Protists and fungi

Eukaryotic cells evolved about 1.8 billion years ago, and for most of the time since then eukaryotes were single cells. Their descendants include the familiar multicellular kingdoms of plants, animals and fungi, but most of the evolutionary diversity of eukaryotes lies elsewhere, among the mostly microscopic organisms traditionally called protists. This lesson surveys protists and fungi: how eukaryotes arose, how they are now classified, and why these organisms matter for ecosystems, food, disease and the history of life.

How eukaryotes arose

BIOL-107 introduced the endosymbiotic theory: mitochondria and chloroplasts descend from bacteria that were engulfed by an ancestral cell and lived inside it. The evidence is strong. Both organelles have their own circular DNA, resembling bacterial chromosomes; their own ribosomes, which are bacterial in size and antibiotic sensitivity; double membranes; and they divide by a process similar to bacterial fission. Their DNA sequences place mitochondria among the alphaproteobacteria and chloroplasts among the cyanobacteria.

Genome studies now suggest the host cell was an archaeon related to the Asgard archaea, first described in 2015 from sediments near a hydrothermal vent field between Greenland and Norway called Loki's Castle. The merger with the mitochondrial ancestor supplied the extra energy that may have allowed larger, more complex cells, with nuclei, internal membranes and big genomes, to evolve. All known eukaryotes have, or once had, mitochondria.

Chloroplasts arose from a cyanobacterium in an ancestor of red algae, green algae and land plants; this is called primary endosymbiosis. Several other lineages acquired chloroplasts secondhand, by engulfing a eukaryotic alga and keeping its chloroplast. This secondary endosymbiosis explains why some protists have chloroplasts surrounded by three or four membranes, and why photosynthesis is scattered across distantly related branches of the eukaryotic tree.

Why protists are not a natural group

The word protist is a convenient label for any eukaryote that is not a plant, an animal or a fungus. Older textbooks placed them all in a kingdom Protista, but molecular phylogenies show that protists do not form a clade. Some are more closely related to animals than to other protists; brown algae such as kelp are more closely related to diatoms and to the water mould that caused the Irish potato famine than to green plants. Modern classification places eukaryotes in several large groups, often called supergroups, though their exact number and boundaries are still being revised.

Protists in ecosystems

Photosynthetic protists, mainly diatoms, dinoflagellates and coccolithophores, are a large part of the phytoplankton that drift in sunlit waters. Together with cyanobacteria, marine phytoplankton carry out roughly half of all photosynthesis on Earth and form the base of ocean food webs that support fish, seabirds and whales. When they die, some sink and carry carbon to the deep ocean; over millions of years, the shells of coccolithophores and foraminiferans have built chalk and limestone deposits, including the white cliffs of Dover.

Diatoms have a peculiar consequence of their glass walls. Each cell lives inside two overlapping halves, like a pillbox. When it divides, each daughter keeps one half and builds a new, smaller half inside it, so the average size of the population shrinks with each generation. When cells reach a minimum size, they restore their size through sexual reproduction.

import numpy as np
# Diatom size reduction: each daughter keeps one half-shell and builds a smaller one inside it
cells = np.array([60.0])                # starting cell length in micrometres
shrink = 1.2                            # the new half is about 1.2 micrometres smaller
for gen in range(1, 13):
    larger = cells                     # daughter keeping the larger half stays the same size
    smaller = cells - shrink           # daughter keeping the smaller half shrinks
    cells = np.concatenate([larger, smaller])
    if gen % 3 == 0:
        print(f"generation {gen:2d}: {len(cells):5d} cells, mean length {cells.mean():.1f}, smallest {cells.min():.1f}")

generation  3:     8 cells, mean length 58.2, smallest 56.4
generation  6:    64 cells, mean length 56.4, smallest 52.8
generation  9:   512 cells, mean length 54.6, smallest 49.2
generation 12:  4096 cells, mean length 52.8, smallest 45.6

Some protists cause harmful algal blooms. Certain dinoflagellates produce toxins that accumulate in shellfish such as mussels and clams, causing paralytic shellfish poisoning in people who eat them. Government agencies monitor shellfish beds and close harvesting when toxins rise.

In Canada, the Canadian Food Inspection Agency and Fisheries and Oceans Canada run the Canadian Shellfish Sanitation Program, testing shellfish for marine biotoxins on both coasts and closing areas such as parts of the Bay of Fundy and the British Columbia coast when levels are unsafe.

Protists and disease

A few protists are among humanity's most important pathogens. Plasmodium, spread by Anopheles mosquitoes, causes malaria, which the World Health Organization estimates caused around 600,000 deaths in 2023, mostly young children in sub-Saharan Africa. Plasmodium has a complex life cycle that alternates between mosquito and human hosts; in human red blood cells it multiplies in synchronized cycles, which cause the periodic fevers typical of the disease.

# Plasmodium blood-stage multiplication (illustrative values for P. falciparum)
merozoites_per_cell = 16      # new parasites released from each infected red blood cell
survival = 0.5                # fraction that successfully invade new red blood cells
cycle_hours = 48
parasites = 1e5               # parasites first released from the liver into the blood
red_cells = 2.5e13            # approximate red blood cells in an adult
for cycle in range(1, 9):
    parasites *= merozoites_per_cell * survival
    pct = 100 * parasites / red_cells
    print(f"day {cycle * cycle_hours // 24:2d}: {parasites:.2e} parasites ({pct:.3f}% of red cells infected)")

day  2: 8.00e+05 parasites (0.000% of red cells infected)
day  4: 6.40e+06 parasites (0.000% of red cells infected)
day  6: 5.12e+07 parasites (0.000% of red cells infected)
day  8: 4.10e+08 parasites (0.002% of red cells infected)
day 10: 3.28e+09 parasites (0.013% of red cells infected)
day 12: 2.62e+10 parasites (0.105% of red cells infected)
day 14: 2.10e+11 parasites (0.839% of red cells infected)
day 16: 1.68e+12 parasites (6.711% of red cells infected)

Each cycle multiplies the parasite load about eightfold in this illustrative model, so the infected fraction of red cells climbs from almost nothing to several per cent in about 16 days. Parasite levels of a few per cent and above are associated with severe malaria, which is why prompt diagnosis and treatment matter so much. Drugs such as artemisinin combinations work by cutting the parasite load at each cycle. Resistance to artemisinin has emerged in Southeast Asia and parts of Africa, another example of evolution by natural selection in action.

Other protist pathogens include Giardia lamblia, which causes giardiasis, known in Canada and the northern United States as beaver fever and caught from untreated stream and lake water; Trypanosoma species, causing sleeping sickness in Africa and Chagas disease in Latin America; Toxoplasma gondii, carried by cats; and Phytophthora infestans, a water mould (an oomycete, related to diatoms, not a true fungus) that destroyed Irish potato crops in the 1840s, contributing to a famine that killed about a million people and drove large-scale emigration to North America.

Fungi: an overview

Fungi are heterotrophic eukaryotes that absorb their food. They secrete digestive enzymes into their surroundings and absorb the broken-down molecules through their cell walls, which are made of chitin, the same tough polysaccharide found in insect exoskeletons. Most fungi grow as networks of thin, branching filaments called hyphae, which together form a mycelium. A mushroom is only the reproductive structure of a much larger mycelium hidden in soil or wood. Yeasts are single-celled fungi.

Fungi are more closely related to animals than to plants. Both belong to the opisthokonts, both store carbohydrate as glycogen rather than starch, and both share chitin-related genes. This close relationship is one reason fungal infections can be hard to treat: drugs that harm fungal cells often harm human cells too.

A mycelium can spread over vast areas. A single individual of the honey fungus Armillaria ostoyae in the Blue Mountains of Oregon is estimated to cover nearly 10 square kilometres and to be thousands of years old, making it one of the largest organisms on Earth. Hyphae extend from their tips, and a mycelium growing outward from a point in uniform soil can form a ring of mushrooms, the fairy rings seen on lawns, whose radius grows each year.

import math
# A fairy ring: a mycelium spreading outward from one point at a steady rate
rate_cm_per_year = 25             # radial growth, within the range reported for lawn fungi
for years in (1, 10, 50, 200):
    r_m = rate_cm_per_year * years / 100
    area = math.pi * r_m ** 2
    print(f"after {years:3d} years: ring radius {r_m:5.1f} m, area enclosed {area:9,.1f} m^2")

after   1 years: ring radius   0.2 m, area enclosed       0.2 m^2
after  10 years: ring radius   2.5 m, area enclosed      19.6 m^2
after  50 years: ring radius  12.5 m, area enclosed     490.9 m^2
after 200 years: ring radius  50.0 m, area enclosed   7,854.0 m^2

Fungal diversity and life cycles

Fungi reproduce both asexually and sexually, usually by producing enormous numbers of spores that travel by air, water or animals. A single large puffball can release trillions. Fungi are classified largely by their sexual structures and, increasingly, by DNA.

Fungi in ecosystems and human life

Fungi are the principal decomposers of wood: they alone can efficiently break down lignin, the tough polymer in woody cell walls. Without them, dead trees and leaves would pile up and nutrients would stay locked away. Mycorrhizal fungi form partnerships with the roots of about 80 to 90 per cent of plant species, extending far into the soil and supplying water, phosphorus and nitrogen in exchange for sugars from the plant. Lichens are partnerships between a fungus and a photosynthetic alga or cyanobacterium. They colonize bare rock and tree bark, and lichens growing on trees and the ground are the main winter food of caribou across the boreal forest and tundra.

Fungi give us bread, beer, wine and cheese (through yeasts and moulds), antibiotics such as penicillin, discovered by Alexander Fleming in 1928, cholesterol-lowering statins and the immunosuppressant cyclosporine used in organ transplants. They also cause disease. Athlete's foot and yeast infections are common human fungal infections, and serious invasive infections threaten people with weakened immune systems; Candida auris, a drug-resistant yeast, has spread in hospitals worldwide since about 2009. Fungal plant diseases destroy significant shares of crops each year.

Two fungal diseases of wildlife show how introduced pathogens can devastate species. Chytridiomycosis, caused by a chytrid fungus spread through the global trade in amphibians, has contributed to the decline of at least 500 amphibian species and the extinction of dozens. White-nose syndrome, caused by Pseudogymnoascus destructans, was first detected in a cave near Albany, New York, in 2006 and has since killed millions of hibernating bats across eastern North America, including in Ontario, Quebec and the Maritime provinces; the little brown bat was listed as endangered in Canada in 2014 as a result.