Learn: EMES 446 Exam 1 Fall 2025

microorganism

an organism that is too small to be seen clearly with the naked eye

symbiosis

the living together of unlike organisms

intracellular endosymbiont

within a host cell, within the host

extracellular endosymbiont

symbiont located within the body cavities of host (but not intracellular)

ectosymbiont

symbiont located on the surface of the host

spontaneous generation hypothesis

hypothesis that some vital force contained in or given to organic matter can create living organisms from inanimate objects

mutualism

an obligatory relationship where there is some reciprocal benefit to both interacting partners

cooperation

both partners benefit from their non-obligatory interactions

predation

involves a predator species that usually attacks and kills its prey to acquire nutrients and support growth

parasitism

beneficial for parasite, harmful for host. Involves a period of coexistence between interacting partners

amensalism

one partner is harmed and the other is unaffected (or benefits)

aposymbiotic

a host that is without its symbiotic partner

microbiome

consists of all of the microbial symbionts within a host

exploitative competition

competition over resources- one organism consumes resources and reduces the resource availability to another organism

interference competition

competition involving direct harming (inhibition or killing) of one organsim by another

chemosynthesis

process by which a living organism harnesses energy from chemical processes to make sugars

xylotrophic

symbiont that derives its food/nutrients from wood

ram ventilation

swim with mouth and gill slits open to force water over gills

active ventilation

Open mouth with gill slits closed to draw in water, close mouth and open gill slits to force water over gills

light organ

organ in squid that houses bioluminescent Vibrio fischeri bacteria

type VI secretion system (T6SS)

secretion system in bacteria used to inject toxic proteins into competitor cells to lyse and kill them

ostia

pores in sponge used for water intake

pinacoderm

outer surface of sponge composed of epithelial cells

oscula

in sponges, where water is expelled once it is filtered

choanocyte

specialized flagellated cells in sponges that pump water through chambers where they filter food particles including bacteria and microalgae

mesohyl

in sponges, an extensive layer of connective tissue where digestion takes place through phagocytosis via archaeocyte cells

archaeocyte cells

in sponges, responsible for digestion via phagocytosis

Vibrio fischeri

bioluminescent marine bacterium that is free-living in seawater or in light organs of hosts

Poribacteria

predominant members of the sponge microbiome, nearly exclusively found in sponges, may be an ancient sponge symbiont

Artemia

brine shrimp larvae, used as a model host for bacterial-host interactions

NW4327 (sponge pathogen)

first isolated sponge pathogen (re-isolated from infected tissue), infection assays performed using healthy sponge

NW001 (sponge commensal)

alphaproteobacterial symbiont that constitutes 75-90% of the total culturable community in healthy sponges

secondary metabolites

organic compounds not directly involved in growth, development, or reproduction

bioprospecting

search for plant/animal/bacterial/fungal species for bioactive products (medicinal/commercially valuable)

Theonella

sponge distributed in Indonesia, Philippines, Japan, Northern Australia. Harbors a massive consortium of uncultivated bacteria belonging to hundreds of distinct phylotypes

Entotheonella

bacterium associated with Theonella, relatively large genomes and account for nearly all bioactive compounds of interest. Entotheonella is found broadly in globally sampled sponges and in seawater

Discodermolide

anti-cancer compound, kills cancer cells by stabilizing microtubules in the cells preventing cellular division

diatoms

ubiquitous photosynthetic eukaryotes responsible for ~20% of photosynthesis on Earth

phycosphere

a region extending outward from an algal cell, chain, or a colony of cells to some distance in which bacterial growth is stimulated by extracellular products of the alga

rhizosphere

zone of soil surrounding a plant root which stimulated bacterial growth through exudates altering physiochemical environment

diffusive boundary layer

thin layer of fluid that is not mixed with the surrounding bulk fluid because turbulence is not sustainable at such small scales

Chondrichthyes

class of fish containing sharks, skates, rays, and chimeras

Ampullae of Lorenzini

pores on a shark nose/facial area filled with a nearly solid jelly containing chitin. AoLs are used by sharks to detect electrical signals

Staphylococcus

common in AoL jelly, contain genes encoding putative biosynthetic gene clusters of biomedical relevance

shipworm

wood-boring bivalves, use shell to bore into wood and endosymbiotic bacteria help digest wood components (lignin and cellulose)

Riftia

tube worms living at deep-sea hydrothermal vents, instead of a digestive tract they have chemosynthetic bacteria within their trophosome

giant shipworm

bivalve that burrows in sediment next to wood falls, contains chemosynthetic bacteria that use sulfide to make sugars for the animal

what year did Leeuwenhoek discover "animalcules"

1676

horizontal versus vertical symbiont transmission

horizontal: involved cyclic occurrence of aposymbiotic and symbiotic phases in the host life cycle, symbiont has host-associated and free living phases (free-living population served as inoculum for the symbiosis)

vertical: transfers the symbiont directly from parent to offspring, usually through the eggs (no aposymbiotic stage)

how to catch a shark

baited long line, baited drumline

methods to find and identify bacterial symbionts

microscopy, culturing, 16S sequencing, metagenome sequencing, single-cell sequencing

core vs variable vs species-specifc microbial communities in sponges

core: global distribution, likely horizontal transmission

variable: present in only some sponges

species-specific: restricted distribution (unique to only one sponge), likely vertical transmission

types of sulfide rich environments (including how they form, types of chemosymbiosis in each habitat)

1. hydrothermal vents: formed from geothermal activity, chemosynthesis done by bacteria located in trophosome of Riftia

2. whale falls: formed from deceased whale sinking to seafloor. Bacteria growing on bones reduce sulfate to sulfide, encouraging a sulphophilic community of chemoautotrophs to form including bivalves with chemosynthetic symbionts

3. wood falls: forms from terrestrial inputs of wood or shipwrecks. Biochemical processes create sulfide-rich sediments near the wood. Giant shipworms living in the sediment have chemosynthetic bacteria

chemosynthesis versus photosynthesis

- light energy used for photosynthesis, chemical energy used for chemosynthesis.

- oxygen is a reactant for chemosynthesis, a product in photosynthesis

-both processes produce sugars

the stepping stone theory for chemosymbiosis

whale falls and wood falls allow chemosynthetic organisms to establish and then disperse to colonize new habitats (hydrothermal vents)

role of T6SS in V. fischeri symbioses

secretion system used for killing bacteria in competition (beneficial in bobtail squid, pathogenic in zebrafish embryos and Artemia nauplii)

sponge anatomy and pumping ability

- no gut, segmentation, circulatory system, or nervous system

- excretion is mediated by diffusion from cell surface

- a 1 kg sponge can filter up to 24,000 liters of water per day

establishment of sponge-microbe associations

1. ancient symbiosis maintained by vertical transmission only

2. parental and environmental symbiont transmission (vertical and environmental transmission)

3. environmental acquisition only

specific enrichment (sponges)

sponges take up specific types of microbes from seawater (would imply a mechanism of symbiont recognition)

subtractive enrichment (sponges)

sponges take in everything and microbes that cannot resist phagocytosis are consumed while others survive and are enriched

unspecific enrichment (sponges)

sponges are filter feeders and concentrate all microbial cells in the water column to the same degree

pathogens in sponges

NW4327, isolated from infected tissue (burrows through collageneous sponging fibres)

cooperation in sponges

microbes and sponges exchange carbon, nitrogen, phosphate, and vitamins

predatory bacteria in sponges

sponge cells eat bacteria and some bacteria eat other bacteria inside sponge tissue

secondary metabolite examples

antibiotics, antitumor agents, antifouling compounds

ecological roles of secondary metabolites

defense, signaling, competition, symbiosis

biomedical/biotech applications of secondary metabolites

used for pharmaceuticals, antifouling coatings, and agriculture

pros and cons for bioprospecting the marine environment

pros: make people care about invertebrates, funding opportunities, diverse options, one organism can contain many bioactive products, benefits environment if invasive, easier than starting from scratch

cons: cost, habitat effects, shift in conservation priorities, replication challenges, sample accessibility

Discodermia and Discodermolide (discovery, applications, challenges)

- Discodermia: deep sea sponge, extracts were tested to see if they can kill bacteria or cancer cells. Discodermolide identified as bioactive compound (kills cancer cells)

- present in low concentrations in the sponge

- issue of supply, needs more optimization to provide enough discodermalide to sustain necessary studies

ecological role and features of diatoms

base of the marine food web

- encased in silica frustules, sink rapidly upon death to bury carbon

how does cell movement effect the shape of the diffusive boundary layer

fluid motion or cell motility can distort the diffusive boundary layer around the cell- bacteria have to hit a moving target to access phycosphere nutrients

Quorum sensing

mechanism that relies on biosynthesis of diffusible small molecules (usually homoserine lactones) that can synchronize cell population density with gene expression to control certain functions

Pheremone signaling

compounds that coordinate activities between individuals of the same species- evidence for diatoms to produce pheremones (nitric oxide) for attracting gametes and influencing different life cycle aspects

where do ice diatoms live

porous layers of ice, brine channels, on top of the ice under the slow, under the ice where it interacts with the seawater

Antarctic ice diatom-bacterial interactions

diatoms with their bacterial epibionts growth better, epibionts detoxify hydrogen peroxide

Pea aphid and Buchnera symbiosis

- Pea aphid feeds on plant phloem sap (deficient in amino acids)

- Buchnera lives inside aphid, aid in amino acid synthesis

- obligate mutualism

- Buchnera transferred to offspring through maternal vertical transmission

- ancestral symbiosis- 160-280 MYA

multispecies dental biofilm symbiosis

- cooperation

- GIbbons and Nygaard observed pure cultures of dental plaque strains would aggregate and sink when mixed together

- benefits to biofilm: expanded habitat, genetic exchange, antimicrobial resistance, protection from predation, increased metabolic diversity

Proteus mirabilis and various hosts/host sites symbiosis

- proteus mirabilis: resident of human gut, halotolerant, ubiquitous in nature

- commensal symbiosis with human gut

- parasitic symbiosis in human urethra and human wounds

- commensal symbiosis with marine filter feeder

Myxococcus and Bdellovibrio symbiosis

- Myxococcus: soil bacterium

- Bdellovibrio: ubiquitous in water/marine

- predation interaction: Myxococcus secretes extracellular enzymes to digest prey from outside "wolf pack predation"

- Bdellovibrio rams target cell and enters/remains in periplasm where it releases enzymes to loosen structure of peptidoglycan cell wall, prey cell becomes a "bdelloplast." Bdellovibrio digests prey cells macromolecules, eventually lyses host

Toxoplasma symbiosis

- protozoan parasite, causes toxoplasmosis

- alters behavior of mice, cats, and can cause psychotic symptoms in humans

- infected mice attracted to pheromones in cat urine --> increased predation and transfer of parasite back into cat

lichen symbiosis

- 3 partners: fungi, photosynthetic cyanobacteria, yeast

- fungal hyphae protects other from environmental hazards

- photosynthetic partner provides others with fixed carbon

- yeast produces toxins, protects from predation

- long term relationship (400 million years)

Vibrio fischeri - squid symbiosis

- V. fischeri located in light organ of squid, squid uses this bioluminescence for counter-illumination

- cooperation

- horizontally transmitted (juveniles hatch aposymbiotic)

Vibrio fischeri - fish embryos and shrimp larvae symbiosis

- pathogenic interaction with zebrafish embryo and Artemia

- can be T6SS independent or dependent

sponge symbiosis

- core, variable, and sponge-specific microbial communities

- ex: Poribacteria: predominant member of sponge microbiome, heterotroph, may be an ancient sponge symbiont (600 million years)

- 3 scenarios for sponge-microbial establishment

- mesoyl harbors dense communities of bacteria and bacterium-digesting archaeocyte cells (some bacteria are consumed, some are not)

shark symbioses (parasitic)

- dead sandbar shark in Baltimore Aquarium, two vibrio bacterial cultures isolated from kidney and liver (culture of each isolate injected into spiny dogfish shark, which died)

shark symbioses (beneficial/commensal)

- sharks caught off coast of Miami, Fl using drum line

- bacterial isolates cultured from mouth, skin, gills, and visible wounds

- Diverse microbial communities found along each part, Vibrio consistently found at wound sites

diatom-bacterial symbiosis examples (cooperative)

- bacteria can supply diatoms with essential vitamins like B12, which many diatoms do not produce

- diatoms can use bacterial iron-bound siderophores as an iron source

- diatoms can produce exopolysaccharides and glycolate, which can be used by bacteria

- nitrogen-fixing bacteria take N2 to ammonia which is easier to assimilate for diatoms

diatom-bacterial symbiosis examples (parasitic/defensive)

- some bacteria produce algicides that can lyse diatoms: allows bacteria to access nutrients by swimming into phycosphere or attaching to diatom

- production of enzymes with algicidal activity are controlled by quorum sensing

- diatom defense mechanisms: secrete fatty acids/esters with antimircobial effects, PUA, production of compounds that disrupt quorum sensing (compounds that mimic or modify HSLs)

chemosynthetic symbioses

- Riftia tube worms at deep sea hydrothermal vents: bacteria inhabit trophosome and produce sugars for tube worms via chemosynthesis

- Giant shipworm: chemosynthetic bacteria makes sugars for shipworm using sulfide

- Nematode covered with a single sulfur-oxidizing symbiont (ectosymbiont)

Marine worm relies on symbiont for nutrition and waste removal (extracellular endosymbiont)

- Mussel harbors symbionts in enlarged gills within specialized bacteriocytes (intracellular endosymbiont)