Hogg S. Essential microbiology

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158 MICROBIAL DIVERSITY

A few words about classification

In this section, we examine the wide diversity of microbial life. In each of the next four

chapters, we shall discuss major structural and functional characteristics, and outline

the main taxonomic divisions within each group. We shall also consider some speciﬁc

examples, particularly with respect to their effect on humans. By way of introduction,

however, we need to say something on the subject of the classiﬁcation of microorganisms.

In any discussion on biological classiﬁcation, it is impossible to avoid mentioning Lin-

naeus, the Swedish botanist who attempted to bring order to the naming of living things

by giving each type a Latin name. He even gave himself one – his real name was Carl

von Linn

e! It was Linnaeus who was responsible for introducing the binomial system

of nomenclature, by which each organism was assigned a genus and a species. To give

a few familiar examples, you and I are Homo sapiens, the fruit ﬂy that has contributed

so much to our understanding of genetics is Drosophila melanogaster, and, in the mi-

crobial world, the bacterium responsible for causing anthrax is Bacillus anthracis. Note

the following conventions, which apply to the naming of all living things (the naming

of viruses is something of a special case, which we’ll consider in Chapter 10):

the generic (genus) name is always given a capital letter

the speciﬁc (species) name is given a small letter

the generic and speciﬁc name are italicised, or, if this isn’t possible, underlined

A taxon is a collec-

tion of related organ-

isms grouped together

for purposes of classifica-

tion. Thus, genus, family,

etc. are taxons.

The science of taxonomy involves not just naming or-

ganisms, but grouping them with other organisms that

share common properties. In the early days, classiﬁca-

tion appeared relatively straightforward, with all living

things apparently ﬁtting into one of two kingdoms.To

oversimplify the matter, if it ran around, it was an an-

imal, if it was green and didn’t, it was a plant! As our

awareness of the microbial world developed, however, it

was clear that such a scheme was not satisfactory to accommodate all life forms, and in

the mid-19th century, Ernst Haeckel proposed a third kingdom, the Protista, to include

the bacteria, fungi, protozoans and algae.

In the 20th century, an increased focus on the cellular and molecular similarities

and dissimilarities between organisms led to proposals for further reﬁnements to the

three-kingdom system. One of the most widely accepted of these has been the ﬁve-

kingdom system proposed by Robert Whittaker in 1969 (Figure A1). Like some of its

predecessors, this took into account the fundamental difference in cell structure between

procaryotes and eucaryotes (Chapter 3), and so placed procaryotes (bacteria) in their

own kingdom, the Monera, separate from single-celled eucaryotes. Another feature of

Whittaker’s scheme was to assign the Fungi to their own kingdom, largely on account of

their distinctive mode of nutrition. Table A1 shows some of the characteristic features

of each kingdom.

Molecular studies in the 1970s revealed that the Archaea differed from all other bac-

teria in their 16S rRNA sequences, as well as in their cell wall structure, membrane lipids

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A FEW WORDS ABOUT CLASSIFICATION 159

FUNGIPLANTAE

PROTISTA

MONERA

ANIMALIA

Figure A.1 Whittaker’s ﬁve-kingdom system of classiﬁcation

and aspects of protein synthesis. These differences were seen as sufﬁciently important

for the recognition of a third basic cell type to add to the procaryotes and eucaryotes.

This led to the proposal of a three-domain scheme of classiﬁcation, in which procary-

otes are divided into the Archaea and the Bacteria (Figure 3.1). The third domain, the

Eucarya represents all eucaryotic organisms. The domains thus represent a level of clas-

siﬁcation that goes even higher than the kingdoms. Although the Archaea (the word

means ‘ancient’) represent a more primitive bacterial form than the Bacteria, they are in

certain respects more closely related to the eucaryotes, causing biologists to revise their

ideas about the evolution of the eucaryotic state.

In hierarchical systems of classiﬁcation, related species are grouped together in the

same genus, genera sharing common features are placed in the same family, and so on.

Table A2 shows a modern classiﬁcation scheme for the gut bacterium Escherichia coli.

The boundaries between long-standing divisions such as algae and protozoa have

become considerably blurred in recent years, and alternative classiﬁcations based on

molecular data have been proposed. This is very much a developing ﬁeld, and no deﬁni-

tive alternative classiﬁcation has yet gained universal acceptance.

In the following chapters, we shall broadly follow the ﬁve-kingdom scheme, although

of course the plant and animal kingdoms, having no microbial members, do not concern

us. Thus, both the Archaea and Bacteria are considered in Chapter 7, and multicellular

fungi form the focus of Chapter 8. Chapter 9 examines the Protists in the modern use

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Table A.1 Characteristics of Whittaker’s ﬁve kingdoms

Monera (procaryotae) Protista Fungi Plantae Animalia

Cell type Procaryotic Eucaryotic Eucaryotic Eucaryotic Eucaryotic

Cell organization Unicellular; occasionally

grouped

Unicellular;

occasionally

multicellular

Unicellular or

multicellular

Multicellular Multicellular

Cell wall Present in most Present in some, absent

in others

Present Present Absent

Nutrition Absorption, some

photosynthetic, some

chemosynthetic

Ingestion or absorption,

some photosynthetic

Absorption Absorptive,

photosynthetic

Ingestion; occasionally

in some parasites by

absorption

Reproduction Asexual, usually by

binary ﬁssion

Mostly asexual,

occasionally both

sexual and asexual

Both sexual and

asexual, often

involving a complex

life cycle

Both sexual and

asexual

Primarily sexual

160

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A FEW WORDS ABOUT CLASSIFICATION 161

Table A.2 A modern hierarchical

classiﬁcation for E. coli; note that in this

classiﬁcation, there are no kingdoms

Domain Bacteria

Phylum Proteobacteria

Class Zymobacteria

Order Enterobacteriales

Family Enterobacteriaceae

Genus Escherichia

Species coli

of the word, that is, unicellular eucaryotic forms. It retains the traditional distinction

between protozoans, algae and other protists (water moulds and slime moulds), but also

offers an alternative, ‘molecular’ scheme, showing the putative phylogenetic relationship

between the various groups of organisms. Microbiology has traditionally embraced

anomalies such as the giant seaweeds, as it has encompassed all organisms that fall

outside of the plant and animal kingdoms. This book offers only a brief consideration

of such macroscopic forms, and for the most part conﬁnes itself to the truly microbial

world.

The viruses, it ought to be clear by now, are special cases, and are considered in

isolation in Chapter 10. Because an understanding of viruses requires an appreciation

of the basics of DNA replication and protein synthesis, it may help to jump ahead and

read the relevant sections of Chapter 11 before embarking on Chapter 10.

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162

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Procaryote Diversity

The phenotype of an or-

ganism refers to its ob-

servable characteristics.

The genotype of an or-

ganism refers to its ge-

netic make-up.

Ever since bacteria were ﬁrst identiﬁed, microbiologists have attempted to bring order

to the way they are named and classiﬁed. The range of morphological features use-

ful in the differentiation of bacteria is fairly limited (compared, say, to animals and

plants), so other characteristics have also been employed. These include metabolic

properties, pathogenicity, nutritional requirements, staining reactions and antigenic

properties. The ﬁrst edition of Bergey’s Manual of Systematic Bacteriology (henceforth

referred to as ‘Bergey’), published in the mid-1980s, mainly used phenotypic character-

istics such as these to classify bacteria. The result placed bacteria into taxonomic groups

that may or may not reﬂect their evolutionary rela-

tionship to one another. In the years since the ﬁrst

edition of Bergey, the remarkable advances made in

molecular genetics have led to a radical reappraisal

of the classiﬁcation of bacteria. Comparison of nu-

cleic acid sequences, notably those of 16S riboso-

mal RNA genes, has led to a new, phylogenetically

based scheme of classiﬁcation, that is, one based on

how closely different groups of bacteria are thought

to be related, rather than what morphological or

physiological features they may share. Ribosomal RNA occurs in all organisms, and

serves a similar function, thus to a large extent these sequences are conserved (remain

similar) in all organisms. The nature and extent of any differences that have crept in

during evolution will, therefore, be an indication of the relatedness of different organ-

isms.

The second edition of Bergey aims to reﬂect this change of approach and reassign

many bacteria according to their phylogenetic relationship, as deduced from molecular

evidence. Due to be issued in ﬁve volumes over a number of years, the ﬁrst volume was

published in 2001. As an example, the genus Pseudomonas previously contained some

70 species on the basis of phenotypic similarities, but in the second edition of Bergey,

taking into account 16S rRNA information, many of these are assigned to newly created

genera.

It must be stressed that Bergey (second edition) does not represent the deﬁnitive

ﬁnal word on the subject, and that the classiﬁcation of bacteria is very much a de-

veloping science, in a constant process of evolution. Indeed, microbiologists are by

no means unanimous in their acceptance of the ‘molecular’ interpretation of bacte-

rial taxonomy. Some point to perceived inadequacies in the collection of data for the

163

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164 PROCARYOTE DIVERSITY

Figure 7.1 Phylogenetic relationships in the Procaryota. A phylogenetic tree based on 16S

ribosomal RNA data, showing the relationships between members of the Archaea and the

Bacteria. The position on the tree of the Eucarya (all eucaryotic organisms) is also indicated

scheme, as well as errors in the data arising from the

sequencing and ampliﬁcation techniques utilised. Other

critics question the validity of a scheme based on 16S

rRNA data when it seems increasingly likely that lateral

gene transfer played an important role in bacterial evo-

lution.

Bacteria may acquire

genes from other or-

ganisms by a variety of

genetic transfer mecha-

nisms (see Chapter 11).

This is known as horizon-

tal or lateral gene trans-

fer, to distinguish it from

vertical inheritance, in

which the parental gen-

otype is passed to the

offspring.

In the following pages, the major taxonomic group-

ings are discussed according to their arrangement in the

second edition of Bergey. Figure 7.1 shows a phyloge-

netic tree, reﬂecting current ideas on the relationship be-

tween the major bacterial groups, as determined by 16S

rRNA sequencing.

Archaea are procary-

otes differing from true

bacteria in cell wall and

plasma membrane che-

mistry as well as 16S rRNA

sequences.

Domain: Archaea

Studies on 16S ribosomal RNA sequences by Carl Woese

and colleagues allowed the construction of phylogenetic

trees for the procaryotes, showing their evolutionary re-

latedness. Figure 7.1 shows how the major procaryotic

groups are thought to be related, based on 16S rRNA

data. The work of Woese also revealed that one group of

procaryotes differed from all the others. As described in

Chapter 3, the Archaea are now regarded as being quite

distinct from the Bacteria (sometimes called Eubacteria). Together with the Eucarya,

these form the three domains of life (Figure 3.1). As can be seen in Table 7.1, archaea

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DOMAIN: ARCHAEA 165

Table 7.1 The three domains of life: Archaea share some features with true bacteria

and others with eucaryotes

Archaea Bacteria Eucarya

Main genetic

material

Single closed circle

of dsDNA

Single closed circle

of dsDNA

True nucleus with

multiple linear

chromosomes

Histones Present Absent Present

Gene structure Introns absent Introns absent Introns present

Plasmids Common Common Rare

Polycistronic

mRNA

Present Present Absent

Ribosomes 70S 70S 80S

Protein synthesis Not sensitive to

streptomycin,

chloramphenicol

Sensitive to

streptomycin,

chloramphenicol

Not sensitive to

streptomycin,

chloramphenicol

Initiator tRNA Methionine N-formyl

methionine

Methionine

Membrane fatty

acids

Ether-linked,

branched

Ester-linked,

straight chain

Ester-linked,

straight chain

Internal organelles Absent Absent Present

Site of energy

generation

Cytoplasmic

membrane

Cytoplasmic

membrane

Mitochondria

Cell wall Muramic acid

absent

Muramic acid

present

Muramic acid

absent

The domain is the high-

est level of taxonomic

grouping.

share some features in common with other bacteria and

some with eucaryotes. Extending nucleic acid analysis to

other genes has shown that members of the Archaea pos-

sess many genes not found in any other type of bacteria.

General features of the Archaea

Members of the Archaea show considerable diversity of both morphology and physiol-

ogy. In view of the fact that the Archaea remained unidentiﬁed as a separate group for so

many years, it should come as no surprise that they do not display any obvious morpho-

logical differences from true bacteria, and all the main cell shapes (see Chapter 2) are rep-

resented. More unusual shapes are also encountered in archaea; members of the genus

Haloarcula have ﬂattened square or triangular cells! Both Gram-positive and Gram-

negative forms of archaea are found, but neither possesses true peptidoglycan. Some

types have a so-called pseudomurein, composed of different substituted polysaccharides

and l-amino acids (Figure 7.2). Most archaea, however, have cell walls composed of

a layer of proteinaceous subunits known as an S-layer, directly associated with the cell

membrane. This difference in cell wall chemistry means that members of the Archaea

are not susceptible to antibacterial agents such as lysozyme and penicillin, whose action

is directed speciﬁcally towards peptidoglycan. Differences are also found in the make-up

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166 PROCARYOTE DIVERSITY

β 1→ 3

N-acetylglucosamine

Glu

Ala

Lys

Glu (NH

)

N-acetyltalosaminuronic acid

Figure 7.2 Pseudomurein, found in the cell walls of certain members of the Archaea,

comprises subunits of N-acetylglucosamine and N-acetyltalosaminuronic acid. The latter

replaces the N-acetylmuramic acid in true peptidoglycan (c.f. Figure 3.6). (Ac represents

the acetyl group). As with peptidoglycan, the amino acids in the peptide chain may vary,

however in pseudomurein they are always of the L-form. The components in parentheses

are not always present.

of archaean membranes, where the lipid component of membranes contains branched

isoprenes instead of fatty acids, and these are joined to glycerol by ether-linkages, rather

than the ester-linkages found in true bacteria (Figure 7.3). The diversity of archaea ex-

tends into their adopted means of nutrition and metabolism: aerobic/anaerobic and

autotrophic/heterotrophic forms are known. Many members of the Archaea are found

in extreme environments such as deep-sea thermal vents and salt ponds. Some extreme

thermophiles are able to grow at temperatures well over 100

◦

C, while psychrophilic

forms constitute a substantial proportion of the microbial population of Antarctica.

Similarly, examples are to be found of archaea that are active at extremes of acidity,

alkalinity or salinity. Initially it was felt that archaea were limited to such environments

because there they faced little competition from true bacteria or eucaryotes. Recent stud-

ies have shown however that archaea are more widespread in their distribution, making

up a signiﬁcant proportion of the bacterial biomass found in the world’s oceans, and

also being found in terrestrial and semiterrestrial niches. The reason that this lay unde-

tected for so long is that these organisms cannot as yet be cultured in the laboratory,

and their presence can only be inferred by the use of modern DNA-based analysis.

Classification of the Archaea

According to the second edition of Bergey, the Archaea are divided into two phyla,

the Euryarchaeota and Crenarchaeota. A third phylum, the Korarchaeota has been

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DOMAIN: ARCHAEA 167

Figure 7.3 Membrane lipids in Archaea and Bacteria. Compositional differences in mem-

brane lipids between (a) Bacteria and (b) Archaea. Note the ether linkages and branched

fatty acids in (b)

proposed, whose members are known only from molecular studies, while the recent

discovery of Nanoarchaeum equitans has led to the proposal of yet another archaean

phylum (see Box 7.1). Countless more species of archaea are thought to exist, which

like the Korarchaeota, have not yet been successfully cultured in the laboratory.

Box 7.1 A new phylum?

In 2002 a novel microorganism, Nanoarchaeum equitans was isolated from a hy-

drothermal vent deep below the sea off the Icelandic coast. Found at tempera-

tures around boiling point, its tiny spherical cells were attached to the surface of

another archaean, Ignicoccus sp., without which it cannot apparently be cultured.

Ribosomal RNA studies showed N. equitans to be sufficiently unlike other members

of the Archaea to justify the creation of a new archaean phylum, the Nanoar-

chaeota. Now fully sequenced, the genome of N. equitans is one of the smallest liv-

ing things to date (490kb). It appears to belong to a very deeply rooted branch of the

Archaea, leading to speculation that it may resemble the first living cells. At 0.4

µm

in diameter, N. equitans is also among the smallest known living organisms. Although

at present it is the only recognised species of the Nanarchaeota, it seems likely to

be joined by isolates reported from other locations around the world.