marine symbiosis MIDTERM 1 study content

microorganism

an organism that is too small to be seen clearly with the naked eye (usually smaller than 1 millimeter in diameter)

• includes viruses, bacteria, many algae, fungi, and protozoa

• exception: bacterium thiomargarita

symbiosis

greek for “living together”

used by German mycologist Anton de Bary

de Bary defines symbiosis as “the living together of unlike organisms”

• symbiotic relationships are close and often long-term interactions

intracellular endosymbiont

endosymbiont- microbe located within the host

intracellular- within host cell

extracellular endosymbiont

endosymbiont- microbe located within the host

extracellular- in body cavities but not intracellular

ectosymbiont

microbe is on the surface of the host

aposymbiotic

a host that is without its symbiotic partner

microbiome

when there are multiple microbial symbionts within a host, the microorganism are collectively referred to as this

holobiont

when there is more than one symbiont, this group of organisms (host and all its microbial symbionts) are called this

mutualism

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

• partners often will not survive if separated

ex. pea aphid and buchnera aphidicola

cooperation

both partners benefit from their non-obligatory interactions

• partners can be separated and remain viable, even if sometimes they don’t function as well

ex. multi-species biofilms

predation

relationship is beneficial for the predator and harmful for prey

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

• several microbes survive by their ability to prey upon others

ex. myxococcus xanthus (soil bacterium) and bdellovibrio (ubiquitous in water/marine)

parasitism

relationship is beneficial for parasite and harmful for the host

• differs from predation in that parasitism involves a period of coexistence between interacting partners

• many examples of parasites influencing host behavior resulting in a fitness benefit to the parasite

• “controlled parasitism” can occur when relationship becomes stable

ex. tapeworms and toxoplasma gondii

amensalism

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

• can be thought as a form of competition

• competition is divided into two types: 1. exploitative 2. interference

exploitative competition

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

ex. competition for limiting nutrient

interference competition

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

ex. toxin production

chemosynthesis

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

• only microorganism do this because they need sugars for biosynthesis and can give sugars away in symbiotic relationship

• use oxygen (O2) to oxidize hydrogens sulfide (H2S) which makes energy (ATP) that can be used to fix carbon dioxide (CO2) to produce sugar (CH2O)

• basically oxidizing hydrogen sulfide releases energy to drive sugar production

energy source- chemicals (sulfide)

other reactants- CO2 and O2

products: sugars and sulfate

use of products: growth and/or given to hosts

ram ventilation

sharks, rays- swim with mouth and gill slits open to force water over gills

active ventilation

AKA buccal pumping

bony fish, also sharks and rays

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

• sharks can allow draw in water through spiracles, often used by bottom-dwelling sharks to prevent taking in sediment during active ventilation through mouth

obligate ram ventilators

• hammerhead

• whale shark

• great white shark

• mako

3 types of shark reproduction

1. oviparous

2. viviparous

3. ovoviviparous

**different reproductive strategies reflect adaptations to a given species’ environment, predation pressures, and life history strategies

oviparous sharks

egg-layering sharks

oviparity is when eggs are fertilized in womb and sharks lays eggs encased in leathery pouch called “mermaid’s purse”

• eggs left unprotected and often eaten by predators before can hatch

• eggs hatch with NO parental care after eggs are laid

oviparous shark species include: catsharks, zebra sharks, and horn sharks

viviparous sharks

viviparity is when an egg develops and hatches INSIDE of womb

• after hatching, pups live on a placenta until being born alive

• have an umbilical cord located between pectoral fins (kinda like belly button)

viviparous shark species include: bull sharks and hammerhead sharks

ovoviviparous sharks

have eggs that hatch inside of womb and shark has LIVE birth

• different from viviparous pups because there is no placenta

• pups live on yolk sac until ready to hatch

• first shark to hatch from its egg will consume other shark fetuses and their yolk sacs

• ovoviviparous sharks give birth to small litters

ovoviviparous sharks include: great white sharks and cookiecutter sharks

shark anatomy

Head → tail landmarks:

• Olfactory bulb = front; smell

• Brain = behind olfactory bulb

• Heart = ventral, behind gills

• Backbone = dorsal/top

• Kidney = just below backbone

• Ovary = cluster of round “grape-like” eggs

• Liver = very large, ventral organ

• Stomach = curved/J-shaped sac

• Intestine = posterior; contains spiral valve

• Uterus = posterior reproductive organ

• Embryo + yolk sac = inside uterus

how to catch a shark

researchers use drumlines with baited hooks. When a shark takes the bait, the line can trigger a satellite/GPS alert, allowing researchers to respond quickly, safely restrain the shark, and collect samples such as skin, gill, mouth, wound, or cloacal samples.

• drumline buoy= whole shark-capture system

• anchored buoy = component attached to an anchor that keeps the system positioned.

light organ

organ in squid (euprymna scolopes) found beneath ink sack

• colonized by vibrio fischeri (multiple strains)

• bi-lobed light organ has six crypts that are colonized independently

type VI secretion system (T6SS)

a gene cluster

• a contact-dependent bacterial weapon that injects toxic effectors into neighboring competitor cells to kill them

• in V. fischeri, T6SS2 is required for killing competing strains and helps determine which strains can coexist within squid light-organ crypts

• different V. fischeri strains can occupy the squid light organ, but some strains are able to kill others. researchers compared killer and non-killer strains and found that killing was associated with the presence of a T6SS-encoding genomic island!!

T6SS helps determine which strains can coexist in the same light-organ crypt

• a killer strain and a non-killer strain tend to occupy different crypts

• when the killer strain has a T6SS mutation, the killer and non-killer strains can occupy the same crypt

ostia

pores in sponge (water intake)

pinacoderm

outer surface of sponge; composed of epithelial cells

oscula

where water filtered is expelled

• estimated that a 1kg sponge can filter up to 24,000 liters of water each day

choanocytes

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

mesohyl

an extensive layer of connective tissue where food particles are transferred to

• harbors dense communities of bacteria alongside bacterium-digesting-archaeocyte cells

archaeocyte cells

help digestion occur by phagocytosis

vibrio fischeri

the SYMBIONT

• bioluminescent marine bacterium (luminescence is required to fully colonize the squid)

• gram-type negative

• gammaproteobacteria

• motile

• found in planktonic, free-living state as well as in association with symbiotic hosts

poribacteria

sponge-specific bacterial symbiont; predominant member of sponge microbiome; representatives nearly exclusively found in sponges; likely ancient

• unculturable (researchers used single cell genome sequencing to study them)

• heterotrophs

• capable of carbohydrate metabolism

• able to degrade diverse substrates, including components of the sponge host matrix

• therefore probably well adapted to the sponge extracellular matrix

poribacteria 16S rRNA sequences differ by as much as 15–20%, which supports the idea of an ancient association, but the distribution pattern suggests both vertical and horizontal transmission may contribute

NW4327

first isolation and description of a sponge pathogen

• disease-causing collagen/spongin-degrading pathogen

• - is an alphaproteobacterium in the Roseobacter clade

• sponge pathogen

NW001

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

• abundant normal symbiont in healthy sponge

• sponge commensal

artemia nauplii

brine shrimp larvae used as a model host

• common aquatic animal; have ecological/economic relevance/emerging model for studying bacterial-host interactions

• v. fischeri can kill Artemia, but T6SS1 dependence is strain-specific: ES114 = T6SS1-independent; ES213 = T6SS1-dependent; PP3 = little killing

***when seeing functions/abilities of v. fischeri in needing to kill hosts it was found that ES114 uses T6SS1 against fish but not Artemia → bacterial virulence mechanisms depend on the host!!!

THUS v. fischeri pathogenicity is host-dependent and strain-dependent

secondary metabolites

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

• functions- defense, signaling, competition, symbiosis

• ex. antibiotics, antitumor agents, antifouling compounds

• these compounds help organisms deter predators, prevent microbial overgrowth, compete for space, & communicate with symbionts

• same molecule can have an ecological function in nature and also a pharmaceutical use for humans

bioprospecting

searching natural environments for useful bioactive compounds

• marine organisms and their microbes are being investigated for compounds that could become: anticancer drugs, antivirals, antibiotics, antifouling agents, natural pesticides

pros: lots of biodiversity, many possible compounds, potential drug discovery

cons: expensive, hard to access samples, replication/supply problems, and harvesting can damage habitats or important species

theonella

sponge HOST

• contains a huge consortium of uncultivated bacteria

• has hundreds of distinct bacterial phylotypes

• is associated with many different natural products

• can have very different metabolite profiles depending on where the sponge was collected

key question regarding it: are compounds actually made by the sponge, or by its bacterial symbionts?

entotheonella

bacterial SYMBIONT living in theonella

• non-culturable; had to use single-cell genome sequencing

• found two genetically distinct Entotheonella phylotypes

• large genomes, about 9 Mb

• one phylotype accounted for nearly all of the bioactive compounds

• Entotheonella occurs in sponges globally and was also found in seawater

key takeaway: many “sponge” secondary metabolites are actually produced by bacterial symbionts

• that matters because if you identify the biosynthetic genes, you could potentially move those genes into another lab organism and produce the compound without harvesting tons of sponge tissue

discodermolide

secondary metabolite from deep-sea sponge Discodermia dissoluta

researchers extracted compounds from sponge and found extracts killed cancer cells

• discodermolide is the active anticancer compound (it stabilizes microtubules, prevents proper cell division, can kill cancer cells, even worked against Taxol-resistant cancer cells)

the big problem was supply:

• it occurs at low concentration

• the sponge is deep-sea

• hard to harvest enough for drug development

two solutions discussed:

• mariculture: farm the sponge

• chemical synthesis: make discodermolide in the lab

eventually, researchers successfully synthesized it, and the synthetic form was used for preclinical work

diatoms

ubiquitous photosynthetic eukaryotes

• responsible for 20% of photosynthesis on Earth

• base of the marine food web

• encased in porous silica shells called frustules

• sink rapidly upon cell death

• carry fixed organic carbon into deep ocean

• important players in shaping carbon cycle and also impact cycling of nitrogen, silicon, and iron

hundred of genes present in diatom genomes have been acquired from bacteria (proteohodopsins)

phycosphere

region immediately surrounding an algal/diatom cell where bacterial growth is stimulated by extracellular products released by alga

• basically nutrient rich microbial zone around diatom/algal cell

• hot spot for interactions b/w bacteria and diatoms

bacteria can get into this region by chemotaxis toward attractant molecules, swimming into region, attaching directly to diatom surface (chemical communication may also happen here)

• aquatic analog of rhizophere

rhizophere

comparable zone around plant roots in soil

both are microenvironments where:

• the host releases compounds into the surrounding area

• those compounds change local chemistry

• microbes gather and interact with the host

• chemotaxis and chemical exchange help establish relationships

diffusive boundary layer

explains why phycosphere can exist

• thin layer of fluid around small aquatic organism that is not well mixed with bulk surrounding water b/c turbulence cannot really be maintained at that tiny scale

because region is not constantly mixed away, molecules released by diatom can temporarily accumulate near cell

• creates concentration gradients with: high conc. near diatom and lower conc. farther away

• concentrated zone helps form phycosphere

• if the cell is swimming, sinking, rising, or there is fluid movement, the boundary layer becomes distorted

diatom releases organic molecules → diffusive boundary layer prevents immediate mixing → molecules become concentrated around the cell → this nutrient-rich area is the phycosphere → bacteria are attracted and interact there

chondrichthyes

one of the three classes of fish

• sharks, skates, rays, and chimeras fall under this class

ampullae of lorenzini (AoL)

sensory structures in sharks/rays made of pores and electroconductive jelly

• jelly connects seawater to sensory system, helping shark detect prey-generated electrical signals and magnetic fields used in navigation

AoL jelly is nearly solid, diffusion-limited, potentially low in oxygen/nutrients, possibly able to concentrate compounds because they do not diffuse away easily

staphylococcus

main bacterial group in AoL jelly

possible role: beneficial/defensive symbiont, but that is not fully proven yet

important event in microbiology: 1676

leewenhoek discovers “animalcules” (aka microbes)

important event in microbiology: 1953

watson and crick propose the double helix structure of DNA

important event in microbiology: 1997

Escherichia coli genome sequenced

important even in microbiology: 2003

first human genome sequence was completed

horizontal transmission

one of two types of symbiont transmission

• involves the cyclic occurrence of aposymbiotic and symbiotic phases in the host’s life cycle

• symbiont has facultative life style consisting of the host-associated and free-living phases

• free-living population serves as the ones that initially enter the host and start the symbiotic relationships

vertical transmission

the second type of symbiont transmission

• transfer symbiont directly from parent to offspring

• no aposymbiotic stage (symbiosis is permanent)

• occurs (most often) through the EGGS (b/c eggs have more space and nutrients= cytoplasm, where endosymbionts can live)

effect of long-term symbiotic associations on genome evolution in host and symbiont

long-term obligate symbiosis can cause symbiont genome reduction and specialization because genes unnecessary inside the host are lost. This increases dependence between host and symbiont

• example: Buchnera lost ~86% of its genome and now depends on the aphid, while the aphid depends on Buchnera for essential amino acids

chemosynthesis vs photosynthesis

similarities:

• both processes use carbon dioxide

• both need energy source to fuel the reaction

• both result in production of sugars

differences:

• use different energy sources- light energy (& CO2) for photo and chemical energy (& CO2 & O2) for chem

• oxygen plays different role= it’s a reactant for chemo (sulfide oxidation) and product for photo

• photo makes O2 too and chem makes sulfate too

core, variable, and species-specific microbial communities

sponge microbiome is NOT one fixed set of microbes- contains microbes that differ in how widely they are shared among hosts

• core community- microbes found in many different sponge species; those present in at least 70% of sponge species (b/c broadly distributed, probably acquired mainly through horizontal/environmental transmission)

• variable community- microbes found in more than one sponge species, but not most of them; more likely host-associated/vertical transmission

• species-specific community- microbes found in only one sponge species; have restricted distribution and may be more closely tied to that particular host, potentially through vertical transmission or strong host specificity

role of T6SS in v. fischeri symbioses

V. fischeri has two Type VI Secretion Systems (T6SSs). T6SSs act like molecular injection systems that deliver proteins/toxins into other cells, but the target and function depend on the specific T6SS.

• T6SS2 → bacterial competition

T6SS2 allows V. fischeri to kill competing bacterial cells through contact-dependent killing. This helps determine which V. fischeri strains can occupy the same regions of the squid light organ. So, even though the squid–V. fischeri relationship is beneficial, V. fischeri can use T6SS2 to compete with other bacteria while establishing that symbiosis.

• T6SS1 → can contribute to pathogenic interactions with animal hosts.

T6SS1 is different. It is similar to a T6SS in Pseudomonas aeruginosa that can inject toxins into eukaryotic cells, which led researchers to test whether V. fischeri T6SS1 contributes to killing animal hosts.

The important finding is that T6SS1's role depends on both the bacterial strain and the host:

- ES114 + zebrafish: T6SS1 is needed for killing.

- ES114 + Artemia: T6SS1 is not needed for killing.

- ES213 + zebrafish: T6SS1 is not needed.

- ES213 + Artemia: T6SS1 is needed.

- PP3: uses T6SS1 against zebrafish but has little effect on Artemia.

• T6SS2: kills other bacteria → helps V. fischeri compete during squid colonization.

• T6SS1: can help kill animal hosts, but whether it is needed depends on the V. fischeri strain and the host.

V. fischeri can use T6SS for both bacterial competition and host interactions

sponge anatomy and pumping ability (liters per hour)

• ostia = small pores where water enters

• choanocytes = flagellated cells that pump water and trap food particles

• mesohyl = inner connective layer where food is transferred and digested

• archaeocytes = cells in the mesohyl that help digest food by phagocytosis

• osculum/oscula = large opening where filtered water exits

water flow:

ostia → choanocyte chambers → osculum

a 1 kg sponge can filter up to 24,000 L/day

convert that to hourly:

24,000 ÷ 24 = 1,000 L/hour

so:

1 kg sponge ≈ 1,000 L/hour

• sponges are powerful filter feeders: choanocytes drive water through ostia, food is processed in the mesohyl, and water exits through the osculum

scenarios of establishment of sponge-microbe symbioses

1. ancient symbiosis + vertical transmission

• symbionts are passed parent → offspring

• the association may be very old and maintained across generations.

2. both vertical + environmental transmission

• some microbes come from the parent

• others are picked up from the environment

3. environmental acquisition

• symbionts are picked up from seawater

• this can happen by:

- specific enrichment = sponge selects certain microbes

- subtractive enrichment = sponge takes in many microbes, but only some survive

- nonspecific enrichment = sponge concentrates microbes from the water generally.

1= parent only

2= parent+environment

3= environment only

specific enrichment, subtractive enrichment, and unspecific enrichment of sponge-associated microbes

• specific enrichment = the sponge selects certain microbes from seawater, and those microbes grow/enrich inside the sponge. This suggests some kind of host recognition or preference.

• subtractive enrichment = the sponge takes in many microbes, but digests/removes the ones that cannot survive, so the resistant microbes remain and become enriched.

• unspecific enrichment = the sponge filters water and concentrates all microbes similarly, without selecting particular ones.

specific= choose some

subtractive= remove some

unspecific= keep/concentrate everything

examples of pathogens, predation, and cooperation in sponges

• pathogen / parasitism: NW4327 infects the sponge Rhopaloeides odorabile. It can degrade collagen/spongin fibers and was re-isolated from infected tissue, supporting that it causes disease

• predation: Bdellovibrio is a predatory bacterium found in sponges that attacks other bacteria.

• cooperation: sponge microbes can help the host by providing useful nutrients:

- cyanobacteria provide fixed carbon/photosynthate

- some microbes use sponge waste nitrogen

- some make vitamins

- some store phosphate that can later be used by the host.

secondary metabolites: examples, ecological roles, and biomedical/biotech applications

pros and cons to bioprospecting in the marine environment

pros of marine bioprospecting

• huge biodiversity = many possible new bioactive compounds

• can lead to useful products like anticancer, antiviral, antibiotic, antifouling, or pesticide compounds

• one organism may produce many different useful compounds-

• can create funding/interest in marine organisms and conservation

• sometimes invasive species can be removed while also being studied for useful products

cons

• expensive and time-consuming

• marine samples can be hard to access

• collecting organisms can damage habitats

• could involve harvesting important/keystone species

• hard to reproduce or obtain enough of a compound

• we may exploit organisms we do not yet understand well

discodermia and discodermolide (discovery, applications, challenges)

ecological role and features of diatoms

diffusive boundary layer- how cell movement impacts its shape

diffusive boundary layer: a thin layer of water around a small aquatic cell where diffusion, not turbulence, controls movement of molecules. This helps secreted molecules stay concentrated near the cell and supports the phycosphere

• effect of cell movement:

if the cell swims, rises, or sinks, the boundary layer is distorted and becomes uneven rather than staying symmetrical around the cell.

still cell = more even boundary layer

moving cell = stretched/distorted boundary layer

• movement changes the shape of the diffusive boundary layer, which changes where nutrients and signals are concentrated around the cell

quorum sensing

pheromone signaling

where ice diatoms are found

antarctic ice diatom-bacterial interactions

ampullae of lorenzini features and biological function