Microorganisms: Timberley M. Roane, Kelly A. Reynolds, Raina M. Maier and Ian L. Pepper

Chapter 2
Microorganisms
Timberley M. Roane, Kelly A. Reynolds, Raina M. Maier and Ian L. Pepper
2.1 Classification of Organisms 2.4 Fungi 2.7.2 Physiological and Ecological

2.2 Eubacteria 2.4.1 Fungal Structure Considerations
2.2.1 Cell Envelope 2.4.2 Fungal Diversity 2.8 Viruses
2.2.2 Cytoplasm 2.4.3 Ecological Considerations 2.8.1 Infective Nature of Viruses
2.2.3 Glycocalyx 2.5 Slime Molds 2.8.2 Procaryotic Viruses
2.2.4 Appendages 2.6 Protozoa 2.8.3 Eucaryotic Viruses
2.2.5 Endospores 2.6.1 Structure and Function 2.9 Other Biological Entities
2.2.6 Information Transfer 2.6.2 Physiological and Ecological 2.9.1 Viroids
2.2.7 Metabolism Considerations 2.9.2 Prions
2.3 The Archaea 2.7 Algae References
2.3.1 Archaean Habitats 2.7.1 Cell Structure
2.3.2 Archaean Function
The purpose of this chapter is to introduce the different

types of microorganisms that will be discussed in this book Information Box 2.1 The Limits of Life?
and provide a general description of their major structural
features and functions that are related to the field of envi-
ronmental microbiology. There are several excellent text-
books listed in the recommended reading list at the end
of the chapter that should be consulted for further detail
on the subject of general microbiology including struc-
ture, function, metabolism, nomenclature, ecology, and
diversity.
Microorganisms, due to their unique ability to adapt
to extreme conditions imposed by oligotrophy (low nutri-
ents), temperature, pH, pressure, and radiation, among
others, have so far been found in every environment imag-
inable (see Information Box 2.1). In fact, microorganisms
are pioneer colonizers and have, over geologic time, had a
profound influence on the climate and environments found We still do not know what the limits of microbial life are.
Bacteria have been successfully recovered even from the hyper-
on Earth (Fig. 2.1). The associated structures and meta-
arid core of the Atacama Desert in Chile shown in the picture
bolic capabilities of a microorganism determine where
above (Maier et al., 2004). This region is currently being carefully
it can be found and the ecological influence it has on the studied by NASA as an analogue for Mars and the question of
surrounding environment. Although microorganisms are whether life exists on Mars. What do you think? Photo courtesy
found everywhere, recently developed detection techniques Julio L. Betancourt, U.S. Geological Survey, Tucson, AZ.
are demonstrating that human perturbations can influence
Environmental Microbiology
Copyright © 2000, 2009 by Academic Press. Inc. All rights of reproduction in any form reserved. 9
10 PART | I Review of Basic Microbiological Concepts
the diversity and distribution of microorganisms in the techniques became available to allow examination of
environment with currently unknown ramifications. nucleic acids, specifically ribosomal RNA (rRNA), which
is a highly conserved sequence involved in translation, the
synthesis of proteins in living things. Based on analysis of
16S rRNA, Carl Woese identified an entirely new group
2.1 CLASSIFICATION OF ORGANISMS
of organisms—the Archaea (Woese and Fox, 1977)—
Until the 1970s, classification of macro- and microorgan- which eventually led to the modern classification of living
isms was based primarily on physiological differences things into a three-domain system consisting of Archaea,
with anywhere from two to six major kingdoms proposed Eucarya, and Bacteria (Fig. 2.2).
for categorizing life as we know it. However, in the 1970s,
2.2 EUBACTERIA
The bacteria are the least structurally complex of the micro-
organisms but offer the greatest metabolic flexibility and
have the greatest diversity. It is estimated that there are
more than 50 bacterial phyla based on the analysis of the
conserved 16S rRNA sequence (Schloss and Handelsman,
2004). Approximately half of these phyla have no cultured
representatives. Thus, we know relatively little about a large
proportion of environmental bacteria and the discussion that
FIGURE 2.1 An evolutionary timeline showing the approximate
follows pertains to cells that have been successfully cultured.
appearance of life on Earth from 4.5 billion years ago to the present time. In the laboratory, bacteria average 0.5–1 m in diam-
Reproduced with permission from the American Society of Microbiology. eter and 1–2 m in length and have the basic composition
P. 1 low T
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Gp. 1 low temp

pSL 12 low temp
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FIGURE 2.2 The three-domain tree of life. From Ward and Brownlee, 2003.
Chapter | 2 Microorganisms 11
shown in Table 2.1. They are generally characterized by strategies for survival in the environment. For example,
high rates of replication (E. coli can replicate by binary fis- the thick cell wall of gram-positive bacteria, such as in
sion in less than 10 minutes), high surface area-to-volume Bacillus and Clostridium, helps them withstand the harsh
ratio, and genetic malleability. They have a single large physical conditions found in soil environments. On the
circular chromosome located in the cytoplasm and there is other hand, the more complex architecture of the cell enve-
no compartmentalization of the cell (Fig. 2.3). The relative lope in gram-negative bacteria such as Pseudomonas and
simplicity of the bacterial cell allows it to rapidly respond Shewanella seems to aid these microbes in interacting with
and adapt to changing environmental conditions. The struc- mineral surfaces and solutes in the environment to obtain
tural features of bacteria are summarized in Information required nutrients for metabolism.
Box 2.2. Starting from the interior side of the cell envelope,
both types of bacteria have a cytoplasmic membrane that
is impermeable to many of the nutrients the cell needs for
growth and energy production (Fig. 2.5). Consequently,
2.2.1 Cell Envelope embedded throughout the cytoplasmic membrane are
Those bacteria that have been cultured can be structurally membrane-spanning proteins specific for the transport of
separated into two major groups based on their cell enve- molecules into and out of the cell. These proteins turn the
lope architecture: gram-positive or gram-negative (Fig. cytoplasmic membrane into a semipermeable structure that
2.4). This major architectural difference helps dictate separates the cytoplasm from the exterior of the cell. Other
TABLE 2.1 Overall Macromolecular Composition of an Average E. coli B/r Cell

Macromolecule Percentage of Weight per cell Molecular Number of Different
total dry weight (1015 weight, weight molecules per cell kinds
grams) of molecules
Protein 55.0 155.0 4.0 104 2,360,000 1050
RNA 20.5 59.0
23S rRNA 1.0 1.0 106 18,700 1
16S rRNA 16.0 5.0 10 5
18,700 1
5S rRNA 1.0 3.9 10 4
18,700 1
Transfer RNA 8.6 2.5 104 205,000 60
Messenger RNA 2.4 1.0 106 1380 400
DNA 3.1 9.0 2.5 10 9
2.13 1
Lipid 9.1 26.0 705 22,000,000 4
Lipopolysaccharide 3.4 10.0 4346 1,200,000 1
Peptidoglycan 2.5 7.0 (904)n 1 1
Glycogen 2.5 7.0 1.0 10 6
4360 1
Total macromolecules 96.1 273.0
Soluble pool 2.9 8.0
Building blocks 7.0
Metabolites, vitamins 1.0
Inorganic ions 1.0 3.0
Total dry weight 100.0 284.0
Total dry weight/cell 2.8 1013 g
Water (at 70% of cell) 6.7 1013 g
Total weight of one cell 9.5 1013 g
Adapted with permission from Neidhardt et al., 1990.

Inner membrane
Plasmid Periplasmic space
Ribosomes Cell wall (peptidoglycan)
Nuclear material Outer membrane
Flagellum
Fimbria
FIGURE 2.3 A bacterial cell showing the lack of interior compartmentalization for nucleic acid transcription and
translation, and for metabolism. This facilitates rapid reproduction and signaling between the cell and the environment.
Appendages that mediate motility (flagella) and attachment to surfaces (fimbriae, pili) can be found on the exterior of the
cell. Drawing courtesy Wayne L. Miller, McGill University, Montreal, Quebec.
Information Box 2.2 Procaryotic Cell Structure and Function
Location Structure Function

Cytoplasm Chromosome Information storage and replication (DNA).
Plasmid Extrachromosomal DNA that often confers a competitive advantage to the cell, e.g.,
antibiotic resistance.
Ribosomes Protein synthesis (rRNA and protein).
Cell envelope Cell membrane Selectively permeable layer found in all bacteria that allows import and export of nutrients,
toxins and waste products. Composed of a phospholipid bilayer with proteins that serve as
ions channels, proton pumps and receptors.
Cell wall Rigid, permeable structure that confers shape and protection to cells.
Periplasmic space Involved in nutrient acquisition, electron transport, and alteration of substances toxic to
the cell. Especially important in gram-negative cells.
Outer membrane A second semipermeable membrane found only in gram-negative cells. The outer leaflet of
the outer membrane contains LPS molecules.
Lipopolysaccharide Found anchored into the outer leaflet of the outer membrane in gram-negative cells. This
(LPS) negatively charged molecule helps mediate interactions of the cell with the environment.
The molecule is an endotoxin and antigenic.
Teichoic acids Found anchored into the peptidoglycan wall of gram-positive cells. This negatively charged
molecule helps mediate interactions of the cell with the environment, e.g., adhesion.
Teichoic acids are antigenic.
S-Layer Monomolecular protein layer on the exterior of cells that can provide protection against
phage, act as a barrier to entry of high molecular weight molecules, help stabilize the
cell, and act as an adhesion site for exoproteins. The S-layer is associated with the LPS in
gram-negative bacteria, with peptidoglycan in gram-positive bacteria, with the lipid
membrane in gram-negative archaea, and with pseudomurein or methanochondroitin in
gram-positive archaea.
Cell exterior Glycocalyx A heterogeneous layer of polysaccharides, protein, and DNA that encapsulates the cell and
provides protection against predation and desiccation. A diffuse irregular layer is known
as a slime layer and a more defined distinct layer is known as a capsule.
Appendages Flagella Long appendages that impart motility to a cell.
Fimbriae or pili Hollow fine protein structures that aid in adhesion to other cells and surfaces.
Teichoic acid Lipoteichoic acid
Lipopolysaccharide
Porins
Outer membrane
Peptidoglycan
Periplasmic space
Proteins
Cell membrane
Lipids
Gram negative Membrane proteins Gram positive
FIGURE 2.4 A comparison of the cell envelope of gram-negative and gram-positive bacteria. The gram-negative cell envelope is
characterized by two membranes, the inner membrane and the outer membrane, which are separated by a thin layer of peptidoglycan
called the cell wall and the periplasmic space. On the exterior side of the cell wall, lipopolysaccharide molecules stretch out and medi-
ate cell interactions with the environment. The gram-positive cell wall is characterized by a single cell membrane that is interior to a
thick layer of peptidoglycan (cell wall). In this case, teichoic acids stretch out from the cell and mediate interactions with the environ-
ment. Drawing courtesy Wayne L. Miller, McGill University, Montreal, Quebec.
Proteins
Phospholipid
O
C O CH2
O
C O CH
O
H2C P O CH2CH2NH2
O
Non-polar Polar head group

fatty acid side chains
FIGURE 2.5 Structure of a cytoplasmic cell membrane. The membrane is composed of phos-
pholipids that spontaneously orient themselves so that the polar head groups are directed to the
exteriors of the membrane and the non-polar fatty acid groups are directed toward the interior of
the membrane. Proteins are embedded throughout the membrane to aid in transport of molecules
into and out of the cell. Drawing courtesy Wayne L. Miller, McGill University, Montreal, Quebec.
important functions of the cytoplasmic membrane and its 2.2.2 Cytoplasm

embedded proteins are electron transport and energy gen-
eration for the cell as well as biosynthesis of structural Cell replication and protein synthesis is centered in the cell
molecules and secondary metabolites such as antibiotics cytoplasm, a complex gel-like matrix composed of water,
that are exported from the cell. enzymes, nutrients, wastes, and gases as well as ribo-
Moving on to the exterior of the cell envelope, both somes responsible for protein synthesis, a single circular
types of bacteria have a cell wall made of peptidoglycan chromosome, and a varied number of small circular aux-
that is external to the cytoplasmic membrane. One impor- iliary plasmids ranging up to several thousand base pairs
tant function of the cell wall is to maintain the shape and (one thousand base pairs 1 kbp) (Fig. 2.3). The chromo-
integrity of the cell, giving rise to various bacterial mor- some is localized in the cytoplasm in a region called the
phologies ranging from the bacillus (rod) and coccus nucleoid. Bacterial chromosomes average 4 million base
(round) to the spirillum (twisted), vibrio (comma-shaped), pairs (Mbp) in size and encode for several thousand genes
and even stalked bacteria. The cell wall is composed (see Information Box 2.3). It is an amazing feat of pack-
of repeating units of N-acetylmuramic acid (NAM) and aging that allows the chromosome to fit into the nucleoid
N-acetylglucosamine (NAG) attached to each other through region. When stretched out, the chromosome is approxi-
peptide cross-linking (Fig. 2.4). This NAM–NAG network mately 1.3 mm in length in comparison to the cell, which
forms a rigid porous structure that freely allows molecules is 1–2 m! Thus, the cell uses a number of tightly regulated
of 15,000 MW to gain access to or diffuse away from proteins including small nucleoid-associated (histone-like)
the cytoplasmic membrane. In gram-negative bacteria the proteins and structural maintenance of chromosomes (SMC)
cell wall is a thin NAM–NAG layer sandwiched between complexes to coil, bend, and ultimately condense the chro-
the periplasmic space and the outer membrane (Fig. 2.4). mosome so that it packs into the cell but yet is available
The periplasmic space is well defined and contains trans- for replication, translation (synthesis of messenger RNA),
port proteins, signaling proteins, and degradative enzymes and recombination (gene rearrangement) (Thanbichler and
that support growth and metabolism. Continuing the jour- Shapiro, 2006). This feat is even more impressive when
ney toward the exterior of the gram-negative cell envelope, one considers that in an actively growing cell, there may be
there is a second membrane called the outer membrane from two to four copies of the chromosome actively being
that is attached to the cell wall by lipoproteins. The inner replicated.
leaflet of the outer membrane is structurally similar to the Plasmids are DNA sequences that are separate from
cytoplasmic membrane, whereas the outer leaflet contains the chromosome. Normally, plasmids encode genes that
immunogenic lipopolysaccharides (LPS) that extend out are not mandatory for cell growth and division but that
from the cell into the environment. LPS confers a nega- make the cell more competitive in a particular niche in the
tive charge to the cell and has both antigenic (causes an environment. Plasmids are often only retained if there is
immune response) and endotoxic (potentially toxic to
humans and animals) properties. The outer membrane has
a variety of functions. It acts as a diffusion barrier against Information Box 2.3 Chromosome Size and
Environmental Niche
large molecules such as antibiotics, it contains phage
receptors and is involved in the process of conjugation
The environment selects for the fittest microorganisms and
(DNA exchange), it has specific nutrient uptake systems
thus each bacterium has only the necessary genes for sur-
(e.g., for iron, vitamins, and sugars), it contains passive
vival (to have additional genes simply requires additional
diffusion pores that allow entry of low molecular weight energy to maintain them). Here we compare two bacteria,
substrates, and finally, it provides protection for periplasmic Pseudomonas aeruginosa (a generalist) and Nitrosomonas europaea
proteins. (a specialist). P. aeruginosa is a versatile gram-negative che-
In gram-positive bacteria, the cell wall is made up of moheterotroph found in soil, marshes, and marine habitats
many stacked layers of peptidoglycan to form a thick as well as on plants and animals, for which it is an oppor-
structure. In addition there are covalently bound nega- tunistic pathogen. The P. aeruginosa genome is 6.3 Mbp with
tively charged teichoic acids, polymers of glycerol or ribi- 5570 predicted genes. Approximately 10% of these genes
tol joined by phosphate groups, which extend out from the are transcriptional regulators or environmental sensors so
surface of the cell wall. They are antigenic and help medi- that the bacterium can quickly respond to its environment.
Compare this to N. europaea, which is a gram-negative che-
ate interactions of the cell (e.g., surface adhesion) with the
moautotroph that specializes in the oxidation of ammonia
environment and other microorganisms. To the interior of
to nitrite. N. europaea is found in soil, freshwater, and sewage
the cell wall, there is a periplasmic space (much less well and in polluted environments with elevated levels of ammo-
defined than for gram-negative bacteria), which has been nia. The N. europaea chromosome is 2.8 Mbp with 2715 pre-
observed in several gram-positive microbes and is thought dicted genes. Thus, the specialist has a chromosome that is
to be involved in peptidoglycan synthesis (Matias and less than half the size of the generalist!
Beveridge, 2006).
a selective pressure, such as the presence of an antibiotic, can harbor a single or several different plasmids with vari-
to maintain a plasmid that confers antibiotic resistance. able copy numbers. Plasmid types are shown in Information
The relationship between plasmids and the chromo- Box 2.5.
some is complex because some plasmids can integrate into The other distinctive feature of the cytoplasm is the
the chromosome during replication and function as part of ribosomes, which transcribe messenger RNA into proteins
the chromosome. During later replications, this process that carry on the basic metabolism of the cell. Ribosomes
can be reversed, with the plasmid DNA being excised and are composed of a large (50S) and a small (30S) subunit
allowed to function as a self-replicating entity within the that each contain both ribosomal RNA (rRNA) and pro-
cell. Some of the more important functions of plasmids are teins. The importance of the ribosomal RNA is illustrated
shown in Information Box 2.4. Plasmids are autonomous by the highly conserved nature of regions of the gene that
in that the plasmid copy number, or number of identical encodes for the rRNA. In fact, because it has a combina-
plasmids per cell, is normally independent of the num- tion of both highly conserved and highly variable regions,
ber of chromosome copies. Plasmids are also expendable, the 16S rRNA gene that encodes for the 16S rRNA com-
meaning that the accessory genetic element is not essential ponent of the small (30S) subunit of the ribosome is cur-
to the growth of the organism in its normal environment. rently used for classification of the bacteria and the archaea
Plasmids range in size from 10 to 1000 kbp and a bacterium (Fig. 2.2 and Information Box 2.6).
Information Box 2.4 Bacterial Plasmid Functions
Plasmid type Function Reference

Resistance plasmids Antibiotic resistance Brooks et al., 2007
Mercury resistance Smit et al., 1998
Degradative plasmids 2,4-D degradation Newby et al., 2000
Plant-interactive plasmids Tumor induction for crown gall disease nodule formation Cho and Winans, 2007
and nitrogen fixation in rhizobia Rogel et al., 2001
Fertility plasmids Conjugative plasmids that contain tra genes van Biesen and Frost, 1992
Col plasmids Code for the production of colicins or proteins that kill Riley and Gordon, 1992
other bacteria
Virulence plasmids Code for toxins in pathogenic bacteria Sayeed et al., 2007
Cryptic plasmids Unknown Srivastava et al., 2006
Information Box 2.5 Types of Plasmids
Low-copy-number plasmids. Plasmids larger than 10 kbp conjugation. The cells can be of the same species or of differ-
that have one or two copies per cell. ent species. Conjugative plasmids are normally large and con-
High-copy-number plasmids. Smaller plasmids (10 kbp) tain transfer genes known as tra genes.
that have 10 to 100 copies per cell. Nonconjugative plasmids. These do not contain tra genes
Relaxed plasmids. Plasmids whose replication does not and are not self-transmissible. However, some plasmids can
depend on initiation of cell replication. Therefore these plas- transfer to other cells by “mobilization” to other conjuga-
mids can be amplified (i.e., copy number increased) relative to tive plasmids, although not all nonconjugative plasmids are
cell number. mobilizable. In the process of mobilization, transfer of non-
Stringent plasmids. These plasmids are dependent on cell conjugative plasmids relies on the tra genes of the conjugative
replication, and plasmid replication is synchronized with replica- plasmids.
tion of the bacterial chromosome. Thus, stringent plasmids have Incompatible plasmids. Plasmids vary in their ability to
low copy numbers that cannot be amplified. Since cells growing coexist within the same cell. Incompatible plasmids can-
rapidly may have three or four chromosomes, stringent plasmids not exist together and give rise to incompatibility groups (Inc
can still be present with copy numbers greater than one per cell. groups). Compatible plasmids belong to different Inc groups
Conjugative plasmids. Self-transmissible plasmids that and vice versa.
can be transferred from one bacterial cell to another during
Information Box 2.6 Classification Using the 16S

RRNA Gene
The 16S rRNA gene is approximately 1500 bp in length. In

terms of DNA sequence, it contains some of the most highly
conserved regions known (because protein synthesis is so Slime layer
important) as well as variable regions. Scientists have taken
advantage of this fact and used the 16S rRNA gene to clas-
sify bacteria.
Capsule
Step 1: anneal universal primers to 16s rRNA gene

FIGURE 2.6 Two different types of glycocalyx: (1) a slime layer that is
~1500 bp
5 3
irregular and diffuse and (2) a capsule that is a more defined and distinct
Step 2: perform PCR to synthesize DNA region between primers
structure.
5 3
Step 3: sequence the DNA product from step 2
Step 4: compare DNA sequences to classify

individual bacteria and create a tree
such as in Figure 2.2 or to the right
The 5 to 3 strand of the 16S rRNA gene

conserved region of the 16s rRNA gene
universal primer and its orientation
synthesized region of DNA containing variable portions of the
gene used for classification
2.2.3 Glycocalyx
FIGURE 2.7 Scanning electron micrograph of a soil bacterium with
Finally, the exterior of the cell can have some important
multiple flagella. The circles are detached flagella that have spontane-
features. Some bacteria have an extracellular layer com- ously assumed the shape of a circle. From Pepper et al., 2006.
posed primarily of polysaccharide but which can contain
proteins and even nucleic acids. This layer is called a glyco-
calyx also known as a slime layer (diffuse and irregular) (negative chemotaxis). Pili and fimbriae are any surface
or capsule (more defined and distinct) (Fig. 2.6). The appendages that are not involved in motility. Fimbriae
resulting sticky layer provides protection against desicca- (singular fimbria) are numerous short surface append-
tion, predation, phagocytosis, and chemical toxicity (such ages. The fimbriae aid in attachment of cells to surfaces
as from antimicrobials), and acts as a means of attach- and so are important for initial colonization for biofilm
ment to surfaces. Glycocalyx producing bacteria, such as formation and also for cell attachment to initiate an infec-
Pseudomonas spp., are often found associated with micro- tion process. Pili (singular pilus) are normally less numer-
bial mats and biofilms (Sections 6.2.3 and 6.2.4). This ous than fimbriae but are longer. They are found only on
material has been found to bind metals and is being used gram-negative bacteria and are involved in a mating pro-
commercially in the binding and removal of heavy metals cess between cells known as conjugation (Fig. 2.8). In this
from industrial waste streams (Chapter 21). process the exchange of DNA is facilitated by a pilus
forming a connection between two cells. Conjugation in
environmental bacteria is important because it enhances
2.2.4 Appendages microbial diversity, often allowing specific populations to
Several accessory structures extend from the cell enve- better adapt to their environmental niche.
lope out into the environment surrounding the cell. These
appendages are not present in all bacterial types, but they
2.2.5 Endospores
are common, and they typically aid bacteria with either
motility or attachment to surfaces. The flagellum (plu- Some gram-positive bacteria, such as Bacillus and
ral flagella) is a complex appendage used for motility Clostridium spp., produce endospores—multilayered struc-
(Fig. 2.7). Motility is important in aiding a bacterial cell to tures capable of withstanding adverse conditions includ-
move short distances (microns) toward nutrients (positive ing radiation, UV light, heat, desiccation, low nutrients, and
chemotaxis) and away from potentially harmful chemicals chemicals—to ensure the survival of the cell. Endospores are
FIGURE 2.8 Bacterial cells exchanging DNA by conjugation using a pilus. From Bacterial
conjugation, 1998.
environmentally significant because they can remain in a met- tra genes, genes coding for the production of the sex pilus.
abolically dormant state for long periods only to germinate When a donor cell encounters a recipient cell, the pilus is
and reactivate when conditions become favorable for growth. formed and allows the replication and transfer of a copy of
Some endospores have remained viable for 100,000 years! the conjugative plasmid from donor to recipient. On receipt
of the plasmid, the recipient now becomes a donor cell capa-
ble of spreading the plasmid and its corresponding genes
2.2.6 Information Transfer to another recipient cell. Conjugation is thought to require
Perhaps the most unique ability of bacteria is their ability a high cell concentration to increase the odds of encounter
to quickly respond to changing environmental conditions. between compatible donor and recipient cells. Conjugation,
This can be attributed to their rapid growth and the since it is dependent on plasmids, is thought to play a sig-
flexibility of the bacterial chromosome. Bacteria readily nificant role in the rapid transfer of plasmid-encoded genes
incorporate new DNA into their genome through homolo- (e.g., antibiotic resistance) among bacterial populations.
gous recombination. Homologous recombination involves Transduction occurs due to the accidental packaging of
the alignment of two DNA strands of similar sequence, a cellular genetic material during bacteriophage replication
crossover between the two DNA strands, and a breaking inside of its host cell (Fig. 2.9). Transducing viruses sacrifice
and repair of the DNA at the crossover point to produce an some of their own genome in place of the host’s genetic mate-
exchange of material between the two strands. The acquisi- rial, resulting in a virus that can still infect a recipient cell but
tion of new DNA generally occurs via lateral gene transfer can no longer replicate. Upon infection of a recipient cell, the
or horizontal gene transfer by one of three mechanisms: replication defective viral genome introduces genetic material
conjugation, transduction, or transformation, which allow from the previous host providing an opportunity for the acqui-
for the exchange of chromosomal and plasmid DNA. The sition of new genes. Since the infecting transducing virus is
relative importance of these DNA transfer mechanisms replication-defective, the recipient cell continues to grow and
is still not known but all have been shown to occur in the metabolize normally. The genetic material picked up by trans-
environment. Variations of the three methods can be used in ducing viruses reflects a variety of genes, some useful for the
the laboratory as well to genetically modify an organism. recipient organism and others not. Transduction can occur at
Conjugation relies on direct cell-to-cell transfer of conju- lower cell concentrations since the process relies on viruses
gative plasmid DNA through a protein pilus (Fig. 2.8). The as carriers of genetic information. This process is extensively
pilus is extended from a donor cell (containing a conjuga- used in biotechnology for the introduction of genes into cells.
tive plasmid) to a recipient cell (lacking a conjugative plas- Transformation occurs when a bacterial cell obtains
mid). The conjugative plasmid is similar to other plasmids free DNA from its surrounding medium (Fig. 2.10). When
in that it can code for a variety of nonessential genes, such cells die, they readily lyse releasing cellular contents
as antibiotic resistance or degradation genes. Unlike other including chromosomal and plasmid genetic material.
plasmids, however, conjugative plasmids also code for the Much of this material is rapidly degraded by nucleases in
Bacterial Transduction the four major types of metabolism based on the source
donor cell of energy and carbon used for growth (Table 2.2). Energy
can be obtained from light through photosynthesis (photo-
trophy) or from the oxidation of organic or inorganic chem-
Lytic cycle icals (chemoorganotrophy or chemolithotrophy). Carbon is
Phage obtained either from carbon dioxide (autotrophy) or from
Transduced
cell
organic compounds such as glucose (heterotrophy). Thus,
chemoorganoheterotrophs are organisms that use glucose
for energy and carbon. Chemolithoautotrophs are organ-
isms that oxidize an inorganic compound for energy and
obtain their carbon from carbon dioxide. Often chemoor-
Recipient
Transducing
cell
ganoheterotrophs are termed chemoheterotrophs indicating
phage that an organic compound is used for energy and carbon.
Chemolithoautotrophs are called chemolithotrophs or
chemoautotrophs, again referring to their use of inorganic
FIGURE 2.9 Transduction is the transfer of host bacterial DNA to a
recipient bacterium via a bacteriophage.
energy and carbon dioxide for carbon. Photoautotrophs
obtain energy from light and fix carbon from carbon diox-
ide, and finally, photoheterotrophs obtain energy from light
Transformation and carbon from organic compounds.
There are two ways in which bacteria can harvest
energy to use for building new cell material: respiration
and fermentation. In respiration, the cell uses a combina-
Donor cell
tion of substrate level phosphorylation (provides a small
amount of ATP) and oxidative phosphorylation which
combines the tricarboxylic acid cycle (TCA cycle) and
Cell lysis electron transport chain (provides a large amount of ATP)
and free DNA to generate ATP energy and reduce power. Key for respira-
tion is the terminal electron acceptor (TEA) that is used to
deliver electrons to the electron transport chain. Under aer-
Recipient cell
obic conditions, the TEA is oxygen, which maximizes the
FIGURE 2.10 Transformation is the uptake of free DNA released from amount of energy produced, a net total of 38 ATP per glu-
a dead or dying cell by a recipient cell.
cose metabolized. Under anaerobic conditions, an alternate
TEA such as NO3, Fe3 , SO42 or CO2 is used. However,
the relative amount of energy that can be derived from
the environment but some can be adsorbed onto the sur- the reduction of alternate terminal electron acceptors is
faces of soil particles and organic matter, which can pro- always less than for oxygen (Information Box 2.7). Thus,
tect the DNA from degradation for long periods of time. respiration under anaerobic conditions is always less effi-
Approximately one in every thousand cells is thought to be cient than under aerobic conditions (less energy is pro-
competent or capable of transporting DNA directly into the duced). It should be noted that some alternate TEAs are
cell. Competency is the ability of a cell to transport DNA very close to oxygen in the amount of energy produced,
from its external environment inside the cell and is depen- most notably nitrate. Thus, many bacteria are facultative
dent on the stage of growth and the cell concentration. For aerobes in that if oxygen is present they use it as a TEA
example, an exponentially growing culture of 107–108 cells/ but if it is not present, they can use NO3 instead. A good
ml of Streptococcus pneumoniae secretes a competency example of a facultative genus is Pseudomonas. Although
protein that initiates the production of several other proteins facultative aerobes can use either oxygen or nitrate, the
that convert the cell into one capable of taking up external range of TEAs they can use is limited. For example, the
DNA (e.g., through the production of DNA-specific trans- sulfate-reducers are obligate anaerobes that specialize in
port proteins). The uptake of DNA is random; however, using sulfate as a TEA.
when it occurs, the DNA can become incorporated into the Fermentation is anaerobic process that uses only substrate
genome of the organism increasing genetic diversity. level phosphorylation with a net generation of 2 ATP per
glucose (thus there is no use of the electron transport chain
or need for an external electron acceptor). Instead, electrons
2.2.7 Metabolism are shunted among organic compounds usually ending in
Full consideration of bacterial metabolism is provided in the production of organic acids or alcohols and resulting
general microbiology textbooks. Here we simply summarize in very small amounts of energy (Information Box 2.7).
TABLE 2.2 Metabolic Classification of Bacteria

Metabolism Electron donor (terminal Carbon source Metabolism type Products
electron acceptor)
chemoheterotroph
Respiration organic compounds organic compounds Pseudomonas, Bacillus CO2, H2O
(aerobic) (O2)
(anaerobic) (e.g., NO3, Fe3, SO42)a Micrococcus, Geobacter, CO2, NO2, N2O, N2,
Desulfovibrio Fe2, S, S2
Fermentation organic compounds organic compounds Escherichia, Clostridium CO2, organic acids, alcohols
(anaerobic only) (organic acids)
chemoautotroph or
chemolithotroph
Chemolithotrophy H2, S2, NH 4, Fe2 CO2 Hydrogen bacteria, H2O, SO42, NO2, Fe3
(aerobic) (O2) Beggiatoa
(anaerobic)a (NO3,) Planctomycetes
Photoautotroph
Photosynthesis Light H2O (NADP) CO2 Cyanobacteria O2
(oxygenic)
(anoxygenic) Light H2S CO2 bacteria including: S0
(bacteriochlorophyll) purple sulfur bacteria
e.g., Chromatium purple
non sulfur bacteria,
e.g., Rhodospirillum green
nonsulfur bacteria, e.g.,
Chloroflexus Heliobacteria,
e.g., Heliobacterium
photoheterotroph
Photoheterotrophy light H2S organic compounds many purple nonsulfur S0

(bacteriochlorophyll) bacteria purple sulfur
bacteria to a limited extent
a
The majority of chemoautotrophs are aerobic. However, there have been several descriptions of anaerobic chemoautotrophs including those that participate in ammonia oxidation
(Anammox) using NO 2 as the terminal electron acceptor (from the order Planctomycetes, e.g., Brocadia anammoxidans) and those that participate in sulfur oxidation using
NO
3 as a terminal electron acceptor (Thiobacillus denitrificans).
Information Box 2.7 Biological Generation of Energy
Growth and metabolism requires energy, which is usually In this case, the logarithm of Keq is also positive; for
stored and transferred in the form adenosine triphosphate example, if Keq 2, then log Keq 0.301.
(ATP). As with any chemical reaction, metabolic reactions are Case 2: If product formation is not favored, then Keq will be
subject to the second law of thermodynamics which says: less than 1. That is, if [A][B]
[C][D] then Keq 1. In this
case, log Keq will be negative; for example, if Keq 0.2, log
In a chemical reaction, only part of the energy is used to do work. The Keq 0.699.
rest of the energy is lost as entropy. For any chemical reaction the free
energy G is the amount of energy available for work.
Thus, for a reaction to have a positive Keq and proceed as writ-
For the reaction A B C D, the thermodynamic equi- ten (from left to right), the energy of the products must be
librium constant, Keq, is defined as lower than the energy of the reactants, meaning that overall,
energy is released during the reaction.
[C] [D]
K eq The relationship between Keq and the Gibbs free energy
[A] [B] change (ΔG0) is given by
Case 1: If the formation of products (C and D) is favored, then

Keq will be positive. That is, if [C][D]
[A][B] then Keq
1. G0 RT log K eq
where R is the universal gas constant and T the absolute C4H6O4 1.75SO42 3.5H 4CO2 1.75H2S 12H2O
temperature (K).
G0 (25C) 257.60 kJ/mol
G0 is negative when log Keq is positive and the reaction will pro-
ceed spontaneously. (c) Aerobic autotrophic respiration: The reactions carried out by
G0 is positive when log Keq is negative and the reaction will not the obligately aerobic chemoautotrophs Nitrosomonas and
proceed as written. Nitrobacter are known as nitrification:
Thus we can use ΔG values for any biochemical reaction mediated
by microbes to determine whether energy is liberated for work and NH3 1.5O2 → H NO2 H2O (Nitrosomonas)
how much energy is liberated. Soil organisms can generate energy G0 (25C) 267.50 kJ/mol
via several mechanisms, which can be divided into three main cat-
egories: photosynthesis, respiration, and fermentation. NO2 0.5O2 → NO3 (Nitrobacter)
G0 (25C) 86.96 kJ/mol
1. Photosynthesis
The following two reactions are examples of chemoauto-
light
trophic sulfur oxidation:
2H2O CO2 → CH2O O2 H2O G0 <115 kcal/mol
biomass
H2S 0. 5O2 → S0 H2O (Beggiatoa)

Note that ΔG0 is positive and so this reaction is not favor-
G0 (25C) 217. 53 kJ/mol
able. It requires reaction energy supplied by sunlight. The
fixed organic carbon is then metabolized to generate energy S0 1.5O2 H2O → SO42 2H (Thiobacillus thiooxidans)
via respiration. Examples of photosynthetic soil organisms are G0 (25C) 532 .09 kJ/mol
Rhodospirillum, Chromatium, and Chlorobium.
The next reaction involves the chemoautotrophic degrada-
2. Respiration tion of carbon monoxide:
(a) Aerobic heterotrophic respiration: Many bacteria function as

either obligate or facultative aerobic chemoheterotrophs CO 0.5O2 → CO2 G0 (25 C) 274.24 kJ/mol
including Pseudomonas, Bacillus, and E. coli.
(d) Anaerobic autotrophic respiration: Thiobacillus denitrificans can
C4H6O4 3.5O2 4CO2 3H2O utilize nitrate as a terminal electron acceptor.
succinic acid
G0 (25)C 1569.25 kJ/ mol S0 1.2NO3 0.4H2O → SO42 0.6N2
G0 (25C) 505.59 kJ/mol
(b) Anaerobic heterotrophic respiration: Anaerobic chemo-heterotrophs
utilize alternate terminal electron acceptors and organic
compounds from the electron donor. The examples below use 3. Fermentation
the same electron donor (succinic acid, C4H6O4) with three
C2H5OH CO2 → 1.5CH3COOH G0 (25C) 27.45 kJ/ mol
different terminal electron acceptors (nitrate, iron, sulfate). ethanol acetic acid
C4H6O4 2.8NO3 2.8H 1.4N2 4CO2 4 .4H2O

All of the preceding reactions illustrate how organisms mediate
G0 (25C) 1507.59 kJ/ mol reactions involved in biogeochemical cycling of carbon, nitro-
C4H6O4 14Fe3 4H2O 4CO2 14Fe2 14H gen, and sulfur (Chapter 14). The ΔG0(25°C) values provided
G0 (25C) 891.00 kJ /mol were compiled from Amend and Shock (2001).
Thus, in fermentation, the end products include a combina- single tiny niche, there may be both aerobic and anaero-
tion of CO2 and organic acids and alcohols. Fermentation bic respiration occurring (as well as fermentation). Each of
is a process that has been taken widely advantage of in the these types of metabolism have energy requirements and
manufacture of alcoholic beverages and a variety of other energy outputs that can actually be calculated, as shown in
food products (vinegar, olives, yogurt, bread, cheese). Information Box 2.7.
In considering metabolism in terms of this textbook, it
is important to consider the environment and which type of
metabolic process (e.g., aerobic respiration versus anaero- 2.3 THE ARCHAEA
bic respiration) will occur given the local availability of
oxygen. In fact, it must be recognized that there is not sim- Archaea are microbes that look somewhat similar to bac-
ply a presence or absence of oxygen in the environment but teria in size and shape under the light microscope but they
rather a continuum of concentrations. As a result, within a are actually genetically and biochemically quite different.
TABLE 2.3 Structural Comparison of Archaea and Information Box 2.8 Thermophilic Archaea—How Do
Bacteria They Survive?
Structure Archaea Bacteria Hyperthermophilic archaea are those that can grow in tem-
Lipid Glycerol based Glycerol based peratures above 80°C. Pyrococcus furiosus can grow in tempera-
phospholipids but phospholipids tures from 73 to 103°C, with an optimum growth temperature
stereochemistry of the of 100°C. Originally isolated from heated marine sediments
glycerol is opposite that of on Vulcano Island, Italy, P. furiosus is an anaerobic bacte-
bacteria and eukaryotes rium capable of fermenting proteins and carbohydrates and
Membranes Composed of glycerol Composed of has one of the fastest growth rates of 40 minutes observed
ether lipids glycerol ester among the hyperthermophiles. In order to survive in such
lipids extreme temperatures, structural modifications of the cell
are required. Heat stabilization of proteins occurs through
Cell wall Lacks peptidoglycan, Peptidoglycan
contains surface layer and S-layer key amino acid substitutions that prevent protein denatur-
proteins or S-layer ation under high temperatures. Membranes have increased
concentrations of saturated fatty acids, which increase the
Flagella Resembles Type IV pili Resembles hydrophobicity and stability of the membrane. Many hyper-
Type III pili
thermophiles have no fatty acids in their membranes, substi-
Chromosome One circular chromosome One circular tuting them with long chain (e.g., C40) hydrocarbons bonded
chromosome together by ether linkages. These hydrocarbon membranes,
conversely, form very temperature stable monolayers instead
of the bilayers observed with fatty acid-based membranes.
Hyperthermophiles also have to prevent their DNA
chromosome from melting under the high temperature.
They appear to be a simpler form of life, and may in fact This is thought to be accomplished through the use of a
be the oldest form of life on Earth. Archaea were originally reverse DNA gyrase enzyme that introduces positive super-
thought to only inhabit extreme environments, leading to coils into DNA. Nonhyperthermophilic bacteria use DNA
the term extremophiles, but more recently they have been gyrase to introduce the negative supercoils found in their
DNA. Positive supercoiling prevents DNA denaturation.
shown to exist in a variety of normal or nonextreme envi-
Additionally, some hyperthermophiles use heat-stable DNA
ronments. For example, Fan et al. (2006) identified simi-
binding proteins that can increase the temperature required
lar archaea from nonextreme environments in four Chinese to melt DNA by several-fold. Obviously, other structural
and American pristine soils. The significance of the pres- modifications exist to stabilize lipids and small molecules
ence of archaea in nonextreme environments has yet to be in the cell. What is the upper temperature limit such modifi-
determined. cations can afford? Because of the instability of ATP beyond
Interestingly, some aspects of archaean cell structure 150°C, scientists think this is the upper limit for life. Only
and metabolism are similar to those of bacterial cells. future research will tell if this is the case.
However, there are key differences in genetic transcription
and translation that are actually more similar to those of
the eukaryotes than to bacteria. Some of the key structural
differences between archaea and bacteria are identified In contrast, methanogens live in anaerobic environments
in Table 2.3. Also of interest is the fact that the archaean and produce methane. Methanogens can be found in low
lipids are based on a 5-carbon isoprene unit (Fig. 7.4) that temperature environments; on the other hand, thermophiles
is also present in rubber. are located in high temperature environments such as hot
springs in Yellowstone Park (Information Box 2.8, Section
7.2). Archaea are also found in high numbers in cold
2.3.1 Archaean Habitats marine environments (Giovannoni and Stingl, 2005).
Many archaea are extremophiles that can survive either
hot or cold temperatures, or extreme salinity or alkalin-
2.3.2 Archaean Function
ity. Nonextreme archaea have been found in a variety of
environments including soil, seawater, or even sewage. No Many archaea remain nonculturable, and this coupled with
pathogenic archaea have yet been isolated (Cavicchioli the relatively short period of time since the discovery of
et al., 2003). Archaea are usually placed into three groups many archaea means that information is limited on archaean
based on habitat. The two major divisions of archaea physiology, function, and the impact on global biochemical
are the Crenarchaeota (mostly thermophiles) and the cycles. Despite this, their presence and role in extreme
Eukaryarchaeota (mostly haloarchaea and methanogens). environments are likely to be critical. For example, it
The halophiles or halobacteria exist in saline environments. was demonstrated that archaea are capable of nitrification
(Konneke et al., 2005). Archaea have also been implicated 2.4.1 Fungal Structure
as mediators of horizontal gene transfer between archaea and
bacteria (Nelson, 1999). Clearly information on the archaea Fungal membranes and cell walls are complex structures
will increase dramatically in the near future, particularly that act as selectively permeable barriers and protective
information on archaea found in nonextreme environments. outer barriers, respectively. The composition of these two
structures varies somewhat among genera, in part due to
the large variation in behaviors and life cycles, habitats,
and physiologies seen in the fungi. As eukaryotes, fungi
2.4 FUNGI have membrane-bound organelles in addition to a cytoplas-
mic membrane composed of a phospholipid bilayer with
Although bacteria may represent the most abundant micro-
interspersed proteins for transport and degradation. Fungal
organisms in terms of numbers of individuals, the fungi,
membranes can be quite complex with structural and com-
which are a physically larger group of eucaryotic micro-
positional differences observed in organelle membranes and
organisms, have the greatest biomass. Conservatively,
in the life cycle stages. In addition to phospholipids, fungal
1.5 million fungal species are estimated to exist, with
membranes can include sterols, glycolipids, and sphingo-
only 7% of them identified so far (Crous et al., 2006).
lipids, which can be used for fungal identification as the
Traditionally, the identification of fungi has been based
ratio, type, and amount of lipids can be species specific.
on morphology, spore structure, and membrane fatty acid
Fungal cell walls are multilayered structures composed
composition. However, similar to use of the 16S rRNA
of chitin, a polymer of the glucose derivative N-acetylglucos-
gene for identification and classification of bacteria, the
amine (Fig. 2.11). Fungal cell walls may also contain cel-
analogous eucaryotic gene, the 18S rRNA gene, is being
lulose, galactosans, chitosans, and mannans. Other cell
used for fungal identification. Even more common thus far
wall components include proteins and lipids. Similar to
has been the use of the nuclear internal transcribed spacer
bacteria, the fungal cell wall lies outside of the cytoplas-
(ITS) region and currently there is a considerably larger
mic membrane, protecting the membrane from damage.
data set for ITS sequences that is being used for identifica-
tion and classification.
Fungi are ubiquitous and primarily found in the soil
environment where they can adapt to a variety of conditions TABLE 2.4 Examples of Fungi and Their Role in the
and have a primary role as decomposers. As with bacteria, Environment
some fungi are pathogenic to both humans and plants (in Fungus Common Role
fact economically, fungi are the most important plant patho- environments
gens). Other fungi are important in industrial processes
Molds
involving fermentation and in biotechnology for the produc- Rhizopus spp. Spoiled food; soil; Degradation; plant
tion of antimicrobial compounds (Table 2.4). Metabolically, crops diseases, e.g., rice
fungi are chemoheterotrophs. Most fungi are obligately seedling blight
aerobic but there are, of course, exceptions. The zoosporic Penicillium spp. Spoiled food; soil Degradation;
fungi found in ruminants are obligately anaerobic. The antibiotic
yeasts are facultative aerobes. These anaerobic fungi gen- (penicillin)
erally ferment sugars and in doing so produce a variety of production
useful by-products, such as ethanol, acetic acid, and lactic Mushrooms
acid, making them important commercially for production Polyporus Dead trees and Decomposition
of many staple foods (e.g., yogurt, cheese, bread, pickles) squamosus plant material
and alcoholic products such as beer and wine. Cryptococcus Soil; can be Degradation; causes
In addition to their primary metabolism that supports neoformans airborne cryptococcosis
biosynthesis and energy production, fungi are known for (infection of the
lungs and central
producing secondary metabolites (compounds produced nervous system in
during the stationary phase of growth). These secondary humans)
metabolites have revolutionized medicine, biotechnology,
Yeasts
and agriculture. For example, fungi are responsible for
such antimicrobials as penicillin produced by Penicillium Saccharomyces Fruits; soils; aquatic Fermentation;
notatum, cephalosporin produced by Cephalosporium acre- cerevisiae environments degradation
monium, and griseofulvin produced by Penicillium griseo- Candida albicans Normal microbiota Causes candidiasis
fulvum. Although the fungal production of antimicrobials of animals (yeast infections)
of the skin or
under in situ conditions is not well understood, it is
mucous membranes
hypothesized that they help reduce competition from other
microorganisms for nutrients.
The cell wall additionally provides the scaffolding for the formation of asexual spores or conidia ranging from 1 to
fairly complex three-dimensional structures characteristic 50 m in diameter. The fuzzy appearance of mold colonies
of some fungi, for example, mushrooms. is due to the aerial hyphae, and the color of fungal colonies
is the result of the coloration of the spores. Some molds
produce sexual spores as the result of sexual reproduction.
2.4.2 Fungal Diversity While not as resistant as bacterial spores, both asexual
Fungi can be divided into three general groups based on and sexual fungal spores can be resistant to extreme tem-
morphological descriptions: molds, mushrooms, and yeasts peratures, desiccation, and chemicals, and are in large part
(Fig. 2.12). Slime molds with phenotypic characteristics responsible for the widespread occurrence of molds.
of both fungi and protozoa will be discussed later (Section The mushrooms are part of the Basidiomycota, which are
2.5). Molds, such as Aspergillus, Penicillium, Rhizopus, filamentous fungi that form the large fruiting bodies referred
and Pilobolus, are filamentous fungi which are found in to as mushrooms. Aerial mycelia come together to form the
many fungal phyla. Each filamentous fungal cell is called macroscopic mushroom, whose main purpose is dispersal of
a hypha (plural hyphae), which grows in masses to form the sexual basidiospores found underneath the cap. The rest
tufts of hyphae or mycelia. Some hyphae extend out from of the mushroom fungus is below ground as a mycelium that
the mycelium to form aerial hyphae responsible for the extends outward for nutrient absorption. Both molds and
FIGURE 2.11 Structure of a fungal cell wall. Drawing

courtesy Wayne L. Miller, McGill University, Montreal,
Glycoproteins
Quebec.
glucans
glucans
Plasma membrane
A B C
FIGURE 2.12 Examples of fungal diversity. (A) Pilobolus kleinii, a member of the Zygomycota, which include molds. The black spores are
ejected several feet into the air. Photo: George Barron, From Simmons (2005). (B) Maiden veil fungus or Dictyophora indusiata, a member of
the Basidiomycota, which include most of the common mushrooms. From Threlfo (2007). (C) Scanning electron micrograph of the budding
yeast Saccharomyces cerevisiae, a member of the Ascomycota. This is the best studied and most widely used yeast for brewing and baking. From
Wheals, 2008.
mushrooms are important decomposers of natural products, exchange for the oxygen and organic carbon provided by
such as wood, paper, and cloth, as discussed later. However, the alga, the fungus provides water and minerals in addi-
both groups of fungi can additionally produce sticky extra- tion to protection from harsh environmental conditions.
cellular substances that bind soil particles to each other
to form stable soil aggregates to reduce soil erosion
(Chapter 4). In some cases, fungi are thought to play a more
2.4.3 Ecological Considerations
important role in controlling erosion than plants. Fungi are chemoheterotrophic microorganisms that rely on
The yeasts are unicellular fungi that are able to fer- simple sugars for carbon and energy. However, simple sug-
ment under anaerobic conditions. Most important are ars are limiting in many environments due to intense com-
Saccharomyces and Candida, which are members of the petition. Consequently, many fungi secrete extracellular
Ascomycota. Although the yeasts do not produce spores, enzymes (exoenzymes) to break down complex polymers
they are prolific in sugary environments and are particularly to simple carbon compounds for cell utilization. Often
associated with fruits, flowers, and sap from trees. With a referred to as saprophytic, fungi are extremely important
few exceptions where sexual reproduction occurs, yeasts in the degradation and recycling of dead plant, insect, and
reproduce by budding where the daughter cell forms as an animal biomass especially the complex polymers asso-
outgrowth from the mother cell eventually pinching off as a ciated with these organisms, for example, cellulose and
single cell. The number of bud scars left behind with each lignin found in plants, and chitin found in insects. The
budding event can be used to estimate the number of repli- filamentous fungi and mushrooms are especially adapted
cation cycles a particular yeast cell has undergone. While to a saprophytic lifestyle due to the large surface area pro-
commonly found in the environment, yeasts (especially vided by their hyphae. Because of their unique ability to
Saccharomyces) play a significant role in commercial degrade complex polymers, fungi have been found to have
applications, including the production of food, alcoholic, the ability to degrade a variety of environmental contami-
and medicinal products. Some yeasts (e.g., Candida) can nants, making them important in waste degradation and
cause vaginal, oral, and respiratory infections, and can recycling (Chapter 18). For example, the yeast-like fungus
experience a filamentous stage during pathogenesis. Aureobasidium pullulans has been found to degrade polyvi-
Certain fungi, usually members of the Ascomycota, nyl chloride (PVC) containing plastics (Webb et al., 2000);
establish symbiotic relationships with algae and cyano- and filamentous fungi such as Penicillium, Stachybotrys,
bacteria to form lichens. These are extremely important Allescheriella, and Phlebia can degrade the aromatic
because lichens encourage mineral weathering through hydrocarbons associated with petroleum products and agri-
the secretion of organic acids that degrade rocks and other cultural pesticides (Boonchan et al., 2000; D’Annibale
inorganic surfaces. The fungus–phototroph relationship et al., 2006). One special fungus is Phanerochaete chryso-
actually occurs when fungal haustoria (hyphal projec- sporium, which is described further in Information Box 2.9.
tions) penetrate the algal cell wall. Both organisms have to A second important environmental group of fungi are
be nutritionally deprived to establish this relationship. In the mycorrhizae. Mycorrhizae form symbiotic relationships
Information Box 2.9 The White-rot Fungi: The Ultimate Fungus?
Fungi, in general, are known for their degradative abilities, and include lignin peroxidase, manganese peroxidase, and laccase.
much of the conversion of recognizable organic matter into The nonspecificity of these enzymes for their substrate target
unrecognizable organic matter is attributed to fungal activity. allows them to act on other substrates, including pollutants, to
One group of fungi, however, far exceeds other groups of fungi in facilitate their degradation. Consequently, white-rot fungi are
their ability to degrade recalcitrant and xenobiotic compounds. being actively pursued in bioremediation. To date, white-rot
These fungi are known as the white-rot fungi. The majority of fungi have been noted to degrade munitions waste, for example,
white-rot fungi are basidiomycetes and include members such TNT (2,4,6-trinitrotoluene); pesticides, for example, DDT (1,1,1-
as Phanerochaete chrysosporium and Trametes versicolor. The white-rot trichloro-2,2-bis(4-chlorophenyl)ethane) and lindane; polychlo-
fungi are especially known for their ability to degrade lignin, a rinated biphenyls used as plasticizers and in hydraulic fluids;
structurally complex component of wood, as a result of a sec- polyaromatic hydrocarbons, benzene homologues found in fos-
ondary metabolic process that yields no energy for the fungus. sil fuels; synthetic dyes such as azo dyes and triphenylmethane
Lignin seems to be accidentally degraded as white-rot fungi used in textiles and plastic; synthetic polymers such as plastics;
release extracellular enzymes to access the polysaccharides and toxic wood preservatives such as creosote and pentachloro-
tied up in the lignin. Because these enzymes are oxidases, the phenol (PCP) (Kullman and Matsumura, 1996; Pointing, 2001).
process of lignin degradation is aerobic. White-rot fungi are the Widespread in the environment and able to withstand harsh
only identified organisms capable of significant lignin degrada- environmental conditions, white-rot fungi are being examined
tion. The three primary enzymes responsible for degradation for in situ and ex situ remediation applications.
with many plants. Through their increased surface area, (developed from more than one ancestral type) group of
mycorrhizae can increase the absorptive area of a plant’s eucaryotic microorganisms that have similar morphologi-
roots by hundreds of thousands of times and help to pre- cal, physiological, reproductive, and ecological characteris-
vent desiccation of the roots. In return, the plant provides tics. All protozoa rely on water, and as such they are most
the fungus with sugars made during photosynthesis (see commonly observed in freshwater and marine habitats,
Chapter 17). although some are terrestrial in moist soils and others are
exclusively found in the gastrointestinal tracts of animals.
However, some protozoa are saprophytic, some are para-
2.5 SLIME MOLDS sitic, and some are photosynthetic. Protozoa are important
environmentally because they serve as the foundation of
Phenotypically similar to both fungi and protozoa, slime the food chain in many aquatic ecosystems, making up a
molds produce spores but move with amoeba-like gliding large part of the plankton fed on by aquatic animals.
motility. Phylogenetically, slime molds are more related to
the amoeboid protozoa than the fungi. There are two types
of slime molds. The cellular slime molds are composed 2.6.1 Structure and Function
of single amoeboid cells during their vegetative stage,
whereas the vegetative acellular slime molds are made up Cell morphology among the protozoa is extremely diverse,
of plasmodia, amorphic masses of protoplasm. Both forms perhaps due the absence of a cell wall and wide range in
can be found in moist environments on decaying organic size (5 m to 1 mm) (Fig. 2.13). In protozoa cell rigidity
matter where they consume bacteria and other microor- is provided, in part, by a gelatinous cytoplasmic material
ganisms via phagocytosis. Environmental factors, such as called the ectoplasm located just inside the cell membrane.
nutrients or stress, can trigger cell accumulation and dif- The ectoplasm is where the cilia and flagella are anchored
ferentiation into fruiting bodies for the production and in motile protozoans. The cell membrane and the ecto-
dispersal of spores. The spores can later germinate into plasm together are known as the pellicle. Finally, inside the
vegetative amoeboid cells. The consensus of individual pellicle is the fluid endoplasm, which contains organelles.
vegetative cells to come together and form fruiting bodies Similar to other microorganisms, the cell membrane is a
implying cell-to-cell communication involving chemical phospholipid bilayer with interspersed proteins for nutrient
signals is of much interest to scientists (see Chapter 16). and waste transport.
Within the protozoal cytoplasm, vacuoles serve a variety
of functions. Phagocytic vacuoles participate in the diges-
2.6 PROTOZOA tion of food; contractile vacuoles maintain osmolarity for
protozoa living in hypotonic environments; and secretory
The 18S rRNA based classification being used for eucary- vacuoles contain enzymes for various cell functions. Also
otic microorganisms has revealed fundamental genetic apparent in the cytoplasm are multiple nuclei. In some pro-
differences among the protozoa. Consequently, it has tozoa the nuclei are identical, while in others, such as the
emerged that the single-celled protozoa are a polyphyletic Ciliophora, there is a macronucleus and a micronucleus.
A B C
FIGURE 2.13 Morphological diversity seen among the protozoa. (A) Infection of an intestinal cell with Cryptosporidium (an apicomplexan); spe-
cifically a sporozoite is attached to an intestinal epithelial cell with several merozoites emerging. For details on the life cycle see Chapter 22. From
Clark (2008). (B) Paramecia are members of the Ciliophora. They are commonly found in freshwater environments where they feed on bacterial cells.
© Dennis Kunkel Microscopy, Inc., reproduced with permission. (C) Ameoba radiosa is a member of the Sarcodina. It is found in many different envi-
ronments and obtains its food by surrounding and engulfing it. From Evarts (2006).
The larger macronucleus is associated with cell growth and Protozoa have an important role in the degradation and
metabolism. The smaller micronucleus is diploid and is cycling of organic matter in the environment. These pro-
involved in genetic recombination during reproduction and tozoa make and release a variety of extracellular enzymes
regeneration of the macronucleus. Many genetically identi- for the degradation of polymers (such as cellulose from
cal copies of each nucleus can exist in a cell. plants) and peptidoglycan from bacterial cell walls. Some
Some protozoa form cysts or oocysts as part of a com- bacteriovorous protozoa release such enzymes to aid in feed-
plex life cycle (Chapter 22). Similar to spores in bacteria ing on bacteria. Other protozoa obtain their nutrients via
and fungi, cysts can increase the survival of the organism. phagocytosis (engulfment), which are then degraded by
Giardia, for example, produces cysts that persist under digestive enzymes stored in phagocytic vacuoles. The abil-
environmental conditions until transmission to an animal ity to degrade large molecules contributes to the complex
host occurs, at which point the cyst will undergo excysta- relationships these organisms have with animals. In fact,
tion to produce a vegetative cell resulting in giardiasis, a protozoa are responsible for up to one-third of fiber diges-
diarrheal disease. Giardia and another cyst forming pro- tion in ruminants and contribute half the microbial mass
tozoan Cryptosporidium have been linked to outbreaks of in the rumen. In the anaerobic environment of the rumen,
waterborne illness. protozoa carry out fermentation, producing organic acids
Many protozoa are distinguished based on their struc- and alcohols.
tural morphology and mechanism of motility. Morphological Water quality is an area where protozoa are having
characterizations are based on colony formation (single an increasingly important impact. Outbreaks of disease
existence or in colonies), swimming style (sedentary or have been attributed to protozoa in drinking water, irriga-
motile), external structures (naked, shelled, or scaled), and tion water, and coastal waters. The three most commonly
pigmentation. Most protozoa are motile and are divided into reported protozoa affecting water quality are Giardia
taxonomic groups based on their mechanism of motility. For (Mastigophora), Cryptosporidium (Apicomplexa) and
example, the Mastigophora use flagella; the Ciliophora use Toxoplasma (Apicomplexa). Originating from infected
cilia (hairlike structures that extend outward from the cell humans and animals, the cysts and oocysts of these organ-
membrane); the Sarcodina use ameboid motility; and the isms can withstand the water temperatures and salinities
Apicomplexa are nonmotile. encountered to survive long periods in the environment
(Fayer et al., 2004). They can also withstand wastewater
treatment disinfection (Chapters 22 and 24).
2.6.2 Physiological and Ecological
Considerations
2.7 ALGAE
Protozoa have a number of important ecological roles
(Information Box 2.10). Many protozoa are chemohetero- Algae are a group of eucaryotic oxygenic photosynthetic
trophic using either aerobic respiration or fermentation. microorganisms that contain chlorophyll a (as seen in
Interestingly, anaerobic and microaerophilic protozoa do not plants). Algae range from single-celled organisms to com-
contain true mitochondria (as found in other eukaryotes). plex multicellular organisms like seaweeds (Fig. 2.14).
Instead they rely on membrane-bound structures called Algae inhabit a wide range of habitats from aquatic envir-
hydrogenosomes for energy production. Hydrogenosomes onments (freshwater, marine, and brackish) to soils and
lack many of the citric acid cycle enzymes normally associ- rocks; only inadequate light or water seems to limit the
ated with mitochondria and use protons as terminal electron presence of algae. Algae are most commonly found in
acceptors forming molecular hydrogen instead of water. saturated environments either suspended (planktonic),
attached to surfaces, or at the air–water interface (neu-
stonic). Endolithic algae can be found in porous rock or
Information Box 2.10 Roles of Protozoa in
as surface crusts on desert soils. Algae are often the pre-
Environmental Microbiology
dominant microorganisms in acidic (below pH 4) habitats,
as seen with the red alga Cyanidium that can grow below
● Serve as the base of the food chain in aquatic systems
pH 2. Generally free-living, some algae have symbiotic
● Population control through the predation of bacteria,
algae, and even other protozoa relationships with fungi (lichens), mollusks, corals, and
● Human and vertebrate parasites, food-borne and plants, and some algae can be parasitic. Classification of
water-borne disease algae is complex, involving numerous cellular proper-
● Degradation of complex organic materials, such as ties. For example, algae can be grouped based on cell wall
cellulose chemistry, cell morphology, chlorophyll molecules and
● Symbioses with some animals, such as termites and accessory pigments, flagella number and type of insertion
ruminants in the cell wall, reproductive structures, life cycle, and hab-
itat. Based on cell properties, algae include the green algae
(Chlorophyta), the euglenoids (Euglenophyta), the dinofla-

gellates (Dinoflagellata), the golden-brown algae, diatoms
(Chrysophyta), the brown algae (Phaeophyta), and the red
alage (Rhodophyta). However, similar to the protozoa, 18S
rRNA criteria reveal a phylogenetically diverse group.
2.7.1 Cell Structure

Algae can be unicellular, colonial (occurring as cell aggre-
gates), or filamentous, resulting in great diversity in over-
all cell morphology. Algal cell walls surround cytoplasmic
A membranes and are thin and rigid but vary in their com-
position. They generally contain cellulose with a variety
of other polysaccharides including pectin, xylans, and
alginic acid. Some walls are calcareous containing calcium
carbonate deposits. Chitin (a polymer of N-acetylglucos-
amine) may also be present in some algae. The euglenoids,
however, differ from other algae by lacking cell walls. In
diatoms, the cell wall is composed of silica, giving rise to
fossils. Other cell wall associated structures include gelati-
nous capsules outside the cell wall for adhesion and pro-
tection, and flagella arranged in different patterns on the
cell for motility.
All algae also contain membrane-bound chloroplasts
containing chlorophyll a and other chlorophylls, such as
chlorophyll b, c, or d. Some contain differently colored
pigments called xanthophylls, which can give rise to differ-
ently colored algae. Many algae also contain pyrenoids that
B serve as sites for storage and synthesis of starch. Starch is
one of the many types of carbohydrate storage that algae
use to support respiration in the absence of photosynthe-
sis. Other types of storage molecules include paramylon
(-1,2-glucan), lipids, and lammarin (-1,3-glucan).
2.7.2 Physiological and Ecological

Considerations
Algae are primarily oxygenic photoautotrophs although a
few are chemoheterotrophic using simple organic compounds
(e.g., acetate) to help support cell metabolism. Oxygenic pho-
tosynthesis produces oxygen as a waste product in obtaining
energy from the breakdown of water. The production of oxy-
C gen is one of the desirable effects of algal growth in some
aquatic systems. Oxygenic photosynthesis by algae is also
FIGURE 2.14 Examples of algal diversity. (A) Spirogyra is a responsible for primary production (production of organic
single celled filamentous freshwater green alga, 10 to 100 m in
length, belonging to the Chlorophyta. From Schagerl (2005). (B) An
matter) in many aquatic habitats. Thus, primary production
algal bloom on Lake Champlain. From EPA (2008). (C) Marine algal sea- by algae sustains the food web in many aquatic environ-
weed belonging to the Rhodophyta. From the Fish and Wildlife Research ments, and is equivalent to the role plants play in terrestrial
Institute (2008). systems.
Found in a variety of disparate habitats, algae have var-
ied reproduction strategies that are partially responsible for
their success. Algae can reproduce sexually and asexually,
with sexual reproduction involving the formation of eggs
within structures called oogonia and sperm within anther- The toxin itself survives cooking and can cause diarrhea
idia. The egg and sperm fuse forming a diploid zygote and central nervous system disorders. Toxin accumula-
resulting in a vegetative algal cell. Asexually, algae repro- tion in fish and shellfish generally occurs during blooms
duce through binary fission or fragmentation, where frag- of dinoflagellates (algal blooms). Unfortunately, the occur-
ments of filamentous algae break off and continue to grow. rence of toxic algal blooms is on the rise nationally and
Binary fission is especially prevalent among the single- internationally due to a number of contributing factors, the
celled algae. Finally, some algae can produce spores (e.g., most prevalent of which is the increasing nutrients, espe-
zoospores or aplanospores) that can germinate into fully cially nitrogen and phosphorus, that are being released into
functioning vegetative cells. coastal waters from sewage and agricultural runoff.
An interesting characteristic of some algae, especially
the coastal dinoflagellates, is the production of secondary
metabolites. Many of these metabolites are in the form of 2.8 VIRUSES
toxins released extracellularly. For example, the dinofla-
gellates Gymnodinium and Gonyaulax species can pro- Viruses are a group of biological entities consisting of a
duce the neurotoxin saxitoxin that paralyzes muscles of the nucleic acid encapsulated within a protein coat known as
respiratory system in vertebrates. The toxin itself, potent the capsid in various different sizes (Fig. 2.15) and mor-
at nanogram concentrations, does not harm shellfish; how- phologies (Fig. 2.16). Viral nucleic acids can consist
ever, shellfish accumulate the toxin making them danger- of single- or double-stranded DNA or RNA. Although
ous for consumption. Ciguatera is a disease resulting from some viruses do contain a few enzymes, they are obligate
the consumption of fish that have ingested or have accumu- parasites that have no metabolic capability and rely on host
lated the toxin of the dinoflagellate Gambierdiscus toxicus. metabolism to produce viral parts that self-assemble. The
MS2 bacteriophage
24 nm
Polio virus 30 nm
Adenovirus
70 nm
Adenovirus DNA Human Immunodeficiency Virus
(HIV) 100 nm
Tobacco Mosaic Virus
18 x 300 nm
T-4 bacteriophage 30 124 nm
Herpes virus 125 nm
Chlamydia elementary
body 450 nm
Vaccinia virus
300 450 nm
T-4 bacteriophage DNA
E. coli bacterium 0.5–2 m
FIGURE 2.15 Comparative sizes of selected viruses in comparison to a bacterial

cell and nucleic acids.
growth cycle of a virus can be described in five steps: (1) vehicle, such as air or water, for transport. Once in con-
adsorption; (2) penetration; (3) replication; (4) maturation; tact with a potential host, viruses find their way into target
and (5) release (Fig. 2.17). All viruses share a common cells using specific receptor sites on their capsid or enve-
mechanism of replication at the molecular level, but differ- lope surfaces. This is why viruses of bacteria or plants do
ent viruses replicate at varying rates. For example, bacterial not normally infect humans and vice versa. Once viruses
viruses (bacteriophage or phage) often replicate rapidly, in invade host cells and replicate, they can invade neighboring
minutes, whereas a typical animal virus replicates in hours cells to continue the infection process. Infection of a cell
to days. All viruses begin infection by adsorption to the by a virus is often but not always debilitating to the cell’s
host via specific receptors and injection of the nucleic acid regular functions. Thus, viral infection may be asymptom-
or uptake of the total virus particle into the cell. The cycle atic or may cause acute, chronic, latent, or slow infections,
then goes into what is known as the eclipse phase, a period or may cause cell death.
of time during which no virus particles can be detected In bacteria, some viral infections appear to cause no
because of release and incorporation of the nucleic acid immediate harm to the host cell. Therefore the phage is
in the host cell machinery. Finally, new viral components carried by the host. These carrier hosts, however, may still
are produced, assembled, and released from the host by be sensitive to other phage populations. This condition is
disruption of the cell or budding at the cell membrane sur- known as lysogeny. With a lysogenic phage, also known
face. The latter release mechanism is less destructive to the as a temperate phage, the nucleic acid is integrated with
host cell and may support a symbiotic condition between the chromosome of the host, persisting indefinitely, and is
the virus and the host. transmitted to host descendants or daughter cells. This sta-
ble, noninfectious form of the virus is known as a prophage.
The phage may remain latent for many generations and
2.8.1 Infective Nature of Viruses
then suddenly be mobilized and initiate replication and
Outside their hosts, viruses are inert objects, incapable eventually cause host lysis. Typically, only a portion of
of movement. Thus, these tiny infectious agents require a temperate phage become lysogenic, while other members
Icosahedral
Glycoprotein nucleocapsid
IIIIIIIIIIIIIIIIIIII
Icosahedral
nucleocapsid IIII
IIIII
IIIII
IIII
IIIIIIIIIIIIIIIIIIII Envelope
A. Naked icosahedral
B. Enveloped icosahedral
C. Naked helical
Helical nucleocapsid
Nucleocapsid
Glycoprotein spikes Nucleic acid

Sheath
Sheath fibers
spikes
I I I I I I I I I
I I I
I
I I I
I I
I I I Helical
I I I II II I I I I I Tail spikes
nucleocapsid
Envelope Base
plates
D. Enveloped helical E. Complex virion

FIGURE 2.16 Simple forms of viruses and their components. The naked icosahedral
viruses (A) resemble small crystals; the enveloped icosahedral viruses (B) are made up of
icosahedral nucleocapsids surrounded by the envelope; naked helical viruses (C) resemble
rods with a fine regular helical pattern in their surface; enveloped helical viruses (D) are heli-
cal nucleocapsids surrounded by the envelope; and complex viruses (E) are mixtures of heli-
cal and icosahedral and other structural shapes.
1. Attachment
2. Penetration
3. Uncoating
4. Transcription of DNA
into early mRNA
5. Translation of early
mRNA into early
proteins
6. Replication of viral
DNA
7. Transcription of DNA
into late mRNA
8. Translation of mRNA
into late proteins
9. Assembly of virions
10. Release
FIGURE 2.17 The basic steps of virus multiplication. Representation of an icosahedral DNA virus
showing the main steps including adsorption, penetration, replication, maturation, and release. Drawing
courtesy of Wayne L. Miller, McGill University, Montreal, Quebec.
of the population remain virulent, multiplying and lys- are predators of prokaryotes. In contrast lysogenic and
ing host cells. Similar to lysogenic bacteriophage, animal chronic infections are actually a parasitic interaction that
retroviruses integrate their nucleic acid into the cell chro- could be described as mutualism (Weinbauer, 2004). In
mosome, producing persistent infections. Such a cycle is the lytic cycle, the number of virions released per cell is
typical of herpesvirus infections in humans. In fact, the known as the burst size. Figure 2.18 shows a bacterial cell
herpesvirus may be passed from grandparent to grand- visibly infected with phage. Overall, the size of phage usu-
child, remaining dormant through two generations. Half ally ranges from 30 to 60 nm. The morphology of environ-
of the human population is estimated to be infected by the mental phage varies considerably. Typically phage consist
age of 1 year, and up to 85% of the population is seroposi- of a head and a tail held together by a connector, but other
tive by puberty. Most latent animal viruses, such as mumps forms can be cubic, spindle, filamentous or pleomorphic.
and measles viruses, lack the ability to lyse the host cell or Details on the metabolic state of phage and methods of
prevent host cell division. Infection is therefore continued viral infection and replication are given in Section 2.8.3 on
by the production of infected daughter host cells. In latent eucaryotic viruses.
infections, an equilibrium is reached between host and
parasite until a nonspecific stimulus, such as compromised
2.8.2.2 Ecology of Procaryotic Viruses
host immunity, evokes active infection.
Procaryotic phage are abundant in a variety of environ-
ments (Table 2.5), and phage populations appear to be cor-
related with bacterial populations. Interestingly, estimates
2.8.2 Procaryotic Viruses of phage populations vary depending on the methodology
utilized, in a manner similar to that for bacteria. When
2.8.2.1 Structure and Life Cycle of Procaryotic Viruses
direct microscopic counts are made utilizing transmis-
The interactions of bacteriophage with a procaryotic host sion electron microscopy, counts are two to three orders
are diverse (outlined in Information Box 2.11). Lytic phage of magnitude higher than when traditional viable plaque
Information Box 2.11 Host–phage Interactions

TABLE 2.5 Incidence of Phage in Different
Environments
Lytic infection. Lytic or virulent phage redirect the host
metabolism toward the production of new phage which are
Environment Number of phage Virus to
released as the host cell lyses.
(g1 or ml1) bacteria
Lysogenic infection. Phage nucleic acid material of the tem-
perate or lysogenic phage remains dormant within the host as ratio (VBR)
prophage. Prophage are replicated along with the host until Marine (deep-sea) 104–105 5–10
the lytic cycle is induced. 5 6
Marine (offshore surface 10 –10 10
Chronic infection. Infected host cells constantly release
water)
phage progeny by budding or extrusion without lysing the
host cell. Coastal environment 106–107
Pseudolysogenic infection. Phage multiply in only a frac- Marine sediments 0.03–11.71 109
tion of the infected host cells. Also known as the phage-
carrier state. Freshwater sediments 0.65–2.90 109 20
Sea ice 9 10 –1.3 10
6 8
Mode of Infection Phage Type

Forest soil 1.31–4.17 109 72
Infection via pili or flagella F-specific phage
Infection via recognition of outer host Capsule phage Agricultural soil 8.7 10 –1.1 10
8 9
1
layer or polysaccharide capsule
Infection via cell wall Somatic phage Data compiled from Weinbauer, 2004, and Williamson et al., 2005.
in the size range 0.2 to 2 m including small protozoa

and bacteria.
Given these large numbers, phage play critical roles in
the environment (Information Box 2.12). The direct role of
phage is to control bacterial populations by induction of
the lytic cycle, which causes bacterial cell lysis. Without
phage as a controlling factor, bacterial populations could
increase significantly. Controlled studies by Wommack and
Colwell (2000) showed that additions of phage to bacte-
rial populations resulted in a 20–40% decrease in bacterial
numbers. Overall, phage and protozoa (nanoflagellates) are
the two major predators of prokaryotes in marine waters.
Control of bacterial populations occurs in both marine and
soil environments and can be general or very specific. For
example, bacteriophage SF-9 is known to specifically lyse
Shigella dysenteriae Type 1 (Faruque et al., 2003). Phage
have also been explored for use in the biological control of
fish disease. In this case two phage were applied to control
FIGURE 2.18 Transmission electron micrograph of a bacterial cell vis- the bacterium Pseudomonas plecoglossicida, the causative
ibly infected with phage. From Weinbauer, 2004. agent of bacterial hemorrhagic ascites disease in cultured
ayu fish (Plecoglossus altivelis) (Park et al., 2000).
Viruses are also influential in controlling marine cya-
nobacteria. Such viruses are known as cyanophage and
counts are used (Ashelford et al., 2003). Virus to bacte- infect numerically dominant primary producers such as the
rium ratios (VBRs) have been used to illustrate the large marine cyanobacteria Prochlorococcus and Synechococcus
number of phage in the environment. VBRs often aver- (Sullivan et al., 2006). Due to the large numbers of bacte-
age around 10, and appear to be higher in marine waters ria that are lysed daily in marine waters, phage are impor-
than in soils, where low VBR values (1) have been tant in both food web processes and biogeochemical cycles
reported (Ashelford et al., 2003). Parada et al. (2007) (Fig. 2.19). Significant amounts (6–26%) of the carbon
reported marine virus to picoplankton ratios ranging from fixed by primary producers enter the dissolved organic
9 at 100 m depth to 110 at a depth of 3500 to 5000 m (see matter carbon (DOC) pool via virus-induced lysis at dif-
Chapter 6). Picoplankton are aquatic microorganisms found ferent trophic levels. In addition it has been estimated that
phage contribute from 1 to 12% of the total dissolved DNA 2.8.3 Eucaryotic Viruses
in samples from freshwater, estuarine, and offshore oligo-
trophic environments (Paul et al., 1991). Eucaryotic viruses infect humans and other animals,
Phage also influence bacterial diversity by mediating plants, and eucaryotic microorganisms including algae
horizontal gene transfer through the process of transduc- and fungi. Eucaryotic viruses are also ubiquitous and are
tion. Two types of transduction are known to be undertaken readily found in marine and soil environments. Most inter-
by phage. For generalized transduction, bacterial host est in eucaryotic viruses has centered on human and plant
genetic material is packed in error into the capsids of vir- pathogens. Human viruses cause ailments to almost every
ulent phage, which is subsequently transferred into a new part of the human body and include smallpox, mumps,
recipient host following infection (Fig. 2.9). In specialized measles, meningitis, hepatitis, encephalitis, colds, influ-
transduction, a host sequence is excised along with the pro- enza, and diarrhea. Information on fate and transport of
phage and subsequently transferred to a host. Information some human viruses is given in Chapter 22; however, a
on transduction rates in natural ecosystems is limited but it detailed discussion of infectious disease is beyond the
is believed that generalized transduction may be important, scope of this book. Examples of important animal viruses
because phage-encapsulated DNA is protected from degra- include the Rhabdoviridae that causes rabies in dogs and
dation (Weinbauer, 2004). the Aphthovirus that causes foot-and-mouth disease in
cows. Studies on plant pathogenic viruses have focused on
those affecting major agricultural crops including tobacco,
potatoes, and tomatoes.
Information Box 2.12 Roles of Phage in Information on eucaryotic viruses that affect algae
Environmental Microbiology have been mostly limited to the marine environment.
Here, viruses have been identified as important agents in
● Control of bacterial populations controlling phytoplankton populations (Brussard, 2004).
● Control of specific bacterial pathogens Eucaryotic viruses not only aid in the control of algal
● Control of marine cyanobacteria blooms, but they are also now being recognized as import-
● Interactions with food web processes ant agents that affect fluxes of energy, nutrients, and
● Interactions with biogeochemical cycles dissolved organic matter in marine waters. Similar to
● Enhanced procaryotic diversity via horizontal gene
the procaryotic viruses, interest in eucaryotic viruses is
transfer
increasing rapidly as it becomes clear that algal viruses are
FIGURE 2.19 Pelagic food chain

Grazing Food Chain model and virus-mediated car-
bon flow. The dotted lines point
Primary to virus-mediated pathways. All
Producers values are in terms of the flux of
Grazers carbon fixed by primary produc-
Carnivores
ers (100%). Only data for viruses
are shown. The data indicate that
between 6 and 26% of the carbon
1% fixed by primary producers enters
the DOC pool via virus-induced
lysis at different trophic levels.
2–10% Adapted from Weinbauer, 2004.
Viruses
6–26%
Viral
Dissolved loop
Inorganic 3–15% Microbial
Organic
Nutrients loop
Carbon
Heterotrophic
Prokaryotes
important in biogeochemical cycles. Thirteen viral infec- in ovules. Viroids have been linked to over 16 plant dis-
tions of marine microalgae have been reported (Brussard, eases, including potato spindle-tuber disease and citrus
2004). As an example, diatoms are the major phytoplank- exocortis disease, and appear to be highly homologous
ton group that play a role in maintaining oxygen levels in to each other, indicating a common evolutionary origin.
the atmosphere and in the carbon cycle that sustains pri- Viroids lack a protein capsid, and the RNA of the viroid
mary production in aquatic environments. The most abun- contains no protein-coding genes. As a result, the mecha-
dant diatom is Chaetocerus, which was recently reported nism of disease for viroids remains unclear. In a given
to have been infected by a previously unknown virus infected cell, however, hundreds to thousands of viroid
(Nagasaki et al., 2005). copies may be present.
Eucaryotic viruses that infect fungi are known as myco-
viruses. Although mycoviruses have been identified in all
major fungal families, information on environmental aspects 2.9.2 Prions
of these viruses is limited. An example of a mycovirus Prions are found in humans and other mammals and con-
with economic repercussions is the causative agent of La sist totally of protein (Fig. 2.20). Abnormal prions are infec-
France disease, which affects the edible common mushroom tious protein that can destroy brain tissue giving it a spongy
Agaricus bisporus (Romaine and Schlagnhaufer, 1995). appearance. Diseases caused by prions are termed trans-
Viral infections of yeasts have also been reported (Schmitt missible spongiform encephalopathy (TSE) diseases. TSE
and Neuhaussen, 1994). Undoubtedly, numerous myco- diseases include the agent of mad cow disease (or bovine
viruses are present in soil environments that most likely spongiform encephalopathy, BSE) in cattle; scrapie in
influence control of fungal populations and biogeochemical sheep; Creutzfeld-Jakob disease in humans; kuru in humans;
cycling, but to this point in time data on such incidence is and chronic wasting disease (CWD) in wild deer and elk.
limited. One intriguing example from Yellowstone National TSE diseases are transmissible from host to host of a
Park involves a fungus, Curvularia protuberata, and a plant, single species or from one species to another, for example,
Dichanthelium lanuginosum, that only grow at high tem- cows to humans. Normal prions are found in the human
perature (65°C) when in a mutualistic association. Research body and are known as PrPc, where
has shown that this association involves a third partner, a
mycovirus. In the absence of viral infection, the fungus PrP prion protein
does not confer thermal tolerance on the plant (Márquez c cellular.
et al., 2007)!
PrPc molecules have three-dimensional configurations that
are easily digested by proteases. The secondary structure
2.9 OTHER BIOLOGICAL ENTITIES of PrPc is dominated by helices (Fig. 2.21A). The abnor-
mal prions are known as PrPsc, where
2.9.1 Viroids sc scrapie.
Viroids are subviral particles that have virus-like properties
but are not viruses. Viroids are infectious circular single- The primary structure of PrPsc is similar to that of PrPc
stranded RNAs from 250 to 400 nucleotides long that rep- (amino acid sequences) but the secondary structure is dom-
licate in their plant host and are transmitted from host to inated by conformations (Fig. 2.21B). PrPsc molecules
host through mechanical means, for example, through a are not easily degraded by proteases. Of critical impor-
wound or through transmission of contaminated pollen or tance is the fact that when PrPsc comes into contact with
PrPc it converts the PrPc into PrPsc. Therefore although
H3N Gly lle Val Cys Glu Gln (A) (B)

− Ala
Ser
Val Leu
Cys
Pro Asp
Arg
Lys −C00
Asn
−
Phe
Lys
Tyr
Thr Leu His
FIGURE 2.20 Primary amino acid sequence of PrPc (a normal prion). FIGURE 2.21 Secondary structures of (A) PrPc and (B) PrPsc.
abnormal prions do not replicate, there exists a mechanism CHAPTER REFERENCES

to increase the numbers of the abnormal form. When num-
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Chapter 2

2.1 Classiﬁcation of Organisms 2.4 Fungi 2.7.2 Physiological and Ecological

The purpose of this chapter is to introduce the different

Gp. 1 low temp

TABLE 2.1 Overall Macromolecular Composition of an Average E. coli B/r Cell

Adapted with permission from Neidhardt et al., 1990.

Plasmid Periplasmic space

Ribosomes Cell wall (peptidoglycan)

Nuclear material Outer membrane

Information Box 2.2 Procaryotic Cell Structure and Function

Location Structure Function

Teichoic acid Lipoteichoic acid

Non-polar Polar head group

important functions of the cytoplasmic membrane and its 2.2.2 Cytoplasm

Information Box 2.4 Bacterial Plasmid Functions

Plasmid type Function Reference

Information Box 2.5 Types of Plasmids

Information Box 2.6 Classiﬁcation Using the 16S

The 16S rRNA gene is approximately 1500 bp in length. In

Step 1: anneal universal primers to 16s rRNA gene

Step 3: sequence the DNA product from step 2

Step 4: compare DNA sequences to classify

The 5 to 3 strand of the 16S rRNA gene

TABLE 2.2 Metabolic Classiﬁcation of Bacteria

Photoheterotrophy light  H2S organic compounds many purple nonsulfur S0

Information Box 2.7 Biological Generation of Energy

Case 1: If the formation of products (C and D) is favored, then

H2S  0. 5O2 → S0  H2O (Beggiatoa)

(a) Aerobic heterotrophic respiration: Many bacteria function as

C4H6O4  2.8NO3  2.8H 1.4N2  4CO2  4 .4H2O

FIGURE 2.11 Structure of a fungal cell wall. Drawing

Information Box 2.9 The White-rot Fungi: The Ultimate Fungus?

(Chlorophyta), the euglenoids (Euglenophyta), the dinofla-

2.7.1 Cell Structure

2.7.2 Physiological and Ecological

T-4 bacteriophage 30 124 nm

Herpes virus 125 nm

T-4 bacteriophage DNA

E. coli bacterium 0.5–2 m

FIGURE 2.15 Comparative sizes of selected viruses in comparison to a bacterial

Glycoprotein spikes Nucleic acid

D. Enveloped helical E. Complex virion

Information Box 2.11 Host–phage Interactions

Mode of Infection Phage Type

in the size range 0.2 to 2 m including small protozoa

FIGURE 2.19 Pelagic food chain

H3N Gly lle Val Cys Glu Gln (A) (B)

abnormal prions do not replicate, there exists a mechanism CHAPTER REFERENCES

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The 5 to 3 strand of the 16S rRNA gene

Photoheterotrophy light H2S organic compounds many purple nonsulfur S0

H2S 0. 5O2 → S0 H2O (Beggiatoa)

C4H6O4 2.8NO3 2.8H 1.4N2 4CO2 4 .4H2O

H3N Gly lle Val Cys Glu Gln (A) (B)