Vaccari D.A., Strom P.F., Alleman J.E. Environmental Biology for Engineers and Scientists

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They have two ﬂagella, one wrapped beltlike around the middle in a transverse groove, the

other extending backward in a longitudinal groove. This gives them a toplike motion, from

which they get their name (from the Greek for ‘‘whirl’’). Although most are free-living,

some are symbionts growing in reef-forming corals, and some are parasitic. The Pyrrophyta

are believed to be close relatives of the ciliated protozoans.

Blooms of dinoﬂagellates in coastal or estuarine waters may sometimes become sufﬁ-

ciently dense to cause red tides (Section 15.2.2). Further, a few dinoﬂagellate species,

such as Gymnodinium, Gonyaulax, and Pﬁsteria, are able to release a neurotoxi n into

the water, which may lead to ﬁsh kills or to human poisoning due to the consumption

of contaminated shellﬁsh (Section 12.3.3). In recent years, Pﬁsteria has received consid-

erable attention in the Chesapeake Bay, apparently ﬁnding a selective advantage by killing

ﬁsh to secure degradable substrates!

Rhodophyta: The Red Algae The red algae, such as Porphyra, are mostly multicellular

and marine, although there are also a few unicellular forms, and some that are freshwater

or soil inhabitants. They have pigments similar to those of cyanobacteria, from which

their chloroplasts may be derived. They produce no ﬂagellated cells, further suggesting

they are not derived from ﬂagellates, as most other algae appear to be. Several red

algae produce mucilaginous polymers that are used com mercially, including the widely

used food additive, carrageenan. Microbiolo gists also owe them a debt of gratitude, as

they are the source of the agar widely used to solidify laboratory media for plating.

Chlorophyta: The Green Algae The green algae are believed to be the group from

which higher plants evolved, and in fact they have the same pigments, cell wall composi-

tion, and storage products. This is an extremely varied and ecologically widespread group,

with habitats that not only include soils and waters (both fresh and salt) but also the

surfaces and internal regions of other organisms. Many are unicellular, but there are

Figure 10.40 Peridinium. (SEM image courtesy of C. J. O’Kelly, D. H. Hopcroft, and R. J.

Bennett.)

278

MICROBIAL GROUPS

also colonial (e.g., Scenedesmus Figure 10.41) and multicellular (but undifferentiated)

forms, and a few that are coenocytic (ﬁlaments in which the cross-walls between cells

deteriorate or do not form, so that they become single cells with many nuclei), like fungi.

10.7.3 Slime Molds

The slime molds are aerobic, mainly terrestrial (a few are aquatic) chemoorganotrophs.

Although they appear to have no major role in environmental engineering or science,

they will be discussed brieﬂy for completeness and because of their interesting life

cycle. There are two separate phyla (Table 10.11), both with similarities to some protozoa.

Myxomycota Myxomycetes, or plasmodial slime molds, often form colorful visible

growths on decaying wood or vegetation. An example is the genus Physarum, which is

bright yellow. The vegetative form is composed of a plasmodium, which is a macroscopic

multinucleated mass of cytoplasm with a single plasma membrane enclosing it (hence,

their other common name, acellular slime molds). Other genera, such as Echinostelium,

however, produce only microscopic plasmodia. The plasmodium crawls over surfaces

with amoeboid motion (cytoplasmic streami ng), engulﬁng food particles—mainly bac-

teria, but also yeasts, spores, and small pieces of organic material—through phagocytosis.

Thus, it behaves much like a giant amoeba. However, when there is insufﬁcient food, or

the surface dries, the plasmodium forms a stalked sporangium and, after meiosis, releases

haploid spores. Under proper conditions a spore germinates to produce a swarm cell

(biﬂagellated) if there is sufﬁcient water for swimming, or a myxamoeba (amoeboid

cell) if the surface is only moist enough for crawling. Two such cells fuse to produce a

diploid cell, which then undergoes mitosis (without cell division) to produce a new plas-

modium.

Acrasiomycota Cellular slime molds, such as Dictyostelium and Polysphondylium,

spend most of their active life as free amoeboid cells. Under unfavorable conditions

Figure 10.41 Scenedesmus.

EUKARYA 279

(inadequate food or water), these individuals aggregate to form a macroscopic pseudo-

plasmodium (because the cells remain individuals with separate membranes), or

‘‘slug’’ (unrelated to true slugs, which are mollusks), which crawls to an exposed location,

forms a fruiting body, and releases spores. (In this way they resemble superﬁcially the

prokaryotic myxobacteria.) The spores can later germinate to produce new amoeboid

TABLE 10.11 The Fungi, Oomycetes (Water Molds), and Slime Molds

Common

Group Phyla Name Motility Feeding Comments Examples

Fungi Zygo- Lower fungi None Absorption Most Entomphthora

mycota mycorrhyzae Mucor

Pilobolus

Rhizopus

Asco- Sac fungi None Absorption Most yeasts and Ceratocystis

mycota lichens; trufﬂes Claviceps

and morels Endothia

Morchella

Neurospora

Tuber

Basidio- Club fungi None Absorption Most Agaricus

mycota mushrooms Amanita

Coprinus

Phanerochaete

Psilocybe

Deutero- Fungi None Absorption Sexual stage Arthrobotrys

mycota imperfecti unknown Aspergillus

(most are Candida

probably Coccidioides

Ascomycetes) Dactylella

Epidermophyton

Fusarium

Geotrichum

Histoplasma

Monilia

Penicillium

Rhizoctonia

Saccharomyces

Trichophyton

Verticillium

Water Oo- Water molds Flagella Absorption Mycelia Allomyces

molds mycota produce Phytophthora

ﬂagellated Plasmopara

zoospores Pythium

Saprolegnia

Slime Myxo- Plasmodial Plasmodium/ Phago- Like giant Echinostelium

molds mycota or acellular amoeboid/ cytosis amoeba; forms Physarum

slime molds ﬂagella sporangium

Acrasio- Cellular Amoeboid/ Phago- Amoebas Dictyostelium

mycota slime molds slug cytosis swarm, Polysphondylium

produce ‘‘slug’’

280 MICROBIAL GROUPS

cells. In addition to this asexual process, cellulose encased macrocysts may occasionally

form in which two amoeba fuse.

10.7.4 Fungi

Fungi are chemoorganotrophic heterotrophs. Most are saprobic, but some are parasites

(the majority of plant pathogens are fungi, as are some animal pathogens) or symbionts.

Although some are found in aquatic or marine environments, most are terrestrial. In addi-

tion to not being photosynthetic, they also differ from plants and algae in having cell walls

composed primarily of chitin rather than cellulose. Fungi are nonmotile, unlike protozo-

ans and slime molds (and some algae). Mitosis in fungi is different from that in plants and

animals.

Like some bacteria, fungi excrete enzymes to digest food externally, then absorb the

smaller organic molecules produced. This makes them especially suited for degradation of

organic solids and for their important ecological role as decomposers of dead biomass

(such as leaves and wood) as well as high-molecular-weight anthropogenic compounds.

They play a major role in the globa l carbon cycle, especially because of the ability of

many to degrade cellulose and of some to attack lignin. Fungi store energy either as gly-

cogen or in lipids.

Fungi usually have one of two growth forms, although a few can take both. Both may

reproduce sexually through spores. Yeasts are unicellular and reproduce asexually by bud-

ding (see below). Molds, which are the much more common form, are multicellular, ﬁla-

mentous organisms and usually reproduce asexually with spores. As with the bacterial

actinomycetes (Section 10.5.7) , an individual ﬁlament is referred to as a hypha (plural,

hyphae), and the intertwined, matted growths they form are known as mycelia (singular,

mycelium). However, unlike with bacterial ﬁlaments, which are essentially colonies of sin-

gle-celled organisms, molds are multicellular. Typically, there is considerable interchange

of materials among cells within the ﬁlament. In fact, often the cross-walls separating cel ls

have holes in them or disappear completely. This can lead to the presence of several nuclei

within a single ‘‘cell,’’ a growth form referred to as coenocytic. Hyphae are usually hap-

loid and produce microscopic spores, usually at the tips of specialized ﬁlaments called

conidia (singular, conidium; Figure 10.42) or in sacs called sporangia (singular, sporan-

gium). After dispersal, the spores may germinate and grow into new hyphae if deposi ted

on a suitable substrate.

The fungal mycelium typically permeates the soil or substrate on which the organism is

growing. Mushrooms are the familiar, large, fruiting bodie s of some fungi and do not

represent the major portion of the organism, which consists of the mycelia below the sur-

face.

Both bacteria and fungi degrade organic material, but bacteria typically grow faster.

However, fungi are less inhibited by dry conditions than bacteria, and so often make

up a majority of the living biomass in drier soils and at the dry edges of compost piles.

Fungi are also able to withstand higher concentrations of salt and sugar, allowing them to

cause spoilage in foods that most bacteria cannot grow on. Some thermophilic fungi can

grow at temperatures up to 62



C. As a group, fungi also can tolerate lower pH than many

common organotrophic bacteria, allowing them to grow competitively, for example, on

fermented fruit. In activated sludge plants for wastewater treatment, if the pH drops

below 5.5 to 6, fungi may grow excessively and interfere with the settling process (fungal

bulking).

EUKARYA 281

The fungi are now classiﬁed into four phyla or divisions: Zygomycetes, Ascomycetes,

Basidiomycetes, and Deuteromycetes (Table 10.11). Previously, another phylum, the

Oomycetes, was included, and is discussed here, but they are now considered a separate

protist group.

Zygomycota The Zygomycetes, or lower fungi, include about 800 known species,

including Rhizopus stolonifer, the common black bread mold. Zygomycete sporangia con-

sist of small stalks that produce spores. In Pilobolus, the ‘‘shotgun fungus,’’ which grows

on horse and cow dung, spore release is dramatic—the sporangium can be shot to a height

of 6 feet! Sexual reproduction occurs through contact of two hyphae (which are haploid)

of opposite mating types (call ed þ and ) and fusing of their nuclei, leading to the pro-

duction of a diploid zygospore. This resistant form later undergoes meiosis, germination,

mitosis, production of a sporangium, and release of haploid spores. Most zygomycetes,

such as the common Mucor, are decomposers in soils and decaying plant material, with

some causing food spoilage. One group forms mycorrhyzae (see below), and a few are

parasitic on plants or animals. Entomophthora, for example, parasitizes houseﬂies, even-

tually killing them. (Look for a white powdery halo of spores around the next dead ﬂy you

ﬁnd on a windowsill.)

Ascomycota The Ascomycetes, or sac fungi , is the largest funga l phylum, with 30,000

species known, including most yeasts, a few mushrooms (such as trufﬂes, morels, and cup

fungi), and many molds. The blue-green mold that grows on citrus fruit and the pink bread

mold Neurospora are Ascomycetes. Many plant diseases are caused by ascomycetes,

including powdery mildew, apple scab, and several rots. Chestnut blight, caused by

Endothia parasitica, has virtually eliminated the American chestnut, once a major forest

tree in the northeastern United States. Ceratocystis ulmi, the cause of Dutch elm disease,

has had a similar effect on the American elm, another major forest and shade tree. Cla-

viceps purpurea infects rye and other cereals, leading to production of a structure called

an ergot in the seed head. Ingestion by cattle or humans can lead to severe nervous system

disorders, including delusions, spasms, and often, death. [One of the chemicals present is

lysurgic acid, a precursor of the hallucinogen, lysurgic acid diethylamide (LSD).] In

Figure 10.42 Aspergillus with conidia. (SEM image courtesy of the University of Iowa Central

Microscopy Research Facility.)

282

MICROBIAL GROUPS

Europe in the Middle Ages, whole villages would sometimes appear to go insane from

eating bread made with infected rye.

Ascomycete molds (yeasts are described below) reproduce asexually by pinching off

conidiospores from special hyphae called conidia. Sexual reproduction occurs through

fusing of two hyphae to form a sac called an ascus (plural, asci), in which (after meiosis

and mitosis) ascospores develop.

Basidiomycota The Basidiomycetes, or club fungi, consist of over 16,000 species,

including most of the familiar mushrooms, toadstools, stinkhorns, puffballs, and jelly

and shelf fungi. In fact, Basidiomycetes are thought to form the major part of living bio-

mass in most soil. Although some mushrooms (e.g., the commercially produced Agaricus

campestris bispo rus) are edible, others are poisonous (e.g., Amanita verna, the destroying

angel) or hallucinogenic (e.g., Psilocybe). Mushrooms are the fruiting bodies that result

from sexual reproduction, serving to release the haploid spores. Some important crop

parasites, such as the rusts and smuts, also are basidiomycetes.

White rot fungi (e.g., Phanerochaete) are basidiomycetes that cause decay of wood by

digesting lignin and cellulose. Because the lignin-degrading enzymes are also effective

against many xenobiotic compounds, P. chrysosporium is being studied for use in engi-

neered processes to degrade industrial pollutants. Brown rot fungi attack cellulose but not

lignin.

Deuteromycota The Deuteromycetes are also referred to as fungi imperfecti, reﬂecting

the fact that they have no known sexual reproduction phase. This is not a true phylum but

rather a form-phylum, containing more than 11,000 ‘‘form-species.’’ Once the sexual

phase is discovered, species in this group are reclassiﬁed into one of the other phyla.

Almost all appear to be Ascomycetes, but a few are Basidiomycetes. Included are

molds of the genus Penicillium, well known as the source of the antibiotic penicillin

and also the source of the ﬂavor and color of Roquefort and other ‘‘blue’’ cheeses. Asper-

gillus (Figu re 10.42) is a common soil saprobe, but during growth on peanuts or other

stored foods, some make aﬂatoxins, among the most toxic natural compounds known.

Aspergillus also can be an aeroallergen (cause allergic reactions) when the spores

become airborne in agriculture and at composting sites, and occasionally can be respon-

sible for lung disease in immunocompromised hosts. Other species of Aspergillus are used

in fermentation of soy sauce and saki. Verticillium cause pink rot of apples and also a wilt

that is affecting many Norway maples planted as municipal street trees in the northeastern

United States. Fusarium causes wilts of several plants, and Rhizoctonia (a Basidiomycete)

can cause damping off and root rot.

On the other hand, some fungi have been found to be helpful in cont rolling nematode

damage of plants. Arthrobotrys and Dactylella, for example, trap and feed on these small

animals—serving as the Venus ﬂytraps of the microbial world! These fungi also are occa-

sionally observed in wastewater treatment systems (Figure 10.43). Geotrichum is another

fungus that is sometimes found in activated sludge plants, where its excessive growth (at

low pH) leads to a problem referred to as fungal bulking.

Among the Fungi Imperfecti that are human pathogens are several species (e.g.,

Epidermophyton and Trichophyton) that cause the skin infections known as athlete’s

foot and ringworm (Section 12.7.7). Hist oplasmosis, which is a potentially fatal

respiratory disease (Section 12.4.7), is cause d by Histoplasma capsulatum. Candida is

a common source of vaginal yeast infections (Section 12.6.7). Both Histoplasma and

EUKARYA 283

Candida are soil organisms and opportunistic pathogens and can invade a variety of

tissues in compromised hosts. They also grow in both yeast and mold form.

Oomycota Because they are nonphotosynthetic, have a cell wall, and produce a myce-

lium, the Oomycetes, or water molds, were considered fungi until fairly recently. How-

ever, unlike fungi, they produce motile spores, and whereas the cell wall contains chitin in

some species, it is made of cellulose in others. Analysis of their 18S rRNA has now con-

ﬁrmed that they are a separate group. Asexual reproduction is by release of biﬂagellated

zoospores from a sporangium that forms at a hyphal tip. Sexual reproduction involves

contact of male and female hyphae, leading to production of oospores. Most oomycetes

are aquatic, with a few, such as Saprolegnia parasitica, parasitic on ﬁsh. A few are

terrestrial, including some very important plant pathogens. Late potato blight,

which may have led to the starvation of as many as 1 million Irish in the 1840s (and

prompted emigr ation of millions more), is caused by Phytophthora infestans. Pythium

causes damping-off disease of seedlings, and Plasmopara and other Oomycetes cause

downy mildew.

Yeasts Yeasts are single-cell ed fungi. There are 60 genera with 500 known species.

Most are ascomycetes, but some are basidiomycetes, zygomycetes, or deuteromycetes.

They reproduce asexually by budding, a mitotic division producing a large and a small

cell (the bud). Yeasts can respire using oxygen, but in the absence of oxygen, they are

limited to glycolysis, which feeds into a fermentation pathway to produce ethanol and

. The ascomycete Saccharomyces cerevisiae has been ‘‘domesticated’’ and developed

into both baker’s and brewer’s yeast.

Mycorrhyzae Some molds, called mycorrhyzae (‘‘fungus roots’’), grow either within or

surrounding the roots of many plants as a symbiotic infection. Their mycelia extend into

the soil, increasing the surface area available for absorption. This increases a plant’s abil-

ity to extract nutrients. In return, the fungus shares in the primary productivity of the

Figure 10.43 Nematode trapping fungus.

284

MICROBIAL GROUPS

plant. The effect is particularly signiﬁcant when minerals are scarce. For example, in one

study (Figure 10.44) tomato plants grown in sterile soil deﬁcient in phosphate grew 6.5

times as much leaf mass when a mycorrhyzal fungus was inoculated into the soil.

Mycorrhyzal fungi are associated with some 90% of terrestrial plants. Most are zygo-

mycetes that grow within the root, with mycelia extending out. Certain trees and shrubs

have mycorrhyzal fungi that grow only on the outside of the root. Most of these are basi-

diomycetes, but some are ascomycetes such as trufﬂes. Mycorrhyzae seem to help plants

grow under adverse conditions such as high altitudes or acidic soils. Plants of the heather

family (Ericaceae) show increased resistance to toxic heavy metals when mycorrhyzae

are present. Orchid seeds will not germinate if an associated fungus is not present.

Lichens Lichens are symbiotic associations between ascomycetes and either algae or

cyanobacteria. The fungus receives carbohydrates and other nutrients from the algae,

and in return, it provides moisture and protection. Lichens are familiar to hikers as the

often-colorful ﬂat growths adhering to rocks. About 17,000 lichen combinations are

known. One of their ecological roles is to hasten the breakdown of the rock substrate,

forming soil. They are very sensitive to sulfur dioxide, and thus can be used as an indi-

cator of air pollution.

10.8 NONCELLULAR INFECTIVE AGENTS: VIRUSES, VIROIDS,

AND PRIONS

Viruses, viroids, and prions are submicrosco pic particles that are not composed of cells.

They can carry out no metabolic activities on their own, and therefore are not considered

‘‘alive.’’ However, they can infect living host cells and cause them to produce new copies

of the infective agent. Thus, many of them produce disease. The viruses (from the Latin

virus, meaning ‘‘poison’’) are the major type of such agent, but we also discuss the others

brieﬂy below.

0.2

0.4

0.6

0.8

g Dry Weight of Leaf

0.6 1.2

mEq Phosphate per Plant

w/o Fungus

w/ Fungus

Figure 10.44 Combined effect of mycorrhyzal fungus and phosphate fertilizer on tomato growth.

(Based on Ricklefs, 1993.)

NONCELLULAR INFECTIVE AGENTS: VIRUSES, VIROIDS, AND PRIONS 285

10.8.1 Viruses

A virus particle, or virion, is composed of a nucleic acid core and a protein coat, or capsid

(Figure 10.45). Some also have an outer envelope composed mainly of lipid and protein.

They are too small—typically 20 to 300 nm (0.02 to 0.3 mm)—to be visible with a light

microscope (or to be removed by normal ﬁltration), but they can be ‘‘seen’’ using electron

microscopy. Although they are strictly intracellular parasites , they also are characterized

by having an extracellular form in which they can be transmitted to infect other host cells.

Although individual virus types often are very speciﬁc as to the organisms (often a single

species, or even a single strain) they can attack, there are varieties of viruses for almost (if

not) all hosts, including animals, plants, fungi , and algae. Viruses that attack bacteria are

called bacteriophage, or simply phage.

The nucleic acid in a virus genome is either DNA or RNA (but not both) and is either

single or double stranded. It encodes for replication of the virion by the host cell. Some

RNA viruses ﬁrst produce a strand of DNA during replication (the reverse of the normal

production of an RNA strand from DNA); such viruses are called retroviruses. The

human immunodeﬁciency virus (HIV), which causes the disease acquired immune deﬁ-

ciency syndrome (AID S; Section 12.6.4) , is a retrovirus. Other RNA viruses are able to

replicate their RNA directly without the intermediate DNA.

The protein coat is composed of subunits called capsomeres, which self-assemble after

production by the host to form the capsid. The two basic forms are helical and the 20-

sided icosahedron (which looks almost spherical), but some capsids are combinations

of the two (e.g., an icosahedron head with a helical tail).

The classiﬁcation of viruses usually depends on the nature of the genetic material, the

kingdom of the host, and the form of the capsid. The Baltimore classiﬁcation system

(Table 10.12) has established six different major groups with a variety of subgroups on

this basis. A ‘‘negative’’ RNA strand must be reversed (by transcription) to the comple-

mentary RNA strand before it can be used as a templat e for the synthesis of proteins.

There are typically several stages to a virus infection. First the virus will attach to the

new host cel l. It must then penetrate the cell surface and inject its genome into the host.

With lytic viruses, replication of the nucleic acid and synthesis of the capsid protein then

occurs, followed by assembly of the new virions. Finally, the host cell lyses (ruptures),

releasing the new viruses.

Figure 10.45 Tableau of viruses (mostly bacteriophage) from saline wetland ponds in

Saskatchewan, Canada. (Photo by David Bird; courtesy of D. Bird and R. Robarts.)

286

MICROBIAL GROUPS

TABLE 10.12 Baltimore Classiﬁcation Groups for Animal, Plant, and Bacteria Viruses

Class Form Host Group Architecture

Representative

I Double- Bacteria Myoviridae C T2, T4

stranded DNA Syphoviridae C l

Podoviridae C T7

Animal Papovaviridae I Papillomavirus,

polyomavirus

Adenoviridae I Adenovirus

Herpesviridae I Herpes simplex,

mononucleosis

Poxviridae C Smallpox

Hepadnaviridae I Hepatitis B

Plant Caulimoviruses I Cauliﬂower mosaic

II Single- Bacteria Microviridae I fX174

stranded DNA Animal Parvoviridae I Parvovirus

Plant Geminiviruses I Maize streak

III Double- Bacteria f6

stranded RNA Animal Reoviridae Rotavirus

Plant

IV Positive- Bacteria Leviviridae I MS2, F2

strand RNA Animal Picornaviridae I Poliovirus, rhinovirus,

hepatitis A,

coxsackievirus

Togaviridiae I Rubella

Flaviviridae I Yellow fever, dengue,

West Nile

Coronaviridae H Murine hepatitis

Caliciviridae I Norwalk virus

Plant Potyvirus H Potato Y

Tymovirus I Turnip yellow mosaic

Tobamovirus H Tobacco mosaic

Comovirus I Cowpea mosaic

V Negative- Bacteria

strand RNA Animal Rhabdoviridae H Rabies

Filoviridae H Ebola

Paramyxoviridae H Mumps, measles,

distemper

Orthomyxoviridae H Inﬂuenza

Bunyaviridae H Hantavirus

Arenaviridae H Lassa

Plant

VI Retrovirus Bacteria

Animal Retroviridae I HIV, oncoviruses

Plant

C, complex; H, helical; I, icosahedral.

Source: Based in part on Voyles (2002).

NONCELLULAR INFECTIVE AGENTS: VIRUSES, VIROIDS, AND PRIONS

287