1
|
Arora J, Buček A, Hellemans S, Beránková T, Arias JR, Fisher BL, Clitheroe C, Brune A, Kinjo Y, Šobotník J, Bourguignon T. Evidence of cospeciation between termites and their gut bacteria on a geological time scale. Proc Biol Sci 2023; 290:20230619. [PMID: 37339742 DOI: 10.1098/rspb.2023.0619] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Termites host diverse communities of gut microbes, including many bacterial lineages only found in this habitat. The bacteria endemic to termite guts are transmitted via two routes: a vertical route from parent colonies to daughter colonies and a horizontal route between colonies sometimes belonging to different termite species. The relative importance of both transmission routes in shaping the gut microbiota of termites remains unknown. Using bacterial marker genes derived from the gut metagenomes of 197 termites and one Cryptocercus cockroach, we show that bacteria endemic to termite guts are mostly transferred vertically. We identified 18 lineages of gut bacteria showing cophylogenetic patterns with termites over tens of millions of years. Horizontal transfer rates estimated for 16 bacterial lineages were within the range of those estimated for 15 mitochondrial genes, suggesting that horizontal transfers are uncommon and vertical transfers are the dominant transmission route in these lineages. Some of these associations probably date back more than 150 million years and are an order of magnitude older than the cophylogenetic patterns between mammalian hosts and their gut bacteria. Our results suggest that termites have cospeciated with their gut bacteria since first appearing in the geological record.
Collapse
Affiliation(s)
- Jigyasa Arora
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Aleš Buček
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
- Faculty of Tropical AgriScience, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
| | - Simon Hellemans
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Tereza Beránková
- Faculty of Tropical AgriScience, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
| | - Johanna Romero Arias
- Faculty of Tropical AgriScience, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
| | - Brian L Fisher
- Madagascar Biodiversity Center, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo 101, Madagascar
- California Academy of Sciences, San Francisco, CA, USA
| | - Crystal Clitheroe
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
| | - Yukihiro Kinjo
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
- College of Economics and Environmental Policy, Okinawa International University, 2-6-1 Ginowan, Ginowan, 901-2701, Okinawa, Japan
| | - Jan Šobotník
- Faculty of Tropical AgriScience, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
- College of Economics and Environmental Policy, Okinawa International University, 2-6-1 Ginowan, Ginowan, 901-2701, Okinawa, Japan
| | - Thomas Bourguignon
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
- Faculty of Tropical AgriScience, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
| |
Collapse
|
2
|
Kashinskaya EN, Simonov EP, Poddubnaya LG, Vlasenko PG, Shokurova AV, Parshukov AN, Andree KB, Solovyev MM. Trophic diversification and parasitic invasion as ecological niche modulators for gut microbiota of whitefish. Front Microbiol 2023; 14:1090899. [PMID: 36998403 PMCID: PMC10043260 DOI: 10.3389/fmicb.2023.1090899] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 02/07/2023] [Indexed: 03/15/2023] Open
Abstract
Introduction The impact of parasites on gut microbiota of the host is well documented, but the role of the relationship between the parasite and the host in the formation of the microbiota is poorly understood. This study has focused on the influence that trophic behavior and resulting parasitism has on the structure of the microbiome. Methods Using 16S amplicon sequencing and newly developed methodological approaches, we characterize the gut microbiota of the sympatric pair of whitefish Coregonus lavaretus complex and the associated microbiota of cestodes parasitizing their intestine. The essence of the proposed approaches is, firstly, to use the method of successive washes of the microbiota from the cestode's surfaces to analyze the degree of bacterial association to the tegument of the parasite. Secondly, to use a method combining the sampling of intestinal content and mucosa with the washout procedure from the mucosa to understand the real structure of the fish gut microbiota. Results and discussion Our results demonstrate that additional microbial community in the intestine are formed by the parasitic helminths that caused the restructuring of the microbiota in infected fish compared to those uninfected. Using the desorption method in Ringer's solution, we have demonstrated that Proteocephalus sp. cestodes possess their own microbial community which is put together from "surface" bacteria, and bacteria which are weakly and strongly associated with the tegument, bacteria obtained after treatment of the tegument with detergent, and bacteria obtained after removal of the tegument from the cestodes.
Collapse
Affiliation(s)
- Elena N. Kashinskaya
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | - Evgeniy P. Simonov
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | - Larisa G. Poddubnaya
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Yaroslavl Region, Russia
| | - Pavel G. Vlasenko
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | - Anastasiya V. Shokurova
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | - Aleksey N. Parshukov
- Institute of Biology of the Karelian Research Centre, Russian Academy of Sciences, Petrozavodsk, Russia
| | - Karl B. Andree
- Institut de Recerca i Tecnologìa Agroalimentaries (IRTA), Sant Carles de la Ràpita, Spain
| | - Mikhail M. Solovyev
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
- Tomsk State University, Biological Institute, Tomsk, Russia
| |
Collapse
|
3
|
Ge X, Pereira FC, Mitteregger M, Berry D, Zhang M, Hausmann B, Zhang J, Schintlmeister A, Wagner M, Cheng JX. SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level. Proc Natl Acad Sci U S A 2022; 119:e2203519119. [PMID: 35727976 PMCID: PMC9245642 DOI: 10.1073/pnas.2203519119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/08/2022] [Indexed: 12/26/2022] Open
Abstract
One of the biggest challenges in microbiome research in environmental and medical samples is to better understand functional properties of microbial community members at a single-cell level. Single-cell isotope probing has become a key tool for this purpose, but the current detection methods for determination of isotope incorporation into single cells do not allow high-throughput analyses. Here, we report on the development of an imaging-based approach termed stimulated Raman scattering-two-photon fluorescence in situ hybridization (SRS-FISH) for high-throughput metabolism and identity analyses of microbial communities with single-cell resolution. SRS-FISH offers an imaging speed of 10 to 100 ms per cell, which is two to three orders of magnitude faster than achievable by state-of-the-art methods. Using this technique, we delineated metabolic responses of 30,000 individual cells to various mucosal sugars in the human gut microbiome via incorporation of deuterium from heavy water as an activity marker. Application of SRS-FISH to investigate the utilization of host-derived nutrients by two major human gut microbiome taxa revealed that response to mucosal sugars tends to be dominated by Bacteroidales, with an unexpected finding that Clostridia can outperform Bacteroidales at foraging fucose. With high sensitivity and speed, SRS-FISH will enable researchers to probe the fine-scale temporal, spatial, and individual activity patterns of microbial cells in complex communities with unprecedented detail.
Collapse
Affiliation(s)
- Xiaowei Ge
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
| | - Fátima C. Pereira
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Matthias Mitteregger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Meng Zhang
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Jing Zhang
- Department of Biomedical Engineering, Photonics Center, Boston University, Boston, MA 02215
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
- Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Ji-Xin Cheng
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
- Department of Biomedical Engineering, Photonics Center, Boston University, Boston, MA 02215
| |
Collapse
|
4
|
Manfredini A, Malusà E, Costa C, Pallottino F, Mocali S, Pinzari F, Canfora L. Current Methods, Common Practices, and Perspectives in Tracking and Monitoring Bioinoculants in Soil. Front Microbiol 2021; 12:698491. [PMID: 34531836 PMCID: PMC8438429 DOI: 10.3389/fmicb.2021.698491] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/28/2021] [Indexed: 12/22/2022] Open
Abstract
Microorganisms promised to lead the bio-based revolution for a more sustainable agriculture. Beneficial microorganisms could be a valid alternative to the use of chemical fertilizers or pesticides. However, the increasing use of microbial inoculants is also raising several questions about their efficacy and their effects on the autochthonous soil microorganisms. There are two major issues on the application of bioinoculants to soil: (i) their detection in soil, and the analysis of their persistence and fate; (ii) the monitoring of the impact of the introduced bioinoculant on native soil microbial communities. This review explores the strategies and methods that can be applied to the detection of microbial inoculants and to soil monitoring. The discussion includes a comprehensive critical assessment of the available tools, based on morpho-phenological, molecular, and microscopic analyses. The prospects for future development of protocols for regulatory or commercial purposes are also discussed, underlining the need for a multi-method (polyphasic) approach to ensure the necessary level of discrimination required to track and monitor bioinoculants in soil.
Collapse
Affiliation(s)
- Andrea Manfredini
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Eligio Malusà
- National Research Institute of Horticulture, Skierniewice, Poland
- Council for Agricultural Research and Economics, Research Centre for Viticulture and Enology, Conegliano, Italy
| | - Corrado Costa
- Council for Agricultural Research and Analysis of the Agricultural Economy, Research Centre for Engineering and Agro-Food Processing, Monterotondo, Italy
| | - Federico Pallottino
- Council for Agricultural Research and Analysis of the Agricultural Economy, Research Centre for Engineering and Agro-Food Processing, Monterotondo, Italy
| | - Stefano Mocali
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| | - Flavia Pinzari
- Institute for Biological Systems, Council of National Research of Italy (CNR), Rome, Italy
- Life Sciences Department, Natural History Museum, London, United Kingdom
| | - Loredana Canfora
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, Rome, Italy
| |
Collapse
|
5
|
Perreau J, Moran NA. Genetic innovations in animal-microbe symbioses. Nat Rev Genet 2021; 23:23-39. [PMID: 34389828 DOI: 10.1038/s41576-021-00395-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2021] [Indexed: 02/07/2023]
Abstract
Animal hosts have initiated myriad symbiotic associations with microorganisms and often have maintained these symbioses for millions of years, spanning drastic changes in ecological conditions and lifestyles. The establishment and persistence of these relationships require genetic innovations on the parts of both symbionts and hosts. The nature of symbiont innovations depends on their genetic population structure, categorized here as open, closed or mixed. These categories reflect modes of inter-host transmission that result in distinct genomic features, or genomic syndromes, in symbionts. Although less studied, hosts also innovate in order to preserve and control symbiotic partnerships. New capabilities to sequence host-associated microbial communities and to experimentally manipulate both hosts and symbionts are providing unprecedented insights into how genetic innovations arise under different symbiont population structures and how these innovations function to support symbiotic relationships.
Collapse
Affiliation(s)
- Julie Perreau
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA
| | - Nancy A Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA.
| |
Collapse
|
6
|
Sogin EM, Kleiner M, Borowski C, Gruber-Vodicka HR, Dubilier N. Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses. Annu Rev Microbiol 2021; 75:695-718. [PMID: 34351792 DOI: 10.1146/annurev-micro-051021-123130] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- E Maggie Sogin
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; ,
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27607, USA
| | - Christian Borowski
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; , .,MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
| | | | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany; , .,MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
| |
Collapse
|
7
|
Caira JN, Jensen K. Electron microscopy reveals novel external specialized organs housing bacteria in eagle ray tapeworms. PLoS One 2021; 16:e0244586. [PMID: 33481793 PMCID: PMC7822281 DOI: 10.1371/journal.pone.0244586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/11/2020] [Indexed: 12/03/2022] Open
Abstract
Nutritionally-based mutualisms with bacteria are known to occur in a wide array of invertebrate phyla, although less commonly in the Platyhelminthes. Here we report what appears to be a novel example of this type of association in two geographically disparate and phylogenetically distant species of tapeworms of eagle rays-the lecanicephalidean Elicilacunosus dharmadii off the island of Borneo and the tetraphyllidean Caulobothrium multispelaeum off Senegal. Scanning and transmission electron microscopy revealed that the grooves and apertures on the outer surfaces of both tapeworms open into expansive cavities housing concentrations of bacteria. This led us to reject the original hypothesis that these structures, and their associated mucopolysaccharides, aid in attachment to the host mucosa. The cavities were found to be specialized in-foldings of the tapeworm body that were lined with particularly elongate filitriches. Given tapeworms lack a gut and employ filitriches to assist in nutrient absorption, enhanced nutrient uptake likely occurs in the cavities. Each tapeworm species appeared to host different bacterial monocultures; those in E. dharmadii were coccoid-like in form, while those in C. multispelaeum were bacillus-like. The presence of bacteria in a specialized structure of this nature suggests the structure is a symbiotic organ. Tapeworms are fully capable of obtaining their own nutrients, and thus the bacteria likely serve merely to supplement their diet. Given the bacteria were also extracellular, this structure is more consistent with a mycetome than a trophosome. To our knowledge, this is not only the first evidence of an external symbiotic organ of any type in a nutritionally-based mutualism, but also the first description of a mycetome in a group of invertebrates that lacks a digestive system. The factors that might account for the independent evolution of this unique association in these unrelated tapeworms are unclear-especially given that none of their closest relatives exhibit any evidence of the phenomenon.
Collapse
Affiliation(s)
- Janine N. Caira
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Kirsten Jensen
- Department of Ecology & Evolutionary Biology and the Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| |
Collapse
|
8
|
Optofluidic Raman-activated cell sorting for targeted genome retrieval or cultivation of microbial cells with specific functions. Nat Protoc 2020; 16:634-676. [PMID: 33311714 DOI: 10.1038/s41596-020-00427-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/25/2020] [Indexed: 12/22/2022]
Abstract
Stable isotope labeling of microbial taxa of interest and their sorting provide an efficient and direct way to answer the question "who does what?" in complex microbial communities when coupled with fluorescence in situ hybridization or downstream 'omics' analyses. We have developed a platform for automated Raman-based sorting in which optical tweezers and microfluidics are used to sort individual cells of interest from microbial communities on the basis of their Raman spectra. This sorting of cells and their downstream DNA analysis, such as by mini-metagenomics or single-cell genomics, or cultivation permits a direct link to be made between the metabolic roles and the genomes of microbial cells within complex microbial communities, as well as targeted isolation of novel microbes with a specific physiology of interest. We describe a protocol from sample preparation through Raman-activated live cell sorting. Subsequent cultivation of sorted cells is described, whereas downstream DNA analysis involves well-established approaches with abundant methods available in the literature. Compared with manual sorting, this technique provides a substantially higher throughput (up to 500 cells per h). Furthermore, the platform has very high sorting accuracy (98.3 ± 1.7%) and is fully automated, thus avoiding user biases that might accompany manual sorting. We anticipate that this protocol will empower in particular environmental and host-associated microbiome research with a versatile tool to elucidate the metabolic contributions of microbial taxa within their complex communities. After a 1-d preparation of cells, sorting takes on the order of 4 h, depending on the number of cells required.
Collapse
|
9
|
Chomicki G, Kiers ET, Renner SS. The Evolution of Mutualistic Dependence. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-110218-024629] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
While the importance of mutualisms across the tree of life is recognized, it is not understood why some organisms evolve high levels of dependence on mutualistic partnerships, while other species remain autonomous or retain or regain minimal dependence on partners. We identify four main pathways leading to the evolution of mutualistic dependence. Then, we evaluate current evidence for three predictions: ( a) Mutualisms with different levels of dependence have distinct stabilizing mechanisms against exploitation and cheating, ( b) less dependent mutualists will return to autonomy more often than those that are highly dependent, and ( c) obligate mutualisms should be less context dependent than facultative ones. Although we find evidence supporting all three predictions, we stress that mutualistic partners follow diverse paths toward—and away from—dependence. We also highlight the need to better examine asymmetry in partner dependence. Recognizing how variation in dependence influences the stability, breakdown, and context dependence of mutualisms generates new hypotheses regarding how and why the benefits of mutualistic partnerships differ over time and space.
Collapse
Affiliation(s)
- Guillaume Chomicki
- Department of Bioscience, Durham University, Durham DH1 3LE, United Kingdom
| | - E. Toby Kiers
- Department of Ecological Science, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Susanne S. Renner
- Systematic Botany and Mycology, Department of Biology, University of Munich (LMU), 80638 Munich, Germany
| |
Collapse
|
10
|
Abstract
To track organisms across all domains of life, the SSU rRNA gene is the gold standard. Many environmental microbes are known only from high-throughput sequence data, but the SSU rRNA gene, the key to visualization by molecular probes and link to existing literature, is often missing from metagenome-assembled genomes (MAGs). The easy-to-use phyloFlash software suite tackles this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based linking to MAGs. Starting from a cleaned reference database, phyloFlash profiles the taxonomic diversity and assembles the sorted SSU rRNA reads. The phyloFlash design is domain agnostic and covers eukaryotes, archaea, and bacteria alike. phyloFlash also provides utilities to visualize multisample comparisons and to integrate the recovered SSU rRNAs in a metagenomics workflow by linking them to MAGs using assembly graph parsing. The small-subunit rRNA (SSU rRNA) gene is the key marker in molecular ecology for all domains of life, but it is largely absent from metagenome-assembled genomes that often are the only resource available for environmental microbes. Here, we present phyloFlash, a pipeline to overcome this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based binning of full metagenomic assemblies. We show that a cleanup of artifacts is pivotal even with a curated reference database. With such a filtered database, the general-purpose mapper BBmap extracts SSU rRNA reads five times faster than the rRNA-specialized tool SortMeRNA with similar sensitivity and higher selectivity on simulated metagenomes. Reference-based targeted assemblers yielded either highly fragmented assemblies or high levels of chimerism, so we employ the general-purpose genomic assembler SPAdes. Our optimized implementation is independent of reference database composition and has satisfactory levels of chimera formation. phyloFlash quickly processes Illumina (meta)genomic data, is straightforward to use, even as part of high-throughput quality control, and has user-friendly output reports. The software is available at https://github.com/HRGV/phyloFlash (GPL3 license) and is documented with an online manual. IMPORTANCE To track organisms across all domains of life, the SSU rRNA gene is the gold standard. Many environmental microbes are known only from high-throughput sequence data, but the SSU rRNA gene, the key to visualization by molecular probes and link to existing literature, is often missing from metagenome-assembled genomes (MAGs). The easy-to-use phyloFlash software suite tackles this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based linking to MAGs. Starting from a cleaned reference database, phyloFlash profiles the taxonomic diversity and assembles the sorted SSU rRNA reads. The phyloFlash design is domain agnostic and covers eukaryotes, archaea, and bacteria alike. phyloFlash also provides utilities to visualize multisample comparisons and to integrate the recovered SSU rRNAs in a metagenomics workflow by linking them to MAGs using assembly graph parsing.
Collapse
|
11
|
Douglas AE. Housing microbial symbionts: evolutionary origins and diversification of symbiotic organs in animals. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190603. [PMID: 32772661 DOI: 10.1098/rstb.2019.0603] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In many animal hosts, microbial symbionts are housed within specialized structures known as symbiotic organs, but the evolutionary origins of these structures have rarely been investigated. Here, I adopt an evolutionary developmental (evo-devo) approach, specifically to apply knowledge of the development of symbiotic organs to gain insights into their evolutionary origins and diversification. In particular, host genetic changes associated with evolution of symbiotic organs can be inferred from studies to identify the host genes that orchestrate the development of symbiotic organs, recognizing that microbial products may also play a key role in triggering the developmental programme in some associations. These studies may also reveal whether higher animal taxonomic groups (order, class, phylum, etc.) possess a common genetic regulatory network for symbiosis that is latent in taxa lacking symbiotic organs, and activated at the origination of symbiosis in different host lineages. In this way, apparent instances of convergent evolution of symbiotic organs may be homologous in terms of a common genetic blueprint for symbiosis. Advances in genetic technologies, including reverse genetic tools and genome editing, will facilitate the application of evo-devo approaches to investigate the evolution of symbiotic organs in animals. This article is part of the theme issue 'The role of the microbiome in host evolution'.
Collapse
Affiliation(s)
- Angela E Douglas
- Department of Entomology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
12
|
Chomicki G, Werner GDA, West SA, Kiers ET. Compartmentalization drives the evolution of symbiotic cooperation. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190602. [PMID: 32772665 DOI: 10.1098/rstb.2019.0602] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Across the tree of life, hosts have evolved mechanisms to control and mediate interactions with symbiotic partners. We suggest that the evolution of physical structures that allow hosts to spatially separate symbionts, termed compartmentalization, is a common mechanism used by hosts. Such compartmentalization allows hosts to: (i) isolate symbionts and control their reproduction; (ii) reward cooperative symbionts and punish or stop interactions with non-cooperative symbionts; and (iii) reduce direct conflict among different symbionts strains in a single host. Compartmentalization has allowed hosts to increase the benefits that they obtain from symbiotic partners across a diversity of interactions, including legumes and rhizobia, plants and fungi, squid and Vibrio, insects and nutrient provisioning bacteria, plants and insects, and the human microbiome. In cases where compartmentalization has not evolved, we ask why not. We argue that when partners interact in a competitive hierarchy, or when hosts engage in partnerships which are less costly, compartmentalization is less likely to evolve. We conclude that compartmentalization is key to understanding the evolution of symbiotic cooperation. This article is part of the theme issue 'The role of the microbiome in host evolution'.
Collapse
Affiliation(s)
- Guillaume Chomicki
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Gijsbert D A Werner
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Road, Oxford OX1 3SZ, UK.,Netherlands Scientific Council for Government Policy, Buitenhof 34, 2513 AH Den Haag, The Netherlands
| | - Stuart A West
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - E Toby Kiers
- Department of Ecological Science, VU University, Amsterdam, The Netherlands
| |
Collapse
|
13
|
Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
Collapse
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
| |
Collapse
|
14
|
Hatzenpichler R, Krukenberg V, Spietz RL, Jay ZJ. Next-generation physiology approaches to study microbiome function at single cell level. Nat Rev Microbiol 2020; 18:241-256. [PMID: 32055027 DOI: 10.1038/s41579-020-0323-1] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2020] [Indexed: 12/14/2022]
Abstract
The function of cells in their native habitat often cannot be reliably predicted from genomic data or from physiology studies of isolates. Traditional experimental approaches to study the function of taxonomically and metabolically diverse microbiomes are limited by their destructive nature, low spatial resolution or low throughput. Recently developed technologies can offer new insights into cellular function in natural and human-made systems and how microorganisms interact with and shape the environments that they inhabit. In this Review, we provide an overview of these next-generation physiology approaches and discuss how the non-destructive analysis of cellular phenotypes, in combination with the separation of the target cells for downstream analyses, provide powerful new, complementary ways to study microbiome function. We anticipate that the widespread application of next-generation physiology approaches will transform the field of microbial ecology and dramatically improve our understanding of how microorganisms function in their native environment.
Collapse
Affiliation(s)
- Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
| | - Viola Krukenberg
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Rachel L Spietz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| |
Collapse
|
15
|
Cleary DFR, Polónia ARM, Huang YM, Swierts T. Compositional variation between high and low prokaryotic diversity coral reef biotopes translates to different predicted metagenomic gene content. Antonie van Leeuwenhoek 2019; 113:563-587. [PMID: 31802337 DOI: 10.1007/s10482-019-01364-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 11/20/2019] [Indexed: 10/25/2022]
Abstract
In a previous study, we identified host species that housed high and low diversity prokaryotic communities. In the present study, we expand on this and assessed the prokaryotic communities associated with seawater, sediment and 11 host species from 7 different phyla in a Taiwanese coral reef setting. The host taxa sampled included hard, octo- and black corals, molluscs, bryozoans, flatworms, fish and sea urchins. There were highly significant differences in composition among host species and all host species housed distinct communities from those found in seawater and sediment. In a hierarchical clustering analysis, samples from all host species, with the exception of the coral Galaxea astreata, formed significantly supported clusters. In addition to this, the coral G. astreata and the bryozoan Triphyllozoon inornatum on the one hand and the coral Tubastraea coccinea, the hermit crab Calcinus laevimanus and the flatworm Thysanozoon nigropapillosum on the other formed significantly supported clusters. In addition to composition, there were highly pronounced differences in richness and evenness among host species from the most diverse species, the bryozoan T. inornatum at 2518 ± 240 OTUs per 10,000 sequences to the least diverse species, the octocoral Cladiella sp. at 142 ± 14 OTUs per 10,000 sequences. In line with the differences in composition, there were significant differences in predicted metagenomic gene counts among host species. Furthermore, there were pronounced compositional and predicted functional differences between high diversity hosts (Liolophura japonica, G. astreata, T. coccinea, C. laevimanus, T. inornatum) and low diversity hosts (Antipathes sp., Pomacentrus coelestis, Modiolus auriculatus, T. nigropapillosum, Cladiella sp. and Diadema savigny). In particular, we found that all tested low diversity hosts were predicted to be enriched for the phosphotransferase system compared to high diversity hosts.
Collapse
Affiliation(s)
- Daniel F R Cleary
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Ana Rita M Polónia
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Yusheng M Huang
- Tropical Island Sustainable Development Research Center, National Penghu University of Science and Technology, Penghu, Taiwan.,Department of Marine Recreation, University of Science and Technology, Penghu, Taiwan
| | - Thomas Swierts
- Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands
| |
Collapse
|
16
|
Seah BKB, Antony CP, Huettel B, Zarzycki J, Schada von Borzyskowski L, Erb TJ, Kouris A, Kleiner M, Liebeke M, Dubilier N, Gruber-Vodicka HR. Sulfur-Oxidizing Symbionts without Canonical Genes for Autotrophic CO 2 Fixation. mBio 2019; 10:e01112-19. [PMID: 31239380 PMCID: PMC6593406 DOI: 10.1128/mbio.01112-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/23/2019] [Indexed: 01/25/2023] Open
Abstract
Since the discovery of symbioses between sulfur-oxidizing (thiotrophic) bacteria and invertebrates at hydrothermal vents over 40 years ago, it has been assumed that autotrophic fixation of CO2 by the symbionts drives these nutritional associations. In this study, we investigated "Candidatus Kentron," the clade of symbionts hosted by Kentrophoros, a diverse genus of ciliates which are found in marine coastal sediments around the world. Despite being the main food source for their hosts, Kentron bacteria lack the key canonical genes for any of the known pathways for autotrophic carbon fixation and have a carbon stable isotope fingerprint that is unlike other thiotrophic symbionts from similar habitats. Our genomic and transcriptomic analyses instead found metabolic features consistent with growth on organic carbon, especially organic and amino acids, for which they have abundant uptake transporters. All known thiotrophic symbionts have converged on using reduced sulfur to gain energy lithotrophically, but they are diverse in their carbon sources. Some clades are obligate autotrophs, while many are mixotrophs that can supplement autotrophic carbon fixation with heterotrophic capabilities similar to those in Kentron. Here we show that Kentron bacteria are the only thiotrophic symbionts that appear to be entirely heterotrophic, unlike all other thiotrophic symbionts studied to date, which possess either the Calvin-Benson-Bassham or the reverse tricarboxylic acid cycle for autotrophy.IMPORTANCE Many animals and protists depend on symbiotic sulfur-oxidizing bacteria as their main food source. These bacteria use energy from oxidizing inorganic sulfur compounds to make biomass autotrophically from CO2, serving as primary producers for their hosts. Here we describe a clade of nonautotrophic sulfur-oxidizing symbionts, "Candidatus Kentron," associated with marine ciliates. They lack genes for known autotrophic pathways and have a carbon stable isotope fingerprint heavier than other symbionts from similar habitats. Instead, they have the potential to oxidize sulfur to fuel the uptake of organic compounds for heterotrophic growth, a metabolic mode called chemolithoheterotrophy that is not found in other symbioses. Although several symbionts have heterotrophic features to supplement primary production, in Kentron they appear to supplant it entirely.
Collapse
Affiliation(s)
| | | | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jan Zarzycki
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Tobias J Erb
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Angela Kouris
- Energy Bioengineering and Geomicrobiology Group, University of Calgary, Calgary, Alberta, Canada
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Manuel Liebeke
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | | |
Collapse
|
17
|
Chemosynthetic symbiont with a drastically reduced genome serves as primary energy storage in the marine flatworm Paracatenula. Proc Natl Acad Sci U S A 2019; 116:8505-8514. [PMID: 30962361 PMCID: PMC6486704 DOI: 10.1073/pnas.1818995116] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Animals typically store their primary energy reserves in specialized cells. Here, we show that in the small marine flatworm Paracatenula, this function is performed by its bacterial chemosynthetic symbiont. The intracellular symbiont occupies half of the biomass in the symbiosis and has a highly reduced genome but efficiently stocks up and maintains carbon and energy, particularly sugars. The host rarely digests the symbiont cells to access these stocks. Instead, the symbionts appear to provide the bulk nutrition by secreting outer-membrane vesicles. This is in contrast to all other described chemosynthetic symbioses, where the hosts continuously digest full cells of a small and ideally growing symbiont population that cannot provide a long-term buffering capacity during nutrient limitation. Hosts of chemoautotrophic bacteria typically have much higher biomass than their symbionts and consume symbiont cells for nutrition. In contrast to this, chemoautotrophic Candidatus Riegeria symbionts in mouthless Paracatenula flatworms comprise up to half of the biomass of the consortium. Each species of Paracatenula harbors a specific Ca. Riegeria, and the endosymbionts have been vertically transmitted for at least 500 million years. Such prolonged strict vertical transmission leads to streamlining of symbiont genomes, and the retained physiological capacities reveal the functions the symbionts provide to their hosts. Here, we studied a species of Paracatenula from Sant’Andrea, Elba, Italy, using genomics, gene expression, imaging analyses, as well as targeted and untargeted MS. We show that its symbiont, Ca. R. santandreae has a drastically smaller genome (1.34 Mb) than the symbiont´s free-living relatives (4.29–4.97 Mb) but retains a versatile and energy-efficient metabolism. It encodes and expresses a complete intermediary carbon metabolism and enhanced carbon fixation through anaplerosis and accumulates massive intracellular inclusions such as sulfur, polyhydroxyalkanoates, and carbohydrates. Compared with symbiotic and free-living chemoautotrophs, Ca. R. santandreae’s versatility in energy storage is unparalleled in chemoautotrophs with such compact genomes. Transmission EM as well as host and symbiont expression data suggest that Ca. R. santandreae largely provisions its host via outer-membrane vesicle secretion. With its high share of biomass in the symbiosis and large standing stocks of carbon and energy reserves, it has a unique role for bacterial symbionts—serving as the primary energy storage for its animal host.
Collapse
|
18
|
Resolving the individual contribution of key microbial populations to enhanced biological phosphorus removal with Raman-FISH. ISME JOURNAL 2019; 13:1933-1946. [PMID: 30894691 PMCID: PMC6776032 DOI: 10.1038/s41396-019-0399-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 02/02/2019] [Accepted: 02/28/2019] [Indexed: 02/05/2023]
Abstract
Enhanced biological phosphorus removal (EBPR) is a globally important biotechnological process and relies on the massive accumulation of phosphate within special microorganisms. Candidatus Accumulibacter conform to the classical physiology model for polyphosphate accumulating organisms and are widely believed to be the most important player for the process in full-scale EBPR systems. However, it was impossible till now to quantify the contribution of specific microbial clades to EBPR. In this study, we have developed a new tool to directly link the identity of microbial cells to the absolute quantification of intracellular poly-P and other polymers under in situ conditions, and applied it to eight full-scale EBPR plants. Besides Ca. Accumulibacter, members of the genus Tetrasphaera were found to be important microbes for P accumulation, and in six plants they were the most important. As these Tetrasphaera cells did not exhibit the classical phenotype of poly-P accumulating microbes, our entire understanding of the microbiology of the EBPR process has to be revised. Furthermore, our new single-cell approach can now also be applied to quantify storage polymer dynamics in individual populations in situ in other ecosystems and might become a valuable tool for many environmental microbiologists.
Collapse
|
19
|
Lee KS, Palatinszky M, Pereira FC, Nguyen J, Fernandez VI, Mueller AJ, Menolascina F, Daims H, Berry D, Wagner M, Stocker R. An automated Raman-based platform for the sorting of live cells by functional properties. Nat Microbiol 2019; 4:1035-1048. [PMID: 30886359 DOI: 10.1038/s41564-019-0394-9] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/30/2019] [Indexed: 12/22/2022]
Abstract
Stable-isotope probing is widely used to study the function of microbial taxa in their natural environment, but sorting of isotopically labelled microbial cells from complex samples for subsequent genomic analysis or cultivation is still in its early infancy. Here, we introduce an optofluidic platform for automated sorting of stable-isotope-probing-labelled microbial cells, combining microfluidics, optical tweezing and Raman microspectroscopy, which yields live cells suitable for subsequent single-cell genomics, mini-metagenomics or cultivation. We describe the design and optimization of this Raman-activated cell-sorting approach, illustrate its operation with four model bacteria (two intestinal, one soil and one marine) and demonstrate its high sorting accuracy (98.3 ± 1.7%), throughput (200-500 cells h-1; 3.3-8.3 cells min-1) and compatibility with cultivation. Application of this sorting approach for the metagenomic characterization of bacteria involved in mucin degradation in the mouse colon revealed a diverse consortium of bacteria, including several members of the underexplored family Muribaculaceae, highlighting both the complexity of this niche and the potential of Raman-activated cell sorting for identifying key players in targeted processes.
Collapse
Affiliation(s)
- Kang Soo Lee
- Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Márton Palatinszky
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Fátima C Pereira
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Jen Nguyen
- Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Vicente I Fernandez
- Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Anna J Mueller
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Filippo Menolascina
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh, UK
| | - Holger Daims
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.,The Comammox Research Platform, University of Vienna, Vienna, Austria
| | - David Berry
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Michael Wagner
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.,The Comammox Research Platform, University of Vienna, Vienna, Austria
| | - Roman Stocker
- Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
20
|
Shitut S, Ahsendorf T, Pande S, Egbert M, Kost C. Nanotube-mediated cross-feeding couples the metabolism of interacting bacterial cells. Environ Microbiol 2019; 21:1306-1320. [PMID: 30680926 DOI: 10.1111/1462-2920.14539] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 01/22/2019] [Indexed: 12/11/2022]
Abstract
Bacteria frequently engage in cross-feeding interactions that involve an exchange of metabolites with other micro- or macroorganisms. The often obligate nature of these associations, however, hampers manipulative experiments, thus limiting our mechanistic understanding of the ecophysiological consequences that result for the organisms involved. Here we address this issue by taking advantage of a well-characterized experimental model system, in which auxotrophic genotypes of E. coli derive essential amino acids from prototrophic donor cells using intercellular nanotubes. Surprisingly, donor-recipient cocultures revealed that the mere presence of auxotrophic genotypes was sufficient to increase amino acid production levels of several prototrophic donor genotypes. Our work is consistent with a scenario, in which interconnected auxotrophs withdraw amino acids from the cytoplasm of donor cells, which delays feedback inhibition of the corresponding amino acid biosynthetic pathway and, in this way, increases amino acid production levels. Our findings indicate that in newly established mutualistic associations, an intercellular regulation of exchanged metabolites can simply emerge from the architecture of the underlying biosynthetic pathways, rather than requiring the evolution of new regulatory mechanisms.
Collapse
Affiliation(s)
- Shraddha Shitut
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena 07745, Germany.,Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück 49076, Germany
| | - Tobias Ahsendorf
- Deutsches Krebsforschungszentrum, Baden-Württemberg 69120, Heidelberg, Germany.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Samay Pande
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Matthew Egbert
- Department of Computer Science, University of Auckland, Auckland 1010, New Zealand
| | - Christian Kost
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena 07745, Germany.,Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück 49076, Germany
| |
Collapse
|
21
|
Chen C, Linse K, Uematsu K, Sigwart JD. Cryptic niche switching in a chemosymbiotic gastropod. Proc Biol Sci 2018; 285:20181099. [PMID: 30051825 PMCID: PMC6053925 DOI: 10.1098/rspb.2018.1099] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/15/2018] [Indexed: 12/25/2022] Open
Abstract
Life stages of some animals, including amphibians and insects, are so different that they have historically been seen as different species. 'Metamorphosis' broadly encompasses major changes in organism bodies and, importantly, concomitant shifts in trophic strategies. Many marine animals have a biphasic lifestyle, with small pelagic larvae undergoing one or more metamorphic transformations before settling into a permanent, adult morphology on the benthos. Post-settlement, the hydrothermal vent gastropod Gigantopelta chessoia experiences a further, cryptic metamorphosis at body sizes around 5-7 mm. The terminal adult stage is entirely dependent on chemoautotrophic symbionts; smaller individuals do not house symbionts and presumably depend on grazing. Using high-resolution X-ray microtomography to reconstruct the internal organs in a growth series, we show that this sudden transition in small but sexually mature individuals dramatically reconfigures the organs, but is in no way apparent from external morphology. We introduce the term 'cryptometamorphosis' to identify this novel phenomenon of a major body change and trophic shift, not related to sexual maturity, transforming only the internal anatomy. Understanding energy flow in ecosystems depends on the feeding ecology of species; the present study highlights the possibility for adult animals to make profound shifts in biology that influence energy dynamics.
Collapse
Affiliation(s)
- Chong Chen
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa 2370061, Japan
| | - Katrin Linse
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Katsuyuki Uematsu
- Marine Works Japan Ltd., 3-54-1 Oppamahigashi, Yokosuka, Kanagawa 2370063, Japan
| | - Julia D Sigwart
- Marine Laboratory, Queen's University Belfast, 12-13 The Strand, Portaferry BT22 1PF, N. Ireland
- Museum of Paleontology, University of California, Berkeley, CA 94720, USA
| |
Collapse
|
22
|
Karimi E, Slaby BM, Soares AR, Blom J, Hentschel U, Costa R. Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges. FEMS Microbiol Ecol 2018; 94:4985835. [DOI: 10.1093/femsec/fiy074] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 04/23/2018] [Indexed: 12/31/2022] Open
Affiliation(s)
- Elham Karimi
- Centre of Marine Sciences (CCMAR), Faculty of Science and Technology (FCT), Algarve University, 8005-139 Faro, Portugal
| | - Beate M Slaby
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany
| | - André R Soares
- Institute of Geography and Earth Sciences, Aberystwyth University, SY23 3DB Aberystwyth, Wales, UK
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Germany
| | - Ute Hentschel
- RD3 Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research Kiel, 24105 Kiel, Germany
- Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany
| | - Rodrigo Costa
- Centre of Marine Sciences (CCMAR), Faculty of Science and Technology (FCT), Algarve University, 8005-139 Faro, Portugal
- Institute for Bioengineering and Biosciences (IBB), Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| |
Collapse
|
23
|
Ivens ABF, Gadau A, Kiers ET, Kronauer DJC. Can social partnerships influence the microbiome? Insights from ant farmers and their trophobiont mutualists. Mol Ecol 2018; 27:1898-1914. [PMID: 29411455 PMCID: PMC5935579 DOI: 10.1111/mec.14506] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/21/2017] [Accepted: 11/28/2017] [Indexed: 01/02/2023]
Abstract
Mutualistic interactions with microbes have played a crucial role in the evolution and ecology of animal hosts. However, it is unclear what factors are most important in influencing particular host–microbe associations. While closely related animal species may have more similar microbiota than distantly related species due to phylogenetic contingencies, social partnerships with other organisms, such as those in which one animal farms another, may also influence an organism's symbiotic microbiome. We studied a mutualistic network of Brachymyrmex and Lasius ants farming several honeydew‐producing Prociphilus aphids and Rhizoecus mealybugs to test whether the mutualistic microbiomes of these interacting insects are primarily correlated with their phylogeny or with their shared social partnerships. Our results confirm a phylogenetic signal in the microbiomes of aphid and mealybug trophobionts, with each species harbouring species‐specific endosymbiont strains of Buchnera (aphids), Tremblaya and Sodalis (mealybugs), and Serratia (both mealybugs and aphids) despite being farmed by the same ants. This is likely explained by strict vertical transmission of trophobiont endosymbionts between generations. In contrast, our results show the ants’ microbiome is possibly shaped by their social partnerships, with ants that farm the same trophobionts also sharing strains of sugar‐processing Acetobacteraceae bacteria, known from other honeydew‐feeding ants and which likely reside extracellularly in the ants’ guts. These ant–microbe associations are arguably more “open” and subject to horizontal transmission or social transmission within ant colonies. These findings suggest that the role of social partnerships in shaping a host's symbiotic microbiome can be variable and is likely dependent on how the microbes are transmitted across generations.
Collapse
Affiliation(s)
- Aniek B F Ivens
- Animal Ecology Section, Department of Ecological Science, Faculty of Science, Vrije Universiteit, Amsterdam, The Netherlands.,Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
| | - Alice Gadau
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
| | - E Toby Kiers
- Animal Ecology Section, Department of Ecological Science, Faculty of Science, Vrije Universiteit, Amsterdam, The Netherlands
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
| |
Collapse
|
24
|
Taerum SJ, De Martini F, Liebig J, Gile GH. Incomplete Co-cladogenesis Between Zootermopsis Termites and Their Associated Protists. ENVIRONMENTAL ENTOMOLOGY 2018; 47:184-195. [PMID: 29325010 DOI: 10.1093/ee/nvx193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Indexed: 06/07/2023]
Abstract
Coevolution is a major driver of speciation in many host-associated symbionts. In the termite-protist digestive symbiosis, the protists are vertically inherited by anal feeding among nest mates. Lower termites (all termite families except Termitidae) and their symbionts have broadly co-diversified over ~170 million yr. However, this inference is based mainly on the restricted distribution of certain protist genera to certain termite families. With the exception of one study, which demonstrated congruent phylogenies for the protist Pseudotrichonympha and its Rhinotermitidae hosts, coevolution in this symbiosis has not been investigated with molecular methods. Here we have characterized the hindgut symbiotic protists (Phylum Parabasalia) across the genus Zootermopsis (Archotermopsidae) using single cell isolation, molecular phylogenetics, and high-throughput amplicon sequencing. We report that the deepest divergence in the Zootermopsis phylogeny (Zootermopsis laticeps [Banks; Isoptera: Termopsidae]) corresponds with a divergence in three of the hindgut protist species. However, the crown Zootermopsis taxa (Zootermopsis angusticollis [Hagen; Isoptera: Termopsidae], Z. nevadensis nevadensis [Hagen; Isoptera: Termopsidae], and Z. nevadensis nuttingi [Haverty & Thorne; Isoptera: Termopsidae]) share the same protist species, with no evidence of co-speciation under our methods. We interpret this pattern as incomplete co-cladogenesis, though the possibility of symbiont exchange cannot be entirely ruled out. This is the first molecular evidence that identical communities of termite-associated protist species can inhabit multiple distinct host species.
Collapse
Affiliation(s)
| | | | - Jürgen Liebig
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Gillian H Gile
- School of Life Sciences, Arizona State University, Tempe, AZ
| |
Collapse
|
25
|
Seah BKB, Schwaha T, Volland JM, Huettel B, Dubilier N, Gruber-Vodicka HR. Specificity in diversity: single origin of a widespread ciliate-bacteria symbiosis. Proc Biol Sci 2018; 284:rspb.2017.0764. [PMID: 28701560 PMCID: PMC5524500 DOI: 10.1098/rspb.2017.0764] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/06/2017] [Indexed: 12/03/2022] Open
Abstract
Symbioses between eukaryotes and sulfur-oxidizing (thiotrophic) bacteria have convergently evolved multiple times. Although well described in at least eight classes of metazoan animals, almost nothing is known about the evolution of thiotrophic symbioses in microbial eukaryotes (protists). In this study, we characterized the symbioses between mouthless marine ciliates of the genus Kentrophoros, and their thiotrophic bacteria, using comparative sequence analysis and fluorescence in situ hybridization. Ciliate small-subunit rRNA sequences were obtained from 17 morphospecies collected in the Mediterranean and Caribbean, and symbiont sequences from 13 of these morphospecies. We discovered a new Kentrophoros morphotype where the symbiont-bearing surface is folded into pouch-like compartments, illustrating the variability of the basic body plan. Phylogenetic analyses revealed that all investigated Kentrophoros belonged to a single clade, despite the remarkable morphological diversity of these hosts. The symbionts were also monophyletic and belonged to a new clade within the Gammaproteobacteria, with no known cultured representatives. Each host morphospecies had a distinct symbiont phylotype, and statistical analyses revealed significant support for host–symbiont codiversification. Given that these symbioses were collected from two widely separated oceans, our results indicate that symbiotic associations in unicellular hosts can be highly specific and stable over long periods of evolutionary time.
Collapse
Affiliation(s)
- Brandon K B Seah
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Thomas Schwaha
- Department of Integrative Zoology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Jean-Marie Volland
- Department of Limnology and Bio-Oceanography, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | | |
Collapse
|
26
|
Schärer L. The varied ways of being male and female. Mol Reprod Dev 2017; 84:94-104. [PMID: 28032683 DOI: 10.1002/mrd.22775] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 12/23/2016] [Indexed: 12/18/2022]
Abstract
Our understanding of sexual reproduction is mainly informed by research on gonochorists (i.e., species with separate sexes), including insects, birds, and mammals. But the male and female sexes are not two types of individuals; they actually represent two different reproductive strategies, and in many organisms, these two strategies are distributed among individuals in a population in a variety of ways. For example, sequential hermaphrodites (or sex-changers) exhibit one strategy early in life and later switch to the other, while simultaneous hermaphrodites exhibit both strategies at the same time. There are also many intermediate sexual systems that mix gonochorists and hermaphrodites in the same species and within many organismal groups, shifts occur between these sexual systems. A fascinating collection of six articles in this special issue on Hermaphroditism & Sex Determination impressively documents some important challenges to our understanding of sex determination, and the specification of male and female reproductive function when these need to occur within the same individual rather than in two separate individuals. Moreover, hermaphroditism changes how we need to think about reproductive allocation to sexual functions, how such allocation can be specified, as well as how the sexual system affects sexual conflict and the resulting antagonistic coevolution. Our understanding of sexual reproduction will profit greatly from exploring the varied ways of being male and female. Mol. Reprod. Dev. 84: 94-104, 2017. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Lukas Schärer
- Evolutionary Biology, Zoological Institute, University of Basel, Basel, Switzerland
| |
Collapse
|
27
|
Singer E, Wagner M, Woyke T. Capturing the genetic makeup of the active microbiome in situ. THE ISME JOURNAL 2017; 11:1949-1963. [PMID: 28574490 PMCID: PMC5563950 DOI: 10.1038/ismej.2017.59] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/02/2017] [Accepted: 03/10/2017] [Indexed: 12/21/2022]
Abstract
More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.
Collapse
Affiliation(s)
- Esther Singer
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Michael Wagner
- University of Vienna, Department of Microbial Ecology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| |
Collapse
|
28
|
Lin HN, Wang KL, Wu ZH, Tian RM, Liu GZ, Xu Y. Biological and Chemical Diversity of Bacteria Associated with a Marine Flatworm. Mar Drugs 2017; 15:md15090281. [PMID: 28862674 PMCID: PMC5618420 DOI: 10.3390/md15090281] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/21/2017] [Accepted: 08/29/2017] [Indexed: 12/16/2022] Open
Abstract
The aim of this research is to explore the biological and chemical diversity of bacteria associated with a marine flatworm Paraplanocera sp., and to discover the bioactive metabolites from culturable strains. A total of 141 strains of bacteria including 45 strains of actinomycetes and 96 strains of other bacteria were isolated, identified and fermented on a small scale. Bioactive screening (antibacterial and cytotoxic activities) and chemical screening (ultra-performance liquid chromatography–mass spectrometry (UPLC-MS)) yielded several target bacterial strains. Among these strains, the ethyl acetate (EA) crude extract of Streptomyces sp. XY-FW47 fermentation broth showed strong antibacterial activity against methicillin-resistant Staphylococcus aureus ATCC43300 (MRSA ATCC43300) and potent cytotoxic effects on HeLa cells. The UPLC-MS spectral analysis of the crude extract indicated that the strain XY-FW47 could produce a series of geldanamycins (GMs). One new geldanamycin (GM) analog, 4,5-dihydro-17-O-demethylgeldanamycin (1), and three known GMs (2–4) were obtained. All of these compounds were tested for antibacterial, cytotoxic, and antifungal activities, yet only GM (3) showed potent cytotoxic (HeLa cells, EC50 = 1.12 μg/mL) and antifungal (Setosphaeria turcica MIC = 2.40 μg/mL) activities. Their structure–activity relationship (SAR) was also preliminarily discussed in this study.
Collapse
Affiliation(s)
- Hui-Na Lin
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
- School of Life Sciences, Xiamen University, Xiamen 361102, China.
| | - Kai-Ling Wang
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
| | - Ze-Hong Wu
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China.
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou 510632, China.
| | - Ren-Mao Tian
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China.
| | - Guo-Zhu Liu
- HEC Research and Development Center, HEC Pharm Group, Dongguan 523871, China.
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
| |
Collapse
|
29
|
Oren A. A plea for linguistic accuracy - also for Candidatus taxa. Int J Syst Evol Microbiol 2017; 67:1085-1094. [PMID: 27926819 DOI: 10.1099/ijsem.0.001715] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
While all names of new taxa submitted to the International Journal of Systematic and Evolutionary Microbiology, either in direct submissions or in validation requests for names effectively published elsewhere, are subject to nomenclatural review to ensure that they are acceptable based on the rules of the International Code of Nomenclature of Prokaryotes, the names of Candidatus taxa have not been subjected to such a review. Formally, this was not necessary because the rank of Candidatus is not covered by the Code, and the names lack the priority afforded validly published names. However, many Candidatus taxa of different ranks are widely discussed in the scientific literature, and a proposal to incorporate the nomenclature of uncultured prokaryotes under the provisions of the Code is currently pending. Therefore, an evaluation of the names of Candidatus taxa published thus far is very timely. Out of the ~400 Candidatus names found in the literature, 120 contradict the current rules of the Code or are otherwise problematic. A list of those names of Candidatus taxa that need correction is presented here and alternative names that agree with the provisions of the Code are proposed.
Collapse
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| |
Collapse
|
30
|
Watanabe T, Kojima H, Fukui M. Identity of major sulfur-cycle prokaryotes in freshwater lake ecosystems revealed by a comprehensive phylogenetic study of the dissimilatory adenylylsulfate reductase. Sci Rep 2016; 6:36262. [PMID: 27824124 PMCID: PMC5099947 DOI: 10.1038/srep36262] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/12/2016] [Indexed: 11/24/2022] Open
Abstract
Adenylylsulfate reductase is a heterodimeric complex of two subunits, AprB and AprA, and is a key enzyme in dissimilatory sulfate reduction and sulfur oxidation. Common use of aprA as a functional marker gene has revealed the diversity of sulfur-cycle prokaryotes in diverse environments. In this study, we established a comprehensive sequence set of apr genes and employed it to reanalyze apr phylogeny, evaluate the coverage of a widely used primer set (AprA-1-FW/AprA-5-RV), and categorize environmental aprA sequences. Phylogenetic tree construction revealed new members of Apr lineage II and several previously unrecognized lateral gene transfer events. Using the established phylogenetic tree, we classified all previously reported aprA sequences amplified from freshwater lakes with the primer pair AprA-1-FW/AprA-5-RV in addition to the aprA sequences newly retrieved from freshwater lakes; the obtained results were complemented by 16S rRNA clone library analysis. Apr-based classifications of some of operational taxonomic units were supported by 16S rRNA-based analysis. This study updates our knowledge on the phylogeny of aprBA and shows the identities of several sulfur-cycle bacteria, which could not be classified to a known taxa until now. The established apr sequence set is publicly available and can be applied to assign environmental sequences to known lineages.
Collapse
Affiliation(s)
- Tomohiro Watanabe
- The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Hisaya Kojima
- The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Manabu Fukui
- The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| |
Collapse
|
31
|
Abstract
Can egalitarian partnerships exist in nature? A new study demonstrates how protist hosts use and abuse their algal symbionts depending on their needs. While this relationship allows protists to survive in low nutrient conditions, it leaves little room for algal retaliation.
Collapse
Affiliation(s)
- E Toby Kiers
- Institute of Ecological Sciences, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands.
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| |
Collapse
|
32
|
Wang Y, Huang WE, Cui L, Wagner M. Single cell stable isotope probing in microbiology using Raman microspectroscopy. Curr Opin Biotechnol 2016; 41:34-42. [PMID: 27149160 DOI: 10.1016/j.copbio.2016.04.018] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 02/17/2016] [Accepted: 04/19/2016] [Indexed: 12/14/2022]
Abstract
Microbial communities are essential for most ecosystem processes and interact in highly complex ways with virtually all eukaryotes. Thus, a detailed understanding of the function of such communities is a fundamental prerequisite for microbial ecologists, applied microbiologists and microbiome researchers. Using single cell Raman microspectroscopy, biochemical fingerprints of individual microbial cells can be obtained in an externally label-free and non-destructive manner. If combined with stable isotope probing (SIP), Raman spectroscopy can directly reveal functions of single microorganisms in their natural habitat. This review provides an update on various SIP-approaches suitable for combination with different Raman scattering techniques and illustrates how single cell Raman SIP can be directly combined with the omics-centric analysis pipelines to investigate microbial communities.
Collapse
Affiliation(s)
- Yun Wang
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics and Single Cell Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom.
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry Meets Microbiology', University of Vienna, 1090 Vienna, Austria
| |
Collapse
|
33
|
Zimmermann J, Wentrup C, Sadowski M, Blazejak A, Gruber-Vodicka HR, Kleiner M, Ott JA, Cronholm B, De Wit P, Erséus C, Dubilier N. Closely coupled evolutionary history of ecto- and endosymbionts from two distantly related animal phyla. Mol Ecol 2016; 25:3203-23. [PMID: 26826340 DOI: 10.1111/mec.13554] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/23/2015] [Accepted: 01/19/2016] [Indexed: 12/21/2022]
Abstract
The level of integration between associated partners can range from ectosymbioses to extracellular and intracellular endosymbioses, and this range has been assumed to reflect a continuum from less intimate to evolutionarily highly stable associations. In this study, we examined the specificity and evolutionary history of marine symbioses in a group of closely related sulphur-oxidizing bacteria, called Candidatus Thiosymbion, that have established ecto- and endosymbioses with two distantly related animal phyla, Nematoda and Annelida. Intriguingly, in the ectosymbiotic associations of stilbonematine nematodes, we observed a high degree of congruence between symbiont and host phylogenies, based on their ribosomal RNA (rRNA) genes. In contrast, for the endosymbioses of gutless phallodriline annelids (oligochaetes), we found only a weak congruence between symbiont and host phylogenies, based on analyses of symbiont 16S rRNA genes and six host genetic markers. The much higher degree of congruence between nematodes and their ectosymbionts compared to those of annelids and their endosymbionts was confirmed by cophylogenetic analyses. These revealed 15 significant codivergence events between stilbonematine nematodes and their ectosymbionts, but only one event between gutless phallodrilines and their endosymbionts. Phylogenetic analyses of 16S rRNA gene sequences from 50 Cand. Thiosymbion species revealed seven well-supported clades that contained both stilbonematine ectosymbionts and phallodriline endosymbionts. This closely coupled evolutionary history of marine ecto- and endosymbionts suggests that switches between symbiotic lifestyles and between the two host phyla occurred multiple times during the evolution of the Cand. Thiosymbion clade, and highlights the remarkable flexibility of these symbiotic bacteria.
Collapse
Affiliation(s)
- Judith Zimmermann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Cecilia Wentrup
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany.,Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Miriam Sadowski
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Anna Blazejak
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | | | - Manuel Kleiner
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany.,Department of Geoscience, University of Calgary, Calgary, 2500 University Drive, AB, T2N 1N4, Canada
| | - Jörg A Ott
- Department of Limnology and Oceanography, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
| | - Bodil Cronholm
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, SE-104 05, Stockholm, Sweden
| | - Pierre De Wit
- Department of Marine Sciences, Sven Lovén Centre for Marine Sciences Tjärnö, University of Gothenburg, Hättebäcksvägen 7, SE-452 96, Strömstad, Sweden
| | - Christer Erséus
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany.,Faculty of Biology/Chemistry, University of Bremen, Bibliothekstrasse 1, D-28359, Bremen, Germany
| |
Collapse
|
34
|
Melnyk RA, Coates JD. The Perchlorate Reduction Genomic Island: Mechanisms and Pathways of Evolution by Horizontal Gene Transfer. BMC Genomics 2015; 16:862. [PMID: 26502901 PMCID: PMC4623255 DOI: 10.1186/s12864-015-2011-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 10/03/2015] [Indexed: 12/03/2022] Open
Abstract
Background Perchlorate is a widely distributed anion that is toxic to humans, but serves as a valuable electron acceptor for several lineages of bacteria. The ability to utilize perchlorate is conferred by a horizontally transferred piece of DNA called the perchlorate reduction genomic island (PRI). Methods We compared genomes of perchlorate reducers using phylogenomics, SNP mapping, and differences in genomic architecture to interrogate the evolutionary history of perchlorate respiration. Results Here we report on the PRI of 13 genomes of perchlorate-reducing bacteria from four different classes of Phylum Proteobacteria (the Alpha-, Beta-, Gamma- and Epsilonproteobacteria). Among the different phylogenetic classes, the island varies considerably in genetic content as well as in its putative mechanism and location of integration. However, the islands of the densely sampled genera Azospira and Magnetospirillum have striking nucleotide identity despite divergent genomes, implying horizontal transfer and positive selection within narrow phylogenetic taxa. We also assess the phylogenetic origin of accessory genes in the various incarnations of the island, which can be traced to chromosomal paralogs from phylogenetically similar organisms. Conclusion These observations suggest a complex phylogenetic history where the island is rarely transferred at the class level but undergoes frequent and continuous transfer within narrow phylogenetic groups. This restricted transfer is seen directly by the independent integration of near-identical islands within a genus and indirectly due to the acquisition of lineage-specific accessory genes. The genomic reversibility of perchlorate reduction may present a unique equilibrium for a metabolism that confers a competitive advantage only in the presence of an electron acceptor, which although widely distributed, is generally present at low concentrations in nature. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2011-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ryan A Melnyk
- Department of Plant and Microbial Biology and Energy Biosciences Institute, University of California, Berkeley, CA, 94720, USA. .,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - John D Coates
- Department of Plant and Microbial Biology and Energy Biosciences Institute, University of California, Berkeley, CA, 94720, USA.
| |
Collapse
|
35
|
West SA, Fisher RM, Gardner A, Kiers ET. Major evolutionary transitions in individuality. Proc Natl Acad Sci U S A 2015; 112:10112-9. [PMID: 25964342 PMCID: PMC4547252 DOI: 10.1073/pnas.1421402112] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The evolution of life on earth has been driven by a small number of major evolutionary transitions. These transitions have been characterized by individuals that could previously replicate independently, cooperating to form a new, more complex life form. For example, archaea and eubacteria formed eukaryotic cells, and cells formed multicellular organisms. However, not all cooperative groups are en route to major transitions. How can we explain why major evolutionary transitions have or haven't taken place on different branches of the tree of life? We break down major transitions into two steps: the formation of a cooperative group and the transformation of that group into an integrated entity. We show how these steps require cooperation, division of labor, communication, mutual dependence, and negligible within-group conflict. We find that certain ecological conditions and the ways in which groups form have played recurrent roles in driving multiple transitions. In contrast, we find that other factors have played relatively minor roles at many key points, such as within-group kin discrimination and mechanisms to actively repress competition. More generally, by identifying the small number of factors that have driven major transitions, we provide a simpler and more unified description of how life on earth has evolved.
Collapse
Affiliation(s)
- Stuart A West
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom; Magdalen College, Oxford OX1 4AU, United Kingdom;
| | - Roberta M Fisher
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
| | - Andy Gardner
- School of Biology, University of St. Andrews, Dyers Brae, St. Andrews KY16 9TH, United Kingdom; and
| | - E Toby Kiers
- Institute of Ecological Sciences, Faculty of Earth and Life Sciences, Vrije Universiteit, 1081 HV, Amsterdam, The Netherlands
| |
Collapse
|
36
|
Affiliation(s)
- E Toby Kiers
- Institute of Ecological Sciences, Vrije Universiteit, 1081 HV Amsterdam, Netherlands.
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| |
Collapse
|
37
|
D Ainsworth T, Krause L, Bridge T, Torda G, Raina JB, Zakrzewski M, Gates RD, Padilla-Gamiño JL, Spalding HL, Smith C, Woolsey ES, Bourne DG, Bongaerts P, Hoegh-Guldberg O, Leggat W. The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts. ISME JOURNAL 2015; 9:2261-74. [PMID: 25885563 PMCID: PMC4579478 DOI: 10.1038/ismej.2015.39] [Citation(s) in RCA: 314] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 02/02/2015] [Accepted: 02/12/2015] [Indexed: 01/15/2023]
Abstract
Despite being one of the simplest metazoans, corals harbor some of the most highly diverse and abundant microbial communities. Differentiating core, symbiotic bacteria from this diverse host-associated consortium is essential for characterizing the functional contributions of bacteria but has not been possible yet. Here we characterize the coral core microbiome and demonstrate clear phylogenetic and functional divisions between the micro-scale, niche habitats within the coral host. In doing so, we discover seven distinct bacterial phylotypes that are universal to the core microbiome of coral species, separated by thousands of kilometres of oceans. The two most abundant phylotypes are co-localized specifically with the corals' endosymbiotic algae and symbiont-containing host cells. These bacterial symbioses likely facilitate the success of the dinoflagellate endosymbiosis with corals in diverse environmental regimes.
Collapse
Affiliation(s)
- Tracy D Ainsworth
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Lutz Krause
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
| | - Thomas Bridge
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Gergely Torda
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Queensland, Australia
| | - Jean-Baptise Raina
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Queensland, Australia
| | - Martha Zakrzewski
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
| | - Ruth D Gates
- Hawaii Institute for Marine Biology, University of Hawai'i, Mānoa, HI, USA
| | - Jacqueline L Padilla-Gamiño
- Hawaii Institute for Marine Biology, University of Hawai'i, Mānoa, HI, USA.,Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | | | - Celia Smith
- Department of Botany, University of Hawai'i, Mānoa, HI, USA
| | - Erika S Woolsey
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - David G Bourne
- Australian Institute for Marine Science, PMB 3, Townsville, Queensland, Australia
| | - Pim Bongaerts
- The Global Change Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Ove Hoegh-Guldberg
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,The Global Change Institute, University of Queensland, Brisbane, Queensland, Australia
| | - William Leggat
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Queensland, Australia
| |
Collapse
|
38
|
Ott JA, Gruber-Vodicka HR, Leisch N, Zimmermann J. Phylogenetic confirmation of the genus Robbea (Nematoda: Desmodoridae, Stilbonematinae) with the description of three new species. SYST BIODIVERS 2014; 12:434-455. [PMID: 27630534 PMCID: PMC5002938 DOI: 10.1080/14772000.2014.941038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 06/12/2014] [Indexed: 11/04/2022]
Abstract
The Stilbonematinae are a monophyletic group of marine nematodes that are characterized by a coat of thiotrophic bacterial symbionts. Among the ten known genera of the Stilbonematinae, the genus Robbea Gerlach 1956 had a problematic taxonomic history of synonymizations and indications of polyphyletic origin. Here we describe three new species of the genus, R. hypermnestra sp. nov., R. ruetzleri sp. nov. and R. agricola sp. nov., using conventional light microscopy, interference contrast microscopy and SEM. We provide 18S rRNA gene sequences of all three species, together with new sequences for the genera Catanema and Leptonemella. Both our morphological analyses as well as our phylogenetic reconstructions corroborate the genus Robbea. In our phylogenetic analysis the three species of the genus Robbea form a distinct clade in the Stilbonematinae radiation and are clearly separated from the clade of the genus Catanema, which has previously been synonymized with Robbea. Surprisingly, in R. hypermnestra sp. nov. all females are intersexes exhibiting male sexual characters. Our extended dataset of Stilbonematinae 18S rRNA genes for the first time allows the identification of the different genera, e.g. in a barcoding approach. http://zoobank.org/urn:lsid:zoobank.org:pub:D37C3F5A-CF2B-40E6-8B09-3C72EEED60B0.
Collapse
Affiliation(s)
- Jörg A. Ott
- Department of Limnology and Biooceanography, University of Vienna, Althanstr. 14, A-1090Vienna, Austria
| | - Harald R. Gruber-Vodicka
- Department of Symbiosis, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359Bremen, Germany
| | - Nikolaus Leisch
- Department of Ecogenomics and System Biology, University of Vienna, Althanstr. 14, A-1090Vienna, Austria
| | - Judith Zimmermann
- Department of Symbiosis, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359Bremen, Germany
| |
Collapse
|
39
|
Eichinger I, Schmitz-Esser S, Schmid M, Fisher CR, Bright M. Symbiont-driven sulfur crystal formation in a thiotrophic symbiosis from deep-sea hydrocarbon seeps. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:364-372. [PMID: 24992535 PMCID: PMC4232855 DOI: 10.1111/1758-2229.12149] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 01/15/2014] [Indexed: 06/03/2023]
Abstract
The siboglinid tubeworm Sclerolinum contortum symbiosis inhabits sulfidic sediments at deep-sea hydrocarbon seeps in the Gulf of Mexico. A single symbiont phylotype in the symbiont-housing organ is inferred from phylogenetic analyses of the 16S ribosomal ribonucleic acid (16S rRNA) gene and fluorescent in situ hybridization. The phylotype we studied here, and a previous study from an arctic hydrocarbon seep population, reveal identical 16S rRNA symbiont gene sequences. While sulfide is apparently the energy source for the symbionts (and ultimately the gutless host), both partners also have to cope with its toxicity. This study demonstrates abundant large sulfur crystals restricted to the trophosome area. Based on Raman microspectroscopy and energy dispersive X-ray analysis, these crystals have the same S8 sulfur configuration as the recently described small sulfur vesicles formed in the symbionts. The crystals reside adjacent to the symbionts in the trophosome. This suggests that their formation is either extra- or intracellular in symbionts. We propose that formation of these crystals provides both energy-storage compounds for the symbionts and serves the symbiosis by removing excess toxic sulfide from host tissues. This symbiont-mediated sulfide detoxification may have been crucial for the establishment of thiotrophic symbiosis and continues to remain an important function of the symbionts.
Collapse
Affiliation(s)
- Irmgard Eichinger
- Department of Limnology and Oceanography, Faculty of Life Sciences, University of ViennaAlthanstr. 14, 1090, Vienna, Austria
| | - Stephan Schmitz-Esser
- Department of Microbial Ecology, Faculty of Life Sciences, University of ViennaAlthanstr. 14, 1090, Vienna, Austria
| | - Markus Schmid
- Institute for Milk Hygiene, University of Veterinary Medicine ViennaVeterinärplatz 1, 1210, Vienna, Austria
| | - Charles R Fisher
- Department of Biology, Pennsylvania State University208 Mueller Laboratory, University Park, Schuylkill, PA, 16802, USA
| | - Monika Bright
- Department of Limnology and Oceanography, Faculty of Life Sciences, University of ViennaAlthanstr. 14, 1090, Vienna, Austria
| |
Collapse
|
40
|
Dittami SM, Barbeyron T, Boyen C, Cambefort J, Collet G, Delage L, Gobet A, Groisillier A, Leblanc C, Michel G, Scornet D, Siegel A, Tapia JE, Tonon T. Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae. Front Genet 2014; 5:241. [PMID: 25120558 PMCID: PMC4110880 DOI: 10.3389/fgene.2014.00241] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 07/07/2014] [Indexed: 11/18/2022] Open
Abstract
Rhizobiales and related orders of Alphaproteobacteria comprise several genera of nodule-inducing symbiotic bacteria associated with plant roots. Here we describe the genome and the metabolic network of “Candidatus Phaeomarinobacter ectocarpi” Ec32, a member of a new candidate genus closely related to Rhizobiales and found in association with cultures of the filamentous brown algal model Ectocarpus. The “Ca. P. ectocarpi” genome encodes numerous metabolic pathways that may be relevant for this bacterium to interact with algae. Notably, it possesses a large set of glycoside hydrolases and transporters, which may serve to process and assimilate algal metabolites. It also harbors several proteins likely to be involved in the synthesis of algal hormones such as auxins and cytokinins, as well as the vitamins pyridoxine, biotin, and thiamine. As of today, “Ca. P. ectocarpi” has not been successfully cultured, and identical 16S rDNA sequences have been found exclusively associated with Ectocarpus. However, related sequences (≥97% identity) have also been detected free-living and in a Fucus vesiculosus microbiome barcoding project, indicating that the candidate genus “Phaeomarinobacter” may comprise several species, which may colonize different niches.
Collapse
Affiliation(s)
- Simon M Dittami
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Tristan Barbeyron
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Catherine Boyen
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Jeanne Cambefort
- CNRS, IRISA UMR 6074 Rennes, France ; IRISA UMR 6074, Université de Rennes 1 Rennes, France ; INRIA, Centre Rennes-Bretagne-Atlantique, Projet Dyliss Rennes, France
| | - Guillaume Collet
- CNRS, IRISA UMR 6074 Rennes, France ; IRISA UMR 6074, Université de Rennes 1 Rennes, France ; INRIA, Centre Rennes-Bretagne-Atlantique, Projet Dyliss Rennes, France
| | - Ludovic Delage
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Angélique Gobet
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Agnès Groisillier
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Catherine Leblanc
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Gurvan Michel
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Delphine Scornet
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Anne Siegel
- CNRS, IRISA UMR 6074 Rennes, France ; IRISA UMR 6074, Université de Rennes 1 Rennes, France ; INRIA, Centre Rennes-Bretagne-Atlantique, Projet Dyliss Rennes, France
| | - Javier E Tapia
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile Santiago, Chile
| | - Thierry Tonon
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| |
Collapse
|
41
|
Bright M, Espada-Hinojosa S, Lagkouvardos I, Volland JM. The giant ciliate Zoothamnium niveum and its thiotrophic epibiont Candidatus Thiobios zoothamnicoli: a model system to study interspecies cooperation. Front Microbiol 2014; 5:145. [PMID: 24778630 PMCID: PMC3985026 DOI: 10.3389/fmicb.2014.00145] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/20/2014] [Indexed: 02/05/2023] Open
Abstract
Symbioses between chemoautotrophic sulfur-oxidizing (thiotrophic) bacteria and protists or animals are among the most diverse and prevalent in the ocean. They are extremely difficult to maintain in aquaria and no thiotrophic symbiosis involving an animal host has ever been successfully cultivated. In contrast, we have cultivated the giant ciliate Zoothamnium niveum and its obligate ectosymbiont Candidatus Thiobios zoothamnicoli in small flow-through aquaria. This review provides an overview of the host and the symbiont and their phylogenetic relationships. We summarize our knowledge on the ecology, geographic distribution and life cycle of the host, on the vertical transmission of the symbiont, and on the cultivation of this symbiosis. We then discuss the benefits and costs involved in this cooperation compared with other thiotrophic symbioses and outline our view on the evolution and persistence of this byproduct mutualism.
Collapse
Affiliation(s)
- Monika Bright
- Department of Limnology and Oceanography, University of ViennaVienna, Austria
| | | | - Ilias Lagkouvardos
- Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
| | - Jean-Marie Volland
- Department of Limnology and Oceanography, University of ViennaVienna, Austria
| |
Collapse
|
42
|
Ebert D. The Epidemiology and Evolution of Symbionts with Mixed-Mode Transmission. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-032513-100555] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dieter Ebert
- Universität Basel, Zoologisches Institut, 4051 Basel, Switzerland; Wissenschaftskolleg zu Berlin, 14193 Berlin, Germany;
| |
Collapse
|
43
|
Nováková E, Hypša V, Klein J, Foottit RG, von Dohlen CD, Moran NA. Reconstructing the phylogeny of aphids (Hemiptera: Aphididae) using DNA of the obligate symbiont Buchnera aphidicola. Mol Phylogenet Evol 2013; 68:42-54. [DOI: 10.1016/j.ympev.2013.03.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 03/07/2013] [Accepted: 03/13/2013] [Indexed: 01/16/2023]
|
44
|
Mori Y, Kataoka T, Okamura T, Kondo R. Dominance of green sulfur bacteria in the chemocline of the meromictic Lake Suigetsu, Japan, as revealed by dissimilatory sulfite reductase gene analysis. Arch Microbiol 2013; 195:303-12. [PMID: 23455488 DOI: 10.1007/s00203-013-0879-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 12/18/2012] [Accepted: 02/16/2013] [Indexed: 10/27/2022]
Abstract
This study investigated the spatiotemporal abundance and diversity of the α-subunit of the dissimilatory sulfite reductase gene (dsrA) in the meromictic Lake Suigetsu for assessing the sulfur-oxidizing bacterial community. The density of dsrA in the chemocline reached up to 3.1 × 10(6) copies ml(-1) in summer by means of quantitative real-time PCR and it was generally higher than deeper layers. Most of the dsrA clones sequenced were related to green sulfur bacteria such as Chlorobium phaeovibrioides, C. limicola, and C. luteolum. Below the chemocline of the lake, we also detected other dsrA clones related to the purple sulfur bacterium Halochromatium salexigens and some branching lineages of diverse sequences that were related to chemotrophic sulfur bacterial species such as Magnetospirillum gryphiswaldense, Candidatus Ruthia magnifica, and Candidatus Thiobios zoothamnicoli. The abundance and community compositions of sulfur-oxidizing bacteria changed depending on the water depth and season. This study indicated that the green sulfur bacteria dominated among sulfur-oxidizing bacterial population in the chemocline of Lake Suigetsu and that certain abiotic environmental variables were important factors that determined sulfur bacterial abundance and community structure.
Collapse
Affiliation(s)
- Yumi Mori
- Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui 917-0003, Japan.
| | | | | | | |
Collapse
|
45
|
Kleiner M, Petersen JM, Dubilier N. Convergent and divergent evolution of metabolism in sulfur-oxidizing symbionts and the role of horizontal gene transfer. Curr Opin Microbiol 2012; 15:621-31. [DOI: 10.1016/j.mib.2012.09.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 09/17/2012] [Accepted: 09/19/2012] [Indexed: 10/27/2022]
|
46
|
Petersen JM, Wentrup C, Verna C, Knittel K, Dubilier N. Origins and evolutionary flexibility of chemosynthetic symbionts from deep-sea animals. THE BIOLOGICAL BULLETIN 2012; 223:123-137. [PMID: 22983038 DOI: 10.1086/bblv223n1p123] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Bathymodiolin mussels dominate hydrothermal vent and cold seep communities worldwide. Symbiotic associations with chemosynthetic sulfur- and methane-oxidizing bacteria that provide for their nutrition are the key to their ecological and evolutionary success. The current paradigm is that these symbioses evolved from two free-living ancestors, one methane-oxidizing and one sulfur-oxidizing bacterium. In contrast to previous studies, our phylogenetic analyses of the bathymodiolin symbionts show that both the sulfur and the methane oxidizers fall into multiple clades interspersed with free-living bacteria, many of which were discovered recently in metagenomes from marine oxygen minimum zones. We therefore hypothesize that symbioses between bathymodiolin mussels and free-living sulfur- and methane-oxidizing bacteria evolved multiple times in convergent evolution. Furthermore, by 16S rRNA sequencing and fluorescence in situ hybridization, we show that close relatives of the bathymodiolin symbionts occur on hosts belonging to different animal phyla: Raricirrus beryli, a terebellid polychaete from a whale-fall, and a poecilosclerid sponge from a cold seep. The host range within the bathymodiolin symbionts is therefore greater than previously recognized, confirming the remarkable flexibility of these symbiotic associations.
Collapse
Affiliation(s)
- Jillian M Petersen
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany.
| | | | | | | | | |
Collapse
|
47
|
Dirks U, Gruber-Vodicka HR, Egger B, Ott JA. Proliferation pattern during rostrum regeneration of the symbiotic flatworm Paracatenula galateia: a pulse-chase-pulse analysis. Cell Tissue Res 2012; 349:517-25. [PMID: 22729484 PMCID: PMC3414702 DOI: 10.1007/s00441-012-1426-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 03/30/2012] [Indexed: 12/16/2022]
Abstract
The remarkable totipotent stem-cell-based regeneration capacities of the Platyhelminthes have brought them into the focus of stem cell and regeneration research. Although selected platyhelminth groups are among the best-studied invertebrates, our data provide new insights into regenerative processes in the most basally branching group of the Platyhelminthes, the Catenulida. The mouth- and gutless free-living catenulid flatworm Paracatenula galateia harbors intracellular bacterial symbionts in its posterior body region, the trophosome region, accounting for up to 50% of the volume. Following decapitation of this flatworm, we have analyzed the behavior of the amputated fragments and any anterior and posterior regeneration. Using an EdU-pulse-chase/BrdU-pulse thymidine analog double-labeling approach combined with immunohistochemistry, we show that neoblasts are the main drivers of the regeneration processes. During anterior (rostrum) regeneration, EdU-pulse-chase-labeled cells aggregate inside the regenerating rostrum, whereas BrdU pulse-labeling before fixation indicates clusters of S-phase neoblasts at the same position. In parallel, serotonergic nerves reorganize and the brain regenerates. In completely regenerated animals, the original condition with S-phase neoblasts being restricted to the body region posterior to the brain is restored. In contrast, no posterior regeneration or growth of the trophosome region in anterior fragments cut a short distance posterior to the brain has been observed. Our data thus reveal interesting aspects of the cellular processes underlying the regeneration of the emerging catenulid-bacteria symbiosis model P. galateia and show that a neoblast stem cell system is indeed a plesiomorphic feature of basal platyhelminths.
Collapse
Affiliation(s)
- Ulrich Dirks
- Department of Marine Biology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
| | | | | | | |
Collapse
|
48
|
Dirks U, Gruber-Vodicka HR, Leisch N, Bulgheresi S, Egger B, Ladurner P, Ott JA. Bacterial symbiosis maintenance in the asexually reproducing and regenerating flatworm Paracatenula galateia. PLoS One 2012; 7:e34709. [PMID: 22509347 PMCID: PMC3317999 DOI: 10.1371/journal.pone.0034709] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 03/05/2012] [Indexed: 12/14/2022] Open
Abstract
Bacteriocytes set the stage for some of the most intimate interactions between animal and bacterial cells. In all bacteriocyte possessing systems studied so far, de novo formation of bacteriocytes occurs only once in the host development, at the time of symbiosis establishment. Here, we present the free-living symbiotic flatworm Paracatenula galateia and its intracellular, sulfur-oxidizing bacteria as a system with previously undescribed strategies of bacteriocyte formation and bacterial symbiont transmission. Using thymidine analogue S-phase labeling and immunohistochemistry, we show that all somatic cells in adult worms - including bacteriocytes - originate exclusively from aposymbiotic stem cells (neoblasts). The continued bacteriocyte formation from aposymbiotic stem cells in adult animals represents a previously undescribed strategy of symbiosis maintenance and makes P. galateia a unique system to study bacteriocyte differentiation and development. We also provide morphological and immunohistochemical evidence that P. galateia reproduces by asexual fragmentation and regeneration (paratomy) and, thereby, vertically transmits numerous symbiont-containing bacteriocytes to its asexual progeny. Our data support the earlier reported hypothesis that the symbiont population is subjected to reduced bottleneck effects. This would justify both the codiversification between Paracatenula hosts and their Candidatus Riegeria symbionts, and the slow evolutionary rates observed for several symbiont genes.
Collapse
Affiliation(s)
- Ulrich Dirks
- Department of Marine Biology, University of Vienna, Vienna, Austria.
| | | | | | | | | | | | | |
Collapse
|
49
|
Donia MS, Fricke WF, Partensky F, Cox J, Elshahawi SI, White JR, Phillippy AM, Schatz MC, Piel J, Haygood MG, Ravel J, Schmidt EW. Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis. Proc Natl Acad Sci U S A 2011; 108:E1423-32. [PMID: 22123943 PMCID: PMC3251135 DOI: 10.1073/pnas.1111712108] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The relationship between tunicates and the uncultivated cyanobacterium Prochloron didemni has long provided a model symbiosis. P. didemni is required for survival of animals such as Lissoclinum patella and also makes secondary metabolites of pharmaceutical interest. Here, we present the metagenomes, chemistry, and microbiomes of four related L. patella tunicate samples from a wide geographical range of the tropical Pacific. The remarkably similar P. didemni genomes are the most complex so far assembled from uncultivated organisms. Although P. didemni has not been stably cultivated and comprises a single strain in each sample, a complete set of metabolic genes indicates that the bacteria are likely capable of reproducing outside the host. The sequences reveal notable peculiarities of the photosynthetic apparatus and explain the basis of nutrient exchange underlying the symbiosis. P. didemni likely profoundly influences the lipid composition of the animals by synthesizing sterols and an unusual lipid with biofuel potential. In addition, L. patella also harbors a great variety of other bacterial groups that contribute nutritional and secondary metabolic products to the symbiosis. These bacteria possess an enormous genetic potential to synthesize new secondary metabolites. For example, an antitumor candidate molecule, patellazole, is not encoded in the genome of Prochloron and was linked to other bacteria from the microbiome. This study unveils the complex L. patella microbiome and its impact on primary and secondary metabolism, revealing a remarkable versatility in creating and exchanging small molecules.
Collapse
Affiliation(s)
- Mohamed S. Donia
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112
| | - W. Florian Fricke
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Frédéric Partensky
- Station Biologique de Roscoff, Université Pierre et Marie Curie–Université Paris 6, 29680 Roscoff, France
- Oceanic Plankton Group, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7144, 29680 Roscoff, France
| | - James Cox
- Metabolomics Core Research Facility, University of Utah, Salt Lake City, UT 84112
| | - Sherif I. Elshahawi
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health and Science University, Beaverton, OR 97006
| | - James R. White
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Adam M. Phillippy
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Michael C. Schatz
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Joern Piel
- Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, D-53121 Bonn, Germany; and
| | - Margo G. Haygood
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health and Science University, Beaverton, OR 97006
| | - Jacques Ravel
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112
- Department of Biology, University of Utah, Salt Lake City, UT 84112
| |
Collapse
|
50
|
Microanatomy of the trophosome region of Paracatenula cf. polyhymnia (Catenulida, Platyhelminthes) and its intracellular symbionts. ZOOMORPHOLOGY 2011; 130:261-271. [PMID: 22131640 PMCID: PMC3213344 DOI: 10.1007/s00435-011-0135-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 08/11/2011] [Accepted: 08/13/2011] [Indexed: 11/03/2022]
Abstract
Marine catenulid platyhelminths of the genus Paracatenula lack mouth, pharynx and gut. They live in a symbiosis with intracellular bacteria which are restricted to the body region posterior to the brain. The symbiont-housing cells (bacteriocytes) collectively form the trophosome tissue, which functionally replaces the digestive tract. It constitutes the largest part of the body and is the most important synapomorphy of this group. While some other features of the Paracatenula anatomy have already been analyzed, an in-depth analysis of the trophosome region was missing. Here, we identify and characterize the composition of the trophosome and its surrounding tissue by analyzing series of ultra-thin cross-sections of the species Paracatenula cf. polyhymnia. For the first time, a protonephridium is detected in a Paracatenula species, but it is morphologically reduced and most likely not functional. Cells containing needle-like inclusions in the reference species Paracatenula polyhymnia Sterrer and Rieger, 1974 were thought to be sperm, and the inclusions interpreted as the sperm nucleus. Our analysis of similar cells and their inclusions by EDX and Raman microspectroscopy documents an inorganic spicule consisting of a unique magnesium–phosphate compound. Furthermore, we identify the neoblast stem cells located underneath the epidermis. Except for the modifications due to the symbiotic lifestyle and the enigmatic spicule cells, the organization of Paracatenula cf. polyhymnia conforms to that of the Catenulida in all studied aspects. Therefore, this species represents an excellent model system for further studies of host adaptation to an obligate symbiotic lifestyle.
Collapse
|