundances in the 11 representative Planctomycetaceae genomes with them in genomes of 16 taxonomically varied microorganisms: nine bacteria, two archaea and five fungi. In the 27 strains, 29 NLS types and 1101 NLS-bearing proteins were identified, principal component analysis showed a significant transitional gradient from bacteria to Planctomycetaceae to fungi on their NLS-bearing protein abundance profiles. Then, we clustered the 993 non-redundant NLS-bearing proteins into 181 families and annotated their involved metabolic pathways. Afterwards, we aligned the ten types of NLS motifs from the 13 families containing NLS-bearing proteins among bacteria, Planctomycetaceae or fungi, considering their diversity, length and origin. A transition towards increased complexity from non-planctomycete bacteria to Planctomycetaceae to archaea and fungi was detected based on the complexity of the 10 types of NLS-like motifs in the 13 NLS-bearing proteins families. CONCLUSION The results of this study reveal that Planctomycetaceae separates slightly from the members of non-planctomycete bacteria but still has substantial differences from fungi, based on the NLS-like motifs and NLS-bearing protein analysis.
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Affiliation(s)
- Min Guo
- State Key Laboratory of Quality Research of Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Chen Huang
- State Key Laboratory of Quality Research of Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Qiwen Liao
- State Key Laboratory of Quality Research of Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Guangyi Fan
- State Key Laboratory of Quality Research of Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Chenghang Sun
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research of Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macao, China.
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10
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King T, Kocharunchitt C, Gobius K, Bowman JP, Ross T. Physiological Response of Escherichia coli O157:H7 Sakai to Dynamic Changes in Temperature and Water Activity as Experienced during Carcass Chilling. Mol Cell Proteomics 2016; 15:3331-3347. [PMID: 27615263 PMCID: PMC5098033 DOI: 10.1074/mcp.m116.063065] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 09/04/2016] [Indexed: 02/03/2023] Open
Abstract
Enterohemeorrhagic Escherichia coli is a leading cause of foodborne illness, with the majority of cases linked to foods of bovine origin. Currently, no completely effective method for controlling this pathogen during carcass processing exists. Understanding how this pathogen behaves under those stress conditions experienced on the carcass during chilling in cold air could offer opportunities for development or improvement of effective decontamination processes. Therefore, we studied the growth kinetics and physiological response of exponential phase E. coli O157:H7 Sakai cultures upon an abrupt downshift in temperature and water activity (from 35 °C aw 0.993 to 14 °C aw 0.967). A parallel Biolog study was conducted to follow the phenotypic responses to 190 carbon sources. Exposure of E. coli to combined cold and water activity stresses resulted in a complex pattern of population changes. This pattern could be divided into two main phases, including adaptation and regrowth phases, based on growth kinetics and clustering analyses. The transcriptomic and proteomic studies revealed that E. coli exhibited a "window" of cell susceptibility (i.e. weaknesses) during adaptation phase. This included apparent DNA damage, the downregulation of molecular chaperones and proteins associated with responses to oxidative damage. However, E. coli also displayed a transient induction in the RpoE-controlled envelope stress response and activation of the master stress regulator RpoS and the Rcs phosphorelay system involved in colanic acid biosynthesis. Increased expression was observed for several genes and/or proteins involved in DNA repair, protein and peptide degradation, amino acid biosynthesis, and carbohydrate catabolism and energy generation. Furthermore, the Biolog study revealed reduced carbon source utilization during adaptation phase, indicating the disruption of energy-generating processes. This study provides insight into the physiological response of E. coli during exposure to combined cold and water activity stress, which could be exploited to enhance the microbiological safety of carcasses and related foods.
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Affiliation(s)
- Thea King
- From the ‡CSIRO Agriculture and Food, North Ryde, NSW 2113, Australia;
| | - Chawalit Kocharunchitt
- §Food Safety Centre, Tasmanian Institute of Agriculture, School of Agricultural Science, University of Tasmania, Private Bag 54, Hobart TAS 7001, Australia
| | - Kari Gobius
- ¶CSIRO Agriculture and Food, Werribee, VIC 3030, Australia
| | - John P Bowman
- §Food Safety Centre, Tasmanian Institute of Agriculture, School of Agricultural Science, University of Tasmania, Private Bag 54, Hobart TAS 7001, Australia
| | - Tom Ross
- §Food Safety Centre, Tasmanian Institute of Agriculture, School of Agricultural Science, University of Tasmania, Private Bag 54, Hobart TAS 7001, Australia
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11
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Geographic distribution at subspecies resolution level: closely related Rhodopirellula species in European coastal sediments. ISME JOURNAL 2016; 11:478-489. [PMID: 27801907 DOI: 10.1038/ismej.2016.123] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/19/2016] [Accepted: 08/05/2016] [Indexed: 11/08/2022]
Abstract
Members of the marine genus Rhodopirellula are attached living bacteria and studies based on cultured Rhodopirellula strains suggested that three closely related species R. baltica, 'R. europaea' and 'R. islandica' have a limited geographic distribution in Europe. To address this hypothesis, we developed a nested PCR for a single gene copy detection of a partial acetyl CoA synthetase (acsA) from intertidal sediments collected all around Europe. Furthermore, we performed growth experiments in a range of temperature, salinity and light conditions. A combination of Basic Local Alignment Search Tool (BLAST) and Minimum Entropy Decomposition (MED) was used to analyze the sequences with the aim to explore the geographical distribution of the species and subspecies. MED has been mainly used for the analysis of the 16S rRNA gene and here we propose a protocol for the analysis of protein-coding genes taking into account the degeneracy of the codons and a possible overestimation of functional diversity. The high-resolution analysis revealed differences in the intraspecies community structure in different geographic regions. However, we found all three species present in all regions sampled and in agreement with growth experiments we demonstrated that Rhodopirellula species do not have a limited geographic distribution in Europe.
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12
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Ferreira C, Soares AR, Lamosa P, Santos MA, da Costa MS. Comparison of the compatible solute pool of two slightly halophilic planctomycetes species, Gimesia maris and Rubinisphaera brasiliensis. Extremophiles 2016; 20:811-820. [PMID: 27502056 DOI: 10.1007/s00792-016-0868-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/30/2016] [Indexed: 11/29/2022]
Abstract
Gimesia maris and Rubinisphaera brasiliensis are slightly halophilic representatives of the deep-branching phylum Planctomycetes. For osmoadaptation both species accumulated α-glutamate, sucrose, ectoine and hydroxyectoine. A major role was found for ectoine, hydroxyectoine as well as sucrose under hyper-osmotic shock conditions. Nevertheless, the levels of sucrose were up-regulated by the increased salinity levels and also by low nitrogen availability. Additionally, G. maris accumulated glucosylglycerate (GG) as major solute specifically under low nitrogen levels, which prompted us to analyse the transcript abundance of two homologues genes known for the biosynthesis of GG, namely glucosyl-3-phosphoglycerate synthase (GpgS) and glucosyl-3-phosphoglycerate phosphatase (GpgP). By qPCR using a suitable reference gene selected in this study, the transcript abundance of the biosynthetic genes was quantified in G. maris cells under hyper-osmotic shock or under low nitrogen conditions. The gpgS gene was induced under nitrogen-limiting conditions suggesting that GG synthesis is regulated primarily at the transcription level. Moreover, the expression of a gene coding for a putative sucrose-phosphorylase (Spase) located upstream the gpgS and gpgP genes was up-regulated, predicting a metabolic role of Spase probably related to GG synthesis.
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Affiliation(s)
- Catarina Ferreira
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
| | - Ana R Soares
- Department of Medical Sciences and Institute for Biomedicine-iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Pedro Lamosa
- Centro de Ressonância Magnética António Xavier, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901, Oeiras, Portugal
| | - Manuel A Santos
- Department of Medical Sciences and Institute for Biomedicine-iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Milton S da Costa
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal.
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13
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de Barsy M, Frandi A, Panis G, Théraulaz L, Pillonel T, Greub G, Viollier PH. Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum. ISME JOURNAL 2016; 10:2129-44. [PMID: 26953603 PMCID: PMC4989314 DOI: 10.1038/ismej.2016.23] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 01/19/2016] [Accepted: 01/21/2016] [Indexed: 01/17/2023]
Abstract
Like other obligate intracellular bacteria, the Chlamydiae feature a compact regulatory genome that remains uncharted owing to poor genetic tractability. Exploiting the reduced number of transcription factors (TFs) encoded in the chlamydial (pan-)genome as a model for TF control supporting the intracellular lifestyle, we determined the conserved landscape of TF specificities by ChIP-Seq (chromatin immunoprecipitation-sequencing) in the chlamydial pathogen Waddlia chondrophila. Among 10 conserved TFs, Euo emerged as a master TF targeting >100 promoters through conserved residues in a DNA excisionase-like winged helix-turn-helix-like (wHTH) fold. Minimal target (Euo) boxes were found in conserved developmentally-regulated genes governing vertical genome transmission (cytokinesis and DNA replication) and genome plasticity (transposases). Our ChIP-Seq analysis with intracellular bacteria not only reveals that global TF regulation is maintained in the reduced regulatory genomes of Chlamydiae, but also predicts that master TFs interpret genomic information in the obligate intracellular α-proteobacteria, including the rickettsiae, from which modern day mitochondria evolved.
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Affiliation(s)
- Marie de Barsy
- Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Antonio Frandi
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Gaël Panis
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Laurence Théraulaz
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Trestan Pillonel
- Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Medicine, University of Geneva, Geneva, Switzerland
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14
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Mock T, Daines SJ, Geider R, Collins S, Metodiev M, Millar AJ, Moulton V, Lenton TM. Bridging the gap between omics and earth system science to better understand how environmental change impacts marine microbes. GLOBAL CHANGE BIOLOGY 2016; 22:61-75. [PMID: 25988950 PMCID: PMC4949645 DOI: 10.1111/gcb.12983] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/05/2015] [Accepted: 05/12/2015] [Indexed: 05/17/2023]
Abstract
The advent of genomic-, transcriptomic- and proteomic-based approaches has revolutionized our ability to describe marine microbial communities, including biogeography, metabolic potential and diversity, mechanisms of adaptation, and phylogeny and evolutionary history. New interdisciplinary approaches are needed to move from this descriptive level to improved quantitative, process-level understanding of the roles of marine microbes in biogeochemical cycles and of the impact of environmental change on the marine microbial ecosystem. Linking studies at levels from the genome to the organism, to ecological strategies and organism and ecosystem response, requires new modelling approaches. Key to this will be a fundamental shift in modelling scale that represents micro-organisms from the level of their macromolecular components. This will enable contact with omics data sets and allow acclimation and adaptive response at the phenotype level (i.e. traits) to be simulated as a combination of fitness maximization and evolutionary constraints. This way forward will build on ecological approaches that identify key organism traits and systems biology approaches that integrate traditional physiological measurements with new insights from omics. It will rely on developing an improved understanding of ecophysiology to understand quantitatively environmental controls on microbial growth strategies. It will also incorporate results from experimental evolution studies in the representation of adaptation. The resulting ecosystem-level models can then evaluate our level of understanding of controls on ecosystem structure and function, highlight major gaps in understanding and help prioritize areas for future research programs. Ultimately, this grand synthesis should improve predictive capability of the ecosystem response to multiple environmental drivers.
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Affiliation(s)
- Thomas Mock
- School of Environmental SciencesUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Stuart J. Daines
- College of Life and Environmental SciencesUniversity of ExeterEX4 4QEExeterUK
| | - Richard Geider
- School of Biological SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
| | - Sinead Collins
- Ashworth LaboratoriesEdinburgh UniversityEH9 3JFEdinburghUK
| | - Metodi Metodiev
- School of Biological SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
| | - Andrew J. Millar
- SynthSys and School of Biological SciencesEdinburgh UniversityEH9 3BFEdinburghUK
| | - Vincent Moulton
- School of Computing SciencesUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Timothy M. Lenton
- College of Life and Environmental SciencesUniversity of ExeterEX4 4QEExeterUK
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15
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Chen X, Song Y, Xu H, Menghe B, Zhang H, Sun Z. Genetic relationships among Enterococcus faecalis isolates from different sources as revealed by multilocus sequence typing. J Dairy Sci 2015; 98:5183-93. [DOI: 10.3168/jds.2015-9571] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 04/27/2015] [Indexed: 11/19/2022]
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16
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Pereira MA, Faustino MAF, Tomé JPC, Neves MGPMS, Tomé AC, Cavaleiro JAS, Cunha Â, Almeida A. Influence of external bacterial structures on the efficiency of photodynamic inactivation by a cationic porphyrin. Photochem Photobiol Sci 2014; 13:680-90. [PMID: 24549049 DOI: 10.1039/c3pp50408e] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The main targets of photodynamic inactivation (PDI) are the external bacterial structures, cytoplasmic membrane and cell wall. In this work it was evaluated how the external bacterial structures influence the PDI efficiency. To reach this objective 8 bacteria with distinct external structures were selected; 4 Gram-negative bacteria (Escherichia coli, with typical Gram-negative external structures; Aeromonas salmonicida, Aeromonas hydrophila both with an S-layer and Rhodopirellula sp., with a peptidoglycan-less proteinaceous cell wall and with cytoplasm compartmentalization) and 4 Gram-positive bacteria (Staphylococcus aureus, with typical Gram-positive external structures; Truepera radiovictrix, Deinococcus geothermalis and Deinococcus radiodurans, all with thick cell walls that give them Gram-positive stains, but including a second complex multi-layered membrane and structurally analogous to that of Gram-negative bacteria). The studies were performed in the presence of 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin tetraiodide (Tetra-Py(+)-Me) at 5.0 μM with white light (40 W m(-2)). The susceptibility of each bacteria to PDI by Tetra-Py(+)-Me was dependent on bacteria external structures. Although all Gram-positive bacteria were inactivated to the detection limit (reduction of ∼8 log) after 60-180 min of irradiation, the inactivation followed distinct patterns. Among the Gram-negative bacteria, E. coli was the only species to be inactivated to the detection limit (∼8 log after 180 min). The efficiency of inactivation of the two species of Aeromonas was similar (reduction of ∼5-6 log after 270 min). Rhodopirellula was less susceptible (reduction of ∼4 log after 270 min). As previously observed, the Gram-positive bacteria are more easily inactivated than Gram-negative strains, and this is even true for T. radiovictrix, D. geothermalis and D. radiodurans, which have a complex multi-layered cell wall. The results support the theory that the outer cell structures are major bacterial targets for PDI. Moreover, the chemical composition of the external structures has a stronger effect on PDI efficiency than complexity and the number of layers of the external coating, and lipids seem to be an important target of PDI.
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Affiliation(s)
- M A Pereira
- Department of Biology & CESAM, University of Aveiro, 3810-193 Aveiro, Portugal.
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17
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Withers R, Doherty GP, Jordan M, Yang X, Dixon NE, Lewis PJ. AtfA, a new factor in global regulation of transcription in Acinetobacter spp. Mol Microbiol 2014; 93:1130-43. [PMID: 25047957 DOI: 10.1111/mmi.12723] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2014] [Indexed: 11/29/2022]
Abstract
Acinetobacter species are widely distributed bacteria in the environment, and have recently gained notoriety as opportunistic nosocomial pathogens. Here we characterize a novel RNA polymerase-interacting protein named acidic transcription factor A, AtfA. It is small and highly acidic, and is widely distributed throughout the γ proteobacteria, including other significant pathogens in the genera Moraxella, Pseudomonas, Legionella and Vibrio. In the model species A. baylyi ADP1, deletion of atfA significantly affects expression of over 500 genes, resulting in a large cell phenotype, reduced cell fitness, impaired biofilm formation and twitching motility, and increased sensitivity to antibiotics. Deletion of atfA also causes dramatically enhanced sensitivity to ethanol, which is an important growth promoter and virulence factor in Acinetobacter spp. The results suggest that auxiliary factors of RNA polymerase with important biological roles remain to be discovered.
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Affiliation(s)
- Ryan Withers
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
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18
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Lage OM, Bondoso J. Planctomycetes and macroalgae, a striking association. Front Microbiol 2014; 5:267. [PMID: 24917860 PMCID: PMC4042473 DOI: 10.3389/fmicb.2014.00267] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/15/2014] [Indexed: 12/31/2022] Open
Abstract
Planctomycetes are part of the complex microbial biofilm community of a wide range of macroalgae. Recently, some studies began to unveil the great diversity of Planctomycetes present in this microenvironment and the interactions between the two organisms. Culture dependent and independent methods revealed the existence of a great number of species but, so far, only less than 10 species have been isolated. Planctomycetes comprise the genera Rhodopirellula, Blastopirellula, and Planctomyces, Phycisphaera and the uncultured class OM190 and some other taxa have only been found in this association. Several factors favor the colonization of macroalgal surfaces by planctomycetes. Many species possess holdfasts for attachment. The macroalgae secrete various sulfated polysaccharides that are the substrate for the abundant sulfatases produced by planctomycetes. Specificity between planctomycetes and macroalgae seem to exist which may be related to the chemical nature of the polysaccharides produced by each macroalga. Furthermore, the peptidoglycan-free cell wall of planctomycetes allows them to resist the action of several antimicrobial compounds produced by the macroalgae or other bacteria in the biofilm community that are effective against biofouling by other microorganisms. Despite the increase in our knowledge on the successful planctomycetes-macroalgae association, a great effort to fully understand this interaction is needed.
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Affiliation(s)
- Olga M Lage
- Department of Biology, Faculty of Sciences, University of Porto Porto, Portugal ; CIMAR/CIIMAR - Interdisciplinary Centre for Marine and Environmental Research, University of Porto Porto, Portugal
| | - Joana Bondoso
- Department of Biology, Faculty of Sciences, University of Porto Porto, Portugal ; CIMAR/CIIMAR - Interdisciplinary Centre for Marine and Environmental Research, University of Porto Porto, Portugal
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19
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Kocharunchitt C, King T, Gobius K, Bowman JP, Ross T. Global genome response of Escherichia coli O157∶H7 Sakai during dynamic changes in growth kinetics induced by an abrupt downshift in water activity. PLoS One 2014; 9:e90422. [PMID: 24594867 PMCID: PMC3940904 DOI: 10.1371/journal.pone.0090422] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 01/30/2014] [Indexed: 01/10/2023] Open
Abstract
The present study was undertaken to investigate growth kinetics and time-dependent change in global expression of Escherichia coli O157∶H7 Sakai upon an abrupt downshift in water activity (aw). Based on viable count data, shifting E. coli from aw 0.993 to aw 0.985 or less caused an apparent loss, then recovery, of culturability. Exponential growth then resumed at a rate characteristic for the aw imposed. To understand the responses of this pathogen to abrupt osmotic stress, we employed an integrated genomic and proteomic approach to characterize its cellular response during exposure to a rapid downshift but still within the growth range from aw 0.993 to aw 0.967. Of particular interest, genes and proteins with cell envelope-related functions were induced during the initial loss and subsequent recovery of culturability. This implies that cells undergo remodeling of their envelope composition, enabling them to adapt to osmotic stress. Growth at low aw, however, involved up-regulating additional genes and proteins, which are involved in the biosynthesis of specific amino acids, and carbohydrate catabolism and energy generation. This suggests their important role in facilitating growth under such stress. Finally, we highlighted the ability of E. coli to activate multiple stress responses by transiently inducing the RpoE and RpoH regulons to control protein misfolding, while simultaneously activating the master stress regulator RpoS to mediate long-term adaptation to hyperosmolality. This investigation extends our understanding of the potential mechanisms used by pathogenic E. coli to adapt, survive and grow under osmotic stress, which could potentially be exploited to aid the selection and/or development of novel strategies to inactivate this pathogen.
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Affiliation(s)
- Chawalit Kocharunchitt
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
- * E-mail:
| | - Thea King
- Commonwealth Scientific and Industrial Research Organisation Animal, Food and Health Sciences, North Ryde, New South Wales, Australia
| | - Kari Gobius
- Commonwealth Scientific and Industrial Research Organisation Animal, Food and Health Sciences, Werribee, Victoria, Australia
| | - John P. Bowman
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Tom Ross
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
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20
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Guo M, Zhou Q, Zhou Y, Yang L, Liu T, Yang J, Chen Y, Su L, Xu J, Chen J, Liu F, Chen J, Dai W, Ni P, Fang C, Yang R. Genomic evolution of 11 type strains within family Planctomycetaceae. PLoS One 2014; 9:e86752. [PMID: 24489782 PMCID: PMC3906078 DOI: 10.1371/journal.pone.0086752] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 12/16/2013] [Indexed: 11/18/2022] Open
Abstract
The species in family Planctomycetaceae are ideal groups for investigating the origin of eukaryotes. Their cells are divided by a lipidic intracytoplasmic membrane and they share a number of eukaryote-like molecular characteristics. However, their genomic structures, potential abilities, and evolutionary status are still unknown. In this study, we searched for common protein families and a core genome/pan genome based on 11 sequenced species in family Planctomycetaceae. Then, we constructed phylogenetic tree based on their 832 common protein families. We also annotated the 11 genomes using the Clusters of Orthologous Groups database. Moreover, we predicted and reconstructed their core/pan metabolic pathways using the KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology system. Subsequently, we identified genomic islands (GIs) and structural variations (SVs) among the five complete genomes and we specifically investigated the integration of two Planctomycetaceae plasmids in all 11 genomes. The results indicate that Planctomycetaceae species share diverse genomic variations and unique genomic characteristics, as well as have huge potential for human applications.
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Affiliation(s)
- Min Guo
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI-Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | | | - Yizhuang Zhou
- Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | | | | | - Jinlong Yang
- Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | | | - Longxiang Su
- Medical College, Nankai University, Tianjin, China
| | - Jin Xu
- BGI-Shenzhen, Shenzhen, China
| | - Jing Chen
- Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | | | - Chengxiang Fang
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI-Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Ruifu Yang
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI-Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Bioenergy, BGI-Shenzhen, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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21
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Paparoditis P, Vastermark A, Le AJ, Fuerst JA, Saier MH. Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1838:193-215. [PMID: 23969110 PMCID: PMC3905805 DOI: 10.1016/j.bbamem.2013.08.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 08/08/2013] [Accepted: 08/09/2013] [Indexed: 02/04/2023]
Abstract
Rhodopirellula baltica (R. baltica) is a Planctomycete, known to have intracellular membranes. Because of its unusual cell structure and ecological significance, we have conducted comprehensive analyses of its transmembrane transport proteins. The complete proteome of R. baltica was screened against the Transporter Classification Database (TCDB) to identify recognizable integral membrane transport proteins. 342 proteins were identified with a high degree of confidence, and these fell into several different classes. R. baltica encodes in its genome channels (12%), secondary carriers (33%), and primary active transport proteins (41%) in addition to classes represented in smaller numbers. Relative to most non-marine bacteria, R. baltica possesses a larger number of sodium-dependent symporters but fewer proton-dependent symporters, and it has dimethylsulfoxide (DMSO) and trimethyl-amine-oxide (TMAO) reductases, consistent with its Na(+)-rich marine environment. R. baltica also possesses a Na(+)-translocating NADH:quinone dehydrogenase (Na(+)-NDH), a Na(+) efflux decarboxylase, two Na(+)-exporting ABC pumps, two Na(+)-translocating F-type ATPases, two Na(+):H(+) antiporters and two K(+):H(+) antiporters. Flagellar motility probably depends on the sodium electrochemical gradient. Surprisingly, R. baltica also has a complete set of H(+)-translocating electron transport complexes similar to those present in α-proteobacteria and eukaryotic mitochondria. The transport proteins identified proved to be typical of the bacterial domain with little or no indication of the presence of eukaryotic-type transporters. However, novel functionally uncharacterized multispanning membrane proteins were identified, some of which are found only in Rhodopirellula species, but others of which are widely distributed in bacteria. The analyses lead to predictions regarding the physiology, ecology and evolution of R. baltica.
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Affiliation(s)
- Philipp Paparoditis
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116
| | - Ake Vastermark
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116
| | - Andrew J. Le
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116
| | - John A. Fuerst
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116
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Abstract
Alpha-solenoids are flexible protein structural domains formed by ensembles of alpha-helical repeats (Armadillo and HEAT repeats among others). While homology can be used to detect many of these repeats, some alpha-solenoids have very little sequence homology to proteins of known structure and we expect that many remain undetected. We previously developed a method for detection of alpha-helical repeats based on a neural network trained on a dataset of protein structures. Here we improved the detection algorithm and updated the training dataset using recently solved structures of alpha-solenoids. Unexpectedly, we identified occurrences of alpha-solenoids in solved protein structures that escaped attention, for example within the core of the catalytic subunit of PI3KC. Our results expand the current set of known alpha-solenoids. Application of our tool to the protein universe allowed us to detect their significant enrichment in proteins interacting with many proteins, confirming that alpha-solenoids are generally involved in protein-protein interactions. We then studied the taxonomic distribution of alpha-solenoids to discuss an evolutionary scenario for the emergence of this type of domain, speculating that alpha-solenoids have emerged in multiple taxa in independent events by convergent evolution. We observe a higher rate of alpha-solenoids in eukaryotic genomes and in some prokaryotic families, such as Cyanobacteria and Planctomycetes, which could be associated to increased cellular complexity. The method is available at http://cbdm.mdc-berlin.de/~ard2/.
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Viana F, Lage OM, Oliveira R. High ultraviolet C resistance of marine Planctomycetes. Antonie van Leeuwenhoek 2013; 104:585-95. [PMID: 24052365 DOI: 10.1007/s10482-013-0027-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 09/03/2013] [Indexed: 02/07/2023]
Abstract
Planctomycetes are bacteria with particular characteristics such as internal membrane systems encompassing intracellular compartments, proteinaceous cell walls, cell division by yeast-like budding and large genomes. These bacteria inhabit a wide range of habitats, including marine ecosystems, in which ultra-violet radiation has a potential harmful impact in living organisms. To evaluate the effect of ultra-violet C on the genome of several marine strains of Planctomycetes, we developed an easy and fast DNA diffusion assay in which the cell wall was degraded with papain, the wall-free cells were embedded in an agarose microgel and lysed. The presence of double strand breaks and unwinding by single strand breaks allow DNA diffusion, which is visible as a halo upon DNA staining. The number of cells presenting DNA diffusion correlated with the dose of ultra-violet C or hydrogen peroxide. From DNA damage and viability experiments, we found evidence indicating that some strains of Planctomycetes are significantly resistant to ultra-violet C radiation, showing lower sensitivity than the known resistant Arthrobacter sp. The more resistant strains were those phylogenetically closer to Rhodopirellula baltica, suggesting that these species are adapted to habitats under the influence of ultra-violet radiation. Our results provide evidence indicating that the mechanism of resistance involves DNA damage repair and/or other DNA ultra-violet C-protective mechanism.
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Affiliation(s)
- Flávia Viana
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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Genetic diversity of Rhodopirellula strains. Antonie van Leeuwenhoek 2013; 104:547-50. [DOI: 10.1007/s10482-013-0004-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 08/14/2013] [Indexed: 02/07/2023]
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d’Avó AF, Cunha S, Mingote A, Lamosa P, da Costa MS, Costa J. A Unique Pool of Compatible Solutes on Rhodopirellula baltica, Member of the Deep-Branching Phylum Planctomycetes. PLoS One 2013; 8:e68289. [PMID: 23826385 PMCID: PMC3694870 DOI: 10.1371/journal.pone.0068289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 05/28/2013] [Indexed: 11/21/2022] Open
Abstract
The intracellular accumulation of small organic solutes was described in the marine bacterium Rhodopirellula baltica, which belongs to the globally distributed phylum Planctomycetes whose members exhibit an intriguing lifestyle and cell morphology. Sucrose, α-glutamate, trehalose and mannosylglucosylglycerate (MGG) are the main solutes involved in the osmoadaptation of R. baltica. The ratio and total intracellular organic solutes varied significantly in response to an increase in salinity, temperature and nitrogen content. R. baltica displayed an initial response to both osmotic and thermal stresses that includes α-glutamate accumulation. This trend was followed by a rather unique and complex osmoadaptation mechanism characterized by a dual response to sub-optimal and supra-optimal salinities. A reduction in the salinity to sub-optimal conditions led primarily to the accumulation of trehalose. In contrast, R. baltica responded to salt stress mostly by increasing the intracellular levels of sucrose. The switch between the accumulation of trehalose and sucrose was by far the most significant effect caused by increasing the salt levels of the medium. Additionally, MGG accumulation was found to be salt- as well as nitrogen-dependent. MGG accumulation was regulated by nitrogen levels replacing α-glutamate as a K+ counterion in nitrogen-poor environments. This is the first report of the accumulation of compatible solutes in the phylum Planctomycetes and of the MGG accumulation in a mesophilic organism.
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Affiliation(s)
- Ana Filipa d’Avó
- Center for Neurosciences and Cellular Biology, University of Coimbra, Coimbra, Portugal
| | - Sofia Cunha
- Center for Neurosciences and Cellular Biology, University of Coimbra, Coimbra, Portugal
| | - Ana Mingote
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Pedro Lamosa
- Centro de Ressonância Magnética António Xavier, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Milton S. da Costa
- Center for Neurosciences and Cellular Biology, University of Coimbra, Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Joana Costa
- Center for Neurosciences and Cellular Biology, University of Coimbra, Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- * E-mail:
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Dressaire C, Picard F, Redon E, Loubière P, Queinnec I, Girbal L, Cocaign-Bousquet M. Role of mRNA stability during bacterial adaptation. PLoS One 2013; 8:e59059. [PMID: 23516597 PMCID: PMC3596320 DOI: 10.1371/journal.pone.0059059] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 02/11/2013] [Indexed: 11/18/2022] Open
Abstract
Bacterial adaptation involves extensive cellular reorganization. In particular, growth rate adjustments are associated with substantial modifications of gene expression and mRNA abundance. In this work we aimed to assess the role of mRNA degradation during such variations. A genome-wide transcriptomic-based method was used to determine mRNA half-lives. The model bacterium Lactococcus lactis was used and different growth rates were studied in continuous cultures under isoleucine-limitation and in batch cultures during the adaptation to the isoleucine starvation. During continuous isoleucine-limited growth, the mRNAs of different genes had different half-lives. The stability of most of the transcripts was not constant, and increased as the growth rate decreased. This half-life diversity was analyzed to investigate determinants of mRNA stability. The concentration, length, codon adaptation index and secondary structures of mRNAs were found to contribute to the determination of mRNA stability in these conditions. However, the growth rate was, by far, the most influential determinant. The respective influences of mRNA degradation and transcription on the regulation of intra-cellular transcript concentration were estimated. The role of degradation on mRNA homeostasis was clearly evidenced: for more than 90% of the mRNAs studied during continuous isoleucine-limited growth of L. lactis, degradation was antagonistic to transcription. Although both transcription and degradation had, opposite effects, the mRNA changes in response to growth rate were driven by transcription. Interestingly, degradation control increased during the dynamic adaptation of bacteria as the growth rate reduced due to progressive isoleucine starvation in batch cultures. This work shows that mRNA decay differs between gene transcripts and according to the growth rate. It demonstrates that mRNA degradation is an important regulatory process involved in bacterial adaptation. However, its impact on the regulation of mRNA levels is smaller than that of transcription in the conditions studied.
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Affiliation(s)
- Clémentine Dressaire
- Université de Toulouse; The Institut National des Sciences Appliquées, UPS, INP, LISBP, Toulouse, France.
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Feller G. Psychrophilic enzymes: from folding to function and biotechnology. SCIENTIFICA 2013; 2013:512840. [PMID: 24278781 PMCID: PMC3820357 DOI: 10.1155/2013/512840] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/06/2012] [Indexed: 05/10/2023]
Abstract
Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Several open questions in the field are also highlighted.
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Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Centre for Protein Engineering, Institute of Chemistry, University of Liège, B6a, 4000 Liège, Belgium
- *Georges Feller:
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Wegner CE, Richter-Heitmann T, Klindworth A, Klockow C, Richter M, Achstetter T, Glöckner FO, Harder J. Expression of sulfatases in Rhodopirellula baltica and the diversity of sulfatases in the genus Rhodopirellula. Mar Genomics 2012; 9:51-61. [PMID: 23273849 DOI: 10.1016/j.margen.2012.12.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 12/10/2012] [Accepted: 12/10/2012] [Indexed: 10/27/2022]
Abstract
The whole genome sequence of Rhodopirellula baltica SH1(T), published nearly 10years ago, already revealed a high amount of sulfatase genes. So far, little is known about the diversity and potential functions mediated by sulfatases in Planctomycetes. We combined in vivo and in silico techniques to gain insights into the ecophysiology of planktomycetal sulfatases. Comparative genomics of nine recently sequenced Rhodopirellula strains detected 1120 open reading frames annotated as sulfatases (Enzyme Commission number (EC) 3.1.6.*). These were clustered into 173 groups of orthologous and paralogous genes. To analyze the functional aspects, 708 sulfatase protein sequences from these strains were aligned with 67 sulfatase reference sequences of reviewed functionality. Our analysis yielded 22 major similarity clusters, but only five of these clusters contained Rhodopirellula sequences homologous to reference sequences, indicating a surprisingly high diversity. Exemplarily, R. baltica SH1(T) was grown on different sulfated polysaccharides, chondroitin sulfate, λ-carrageenan and fucoidan. Subsequent gene expression analyses using whole genome microarrays revealed distinct sulfatase expression profiles based on substrates tested. This might be indicative for a high structural diversity of sulfated polysaccharides as potential substrates. The pattern of sulfatases in individual planctomycete species may reflect ecological niche adaptation.
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Affiliation(s)
- Carl-Eric Wegner
- Microbial Genomics and Bioinformatics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, 28359 Bremen, Germany
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Lage OM, Bondoso J. Bringing Planctomycetes into pure culture. Front Microbiol 2012; 3:405. [PMID: 23335915 PMCID: PMC3538630 DOI: 10.3389/fmicb.2012.00405] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 11/11/2012] [Indexed: 01/09/2023] Open
Abstract
Planctomycetes have been known since the description of Planctomyces bekefii by Gimesi at the beginning of the twentieth century (1924), although the first axenic cultures were only obtained in the 1970s. Since then, 11 genera with 14 species have been validly named and five candidatus genera belonging to the anaerobic ammonium oxidation, anammox bacteria have also been discovered. However, Planctomycetes diversity is much broader than these numbers indicate, as shown by environmental molecular studies. In recent years, the authors have attempted to isolate and cultivate additional strains of Planctomycetes. This paper provides a summary of the isolation work that was carried out to obtain in pure culture Planctomycetes from several environmental sources. The following strains of planctomycetes have been successfully isolated: two freshwater strains from the sediments of an aquarium, which were described as a new genus and species, Aquisphaera giovannonii; several Rhodopirellula strains from the sediments of a water treatment recycling tank of a marine fish farm; and more than 140 planctomycetes from the biofilm community of macroalgae. This collection comprises several novel taxa that are being characterized and described. Improvements in the isolation methodology were made in order to optimize and enlarge the number of Planctomycetes isolated from the macroalgae. The existence of an intimate and an important relationship between planctomycetes and macroalgae reported before by molecular studies is therefore supported by culture-dependent methods.
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Affiliation(s)
- Olga M Lage
- Department of Biology, Faculty of Sciences, University of Porto Porto, Portugal ; CIMAR/CIIMAR - Interdisciplinary Centre for Marine and Environmental Research University of Porto Porto, Portugal
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Melvin Blaze MT, Aydin B, Carlson R, Hanley L. Identification and imaging of peptides and proteins on Enterococcus faecalis biofilms by matrix assisted laser desorption ionization mass spectrometry. Analyst 2012; 137:5018-25. [PMID: 22962657 PMCID: PMC3654527 DOI: 10.1039/c2an35922g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The heptapeptide ARHPHPH was identified from biofilms and planktonic cultures of two different strains of Enterococcus faecalis, V583 and ATCC 29212, using matrix assisted laser desorption ionization mass spectrometry (MALDI-MS). ARHPHPH was also imaged at the boundary of cocultured, adjacent E. faecalis and Escherichia coli (ATCC 25922) biofilms, appearing only on the E. faecalis side. ARHPHPH was proteolyzed from κ-casein, a component in the growth media, by E. faecalis microbes. Additionally, top down and bottom up proteomic approaches were combined to identify and spatially locate multiple proteins within intact E. faecalis V583 biofilms by MALDI-MS. The resultant tandem MS data were searched against the NCBInr E. faecalis V583 database to identify thirteen cytosolic and membrane proteins which have functional association with the cell surface. Two of these proteins, enolase and GAPDH, are glycolytic enzymes known to display multiple functions in bacterial virulence in related bacterial strains. This work illustrates a powerful approach for discovering and localizing multiple peptides and proteins within intact biofilms.
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Affiliation(s)
- M. T. Melvin Blaze
- Department of Chemistry, MC 111, University of Illinois at Chicago, Chicago, IL 60607-7061
| | - Berdan Aydin
- Department of Chemistry, MC 111, University of Illinois at Chicago, Chicago, IL 60607-7061
| | - Ross Carlson
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
| | - Luke Hanley
- Department of Chemistry, MC 111, University of Illinois at Chicago, Chicago, IL 60607-7061
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Afzal MI, Delaunay S, Paris C, Borges F, Revol-Junelles AM, Cailliez-Grimal C. Identification of metabolic pathways involved in the biosynthesis of flavor compound 3-methylbutanal from leucine catabolism by Carnobacterium maltaromaticum LMA 28. Int J Food Microbiol 2012; 157:332-9. [DOI: 10.1016/j.ijfoodmicro.2012.05.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 04/30/2012] [Accepted: 05/09/2012] [Indexed: 11/29/2022]
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Kostadinov I, Kottmann R, Ramette A, Waldmann J, Buttigieg PL, Glöckner FO. Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes. MICROBIAL INFORMATICS AND EXPERIMENTATION 2011; 1:9. [PMID: 22587903 PMCID: PMC3372289 DOI: 10.1186/2042-5783-1-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 09/07/2011] [Indexed: 11/14/2022]
Abstract
Background DNA-binding transcription factors (TFs) regulate cellular functions in prokaryotes, often in response to environmental stimuli. Thus, the environment exerts constant selective pressure on the TF gene content of microbial communities. Recently a study on marine Synechococcus strains detected differences in their genomic TF content related to environmental adaptation, but so far the effect of environmental parameters on the content of TFs in bacterial communities has not been systematically investigated. Results We quantified the effect of environment stability on the transcription factor repertoire of marine pelagic microbes from the Global Ocean Sampling (GOS) metagenome using interpolated physico-chemical parameters and multivariate statistics. Thirty-five percent of the difference in relative TF abundances between samples could be explained by environment stability. Six percent was attributable to spatial distance but none to a combination of both spatial distance and stability. Some individual TFs showed a stronger relationship to environment stability and space than the total TF pool. Conclusions Environmental stability appears to have a clearly detectable effect on TF gene content in bacterioplanktonic communities described by the GOS metagenome. Interpolated environmental parameters were shown to compare well to in situ measurements and were essential for quantifying the effect of the environment on the TF content. It is demonstrated that comprehensive and well-structured contextual data will strongly enhance our ability to interpret the functional potential of microbes from metagenomic data.
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Affiliation(s)
- Ivaylo Kostadinov
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany.
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Abstract
Planctomycetes associated with 12 macroalgae from the north coast of Portugal were isolated, using an improved method. A total of 138 isolates were found to comprise 10 operational taxonomic units (OTUs), with 65% of the strains being closely related to the species Rhodopirellula baltica. The other strains are probably new species or genera related to Rhodopirellula, Blastopirellula and Planctomyces. Some of the OTUs isolated are unique and have never been found before in previous studies. Catalyzed reporter deposition-FISH confirmed the presence of Planctomycetes on macroalgal surfaces. This study provides the first report of the cultured diversity of Planctomycetes on the epiphytic macroalgae community and presents clear evidence of their nutritional and intimate relationship.
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Affiliation(s)
- Olga Maria Lage
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.
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Williams TJ, Lauro FM, Ertan H, Burg DW, Poljak A, Raftery MJ, Cavicchioli R. Defining the response of a microorganism to temperatures that span its complete growth temperature range (-2°C to 28°C) using multiplex quantitative proteomics. Environ Microbiol 2011; 13:2186-203. [PMID: 21443741 DOI: 10.1111/j.1462-2920.2011.02467.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The growth of all microorganisms is limited to a specific temperature range. However, it has not previously been determined to what extent global protein profiles change in response to temperatures that incrementally span the complete growth temperature range of a microorganism. As a result it has remained unclear to what extent cellular processes (inferred from protein abundance profiles) are affected by growth temperature and which, in particular, constrain growth at upper and lower temperature limits. To evaluate this, 8-plex iTRAQ proteomics was performed on the Antarctic microorganism, Methanococcoides burtonii. Methanococcoides burtonii was chosen due to its importance as a model psychrophilic (cold-adapted) member of the Archaea, and the fact that proteomic methods, including subcellular fractionation procedures, have been well developed. Differential abundance patterns were obtained for cells grown at seven different growth temperatures (-2°C, 1°C, 4°C, 10°C, 16°C, 23°C, 28°C) and a principal component analysis (PCA) was performed to identify trends in protein abundances. The multiplex analysis enabled three largely distinct physiological states to be described: cold stress (-2°C), cold adaptation (1°C, 4°C, 10°C and 16°C), and heat stress (23°C and 28°C). A particular feature of the thermal extremes was the synthesis of heat- and cold-specific stress proteins, reflecting the important, yet distinct ways in which temperature-induced stress manifests in the cell. This is the first quantitative proteomic investigation to simultaneously assess the response of a microorganism to numerous growth temperatures, including the upper and lower growth temperatures limits, and has revealed a new level of understanding about cellular adaptive responses.
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Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
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Rebuffet E, Groisillier A, Thompson A, Jeudy A, Barbeyron T, Czjzek M, Michel G. Discovery and structural characterization of a novel glycosidase family of marine origin. Environ Microbiol 2011; 13:1253-70. [PMID: 21332624 DOI: 10.1111/j.1462-2920.2011.02426.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The genomic data on heterotrophic marine bacteria suggest the crucial role that microbes play in the global carbon cycle. However, the massive presence of hypothetical proteins hampers our understanding of the mechanisms by which this carbon cycle is carried out. Moreover, genomic data from marine microorganisms are essentially annotated in the light of the biochemical knowledge accumulated on bacteria and fungi which decompose terrestrial plants. However marine algal polysaccharides clearly differ from their terrestrial counterparts, and their associated enzymes usually constitute novel protein families. In this study, we have applied a combination of bioinformatics, targeted activity screening and structural biology to characterize a hypothetical protein from the marine bacterium Zobellia galactanivorans, which is distantly related to GH43 family. This protein is in fact a 1,3-α-3,6-anhydro-l-galactosidase (AhgA) which catalyses the last step in the degradation pathway of agars, a family of polysaccharides unique to red macroalgae. AhgA adopts a β-propeller fold and displays a zinc-dependent catalytic machinery. This enzyme is the first representative of a new family of glycoside hydrolases, especially abundant in coastal waters. Such genes of marine origin have been transferred to symbiotic microbes associated with marine fishes, but also with some specific human populations.
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Affiliation(s)
- Etienne Rebuffet
- UPMC University Paris 6 CNRS, UMR 7139 Marine Plants and Biomolecules, Station Biologique de Roscoff, Roscoff, Bretagne, France
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Bull AT. The renaissance of continuous culture in the post-genomics age. J Ind Microbiol Biotechnol 2010; 37:993-1021. [PMID: 20835748 DOI: 10.1007/s10295-010-0816-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 08/11/2010] [Indexed: 01/08/2023]
Abstract
The development of continuous culture techniques 60 years ago and the subsequent formulation of theory and the diversification of experimental systems revolutionised microbiology and heralded a unique period of innovative research. Then, progressively, molecular biology and thence genomics and related high-information-density omics technologies took centre stage and microbial growth physiology in general faded from educational programmes and research funding priorities alike. However, there has been a gathering appreciation over the past decade that if the claims of systems biology are going to be realised, they will have to be based on rigorously controlled and reproducible microbial and cell growth platforms. This revival of continuous culture will be long lasting because its recognition as the growth system of choice is firmly established. The purpose of this review, therefore, is to remind microbiologists, particularly those new to continuous culture approaches, of the legacy of what I call the first age of continuous culture, and to explore a selection of researches that are using these techniques in this post-genomics age. The review looks at the impact of continuous culture across a comprehensive range of microbiological research and development. The ability to establish (quasi-) steady state conditions is a frequently stated advantage of continuous cultures thereby allowing environmental parameters to be manipulated without causing concomitant changes in the specific growth rate. However, the use of continuous cultures also enables the critical study of specified transition states and chemical, physical or biological perturbations. Such dynamic analyses enhance our understanding of microbial ecology and microbial pathology for example, and offer a wider scope for innovative drug discovery; they also can inform the optimization of batch and fed-batch operations that are characterized by sequential transitions states.
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Affiliation(s)
- Alan T Bull
- School of Biosciences, University of Kent, Canterbury, Kent CT27NJ, UK.
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Wecker P, Klockow C, Schüler M, Dabin J, Michel G, Glöckner FO. Life cycle analysis of the model organism Rhodopirellula baltica SH 1(T) by transcriptome studies. Microb Biotechnol 2010; 3:583-94. [PMID: 21255355 PMCID: PMC3815771 DOI: 10.1111/j.1751-7915.2010.00183.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The marine organism Rhodopirellula baltica is a representative of the globally distributed phylum Planctomycetes whose members exhibit an intriguing lifestyle and cell morphology. The analysis of R. baltica's genome has revealed many biotechnologically promising features including a set of unique sulfatases and C1‐metabolism genes. Salt resistance and the potential for adhesion in the adult phase of the cell cycle were observed during cultivation. To promote the understanding of this model organism and to specify the functions of potentially useful genes, gene expression throughout a growth curve was monitored using a whole genome microarray approach. Transcriptional profiling suggests that a large number of hypothetical proteins are active within the cell cycle and in the formation of the different cell morphologies. Numerous genes with potential biotechnological applications were found to be differentially regulated, revealing further characteristics of their functions and regulation mechanisms. More specifically, the experiments shed light on the expression patterns of genes belonging to the organism's general stress response, those involved in the reorganization of its genome and those effecting morphological changes. These transcriptomic results contribute to a better understanding of thus far unknown molecular elements of cell biology. Further, they pave the way for the biotechnological exploitation of R. baltica's distinctive metabolic features as a step towards sourcing the phylum Planctomycetes at large.
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Affiliation(s)
- Patricia Wecker
- Max Planck Institute for Marine Microbiology, Microbial Genomics Group, Celsiusstr. 1, 28359 Bremen, Germany
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