151
|
Huys GR, Raes J. Go with the flow or solitary confinement: a look inside the single-cell toolbox for isolation of rare and uncultured microbes. Curr Opin Microbiol 2018; 44:1-8. [PMID: 29908491 DOI: 10.1016/j.mib.2018.05.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/24/2018] [Indexed: 01/01/2023]
Abstract
With the vast majority of the microbial world still considered unculturable or undiscovered, microbiologists not only require more fundamental insights concerning microbial growth requirements but also need to implement miniaturized, versatile and high-throughput technologies to upscale current microbial isolation strategies. In this respect, single-cell-based approaches are increasingly finding their way to the microbiology lab. A number of recent studies have demonstrated that analysis and separation of free microbial cells by flow-based sorting as well as physical stochastic confinement of individual cells in microenvironment compartments can facilitate the isolation of previously uncultured species and the discovery of novel microbial taxa. Still, while most of these methods give immediate access to downstream whole genome sequencing, upscaling to higher cell densities as required for metabolic readouts and preservation purposes can remain challenging. Provided that these and other technological challenges are addressed in future innovation rounds, integration of single-cell tools in commercially available benchtop instruments and service platforms is expected to trigger more targeted explorations in the microbial dark matter at a depth comparable to metagenomics.
Collapse
Affiliation(s)
- Geert Rb Huys
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium; VIB, Center for Microbiology, Leuven, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium; VIB, Center for Microbiology, Leuven, Belgium.
| |
Collapse
|
152
|
Oyserman BO, Medema MH, Raaijmakers JM. Road MAPs to engineer host microbiomes. Curr Opin Microbiol 2018; 43:46-54. [DOI: 10.1016/j.mib.2017.11.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 01/07/2023]
|
153
|
Plewniak F, Crognale S, Rossetti S, Bertin PN. A Genomic Outlook on Bioremediation: The Case of Arsenic Removal. Front Microbiol 2018; 9:820. [PMID: 29755441 PMCID: PMC5932151 DOI: 10.3389/fmicb.2018.00820] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/10/2018] [Indexed: 01/07/2023] Open
Abstract
Microorganisms play a major role in biogeochemical cycles. As such they are attractive candidates for developing new or improving existing biotechnological applications, in order to deal with the accumulation and pollution of organic and inorganic compounds. Their ability to participate in bioremediation processes mainly depends on their capacity to metabolize toxic elements and catalyze reactions resulting in, for example, precipitation, biotransformation, dissolution, or sequestration. The contribution of genomics may be of prime importance to a thorough understanding of these metabolisms and the interactions of microorganisms with pollutants at the level of both single species and microbial communities. Such approaches should pave the way for the utilization of microorganisms to design new, efficient and environmentally sound remediation strategies, as exemplified by the case of arsenic contamination, which has been declared as a major risk for human health in various parts of the world.
Collapse
Affiliation(s)
- Frédéric Plewniak
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS, Université de Strasbourg, Strasbourg, France
| | - Simona Crognale
- Istituto di Ricerca sulle Acque, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Simona Rossetti
- Istituto di Ricerca sulle Acque, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS, Université de Strasbourg, Strasbourg, France
| |
Collapse
|
154
|
McKenzie VJ, Kueneman JG, Harris RN. Probiotics as a tool for disease mitigation in wildlife: insights from food production and medicine. Ann N Y Acad Sci 2018; 1429:18-30. [PMID: 29479716 DOI: 10.1111/nyas.13617] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/05/2017] [Accepted: 01/05/2018] [Indexed: 12/17/2022]
Abstract
The use of beneficial microbes to improve host attributes, referred to as probiotic therapy, has been increasingly applied to industries, including aquaculture, agriculture, and human medicine, and is emerging in the field of wildlife medicine. However, there is a general lack of shared knowledge regarding successful practices as well as ecological processes that underlie host-microbe interactions. Presently, probiotics are being developed specifically for preventing and treating particular infectious diseases as an alternative to antibiotic treatments and chemotherapy. We review research on probiotics developed for mitigation of infectious disease in the aforementioned industries to gain insight into how probiotics may be effective in reducing wildlife disease risk. We examine the trends of successful in vivo probiotic applications for disease systems and identify common objectives to reduce intestinal pathogens and sexually transmitted and respiratory diseases, inhibit skin pathogens, and serve as environmental prophylaxis to reduce pathogen loads in the environment. We conclude by highlighting the frontier of wildlife probiotics research and identifying knowledge gaps where research is needed.
Collapse
Affiliation(s)
- Valerie J McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado
| | - Jordan G Kueneman
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado.,Smithsonian Tropical Research Institute, Panama City, Panama
| | - Reid N Harris
- Department of Biology, James Madison University, Harrisonburg, Virginia.,Amphibian Survival Alliance, London, United Kingdom
| |
Collapse
|
155
|
Raina JB, Eme L, Pollock FJ, Spang A, Archibald JM, Williams TA. Symbiosis in the microbial world: from ecology to genome evolution. Biol Open 2018; 7:7/2/bio032524. [PMID: 29472284 PMCID: PMC5861367 DOI: 10.1242/bio.032524] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The concept of symbiosis – defined in 1879 by de Bary as ‘the living together of unlike organisms’ – has a rich and convoluted history in biology. In part, because it questioned the concept of the individual, symbiosis fell largely outside mainstream science and has traditionally received less attention than other research disciplines. This is gradually changing. In nature organisms do not live in isolation but rather interact with, and are impacted by, diverse beings throughout their life histories. Symbiosis is now recognized as a central driver of evolution across the entire tree of life, including, for example, bacterial endosymbionts that provide insects with vital nutrients and the mitochondria that power our own cells. Symbioses between microbes and their multicellular hosts also underpin the ecological success of some of the most productive ecosystems on the planet, including hydrothermal vents and coral reefs. In November 2017, scientists working in fields spanning the life sciences came together at a Company of Biologists’ workshop to discuss the origin, maintenance, and long-term implications of symbiosis from the complementary perspectives of cell biology, ecology, evolution and genomics, taking into account both model and non-model organisms. Here, we provide a brief synthesis of the fruitful discussions that transpired. Summary: At a recent Company of Biologists workshop, evolutionary biologists discussed the major outstanding questions in symbiosis research.
Collapse
Affiliation(s)
- Jean-Baptiste Raina
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Laura Eme
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden
| | - F Joseph Pollock
- Eberly College of Science, Department of Biology, Pennsylvania State University, University Park, PA 16801, USA
| | - Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden.,NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB Den Burg, The Netherlands
| | - John M Archibald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, 24 Tyndall Ave, Bristol, BS8 1TH, UK
| |
Collapse
|
156
|
Pascual J, Foesel BU, Geppert A, Huber KJ, Boedeker C, Luckner M, Wanner G, Overmann J. Roseisolibacter agri gen. nov., sp. nov., a novel slow-growing member of the under-represented phylum Gemmatimonadetes. Int J Syst Evol Microbiol 2018; 68:1028-1036. [PMID: 29458671 DOI: 10.1099/ijsem.0.002619] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
A novel slow-growing bacterium, designated strain AW1220T, was isolated from agricultural floodplain soil sampled at Mashare (Kavango region, Namibia) by using a high-throughput cultivation approach. Strain AW1220T was characterized as a Gram-negative, non-motile, rod-shaped bacterium. Occasionally, some cells attained an unusual length of up to 35 µm. The strain showed positive responses for catalase and cytochrome-c oxidase and divided by binary fission and/or budding. The strain had an aerobic chemoorganoheterotrophic metabolism and was also able to grow under micro-oxic conditions. Colonies were small and pink pigmented. Strain AW1220T was found to be a mesophilic, neutrophilic and non-halophilic bacterium. Cells accumulated polyphosphate intracellularly and mainly utilized complex protein substrates for growth. 16S rRNA gene sequence comparisons revealed that strain AW1220T belonged to the class Gemmatimonadetes (=group 1). Its closest relatives were found to be Gemmatimonas aurantiaca T-27T (90.9 % gene sequence similarity), Gemmatimonas phototrophica AP64T (90.8 %) and Longimicrobiumterrae CB-286315T (84.2 %). The genomic G+C content was 73.3 mol%. The major fatty acids were iso-C15 : 0, C16 : 1ω7c and/or iso-C15 : 0 2-OH, iso-C17 : 1ω9c, iso-C15 : 0 3-OH and C16 : 0. The predominant respiratory quinone was MK-9, albeit minor amounts of MK-8 and MK-10 are also present. The polar lipids comprised major amounts of phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and one unidentified phosphoglycolipid. On the basis of its polyphasic characterization, strain AW1220T represents a novel genus and species of the class Gemmatimonadetes for which the name Roseisolibacter agri gen. nov., sp. nov. is proposed, with the type strain AW1220T (=DSM 104292T=LMG 29977T).
Collapse
Affiliation(s)
- Javier Pascual
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Bärbel U Foesel
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.,Present address: Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Alicia Geppert
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Katharina J Huber
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Christian Boedeker
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Manja Luckner
- Department of Biology I, Biozentrum Ludwig Maximilian University Munich, Planegg-Martinsried, Germany
| | - Gerhard Wanner
- Department of Biology I, Biozentrum Ludwig Maximilian University Munich, Planegg-Martinsried, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.,Technische Universität Braunschweig, Braunschweig, Germany
| |
Collapse
|
157
|
Dunivin TK, Miller J, Shade A. Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire. PLoS One 2018; 13:e0191893. [PMID: 29370270 PMCID: PMC5785013 DOI: 10.1371/journal.pone.0191893] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/12/2018] [Indexed: 02/05/2023] Open
Abstract
Arsenic (As), a toxic element, has impacted life since early Earth. Thus, microorganisms have evolved many As resistance and tolerance mechanisms to improve their survival outcomes given As exposure. We isolated As resistant bacteria from Centralia, PA, the site of an underground coal seam fire that has been burning since 1962. From a 57.4°C soil collected from a vent above the fire, we isolated 25 unique aerobic As resistant bacterial strains spanning seven genera. We examined their diversity, resistance gene content, transformation abilities, inhibitory concentrations, and growth phenotypes. Although As concentrations were low at the time of soil collection (2.58 ppm), isolates had high minimum inhibitory concentrations (MICs) of arsenate and arsenite (>300 mM and 20 mM respectively), and most isolates were capable of arsenate reduction. We screened isolates (PCR and sequencing) using 12 published primer sets for six As resistance genes (AsRGs). Genes encoding arsenate reductase (arsC) and arsenite efflux pumps (arsB, ACR3(2)) were present, and phylogenetic incongruence between 16S rRNA genes and AsRGs provided evidence for horizontal gene transfer. A detailed investigation of differences in isolate growth phenotypes across As concentrations (lag time to exponential growth, maximum growth rate, and maximum OD590) showed a relationship with taxonomy, providing information that could help to predict an isolate's performance given As exposure in situ. Our results suggest that microbiological management and remediation of environmental As could be informed by taxonomically-linked As tolerance, potential for resistance gene transferability, and the rare biosphere.
Collapse
Affiliation(s)
- Taylor K. Dunivin
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- Environmental and Integrative Toxicological Sciences Doctoral Program, Michigan State University, East Lansing, Michigan, United States of America
| | - Justine Miller
- Lyman Briggs College, Michigan State University, East Lansing, Michigan, United States of America
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan, United States of America
| |
Collapse
|