Part 3 - BOTANY

Bruce Baldwin
[email protected]
Office Hours:
9:10-10 AM (M,W, F)
VLSB 2011

Lectures posted on bCourses

Readings on Bio 1B site
Exams on lecture material

Readings are helpful to reinforce and contextualize the lecture material and are an important aid to learning the material presented in the
lectures and lecture notes (here).

Exam questions will be drawn from the lecture material.

 Lecture 1
Introduction & Fungi

Outline
i) Introduction - what are plants?

ii) Fungi
- important characteristics
 Aristotle Linnaeus
(384 - 322 BC) (1701-1778)

From time of Aristotle until late 1960s, most biologists subscribed to a two-kingdom view of life: plants (botany) and animals (zoology)

Animals: Organisms that move about, have sense-perceptive capacity (pleasure, pain, imagination, desire, voluntary motion)

Plants: Nutritive and reproductive capacity, but not sensory or perceptive abilities --- and don’t move about freely
 Old view of animals vs. plants
• Animals: Can move about; have sensory
and perceptive capability (literally, “soul”).
• Zoology: Science focused on animals
• Plants: Every other living thing; have
bodies, nutritive and reproductive
capabilities, but do not move about or have
sensory abilities
• Botany: Science focused on plants
Late 1960s, five-kingdom view of life became widely accepted:
Animals (mostly as before), plants (most multicellular photosynthetic organisms), fungi (non-photosynthetic, macroscopic), protista (mostly
microscopic eukaryotes), monera (all prokaryotes)
 Prokaryotes vs. eukaryotes
• Eukaryotes: Possess membrane-bound
nucleus and organelles (e.g., mitochondria,
plastids)
• Eukaryotes include protists, animals, plants,
and fungi in old 5-kingdom system
• Prokaryotes: Lack a nucleus and organelles
• Prokaryotes represent only 1 kingdom
(monera) in old 5-kingdom system

Plastid is a general term that includes chloroplasts (organelles involved directly in photosynthesis) as well as the same basic type of organelle
serving a different function in the same organism (e.g., for starch storage in root cells, where light penetration and photosynthesis do not
occur); not all eukaryotes have plastids (for example, animals and fungi lack them).
 Prokaryotes:

2 of 3 major clades (“domains”) of life

(archaea & bacteria)

Archaea may be more closely related, in

part, to eukaryotes than to bacteria

Molecular biology revealed that prokaryotes are vastly more diverse than previously thought (most cannot be cultured)

Prokaryotes are 1st evident from stromatolites ~3.5 billion years ago, well before the origin of eukaryotes (~2 billion years ago)

As we will see later, some key components of eukaryotic cells (including genomic components) are from bacteria, so relationships shown
above are simplistic

Evolutionary relationships among prokaryotes and eukaryotes have been studied using DNA sequence data. Much of the diversity of
prokaryotes has been discovered by DNA data, as well (often from environmental samples rather than from isolated organisms).
 Extremophiles
• Literally, “lovers of extreme conditions”;
many archaea. These include:
• Halophiles: In highly saline environments
(e.g., inland seas or lakes)
• Thermophiles: In very hot environments
(e.g., hydrothermic or volcanic vents)
• Methanogens: Live in anaerobic guts, & also
include true extremophiles
• Highly valuable for molecular biology,
including resolution of the tree-of-life

Extreme halophiles include bacteria and archaea, in environments toxic to the vast majority of eukaryotes.

The most extreme thermophiles are archaea, which include many that can survive in truly boiling conditions. True bacteria of hot springs, for
example, are found under less extreme thermal conditions (not truly boiling).

Methanogens are represented here as a clade of archaea of unique metabolism (producing methane as waste) that occur under various
anaerobic (oxygen-free) conditions, as do many bacteria and some eukaryotes (e.g., as gut microbes), but some methanogens are good
examples of thermophiles and other true extremophiles (e.g., those living under kilometers of ice in Greenland).
 Archaea “extremophiles”

Left:
Some Would Call It Hell; Archaea Call It Home. Masses of heat- and acid-loving archaea form an orange mat inside a volcanic vent on the
island of Kyushu, Japan. Sulfurous residue is visible at the edges of the archaean mat.

Center
Deep-sea hydrothermal vents include a diversity of chemoautotrophic (see slide 11) archaea that form the base of the food chain, supporting
organisms such as giant tube worms, shown here.

Right:
Extreme Halophiles. Commercial seawater evaporating ponds, such as these in San Francisco Bay, are attractive homes for salt-loving
archaea.
 Bacteria

-Highly diverse group, representing every major mode of

nutrition and metabolism
-Some (cyanobacteria) capable of photosynthesis, unlike all
known archaea; led to O2-rich atmosphere 1.8 billion years ago
(also critical for nitrogen fixation, along with other bacteria)

Bacteria play other critical ecological roles. For example, some are decomposers that release elements trapped in bodies or waste products
of other organisms to the environment, thereby serving as recyclers; others are mutualists (e.g., in human gut, where they are important for
digestion and receive nourishment from food ingestion).
Bacteria also include important pathogens (responsible for a wide diversity of diseases of plants and animals).

Adaptations of bacteria were co-opted in eukaryotes (more on that soon)

 Diversity of Modes of Living

1) Autotrophs: Generate food from inorganic carbon

(e.g., carbon dioxide)
a) photo-autotroph b) chemo-autotroph

2) Heterotrophs: Feed on organic substances (other

organisms or their products)

Photo-autotrophs capture energy from light; they capture carbon from the atmosphere, as CO2.

Chemo-autotrophs capture energy from oxidizing inorganic substances, such as hydrogen sulfide, ammonia, and ferrous ions; they capture
carbon as CO2.
The modern three domain system of classification (two prokaryotic & one eukaryotic) highlights the ancient divergence within prokaryotes,
which pre-dates the origin of eukaryotes
Recognition of only one eukaryotic domain is not because eukaryotes are less diverse than previously thought; instead, their diversity is vast
and much richer than earlier thought, with supergroups that do not correspond well with the four in the 5-kingdom system
 The Tree of Life
(www.tolweb.org)

The fungi, animals, and land plants are just minor twigs in the overall tree of life, as shown here.

See the tree-of-life website for more material on many of the prokaryotic and eukaryotic lineages that we will not have time to cover (& on
those that we are covering)
 Viruses

Bacteria Archaea Eukarya

Viruses

???

Viruses have been left out of the 3-domain classification and often are treated as non-living, because they are inert in isolation of the living
cells of organisms, and their relationships to living things are poorly known.

Evolutionary relationships of viruses are difficult to resolve because of their very small genomes and rapid evolutionary rates (that is, the
small amount of phylogenetic signal that can be contained within such short stretches of DNA or RNA is rapidly swamped out by new
mutations).
 What is covered
in the “Plants”
section of Bio 1B:

Fungi
“Algae”
Land Plants

“Plants” (as originally conceived) are extremely polyphyletic, as are the so-called “algae”. The term “algae” is generally used to refer to all of
the disparate assemblages of photosynthetic organisms except for the (monophyletic) land plants.

Fungi, on the other hand, do constitute a clade, with some traditionally included groups removed, such as the slime molds, which are no more
closely related to fungi than to animals.
 Fungi distantly related
to land plants (independently Fungi
evolved multicellularity)

Fungi, although traditionally placed in the field of botany, are in fact much more closely related to animals than to land plants or any groups of
“algae.” This is seen in the posterior flagellum shared by animals and fungi (that is, among those members of both groups that have flagella).
In contrast, flagella of land plants (and “algae”) are anterior.
 Animals

Fungi
Fungi more closely related to ~1 billion
animals than to any photosynthetic years ago
clades

Fungi and animals shared a common ancestor ~ 1 billion years ago; much more recently than either shared a common ancestor with land
plants.

Fungi and plants are each more closely related to unicellular groups than to each other; the multicellular body evolved independently in fungi,
plants, and animals.
 Characteristics of Fungi

Most of our familiarity with fungi (especially macro-fungi) is from their reproductive structures; most of the fungal body is hidden from view and
can be immense by comparison with the reproductive structures (often called “fruiting bodies”, even though technically fungi do not produce
fruit, which is a unique innovation of flowering plants).
 Fungi: Characteristics
• Eukaryotes (have nuclei, mitochondria)
• Bodies are non-motile
• Multicellular fungi are filamentous (hyphae,
making up mycelium)
• Absorptive mode of nutrition; heterotrophic
• Cell walls present, contain chitin (not cellulose)
• Store carbon as glycogen (not starch)
• Life cycle includes spores
• Unicellular & multicellular

High surface-to-volume ratio promotes absorptive heterotrophy; also makes fungi more vulnerable to desiccation (therefore most common in
moist environments)

Fungi include a huge diversity of decomposers, which derive nourishment from dead or decaying matter; fungi that are decomposers
historically have been called saprophytes (“putrid plant”); fungi include the most important decomposers among eukaryotes --> recyclers of
elements needed by living things (more on their critical role later)

Many fungi are parasites (gain nutrients from living hosts, to the detriment of the host); and many others are mutualists (having an intimate
association with another organism, to the benefit of both --- examples later)
 Hyphae: tubular filaments of high surface area/volume ratio
(enhances absorption)

Hyphae are often broken into cell-like compartments by partitions called septa. These electron micrographs show that septa are broken by
pores. As a result, the cytoplasm of different compartments is continuous. The hyphae from an individual make up a feeding body called a
mycelium. Hyphae can grow and respond quickly in response to food availability. During sexual reproduction, hyphae form fruiting bodies.
Frequently, these fruiting bodies erupt from the ground or substrate, allowing spores to be dispersed by wind. Production of fruiting bodies
can be stimulated by environmental cues, such as a change in the availability of nutrients.

Fungi can concentrate resources in production of a fruiting body in just a few hours; the common meadow mushroom can release a billion
spores from a single fruiting body (trillions can be released from some fungal fruiting bodies).