Biller, Et Al., 2014. “Prochlorococcus: the Structure and Function Of

Total Page:16

File Type:pdf, Size:1020Kb

Biller, Et Al., 2014. “Prochlorococcus: the Structure and Function Of Nature Reviews Microbiology | AOP, published online 1 December 2014; doi:10.1038/nrmicro3378 REVIEWS Prochlorococcus: the structure and function of collective diversity Steven J. Biller1, Paul M. Berube1, Debbie Lindell2 and Sallie W. Chisholm1,3 Abstract | The marine cyanobacterium Prochlorococcus is the smallest and most abundant photosynthetic organism on Earth. In this Review, we summarize our understanding of the diversity of this remarkable phototroph and describe its role in ocean ecosystems. We discuss the importance of interactions of Prochlorococcus with the physical environment, with phages and with heterotrophs in shaping the ecology and evolution of this group. In light of recent studies, we have come to view Prochlorococcus as a ‘federation’ of diverse cells that sustains its broad distribution, stability and abundance in the oceans via extensive genomic and phenotypic diversity. Thus, it is proving to be a useful model system for elucidating the forces that shape microbial populations and ecosystems. 1 Phytoplankton Since the discovery of Prochlorococcus in 1985 , con- constrained and less variable than many other microbial Free-floating aquatic siderable progress has been made in understanding the habitats (such as the soil), and exhibits gradual changes photosynthetic microorganisms characteristics that make this bacterium unique in the on monthly to annual timescales. that require sunlight and microbial world. It is the smallest (the cell diameter is From the perspective of its microbial inhabitants, the inorganic nutrients for growth 0.5–0.7 μm)2 and most abundant photosynthetic organ- oligotrophic ocean is an extremely dilute environment Euphotic zone ism on the planet, with an estimated global population of in terms of both its chemistry and biology (FIG. 1a). For The sunlit upper region of the ~1027 cells3–5. Prochlorococcus has the smallest genome of example, the average Prochlorococcus bacterium may ocean water column that any free-living phototroph6; some isolates have genomes be hundreds of cell diameters away from another cell receives sufficient light energy as small as 1.65 Mbp, with only ~1,700 genes7. It is the of any type, and even a few cell diameters away from to sustain photosynthesis. The phytoplankton depth can vary depending on only type of marine that uses the divinyl essential nutrients, which are found at picomolar to local conditions, but it is form of chlorophyll a and chlorophyll b to harvest light nanomolar concentrations. By contrast, well-studied generally the upper ~200 m energy8, which causes a slight red shift in its absorption model microorganisms, such as Escherichia coli, tend to in oligotrophic waters. spectra2,9. This unique pigmentation has made it possi- reside in relatively nutrient-rich and densely populated ble to determine that Prochlorococcus accounts for 50% environments, such as the gut. Studies have shown that, of the total chlorophyll in vast stretches of the surface to overcome the challenges associated with their dilute 10,11 1Department of Civil and oceans . Collectively, this cyanobacterium produces environment, some marine microorganisms attach to 3 20 Environmental Engineering, an estimated 4 gigatons of fixed carbon each year , which particles or form close associations with other bac- Massachusetts Institute of is approximately the same net primary productivity as teria21. Although microscale patchiness of some form Technology, Cambridge, global croplands12. may contribute to the survival of Prochlorococcus, direct Massachusetts 02139, USA. Prochlorococcus thrives throughout the euphotic zone evidence to support or reject this hypothesis is lacking. 2Faculty of Biology, oligotrophic 1,13 Technion – Israel Institute of of the tropical and subtropical ocean . Nevertheless, the dilute nature of oligotrophic ecosys- Technology, Haifa 32000, The daily light–dark cycle synchronizes cell division in tems clearly imposes a unique set of selective pressures Israel. Prochlorococcus14 and is an important driver of highly on microbial life. 3Department of Biology, choreographed gene expression patterns throughout Prochlorococcus has several traits that make it well- Massachusetts Institute of 15–19 Technology, Cambridge, the day . The euphotic zone is shaped by continuous suited to this dilute habitat. Compared with other phyto- Massachusetts 02139, USA. macroscale gradients of light, temperature and nutrients plankton, Prochlorococcus has a low phosphorus require- Correspondence to S.J.B., (FIG. 1); both light intensity and temperature are highest ment (it has high C/P and N/P ratios)22–24, partly owing S.W.C. at the surface and decrease with depth, whereas nutri- to its relatively small genome22 and the substitution of e-mails: [email protected]; ent levels are typically low at the surface and gradually sulpholipids for phospholipids in the cell membrane25. Its [email protected] doi:10.1038/nrmicro3378 increase with depth. Although there is fine-scale varia- small size results in a high surface-to-volume ratio that Published online tion within the water column, the physical and chemi- facilitates efficient nutrient acquisition and enhances 1 December 2014 cal environment of the ocean as a whole tends to be light absorption, which, when combined with its unique NATURE REVIEWS | MICROBIOLOGY ADVANCE ONLINE PUBLICATION | 1 © 2014 Macmillan Publishers Limited. All rights reserved REVIEWS a Upper Phage mixed Wind-driven Vesicle Diatom layer mixing Light absorbed 40 cell lengths 447 nm Fe 673 nm 2 cell lengthsPO 3– 4 cell lengths 4 Co <1 cell length Zooplankton 200 m + NH4 Prochlorococcus 200 cell lengths Light Temperature Nutrients 100 cell lengths Heterotroph (such as SAR11) Low High b Culture c Field 1.0 0 HL HL 0.8 50 0.6 Light 100 LL 0.4 Depth (m) LL Growth rate (μ) rate Growth 150 0.2 0 200 100 101 102 103 Low High 3 4 5 6 7 8 9 Light intensity (μmol photon per m2 per s) Light intensity Abundance (log cells per L) d Culture e Field 60 HLII 0.6 40 0.5 HLII 20 0.4 0 HLI 0.3 N latitude HLI -20 Growth rate (μ) rate Growth 0.2 -40 0.1 -60 10 15 20 25 30 80 60 40 20 0 10 25 3 5 7 Temperature (°C) W longitude Surface Abundance temperature (log cells per mm2) (°C) Nature Reviews | Microbiology pigmentation9, make it the most efficient light absorber of deep waters grow optimally at substantially lower light any photosynthetic cell; Prochloroccocus is the only phyto­ intensities (termed low-light (LL)-adapted ecotypes) plankton known to absorb more light than it scatters2. than those isolated from the surface (termed high- Oligotrophic Thus, Prochlorococcus can thrive at lower light intensi- light (HL)-adapted ecotypes) (FIG. 1b), which results in A term used to describe an 9 28–30 environment with low ties than those required by most other phytoplankton niche-partitioning in the water column : HL‑adapted concentrations of available and its populations extend deeper in the water column cells are orders of magnitude more abundant in surface nutrients. than almost any other phototroph26, essentially defining waters31–33 but are outnumbered by LL‑adapted cells the lower boundary of photosynthetic life in the oceans. at the base of the euphotic zone (FIG. 1c). Despite the Ecotypes The ability of Prochlorococcus to occupy the entire complexity of ocean dynamics, these distinct groups of Genetically and physiologically differentiated subgroups of a euphotic zone can be largely explained by its micro­ Prochlorococcus shift in relative abundance in reproduc- 34,35 species that occupy a distinct diversity, as different subgroups are adapted to differ- ible annual cycles , which demonstrates the remark- ecological niche. ent light optima for growth9,27. Strains isolated from able robustness of Prochlorococcus populations. The 2 | ADVANCE ONLINE PUBLICATION www.nature.com/reviews/micro © 2014 Macmillan Publishers Limited. All rights reserved REVIEWS ◀ Figure 1 | The Prochlorococcus habitat. a | Prochlorococcus inhabits the entire Although the initial partitioning of Prochlorococ­ euphotic zone, which is characterized by gradients of light, temperature and nutrients. cus into the broad categories of HL- and LL‑adapted The ocean water column is divided into an upper ‘mixed’ layer (where wind and strains was based solely on phenotype9,27,46, molecular heat-driven turbulence homogenizes the distribution of nutrients and cells) and the phylogenetic analyses have shown that this division is stratified and less turbulent deeper waters, where gradients in nutrients form as a result consistent with the earliest phylogenetic split within the of biogeochemical activity. Light levels decrease exponentially with depth; gradients of 31,37,38,40 temperature and nutrient concentrations are largely similar in the mixed layer, whereas Prochlorococcus lineage . HL‑adapted Prochlo­ temperature decreases, and nutrient concentrations increase, with depth. The rococcus strains form a coherent, monophyletic group oligotrophic ocean represents an extremely dilute environment in terms of organisms that resolves into at least six clades (HLI–HLVI)9,27,31,46, and nutrients. Some key players in oligotrophic marine communities are shown, along whereas the LL‑adapted strains are polyphyletic and par- with the distances between them as estimated from their average concentrations. tition into at least six clades (LLI–LLVII)36,47,48 (FIG. 2a). According to these metrics, each Prochlorococcus bacterium is hundreds of cell Although alternative nomenclature has been proposed, diameters away from other members of its
Recommended publications
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • Strong Purifying Selection Contributes to Genome Streamlining in Epipelagic Marinimicrobia
    bioRxiv preprint doi: https://doi.org/10.1101/653261; this version posted May 30, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Strong Purifying Selection Contributes to Genome Streamlining in Epipelagic Marinimicrobia Carolina Alejandra Martinez-Gutierrez and Frank O. Aylward Department of Biological Sciences, Virginia Tech, Blacksburg, VA Email for correspondence: [email protected] Abstract Marine microorganisms inhabiting nutrient-depleted waters play critical roles in global biogeochemical cycles due to their abundance and broad distribution. Many of these microbes share similar genomic features including small genome size, low % G+C content, short intergenic regions, and low nitrogen content in encoded amino acids, but the evolutionary drivers of these characteristics are unclear. Here we compared the strength of purifying selection across the Marinimicrobia, a candidate phylum which encompasses a broad range of phylogenetic groups with disparate genomic features, by estimating the ratio of non-synonymous and synonymous substitutions (dN/dS) in conserved marker genes. Our analysis shows significantly lower dN/dS values in epipelagic Marinimicrobia that exhibit features consistent with genome streamlining when compared to their mesopelagic counterparts. We found a significant positive correlation between median dN/dS values and genomic traits associated to streamlined organisms, including % G+C content, genome size, and intergenic region length. Our findings are consistent with genome streamlining theory, which postulates that small, compact genomes with low G+C contents are adaptive and the product of strong purifying selection.
    [Show full text]
  • Consistent Responses of Soil Microbial Communities to Elevated Nutrient Inputs in Grasslands Across the Globe
    Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe Jonathan W. Leffa,b, Stuart E. Jonesc, Suzanne M. Proberd, Albert Barberána, Elizabeth T. Borere, Jennifer L. Firnf, W. Stanley Harpoleg,h,i, Sarah E. Hobbiee, Kirsten S. Hofmockelj, Johannes M. H. Knopsk, Rebecca L. McCulleyl, Kimberly La Pierrem, Anita C. Rischn, Eric W. Seabloomo, Martin Schützn, Christopher Steenbockb, Carly J. Stevensp, and Noah Fierera,b,1 aCooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309; bDepartment of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309; cDepartment of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556; dCommonwealth Scientific and Industrial Research Organisation Land and Water Flagship, Wembley, WA 6913, Australia; eDepartment of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108; fSchool of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, QLD 4001, Australia; gDepartment of Physiological Diversity, Helmholtz Center for Environmental Research UFZ, 04318 Leipzig, Germany; hGerman Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, D-04103 Leipzig, Germany; iInstitute of Biology, Martin Luther University Halle-Wittenberg, 06108 Halle (Saale), Germany; jEcology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50011; kSchool of Biological Sciences, University of Nebraska, Lincoln, NE 68588; lDepartment of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546; mDepartment of Integrative Biology, University of California, Berkeley, CA 94720; nCommunity Ecology, Swiss Federal Institute for Forest, Snow and Landscape Research, 8903 Birmensdorf, Switzerland; oDepartment of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108; and pLancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, United Kingdom Edited by Peter M.
    [Show full text]
  • Biogeographic Variations of Picophytoplankton in Three Contrasting Seas: the Bay of Bengal, South China Sea and Western Pacific Ocean
    Vol. 84: 91–103, 2020 AQUATIC MICROBIAL ECOLOGY Published online April 9 https://doi.org/10.3354/ame01928 Aquat Microb Ecol OPENPEN ACCESSCCESS Biogeographic variations of picophytoplankton in three contrasting seas: the Bay of Bengal, South China Sea and Western Pacific Ocean Yuqiu Wei1, Danyue Huang1, Guicheng Zhang2,3, Yuying Zhao2,3, Jun Sun2,3,* 1Institute of Marine Science and Technology, Shandong University, 72 Binhai Road, Qingdao 266200, PR China 2Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, PR China 3Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin 300457, PR China ABSTRACT: Marine picophytoplankton are abundant in many oligotrophic oceans, but the known geographical patterns of picophytoplankton are primarily based on small-scale cruises or time- series observations. Here, we conducted a wider survey (5 cruises) in the Bay of Bengal (BOB), South China Sea (SCS) and Western Pacific Ocean (WPO) to better understand the biogeographic variations of picophytoplankton. Prochlorococcus (Pro) were the most abundant picophytoplank- ton (averaging [1.9−3.6] × 104 cells ml−1) across the 3 seas, while average abundances of Syne- chococcus (Syn) and picoeukaryotes (PEuks) were generally 1−2 orders of magnitude lower than Pro. Average abundances of total picophytoplankton were similar between the BOB and SCS (4.7 × 104 cells ml−1), but were close to 2-fold less abundant in the WPO (2.5 × 104 cells ml−1). Pro and Syn accounted for a substantial fraction of total picophytoplankton biomass (70−83%) in the 3 con- trasting seas, indicating the ecological importance of Pro and Syn as primary producers.
    [Show full text]
  • Sea Squirt Symbionts! Or What I Did on My Summer Vacation… Leah Blasiak 2011 Microbial Diversity Course
    Sea Squirt Symbionts! Or what I did on my summer vacation… Leah Blasiak 2011 Microbial Diversity Course Abstract Microbial symbionts of tunicates (sea squirts) have been recognized for their capacity to produce novel bioactive compounds. However, little is known about most tunicate-associated microbial communities, even in the embryology model organism Ciona intestinalis. In this project I explored 3 local tunicate species (Ciona intestinalis, Molgula manhattensis, and Didemnum vexillum) to identify potential symbiotic bacteria. Tunicate-specific bacterial communities were observed for all three species and their tissue specific location was determined by CARD-FISH. Introduction Tunicates and other marine invertebrates are prolific sources of novel natural products for drug discovery (reviewed in Blunt, 2010). Many of these compounds are biosynthesized by a microbial symbiont of the animal, rather than produced by the animal itself (Schmidt, 2010). For example, the anti-cancer drug patellamide, originally isolated from the colonial ascidian Lissoclinum patella, is now known to be produced by an obligate cyanobacterial symbiont, Prochloron didemni (Schmidt, 2005). Research on such microbial symbionts has focused on their potential for overcoming the “supply problem.” Chemical synthesis of natural products is often challenging and expensive, and isolation of sufficient quantities of drug for clinical trials from wild sources may be impossible or environmentally costly. Culture of the microbial symbiont or heterologous expression of the biosynthetic genes offers a relatively economical solution. Although the microbial origin of many tunicate compounds is now well established, relatively little is known about the extent of such symbiotic associations in tunicates and their biological function. Tunicates (or sea squirts) present an interesting system in which to study bacterial/eukaryotic symbiosis as they are deep-branching members of the Phylum Chordata (Passamaneck, 2005 and Buchsbaum, 1948).
    [Show full text]
  • A Genomic View of Trophic and Metabolic Diversity in Clade-Specific Lamellodysidea Sponge Microbiomes
    UC San Diego UC San Diego Previously Published Works Title A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes. Permalink https://escholarship.org/uc/item/6z2365ft Journal Microbiome, 8(1) ISSN 2049-2618 Authors Podell, Sheila Blanton, Jessica M Oliver, Aaron et al. Publication Date 2020-06-23 DOI 10.1186/s40168-020-00877-y Peer reviewed eScholarship.org Powered by the California Digital Library University of California Podell et al. Microbiome (2020) 8:97 https://doi.org/10.1186/s40168-020-00877-y RESEARCH Open Access A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes Sheila Podell1 , Jessica M. Blanton1, Aaron Oliver1, Michelle A. Schorn2, Vinayak Agarwal3, Jason S. Biggs4, Bradley S. Moore5,6,7 and Eric E. Allen1,5,7,8* Abstract Background: Marine sponges and their microbiomes contribute significantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponges obtain additional energy from abundant photosynthetic Hormoscilla cyanobacterial symbionts, which also produce polybrominated diphenyl ethers (PBDEs) chemically similar to anthropogenic pollutants of environmental concern. Potential contributions of non-Hormoscilla bacteria to Lamellodysidea microbiome metabolism and the synthesis and degradation of additional secondary metabolites are currently unknown. Results: This study has determined relative abundance, taxonomic novelty, metabolic
    [Show full text]
  • The Trophic-Dynamic Aspect of Ecology Author(S): Raymond L
    The Trophic-Dynamic Aspect of Ecology Author(s): Raymond L. Lindeman Reviewed work(s): Source: Ecology, Vol. 23, No. 4 (Oct., 1942), pp. 399-417 Published by: Ecological Society of America Stable URL: http://www.jstor.org/stable/1930126 . Accessed: 30/01/2012 10:50 Your use of the JSTOR archive indicates your acceptance of the Terms & Conditions of Use, available at . http://www.jstor.org/page/info/about/policies/terms.jsp JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact [email protected]. Ecological Society of America is collaborating with JSTOR to digitize, preserve and extend access to Ecology. http://www.jstor.org THE TROPHIC-DYNAMIC ASPECT OF ECOLOGY RAYMOND L. LINDEMAN OsbornZoological Laboratory,Yale University Recent progressin the studyof aquatic community. A more "bio-ecological" food-cycle relationships invites a re- species-distributionalapproach would appraisal of certain ecological tenets. recognize both the plants and animals Quantitative productivitydata provide as co-constituentsof restricted"biotic" a basis for enunciating certain trophic communities,such as "plankton com- principles, which, when applied to a munities," "benthic communities,"etc., series of successional stages, shed new in which membersof the living commu- light on the dynamics of ecological nity "co-act" with each other and "re- succession. act" with the non-livingenvironment (Clementsand Shelford,'39; Carpenter, "COMMUNITY" CONCEPTS '39, '40; T. Park, '41).
    [Show full text]
  • Directed Isolation of Prochlorococcus
    Directed isolation of Prochlorococcus Selected tools for the Prochlorococcus model system Berube PM*, Becker JW*, Biller SJ, Coe AC, Cubillos-Ruiz A, Ding H, Kelly L, Thompson JW, Chisholm SW Sampling within the euphotic * co-presenters Massachusetts Institute of Technology, Cambridge, MA zone of oligotrophic ocean regions • Depth specific targeting of Prochlorococcus ecotypes Isolation and characterization of vesicles from marine bacteria • Utilization of ecotype abundance data from time-series Density measurements when available 0.2 µm TFF Pellet by Obtain final gradient Tips for optimal vesicle preparations filter concentration ultracentrifugation sample purification Keep TFF feed pressure < 10 psi at all times Low-light adapted Prochlorococcus populations when concentrating samples. are underrepresented in culture collections Total Prochlorococcus (Flow Cytometry) Ecotype Counts / Flow Cytometry Counts Vesicle pellets are usually colorless, but don’t 0 6 0 6 5 4 worry, it’ll be there! 50 50 100 4 100 2 3 0 150 150 Depth [m] 2 Depth [m] -2 Resuspension of vesicles by gentle manual 200 log cells/mL 200 1 -4 Prochlorococcus Vesicle Other media components 250 250 pipetting works best; keep resuspension 0 -6 log2 ratio (ecotype/FCM) volumes to an absolute minimum. 100 W 90 W 80 W 70W 100 W 90 W 80 W 70W Pre-filtration of Tangential Flow Filtration (TFF) TEM of purified Prochlorococcus Culture Prochlorococcus vesicles Field samples require careful collection of Targeting of low-light adapted Prochlorococcus smaller density gradient fractions
    [Show full text]
  • Supplementary Information
    Supplementary Information A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes Sheila Podell, Jessica M. Blanton, Aaron Oliver, Michelle A. Schorn, Vinayak Agarwal, Jason S. Biggs, Bradley S. Moore, Eric E. Allen Contents Supplementary Figures S1-S13 ....................................................................................................... 2 Supplementary Tables S1-S8 ........................................................................................................ 16 References ..................................................................................................................................... 26 Supplementary Figure 1. Cyanobacteria MAGs classified taxonomically. A) PhyloPhlAn multi-locus concatenated tree [1], with Crinalium epipsammum as an outgroup. B) 16S rRNA gene/and average amino acid identity matrix with closest database relatives. Guidelines for assigning species, genus, family, and order-level taxonomic granularity were based on [2, 3] for AAI and [4] for 16S rRNA gene percent nucleotide identity. A B Pleurocapsa_PCC_7327 1 Stanieria_cyanosphaera 1 SP5CPC1 1 0.993 Prochloron_didemni_P3 1 Prochloron_didemni_P4 Gloeobacter_violaceus Stanieria_cyanosphaera SP5CPC Prochloron_didemni_P3 Prochloron_didemni_P4 Gloeobacter_violaceus Crinalium_epipsammum Desertifilum_IPPASB1220 GM7CHS1 GM202CHS1 GM102CHS1 SP12CHS1 SP5CHS1 Nostoc_punctiforme 92/65 89/61 89/61 89/61 88/51 90/63 91/62 90/60 90/60 -/60 89/60 90/60 88/63 Pleurocapsa_PCC_7327 Crinalium_epipsammum
    [Show full text]
  • 1 Strong Purifying Selection Is Associated with Genome
    1 Strong Purifying Selection is Associated with Genome Streamlining in Epipelagic Marinimicrobia Carolina Alejandra Martinez-Gutierrez and Frank O. Aylward Department of Biological Sciences, Virginia Tech, Blacksburg, VA Email for correspondence: [email protected] Abstract Marine microorganisms inhabiting nutrient-depleted waters play critical roles in global biogeochemical cycles due to their abundance and broad distribution. Many of these microbes share similar genomic features including small genome size, low % G+C content, short intergenic regions, and low nitrogen content in encoded amino acid residue side chains (N-ARSC), but the evolutionary drivers of these characteristics are unclear. Here we compared the strength of purifying selection across the Marinimicrobia, a candidate phylum which encompasses a broad range of phylogenetic groups with disparate genomic features, by estimating the ratio of non-synonymous and synonymous substitutions (dN/dS) in conserved marker genes. Our analysis reveals that epipelagic Marinimicrobia that exhibit features consistent with genome streamlining have significantly lower dN/dS values when compared to the mesopelagic counterparts. We also found a significant positive correlation between median dN/dS values and % G+C content, N-ARSC, and intergenic region length. We did not identify a significant correlation between dN/dS ratios and estimated genome size, suggesting the strength of selection is not a primary factor shaping genome size in this group. Our findings are generally consistent with genome streamlining theory, which postulates that many genomic features of abundant epipelagic bacteria are the result of adaptation to oligotrophic nutrient conditions. Our results are also in agreement with previous findings that genome streamlining is common in epipelagic waters, suggesting that genomes inhabiting this region of the ocean have been shaped by strong selection together with prevalent nutritional constraints characteristic of this environment.
    [Show full text]
  • Picophytoplankton Biomass Distribution in the Global Ocean
    CMYK RGB History of Geo- and Space Open Access Open Sciences Advances in Science & Research Open Access Proceedings Drinking Water Drinking Water Engineering and Science Engineering and Science Open Access Access Open Discussions Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Discussions Earth Syst. Sci. Data Discuss., 5, 221–242, Earth 2012 System Earth System www.earth-syst-sci-data-discuss.net/5/221/2012/ Science Science doi:10.5194/essdd-5-221-2012 ESSDD © Author(s) 2012. CC Attribution 3.0 License. 5, 221–242, 2012 Open Access Open Open Access Open Data Data This discussion paper is/has been under review for the journal Earth System Science Discussions Picophytoplankton Data (ESSD). Please refer to the corresponding final paper in ESSD if available. Social Social biomass distribution in the global ocean Open Access Open Geography Open Access Open Geography Picophytoplankton biomass distribution E. T. Buitenhuis et al. in the global ocean Title Page E. T. Buitenhuis1, W. K. W. Li2, D. Vaulot3, M. W. Lomas4, M. Landry5, F. Partensky3, D. M. Karl6, O. Ulloa7, L. Campbell8, S. Jacquet9, F. Lantoine10, Abstract Instruments F. Chavez11, D. Macias12, M. Gosselin13, and G. B. McManus14 Data Provenance & Structure 1Tyndall Centre for Climate Change Research and School of Environmental Sciences, Tables Figures University of East Anglia, Norwich NR4 7TJ, UK 2Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada J I 3UMR 7144 (CNRS and UPMC, Paris 06), Station Biologique, 29680
    [Show full text]
  • A Novel Species of the Marine Cyanobacterium Acaryochloris With
    www.nature.com/scientificreports OPEN A novel species of the marine cyanobacterium Acaryochloris with a unique pigment content and Received: 12 February 2018 Accepted: 1 June 2018 lifestyle Published: xx xx xxxx Frédéric Partensky 1, Christophe Six1, Morgane Ratin1, Laurence Garczarek1, Daniel Vaulot1, Ian Probert2, Alexandra Calteau 3, Priscillia Gourvil2, Dominique Marie1, Théophile Grébert1, Christiane Bouchier 4, Sophie Le Panse2, Martin Gachenot2, Francisco Rodríguez5 & José L. Garrido6 All characterized members of the ubiquitous genus Acaryochloris share the unique property of containing large amounts of chlorophyll (Chl) d, a pigment exhibiting a red absorption maximum strongly shifted towards infrared compared to Chl a. Chl d is the major pigment in these organisms and is notably bound to antenna proteins structurally similar to those of Prochloron, Prochlorothrix and Prochlorococcus, the only three cyanobacteria known so far to contain mono- or divinyl-Chl a and b as major pigments and to lack phycobilisomes. Here, we describe RCC1774, a strain isolated from the foreshore near Roscof (France). It is phylogenetically related to members of the Acaryochloris genus but completely lacks Chl d. Instead, it possesses monovinyl-Chl a and b at a b/a molar ratio of 0.16, similar to that in Prochloron and Prochlorothrix. It difers from the latter by the presence of phycocyanin and a vestigial allophycocyanin energetically coupled to photosystems. Genome sequencing confrmed the presence of phycobiliprotein and Chl b synthesis genes. Based on its phylogeny, ultrastructural characteristics and unique pigment suite, we describe RCC1774 as a novel species that we name Acaryochloris thomasi. Its very unusual pigment content compared to other Acaryochloris spp.
    [Show full text]