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Bapteste E, Huneman P, Keller L, Teulière J, Lopez P, Teeling EC, Lindner AB, Baudisch A, Ludington WB, Franceschi C. Expanding evolutionary theories of ageing to better account for symbioses and interactions throughout the Web of Life. Ageing Res Rev 2023; 89:101982. [PMID: 37321383 PMCID: PMC10771319 DOI: 10.1016/j.arr.2023.101982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/26/2023] [Accepted: 06/11/2023] [Indexed: 06/17/2023]
Abstract
How, when, and why organisms age are fascinating issues that can only be fully addressed by adopting an evolutionary perspective. Consistently, the main evolutionary theories of ageing, namely the Mutation Accumulation theory, the Antagonistic Pleiotropy theory, and the Disposable Soma theory, have formulated stimulating hypotheses that structure current debates on both the proximal and ultimate causes of organismal ageing. However, all these theories leave a common area of biology relatively under-explored. The Mutation Accumulation theory and the Antagonistic Pleiotropy theory were developed under the traditional framework of population genetics, and therefore are logically centred on the ageing of individuals within a population. The Disposable Soma theory, based on principles of optimising physiology, mainly explains ageing within a species. Consequently, current leading evolutionary theories of ageing do not explicitly model the countless interspecific and ecological interactions, such as symbioses and host-microbiomes associations, increasingly recognized to shape organismal evolution across the Web of Life. Moreover, the development of network modelling supporting a deeper understanding on the molecular interactions associated with ageing within and between organisms is also bringing forward new questions regarding how and why molecular pathways associated with ageing evolved. Here, we take an evolutionary perspective to examine the effects of organismal interactions on ageing across different levels of biological organisation, and consider the impact of surrounding and nested systems on organismal ageing. We also apply this perspective to suggest open issues with potential to expand the standard evolutionary theories of ageing.
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Affiliation(s)
- Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France.
| | - Philippe Huneman
- Institut d'Histoire et de Philosophie des Sciences et des Techniques (CNRS/ Université Paris I Sorbonne), Paris, France
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jérôme Teulière
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Ireland
| | - Ariel B Lindner
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), Paris, France
| | - Annette Baudisch
- Interdisciplinary Centre on Population Dynamics, University of Southern Denmark, 5230 Odense M, Denmark
| | - William B Ludington
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Claudio Franceschi
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40138 Bologna, Italy; Department of Applied Mathematics and Laboratory of Systems Medicine of Aging, Lobachevsky University, Nizhny Novgorod 603950, Russia
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Matthews AE, Boves TJ, Percy KL, Wijeratne AJ. Draft genome sequencing data of a feather mite, Amerodectes protonotaria Hernandes 2018 (Acariformes: Proctophyllodidae). Data Brief 2022; 46:108835. [PMID: 36591378 PMCID: PMC9801072 DOI: 10.1016/j.dib.2022.108835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Feather mites are ubiquitous, permanent, obligate ectosymbionts of avian hosts and are a valuable natural system for studying host-symbiont evolutionary and ecological dynamics at multiple levels of biological organization. However, a lack of a sequenced genome impedes molecular studies using this system. Therefore, we present the first draft genome of a symbiotic feather mite, Amerodectes protonotaria Hernandes 2018. The genome sequence data presented here were derived from an individual female mite that was collected in the field from Protonotaria citrea, its only known host species. Short read sequence data were obtained using an Illumina NovaSeq 6000 platform. From these data, we assembled a 59,665,063 bp draft genome consisting of 2,399 contigs. Raw short reads and the assembled genome sequence are available at the National Center for Biotechnology Information (NCBI)'s Sequence Read Archive (SRA) under BioProject PRJNA884722. The data presented here are beneficial for future research on the biology and evolution of closely related mites and the genomics of host-symbiont interactions.
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Affiliation(s)
- Alix E. Matthews
- College of Sciences and Mathematics and Molecular Biosciences Program, Arkansas State University, Jonesboro, Arkansas, United States,Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, United States,Corresponding author. @matthews_ae
| | - Than J. Boves
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, United States
| | - Katie L. Percy
- Audubon Delta, National Audubon Society, Baton Rouge, Louisiana, United States,United States Department of Agriculture, Natural Resources Conservation Service, Addis, Louisiana, United States
| | - Asela J. Wijeratne
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, United States
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Zou G, Liu Y, Kong F, Liao L, Deng G, Jiang X, Cai J, Liu W. Depression of the soil arbuscular mycorrhizal fungal community by the canopy gaps in a Japanese cedar ( Cryptomeria japonica) plantation on Lushan Mountain, subtropical China. PeerJ 2021; 9:e10905. [PMID: 33777516 PMCID: PMC7971093 DOI: 10.7717/peerj.10905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/14/2021] [Indexed: 11/20/2022] Open
Abstract
Both canopy gaps (CG) and arbuscular mycorrhizal fungi (AMF) play key roles in seedling establishment and increasing species diversity in forests. The response of AMF to canopy gaps is poorly understood. To assess the long-term effects of canopy gaps on soil AMF community, we sampled soil from plots in a 50-year Cryptomeria japonica (L.f.) D. Don. plantation, located in Lushan Mountain, subtropical China. We analyzed the AMF community, identified through 454 pyrosequencing, in soil and edaphic characteristics. Both richness and diversity of AMF in CG decreased significantly compared to the closed canopy (CC). The differences of the AMF community composition between CG and CC was also significant. The sharp response of the AMF community appears to be largely driven by vegetation transformation. Soil nutrient content also influenced some taxa, e.g., the low availability of phosphorus increased the abundance of Acaulospora. These results demonstrated that the formation of canopy gaps can depress AMF richness and alter the AMF community, which supported the plant investment hypothesis and accentuated the vital role of AMF-plant symbioses in forest management.
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Affiliation(s)
- Guiwu Zou
- Jiangxi Provincial Key Laboratory of Silviculture, Collaborative Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, College of Forestry/College of Art and Landscape, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Positioning Observation Station of Forest Ecosystem in Lushan, Lushan National Nature Reserve of Jiangxi, Jiujiang, Jiangxi, China
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuanqiu Liu
- Jiangxi Provincial Key Laboratory of Silviculture, Collaborative Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, College of Forestry/College of Art and Landscape, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Positioning Observation Station of Forest Ecosystem in Lushan, Lushan National Nature Reserve of Jiangxi, Jiujiang, Jiangxi, China
| | - Fanqian Kong
- Positioning Observation Station of Forest Ecosystem in Lushan, Lushan National Nature Reserve of Jiangxi, Jiujiang, Jiangxi, China
| | - Liqin Liao
- Jiangxi Provincial Key Laboratory of Silviculture, Collaborative Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, College of Forestry/College of Art and Landscape, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Positioning Observation Station of Forest Ecosystem in Lushan, Lushan National Nature Reserve of Jiangxi, Jiujiang, Jiangxi, China
| | - Guanghua Deng
- Jiangxi Provincial Key Laboratory of Silviculture, Collaborative Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, College of Forestry/College of Art and Landscape, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Xueru Jiang
- Jiangxi Provincial Key Laboratory of Silviculture, Collaborative Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, College of Forestry/College of Art and Landscape, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Junhuo Cai
- Jiangxi Provincial Key Laboratory of Silviculture, Collaborative Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, College of Forestry/College of Art and Landscape, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Wei Liu
- Jiangxi Provincial Key Laboratory of Silviculture, Collaborative Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, College of Forestry/College of Art and Landscape, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Positioning Observation Station of Forest Ecosystem in Lushan, Lushan National Nature Reserve of Jiangxi, Jiujiang, Jiangxi, China
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Liu Y, Liu Y, Jiao D, Lu C, Lou Y, Li N, Wang G, Wang H. Synthesis and release of fatty acids under the interaction of Ulva pertusa and Heterosigma akashiwo by stable isotope analysis. Ecotoxicol Environ Saf 2021; 210:111852. [PMID: 33418155 DOI: 10.1016/j.ecoenv.2020.111852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Symbiosis of marine algae is inevitable in the marine environment, and species may occur interaction on the growth. In this study, the macroalgae Ulva pertusa and marine microalgae Heterosigma akashiwo were selected as target species to study the interaction mechanism between them. After the 8 days of co-cultivation, the inhibition on growth was observed for both of U. pertusa and H. akashiwo. Eight fatty acids in U. pertusa was detected, with the significant decrease in contents of polyunsaturated fatty acids (PUFAs) especially for C18:2, C18:3n-3 and C18:3n-6. Twelve fatty acids in H. akashiwo was detected, with the significant change for PUFAs. PUFA concentrations in the co-culture group were less than those in the mono-culture. Meanwhile the principal component analysis was conducted to insight into the interaction between U. pertusa and H. akashiwo by fatty acids content and carbon stable isotope ratio of fatty acids (δ13CFAs). Fatty acid content could not distinguish mono and co-culture. However, δ13CFAs could distinguish not only the culture time of algae, but also the living environment of algae. In addition, this study combined fatty acids content and δ13CFAs to explore the release of fatty acids by algae into the seawater. The C18:3n-3 was identified as the allelochemical released by U. pertusa to inhibit the growth of H. akashiwo. The ratio of δ13CFAs in seawater decreased. This study provides a theoretical basis for the symbiosis of marine algae, and a new method of compound-specific stable carbon isotopes was used to better explore the metabolism of fatty acids in algae.
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Affiliation(s)
- Yuxin Liu
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yu Liu
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China; Environmental Information Institute, Dalian Maritime University, Dalian 116026, China.
| | - Dian Jiao
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Chao Lu
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Yadi Lou
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Na Li
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Guoguang Wang
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China.
| | - Haixia Wang
- Navigation College, Dalian Maritime University, Dalian 116026, China
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5
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Kowallik KV, Martin WF. The origin of symbiogenesis: An annotated English translation of Mereschkowsky's 1910 paper on the theory of two plasma lineages. Biosystems 2021; 199:104281. [PMID: 33279568 PMCID: PMC7816216 DOI: 10.1016/j.biosystems.2020.104281] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 02/02/2023]
Abstract
In 1910, the Russian biologist Konstantin Sergejewitch Mereschkowsky (Константин Сергеевич Мережковский, in standard transliterations also written as Konstantin Sergeevič Merežkovskij and Konstantin Sergeevich Merezhkovsky) published a notable synthesis of observations and inferences concerning the origin of life and the origin of nucleated cells. His theory was based on physiology and leaned heavily upon the premise that thermophilic autotrophs were ancient. The ancestors of plants and animals were inferred as ancestrally mesophilic anucleate heterotrophs (Monera) that became complex and diverse through endosymbiosis. He placed a phylogenetic root in the tree of life among anaerobic autotrophic bacteria that lack chlorophyll. His higher level classification of all microbes and macrobes in the living world was based upon the presence or absence of past endosymbiotic events. The paper's primary aim was to demonstrate that all life forms descend from two fundamentally distinct organismal lineages, called mykoplasma and amoeboplasma, whose very nature was so different that, in his view, they could only have arisen independently of one another and at different times during Earth history. The mykoplasma arose at a time when the young Earth was still hot, it later gave rise to cyanobacteria, which in turn gave rise to plastids. The product of the second origin of life, the amoeboplasma, arose after the Earth had cooled and autotrophs had generated substrates for heterotrophic growth. Lineage diversification of that second plasma brought forth, via serial endosymbioses, animals (one symbiosis) and then plants (two symbioses, the second being the plastid). The paper was published in German, rendering it inaccessible to many interested scholars. Here we translate the 1910 paper in full and briefly provide some context.
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Affiliation(s)
- Klaus V Kowallik
- Institute for Molecular Evolution, Heinrich-Heine-University of Düsseldorf, Düsseldorf, Germany.
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine-University of Düsseldorf, Düsseldorf, Germany.
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6
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Shih JL, Selph KE, Wall CB, Wallsgrove NJ, Lesser MP, Popp BN. Trophic Ecology of the Tropical Pacific Sponge Mycale grandis Inferred from Amino Acid Compound-Specific Isotopic Analyses. Microb Ecol 2020; 79:495-510. [PMID: 31312870 DOI: 10.1007/s00248-019-01410-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/02/2019] [Indexed: 06/10/2023]
Abstract
Many sponges host abundant and active microbial communities that may play a role in the uptake of dissolved organic matter (DOM) by the sponge holobiont, although the mechanism of DOM uptake and metabolism is uncertain. Bulk and compound-specific isotopic analysis of whole sponge, isolated sponge cells, and isolated symbiotic microbial cells of the shallow water tropical Pacific sponge Mycale grandis were used to elucidate the trophic relationships between the host sponge and its associated microbial community. δ15N and δ13C values of amino acids in M. grandis isolated sponge cells are not different from those of its bacterial symbionts. Consequently, there is no difference in trophic position of the sponge and its symbiotic microbes indicating that M. grandis sponge cell isolates do not display amino acid isotopic characteristics typical of metazoan feeding. Furthermore, both the isolated microbial and sponge cell fractions were characterized by a similarly high ΣV value-a measure of bacterial-re-synthesis of organic matter calculated from the sum of variance among individual δ15N values of trophic amino acids. These high ΣV values observed in the sponge suggest that M. grandis is not reliant on translocated photosynthate from photosymbionts or feeding on water column picoplankton, but obtains nutrition through the uptake of amino acids of bacterial origin. Our results suggest that direct assimilation of bacterially synthesized amino acids from its symbionts, either in a manner similar to translocation observed in the coral holobiont or through phagotrophic feeding, is an important if not primary pathway of amino acid acquisition for M. grandis.
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Affiliation(s)
- Joy L Shih
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Karen E Selph
- Department of Oceanography, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Christopher B Wall
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, PO Box 1346, Kāne'ohe, HI, 96744, USA
| | - Natalie J Wallsgrove
- Department of Earth Sciences, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Michael P Lesser
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | - Brian N Popp
- Department of Earth Sciences, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.
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Colin S, Coelho LP, Sunagawa S, Bowler C, Karsenti E, Bork P, Pepperkok R, de Vargas C. Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes. eLife 2017. [PMID: 29087936 DOI: 10.7554/elife.26066.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
We present a 3D-fluorescence imaging and classification tool for high throughput analysis of microbial eukaryotes in environmental samples. It entails high-content feature extraction that permits accurate automated taxonomic classification and quantitative data about organism ultrastructures and interactions. Using plankton samples from the Tara Oceans expeditions, we validate its applicability to taxonomic profiling and ecosystem analyses, and discuss its potential for future integration of eukaryotic cell biology into evolutionary and ecological studies.
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Affiliation(s)
- Sebastien Colin
- UMR 7144, team EPEP, Station Biologique de Roscoff, Centre Nationnal de la Recherche Scientifique, Roscoff, France
- Université Pierre et Marie Curie, Sorbonne Universités, Roscoff, France
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, Paris Sciences et Lettres Research University, Paris, France
| | - Eric Karsenti
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, Paris Sciences et Lettres Research University, Paris, France
- Directors' Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rainer Pepperkok
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Colomban de Vargas
- UMR 7144, team EPEP, Station Biologique de Roscoff, Centre Nationnal de la Recherche Scientifique, Roscoff, France
- Université Pierre et Marie Curie, Sorbonne Universités, Roscoff, France
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8
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Colin S, Coelho LP, Sunagawa S, Bowler C, Karsenti E, Bork P, Pepperkok R, de Vargas C. Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes. eLife 2017; 6. [PMID: 29087936 PMCID: PMC5663481 DOI: 10.7554/elife.26066] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 09/25/2017] [Indexed: 01/01/2023] Open
Abstract
We present a 3D-fluorescence imaging and classification tool for high throughput analysis of microbial eukaryotes in environmental samples. It entails high-content feature extraction that permits accurate automated taxonomic classification and quantitative data about organism ultrastructures and interactions. Using plankton samples from the Tara Oceans expeditions, we validate its applicability to taxonomic profiling and ecosystem analyses, and discuss its potential for future integration of eukaryotic cell biology into evolutionary and ecological studies. Our planet’s ecosystems – from its oceans to its forests – are teeming with microbes. DNA analysis of environmental samples shows that many of these microbes belong to a group known as protists. This group consists of single-celled organisms that are close relatives of fungi, plants and animals. Though protists are a widespread and diverse group, scientists know little about them. One reason for this is the lack of high-throughput ways to recognize and count protists in environmental samples. Colin, Coelho et al. set out to tackle this blind spot in ecology and cell biology by developing an automated imaging system. The system needed to image many kinds of protist cells in enough detail to see the features inside. The end-result was a 3D-imaging technique called e-HCFM – which is short for “environmental high content fluorescence microscopy”. Colin, Coelho et al. went on to use the technique on 72 samples collected on an expedition across the world’s oceans. This allowed them to automatically image, recognize and classify over 330,000 organisms. This approach and new dataset will benefit researchers working in many fields, from cell biology to ecology, computational biology and beyond. In the future, this imaging method might integrate with techniques that can analyze the DNA in individual cells. This would allow scientists to link protists’ visible features to their genetic information, in a way that will scale from single cells up to entire ecosystems.
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Affiliation(s)
- Sebastien Colin
- UMR 7144, team EPEP, Station Biologique de Roscoff, Centre Nationnal de la Recherche Scientifique, Roscoff, France.,Université Pierre et Marie Curie, Sorbonne Universités, Roscoff, France.,Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, Paris Sciences et Lettres Research University, Paris, France
| | - Eric Karsenti
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, Paris Sciences et Lettres Research University, Paris, France.,Directors' Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rainer Pepperkok
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Colomban de Vargas
- UMR 7144, team EPEP, Station Biologique de Roscoff, Centre Nationnal de la Recherche Scientifique, Roscoff, France.,Université Pierre et Marie Curie, Sorbonne Universités, Roscoff, France
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Ormeño-Orrillo E, Gomes DF, Del Cerro P, Vasconcelos ATR, Canchaya C, Almeida LGP, Mercante FM, Ollero FJ, Megías M, Hungria M. Genome of Rhizobium leucaenae strains CFN 299(T) and CPAO 29.8: searching for genes related to a successful symbiotic performance under stressful conditions. BMC Genomics 2016; 17:534. [PMID: 27485828 PMCID: PMC4971678 DOI: 10.1186/s12864-016-2859-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 06/27/2016] [Indexed: 01/02/2023] Open
Abstract
Background Common bean (Phaseolus vulgaris L.) is the most important legume cropped worldwide for food production and its agronomic performance can be greatly improved if the benefits from symbiotic nitrogen fixation are maximized. The legume is known for its high promiscuity in nodulating with several Rhizobium species, but those belonging to the Rhizobium tropici “group” are the most successful and efficient in fixing nitrogen in tropical acid soils. Rhizobium leucaenae belongs to this group, which is abundant in the Brazilian “Cerrados” soils and frequently submitted to several environmental stresses. Here we present the first high-quality genome drafts of R. leucaenae, including the type strain CFN 299T and the very efficient strain CPAO 29.8. Our main objective was to identify features that explain the successful capacity of R. leucaenae in nodulating common bean under stressful environmental conditions. Results The genomes of R. leucaenae strains CFN 299T and CPAO 29.8 were estimated at 6.7–6.8 Mbp; 7015 and 6899 coding sequences (CDS) were predicted, respectively, 6264 of which are common to both strains. The genomes of both strains present a large number of CDS that may confer tolerance of high temperatures, acid soils, salinity and water deficiency. Types I, II, IV-pili, IV and V secretion systems were present in both strains and might help soil and host colonization as well as the symbiotic performance under stressful conditions. The symbiotic plasmid of CPAO 29.8 is highly similar to already described tropici pSyms, including five copies of nodD and three of nodA genes. R. leucaenae CFN 299T is capable of synthesizing Nod factors in the absence of flavonoids when submitted to osmotic stress, indicating that under abiotic stress the regulation of nod genes might be different. Conclusion A detailed study of the genes putatively related to stress tolerance in R. leucaenae highlighted an intricate pattern comprising a variety of mechanisms that are probably orchestrated to tolerate the stressful conditions to which the strains are submitted on a daily basis. The capacity to synthesize Nod factors under abiotic stress might follow the same regulatory pathways as in CIAT 899T and may help both to improve bacterial survival and to expand host range to guarantee the perpetuation of the symbiosis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2859-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Douglas Fabiano Gomes
- Embrapa Soja, C.P. 231, 86001-970, Londrina, Paraná, Brazil.,CAPES, SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, 70.040-020, Brasília, Federal District, Brazil
| | - Pablo Del Cerro
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes, 6 Apdo Postal, 41012, Sevilla, Spain
| | - Ana Tereza Ribeiro Vasconcelos
- Laboratório Nacional de Computação Científica (LNCC), Labinfo, Rua Getúlio Vargas 333, 25651-071, Petrópolis, Rio de Janeiro, Brazil
| | - Carlos Canchaya
- Department Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, 36310, Vigo, Spain
| | - Luiz Gonzaga Paula Almeida
- Laboratório Nacional de Computação Científica (LNCC), Labinfo, Rua Getúlio Vargas 333, 25651-071, Petrópolis, Rio de Janeiro, Brazil
| | | | - Francisco Javier Ollero
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes, 6 Apdo Postal, 41012, Sevilla, Spain
| | - Manuel Megías
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes, 6 Apdo Postal, 41012, Sevilla, Spain
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Muggia L, Fleischhacker A, Kopun T, Grube M. Extremotolerant fungi from alpine rock lichens and their phylogenetic relationships. FUNGAL DIVERS 2015; 76:119-142. [PMID: 26877720 PMCID: PMC4739527 DOI: 10.1007/s13225-015-0343-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/06/2015] [Indexed: 01/23/2023]
Abstract
Fungi other than the lichen mycobiont frequently co-occur within lichen thalli and on the same rock in harsh environments. In these situations dark-pigmented mycelial structures are commonly observed on lichen thalli, where they persist under the same stressful conditions as their hosts. Here we used a comprehensive sampling of lichen-associated fungi from an alpine habitat to assess their phylogenetic relationships with fungi previously known from other niches. The multilocus phylogenetic analyses suggest that most of the 248 isolates belong to the Chaetothyriomycetes and Dothideomycetes, while a minor fraction represents Sordariomycetes and Leotiomycetes. As many lichens also were infected by phenotypically distinct lichenicolous fungi of diverse lineages, it remains difficult to assess whether the culture isolates represent these fungi or are from additional cryptic, extremotolerant fungi within the thalli. Some of these strains represent yet undescribed lineages within Chaethothyriomycetes and Dothideomycetes, whereas other strains belong to genera of fungi, that are known as lichen colonizers, plant and human pathogens, rock-inhabiting fungi, parasites and saprotrophs. The symbiotic structures of the lichen thalli appear to be a shared habitat of phylogenetically diverse stress-tolerant fungi, which potentially benefit from the lichen niche in otherwise hostile habitats.
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Affiliation(s)
- Lucia Muggia
- Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010 Graz, Austria ; Department of Life Sciences, Università degli Studi di Trieste, Via Valerio 12/2, 34128 Trieste, Italy
| | | | - Theodora Kopun
- Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010 Graz, Austria
| | - Martin Grube
- Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010 Graz, Austria
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