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Microbial Diversity: Understanding the Complexity of Microorganisms in ESGN 586, Fall 2007, Study notes of Engineering

This document from esgn 586, fall 2007, explores the complexity and diversity of microorganisms, discussing their energy sources, responses to environments, gene regulation, growth, and survival strategies. It also covers the historical focus on macroorganisms and the importance of microbial communities, communication between organisms, and the challenges in taxonomy and phylogenetic relationships.

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ESGN 586, Fall 2007, John R. Spear Page 1
ESGN586 Lecture 2 Fall ’07
Readings: Brock, Chapters 1-5
Chapter 1 - 5 Key Points:
What is a microbe?
Webster’s: A microorganism
Brock: A microscopic organism consisting of a single cell or cell cluster, also including
the viruses, which are not cellular.
FYI: A virus is a genetic element, containing either DNA or RNA that replicates in cells,
but is characterized by having an extracellular state. It is a non-living particle.
Why do we care?
Responsible for SO many things…
Health & The Pathogens—but remember there are only 7 divisions of Bacteria
that have pathogens, and there are no archaeal pathogens.
Refrigeration
Ex: Hurricanes Katrina and Rita
Packaging
How we touch, what we touch
How we are social, or not, with each other. Handle a baby?
Cleanliness—of everything:
What is body odor?
Sleeping Bags
Clothes
Hands
Teeth
Other orifices
How we taste, How we smell, How we hear, How we feel
Microbes are intimately involved in all of these senses.
Environmental Microbiology—Here We Go:
1. “Microbial diversity” reflects the different ways in which microbial organisms:
--Obtain energy and nutrients
--Respond to the environment and other organisms
--Regulate genes and metabolism
--Grow and divide
--Survive adverse conditions
2. Microbial organisms have the same needs as macrobes— Indeed, most of biological
diversity is microbial in nature; historical focus aside, most eucaryotes are microbial.
3. Note the differing biological strategies manifest by macrobial and microbial phenotypes:
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Download Microbial Diversity: Understanding the Complexity of Microorganisms in ESGN 586, Fall 2007 and more Study notes Engineering in PDF only on Docsity!

ESGN586 Lecture 2 Fall ’

Readings: Brock , Chapters 1- 5

Chapter 1 - 5 Key Points:

What is a microbe?

Webster’s : A microorganism

Brock: A microscopic organism consisting of a single cell or cell cluster, also including

the viruses, which are not cellular.

FYI: A virus is a genetic element, containing either DNA or RNA that replicates in cells,

but is characterized by having an extracellular state. It is a non-living particle.

Why do we care?

Responsible for SO many things…

Health & The Pathogens—but remember there are only 7 divisions of Bacteria

that have pathogens, and there are no archaeal pathogens.

Refrigeration

Ex: Hurricanes Katrina and Rita

Packaging

How we touch, what we touch

How we are social, or not, with each other. Handle a baby?

Cleanliness—of everything:

What is body odor?

Sleeping Bags

Clothes

Hands

Teeth

Other orifices

How we taste, How we smell, How we hear, How we feel

Microbes are intimately involved in all of these senses.

Environmental Microbiology—Here We Go:

  1. “Microbial diversity” reflects the different ways in which microbial organisms:

--Obtain energy and nutrients

--Respond to the environment and other organisms

--Regulate genes and metabolism

--Grow and divide

--Survive adverse conditions

  1. Microbial organisms have the same needs as macrobes— Indeed, most of biological

diversity is microbial in nature; historical focus aside, most eucaryotes are microbial.

  1. Note the differing biological strategies manifest by macrobial and microbial phenotypes:

a. Large creatures are comprised of different cell-types, differentiated from a

common germ-line that collectively and interdependently form the functioning

community (the macroorganism).

b. The constituents of communities of microbial organisms are selected upon by the

local chemistry and physical properties, and collectively and interdependently

form the functioning community (e.g. a "biofilm").

In the macro case the organism carries the information for the required cell-types; in the micro

case the environment selects for the suite of required cell-types. Different strategies of life-stuff.

  1. Traditional large-organism biology has focused on organism shape: general biology texts

usually paint “prokaryotes” as simple cells:

rods (bacilli, s. bacillus; note contrast with Bacillus , a “genus” name)

cocci (s. coccus)

“spirals” (misnomer—really helices)

“vibrios” (partial helices)

  1. But many other forms occur—e.g.:

--Long filaments (> 100 μm = 0.1 mm common, e.g. Beggiatoa , Thioploca )

--Branched filaments (e.g. Streptomyces )

--Star-shaped ( Stella )

--Amorphous-shaped (e.g. Sulfolobus )

--Flat-looking (e.g. Haloarcula )

  1. General texts often emphasize individual cells, but aggregates are the common theme

in nature:

Chains (strepto-, e.g. streptococci)

Tetrads—and higher regular clusters

Rosettes

e.g. Planctomyces

  1. Seldom do organisms in nature occur in isolation, “free-living” cell-types:

Microbes form complex “communities” (ensembles of different organisms— in contrast

to a “population,” which refers to a collection of the same type of organism)

oxymoron. (People who use that term are usually referring to a representative of the bacterial

division “Proteobacteria”)

b. Many different external structures, e.g.:

Flagella, pili, stalks and holdfasts, capsules, sheaths (sometimes with

multiple types of organisms), etc.

c. Many different internal structures, e.g.:

“Nucleoid” (bacterial nucleus), spores, “inclusions” of energy -- reserves

(e.g. sulfur, poly beta-hydroxybutyrate, glycogen), etc.

  1. Metabolic diversity - switch-hitters common, capable of markedly different

metabolisms:

a. “Chemoheterotrophs” - obtain energy and carbon from reduced organics, e.g.

Escherichia , Bacillus

b. “Chemoautotrophs” - energy from reduced inorganics (e.g. H 2

S, Beggiatoa ; Fe

Gallionella ); carbon by “fixing” CO 2

c. “Photoheterotrophs” - carbon from organics, energy from light (e.g. Rhodobacter )

d. Photoautotrophs” - carbon from CO 2

, energy from light (cyanobacteria, plants

[the chloroplast is a cyanobacterium!])

  1. Ecological diversity: Microbial character is far more robust than the macrobial form

a. Extremes of ionic strength—distilled H 2

O to NaCl-saturated brines (south SF

Bay, Dead Sea, e.g. Haloarcula )

b. Extremes of temperature—ca. −5˚C to 113˚C ( Pyrodictium ) to 121°C

c. pH -- pH < 0 to 12

d. All over the planet -- from deep-subsurface to clouds in the sky, any place there

is liquid water and an energy gradient

  1. Behavioral diversity:

a. Motility and taxis -- chemotaxis, phototaxis, magnetotaxis

b. Developmental processes -- sporulation ( Bacillus ),

developmental growth phases

( Caulobacter ), metabolic differentiation ( Anabaena “heterocysts” for N 2

fixation)

c. Communication -- between like cells (“Quorum-sensing”) and unlike

(symbioses, antibiotics)

  1. Evolutionary diversity -- the basis of it all!

a. For all the differences between different organisms, the underlying

biochemistries are pretty much the same:

DNA/RNA-based information transfer

ATP / NAD(P) chemiosmosis-based energy

same (general) pathways for carbon-metabolism and biosynthesis

b. All life (on Earth) is related ancestrally.

A Pretty Amazing Property of Life!

Describing Microbial Diversity: the Changing Paradigm

  1. Traditional taxonomy (classification) of microbes, both “prokaryote” and eucaryote, is in a

mess--but we are stuck with it for traditional reasons.

a. A “natural” taxonomy would be based on evolutionary relatedness:

Thus, organisms in same “genus” (a collection of “species”) would have similar

properties in a fundamental sense.

b. A natural taxonomy of m a crobes has long been possible:

Large organisms have many easily distinguished features, e.g. body-

plans and developmental processes, that can be used to describe hierarchies of

relatedness.

c. Microbes usually have few distinguishing properties that relate them, so a hierarchical

taxonomy mainly has not been possible.

  1. Recent advances in molecular phylogeny have changed the picture a lot: we now have a

relatively non-subjective, quantitative way to view “biodiversity”, in the context of phylogenetic

maps - evolutionary trees.

a. Slowly evolving molecules (e.g. rRNA) used for large-scale structure; “fast-clock”

molecules for fine-structure.

  1. e.g. if want to study an uncultivatable symbiont, identify a cultivatable free-living form.

E.g. the Riftia symbiont?

c. Phylogenetic perspective even on macrobes is quite recent -- say a century, and on microbes

only ca. 20 years. Many microbiology texts don’t have it and many (even most) general

biology texts get it wrong!

A Bit on the Evolution of Evolutionary Thought

  1. Prior to the late 19th century, the concept of evolution was on the “evolutionary ladder”:

Man

Apes

Marsupials

Reptiles

Amphibia

Fish

Invertebrates

Plants

Fungi

Leewenhoek’s “animacules”

Thus, we still deal in “higher and lower” eucaryotes (I try not to use these

terms -- they are dumb), “missing links,” and “primitive” organisms.

a. In its milieu, E. coli is as highly evolved as are we. E. coli is simple (~5× 10

bp genome), we are complex (~3× 10

bps); complexity has nothing to do with

“evolutionary advancement”.

b. Lineages evolve by diversification, "radiation", not “progression”. (!!)

c. There is no such thing as a “primitive” organism alive today. Simple, yes, but

still a finely honed product of 4 billion years under the selective hammer of

the niches that it and its progenetors have occupied.

  1. By the late 1800s the concept of “evolutionary trees” was on the

table -- e.g. Ernst Haeckel, 1866 (Note that Darwin’s “Origin of

Species” was first presented in 1858).

Note “kingdoms” of

Plants, Animals, Protists

(non-plants and animals, mostly

microbial), and

“monera” (procaryotes, in

retrospect) at base.

  1. The conceptual basis for biological diversity was pretty much stalled at the Haeckel stage for

the next century -- and still is in many/most general texts of biology. The current articulation

is as the “five kingdoms of life”, here taken from a 1969 Science lead article.

  1. Relationships among microbes, both “procaryote” and eucaryote

speculative, at best

  1. No criteria to relate organisms between “kingdoms” (even between e.g. phyla of

animals)-- a universal phylogeny was impossible

  1. Implicit timeline remained -- “procaryotes”, protists “primitive”

  2. Suggestion that eucaryotic nucleus was derived from a “procaryote”progenitor

turned out to be fundamentally incorrect (the often- cited date of 1.5 billion years ago for

the origin of eucaryotes is B.S.) -

  1. Studies in “molecular phylogeny” over the past two decades have

changed the “paradigm” significantly. (ala Thomas Kuhn -- “The

Stucture of Scientific Revolutions”

a) By comparing macromolecular sequences, can extract

evolutionary relationships -- “evolutionary distances” -- between

organisms

  1. The goal of molecular phylogeny is to relate molecules (hence in

principle organisms) quantitatively, so as to reconstruct their

evolutionary histories, e.g. as a “phylogenetic tree.”

a. There are many ways to "relate" molecules. Some subjective ways are:

e.g. immunologically (fractional gross reactivity)

e.g. DNA-DNA “heterologous hybridization” (more below)

But these are difficult (impossible) to precisely quantitate in

terms of relationships

b. The best way is by direct comparison of sequences of nucleic

acids or proteins. This provides “precise” numbers for defining

relationships between molecules -- and, ideally, organisms

  1. For “homologous” (of common ancestry) nucleic acid (or protein) sequences:

A. Consider”

--Organism A • • • A G C U G C C A G U • • •

X X X

--Organism B • • • A A C U C C C A A U • • •

↑DNA OR RNA?

Sequence A is 70% identical to Sequence B,

Fractional identity is 0.

Fractional difference is 0.3 (1-0.7)

  1. Note that the term “homology” is commonly, and incorrectly, used when “identity”

is meant. Note that gene sequences are not “##% similar”, they are “##% identical”;

protein seqs, on the other hand, can be “similar.”

  1. You cannot meaningfully compare sequences unless they are

"homologous" -- of common ancestry. Homologous sequences are

not necessarily identical; identical sequences are not necessarily

homologous (e.g. promoters, translation punctuation, etc.).

B. Do difference (1-identity) count for all pairs of organisms considered. This difference count

is a measure of the extent of evolution - evolutionary distance - separating the pairs of

organisms.

e.g. with organisms A,B,C,D and E:

C. To build relationships, construct a “difference matrix” for organisms A-E:

A B C D E

A  0.1 0.2 0.2 0.4 Fractional Difference

B 0.9  0.2 0.2 0.

C 0.8 0.8  0.1 0.

D 0.8 0.8 0.9  0.

E 0.6 0.6 0.6 0.6 

Fractional Identity

Can relate in a “tree”- like figure, a “dendrogram”

A. Doesn’t really matter so long as:

  1. “Homologous” molecule occurs in all organisms considered

a) More specifically, you need to know that the molecules are

“orthologs,” not “paralogs”

b) “Orthologs” share ancestry and retain the same function in

the different organisms

c) “Paralogs” result from an ancestral duplication, with

potentially different functions taken on subsequent to the

duplication -- produce “gene families”.

d) For instance, the α and β globins are a gene family; they have

ancient common ancestry -- the α - type and β - type globins have evolved

independently since the ancestral duplication:

α - globins are orthologs; β - globins are orthologs.

α and β globins are paralogs

e) The tree of the gene family would look like:

f) If you did not keep your orthologs and paralogs straight (sometimes a tough

call) when you build the dataset, you might get some most unexpected trees,

e.g.:

Human (α-globin)

Frog (α-globin)

Mouse (β-globin)

  1. Need a sufficient number of nucleotides (or amino acids) to be

statistically significant -- more is always better.

  1. Changes span evolutionary distance inspected -- i.e., compared

sequences must not be randomized.

Human α-globin

Mouse α-globin

Frog α-globin

Human β-globin

Mouse β-globin

Frog β-globin

  1. No lateral transfer -- the evolution of the gene must reflect the

evolution of the organisms considered.

a) Genes that are known to undergo lateral transfer are called

“xenologs.” If you are interested in metabolic genes, there is a good

chance, at least among Bacteria, that you are dealing with

genes/pathways that can move.

b) e.g. penicillinase and other commonly transferred antibiotic

resistance genes.

  1. Note the evident impact of lateral transfers throughout evolution. Much of

microbial physiological diversity (probably) is dependent on laterally transferred genes.

a. Note also that portions of genes can transfer (e.g. with two- component

systems) so that homologous blocks of sequence can show-up in functionally

unrelated genes. Formation of intralineage "gene families" also results in mixing-

up functional modules of macromolecules.

B. Considerable work done in past with protein sequences, e.g. cytochrome C,

hemoglobin.

  1. But proteins hard to get and sequence; it is now easier to isolate/sequence genes.

  2. Most protein genes are “shallow” clocks; e.g. E. coli doesn’t have

hemoglobin.

  1. Choice of molecules for comprehensive (all organisms) phylogeny -- ribosomal RNAs

(rRNAs).

A. Ribosome -- carrys out protein synthesis

Small subunit Large subunit

S L “23S” rRNA (LSU): 3000-5000nt

“16S” (SSU) rRNA: 15 00 - 2000nt “5S” rRNA - 120 nt

ca. 25 proteins ca. 30-40 proteins

B. rRNAs present in all organisms and the major organelles (mitochondria and chloroplasts).

C. Highly conserved throughout evolution; e.g., ca. 50% identity between E. coli and human

SSU rRNAs over alignable nt

  1. Sometimes see referred to as “kingdoms,” but usage in this context

is probably not a good idea -- too historically loaded.

  1. You can inject "time" into tree, but sequence change is not necessarily linear with time
  • indeed, probably it usually isn't.

C. The eucaryote nuclear line of descent is as old as the "procaryote"

lines

D. Two primary lineages of “procaryotes,” Bacteria (formerly

eubacteria) and Archaea (formerly archaebacteria -- try to avoid using term;

they aren’t bacteria)

  1. The term “procaryote” is inappropriate in the light of the relationships.
  1. Are there still more domain-level divergences to be discovered??

E. Note that lines connecting organisms to nodes are not all the same

length -- the evolutionary clock is not constant between different lineages (e.g.

Haloferax vs. Methanopyrus , Aquifex vs. Bacillus , Eucarya in general vs. any

representative of Archaea or Bacteria)

  1. Rate of evolution not necessarily the same for a particular lineage

at all stages in the evolution of the line, e.g. Agrobacterium vs.

mitochondrion

  1. Note domain-level tendencies:

Eucarya -- fast clocks

Bacteria

Archaea

Eucarya

"Time"

indicating: The root of the Big Tree is (presumably deep) on the

bacterial line of descent.

B. This means also that Eucarya and Archaea shared common history after

divergence from Bacteria

  1. This explains many similarities between archaeal and eucaryal

machineries.

e.g. similar transcription machineries; Archaea and Eucarya use TATA-binding

proteins whereas Bacteria use σ factors for specification of transcription initiation.

e.g. Archaeal and eucaryal DNA-synthetic machineries far more like one another

than either is to bacteria (for good overview, Bernander, “Archaea and the cell

cycle,” Molec. Microbiol. 29:955-961[1998])

  1. Note that the Big Tree shown is a limited set of specific organisms: ca. 30,000 16S (SSU)

sequences are now available.

A. One database of rRNA sequences -- Ribosomal Database Project:

http://www.cme.msu.edu/RDP/

You can download trees, carry out functions, get programs, etc.

  1. A few domain-level trees for reference:
  2. Bacteria (next page)

A. This is a diagrammatic tree. The wedge indicates multiple

lineages; the depth of the wedge the depth of the deepest branches. These

groups represent the phylogenetic “divisions” of bacteria (referred to as

“kingdoms” by Woese). There is no formal taxonomic status of these divisions at

this time:

B. ca. 35 divisions identified so far, only ca. 25 containing cultivated representatives

(black wedges; open wedges have no cultivated representatives).