BIOS 044: Bacteria and Archaea

Vocabulary practice flashcards covering the key terms, identification techniques, metabolic classifications, and lineages of Bacteria and Archaea from BIOS 044.

Microbiome

A community of microorganisms (including bacteria, archaea, fungi, and other microbes) that inhabit a particular environment or host organism, playing essential roles in biological and ecological processes.

Harmful Algal Bloom (HAB)

A rapid proliferation of algae or cyanobacteria (such as Microcystis) that can release harmful toxins, degrade aquatic habitats, and lead to public safety advisories.

Shannon Diversity ($H$)

A diversity metric that accounts for both the richness (number of different taxa) and evenness (relative abundance of each taxon) of species within a community.

Lemur Microbiome Case Study

A 16S rRNA sequencing study by Bornbusch et al. (2022) of $n = 209$ ring-tailed lemurs (Lemur catta) across up to 13 settings, demonstrating higher gut microbial Shannon diversity in wild Madagascar lemurs compared to captive Madagascar lemurs, while captive U.S. lemurs were closer to wild values without a statistically significant difference.

Three-Domain System

A phylogenetic classification model widely accepted from 1980 to 2010 that categorizes all cellular life into three separate, distinct domains: Bacteria, Archaea, and Eukarya.

Two-Domain System

A phylogenetic hypothesis supported post-2010 proposing that Bacteria and Archaea are the two primary domains of life, with domain Eukarya branching directly from within the archaeal lineage.

Last Universal Common Ancestor (LUCA)

The most recent shared ancestral cell or population of organisms from which all contemporary domains of cellular life on Earth descended.

Extremophile

An organism that thrives under extreme conditions, such as high salinity, high temperature, low temperature, or high hydrostatic pressure.

Tardigrade (Water Bear)

A microscopic animal capable of enduring and surviving extreme environmental stress, but not classified as an extremophile because surviving or tolerating conditions is not the same as thriving in them.

Formylmethionine

The specialized modified initiator amino acid incorporated as the first residue during protein translation in Bacteria, contrasting with methionine used by Archaea and Eukarya.

Peptidoglycan

A mesh-like structural polymer composed of repeating sugars cross-linked by amino acids that forms the cell wall of Bacteria, but is completely absent from the cell walls of Archaea.

Bacterial Colony

A visible cluster of bacterial cells that have grown and multiplied on a solid agar medium, typically originating from a single cell or small group of identical cells.

Enrichment Culture

A laboratory method designed to detect and isolate cells with specific characteristics by inoculating an environmental sample into selective media (varying temperature, salinity, or nutrients) so suited cells outcompete others over serial transfers.

Gram-Positive Bacteria

Bacteria possessing a cell wall with a thick layer of peptidoglycan that retains the crystal violet dye during Gram staining, appearing purple under a light microscope.

Gram-Negative Bacteria

Bacteria possessing a two-component cell wall composed of a thin peptidoglycan layer surrounded by an outer phospholipid membrane; they decolorize and retain counterstain, appearing pink.

Cytochrome c Oxidase Test

A biochemical identification assay that detects the presence of cytochrome c oxidase, an enzyme of the bacterial electron transport chain; used to differentiate oxidase-positive bacteria like Alcaligenes and Pseudomonas from oxidase-negative enteric rods.

Citrate Utilization Test

A metabolic assay used to determine an organism's ability to use citrate as its sole carbon source, indicated by a medium color change where green represents a negative result and blue represents a positive result.

16S rRNA Gene Profiling

A culture-independent molecular identification method that extracts community DNA, amplifies the 16S rRNA gene via PCR, and sequences it to identify taxonomic composition and relative abundance.

Conserved Regions (16S rRNA)

Relatively invariant nucleotide stretches of the 16S rRNA gene that serve as universal primer-binding sites for non-specific PCR amplification across diverse bacterial and archaeal lineages.

Variable Regions (16S rRNA)

Nine hypervariable segments ($V_1$ to $V_9$) within the 16S rRNA gene whose distinct sequence variations allow discrimination of specific microbial groups, genera, or species.

Operational Taxonomic Unit (OTU)

A pragmatic taxonomic classification unit used in marker-gene sequencing studies to group closely related sequence reads based on a shared similarity threshold.

Shotgun Metagenomics

A comprehensive sequencing approach that sequences all fragmented DNA extracted from an environmental sample, revealing both taxonomic composition and functional genetic potential (putative pathways) across whole genomes.

Transformation

A mechanism of lateral (horizontal) gene transfer in which bacteria or archaea naturally take up free, naked donor DNA from the surrounding environment released by cell lysis or secretion.

Transduction

A mechanism of lateral (horizontal) gene transfer mediated by a virus (bacteriophage) that accidentally packages donor prokaryotic DNA and injects it into a recipient cell.

Conjugation

A lateral (horizontal) gene transfer process involving direct physical cell-to-cell contact through a conjugation tube, enabling the transfer of a plasmid or copied portion of the main chromosome.

Binary Fission

The standard asexual reproductive process in prokaryotes where a single cell replicates its chromosome and divides into two genetically identical daughter cells.

Photoautotroph

An organism that captures energy from sunlight to synthesize ATP and fixes carbon from inorganic sources such as $CO_2$ (e.g., Cyanobacteria).

Photoheterotroph

An organism that absorbs sunlight for ATP synthesis while obtaining organic carbon compounds produced by other organisms for building blocks (e.g., Heliobacteria in waterlogged soil).

Chemoorganoautotroph

An organism that obtains chemical energy from organic molecules while fixing its carbon from inorganic simple molecules like $CO_2$ or $CH_4$ (e.g., Methylomonas).

Chemoorganoheterotroph

An organism that relies on organic molecules as both its energy source to make ATP and its carbon source for building cellular components (e.g., Escherichia coli).

Chemolithoautotroph

An organism that derives energy by oxidizing inorganic molecules (such as ammonia or hydrogen sulfide) and uses inorganic carbon ($CO_2$) to synthesize complex organic molecules (e.g., Nitrosopumilus maritimus).

Chemolithoheterotroph

An organism that obtains energy from inorganic chemical compounds (such as hydrogen sulfide) but requires preformed organic molecules from other organisms as a carbon source (e.g., Beggiatoa).

Cyanobacteria

A bacterial lineage found in freshwater, brackish, and marine habitats composed of photoautotrophs capable of oxygenic photosynthesis, known for occasionally forming harmful algal blooms (e.g., Microcystis).

Spirochaetes

A bacterial lineage characterized by corkscrew-shaped individual cells with chemoheterotrophic metabolism, including the Lyme disease pathogen Borrelia burgdorferi.

Crenarchaeota

An archaeal lineage commonly inhabiting extreme environments, possessing variable shapes that often bear flagella, and functioning metabolically as chemoheterotrophs or chemolithoautotrophs.

Euryarchaeota

An archaeal lineage found in freshwater, saltwater, and soil habitats, typically rod-shaped as individual cells, including chemolithoautotrophs and extreme halophiles.

Thiomargarita namibiensis

One of the largest known bacterial species, with cell diameters reaching up to $50\,\mu\text{m}$ or larger, exemplifying morphological size variation in prokaryotes.

Mycoplasma mycoides

One of the smallest known bacterial species, with cell diameters around $0.3\,\mu\text{m}$, illustrating the lower limit of bacterial cellular size.