Aquatic Microbiology: Archaea, Bacteria, and Microbial Ecology in Aquatic Ecosystems

Comprehensive practice flashcards covering the morphology, physiology, reproduction, quantification, pathogenic impacts, ecological roles, food webs, and biogeochemical cycles of Archaea and Bacteria in aquatic environments.

Archaea

Prokaryotic microorganisms belonging to the third branch or domain of life, distinct from Bacteria and Eukarya, featuring unique plasma membrane and cell wall structures that enable survival in hostile environments.

Bacteria (Eubacteria)

Microscopic, single-celled prokaryotic organisms with peptidoglycan cell walls that lack chlorophyll and true branching (except in higher actinomycetales), thriving in diverse environments.

Peptidoglycan

The essential structural polymer present in all bacterial cell walls that provides rigidity, structural strength against adverse osmotic environments, and determines cell shape.

Gram-Positive Bacteria

Bacteria possessing thick cell walls composed of several layers of peptidoglycan that become dehydrated by alcohol during Gram staining, trapping crystal violet-iodine complexes to stain blue/purple.

Gram-Negative Bacteria

Bacteria possessing fragile, thin peptidoglycan layers with larger pores that lose the crystal violet-iodine complex during alcohol decolorization and stain red following the addition of safranin counterstain.

Extreme Halophiles

A physiological group of Archaea requiring at least $12\text{--}15\%\,\text{NaCl}$ up to saturation to survive and grow, forming bright red colonies due to high carotenoid content.

Thermoacidophiles

A group of Archaea that thrive in high-temperature and highly acidic environments, such as hydrothermal vents, hot springs, deep subterranean settings, oil reservoirs, and burning coal refuse piles.

Methanogenic Bacteria (Methanogens)

Chemoautotrophic, strictly anaerobic Archaea that generate environmental methane by utilizing limited simple carbon compounds ($H_2$, $CO_2$, formate, acetate, methanol, or trimethylamine) for energy-generating metabolism.

Epulopiscium fishelsoni

The largest reported prokaryote to date, measuring $>500\,\mu\text{m}$ in length and $40\,\mu\text{m}$ in width, found exclusively in the intestinal tract of certain tropical fish.

Coccus

A spherical bacterial morphology with typical dimensions ranging between $0.4\,\mu\text{m}$ and $2.0\,\mu\text{m}$ in diameter.

Bacillus (Cell Morphology)

A rod-shaped bacterial morphology typically ranging from $1\,\mu\text{m}$ to $10\,\mu\text{m}$ in length, capable of exceeding lengths of $60\,\mu\text{m}$ or even $100\,\mu\text{m}$ in the presence of cell division inhibitors.

Spirillum and Spirochete

Spiral bacterial morphologies categorized by flexibility; spirilla are rigid helical cells, whereas spirochetes are flexible helical cells.

Pleomorphic Bacteria

Bacterial species possessing atypical, stable, genetically determined shapes that diverge from standard cocci, bacilli, or spirals, including filamentous, star-shaped, or square cells.

Streptomyces sp.

A genus of filamentous bacteria forming long, threadlike multicellular strands resembling fungal hyphae that develop reproductive spores at their filament tips.

Stella sp.

A genus of pleomorphic bacteria exhibiting a distinct, genetically stable star-shaped cell morphology.

Arcula sp.

A square-shaped bacterium isolated from natural salt ponds along the Red Sea, resembling flat boxes with perfectly straight edges and sharp $90^{\circ}$ corner angles.

Diplo- Arrangement

A stable bacterial cellular grouping formed when cells divide in a single plane and remain attached in pairs or duplexes (e.g., diplococci or diplobacilli).

Strepto- Arrangement

A bacterial cell grouping formed when repeated divisions occur in a single continuous plane, producing extended linear chains (e.g., streptococci or streptobacilli).

Staphylo- Arrangement

A bacterial cellular arrangement resulting from divisions in multiple random planes, forming irregular aggregates resembling bunches of grapes (e.g., staphylococci).

Bacterial Flagellum

A rigid, spinning, helical surface appendage approximately $20\,\text{nm}$ in diameter, comprised of a basal body, hook, and filament, capable of rotation speeds up to $300\,\text{revolutions per second}$.

Monotrichous Flagellation

A bacterial motility arrangement characterized by the presence of a single flagellum located at one pole of the cell.

Lophotrichous Flagellation

A polar bacterial flagellar arrangement in which a cell possesses a cluster or tuft of multiple flagella at one pole.

Amphitrichous Flagellation

A bacterial flagellation pattern featuring flagella situated at both opposite ends of the cell, occurring singly or in tufts.

Peritrichous Flagellation

A non-polar bacterial flagellar distribution wherein flagella project around the entire external surface of the bacterial cell.

Axial Filaments

Motility appendages characteristic of spirochetes, composed of two bundles of overlapping fibers originating from opposite cellular poles beneath the outer sheath.

Pili (Fimbriae)

Short, straight, non-motile protein tubes found primarily on certain Gram-negative bacteria that mediate physical attachment to surfaces and facilitate colonization.

F Pilus

A specialized, elongated bacterial pilus that facilitates horizontal genetic transfer between bacterial cells during conjugation.

Binary Fission

The predominant mode of bacterial reproduction wherein an individual cell doubles in size, replicates its circular chromosome, forms a transverse septum, and cleaves into two independent, identical daughter cells.

Doubling Time

The time required for a bacterial population to double in number through binary fission, remaining constant for a given species under stable physical and chemical conditions.

Lag Phase

The initial growth phase of bacteria in batch culture characterized by cellular acclimation, enzyme synthesis, and chromosome replication without an immediate increase in cell population.

Logarithmic Phase (Log Phase)

The active phase of exponential population growth in batch culture where cells divide at a constant maximal rate, doubling the population at regular intervals.

Stationary Phase

The growth phase in batch culture where the rate of cell division equals the rate of cell death due to nutrient depletion and accumulation of toxic waste, resulting in a stable population plateau.

Death Phase

The final stage in a closed batch culture where the rate of microbial mortality exceeds cell division, leading to an exponential decline in viable cell numbers.

Total Plate Count

A quantitative cultivation technique that measures viable living bacteria on agar media, based on the principle that each viable cell forms a single macroscopic colony.

Colony-Forming Unit (CFU)

The standard microbiological unit of measurement representing an individual viable bacterial cell or clump of cells capable of multiplying into a distinct colony on solid media.

Turbidity (Optical Density)

An indirect measurement of microbial biomass in liquid broth that assesses cloudiness using a spectrophotometer based on light scattering against a standard growth curve.

Fastidious Bacteria

Microorganisms that possess strict, complex nutritional demands, requiring specialized enriched culture media (e.g., chocolate agar or MacConkey's agar) for cultivation.

Selective Media

Culture media formulated with specific chemical agents, salts, or dyes that promote the growth of targeted microorganisms while inhibiting competing species.

Differential Media

Culture media incorporating biochemical indicators that distinguish between different bacterial taxa based on recognizable visual changes in colony appearance or surrounding agar.

Eosine Methylene Blue (EMB) Agar

A selective and differential medium containing dyes that inhibit Gram-positive bacteria while allowing Gram-negative bacteria to grow and differentiate based on lactose fermentation.

Thiosulfate Bile Salt Citrate (TCBS) Agar

A specialized selective and differential culture medium formulated specifically for the isolation and identification of marine and estuarine Vibrio species.

Blood Agar

A differential culture medium containing intact mammalian red blood cells used to detect bacterial hemolytic activity (the enzymatic lysis of erythrocytes).

General Media (Complex Media)

Nutrient-rich, non-selective culture media (such as Nutrient Agar) containing peptone, yeast, or beef extract used for routine cultivation and total plate counts.

Proteorhodopsin

A light-driven retinal proton-pumping protein widespread in surface ocean bacterioplankton that enables bacterial cells to harvest solar energy and supplement respiration during oxygen deprivation.

Sulphate-Reducing Bacteria (Sediments)

Chemoautotrophic, anaerobic bacteria (such as Desulfovibrio, Desulfomonas, and Desulfococcus) that account for over $50\%$ of carbon turnover in coastal marine sediments.

Luminous Bacteria

Motile, Gram-negative, heterotrophic marine rod-shaped bacteria (e.g., Vibrio fischeri, Photobacterium leiognathi) capable of emitting visible light through bioluminescence.

Luciferin

A protein-like light-emitting substrate that reacts with molecular oxygen in luminous bacteria to produce bioluminescent light used for defense, prey attraction, and camouflage.

Extracellular Products (ECP)

Highly toxic metabolic enzymes (including proteases, hemolysins, and cytotoxins) secreted by pathogenic bacteria that disrupt host defenses and cause tissue necrosis in aquatic hosts.

Koch's Postulates

The formal scientific criteria required to establish an organism as the cause of a disease: consistent presence in diseased hosts, pure culture isolation, disease reproduction in susceptible hosts, and re-isolation.

Motile Aeromonad Septicemia (MAS)

A serious freshwater fish disease (also called ulcer disease, red-sore disease, or hemorrhagic septicemia) caused by motile Aeromonas species and characterized by body ulcerations and fin hemorrhaging.

Aeromonas hydrophila

A Gram-negative, motile rod-shaped freshwater bacterium that causes motile aeromonad septicemia, exophthalmia, dropsy, and tissue necrosis in cultured and wild fishes.

Aeromonas caviae

A pathogenic freshwater bacterial species involved alongside A. hydrophila and A. sobria in producing motile aeromonad septicemia and skin lesions in fishes.

Vibriosis

The most economically impactful infectious disease affecting cultured and wild marine and estuarine finfish, caused by halophilic bacteria of the genus Vibrio.

Vibrio sp.

A genus of Gram-negative, curved rod-shaped, facultatively anaerobic bacteria that dominate marine and estuarine environments, containing pathogenic, saprophytic, and bioluminescent species.

Vibrio harveyi

A luminous, Gram-negative marine bacterium that serves as the primary etiologic agent of luminous bacterial disease in penaeid shrimp hatcheries and aquaculture ponds.

Luminous Bacterial Disease

A devastating penaeid shrimp disease (chiefly affecting Penaeus monodon) causing severe hepatopancreas necrosis, systemic infection, continuous greenish glow in darkness, and up to $100\%$ larval mortality.

Green-Water Culture System

An ecological aquaculture management method using microalgae-rich water from finfish culture (e.g., tilapia or milkfish) to competitively inhibit and suppress pathogenic luminous Vibrio harveyi in shrimp ponds.

Microbial Ecology

The scientific study of relationships among microorganisms and between microorganisms and their physical, chemical, and biological environment across diverse aquatic habitats.

Marine Ecosystems

Saline aquatic environments covering approximately $71\%$ of Earth's surface and $97\%$ of planetary water, characterized by an average salinity of approximately $35\,\text{ppt}$ ($3.5\%$).

Freshwater Ecosystems

Aquatic environments containing less than $0.5\,\text{ppt}$ salinity, including lakes, rivers, streams, ponds, and wetlands, whose microbial communities frequently originate from surrounding soils and runoff.

Brackishwater Ecosystems

Transitional aquatic habitats where freshwater mixes with seawater (such as estuaries and mangroves), exhibiting fluctuating salinity concentrations between $0.5\,\text{ppt}$ and $30\,\text{ppt}$.

Mutualism

An ecological symbiotic interaction in which both participating organisms derive fitness or physiological benefits (e.g., intestinal microbiota providing digestive enzymes to fish hosts in exchange for nutrients).

Commensalism

A symbiotic relationship in which one organism benefits while the other organism remains unaffected and unharmed (e.g., harmless bacteria colonizing aquatic plant surfaces).

Parasitism

An asymmetrical interaction in which one organism (the parasite or pathogen) benefits by extracting resources from and causing physiological harm or pathology to the host organism.

Microbial Competition

An interaction where microorganisms compete for limited shared ecological resources, such as dissolved nutrients, molecular oxygen, and surface attachment area.

Microbial Predation

The direct grazing and consumption of bacteria by larger aquatic protists (such as ciliates and flagellates), which serves to regulate bacterial population densities.

Food Web

A complex network of interconnected food chains with multiple energy pathways, illustrating trophic feeding relationships and providing greater ecological stability than simple food chains.

Microbial Loop (Microbial Food Web)

An ecological pathway wherein heterotrophic bacteria reclaim dissolved organic carbon (DOC), converting it into bacterial biomass that is consumed by protozoa and channeled back into classic grazing food webs.

Marine Microbial Food Web (Barber Model)

A comprehensive conceptual framework illustrating trophic transfers linking autotrophic picoplankton, dissolved organic carbon excretion, coagulation into marine snow, bacterial uptake, and grazing by unicellular protozoa.

Autotrophic Picoplankton

Minute photosynthetic microorganisms ($0.2\text{--}5.0\,\mu\text{m}$), including cyanobacteria such as Prochlorococcus and Synechococcus, that generate primary organic matter at the base of open-ocean food webs.

Dissolved Organic Carbon (DOC)

Soluble organic molecules (sugars, amino acids, proteins, organic acids) excreted by living phytoplankton or released by cell lysis, functioning as primary nutrient substrates for heterotrophic bacterioplankton.

Marine Snow (Organic Aggregates)

Macroscopic, sinking particulate organic aggregates composed of dead plankton, mucus, bacterial cells, fecal material, and detritus that transfer carbon from surface waters into deeper ocean strata.

Particulate Organic Detritus

Suspended or benthic non-living organic matter consisting of fecal pellets, dead plant tissue, and decomposing animal carcasses that undergo continuous microbial colonization and degradation.

Biological Carbon Pump

The microbially driven ecological mechanism by which organically fixed carbon aggregates sink from the photic ocean surface into deep waters and benthic sediments.

Dissolved Inorganic Carbon (DIC)

Inorganic aqueous carbon forms, including dissolved carbon dioxide ($CO_2$), carbonic acid ($H_2CO_3$), bicarbonate ($HCO_3^-$), and carbonate ($CO_3^{2-}$), utilized by autotrophs during photosynthesis.

Biogeochemical Cycles

Natural cyclical pathways through which essential chemical elements (C, N, S, P) circulate through biological, geological, and chemical processes driven primarily by microbial transformations.

Aquatic Carbon Cycle

The microbially driven biogeochemical cycle wherein carbon moves continuously between atmospheric gas, dissolved ionic pools, autotrophic biomass, aquatic consumer food webs, and bottom sediment sinks.

Long-Term Carbon Storage

The burial of particulate organic carbon in aquatic bottom sediments for centuries or millennia, potentially forming fossil fuels and removing carbon from atmospheric circulation.

Saprophytic Microorganisms

Specialized heterotrophic decomposer bacteria and fungi (e.g., Bacillus, Pseudomonas, Aspergillus) that obtain energy by secreting enzymes to degrade dead organisms, feces, and uneaten feed.

Aquatic Nitrogen Cycle

The continuous microbially mediated transformation of nitrogen through nitrogen fixation, assimilation, consumption, ammonification, nitrification, and denitrification across aquatic environments.

Nitrogen Fixation

The enzymatic reduction of inert atmospheric dinitrogen gas ($N_2$) into bioavailable ammonia ($NH_3$) or ammonium ($NH_4^+$) by specialized cyanobacteria (Anabaena, Nostoc) and bacteria.

Nitrogenase

The complex, oxygen-sensitive metalloenzyme found in diazotrophic bacteria and cyanobacteria that catalyzes the reduction of atmospheric $N_2$ into biologically usable ammonia.

Assimilation (Nitrogen)

The biochemical uptake and incorporation of inorganic dissolved nitrogen compounds ($NH_4^+$, $NO_2^-$, $NO_3^-$) by phytoplankton, algae, and plants into amino acids, proteins, and nucleic acids.

Ammonification (Mineralization)

The microbial degradation of organic nitrogenous materials (dead fish, plant debris, fish feces, uneaten feed) into inorganic ammonia ($NH_3$) or ammonium ($NH_4^+$) by heterotrophic bacteria.

Nitrification

The two-step obligate aerobic biological oxidation of toxic ammonia to nitrite ($NO_2^-$) and sequentially to nitrate ($NO_3^-$) mediated by chemolithoautotrophic nitrifying bacteria.

Nitrosomonas

A genus of obligate aerobic, chemolithoautotrophic ammonia-oxidizing bacteria that perform Step 1 of nitrification by converting ammonia into nitrite ($NH_3 \rightarrow NO_2^-$).

Nitrobacter

A genus of aerobic, chemolithoautotrophic nitrite-oxidizing bacteria that execute Step 2 of nitrification by converting toxic nitrite into less harmful nitrate ($NO_2^- \rightarrow NO_3^-$).

Azotobacter

A genus of free-living, aerobic heterotrophic bacteria that contribute to aquatic and terrestrial nitrogen fertility through independent atmospheric nitrogen fixation.

Denitrification

The anaerobic microbial reduction of nitrate ($NO_3^-$) to nitrite, nitrous oxide, and ultimately inert atmospheric nitrogen gas ($N_2$) by facultative bacteria (e.g., Pseudomonas, Paracoccus).

Volatilization (Ammonia)

The chemical and physical release and diffusion of gaseous, un-ionized ammonia ($NH_3$) from surface waters directly into the atmosphere.

Aquatic Sulfur Cycle

The biogeochemical cycle governing the continuous biological, chemical, and physical transformations between sulfate, hydrogen sulfide, elemental sulfur, and organic sulfur in aquatic environments.

Sulfate Assimilation

The biochemical uptake of dissolved sulfate ($SO_4^{2-}$) by algae, aquatic plants, and bacteria to synthesize sulfur-bearing amino acids such as cysteine and methionine.

Sulfate Reduction

The anaerobic respiratory process wherein sulfate-reducing bacteria (e.g., Desulfovibrio, Desulfobacter) use sulfate ($SO_4^{2-}$) as a terminal electron acceptor, converting it into toxic hydrogen sulfide ($H_2S$).

Hydrogen Sulfide ($H_2S$)

A highly toxic, reduced gaseous sulfur compound characterized by a rotten egg odor that accumulates in oxygen-depleted, organic-rich pond sediments and causes severe aquatic mortality.

Sulfur Oxidation

The aerobic or microaerophilic microbial conversion of toxic hydrogen sulfide ($H_2S$) back into harmless dissolved sulfate ($SO_4^{2-}$) by specialized sulfur bacteria (e.g., Thiobacillus, Beggiatoa).

Aquatic Phosphorus Cycle

A sedimentary biogeochemical cycle that lacks a major atmospheric gas phase, in which phosphorus circulates among rocks, water, living biomass, and sediments via assimilation, mineralization, and sedimentation.

Phosphatases

Extracellular hydrolytic enzymes secreted by mineralizing microorganisms (such as Bacillus, Pseudomonas, and Aspergillus) that cleave phosphate groups from organic matter, releasing dissolved orthophosphate ($PO_4^{3-}$).

Eutrophication

The excessive nutrient enrichment of water bodies (primarily driven by surplus phosphorus and nitrogen), which triggers dense algal blooms, reduced water transparency, and nighttime dissolved oxygen depletion.

Biofilm

A highly organized, surface-attached consortium of microorganisms (bacteria, cyanobacteria, diatoms, fungi, and protozoa) enclosed within a self-produced matrix of extracellular polymeric substances.

Extracellular Polymeric Substances (EPS)

The protective, sticky biochemical matrix consisting of polysaccharides, structural proteins, extracellular DNA, lipids, and water that holds biofilm communities together and confers resistance to environmental stresses.