Overview

Brief Summary

Introduction

The name Bacillariophyceae has been used in several ways: to refer to all diatoms (e.g. when the diatoms are trated as a class within the Heterokontophyta, as by van den Hoek et al. 1995), or to refer to the raphe-bearing pennate diatoms (e.g. Round et al. 1990), or to refer to all pennate diatoms (Medlin & Kaczmarska 2004). Here, we adopt the third of these: all pennate diatoms.

The pennate diatoms are characterized morphologically by the feather-like organization of their valve pattern, which is evident in the title illustrations. The distinction between this kind of pattern and the centric patterns found in other clades of diatoms was first discussed by Schütt (1896) and Karsten (1928). In pennates, a long rib or strip of plain silica runs along the length of the valve, subtending transverse ribs and lines of pores on either side. In contrast, the clades of centric diatoms possess a radial organization of the pattern. Electron microscopy has revealed that, at the centre of the radial pattern, there is a ring-like annulus (although the annulus can be elliptical or elongate in some species, such as Odontella sinensis and Attheya species: Pickett-Heaps et al. 1990, Stonik et al. 2006). Because of the resemblance of the pennate valve to the human rib-cage, the longitudinal rib or strip is called the sternum.

Most pennate diatoms have elongate cells, shaped like boats, rods, spicules or bananas and it is sometimes stated that this, rather than the organization of the valve pattern, is the essential feature of the group. However, elongate shape is not confined to pennate diatoms, being found in several clades of polar centric diatoms.

Pennate diatoms are monophyletic according to molecular phylogenies (e.g. Medlin & Kaczmarska 2004, Sorhannus 2007): the sternum has apparently evolved only once. Another autapomorphy of pennates is the loss of all flagellate stages: during sexual reproduction, fusion takes place between large amoeboid or motionless gametes, which are usually ± equal in size (morphological isogamy).

The pennates are more species-rich than other diatom groups. Most species are benthic, growing attached to solid substrata or moving through sediments and over surfaces, but the group also contains some common and important planktonic genera, such as the toxin-producing Pseudo-nitzschia, and the remarkable hair-like Thalassiothrix, which can grow up to 5 mm long.

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Comprehensive Description

Characteristics

  • Valve pattern feather-like, organized with respect to a longitudinal sternum.
  • Sexual reproduction via morphological isogamy (or slight anisogamy) of amoeboid or swelling static gametes.
  • Cells mostly elongate, bipolar.
  • Shape usually created through the constraining effects of a set of special silicified bands (the perizonium), formed during auxospore expansion.
  • Predominantly benthic.
  • Rimoportulae or their presumed homologues, the raphe slits, present in most genera and species.

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Ecology

Associations

Known predators

Bacillariophyceae (Benthic diatoms) is prey of:
Acartia
Porifera
Bivalvia
Ethmidium maculatum
Rangia
Gammarus
Mugil
Baetis
Ephemerella
Leuctra
Philopotamus
Ecdyonurus
Hydropsyche
Rhyacophila
Diplectrona
Asellus
Epeorus
Pseudocloeon
Centroptilum
Paraleptophlebia
Neophylax
Glossosoma
Tendipedidae
Simulium
Oreochromis mossambicus
Podophthalmus vigil
Copepoda
Metopograpsis messor
Macrobrachium
Oxyurichthyes lonchotus
Palaemonetes
Charybdis orientalis
Mugil cephalus
Chonophorous genivittatus
Nodolittorina tuberculata
Littorina
Fissurella barbadensis
Enchinometra lucunter
Acanthopleura granulata
Rhithrogena
Amphinemura
Oligochaeta
Cladocera
Chironomidae
Chloroperla
Stenonema
Chimarra
Habrophleboides
Prosimulium
Psychomyia
Corynoneura
Polypedilum
Isonychia
Psephenus
Stenelmis
Psilotreta
Helicopsyche
Agapetus
Antocha
Eukiefferiella
Chenmatopsyche
Calanoida
Parathemisto
Rheotanytarsus
Heptagenia
Simuliidae
Cricotopus
Orthocladius
Cricotopus bicinctus
Trichoptera
Limnophilus
Ephemeroptera
Suidasia
Tegula funebralis
Littorina planaxis
Littorina scutulata
Acmaea digitalis
Acmaea pelta
Acmaea scabra
Cyanoplax dientens
Dynamenella glabra
Allochertes ptilocerus
Diaulota densissima
Syllis vittata
Syllis spenceri
Hydropsyche instabilis
Leuctra fusciventris
Baetis rhodani
Ephemerella notata
Dicranota
Pentaneura
Philopotamus montanus
Ecdyonurus venosus
Sericostoma personatum
Siphlonurus lacustris
Pacifastacus gambelli
Gammarus lacustris
Limnephilus frijole
Sigara
Diplectrona modesta
Phyacophila parantra
Caecidotea brevicauda
Baetis flavistriga
Baetis herodes
Centroptilium rufostrigatum
Epeorus pleuralis
Neophylax autumnus
Glossosoma intermedium
Baetis binoculatus
Baetis pumilus
Ecdyurus venosus
Rhithrogena semicolorata
Heptagenia sulphurea
Caenis rivulorum
Halesus auricollis
Agapetus fuscipes
Glossosoma vernale
Psychomyia pusilla
Tinodes waeneri
Hydroptila
Orthocladiariae
Tanypodinae
Tanytarsus
Simulium reptans
Hexatoma
Nais
Sphaerium
Pisidium
Cyclops
Chydorus
Bosmina
Pleuroxus
Ostracoda
Najna consiliorum
Araneidae
Catostomus commersoni
Ancylastrum fluviatile
Gammarus pulex
Glossosoma boltoni
Chimarrha marginata
Stenophylax stellatus
Helmidae
Salmo salar
Phoxinus phoxinus
Bacillariophyceae
Free bacteria in water column/DOC
Heterotrophic microflagellates
microzooplankton
zooplankton
Ctenophora
Polychaeta
Brevoortia tyrannus
Leiostomus xanthurus
Morone americana
Arius felis
Pomatomus saltatrix

Based on studies in:
USA: Rhode Island (Coastal)
Barbados (Littoral, Rocky shore)
USA: North Carolina, Pamlico (Estuarine)
USA: Kentucky (River)
Wales, River Clydach (River)
Wales, River Rheidol (River)
England, River Cam (River)
Wales, Dee River (River)
Finland (River)
USA: Pennsylvania (River)
USA: Kentucky, Station 1 (River)
USA: Hawaii (Swamp)
Canada, high Arctic (Ice cap)
USA: Idaho-Utah, Deep Creek (River)
UK: Yorkshire, Aire, Nidd & Wharfe Rivers (River)
Canada: Ontario, Mad River (River)
USA: California, Monterey Bay (Littoral, Rocky shore)
Canada: Ontario (River)
USA: Maryland, Chesapeake Bay (Estuarine)

This list may not be complete but is based on published studies.
  • J. N. Kremer and S. W. Nixon, A Coastal Marine Ecosystem: Simulation and Analysis, Vol. 24 of Ecol. Studies (Springer-Verlag, Berlin, 1978), from p. 12.
  • B. J. Copeland, K. R. Tenore, D. B. Horton, Oligohaline regime. In: Coastal Ecological Systems of the United States, H. T. Odum, B. J. Copeland, E. A. McMahan, Eds. (Conservation Foundation, Washington, DC, 1974) 2:315-357, from p. 318.
  • J. R. E. Jones, A further ecological study of calcareous streams in the "Black Mountain" district of South Wales, J. Anim. Ecol. 18:142-159, from p. 157 (1949).
  • G. W. Minshall, Role of allochthonous detritus in the trophic structure of a woodland springbrook community, Ecology 48(1):139-149, from p. 148 (1967).
  • G. E. Walsh, An ecological study of a Hawaiian mangrove swamp. In: Estuaries, G. H. Lauff, Ed. (AAAS Publication 83, Washington, DC, 1967), pp. 420-431, from p. 429.
  • F. Briand, unpublished observations
  • J. R. E. Jones, A further ecological study of the river Rheidol: the food of the common insects of the main-stream, J. Anim. Ecol. 19:159-174, from p. 172 (1950).
  • K. W. Cummins, W. P. Coffman, P. A. Roff, Trophic relationships in a small woodland stream, Verh. Int. Ver. Theor. Angew. Limnol. 16:627-638, from p. 630 (1966).
  • K. Kuusela, Early summer ecology and community structure of the macrozoobenthos on stones in the Javajankoski rapids on the river Lestijoki, Finland, Acta Universitatis Ouluensis (Ser. A, no. 87, Oulu, Finland, 1979).
  • P. W. Glynn, Community composition, structure, and interrelationships in the marine intertidal Endocladia Muricata - Balanus glandula association in Monterey Bay, California, Beaufortia 12(148):1-198, from p. 133 (1965).
  • J. R. E. Jones, 1949. A further ecological study of calcareous streams in the "Black Mountain" district of South Wales. J. Anim. Ecol. 18:142-159, from pp. 154-55, 157.
  • D. G. Koslucher and G. W. Minshall, 1973. Food habits of some benthic invertebrates in a northern cool-desert stream (Deep Creek, Curlew Valley, Idaho-Utah). Trans. Amer. Micros. Soc. 92:441-452, from pp. 446-50.
  • G. W. Minshall, 1967. Role of allochthonous detritus in the trophic structure of a woodland springbrook community. Ecology 48:139-149, from pp. 145, 148.
  • E. Percival and H. Whitehead, 1929. A quantitative study of the fauna of some types of stream-bed. J. Ecol. 17:282-314, from p. 311 & overleaf.
  • W. E. Ricker, 1934. An ecological classification of certain Ontario streams. Univ. Toronto Studies, Biol. Serv. 37, Publ. Ontario Fish. Res. Lab. 49:7-114, from pp. 78, 89.
  • R. M. Badcock, 1949. Studies in stream life in tributaries of the Welsh Dee. J. Anim. Ecol. 18:193-208, from pp. 202-206 and Price, P. W., 1984, Insect Ecology, 2nd ed., New York: John Wiley, p. 23
  • M. S. W. Bradstreet and W. E. Cross, Trophic relationships at High Arctic ice edges, Arctic 3(1)5:1-12, from p. 9 (1982).
  • W. E. Ricker, 1934. An ecological classification of certain Ontario streams. Univ. Toronto Studies, Biol. Serv. 37, Publ. Ontario Fish. Res. Lab. 49:7-114, from pp. 105-106.
  • P. H. T. Hartley, Food and feeding relationships in a community of fresh-water fishes, J. Anim. Ecol. 17(1):1-14, from p. 12 (1948).
  • Baird D, Ulanowicz RE (1989) The seasonal dynamics of the Chesapeake Bay ecosystem. Ecol Monogr 59:329–364
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Known prey organisms

Bacillariophyceae (Benthic diatoms) preys on:
phytoplankton
Bacteria attached to suspended POM
Bacteria attached to sediment POM
Bacillariophyceae

Based on studies in:
USA: Maryland, Chesapeake Bay (Estuarine)

This list may not be complete but is based on published studies.
  • Baird D, Ulanowicz RE (1989) The seasonal dynamics of the Chesapeake Bay ecosystem. Ecol Monogr 59:329–364
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General Ecology

DMS in the odor landscape of the sea

Dimethyl Sulfide or DMS is present throughout the ocean(1). It’s an important odor component of many fish and shellfish, including clams, mussels, oysters, scallops, crabs and shrimp(2-9). Where does it come from? Usually from the marine plants they feed on.

Many species of plants and algae produce DMS, but not all species produce significant amounts of it. Nearly all of these are marine, and they tend to be in closely related groups with other DMS-producers, including Chlorophyte (green) seaweeds, the Dinophyceae in the dinoflagellates, and some members of the Chrysophyceae and the Bacillariophyceae (two classes of diatoms). Other large groups, like cyanobacteria and freshwater algae, tend not to produce DMS. (10,11)

Why do these groups produce DMS? In algae, most researchers believe a related chemical, DMSP, is used by the algae for osmoregulation- by ensuring the ion concentration inside their cells stays fairly close to the salinity in the seawater outside, they prevent osmotic shock. Otherwise, after a sudden exposure to fresh water (rain at the sea surface, for instance) cells could swell up and explode. In vascular plants, like marsh grasses and sugar cane, it’s not clear what DMS is used for. (12,13)

Freshly harvested shellfish can smell like DMS because DMSP has accumulated in their tissue from the algae in their diet. Some animals, including giant Tridacna clams and the intertidal flatworm Convoluta roscoffensis, harbor symbiotic algae in their tissues, which produce DMSP; this may not be important to their symbioses, but for Tridacna, the high DMS levels can be a problem for marketing the clams to human consumers. After death, DMSP begins to break down into DMS. A little DMS creates a pleasant flavor, but high concentrations offend the human palate.(2,14)

Not all grazers retain DMS in their tissues, though. At sea, DMS is released when zooplankton feed on algae. It’s been shown in the marine copepods Labidocera aestiva and Centropages hamatus feeding on the dinoflagellate Gymnodinium nelson that nearly all the DMS in the consumed algae is quickly released during feeding and digestion.(15) This has a disadvantage for the grazing zooplankton. Marine predators, like procellariiform seabirds, harbor seals, penguins, whale sharks, cod, and coral reef fishes like brown chromis, Creole wrasse and boga, can use the smell of DMS to locate zooplankton to feed on. (8,16,17)

It’s not easy to measure how much DMS is released from the Ocean into the air every year. Recent estimates suggest 13-37 Teragrams, or 1.3-3.7 billion kilograms. This accounts for about half the natural transport of Sulfur into the atmosphere, is the conveyor belt by which Sulfur cycles from the ocean back to land. In the atmosphere, DMS is oxidized into several compounds that serve as Cloud Condensation Nuclei (CCN). The presence of CCN in the air determines when and where clouds form, which affects not only the Water cycle, but the reflection of sunlight away from the Earth. This is why climate scientists believe DMS plays an important role in regulating the Earth’s climate. (12,18)

  • 1) BATES, T. S., J. D. Cline, R. H. Gammon, and S. R. Kelly-Hansen. 1987. Regional and seasonal variations in the flux of oceanic dimethylsulfide to the atmosphere. J. Geophys. Res.92: 2930- 2938
  • 2) Hill, RW, Dacey, JW and A Edward. 2000. Dimethylsulfoniopropionate in giant clams (Tridacnidae). The Biological Bulletin, 199(2):108-115
  • 3) Brooke, R.O., Mendelsohn, J.M., King, F.J. 1968. Significance of Dimethyl Sulfide to the Odor of Soft-Shell Clams. Journal of the Fisheries Research Board of Canada, 25:(11) 2453-2460
  • 4) Linder, M., Ackman, R.G. 2002. Volatile Compounds Recovered by Solid-Phase Microextraction from Fresh Adductor Muscle and Total Lipids of Sea Scallop (Placopecten magellanicus) from Georges Bank (Nova Scotia). Journal of Food Science, 67(6): 2032–2037
  • 5) Le Guen, S., Prost, C., Demaimay, M. 2000. Critical Comparison of Three Olfactometric Methods for the Identification of the Most Potent Odorants in Cooked Mussels (Mytilus edulis). J. Agric. Food Chem., 48(4): 1307–1314
  • 6) Piveteau, F., Le Guen, S., Gandemer, G., Baud, J.P., Prost, C., Demaimay, M. 2000. Aroma of Fresh Oysters Crassostrea gigas: Composition and Aroma Notes. J. Agric. Food Chem., 48(10): 4851–4857
  • 7) Tanchotikul, U., Hsieh, T.C.Y. 2006. Analysis of Volatile Flavor Components in Steamed Rangia Clam by Dynamic Headspace Sampling and Simultaneous Distillation and Extraction. Journal of Food Science, 56(2): 327–331
  • 8) Ellingsen, O.F., Doving, K.B. 1986. Chemical fractionation of shrimp extracts inducing bottom food search behavior in cod (Gadus morhua L.). J. Chem. Ecol., 12(1): 155-168
  • 9) Sarnoski, P.J., O’Keefe, S.F., Jahncke, M.L., Mallikarjunan, P., Flick, G. 2010. Analysis of crab meat volatiles as possible spoilage indicators for blue crab (Callinectes sapidus) meat by gas chromatography–mass spectrometry. Food Chemistry, 122(3):930–935
  • 10) Malin, G., Kirst, G.O. 1997. Algal Production of Dimethyl Sulfide and its Atmospheric Role. J. Phycol., 33:889-896
  • 11) Keller, M.D., Bellows, W.K., Guillard, R.L. 1989. Dimethyl Sulfide Production in Marine Phytoplankton. Biogenic Sulfur in the Environment. Chapter 11, pp 167–182. ACS Symposium Series, Vol. 393. ISBN13: 9780841216129eISBN: 9780841212442.
  • 12) Yoch, D.C. 2002. Dimethylsulfoniopropionate: Its Sources, Role in the Marine Food Web, and Biological Degradation to Dimethylsulfide. Appl Environ Microbiol., 68(12):5804–5815.
  • 13) Otte ML, Wilson G, Morris JT, Moran BM. 2004. Dimethylsulphoniopropionate (DMSP) and related compounds in higher plants. J Exp Bot., 55(404):1919-25
  • 14) Van Bergeijk, S.A., Stal, L.J. 2001. Dimethylsulfonopropionate and dimethylsulfide in the marine flatworm Convoluta roscoffensis and its algal symbiont. Marine Biology, 138:209-216
  • 15) Dacey , J.W.H. and Stuart G. Wakeham. 1986. Oceanic Dimethylsulfide: Production during Zooplankton Grazing on Phytoplankton. Science, 233( 4770):1314-1316
  • 16) Nevitt, G. A., Veit, R. R. & Kareiva, P. (1995) Dimethyl Sulphide as a Foraging Cue for Antarctic Procellariiform Seabirds. Nature 376, 680-682.
  • 17) Debose, J.L., Lema, S.C., & Nevitt, G.A. (2008). Dimethylsulfionoproprianate as a foraging cue for reef fishes. Science, 319, 1356.
  • 18) Charlson, R.J., Lovelock, J.E., Andraea, M.O., Warren, S.G. 1987. Oceanic phytoplankton, atmospheric sulphur, cloud albedo and climate. Nature, 326:655-661
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Evolution and Systematics

Evolution

Discussion of Phylogenetic Relationships

View Bacillariophyceae Tree

Evolution within the Bacillariophyceae is better understood than among the radial and polar centric diatoms. The earliest molecular systematic paper on diatom evolution (Medlin et al. 1993) indicated three clades:

  1. A clade of pennate diatoms lacking a raphe system (Rhaphoneis, Asterionellopsis)
  2. A second clade of pennate diatoms lacking a raphe system (Thalassionema, Fragilaria)
  3. Raphid pennate diatoms (Bacillaria, Nitzschia, Cylindrotheca)

The relationship among these was {1(2,3)}. In other words, the raphid diatoms are not the sister group to all of the other pennate diatoms, which lack a raphe system. Instead they are the sister group of a particular subset of the araphid pennate diatoms. At present, none of the three clades, nor the (2,3) clade, have agreed names. Clade 3 corresponds to the Bacillariophyceae sensu Round et al. (1990), but Medlin & Kaczmarska (2004), followed by Adl et al. (2005) used this name for all pennate diatoms, as here.

Phylogenetic analyses published since 1993, including many more taxa, still generally show the same {1(2,3)} structure (e.g. Kooistra et al. 2007, Sorhannus 2007). For the moment, the three clades are given informal names here. Clade I araphids comprise a small, morphologically disparate group, which are all marine. Clade II araphids comprise the majority of the Fragilariophyceae sensu Round et al. (1990), i.e. of the pennate diatoms that lack a raphe system. The sister relationship between the raphid diatoms and clade II shows that none of the subclades within clade II are likely to furnish clues as to how the raphe evolved.

The consequence of the {1(2,3)} relationship is that the pennate diatoms that lack a raphe system, which were recognized as the class Fragilariophyceae by Round et al. (1990), are a paraphyletic assemblage. Some people therefore reject any use of the phrase 'araphid pennate diatoms'.

The position of the family Striatellaceae, containing Striatella and Pseudostriatella (but not Hyalosira and Grammatophora as Round et al. 1990 thought) is currently unclear, since it varies greatly from analysis to analysis.

The earliest known pennates in the fossil record are Sceptroneis and Incisoria from the Late Cretaceous (Hajós & Stradner 1975), which appear to belong to the clade I family Rhaphoneidaceae, and Rhaphoneis itself is also reported from the Late Cretaceous (Sims et al. 2006). A few further araphid pennates occur in Cretaceous deposits but their affinities are less clear. Fossil raphid diatoms are not known until the Tertiary (Palaeocene: Sims et al. 2006), but the group probably arose slightly earlier, in the Late Cretaceous (Sorhannus 2007 estimates 75 Mya for the primary diversification of the raphids and 93.8 Ma for the separation of the raphids and clade II).

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Functional Adaptations

Functional adaptation

Estuaries rely on ecosystem engineers: diatoms
 

Estuarine ecosystems rely on diatoms because they act as ecosystem engineers by binding sand to stabilize the environment.

     
  "Many organisms modulate the availability of resources to other species by causing state changes in biotic or abiotic materials (ecosystem engineering), in the process frequently changing the selection to which the ecosystem engineers and other organisms are exposed (niche construction)…In the Bay of Fundy, Canada, estuarine sediments are dominated by benthic diatoms that produce carbohydrate exudates. These secretions bind the sand and stabilize its movement, which causes a physical state change in the environment that allows other species to colonize the area (figure 1;Daborn et al. 1993, Jones et al. 1997). An amphipod (Corophium volutator) that grazes on the diatoms affects soil stability; where these amphipods are abundant, sand stabilization by diatoms is reduced. In turn, migratory sandpipers (Calidris pusilla) feed on the amphipods (figure 2). With the appearance of these birds, amphipod numbers decline, promoting restabilization of the habitat by diatoms. Jones and colleagues (1997) point out that the sandpiper might be seen as the keystone species in the system, since it meets keystone definitions, and variation in its abundance has great knock-on effects on the ecosystem. However, these effects transpire only because of the engineering activities of the diatoms, which are the key ecosystem engineers. Conservation efforts to counteract sediment erosion would be misguided if directed solely at the keystone predators." (Boogert et al. 2006:570, 572)
  Learn more about this functional adaptation.
  • Boogert, Neeltje J.; Paterson, David M.; Laland, Kevin N. 2006. The Implications of Niche Construction and Ecosystem Engineering for Conservation Biology. BioScience. 56(7): 570-578.
  • Jones, CG; Lawton, JH; Shachak, M. 1997. Positive and negative effects of organisms as physical ecosystem engineers. Ecology. 78(6): 1946-1957.
  • Jones CG; Lawton JH; Shachak M. 1994. Organisms as ecosystem engineers. Oikos. 69: 373-386.
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Molecular Biology and Genetics

Molecular Biology

Statistics of barcoding coverage

Barcode of Life Data Systems (BOLD) Stats
Specimen Records: 1466
Specimens with Sequences: 1750
Specimens with Barcodes: 43
Species: 378
Species With Barcodes: 370
Public Records: 969
Public Species: 324
Public BINs: 34
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Barcode data

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