Small but Mighty: Cell Size and Bacteria

Total Page:16

File Type:pdf, Size:1020Kb

Small but Mighty: Cell Size and Bacteria Downloaded from http://cshperspectives.cshlp.org/ on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Small but Mighty: Cell Size and Bacteria Petra Anne Levin1 and Esther R. Angert2 1Department of Biology, Washington University, St. Louis, Missouri 63130 2Department of Microbiology, Cornell University, Ithaca, New York 14853 Correspondence: [email protected]; [email protected] Our view of bacteria is overwhelmingly shaped by their diminutive nature. The most ancient of organisms, their very presence was not appreciated until the 17th century with the inven- tion of the microscope. Initially, viewed as “bags of enzymes,” recent advances in imaging, molecular phylogeny,and, most recently,genomics have revealed incredible diversity within this previously invisible realm of life. Here, we review the impact of size on bacterial evo- lution, physiology, and morphogenesis. umanity has always experienced the im- bolic support. Although less than 1% of bacteria Hpact of microorganisms, most obviously canbeculturedreadily inthelaboratory(Amann through their ability to cause devastating dis- et al. 1995), the biochemical versatility among ease. For the vast majority of human history, these tiny creatures exceeds that of the plants, we were unaware of their presence, much less animals, and fungi combined (Pace 1997). the fundamental microbial processes to which Anton van Leeuwenhoek’s illustrations in a we owe our existence: from the production of letter to the Royal Society of London in the late energy by our ancient bacterial endosymbionts 17th century provide one of the earliest records (the mitochondria) to the generation of oxygen of bacterial cell form (Dobell 1960). Viewed in our atmosphere. Despite their astounding through a single lens, Leeuwenhoek pioneered global abundance (1030 cells) and their sub- studies of the human microbiome, describing stantial contribution to the total biomass of motile bacilli, cocci, and spirochetes he found planet earth (Whitman et al. 1998; Kallmeyer in scrapings taken from between his teeth (and et al. 2012), our inability to see these tiny life the teeth of others). This triumph was made forms shrouded their nearly limitless diversity possible by incomparable curiosity, lens con- in mystery. It was not until the 17th century, struction, and exceptional lighting. The simple with the careful observations and reports of An- cellular structure and glassy nature of most un- ton van Leeuwenhoek, that we became aware of stained bacteria viewed with a light microscope this previously invisible world on and around generated little interest in bacterial cell biology us. Today, we know that there are more bacteria with the exception of objects of unusual con- living in our intestinal tract than stars in the trast, such as endospores described by Robert Milky Way galaxy (and that they far outnumber Koch and the wonderfully colorful and large all the people who have ever lived). We also cyanobacteria. The bacterial nature of the latter know now that we thrive because of their meta- was itself only appreciated late in the 20th cen- Editors: Rebecca Heald, Iswar K. Hariharan, and David B. Wake Additional Perspectives on Size Control in Biology: From Organelles to Organisms available at www.cshperspectives.org Copyright # 2015 Cold Spring Harbor Laboratory Press; all rights reserved; doi: 10.1101/cshperspect.a019216 Cite this article as Cold Spring Harb Perspect Biol 2015;7:a019216 1 Downloaded from http://cshperspectives.cshlp.org/ on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press P.A. Levin and E.R. Angert tury (Oren 2004). For the most part, bacteria or 0.22 mL). Thiomargarita is slightly larger were viewed as primitive “bags of enzymes” un- than a Drosophila eye (Schulz et al. 1999) and til the 1990s, when the complexity of bacterial big enough to be seen by the human eye (Fig. 1). subcellular structure and regulators of cell re- A closer look at Thiomargarita reveals a central- production finally began to emerge. Tools and ly located fluid-filled vacuole, which takes up reagents developed for eukaryotic cell biol- 98% of the cell volume and is a nitrate reser- ogy (e.g., stains for DNA, membranes, and fluo- voir used to fuel sulfide oxidation. Even when rescent protein tags), once applied to bacterial accounting for the intracellular vacuole, a large cells, revealed astonishing insights including the Thiomargarita cell has a tremendous biovolume specific and even dynamic localization patterns to support (4.4  106 fL). Epulopiscium spp., of proteins, and the accuracy of chromosome intestinal symbionts of certain marine surgeon- organization. fish, are the largest known heterotrophic bacte- ria. These cigar-shaped cells are up to 600 mm  80 mm with an active cytoplasmic volume of BACTERIAL SIZE RANGE 2  106 mm3 or 0.02 mL (Angert et al. 1993). Bacillus subtilis, Staphylococcus aureus, Escheri- Unlike Thiomargarita, Epulopiscium cells con- chia coli, and Caulobacter crescentus, the prima- tain no storage vacuoles or other inert inclu- ry models for bacterial cell biology, are more sions (Fig. 1). The difference in size between or less typical in size, with individual cell vol- Candidatus Actinomarina minuta and these gi- umes between 0.4–3 mm3 (or 0.4–3.0 femto- ants is equivalent to the difference between a liters; femtoliter or fL is equal to 10215 L). Free- mouse and the Empire State Building (E. coli living marine ultramicrobacteria, appropriately could be represented by a small skunk or a rabbit named Candidatus Actinomarina minuta, have on this scale). We refer the reader to Niklas an average cell volume 1% that of E. coli (2015), wherein he discusses how cell features (0.013 mm3, range 0.6  1022 to 2.4  and geometry factor into considerations of cell 1022 fL). At the other end of the spectrum, size. the marine sediment–dwelling Thiomargarita What limits bacterial cell size? The smallest namibiensis, the “Sulfur pearl of Namibia,” is cells need enough volume to accommodate ad- a spherical organism with a volume eight or- equate genetic resources to support the cell’s ders of magnitude more than that of E. coli lifestyle (Koch 1996). The cell must also contain (750 mm in diameter, volume 2.2  108 fL the basic machinery required to express those Figure 1. Giant bacteria. On the left is a chain of Thiomargarita namibiensis cells. In this bright-field image, sulfur granules can be seen in the cytoplasm. The panel on the right shows an exceptionally large Epulopiscium cell with two large internal offspring. Scale bars, 100 mm. 2 Cite this article as Cold Spring Harb Perspect Biol 2015;7:a019216 Downloaded from http://cshperspectives.cshlp.org/ on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Cell Size and Bacteria genes as well as housekeeping proteins and port becomes numbingly unreliable. A small biochemicals to maintain its metabolism and molecule like oxygen at room temperature cellular reproduction. Genomic and metabol- would typically take about an hour to diffuse ic streamlining is seen in obligate intracellular 1 mm (Schulz and Jorgensen 2001). Similarly, symbionts, pathogens, and organelles that have the acquisition of nutrients relies on diffusion given up metabolic capabilities because those and capture of molecules at the surface of a cell. needs are supplied by the host (McCutcheon Consequently, free-living cells tend to be small, and Moran 2012; Wernegreen 2012). The loss with a large surface area relative to their cyto- of genes for sensing environmental change and plasmic volume, so that capture of nutrients, at responding to those contingencies can allow for low concentrations, can support the cell’s met- substantial genome reduction but not always a abolic needs. Cell form and function have been corresponding reduction in cell size. subjected to these constraints. For comparison, The structure and function of all large cells E. coli has a surface-area-to-volume ratio of appear bounded by the limits of diffusion 3.7 mm2 to 1 mm3, whereas the largest Thio- (Schulz and Jorgensen 2001). Encounters with margarita cell has a surface-to-volume ratio of nutrients, elimination of waste, and the timely 8.2  1023 mm2 to 1 mm3. Clearly, these large movement of biomolecules within the cell to bacteria are bending the rules. support metabolic needs all impact the ability of a large bacterium to survive in its environ- How Epulopisicum Has Overcome ment. The compartmentalization of cellular the Issue of Diffusion functions, the motor protein-facilitated traf- ficking over a complex cytoskeletal network, Most large bacteria either maintain a high sur- the expansion of genomic resources, and the face-to-volume ratio by being long and thin acquisition of endosymbionts that became en- like Spirochaeta plicatilis (a 250-mm-long, ergy-generating organelles have all been credit- 0.75-mm-diameter corkscrew-shaped bacte- ed for the advancement of the size and com- rium) or adopt a morphology in which no plexity of eukaryotic cells (Angert 2012). part of the cytoplasm is much more than a mi- cron away from the external environment. Thi- omargarita is an example of the latter, maintain- THE PROBLEM OF DIFFUSION ing a thin layer of cytoplasm surrounding a large The identification of giant bacteria required a fluid-filled vacuole. Epulopiscium spp. are the reexamination of the long-held beliefs about exception to this rule. maximum bacterial cell size. For all cells, growth Although their elongated form undoubted- and reproduction is limited by the speed of ly helps increase their surface-area-to-volume chemical communication and the availability ratio (Koch 1996), the largest Epulopiscium has of nutrients to fuel metabolism. Diffusion is a ratio of 0.6 mm2 to 1 mm3, 1/6 that of E. coli. the random, three-dimensional movement of Despite this difference, Epulopiscium maintains a molecule. For movement of molecules inside a high metabolic rate.
Recommended publications
  • Sporulation Evolution and Specialization in Bacillus
    bioRxiv preprint doi: https://doi.org/10.1101/473793; this version posted March 11, 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 4.0 International license. Research article From root to tips: sporulation evolution and specialization in Bacillus subtilis and the intestinal pathogen Clostridioides difficile Paula Ramos-Silva1*, Mónica Serrano2, Adriano O. Henriques2 1Instituto Gulbenkian de Ciência, Oeiras, Portugal 2Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal *Corresponding author: Present address: Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands Phone: 0031 717519283 Email: [email protected] (Paula Ramos-Silva) Running title: Sporulation from root to tips Keywords: sporulation, bacterial genome evolution, horizontal gene transfer, taxon- specific genes, Bacillus subtilis, Clostridioides difficile 1 bioRxiv preprint doi: https://doi.org/10.1101/473793; this version posted March 11, 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 4.0 International license. Abstract Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of a highly resistant, dormant spore. Spores allow environmental persistence, dissemination and for pathogens, are infection vehicles. In both the model Bacillus subtilis, an aerobic species, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes.
    [Show full text]
  • Nocturnal Production of Endospores in Natural Populations of Epulopiscium-Like Surgeonfish Symbionts Joseph F
    JOURNAL OF BACTERIOLOGY, Nov. 2005, p. 7460–7470 Vol. 187, No. 21 0021-9193/05/$08.00ϩ0 doi:10.1128/JB.187.21.7460–7470.2005 Copyright © 2005, American Society for Microbiology. All Rights Reserved. Nocturnal Production of Endospores in Natural Populations of Epulopiscium-Like Surgeonfish Symbionts Joseph F. Flint,1 Dan Drzymalski,1 W. Linn Montgomery,2 Gordon Southam,3 and Esther R. Angert1* Department of Microbiology, Cornell University, Ithaca, New York 148531; Department of Biological Sciences, Downloaded from Northern Arizona University, Flagstaff, Arizona 860112; and Department of Earth Sciences, University of Western Ontario, London, Ontario N6A 5B7, Canada3 Received 27 April 2005/Accepted 19 August 2005 Prior studies have described a morphologically diverse group of intestinal microorganisms associated with surgeonfish. Despite their diversity of form, 16S rRNA gene surveys and fluorescent in situ hybridizations indicate that these bacteria are low-G؉C gram-positive bacteria related to Epulopiscium spp. Many of these bacteria exhibit an unusual mode of reproduction, developing multiple offspring intracellularly. Previous http://jb.asm.org/ reports have suggested that some Epulopiscium-like symbionts produce dormant or phase-bright intracellular offspring. Close relatives of Epulopiscium, such as Metabacterium polyspora and Clostridium lentocellum, are endospore-forming bacteria, which raises the possibility that the phase-bright offspring are endospores. Structural evidence and the presence of dipicolinic acid demonstrate that phase-bright offspring of Epulopis- cium-like bacteria are true endospores. In addition, endospores are formed as part of the normal daily life cycle of these bacteria. In the populations studied, mature endospores were seen only at night and the majority of cells in a given population produced one or two endospores per mother cell.
    [Show full text]
  • Initiation of Intracellular Offspring in Epulopiscium
    Blackwell Science, LtdOxford, UKMMIMolecular Microbiology 1365-2958Blackwell Publishing Ltd, 2003513827835Original ArticleIntracellular offspring of EpulopisciumE. R. Angert and K. D. Clements Molecular Microbiology (2004) 51(3), 827–835 doi:10.1046/j.1365-2958.2003.03869.x Initiation of intracellular offspring in Epulopiscium Esther R. Angert1* and Kendall D. Clements2 of surgeonfish (Family Acanthuridae) (Fishelson et al., 1Department of Microbiology, Cornell University, Ithaca, 1985; Montgomery and Pollak, 1988; Clements et al., NY, USA. 1989). The largest Epulopiscium cells are cigar shaped 2School of Biological Sciences, University of Auckland, and reach lengths in excess of 600 mm. Phylogenetic Auckland, New Zealand. analyses based on small subunit rRNA sequence compar- isons revealed that Epulopiscium spp. are members of the low G + C Gram-positive group of bacteria (Angert et al., Summary 1993), affiliated with Cluster XIVb of the clostridia (Collins Epulopiscium spp. are the largest heterotrophic bac- et al., 1994). A diagnostic feature of the genus Epulopis- teria yet described. A distinguishing feature of the cium is the ability of individuals to produce multiple, active, Epulopiscium group is their viviparous production of intracellular offspring. Depending on the strain, an individ- multiple, internal offspring as a means of cellular ual cell (mother cell) can produce 1–7 internal offspring reproduction. Based on their phylogenetic position, (daughter cells), but generally two are produced (Clem- among low G + C Gram-positive endospore-forming ents et al., 1989). Offspring primordia are closely associ- bacteria, and the remarkable morphological similarity ated with the tips of the mother cell but occasionally between developing endospores and Epulopiscium similar structures are seen associated with the internal offspring, we hypothesized that intracellular offspring side wall of a mother cell (Robinow and Angert, 1998).
    [Show full text]
  • Sporulation in Bacteria: Beyond the Standard Model
    SUNY Geneseo KnightScholar Biology Faculty/Staff Works Department of Biology 2014 Sporulation in Bacteria: Beyond the Standard Model Elizabeth Hutchison SUNY Geneseo, [email protected] Follow this and additional works at: https://knightscholar.geneseo.edu/biology Part of the Bacteriology Commons Recommended Citation Hutchison, E. A., Miller, D. A., & Angert, E. R. (2014). Sporulation in Bacteria: Beyond the Standard Model. Microbiology Spectrum, 2(5). This Article is brought to you for free and open access by the Department of Biology at KnightScholar. It has been accepted for inclusion in Biology Faculty/Staff Works by an authorized administrator of KnightScholar. For more information, please contact [email protected]. SporulationinBacteria: Beyond the Standard Model ELIZABETH A. HUTCHISON,1 DAVID A. MILLER,2 and ESTHER R. ANGERT3 1Department of Biology, SUNY Geneseo, Geneseo, NY 14454; 2Department of Microbiology, Medical Instill Development, New Milford, CT 06776; 3Department of Microbiology, Cornell University, Ithaca, NY 14853 ABSTRACT Endospore formation follows a complex, highly in nature (1). These highly resistant, dormant cells can regulated developmental pathway that occurs in a broad range withstand a variety of stresses, including exposure to Firmicutes Bacillus subtilis of . Although has served as a powerful temperature extremes, DNA-damaging agents, and hy- model system to study the morphological, biochemical, and drolytic enzymes (2). The ability to form endospores genetic determinants of sporulation, fundamental aspects of the program remain mysterious for other genera. For example, appears restricted to the Firmicutes (3), one of the ear- it is entirely unknown how most lineages within the Firmicutes liest branching bacterial phyla (4). Endospore formation regulate entry into sporulation.
    [Show full text]
  • Bacterial Symbiont Subpopulations Have Different Roles in a Deep-Sea
    RESEARCH ARTICLE Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis Tjorven Hinzke1,2,3, Manuel Kleiner4, Mareike Meister5,6, Rabea Schlu¨ ter7, Christian Hentschker8, Jan Pane´ -Farre´ 9, Petra Hildebrandt8, Horst Felbeck10, Stefan M Sievert11, Florian Bonn12, Uwe Vo¨ lker8, Do¨ rte Becher5, Thomas Schweder1,2, Stephanie Markert1,2* 1Institute of Pharmacy, University of Greifswald, Greifswald, Germany; 2Institute of Marine Biotechnology, Greifswald, Germany; 3Energy Bioengineering Group, University of Calgary, Calgary, Canada; 4Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States; 5Institute of Microbiology, University of Greifswald, Greifswald, Germany; 6Leibniz Institute for Plasma Science and Technology, Greifswald, Germany; 7Imaging Center of the Department of Biology, University of Greifswald, Greifswald, Germany; 8Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany; 9Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany; 10Scripps Institution of Oceanography, University of California San Diego, San Diego, United States; 11Biology Department, Woods Hole Oceanographic Institution, Woods Hole, United States; 12Institute of Biochemistry, University Hospital, Goethe University School of Medicine Frankfurt, Frankfurt, Germany Abstract The hydrothermal vent tubeworm Riftia pachyptila hosts a single 16S rRNA phylotype of intracellular sulfur-oxidizing symbionts, which
    [Show full text]
  • Recombination Contributes to Population Diversification in The
    The ISME Journal (2019) 13:1084–1097 https://doi.org/10.1038/s41396-018-0339-y ARTICLE Recombination contributes to population diversification in the polyploid intestinal symbiont Epulopiscium sp. type B 1 2 3 4 1 Francine A. Arroyo ● Teresa E. Pawlowska ● J. Howard Choat ● Kendall D. Clements ● Esther R. Angert Received: 18 May 2018 / Revised: 15 November 2018 / Accepted: 13 December 2018 / Published online: 14 January 2019 © International Society for Microbial Ecology 2019 Abstract Epulopiscium sp. type B (Lachnospiraceae) is an exceptionally large, highly polyploid, intestinal symbiont of the coral reef dwelling surgeonfish Naso tonganus. These obligate anaerobes do not form mature endospores and reproduce solely through the production of multiple intracellular offspring. This likely makes them dependent on immediate transfer to a receptive host for dispersal. During reproduction, only a small proportion of Epulopiscium mother-cell DNA is inherited. To explore the impact of this unusual viviparous lifestyle on symbiont population dynamics, we investigated Epulopiscium sp. type B and their fish hosts collected over the course of two decades, at island and reef habitats near Lizard Island, Australia. Using multi-locus sequence analysis, we found that recombination plays an important role in maintaining diversity of these 1234567890();,: 1234567890();,: symbionts and yet populations exhibit linkage disequilibrium (LD). Symbiont populations showed spatial but not temporal partitioning. Surgeonfish are long-lived and capable of traveling long distances, yet the population structures of Epulopiscium suggest that adult fish tend to not roam beyond a limited locale. Codiversification analyses and traits of this partnership suggest that while symbionts are obligately dependent on their host, the host has a facultative association with Epulopiscium.
    [Show full text]
  • Supplemental Material
    Supplemental Material: Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules Authors: Baker, J.L.1,*, Morton, J.T.2., Dinis, M.3, Alverez, R.3, Tran, N.C.3, Knight, R.4,5,6,7, Edlund, A.1,5,* 1 Genomic Medicine Group J. Craig Venter Institute 4120 Capricorn Lane La Jolla, CA 92037 2Systems Biology Group Flatiron Institute 162 5th Avenue New York, NY 10010 3Section of Pediatric Dentistry UCLA School of Dentistry 10833 Le Conte Ave. Los Angeles, CA 90095-1668 4Center for Microbiome Innovation University of California at San Diego La Jolla, CA 92023 5Department of Pediatrics University of California at San Diego La Jolla, CA 92023 6Department of Computer Science and Engineering University of California at San Diego 9500 Gilman Drive La Jolla, CA 92093 7Department of Bioengineering University of California at San Diego 9500 Gilman Drive La Jolla, CA 92093 *Corresponding AutHors: JLB: [email protected], AE: [email protected] ORCIDs: JLB: 0000-0001-5378-322X, AE: 0000-0002-3394-4804 SUPPLEMENTAL METHODS Study Design. Subjects were included in tHe study if tHe subject was 3 years old or older, in good general HealtH according to a medical History and clinical judgment of tHe clinical investigator, and Had at least 12 teetH. Subjects were excluded from tHe study if tHey Had generalized rampant dental caries, cHronic systemic disease, or medical conditions tHat would influence tHe ability to participate in tHe proposed study (i.e., cancer treatment, HIV, rHeumatic conditions, History of oral candidiasis). Subjects were also excluded it tHey Had open sores or ulceration in tHe moutH, radiation tHerapy to tHe Head and neck region of tHe body, significantly reduced saliva production or Had been treated by anti-inflammatory or antibiotic tHerapy in tHe past 6 montHs.
    [Show full text]
  • Propagation by Sporulation in the Guinea Pig Symbiont Metabacterium Polyspora
    Proc. Natl. Acad. Sci. USA Vol. 95, pp. 10218–10223, August 1998 Microbiology Propagation by sporulation in the guinea pig symbiont Metabacterium polyspora ESTHER R. ANGERT AND RICHARD M. LOSICK* Department of Molecular and Cellular Biology, Harvard University, The Biological Laboratories, 16 Divinity Avenue, Cambridge, MA 02138 Contributed by Richard M. Losick, June 17, 1998 ABSTRACT The Gram-positive bacterium Metabacterium M. polyspora is modified to allow for the production of multiple polyspora is an uncultivated symbiont of the guinea pig gas- endospores. trointestinal tract. Here we present evidence that in M. In the case of the endospore-forming bacterium Bacillus polyspora vegetative cell division has taken on a minor, and subtilis, which produces only a single endospore, development apparently dispensable, role in propagation. Instead, this occurs by a modification of the process of binary fission. unusual bacterium has evolved the capacity to produce prog- Vegetative cells divide by the formation of a medially posi- eny in the form of multiple endospores. Endospore formation tioned ring of the tubulin-like protein FtsZ (6). The FtsZ ring, is coordinated with transit of the bacterium through the in turn, recruits additional cell division proteins that drive the gastrointestinal tract of the guinea pig. For the majority of formation of the septum. Endospore formation, in contrast, cells, sporulation is initiated in the ileum, whereas later stages takes place by the formation of two rings of FtsZ, one near of development take place in the cecum. We show that multiple each pole of the cell (7). Normally, only one ring becomes endospores are generated both by asymmetric division at both functional and produces a single septum located near one pole poles of the cell and by symmetric division of the endospores of the cell.
    [Show full text]
  • Protists Are Microbes Too: a Perspective
    The ISME Journal (2009) 3, 4–12 & 2009 International Society for Microbial Ecology All rights reserved 1751-7362/09 $32.00 www.nature.com/ismej PERSPECTIVE Protists are microbes too: a perspective David A Caron1, Alexandra Z Worden2, Peter D Countway1, Elif Demir2 and Karla B Heidelberg1 1Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA and 2Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA Our understanding of the composition and activities of microbial communities from diverse habitats on our planet has improved enormously during the past decade, spurred on largely by advances in molecular biology. Much of this research has focused on the bacteria, and to a lesser extent on the archaea and viruses, because of the relative ease with which these assemblages can be analyzed and studied genetically. In contrast, single-celled, eukaryotic microbes (the protists) have received much less attention, to the point where one might question if they have somehow been demoted from the position of environmentally important taxa. In this paper, we draw attention to this situation and explore several possible (some admittedly lighthearted) explanations for why these remarkable and diverse microbes have remained largely overlooked in the present ‘era of the microbe’. The ISME Journal (2009) 3, 4–12; doi:10.1038/ismej.2008.101; published online 13 November 2008 Keywords: protists; eukaryotic genomics; species concept; diversity; biogeography Introduction research activity has lagged behind that of other microbes despite their rather impressive contribu- Environmental science has clearly entered the ‘era tions to microbiological history, microbial diversity of the microbe’ during the past decade.
    [Show full text]
  • Developmental Intestinal Microbiome Alterations in Canine Fading Puppy Syndrome
    www.nature.com/npjbiofilms ARTICLE OPEN Developmental intestinal microbiome alterations in canine fading puppy syndrome: a prospective observational study ✉ Smadar Tal1,3, Evgenii Tikhonov2,3, Itamar Aroch1, Lior Hefetz1, Sondra Turjeman 2, Omry Koren2,4 and Sharon Kuzi 1,4 Fading puppy syndrome (FPS) is a fatal condition in neonatal dogs. Intestinal microbial alterations, although never investigated, may be involved in its pathophysiology. The study examined the occurrence of FPS and its associations with dam, puppy, and husbandry characteristics, compared the intestinal microbial diversity of healthy puppies and those with FPS, and examined whether intestinal microbiomes are predictive of FPS. Day 1 and 8 post-partum (PP) rectal swabs were collected from healthy puppies and puppies which later developed FPS. Microbial compositional structure, including alpha and beta diversities and relative abundance of specific taxa were compared between groups, and microbial data was applied to a machine-learning model to assess the predictive performance of microbial indices of FPS or death. FPS occurred in 22/165 puppies (13%), with a 100% mortality rate. FPS was associated (P < 0.001) with decreased Day 1 PP puppy activity. Day 1 (P = 0.003) and 8 (P = 0.005) PP rectal beta diversities were different in puppies with FPS vs healthy ones. Increased Proteobacteria/Firmicutes ratio, increased relative abundance of Pasteurellaceae, and decreased relative abundance of Clostridia and Enterococcus were associated with FPS. A machine-learning model showed that Day 1 PP rectal microbiome composition accurately predicted FPS-related death. We found that specific rectal microbial phenotypes are associated with FPS, reflecting the significant role of microbiome alterations in this phenomenon.
    [Show full text]
  • Cell Size Control in Bacteria Review
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Current Biology 22, R340–R349, May 8, 2012 ª2012 Elsevier Ltd All rights reserved DOI 10.1016/j.cub.2012.02.032 Cell Size Control in Bacteria Review An-Chun Chien, Norbert S. Hill, and Petra Anne Levin exhibit a vast array of morphologies ranging from rods and filaments to cocci, spirals and amoeboid-like forms. The diversity of bacteria is mirrored in the size of individual Like eukaryotes, bacteria must coordinate division with species, which range from w0.3 mm for obligate intracellular growth to ensure cells are the appropriate size for a pathogenic members of the genus Mycoplasma,tow600 mm given environmental condition or developmental fate. As for Epulopiscium fishelsoni, a Gram-positive commensal single-celled organisms, nutrient availability is one of the inhabitant of Surgeonfish guts, and 750 mm for Thiomargarita strongest influences on bacterial cell size. Classic physio- namibiensis, a chemilithotrophic Gram-negative bacterium logical experiments conducted over four decades ago native to coastal Namibia [1–3]. While T. namibiensis is first demonstrated that cell size is directly correlated essentially a large gas vesicle surrounded by a thin layer of with nutrient source and growth rate in the Gram-negative cytoplasm, Epulopiscium has managed to overcome diffu- bacterium Salmonella typhimurium. This observation sub- sion-dependent limitations on cell size, in part by increasing sequently served as the basis for studies revealing a role genome number along with cell size. These tens-of-thou- for cell size in cell cycle progression in a closely related sands of genomes are arranged around the periphery of organism, Escherichia coli.
    [Show full text]
  • Protists Are Microbes Too: a Perspective
    The ISME Journal (2008), 1–9 & 2008 International Society for Microbial Ecology All rights reserved 1751-7362/08 $32.00 www.nature.com/ismej PERSPECTIVE Protists are microbes too: a perspective David A Caron1, Alexandra Z Worden2, Peter D Countway1, Elif Demir2 and Karla B Heidelberg1 1Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA and 2Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA Our understanding of the composition and activities of microbial communities from diverse habitats on our planet has improved enormously during the past decade, spurred on largely by advances in molecular biology. Much of this research has focused on the bacteria, and to a lesser extent on the archaea and viruses, because of the relative ease with which these assemblages can be analyzed and studied genetically. In contrast, single-celled, eukaryotic microbes (the protists) have received much less attention, to the point where one might question if they have somehow been demoted from the position of environmentally important taxa. In this paper, we draw attention to this situation and explore several possible (some admittedly lighthearted) explanations for why these remarkable and diverse microbes have remained largely overlooked in the present ‘era of the microbe’. The ISME Journal advance online publication, 13 November 2008; doi:10.1038/ismej.2008.101 Keywords: protists; eukaryotic genomics; species concept; diversity; biogeography Introduction research activity has lagged behind that of other microbes despite their rather impressive contribu- Environmental science has clearly entered the ‘era tions to microbiological history, microbial diversity of the microbe’ during the past decade. At no other and biogeochemical processes.
    [Show full text]