Microbial Ecology

Question 1

How are microbes organized / trait-based?

Answer 1

Taxonomic groups, size, throphy (auto, hetero, mixo), functional groups.

Question 2

Hvad er en Appendicularian? Hvordan fungerer de og hvordan er de vigtige for vertical flux of carbon?

Answer 2

Lever i en stor skal men er små indeni. De er store ift hvad de spiser. De filtrere bakterier i deres skal. Når deres skal bliver for fyldt med shit fx fytoplankton, kan de hoppe ud af deres skal og lave et nyt hus. De skaller de smider, falder til bunden. Det er vigtigt for livet på bunden - vertical flux of carbon fordi der kommer HELE fytoplankton ned ift. ting der allerede er fordøjet med pøller der falder ned.

Question 3

What is the abundance of bacteria pr milliliter havvand?

Answer 3

Abundance: 1 million bacteria per milliliter

Question 4

Respirerer bakterier?

Answer 4

Respiration: Bakterier respirerer. Selv når man fjerner større organismer, ser man respiration.

Question 5

Hvad er detritus?

Answer 5

Waste or debris of any kind.

Things that have been broken down. Detritus kan breakes i endnu mindre dele og være DOC

Question 6

Hvad er DOC? hvad består det af?

Answer 6

DOC: Dissolved organic carbon. Broken down from blandt andet detritus.
DOC er et heterogent mix af organisk compounds som kommer fra biotic and abiotic degradation of organisms.
* Marine organisms are by far the dominant source
* Compounds released as dissolved or particulate from every level of the food web

Question 7

Hvad er bakteriers rolle i marine ecosystems?

Answer 7

Active component of the foodweb: De er productive. Bakterieplankton er en major carbon pool, also in Arctic systems. De er responsible for cycling a large fraction of the PP.
Primary role of bacteria in the food webs: The only group that efficiently can take up dissolved organic matter.

MAIN roller
Breaking down of organic matter.
Photosyntese.
Remineralization.
Bring back “lost DOC” to the food web.

Decomposers, like fungi and bacteria, complete the food chain. Decomposers turn organic wastes, such as decaying plants, into inorganic materials, such as nutrient-rich soil. They complete the cycle of life, returning nutrients to the soil or oceans for use by autotrophs

bacteria play a crucial role in nutrient cycling through remineralization of organic matter benefiting phytoplankton production

Question 8

Er bakterier meget adaptive?

Answer 8

Meget adaptive: De kan være over det hele også kolde Arktis. De er gode til at overleve steder.

Question 9

Forklar bakteriers rolle i long food webs

Answer 9

Long food webs where bacteria er main PP: Der er nogle steder, især nær ækvator hvor bakterier er the main PP. Her er der lange food webs, fordi carbon skal transporteres gennem mange, mange led før de når op.

Hvis der er meget næring til stede, så vil de større fytoplankton være flere af. Hvis der ikke er så meget og kun små ting, så skal næring igennem en længere kæde af mindre dyr.

Question 10

Hvad er bakteriers predatorer?

Answer 10

Prædatorer: Unicellular flagellates. De vokser samme speed som bakterier og følger deres bytte ret tæt i tid - hvor copepods har en anden langsommere livscyklus (det skaber relativ konstant biomasse for bakterier).
Derudover er deres prædatorer vira.

Question 11

Hvad er “The microbial loop”?

Answer 11

Flow of energy.
Nogle gange er fytoplankton så små at de ikke kan spises af copepods. Så spises de af predator microbes fx dinoflagellater og ciliates, som kan spises af copepods.
Eller : molecules are too small for the average consumer but are perfect sources of fuel for bacteria. By consuming the molecules, bacteria are reintroducing critical energy back into the food web when slightly larger creatures, like krill, eat the bacteria. This process is known as the microbial loop.

Phytoplankton and other marine organisms release organic molecules called Dissolved Organic Matter (DOM) or Dissolved Organic Carbon (DOC). DOM includes liquid wastes of zooplankton and cytoplasm that leaks out of phytoplankton cells. In the microbial loop, bacteria consume DOM that cannot be directly ingested by larger organisms. Each millilitre of seawater contains approximately 1 million bacterial cells, many of which utilise DOM as a source of energy and nutrition.

Bacteria are eaten by microflagellates. The abundance of the bacteria is, to a large extent, regulated by the grazing effects of heterotrophic nano-flagellates (2 – 20 μm in diameter). Ciliates, which are small enough to eat microflagellates, are eaten by zooplankton. Micro-flagellates and ciliates help to recycle organic matter back into the marine food web. Bacteria also help to facilitate phytoplankton growth by releasing nutrients when they absorb DOM. Viruses are the smallest and most abundant organisms in the sea, viral activity produces DOM, thus helping to drive energy cycles for ocean life. The main difference of the microbial loop between estuarine and coastal waters is that coastal waters tend to have lower population densities of bacteria and of the organism that prey on them.

Question 12

How will the relative importance vary / hvordan varierer bakterier from the poles towards equator?

Relative importance er det her med ruten energi tager i fødenettet, kort eller lang.

Answer 12

Arctic der er “kortere” foodwebs, større celler. Når man kommer nærmere ækvator er der flere mindre celler og længere food web, respiratory loss.

Question 13

Describe major “short cuts” in the food web and argue why and where they are relevant to integrate in our understanding of the flow of energy/matter trough the pelagic ecosystem.

Answer 13

De der seje celler Appendicularians der er mega store men som spiser meget små ting - feeder on the base of the food web. Dinoflagellates spiser også mindre ting end den 1:10 ratio.

These cosmopolitan primary producers are fast growing in nutrientrich waters 13 and their large size enables direct consumption by crustacean zooplankton such as copepods and hence a shortcut to fish

Question 14

Hvad gør phages og Hvordan kontrollerer phages the microbial abundance og bakterie populationer?

Answer 14

On the most basic level, viruses exist to replicate themselves, a process that most often involves killing their hosts.
By killing bacteria, phages control microbial abundance and release dissolved organic matter, influencing global biogeochemical cycles.

Virus affect bacteria population dynamics: Vira er meget specifikke med hvem de går efter. Fluctuation selection / killing the winner. Dvs. når der fx sker blooms I specifikke bakterier så er det også dem som virus går mest efter. Derfor er der en vis regulering af bakterie sub populationer.

Question 15

Hvor mange virus er der pr. milliliter i havet? Hvor mange i hele havet?

Answer 15

At concentrations of approximately 10^7 viruses per milliliter of surface seawater, viruses are the most abundant biological entities in the oceans.

There are an estimated 10^30 viruses in the global oceans.

Question 16

Hvor mange daily infections af virusser er der i havet om dagen? Og hvorfor er det godt/hvordan er virus the drivers of biochemical cycling in the ocean?

Answer 16

Each day, an estimated 10^28 viral infections occur in the world’s oceans, releasing up to 109 tons of carbon from biological cells.

Viruses as drivers of biochemical cycling in the ocean: Fordi der sker så mange infektioner hele tiden, så bliver der frigivet 50 Gt C per year. Det er nærmest lige så meget som the primary production. Det er meget. Viral activity stimulates primary production. Det ammonia de producerer ved lysing er godt for primær produktionen

Question 17

Hvad er phages? Er der mange af dem? Hvad gør de mod bakterier?

Answer 17

Phage: The majority of the viruses in the oceans are believed to be phages.
Phages er vira der infecter bakterier. They iinfluence their hosts through selection for resistance, horizontal gene transfer and manipulation of bacterial metabolism. Marine phages are extremely diverse and can carry a variety of auxiliary metabolic genes encoding critical ecological functions.

Question 18

Har virus deres eget metabolism?

Answer 18

Metabolism: Virus har ikke deres egen metabolism - de er afhængige af, at kunne infecte en hosts. De er på en måde stykker af DNA / genomsizes der flyder rundt. De er parasites på en måde.

Question 19

Hvad betyder det, at virus lysing their hosts?

Answer 19

Vira lysing their hosts: Break down of bacteria cells. Makes phages efficient killers. De injecter ligesom deres DNA ind I en host. Det hijacker the host og får dem til at gøre ting. Til sidst expoderer cellen og nye virus sendes ud. Når bakterie cellen exploderer bliver den til mad for andre bakterier (den indeholder jo hvad de har brug for). Baceria efficiency uptake of this is 74%.

Carbon release during viral lysis: Peptide release. Large release of amino acids.

Question 20

Hvad er byttedyr for virus i havet?

Answer 20

Bakterier og fytoplankton.

Question 21

Hvad er Auxiliary metabolic genes AMGs? Og hvordan kan de benefitte bakterierne som får dem af virus?

Answer 21

AMGs modulate host cell metabolism during infection so that the phage can replicate more efficiently.

Enrichment with phage DNA through integration in host genome and transfer of genes between hosts: På en måde er the hosts DNA enriched nogle gange af ny DNA. Deres DNA kan integreres i hosts. Fx kan et AMG som tilføres, gøre, så hosten faktisk bliver bedre til at optage nogle ting i mad, så den vokser mere (dog ender den vist stadig med at dø). Mutual benefits. Hosten har nogle gange også noget at sige ift. hvad der sker.

Question 22

Er virus diverse??? og hvad er deres generation time?

Answer 22

Diverse group: De er virkelig diverse og der er mange. Især fordi de har så kort generation time.

Generation times for viruses: A few hours to a day.

Question 23

Kan bakterier udvikle resistens for virusserne? og hvis ja, hvorfor er der så virus overhovedet?

Answer 23

Bacteria evolve resistance from virus (phage sensitive or phage resistant): Hvis man tilføjer en virus til nogle bakterier så vil antallet falde først - men efter noget tid vil bakterie antal stige igen, fordi nogle bliver resistente (ved mutation) og så føres disse videre og kan overleve.

Hvorfor er der så virus?: Fordi det koster meget at komme resistent. Reduced growth rate. Loss of motility. Enhanced mortality by other phages.

Question 24

Forklar nutrient remineralisation ?

Answer 24

Nutrient remineralization i havet er processen, hvor organismer som fisk, plankton og andre dyr bruger næringsstoffer som kulstof, kvælstof og fosfor til at vokse og leve. Når disse organismer dør eller producerer affald, falder de til bunden af havet og nedbrydes af bakterier og andre små organismer.

Under nedbrydningsprocessen bliver de næringsstoffer, som var låst inde i organismerne, frigivet tilbage i vandet i form af mineraler. Disse mineraler kan derefter genbruges af andre organismer i havet til at vokse og opretholde deres liv. Så kort sagt, nutrient remineralization handler om at genbruge næringsstoffer fra døde organismer, så de kan bruges igen af andre havorganismer

Der er flere ting der kan lave nutrient remineralisering.
- Decomposition of DOM and POM
- Living organisms som bakterier fx

Experiments indicate that very small organisms dominate nutrient remineralization in many planktonic systems.
Another route for nutrient remineralization is called the microbial loop, where small, unicellular algae, bacteria, viruses, protozoa (particularly very small flagellates), and rotifers rapidly recycle carbon and nutrients.

Question 25

Der kan være trade-offs for competition specialists (fx osmotrophs - organisms that feed on dissolved substrates) mellem deres uptake capability and protection against infections fra virus.
Hvordan kan det være?

Answer 25

The uptake porins used for nutrient transport through the cellular membrane can also be the locus for viral attachment and nucleic acid injection.
Modifying the porins to reduce viral attack would, presumably, be likely to reduce transport.

Question 26

Artikel i Modelling Concepts:
Use of non-limiting substrates to increase size; a generic strategy to simultaneously optimize uptake and minimize predation in pelagic osmotrophs?

We here discuss three cases of pelagic osmotrophs, covering a wide spectrum in physiology and cell size:

(1) the heterotrophic bacterium Vibrio splendidus, hypothesized here
to have the potential to….. what

(2) the autotrophic cyanobacterium Synechococccus, hypothesized
to use the same strategy, but based on … what

(3) diatoms using silicate to build …. what

Answer 26

We here discuss three cases of pelagic osmotrophs, covering a wide spectrum in physiology and cell size:

(1) the heterotrophic bacterium Vibrio splendidus, hypothesized here
to have the potential to use an excess of organic carbon substrates to increase cell size without a concomitant increase in its requirement for nitrogen or phosphorous;

(2) the autotrophic cyanobacterium Synechococccus, hypothesized
to use the same strategy, but based on photosynthesizing the organic-C required; and

(3) diatoms using silicate to build an exoskeleton allowing a large vacuole (en lomme med væske fx) that can be emptied for the limiting element.

The price paid for this strategy thus differs, but all cases imply that the strategy can only be used under specific environmental conditions, characterized respectively by an excess of organic substrates for bacterial growth, an excess of light energy for primary production, or
the presence of free dissolved silicate

Question 27

Normale bakterie communities, hvor bakterier indeholder både C, N og P. Hvad er C : P ratio normally found in natural bacterial communities

Answer 27

Average 50 : 1
C : P ratio normally found in natural bacterial communities

Question 28

Nogle mikroorganismer kan optage et bestemt stof hvis der er excess af det. Fx hvis der er meget glucose eller meget DOM kan de ligesom optage dette, blive større (men blive større uden at have brug for mere af the limiting shit i vandet, som der stadig ikke er nok af, adjusting cell quotas) for at på den måde få flere fordele. Hvilke fordele kan det være?

Answer 28

• increased nutrient uptake
• decreased predation pressure,
• storage of energy and carbon for potential later use under C-limited conditions.

Question 29

The ability of osmotroph organisms to adjust cell quotas according to the availability of an element is well known, both for phytoplankton and heterotrophic bacteria. Hvad betyder dette?

Answer 29

Nogle organismer kan optage en non-limited ressource (fx hvis der er meget DOM i området C) så kan de optage meget af det og enten gemme det til senere eller de kan vokse i størrelsen UDEN at behøve at optage flere andre limited nutrients for eksempel. Det hedder at de adjuster deres cell quotas (for fx C, N, P osv så de ikke behøver optage mere af alle)

Det giver organismerne competitive advantages i forskellige miljøer.
Storage capacity for a non-limiting element may provide a competitive advantage in both stable and changing environments

Question 30

Hvad er the small-celled competitor strategy. Og nævn et eksempel på nogle fytoplankton som bruger denne strategi

Answer 30

Jo mindre celler er, jo mere effektive er de til at optage næringsstoffer, mineraler osv. Pga. deres size : volume ratio. Det er small-celled competitors.
De bliver dog spist af andre, fordi de er små. Derfor er der nogle der laver defence against predators/bliver større som en anden metode.
De er ofte mere effektive i oligotrofe vande

Small autotrophic picoplankton with < 1 lm cells, such as Synechococcus and Prochlorococcus, have been thought of as examples of extreme adaptations to the small-celled competitor strategy discussed above, obviously successful considering their abundance in the ocean’s oligotrophic regions

Question 31

Forklar hvad Winnie the Poo strategists er. Og er det maximizing eller minimizing the r : m ratio.

Answer 31

Winnie the poo - when the Rabbit said “Honey or condensed milk with your bread”? he was so excited that he said, “Both”

Det er hvis man ikke behøver at gå ned på det ene for at få det andet.

For fotosyntese bakterier:
maximizing the r : m-ratio by storing photosynthesized carbon inside the cell and, in extreme cases, minimizing m by abandoning genes not strictly required.

m the amount needed to make a new cell
m the cell quota of the limiting element

Maximum diffusive transport towards a spherical cell of radius r is given by the expression 4pDrS, where D is the molecular diffusion constant for the substrate in water and S the concentration at an infinite distance from the cell

The essence of the discussion above is that optimizing either nutrient uptake or predator defence can both be successful strategies in a tightly coupled microbial food web, depending on the environmental conditions. The most universally successful strategy would, however, be one that can simultaneously maximize uptake and defence (the
proposed Winnie-the-Pooh strategists)

Question 32

hvor meget af O2 i atmosfæren er produceret af havets fytoplankton?

Answer 32

Omkring 50% med fotosyntese

Question 33

Hvordan kan fytoplankton i havet regulere vores klima??

Answer 33

De optager CO2 fra luften og omdanner det til ilt. fotosyntese

Question 34

hvad er en anaerob bakterie?

Answer 34

Anaerobic bacteria – bacteria that can survive without oxygen – are active in the ocean floor. They process the methane with the help of sulphate (SO42-), thus producing hydrogen sulphide anions (HS-), hydrogen sulphide (H2S) and bicarbonate (HCO3-).

Anaerobes are microorganisms that don’t require oxygen in order to survive or proliferate. Instead of oxygen, anaerobic organisms use electron acceptors such as nitrate or sulfate and other inorganic acceptors that have a lower reduction potential than oxygen, thus resulting in less efficient respiration.

Question 35

Hvad er en aerob bakterie?

Answer 35

Aerobic bacteria – which need oxygen – are active in seawater.

Aerobic respiration breaks down glucose and combines the broken down products with oxygen, making water and carbon dioxide. The carbon dioxide is a waste product of aerobic respiration because cells do not need it.

Most of the organic matter in the world’s oceans is remineralized via aerobic respiration by heterotrophic microorganisms. Only when oxygen (O2) becomes scarce, microorganisms use thermodynamically less favourable electron acceptors, predominantly nitrate (NO3 -), for the oxidation of organic matter.

Question 36

Forklar et eksempel som ikke er winnie the poo strategists -

Answer 36

Når plankton går sammen for at lave kolonier i stedet for at stå alene:

However, from geometrical considerations, it is difficult to see how nutrient uptake can be improved by arranging the cells on the surface
of a sphere, as opposed to distributing them as small swimming flagellates. Phaeocystis may thus be an example of a successful organism that cannot really be classified in the same category as our proposed Winnie-the-Pooh strategists.
Rather, it seems to have chosen to either optimize nutrient uptake in the free flagellate form or to minimize predation in the colony form

Derudover er både uptake specialist og defense specialists heller ikke winnie the poo strategists da de fokuserer på én af tingene

Question 37

Vækst under diffusionsbegrænsning (uptake af næringsstoffer gennem diffusion) afhænger af

Answer 37

forholdet mellem cellens overflade og cellernes behov for det begrænsende element

Question 38

Hvad er Metazoans?

Answer 38

Metazoan are those animals whose body is arranged into tissues, organs and organ system. They are multicellular organisms. Example - fish, birds, amphibians, reptiles and mammals.

Question 39

What are the three main carbon pumps in the ocean?

Three main processes (or pumps) that make up the marine carbon cycle bring atmospheric carbon dioxide (CO2) into the ocean interior and distribute it through the oceans.

Answer 39

Three main processes (or pumps) that make up the marine carbon cycle bring atmospheric carbon dioxide (CO2) into the ocean interior and distribute it through the oceans.
These three pumps are:

(1) the solubility pump,
(2) the carbonate pump,
(3) the biological pump.

Question 40

Hvad er the biological carbon pump in the ocean?

Answer 40

The biological pump is the set of processes by which inorganic carbon (e.g., carbon dioxide) is fixed into organic matter via photosynthesis and then sequestered away from the atmosphere generally by transport into the deep ocean.

The biological pump is a process of oceanic carbon sequestration that is driven mainly by autotrophic phytoplankton that inhabits the surface waters. This method of autotrophy, photosynthesis, converts CO2 (dissolved inorganic carbon (DIC)) into organic biomass (particulate organic carbon (POC)) (Passow & Carlson, 2012; Sigman & Hain, 2012). Photosynthesis is the initial method of bringing carbon into the biological pump. It is further moved throughout the ocean by entering the food web after phytoplankton, which are primary producers at the lowest trophic level, are eaten by consumers. Carbon can then stay in the food web as higher trophic levels continuously consume organisms, or it can be released from the food web in the form of defecation or dead tissue (Passow & Carlson, 2012). This carbon sequestration process by primary production accounts for a vast majority of carbon fixation on Earth

Question 41

Hvad er the solubility pump?

Answer 41

The solubility pump is one of the two ways carbon (in the form of carbon dioxide, or CO2) is moved through the ocean and back into the atmosphere. The solubility pump utilizes ocean temperatures, deep currents, and upwelling

The solubility pump refers to the fact that carbon dioxide is more soluble in cold water and that cold water is also denser and more likely to sink into the deep ocean. The solubility pump is thus driven by a combination of ocean physics and chemistry.

Question 42

Hvad er the calcium carbonate (counter) pump? og hvorfor hedder den det?

Answer 42

The carbonate pump is a process driven by organisms like coccolithophores that produce calcium carbonate (CaCO3) shells. These organisms take up dissolved carbon and calcium to create CaCO3 and CO2. This process helps remove carbon from the ocean’s surface and transport it to the seafloor as sediments, where it can be stored for a long time. Ultimately, this helps reduce the amount of CO2 in the atmosphere over geological timescales. Organisms like coccolithophores play a crucial role in this process by producing a significant amount of calcite, which contributes to carbon transport and burial in marine sediment.

Kalkdannende organismer optager opløst CO2 og calcium for at danne calciumcarbonat (CaCO3), samtidig med at de frigiver CO2 som en biprodukt af denne proces.
Den nettoeffekt er imidlertid en fjernelse af CO2 fra havoverfladen på lang sigt. Selvom CO2 frigives under kalkdannelsen, bidrager den resulterende ophobning af CaCO3 i havbunden til en netto-opbevaring af carbon, hvilket hjælper med at reducere CO2-niveauerne i atmosfæren over geologisk tidsskala.