Marine Exam 2 Review - Exam 2 study guide with notes from the book and lecture PDF

Preview

Summary

Exam 2 study guide with notes from the book and lecture...

Description

Marine Exam 2 Review 

PP 1- The Marine Environment:



There is one ocean that is divided into several parts  Pacific- thought to be peaceful, fairly cold o Large, average depth is 4,000 meters o Covers half of the ocean o 50.1 % of ocean surface area 

Atlantico Quarter of the ocean o 3,800 meters of average depth o 26.0% of ocean surface area



Indiano 20% of the ocean o Same depth as the Atlantic

10/12/2015

o 20.5% of ocean surface area 

Artico 3.4% of ocean surface area o 1,000 meters o More oil deposits  Antarctic ocean- southern ocean  Circumpolar, current does around the south pole

  

Current acts as a barrier that some things can’t penetrate

Some great lakes are bigger than seas The ocean takes up 72% of the Earth’s surface- primarily Oceanic*

What makes water flow?  Wind/ air flow, primarily b/c cold water is more dense than warm water (cold water   

sinks to the bottom) North of the equator water flows in clockwise South of the equator water flows counter clockwise Rainfall changes salinity and that effects density

  

Gulf stream flows in the bowl- easy to get caught in Gyers  a portion of the ocean that have a strong current (circulating body of water) Some parts of the ocean are deeper than our highest mountains  Continental shelf30m       



Abyssal plain -4,000m



  

Mid Atlantic ridge  hydrothermal vents along these ridges  Plates are separating, sea floor spreads and magma comes up to form ridges o A lot of activity builds the ridge up o Occurs in the other oceans as well Sea mounts  islands such as the Bermuda Western Africa has a thin continental margin If you sample in the Chesapeake,  Marine level salinity, no hydrostatic pressure, fairly constant conditions



If you sample from Bermuda,  Rapid movement of currents, colder, not the same as the Chesapeake



Composition of seawater  Salinity of the ocean, predominately sodium (NA 31%) and chloride (Cl 55%)  Some sulfate & magnesium 



o Small amounts of calcium, potassium, bicarbonate, etc. [The average composition of seawater  35 parts per thousand] o Some areas are over the average o The colder temperatures tend to have less salinity Varies a little depending on where you are



Temperature, depth, sunlight, && SALINITY effect the microbes on the ocean



halophiles love salt Obligate halophiles grow in the ocean  uniquely adapted to the marine environment Halotolerant organisms also live here such as E coli

 

      

Why is there higher salinity along the tropics and not at the equator?  The warm humid air along the equator rises (because of its low density) and cools, allowing water vapor to condense, which results in rainfall, causing precipitation to exceed evaporation Temperature vs. Depth  Between the surface of the ocean and the bottom there is a thermocline Forms a barrier because of change in density Temperature drives the change in density Change in density causes a thermocline The thermocline is a boundary layer, just as the top of the ocean and bottom are Ocean is predominately 5 degrees C  Ocean has high salinity, low temperature, high hydrostatic pressure, dynamic, and 

mostly dark, change in oxygen and CO2****** Thermocline may be more pronounced in the

summer The tropics have a very distinct thermocline CO2 and O2 vs. Depth   Oxygen decreases as you go deeper & CO2

 

increases! A lot of photosynthesis activity at the top Light penetration vs. Depth   Photosynthesis occurs at the top 60 meters where

 

there’s plenty of sunlight and consumption of oxygen  Below 600 meters is permanently dark, no photosynthesis, 5 degrees C, very low oxygen 

 

There is high productivity along the tropics! PH of seawater   Calcium interactions with carbonate and forms calcium carbonate rock  As we add CO2 the water gets more acidic and affects the pH 

Carbonate is a more basic solution

D



PP 2- The ocean as a microbial habitat  The ocean covers 72% of Earth’s surface, 3 times as much area than land  

It is the largest microbial environment on Earth The average depth is 3.8 km- 4,000 meters o Mariana trench is 11 km  It is on a subduction zone, the plate is moving underneath another  

 

plate Continues to get deeper James Cameron  Has been to the bottom of the Mariana Trench  Built his own vessel for the trip, took multiple hours to get

back and to get back up Salinity is generally 34-37 parts per thousand PH = 7.5 -8.4

Weight percent: o Sodium 55 o Chlorine 31 o Sulfate 8 o Magnesium 4 o Calcium 1







o Potassium 1 o & Trace elements Barophile  microbes that do better under some pressure  

10 m = 1 atm increase Mariana trench is 11,000 meters & 1,000 atm

 

Extreme barophiles require some pressure Ocean has hydrostatic pressure, pressure under water o How does this affect our bacteria?  E. Coli can handle some pressure,

bareotolerant Physiology of marine microbes   Halophile – require sodium   

Barophile- may require pressure

 

Oligotrophic- adapted to low nutrient levels Role of sunlight o Primary productivity o Drives proton pump- proteohodpsin o Aerobic Anoxygenic photoheterotrophy

Psychrophile to hyperthermophile- temperature >90% of the ocean is 5 degrees C or less

Estimated number of Bacteria and Archaea in the marine environment  Fewer on the continental shelf than the open ocean

o Open ocean – upper 200 m = 3.6 x 1028 o Open ocean – below 200 m = 6.5 x 1028 o Open ocean – top 10 cm of sediment = 1.7 x 1028 o Continental shelf - 1 x 1026    

Most are in the subsurface sediments Total oceans- 1.29 x1029 o (67% are beneath deep oceans) = 3.8 x 1030 Total marine microbial biomass- 4.2 x 1030

Distribution of Bacteria vs. Archaea  Around 500 meters the amount of bacteria  

and archaeal are pretty even (Has to do with pressure) BACTERIA: o Based on cultures  Gamma proteobacteria are predominate o Based on 16S rRNA  Alpha proteobacteria are predominate o Purple & green sulfur bacteria o Nitrifying bacteria o Cyanobacteria  Prochlorococcus & Synechococcus dominate the picoplankton o Vibrio, Pseudomonas, Aeromonas, Photobacerium, Bdellovibrio  Bdellovibrio- comma shaped organisms, gets up to very fast speed and rams its way through the cell wall of bacteria



ARCHAEA

o Euryarchaeota  Methanogens- anaerobes that produce methane  

Thermococcus & Pyrococcus- hyperthermophiles

Archaeoglobus- oxidize H2 and reduce sulfate, hyperthermophile o Crenarchaeota  Pyrolobus- grows at 113 degrees C, protein cell walls, 

chemolithotrophs Types of Niskin water samplers:  General Oceanics, Florida, collect water samples aseptically o Rosette Array o Single bottle sampler



HYDROTHERMAL VENTS:  Chemolithotrophic driven ecosystem  Unique syntrophic relationships  

High temps, low temps, dark, IR light, barophilic pressure Black smokers- hot vents (INCREDIBLY hot), this type of heat extracts a lot



vitamins/minerals, microbe-eukaryote associations All the minerals from the Basalt leave through the vent and as they hit the 5 degrees



water they precipitate, high levels of minerals surrounding the vents. Primary producers: chemolithoautotrophs and



chemolithoheterotrophs Warm bents are not as hot, less mineral



precipitation, less microbe presence IR light light is not naturally occurring that far down in the ocean but it is produced by the hot vents

Bermuda Atlantic Times Series (BATS)  Bermuda is 500-600 miles away from SC

 

Tip of a sea mountain that originates on the ocean floor Oligotrophic in the south part of the N Atlantic

Hawaii Ocean Time Series (HOT) David Carl & Ed Delong are the oceanographers who work there HOT-ALOHA o Objective is to provide a comprehensive description of the ocean at a site representative of the North Pacific subtropical gyre o Each month cruise to ALOHA about 100 km north of Oahu, Hawaii o Scientists working on the Hawaii ocean time-series program since October 1988 o Measurements include: thermohaline structures, water column chemistry, primary production, plankton community structure, etc. Global ocean survey sampling locations are along the East coast of the US, Honduras, Costa Rica, Panama, and the Galapagos Islands

Structure of the Marine Ecosystem- IMPORTANT! *Microbial loop -What comes off the land (watershed) is nutrients, pathogens, pollutants, etc. -Sun: light energy reaches the surface layer of the ocean (upper 60m), which is captured by photosynthetic bacteria o The surface (NEUSTON LAYER ~10 μm (around 10 microbes)) has the most intense light rays/highest amt. of light energy, consumption/production of CO2 and O2 drastically changes the pH, DOM: dissolved organic matter, DOC: dissolved organic carbon, viruses attack phytoplankton, produce POM, protozoa (eat bacteria), trophic levels of (produces/uses CO2/O2): Photosynthesis, heterotrophs, phototrophs, viral lysis o 2 boundary layers: atmosphere/ ocean & ocean/sediments o Organisms settle at the bottom of both boundaries o Surface of the ocean  barrier/ boundary layer (SEPARATES ATMOPSHERE FROM WATER) Carbon dioxide is soluble in the ocean and is being produced and moving out of atmosphere, oxygen dissolves into oceanic waters There is an interaction Sunlight, air temp and ocean temp are different Interaction between land and water (constituents- pollutants & nutrients)



Two loops into the ocean: Phytoplankton  zooplankton  Fish Phytoplankton (plant like)= algae, diatoms, dinoflagulates (float & under control of ocean) Zooplankton (animal like) = juvenile shrimp, fish, other small organisms (above 8 micrometers) Classic school web primary producers  secondary  tertiary Microbial loop  POM- particulate organic matter (has structure- can be filtered) Anything larger than .8 DOM- dissolved organic matter Amino acids, carbohydrates, small peptides, viruses Talking about all carbon together Phytoplankton provide food for zooplankton & release DOM (primarily carbon)

   

As they die they become part of the POM When POM gets larger it tends to sink & then comes to benthic portion & becomes part of the seafloor Bacteria are a sink for the nutrients C, N, P, Si, Fe loop Bacteriophage viruses infect and break up the bacteria to release more phage materials



Pieces of microbial cells are released Advection- flow (can be turbulent or less mixing)

Microbial Oceanography Carbon Cycle  >50% primary productivity of the Earth o ½ of the Earth’s carbon is fixed in the ocean by marine microorganisms not plants o Bacteria dominate the ecosystem o REMEMBER: the ocean is THE microbiological habitat of the planet   

Spatio-temporal patterns of carbon and energy flux Initially bacteria were ignored Now know that bacteria dominate the abundance, diversity, and metabolic activity

of the ocean Bacterial Microenvironment: Volume = 1μL • 10,000 viruses; 1,000 bacteria; 100 Prochlorococcus cells; 10 Synechococcus cells; 10 eukaryotic algae; and 10 protists • Close proximity (0–1 mm)  really close together! •

DOM hot spots • Photosynthetic regions

• Bacteria with flagella have an advantage to move to that area 1 cubic millimeter  1 mm by 1mm by 1 mm

• Organic matter in the ocean size range:

Macrogels & microgels are great sources of carbon and may be food Colloidal= some materials that generally dissolve together

Microspatial environments in the ocean:  Surfaces o Bacterial surface is a dominant biotic surface o DOM interactions with bacterial surfaces o Many microbes attach to surfaces for safety

o Mainly gram negative bacteria 

Pelagic o Motile bacterium- leaves monomers & oligomers behind



Transparent gels- colloids, sheets & bundle o Polymeric components o 10% of all the DOM (70 x 10^15 grams of carbon) o Bacteria can attach to gels- hydrolases convert gels to soluble nutrients

Uptake: multiple transporters- km (Km- kinetic measure of the rate at which microbes are taken up) Need to better understand the biochemical mechanism that couple OM transport and hydrolysis Bacteria in the ocean adaptive strategies Detritus- broken particles of phytoplankton (food for microbes) Ability to take things up from the environment = permeases OR they can attach to a polymer and break them up to bring them in Diagram below shows the ability of bacterium to take in nutrients:



Bacteria- Plankton interactions:  Phytoplankton- attach & carry out hydrolysis  Phycosphere o Mucus production by phytoplankton o Dimethylsulphoniopropionate (DMSP)  Dimethylsulfide (DMS)  Algae use DMSP and produce DMS  DMS goes up into the atmosphere and forms a cloud above the ocean o SAR 11 cluster 

Protists o Half of primary productivity consumed by protists o Eat up the bacteria o Bacteria colonize dead protists

Marine snow microbial cycling: Aggregate material that falls through water column  Serves as good source for bacteria for larger animals (metazoa)  Leaves a trail of carbon, nitrogen, silica, etc. behind

o (Tear drop shape) 

Microbes follow behind it to get the food



Marine snow is made of aggregates of POMs & DOMs (white in color)

PP 3: Microbial primary production About 50% of carbon fixed on our planet is fixed in the ocean Photosynthesis: requires light, consumes carbon dioxide, generates energy • Light reactions - energy from light trapped •

Dark reactions - chemical energy used to reduce CO2

• •

Oxidize H2O to O2 and reduce NADP+ to NADPH - oxygenic photosynthesis Oxidize another substrate and reduce NADP+ to NADPH - anoxygenic photosynthesis



~There are some reactions of photosynthesis that require light, respiration reactions

occur in the dark at night and in the day  ~Utilize the energy in sunlight to generate the chemical energy to reduce carbon dioxide to produce carbohydrates  Carbs consumed by microbes 24/7   

~Dark reactions don’t only occur in the dark they just don’t require light for energy NADP is used by microbes differently than NAD NADPH is the reduced form of NADP+



[Reduced means it gained an electron] o NAD carries electrons that are being produced in the microbe metabolism!!!

 

To reduce oxygen in catabolic reactions NADP+ is also an electron carrier but takes them to anabolic functions to

build biomass***** • •

[We need energy to drive anabolic & catabolic reactions] Anoxygenic photosynthesis does not produce oxygen

Take electrons not from water but from another substrate such as hydrogen sulfide What’re the pigments involved in photosynthetic processes? • Anoxygenic microbes  green and purple bacteria •

• • •

Do not have chlorophyll a

Look for chlorophyll a if you want to look for oxygenic photosynthesis Difference from bacterial photosynthesis and eukaryotic photosynthesis? • Use below .8 filtration • Green & purples only have photosystem 1  •

distinguishing characteristic* Can be photoheterotrophs because we can use CO2 and organic compounds as carbon source

The light reaction – Eukaryotes & Cyanobacteria

•

•

Chlorophylls • Major light-absorbing pigments • Can not catch all wavelengths so we have accessory pigments Accessory pigments • Broaden the spectrum of light • •

• •

Transfer light energy to chlorophylls E.g., carotenoids and phycobiliproteins

Organization of pigments • Antennas - highly organized arrays of chlorophylls and accessory pigments Photosystems – I and II • Antenna and its associated reaction-center chlorophyll Light harvesting molecules are found in highly organized systems Light harvesting antenna some structure of pigments so that light energy can be harvested

Collect light from different wavelengths Represent energy to the microbes The photosynthetic system consists of… 1. Light harvesting molecules & reaction centers 2. Photosynthetic membrane

3. Absorbance spectrum Prokaryotes do not have chloroplasts  Only found in eukaryotic organisms Purple bacteria- invagination of the cytoplasmic membrane  Green bacteria- chlorosomes; specialized non-unit membranes Eukaryote and Prokaryote chlorophylls: Phytol has 20 carbons hanging off of it, acts as a stability/anchoring component Anchors into a lipid membrane Many anchor close together as the antenna The unsaturated bonds = double bonds, missing hydrogen aka electrons Can have electron flow within the biological molecule No iron the middle  magnesium Difference between chlorophyll a and bacteriochlorophyll a  Both are similar in structure, allow for electron flow, have anchoring units  Some constituent groups make them uniquely different The different chlorophylls found in different bacteria capture light at different wavelengths (see table below)

Carotenoids- absorb blue light  Various types- distinctive for purple & green bacteria  Accessory pigments  Transfer energy to RC  Photoprotective= absorbs electrons and serves as an antioxidant  A lot of free radicals are generated at the surface of the water (why we need to use 

sunscreen) Isoprenoid units- excellent as electron carriers o Transfer electrons and uses them

Photosynthetic Microbes: ecological niches & light pigments  Different photosynthetic pigments  Distinct absorption spectra o Red wavelengths 620- 700 nm o Purple bacteria can absorb light in the infrared part of the spectrum o 500-580 nm  green o Violet  400-450 nm o Humans can see 400-700 nm range  

Oxygen requirements The most energy is found in the blue/ violet spectrum because they have shorter



wavelengths Bacteria find a place where they can generate energy Around the blue/ violet spectrum mainly,



some around red Phycobiliporteins are unique to cyanobacteria

Visible light spectrum-

We can detect light in a vary narrow range Ultra violet violet  blue  green  yellow  orange  red  near infrared   

Major groups of photosynthetic bacteria:

Phylum Cyanobacteria  Largest most diverse group of photosynthetic bacteria  Many are obligate photolithoautotrophs 

Resembles the plastid (chloroplast) of eukaryotes o Have photosystem I & II o Has chlorophyll a  Prochlorophytes have chlorophyll a and b



Oxygenic photosynthesis o One species can carry out anoxygenic photosynthesis uses H2S as electron



source Tolerant of environmental extremes

o Thermophilic species can grow at temperatures up to 75 degrees C o Often are primary colonizers 

Can cause blooms in nutrient rich water bodies (most pronounced in lakes and ponds but being observed more in marine waters) o Some produce toxins

...