1980 Preface * 1999 Preface * 1999 Acknowledgements * Introduction * 1 Circular Logic * 2 Phase Singularities (Screwy Results of Circular Logic) * 3 The Rules of the Ring * 4 Ring Populations * 5 Getting Off the Ring * 6 Attracting Cycles and Isochrons * 7 Measuring the Trajectories of a Circadian Clock * 8 Populations of Attractor Cycle Oscillators * 9 Excitable Kinetics and Excitable Media * 10 The Varieties of Phaseless Experience: In Which the Geometrical Orderliness of Rhythmic Organization Breaks Down in Diverse Ways * 11 The Firefly Machine 12 Energy Metabolism in Cells * 13 The Malonic Acid Reagent ('Sodium Geometrate') * 14 Electrical Rhythmicity and Excitability in Cell Membranes * 15 The Aggregation of Slime Mold Amoebae * 16 Numerical Organizing Centers * 17 Electrical Singular Filaments in the Heart Wall * 18 Pattern Formation in the Fungi * 19 Circadian Rhythms in General * 20 The Circadian Clocks of Insect Eclosion * 21 The Flower of Kalanchoe * 22 The Cell Mitotic Cycle * 23 The Female Cycle * References * Index of Names * Index of Subjects

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/596B270197FE27DE5FABB598B6210622/S0025557200150892a.pdf/div-class-title-span-class-italic-the-geometry-of-biological-time-span-by-a-t-winfree-pp-544-dm68-corrected-second-printing-1990-isbn-3-540-52528-9-springer-div.pdf

The geometry of biological time , by A. T. Winfree. Pp 544. DM68. Corrected Second Printing 1990. ISBN 3-540-52528-9 (Springer)

The microphytobenthos consists of unicellular eukaryotic algae and cyanobacteria that grow within the upper several millimeters of illuminated sediments, typically appearing only as a subtle brownish or greenish shading. The surficial layer of the sediment is a zone of intense microbial and geochemical activity and of considerable physical reworking. In many shallow ecosystems, the biomass of benthic microalgae often exceeds that of the phytoplankton in the overlying waters. Direct comparison of the abundance of benthic and suspended microalgae is complicated by the means used to measure biomass and by the vertical and horizontal distribution of the microphytobenthos in the sediment. Where biomass has been estimated as chlorophyll a, there may be negligible to large (40%) error due to interference by degradation products, except where chlorophyll is measured by high-performance liquid chromatography. The vertical distribution of microphytobenthos, aside from mat-forming species, is determined by the opposing effects of their vertical migration, which tends to concentrate them near the surface, and physical mixing by overlying currents, which tends to cause an even vertical distribution through the mixed layer of sediment. Uncertainties in vertical distribution are compounded by frequently patchy horizontal distribution. Under-sampling on small (<1 m) scales can lead to errors in the estimate that are comparable to the ranges of seasonal and geographic variation. These uncertainties are compounded by biases in the techniques used to estimate production by the microphytobenthos. In most environments studied, biomass (as chlorophyll a) and light availability appear to be the principal determinants of benthic primary production. The effect of variable light intensities on integral production can be described by a functional response curve. When normalized to the chlorophyll content of the surficial sediment, the residual variation in the data described by the functional response curve is due to changes in the chlorophyll-specific response to irradiance. Production by the benthos is often a significant fraction of production in the water column and microphytobenthos may contribute directly to water column production when they are resuspended. Thus on both the basis of biomass and biogeochemical reactivity, benthic microalgae play significant roles in system productivity and trophic dynamics, as well as such habitat characteristics as sediment stability. *** DIRECT SUPPORT *** A01BY074 00003

https://www.jstor.org/stable/info/1352224

Microphytobenthos: The ecological role of the “secret garden” of unvegetated, shallow-water marine habitats. I. Distribution, abundance and primary production

Publisher Summary Mangroves are trees or bushes growing between the level of high water of spring tides and a level close to but above mean sea-level Very few species of mangrove are deep rooted, or have persistent tap roots Almost all are shallow rooted but the root systems are often extensive and may cover a wide area Rhizophoraceous trees have seedlings with a long radicle which would seem well suited to develop into a tap root, but as soon as the seedling becomes established in the mud the radicle develops little further Trees of Avicennia and of Sonneratia develop several different kinds of roots The main rooting system consists of large cable roots which give off anchoring roots downwards and aerial roots or pneumatophores upwards These pneumatophores in their turn produce a large number of nutritive roots which penetrate the mineral-rich subsurface layers of the soil The land animals found in mangrove forests include roosting flocks of fruit bats, fishing and insectivorous birds, and many insects are conspicuous Of the marine animals, crabs and molluscs live permanently in the forest, and prawns and fishes come in on the tide to feed on the apparently abundant nutriment provided by the mangrove soils In South East Asia man uses mangrove areas for the establishment of ponds for the culture of fish and prawns, and for timber

A General Account of the Fauna and Flora of Mangrove Swamps and Forests in the Indo-West-Pacific Region

Primary Production by Phytoplankton and Microphytobenthos in Estuaries

Recovery of a desert stream after an intense flash flooding event is described as a model of temporal succession in lotic ecosystems. A late summer flood in Sycamore Creek, Arizona, virtually eliminated algae and reduced invertebrate standing crop by 98%. Physical and morphometric conditions typical of the preflood period were restored in 2 d and the biota recovered in 2—3 wk. Algal communities responded rapidly and achieved a standing crop of nearly 100 g/m2 in 2 wk. Community composition was dominated by diatoms early in succession and by filamentous greens and blue—greens later. Macroinvertebrates also recolonized denuded substrates rapidly, largely by immigration of aerial adults and subsequent oviposition. Growth and development were rapid and several generations of the dominant mayfly and dipteran taxa were completed during the 1st mo of recovery. Invertebrate dry biomass reached 7.3 g/m2 in 1 mo. Gross primary production (Pg) measured as O2 increased in a similar asymptotic fashion and reached 6.6 g°m—2°d—1 in 30 d. Pg exceeded community respiration (R) after day 5 and Pg/R averaged 1.46 for the remainder of the 2—mo sequence. This ecosystem is thus autotrophic and exports organic matter downstream and by drying, laterally. Uptake of nitrate and phosphorus were proportional to net primary production and exhibited a marked downstream decline in concentration during both light and dark periods. Temporal trajectories of various community and ecosystem attributes are compared with those suggested by Odum (1969) to be diagnostic of successional status. Agreement was poor in attributes which are especially modified in open, frequently disturbed ecosystems such as streams.

Temporal succession in a desert stream ecosystem following flash flooding

The vertical migration of two Euglena species and several diatom species into and out of the sediment on the banks of the River Avon has been studied under natural conditions. All species have been shown to migrate vertically upwards when exposed during daylight. Tidal flooding of the sediment is generally preceded by re-burrowing of the algae beneath the surface. Methods have been devised to follow these migrations in both the field and laboratory. Laboratory experiments show that these migrations are rhythmic, continuing under constant illumination and temperature and removed from tidal influence. The effect of three different temperatures and three different light intensities has been investigated. Transfer from low to high temperatures has been shown to reset the phase of the rhythm. The results are discussed in relation to other work and to the ‘biological clock’ hypothesis.

Persistent, vertical-migration rhythms in benthic microflora.: II. Field and Laboratory Studies On Diatoms From The Banks Of The River Avon

Summary
1. A great number of vital processes are rhythmic and the rhythms quite often persist in constant conditions. The best-known rhythms are circadian; much less is known about circalunadian rhythms, and this review was prepared in an attempt to rectify this deficiency. All through the article comparisons are drawn between circalunadian and circacian rhythms.

2. Activity rhythms.

(a) The activity patterns of 28 intertidal animals are discussed. All describe a periodicity with a basic component of 24.8 hours, and this approximate period persists in the laboratory in constant light and temperature and in the absence of the tides. The duration of persistence ranges from a few cycles to months, and is a function of the species studied, the conditions imposed, and individual tenacity.

(b) In those few cases where relatively long-term observations have been made, there is a trend for the period of the rhythm to become circatidal, or better, circalunadian.

(c) The ‘desired’ phase relationship between rhythm and tidal cycle is species-specific. Geographical translocation experiments have shown that the phase is set by the local tides.

(d) In some cases the amplitude of the persistent rhythm mimics the semidiurnal inequality of the tides.

(e) In about a third of the species discussed, a circadian component has been found combined with the tidal component. Many of the other studies were of such short duration that a low-amplitude circadian component would have gone unnoticed.

(f) The tidal rhythm is innate. However, the rhythm is (i) sometimes lacking in organisms living in non-tidal habitats, or (ii) fades after a spell of incarceration in constant conditions. Various treatments — some aperiodic — can induce the expression of the missing tidal rhythm.

(g) In the green crab, removal of the eyestalks destroys the activity rhythm.

3. Vertical migration rhythms.

(a) A rather surprisingly large number of intertidal animals have been found to undergo migration rhythms between the upper layers of the substratum and its surface. The movements are synchronized with the tides in nature, but most species have either been shown to be diurnal in constant conditions, or in cases where adequate testing has not been done, suspected of being so.

(b) In only one species has confirming work shown that the fundamental frequency is truly tidal. This finding is especially important as it shows that tidal rhythms need only the single-cell level of organization for expression. Even at this level there appears to be a dictatorial override by a circadian clock.

4. Colour change. Low-amplitude tidal rhythms in colour change — superimposed on a more dominant circadian change — have been reported to be intrinsic in four species and inducible in a fifth.

5. Oxygen consumption. Tidal rhythms in oxygen consumption have been described for seven invertebrates and one alga; six of the species have superimposed solar-day rhythmic components also.

6. Translocation. A total of five geographical translocation experiments, in which the organisms were maintained in constant conditions throughout, have been tried. Unequivocally in one case, and possibly in a second, the test organisms rephased spontaneously to the times commensurate with local tidal conditions. In two other cases, the pretranslocation phase was retained. The fifth experiment has not been reproducible.

7. Determination of phase.

(a) The tidal cycle on the home shoreline sets the phase of the inhabitant's rhythms. Even the location of a crab's burrow on the beach incline can play a determining role.

(b) Paradoxically, the periodic wetting by inundation is not an important entraining factor for most intertidal organisms. Instead, the effective portions of the tidal cycle include one or more of the following. (i) Mechanical agitation, especially for animals living in an uprush zone where they are periodically subjected to the pounding surf, (ii) Temperature cycles, though they have not yet been systematically investigated, have very pronounced entraining roles in crabs. (iii) Pressure is probably not a generally important entraining agent for most intertidal organisms, but it is so for the green crab.

(c) Light-dark cycles in general, whether daily or tidal in length, have no effect on the entrainment or phase setting of many tidal rhythms. There are two exceptions: (i) a 24-hour light-dark cycle is known to keep a tidal locomotor rhythm (one that becomes circalunadian in constant conditions) at a strict tidal frequency. (ii) In rhythms with both daily and tidal components, when the former is shifted by light stimuli, the latter is affected in a nearly identical manner.

8. Temperature.

(a) The role of temperature on tidal rhythms is compared with its role on circadian rhythms.

(b) The effects of different constant temperatures have so far been studied on only four tidal rhythms. All studies indicate a lack of any permanent change in period, which is not so with most circadian rhythms; the latter having temperature coefficients around 1.1. In two of the studies the rhythms under test temperatures were followed for less than a day, and a third study cannot be repeated.

(c) Short exposure to very cold temperature pulses produced a response that may be interpreted as a temporary stoppage of the clock. Exposure to relatively less-cold pulses appear simply to reset the hands of the clock. The same responses have been demonstrated with circadian rhythms.

(d) In the case of green crabs, which had become arrhythmic during prolongued captivity in the laboratory, a tidal rhythm could be reinitiated by a single short cold treatment. The cold pulse also set the phase of the rhythm.

(e) A few superficial studies employing temperature steps or pulses have produced results which suggest that a phase-change sensitivity rhythm — just like that found associated with circadian rhythms — may underlie tidal rhythms. Certainly a determined search for this rhythm should be made in the near future.

9. Clock control of rhythms.

(a) An argument is constructed claiming that tidal rhythms have a basic period of about 24–8 hours rather than the more expected tidal interval of 12.4 hours. In constant conditions, a circalunadian period is usually displayed.

(b) After speculating that a frequency-transforming coupler may function between the clock and the overt rhythm, reasons are given that lead to the further speculation that both circadian and circalunadian rhythms could be generated by a single clock, via specific coupling mechanisms.

(c) Two current hypotheses concerning the nature of the clockworks are reviewed and discussed.

(d) Suggestions are made for future investigations.

Tidal rhythms: the clock control of the rhythmic physiology of marine organisms

1. The diatom, Hantzschia virgata, appears on the surface sands of Barnstable Harbor, Mass., during daytime low tides. Surface accumulations of this organism reach such concentrations that the sand takes on a golden-brown color. As the tide returns the cells re-burrow into the sand.2. The cells can be prevented from emerging onto the surface sands at low tide by artificially darkening the area with an opaque covering just as the tide recedes. Cells already on the surface can be made to re-burrow by similarly placing them in darkness.3. The vertical-migration rhythm will persist in the laboratory in constant illumination, constant temperature, and away from the influence of the tide for as long as eleven days. During this time the cells remain in approximate synchrony with the feral cells in nature.4. In nature, when the times of low tide approach sunset, the cells rephase their rhythm to the early morning hours of daylight. Cells collected during late afternoon low tides and returned to L:D or L:L in the ...

Persistent, vertical-migration rhythms in benthic microflora. vi. the tidal and diurnal nature of the rhythm in the diatom hantzschia virgata

During daytime low tides on the River Avon at Bristol, England, the exposed river banks become a deep green colour owing to the presence of enormous numbers of Euglena obtusa which emerge out of the black mud. Cell densities on the surface surpass 105 cells/cm2. Before the tide returns to cover the area, the cells re-burrow back into the mud and remain there during high tide and throughout the night.The cells can be prevented from emerging on to the surface mud at low tide by artificially darkening the area with an opaque covering just as the tide recedes. Cells which are already on the surface can be made to re-burrow by similarly placing them in darkness.The vertical-migration rhythm will persist in the laboratory in constant illumi-nation, constant temperature, and away from the influence of the tide, for nearly one month. In these conditions the rhythm is diurnal, rather than tidal. The rhythm will not persist in constant darkness.Because of the excessive turbidity of Avon water, each high tide imposes a period of darkness on the surface mud. It is thought that these dark periods transform the fundamental diurnal rhythm into one of tidal frequency.Various intensities of constant illumination alter the form and amplitude of the rhythm, but not the period. The stable nature of the period, under different light intensities, is thought to be due to a unique, self-stabilizing feature inherent in this type of rhythm.The rhythm is inhibited at 2° C. Between 5° and 15° C, the period of the rhythm is virtually unaltered; it remains approximately 24 h in length.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0025315400016428

Persistent, vertical-migration rhythms in benthic microflora: I. The effect of light and temperature on the rhythmic behaviour of Euglena obtusa

IN intertidal organisms the rates at which various physiological functions proceed are often related to the state of the tide. In a habitat in which environmental conditions change so drastically with the ebb and flow of the tidal waters, this is not particularly surprising. What is remarkable is that the rate of many of these functions continues to vacillate in approximate synchrony with the tide when organisms are removed to non-tidal, constant conditions in the laboratory. These persistent vacillations are referred to as tidal or bimodal lunar day rhythms. By way of example, persistent tidal rhythms have been described for oxygen consumption in crabs1; vertical migrations of planarians2 and diatoms3; colour change in crabs4; spontaneous activity in crabs5,6, amphipods7,8, and fish9; and filtration rate in mussels10.

John D. Palmer

Papers

Persistent, vertical-migration rhythms in benthic microflora.: II. Field and Laboratory Studies On Diatoms From The Banks Of The River Avon

Tidal rhythms: the clock control of the rhythmic physiology of marine organisms

Persistent, vertical-migration rhythms in benthic microflora. vi. the tidal and diurnal nature of the rhythm in the diatom hantzschia virgata

Persistent, vertical-migration rhythms in benthic microflora: I. The effect of light and temperature on the rhythmic behaviour of Euglena obtusa

Daily and Tidal Components in the Persistent Rhythmic Activity of the Crab, Sesarma