HETEROTROPHIC ACTIVITY IN THE SEA NATO CONFERENCE SERIES II III IV V VI Ecology Systems Science Human Factors Marine Sciences Air-Sea Interactions Materials Science IV MARINE SCIENCES Recent volumes in this series Volume Structure and Development of the Greenland-Scotland Ridge edited by Martin H P Bott, Svend Saxov, Manik Talwani, and Jarn Thiede Volume Trace Metals in Sea Water edited by C S Wong, Edward Boyle, Kenneth W Bruland, J D Burton, and Edward D Goldberg Volume 10A Coastal Upwelling: Its Sediment Record Responses of the Sedimentary Regime to Present Coastal Upwelling edited by Erwin Suess and Jarn Thiede Volume 10B Coastal Upwelling: Its Sediment Record Sedimentary Records of Ancient Coastal Upwelling edited by Jarn Thiede and Erwin Suess Volume 11 Coastal Oceanography edited by Herman G Gade, Anton Edwards, and Harald Svendsen Volume 12 Hydrothermal Processes at Seafloor Spreading Centers edited by Peter A Rona, Kurt Bostrom, Lucien Laubier, and Kenneth L Smith, Jr Volume 13 Flows of Energy and Materials in Marine Ecosystems: Theory and Practice edited by M J R Fasham Volume 14 Mechanisms of Migration in Fishes edited by James D McCleave, Geoffrey P Arnold, Julian J Dodson, and William H Neill Volume Heterotrophic Activity in the Sea edited by John E Hobbie and Peter J IeB Williams HETEROTROPHIC ACTIVITY IN THE SEA Edited by John E Hobbie Marine Biological Laboratory Woods Hole, Massachusetts, USA and Peter J le8 Williams Department of Marine Microbiology Gothenburg University Gothenburg, Sweden Published in cooperation with NATO Scientific Affairs Division PLENUM PRESS· NEW YORK AND LONDON Library of Congress Cataloging in Publication Data NATO Advanced, Research Institute on Microbial Metabolism and the Cycling of Organic Matter in the Sea (1981: Cascais, Portugal) Heterotrophic activity in the sea (NATO conference series IV, Marine Sciences; v 15) "Published in cooperation with NATO Scientific Affairs Division." Bibliography: p Includes index Bacteria, Heterotrophic-Congresses Marine bacteria-Congresses Marine microbiology-Congresses I Hobbie, John E II Williams, Peter J leB III Title IV Series 576'.15'09162 84-11601 QR106.N37 1981 ISBN 978-1-4684-9012-1 ISBN 978-1-4684-9010-7 (eBook) 001 10.1007/978-1-4684-9010-7 Proceedings of a NATO Advanced Research Institute on Microbial Metabolism and the Cycling of Organic Matter in the Sea, held November 1981 in Cascais, Portugal © 1984 Plenum Press, New York Softcover reprint of the hardcover 1st edition 1984 A Division of Plenum Publishing Corporation 233 Spring Street, New York, N.Y 10013 All rights reserved No part of this book may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without written permission from the Publisher PREFACE Introduction This book contains papers given at a NATO Advanced Research Institute (A.R.I.) held at Caiscais, Portugal, in November, 1981 The subject of the A.R.I was marine heterotrophy; this is defined as the process by which the carbon autotrophically fixed into organic compounds by photosynthesis is transformed and respired Obviously all animals and many microbes are heterotrophs but here we will deal only with the microbes Also, we restricted the A.R.I primarily to microbial heterotrophy in the water column even though we recognize that a great deal occurs in sediments Most of the recent advances have, in fact, been made in the water column because it is easier to work in a fluid, apparently uniform medium The reason for the A.R.I was the rapid development of this subject over the past few years Methods and arguments have flourished so it is now time for a review and for a sorting out We wish to thank the NATO Marine Science Committee for sharing this view, F Azam, A.-L Meyer-Reil, L Pomeroy, C Lee, and B Hargrave for organizational help, and H Lang and S Semino for valuable editing aid Autoecology vs Synecology The techniques of microbiology were developed for laboratory use When they are applied to seawater they also appear to work; at least microbes can be isolated and identified, organic compounds disappear and are oxidized, and oxygen decreases However, have these techniques identified the important organisms, rates, and controls occurring in nature? This must still be the overriding question for the study of marine heterotrophy With this emphasis on the process in nature, one concludes that most of the traditional laboratory techniques become unusable: most microbes from seawater not grow on agar plates, microbes quickly multiply or die in incubation bottles, and incubations in the past have often been carried out for extended periods in order to measure change in substrate concentration Whereas it may be too extreme to say that most of the measurements in the past have been artifacts, the probability of artifacts caused by experimental conditions is quite high v PREFACE and has to be considered in every measurement The great advances in methods in the past decades have been in synecology: the study of organisms as communities or as parts of cycles or processes The other approach, autecology, or the study of individual species, has been in eclipse because of an inability to relate microbial species, isolated from nature and studied in laboratory cultures, back to their role in natural processes Synecology has flourished recently in large part due to advances in biochemical and biomedical techniques and instruments and to their adaptation to ecological problems For example, bacteria may now be counted in natural waters because of greatly improved epifluorescent microscopes and new types of membrane filters, both developed initially for medical and industrial research Yet, in spite of new methods and instrume~ts, the problem of how to measure the various aspects of microbial heterotrophy in the sea has not been resolved This is due in part to the necessity for making measurements in the field and in part to the very low levels of bacterial activity There is still no single, agreed upon method for measuring bacterial growth or respiration so the literature is filled with arguments about different methods Many of the arguments would be ended if a single method were available, no matter how laborious or difficult, as a standard for calibration of other easier methods The Problem of Production Measurements Throughout this book and in discussions at conferences and in the literature, the emphasis is on production or growth of microbes Heterotrophy is also a degradative process and it would appear that the rate and controls of the process could be measured without measuring production For some questions it is true that a rate measurement would have also been adequate to answer the question There are also major questions about the pathways of carbon and energy flow in marine food webs that can only be answered with a production measure For example, if microbes are being fed upon by protozoans and higher filter feeders, then the production rate of microbes is an integral part of the calculation of energy flow The techniques for measuring production have been developed for a number of groups of marine organisms Hhy then is there a problem for heterotrophic microbes? The general answer is that marine microbes live in a dilute environment where every process is difficult to measure; this is further confounded by the fact that microbes respond rapidly to any change in their surroundings so all incubations may influence results Some detailed comments about the production problem follow PREFACE Microbes degrade and eventually take up, grow on, and respire an enormous variety of organic compounds At one point in time each species or even each cell may be specializing on one or several compounds or may be simultaneously taking up a large number of compounds The practical effect is that production cannot be measured by adding a single radioactively labelled compound (e.g., glucose) and measuring the rate of use by microbes This contrasts wth algal primary production which may be estimated by following the metabolism of a single compound such as oxygen or carbon dioxide Microbes in the sea are able to increase and decrease their activity over wider ranges than any other group of organisms If environmental conditions are favorable they grow rapidly If conditions are unfavorable they may become nearly dormant The result is that merely demonstrating the presence of x 10 6cells per ml in the environment tells us nothing immediately about their production rate Higher organisms either respire continuously or must enter distinctive resting states For this reason, we learn a great deal more from their presence when we try to interpret energy flow The continuous processes that remove microbes - that is, death and grazing -occur at the same time as production The result is that neither a steady state nor changes in the numbers of bacteria necessarily reflect bacterial production or lack of production In this context, death may occur as attack by other microbes or as natural lysis Both are possible but their importance in the sea is unknown Other organisms compete for substrates with the microbes While a small flagellate taking up dissolved organic carbon is a part of a heterotrophic process, it can interfere with a measurement of prokaryotic microbial production It is also known that higher organisms, such as mussels, can remove large amounts of dissolved organic matter from solution and this makes it difficult to infer microbial production from mass balance Some microbes rapidly respond to changed conditions When water samples are collected and incubated over time, some microbes flourish and some may die In a practical sense, only those techniques may be used that have short incubations of minutes or perhaps a few hours Microbial production is low in most of the sea, at times less than 10 ~g C liter- l day-I, so that techniques such as measuring the loss of oxygen or the production of ammonia are analytically very demanding vii PREFACE The General Questions of Marine Heterotrophy The discussion above stresses the difficulties of studying marine heterotrophy In this way we have attempted to explain without being too negative why the workers in this field not have a better idea of microbial processes in the sea Yet, in this NATO Advanced Research Institute the participants dealt with the recent progress in measuring and understanding marine heterotrophy; a feeling of accomplishment and optimism prevailed We now will give an overview of the outcome of the discussions organized around four general questions: What is the identity and abundance of marine microbial heterotrophs such as bacteria and microflagellates? What are the rates of heterotrophic processes such as growth, respiration, and mineralization of nitrogen and phosphorus? What is the role of the marine heterotrophs in the food web of the ~ea? What are the controls of the various processes that make up heterotrophy in the sea? The Identity and Abundance of Heterotrophs Despite our progress in measuring rates and identifying the role of marine microbes in the heterotrophic process, we are uncertain about the species composition of the community The classic techniques of plate or dilution cultures yield data on abundance and identity of the organisms we are able to cultivate Within the last decade it has become clear that the resulting numbers were wrong and that a very small percentage of the marine bacteria grow in enrichment cultures This leaves us uncertain as to whether the species isolated are representative of the community as a whole Monoclonal antibody techniques may well resolve this particular question but will, of course, only work with species amenable to culture If we did know the identity of all the bacteria in a water body, then we could answer the recurring question of whether the sea is populated by microbial specialists or microbial generalists The incomplete evidence so far would indicate that Pseudomonas-like generalists predominate Advances in microscopic techniques in recent years have finally allowed direct counts to be made of microbes in seawater These somewhat labor intensive methods utilize an epifluorescent microscope to count the bacteria which have been dyed with a fluorescent nuclear stain and filtered onto a membrane Important findings have included the large number of bacteria (10 5-10 ml- l ) and the PREFACE ix generally small size of the cells (0.2-0.4 ~m in diameter) It appears that the technique can be automated with computer image analysis (J Sieburth, personal communication) With slight modifications, the epifluorescent methods can also be used to count small flagellates in the 2-20 ~m size range and to differentiate between the autotrophic and heterotrophic forms An extension of fluorescent dye techniques, flow cytometer cell sorting, can be used to effect some physical partitioning of the microbial community The technique has been successful for larger bacteria such as nitrifiers While it is now relatively easy to obtain numbers of microbes, it is more difficult to convert these numbers to biomass or carbon It is clearly difficult to determine with any precision the exact dimensions of cells close to the limit of resolution of the light microscope Even after a biovolume is obtained, it often needs to be converted for ecological reasons to units of carbon and these factors have so far been derived entirely from laboratory cultures of large bacteria An alternative approach to the problem has been to measure some biochemical component of the bacterial cell Some of these components, such as ATP, are not specific to bacteria Most have the same problem of the conversion factors which might well vary from population to population and from time to time For example, a muramic acid conversion factor will change by almost an order of magnitude depending on whether the bacteria are gram negative or gram positive In summary, whereas we now know that microbes are abundant and have a significant biomass relative to other heterotrophs such as the metazoa, the indigenous species composition is still a closed book Rates of Heterotrophic Processes As a result of growth and activity, heterotrophs are involved in a number of interrelated processes such as decomposition of complex molecules, respiration, remineralization, mineralization, and the uptake of dissolved organic compounds and their conversion to particulate mate.rial Measurements of any of these has been very difficult in the past but in the last decade very real advances have been made Bacterial growth, a fundamental property, has been estimated both directly and indirectly Direct measures depend upon changes in biomass (or related parameters) and will only work when grazers are unimportant or are removed from the &ystem In practice, it has proven difficult to remove the grazers, particularly microflagellates, without disrupting the system Because of these problems, indirect methods of measuring growth have been developed One technique, the frequency of dividing cells, involves no incubation but instead relies upon determination of the percentage of the population in the dividing state The technique x PREFACE is promising but needs testing in a wide variety of environments Another set of techniques involves short incubations in order to determine the rate of incorporation of labelled precursors into RNA and DNA These approaches are in an active state of development at present and seem to have great potential However, they still need testing in a variety of environments and clarification of their biochemistries Until these problems are resolved, the usefulness of the techniques remains in question The measurement of a change in concentration of oxygen, carbon dioxide, or inorganic nutrients is a further way to determine heterotrophic rates So far, the oxygen change method has been most widely used for in vitro studies With recent improvements in instrumental analysis,-rt may be expected that both the oxygen technique and the total carbon dioxide measurements will be more widely used in the study of overall microbial activity In situ studies depend both on analytical sensitivity and on the ability~describe mixing and gas exchange in the environment In spite of the long history of this approach, there are only a few measurements that pertain to the upper mixed layers of the ocean where the biology is interesting but the mixing is difficult to ·measure In situations where recycling is important, then isotope dilution techniques are often used For example, 15N techniques allow both uptake and production of ammonia to be calculated Another system in which uptake and production are closely coupled is the production of dissolved organic compounds by algae and their rapid uptake by bacteria The algal compounds can be labelled with 14C and the separation of algae and bacteria attempted by filtration However, even after very short incubations, some of the photoassimilated 14C will have already been respired by the bacteria so the method underestimates bacterial production from algal exudates In addition to the exudates, bacterial growth will also be sustained by the breakdown of algal particulate matter The first useful isotope method for investigating heterotrophy was the measurement of the uptake and respiration of single organic compounds, such as glucose, amino acids, or acetate This approach gives a relative measure of activity and information on conversion efficiency of these compounds, but can not be expected to give a measure of overall microbial metabolism A method that stands by itself is the enzymatic measure of the activity of the electron transport system This has the great advantage of not involving an incubation of cells, but in order to interpret the results in conventional ecological terms either biochemical assumptions have to be made or the method has to be cross calibrated against other methods CONTRIBUTORS Dr Farooq Azam Institute of Marine Resources University of California, San Diego A-018 La Jolla, California 92093 Dr Robert Bertoni Istituto Italiano di Idrobiologia 28048 Pallanza, Italy Dr Gilles Billen Laboratory of Oceanography Universite Libre de Bruxelles Avenue F D Roosevelt 50 1050 Brussels, Belgium Dr Angelo F Carlucci Scripps Institute of Oceanography A-018 La Jolla, California 92093 Dr John Davies Department of Agriculture and Fisheries Marine Laboratory Aberdeen, Scotland, United Kingdom Dr I Dundas Department of General Microbiology University Bergen Allegt 70, Bergen, Norway Dr Geoffrey Eglinton Organic Geochemistry Unit School of Chemistry University of Bristol, Cantock's Close Bristol BS8 ITS, United Kingdom Dr Gloria Cruz Ferreia Departamento da Quimica 3800 ACErRO, Portugal 555 CONTRIBUTORS 556 o Dr Ake Hagstrom Department of Microbiology University of Umel S-901 87 Umel, Sweden Dr Barry T Hargrave Marine Ecology Laboratory Bedford Institute of Oceanography Dartmouth, Nova Scotia Canada B2Y 4A2 Dr A Herb1and Antenne O.R.S.T.O.M Center Oceano1ogica de Bretagne B P 337, Cedex, France Dr John E Hobbie Marine Biological Laboratory Woods Hole, Massachusetts 02543 Dr Ho1ger Jannasch Woods Hole Oceanographic Institution Woods Hole, Massachusetts 02543 Dr William J Jenkins Woods Hole Oceanographic Institution Woods Hole, Massachusetts 02543 Dr Carl C Barker J~rgensen Zoophysio1ogica1 Laboratory University of Copenhagen Universitetsparken 13 DK-21 Copenhagen ~, Denmark Dr David M Karl Department of Oceanography University of Hawaii Honolulu, Hawaii 96822 Dr Cindy Lee Woods Hole Oceanographic Institution Woods Hole, Massachusetts 02543 Dr William Li Marine Ecology Laboratory Bedford Institute of Oceanography Dartmouth, Nova Scotia Canada B2Y 4A2 CONTRIBUTORS 557 Dr Lutz Meyer-Rei1 Institut fur Meereskunde an der Universitat Kie1 Abtei1ung Marine Mikrobio1ogie Kie1, Federal Republic of Germany Dr David J W Moriarty Division of Fisheries and Oceanography CSIRO, P O Box 120 Cleveland, QLD 4163, Australia Dr Richard Morita Department of Microbiology Oregon State University Corvallis, Oregon 97331 Dr R C Newell Institute for Marine Environmental Research Prospect Place, The Hoe Plymouth PLl 3DH, United Kingdom Dr Bruce J Peterson Marine Biological Laboratory Woods Hole, Massachusetts 02543 Dr Lawrence R Pomeroy Institute of Ecology University of Georgia Athens, Georgia 30602 Dr Francis A Richards Department of the Navy Office of Naval Research Branch Office, London, Box 39 FPO New York 09510 Dr Bo Riemann University of Copenhagen Freshwater-Biological Laboratory 51 He1sing~rsgade -DK 3400 Hil1er~d, Denmark Dr Jonathan Sharp College of Marine Studies University of Delaware Lewes, Delaware 19958 Dr John MeN Sieburth Graduate School of Oceanography University of Rhode Island, Bay Campus Narragansett, Rhode Island 02882-1197 558 CONTRIBUTORS Dr Frank B van Es BioI Res Eurs Estuary Department of Microbiology Groningen University Kerklaan 30 9751 NN, Haren, The Netherlands Dr Hans van Gemerden Department of Microbiology Groningen University Kerklaan 30 9751 NN, Haren, The Netherlands Dr Peter Wangersky Department of Oceanography Dalhousie University Halifax, Nova Scotia Canada B3H 4Jl Dr William Wiebe Department of Microbiology University of Georgia Athens, Georgia 30602 Dr Peter J leBo Williams Department of Oceanography The University Southampton S09 SNH, United Kingdom Dr Richard T Wright Department of Biology Gordon College Wenham, Massachusetts 01984 INDEX Acanthoepsis unguiculata electron micrograph of, 420 Acetate uptake, 331, 335 Acinetobacter effect of substrate on, 60 Actinomonas as bacteria grazer, 407 photomicrograph of, 419 Active transport, 68 Active transport systems, 327-329 Activity determinations, 508 Adaptation in microorganisms, 25, 27-45 Adenine incorporation into nucleic acids, 182, 184, 198-213, 219, 222 Adenine metabolism, 199-206 Advection-diffusion equations, 392-393 Advection-diffusion models, 304-306, 308, 393-402 Aerobacter enzyme synthesis in, 41 growth rate, 43-44 Aerobic respiration, 57 Affinity, 26-30, 32-33, 35, 36, 40-42, 47, 49, 69, 87-88 Aggregate formation, 7-8 Alanine uptake, 332, 336 Algal exudation, 189-190, 192, 255 Allochthonous inputs, 102-104, 111 Alteromonas ha1op1anktis transport constants of, 328 Amines primary, 318, 472 Amino acids, 84-93, 101, 112, 122, 126, 131, 135, 315, 559 Amino acids (continued) 317, 321-322, 472 Amino acid uptake, 331-339 Amino acid utilization, 317, 320, 344-346 Ammonia release, 339-340 Ammonia uptake, 332, 340 Ammonium nitrification, 307 Amoebae as bacteria-eating rhizopods, 406-407 Anaerobic respiration, 57-58 Anca1omicrobium prosthecae development, 31, 46 Anoxic marine environments, 298-302 ANT 300 arginine binding in, 93-95 arginine uptake by, 87-88 chemotactic response of, 93-94 glutamic acid uptake by, 88 survival of, 72 AODC, 136-137, 141-145 Apparent oxygen utilization, 296-297, 391, 396 Appendicu1arians filter feeding, 452-453 grazing impact, 455-456 Arginine binding, 93-95 Arthrobacter as prey, 410 endogenous growth of, 49-50 Aspergi111us nidu1ans thymidine kinase in, 220 Assimilation efficiency of bacteria, 58, 66 Atmospheric inputs, 102-104 ATP increase growth method, 182, 185, 202-205, 211-213 560 Attached bacteria, 61, 74 on detritus, 63-64 on living organisms, 64-65 types of attraction, 63 Autochthonous inputs, 102 Azoic zone, 290 Bacillus as prey, 410 group translocation in, 69 Bacteria attached (see Attached bacteria) biomass of, 525-528, 538-542 counting of, 2-3 distribution and dynamics of, 420-423 growth of, 180-186, 188-192, 211-212, 217-219, 223, 225-228, 234, 239, 249-260 growth cycle of, 61 growth rate of in situ, 59 role of substrate composition, 60 role of substrate concentration, 60, 86 role of temperature, 60, 233, 255-256 growth state in situ, 72 growth yields-of:-sG-60, 74 number of, 524-528 population survival strategies of, 16-17 roles in marine ecosystems, 2, 179-181, 189, 192 significance in food web, 188 size of, 60-63, 74, 235, 255, 257 starvation and survival of, 71-75, 191 Bacterial activity, 128, 134 Bacterial decomposition, 274-275 Bacterial hopanoids, 489-494 Bacterial production, 6-7, 122, 130-134, 152, 145-146, 180-181, 186-188, 192, 226-228, 237-238, 241245, 249, 252, 539-542 INDEX Bacterial secondary production, 188, 233, 237, 239, 242, 244-245 Bacterial utilization, 104, Ill, 338 Bacteriop1ankton communities, 148-149 Bacteriop1ankton growth measurement, 172-192 Bacterivory ciliate, 408-411, 430 flagellate, 407-408, 428 protozoan, 405-435 rhizopod, 405-407 Balanced growth, 180-181, 213 Ba1antiophorus minutus prey aggregation by, 412 Barophi1ism, 505, 511-513, 517 Baroto1erance, 505, 511-513, 517 Beggiotoa chemoautotrophism in, 303 occurrence of, 516 Benekea group translocation in, 69 Binding proteins, 88-89, 93, 96 Biological marker compounds, 485 Biomass determinations, 506-507 Biva1 ve gill fluid mechanics of, 449-451 Bodo ~ bacterial grazer, 407 electron micrograph of, 420 and phosphate excretion, 15-16 photomicrograph of, 419 Bottle effect, 358 Bubbles and particle formation, 273-274 Calibration of growth methods, 185-186, 190, 206-207, 209 Ca1athrix occurrence of, 516 Carbohydrates, 101, 112-113, 126, 131, 133, 147 Carbon dissolved organic, 4, 71, 83, 85, 158 composition of, 122, 124-127 INDEX 561 Carbon (continued) Choanocytes, 448 dissolved organic (continued) Chore11a cordata humus, 14-16 in adenine calibration labile, 122, 134 experiment, 209 refractory, 122 Chromatium seasonal variation in, 125 growth rate of, 33-35, 45 sources and sinks of, 11-12, Chromatium vinosum 122-123 growth vs storage in, 33-34 turnover of, 127-134, 531-533 substrate use by, 39 Chromatium weissei uptake of, 529-535 extracellular organic, 233-245 growth vs storage in, 33-35 global cycle of, 4-12 Ciliary feeding, 449-451, 454 mineralization of, 337 Ciliate bacterivory, 408-411, 430 particulate organic,S, 7-8, Ciona intestina1is 83-84 mucus filter of, 452 decomposition of, 535-538 Cirri, 449-450 distribution of, 271-273 Ca1yptogena magnifica sedimentation of, 156-157, occurrence of, 516 160-174 Clostridium Carbonate substrate use by, 37-38 in ocean, 167 Cluster hypothesis, 190 Carbon budgets, 105-107, 110, 14C02 production 233-234 from labelled organic Carbon dioxide production, 367-373 additions, 367, 372 Carbon flow diagrams, 547-554 C02 reduction, 301 Carbon production, 211-213 Cocco1ithus hux1eyi Carchesium transport constants of, 328 prey aggregation by, 412 Co-metabo1ism, 67, 122 Cau10bacter Competition enzyme synthesis in, 41 in microorganisms, 25-30, 33-34, growth rate of, 44, 49-50, 86 37-39, 41, 43, 45, 258 Cell increase growth method, Conceptual model, 148-149 182, 185 Continuous culture CEPEX, 134, 341, 381, 456 ("chemostat"), 26-28, 37Chaetoceros pe1agicus 38, 42, 65, 86, 102-110, adenine uptake and 113, 183, 186, 250, 252, assimilation, 203 255-256, 509 Challenger Expedition, 290 Creatin, 319 Chemical approach, 124-127, Cricosphaera carterae 132-133 adenine uptake and Chemoautotrophic bacteria, 506, assimilation, 203 508, 513-517 Cyanobacteria, 4, 13, 45 Chemosynthesis, 514-518 thymidine kinase in, 220-221 Chemosynthetic bacteria, 435 Cyc1osa1pa spp Chemosynthetic uptake, 308 filter characteristics of, Chemotaxis, 92 452-453 Ch1orella, 416 Cyc10tella ~ Ch1orobium adenine uptake and maintenance energy of, 45 assimilation, 203 562 Cyclotella nana transport constants of, 328 Cylindrotheca sp in adenine calibration experiment, 209 Dark l4C02 production, 371 Dark l4C02 uptake, 242-243 Decomposition role of marine bacteria, 12-16, 67, 84 Decompression, 511-513 Deep sea, 505-518 Denitrification, 300, 306 Desulfovibrio thymidine incorporation in, 221 Detritus, 14-15 Detritus hydrolysis, 325-326 Diatom bloom, 234-236, 238, 259, 471 (see also Spring bloom-)- - Diel changes in dissolved carbohydrate concentrations, 423-424 in oxygen concentrations, 369, 362-366, 369 Diel cycles of carbon, 424 of growth, 190-192, 227-228, 239-245, 249, 251, 255, 257-260 Diel effects on DOC pool, 125-126 Dinoflagellate bloom, 471 Dissolved organic matter, 101, 103, 188-189, 314, 320-321 uptake in bivalves, 453 Ditylum brightwellii transport constants of, 328 DNA purification of, 222-224 synthesis, 198-213, Z17-229 DOC, see Carbon, dissolved organic Dormancy, 139, 149, 191 Dunaliella sp osmoregulation in, 110 INDEX Dunaliella tertiolecta respiration and excretion losses from, 108 transport constants of, 328 Electron microscopy, 413-420 Electron transport system activity of, 373, 375-379 Emiliania huxleyi adenine uptake and assimilation, 203 lipids in, 495, 497-499 Emiliania ovata lipids in, 495 Enclosure experiments large scale 465-477 Energy metabolism, 57 Enrichment experiments, 134-140, 146-147 EOC, see Carbon, extracellular organic Epibacteria, 421-422, 428, 430 Epifluorescence microscopy, 413419, 525 Epistylis prey aggregation by, 412 Escherichia coli binding protein, 89 DNA synthesis, 226 episomal transfer, 70 glycerol uptake by, 69 growth rate of, 59-60 as prey, 411 survival of, 71 transport system in, 327 use of exogenous adenine, 201-202 Estuarine bacteria, 136-147 Euglena assimilation:respiration ratio, 57-58 Euglena gracilis thymidine kinase in, 220 Euplotes photomicrograph of, 419 Evolution of micrographs, 25-27, 32, 45 Exoenzymatic hydrolysis, 322-326 Extracellular enzymes, 535-537 563 INDEX Exudation of DOC, 123, 140-141 Exuviella sp adenine uptake and assimilation, 203 Fecal pellets, 482-483 settling of, 166-167, 171 Fermentation, 57 Filter feeding, 445-462 (see also Suspension feeding) Flagella, 448-449, 452 Flagellate bacterivory, 407-408, 428 Flavobacterium group translocation in, 69 FLEX, 369 Flocculation of bacteria, 412-413 Food chains allochthonous materials in, 4-6 detritus in, 14-16 heterotrophic uptake in, 9-10 primary production in, 4, 101-106, Ill, 114 secondary production in, 6-7 trophic efficiency of, 1, 427, 428, 430, 472-476 Forbes-Thompson debate, 290 Free-living bacteria, 189-190, 192, 275, 278 Frequency, of dividing cells, 182-183, 187, 192, 217, 242-245, 249-253, 255-259, 426 Geochronology, 168-169 Geological record, of microbial lipids, 489-495 Geostrophic estimates, 394-396 Geothermal energy, 516-517 Geukensia demissa grazing impact of, 459, 461-462 Glaucoma bacterivory by, 410 Glucose respiration of, 534-535 turnover time, 534 uptake of, 235-236, 239, 241, Glucose (continued) uptake of (continued) 242, 330, 335, 475, 531 Glycollate uptake, 339 Gravitational settling, 155, 163 Grazer-controlled community, 148 Grazing impact, of suspension feeders, 454-462 Grazing pressures, 254-255, 258-259 Ground water inputs, 102-104 Group translocation, 69 Growth efficiency, 58-59 Growth-nutrient regime relationships, 189-190 Growth rate, 26-36, 42-50, 180-186, 188-192, 211 of bacteria, 59-61, 86, 180-186, 188-192, 217219, 223, 225-228, 234, 239, 249-260 of phytoplankton, 101-102, 104105, 107, 113-114, 160 Growth state of bacteria, 72 Growth yields of bacteria, 56-60, 74 Gymnodinium adenine uptake and assimilation, 203 Hartmanella bacterivory by, 407 History of marine microbiology, 2, 290-291 Humus marine, 14-16 Hydrolysis of particles and polymers, 189-190, 192 Hydrothermal vents, 513-517 Hyphomicrobium endogenous growth of, 44, 49-50 methanol affinity of, 32-33 stalk length of, 32-33, 46 In situ production, 104 Intestinal microflora, 511 564 Intracellular compartmentalization 204 207 Intrusive sampling approach 127-129 Isochrysis thymidine incorporation by 220 Isotope dilution 224-227 243 340 Kerogen breakdown during catagenesis 494 Kinetic approach 129-129 133134 139-140 Klebsiella as prey 411 Labile DOC 122 134 Lauderia borealis adenine uptake and assimilation 203 and carbohydrates in sea water 112 Lipid composition influence of growth conditions 497 Lipid indicators of microbial activity 481-500 Lipids of marine sediment 484-487 489-500 Macromolecular synthesis 204 226 Maintenance energy 42-45 96 Manganese oxidizing bacteria 516 Marine snow 166 421-422 431 433 510 Material balance studies 157-163 Mathematical model, 147-148 Mayorella photomicrograph of 419 Melosira nummuloides transport constants of 328 Mesodinium rubrum biomass of, 254 Methanogenic bacteria 516 Methanogenic bacterial lipids 484 INDEX Microbial lipid signatures 494 499 Microbial mats 516 Microbial niches 511 Micrococcus cryophilus wax ester profile of 497 M!cromonas pusilla 416-417 Microplankton 413-414 Mineralization 30 260 336-338 472 Mineral nitrogen assimilation 326-327 uptake 333 Molecular evolution 495 Monas ~bacterial grazer 407 Monochrysis lutheri adenine uptake and assimilation 203 respiration and excretion losses from 108 Monosaccharide uptake 339 Mucus filter 447 451-454 Mucus net feeding 451-453 457 Mytilus californianus uptake of dissolved organic matter 453 Mytllus edul1s filter feeding by 449-451 grazing impact of, 456-461 uptake of dissolved organic matter by 453 Naegleria bacterivory by 407 Nanochloris 416 Nanoplankton 413-414 418, 422-423 425-428 430 Navicula pavillardi transport constants of 328 Neurospora crassa thymidine kinase in, 220 Nitrate reduction, 300, 306-307 Nitrate uptake, 332 Nitrification 333 Nitrite production rate 307 Nitrocystis oceanus transport constants of, 328 INDEX Nitrogen cycle, 292, 342-343, 471-472 dissolved organic, 314-316, 318-320, 322, 325-326 characterization of, 315 fixation, 517 mineralization, 336-338, 472 regeneration, planktonic, 343, 472 uptake kinetics, 329-333 uptake mechanisms, 326 Nitrogenous material in seawater, 85 Nitrosococcus role in nitrification, 307 Nitrosomonas role in nitrification, 307 Nitrosomonas europaea transport constants of, 328 Nitzchia sp adenine uptake and assimilation, 203 Nucleic acid synthesis, 198-213, 217-219 Nucleotide fingerprinting, 198 Nutrient cycling, 471-472 Nutrient regeneration, 266, 268, 277-278 Ocean General Circulation Models, 402 Oicomonas as bacterial grazer, 407 Oicomonas termo prey aggreation by, 412 Oikopleura ~ as predator, 473-474 Oikopleura spp filter feeding by, 452 grazing impact of, 454-456, 461-462 Oil decomposition by bacteria, 67, 268, 276-277, 489, 494 Oligotroph "model" characteristics, 46-51 Oochromonas danica prey aggregation by, 413 565 Opal in ocean, 167 Organic excretion, 102, 107-114 Organic geochemistry, 481, 483, 499 Organic matter inputs, 101-104 Oxygen consumption rates, 303-306, 358-366, 377-379, 383, 395 development of atmosphere, 12-13 in ocean, 14, 83 uptake, 156-158, 174 utilization rates, 391, 399 Paramecium and phosphate excretion, 15 Paramecium caudatum prey aggregation by, 412 Paramoeba photomicrograph of, 419 Paraphysomonas as bacterial grazer, 407 electron micrograph of, 420 photomicrograph of, 419 Particle counter, 446-447 Particle retention by suspension feeders, 446-462 Particle settling, 155-157, 160-174 Particulate matter aggregate formation, 7-8 composition of, 270-271, 294-295 in estuaries, 264-265 fecal pellets, 8-9, 15, 64, 267-268 formation of, 273-274 microorganisms in, 7-9, 64 sources of, 7, 263-270 Passive transport, 68 Patchiness, 507, 510-511 2l0Pb flux, 162, 167, 169-171 pe02 changes, 367-368 Peridinium foliaceus adenine uptake and assimilation, 203 INDEX 566 Peritromus photomicrograph of, 419 Petroleum (see also Oil) in ocean, Phaeocystis poucheti excretion by, 321 Phaeocystls sp adenine uptake and assimilation, 203 Phallusia mammillata mucus filter of, 452 pH changes, 367-369 Phenotypic response, 25, 32 Phosphate in water column, 297 Phosphate reduction, 301-302 Phosphorous regeneration, 156-158 Photobacterium group translocation in, 69 Phytoplankton, 101-114 bloom, 237-238, 269, 272, 321 death of, 102, 113, 321 excretion by, 320-321, 326, 342, 467-471 growth rates of, 101-102, 104105, 107, 113-114, 160 lipids, 482-483 nitrogen composition, 322 production, 160-162, 168, 172173, 245, 254, 257 Phytoplankton-bacteria interactions, 188-189 Phytoplankton bloom (see Spring bloom) -Picoplankton, 413-414, 416-418, 422-423, 425-431 Platyamoeba photomicrograph of, 419 Platymonas thymidine incorporation by, 220 Platymonas subcordiformis transport constants of, 328 Pleurosiga minima electron micrograph of, 420 POC (see Carbon, particulate organic) Pollutants and particulate matter in ocean, 268-269, 276-277 -rr Potomacus pottsi bacterivory by, 410 Predator-prey interactions, 425426, 428-430, 473-474 ,Pressure retaining samplers, 511-512 Prey aggregation, 411-413 Primary production, 4, 101-106, 111, lIS, 160-162, 167, 228, 233,234, 239, 243, 250, 252~255, 257,259260, 268, 341, 343, 472, 516 Proteolytic activity, 324 Proton motive force, 42 Protozoan bacterivory, 405-435 PRPOOS, lOS, 211 Pseudoemiliania 1acunosa lipids in, 495 Pseudomonas as prey, 410 effect of substrate on, 60 group translocation in, 69 growth rate of, 28-32 steady state population of, 509 surface to volume ratio, 31-32 survival of, 71 thymidine incorporation in, 221 Pseudomonas aeruginosa transport systems in, 327-328 Pseudomonas denitrificans assimilation efficiency, 58 Psychrophi1ism, 50S, 513 Pure culture studies of marine bacteria, 55-59, 65, 67-69, 71-72, 75 Redfield Ratio, 104, 107, 289, 291-292, 294-298, 304 Refractory DOC, 122 Regional variation in dissolved organic nitrogen, 315-316 Remineralization, 296, 306, 338, 342, 375, 380 Respiration, 357-383 of bacteria, 10-11, 307, 529 of phytoplankton, 105-109 INDEX Respiratory C02 production autotrophic, 369-371 heterotrophic, 371-373 Rhizobium as prey, 411 Rhizopod bacterivory, 405-407 Rhizoso1enia robusta adenine uptake and assimilation, 203 Rhodopseudomonas capsu1ata substrate use by, 39 Rhynchomonas as bacterial grazer, 407 photomicrograph of, 419 Riftia pachyptila occurrence of, 516 River inputs, 102-103 ~ model, 292-298, 306 RNA synthesis, 199-213, 218-219, 225-226 in oxygen-minimum layer, 14 Sabella pavon ina filter feeding by, 451 Saccharomyces cerevisiae thymidine kinase in, 220 transport systems in, 327-328 Salmonella typhimurium glycerol uptake by, 69 Salps filter feeding by, 451-453 grazing impact of, 456-457 Salvage pathways, 199-202, 204, 221 Sargassum clumps, 266 Saturation constant (Ks), 26-27, 29 Scavenging potential, 30 Sea-air interface, 433 SEAREX, 104 Seasonal variation in dissolved organic nitrogen, 315, 317 in growth rate, 254, 257-260 Seawater cultures, 186 Sediment lipids of, 484-487, 489-500 microbial colonization of, 524 microbiology of, 523-542 567 Sedimentation, 155-174 Sediment trap studies, 170-172, 174, 294-295, 495-498 Selection, 25-28 Serratia marinorubra in adenine calibration experiment, 207 glucose uptake by, 69 as prey, 410 Setae, 447-448 Shift-down, 190-192 Shift-up, 190-192, 255 Sinking rate, 163-165 Size fractionation studies, 377380, 475-476 Ske1etonema costatum respiration and excretion losses from, 109 transport constants of, 328 Soluble organic material nature of, 470-471 production of, 467-470, 476-477 utilization of, 468, 470-471, 477 Spartina exudation by, 123 Specialization of substrate use, 34-41, 43, 67-71, 75 Spirillum growth rate of, 28-32, 36 surface to volume ratio of, 31-32 uptake of nutrients by, 38-39, 49 Spongia filter characteristics of, 448-449 grazing impact of, 455-456 Spring bloom, 253, 259, 368 Starvation of bacteria, 71-75, 88, 91-92, 191 Steady-state conditions, 105, 110, 113-114, 160-163, 165, 183, 334, 508-509 Stegosoma magnum grazing impact of, 455-456 568 Sterols in marine sediments, 490 Stokes Law, 163 165, 167 Strategic sampling approach, 127, 129, 132 Stratification of ocean, 13-14 Structured nutrient fields, 190-191 Substrate binding, 88-95 Substrate capture, 84-86, 96 Substrate-limited community, 148-149 Substrate utilization, 57, 62, 123, 330 pure culture studies, 65, 67-68 specialism vs versatility, 34-41, 43, 67-71, 75 Succession of bacteria, 70, 259 Sulfate assimilation, 182-184, 242-244 Sulfate reduction, 301 Sulfur bacteria, 28, 35, 45 Sulfur oxidizing bacteria, 517 Surface to volume ratio, 30-33, 46-47, 61-62 Survival of bacteria, 44-45, 71-75 Suspension feeding, 445-462 (see also Filter feeding) Synechococcus thymidine incorporation by, 220 Tetrahymena pyriformis as bacterial grazer, 411 Thalassiosira thymidine incorporation by, 220 Tha1assiosira allenii respiration and excretion losses from, 108 Thermistor flow meters, 446 Thiobacillus, 28 metabolic versatility of, 35-40, 43 Thiomicrospira pe10phila, 28, 32 Thiomicrospira sp barotolerance in, 517 Threshold concentrations, 509-510 INDEX Thymidine incorporation into DNA, 182, 184 192, 198, 217-227, 239-245 Thymidine kinase, 219-222 Time scale of growth variability, 191, 250 Tindaria ca11istiformis growth rate of, 84 Tracer approach, 128 Tracer estimates steady state, 393-394 transient, 396-401 Trichodesmium in marine humus, 14 Tritium distribution in ocean, 396-399 Trophic approach, 121-122 Trophic transfer efficiencies, 426, 428, 430, 474-475 Trophic transfer models, 433-435 Turnover· of DOC, 127-134 U1va ~tached bacteria, 65 Urea, 319, 328 Uronema as bacterial grazer, 407, 410, 416 growth rate of, 407 photomicrograph of, 419 Ventilation-transport models, 402 Vernal bloom, 368 Versatility of substrate use, 34-40, 43, 67-71, 75 VERTEX, 206, 208-210, 212 Vertical flux of particulate matter, 163-168, 172, 174 Vibrio as prey, 410 changes during growth, 61 Vibrio marinus amino acids of, 91 Vibrio natriegen growth rate of, 59 INDEX Vorticella prey aggregation by, 412 Water processing by suspension feeders, 446-462 Winkler method, 290, 359, 362 Yield, coefficient, 508-509 Zooplankton excretion, 322, 340-342 grazing, 102, 113, 141, 237238, 255-256, 259, 321, 342, 471-472 569