DOCSLIB.ORG

Marine Environmental Genomics: New Secrets from a Mysterious Ocean

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Marine Environmental Genomics: New Secrets from a Mysterious Ocean PAPER Marine Environmental Genomics: New Secrets from a Mysterious Ocean AUTHORS ABSTRACT Karla B. Heidelberg Ocean microbes play critical roles in ecosystem dynamics and biogeochemical cycles. J. Craig Venter Institute For a number of reasons, these organisms have been hard to study; among other character- John F. Heidelberg istics, they are difficult or maybe impossible to culture. The recent application of cultivation- Institute for Genomic Research and independent genomic techniques to study bacterial communities has begun to fundamen- J. Craig Venter Institute tally change our views of microbial ecology and function. These approaches are providing more comprehensive insights into the structure and function of natural assemblages of microbial populations. Genomics-based technologies are revealing previously unknown groups of microorganisms and novel metabolic pathways, leading to a deeper appreciation oday we are witnessing an explosion in of the fundamental genetic and potential functional diversity of ocean microbes. When interest in marine microbial communities. evaluated in the context of observed ecosystem functions, we can begin to understand the TMicroscopic marine organisms, including complex interactions of individuals and populations with their physical and chemical envi- communities of phytoplankton, Bacteria, ronment. The continuing study and interpretation of the community genomic data will Archaea, protists and viruses, play critical roles require a close synergy among interdisciplinary researchers working throughout the world’s in the biosphere by participating in virtually ocean basins. Community genomic approaches have and will become a powerful tool for all of the Earth’s biogeochemical cycles and understanding marine microbial ecology in the future. thereby affecting geology, hydrology, and even possibly global climate change. These prolific and diverse microbial communities, while not powerful as these studies are, they do not pro- phylogentic genes. Amplification and se- seen by casual observers, by some estimates vide information on which microbes are re- quencing of the conserved regions of the 16S account for more than 90 percent of the ocean’s sponsible for specific biogeochemical processes. ribosomal RNA (rRNA) gene (part of the pro- biomass and 98 percent of the primary pro- Additional studies were designed to evalu- tein synthesis machinery found in all living duction in the marine environment (e.g. ate ocean function with the use of culturing cells), can provide the identity of the specific Whitman et al., 1998). Therefore, for hu- technologies. However, a significant challenge organisms in the sample. Initial application of mans to truly begin to understand the impact to our ability to study and understand these this methodology resulted in an explosion of of our activities on our environment, and to microorganisms is that the vast majority are information, providing for the first time a being to develop new tools to combat nega- not easily cultured on typical growth media, mechanism to evaluate microbial diversity for tive effects, it is important for us to under- the traditional approach in much of microbi- the > 99% of the microbial population that stand both diversity and function of the ma- ology dating back to the early days of medical could not be grown in the laboratory (e.g. rine microbial assemblages. microbiology and Koch’s principles. Cultur- DeLong et al., 1989; Giovannoni et al.; 1990; Traditional ‘black box’ microbial ecology ing methods were thought to be the necessary Pace, 1996, 1997). set the foundation for understanding ocean first step towards evaluating microbial diver- Despite the impact of these rRNA based function and taught us that unseen biology is sity and function, but we now know that surveys, a phylogenetic identification of a mi- of critical importance in the ocean. Through studying only microbial populations that can croorganism based solely on an rRNA sequence these studies we learned that microbes were at be grown in culture provides very little infor- does not allow inference of physiology, bio- the core of virtually all the biogeochemical mation on natural diversity or environmental chemistry, or ecological significance. Therefore, carbon (e.g. Carlson et al., 2001) and nutri- function (e.g. Beja et al., 2002a). Conse- the specific biological properties of abundant ent (e.g. Redfeld, 1958) cycles. For example, quently, over the past decade, scientists have uncultured microorganisms remain almost the global dissolved organic carbon pool is developed molecular tools to explore environ- entirely unknown. Another limitation of the estimated to be approximately 700 Pg C, a mental diversity without relying on culturing 16S rRNA sequencing technique is that it does value comparable to the mass of inorganic C technologies. The most commonly used cul- not distinguish between strains of the same in the atmosphere. Interaction of microbes ture-independent method relies on compari- species that may fill significantly different bio- within the dissolved organic pool could sons of homologous genes between organisms logical niches and habitats. For example, Es- strongly impact the balance between oceanic by using techniques such as polymerase chain cherichia coli, which persist in the human gut and atmospheric carbon dioxide. However, reaction (PCR) products typically targeting in a mutualistic relationship, may not be dis- 94 Marine Technology Society Journal tinguished from a closely related strain that erotrophic bacteria (Moran et al., 2004; trying to isolate a single organism, the total has acquired various toxins and is a deadly Giovannoni et al., 2005), and several community DNA is isolated en mass, the DNA human pathogen. cyanobacteria (e.g. Dufresne et al., 2003; is extracted, and this community of DNA Recent advances in genomic science have Palenik et al., 2003; Rocap et al., 2003)— serves as the template for sequencing. Once helped scientists to study cultured microor- are providing exciting information on the extracted, the DNA can be shotgun sequenced ganisms with much greater precision than detailed physiological and genetic controls as short insert libraries or analyzed with tar- ever before. Through the merging of DNA of photosynthesis, and the cycling of carbon geted large insert libraries (Figure 2). These are sequencing technologies and the use of newly and nitrogen in the world’s oceans. With re- powerful meta- or community genomics ap- developed computational methodologies a cent efforts funded by the Gordon and Betty proaches and allow for the gene compliment complete set of genetic blueprints of the or- Moore Foundation’s Marine Microbial se- of the entire community to be sequenced to ganism (the genomes) can now be ascertained quencing program (see Marine Microbial Ini- yield information on the potential biological in a very short period of time. Since the first tiative, http://www.moore.org/), the possible functions of the genes to be catalogued at a bacterial genome was sequenced a decade ago, addition of up to approximately 150 ge- very rapid pace. Analysis of small insert clones (Fleischmann et al., 1995), the number of nomes from cultured marine prokaryotes will from the Sargasso Sea (Venter et al., 2004), for fully sequenced deposited prokaryotic ge- greatly expand the existing marine genome example, yielded over one million previously nomes into public databases has grown tre- reference library. unknown genes, including almost 800 mendously (Figure 1). Genome sequencing However, perhaps the real potential of rhodopsins (a light absorbing molecule). In of microorganisms was initially prioritized to genomics may be in the newly developed addition to entire genome sequencing, studies study cultured pathogens, but recently there methods applied to study uncultured organ- using large insert libraries to evaluate detailed has been an expansion and focus on envi- isms—both prokaryotes and viruses. Several parts of organism’s genomes have helped make ronmentally important marine microbes. As key studies in 2004 (Tysen et al., Venter et al., important new discoveries, such as finding of expected, having the completed manually Tringe et al.) show that much could be learned a new form of phototrophy (Béjà et al., 2002b; curated genomes of key ocean organism ge- about entire communities of uncultured or- reviewed by Karl, 2002). It is clear that micro- nomes—e.g. a diatom, Thalassiosira ganisms by using high-throughput, shotgun bial communities have an extraordinary di- pseudonana (Armbrust et al., 2004), two het- DNA sequencing technologies. Rather than verse suite of mechanisms and pathways that are still yet to be discovered. Figure 1 As often is the case with new technologi- Publicly available completed genomes. Data reported by publication date, or if not published, the date cal advances, genomic technologies are being that genome data was deposited into the Comprehensive Microbial Database (CMR; http://cmr.tigr.org/ used by scientists based, for the most part, in tigr-scripts/CMR/CmrHomePage.cgi). Data for 2005 as of May. Data presented represent a total of 226 the developed world. It is tempting, for rea- genomes (199 Bacteria and 20 Archae and 3 Viruses). sons of convenience, to maintain research pro- grams in well-studied waters of one’s own coun- try. Ocean communities, however, function irrespective of political boundaries, and glo- bally, these new technologies have so much potential for informing marine management, sustainability,
Load more

Recommended publications
  • Taurine Is a Major Carbon and Energy Source for Marine Prokaryotes in the North Atlantic Ocean Off the Iberian Peninsula
    Microbial Ecology https://doi.org/10.1007/s00248-019-01320-y MICROBIOLOGY OF AQUATIC SYSTEMS Taurine Is a Major Carbon and Energy Source for Marine Prokaryotes in the North Atlantic Ocean off the Iberian Peninsula Elisabeth L. Clifford1 & Marta M. Varela2 & Daniele De Corte3 & Antonio Bode2 & Victor Ortiz1 & Gerhard J. Herndl1,4 & Eva Sintes1,5 Received: 28 June 2018 /Accepted: 3 January 2019 # The Author(s) 2019 Abstract Taurine, an amino acid-like compound, acts as an osmostress protectant in many marine metazoans and algae and is released via various processes into the oceanic dissolved organic matter pool. Taurine transporters are widespread among members of the marine prokaryotic community, tentatively indicating that taurine might be an important substrate for prokaryotes in the ocean. In this study, we determined prokaryotic taurine assimilation and respiration throughout the water column along two transects in the North Atlantic off the Iberian Peninsula. Taurine assimilation efficiency decreased from the epipelagic waters from 55 ± 14% to 27 ± 20% in the bathypelagic layers (means of both transects). Members of the ubiquitous alphaproteobacterial SAR11 clade accounted for a large fraction of cells taking up taurine, especially in surface waters. Archaea (Thaumarchaeota + Euryarchaeota) were also able to take up taurine in the upper water column, but to a lower extent than Bacteria. The contribution of taurine assimilation to the heterotrophic prokaryotic carbon biomass production ranged from 21% in the epipelagic layer to 16% in the bathypelagic layer. Hence, we conclude that dissolved free taurine is a significant carbon and energy source for prokaryotes throughout the oceanic water column being utilized with similar efficiencies as dissolved free amino acids.
    [Show full text]
  • Specificity Re-Evaluation of Oligonucleotide Probes for the Detection of Marine Picoplankton by Tyramide Signal Amplification-Fl
    fmicb-08-00854 May 24, 2017 Time: 20:18 # 1 ORIGINAL RESEARCH published: 29 May 2017 doi: 10.3389/fmicb.2017.00854 Specificity Re-evaluation of Oligonucleotide Probes for the Detection of Marine Picoplankton by Tyramide Signal Amplification-Fluorescent In Situ Hybridization Virginie Riou, Marine Périot and Isabelle C. Biegala* Centre National de la Recherche Scientifique, Mediterranean Institute of Oceanography – Institut de Recherche pour le Développement, Aix Marseille Université – Université de Toulon, Marseille, France Edited by: Sophie Rabouille, Oligonucleotide probes are increasingly being used to characterize natural microbial Centre National de la Recherche Scientifique (CNRS), France assemblages by Tyramide Signal Amplification-Fluorescent in situ Hybridization (TSA- Reviewed by: FISH, or CAtalysed Reporter Deposition CARD-FISH). In view of the fast-growing rRNA Fernanda De Avila Abreu, databases, we re-evaluated the in silico specificity of eleven bacterial and eukaryotic Federal University of Rio de Janeiro, Brazil probes and competitor frequently used for the quantification of marine picoplankton. Tom Bibby, We performed tests on cell cultures to decrease the risk for non-specific hybridization, University of Southampton, before they are used on environmental samples. The probes were confronted to recent United Kingdom databases and hybridization conditions were tested against target strains matching *Correspondence: Isabelle C. Biegala perfectly with the probes, and against the closest non-target strains presenting one [email protected]
    [Show full text]
  • Archaeal Distribution and Abundance in Water Masses of the Arctic Ocean, Pacific Sector
    Vol. 69: 101–112, 2013 AQUATIC MICROBIAL ECOLOGY Published online April 30 doi: 10.3354/ame01624 Aquat Microb Ecol FREEREE ACCESSCCESS Archaeal distribution and abundance in water masses of the Arctic Ocean, Pacific sector Chie Amano-Sato1, Shohei Akiyama1, Masao Uchida2, Koji Shimada3, Motoo Utsumi1,* 1University of Tsukuba, Tennodai, Tsukuba, Ibaraki 305-8572, Japan 2National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki 305-8506, Japan 3Tokyo University of Marine Science and Technology, Konan, Minato-ku, Tokyo 108-8477, Japan ABSTRACT: Marine planktonic Archaea have been recently recognized as an ecologically impor- tant component of marine prokaryotic biomass in the world’s oceans. Their abundance and meta- bolism are closely connected with marine geochemical cycling. We evaluated the distribution of planktonic Archaea in the Pacific sector of the Arctic Ocean using fluorescence in situ hybridiza- tion (FISH) with catalyzed reporter deposition (CARD-FISH) and performed statistical analyses using data for archaeal abundance and geochemical variables. The relative abundance of Thaum - archaeota generally increased with depth, and euryarchaeal abundance was the lowest of all planktonic prokaryotes. Multiple regression analysis showed that the thaumarchaeal relative abundance was negatively correlated with ammonium and dissolved oxygen concentrations and chlorophyll fluorescence. Canonical correspondence analysis showed that archaeal distributions differed with oceanographic water masses; in particular, Thaumarchaeota were abundant from the halocline layer to deep water, where salinity was higher and most nutrients were depleted. However, at several stations on the East Siberian Sea side of the study area and along the North- wind Ridge, Thaumarchaeota and Bacteria were proportionally very abundant at the bottom in association with higher nutrient conditions.
    [Show full text]
  • Oceans of Archaea Abundant Oceanic Crenarchaeota Appear to Derive from Thermophilic Ancestors That Invaded Low-Temperature Marine Environments
    Oceans of Archaea Abundant oceanic Crenarchaeota appear to derive from thermophilic ancestors that invaded low-temperature marine environments Edward F. DeLong arth’s microbiota is remarkably per- karyotes), Archaea, and Bacteria. Although al- vasive, thriving at extremely high ternative taxonomic schemes have been recently temperature, low and high pH, high proposed, whole-genome and other analyses E salinity, and low water availability. tend to support Woese’s three-domain concept. One lineage of microbial life in par- Well-known and cultivated archaea generally ticular, the Archaea, is especially adept at ex- fall into several major phenotypic groupings: ploiting environmental extremes. Despite their these include extreme halophiles, methanogens, success in these challenging habitats, the Ar- and extreme thermophiles and thermoacido- chaea may now also be viewed as a philes. Early on, extremely halo- cosmopolitan lot. These microbes philic archaea (haloarchaea) were exist in a wide variety of terres- first noticed as bright-red colonies trial, freshwater, and marine habi- Archaea exist in growing on salted fish or hides. tats, sometimes in very high abun- a wide variety For many years, halophilic isolates dance. The oceanic Marine Group of terrestrial, from salterns, salt deposits, and I Crenarchaeota, for example, ri- freshwater, and landlocked seas provided excellent val total bacterial biomass in wa- marine habitats, model systems for studying adap- ters below 100 m. These wide- tations to high salinity. It was only spread Archaea appear to derive sometimes in much later, however, that it was from thermophilic ancestors that very high realized that these salt-loving invaded diverse low-temperature abundance “bacteria” are actually members environments.
    [Show full text]
  • Experimental Warming Effects on Prokaryotic Growth and Viral Production in Coastal Waters of the Northwest Pacific During the Cold Season
    diversity Brief Report Experimental Warming Effects on Prokaryotic Growth and Viral Production in Coastal Waters of the Northwest Pacific during the Cold Season An-Yi Tsai 1,2,*, Gwo-Ching Gong 1,2 and Vladimir Mukhanov 3 1 Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung 202-24, Taiwan; [email protected] 2 Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 202-24, Taiwan 3 A.O. Kovalevsky Institute of Biology of the Southern Seas, Russian Academy of Sciences, 299011 Sevastopol, Russia; [email protected] * Correspondence: [email protected]; Tel.: +886-2-2462-2192 (ext. 5705); Fax: +886-2-2462-0892 Abstract: Climate warming can directly affect biological processes in marine environments. Here, we investigated if warming (+2 ◦C) can change dynamics in viral and prokaryotic populations in the cold seasons in natural seawaters. We monitored the changes in viral production and prokaryotic growth rate. The prokaryotic average gross growth rates were 0.08 and 0.34 h−1 in November and 0.06 and 0.41 h−1 in December in the in situ and warming experiments, respectively. We found that warming water temperature resulted in a significant increase in prokaryotic growth rates. In warming experiments, the overall viral production rate was about 0.77–14.4 × 105 viruses mL−1 h−1, and a rough estimate of prokaryotic mortality was about 5.6–6.8 × 104 cells mL−1 h−1. Based on our estimation, burst sizes of about 21 and 14 viruses prokaryotes−1 were measured under the Citation: Tsai, A.-Y.; Gong, G.-C.; experimental warming period.
    [Show full text]
  • Cobalamin Cobalamin in Which Adenine Substitutes for DMB As the Α Ligand
    Two distinct pools of B12 analogs reveal community interdependencies in the ocean Katherine R. Heala, Wei Qinb, Francois Ribaleta, Anthony D. Bertagnollib,1, Willow Coyote-Maestasa,2, Laura R. Hmeloa, James W. Moffettc,d, Allan H. Devola, E. Virginia Armbrusta, David A. Stahlb, and Anitra E. Ingallsa,3 aSchool of Oceanography, University of Washington, Seattle, WA 98195; bDepartment of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195; cDepartment of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0894; and dDepartment of Civil and Environmental Engineering, University of Southern California, Los Angeles, CA 90089-0894 Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved November 28, 2016 (received for review May 25, 2016) Organisms within all domains of life require the cofactor cobalamin cobalamin in which adenine substitutes for DMB as the α ligand (vitamin B12), which is produced only by a subset of bacteria and (12) (Fig. 1). Production of pseudocobalamin in a natural marine archaea. On the basis of genomic analyses, cobalamin biosynthesis environment has not been shown, nor have reasons for the pro- in marine systems has been inferred in three main groups: select duction of this compound in place of cobalamin been elucidated. heterotrophic Proteobacteria, chemoautotrophic Thaumarchaeota, To explore the pervasiveness of cobalamin and pseudocobala- and photoautotrophic Cyanobacteria. Culture work demonstrates min supply and demand in marine systems, we determined the that many Cyanobacteria do not synthesize cobalamin but rather standing stocks of these compounds in microbial communities produce pseudocobalamin, challenging the connection between the from surface waters across the North Pacific Ocean using liquid occurrence of cobalamin biosynthesis genes and production of the chromatography mass spectrometry (LC-MS).
    [Show full text]
  • Microbial Ecology of the Oceans David L. Kirchman (Editor)
    Microbial Ecology of the Oceans David L. Kirchman (Editor) John Wiley & Sons, August 2000, ISBN 0471299928 552 pages Microbial ecology is now recognized to be fundamental for understanding the natural world around us and is essential for examining life in the oceans. For the first time, this book brings together international experts to explore the incredibly diverse collection of microbes (and viruses) found in the oceans and to dissect many of the processes mediated by these microbes in aquatic environments. Although the oceans are emphasized, the organisms and processes discussed in the book occur in nearly all natural environments, including rivers and lakes. « Microbial Ecology of the Oceans » reviews some basics of marine microbiology and provides a foundation for researchers and students new to the field while also examining several questions currently being discussed in modern microbial ecology. The book brings together concepts from autoecological studies of individual bacterial groups and from ecological studies of microbial assemblages in the oceans. In addition to drawing on the rich history of microbiology, Microbial Ecology of the Oceans uses the latest advances in biological and chemical oceanography and limnology to examine the role of marine microbes and viruses in the oceans. « Microbial Ecology of the Oceans » elucidates the role of microbes in food web dynamics and biogeochemical cycles in the ocean. It will prove to be an indispensable resource for students and researchers in biological and chemical oceanography, geochemistry, marine chemistry, freshwater ecology, and microbiology. Some of the topics covered by this informative book include: * Microbial evolution, as revealed by molecular techniques * Microbes in carbon budgets and cycles * Viruses and grazers of bacteria * Competition between bacteria and phytoplankton for limited nutrients * Marine symbiosis Introduction (D.
    [Show full text]
  • Ecological Dynamics and Co-Occurrence Among Marine Phytoplankton, Bacteria and Myoviruses Shows Microdiversity Matters
    The ISME Journal (2017) 11, 1614–1629 © 2017 International Society for Microbial Ecology All rights reserved 1751-7362/17 www.nature.com/ismej ORIGINAL ARTICLE Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters David M Needham, Rohan Sachdeva and Jed A Fuhrman Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA Numerous ecological processes, such as bacteriophage infection and phytoplankton–bacterial interactions, often occur via strain-specific mechanisms. Therefore, studying the causes of microbial dynamics should benefit from highly resolving taxonomic characterizations. We sampled daily to weekly over 5 months following a phytoplankton bloom off Southern California and examined the extent of microdiversity, that is, significant variation within 99% sequence similarity clusters, operational taxonomic units (OTUs), of bacteria, archaea, phytoplankton chloroplasts (all via 16S or intergenic spacer (ITS) sequences) and T4-like-myoviruses (via g23 major capsid protein gene sequence). The extent of microdiversity varied between genes (ITS most, g23 least) and only temporally common taxa were highly microdiverse. Overall, 60% of taxa exhibited microdiversity; 59% of these had subtypes that changed significantly as a proportion of the parent taxon, indicating ecologically distinct taxa. Pairwise correlations between prokaryotes and myoviruses or phytoplank- ton (for example, highly microdiverse Chrysochromulina sp.) improved when using single-base variants. Correlations between myoviruses and SAR11 increased in number (172 vs 9, Spear- man40.65) and became stronger (0.61 vs 0.58, t-test: Po0.001) when using SAR11 ITS single-base variants vs OTUs. Whole-community correlation between SAR11 and myoviruses was much improved when using ITS single-base variants vs OTUs, with Mantel rho = 0.49 vs 0.27; these results are consistent with strain-specific interactions.
    [Show full text]
  • The Biomass Distribution on Earth
    The biomass distribution on Earth Y. M. Bar-On, R. Phillips, R. Milo Supplementary Information Appendix Contents Overview ......................................................................................................................... 3 Plants ............................................................................................................................... 4 Biomass ....................................................................................................................... 4 Biomass of roots and leaves ........................................................................................ 6 Comparison of plant and bacterial biomass ................................................................ 7 Bacteria and Archaea (Prokaryotes) ............................................................................... 7 Marine ......................................................................................................................... 8 Soil ............................................................................................................................ 11 Marine deep subsurface sediment ............................................................................. 13 Terrestrial deep subsurface ....................................................................................... 18 Fungi ............................................................................................................................. 22 Soil fungi ..................................................................................................................
    [Show full text]
  • Molecular Marine Microbiology
    J. Molec. Microbiol. Biotechnol. (1999) 1(1): 3-4. JMMBMarine Symposium Microbiology 3 Molecular Marine Microbiology Douglas H. Bartlett* describes the bacterial manufacturing of magnetic iron containing organelles (magnetosomes) within certain Center for Marine Biotechnology and Biomedicine benthic bacteria and their biotechnological promise in Scripps Institution of Oceanography products ranging from magnetic tapes to magnetic University of California, San Diego resonance imaging devices. La Jolla, CA 92093-0202, USA Two articles deal with mysterious motility mechanisms operating in marine microbes. Linda McCarter introduces surface-regulated phenomena, including swarming motility The following thirteen minireviews introduce some of the via lateral flagella, in the human pathogen and marine exciting milestones being covered in molecular marine resident, V. parahaemolyticus. Bianca Brahamsha details microbiology today, and in many cases, their biomedical the only known case of liquid motility in the absence of or biotechnological relevance. The issues covered include flagella, a phenotype displayed by many marine quorum and anti-quorum sensing, selected symbioses, Synechococcus species. DNA shuffling in the environment, the evolution and devel- The minireviews end with descriptions of the opment of novel motility mechanisms, hydrocarbon deg- adaptations of certain deep-sea prokaryotes to extremes radation, the interactions of microbes with metals, and of pressure and temperature. Kato and Qureshi present a adaptations to extremes of pressure and temperature. Al- taxomonic overview of deep-sea bacteria and genetic and though most of these topics are not exclusive to marine biophysical analyses of respiratory chain adaptations to realms, they all have as a common thread a profound rel- elevated pressure. My article describes genetic evidence evance to the ocean environment.
    [Show full text]
  • Prokaryotic Growth and Nutrition
    37623_CH05_137_160.pdf 11/11/06 7:23 AM Page 137 © Jones and Bartlett Publishers. NOT FOR SALE OR DISTRIBUTION 5 Chapter Preview and Key Concepts 5.1 Prokaryotic Reproduction Prokaryotic • Binary fission produces genetically-identical daughter cells. • Prokaryotes vary in their generation times. Growth and 5.2 Prokaryotic Growth • Bacterial population growth goes through four phases. • Endospores are dormant structures to endure Nutrition times of nutrient stress. • Growth of prokaryotic populations is sensitive to temperature, oxygen gas, and pH. But who shall dwell in these worlds if they be inhabited? . Are we or 5.3 Culture Media and Growth Measurements • Culture media contain the nutrients needed for they Lords of the World? . optimal prokaryotic growth. —Johannes Kepler (quoted in The Anatomy of Melancholy) • Special chemical formulations can be devised to isolate and identify some prokaryotes. MicroInquiry 5: Identification of Bacterial Species Books have been written about it; movies have been made; even a • Two standard methods are available to produce radio play in 1938 about it frightened thousands of Americans. What pure cultures. is it? Martian life. In 1877 the Italian astronomer, Giovanni Schiapar- • Prokaryotic growth can be measured by direct elli, saw lines on Mars, which he and others assumed were canals built and indirect methods. by intelligent beings. It wasn’t until well into the 20th century that this notion was disproved. Still, when we gaze at the red planet, we won- der: Did life ever exist there? We are not the only ones wondering. Astronomers, geologists, and many other scientists have asked the same question. Today microbiol- ogists have joined their comrades, wondering if microbial life once existed on the Red Planet or, for that matter, elsewhere in our Solar System.
    [Show full text]
  • Mechanisms of Microbial Carbon Sequestration in the Ocean – Future Research Directions
    Biogeosciences, 11, 5285–5306, 2014 www.biogeosciences.net/11/5285/2014/ doi:10.5194/bg-11-5285-2014 © Author(s) 2014. CC Attribution 3.0 License. Mechanisms of microbial carbon sequestration in the ocean – future research directions N. Jiao1, C. Robinson2, F. Azam3, H. Thomas4, F. Baltar5, H. Dang1, N. J. Hardman-Mountford6, M. Johnson2, D. L. Kirchman7, B. P. Koch8, L. Legendre9,10, C. Li11, J. Liu1, T. Luo1, Y.-W. Luo1, A. Mitra12, A. Romanou13, K. Tang1, X. Wang14, C. Zhang15, and R. Zhang1 1State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China 2School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK 3Scripps Institution of Oceanography, UCSD, La Jolla, CA 920193, USA 4Dalhousie University, Halifax, Nova Scotia, Canada 5Department of Marine Science, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand 6CSIRO Marine and Atmospheric Research, Floreat, WA 6014, Australia 7School of Marine Science and Policy, University of Delaware, DE 19958, USA 8Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, 27570 Bremerhaven, Germany 9Sorbonne Universités, UPMC Univ. Paris 06, UMR7093, Laboratoire d’Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France 10CNRS, UMR7093, Laboratoire d’Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France 11Chinese University of Geology, Wuhan, China 12Centre for Sustainable Aquatic Research, Swansea University, Swansea, UK 13Dept. of Applied Physics and Applied Math., Columbia University and NASA-Goddard Institute for Space Studies, 2880 Broadway, New York, NY 10025, USA 14South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China 15Tongji University, Shanghai, China Correspondence to: N.
    [Show full text]