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Biological Oceanography, 2nd edition

May 2012, ©2012, Wiley-Blackwell
Biological Oceanography, 2nd edition (EHEP002684) cover image
This new edition of Biological Oceanography has been greatly updated and expanded since its initial publication in 2004. It presents current understanding of ocean ecology emphasizing the character of marine organisms from viruses to fish and worms, together with their significance to their habitats and to each other.

The book initially emphasizes pelagic organisms and processes, but benthos, hydrothermal vents, climate-change effects, and fisheries all receive attention. The chapter on oceanic biomes has been greatly expanded and a new chapter reviewing approaches to pelagic food webs has been added. Throughout, the book has been revised to account for recent advances in this rapidly changing field. The increased importance of molecular genetic data across the field is evident in most of the chapters.

As with the previous edition, the book is primarily written for senior undergraduate and graduate students of ocean ecology and professional marine ecologists.

Visit www.wiley.com/go/miller/oceanography to access the artwork from the book.

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Preface to the second edition vii

Acknowledgements viii

1 Ocean ecology: some fundamental aspects 1

2 The phycology of phytoplankton 19

3 Habitat determinants of primary production in the sea 49

4 Numerical models: the standard form of theory in pelagic ecology 73

5 A sea of microbes: archaea, bacteria, protists, and viruses in the marine pelagial 96

6 The zoology of zooplankton 115

7 Production ecology of marine zooplankton 130

8 Population biology of zooplankton 158

9 Pelagic food webs 181

10 Biogeography of pelagic habitats 202

11 Biome and province analysis of the oceans 230

12 Adaptive complexes of meso- and bathypelagic organisms 276

13 The fauna of deep-sea sediments 292

14 Some benthic community ecology 321

Biological oceanography

15 Submarine hydrothermal vents 351

16 Ocean ecology and global climate change 367

17 Fisheries oceanography 396

References 427


Colour plates appear between pages 230 and 231

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Charlie Miller, now Emeritus Professor of Oceanography at Oregon State University, taught biological oceanography and zooplankton biology for many years. His research contributions have concentrated on seasonal processes in the ecology of marine zooplankton, particularly copepods, in the Oregon coastal zone and estuaries, the Gulf of Alaska, Georges Bank and the Gulf of Maine.

Patricia Wheeler, now Emeritus Distinguished Professor of Oceanic and Atmospheric Sciences at Oregon State University, taught biological oceanography and phytoplankton physiology there for many years. Her research contributions address phytoplankton nutrient dynamics and include work on dissolved organic carbon and nitrogen. She conducted field work in the Equatorial Pacific, the northern California Current system and the Arctic Ocean.

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Requests for additional content have come from teachers using the first edition of Biological Oceanography.  To cover that content, we propose a book about one-quarter to one-third larger than the OE. Specifically proposed additions are as follows:


I. A chapter on Pelagic Food Webs


In a sense many chapters in first edition are about pelagic food webs, but there was no explicit treatment of several important topics.  A new chapter will address them: 


(1)  Food web complexity. This has long been recognized regarding trophic relations in ocean waters, for example by Alister Hardy’s North Sea food web centering on herring that shows dozens of connections.  There are in fact more layers and links than Hardy could discern.  We will show some of these diagrams, older and more recent, and discuss the issues they raise.

(2) There is expanding knowledge of the complexity of lower levels – with protistan heterotrophs in key roles.  We will review at greater length the food chain fractionation experiments, which show distinct trophic levels down to bacterial cell sizes. 

(3) Several old and new techniques allow identification of an animal’s food and its general trophic level, including gut content analysis, isotopic composition of tissues and characterization of stored fatty acids that can identify specific food sources (“lipid tracking”).  These methods are popular and widely applied.  The data usually are subject to multiple explanations, which will be discussed.

 (4)  Food-chain amplification of elements, molecules and pollutants.  Amplification of heavy isotopes of carbon and nitrogen, of heavy metals and anthrogenic molecules will be reviewed, together with some of the consequences.

(5) Effects of removal of top predators will be discussed, including stock bursts of previously suppressed competitors and rapidly growing forms (jellyfish and squid).  The replacement of slow-growing, heavily-exploited forms (fish) will be examined.

(6) Food-web modeling – Ecopath/Ecosim and relatives - will be introduced and considered.


II. Modifications of present chapters.


Chapter 1 in OE on the spring bloom phenomenon was intended to give the student a general overview of the dynamics of seasonal cycling in pelagic ecosystems before tackling detailed information on their biological components.  We will review and revise this as new information suggests (study lying ahead of us).  Some users of OE recommend beginning with something else; others like this entry point very much.  We will keep thinking about the most effective overall arrangement.  The presentation on the interaction of cell dimensions, shape and surface area will be revised to emphasize the greater rates of diffusive supply of nutrients and removal of metabolites for smaller cells (rather than simplistic effects of area per se).  This will incorporate a brief presentation of encounter theory following the development in T. Kiorboe’s (2008) book, A Mechanistic Approach to Plankton Ecology, together with a statement of its applicability to a wide range of interactions in the water column.


Recent work on phytoplankton (chapter 2 in OE) has taken strong advantage of developments in molecular biology.  Emerging results from algal genomics provide important insights into the diversity of metabolic processes in the ocean and the evolutionary relationships of the phytoplankton.   Messenger-RNA analyses are revealing adaptive strategies by characterizing variation of gene activity in varying environmental settings.  This progress will be characterized, while the descriptions of gross and fine-scale structure will be retained.


There is a great deal of new information on the regulation of photosynthesis and algal cell cycles in pelagic ecosystems (chapter 3 in OE).  The roles of trace metal limitation and toxicity, particularly iron limitation, and nutrient recycling have been analyzed with new methods.  Details of the biophysics of light in photosynthetic systems are being exploited to evaluate production rates and physiologic status of phytoplankton.  New algorithms have been developed for estimating both phytoplankton stocks and production rates from satellite data.  This new information will be incorporated, some of it replacing the content of OE.


Thus, our considerations for chapters 2 and 3 will cover:

Ø  Revised classification of phytoplankton (How much has it changed?  Have the bases of identification changed enough to warrant explanation?)

Ø  Fast Repetition Rate Fluorometry (FRR) – in situ primary production measures or egregious hype?  (We would not put it that way.)

Ø  Fv/Fm more generally – application of chlorophyll fluorescence to of phytoplankton physiological status (work of Behrenfeld, Milligan, O’Malley, …)

Ø  Carbon/Chlorophyll ratio variation (evaluated from space and in situ)

Ø  Updated algorithms for chlorophyll, carbon and production. from satellites

Ø  Updated regional and global productivity estimates

Ø  Revision of nutrient limitation dynamics – new views of new vs. recyled production, iron limitation (oceanic and coastal) and HNLC mechanics, iron-copper-zinc interactions, siderophores (cell surface and extra-cellular), silicic acid limitation of diatoms, nitrogen fixation and ecological stoichiometry (ideas reaching “beyond Redfield”)

Ø  Update on ecologic roles of prokaryotic autotrophs and eukaryote picoplankton

Ø  Update on harmful algal blooms


Not much important progress has been made in pelagic ecosystem modeling (chapter 4 in OE) in our opinion since 2003.  Perhaps the most important advances have been better coupling of NPZD (and NNPPZD, etc.) models to regional and global physical models of advection and mixing.  A brief section will be added on those couplings, possibly using references to one or more ‘stable’ web sites offering animations of such model results.  It has been proposed by users that the programs for simple models presented in OE be converted to Matlab scripts, because that is the programming mode most widely taught and used in oceanographic education at present.  That will be done.


The chapter on microbiology (# 5 in OE) will have expanded information on protozoans (‘microheterotrophs’) and their feeding activity.  Interactions at the cellular level, molecular signaling and molecular defenses, will be reviewed.  Some of that will also go into the food-web chapter described above.  The biology of marine bacteria, archaea and viruses, with hints about their functional ecology, has moved rapidly since 2003 (the last information in OE).  There is some new information on DOM – one “flywheel” of the pelagic food web.  There are good review materials on these topics from which to update the text. 


Chapters on mesozooplankton (6-8 in OE) will be updated.  The level of detail in description of animals is praised by biology students, disliked by those from physics and chemistry.  The teachers tend to like it, so it will remain about the same.  Teachers and students can skip some or all of it if they choose.  Discussion will be improved and updated on

Ø  the mechanics of propulsion – the poise of animal size on the inertial-viscous cusp, jets and paddles, energy dissipation and contributions to ocean mixing

Ø  seasonal adaptive complexes and other issues of phenology

Ø  reproductive and mortality rate studies – to be updated

The section on estimation of secondary production is long and likely excessively detailed for the intended audience.  This is particularly true because the estimates are seriously imprecise and based on shaky assumptions.  The section will be reviewed and probably simplified.  A ‘bridge’ will be provided to the Ecopath/Ecosim modeling in the proposed new chapter on pelagic food web ecology.


Chapter 9 of OE on oceanic, pelagic biogeography will be reviewed. Very little new information is likely to apply.  Specific criticism has been received from Alan Longhurst, the author of two editions of Ecological Geography of the Sea (Academic Press).  That is because he chooses a wholly different basis for classification of regions, one mildly criticized in OE.  His 2007 version will be examined, and significant, valid insights will be incorporated.  Our chapter will continue the approach that species distributions can be taken as defining distinctive regions.


Chapter 10, “Biome and province analysis of the oceans” will take areas defined by a species patterns, combine those areas with similar physical regimes, then review their typical ecology in detail.  This chapter has been criticized as falling far short of the level of information available about major pelagic ecosystems.  Sections will be prepared on

Ø  Polar seas

Ø  Subpolar gyres: contrasting Pacific and Atlantic subarctic areas, and comparing those to the subantarctic zone.

Ø  Subtropical gyres: five generally similar, oligotrophic regions in all three major oceans, review of the HOTS and BATS time series results

Ø  Equatorial ecosystems: zonal upwelling, tropical instability wave effects, population maintenance, El Niño-Southern Oscillation variability

Ø  Coastal upwelling ecosystems: emphasis on Coastal California and Oregon

Ø  Adaptations to thermal and other gradients

We propose a much more extended treatment than in OE, expanding the chapter from 17 pages to about 40.


Chapter 11 on life in mesopelagic depths (~300 to 1200 m) is about the right length and has good content in OE.  However, there are many new insights about vision in limited light, bioluminescence and metabolic adaptations, particularly to hypoxia in oxygen-minimum layers.  Some of the recent insights have been catalogued by Tony Koslow in The Silent Deep (U. Chicago), which we will review for appropriate facts and examples.  The intent of the chapter will still be to demonstrate the extraordinary adaptive complexes that enable animals to sustain their lives in the face of complex challenges of the mesopelagic


The characterization of benthic fauna in OE Chapter 12 will remain much the same.  To much too great an extent, this chapter is just a précis of Gage and Taylor’s Deep-Sea Biology.  On the other hand, it will be difficult to do better than that in a chapter of reasonable length.  Dr. Miller will spend a month or so studying recent literature as a basis for revising this.


Chapter 13 in OE ‘used’ benthic ecology to demonstrate the sorts of multivariate statistical techniques popular all across biological oceanography.  Such a demonstration remains important, and examples from the benthos are better than most.  As for chapter 12, a literature review may produce better, at least more recent, examples than in OE.  We are almost tempted to view the new edition as a separate book, since OE will still exist.  That would allow a completely new selection of examples.  However, new students are only going to buy one book, so we propose to stick with the best examples, even if they are already in the old edition. 


Hydrothermal vents will again be covered in Chapter 14.  The story of vents will be updated with recent discoveries.  For example the calcitic chimneys initially discovered by Deborah Kelly had just been reported in 2003, not described in any detail.  Those vents are now reasonably well known and similar structures and hydrothermal flow have been found in many other locations including a deep-sea basin north of Fiji.  The update will include recent revisions of arguments that vents could have supported the origin of life.  A less historical perspective will be taken on this issue in the interests of space. An interesting approach to the most primordial life has been taken by Paul Falkowski and colleagues, who examine the most fundamental biological redox reactions, trying to trace how they might have been initiated.  Those papers will be studied for the proposed new edition.


Revision of chapter 15 on fisheries oceanography should give it a more urgent tone.  Fisheries are a very serious problem area.  Advantage will be taken of analyses by Boris Worm and the late Ransom Myers, particularly (1) their time-series of global results from the Japanese tuna fishery and (2) their conclusions about fisheries for very large predators (down in very recent decades to 10% of initial catch rates).  The more anecdotal study by Callum Roberts (The Unnatural History of the Sea) provides usable quotes (the entire bed of the North Sea was an oyster bed, …) that will be considered in reviewing the impacts of fishing technology on marine habitats, impacts likely just as important as the removal of fish and shellfish.  A basic introduction to fisheries management thinking should remain.  The potential and social difficulties of establishing and enforcing marine protected areas will be discussed briefly, using the excellent examples showing that reserves work.  They have been termed “mystical fisheries thinking” by Ray Hilborn, a famous fisheries scholar, but the data show they are a solid, effective conservation measure.  In one chapter, the topic can only be touched upon.  However, we feel it remains important for oceanographers-in-training to think of fisheries as integral to the subject matter in their field.


Chapter 16 on climate change requires thorough updating.  Partly that is because climate change and its effects are moving much faster than anticipated when OE was written.  For examples, the increasing rate of fossil fuel burning exceeds even the most extreme projections by the Intergovernmental Panel on Climate Change (IPCC) in its 2007 report, and summer reductions of Arctic Ocean ice coverage were substantially greater in 2007 and 2008 than predicted by the previous trend line.  The chapter will be improved by (1) better analysis of the role of oceans in glacial-interglacial cycling of atmospheric CO2, correctly scaling the global role of the biological carbon ‘pump’.  Statements will be revised concerning the roles atmospheric delivery of iron and phytoplankton nutrition had in carbon sequestration during the ice ages, taking particular care with leading vs. following effects.  That is, we will review the status of the iron question: Does decreased atmospheric CO2, with attendant cooling, cause enhanced dust delivery, or does iron in dust supplied by greater winds in early glacial eras promote sequestration of CO2, locking in glacial-era cooling. 


(2) A much better catalogue will be provided of possible oceanographic effects  of warming (while still avoiding more shore-bound ones like coral bleaching (and death), polar bears drowning, etc.).  Particularly attention will be given to effects of enhanced thermal stratification.  We will again use biological responses in the ocean to long-term ‘weather’ variations, such as the North Atlantic Oscillation (NAO) and the Pacific Decadal Oscillation (PDO) to ‘guess’ at the impacts of permanent climate change, presumed by everyone to be warming.  Excellent examples have been developed of the sorts of change accompany these pattern shifts since the writing of the OE.  This is the part of the book mostly likely to overlap some with the text by Mann and Lazier (discussed below), but climate change is so important in current work that it must be correctly characterized in our book.


(3) In the context of carbon-cycle changes in the face of increasing fossil fuel carbon inputs, we will write briefly about some related issues:  

Ø  Acidification of the ocean from carbon dioxide absorption is now definitively measurable, a prelude to likely ecologic disruptions of serious magnitude.

Ø  Effects of declining oxygen (now apparent in oxygen-minimun zones as well as in coastal hypoxic and dead zones).


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“The book is extremely well referenced for further study and the impression is that most of the work cited is from within about the last twenty years. Altogether a worthy addition to any marine departmental library.”  (British Ecological Society Bulletin, 1 December 2012)

“Overall I found it to be an immensely informative and entertaining read. This book will make an excellent core text for any graduate level course in Biological Oceanography whether introductory or advanced...I also think that every Biological Oceanographer should read it. It is an enlightening experience to view your field through the eyes of two colleagues who have been in this business for a long time. I also found reading this book a humbling experience.  Charlie Miller and Pat Wheeler demonstrate an amazing depth and diversity of understanding in almost every topic that is taken up. I hope by the time I get to where they are in their careers I have achieved this level of scholarship in Biological Oceanography.”  (Limnology and Oceanography Bulletin, 1 May 2013)


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Biological Oceanography, 2nd Edition
ISBN : 978-1-118-22318-5
504 pages
April 2012
$58.99   BUY

Biological Oceanography, 2nd Edition
ISBN : 978-1-4443-3302-2
480 pages
May 2012
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Biological Oceanography, 2nd Edition
ISBN : 978-1-4443-3301-5
474 pages
May 2012
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Wiley E-Text   
Biological Oceanography, 2nd Edition
ISBN : 978-1-118-40954-1
504 pages
January 2013
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