bio 1070 unit #3

Human microbiome

All microorganisms living in and on the human body (skin, mouth, gut, etc).

Body-site microbiomes

Different body parts host different microbial communities (e.g., mouth vs gut vs skin).

Main microbiome groups

Bacteria (majority), archaea, unicellular eukaryotes, multicellular eukaryotes (mites), viruses.

Demodex folliculorum

Microscopic face mite living in hair follicles and oil glands; almost all adults have them.

Microbiome services

Vitamin production, digestion help, pathogen protection, immune modulation, other health functions.

Viruses in microbiome

Viral particles are extremely abundant on and in the body, infecting host cells and microbes.

Microbe

General term for microscopic organisms; often includes bacteria, archaea, small eukaryotes, and sometimes viruses.

Three domains of life

Bacteria, Archaea, Eukarya.

Prokaryote (usage in this course)

Any organism in Bacteria or Archaea; no nucleus or membrane-bound organelles.

Prokaryote is not a domain

"Prokaryote" is a descriptive category, not one of the three domains.

Eukaryote (basic)

Organism in domain Eukarya; has nucleus and membrane-bound organelles.

Uncertainty of domain relationships

Evolutionary relationships among Bacteria, Archaea, and Eukarya are unclear and still debated.

Course simplification of domains

For this course, domains are treated as three independent, non-nested groups.

Core functions of living organisms (cells)

Obtain energy and nutrients, regulate internal conditions, metabolize and eliminate waste, grow, reproduce, respond to environment.

Homeostasis

Maintenance of stable internal conditions for molecular machinery to work properly.

Metabolism

All chemical reactions in cells that use energy and nutrients and produce waste.

Virus cellular status

Acellular; not made of cells and do not perform typical cellular functions independently.

Virus life-like properties

Contain genetic material, evolve, replicate using host, respond to some stimuli.

Virus non-life properties

No metabolism, no homeostasis, no independent reproduction, no growth or development.

Obligate intracellular parasite

Organism (virus) that must live and replicate inside host cells and cannot survive independently.

Functions required by viruses

Must replicate and respond to environment (do not need to grow, metabolize, or maintain homeostasis by themselves).

Prokaryote diversity uncertainty

Estimated species numbers range from ~10 million to ~1 trillion; exact number unknown.

Prokaryote ubiquity

Prokaryotes (bacteria and archaea) are found in almost every environment on Earth.

Prokaryote roles

Primary producers, decomposers, symbionts, pathogens, and industrially useful organisms.

Bacteria - cell structure

Unicellular, no nucleus, no membrane-bound organelles, circular double-stranded DNA chromosome.

Bacterial cell wall

Contains peptidoglycan; this trait is unique to bacteria.

Peptidoglycan

Complex polymer in bacterial cell walls; main target of many antibiotics.

Bacterial plasmids

Small circular DNA molecules that can be transferred between individuals.

Bacterial reproduction

Asexual, typically by binary fission.

Bacterial chromosome shape

Single circular double-stranded DNA.

Bacterial multicellularity

Most bacteria are single-celled, but some form simple multicellular filaments or chains.

Filamentous cyanobacteria

Bacteria that form chains of cells; example of simple multicellularity in bacteria.

Bacterial ubiquity

Bacteria are present everywhere, including clouds, soil, water, organisms, and extreme environments.

Bacterial metabolic diversity

Include phototrophs, chemotrophs, decomposers, symbionts, heterotrophs, pathogens.

Photosynthetic bacteria

Bacteria that perform photosynthesis and act as primary producers.

Chemosynthetic bacteria

Bacteria that build organic molecules using chemical energy instead of light.

Heterotrophic bacteria

Bacteria that obtain organic carbon by consuming other organisms or organic matter.

Bacterial pathogens

Disease-causing bacteria such as Streptococcus.

Plastic-eating bacteria

Recently discovered bacteria that can use plastic as an energy or carbon source.

Aerobic bacterial respiration

Uses oxygen to generate ATP.

Anaerobic bacterial respiration

Respiration without oxygen; uses alternative electron acceptors.

Bacterial fermentation

Energy generation without electron transport chain, typically in anaerobic conditions.

Archaea - cell structure

Unicellular, no nucleus, no membrane-bound organelles, circular double-stranded DNA, plasmids.

Archaeal histone-like proteins

Proteins that package DNA in archaea; similar function to eukaryotic histones.

Archaeal cell membrane uniqueness

Archaeal membranes contain unique lipids distinct from bacteria and eukaryotes.

Archaeal reproduction

Asexual reproduction.

Archaeal metabolism

Chemosynthesis, heterotrophy, decomposition, symbiosis; diverse energy strategies.

Archaea as extremophiles

Frequently inhabit extreme environments like high salinity lakes, hot springs, deep-sea vents.

Photosynthetic archaea

Do not exist; archaea are not known to perform photosynthesis.

Archaeal pathogens

No confirmed archaeal pathogens are known to infect humans.

Archaeal methionine start

Protein synthesis in archaea starts with unmodified methionine, a diagnostic trait.

Shared traits - bacteria and archaea

Unicellular, no nucleus, no organelles, circular chromosomes, plasmids, asexual reproduction.

Diagnostic trait of bacteria

Presence of peptidoglycan in the cell wall.

Diagnostic trait of archaea (for this course)

Protein synthesis starts with unmodified methionine.

Archaeal extremophily vs bacteria

Both can live in extreme environments, but many classic extremophiles are archaea.

Eukaryote - synapomorphies

Double-membraned nucleus, membrane-bound organelles, sexual reproduction via meiosis.

Eukaryotic chromosomes

Typically linear chromosomes.

Eukaryotic histones

True histone proteins that wrap DNA into chromatin.

Eukaryotic reproduction

Capable of sexual reproduction; many lineages can also reproduce asexually.

Unicellular vs multicellular eukaryotes

Eukaryotes can be single-celled or multicellular, depending on lineage.

Eukaryotes as chimeras

Share features with archaea (information processing) and bacteria (membrane structure), reflecting a mixed origin.

Eukaryotic cytoskeleton

Complex internal protein network for shape, transport, and movement.

Endosymbiosis definition

Mutualistic relationship where one organism lives inside another and becomes a permanent part.

Origin of mitochondria

From endosymbiosis of a bacterium inside an early eukaryotic or archaeal host.

Primary endosymbiosis

Host cell engulfs a free-living bacterium that becomes mitochondrion or chloroplast.

Secondary endosymbiosis

Host eukaryote engulfs another eukaryote that already has a primary endosymbiont (e.g., some algae chloroplasts).

Virus components

Genetic material (DNA or RNA), protein capsid, sometimes lipid envelope.

Virus and host energy/nutrients

Use host machinery and resources but do not carry out independent metabolism.

Virus size

Much smaller than bacteria and most organelles; among the smallest biological entities.

Viral burst size example

One infected cell (e.g., human cell infected by SARS-CoV-2) can release 100,000 to 1,000,000 virions.

Global viral abundance

Estimated ~10³¹ virus particles, more than number of stars in the universe.

Virus ecological role

Influence population dynamics, gene transfer, and evolution of virtually all life.

Viruses and biodiversity metrics

Present in nearly every eukaryotic lineage; high viral diversity.

Archaeplastida

Group including red algae, green algae, and land plants; chloroplasts from primary endosymbiosis.

Epistokonts (Opisthokonts)

Group including animals and fungi (and some protists).

SAR supergroup

Large eukaryotic group including many algae and protists; not required to memorize details.

Amoebozoans

Group of eukaryotes that often move with amoeboid movement; not primary focus for this course.

Algae (conceptual)

Non-monophyletic collection of mostly aquatic, photosynthetic eukaryotes from different lineages.

Multicellularity in eukaryotes

Evolved multiple times independently (plants, fungi, animals, some algae).

Photosynthesis in eukaryotes

Also evolved multiple times via different endosymbiotic events across lineages.

Implication of multiple origin traits

Presence of photosynthesis or multicellularity alone does not identify a specific eukaryotic group.

Plant definition for this course

Archaeplastids: red algae, green algae, and land plants.

Plant universal trait

Chloroplasts from primary endosymbiosis.

Land plant cellulose

Cell walls of land plants contain cellulose; red and many green algae may have different wall components.

Stomata and cuticle

Traits of land plants that reduce water loss and regulate gas exchange.

Vascular tissue

Xylem and phloem; present only in vascular plants (subset of land plants).

Seeds and pollen

Traits of seed plants (subset of vascular plants).

Flowers and fruits

Traits of angiosperms (subset of seed plants).

Inference from flowers

If an organism has flowers, it is an angiosperm and therefore has seeds, pollen, vascular tissue, stomata, and cuticle.

Inference from 'plant' label

If something is a plant, it is a eukaryote and has chloroplasts from primary endosymbiosis, but may lack flowers, seeds, or vascular tissue.

Plant ecological roles

Primary producers, oxygen production, habitat structure, water and nutrient cycling, symbiosis with fungi and some animals.

Fungi as a group

Monophyletic eukaryotic group; not synonymous with 'mushroom'.

Yeast definition

Any unicellular fungus.

Mushroom definition

Fruiting body of some multicellular fungi used for reproduction.

Hyphae

Thread-like fungal filaments forming the structural body of many fungi.

Mycelium

Network of hyphae forming the main feeding structure of many fungi.

Fungal cell wall

Contains chitin; key synapomorphy for fungi.

Absorptive heterotrophy

Fungi secrete digestive enzymes externally and absorb breakdown products.

Mycorrhizae

Mutualistic associations between fungal mycelium and plant roots.

Mycorrhizal prevalence

Approximately 90 percent of land plants form mycorrhizal associations.