13.E: Diversity of Microbes, Fungi, and Protists (Exercises) - Biology

13.E: Diversity of Microbes, Fungi, and Protists (Exercises) - Biology

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13.E: Diversity of Microbes, Fungi, and Protists (Exercises)

Microbes known as protists are understudied, but their impact on ecosystems could be huge

Among the large cast of microbiome players, bacteria have long been hogging the spotlight. But the single-celled organisms known as protists are finally getting the starring role they deserve.

A group of scientists who study the interactions between plants and microbes have released a new study detailing the dynamic relationships between soil-dwelling protists and developing plants, demonstrating that soil protists respond to plant signals much like bacteria do.

An enormous variety and diversity of microbes live in soil, and studying how these organisms interact with each other and with plant roots is a hot topic in biology, as it has applications for agriculture, land stewardship, and climate change resilience technologies.

"Protists represent a new frontier in the study of soil microbial ecology," said lead author Javier A. Ceja Navarro, a research scientist at Lawrence Berkeley National Laboratory (Berkeley Lab). "Here we show that this group of organisms really must be included in microbial studies aiming to understand how microbes interact with plants."

Protists are not a distinct lineage of organisms, but rather a category assigned to any single-celled eukaryotic organism (an organism whose cells contain a nucleus) that is not a plant, fungi, or animal. This diverse group of 200,000+ species (new ones are being discovered continuously) includes amoebas, diatoms, dinoflagellates, slime molds, and even various parasites -- such as the malaria-causing Plasmodium and the eponymous Giardia-causing genus of protozoans.

Protists are found across the planet in a variety of ecosystems. Some species, like certain marine plankton protists and human disease-causing protists have been studied closely. Yet for the majority of species, scientists are just beginning to scratch the surface of what the organism does and how they respond to the environment. Such is the case for soil protists.

According to Navarro, protists are known to control soil microbial dynamics and nutrient cycling by feeding on other microbes. Although there is a good body of knowledge about their interactions with other members of the soil microbiome, little is known about how protists respond to changes in their environment.

"Even though protists are important and their relevance has been known for decades, our study is the first one showing an association of protists with plants in a large-scale field experiment," noted project leader Mary Firestone, a faculty scientist in Berkeley Lab's Earth and Environmental Sciences Area and a professor at UC Berkeley. The project was a collaboration among scientists from Berkeley Lab, UC Berkeley, Lawrence Livermore National Laboratory (LLNL), the Noble Research Institute, and the University of Oklahoma.

The team grew switchgrass -- a crop proposed for large-scale biofuel production -- from seedlings at two large-scale field sites, and took samples of the soil surrounding the roots of plants at different stages of growth. They used next-generation genome sequencing to identify the types of protists present in each sample and the abundance of each species.

"As plants grow, the cells in their roots release metabolites that send signals out to the surrounding soil environment," added Jennifer Pett-Ridge, a senior staff scientist from LLNL. "We saw that protists communities shift and change in response to the plant's effects -- in a manner that is similar to what we've observed for bacterial communities."

"Future studies focusing on understanding the mechanisms of plant establishment in soil will need to consider protists as a key part of the plant microbiome," added Navarro, who is part of Berkeley Lab's Biosciences Area. "Ignoring protists in terrestrial ecological studies will result in a big knowledge gap that will make our understanding of the environmental microbiome incomplete."

13.E: Diversity of Microbes, Fungi, and Protists (Exercises) - Biology

Featured Organisms and Locality (p. 127):
Spider crabs and seaslugs of Sagami Bay, Japan

I. Classification
a) The Five Kingdoms System of Whittaker
(Note: While still wildly popular with textbook
authors, and advocated by some biologists such
as Lynn Margulis, this is really a breakdown of
life by functional and nutritional categories.
An alternative view, proposed by Carl Woese,
is gaining in popularity because it more accurately
reflects the actual historical relationships of life forms:
This view is called the Three Domains of Life System -
Bacteria, Archaea, Eukarya)
terms: kingdoms, Plantae = vascular plants, Fungi,
Animalia = Metazoa or multicellular animals,
Protista = arbitrary grouping of organisms whose
cells have a nucleus (i.e., eukaryotes) but excluding
multicellular plants, fungi, and animals,
not to be confused with prokaryotes (or Monera)
= arbitrary grouping of all organisms except those
whose cells have a nucleus (eukaryotes)
Note: Most current taxonomists try to only formally name
groupings that are clearly monophyletic. In contrast, many
traditional names, including "prokaryotes," "protists,"
"invertebrates," and "agnathans" are paraphyletic groupings
defined by features they lack, such as a cell nucleus, multicellularity,
a backbone, or a jaw, respectively. Another way to try to carve
up biotic diversity into monophyletic groups is to increase the
number of kingdoms, for example with the 10 Kingdom approach.

RQ 6.1: Contrast how life is classified in the Five Kingdoms System
vs. the Three Domains System. Which kingdom is broken up
into separate domains and which kingdoms are combined into
a single domain?

b) The Names of Organisms
terms: phylum, class, order, family, genus, species
(these are "ranks" used in a "ranked" hierarchical
taxonomy - it is also possible to classify all of life
without them in an "unranked" hierarchical taxonomy)
taxon (plural is taxa), taxonomist, systematist,
taxonomy (= classifying life), systematics (taxonomy
+ evolutionary history of life, includes taxonomy),
scientific binomial name, e.g., Glyptocephalus zachirus
abbreviated G. zachirus. Note genus is capitalized,
species is not, scientific name is always in italics or
underlined, common name is not: West Coast flatfish
but note this common name refers to multiple species
of other "flatfish" species, and even if one refers to
a more specific common name, such as "Rex sole,"
this has problems because it is known by different
common names elsewhere. See Fig. 6.4 for more
examples of a common name varing with location.
The definition of a species is also problematic. The
most popular (but not necessarily the best) is the
biological species concept, proposed by Ernst Mayr.
This species concept generally works best for
living populations whose members engage in sexual
interbreeding, and less well for fossils or "species"
that reproduce without sexual cross-fertilization.

RQ 6.2: Why is a scientific binomial name sometimes more
precise than a common name?

II. Bacteria (includes Cyanobacteria)
terms (Box 6.1, p. 134): meter (m), millimeter (mm),
micrometer (µm), nanometer (nm) (1 m = 1000 mm,
1 mm = 1000 µm, 1 µm = 1000 nm)
terms (p. 135): anaerobic or aerobic photosynthesis

RQ 6.3: How big are typical "microbial" organisms?

a) Cyanobacteria - Ancient Transformers of the Earth
terms: formerly known as "blue-green algae" but
cyanobacteria are bacteria that engage in aerobic
photosynthesis, stromatolites are the fossilized
slime secreted by ancient cyanobacteria, as still
being produced in some salty bays such as
Sharks Bay, Australia

RQ 6.4: Based on abundant ancient stromatolite fossils, it
is apparent that cyanobacteria had an extremely important
role in transforming the Earth as a habitat for life billions
of years ago. What did they do that was so important?

b) (Other) Bacteria - Essential to Closure of Ecological Cycles
Note: Bacteria reproduce very rapidly so can quickly exhaust
available O2 dissolved in seawater (see Chapter 3 notes).
terms: refractory materials (are indigestable to all but
bacteria, who make them available to other organisms)

c) Archaea (no section in the book but there should be we
are just beginning to characterize the diverse organisms
included in this domain of life - including some that live
at near boiling temperatures in deep-sea - hot vents)

RQ 6.5: Give three examples of where one could find a
member of the most recently recognized domain of life,

III. Protists (i.e., members of Eukarya that are not plants,
fungi, or animals)

RQ 6.6: What problem do auxospores help solve for diatoms?

2) Dinoflagellates are distinguished by cellulose, flagella,
and diversity
terms: armored (with cellulose plates) vs. unarmored, flagella,
bioluminescence, red tides, toxic red tides, paralytic shellfish poisoning,
ciguatera (important concern in Caribbean and elsewhere in tropics),
zooxanthellae (symbiotic cells in corals and anemones), coral reef

RQ 6.7: How do zooxanthellae and their anemone, coral (or other animal)
hosts mutually benefit from their association?

3) Microflagellates are tiny, diverse, abundant, and dominant?
terms: microflagellates (includes coccolithophores with coccolith
plates, also green flagellates such as Chlamydomonas)

RQ 6.8: If microflagellates are sometimes even more abundant than
diatoms and dinoflagellates, why was this not generally appreciated
until recently?

b) Nonphotosynthetic Protists
terms: forams, ciliates, cilia, radiolarians

a) Seaweeds, Kelp, and Other Algae
terms: gametophyte, sporophyte, gametes, meiosis, spores, zygote

RQ 6.9: Why are brown algae brown? What are some ways they are

2) Green algae resemble land plants in several ways
terms: chlorophyll a, starch, chlorophytes (green algae + land plants)

RQ 6.10: What main evidence suggests land (vascular) plants share a
common ancestor with green algae, relative to other algae?

b) Land Plants in the Sea
terms: vascular tissue, roots

RQ 6.11: What is at least one advantage that land plants have, relative
to algae, for life in the sea? Why, then, are land plants not more
common in the sea?

1) Grasses and grasslike plants are prominent in salt marshes
and submerged meadows
terms: salt marsh plants (Spartina), eelgrass, rhizomes, sea grasses

Chapter Summary

Prokaryotes existed for billions of years before plants and animals appeared. Microbial mats are thought to represent the earliest forms of life on Earth, and there is fossil evidence, called stromatolites, of their presence about 3.5 billion years ago. During the first 2 billion years, the atmosphere was anoxic and only anaerobic organisms were able to live. Cyanobacteria began the oxygenation of the atmosphere. The increase in oxygen concentration allowed the evolution of other life forms.

Prokaryotes (domains Archaea and Bacteria) are single-celled organisms lacking a nucleus. They have a single piece of circular DNA in the nucleoid area of the cell. Most prokaryotes have cell wall outside the plasma membrane. Bacteria and Archaea differ in the compositions of their cell membranes and the characteristics of their cell walls.

Bacterial cell walls contain peptidoglycan. Archaean cell walls do not have peptidoglycan. Bacteria can be divided into two major groups: Gram-positive and Gram-negative. Gram-positive organisms have a thick cell wall. Gram-negative organisms have a thin cell wall and an outer membrane. Prokaryotes use diverse sources of energy to assemble macromolecules from smaller molecules. Phototrophs obtain their energy from sunlight, whereas chemotrophs obtain it from chemical compounds.

Infectious diseases caused by bacteria remain among the leading causes of death worldwide. The excessive use of antibiotics to control bacterial infections has resulted in resistant forms of bacteria being selected. Foodborne diseases result from the consumption of contaminated food, pathogenic bacteria, viruses, or parasites that contaminate food. Prokaryotes are used in human food products. Microbial bioremediation is the use of microbial metabolism to remove pollutants. The human body contains a huge community of prokaryotes, many of which provide beneficial services such as the development and maintenance of the immune system, nutrition, and protection from pathogens.

13.2 Eukaryotic Origins

The first eukaryotes evolved from ancestral prokaryotes by a process that involved membrane proliferation, the loss of a cell wall, the evolution of a cytoskeleton, and the acquisition and evolution of organelles. Nuclear eukaryotic genes appear to have had an origin in the Archaea, whereas the energy machinery of eukaryotic cells appears to be bacterial in origin. The mitochondria and plastids originated from endosymbiotic events when ancestral cells engulfed an aerobic bacterium (in the case of mitochondria) and a photosynthetic bacterium (in the case of chloroplasts). The evolution of mitochondria likely preceded the evolution of chloroplasts. There is evidence of secondary endosymbiotic events in which plastids appear to be the result of endosymbiosis after a previous endosymbiotic event.

13.3 Protists

Protists are extremely diverse in terms of biological and ecological characteristics due in large part to the fact that they are an artificial assemblage of phylogenetically unrelated groups. Protists display highly varied cell structures, several types of reproductive strategies, virtually every possible type of nutrition, and varied habitats. Most single-celled protists are motile, but these organisms use diverse structures for transportation.

The process of classifying protists into meaningful groups is ongoing, but genetic data in the past 20 years have clarified many relationships that were previously unclear or mistaken. The majority view at present is to order all eukaryotes into six supergroups. The goal of this classification scheme is to create clusters of species that all are derived from a common ancestor.

13.4 Fungi

Fungi are eukaryotic organisms that appeared on land over 450 million years ago. They are heterotrophs and contain neither photosynthetic pigments such as chlorophylls nor organelles such as chloroplasts. Because they feed on decaying and dead matter, they are saprobes. Fungi are important decomposers and release essential elements into the environment. External enzymes digest nutrients that are absorbed by the body of the fungus called a thallus. A thick cell wall made of chitin surrounds the cell. Fungi can be unicellular as yeasts or develop a network of filaments called a mycelium, often described as mold. Most species multiply by asexual and sexual reproductive cycles, and display an alternation of generations.

The divisions of fungi are the Chytridiomycota, Zygomycota, Ascomycota, Basidiomycota, and Glomeromycota.

Fungi establish parasitic relationships with plants and animals. Fungal diseases can decimate crops and spoil food during storage. Compounds produced by fungi can be toxic to humans and other animals. Mycoses are infections caused by fungi. Superficial mycoses affect the skin, whereas systemic mycoses spread through the body. Fungal infections are difficult to cure.

Fungi have colonized all environments on Earth but are most often found in cool, dark, moist places with a supply of decaying material. Fungi are important decomposers because they are saprobes. Many successful mutualistic relationships involve a fungus and another organism. They establish complex mycorrhizal associations with the roots of plants. Lichens are a symbiotic relationship between a fungus and a photosynthetic organism, usually an alga or cyanobacterium.

Fungi are important to everyday human life. Fungi are important decomposers in most ecosystems. Mycorrhizal fungi are essential for the growth of most plants. Fungi, as food, play a role in human nutrition in the form of mushrooms and as agents of fermentation in the production of bread, cheeses, alcoholic beverages, and numerous other food preparations. Secondary metabolites of fungi are used in medicine as antibiotics and anticoagulants. Fungi are used in research as model organisms for the study of eukaryotic genetics and metabolism.

13.E: Diversity of Microbes, Fungi, and Protists (Exercises) - Biology

Living things are very diverse, from simple, single-celled bacteria to complex, multicellular organisms. (credit “ringworm”: modification of work by Dr. Lucille K. Georg, CDC credit “Trypanosomes”: modification of work by Dr. Myron G. Schultz, CDC credit “tree mold”: modification of work by Janice Haney Carr, Robert Simmons, CDC credit “coral fungus”: modification of work by Cory Zanker credit “bacterium”: modification of work by Dr. David Cox, CDC credit “cup fungus”: modification of work by “icelight”/Flickr credit “MRSA”: modification of work by Janice Haney Carr, CDC credit “moldy grapefruit”: modification of work by Joseph Smilanick)

Until the late twentieth century, scientists most commonly grouped living things into five kingdoms—animals, plants, fungi, protists, and bacteria—based on several criteria, such as absence or presence of a nucleus and other membrane-bound organelles, absence or presence of cell walls, multicellularity, and mode of nutrition. In the late twentieth century, the pioneering work of Carl Woese and others compared nucleotide sequences of small-subunit ribosomal RNA (SSU rRNA), which resulted in a dramatically different way to group organisms on Earth. Based on differences in the structure of cell membranes and in rRNA, Woese and his colleagues proposed that all life on Earth evolved along three lineages, called domains. The three domains are called Bacteria, Archaea, and Eukarya.

Two of the three domains—Bacteria and Archaea—are prokaryotic, meaning that they lack both a nucleus and true membrane-bound organelles. However, they are now considered, on the basis of membrane structure and rRNA, to be as different from each other as they are from the third domain, the Eukarya. Prokaryotes were the first inhabitants on Earth, perhaps appearing approximately 3.9 billion years ago. Today they are ubiquitous—inhabiting the harshest environments on the planet, from boiling hot springs to permanently frozen environments in Antarctica, as well as more benign environments such as compost heaps, soils, ocean waters, and the guts of animals (including humans). The Eukarya include the familiar kingdoms of animals, plants, and fungi. They also include a diverse group of kingdoms formerly grouped together as protists.

Watch the video: Protists and Fungi (July 2022).


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