Beyond the "Code": A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora)

Abstract

Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigations of biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversity of ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from a workshop that explored ways to implement six Grand Challenges proposed by the International Research Coordination Network for Biodiversity of Ciliates (IRCN-BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN-BC proposes to populate The Ciliate Guide, an online database, with biodiversity-related data and metadata to create a resource that will facilitate accurate taxonomic identifications and promote sharing of data.

Keywords: Cultivation; information resources; molecular phylogeny; morphology; nomenclature; phylogenetics; systematics; taxonomy; type specimens.

Figure 1

Ciliate sequences of the small subunit ribosomal RNA gene in the NCBI GenBank (http://www.ncbi.nlm.nih.gov; accessed on 6/4/2015).

Figure 2

Photomicrographs of representative ciliate taxa (originals from D. J. Patterson). (A) Homalozoon vermiculare, a crawling, ribbon‐shaped haptorian predator. The cell has been fixed and stained with Feulgen reagent. The anterior mouth, at the top of the image, is underlain with a dense band of extrusomes that are used to capture food. The structures stained pink are the irregular ribbon of macronuclear nodules, the micronuclei, and a few developing extrusomes. Scale bar = 50 μm. (B) Tetrahymena pyriformis, a hymenostome ciliate. The cell has been fixed and stained with protargol that impregnates the bases of the cilia (basal bodies) and the nucleus. The somatic cilia are arranged in longitudinal rows; the oral cilia are densely packed and appear as short bands. A system of microtubules that forms the cytopharynx extends from the mouth into the cell. The macronucleus is the globular structure near the center of the cell. Scale bar = 20 μm. (C) Pattersoniella vitiphila, a hypotrich ciliate. Fixed cell stained with protargol. The C‐shaped collar around the front (top) of the cell is the adoral zone of membranelles (ciliary fans). The spots near the front of the cell, forming marginal bands and a curving row in the center of the cell, are cirri (ciliary bristles). The macronuclear nodules are the globular inclusions within the cell. Scale bar = 50 μm. (D) Vorticella convallaria, a peritrich ciliate. Two living cells under Nomarski differential interference contrast optics, the one to the right is extended and feeding, the one to the left is contracted. The feeding cilia (haplokinety and polykineties) extend around the edge of the anterior of the cell and curve into the mouth. The cells contain many food vacuoles. The stalk contains a spasmoneme that causes it to contract in a spiral fashion, while an elastic envelope acts as antagonist. Scale bar = 50 μm. (E) Trithigmostoma sp., a cyrtophorid ciliate. Living cell under phase‐contrast optics. The cell eats small algae, using the basket‐shaped mouth (upper right). Several ingested diatoms can be seen inside the cell. The large central structure is the macronucleus. There are multiple small contractile vacuoles in the cell that are used for osmoregulation. Scale bar = 50 μm. (F) Paramecium bursaria, a peniculid ciliate with endosymbiotic zoochlorellae. Living cell under Nomarski differential interference contrast optics. The cell surface is underlain with many rod‐shaped extrusomes (minute harpoon‐like structures). The pear‐shaped area in the center of the cell is the cytopharynx. Scale bar = 50 μm. (G) Acineta sp., a suctorian ciliate. Living cell under Nomarski differential interference contrast optics. This predator captures other ciliates and flagellates that swim into the extending sticky tentacles. Each tentacle is a mouth and has an expanded apex containing extrusomes that catch hold of any prey. The cell is attached to substrates by means of a stalk. Cilia are absent in the trophic cell, but present in the swarmers. Scale bar = 50 μm. (H) Eudiplodinium sp., an entodiniomorphid ciliate from the stomach of a bison. Living cell under phase‐contrast optics. The body is very stiff, sculpted with longitudinal grooves that form a rounded extension at the posterior end of the cell. There are two zones of cilia at the anterior end. The ciliate feeds on bacteria, many of which can be seen around the cell, and on small particles of wood. Two contractile vacuoles and associated vesicles lie over the macronucleus in the left cell half. Scale bar = 20 μm. (I) Cryptopharynx sp., a small and rarely encountered karyorelictean ciliate. Living cell under phase‐contrast optics. The mouth is the extension to the anterior right. The cilia form dimpled rows (kineties) that extend along the length of the body. Scale bar = 20 μm. (J) Mesodinium rubrum (=Myrionecta rubra), a small marine planktonic haptorian ciliate that contains endosymbiotic cryptomonad algae giving the cell its red color. Living cell under phase‐contrast optics. Stiff bundles of equatorial cilia extend from the cell and their action causes a jumping motion; further cilia lay adpressed to the posterior portion of the body. Scale bar = 20 μm. (K) Stentor coeruleus, a trumpet‐shaped heterotrich ciliate. Living cell under Nomarski differential interference contrast optics. The cell attaches to immersed surfaces via its posterior end and, when feeding, the cell has a characteristic conical form with the adoral zone of membranelles at the anterior of the cell. Cilia also extend from the remaining body surface. The blue color comes from minute inclusions (cortical granules) lying just under the cell surface. Scale bar = 100 μm. (L) Lacrymaria olor, a predatory haptorid ciliate. Living cell under phase‐contrast optics. The extensible and contractile anterior portion moves around, searching for prey, while the posterior end of the body often remains attached to the substrate. The mouth is at the tip of the extensible neck and is expanded because of the extrusomes that are used to kill prey—often small ciliates. Scale bar = 50 μm. (M) Litonotus sp., a pleurostomatid predatory ciliate. Living cell seen from the side under phase‐contrast optics. There are two large macronuclear nodules in the center of the cell. The mouth lies along the bottom edge of the cell, extending from near the middle to the anterior end, and is underlain with extrusomes that are used to kill prey. Somatic cilia extend from the ventral surface of the cell. Scale bar = 20 μm. (N) Loxodes sp., a karyorelictid ciliate from freshwater habitats. Living cell under phase‐contrast optics. The sickle‐shaped mouth region is located to the anterior right of the cell, which engulfs mostly algae, such as diatoms, and cyanobacteria. One of the macronuclear nodules is evident just above the mid‐line and in the left cell half; it has a dark core and a light peripheral region. Anteriorly and posteriorly to it are two vacuoles of a similar size but each with a bright refractile granule. These are Müller's bodies that inform the cell as to the direction of gravitational pull. Scale bar = 50 μm. (O) Bursaria sp., a huge colpodid ciliate. Living cell under dark field optics. There is a large, curved channel that leads form the anterior of the cell to the cytostome. The ciliate is mostly found in still‐freshwater habitats, where it feeds on planktonic algae. Scale bar = 50 μm.