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Ivanova AA, Kulichevskaya IS, Dedysh SN. Gemmata palustris sp. nov., a Novel Planctomycete from a Fen in Northwestern Russia. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721050076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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2
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Mu Z, Dong S, Li Y, Li S, Shen H, Zhang J, Han Y, Xu Y, Zhao Z. Soil Bacterial Community Responses to N Application and Warming in a Qinghai-Tibetan Plateau Alpine Steppe. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.709518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nitrogen deposition and climate warming can alter soil bacterial communities. However, the response of soil bacteria in an alpine steppe to these changes is largely unknown. In this study, a field experiment was performed on the northeastern Qinghai-Tibetan Plateau to determine the changes in soil bacterial communities of alpine steppes in response to nitrogen application and warming. The experiment consisted of four treatments, namely no-N application with no-warming (CK), N application (8 kg N ha−1 year−1) with no-warming (N), warming with no-N application (W), and N application (8 kg N ha−1 year−1) with warming (W&N). This study aimed to investigate (1) the changes in soil bacterial diversity and community structure under simulated nitrogen deposition and warming conditions, and (2) the key environmental factors responsible for these changes. Based on the results, soil bacterial diversity and community composition did not change significantly in the short term. Warming had a significant effect on overall bacterial composition, rare species composition, and individual bacterial taxa. Besides, the interaction between nitrogen application and warming had a significant effect on community β-diversity. Above-ground plant variables were highly correlated with bacterial community characteristics. Nitrogen application and warming did not significantly alter the distribution range of the bacterial community. Overall, this study suggests that soil bacterial communities can remain relatively stable at the level of simulated nitrogen application and warming and that short-term climatic changes may have no significant impacts on soil bacterial communities.
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Godinho O, Botelho R, Albuquerque L, Wiegand S, Kallscheuer N, da Costa MS, Lobo-da-Cunha A, Jogler C, Lage OM. Bremerella alba sp. nov., a novel planctomycete isolated from the surface of the macroalga Fucus spiralis. Syst Appl Microbiol 2021; 44:126189. [PMID: 33852992 DOI: 10.1016/j.syapm.2021.126189] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/25/2022]
Abstract
A bacterial strain, designated FF15T, was isolated from the thallus surface of the macroalga Fucus spiralis sampled on a rocky beach in Porto, Portugal. Based on the 16S rRNA gene sequence, strain FF15T was affiliated to the phylum Planctomycetes. This strain forms white colonies on modified M13 medium and the cells are pear-shaped, can form rosettes, divide by polar budding and are motile. The novel isolate is mesophilic and neutrophilic with an optimum growth temperature of about 30 °C and an optimum pH for growth between 6.5 and 7.5. It showed growth over a broad range of salinities (0-9% NaCl - optimum at 1.5%). No additional vitamins are required for growth. It is cytochrome c oxidase and catalase positive. The major respiratory quinone was menaquinone 6 (MK-6). Genome sequencing revealed a genome size of 6.37 Mbp and a DNA G + C content of 54.2%. Analysis of phylogenetic markers, including similarities of the 16S rRNA gene sequence, rpoB gene sequence, as well as Percentage of Conserved Proteins (POCP), Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI), suggest the affiliation of strain FF15T to "Bremerella", a recently described genus in the family Pirellulaceae. Based on the genotypic, phylogenetic, chemotaxonomic, physiological and biochemical characterization, we described a new species represented by strain FF15T (=CECT 8078T = LMG 31936T), for which we propose the name Bremerella alba snov.
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Affiliation(s)
- Ofélia Godinho
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
| | - Raquel Botelho
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Luciana Albuquerque
- Centro de Neurociências e Biologia Celular, Universidade de Coimbra, 3004-504 Coimbra, Portugal
| | - Sandra Wiegand
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands; Institute for Biological Surfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Nicolai Kallscheuer
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Milton S da Costa
- Centro de Neurociências e Biologia Celular, Universidade de Coimbra, 3004-504 Coimbra, Portugal; Departamento de Ciências da Vida, Universidade de Coimbra, 3000-456 Coimbra, Portugal
| | - Alexandre Lobo-da-Cunha
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal; Laboratório de Biologia Celular, Instituto de Ciências Biomédicas Abel Salazar, ICBAS, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Christian Jogler
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands; Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal.
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Kaboré OD, Godreuil S, Drancourt M. Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories. Front Cell Infect Microbiol 2020; 10:519301. [PMID: 33330115 PMCID: PMC7734314 DOI: 10.3389/fcimb.2020.519301] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients' specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.
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Affiliation(s)
- Odilon D. Kaboré
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sylvain Godreuil
- Université de Montpellier UMR 1058 UMR MIVEGEC, UMR IRD 224-CNRS Inserm, Montpellier, France
| | - Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
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Bacterial analysis in the early developmental stages of the black tiger shrimp (Penaeus monodon). Sci Rep 2020; 10:4896. [PMID: 32184459 PMCID: PMC7078212 DOI: 10.1038/s41598-020-61559-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/28/2020] [Indexed: 12/17/2022] Open
Abstract
Microbial colonization is an essential process in the early life of animal hosts—a crucial phase that could help influence and determine their health status at the later stages. The establishment of bacterial community in a host has been comprehensively studied in many animal models; however, knowledge on bacterial community associated with the early life stages of Penaeus monodon (the black tiger shrimp) is still limited. Here, we examined the bacterial community structures in four life stages (nauplius, zoea, mysis and postlarva) of two black tiger shrimp families using 16S rRNA amplicon sequencing by a next-generation sequencing. Although the bacterial profiles exhibited different patterns in each developmental stage, Bacteroidetes, Proteobacteria, Actinobacteria and Planctomycetes were identified as common bacterial phyla associated with shrimp. Interestingly, the bacterial diversity became relatively stable once shrimp developed to postlarvae (5-day-old and 15-day-old postlarval stages), suggesting an establishment of the bacterial community in matured shrimp. To our knowledge, this is the first report on bacteria establishment and assembly in early developmental stages of P. monodon. Our findings showed that the bacterial compositions could be shaped by different host developmental stages where the interplay of various host-associated factors, such as physiology, immune status and required diets, could have a strong influence.
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Kaboré OD, Loukil A, Godreuil S, Drancourt M. Co-culture models illustrate the digestion of Gemmata spp. by phagocytes. Sci Rep 2018; 8:13311. [PMID: 30190504 PMCID: PMC6127157 DOI: 10.1038/s41598-018-31667-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 08/10/2018] [Indexed: 11/25/2022] Open
Abstract
Gemmata spp. bacteria thrive in the same aquatic environments as free-living amoebae. DNA-based detection of Gemmata spp. sequences in the microbiota of the human digestive tract and blood further questioned the susceptibility of Gemmata spp. to phagocytes. Here, Gemmata obscuriglobus and Gemmata massiliana were co-cultured with the amoebae Acanthamoeba polyphaga, Acanthamoeba castellanii, Acanthamoeba griffini and THP-1 macrophage-like phagocytes. All experiments were performed in five independant replicates. The ratio amoeba/bacteria was 1:20 and the ratio THP-1/bacteria was 1:10. After a 2-hour co-culture, extracellular bacteria were killed by kanamycin or amikacin and eliminated. The intracellular location of Gemmata bacteria was specified by confocal microscopy. Microscopic enumerations and culture-based enumerations of colony-forming units were performed at T = 0, 1, 2, 3, 4, 8, 16, 24, 48 and 72 hours post-infection. Then, Gemmata bacteria were engulfed into the phagocytes’ cytoplasmic vacuoles, more than (98 ± 2)% of Gemmata bacteria, compared to controls, were destroyed by phagocytic cells after a 48-h co-culture according to microscopy and culture results, and no positive culture was observed at T = 72-hours. Under our co-culture conditions, Gemmata bacteria were therefore susceptible to the environmental and host phagocytes here investigated. These data suggest that these Acanthamoeba species and THP-1 cells cannot be used to isolate G. massiliana and G. obscuriglobus under the co-culture conditions applied in this study. Although the THP-1 response can point towards potential responses that might occur in vivo, these responses should first bevalidated by in vivo studies to draw definite conclusions.
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Affiliation(s)
- Odilon D Kaboré
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Ahmed Loukil
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sylvain Godreuil
- Université de Montpellier UMR 1058 UMR MIVEGEC, UMR IRD 224-CNRS Inserm, 1058, Montpellier, France
| | - Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France.
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Genome Analysis of Fimbriiglobus ruber SP5 T, a Planctomycete with Confirmed Chitinolytic Capability. Appl Environ Microbiol 2018; 84:AEM.02645-17. [PMID: 29374042 DOI: 10.1128/aem.02645-17] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 01/21/2018] [Indexed: 11/20/2022] Open
Abstract
Members of the bacterial order Planctomycetales have often been observed in associations with Crustacea. The ability to degrade chitin, however, has never been reported for any of the cultured planctomycetes although utilization of N-acetylglucosamine (GlcNAc) as a sole carbon and nitrogen source is well recognized for these bacteria. Here, we demonstrate the chitinolytic capability of a member of the family Gemmataceae, Fimbriiglobus ruber SP5T, which was isolated from a peat bog. As revealed by metatranscriptomic analysis of chitin-amended peat, the pool of 16S rRNA reads from F. ruber increased in response to chitin availability. Strain SP5T displayed only weak growth on amorphous chitin as a sole source of carbon but grew well with chitin as a source of nitrogen. The genome of F. ruber SP5T is 12.364 Mb in size and is the largest among all currently determined planctomycete genomes. It encodes several enzymes putatively involved in chitin degradation, including two chitinases affiliated with the glycoside hydrolase (GH) family GH18, GH20 family β-N-acetylglucosaminidase, and the complete set of enzymes required for utilization of GlcNAc. The gene encoding one of the predicted chitinases was expressed in Escherichia coli, and the endochitinase activity of the recombinant enzyme was confirmed. The genome also contains genes required for the assembly of type IV pili, which may be used to adhere to chitin and possibly other biopolymers. The ability to use chitin as a source of nitrogen is of special importance for planctomycetes that inhabit N-depleted ombrotrophic wetlands.IMPORTANCE Planctomycetes represent an important part of the microbial community in Sphagnum-dominated peatlands, but their potential functions in these ecosystems remain poorly understood. This study reports the presence of chitinolytic potential in one of the recently described peat-inhabiting members of the family Gemmataceae, Fimbriiglobus ruber SP5T This planctomycete uses chitin, a major constituent of fungal cell walls and exoskeletons of peat-inhabiting arthropods, as a source of nitrogen in N-depleted ombrotrophic Sphagnum-dominated peatlands. This study reports the chitin-degrading capability of representatives of the order Planctomycetales.
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Storesund JE, Lanzèn A, García-Moyano A, Reysenbach AL, Øvreås L. Diversity patterns and isolation of Planctomycetes associated with metalliferous deposits from hydrothermal vent fields along the Valu Fa Ridge (SW Pacific). Antonie van Leeuwenhoek 2018; 111:841-858. [PMID: 29423768 DOI: 10.1007/s10482-018-1026-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 01/25/2018] [Indexed: 02/06/2023]
Abstract
The microbial diversity associated with diffuse venting deep-sea hydrothermal deposits is tightly coupled to the geochemistry of the hydrothermal fluids. Previous 16S rRNA gene amplicon sequencing (metabarcoding) of marine iron-hydroxide deposits along the Arctic Mid Ocean Ridge, revealed the presence of diverse bacterial communities associated with these deposits (Storesund and Øvreås in Antonie van Leeuwenhoek 104:569-584, 2013). One of the most abundant and diverse phyla detected was the enigmatic Planctomycetes. Here we report on the comparative analyses of the diversity and distribution patterns of Planctomycetes associated with metalliferous deposits from two diffuse-flow hydrothermal vent fields (Mariner and Vai Lili) from the Valu Fa Ridge in the Southwestern Pacific. Metabarcoding of 16S rRNA genes showed that the major prokaryotic phyla were Proteobacteria (51-73% of all 16S rRNA gene reads), Epsilonbacteraeota (0.5-19%), Bacteriodetes (5-17%), Planctomycetes (0.4-11%), Candidatus Latescibacteria (0-5%) and Marine Benthic Group E (Hydrothermarchaeota) (0-5%). The two different sampling sites differed considerably in overall community composition. The abundance of Planctomycetes also varied substantially between the samples and the sites, with the majority of the sequences affiliated with uncultivated members of the classes Planctomycetacia and Phycisphaerae, and other deep branching lineages. Seven different strains affiliated with the order Planctomycetales were isolated, mostly from the Vai Lili samples, where also the highest Planctomycetales diversity was seen. Most of the isolates were affiliated with the genera Gimesia, Rhodopirellula and Blastopirellula. One isolate was only distantly related to known cultured, but uncharacterized species within the Pir4 group. This study shows that the deep-sea Planctomycetes represent a very heterogeneous group with a high phylogenetic diversity and a substantial potential for novel organism discovery in these deep ocean environments.
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Affiliation(s)
- Julia Endresen Storesund
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 53B, Postboks 7803, 5006, Bergen, Norway
| | - Anders Lanzèn
- AZTI, Marine Research Division, Herrera Kaia, Portualdea s/n, 20110, Pasaia, Spain.,IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain
| | - Antonio García-Moyano
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 53B, Postboks 7803, 5006, Bergen, Norway
| | | | - Lise Øvreås
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 53B, Postboks 7803, 5006, Bergen, Norway.
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Marinho MC, Lage OM, Catita J, Antunes SC. Adequacy of planctomycetes as supplementary food source for Daphnia magna. Antonie van Leeuwenhoek 2017; 111:825-840. [PMID: 29222603 DOI: 10.1007/s10482-017-0997-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/01/2017] [Indexed: 11/30/2022]
Abstract
The nutritional quality of daphnids diet can influence their growth, reproduction and survival. In aquatic ecosystems, bacteria can contribute significantly to Daphnia diet by supporting, for instances, their high needs for phosphorus. The laboratory feeding of the model organisms Daphnia spp. is algal based, but should be improved to allow their better performance. The aim of this study was to evaluate the potential of two planctomycetes, Gemmata obscuriglobus and Rhodopirellula rubra, from exponential and stationary growth phases as alternative or supplementary food source for Daphnia magna. The actinobacterium Arthrobacter sp. was used for comparison. The feeding with only bacteria showed the inefficacy of both planctomycetes and actinobacteria as the only food source. However, when used in supplement to Raphidocelis subcapitata, a decrease in the age of first reproduction, a significant increase in reproductive output, in somatic growth and in rate of population increase was found for the highest cell densities of bacteria tested. The typical pink coloration of these bacteria present in daphnids body and eggs confirmed bacterial absorption and metabolization of their pigment. Planctomycetes yielded better results than the actinobacteria Arthrobacter but G. obscuriglobus that possesses sterols did not induce a better performance comparatively to R. rubra. No relation could be established between the feeding treatments that allowed improvement of Daphnia performance and the different kind of Daphnia' Fatty Acid Methyl Esters. The use of sonication to separate planctomycetal cells before feeding the daphnids proved to be efficient. We confirmed that R. subcapitata supplemented by bacteria allows a better growth performance of D. magna.
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Affiliation(s)
- M C Marinho
- Departamento de Biologia da Faculdade de Ciências da, Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - O M Lage
- Departamento de Biologia da Faculdade de Ciências da, Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal. .,Centro Interdisciplinar de Investigação Marinha e A8 Ambiental (CIIMAR/CIMAR), Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal.
| | - José Catita
- Paralab, SA, Valbom, Portugal.,CEBIMED - Faculty of Health Sciences, University Fernando Pessoa, Porto, Portugal
| | - S C Antunes
- Departamento de Biologia da Faculdade de Ciências da, Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,Centro Interdisciplinar de Investigação Marinha e A8 Ambiental (CIIMAR/CIMAR), Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, 4450-208, Matosinhos, Portugal
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Mestre M, Ferrera I, Borrull E, Ortega-Retuerta E, Mbedi S, Grossart HP, Gasol JM, Sala MM. Spatial variability of marine bacterial and archaeal communities along the particulate matter continuum. Mol Ecol 2017; 26:6827-6840. [PMID: 29117634 DOI: 10.1111/mec.14421] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 01/26/2023]
Abstract
Biotic and abiotic particles shape the microspatial architecture that defines the microbial aquatic habitat, being particles highly variable in size and quality along oceanic horizontal and vertical gradients. We analysed the prokaryotic (bacterial and archaeal) diversity and community composition present in six distinct particle size classes ranging from the pico- to the microscale (0.2 to 200 μm). Further, we studied their variations along oceanographic horizontal (from the coast to open oceanic waters) and vertical (from the ocean surface into the meso- and bathypelagic ocean) gradients. In general, prokaryotic community composition was more variable with depth than in the transition from the coast to the open ocean. Comparing the six size-fractions, distinct prokaryotic communities were detected in each size-fraction, and whereas bacteria were more diverse in the larger size-fractions, archaea were more diverse in the smaller size-fractions. Comparison of prokaryotic community composition among particle size-fractions showed that most, but not all, taxonomic groups have a preference for a certain size-fraction sustained with depth. Species sorting, or the presence of diverse ecotypes with distinct size-fraction preferences, may explain why this trend is not conserved in all taxa.
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Affiliation(s)
- Mireia Mestre
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Encarna Borrull
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| | - Eva Ortega-Retuerta
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain.,Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, UMR 7621, Université Pierre and Marie Curie (Paris 06), Sorbonne Universités, Banyuls-sur-Mer, France
| | - Susan Mbedi
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany.,Museum für Naturkunde - Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Hans-Peter Grossart
- Experimental Limnology, IGB-Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany.,Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
| | - M Montserrat Sala
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, ICM-CSIC, Barcelona, Catalunya, Spain
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11
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Seeger C, Butler MK, Yee B, Mahajan M, Fuerst JA, Andersson SGE. Tuwongella immobilis gen. nov., sp. nov., a novel non-motile bacterium within the phylum Planctomycetes. Int J Syst Evol Microbiol 2017; 67:4923-4929. [PMID: 29087267 PMCID: PMC5845749 DOI: 10.1099/ijsem.0.002271] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A gram-negative, budding, catalase negative, oxidase positive and non-motile bacterium (MBLW1T) with a complex endomembrane system has been isolated from a freshwater lake in southeast Queensland, Australia. Phylogeny based on 16S rRNA gene sequence analysis places the strain within the family Planctomycetaceae, related to Zavarzinella formosa (93.3 %), Telmatocola sphagniphila (93.3 %) and Gemmata obscuriglobus (91.9 %). Phenotypic and chemotaxonomic analysis demonstrates considerable differences to the type strains of the related genera. MBLW1T displays modest salt tolerance and grows optimally at pH values of 7.5–8.0 and at temperatures of 32–36 °C. Transmission electron microscopy analysis demonstrates the presence of a complex endomembrane system, however, without the typically condensed nucleoid structure found in related genera. The major fatty acids are 16 : 1 ω5c, 16 : 0 and 18 : 0. Based on discriminatory results from 16S rRNA gene sequence analysis, phenotypic, biochemical and chemotaxonomic analysis, MBLW1T should be considered as a new genus and species, for which the name Tuwongella immobilis gen. nov., sp. nov. is proposed. The type strain is MBLW1T (=CCUG 69661T=DSM 105045T).
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Affiliation(s)
- Christian Seeger
- Department of Cell and Molecular Biology, Molecular Evolution, Uppsala University, Box 596, 751 24 Uppsala, Sweden
| | - Margaret K Butler
- Australian Center for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Benjamin Yee
- Department of Cell and Molecular Biology, Molecular Evolution, Uppsala University, Box 596, 751 24 Uppsala, Sweden
| | - Mayank Mahajan
- Department of Cell and Molecular Biology, Molecular Evolution, Uppsala University, Box 596, 751 24 Uppsala, Sweden
| | - John A Fuerst
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Siv G E Andersson
- Department of Cell and Molecular Biology, Molecular Evolution, Uppsala University, Box 596, 751 24 Uppsala, Sweden
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12
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Patterns of bacterial diversity in the marine planktonic particulate matter continuum. ISME JOURNAL 2017; 11:999-1010. [PMID: 28045454 DOI: 10.1038/ismej.2016.166] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 10/04/2016] [Accepted: 10/17/2016] [Indexed: 12/24/2022]
Abstract
Depending on their relationship with the pelagic particulate matter, planktonic prokaryotes have traditionally been classified into two types of communities: free-living (FL) or attached (ATT) to particles, and are generally separated using only one pore-size filter in a differential filtration. Nonetheless, particulate matter in the oceans appears in a continuum of sizes. Here we separated this continuum into six discrete size-fractions, from 0.2 to 200 μm, and described the prokaryotes associated to each of them. Each size-fraction presented different bacterial communities, with a range of 23-42% of unique (OTUs) in each size-fraction, supporting the idea that they contained distinct types of particles. An increase in richness was observed from the smallest to the largest size-fractions, suggesting that increasingly larger particles contributed new niches. Our results show that a multiple size-fractionation provides a more exhaustive description of the bacterial diversity and community structure than the use of only one filter. In addition, and based on our results, we propose an alternative to the dichotomy of FL or ATT lifestyles, in which we differentiate the taxonomic groups with preference for the smaller fractions, those that do not show preferences for small or large fractions, and those that preferentially appear in larger fractions.
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Kohn T, Heuer A, Jogler M, Vollmers J, Boedeker C, Bunk B, Rast P, Borchert D, Glöckner I, Freese HM, Klenk HP, Overmann J, Kaster AK, Rohde M, Wiegand S, Jogler C. Fuerstia marisgermanicae gen. nov., sp. nov., an Unusual Member of the Phylum Planctomycetes from the German Wadden Sea. Front Microbiol 2016; 7:2079. [PMID: 28066393 PMCID: PMC5177795 DOI: 10.3389/fmicb.2016.02079] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/08/2016] [Indexed: 11/23/2022] Open
Abstract
Members of the phylum Planctomycetes are ubiquitous bacteria that dwell in aquatic and terrestrial habitats. While planctomycetal species are important players in the global carbon and nitrogen cycle, this phylum is still undersampled and only few genome sequences are available. Here we describe strain NH11T, a novel planctomycete obtained from a crustacean shell (Wadden Sea, Germany). The phylogenetically closest related cultivated species is Gimesia maris, sharing only 87% 16S rRNA sequence identity. Previous isolation attempts have mostly yielded members of the genus Rhodopirellula from water of the German North Sea. On the other hand, only one axenic culture of the genus Pirellula was obtained from a crustacean thus far. However, the 16S rRNA gene sequence of strain NH11T shares only 80% sequence identity with the closest relative of both genera, Rhodopirellula and Pirellula. Thus, strain NH11T is unique in terms of origin and phylogeny. While the pear to ovoid shaped cells of strain NH11T are typical planctomycetal, light-, and electron microscopic observations point toward an unusual variation of cell division through budding: during the division process daughter- and mother cells are connected by an unseen thin tubular-like structure. Furthermore, the periplasmic space of strain NH11T was unusually enlarged and differed from previously known planctomycetes. The complete genome of strain NH11T, with almost 9 Mb in size, is among the largest planctomycetal genomes sequenced thus far, but harbors only 6645 protein-coding genes. The acquisition of genomic components by horizontal gene transfer is indicated by the presence of numerous putative genomic islands. Strikingly, 45 “giant genes” were found within the genome of NH11T. Subsequent analysis of all available planctomycetal genomes revealed that Planctomycetes as such are especially rich in “giant genes”. Furthermore, Multilocus Sequence Analysis (MLSA) tree reconstruction support the phylogenetic distance of strain NH11T from other cultivated Planctomycetes of the same phylogenetic cluster. Thus, based on our findings, we propose to classify strain NH11T as Fuerstia marisgermanicae gen. nov., sp. nov., with the type strain NH11T, within the phylum Planctomycetes.
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Affiliation(s)
- Timo Kohn
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Anja Heuer
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Mareike Jogler
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - John Vollmers
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Christian Boedeker
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Patrick Rast
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Daniela Borchert
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Ines Glöckner
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Heike M Freese
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | | | - Jörg Overmann
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Anne-Kristin Kaster
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Manfred Rohde
- Helmholtz Centre for Infectious Disease Braunschweig, Germany
| | - Sandra Wiegand
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
| | - Christian Jogler
- Leibniz Institut Deutsche Sammlung Von Mikroorganismen und Zellkulturen Braunschweig, Germany
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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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Abstract
The Planctomycetes genus Gemmata is represented by both uncultured organisms and cultured Gemmata obscuriglobus and 'Gemmata massiliana' organisms. Their plasmidless 9.2 Mb genomes encode a complex cell plan, cell signaling capacities, antibiotic and trace metal resistance and multidrug resistance efflux pumps. As they lack iron metabolism pathways, they are fastidious. Gemmata spp. are mainly found in aquatic and soil environments but have also been found in hospital water networks in close proximity to patients, in animals, on human skin, the gut microbiota and in the blood of aplastic leukemic patients. Due to their panoply of attack and defense mechanisms and their recently demonstrated association with humans, the potential of Gemmata organisms to behave as opportunistic pathogens should be more widely recognized.
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Affiliation(s)
- Rita Aghnatios
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095. Faculté de Médecine, Marseille 13005, France
| | - Michel Drancourt
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095. Faculté de Médecine, Marseille 13005, France
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16
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Žure M, Munn CB, Harder J. Diversity ofRhodopirellulaand related planctomycetes in a North Sea coastal sediment employingcarBas molecular marker. FEMS Microbiol Lett 2015; 362:fnv127. [DOI: 10.1093/femsle/fnv127] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2015] [Indexed: 01/28/2023] Open
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17
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Campbell AM, Fleisher J, Sinigalliano C, White JR, Lopez JV. Dynamics of marine bacterial community diversity of the coastal waters of the reefs, inlets, and wastewater outfalls of southeast Florida. Microbiologyopen 2015; 4:390-408. [PMID: 25740409 PMCID: PMC4475383 DOI: 10.1002/mbo3.245] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 01/09/2015] [Accepted: 01/26/2015] [Indexed: 02/01/2023] Open
Abstract
Coastal waters adjacent to populated southeast Florida possess different habitats (reefs, oceanic inlets, sewage outfalls) that may affect the composition of their inherent microbiomes. To determine variation according to site, season, and depth, over the course of 1 year, we characterized the bacterioplankton communities within 38 nearshore seawater samples derived from the Florida Area Coastal Environment (FACE) water quality survey. Six distinct coastal locales were profiled – the Port Everglades and Hillsboro Inlets, Hollywood and Broward wastewater outfalls, and associated reef sites using culture-independent, high-throughput pyrosequencing of the 16S rRNA V4 region. More than 227,000 sequences helped describe longitudinal taxonomic profiles of marine bacteria and archaea. There were 4447 unique operational taxonomic units (OTUs) identified with a mean OTU count of 5986 OTUs across all sites. Bacterial taxa varied significantly by season and by site using weighted and unweighted Unifrac, but depth was only supported by weighted Unifrac, suggesting a change due to presence/absence of certain OTUs. Abundant microbial taxa across all samples included Synechococcus, Pelagibacteraceae, Bacteroidetes, and various Proteobacteria. Unifrac analysis confirmed significant differences at inlet sites relative to reef and outfalls. Inlet-based bacterioplankton significantly differed in greater abundances of Rhodobacteraceae and Cryomorphaceae, and depletion of SAR406 sequences. This study also found higher counts of Firmicutes, Chloroflexi, and wastewater associated SBR1093 bacteria at the outfall and reef sites compared to inlet sites. This study profiles local bacterioplankton populations in a much broader context, beyond culturing and quantitative PCR, and expands upon the work completed by the National Oceanic and Atmospheric Administration FACE program.
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Affiliation(s)
- Alexandra M Campbell
- Center of Excellence in Coral Reef Ecosystem Research, Nova Southeastern University, Dania Beach, Florida, 33004
| | - Jay Fleisher
- School of Osteopathic Medicine, Nova Southeastern University, 3301 College Avenue, Davie, Florida, 33004
| | - Christopher Sinigalliano
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, Florida, 33149
| | | | - Jose V Lopez
- Center of Excellence in Coral Reef Ecosystem Research, Nova Southeastern University, Dania Beach, Florida, 33004
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18
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Scheuner C, Tindall BJ, Lu M, Nolan M, Lapidus A, Cheng JF, Goodwin L, Pitluck S, Huntemann M, Liolios K, Pagani I, Mavromatis K, Ivanova N, Pati A, Chen A, Palaniappan K, Jeffries CD, Hauser L, Land M, Mwirichia R, Rohde M, Abt B, Detter JC, Woyke T, Eisen JA, Markowitz V, Hugenholtz P, Göker M, Kyrpides NC, Klenk HP. Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. Stand Genomic Sci 2014; 9:10. [PMID: 25780503 PMCID: PMC4334474 DOI: 10.1186/1944-3277-9-10] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 06/16/2014] [Indexed: 12/21/2022] Open
Abstract
Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448(T), were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.
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Affiliation(s)
- Carmen Scheuner
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Brian J Tindall
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Megan Lu
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Cynthia D Jeffries
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Romano Mwirichia
- Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Manfred Rohde
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Birte Abt
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - John C Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jonathan A Eisen
- DOE Joint Genome Institute, Walnut Creek, California, USA
- University of California Davis Genome Center, Davis, California, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Markus Göker
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hans-Peter Klenk
- DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
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19
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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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Bondoso J, Albuquerque L, Lobo-da-Cunha A, da Costa MS, Harder J, Lage OM. Rhodopirellula lusitana sp. nov. and Rhodopirellula rubra sp. nov., isolated from the surface of macroalgae. Syst Appl Microbiol 2014; 37:157-64. [DOI: 10.1016/j.syapm.2013.11.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 11/13/2013] [Accepted: 11/19/2013] [Indexed: 10/25/2022]
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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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Izumi H, Sagulenko E, Webb RI, Fuerst JA. Isolation and diversity of planctomycetes from the sponge Niphates sp., seawater, and sediment of Moreton Bay, Australia. Antonie van Leeuwenhoek 2013; 104:533-46. [DOI: 10.1007/s10482-013-0003-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/13/2013] [Indexed: 11/29/2022]
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Characterization of a planctomycete associated with the marine dinoflagellate Prorocentrum micans Her. Antonie van Leeuwenhoek 2013; 104:499-508. [PMID: 23929089 DOI: 10.1007/s10482-013-9991-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/26/2013] [Indexed: 10/26/2022]
Abstract
During attempts to obtain axenic the cultures of the marine dinoflagellate Prorocentrum micans, a microorganism with peculiar features was isolated. This contaminant resisted the physical and antibiotic treatments performed. Subsequent characterization showed that in agar plates this microorganism develops round granular pink colonies. It is a salt-dependent mesophilic and chemoheterotrophic Gram negative bacterium with a rod to ovoid shape, presenting cell motility in young cultures. Cell division occurs by cell budding. The bacterium forms aggregates with a variable number of cells that are stacked by fibrillar glycoproteic material, the holdfast. A tuft of numerous short glycoproteic fimbriae emerges from one pole of the cell. Preeminent granular inclusions, also of glycoproteic nature, are present in the cytoplasm. Several structural and compositional aspects of the cell envelope and cytoplasm are provided. The production of fibrillar material and the existence of the polar appendages suggest that this microorganism should occur in aquatic environments bound to substrates and could be associated with P. micans in natural marine habitats. Based on the characteristics displayed, this microorganism is a member of the Planctomycetes, order Planctomycetales.
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Lage OM, Bondoso J, Lobo-da-Cunha A. Insights into the ultrastructural morphology of novel Planctomycetes. Antonie van Leeuwenhoek 2013; 104:467-76. [PMID: 23857394 DOI: 10.1007/s10482-013-9969-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 07/03/2013] [Indexed: 12/21/2022]
Abstract
Knowledge of the interesting phylum of Planctomycetes has increased in the last decades both due to cultural and molecular methods. Although a restricted number of species have been described to date, this group presents a much larger diversity that has been mainly revealed by molecular ecology studies. Isolation experiments allowed us to get a number of new Planctomycetes taxa that extend the already described ones. In this work we present the ultrastructural morphological characterization of these new taxa as well as we give new details of Aquisphaera giovannonii ultrastructure. Furthermore, our interpretation on Planctomycetes cell envelope is provided.
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Affiliation(s)
- Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/nº, 4169-007, Porto, Portugal,
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Lage OM, Bondoso J, Catita JAM. Determination of zeta potential in Planctomycetes and its application in heavy metals toxicity assessment. Arch Microbiol 2012; 194:847-55. [PMID: 22576374 DOI: 10.1007/s00203-012-0818-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 04/19/2012] [Accepted: 04/20/2012] [Indexed: 11/25/2022]
Abstract
Zeta potential of Planctomycetes was evaluated under different environmental conditions and correlated to cell viability. Phylogenetically distinct strains of the Planctomycetes presented different negative zeta potential values. More negative values were associated with Rhodopirellula spp. and related to the great amount of fimbriae in these species. Milli-Q water was chosen as the best dispersion media to perform the measurements. Zeta potential increased with ionic strength and varied with pH. In the physiological range of pH 5.0-9, zeta potential remained low and Rhodopirellula sp. strain LF2 cells were viable. Out of this range, zeta potential increased significantly and viability decreased. The effect on zeta potential of arsenic, cadmium, chromium, copper, lead, nickel, and zinc was assessed in Rhodopirellula sp. strain LF2. Zeta potential increased with increasing toxicity of the heavy metals in a dose-response way. This result was confirmed by the results observed for Rhodopirellula baltica strain SH1 under copper toxicity. Lead was the most toxic metal and zinc was the least toxic as observed by zeta potential and viability. The results support a correlation between zeta potential and cell viability which seem to indicate the possibility to use it as a viability predictor for the effects of heavy metals toxicity.
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Affiliation(s)
- Olga Maria Lage
- CIMAR/CIIMAR, Interdisciplinary Centre for Marine and Environmental Research, University of Porto, Porto, Portugal.
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26
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Anammox bacteria in different compartments of recirculating aquaculture systems. Biochem Soc Trans 2012; 39:1817-21. [PMID: 22103532 DOI: 10.1042/bst20110743] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Strict environmental restrictions force the aquaculture industry to guarantee optimal water quality for fish production in a sustainable manner. The implementation of anammox (anaerobic ammonium oxidation) in biofilters would result in the conversion of both ammonium and nitrite (both toxic to aquatic animals) into harmless dinitrogen gas. Both marine and freshwater aquaculture systems contain populations of anammox bacteria. These bacteria are also present in the faeces of freshwater and marine fish. Interestingly, a new planctomycete species appears to be present in these recirculation systems too. Further exploitation of anammox bacteria in different compartments of aquaculture systems can lead to a more environmentally friendly aquaculture practice.
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van Kessel MAHJ, Dutilh BE, Neveling K, Kwint MP, Veltman JA, Flik G, Jetten MSM, Klaren PHM, Op den Camp HJM. Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.). AMB Express 2011; 1:41. [PMID: 22093413 PMCID: PMC3226434 DOI: 10.1186/2191-0855-1-41] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 11/18/2011] [Indexed: 11/19/2022] Open
Abstract
The microbes in the gastrointestinal (GI) tract are of high importance for the health of the host. In this study, Roche 454 pyrosequencing was applied to a pooled set of different 16S rRNA gene amplicons obtained from GI content of common carp (Cyprinus carpio) to make an inventory of the diversity of the microbiota in the GI tract. Compared to other studies, our culture-independent investigation reveals an impressive diversity of the microbial flora of the carp GI tract. The major group of obtained sequences belonged to the phylum Fusobacteria. Bacteroidetes, Planctomycetes and Gammaproteobacteria were other well represented groups of micro-organisms. Verrucomicrobiae, Clostridia and Bacilli (the latter two belonging to the phylum Firmicutes) had fewer representatives among the analyzed sequences. Many of these bacteria might be of high physiological relevance for carp as these groups have been implicated in vitamin production, nitrogen cycling and (cellulose) fermentation.
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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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Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function. Nat Rev Microbiol 2011; 9:403-13. [PMID: 21572457 DOI: 10.1038/nrmicro2578] [Citation(s) in RCA: 280] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Planctomycetes form a distinct phylum of the domain Bacteria and possess unusual features such as intracellular compartmentalization and a lack of peptidoglycan in their cell walls. Remarkably, cells of the genus Gemmata even contain a membrane-bound nucleoid analogous to the eukaryotic nucleus. Moreover, the so-called 'anammox' planctomycetes have a unique anaerobic, autotrophic metabolism that includes the ability to oxidize ammonium; this process is dependent on a characteristic membrane-bound cell compartment called the anammoxosome, which might be a functional analogue of the eukaryotic mitochondrion. The compartmentalization of planctomycetes challenges our hypotheses regarding the origins of eukaryotic organelles. Furthermore, the recent discovery of both an endocytosis-like ability and proteins homologous to eukaryotic clathrin in a planctomycete marks this phylum as one to watch for future research on the origin and evolution of the eukaryotic cell.
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Pollet T, Tadonléké RD, Humbert JF. Comparison of primer sets for the study of Planctomycetes communities in lentic freshwater ecosystems. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:254-261. [PMID: 23761258 DOI: 10.1111/j.1758-2229.2010.00219.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In search of a primer set that could be used to study Planctomycetes dynamics in lakes and especially via fingerprinting methods, e.g. denaturing gradient gel electrophoresis (DGGE), three existing specific primer sets, developed for marine and soil systems, have been tested on water samples from four freshwater ecosystems. The first primer set (PLA46F/PLA886R) allowed PCR amplification of Planctomycetes sequences in only one of the four ecosystems, whereas the second primer set (PLA40F/P518R) amplified Planctomycetes sequences in all the studied ecosystems but with a low specificity, since sequences belonging to Verrucomicrobiales and Chlamydiales clades were also amplified. Finally, the third primer set (PLA352F/PLA920R) allowed amplification of Planctomycetes sequences in the four ecosystems with a very high specificity. It amplified all known Planctomycetes genera and yielded the highest Operational Taxonomic Unit (OTU) richness and diversity estimates. In silico analyses supported these results. Further experiments comparing PLA352F/PLA920R to PLA46F/P1390R (a primer set generating a longer PCR fragment, also used to study Planctomycetes) yielded very similar results. Our findings suggest that the primer set PLA352F/PLA920R provides good estimates of Planctomycetes richness and diversity compared with other, and can thus be used to study Planctomycetes dynamics in lentic freshwater ecosystems.
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Affiliation(s)
- Thomas Pollet
- INRA-UMR CARRTEL, 74203 Thonon les Bains cedex, France. INRA, UMR 7618 BIOEMCO, Site de l'ens, 75005 Paris, France
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Bengtsson MM, Øvreås L. Planctomycetes dominate biofilms on surfaces of the kelp Laminaria hyperborea. BMC Microbiol 2010; 10:261. [PMID: 20950420 PMCID: PMC2964680 DOI: 10.1186/1471-2180-10-261] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 10/15/2010] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Bacteria belonging to Planctomycetes display several unique morphological and genetic features and are found in a wide variety of habitats on earth. Their ecological roles in these habitats are still poorly understood. Planctomycetes have previously been detected throughout the year on surfaces of the kelp Laminaria hyperborea from southwestern Norway. We aimed to make a detailed investigation of the abundance and phylogenetic diversity of planctomycetes inhabiting these kelp surfaces. RESULTS Planctomycetes accounted for 51-53% of the bacterial biofilm cells in July and September and 24% in February according to fluorescence in situ hybridization (FISH) results. Several separate planctomycetes lineages within Pirellulae, Planctomyces and OM190 were represented in 16S rRNA gene clone libraries and the most abundant clones belonged to yet uncultured lineages. In contrast to the abundance, the diversity of the planctomycete populations increased from July to February and was probably influenced by the aging of the kelp tissue. One planctomycete strain that was closely related to Rhodopirellula baltica was isolated using selective cultivation techniques. CONCLUSIONS Biofilms on surfaces of L. hyperborea display an even higher proportion of planctomycetes compared to other investigated planctomycete-rich habitats such as open water, sandy sediments and peat bogs. The findings agree well with the hypothesis of the role of planctomycetes as degraders of sulfated polymeric carbon in the marine environment as kelps produce such substances. In addition, the abundant planctomycete populations on kelp surfaces and in association with other eukaryotes suggest that coexistence with eukaryotes may be a key feature of many planctomycete lifestyles.
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Affiliation(s)
- Mia M Bengtsson
- Department of Biology, University of Bergen, Box 7803, N-5020 Bergen, Norway
| | - Lise Øvreås
- Department of Biology, University of Bergen, Box 7803, N-5020 Bergen, Norway
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Wecker P, Klockow C, Ellrott A, Quast C, Langhammer P, Harder J, Glöckner FO. Transcriptional response of the model planctomycete Rhodopirellula baltica SH1(T) to changing environmental conditions. BMC Genomics 2009; 10:410. [PMID: 19725962 PMCID: PMC2754498 DOI: 10.1186/1471-2164-10-410] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Accepted: 09/02/2009] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The marine model organism Rhodopirellula baltica SH1(T) was the first Planctomycete to have its genome completely sequenced. The genome analysis predicted a complex lifestyle and a variety of genetic opportunities to adapt to the marine environment. Its adaptation to environmental stressors was studied by transcriptional profiling using a whole genome microarray. RESULTS Stress responses to salinity and temperature shifts were monitored in time series experiments. Chemostat cultures grown in mineral medium at 28 degrees C were compared to cultures that were shifted to either elevated (37 degrees C) or reduced (6 degrees C) temperatures as well as high salinity (59.5 per thousand) and observed over 300 min. Heat shock showed the induction of several known chaperone genes. Cold shock altered the expression of genes in lipid metabolism and stress proteins. High salinity resulted in the modulation of genes coding for compatible solutes, ion transporters and morphology. In summary, over 3000 of the 7325 genes were affected by temperature and/or salinity changes. CONCLUSION Transcriptional profiling confirmed that R. baltica is highly responsive to its environment. The distinct responses identified here have provided new insights into the complex adaptation machinery of this environmentally relevant marine bacterium. Our transcriptome study and previous proteome data suggest a set of genes of unknown functions that are most probably involved in the global stress response. This work lays the foundation for further bioinformatic and genetic studies which will lead to a comprehensive understanding of the biology of a marine Planctomycete.
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Affiliation(s)
- Patricia Wecker
- Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Microbial Genomics Group, Celsiusstr. 1, 28359 Bremen, Germany
- Jacobs University Bremen gGmbH, Campusring 1, 28759 Bremen, Germany
| | - Christine Klockow
- Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Microbial Genomics Group, Celsiusstr. 1, 28359 Bremen, Germany
- Jacobs University Bremen gGmbH, Campusring 1, 28759 Bremen, Germany
| | - Andreas Ellrott
- Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Microbial Genomics Group, Celsiusstr. 1, 28359 Bremen, Germany
| | - Christian Quast
- Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Microbial Genomics Group, Celsiusstr. 1, 28359 Bremen, Germany
| | - Philipp Langhammer
- Department of Microbiology, Max Planck Institute for Marine Microbiology, Microbiology, Celsiusstr. 1, 28359 Bremen, Germany
| | - Jens Harder
- Department of Microbiology, Max Planck Institute for Marine Microbiology, Microbiology, Celsiusstr. 1, 28359 Bremen, Germany
| | - Frank Oliver Glöckner
- Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Microbial Genomics Group, Celsiusstr. 1, 28359 Bremen, Germany
- Jacobs University Bremen gGmbH, Campusring 1, 28759 Bremen, Germany
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Winkelmann N, Harder J. An improved isolation method for attached-living Planctomycetes of the genus Rhodopirellula. J Microbiol Methods 2009; 77:276-84. [DOI: 10.1016/j.mimet.2009.03.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 03/04/2009] [Accepted: 03/04/2009] [Indexed: 11/16/2022]
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Boomer SM, Noll KL, Geesey GG, Dutton BE. Formation of multilayered photosynthetic biofilms in an alkaline thermal spring in Yellowstone National Park, Wyoming. Appl Environ Microbiol 2009; 75:2464-75. [PMID: 19218404 PMCID: PMC2675224 DOI: 10.1128/aem.01802-08] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Accepted: 02/09/2009] [Indexed: 11/20/2022] Open
Abstract
In this study, glass rods suspended at the air-water interface in the runoff channel of Fairy Geyser, Yellowstone National Park, WY, were used as a substratum to promote the development of biofilms that resembled multilayered mat communities in the splash zone at the geyser's source. This approach enabled the establishment of the temporal relationship between the appearance of Cyanobacteria, which ultimately formed the outer green layer, and the development of a red underlayer containing Roseiflexus-like Chloroflexi. This is the first study to define time-dependent successional events involved in the development of differently colored layers within microbial mats associated with many thermal features in Yellowstone National Park. Initial (1-month) biofilms were localized below the air-water interface (60 to 70 degrees C), and the majority of retrieved bacterial sequence types were similar to Synechococcus and Thermus isolates. Biofilms then shifted, becoming established at and above the air-water interface after 3 months. During winter sampling (6 to 8 months), distinct reddish orange microcolonies were observed, consistent with the appearance of Roseiflexus-like sequences and bacteriochlorophyll a pigment signatures. Additionally, populations of Cyanobacteria diversified to include both unicellular and filamentous cell and sequence types. Distinct green and red layers were observed at 13 months. Planctomycetes-like sequences were also retrieved in high abundance from final biofilm layers and winter samples. Finally, biomass associated with geyser vent water contained Roseiflexus-like sequence types, in addition to other high-abundance sequence types retrieved from biofilm samples, supporting the idea that geothermal water serves as an inoculum for these habitats.
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Affiliation(s)
- Sarah M Boomer
- Western Oregon University, Department of Biology, Monmouth, Oregon 97361, USA.
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Kulichevskaya IS, Ivanova AO, Belova SE, Baulina OI, Bodelier PLE, Rijpstra WIC, Sinninghe Damsté JS, Zavarzin GA, Dedysh SN. Schlesneria paludicola gen. nov., sp. nov., the first acidophilic member of the order Planctomycetales, from Sphagnum-dominated boreal wetlands. Int J Syst Evol Microbiol 2007; 57:2680-2687. [DOI: 10.1099/ijs.0.65157-0] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three strains of budding, ellipsoid-shaped and rosette-forming bacteria were isolated from acidic Sphagnum-dominated boreal wetlands of northern Russia and were designated strains MPL7T, MOB77 and SB2. The presence of crateriform pits and numerous fibrillar appendages on the cell surface and an unusual spur-like projection on one pole of the cell indicated a planctomycete morphotype. These isolates are moderately acidophilic, mesophilic organisms capable of growth at pH values between 4.2 and 7.5 (with an optimum at pH 5.0–6.2) and at temperatures between 4 and 32 °C (optimum 15–26 °C). The major fatty acids are C16 : 0 and C16 : 1
ω7c; the major quinone is MK-6. The G+C content of the DNA is 54.4–56.5 mol%. Strains MPL7T, MOB77 and SB2 possess nearly identical 16S rRNA gene sequences and belong to the planctomycete lineage defined by the genus Planctomyces, being most closely related to Planctomyces limnophilus DSM 3776T (86.9–87.1 % sequence similarity). However, strain MPL7T showed only 28 % DNA–DNA hybridization with P. limnophilus DSM 3776T. Compared with currently described members of the genus Planctomyces, the isolates from northern wetlands do not form long and distinctive stalks, have greater tolerance of acidic conditions and low temperatures, are more sensitive to NaCl, lack pigmentation and degrade a wider range of biopolymers. The data therefore suggest that strains MPL7T, MOB77 and SB2 represent a novel genus and species, for which the name Schlesneria paludicola gen. nov., sp. nov., is proposed. Strain MPL7T (=ATCC BAA-1393T =VKM B-2452T) is the type strain of Schlesneria paludicola.
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Affiliation(s)
- Irina S. Kulichevskaya
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | - Anastasia O. Ivanova
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | - Svetlana E. Belova
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | - Olga I. Baulina
- M. V. Lomonosov Moscow State University, Faculty of Biology Science, GSP-2, Leninskie Gory, Moscow 119992, Russia
| | | | - W. Irene C. Rijpstra
- Royal Netherlands Institute for Sea Research, Department of Marine Biogeochemistry and Toxicology, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Jaap S. Sinninghe Damsté
- Royal Netherlands Institute for Sea Research, Department of Marine Biogeochemistry and Toxicology, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - George A. Zavarzin
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | - Svetlana N. Dedysh
- S. N. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
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Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes. ISME JOURNAL 2007; 1:419-35. [DOI: 10.1038/ismej.2007.63] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Elshahed MS, Youssef NH, Luo Q, Najar FZ, Roe BA, Sisk TM, Bühring SI, Hinrichs KU, Krumholz LR. Phylogenetic and metabolic diversity of Planctomycetes from anaerobic, sulfide- and sulfur-rich Zodletone Spring, Oklahoma. Appl Environ Microbiol 2007; 73:4707-16. [PMID: 17545322 PMCID: PMC1951033 DOI: 10.1128/aem.00591-07] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 05/27/2007] [Indexed: 11/20/2022] Open
Abstract
We investigated the phylogenetic diversity and metabolic capabilities of members of the phylum Planctomycetes in the anaerobic, sulfide-saturated sediments of a mesophilic spring (Zodletone Spring) in southwestern Oklahoma. Culture-independent analyses of 16S rRNA gene sequences generated using Planctomycetes-biased primer pairs suggested that an extremely diverse community of Planctomycetes is present at the spring. Although sequences that are phylogenetically affiliated with cultured heterotrophic Planctomycetes were identified, the majority of the sequences belonged to several globally distributed, as-yet-uncultured Planctomycetes lineages. Using complex organic media (aqueous extracts of the spring sediments and rumen fluid), we isolated two novel strains that belonged to the Pirellula-Rhodopirellula-Blastopirellula clade within the Planctomycetes. The two strains had identical 16S rRNA gene sequences, and their closest relatives were isolates from Kiel Fjord (Germany), Keauhou Beach (HI), a marine aquarium, and tissues of marine organisms (Aplysina sp. sponges and postlarvae of the giant tiger prawn Penaeus monodon). The closest recognized cultured relative of strain Zi62 was Blastopirellula marina (93.9% sequence similarity). Detailed characterization of strain Zi62 revealed its ability to reduce elemental sulfur to sulfide under anaerobic conditions, as well as its ability to produce acids from sugars; both characteristics may potentially allow strain Zi62 to survive and grow in the anaerobic, sulfide- and sulfur-rich environment at the spring source. Overall, this work indicates that anaerobic metabolic abilities are widely distributed among all major Planctomycetes lineages and suggests carbohydrate fermentation and sulfur reduction as possible mechanisms employed by heterotrophic Planctomycetes for growth and survival under anaerobic conditions.
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Affiliation(s)
- Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA.
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Drees KP, Neilson JW, Betancourt JL, Quade J, Henderson DA, Pryor BM, Maier RM. Bacterial community structure in the hyperarid core of the Atacama Desert, Chile. Appl Environ Microbiol 2006; 72:7902-8. [PMID: 17028238 PMCID: PMC1694221 DOI: 10.1128/aem.01305-06] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Soils from the hyperarid Atacama Desert of northern Chile were sampled along an east-west elevational transect (23.75 to 24.70 degrees S) through the driest sector to compare the relative structure of bacterial communities. Analysis of denaturing gradient gel electrophoresis (DGGE) profiles from each of the samples revealed that microbial communities from the extreme hyperarid core of the desert clustered separately from all of the remaining communities. Bands sequenced from DGGE profiles of two samples taken at a 22-month interval from this core region revealed the presence of similar populations dominated by bacteria from the Gemmatimonadetes and Planctomycetes phyla.
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Affiliation(s)
- Kevin P Drees
- University of Arizona Department of Soil, Water, and Environmental Science, Shantz Building #38, Room 429, Tucson, AZ 85721, USA
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Kirkpatrick J, Oakley B, Fuchsman C, Srinivasan S, Staley JT, Murray JW. Diversity and distribution of Planctomycetes and related bacteria in the suboxic zone of the Black Sea. Appl Environ Microbiol 2006; 72:3079-83. [PMID: 16598025 PMCID: PMC1449031 DOI: 10.1128/aem.72.4.3079-3083.2006] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Samples from six depths of the Black Sea's suboxic zone were analyzed for 16S rRNA gene sequence information. A gradient in phylotype diversity was found. The distributions of known anaerobic ammonium oxidation (anammox) bacteria, many unknown Planctomycetes, and other phylotypes were examined in relation to the local nutrient and redox conditions.
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Affiliation(s)
- John Kirkpatrick
- School of Oceanography, University of Washington, Box 357242, Seattle, WA 98195, USA
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41
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Wagner M, Horn M. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr Opin Biotechnol 2006; 17:241-9. [PMID: 16704931 DOI: 10.1016/j.copbio.2006.05.005] [Citation(s) in RCA: 321] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 05/03/2006] [Accepted: 05/05/2006] [Indexed: 01/20/2023]
Abstract
In the rRNA-based tree of life four bacterial phyla, comprising the Planctomycetes, Verrucomicrobia, Chlamydiae and Lentisphaerae, form together with the candidate phyla Poribacteria and OP3 a monophyletic group referred to as the PVC superphylum. This assemblage contains organisms that possess dramatically different lifestyles and which colonize sharply contrasting habitats. Some members of this group are among the most successful human pathogens, others are abundant soil microbes, and others still are of major importance for the marine nitrogen cycle and hold much promise for sustainable wastewater treatment. Recent comparative genomic and metagenomic analyses of a few representatives of this group revealed many unusual features and generated unexpected hypotheses regarding their physiology, some of which have already been confirmed experimentally. Furthermore, the availability of these genome sequences offered new insights into the evolutionary history of this peculiar group of microbes with major medical, ecological and biotechnological relevance.
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Affiliation(s)
- Michael Wagner
- Department of Microbial Ecology, University of Vienna, Austria.
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42
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Davis KER, Joseph SJ, Janssen PH. Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria. Appl Environ Microbiol 2005; 71:826-34. [PMID: 15691937 PMCID: PMC546801 DOI: 10.1128/aem.71.2.826-834.2005] [Citation(s) in RCA: 295] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Soils are inhabited by many bacteria from phylogenetic groups that are poorly studied because representatives are rarely isolated in cultivation studies. Part of the reason for the failure to cultivate these bacteria is the low frequency with which bacterial cells in soil form visible colonies when inoculated onto standard microbiological media, resulting in low viable counts. We investigated the effects of three factors on viable counts, assessed as numbers of CFU on solid media, and on the phylogenetic groups to which the isolated colony-forming bacteria belong. These factors were inoculum size, growth medium, and incubation time. Decreasing the inoculum size resulted in significant increases in the viable count but did not appear to affect colony formation by members of rarely isolated groups. Some media that are traditionally used for soil microbiological studies returned low viable counts and did not result in the isolation of members of rarely isolated groups. Newly developed media, in contrast, resulted in high viable counts and in the isolation of many members of rarely isolated groups, regardless of the inoculum size. Increased incubation times of up to 3 months allowed the development of visible colonies of members of rarely isolated groups in conjunction with the use of appropriate media. Once isolated, pure cultures of members of rarely isolated groups took longer to form visible colonies than did members of commonly isolated groups. Using these new media and extended incubation times, we were able to isolate many members of the phyla Acidobacteria (subdivisions 1, 2, 3, and 4), Gemmatimonadetes, Chloroflexi, and Planctomycetes (including representatives of the previously uncultured WPS-1 lineage) as well as members of the subclasses Rubrobacteridae and Acidimicrobidae of the phylum Actinobacteria.
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Affiliation(s)
- Kathryn E R Davis
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia.
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Langó Z. "Who has first observed planctomyces" (or data to the history of Planctomyces bekefii). Acta Microbiol Immunol Hung 2005; 52:73-84. [PMID: 15957235 DOI: 10.1556/amicr.52.2005.1.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The first description of Planctomyces bekefii was published in eighty years ago by N. Gimesi in Hungary. The history and importance of this species is revealed in this article.
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Affiliation(s)
- Zsuzsanna Langó
- General Microbiological Committee of the Hungarian Academy of Sciences, Roosevelt tér 9, H-1051 Budapest, Hungary.
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Nocker A, Lepo JE, Snyder RA. Influence of an oyster reef on development of the microbial heterotrophic community of an estuarine biofilm. Appl Environ Microbiol 2005; 70:6834-45. [PMID: 15528551 PMCID: PMC525144 DOI: 10.1128/aem.70.11.6834-6845.2004] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterized microbial biofilm communities developed over two very closely located but distinct benthic habitats in the Pensacola Bay estuary using two complementary cultivation-independent molecular techniques. Biofilms were grown for 7 days on glass slides held in racks 10 to 15 cm over an oyster reef and an adjacent muddy sand bottom. Total biomass and optical densities of dried biofilms showed dramatic differences for oyster reef versus non-oyster reef biofilms. This study assessed whether the observed spatial variation was reflected in the heterotrophic prokaryotic species composition. Genomic biofilm DNA from both locations was isolated and served as a template to amplify 16S rRNA genes with universal eubacterial primers. Fluorescently labeled PCR products were analyzed by terminal restriction fragment length polymorphism, creating a genetic fingerprint of the composition of the microbial communities. Unlabeled PCR products were cloned in order to construct a clone library of 16S rRNA genes. Amplified ribosomal DNA restriction analysis was used to screen and define ribotypes. Partial sequences from unique ribotypes were compared with existing database entries to identify species and to construct phylogenetic trees representative of community structures. A pronounced difference in species richness and evenness was observed at the two sites. The biofilm community structure from the oyster reef setting had greater evenness and species richness than the one from the muddy sand bottom. The vast majority of the bacteria in the oyster reef biofilm were related to members of the gamma- and delta-subdivisions of Proteobacteria, the Cytophaga-Flavobacterium -Bacteroides cluster, and the phyla Planctomyces and Holophaga-Acidobacterium. The same groups were also present in the biofilm harvested at the muddy sand bottom, with the difference that nearly half of the community consisted of representatives of the Planctomyces phylum. Total species richness was estimated to be 417 for the oyster reef and 60 for the muddy sand bottom, with 10.5% of the total unique species identified being shared between habitats. The results suggest dramatic differences in habitat-specific microbial diversity that have implications for overall microbial diversity within estuaries.
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Affiliation(s)
- Andreas Nocker
- Center for Environmental Diagnostics and Bioremediation, University of West Florida, Pensacola, Florida 32514, USA
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Brümmer IHM, Felske ADM, Wagner-Döbler I. Diversity and seasonal changes of uncultured Planctomycetales in river biofilms. Appl Environ Microbiol 2004; 70:5094-101. [PMID: 15345387 PMCID: PMC520923 DOI: 10.1128/aem.70.9.5094-5101.2004] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cell counts of planctomycetes showed that there were high levels of these organisms in the summer and low levels in the winter in biofilms grown in situ in two polluted rivers, the Elbe River and the Spittelwasser River. In this study 16S rRNA-based methods were used to investigate if these changes were correlated with changes in the species composition. Planctomycete-specific clone libraries of the 16S rRNA genes found in both rivers showed that there were seven clusters, which were distantly related to the genera Pirellula, Planctomyces, and Gemmata. The majority of the sequences from the Spittelwasser River were affiliated with a cluster related to Pirellula, while the majority of the clones from the Elbe River fell into three clusters related to Planctomyces and one deeply branching cluster related to Pirellula. Some clusters also contained sequences derived from freshwater environments worldwide, and the similarities to our biofilm clones were as high as 99.8%, indicating the presence of globally distributed freshwater clusters of planctomycetes that have not been cultivated yet. Community fingerprints of planctomycete 16S rRNA genes were generated by temperature gradient gel electrophoresis from Elbe River biofilm samples collected monthly for 1 year. Sixteen bands were identified, and for the most part these bands represented organisms related to the genus Planctomyces. The fingerprints showed that there was strong seasonality of most bands and that there were clear differences in the summer and the winter. Thus, seasonal changes in the abundance of Planctomycetales in river biofilms were coupled to shifts in the community composition.
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Affiliation(s)
- I H M Brümmer
- German Research Centre for Biotechnology, Department of Microbiology, Mascheroder Weg 1, D-38124 Braunschweig, Germany
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Schlesner H, Rensmann C, Tindall BJ, Gade D, Rabus R, Pfeiffer S, Hirsch P. Taxonomic heterogeneity within the Planctomycetales as derived by DNA–DNA hybridization, description of Rhodopirellula baltica gen. nov., sp. nov., transfer of Pirellula marina to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov. and emended description of the genus Pirellula. Int J Syst Evol Microbiol 2004; 54:1567-1580. [PMID: 15388712 DOI: 10.1099/ijs.0.63113-0] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ninety-seven strains of budding bacteria originating from various aquatic habitats and morphologically resembling planctomycetes were investigated taxonomically. Taxonomic differentiation was based on DNA–DNA hybridization, physiological properties and chemotaxonomic tests. Nineteen hybridization groups, containing 79 of the tested strains, were established. Eighteen strains, however, did not fit into any of these groups. Rhodopirellula baltica gen. nov., sp. nov. is described, with strain SH 1T (=IFAM 1310T=DSM 10527T=NCIMB 13988T) as the type strain. Pirellula marina is transferred to the genus Blastopirellula gen. nov. as Blastopirellula marina comb. nov., with strain SH 106T (=IFAM 1313T=DSM 3645T=ATCC 49069T) as the type strain. An emended description of the genus Pirellula is also provided. Differentiation between R. baltica, B. marina and Pirellula staleyi was achieved by the integration of morphological, physiological, chemotaxonomic and genetic characteristics.
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Affiliation(s)
- Heinz Schlesner
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - Christina Rensmann
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | - Brian J Tindall
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
| | - Dörte Gade
- Max-Planck-Institut für Marine Mikrobiologie, Celsiusstraße 1, D-28359 Bremen, Germany
| | - Ralf Rabus
- Max-Planck-Institut für Marine Mikrobiologie, Celsiusstraße 1, D-28359 Bremen, Germany
| | - Stefan Pfeiffer
- Zentrale Mikroskopie, Christian-Albrechts-Universität, Am Botanischen Garten 5, D-24098 Kiel, Germany
| | - Peter Hirsch
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
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Teeling H, Lombardot T, Bauer M, Ludwig W, Glöckner FO. Evaluation of the phylogenetic position of the planctomycete 'Rhodopirellula baltica' SH 1 by means of concatenated ribosomal protein sequences, DNA-directed RNA polymerase subunit sequences and whole genome trees. Int J Syst Evol Microbiol 2004; 54:791-801. [PMID: 15143026 DOI: 10.1099/ijs.0.02913-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In recent years, the planctomycetes have been recognized as a phylum of environmentally important bacteria with habitats ranging from soil and freshwater to marine ecosystems. The planctomycetes form an independent phylum within the bacterial domain, whose exact phylogenetic position remains controversial. With the completion of sequencing of the genome of 'Rhodopirellula baltica' SH 1, it is now possible to re-evaluate the phylogeny of the planctomycetes based on multiple genes and genome trees in addition to single genes like the 16S rRNA or the elongation factor Tu. Here, evidence is presented based on the concatenated amino acid sequences of ribosomal proteins and DNA-directed RNA polymerase subunits from 'Rhodopirellula baltica' SH 1 and more than 90 other publicly available genomes that support a relationship of the Planctomycetes and the Chlamydiae. Affiliation of 'Rhodopirellula baltica' SH 1 and the Chlamydiae was reasonably stable regarding site selection since, during stepwise filtering of less-conserved sites from the alignments, it was only broken when rigorous filtering was applied. In a few cases, 'Rhodopirellula baltica' SH 1 shifted to a deep branching position adjacent to the Thermotoga/Aquifex clade. These findings are in agreement with recent publications, but the deep branching position was dependent on site selection and treeing algorithm and thus not stable. A genome tree calculated from normalized BLASTP scores did not confirm a close relationship of 'Rhodopirellula baltica' SH 1 and the Chlamydiae, but also indicated that the Planctomycetes do not emerge at the very root of the Bacteria. Therefore, these analyses rather contradict a deep branching position of the Planctomycetes within the bacterial domain and reaffirm their earlier proposed relatedness to the Chlamydiae.
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Affiliation(s)
- Hanno Teeling
- Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Thierry Lombardot
- Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Margarete Bauer
- Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Wolfgang Ludwig
- Department of Microbiology, Technical University Munich, D-85350 Freising, Germany
| | - Frank Oliver Glöckner
- Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
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Fieseler L, Horn M, Wagner M, Hentschel U. Discovery of the novel candidate phylum "Poribacteria" in marine sponges. Appl Environ Microbiol 2004; 70:3724-32. [PMID: 15184179 PMCID: PMC427773 DOI: 10.1128/aem.70.6.3724-3732.2004] [Citation(s) in RCA: 247] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2003] [Accepted: 02/23/2004] [Indexed: 11/20/2022] Open
Abstract
Marine sponges (Porifera) harbor large amounts of commensal microbial communities within the sponge mesohyl. We employed 16S rRNA gene library construction using specific PCR primers to provide insights into the phylogenetic identity of an abundant sponge-associated bacterium that is morphologically characterized by the presence of a membrane-bound nucleoid. In this study, we report the presence of a previously unrecognized evolutionary lineage branching deeply in the domain Bacteria that is moderately related to the Planctomycetes, Verrucomicrobia, and Chlamydia lines of decent. Because members of this lineage showed <75% 16S rRNA gene sequence similarity to known bacterial phyla, we suggest the status of a new candidate phylum, named "Poribacteria", to acknowledge the affiliation of the new bacterium with sponges. The affiliation of the morphologically conspicuous sponge bacterium with the novel phylogenetic lineage was confirmed by fluorescence in situ hybridization with newly designed probes targeting different sites of the poribacterial 16S rRNA. Consistent with electron microscopic observations of cell compartmentalization, the fluorescence signals appeared in a ring-shaped manner. PCR screening with "Poribacteria"-specific primers gave positive results for several other sponge species, while samples taken from the environment (seawater, sediments, and a filter-feeding tunicate) were PCR negative. In addition to a report for Planctomycetes, this is the second report of cell compartmentalization, a feature that was considered exclusive to the eukaryotic domain, in prokaryotes.
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Affiliation(s)
- Lars Fieseler
- Zentrum für Infektionsforschung, Universität Würzburg, D-97070 Wuerzburg, Germany
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Gade D, Schlesner H, Glöckner FO, Amann R, Pfeiffer S, Thomm M. Identification of planctomycetes with order-, genus-, and strain-specific 16S rRNA-targeted probes. MICROBIAL ECOLOGY 2004; 47:243-251. [PMID: 14994173 DOI: 10.1007/s00248-003-1016-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2003] [Accepted: 04/28/2003] [Indexed: 05/24/2023]
Abstract
A specific 16S rRNA-targeted oligonucleotide probe (PIR1223) for the genus Pirellula and a species-specific probe (RB454) for Pirellula sp. strain SH1 have been designed and optimized. Together with the already existing order-specific probe PLA886, the two newly designed probes were used to detect and identify planctomycetes, pirellulae, and close relatives of Pirellula sp. strain SH1 in different habitats. With the help of these probes for detection and identification, bacteria of the genus Pirellula were detected and cultivated from tissue of the Mediterranean sponge Aplysina aerophoba and from the water column of the Kiel Fjord. An unexpected result was the close phylogenetic relationship of the isolate from the sponge and the brackish water habitat Kiel Fjord as revealed by DNA/DNA hybridization.
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Affiliation(s)
- D Gade
- Max-Planck-Institut für Marine Mikrobiologie, Celsiusstr. 1, D-28359 Bremen, Germany.
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Joseph SJ, Hugenholtz P, Sangwan P, Osborne CA, Janssen PH. Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 2003; 69:7210-5. [PMID: 14660368 PMCID: PMC309996 DOI: 10.1128/aem.69.12.7210-7215.2003] [Citation(s) in RCA: 283] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2003] [Accepted: 09/16/2003] [Indexed: 11/20/2022] Open
Abstract
Most soil bacteria belong to family-level phylogenetic groups with few or no known cultivated representatives. We cultured a collection of 350 isolates from soil by using simple solid media in petri dishes. These isolates were assigned to 60 family-level groupings in nine bacterial phyla on the basis of a comparative analysis of their 16S rRNA genes. Ninety-three (27%) of the isolates belonged to 20 as-yet-unnamed family-level groupings, many from poorly studied bacterial classes and phyla. They included members of subdivisions 1, 2, 3, and 4 of the phylum Acidobacteria, subdivision 3 of the phylum Verrucomicrobia, subdivision 1 of the phylum Gemmatimonadetes, and subclasses Acidimicrobidae and Rubrobacteridae of the phylum ACTINOBACTERIA: In addition, members of 10 new family-level groupings of subclass Actinobacteridae of the phylum Actinobacteria and classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria of the phylum Proteobacteria were obtained. The high degree of phylogenetic novelty and the number of isolates affiliated with so-called unculturable groups show that simple cultivation methods can still be developed further to obtain laboratory cultures of many phylogenetically novel soil bacteria.
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Affiliation(s)
- Shayne J Joseph
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
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