251
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Kent AG, Dupont CL, Yooseph S, Martiny AC. Global biogeography of Prochlorococcus genome diversity in the surface ocean. ISME JOURNAL 2016; 10:1856-65. [PMID: 26836261 DOI: 10.1038/ismej.2015.265] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 12/05/2015] [Accepted: 12/15/2015] [Indexed: 01/08/2023]
Abstract
Prochlorococcus, the smallest known photosynthetic bacterium, is abundant in the ocean's surface layer despite large variation in environmental conditions. There are several genetically divergent lineages within Prochlorococcus and superimposed on this phylogenetic diversity is extensive gene gain and loss. The environmental role in shaping the global ocean distribution of genome diversity in Prochlorococcus is largely unknown, particularly in a framework that considers the vertical and lateral mechanisms of evolution. Here we show that Prochlorococcus field populations from a global circumnavigation harbor extensive genome diversity across the surface ocean, but this diversity is not randomly distributed. We observed a significant correspondence between phylogenetic and gene content diversity, including regional differences in both phylogenetic composition and gene content that were related to environmental factors. Several gene families were strongly associated with specific regions and environmental factors, including the identification of a set of genes related to lower nutrient and temperature regions. Metagenomic assemblies of natural Prochlorococcus genomes reinforced this association by providing linkage of genes across genomic backbones. Overall, our results show that the phylogeography in Prochlorococcus taxonomy is echoed in its genome content. Thus environmental variation shapes the functional capabilities and associated ecosystem role of the globally abundant Prochlorococcus.
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Affiliation(s)
- Alyssa G Kent
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Chris L Dupont
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, San Diego, CA, USA
| | - Shibu Yooseph
- Informatics Group, J. Craig Venter Institute, San Diego, CA, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.,Department of Earth System Science, University of California, Irvine, CA, USA
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252
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Larkin AA, Blinebry SK, Howes C, Lin Y, Loftus SE, Schmaus CA, Zinser ER, Johnson ZI. Niche partitioning and biogeography of high light adapted Prochlorococcus across taxonomic ranks in the North Pacific. ISME JOURNAL 2016; 10:1555-67. [PMID: 26800235 DOI: 10.1038/ismej.2015.244] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/30/2015] [Accepted: 11/18/2015] [Indexed: 02/08/2023]
Abstract
The distribution of major clades of Prochlorococcus tracks light, temperature and other environmental variables; yet, the drivers of genomic diversity within these ecotypes and the net effect on biodiversity of the larger community are poorly understood. We examined high light (HL) adapted Prochlorococcus communities across spatial and temporal environmental gradients in the Pacific Ocean to determine the ecological drivers of population structure and diversity across taxonomic ranks. We show that the Prochlorococcus community has the highest diversity at low latitudes, but seasonality driven by temperature, day length and nutrients adds complexity. At finer taxonomic resolution, some 'sub-ecotype' clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Intriguingly, biogeographies of the HL-I sub-ecotypes are driven by unique combinations of environmental traits, rather than through trait hierarchy, while the HL-II sub-ecotypes appear ecologically similar, thus demonstrating differences among these dominant HL ecotypes. Examining biodiversity across taxonomic ranks reveals high-resolution dynamics of Prochlorococcus evolution and ecology that are masked at phylogenetically coarse resolution. Spatial and seasonal trends of Prochlorococcus communities suggest that the future ocean may be comprised of different populations, with implications for ecosystem structure and function.
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Affiliation(s)
- Alyse A Larkin
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Sara K Blinebry
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Caroline Howes
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Yajuan Lin
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Sarah E Loftus
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Carrie A Schmaus
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
| | - Erik R Zinser
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Zackary I Johnson
- Marine Laboratory, Nicholas School of the Environment, and Biology Department, Duke University, Beaufort, NC, USA
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253
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Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria. ISME JOURNAL 2016; 10:1902-14. [PMID: 26784354 PMCID: PMC5029164 DOI: 10.1038/ismej.2015.260] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/24/2015] [Accepted: 12/10/2015] [Indexed: 11/08/2022]
Abstract
Most free-living planktonic cells are streamlined and in spite of their limitations in functional flexibility, their vast populations have radiated into a wide range of aquatic habitats. Here we compared the metabolic potential of subgroups in the Alphaproteobacteria lineage SAR11 adapted to marine and freshwater habitats. Our results suggest that the successful leap from marine to freshwaters in SAR11 was accompanied by a loss of several carbon degradation pathways and a rewiring of the central metabolism. Examples for these are C1 and methylated compounds degradation pathways, the Entner–Doudouroff pathway, the glyoxylate shunt and anapleuretic carbon fixation being absent from the freshwater genomes. Evolutionary reconstructions further suggest that the metabolic modules making up these important freshwater metabolic traits were already present in the gene pool of ancestral marine SAR11 populations. The loss of the glyoxylate shunt had already occurred in the common ancestor of the freshwater subgroup and its closest marine relatives, suggesting that the adaptation to freshwater was a gradual process. Furthermore, our results indicate rapid evolution of TRAP transporters in the freshwater clade involved in the uptake of low molecular weight carboxylic acids. We propose that such gradual tuning of metabolic pathways and transporters toward locally available organic substrates is linked to the formation of subgroups within the SAR11 clade and that this process was critical for the freshwater clade to find and fix an adaptive phenotype.
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254
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Shilova IN, Robidart JC, DeLong EF, Zehr JP. Genetic Diversity Affects the Daily Transcriptional Oscillations of Marine Microbial Populations. PLoS One 2016; 11:e0146706. [PMID: 26751368 PMCID: PMC4709009 DOI: 10.1371/journal.pone.0146706] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/21/2015] [Indexed: 11/18/2022] Open
Abstract
Marine microbial communities are genetically diverse but have robust synchronized daily transcriptional patterns at the genus level that are similar across a wide variety of oceanic regions. We developed a microarray-inspired gene-centric approach to resolve transcription of closely-related but distinct strains/ecotypes in high-throughput sequence data. Applying this approach to the existing metatranscriptomics datasets collected from two different oceanic regions, we found unique and variable patterns of transcription by individual taxa within the abundant picocyanobacteria Prochlorococcus and Synechococcus, the alpha Proteobacterium Pelagibacter and the eukaryotic picophytoplankton Ostreococcus. The results demonstrate that marine microbial taxa respond differentially to variability in space and time in the ocean. These intra-genus individual transcriptional patterns underlie whole microbial community responses, and the approach developed here facilitates deeper insights into microbial population dynamics.
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Affiliation(s)
- Irina N. Shilova
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Julie C. Robidart
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Edward F. DeLong
- School of Ocean and Earth Science and Technology, University of Hawai’i at Manoa, Honolulu, Hawaii, United States of America
| | - Jonathan P. Zehr
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
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255
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Mock T, Daines SJ, Geider R, Collins S, Metodiev M, Millar AJ, Moulton V, Lenton TM. Bridging the gap between omics and earth system science to better understand how environmental change impacts marine microbes. GLOBAL CHANGE BIOLOGY 2016; 22:61-75. [PMID: 25988950 PMCID: PMC4949645 DOI: 10.1111/gcb.12983] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/05/2015] [Accepted: 05/12/2015] [Indexed: 05/17/2023]
Abstract
The advent of genomic-, transcriptomic- and proteomic-based approaches has revolutionized our ability to describe marine microbial communities, including biogeography, metabolic potential and diversity, mechanisms of adaptation, and phylogeny and evolutionary history. New interdisciplinary approaches are needed to move from this descriptive level to improved quantitative, process-level understanding of the roles of marine microbes in biogeochemical cycles and of the impact of environmental change on the marine microbial ecosystem. Linking studies at levels from the genome to the organism, to ecological strategies and organism and ecosystem response, requires new modelling approaches. Key to this will be a fundamental shift in modelling scale that represents micro-organisms from the level of their macromolecular components. This will enable contact with omics data sets and allow acclimation and adaptive response at the phenotype level (i.e. traits) to be simulated as a combination of fitness maximization and evolutionary constraints. This way forward will build on ecological approaches that identify key organism traits and systems biology approaches that integrate traditional physiological measurements with new insights from omics. It will rely on developing an improved understanding of ecophysiology to understand quantitatively environmental controls on microbial growth strategies. It will also incorporate results from experimental evolution studies in the representation of adaptation. The resulting ecosystem-level models can then evaluate our level of understanding of controls on ecosystem structure and function, highlight major gaps in understanding and help prioritize areas for future research programs. Ultimately, this grand synthesis should improve predictive capability of the ecosystem response to multiple environmental drivers.
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Affiliation(s)
- Thomas Mock
- School of Environmental SciencesUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Stuart J. Daines
- College of Life and Environmental SciencesUniversity of ExeterEX4 4QEExeterUK
| | - Richard Geider
- School of Biological SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
| | - Sinead Collins
- Ashworth LaboratoriesEdinburgh UniversityEH9 3JFEdinburghUK
| | - Metodi Metodiev
- School of Biological SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
| | - Andrew J. Millar
- SynthSys and School of Biological SciencesEdinburgh UniversityEH9 3BFEdinburghUK
| | - Vincent Moulton
- School of Computing SciencesUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Timothy M. Lenton
- College of Life and Environmental SciencesUniversity of ExeterEX4 4QEExeterUK
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256
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Cullen JJ, MacIntyre HL. On the use of the serial dilution culture method to enumerate viable phytoplankton in natural communities of plankton subjected to ballast water treatment. JOURNAL OF APPLIED PHYCOLOGY 2016; 28:279-298. [PMID: 26893536 PMCID: PMC4735243 DOI: 10.1007/s10811-015-0601-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 04/21/2015] [Indexed: 05/07/2023]
Abstract
Discharge standards for ballast water treatment (BWT) systems are based on concentrations of living cells, for example, as determined with vital stains. Ultraviolet radiation (UV) stops the reproduction of microorganisms without killing them outright; they are living, but not viable, and ecologically as good as dead. Consequently, UV-treated discharge can be compliant with the intent of regulation while failing a live/dead test. An alternative evaluation of BWT can be proposed based on the assessment of viable, rather than living, cells in discharge water. In principle, the serial dilution culture-most probable number (SDC-MPN) method provides the appropriate measure for phytoplankton. But, the method has been criticized, particularly because it is thought that many phytoplankton species cannot be cultured. A review of the literature shows that although SDC-MPN has been used for more than 50 years-generally to identify and count phytoplankton species that cannot be preserved-its application to enumerate total viable phytoplankton seems to be new, putting past criticisms of the method in a different light. Importantly, viable cells need to grow only enough to be detected, not to be brought into sustained culture, and competition between species in a dilution tube is irrelevant as long as the winner is detectable. Thorough consideration of sources of error leads to recommendations for minimizing and quantifying uncertainties by optimizing growth conditions and conducting systematic comparisons. We conclude that with careful evaluation, SDC-MPN is potentially an effective method for assessing the viability of phytoplankton after BWT.
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Affiliation(s)
- John J. Cullen
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia Canada B3H 4R2
| | - Hugh L. MacIntyre
- Department of Oceanography, Dalhousie University, Halifax, Nova Scotia Canada B3H 4R2
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257
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Weakly Deleterious Mutations and Low Rates of Recombination Limit the Impact of Natural Selection on Bacterial Genomes. mBio 2015; 6:e01302-15. [PMID: 26670382 PMCID: PMC4701828 DOI: 10.1128/mbio.01302-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Free-living bacteria are usually thought to have large effective population sizes, and so tiny selective differences can drive their evolution. However, because recombination is infrequent, “background selection” against slightly deleterious alleles should reduce the effective population size (Ne) by orders of magnitude. For example, for a well-mixed population with 1012 individuals and a typical level of homologous recombination (r/m = 3, i.e., nucleotide changes due to recombination [r] occur at 3 times the mutation rate [m]), we predict that Ne is <107. An argument for high Ne values for bacteria has been the high genetic diversity within many bacterial “species,” but this diversity may be due to population structure: diversity across subpopulations can be far higher than diversity within a subpopulation, which makes it difficult to estimate Ne correctly. Given an estimate of Ne, standard population genetics models imply that selection should be sufficient to drive evolution if Ne × s is >1, where s is the selection coefficient. We found that this remains approximately correct if background selection is occurring or when population structure is present. Overall, we predict that even for free-living bacteria with enormous populations, natural selection is only a significant force if s is above 10−7 or so. Because bacteria form huge populations with trillions of individuals, the simplest theoretical prediction is that the better allele at a site would predominate even if its advantage was just 10−9 per generation. In other words, virtually every nucleotide would be at the local optimum in most individuals. A more sophisticated theory considers that bacterial genomes have millions of sites each and selection events on these many sites could interfere with each other, so that only larger effects would be important. However, bacteria can exchange genetic material, and in principle, this exchange could eliminate the interference between the evolution of the sites. We used simulations to confirm that during multisite evolution with realistic levels of recombination, only larger effects are important. We propose that advantages of less than 10−7 are effectively neutral.
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258
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259
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Louca S, Doebeli M. Transient dynamics of competitive exclusion in microbial communities. Environ Microbiol 2015; 18:1863-74. [DOI: 10.1111/1462-2920.13058] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/15/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Stilianos Louca
- Biodiversity Research Centre; University of British Columbia; Vancouver BC V6T 1Z4 Canada
| | - Michael Doebeli
- Department of Zoology; University of British Columbia; Vancouver BC V6T 1Z4 Canada
- Department of Mathematics; University of British Columbia; Vancouver BC V6T 1Z2 Canada
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260
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Lassalle F, Muller D, Nesme X. Ecological speciation in bacteria: reverse ecology approaches reveal the adaptive part of bacterial cladogenesis. Res Microbiol 2015; 166:729-41. [DOI: 10.1016/j.resmic.2015.06.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/28/2015] [Accepted: 06/30/2015] [Indexed: 11/30/2022]
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261
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Interactions between closely related bacterial strains are revealed by deep transcriptome sequencing. Appl Environ Microbiol 2015; 81:8445-56. [PMID: 26431969 DOI: 10.1128/aem.02690-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/27/2015] [Indexed: 01/15/2023] Open
Abstract
Comparative genomics, metagenomics, and single-cell technologies have shown that populations of microbial species encompass assemblages of closely related strains. This raises the question of whether individual bacterial lineages respond to the presence of their close relatives by modifying their gene expression or, instead, whether assemblages simply act as the arithmetic addition of their individual components. Here, we took advantage of transcriptome sequencing to address this question. For this, we analyzed the transcriptomes of two closely related strains of the extremely halophilic bacterium Salinibacter ruber grown axenically and in coculture. These organisms dominate bacterial assemblages in hypersaline environments worldwide. The strains used here cooccurred in the natural environment and are 100% identical in their 16S rRNA genes, and each strain harbors an accessory genome representing 10% of its complete genome. Overall, transcriptomic patterns from pure cultures were very similar for both strains. Expression was detected along practically the whole genome albeit with some genes at low levels. A subset of genes was very highly expressed in both strains, including genes coding for the light-driven proton pump xanthorhodopsin, genes involved in the stress response, and genes coding for transcriptional regulators. Expression differences between pure cultures affected mainly genes involved in environmental sensing. When the strains were grown in coculture, there was a modest but significant change in their individual transcription patterns compared to those in pure culture. Each strain sensed the presence of the other and responded in a specific manner, which points to fine intraspecific transcriptomic modulation.
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262
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Puxty RJ, Millard AD, Evans DJ, Scanlan DJ. Shedding new light on viral photosynthesis. PHOTOSYNTHESIS RESEARCH 2015; 126:71-97. [PMID: 25381655 DOI: 10.1007/s11120-014-0057-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 10/29/2014] [Indexed: 06/04/2023]
Abstract
Viruses infecting the environmentally important marine cyanobacteria Prochlorococcus and Synechococcus encode 'auxiliary metabolic genes' (AMGs) involved in the light and dark reactions of photosynthesis. Here, we discuss progress on the inventory of such AMGs in the ever-increasing number of viral genome sequences as well as in metagenomic datasets. We contextualise these gene acquisitions with reference to a hypothesised fitness gain to the phage. We also report new evidence with regard to the sequence and predicted structural properties of viral petE genes encoding the soluble electron carrier plastocyanin. Viral copies of PetE exhibit extensive modifications to the N-terminal signal peptide and possess several novel residues in a region responsible for interaction with redox partners. We also highlight potential knowledge gaps in this field and discuss future opportunities to discover novel phage-host interactions involved in the photosynthetic process.
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Affiliation(s)
- Richard J Puxty
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- School of Biological Sciences, University of California, Irvine, CA 92697, USA
| | - Andrew D Millard
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - David J Evans
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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263
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Davison M, Hall E, Zare R, Bhaya D. Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity. PHOTOSYNTHESIS RESEARCH 2015; 126:135-146. [PMID: 25515769 DOI: 10.1007/s11120-014-0066-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 12/10/2014] [Indexed: 06/04/2023]
Abstract
Cyanobacteria have played a crucial role in the history of early earth and continue to be instrumental in shaping our planet, yet applications of cutting edge technology have not yet been widely used to explore cyanobacterial diversity. To provide adequate background, we briefly review current sequencing technologies and their innovative uses in genomics and metagenomics. Next, we focus on current cell capture technologies and the challenges of using them with cyanobacteria. We illustrate the utility in coupling breakthroughs in DNA amplification with cell capture platforms, with an example of microfluidic isolation and subsequent targeted amplicon sequencing from individual terrestrial thermophilic cyanobacteria. Single cells of thermophilic, unicellular Synechococcus sp. JA-2-3-B'a(2-13) (Syn OS-B') were sorted in a microfluidic device, lysed, and subjected to whole genome amplification by multiple displacement amplification. We amplified regions from specific CRISPR spacer arrays, which are known to be highly diverse, contain semi-palindromic repeats which form secondary structure, and can be difficult to amplify. Cell capture, lysis, and genome amplification on a microfluidic device have been optimized, setting a stage for further investigations of individual cyanobacterial cells isolated directly from natural populations.
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Affiliation(s)
- Michelle Davison
- Department of Plant Biology, Carnegie Institution of Science, 260 Panama Street, Stanford, CA, 94305, USA.
| | - Eric Hall
- SRI International, 333 Ravenswood Ave, Menlo Park, CA, 94025, USA
| | - Richard Zare
- Department of Chemistry, Stanford University, 333 Campus Drive Mudd Building, Room 121, Stanford, CA, 94305-4401, USA
| | - Devaki Bhaya
- Department of Plant Biology, Carnegie Institution of Science, 260 Panama Street, Stanford, CA, 94305, USA
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264
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Ikuta T, Takaki Y, Nagai Y, Shimamura S, Tsuda M, Kawagucci S, Aoki Y, Inoue K, Teruya M, Satou K, Teruya K, Shimoji M, Tamotsu H, Hirano T, Maruyama T, Yoshida T. Heterogeneous composition of key metabolic gene clusters in a vent mussel symbiont population. ISME JOURNAL 2015; 10:990-1001. [PMID: 26418631 PMCID: PMC4796938 DOI: 10.1038/ismej.2015.176] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 08/10/2015] [Accepted: 08/13/2015] [Indexed: 11/09/2022]
Abstract
Chemosynthetic symbiosis is one of the successful systems for adapting to a wide range of habitats including extreme environments, and the metabolic capabilities of symbionts enable host organisms to expand their habitat ranges. However, our understanding of the adaptive strategies that enable symbiotic organisms to expand their habitats is still fragmentary. Here, we report that a single-ribotype endosymbiont population in an individual of the host vent mussel, Bathymodiolus septemdierum has heterogeneous genomes with regard to the composition of key metabolic gene clusters for hydrogen oxidation and nitrate reduction. The host individual harbours heterogeneous symbiont subpopulations that either possess or lack the gene clusters encoding hydrogenase or nitrate reductase. The proportions of the different symbiont subpopulations in a host appeared to vary with the environment or with the host's development. Furthermore, the symbiont subpopulations were distributed in patches to form a mosaic pattern in the gill. Genomic heterogeneity in an endosymbiont population may enable differential utilization of diverse substrates and confer metabolic flexibility. Our findings open a new chapter in our understanding of how symbiotic organisms alter their metabolic capabilities and expand their range of habitats.
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Affiliation(s)
- Tetsuro Ikuta
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yukiko Nagai
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Shigeru Shimamura
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Miwako Tsuda
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Shinsuke Kawagucci
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Yui Aoki
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Koji Inoue
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Morimi Teruya
- Okinawa Industrial Technology Center, 12-2 Suzaki, Uruma, Okinawa, Japan
| | - Kazuhito Satou
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Kuniko Teruya
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Makiko Shimoji
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Hinako Tamotsu
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan
| | - Takashi Hirano
- Okinawa Institute of Advanced Sciences (OIAS), 5-1 Suzaki, Uruma, Okinawa, Japan.,Okinawa Science and Technology Promotion Center (OSTC), 112-18 Asahimachi, Naha, Okinawa, Japan
| | - Tadashi Maruyama
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
| | - Takao Yoshida
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, Kanagawa, Japan
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265
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ConStrains identifies microbial strains in metagenomic datasets. Nat Biotechnol 2015; 33:1045-52. [PMID: 26344404 PMCID: PMC4676274 DOI: 10.1038/nbt.3319] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 07/16/2015] [Indexed: 01/21/2023]
Abstract
An important fraction of microbial diversity is harbored in strain individuality, so identification of conspecific bacterial strains is imperative for improved understanding of microbial community functions. Limitations in bioinformatics and sequencing technologies have to date precluded strain identification owing to difficulties in phasing short reads to faithfully recover the original strain-level genotypes, which have highly similar sequences. We present ConStrains, an open-source algorithm that identifies conspecific strains from metagenomic sequence data and reconstructs the phylogeny of these strains in microbial communities. The algorithm uses single-nucleotide polymorphism (SNP) patterns in a set of universal genes to infer within-species structures that represent strains. Applying ConStrains to simulated and host-derived datasets provides insights into microbial community dynamics.
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266
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Acosta S, Carela M, Garcia-Gonzalez A, Gines M, Vicens L, Cruet R, Massey SE. DNA Repair Is Associated with Information Content in Bacteria, Archaea, and DNA Viruses. J Hered 2015; 106:644-59. [PMID: 26320243 DOI: 10.1093/jhered/esv055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 07/07/2015] [Indexed: 11/13/2022] Open
Abstract
The concept of a "proteomic constraint" proposes that DNA repair capacity is positively correlated with the information content of a genome, which can be approximated to the size of the proteome (P). This in turn implies that DNA repair genes are more likely to be present in genomes with larger values of P. This stands in contrast to the common assumption that informational genes have a core function and so are evenly distributed across organisms. We examined the presence/absence of 18 DNA repair genes in bacterial genomes. A positive relationship between gene presence and P was observed for 17 genes in the total dataset, and 16 genes when only nonintracellular bacteria were examined. A marked reduction of DNA repair genes was observed in intracellular bacteria, consistent with their reduced value of P. We also examined archaeal and DNA virus genomes, and show that the presence of DNA repair genes is likewise related to a larger value of P. In addition, the products of the bacterial genes mutY, vsr, and ndk, involved in the correction of GC/AT mutations, are strongly associated with reduced genome GC content. We therefore propose that a reduction in information content leads to a loss of DNA repair genes and indirectly to a reduction in genome GC content in bacteria by exposure to the underlying AT mutation bias. The reduction in P may also indirectly lead to the increase in substitution rates observed in intracellular bacteria via loss of DNA repair genes.
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Affiliation(s)
- Sharlene Acosta
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Miguelina Carela
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Aurian Garcia-Gonzalez
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Mariela Gines
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Luis Vicens
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Ricardo Cruet
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey)
| | - Steven E Massey
- From the Department of Biology, University of Puerto Rico-Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico (Acosta, Carela, Garcia-Gonzalez, Gines, Vicens, Cruet, and Massey).
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267
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Krause DJ, Whitaker RJ. Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes. Syst Biol 2015; 64:926-35. [PMID: 26316424 PMCID: PMC4604833 DOI: 10.1093/sysbio/syv050] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 06/09/2015] [Indexed: 01/22/2023] Open
Abstract
Microbial species concepts have long been the focus of contentious debate, fueled by technological limitations to the genetic resolution of species, by the daunting task of investigating phenotypic variation among individual microscopic organisms, and by a lack of understanding of gene flow in reproductively asexual organisms that are prone to promiscuous horizontal gene transfer. Population genomics, the emerging approach of analyzing the complete genomes of a multitude of closely related organisms, is poised to overcome these limitations by providing a window into patterns of genome variation revealing the evolutionary processes through which species diverge. This new approach is more than just an extension of previous multilocus sequencing technologies, in that it provides a comprehensive view of interacting evolutionary processes. Here we argue that the application of population genomic tools in a rigorous population genetic framework will help to identify the processes of microbial speciation and ultimately lead to a general species concept based on the unique biology and ecology of microorganisms.
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Affiliation(s)
- David J Krause
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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268
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Abstract
This review summarizes usage of genome-editing technologies for metagenomic studies; these studies are used to retrieve and modify valuable microorganisms for production, particularly in marine metagenomics. Organisms may be cultivable or uncultivable. Metagenomics is providing especially valuable information for uncultivable samples. The novel genes, pathways and genomes can be deducted. Therefore, metagenomics, particularly genome engineering and system biology, allows for the enhancement of biological and chemical producers and the creation of novel bioresources. With natural resources rapidly depleting, genomics may be an effective way to efficiently produce quantities of known and novel foods, livestock feed, fuels, pharmaceuticals and fine or bulk chemicals.
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Affiliation(s)
- Rimantas Kodzius
- Computational Bioscience Research Center (CBRC), Saudi Arabia; Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Saudi Arabia.
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269
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Garcia SL, Buck M, McMahon KD, Grossart HP, Eiler A, Warnecke F. Auxotrophy and intrapopulation complementary in the ‘interactome’ of a cultivated freshwater model community. Mol Ecol 2015; 24:4449-59. [DOI: 10.1111/mec.13319] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/09/2015] [Accepted: 07/10/2015] [Indexed: 01/05/2023]
Affiliation(s)
- Sarahi L. Garcia
- Department of Ecology and Genetics; Limnology and Science for Life Laboratory; Uppsala University; Norbyvägen 18D 752 36 Uppsala Sweden
| | - Moritz Buck
- Department of Ecology and Genetics; Limnology and Science for Life Laboratory; Uppsala University; Norbyvägen 18D 752 36 Uppsala Sweden
- BILS; Swedish Bioinformatics Infrastructure for Life Sciences; Husargatan 3 751 23 Uppsala Sweden
| | - Katherine D. McMahon
- Department of Bacteriology and Department of Civil and Environmental Engineering; University of Wisconsin-Madison; 5552 Microbial Sciences Building 1550 Linden Drive Madison WI 53706 USA
| | - Hans-Peter Grossart
- Department Experimental Limnology; Leibniz-Institute for Freshwater Ecology and Inland Fisheries; Alte Fischerhütte 2 OT Neuglobsow 16775 Stechlin Germany
- Institute for Biochemistry and Biology; Potsdam University; Karl-Liebknecht-Straße 24-25 Haus 25 14476 Potsdam Germany
| | - Alexander Eiler
- Department of Ecology and Genetics; Limnology and Science for Life Laboratory; Uppsala University; Norbyvägen 18D 752 36 Uppsala Sweden
| | - Falk Warnecke
- Jena School for Microbial Communication at Friedrich Schiller University Jena; Philosophenweg 12 07743 Jena Germany
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270
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Roux S, Hallam SJ, Woyke T, Sullivan MB. Viral dark matter and virus-host interactions resolved from publicly available microbial genomes. eLife 2015. [PMID: 26200428 PMCID: PMC4533152 DOI: 10.7554/elife.08490] [Citation(s) in RCA: 294] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus–host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7–38% of ‘unknown’ sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 new viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus–host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes. DOI:http://dx.doi.org/10.7554/eLife.08490.001 Viruses are infectious particles that can only multiply inside the cells of microbes and other organisms. Little is known about the genetic differences between virus particles (so-called ‘genetic diversity’), especially compared to what we know about the diversity of bacteria, archaea, and other single-celled microbes. This lack of knowledge hampers our understanding of the role viruses play in the evolution of microbial communities and their associated ecosystems. Studying the genetics of the viruses in these communities is challenging. There is no single ‘marker’ gene that can be used to identify all viruses in environmental samples. Also, many of the fragments of viral genomes that have been identified have not yet been linked to their host microbes. Many viruses integrate their genome into the DNA of their host cell, and there are computational tools available that exploit this ability to identify viruses and link them to their host. However, other viruses can live and multiply inside cells without integrating their genome into the host's DNA. Earlier in 2015, researchers developed a new computational tool called VirSorter that can predict virus genome sequences within the DNA extracted from microbes. VirSorter identifies viral genome sequences based on the presence of ‘hallmark’ genes that encode for components found in many virus particles, together with a reference database of genomes from many viruses. Now, Roux et al.—including some of the researchers from the earlier work—use VirSorter to predict viral DNA from publicly available bacteria and archaea genome data. The study identifies over 12,000 viral genomes and links them to their microbial hosts. These data increase the number of viral genome sequences that are publically available by a factor of ten and identify the first viruses associated with 13 new types of bacteria, which include species that are abundant in particular environments. It is possible for several different viruses to infect a single cell at the same time. Some viruses are known to be able to exchange DNA, and if this happens frequently in other viruses, it could have a big impact on how viruses evolve. Roux et al.'s findings suggest that although it is common for several different viruses to infect the same cell, it is relatively rare for these viruses to exchange genetic material. Roux et al.'s findings demonstrate the value of searching publicly available microbial genome data for fragments of viral genomes. These new viral genomes will serve as a useful resource for researchers as they explore the communities of viruses and microbes in natural environments, the human body and in industrial processes. DOI:http://dx.doi.org/10.7554/eLife.08490.002
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Affiliation(s)
- Simon Roux
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Tanja Woyke
- U.S Department of Energy Joint Genome Institute, Walnut Creek, United States
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, United States
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271
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Rosen MJ, Davison M, Bhaya D, Fisher DS. Microbial diversity. Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche. Science 2015; 348:1019-23. [PMID: 26023139 DOI: 10.1126/science.aaa4456] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Extensive fine-scale genetic diversity is found in many microbial species across varied environments, but for most, the evolutionary scenarios that generate the observed variation remain unclear. Deep sequencing of a thermophilic cyanobacterial population and analysis of the statistics of synonymous single-nucleotide polymorphisms revealed a high rate of homologous recombination and departures from neutral drift consistent with the effects of genetic hitchhiking. A sequenced isolate genome resembled an unlinked random mixture of the allelic diversity at the sampled loci. These observations suggested a quasisexual microbial population that occupies a broad ecological niche, with selection driving frequencies of alleles rather than whole genomes.
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Affiliation(s)
- Michael J Rosen
- Applied Physics Department, Stanford University, Stanford, CA 94305, USA
| | - Michelle Davison
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Devaki Bhaya
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
| | - Daniel S Fisher
- Applied Physics Department, Stanford University, Stanford, CA 94305, USA. Bioengineering Department, Stanford University, Stanford, CA 94305, USA.
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272
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Becraft ED, Wood JM, Rusch DB, Kühl M, Jensen SI, Bryant DA, Roberts DW, Cohan FM, Ward DM. The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park. Front Microbiol 2015; 6:590. [PMID: 26157420 PMCID: PMC4475828 DOI: 10.3389/fmicb.2015.00590] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/29/2015] [Indexed: 01/18/2023] Open
Abstract
Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species [putative ecotypes (PEs)], which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same PE formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the PEs are ecologically distinct, the members of each ecotype are ecologically homogeneous. PEs responded differently to experimental perturbations of temperature and light, but the genetic variation within each PE was maintained as the relative abundances of PEs changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to PEs that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for PEs that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time.
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Affiliation(s)
- Eric D. Becraft
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MTUSA
- Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences, East Boothbay, MEUSA
| | - Jason M. Wood
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MTUSA
| | | | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, HelsingørDenmark
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Ultimo, NSWAustralia
| | - Sheila I. Jensen
- Marine Biological Section, Department of Biology, University of Copenhagen, HelsingørDenmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, HellerupDenmark
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PAUSA
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MTUSA
| | | | | | - David M. Ward
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MTUSA
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273
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Coutinho FH, Meirelles PM, Moreira APB, Paranhos RP, Dutilh BE, Thompson FL. Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review. PeerJ 2015; 3:e1008. [PMID: 26157601 PMCID: PMC4476133 DOI: 10.7717/peerj.1008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 05/19/2015] [Indexed: 12/14/2022] Open
Abstract
Associations between microorganisms occur extensively throughout Earth’s oceans. Understanding how microbial communities are assembled and how the presence or absence of species is related to that of others are central goals of microbial ecology. Here, we investigate co-occurrence associations between marine prokaryotes by combining 180 new and publicly available metagenomic datasets from different oceans in a large-scale meta-analysis. A co-occurrence network was created by calculating correlation scores between the abundances of microorganisms in metagenomes. A total of 1,906 correlations amongst 297 organisms were detected, segregating them into 11 major groups that occupy distinct ecological niches. Additionally, by analyzing the oceanographic parameters measured for a selected number of sampling sites, we characterized the influence of environmental variables over each of these 11 groups. Clustering organisms into groups of taxa that have similar ecology, allowed the detection of several significant correlations that could not be observed for the taxa individually.
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Affiliation(s)
- Felipe H Coutinho
- Universidade Federal do Rio de Janeiro (UFRJ)/Instituto de Biologia (IB) , Rio de Janeiro , Brazil ; Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI) , Nijmegen , The Netherlands
| | - Pedro M Meirelles
- Universidade Federal do Rio de Janeiro (UFRJ)/Instituto de Biologia (IB) , Rio de Janeiro , Brazil
| | - Ana Paula B Moreira
- Universidade Federal do Rio de Janeiro (UFRJ)/Instituto de Biologia (IB) , Rio de Janeiro , Brazil
| | - Rodolfo P Paranhos
- Universidade Federal do Rio de Janeiro (UFRJ)/Instituto de Biologia (IB) , Rio de Janeiro , Brazil
| | - Bas E Dutilh
- Universidade Federal do Rio de Janeiro (UFRJ)/Instituto de Biologia (IB) , Rio de Janeiro , Brazil ; Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Centre for Molecular and Biomolecular Informatics (CMBI) , Nijmegen , The Netherlands ; University of Utrecht (UU), Theoretical Biology and Bioinformatics , Utrecht , The Netherlands
| | - Fabiano L Thompson
- Universidade Federal do Rio de Janeiro (UFRJ)/Instituto de Biologia (IB) , Rio de Janeiro , Brazil ; Universidade Federal do Rio de Janeiro (UFRJ)/COPPE, SAGE , Rio de Janeiro , Brazil
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274
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Abstract
Rapid genetic exchange leads to mosaic genomes in cyanobacterial populations
[Also see Report by
Rosen
et al.
]
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Affiliation(s)
- Michael M. Desai
- Departments of Organismic and Evolutionary Biology and of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Aleksandra M. Walczak
- CNRS, Laboratoire de Physique Theorique, Ecole Normale Superieure, 75 231 Paris Cedex 05, France
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275
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Roux S, Enault F, Hurwitz BL, Sullivan MB. VirSorter: mining viral signal from microbial genomic data. PeerJ 2015; 3:e985. [PMID: 26038737 PMCID: PMC4451026 DOI: 10.7717/peerj.985] [Citation(s) in RCA: 681] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/08/2015] [Indexed: 01/01/2023] Open
Abstract
Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome), new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs) of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter’s prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages). Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs) as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision) on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in “reverse” to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made available through the iPlant Cyberinfrastructure that provides a web-based user interface interconnected with the required computing resources. VirSorter thus complements existing prophage prediction softwares to better leverage fragmented, SAG and metagenomic datasets in a way that will scale to modern sequencing. Given these features, VirSorter should enable the discovery of new viruses in microbial datasets, and further our understanding of uncultivated viral communities across diverse ecosystems.
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Affiliation(s)
- Simon Roux
- Ecology and Evolutionary Biology, University of Arizona , USA
| | - Francois Enault
- Clermont Université, Université Blaise Pascal, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand , France ; CNRS UMR 6023, LMGE , Aubière , France
| | - Bonnie L Hurwitz
- Department of Agricultural and Biosystems Engineering, University of Arizona , USA
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276
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Irwin AJ, Finkel ZV, Müller-Karger FE, Troccoli Ghinaglia L. Phytoplankton adapt to changing ocean environments. Proc Natl Acad Sci U S A 2015; 112:5762-6. [PMID: 25902497 PMCID: PMC4426419 DOI: 10.1073/pnas.1414752112] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Model projections indicate that climate change may dramatically restructure phytoplankton communities, with cascading consequences for marine food webs. It is currently not known whether evolutionary change is likely to be able to keep pace with the rate of climate change. For simplicity, and in the absence of evidence to the contrary, most model projections assume species have fixed environmental preferences and will not adapt to changing environmental conditions on the century scale. Using 15 y of observations from Station CARIACO (Carbon Retention in a Colored Ocean), we show that most of the dominant species from a marine phytoplankton community were able to adapt their realized niches to track average increases in water temperature and irradiance, but the majority of species exhibited a fixed niche for nitrate. We do not know the extent of this adaptive capacity, so we cannot conclude that phytoplankton will be able to adapt to the changes anticipated over the next century, but community ecosystem models can no longer assume that phytoplankton cannot adapt.
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Affiliation(s)
- Andrew J Irwin
- Department of Mathematics and Computer Science, Mount Allison University, Sackville, NB, Canada E4L 1E6;
| | - Zoe V Finkel
- Environmental Science Program, Mount Allison University, Sackville, NB, Canada E4L 1A7
| | - Frank E Müller-Karger
- Institute for Marine Remote Sensing/IMaRS, College of Marine Science, University of South Florida, St. Petersburg, FL 33701; and
| | - Luis Troccoli Ghinaglia
- Escuela de Ciencias Aplicadas del Mar, Universidad de Oriente, Boca de Río, Isla de Margarita, Venezuela
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277
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Unraveling interactions in microbial communities - from co-cultures to microbiomes. J Microbiol 2015; 53:295-305. [PMID: 25935300 DOI: 10.1007/s12275-015-5060-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/02/2014] [Accepted: 04/09/2014] [Indexed: 12/15/2022]
Abstract
Microorganisms do not exist in isolation in the environment. Instead, they form complex communities among themselves as well as with their hosts. Different forms of interactions not only shape the composition of these communities but also define how these communities are established and maintained. The kinds of interaction a bacterium can employ are largely encoded in its genome. This allows us to deploy a genomescale modeling approach to understand, and ultimately predict, the complex and intertwined relationships in which microorganisms engage. So far, most studies on microbial communities have been focused on synthetic co-cultures and simple communities. However, recent advances in molecular and computational biology now enable bottom up methods to be deployed for complex microbial communities from the environment to provide insight into the intricate and dynamic interactions in which microorganisms are engaged. These methods will be applicable for a wide range of microbial communities involved in industrial processes, as well as understanding, preserving and reconditioning natural microbial communities present in soil, water, and the human microbiome.
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278
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Berube PM, Biller SJ, Kent AG, Berta-Thompson JW, Roggensack SE, Roache-Johnson KH, Ackerman M, Moore LR, Meisel JD, Sher D, Thompson LR, Campbell L, Martiny AC, Chisholm SW. Physiology and evolution of nitrate acquisition in Prochlorococcus. THE ISME JOURNAL 2015; 9:1195-207. [PMID: 25350156 PMCID: PMC4409163 DOI: 10.1038/ismej.2014.211] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 09/08/2014] [Accepted: 09/23/2014] [Indexed: 01/01/2023]
Abstract
Prochlorococcus is the numerically dominant phototroph in the oligotrophic subtropical ocean and carries out a significant fraction of marine primary productivity. Although field studies have provided evidence for nitrate uptake by Prochlorococcus, little is known about this trait because axenic cultures capable of growth on nitrate have not been available. Additionally, all previously sequenced genomes lacked the genes necessary for nitrate assimilation. Here we introduce three Prochlorococcus strains capable of growth on nitrate and analyze their physiology and genome architecture. We show that the growth of high-light (HL) adapted strains on nitrate is ∼17% slower than their growth on ammonium. By analyzing 41 Prochlorococcus genomes, we find that genes for nitrate assimilation have been gained multiple times during the evolution of this group, and can be found in at least three lineages. In low-light adapted strains, nitrate assimilation genes are located in the same genomic context as in marine Synechococcus. These genes are located elsewhere in HL adapted strains and may often exist as a stable genetic acquisition as suggested by the striking degree of similarity in the order, phylogeny and location of these genes in one HL adapted strain and a consensus assembly of environmental Prochlorococcus metagenome sequences. In another HL adapted strain, nitrate utilization genes may have been independently acquired as indicated by adjacent phage mobility elements; these genes are also duplicated with each copy detected in separate genomic islands. These results provide direct evidence for nitrate utilization by Prochlorococcus and illuminate the complex evolutionary history of this trait.
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Affiliation(s)
- Paul M Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven J Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alyssa G Kent
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | - Jessie W Berta-Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sara E Roggensack
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kathryn H Roache-Johnson
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
- Department of Biological Sciences, University of Southern Maine, Portland, ME, USA
| | - Marcia Ackerman
- Department of Biological Sciences, University of Southern Maine, Portland, ME, USA
| | - Lisa R Moore
- Department of Biological Sciences, University of Southern Maine, Portland, ME, USA
| | - Joshua D Meisel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel Sher
- Department of Marine Biology, University of Haifa, Haifa, Israel
| | - Luke R Thompson
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA
| | - Lisa Campbell
- Department of Oceanography, Texas A&M University, College Station, TX, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, Irvine, CA, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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279
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Massey SE. Genetic code evolution reveals the neutral emergence of mutational robustness, and information as an evolutionary constraint. Life (Basel) 2015; 5:1301-32. [PMID: 25919033 PMCID: PMC4500140 DOI: 10.3390/life5021301] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/02/2015] [Accepted: 04/03/2015] [Indexed: 01/09/2023] Open
Abstract
The standard genetic code (SGC) is central to molecular biology and its origin and evolution is a fundamental problem in evolutionary biology, the elucidation of which promises to reveal much about the origins of life. In addition, we propose that study of its origin can also reveal some fundamental and generalizable insights into mechanisms of molecular evolution, utilizing concepts from complexity theory. The first is that beneficial traits may arise by non-adaptive processes, via a process of "neutral emergence". The structure of the SGC is optimized for the property of error minimization, which reduces the deleterious impact of point mutations. Via simulation, it can be shown that genetic codes with error minimization superior to the SGC can emerge in a neutral fashion simply by a process of genetic code expansion via tRNA and aminoacyl-tRNA synthetase duplication, whereby similar amino acids are added to codons related to that of the parent amino acid. This process of neutral emergence has implications beyond that of the genetic code, as it suggests that not all beneficial traits have arisen by the direct action of natural selection; we term these "pseudaptations", and discuss a range of potential examples. Secondly, consideration of genetic code deviations (codon reassignments) reveals that these are mostly associated with a reduction in proteome size. This code malleability implies the existence of a proteomic constraint on the genetic code, proportional to the size of the proteome (P), and that its reduction in size leads to an "unfreezing" of the codon - amino acid mapping that defines the genetic code, consistent with Crick's Frozen Accident theory. The concept of a proteomic constraint may be extended to propose a general informational constraint on genetic fidelity, which may be used to explain variously, differences in mutation rates in genomes with differing proteome sizes, differences in DNA repair capacity and genome GC content between organisms, a selective pressure in the evolution of sexual reproduction, and differences in translational fidelity. Lastly, the utility of the concept of an informational constraint to other diverse fields of research is explored.
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Affiliation(s)
- Steven E Massey
- Biology Department, PO Box 23360, University of Puerto Rico-Rio Piedras, San Juan, PR 00931, USA.
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280
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Zimmermann M, Escrig S, Hübschmann T, Kirf MK, Brand A, Inglis RF, Musat N, Müller S, Meibom A, Ackermann M, Schreiber F. Phenotypic heterogeneity in metabolic traits among single cells of a rare bacterial species in its natural environment quantified with a combination of flow cell sorting and NanoSIMS. Front Microbiol 2015; 6:243. [PMID: 25932020 PMCID: PMC4399338 DOI: 10.3389/fmicb.2015.00243] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/12/2015] [Indexed: 11/24/2022] Open
Abstract
Populations of genetically identical microorganisms residing in the same environment can display marked variability in their phenotypic traits; this phenomenon is termed phenotypic heterogeneity. The relevance of such heterogeneity in natural habitats is unknown, because phenotypic characterization of a sufficient number of single cells of the same species in complex microbial communities is technically difficult. We report a procedure that allows to measure phenotypic heterogeneity in bacterial populations from natural environments, and use it to analyze N2 and CO2 fixation of single cells of the green sulfur bacterium Chlorobium phaeobacteroides from the meromictic lake Lago di Cadagno. We incubated lake water with 15N2 and 13CO2 under in situ conditions with and without NH4+. Subsequently, we used flow cell sorting with auto-fluorescence gating based on a pure culture isolate to concentrate C. phaeobacteroides from its natural abundance of 0.2% to now 26.5% of total bacteria. C. phaeobacteroides cells were identified using catalyzed-reporter deposition fluorescence in situ hybridization (CARD-FISH) targeting the 16S rRNA in the sorted population with a species-specific probe. In a last step, we used nanometer-scale secondary ion mass spectrometry to measure the incorporation 15N and 13C stable isotopes in more than 252 cells. We found that C. phaeobacteroides fixes N2 in the absence of NH4+, but not in the presence of NH4+ as has previously been suggested. N2 and CO2 fixation were heterogeneous among cells and positively correlated indicating that N2 and CO2 fixation activity interact and positively facilitate each other in individual cells. However, because CARD-FISH identification cannot detect genetic variability among cells of the same species, we cannot exclude genetic variability as a source for phenotypic heterogeneity in this natural population. Our study demonstrates the technical feasibility of measuring phenotypic heterogeneity in a rare bacterial species in its natural habitat, thus opening the door to study the occurrence and relevance of phenotypic heterogeneity in nature.
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Affiliation(s)
- Matthias Zimmermann
- Department of Environmental Systems Sciences, ETH Zurich - Swiss Federal Institute of Technology Zurich, Switzerland ; Molecular Microbial Ecology Group, Department of Environmental Microbiology, Eawag - Swiss Federal Institute of Aquatic Science and Technology Zurich, Switzerland
| | - Stéphane Escrig
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Leipzig Germany
| | - Thomas Hübschmann
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Leipzig Germany
| | - Mathias K Kirf
- Department of Environmental Systems Sciences, ETH Zurich - Swiss Federal Institute of Technology Zurich, Switzerland ; Department of Surface Waters, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum Switzerland
| | - Andreas Brand
- Department of Environmental Systems Sciences, ETH Zurich - Swiss Federal Institute of Technology Zurich, Switzerland ; Department of Surface Waters, Eawag - Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum Switzerland
| | - R Fredrik Inglis
- Department of Environmental Systems Sciences, ETH Zurich - Swiss Federal Institute of Technology Zurich, Switzerland ; Molecular Microbial Ecology Group, Department of Environmental Microbiology, Eawag - Swiss Federal Institute of Aquatic Science and Technology Zurich, Switzerland
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz-Centre for Environmental Research, Leipzig Germany
| | - Susann Müller
- Department of Environmental Systems Sciences, ETH Zurich - Swiss Federal Institute of Technology Zurich, Switzerland
| | - Anders Meibom
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland ; Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne Switzerland
| | - Martin Ackermann
- Department of Environmental Systems Sciences, ETH Zurich - Swiss Federal Institute of Technology Zurich, Switzerland ; Molecular Microbial Ecology Group, Department of Environmental Microbiology, Eawag - Swiss Federal Institute of Aquatic Science and Technology Zurich, Switzerland
| | - Frank Schreiber
- Department of Environmental Systems Sciences, ETH Zurich - Swiss Federal Institute of Technology Zurich, Switzerland ; Molecular Microbial Ecology Group, Department of Environmental Microbiology, Eawag - Swiss Federal Institute of Aquatic Science and Technology Zurich, Switzerland
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281
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Takeuchi N, Cordero OX, Koonin EV, Kaneko K. Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection. BMC Biol 2015; 13:20. [PMID: 25928466 PMCID: PMC4410459 DOI: 10.1186/s12915-015-0131-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 03/13/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Fixation of beneficial genes in bacteria and archaea (collectively, prokaryotes) is often believed to erase pre-existing genomic diversity through the hitchhiking effect, a phenomenon known as genome-wide selective sweep. Recent studies, however, indicate that beneficial genes spread through a prokaryotic population via recombination without causing genome-wide selective sweeps. These gene-specific selective sweeps seem to be at odds with the existing estimates of recombination rates in prokaryotes, which appear far too low to explain such phenomena. RESULTS We use mathematical modeling to investigate potential solutions to this apparent paradox. Most microbes in nature evolve in heterogeneous, dynamic communities, in which ecological interactions can substantially impact evolution. Here, we focus on the effect of negative frequency-dependent selection (NFDS) such as caused by viral predation (kill-the-winner dynamics). The NFDS maintains multiple genotypes within a population, so that a gene beneficial to every individual would have to spread via recombination, hence a gene-specific selective sweep. However, gene loci affected by NFDS often are located in variable regions of microbial genomes that contain genes involved in the mobility of selfish genetic elements, such as integrases or transposases. Thus, the NFDS-affected loci are likely to experience elevated rates of recombination compared with the other loci. Consequently, these loci might be effectively unlinked from the rest of the genome, so that NFDS would be unable to prevent genome-wide selective sweeps. To address this problem, we analyzed population genetic models of selective sweeps in prokaryotes under NFDS. The results indicate that NFDS can cause gene-specific selective sweeps despite the effect of locally elevated recombination rates, provided NFDS affects more than one locus and the basal rate of recombination is sufficiently low. Although these conditions might seem to contradict the intuition that gene-specific selective sweeps require high recombination rates, they actually decrease the effective rate of recombination at loci affected by NFDS relative to the per-locus basal level, so that NFDS can cause gene-specific selective sweeps. CONCLUSION Because many free-living prokaryotes are likely to evolve under NFDS caused by ubiquitous viruses, gene-specific selective sweeps driven by NFDS are expected to be a major, general phenomenon in prokaryotic populations.
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Affiliation(s)
- Nobuto Takeuchi
- Department of Basic Science, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan.
| | - Otto X Cordero
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland.
| | - Eugene V Koonin
- National Institutes of Health, National Library of Medicine, National Center for Biotechnology Information, Bethesda, USA.
| | - Kunihiko Kaneko
- Department of Basic Science, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan.
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282
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Christie-Oleza JA, Armengaud J, Guerin P, Scanlan DJ. Functional distinctness in the exoproteomes of marine Synechococcus. Environ Microbiol 2015; 17:3781-94. [PMID: 25727668 PMCID: PMC4949707 DOI: 10.1111/1462-2920.12822] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 02/21/2015] [Indexed: 12/31/2022]
Abstract
The exported protein fraction of an organism may reflect its life strategy and, ultimately, the way it is perceived by the outside world. Bioinformatic prediction of the exported pan‐proteome of Prochlorococcus and Synechococcus lineages demonstrated that (i) this fraction of the encoded proteome had a much higher incidence of lineage‐specific proteins than the cytosolic fraction (57% and 73% homologue incidence respectively) and (ii) exported proteins are largely uncharacterized to date (54%) compared with proteins from the cytosolic fraction (35%). This suggests that the genomic and functional diversity of these organisms lies largely in the diverse pool of novel functions these organisms export to/through their membranes playing a key role in community diversification, e.g. for niche partitioning or evading predation. Experimental exoproteome analysis of marine Synechococcus showed transport systems for inorganic nutrients, an interesting array of strain‐specific exoproteins involved in mutualistic or hostile interactions (i.e. hemolysins, pilins, adhesins), and exoenzymes with a potential mixotrophic goal (i.e. exoproteases and chitinases). We also show how these organisms can remodel their exoproteome, i.e. by increasing the repertoire of interaction proteins when grown in the presence of a heterotroph or decrease exposure to prey when grown in the dark. Finally, our data indicate that heterotrophic bacteria can feed on the exoproteome of Synechococcus.
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Affiliation(s)
| | - Jean Armengaud
- CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory 'Technological Innovations for Detection and Diagnostic', Bagnols-sur-Cèze, F-30207, France
| | - Philippe Guerin
- CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory 'Technological Innovations for Detection and Diagnostic', Bagnols-sur-Cèze, F-30207, France
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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283
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Convergent evolution toward an improved growth rate and a reduced resistance range in Prochlorococcus strains resistant to phage. Proc Natl Acad Sci U S A 2015; 112:E2191-200. [PMID: 25922520 DOI: 10.1073/pnas.1420347112] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Prochlorococcus is an abundant marine cyanobacterium that grows rapidly in the environment and contributes significantly to global primary production. This cyanobacterium coexists with many cyanophages in the oceans, likely aided by resistance to numerous co-occurring phages. Spontaneous resistance occurs frequently in Prochlorococcus and is often accompanied by a pleiotropic fitness cost manifested as either a reduced growth rate or enhanced infection by other phages. Here, we assessed the fate of a number of phage-resistant Prochlorococcus strains, focusing on those with a high fitness cost. We found that phage-resistant strains continued evolving toward an improved growth rate and a narrower resistance range, resulting in lineages with phenotypes intermediate between those of ancestral susceptible wild-type and initial resistant substrains. Changes in growth rate and resistance range often occurred in independent events, leading to a decoupling of the selection pressures acting on these phenotypes. These changes were largely the result of additional, compensatory mutations in noncore genes located in genomic islands, although genetic reversions were also observed. Additionally, a mutator strain was identified. The similarity of the evolutionary pathway followed by multiple independent resistant cultures and clones suggests they undergo a predictable evolutionary pathway. This process serves to increase both genetic diversity and infection permutations in Prochlorococcus populations, further augmenting the complexity of the interaction network between Prochlorococcus and its phages in nature. Last, our findings provide an explanation for the apparent paradox of a multitude of resistant Prochlorococcus cells in nature that are growing close to their maximal intrinsic growth rates.
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284
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285
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Stepanauskas R. Wiretapping into microbial interactions by single cell genomics. Front Microbiol 2015; 6:258. [PMID: 25904902 PMCID: PMC4389542 DOI: 10.3389/fmicb.2015.00258] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/16/2015] [Indexed: 11/13/2022] Open
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286
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Mareš J, Lara Y, Dadáková I, Hauer T, Uher B, Wilmotte A, Kaštovský J. Phylogenetic analysis of cultivation-resistant terrestrial cyanobacteria with massive sheaths (Stigonema spp. and Petalonema alatum, Nostocales, Cyanobacteria) using single-cell and filament sequencing of environmental samples. JOURNAL OF PHYCOLOGY 2015; 51:288-297. [PMID: 26986524 DOI: 10.1111/jpy.12273] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 11/22/2014] [Indexed: 06/05/2023]
Abstract
Molecular assessment of a large portion of traditional cyanobacterial taxa has been hindered by the failure to isolate and grow them in culture. In this study, we developed an optimized protocol for single cell/filament isolation and 16S rRNA gene sequencing of terrestrial cyanobacteria with large mucilaginous sheaths, and applied it to determine the phylogenetic position of typical members of the genera Petalonema and Stigonema. A methodology based on a glass-capillary isolation technique and a semi-nested PCR protocol enabled reliable sequencing of the 16S rRNA gene from all samples analyzed. Ten samples covering seven species of Stigonema from Europe, North and Central America, and Hawaii, and the type species of Petalonema from Slovakia were sequenced. Contrary to some previous studies, which proposed a relationship with heteropolar nostocalean cyanobacteria, Petalonema appeared to belong to the family Scytonemataceae. Analysis of Stigonema specimens recovered a unique coherent phylogenetic cluster, substantially broadening our knowledge of the molecular diversity within this genus. Neither the uni- to biseriate species nor the multiseriate species formed monophyletic subclusters within the genus. Typical multiseriate species of Stigonema clustered in a phylogenetic branch derived from uni- to biseriate S. ocellatum Thuret ex Bornet & Flahault in our analysis, suggesting that species with more complex thalli may have evolved from the more simple ones. We propose the technique tested in this study as a promising tool for a future revision of the molecular taxonomy in cyanobacteria.
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Affiliation(s)
- Jan Mareš
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
- Centre for Phycology, Institute of Botany ASCR, v.v.i., Dukelská 135, Třeboň, CZ-379 82, Czech Republic
| | - Yannick Lara
- Center for Protein Engineering, University of Liège, Liège, 4000, Belgium
| | - Iva Dadáková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ-61137, Czech Republic
| | - Tomáš Hauer
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
- Centre for Phycology, Institute of Botany ASCR, v.v.i., Dukelská 135, Třeboň, CZ-379 82, Czech Republic
| | - Bohuslav Uher
- Department of Limnology and Bio-Oceanography, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, A-1090, Austria
| | - Annick Wilmotte
- Center for Protein Engineering, University of Liège, Liège, 4000, Belgium
| | - Jan Kaštovský
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
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287
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Luo H. The use of evolutionary approaches to understand single cell genomes. Front Microbiol 2015; 6:174. [PMID: 25806025 PMCID: PMC4354383 DOI: 10.3389/fmicb.2015.00191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/20/2015] [Indexed: 11/13/2022] Open
Abstract
The vast majority of environmental bacteria and archaea remain uncultivated, yet their genome sequences are rapidly becoming available through single cell sequencing technologies. Reconstructing metabolism is one common way to make use of genome sequences of ecologically important bacteria, but molecular evolutionary analysis is another approach that, while currently underused, can reveal important insights into the function of these uncultivated microbes in nature. Because genome sequences from single cells are often incomplete, metabolic reconstruction based on genome content can be compromised. However, this problem does not necessarily impede the use of phylogenomic and population genomic approaches that are based on patterns of polymorphisms and substitutions at nucleotide and amino acid sites. These approaches explore how various evolutionary forces act to assemble genetic diversity within and between lineages. In this mini-review, I present examples illustrating the benefits of analyzing single cell genomes using evolutionary approaches.
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Affiliation(s)
- Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong Hong Kong, China
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288
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Sudek S, Everroad RC, Gehman ALM, Smith JM, Poirier CL, Chavez FP, Worden AZ. Cyanobacterial distributions along a physico-chemical gradient in the Northeastern Pacific Ocean. Environ Microbiol 2015; 17:3692-707. [PMID: 25522910 DOI: 10.1111/1462-2920.12742] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 12/01/2014] [Accepted: 12/01/2014] [Indexed: 12/11/2022]
Abstract
The cyanobacteria Prochlorococcus and Synechococcus are important marine primary producers. We explored their distributions and covariance along a physico-chemical gradient from coastal to open ocean waters in the Northeastern Pacific Ocean. An inter-annual pattern was delineated in the dynamic transition zone where upwelled and eastern boundary current waters mix, and two new Synechococcus clades, Eastern Pacific Clade (EPC) 1 and EPC2, were identified. By applying state-of-the-art phylogenetic analysis tools to bar-coded 16S amplicon datasets, we observed higher abundance of Prochlorococcus high-light I (HLI) and low-light I (LLI) in years when more oligotrophic water intruded farther inshore, while under stronger upwelling Synechococcus I and IV dominated. However, contributions of some cyanobacterial clades were proportionally relatively constant, e.g. Synechococcus EPC2. In addition to supporting observations that Prochlorococcus LLI thrive at higher irradiances than other LL taxa, the results suggest LLI tolerate lower temperatures than previously reported. The phylogenetic precision of our 16S rRNA gene analytical approach and depth of bar-coded sequencing also facilitated detection of clades at low abundance in unexpected places. These include Prochlorococcus at the coast and Cyanobium-related sequences offshore, although it remains unclear whether these came from resident or potentially advected cells. Our study enhances understanding of cyanobacterial distributions in an ecologically important eastern boundary system.
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Affiliation(s)
- Sebastian Sudek
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - R Craig Everroad
- Exobiology Branch, NASA Ames Research Center, MS 239-4, Moffett Field, CA, 94035, USA
| | - Alyssa-Lois M Gehman
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Jason M Smith
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Camille L Poirier
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Francisco P Chavez
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA.,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, ON, M5G 1Z8, Canada
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289
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Voorhies AA, Eisenlord SD, Marcus DN, Duhaime MB, Biddanda BA, Cavalcoli JD, Dick GJ. Ecological and genetic interactions between cyanobacteria and viruses in a low-oxygen mat community inferred through metagenomics and metatranscriptomics. Environ Microbiol 2015; 18:358-71. [DOI: 10.1111/1462-2920.12756] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 12/15/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Alexander A. Voorhies
- Department of Earth and Environmental Sciences; University of Michigan; Ann Arbor MI 48109 USA
| | - Sarah D. Eisenlord
- School of Natural Resources and Environment; University of Michigan; Ann Arbor MI 48109 USA
| | - Daniel N. Marcus
- Department of Earth and Environmental Sciences; University of Michigan; Ann Arbor MI 48109 USA
| | - Melissa B. Duhaime
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI 48109 USA
| | - Bopaiah A. Biddanda
- Annis Water Resources Institute; Grand Valley State University; Muskegon MI 49441 USA
| | - James D. Cavalcoli
- Department of Computational Medicine and Bioinformatics; University of Michigan; Ann Arbor MI 48109 USA
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences; University of Michigan; Ann Arbor MI 48109 USA
- Department of Ecology and Evolutionary Biology; University of Michigan; Ann Arbor MI 48109 USA
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290
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Astorga-Eló M, Ramírez-Flandes S, DeLong EF, Ulloa O. Genomic potential for nitrogen assimilation in uncultivated members of Prochlorococcus from an anoxic marine zone. ISME JOURNAL 2015; 9:1264-7. [PMID: 25700337 PMCID: PMC4409168 DOI: 10.1038/ismej.2015.21] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 12/19/2014] [Accepted: 12/31/2014] [Indexed: 11/09/2022]
Abstract
Cyanobacteria of the genus Prochlorococcus are the most abundant photosynthetic marine organisms and key factors in the global carbon cycle. The understanding of their distribution and ecological importance in oligotrophic tropical and subtropical waters, and their differentiation into distinct ecotypes, is based on genetic and physiological information from several isolates. Currently, all available Prochlorococcus genomes show their incapacity for nitrate utilization. However, environmental sequence data suggest that some uncultivated lineages may have acquired this capacity. Here we report that uncultivated low-light-adapted Prochlorococcus from the nutrient-rich, low-light, anoxic marine zone (AMZ) of the eastern tropical South Pacific have the genetic potential for nitrate uptake and assimilation. All genes involved in this trait were found syntenic with those present in marine Synechococcus. Genomic and phylogenetic analyses also suggest that these genes have not been aquired recently, but perhaps were retained from a common ancestor, highlighting the basal characteristics of the AMZ lineages within Prochlorococcus.
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Affiliation(s)
- Marcia Astorga-Eló
- 1] Departamento de Oceanografía and Instituto Milenio de Oceanografía, Universidad de Concepción, Concepción, Chile [2] Programa de Magíster en Bioquímica y Bioinformática, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Salvador Ramírez-Flandes
- 1] Departamento de Oceanografía and Instituto Milenio de Oceanografía, Universidad de Concepción, Concepción, Chile [2] Programa de Doctorado en Ingeniería de Sistemas Complejos, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Edward F DeLong
- 1] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA [2] Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA [3] Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, USA
| | - Osvaldo Ulloa
- Departamento de Oceanografía and Instituto Milenio de Oceanografía, Universidad de Concepción, Concepción, Chile
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291
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Pierella Karlusich JJ, Ceccoli RD, Graña M, Romero H, Carrillo N. Environmental selection pressures related to iron utilization are involved in the loss of the flavodoxin gene from the plant genome. Genome Biol Evol 2015; 7:750-67. [PMID: 25688107 PMCID: PMC5322553 DOI: 10.1093/gbe/evv031] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Oxidative stress and iron limitation represent the grim side of life in an oxygen-rich atmosphere. The versatile electron transfer shuttle ferredoxin, an iron-sulfur protein, is particularly sensitive to these hardships, and its downregulation under adverse conditions severely compromises survival of phototrophs. Replacement of ferredoxin by a stress-resistant isofunctional carrier, flavin-containing flavodoxin, is a widespread strategy employed by photosynthetic microorganisms to overcome environmental adversities. The flavodoxin gene was lost in the course of plant evolution, but its reintroduction in transgenic plants confers increased tolerance to environmental stress and iron starvation, raising the question as to why a genetic asset with obvious adaptive value was not kept by natural selection. Phylogenetic analyses reveal that the evolutionary history of flavodoxin is intricate, with several horizontal gene transfer events between distant organisms, including Eukarya, Bacteria, and Archaea. The flavodoxin gene is unevenly distributed in most algal lineages, with flavodoxin-containing species being overrepresented in iron-limited regions and scarce or absent in iron-rich environments. Evaluation of cyanobacterial genomic and metagenomic data yielded essentially the same results, indicating that there was little selection pressure to retain flavodoxin in iron-rich coastal/freshwater phototrophs. Our results show a highly dynamic evolution pattern of flavodoxin tightly connected to the bioavailability of iron. Evidence presented here also indicates that the high concentration of iron in coastal and freshwater habitats may have facilitated the loss of flavodoxin in the freshwater ancestor of modern plants during the transition of photosynthetic organisms from the open oceans to the firm land.
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Affiliation(s)
- Juan J Pierella Karlusich
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina
| | - Romina D Ceccoli
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina Present address: Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario; CONICET, Rosario, Argentina
| | - Martín Graña
- Unidad de Bioinformática, Institut Pasteur Montevideo, Uruguay
| | - Héctor Romero
- Departamento de Ecología y Evolución, Facultad de Ciencias/CURE, Universidad de la República, Montevideo, Uruguay
| | - Néstor Carrillo
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET-Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina
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292
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Abstract
Recent advances in studying the dynamics of marine microbial communities have shown that the composition of these communities follows predictable patterns and involves complex network interactions, which shed light on the underlying processes regulating these globally important organisms. Such 'holistic' (or organism- and system-based) studies of these communities complement popular reductionist, often culture-based, approaches for understanding organism function one gene or protein at a time. In this Review, we summarize our current understanding of marine microbial community dynamics at various scales, from hours to decades. We also explain how the data illustrate community resilience and seasonality, and reveal interactions among microorganisms.
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293
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Stepanauskas R. Re-defining microbial diversity from its single-celled building blocks. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:36-37. [PMID: 25721601 PMCID: PMC4374662 DOI: 10.1111/1758-2229.12226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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294
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Bhattacharya D, Qiu H, Price DC, Yoon HS. Why we need more algal genomes. JOURNAL OF PHYCOLOGY 2015; 51:1-5. [PMID: 26986254 DOI: 10.1111/jpy.12267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/10/2014] [Indexed: 06/05/2023]
Affiliation(s)
- Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources and Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, 08901, USA
| | - Huan Qiu
- Department of Ecology, Evolution and Natural Resources and Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, 08901, USA
| | - Dana C Price
- Department of Ecology, Evolution and Natural Resources and Institute of Marine and Coastal Science, Rutgers University, New Brunswick, New Jersey, 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 440-746, Korea
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295
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Clingenpeel S, Clum A, Schwientek P, Rinke C, Woyke T. Reconstructing each cell's genome within complex microbial communities-dream or reality? Front Microbiol 2015; 5:771. [PMID: 25620966 PMCID: PMC4287102 DOI: 10.3389/fmicb.2014.00771] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/17/2014] [Indexed: 11/24/2022] Open
Abstract
As the vast majority of microorganisms have yet to be cultivated in a laboratory setting, access to their genetic makeup has largely been limited to cultivation-independent methods. These methods, namely metagenomics and more recently single-cell genomics, have become cornerstones for microbial ecology and environmental microbiology. One ultimate goal is the recovery of genome sequences from each cell within an environment to move toward a better understanding of community metabolic potential and to provide substrate for experimental work. As single-cell sequencing has the ability to decipher all sequence information contained in an individual cell, this method holds great promise in tackling such challenge. Methodological limitations and inherent biases however do exist, which will be discussed here based on environmental and benchmark data, to assess how far we are from reaching this goal.
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Affiliation(s)
| | - Alicia Clum
- DOE Joint Genome Institute Walnut Creek, CA, USA
| | | | | | - Tanja Woyke
- DOE Joint Genome Institute Walnut Creek, CA, USA
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296
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Kirkup BC. Bacterial Strain Diversity Within Wounds. Adv Wound Care (New Rochelle) 2015; 4:12-23. [PMID: 25566411 DOI: 10.1089/wound.2014.0560] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 06/23/2014] [Indexed: 12/17/2022] Open
Abstract
Significance: Rare bacterial taxa (taxa of low relative frequency) are numerous and ubiquitous in virtually any sample-including wound samples. In addition, even the high-frequency genera and species contain multiple strains. These strains, individually, are each only a small fraction of the total bacterial population. Against the view that wounds contain relatively few kinds of bacteria, this newly recognized diversity implies a relatively high rate of migration into the wound and the potential for diversification during infection. Understanding the biological and medical importance of these numerous taxa is an important new element of wound microbiology. Recent Advances: Only recently have these numerous strains been discovered; the technology to detect, identify, and characterize them is still in its infancy. Multiple strains of both gram-negative and gram-positive bacteria have been found in a single wound. In the few cases studied, the distribution of the bacteria suggests microhabitats and biological interactions. Critical Issues: The distribution of the strains, their phenotypic diversity, and their interactions are still largely uncharacterized. The technologies to investigate this level of genomic detail are still developing and have not been largely deployed to investigate wounds. Future Directions: As advanced metagenomics, single-cell genomics, and advanced microscopy develop, the study of wound microbiology will better address the complex interplay of numerous individually rare strains with both the host and each other.
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Affiliation(s)
- Benjamin C. Kirkup
- FE Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
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297
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Abstract
The biodiversity of phytoplankton is a core measurement of the state and activity of marine ecosystems. In the context of historical approaches, we review recent major advances in the technologies that have enabled deeper characterization of the biodiversity of phytoplankton. In particular, high-throughput sequencing of single loci/genes, genomes, and communities (metagenomics) has revealed exceptional phylogenetic and genomic diversity whose breadth is not fully constrained. Other molecular tools-such as fingerprinting, quantitative polymerase chain reaction, and fluorescence in situ hybridization-have provided additional insight into the dynamics of this diversity in the context of environmental variability. Techniques for characterizing the functional diversity of community structure through targeted or untargeted approaches based on RNA or protein have also greatly advanced. A wide range of techniques is now available for characterizing phytoplankton communities, and these tools will continue to advance through ongoing improvements in both technology and data interpretation.
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Affiliation(s)
- Zackary I Johnson
- Marine Laboratory (Nicholas School of the Environment) and Department of Biology, Duke University, Beaufort, North Carolina 28516;
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298
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Martin-Cuadrado AB, Garcia-Heredia I, Moltó AG, López-Úbeda R, Kimes N, López-García P, Moreira D, Rodriguez-Valera F. A new class of marine Euryarchaeota group II from the Mediterranean deep chlorophyll maximum. ISME JOURNAL 2014; 9:1619-34. [PMID: 25535935 DOI: 10.1038/ismej.2014.249] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 11/14/2014] [Accepted: 11/19/2014] [Indexed: 11/09/2022]
Abstract
We have analyzed metagenomic fosmid clones from the deep chlorophyll maximum (DCM), which, by genomic parameters, correspond to the 16S ribosomal RNA (rRNA)-defined marine Euryarchaeota group IIB (MGIIB). The fosmid collections associated with this group add up to 4 Mb and correspond to at least two species within this group. From the proposed essential genes contained in the collections, we infer that large sections of the conserved regions of the genomes of these microbes have been recovered. The genomes indicate a photoheterotrophic lifestyle, similar to that of the available genome of MGIIA (assembled from an estuarine metagenome in Puget Sound, Washington Pacific coast), with a proton-pumping rhodopsin of the same kind. Several genomic features support an aerobic metabolism with diversified substrate degradation capabilities that include xenobiotics and agar. On the other hand, these MGIIB representatives are non-motile and possess similar genome size to the MGIIA-assembled genome, but with a lower GC content. The large phylogenomic gap with other known archaea indicates that this is a new class of marine Euryarchaeota for which we suggest the name Thalassoarchaea. The analysis of recruitment from available metagenomes indicates that the representatives of group IIB described here are largely found at the DCM (ca. 50 m deep), in which they are abundant (up to 0.5% of the reads), and at the surface mostly during the winter mixing, which explains formerly described 16S rRNA distribution patterns. Their uneven representation in environmental samples that are close in space and time might indicate sporadic blooms.
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Affiliation(s)
- Ana-Belen Martin-Cuadrado
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Inmaculada Garcia-Heredia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Aitor Gonzaga Moltó
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Rebeca López-Úbeda
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Nikole Kimes
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Purificación López-García
- Unité d'Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Orsay Cedex, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Orsay Cedex, France
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
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299
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Microbial taxonomy in the post-genomic era: rebuilding from scratch? Arch Microbiol 2014; 197:359-70. [PMID: 25533848 DOI: 10.1007/s00203-014-1071-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 12/20/2022]
Abstract
Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. Its cornerstone, the prokaryote species has been re-evaluated twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. Ultimately, we will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.
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