Molecular Ecology of Aquatic Microbes

421 Pages·1995·14.709 MB·English

by  Ian Joint (auth.), Ian Joint (eds.)

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Series G: Ecological Sciences, Vol. 38
Molecular Ecology
of Aquatic Microbes
Edited by
Ian Joint
Plymouth Marine Laboratory
Natural Environment Research Council
Prospect Place, The Hoe
Plymouth, PL1 3DH, UK
Springer
Proceedings of the NATO Advanced Study Institute on Molecular Ecology of
Aquatic Microbes, held at II Ciocco, Lucca, Italy, 28 August -9 September
1994.
Library of Congress Cataloging-in-Publication Data
Molecular ecology of aquatic microbes I edited by Ian Joint.
p. cm. -- (NATO ASI series. Series G, Ecological sciences
no. 38)
Includes bibliographical references and index.
1. Water--Microbiology. 2. Molecular microbiology. 1. Joint,
Ian, 1947- II. Series.
QR105.M65 1995
576' • 192--dc20 95-24508
CIP
ISBN-13: 978-3-642-79925-9 e-ISBN-13: 978-3-642-79923-5
DOl: 10.1007/978-3-642-79923-5
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Preface
A NATO ASI on "Molecular Ecology of Aquatic Microbes" was held at II
Ciocco, Lucca, Italy from 28 August - 9 September 1994. The aims of the ASI
were to evaluate the potential for molecular biology to solve some important
questions in aquatic microbiology, particularly in relation to biogeochemical
cycling and microbial physiology.
Techniques developed by molecular biologists have now been adopted by a
wide range of scientific disciplines. In the last 5 years, aquatic microbial
ecologists have begun to incorporate these methods into their research and, as a
result, are developing a much clearer understanding of phylogenetic diversity, the
molecular basis of physiological acclimations and the transduction of
environmental signals and organism responses. The aim of this ASI was to assess
progress in this new field of research, to compare and describe techniques and
experimental approaches, and to foster communication between disciplines. The
ASI offered an excellent opportunity to bring together aquatic ecologists with
molecular biologists and to encourage efficient technology transfer. The meeting
provided a forum for detailed and broad exchange of information on the status
and trends of aquatic molecular ecology and to assess how emerging molecular
techniques might solve some important problems in ecology which have prove
intractable because of lack of appropriate methodologies.
The organising committee was Dr Paul Falkowski (Brookhaven National
Laboratory, USA), Professor Noel Carr (University of Warwick, UK) and Dr
Luigi Lazzaro (University of Firenzi, Italy) I would like to express my
appreciation for the efforts they made to ensure a successful meeting.
I would also like to acknowledge financial support from a number of
organisations. NATO provided the majority of the funding which allowed this
meeting to take place. The US Department of Energy gave generous assistance
through grant number DE-FG02-94ER61896, which enabled us to invite 5
additional lecturers. The UK Natural Environment Research Council also gave a
grant from the Special Topic on Molecular and Genetic Advances, which
supported 2 lecturers from the UK. The generous support of all these
organisations is gratefully acknowledged.
Ian Joint
ASI Director
CONTENTS
The Potential of Molecular Ecology
IAN JOINT. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Towards Understanding the Molecular Ecology
of Phytoplankton Photosynthesis
PAUL G. FALKOWSKI. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Bacteria in Oceanic Carbon Cycling as a Molecular Problem
FAROOQ AzAM, DAVID C. SMITH, RICHARD A. LONG, GRIEG F. STEWARD. . . 39
The Role and Regulation of Microbes in Sediment Nitrogen Cycle
HENRY BLACKBURN. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Functional and Taxonomic Probes for Bacteria in the Nitrogen Cycle
BESS B. WARD. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
The Role ofMixotrophy in Pelagic Environments
Bo RIEMANN, HARRy HAVSKUM, FREDE THINGSTAD, AND
CATHERINE BERNARD. ......... .............................. 87
Successional Change in the Planktonic Vegetation:
Species, Structures, Scales
COLIN S. REYNOLDS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Can Molecular Techniques Change Our Ideas
About the Species Concept?
LINDA K. MEDLIN, MARTIN LANGE, GARY L.A. BARKER, AND
PAULK. HAYES. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
How Do Cyanobacteria Perceive and Adjust to Their Environment?
JEAN HOUMARD. . . . . . . .. . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . 153
How Do Cells Express Nutrient Limitation at the Molecular Level?
NICHOLAS H. MANN. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
The Problem of Excess and/or Limitation of the Habitat Conditions:
Do Natural Assemblages Exist?
RICARDO GUERRERO AND JORDI MAS-CASTELLA. . . . . . . . . . . . . . . . . . . . . 191
VIII
Signal Transduction in Microorganisms
MELVIN I. SIMON. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
Microbial Diversity in Oceanic Systems:
rRNA Approaches to the Study ofUnculturable Microbes
STEPHEN J. GIOVANNONI, THOMASD. MULLINS, ANDKATHARINEG. FIELD. 217
Viruses -the New Players in the Game; Their Ecological Role
and Could They Mediate Genetic Exchange by Transduction?
GUNNARBRATBAKANDMIKALHELDAL........................... 249
Molecular Analysis of Plastid Evolution
VVOLFGANGLOFFELHARDT. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
Can VV e Estimate Bacterial Growth Rates from Ribosomal RNA Content?
PAULF. KEMP. . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . 279
The Cell Cycle of Phytoplankton:
Coupling Cell Growth to Population Growth
DANIEL VA ULOT. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 303
Response of Photosynthetic Microorganisms
to Changing Ambient Concentration of C02
MICHAL RONEN-TARAZI, RAKEFET SCHWARZ, ANNE BOUEVITCH,
JUDY LIEMAN-HURWITZ, JONATHAN EREZ AND AARON KAPLAN. . . . . . . . . . 323
Nitrogen Fixation in the Sea: VVhy Only Trichodesmium?
JONATHAN P. ZEHR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335
Molecular Ecology of Marine Methanotrophs
J COLIN MURRELL AND ANDREW J HOLMES. . . . . . . . . . . . . . . . . . . . . . . . . 365
Microbial Cultures andNatural Populations
NOEL G CARR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391
List of Participants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 403
Subject Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411
The Potential of Molecular Ecology
Ian Joint
NERC Plymouth Marine Laboratory
Prospect Place
The Hoe
Plymouth PLl 3DH
UK
Introduction
The solution of major environmental problems requires a clear understanding of
the complex interactions which are part of natural systems. Many important
processes, which are poorly understood but which have clear global implications,
are mediated by the activity of microbes. Although micro-organisms may have
spheres of influence with distance scales of centimetres or less, their combine
effect is truly global. However, within any particular environment, microbial
biomass and activity can be very variable in both time and space. The challenge
to microbial ecologists is to make measurements which are accurate and precise
at the scale of a microbial population but which can also be extrapolated to give
useful information at local, oceanic basin or global scales.
Marine microbial ecologists have an increasing number of powerful
techniques which have allowed great progress to be made in understanding and
quantifying microbial activity in the oceans. However, it is important to recognise
that many of these techniques also have limitations and that existing
methodologies may not be capable of supplying the information which is required
to understand ecological interactions. Molecular techniques may offer the solution
to some of these problems. In this chapter, I will discuss a number of processes
which I have been studying and which I believe are proving intractable with
current methodologies. I will present a personal view, derived from my own
research experience; however, readers may fmd parallels in the development of
their own research which may convince them, as I am convinced, that molecular
biology has a significant role to play in improving our understanding of the
functioning of aquatic microbes.
I will begin by explaining why I have come to believe that current
methodologies have limitations which are not easy to overcome; I will then give a
small number of examples of what I believe is the potential of molecular ecology,
NATO ASI Series, Vol. G 38
Molecular Ecology of Aquatic Microbes
Edited by I. Joint
© Springer-Verlag Berlin Heidelberg 1995
2
although others have already done this effectively (Falkowski and LaRoche,
1991). But a wider justification for molecular ecology comes not from this
chapter but will be found in the rest of this book.
Phytoplankton biomass and production
Two attributes of phytoplankton, chlorophyll and carbon fixation, are amongst the
most commonly measured parameters in oceanography. The simplicity and
physical robustness of fluorometers allows routine deployment of these
instruments by physical, chemical and biological oceanographers. Chlorophyll
fluorescence has become one of the favourite descriptors of the bulk properties of
sea water. Similarly, primary production is measured at great frequency. The
sensitivity of the 14C technique has resulted in a large body of data which relates
to almost every marine province; yet even with frequent use, the 14C method
remains one of the most controversial techniques in current use (Williams, 1993).
The 14C method has been important in my own research and, in spite of
uncertainties about whether we measure gross or net production (Williams,
1993), I believe valuable information on phytoplankton production has been and
will continue to be obtained with this methodology. As an example of what can
be achieved, I used the 14C method to estimate seasonal phytoplankton
production (Joint & Pomroy, 1993) within the context of a large multidisciplinary
study of the southern North Sea (Howarth et al., 1993), a major temperate
European shelf sea. Large variations in annual production were found, ranging
from 79gC m-2y-l in the eastern North Sea to 261gC m-2y-l for the German
Bight. The differences in production were partly a consequence of physical
processes, such as the degree of stratification, tidal mixing and depth, but also
because of different inputs of nutrients from rivers. The regions of highest annual
production were not only those with the shallowest water but also those with the
greatest influence of the Rhine and other major rivers. However, the factor which
resulted in the greatest difference in phytoplankton production was the presence
of a bloom of colony-forming Phaeocystis. The reasons for the development of
blooms of this phytoplankton are not certain, but a number of workers have
suggested that it is direct consequence of increased nutrient supply from rivers
(Cadee, 1990; Lancelot, et al. 1987; Veldhuis, 1986). Although this is a widely
held hypothesis, it has yet to be proven.
Current methods to measure primary production suffer from a number of
limitations. Although giving invaluable data about the activities of complete
assemblages (or at least those assemblages which survive the in vitro
assessment), methods such as 14C assimilation or O2 evolution cannot give any
information on the activity of the individual organisms which make up those
assemblages. It is unusual for any natural phytoplankton population to be
3
unialgal, although under some bloom conditions one species, such as Phaeocystis
may reach pre-eminence and greatly outnumber other phytoplankton. Therefore,
standard methods to assess primary production estimate the mean, or median, rate
of production of all of the phytoplankton which make up an assemblage. For
many applications, such as the study of the North Sea (Joint and Pomroy, 1993)
this limitation is not important. Yet there may be other occasions when it might
be an advantage to have a measure of the growth of individual phytoplankton
species.
Measures of community activity, such as the 14C method assume that the
average activity of the whole population has some validity in relation to the
organisms which make up that assemblage. But is this a realistic assumption? We
can readily recognise the heterogeneity of natural populations; different algal
species can be identified by standard microscopic observation and we have no
difficulty in accepting that organisms are highly variable, with different
morphologies, sizes and growth rate. However, neither this heterogeneity nor the
ecological consequences of the assumptions behind the 14C method are often
considered. Marine phytoplankton exhibit a large range in specific growth rate of
over an order of magnitude (Geider and Osbourne, 1992), from 3 d-1 for small
diatoms to 0.1 d-1 for slow growing dinoflagellates. Therefore, it is possible that
short term incubations of <1 day do not give a true estimate of growth of an
organism which has a generation time of several days. The 14C method may have
a distinct bias towards rapidly growing organisms with generation times equal to
or less than the incubation period of the experiment. Diel variations in
photosynthetic carbon fixation of rapidly growing phytoplankton might be more
closely matched to cell growth and division than in phytoplankton cells with
doubling times of several days.
Does any of this really matter? Most researchers who use these methods
will accept that there are limitations; that the 14C method measures something
between net and gross production, and probably close to net production, is
probably well accepted and for many purposes, these estimates are more than
adequate. However, it could also be argued that the widespread use of the 14C
has constrained the development of ecological concepts. The true limitations of
current measures of community activity become more apparent as a result of new
understandings derived from the study of the organisms which graze the
phytoplankton. We are becoming increasingly aware that grazers can be very
selective in the phytoplankton cells on which they feed. Copepods demonstrate
large differences in growth rate when fed diets comprising different species. In
particular, many dinofiagellates are poor food for copepods (Gill and Harris,
1987) and even the physiological state of phytoplankton can affect grazing by
zooplankton (Estep et al. 1990). Filter feeding bivalves, such as mussels are also