Microbial Ecology of the Oceans

Preface     xvContributors     xviiIntroduction and Overview   David L. Kirchman     1Eukaryotic Phytoplankton and Cyanobacteria     3Photoheterotrophic Bacteria     5Dissolved Organic Material     7Heterotrophic Bacteria     10Marine Archaea     13Heterotrophic Protists     14Nanoflagellates (2-20 [gamma]m)     14Microzooplanktonic Protists (20-200 [gamma]m)     16Dinoflagellates     16Marine Fungi     16Marine Viruses     17N[subscript 2] Fixers     18Nitrifiers and Other Chemolithotrophs     19Denitrifiers     20Concluding Remarks     21Summary     22Acknowledgments     22References     23Understanding Roles of Microbes in Marine Pelagic Food Webs: A Brief History   Evelyn Sherr   Barry Sherr     27Introduction     27Pre-1950s: The Early Years     281950-1974     291970s-1980s     32Improvement in Methods     32Bacterial Abundance     32Bacterial Activity     33Marine Heterotrophic Protists     34The "Microbial Loop"     361990-Present: The Molecular Revolution     39Summary     40References     41Bacterial and Archaeal Community Structure and Its Patterns   Jed A. Fuhrman   Ake Hagstrom     45Introduction     45Major Groups of Prokaryotes in Seawater     47"Classically" Culturable Bacteria     49The Roseobacter Clade of Marine Alphaproteobacteria     50Gammaproteobacteria     51Bacteroidetes     52Cyanobacteria     52"Sea Water" Culturable Bacteria     55SAR11 Cluster     55Not-Yet-Cultured Bacteria     57Marine Gammaproteobacterial Clusters     57Actinobacteria     58SAR116 Cluster     59SAR202     59Marine Group A     59Marine Group B     59Betaproteobacteria     59Marine Archaea     60Bacterioplankton Diversity     63Species Concept     63Microdiversity     64Components of Diversity: Richness and Evenness     65Community Structure: Description and Factors     67Bottom-Up Control     68Sideways Control     69Top-Down Control     70"Kill the Winner" Hypothesis     71Temporal Variation (Days to Seasonal)     72Short-Term Variation     72Seasonal Variation     72Spatial Variation     74Microscale Patterns     74Global Distribution     75Latitudinal Gradient and Degree of Endemism     76Patchiness and Large Eddies     77Summary     79References     80Genomics and Metagenomics of Marine Prokaryotes   Mary Ann Moran     91Introduction     91The Basics of Prokaryotic Genomics     92Genome Sequence and Assembly     92Finding Genes     95Finding Operons     96Functional Annotation     96Tame or Wild? Pure-Culture Genomics Versus Metagenomics     100Genomics in Marine Microbial Ecology     103The Ecology of Genome Composition     103Reverse Biogeochemistry: Discovery of New Ecological Processes     104Environmental Reductionism: New Details About Recognized Processes     106Comparative Genomics and Metagenomics     107Future Directions     122Summary     125Acknowledgments     125References     125Photoheterotrophic Marine Prokaryotes   Oded Beja   Marcelino T. Suzuki     131Introduction     131Facultative Photoheterotrophy by Unicellular Cyanobacteria     132Cyanobacteria as Facultative Heterotrophs     132Uptake of Urea and DMSP     133Uptake of Nucleosides and Amino Acids     134Field Studies Using Light and Dark Incubations     135Implications of Facultative Photoheterotrophy by Cyanobacteria     138Marine AAnP Bacteria: Habitats and Diversity     139Rediscovery of the Marine AAnP Bacteria     139Diversity of AAnP Bacteria     139Physiology of AAnP Bacteria     140AAnP Bacterial Abundance and Ecological Significance     142Proteorhodopsin-Containing Prokaryotes     143Proteorhodopsin Genotypes and Taxonomic Distributions     144Proteorhodopsin Spectral Tuning     145Proteorhodopsin-Containing Prokaryotes: Abundance and Activity      146Proteorhodopsin-Containing Prokaryotes: Ecological Significance     150Summary     151References     151Ecology and Diversity of Picoeukaryotes   Alexandra Z. Worden   Fabrice Not     159Introduction     159Functional Roles, Classification, and Biological Traits     162Photoautotrophs     163Heterotrophs and Alternative Lifestyles     170Environmental Diversity and Molecular Phylogenetics     172Diversity of Uncultured Populations     174Methodological Issues for envPCR Studies     178Distribution, Abundance, and Activities     179Methods for Quantifying Mixed Assemblages     180Distribution, Abundance, and Activity of Mixed Picophytoplankton Assemblages     182Quantifying Specific Picoeukaryote Populations     186Methodological Challenges to Quantifying Specific Populations and Resolving Dynamics     190Mortality, Contributions to Microbial Food Webs, and Microbial Interactions     191Genomic Approaches to Picoeukaryote Ecology     193Integration of Picoeukaryotes to the Microbial Food Web: Research Directions     194Summary     195Acknowledgments      196References     196Organic Matter-Bacteria Interactions in Seawater   Toshi Nagata     207Introduction     207Organic Matter Inventory and Fluxes     208DOM-Bacteria Interactions     211Labile Low-Molecular Weight (LMW) DOM     211Extracellular Hydrolytic Enzymes     215Polymeric DOM-Protein as a Model     217Refractory DOM     220POM-Bacteria Interactions     223POM Continuum     223POM Fluxes     223POM-Mineral Interactions     229Bacterial Community Structure and Utilization of Organic Matter     230Future Challenges     231Summary     232References     232Physiological Structure and Single-Cell Activity in Marine Bacterioplankton   Paul A. del Giorgio   Josep M. Gasol     243Introduction     243Distribution of Physiological States in Bacterioplankton Assemblages     245The Concept of "Physiological Structure" of Bacterioplankton Assemblages     245Starvation, Dormancy, and Viability in Marine Bacterioplankton     246Describing the Physiological Structure of Bacterioplankton      250Single-Cell Properties and Methodological Approaches     250Operational Categories of Single-Cell Activity     259Regulation of Physiological Structure of Marine Bacterioplankton     260Factors Influencing Physiological State of Bacterial Cells in Marine Ecosystems     261Factors Influencing Loss and Persistence of Physiological Fractions     263Distribution of Single-Cell Characteristics in Marine Bacterioplankton Assemblages     265Distribution of Single-Cell Activity and Physiological States in Marine Bacterioplankton     265Simultaneous Determination of Several Aspects of Single-Cell Activity and Physiology     270Patterns in Distribution of Single-Cell Activity and Physiology Along Marine Gradients     271Distribution of Activity and Growth Among Bacterial Size Classes     273Distribution of Activity Across and Within Major Phylogenetic Groups     274Dynamics of Single-Cell Activity and Physiological States     276Ecological Implications of Patterns in Bacterioplankton Single-Cell Activity     279Community Versus Individual Cell Growth and Metabolic Rates     280Linking the Distribution of Single-Cell Parameters and the Bulk Assemblage Response     282Ecological Role of Different Physiological Fractions     283Concluding Remarks     284Summary     285Acknowledgments     285References     285Heterotrophic Bacterial Respiration   Carol Robinson     299Introduction     299Measurement of Bacterial Respiration and Production     301Routine Measurement Techniques for Bacterial Respiration and Their Limitations     301Routine Measurement Techniques for Bacterial Production and Their Limitations     304Magnitude and Variability of Bacterial Respiration     304Temporal Variability     308Spatial Variability     309Relationship Between Bacterial Respiration and Environmental and Ecological Factors     311Bacterial Respiration as a Proportion of Community Respiration     315Predicting Bacterial Respiration     317Comparison Between Measurements and Predictions of Bacterial Respiration     319Magnitude of Bacterial Respiration in Relation to Primary Production     321Bacterial Respiration in a Changing Environment     324Summary     326Acknowledgments     327References     327Resource Control of Bacterial Dynamics in the Sea   Matthew J. Church     335Introduction      335Growth in the Sea     336Growth and Nutrient Uptake Kinetics     339Approaches to Understanding Resource Control of Growth     343Comparative Approaches     343Experimental Approaches for Defining Limitation of Bacterial Growth     349Limitation by Dissolved Organic Matter     351Bacterial Growth on Bulk DOM Pools     353Limitation by Specific DOM Compounds     354Limitation by Inorganic Nutrients     361Nitrogen     361Phosphorus     364Trace Nutrients     365Temperature-DOM Interactions     366Light     368Resource Control of Specific Bacterial Populations in the Sea     369Summary     371Acknowledgments     371References     371Protistan Grazing on Marine Bacterioplankton   Klaus Jurgens   Ramon Massana     383Introduction     383New Insights into Phylogenetic Organization     386Functional Size Classes of Protists     390Natural Assemblages of Marine Heterotrophic Nanoflagellates     391Functional Ecology of Bacterivorous Flagellates     394Living in a Dilute Environment     394Using Culture Experiments to Infer the Ecological Role of HNF     397Impact of Protistan Bacterivory on Marine Bacterioplankton     401Search for the Perfect Method to Quantify Protistan Bacterivory     401Rates of Protistan Bacterivory in the Sea     403Balance of Bacterial Production and Protistan Grazing     404Bottom-Up Versus Top-Down Control of Bacteria and Bacterivorous Protists     405Ecological Functions of Bacterial Grazers     406Grazing as a Shaping Force of Bacterial Assemblages     408Bacterial Cell Size Determines Vulnerability Towards Grazers     408Other Antipredator Traits of Prokaryotes     411Grazing-Mediated Changes in Bacterial Community Composition     414Molecular Tools for Protistan Ecology     414Culturing Bias and Molecular Approaches     414Global Distribution and Diversity of Marine Protists     420Linking Diversity and Function for Uncultured Heterotrophic Flagellates     422Summary     423Acknowledgments     424References     424Marine Viruses: Community Dynamics, Diversity and Impact on Microbial Processes   Mya Breitbart   Mathias Middelboe   Forest Rohwer     443Introduction     443Viruses and the Marine Microbial Food Web     444Direct Counts and Viral Numbers     444Viral Production and Decay Rates     447Viral Decay and Rates of Production in Pelagic Systems     447Measurements of Viral Production in Marine Sediments     449General Rates of Viral Production     449Role of Viruses in Biogeochemical Cycling     450Impact of Viruses on Bacterial Diversity and Community Dynamics     452Marine Viral Diversity     457Methods for Examining Marine Viral Diversity     457Culture-Based Studies of Viral Diversity     458The Need for Culture-Independent Methods     459Culture-Independent Studies of Viral Diversity Using Transmission Electron Microscopy     460Whole-Genome Profiling of Viral Communities Based on Genome Size     461Studies of Viral Diversity Using Signature Genes     461Metagenomic Studies of Viral Diversity     462A Vision for the Future     466Summary     467References     468Molecular Ecological Aspects of Nitrogen Fixation in the Marine Environment   Jonathan P. Zehr   Hans W. Paerl      481Introduction     481Chemistry, Biochemistry, and Genetics of N[subscript 2] Fixation     482Genetics and Enzymology     483Evolution of N[subscript 2] Fixation     485Phylogeny of Nitrogenase     487Genomics of N[subscript 2] Fixation     487Diversity of N[subscript 2]-Fixing Microorganisms     489Regulation in Diazotrophs     489Methods for Assessing Diazotroph Diversity, Gene Expression, and N[subscript 2] Fixation Activity     490Ecophysiological Aspects of N[subscript 2] Fixation     494Ecology of Diazotrophs in the Open Ocean     499Estuarine and Coastal Waters     505Benthic Habitats, Including Microbial Mats and Reefs     506Deep Water and Hydrothermal Vents     507Summary     508Acknowledgments     509References     509Nitrogen Cycling in Sediments   Bo Thamdrup   Tage Dalsgaard     527Introduction     527Inputs     531Transformations     532Microbes and Microbial Processes     532Processes Involving Mn and Fe     548Nitrogen Budgets     550Benthic Budgets      550Oceanic Budgets     552Summary     554References     555Index     569

\ Choice...useful resource for everybody working in this field...well-written material and simple and lucid illustrations...would serve as an excellent primary source of information on virtually any aspects of marine microbial ecology.\ \ \ \ \ SciTech Book NewsThe collection brings together concepts from autoecological studies of individual bacterial groups and from ecological studies of microbial assemblages.\ \ \ Choice...useful resource for everybody working in this field...well-written material and simple and lucid illustrations...would serve as an excellent primary source of information on virtually any aspects of marine microbial ecology.\ \ \ \ \ BooknewsSummarizes basic information known about microbes as components of the food webs and elemental cycles at work in the oceans. The collection brings together concepts from autoecological studies of individual bacterial groups and from ecological studies of microbial assemblages. Topics of the 16 contributions include microbial evolution as revealed by molecular techniques, microbes in carbon budgets and cycles, control of bacterial growth in idealized food webs, the impact of viruses on bacterial processes, interactions between bacteria and their grazers, the marine microbial nitrogen cycle, and symbiosis and mixotrophy among pelagic microorganisms. Annotation c. Book News, Inc., Portland, OR (booknews.com)\ \ \ \ \ From the Publisher"The collection brings together concepts from autoecological studies of individual bacterial groups and from ecological studies of microbial assemblages." (SciTech Book News, Vol. 25, No. 2 June 2001)\ "...useful resource for everybody working in this field...well-written material and simple and lucid illustrations...would serve as an excellent primary source of information on virtually any aspects of marine microbial ecology." (Choice Vol. 38, No. 9 May 2001)\ "...this is an excellent book...will serve as an authoritative source on bacterial life in the water column...I recommend it warmly to anyone interested in biological oceanography and the microbial life in the sea." (Journal of Experimental Marine Biology and Ecology, Vol. 269, 2002)\ \ \