Biology Microscopy - Biodiversity

Organisms known as archaea (archaebacteria) belong to the Domain Archaea, and are typically chemosynthetic. They share the characteristics of prokaryotes (no membrane-bound organelles; genes on a ring of DNA rather than real chromosomes; usually quite small) with the bacteria, which belong to the Domain Bacteria. In lab, we are only concerned with the Domain Bacteria. For these organisms, cell shape (bacillus, coccus or spirillum) and gram-stain (positive or negative) are among the more practical means of classification.

Eubacteria

For many species of "true" bacteria, the known biology still does not allow a reasonable means of classifying them into groups that are both closely related and recognizable. Thus, we consider them Eubacteria. These are typically heterotrophic cells with walls containing peptidoglycan. There are numerous (not always widely agreed upon) phylum-level categories and evolutionary lineages. They may be motile or not. Examples of common types of Eubacteria include the following:

gram negative bacilli
Note the color (pink is negative) and shape (bacillus is rod-shaped).

gram positive bacilli
Note the color (purple is positive) and shape (bacillus is rod-shaped).

gram negative cocci
Note the color (pink is negative) and shape (coccus is spherical).

gram positive cocci
Note the color (purple is positive) and shape (coccus is spherical).

some of these bacteria form endospores, which resist harsh environments.

Phylum Spirochetes

The spirillum (helical) shape distinguishes this group of heterotrophic bacteria, which tend to be large for prokaryotes and often possess flagella.

Spirillum
Note shape and flagella (at ends).

Phylum Cyanobacteria

These autotrophic, algal-like organisms appear plantlike, but their chlorophyll a appears in photosynthetic lamellae (not true chloroplasts). They are, however, prokaryotic, and some species fix nitrogen in specialized cells called heterocysts (see Anabaena). In general, their size is intermediate between other bacteria and the unicellular protists.

Oscillatoria
This apparently multi-cellular form consists of ribbon-like chains of cells.

Anabaena
This form also has chains of cells, but these are smaller and embedded in a gelatinous matrix; note the heterocysts.

Nostoc
Similar in form to Anabaena.

Plants are eukaryotic, multi-cellular autotrophs that possess chlorophyll and cell walls of cellulose. Life cycle includes alternation of generations, with a dependent embryo. 

Bryophytes are now considered to be three separate phyla of non-vascular plants. Bryophytes are terrestrial, but compared to truly terrestrial plants they do not possess real vascular tissue, although some like some Phaeophyta have cells that inefficiently conduct water and dissolved materials. True mosses, liverworts and hornworts comprise the three recognizable groups of bryophytes. 

Moss structures

Moss capsule (l.s.): The spore capsule is the major portion of the sporophyte stage in the moss life cycle. It develops from a fertilized egg, on a stalk on top of the female moss gametophyte. A large sporangium (S) containing spores (P) surrounds the central core of the capsule. A cap on top opens for spore dispersal. 

Moss antheridium (l.s.): The antheridium (M) is the reproductive structure of the male gametophyte stage of the moss life cycle. Antheridia, which produce many motile sperm, are located at the tip of the individual male plant. 

Moss archegonium (l.s.): The archegonium (F) is the reproductive structure of the female gametophyte stage of the moss life cycle. Archegonia, each of which produces an egg (E), are located at the tip of the individual female plant. 

Phylum Lycophyta includes the club mosses. Though vascular, modern club mosses are not terribly significant plants (in terms of either species diversity, abundance or size); during the coal-forming period, several hundred million years ago, however, there were tree-like lycopods. The dominant stage of the life cycle is the sporophyte, and the strobilus is a vaguely cone-like structure that contains the sporangia. The stems have vascular tissue, but are otherwise rather simply constructed; the leaves are not very well developed (microphylls). 

Club moss structures 

Lycopodium stem (c.s.): The stem contains bundles of vascular tissue.  Xylem cells (X) are larger than the phloem cells (P), and they are surrounded mainly by pith-like parenchyma cells and wrapped in epidermis. The structure resembles that of the ferns, though the arrangement of tissues is different. 

Lycopodium strobilus (l.s.) Strobilus is a sort of cone-like structure. Spores (E) are produced in the sporangia (G), the chambers attached to top of the fertile (modified) leaves arranged around the vascular core (C). 

Phylum Pterophyta includes ferns, truly vascular plants with leaves of the most highly developed type (megaphylls). The fern life cycle, with its non-vascular gametophyte stage, and complex leaves, usually arising from an underground stem (or rhizome), are characteristic of the group. Ferns are the most complex non-seed-bearing plants. 

Fern structures 

Leaflet with sorus:  Although some fern sporophytes consist of really obvious modified leaves for producing their spores, most species have inconspicuous structures, sori (U), on the undersides of their typical leaves. Often the shape or location of these structures is useful in identifying fern species. Here, one can observe the sporangia (G) full of spores (E) within the sorus. 

Stem:  The underground stem (or rhizome) of ferns has a reasonably complex structure. Vascular bundles (V) of xylem and phloem and strands of sclerenchyma cells (S), both with much thickened cell walls, function in support in some ferns. They are scattered among simpler, pith cells (P). 

Fern gametophyte (prothallium):  The non-vascular gametophyte (G) stage of the fern life cycle produces antheridia (M) and archegonia, which produce motile sperm cells and non-motile egg cells, respectively. A fertilized egg, or zygote, produces a young sporophyte (S), which grows out of the gametophyte. At higher magnification, vascular tissue (V) can be seen in the young sporophyte. 

Phylum Coniferophyta are seed-bearing vascular plants that possess "naked" seeds (i.e., without protection from the ovary or fruit), and scale-like or needle-like leaves. Many, but not all, are evergreen; many are found in habitats that are at least occasionally quite cold or quite dry. 

Conifer structures 

Leaf (needle) cross-section:  Although conifer needles look much different than flowering plant leaves, they do have generally the same structure. An epidermis (E) covers the surface of the needle and a vascular bundle (V) lies in the center. Much of the volume of the leaf is the photosynthetic region, the mesophyll (M), which usually also contains one or more pitch ducts (P). 

Female strobilus (ovulate cone):  The female reproductive structures take more than one year to mature in most conifers. By the second year in a pine tree, the cone is small but clearly visible, and microscopic examination reveals the following cone structure: cone scale (S), ovule (O) and vascular core (V). 

Male strobilus (pollen cone) The male reproductive structures develop in a single year. The cone is small and contains several sporangia (S) or pollen chambers, where the copious pollen (P), typical of wind-pollinated plants, is produced. A vascular core (V) is present here, too. 

Phylum Anthophyta are seed-bearing vascular plants in which seeds protected by the modified ovary or fruit. Their most obvious unique trait is the involvement of flowers in sexual reproduction. Anthophytes have been traditionally divided into two groups. 

Monocotyledons form a true clade, i.e., all are descended from a common ancestor.  Grasses, lilies and orchids are three of the more familiar families belonging to this group. Monocot characteristics include having flower parts in threes, generally elongate leaves with parallel veins (vascular tissue), and vascular bundles scattered throughout the stem. 

Monocot structures

Allium root tip (l.s.):  Even though onions are monocots, the root tip is like that of dicots in its basic structure. Notice that there are three zones of cells (division (D), elongation (G), and maturation (M)) behind a protective cap of thick-walled cells (R). 

Zea mays root (c.s.):  As a typical monocot root , the corn root has a more organized arrangement of tissues than does its stem. An epidermis (E) covers a thick layer of cortex cells (C), used for storage; inside this, bounded by an endodermis (N), is a vascular core of xylem (X) and phloem (L), with pith at the center (P). Compare to the dicot root. 

Zea mays stem (c.s.):  As a typical monocot stem, the corn stem does not have a very organized arrangement of tissues (especially compared to dicots). Most of the cells in the corn stem are thin-walled pith cells (P), with the vascular bundles, containing xylem (X) and phloem (L), scattered throughout the stem; epidermis (E) covers the outside of the stem.  

Dicotyledons do not make up a true clade, but share many common characteristics.  

Dicot structures

Tilia two-year old stem (c.s.) Basswood, a deciduous tree, has a woody stem, which results from secondary growth produced by the lateral meristem or cambium (U). Like any meristem, this is a region of dividing cells, which is how the secondary tissues, both xylem (X) and phloem (L), are produced. The most recent year's growth of xylem and phloem is adjacent to the cambium , and the concentric rings of xylem (tree rings) in seasonal ecosystems allow one to age a tree. In such a young stem, one can see an outer layer of epidermis (E) and pith (P) cells at the stem's center.  

Ranunculus root (c.s.) Buttercups have a root structure typical of herbaceous dicots . The xylem (X) and phloem (L), form a central, vascular core , surrounded by the endodermis (N). The largest portion of the root lies outside this core, and consists of cortex (C) cells, which store starch in the plastids seen filling the cells. An epidermis (E) covers the outside. 

Coleus stem tip (l.s.) A plant grown for its decorative foliage, the tip of a Coleus stem shows the apical meristem (A), bud meristems (B) and leaf primordia (F). Although none of the cells near the stem tip have matured, they will become the primary tissues seen in stem cross sections. 

Leaf The basic structure of a leaf , seen in cross section, includes both upper (U) and lower (W) epidermis, as well as the mesophyll comprising the bulk of the leaf. The epidermal cells appear empty, and are not photosynthetic; you may see stomata and guard cells in the lower. The mesophyll has an upper, regularly arranged palisade (S) layer and an irregular spongy (Y) layer, and includes veins (V). Veins contain xylem (X) and phloem (L) surrounded by sheath (H) cells. A surface view of the epidermis shows the irregular-shaped epidermal cells (E), with their breathing structures, stoma (O), protected by guard cells (Z).

Fungi are eukaryotic, mostly multi-cellular heterotrophs; their cells possess walls, mostly of chitin, although the chains of cells (termed hyphae) are frequently not completely separated from each other by a wall. Hyphae should be visible in almost any slide. 

Phylum Zygomycota These are often called bread molds, and such species are common and typical. These fungi are identified by being haploid without motility in any stage. 

Rhizopus This is a black bread mold; all molds found on bread are not necessarily this. The dark, spiky zygosporangium found between two suspensors is diagnostic; stalked sporangia, which produce spores, are usually also visible. 

Phylum Ascomycota Although most species in this group are rather small, some fairly large forms look more or less mushroom-like. The distinguishing feature is that they reproduce by spores produced in an ascus, which is typically a tube- or vase-like structure containing eight ascospores. 

Penicillium This is the type of fungus that produces penicillin; frequently found on spoiled fruit. Branching conidiophores are a distinguishing feature. Peziza This group represents one of the more mushroom-like ascomycotans. There are lots of species in this genus, most resembling a saucer with upturned edges; the asci are usually on the upper (inner) spore-producing surface (S). Hyphae (H), and asci (A) with eight ascospores (8) are easily seen. 

Phylum Basidiomycota Most of the species that you would think of as mushrooms or mushroom-like organisms belong to this group. Spores produced on a basidium, a microscopic fist-shaped structure located on the reproductive surface of the fruiting body, are diagnostic.

Puccinia This is a rust that infects wheat. It has a complex life cycle involving several recognizable stages/forms, and a secondary host, barberry. We will see the aecia stage on a barberry leaf; it is haploid. 

Coprinus Named for its habit of occurring on dung, some species are delicious. This is a rather typical mushroom, except that species of this group self-digest soon after the spores ripen. It is a gilled mushroom, and the basidia occur on the gills (G), located on the underside of the cap of the fruiting body or basidiocarp (C). On high power, the basidia (B) and basidiospores (S) are easily seen. 

Lichens are not just fungi, but a symbiotic pairing of a fungus and some type of algae or cyanobacteria (green algae and cyanobacteria are most common). The fact that they are often as large as most macroscopic fungi, and frequently abundant in certain ecosystems, makes having a way to classify them more useful than, e.g., the ecologically similar, but microscopic symbiotic mycorrhizae. When identified, the fungal component is more likely to be an ascomycotan, although basidiomycotans also form lichens. 

lichen The symbiosis is fairly obvious as the algal cells (A) are easily seen enmeshed in the fungal hyphae (H); you can also see where the lichen was attached to the substrate (D). At lower power, the general structure is more apparent.

Unlike Protista, Fungi, and Plantae, there is little argument about what groups are placed in this kingdom. Animals are multi-cellular heterotrophs, whose cells have no cell wall and individuals of which are usually motile or have motile structures. Except for Porifera, animals generally have cells that clearly fit into one of the four basic tissue types: epithelium, connective, muscle and nerve.

Phylum Porifera

The sponges are characterized by having no tissues and a body of only two cell layers (diploblastic). Although there are three levels of complexity of sponge bodies, and sponge bodies are supported by a variety of materials, the basic body plan of a sponge is that a layer of flat cells is on the outside and a layer of flagella-bearing cells is on the inside, surrounding a hollow chamber, the spongocoel. The beating flagella move water through pore-shaped cells, into the spongocoel, and out an opening (osculum); this allows the sponge to filter-feed. An example is:

Grantia

This slide shows cross sections of a sponge of intermediate complexity. You can see the radial canals (R) radiate outward from the spongocoel (S); incurrent canals (I) allow water in from the environment to the porocytes. With a good slide, you may see pointed spicules or recognize the two cell layers.

Phylum Cnidaria

The cnidarians, which include the hydroids, jellyfish, corals and sea anemones, are characterized by having two tissue layers (outer = epithelio-muscle layer; inner = gastrodermis); two body forms (polyp is a cylinder with dorsal tentacles around the mouth, and is normally sedentary; medusa is an umbrella-shaped, free-swimming form with marginal or ventral tentacles); a gastrovascular cavity (or incomplete digestive system = one opening); and, especially, stinging cells. Most are marine; many are colonial. Examples of various forms can be seen in:

Obelia

This species typically occurs as a connected colony of individual polyps produced asexually by budding. Gastrozooids (F) possess tentacles (T) and are specialized for feeding; they also possess a gastrovascular cavity (G). Gonozooids (R) are specialized for reproduction (budding, which produces tiny medusae (M)). The free-living medusa form is the sexual stage; reproductive organs (O) are not visible in immature medusae, but are in mature medusae.

Phylum Platyhelminthes

This phylum contains the free-living flatworms (e.g., planarians) and the parasitic flukes and tapeworms. The most obvious identifying feature of this phylum is the flat, ribbon-like shape of these worms. They do not have a body cavity of any sort between their body wall and their internal organs. Most have a digestive system in the form of a gastrovascular cavity; tapeworms have no digestive system. Many species in this group of worms are parasitic; they are hermaphrodites. Examples are:

Planaria

This is a fairly common aquatic scavenger; it has its mouth in the middle of its ventral surface. An injected specimen shows the extent of the gastrovascular cavity (G), which extends in all directions from the pharynx (P); eye spots (E) are also visible. A cross section of a planarian clearly shows the acoelomate condition, with no space between the body wall (B) and the internal organs; the epidermis (S) is also visible.

Taenia

This tapeworm shows the body form typical of this group of parasites. The scolex (S) is at the "head" end and possesses hooks and suckers for attaching to the gut wall of its host. What appear to be segments (but are more like individual members of a colony) are termed proglottids (P). These do contain such structures as nerves and excretory organs, but are primarily packages of reproductive structures; mature proglottids are mostly filled with eggs (E).

Phylum Nematoda

This phylum contains the roundworms; there are free-living forms as well as parasites of both animals and plants. They have no readily seen unique characters beyond their smooth, round, worm-shaped body; internally, they have a pseudocoelom in which their organs float freely. They have a complete digestive system, the least complex group of animals to have one. There are separate males and females; females are larger than males.

Ascaris

These are simple intestinal roundworms. In both the male and the female, one can see the body wall (B), various sections of the reproductive system (R), the digestive system (G), and the cuticle (C), which serves as a protective coating for the body. Males exhibit a sperm duct (S) with sperm, whereas females have a uterus (U) filled with eggs.

Phylum Rotifera

These animals, too, are pseudocoelomate, and were once grouped in the same phylum as nematodes. Though the size of many protists, they are complex animals with several organ systems, including a complete digestive tract. They have a coronal ring of cilia at the anterior end, surrounding their mouths.

rotifer

At their posterior end, rotifers have a foot (F) which allows them to attach to the substrate for feeding. They possess a muscular grinding structure, the mastax (M), between their mouth and stomach (S); also visible are the ovary (O) and coronal cilia (C).

Phylum Annelida

These are the only group of segmented worms; the segmentation is externally obvious as a series of rings along the body. They have complete digestion, a closed circulatory system, a ventral nerve cord, a nephridial excretory system, and a true body cavity or eucoelom. An example is:

earthworm

The earthworm is fairly typical of one class of annelids. A cross section of the worm allows a view of the basic structure of most of the body. The intestine (I) is most obvious, with the typhlosole (T) protruding into the lumen (inner space). Also visible are the dorsal artery (A) and the ventral nerve cord (N), above and below the intestine, respectively; the muscles of the body wall (B) are quite obvious.

Phylum Arthropoda

Arthropods are characterized by a segmented body covered by an exoskeleton and possessing jointed appendages. This is a very diverse group, and the most advanced group of protostomes. It contains several subphyla and classes.

Class Arachnida

These are members of the subphylum Chelicerata, so named for possessing fang-like chelicerae rather than mandibles (true jaws). Arachnids are distinguished by having four pairs of walking legs, although many have a pair of rather leg-like chelipeds which may be used in feeding or prey capture; they also have the head and thorax body regions fused as a cephalothorax. Examples are:

pseudoscorpion

Only vaguely looking like scorpions, these have "pinchers" at the ends of their large chelipeds but do not possess the sting at the end of the abdomen, however. Note cephalothorax (T), abdomen (A), four pair of legs (L), chelipeds (P) and chelicerae (F). A close-up of the cheliped shows the "pinchers."

Class Insecta

Any arthropod with wings must be an insect. Except for a few immature arachnids, anything with six legs (hexapod) is an insect. This group is extremely diverse. Examples include ants and fleas.

Class Crustacea

Technically, crustaceans are distinguished by two pair of antennae. Practically, an abundance of legs or appearance like crayfish, shrimp or crabs is usually your best bet; they possess gills, though some are terrestrial. An example is Gammarus.