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Vargas S, Leiva L, Wörheide G. Short-Term Exposure to High-Temperature Water Causes a Shift in the Microbiome of the Common Aquarium Sponge Lendenfeldia chondrodes. Microb Ecol 2021; 81:213-222. [PMID: 32767091 PMCID: PMC7794106 DOI: 10.1007/s00248-020-01556-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
Marine sponges harbor diverse microbiomes that contribute to their energetic and metabolic needs. Although numerous studies on sponge microbial diversity exist, relatively few focused on sponge microbial community changes under different sources of environmental stress. In this study, we assess the impact of elevated seawater temperature on the microbiome of cultured Lendenfeldia chondrodes, a coral reef sponge commonly found in marine aquaria. Lendenfeldia chondrodes exhibits high thermal tolerance showing no evidence of tissue damage or bleaching at 5 °C above control water temperature (26 °C). High-throughput sequencing of the bacterial 16S rRNA V4 region revealed a response of the microbiome of L. chondrodes to short-term exposure to elevated seawater temperature. Shifts in abundance and richness of the dominant bacterial phyla found in the microbiome of this species, namely Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes, characterized this response. The observed resilience of L. chondrodes and the responsiveness of its microbiome to short-term increases in seawater temperature suggest that this holobiont may be capable of acclimating to anthropogenic-driven sublethal environmental stress via a re-accommodation of its associated bacterial community. This sheds a new light on the potential for resilience of some sponges to increasing surface seawater temperatures and associated projected regime shifts in coral reefs.
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Affiliation(s)
- Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany.
| | - Laura Leiva
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany
- Biologische Anstalt Helgoland, Shelf Sea System Ecology, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, 27498, Helgoland, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany
- SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Str. 10, 80333, Munich, Germany
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Cui L, Zhu B, Zhang X, Chan Z, Zhao C, Zeng R, Yang S, Chen S. Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems. Genes (Basel) 2020; 12:genes12010040. [PMID: 33396721 PMCID: PMC7823961 DOI: 10.3390/genes12010040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 01/22/2023] Open
Abstract
The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the β-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.
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Affiliation(s)
- Liang Cui
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China; (L.C.); (B.Z.); (X.Z.); (C.Z.)
| | - Bitong Zhu
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China; (L.C.); (B.Z.); (X.Z.); (C.Z.)
| | - Xiaobo Zhang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China; (L.C.); (B.Z.); (X.Z.); (C.Z.)
| | - Zhuhua Chan
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, No. 178 Daxue Road, Xiamen 361005, China; (Z.C.); (R.Z.)
| | - Chungui Zhao
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China; (L.C.); (B.Z.); (X.Z.); (C.Z.)
| | - Runying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, No. 178 Daxue Road, Xiamen 361005, China; (Z.C.); (R.Z.)
| | - Suping Yang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, China; (L.C.); (B.Z.); (X.Z.); (C.Z.)
- Correspondence: (S.Y.); (S.C.)
| | - Shicheng Chen
- Department of Biomedical Diagnostic and Therapeutic Sciences, School of Health Sciences, Oakland University, Rochester, MI 48309, USA
- Correspondence: (S.Y.); (S.C.)
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Wiegand S, Jogler M, Boedeker C, Heuer A, Rast P, Peeters SH, Jetten MSM, Kaster AK, Rohde M, Kallscheuer N, Jogler C. Additions to the genus Gimesia: description of Gimesia alba sp. nov., Gimesia algae sp. nov., Gimesia aquarii sp. nov., Gimesia aquatilis sp. nov., Gimesia fumaroli sp. nov. and Gimesia panareensis sp. nov., isolated from aquatic habitats of the Northern Hemisphere. Antonie Van Leeuwenhoek 2020; 113:1999-2018. [PMID: 33231764 PMCID: PMC7716864 DOI: 10.1007/s10482-020-01489-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/19/2020] [Indexed: 11/29/2022]
Abstract
Thirteen novel planctomycetal strains were isolated from five different aquatic sampling locations. These comprise the hydrothermal vent system close to Panarea Island (Italy), a biofilm on the surface of kelp at Monterey Bay (CA, USA), sediment and algae on Mallorca Island (Spain) and Helgoland Island (Germany), as well as a seawater aquarium in Braunschweig, Germany. All strains were shown to belong to the genus Gimesia. Their genomes cover a size range from 7.22 to 8.29 Mb and have a G+C content between 45.1 and 53.7%. All strains are mesophilic (Topt 26-33 °C) with generation times between 12 and 32 h. Analysis of fatty acids yielded palmitic acid (16:0) and a fatty acid with the equivalent chain length of 15.817 as major compounds. While five of the novel strains belong to the already described species Gimesia maris and Gimesia chilikensis, the other strains belong to novel species, for which we propose the names Gimesia alba (type strain Pan241wT = DSM 100744T = LMG 31345T = CECT 9841T = VKM B-3430T), Gimesia algae (type strain Pan161T = CECT 30192T = STH00943T = LMG 29130T), Gimesia aquarii (type strain V144T = DSM 101710T = VKM B-3433T), Gimesia fumaroli (type strain Enr17T = DSM 100710T = VKM B-3429T) and Gimesia panareensis (type strain Enr10T = DSM 100416T = LMG 29082T). STH numbers refer to the Jena Microbial Resource Collection (JMRC).
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Affiliation(s)
- Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Mareike Jogler
- Department of Microbial Interactions, Friedrich-Schiller-University, Jena, Germany
| | | | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | | | - Stijn H Peeters
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | | | - Christian Jogler
- Department of Microbial Interactions, Friedrich-Schiller-University, Jena, Germany.
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands.
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Kulichevskaya IS, Ivanova AA, Naumoff DG, Beletsky AV, Rijpstra WIC, Sinninghe Damsté JS, Mardanov AV, Ravin NV, Dedysh SN. Frigoriglobus tundricola gen. nov., sp. nov., a psychrotolerant cellulolytic planctomycete of the family Gemmataceae from a littoral tundra wetland. Syst Appl Microbiol 2020; 43:126129. [PMID: 32847778 PMCID: PMC7534041 DOI: 10.1016/j.syapm.2020.126129] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 11/25/2022]
Abstract
Planctomycetes of the family Gemmataceae are characterized by large genome sizes and cosmopolitan distribution in freshwater and terrestrial environments but their ecological functions remain poorly understood. In this study, we characterized a novel representative of this family, strain PL17T, which was isolated from a littoral tundra wetland and was capable of growth on xylan and cellulose. Cells of this isolate were represented by pink-pigmented spheres that multiplied by budding and occurred singly or in short chains and aggregates. Strain PL17T was obligately aerobic, mildly acidophilic chemoorganotrophic bacterium, which displayed good tolerance of low temperatures. The major fatty acids were C18:0, C16:1ω5, and βOH-C16:1; the major polar lipid was trimethylornithine. The genome of strain PL17T consisted of a 9.83 Mb chromosome and a 24.69kb plasmid. The G+C contents of the chromosomal and plasmid DNA were 67.4 and 62.3mol%, respectively. Over 8900 potential protein-coding genes were identified in the genome including a putative cellulase that contains a domain from the GH5 family of glycoside hydrolases. The genome of strain PL17T contained one linked and one unlinked rRNA operons with 16S rRNA gene sequences displaying 94.5% similarity to that in Gemmata obscuriglobus UQM2246T. Based on the results of comparative phenotypic, chemotaxonomic and phylogenomic analyses, we propose to classify strain PL17T (= CECT 9407T=VKM B-3467T) as representing a novel genus and species of the family Gemmataceae, Frigoriglobus tundricola gen. nov., sp. nov.
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Affiliation(s)
- Irina S Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Anastasia A Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Daniil G Naumoff
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - W Irene C Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands; Utrecht University, Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht, The Netherlands
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
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Lu X, Wang K, Sun S, Mou X. Metatranscriptomic identification of polyamine-transforming bacterioplankton in the Gulf of Mexico. Environ Microbiol Rep 2020; 12:258-266. [PMID: 32227463 DOI: 10.1111/1758-2229.12841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/22/2020] [Indexed: 06/10/2023]
Abstract
The importance of short-chained aliphatic polyamines (PAs) to bacterioplankton-mediated carbon and nitrogen cycles has been repeatedly proposed. However, bacterial taxa and genes involved in the transformations of different PA compounds and their potential spatial variations remain unclear. This study collected surface bacterioplankton from nearshore, offshore, and open ocean stations in the Gulf of Mexico and examined how metatranscriptomes responded to additions of three single PA model compounds (i.e. putrescine, spermidine, or spermine). Our data showed an overrepresentation of genes affiliated with γ-glutamylation and spermidine cleavage pathways in metatranscriptomes received PA amendments and the expression level of each pathway varied among different PA compounds and sampling locations. PA-transforming taxa were affiliated with Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, and Proteobacteria and their relative importance was also compound and location specific. These findings suggest that PAs are transformed via multiple pathways and by a diversity of marine bacterioplankton in the Gulf of Mexico. The relative importance of different PA transforming pathways and composition of functional microbial communities may be regulated by nutrient status of local environments.
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Affiliation(s)
- Xinxin Lu
- Department of Biological Sciences, Kent State University, Kent, OH, USA
| | - Kai Wang
- Department of Biological Sciences, Kent State University, Kent, OH, USA
| | - Shulei Sun
- Center for Advanced Laboratory Medicine, University of California, San Diego, CA, USA
| | - Xiaozhen Mou
- Department of Biological Sciences, Kent State University, Kent, OH, USA
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Kulichevskaya IS, Naumoff DG, Miroshnikov KK, Ivanova AA, Philippov DA, Hakobyan A, Rijpstra WIC, Damsté JSS, Liesack W, Dedysh SN. Limnoglobus roseus gen. nov., sp. nov., a novel freshwater planctomycete with a giant genome from the family Gemmataceae. Int J Syst Evol Microbiol 2020; 70:1240-1249. [PMID: 31800383 PMCID: PMC7397252 DOI: 10.1099/ijsem.0.003904] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/16/2019] [Indexed: 11/18/2022] Open
Abstract
The family Gemmataceae accommodates aerobic, chemoorganotrophic planctomycetes, which inhabit various freshwater ecosystems, wetlands and soils. Here, we describe a novel member of this family, strain PX52T, which was isolated from a boreal eutrophic lake in Northern Russia. This isolate formed pink-pigmented colonies and was represented by spherical cells that occurred singly, in pairs or aggregates and multiplied by budding. Daughter cells were highly motile. PX52T was an obligate aerobic chemoorganotroph, which utilized various sugars and some heteropolysaccharides. Growth occurred at pH 5.0-7.5 (optimum pH 6.5) and at temperatures between 10 and 30 °C (optimum 20-25 °C). The major fatty acids were C18 : 1ɷ7c, C18 : 0 and βOH-C16:0; the major intact polar lipid was trimethylornithine, and the quinone was MK-6. The complete genome of PX52T was 9.38 Mb in size and contained nearly 8000 potential protein-coding genes. Among those were genes encoding a wide repertoire of carbohydrate-active enzymes (CAZymes) including 33 glycoside hydrolases (GH) and 87 glycosyltransferases (GT) affiliated with 17 and 12 CAZy families, respectively. DNA G+C content was 65.6 mol%. PX52T displayed only 86.0-89.8 % 16S rRNA gene sequence similarity to taxonomically described Gemmataceae planctomycetes and differed from them by a number of phenotypic characteristics and by fatty acid composition. We, therefore, propose to classify it as representing a novel genus and species, Limnoglobus roseus gen. nov., sp. nov. The type strain is strain PX52T (=KCTC 72397T=VKM B-3275T).
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Affiliation(s)
- Irina S. Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Daniil G. Naumoff
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Kirill K. Miroshnikov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Anastasia A. Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Dmitriy A. Philippov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia
| | - Anna Hakobyan
- Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - W. Irene C. Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands
- Utrecht University, Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht, The Netherlands
| | - Jaap S. Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands
- Utrecht University, Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht, The Netherlands
| | - Werner Liesack
- Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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Alves KJ, da Silva MCP, Cotta SR, Ottoni JR, van Elsas JD, de Oliveira VM, Andreote FD. Mangrove soil as a source for novel xylanase and amylase as determined by cultivation-dependent and cultivation-independent methods. Braz J Microbiol 2019; 51:217-228. [PMID: 31741310 DOI: 10.1007/s42770-019-00162-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/19/2019] [Indexed: 11/25/2022] Open
Abstract
Xylanase and α-amylase enzymes participate in the degradation of organic matter, acting in hemicellulose and starch mineralization, respectively, and are in high demand for industrial use. Mangroves represent a promising source for bioprospecting enzymes due to their unique characteristics, such as fluctuations in oxic/anoxic conditions and salinity. In this context, the present work aimed to bioprospect xylanases from mangrove soil using cultivation-dependent and cultivation-independent methods. Through screening from a metagenomic library, three potentially xylanolytic clones were obtained and sequenced, and reads were assembled into contigs and annotated. The contig MgrBr135 was affiliated with the Planctomycetaceae family and was one of 30 ORFs selected for subcloning that demonstrated only amylase activity. Through the cultivation method, 38 bacterial isolates with xylanolytic activity were isolated. Isolate 11 showed an enzymatic index of 10.9 using the plate assay method. Isolate 39 achieved an enzyme activity of 0.43 U/mL using the colorimetric method with 3,5-dinitrosalicylic acid. Isolate 39 produced xylanase on culture medium with salinity ranging from 1.25 to 5%. Partial 16S rRNA gene sequencing identified isolates in the Bacillus and Paenibacillus genera. The results of this study highlight the importance of mangroves as an enzyme source and show that bacterial groups can be used for starch and hemicellulose degradation.
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Affiliation(s)
- Kelly Jaqueline Alves
- Department of Soil Science, Laboratory of Soil Microbiology, University of Sao Paulo, Padua Dias Avenue, 11 CP 09, Piracicaba, São Paulo, 13418-900, Brazil.
| | - Mylenne Calciolari Pinheiro da Silva
- Department of Soil Science, Laboratory of Soil Microbiology, University of Sao Paulo, Padua Dias Avenue, 11 CP 09, Piracicaba, São Paulo, 13418-900, Brazil
| | - Simone Raposo Cotta
- Center for Nuclear Energy in Agriculture, University of São Paulo, Centenario Avenue, 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Júlia Ronzella Ottoni
- University Center Dinâmica das Cataratas, Castelo Branco Street, 349, Foz do Iguaçu, Paraná, 85852-010, Brazil
| | - Jan Dirk van Elsas
- Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, the Netherlands
| | - Valeria Maia de Oliveira
- Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Alexandre Cazellato Avenue, 999, Paulínia, São Paulo, 13140-000, Brazil
| | - Fernando Dini Andreote
- Department of Soil Science, Laboratory of Soil Microbiology, University of Sao Paulo, Padua Dias Avenue, 11 CP 09, Piracicaba, São Paulo, 13418-900, Brazil
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Jiang B, Adebayo A, Jia J, Xing Y, Deng S, Guo L, Liang Y, Zhang D. Impacts of heavy metals and soil properties at a Nigerian e-waste site on soil microbial community. J Hazard Mater 2019; 362:187-195. [PMID: 30240992 DOI: 10.1016/j.jhazmat.2018.08.060] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/05/2018] [Accepted: 08/18/2018] [Indexed: 05/12/2023]
Abstract
Heavy metal contamination is a serious problem worldwide threatening soil environment and human health. In the present study, concentrations of 6 heavy metals at an electronic waste (e-waste) site in Nigeria were correlated to their mobility, showing distinct distribution pattern between surface soils and subsoils. Proteobacteria, Firmicutes, Acidobacteria and Planctomycetes dominated the indigenous soil microbial communities, and there was significant discrimination of bacterial taxonomic composition between the heavy metal contaminated and uncontaminated areas. The abundance of most bacterial taxa changed with heavy metal contamination level to different extent. The multivariate regression tree (MRT) analyses illustrated that main environmental variables influencing bacterial taxonomic composition included soil texture (31%) and organic carbon (14%), whereas microbial diversity was affected by soil pH (32%) and soil texture (14%). Our results surprisingly indicated that soil properties were more influential in determining soil bacterial composition and diversity than heavy metals even at the e-waste site which was seriously contaminated by heavy metals. The present study contributes to a deeper insight into the key environmental variables shaping the diversity and composition of soil microbes at heavy metal contaminated e-waste sites.
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Affiliation(s)
- Bo Jiang
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China
| | - Adedoyin Adebayo
- Department of Environmental Management and Toxicology, Federal University of Petroleum Resources, Effurun, Delta State, Nigeria
| | - Jianli Jia
- School of Chemical and Environmental Engineering, China University of Mining & Technology, Beijing, 100083, PR China
| | - Yi Xing
- School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing, 100083, PR China.
| | - Songqiang Deng
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, Hubei 430074, PR China
| | - Limin Guo
- School of Environmental Science and Engineering, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, Hubei 430074, PR China
| | - Yuting Liang
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China.
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing, 100084, PR China; Research Institute for Environmental Innovation (Suzhou), Tsinghua, Suzhou 215163, PR China.
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Boedeker C, Schüler M, Reintjes G, Jeske O, van Teeseling MCF, Jogler M, Rast P, Borchert D, Devos DP, Kucklick M, Schaffer M, Kolter R, van Niftrik L, Engelmann S, Amann R, Rohde M, Engelhardt H, Jogler C. Determining the bacterial cell biology of Planctomycetes. Nat Commun 2017; 8:14853. [PMID: 28393831 PMCID: PMC5394234 DOI: 10.1038/ncomms14853] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 02/07/2017] [Indexed: 02/08/2023] Open
Abstract
Bacteria of the phylum Planctomycetes have been previously reported to possess several features that are typical of eukaryotes, such as cytosolic compartmentalization and endocytosis-like macromolecule uptake. However, recent evidence points towards a Gram-negative cell plan for Planctomycetes, although in-depth experimental analysis has been hampered by insufficient genetic tools. Here we develop methods for expression of fluorescent proteins and for gene deletion in a model planctomycete, Planctopirus limnophila, to analyse its cell organization in detail. Super-resolution light microscopy of mutants, cryo-electron tomography, bioinformatic predictions and proteomic analyses support an altered Gram-negative cell plan for Planctomycetes, including a defined outer membrane, a periplasmic space that can be greatly enlarged and convoluted, and an energized cytoplasmic membrane. These conclusions are further supported by experiments performed with two other Planctomycetes, Gemmata obscuriglobus and Rhodopirellula baltica. We also provide experimental evidence that is inconsistent with endocytosis-like macromolecule uptake; instead, extracellular macromolecules can be taken up and accumulate in the periplasmic space through unclear mechanisms.
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Affiliation(s)
| | - Margarete Schüler
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Greta Reintjes
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Olga Jeske
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Muriel C. F. van Teeseling
- Department of Microbiology, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands
- Department of Cellular Microbiology, Philipps-University Marburg, Faculty of Biology, Hans-Meerwein-Straße 4, 35043 Marburg, Germany
| | - Mareike Jogler
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Patrick Rast
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Daniela Borchert
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Damien P. Devos
- Department of Cell biology and Biotechnology, CABD, Pablo de Olavide University-CSIC, Carretera de Utrera km1, 41013 Sevilla, Spain
| | - Martin Kucklick
- Helmholtz Center for Infection Research GmbH, Inhoffenstraße 7, 38124 Braunschweig, Germany
- Department of Microbial Proteomics, Technical University Braunschweig, Institute for Microbiology, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Roberto Kolter
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Laura van Niftrik
- Department of Microbiology, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands
| | - Susanne Engelmann
- Helmholtz Center for Infection Research GmbH, Inhoffenstraße 7, 38124 Braunschweig, Germany
- Department of Microbial Proteomics, Technical University Braunschweig, Institute for Microbiology, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Manfred Rohde
- Helmholtz Center for Infection Research GmbH, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Harald Engelhardt
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christian Jogler
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
- Department of Microbiology, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands
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10
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Zdanowski MK, Bogdanowicz A, Gawor J, Gromadka R, Wolicka D, Grzesiak J. Enrichment of Cryoconite Hole Anaerobes: Implications for the Subglacial Microbiome. Microb Ecol 2017; 73:532-538. [PMID: 27822618 PMCID: PMC5348551 DOI: 10.1007/s00248-016-0886-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/24/2016] [Indexed: 05/30/2023]
Abstract
Glaciers have recently been recognized as ecosystems comprised of several distinct habitats: a sunlit and oxygenated glacial surface, glacial ice, and a dark, mostly anoxic glacial bed. Surface meltwaters annually flood the subglacial sediments by means of drainage channels. Glacial surfaces host aquatic microhabitats called cryoconite holes, regarded as "hot spots" of microbial abundance and activity, largely contributing to the meltwaters' bacterial diversity. This study presents an investigation of cryoconite hole anaerobes and discusses their possible impact on subglacial microbial communities, combining 16S rRNA gene fragment amplicon sequencing and the traditional enrichment culture technique. Cryoconite hole sediment harbored bacteria belonging mainly to the Proteobacteria (21%), Bacteroidetes (16%), Actinobacteria (14%), and Planctomycetes (6%) phyla. An 8-week incubation of those sediments in Postgate C medium for sulfate reducers in airtight bottles, emulating subglacial conditions, eliminated a great majority of dominant taxa, leading to enrichment of the Firmicutes (62%), Proteobacteria (14%), and Bacteroidetes (13%), which consisted of anaerobic genera like Clostridium, Psychrosinus, Paludibacter, and Acetobacterium. Enrichment of Pseudomonas spp. also occurred, suggesting it played a role as a dominant oxygen scavenger, providing a possible scenario for anaerobic niche establishment in subglacial habitats. To our knowledge, this is the first paper to provide insight into the diversity of the anaerobic part of the cryoconite hole microbial community and its potential to contribute to matter turnover in anoxic, subglacial sites.
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Affiliation(s)
- Marek K Zdanowski
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Albert Bogdanowicz
- Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Jan Gawor
- Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Robert Gromadka
- Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Dorota Wolicka
- Institute of Geochemistry, Mineralogy and Petrology, Faculty of Geology, Warsaw University, Warsaw, Poland
| | - Jakub Grzesiak
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland.
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11
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Danilova OV, Belova SE, Gagarinova IV, Dedysh SN. Microbial Community Composition and Methanotroph Diversity of a Subarctic Wetland in Russia. Mikrobiologiia 2016; 85:545-554. [PMID: 29364602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This study assessed the microbial diversity, activity, and composition of methane-oxidizing communities of a subarctic wetland in Russia,with mosaic cover of Sphagnum mosses and lichens of the genera Cladonia and Cetraria. Potential methane-oxidizing activity of peat sampled from lichen-dominated wetland sites was higher than that in the sites dominated by Sphagnum mosses. In peat from lichendominated sites, major bacterial groups identified by high-throughput sequencing of the 16S rRNA genes were the Acidobacteria (35.4-41.2% of total 16S rRNA gene reads), Alphaproteobacteria (19.1-24.2%), Gammaproteobacteria (7.9-11.1%), Actinobacteria (5.5-13.2%), Planctomycetes (7.2-9.5%), and Verrucomicrobia (5.1-9.5%). The distinctive feature of this community was high proportion of Subdivision 2 Acidobacteria, which are not char- acteristic for boreal Sphagnum peat bogs. Methanotrophic community composition was determined by mo- lecular analysis of the pmoA gene encoding particulate methane monooxygenase. Most (-80%) of all pmoA gene fragments revealed in peat from lichen-dominated sites belonged to the phylogenetic lineage represented by a microaerobic spiral-shaped methanotroph, "Candidatus Methylospira mobilis." Members of the genus Methylocystis, which are typical inhabitants of boreal Sphagnum peat bogs, represented only a minor group of indigenous methanotrophs. The specific feature of a methanotrophic community in peat from lichen-dominated sites was the presence of uncultivated USCa (Upland Soil Cluster alpha) methanotrophs, which are typical for acidic upland soils showing atmospheric methane oxidation. The methanotrophic community composition in lichen-dominated sites of a tundra wetland, therefore, was markedly different from that in bo- real Sphagnum peat bogs.
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12
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Chernitsyna SM, Khal'zov IA, Khanaeva TA, Morozov IV, Klimenkov IV, Pimenov NV, Zemskayal TI. Microbial Community Associated with Thioploca sp. Sheaths in the Area of the Posolski Bank Methane Seep, Southern Baikal. Mikrobiologiia 2016; 85:522-530. [PMID: 29364600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacterial mats formed by a colorless sulfur bacterium Thioploca sp. in the area of the Posolski Bank cold methane seep (southern Baikal) were -studied using electron microscopy and phylogenetic analysis. Morphologically the bacteria were identified as Thioploca ingrica.- Confocal microscopy of DAPI-stained samples revealed numerous rod-shaped, filamentous, and spiral microorganisms in the sheaths, as well as in- side and between the trichomes. Transmission electron microscopy revealed nonvacuolated bacteria and small cells-without cell envelopes within the sheath. Bacteria with pronounced intracytoplasmic membranes characteristic; of type I methanotrophs were observed at the outer side of the sheath. Based on analysis of the 16S rRNA gene sequences, the following phyla were idenified in the sheath community: Bacteroidetes, Nitro- spira, Chloroflexi, Planctomycetes, Verrucomicrobia,'y-, and 6-Proteobacteria, Euryarchaeota, Crenarchaeota, and Thaumarchaeota, as well as anammox bacteria. A hypothetical scheme of matter flows in the Lake Baikal bacterial mats was proposed based on the data on metabolism of the cultured homologues.
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13
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Nikolaev A, Kozlov MN, Kevbrina MV, Dorofeev AG, Pimenov NV, Kallistova AY, Grachev VA, Kazakova EA, Zharkov AV, Kuznetsov BB, Patutina EO, Bumazhkin BK. [Candidatus "Jettenia moscovienalis" sp. nov., a New Species of Bacteria Carrying out Anaerobic Ammonium Oxidation]. Mikrobiologiia 2015; 84:236-243. [PMID: 26263630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A new species of bacteria oxidizing ammonium with nitrite under anoxic conditions was isolated from the activated sludge of a semi-industrial bioreactor treating digested sludge of the Kuryanovo wastewater treatment plant (Moscow, Russia). Physiological, morphological, and molecular genetic characterization of the isolate was carried out. The cells were ovoid (-0.5 x 0.8 μm), with the intracellular membrane structures characteristic of anammox bacteria (anammoxosome and paryphoplasm); unlike other anammox bacteria, it possessed extensive intracellular membrane structures located in layers parallel to the cytoplasmic membrane, but never close to the anammoxosome. The cells formed aggregates 5-28 μm in diameter and readily attached to solid surfaces. The cells were morphologically labile, easily plasmolyzed, and lost their content. Doubling time was 28 days, μ(max) = 0.025 day(-1); optimal temperature and pH for growth were 20-45 degrees C and 8.0, respectively. Phylogenetic analysis of the 16S rRNA gene sequences suggested its classification as a new species of the candidate genus Jettenia (order Planctomycetales). The name Candidatus "Jettenia moscovienalis" sp. nov. was proposed for the new bacterium.
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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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. Biochim Biophys 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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Cai HY, Yan ZS, Wang AJ, Krumholz LR, Jiang HL. Analysis of the attached microbial community on mucilaginous cyanobacterial aggregates in the eutrophic Lake Taihu reveals the importance of Planctomycetes. Microb Ecol 2013; 66:73-83. [PMID: 23571665 DOI: 10.1007/s00248-013-0224-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 03/22/2013] [Indexed: 05/12/2023]
Abstract
The phylogenetic diversity of the microbial community assemblage of the carpet-like mucilaginous cyanobacterial blooms in the eutrophic Lake Taihu was investigated. 16S ribosomal DNA clone libraries produced from the DNA of cyanobacterial assemblages that had been washed to remove unattached bacteria contained only cyanobacteria. However, a further treatment which included grinding the freeze-dried material to physically detach cells followed by the removal of larger cells by filtration allowed us to detect a large variety of bacteria within the cyanobacterial bloom community. Interestingly, the dominant members of the microbial community were Planctomycetes followed by Cytophaga-Flavobacterium-Bacteroides (CFB), Betaproteobacteria, and Gammaproteobacteria. The analysis of the 16S ribosomal DNA clone libraries made from enrichment culture revealed much higher phylogenetic diversity of bacteria. Dominant bacterial groups in the enrichment system were identified as members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria subdivisions, CFB group, and Planctomycetes. In addition, the clone libraries constructed from Planctomycetes-specific 16S ribosomal RNA primers also verified that the enrichment allowed a diversity of Planctomycetes to proliferate, although the community composition was altered after enrichment.
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Affiliation(s)
- Hai-Yuan Cai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, People's Republic of China
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17
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Hu BL, Shen LD, Liu S, Cai C, Chen TT, Kartal B, Harhangi HR, Op den Camp HJM, Lou LP, Xu XY, Zheng P, Jetten MSM. Enrichment of an anammox bacterial community from a flooded paddy soil. Environ Microbiol Rep 2013; 5:483-489. [PMID: 23754729 DOI: 10.1111/1758-2229.12038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 01/03/2013] [Accepted: 01/18/2013] [Indexed: 06/02/2023]
Abstract
This study describes the enrichment of anammox bacteria in a column simulating oxygen limited flooded paddy soils, which are important man-made ecosystems that receive substantial amounts of fixed nitrogen. The upper 50 cm of the paddy soil, containing a high amount of ammonium [1.6-10.4 mmol N kg (dry weight)(-1)], was selected as the inoculum for anammox enrichment. After 18 months of incubation with freshwater from the paddy soil ecosystem, the enrichment culture consumed approximately 4 mmol ammonium l(-1) day(-1) and 5 mmol nitrite l(-1) day(-1). The maximum specific anammox activity of the culture was 35.7 μmol N g (dry weight)(-1) h(-1). Fluorescence in situ hybridization indicated that anammox cells constituted 50% ± 10% of the enrichment culture. The phylogenetic analyses of 16S rRNA and the diagnostic hydrazine synthase (hzsA) genes showed that two dominant anammox species were enriched from paddy soil. The enriched Candidatus Anammoxoglobus-like organisms showed a 16S rRNA gene similarity of 97.5-99.2% to Candidatus Anammoxoglobus propionicus and the Candidatus Jettenia-like organisms showed 92.1-93.1% 16S rRNA gene identity to Candidatus Jettenia asiatica. Real-time quantitative PCR of hzsA gene suggested that up to 10(10) copies g (dry weight)(-1) of soil anammox bacteria were present in the enrichment culture.
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Affiliation(s)
- Bao-lan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
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18
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van de Vossenberg J, Woebken D, Maalcke WJ, Wessels HJCT, Dutilh BE, Kartal B, Janssen-Megens EM, Roeselers G, Yan J, Speth D, Gloerich J, Geerts W, van der Biezen E, Pluk W, Francoijs KJ, Russ L, Lam P, Malfatti SA, Tringe SG, Haaijer SCM, Op den Camp HJM, Stunnenberg HG, Amann R, Kuypers MMM, Jetten MSM. The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium. Environ Microbiol 2013; 15:1275-89. [PMID: 22568606 PMCID: PMC3655542 DOI: 10.1111/j.1462-2920.2012.02774.x] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 04/11/2012] [Accepted: 04/12/2012] [Indexed: 11/28/2022]
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the 'Candidatus Scalindua' species, but the molecular basis of their metabolism and competitive fitness is presently unknown. We applied community sequencing of a marine anammox enrichment culture dominated by 'Candidatus Scalindua profunda' to construct a genome assembly, which was subsequently used to analyse the most abundant gene transcripts and proteins. In the S. profunda assembly, 4756 genes were annotated, and only about half of them showed the highest identity to the only other anammox bacterium of which a metagenome assembly had been constructed so far, the freshwater 'Candidatus Kuenenia stuttgartiensis'. In total, 2016 genes of S. profunda could not be matched to the K. stuttgartiensis metagenome assembly at all, and a similar number of genes in K.stuttgartiensis could not be found in S. profunda. Most of these genes did not have a known function but 98 expressed genes could be attributed to oligopeptide transport, amino acid metabolism, use of organic acids and electron transport. On the basis of the S. profunda metagenome, and environmental metagenome data, we observed pronounced differences in the gene organization and expression of important anammox enzymes, such as hydrazine synthase (HzsAB), nitrite reductase (NirS) and inorganic nitrogen transport proteins. Adaptations of Scalindua to the substrate limitation of the ocean may include highly expressed ammonium, nitrite and oligopeptide transport systems and pathways for the transport, oxidation, and assimilation of small organic compounds that may allow a more versatile lifestyle contributing to the competitive fitness of Scalindua in the marine realm.
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Affiliation(s)
- Jack van de Vossenberg
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Dagmar Woebken
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, Germany
| | - Wouter J Maalcke
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Hans J C T Wessels
- Nijmegen Centre for Mitochondrial Disorders, Nijmegen Proteomics Facility, Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic disease, Radboud University Nijmegen Medical CentreNijmegen, the Netherlands
| | - Bas E Dutilh
- CMBI, Radboud University Nijmegen Medical CentreNijmegen, the Netherlands
| | - Boran Kartal
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Eva M Janssen-Megens
- Nijmegen Center for Molecular Life Sciences, Department of Molecular Biology, Radboud University NijmegenNijmegen, the Netherlands
| | - Guus Roeselers
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Jia Yan
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Daan Speth
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Jolein Gloerich
- Nijmegen Proteomics Facility, Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic disease, Radboud University Nijmegen Medical CentreNijmegen, the Netherlands
| | - Wim Geerts
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Erwin van der Biezen
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Wendy Pluk
- Nijmegen Proteomics Facility, Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic disease, Radboud University Nijmegen Medical CentreNijmegen, the Netherlands
| | - Kees-Jan Francoijs
- Nijmegen Center for Molecular Life Sciences, Department of Molecular Biology, Radboud University NijmegenNijmegen, the Netherlands
| | - Lina Russ
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Phyllis Lam
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, Germany
| | | | | | - Suzanne C M Haaijer
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
| | - Henk G Stunnenberg
- Nijmegen Center for Molecular Life Sciences, Department of Molecular Biology, Radboud University NijmegenNijmegen, the Netherlands
| | - Rudi Amann
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, Germany
| | - Marcel M M Kuypers
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, Bremen, Germany
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen6525 AJ Nijmegen, the Netherlands
- Department of Biotechnology, Delft University of TechnologyDelft, the Netherlands
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19
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DeLorenzo S, Bräuer SL, Edgmont CA, Herfort L, Tebo BM, Zuber P. Ubiquitous dissolved inorganic carbon assimilation by marine bacteria in the Pacific Northwest coastal ocean as determined by stable isotope probing. PLoS One 2012; 7:e46695. [PMID: 23056406 PMCID: PMC3463544 DOI: 10.1371/journal.pone.0046695] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Accepted: 09/06/2012] [Indexed: 11/25/2022] Open
Abstract
In order to identify bacteria that assimilate dissolved inorganic carbon (DIC) in the northeast Pacific Ocean, stable isotope probing (SIP) experiments were conducted on water collected from 3 different sites off the Oregon and Washington coasts in May 2010, and one site off the Oregon Coast in September 2008 and March 2009. Samples were incubated in the dark with 2 mM (13)C-NaHCO(3), doubling the average concentration of DIC typically found in the ocean. Our results revealed a surprising diversity of marine bacteria actively assimilating DIC in the dark within the Pacific Northwest coastal waters, indicating that DIC fixation is relevant for the metabolism of different marine bacterial lineages, including putatively heterotrophic taxa. Furthermore, dark DIC-assimilating assemblages were widespread among diverse bacterial classes. Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes dominated the active DIC-assimilating communities across the samples. Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia were also implicated in DIC assimilation. Alteromonadales and Oceanospirillales contributed significantly to the DIC-assimilating Gammaproteobacteria within May 2010 clone libraries. 16S rRNA gene sequences related to the sulfur-oxidizing symbionts Arctic96BD-19 were observed in all active DIC assimilating clone libraries. Among the Alphaproteobacteria, clones related to the ubiquitous SAR11 clade were found actively assimilating DIC in all samples. Although not a dominant contributor to our active clone libraries, Betaproteobacteria, when identified, were predominantly comprised of Burkholderia. DIC-assimilating bacteria among Deltaproteobacteria included members of the SAR324 cluster. Our research suggests that DIC assimilation is ubiquitous among many bacterial groups in the coastal waters of the Pacific Northwest marine environment and may represent a significant metabolic process.
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Affiliation(s)
- Suzanne DeLorenzo
- Center for Coastal Margin Observation & Prediction and Division of Environmental & Biomolecular Systems, Oregon Health & Science University, Beaverton, Oregon, United States of America.
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Kulichevskaia IS, Ivanova AA, Belova SE, Dedysh SN. [A novel filamentous planctomycete of the Isosphaera-Singulisphaera group isolated from a Sphagnum peat bog]. Mikrobiologiia 2012; 81:486-492. [PMID: 23156692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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McInerney JO, Martin WF, Koonin EV, Allen JF, Galperin MY, Lane N, Archibald JM, Embley TM. Planctomycetes and eukaryotes: a case of analogy not homology. Bioessays 2011; 33:810-7. [PMID: 21858844 PMCID: PMC3795523 DOI: 10.1002/bies.201100045] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 07/13/2011] [Accepted: 07/15/2011] [Indexed: 11/11/2022]
Abstract
Planctomycetes, Verrucomicrobia and Chlamydia are prokaryotic phyla, sometimes grouped together as the PVC superphylum of eubacteria. Some PVC species possess interesting attributes, in particular, internal membranes that superficially resemble eukaryotic endomembranes. Some biologists now claim that PVC bacteria are nucleus-bearing prokaryotes and are considered evolutionary intermediates in the transition from prokaryote to eukaryote. PVC prokaryotes do not possess a nucleus and are not intermediates in the prokaryote-to-eukaryote transition. Here we summarise the evidence that shows why all of the PVC traits that are currently cited as evidence for aspiring eukaryoticity are either analogous (the result of convergent evolution), not homologous, to eukaryotic traits; or else they are the result of horizontal gene transfers.
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Affiliation(s)
- James O McInerney
- Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland.
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Pollet T, Tadonléké RD, Humbert JF. Spatiotemporal changes in the structure and composition of a less-abundant bacterial phylum (Planctomycetes) in two perialpine lakes. Appl Environ Microbiol 2011; 77:4811-21. [PMID: 21602381 PMCID: PMC3147387 DOI: 10.1128/aem.02697-10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Accepted: 05/04/2011] [Indexed: 11/20/2022] Open
Abstract
We used fingerprinting and cloning-sequencing to study the spatiotemporal dynamics and diversity of Planctomycetes in two perialpine lakes with contrasting environmental conditions. Planctomycetes, which are less-abundant bacteria in freshwater ecosystems, appeared to be structured in the same way as the entire bacterial community in these ecosystems. They were more diversified and displayed fewer temporal variations in the hypolimnia than in the epilimnia. Like the more-abundant bacterial groups in aquatic systems, Planctomycetes communities seem to be composed of a very small number of abundant and widespread operational taxonomic units (OTUs) and a large number of OTUs that are present at low abundance. This indicates that the concept of "abundant or core" and "rare" bacterial phylotypes could also be applied to less-abundant freshwater bacterial phyla. The richness and diversity of Planctomycetes were mainly driven by pH and were similar in both of the lakes studied, whereas the composition of the Planctomycetes community seemed to be determined by a combination of factors including temperature, pH, and nutrients. The relative abundances of the dominant OTUs varied over time and were differently associated with abiotic factors. Our findings demonstrate that less-abundant bacterial phyla, such as Planctomycetes, can display strong spatial and seasonal variations linked to environmental conditions and suggest that their functional role in the lakes studied might be attributable mainly to a small number of phylotypes and vary over space and time in the water column.
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Affiliation(s)
- Thomas Pollet
- INRA-UMR CARRTEL, BP511, 74203 Thonon-les-Bains Cedex, France
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