Aquatic Microbiology - Topic and Lecture note summary PDF

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Aquatic Microbiology Aquatic environments are highly variable in the resources and conditions available for microbial growth. The balance between photosynthesis and respiration controls the oxygen and carbon cycles. Phytoplankton: oxygenic phototrophs suspended freely in water; include algae and cyanobacteria. Benthic species: are attached to the bottom or sides of a lake or stream. ●

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The activity of heterotrophic microbes in aquatic systems is highly dependent upon activity of primary producers; oxygenic phototrophs produce organic material and oxygen. Oxygen has limited solubility in water; the deep layers of freshwater lakes can become ANOXIC once the oxygen is consumed Oxygen concentrations in aquatic systems are dependent on the amount of organic matter present and the physical mixing of the system.

Types of aquatic habitats - Lakes and reservoirs - Rivers and streams - Oceans (coastal seas, deep oceans) - Groundwater - Wastewater - Wetlands, waterlogged soil and swamps - Salt-marsh sediments - Estuaries Freshwater habitats LENTIC (Sluggish) Lakes, ponds, reservoirs Lakes: Seasonal Stratification - In many temperate lakes, the water column becomes stratified during the summer. - In the winter there is low concentration of oxygen on the bottom, high oxygen conc in the middle and medium oxygen conc at the top. - In Spring, is convection where there is a constant conc of oxygen at all depths. - In Summer, the deepest depth has low oxygen conc, in the thermocline there is medium oxygen conc and at the top there is high oxygen conc - In autumn , convection, constant conc of oxygen. Microbiological habitats in Lakes ● Planktonic - the water column, floating free in water ● Neustonic- the surface film ● Benthic - in and on permanently submerged sediments ● Sestonic - On floating organic matter Shallow near shore waters- light absorbance spectrum of phytoplankton algae and photosynthetic bacteria (Chlorophycophyta: 400-700 nm , green algae & Rhodophycophyta:

400-700 nm, red algae). Central lake waters > microbes form distinct community gradient based upon the wavelength - Cyanobacteria: 400-700 nm - Green sulfur bacteria: 400-800 nm - Nonsulfur purple bacteria: 400-900 nm CO2 uptake -> Phytoplankton -> Zooplankton Distribution of Bacteria in a Lake Sunlight ● Cyanobacteria - Epilimnion - Thermocline ● Green and purple bacteria - Hypolimnion So4^2- reducing bacteria - Hypolimnion CH4, NH4+, H2S ^^^^ from Anaerobes (Bacillus, Clostridium, Pseudomonas, Desulfovibrio) Sediment High microbial diversity reflects dynamic character of lake Eutrophication is a natural process that occurs to lakes over time - weathering of rocks and soils from surrounding catchment area leads to an accumulation of nutrients in the water and associated sediments. Young lakes - usually have low levels of nutrients and correspondingly low levels of biological activity. OLIGOTROPHIC (little/few - nourishment) Eutrofication: ● After artificial input of nutrients (eg run-off from agricultural land and effluent containing detergent or partially treated sewage). ● Eutrophic lake with high conc of plant nutrients PO4 so NO3- and PO43- high. ● Rapid growth of algae/cyanobacteria where there is heavy algal growth, increased turbidity and increased sedimentation. ● Increased growth of plants e.g reeds ● Algal blooms followed by lysis ● Development of anaerobic conditions -> anoxic conditions sediment The low oxygen concentrations result in fish death Old lakes - usually high levels of nutrients and corresponding high levels of biological activity. EUTROPHIC (well - nourished) Pollution of lakes and rivers can cause eutrophication. Water pollution has different effects on lakes and rivers. Lake water is not quickly replaced the effects can accumulate gradually, In rivers pollution is eventually washed away to the sea. Waste (wastewater especially) from human or animal origin can contain pathogens. LOTIC (Washed) Rivers and streams Rivers : - May be well mixed because of rapid water flow - Can still suffer from oxygen deficiencies because of high inputs of

● Organic matter from sewage ● Agricultural and industrial pollution Biochemical oxygen demand (BOD) - The microbial oxygen-consuming capacity of a body of water Richness vs abundance: High spp richness = cyanobacteria, diatoms, green algae, flagellates and bacteria. Following an algal bloom high abundance of cyanobacterium but low richness.

Extent of the marine environment ● Largest part of the biosphere ● 97-98% of all the water on Earth ● ~75% of the ocean is below 1000 m depth and is constantly cold (~3 oC) ● The deepest part of the oceans is ~ 11,000 m deep with 1000 atm pressure. ● Microbes have developed adaptations to the different environments. Research challenges ● Most research - near-shore and estuarine environments ● Off-shore interest where true offshore is ocean >1000 m ● 62% of the Earth’s surface is in the pelagic and deep sea region ● Little is known of geochemical activities involving microbes at this depth Use of light by phytoplankton ● Chlorophyll is key diagnostic marker ● Primary photosynthetic pigments - Different species have different types - Those with chloroplasts have chlorophyll ● Accessory pigments - Help with light harvesting - Chromatic adaptation - response to quality of light >carotenoids >xanthophylls >phycobilins Seawater composition ● The composition of seawater is ~36 parts per 1000 of salt. ● More than 80 elements ● Main ions (%): Na2+, Mg2+, Ca2+, K+, Sr2+, HBO3, Cl-, SO42-, Br-, CO3- and HCO3● N&P - Not major elements in oceans - But are present in sufficient quantity for biological activity. ● pH - 7.5 - 8.4 Temperature ● Usually in range of 2-4oC

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Growth of marine bacteria is usually optimum at 18oC Most of ocean is at lower T range In different currents at different depths, there are often sharp and clear differences in T. Dissolved gases ● CO2 input - most important gaseous exchange ● Atmosphere CO2 content - 600 billion tons. ● Seawater 100x as - CO2, carbonate and bicarbonate ● CO2 and bicarbonate ions - Used by photosynthetic organisms - Availability dependent on pH > photosynthesis stops : in seawater at pH 9.4 even in bright light; in fresh water at pH levels up to 10.1 (low calcium levels). Marine microorganisms ● Nutrients limiting but higher in coastal zones - Microbial counts lower than fresh water - Prochlorophytes(picoplankton) active even at great depths (photic zone down to 300 m) - Trichodesmium (cyanobacteria) fixes N in tropical and sub-tropical oceans ● Open oceans - Largest biomass on Earth - Decrease with depth (prokaryotes) - Oxygenic and anoxygenic photosynthesis - Bacteria with proteorhodopsin pigments - Slight predominance of Archaea below 1000m Smaller the size, greater the abundance. Surface Microbiology - Neuston ● Surface microlayer (SML) - Stable layer (1-1000 microlitres) - Hydrated gel-like layer - Microbial- and organic-rich - Biofilm environment - May give rise to marine aerosols - Modified chemical/physical properties ● At atmospheric interface - Harsh conditions - high UV, pollutants, pigmentation common ● Oily, mostly lipids, from marine organisms and natural hydrocarbon seeps but also surfactants - Bacteria arrive by upwelling on gas bubbles or are naturally hydrophobic - Consortia develop to degrade oils/pollutants - Increased bacterial respiration - control of O2/Co2 fluxes through interface ● Sampling the neuston - manta trawl, 300 micrometers, uppermost 20cm surface layer ocean, anthropogenic particles & neuston - Use synthetic aperture radar (SAR) to locate target (slit) - Identify the actual vicinity

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Sample following the new protocol Analyse samples through Pyrosequencing

Epipelagic zone ● Down to 150m; photosynthetic; mixed by solar convection currents - Seperated from deep ocean by thermocline - Cyanobacteria and prochlorophytes - Synechococcus at base (absorbs 400-500nm) small cocci to minimise sinking - Some Eubacteria synthesise bacteriochlorophyll; strict aerobe Erythrobacter - 60% ATP synthesis light driven to enhance organic carbon use under limiting conditions. ● Oxic but can bereduced by bacterial metabolism, esp after blooms - Anoxygenic phototrophs not usual except in stratified marine basins e.g Black Sea - Chlorobium green sulphur bacteria develop at 60-110m. Primary productivity - Capture of energy and fixation of CO2 - Oceans account for 50% Earth’s productivity - Equivalent to role of forests on land - Transferred to different layers and then to deep ocean - 10 gigatonnes/annum - Much of the primary productivity in the open oceans due to the photosynthetic activities of prochlorophytes > Prochlorococcus & Synechoccus > in tropical and sub-tropical areas: Trichodesmium - Eukaryotic diatoms also important Prokaryotic phytoplankton Synechococcus: - Very small (0.8-1.5 micrometers) - Widespread and ubiqitous - Contains chl a & phycoerythrin - Can fluoresce orange or red - Counted with epifluorescence or flow cytometry Prochlorococcus: - High densities - Smallest known (0.5-0.8 micrometers) - Divinyl chl a (modified chl b) - Counted by flow cytometry - Most abundant autotroph on Earth Ocean prokaryotic diversity ● The most important SAR11 clade alpha-Proteobacterium -> found throughout oceans ● 16s rRNA -> could not be cultured ● 2002 finally cultured and called Pelagibacter ubique -> study of its physiology ● ~⅓ of all bacterial cells in the ocean are from SAR11 lineage ● Shallow and deep water ● Successful -> genome survive and reproduce at even low nutrient conc.

Sargasso Sea experiment - The Power of Environmental Metagenomics - 1 billion bp of non-redundant sequence - Displayed the gene content, diversity and relative abundance of the organism - Sequences from at least 1800 genomic species including 148 previously unknown Nutrient upwelling: ● Movement of deeper colder water to shallower depths ● Rich in nutrients ● Wind direction/ strength and coastal topography important ● Surface water moves at 90o (left southern hemisphere, to right northern hemisphere) ● Extremely dynamic patterns ● Causes blooms of phytoplankton - Form basis of important food chains ● Coastal upwelling ecosystems - Most productive in world - 1% ocean surface = 50% world fisheries ● Affect movement of animal larvae Biological pump ● Phytoplankton live in the sunlit surface waters of the ocean, and through photosynthesis they convert atmospherically derived CO2 into their biomass. ● A fraction of this biomass sinks into the darker depths where it is colonized by bacteria that turn it back into CO2 through respiration. ● Thus, phytoplankton - bacteria interactions effectively transport CO2 from the atmosphere deep into the ocean. High nutrient low chlorophyll (HNLC) Iron sulphate added to ocean -> availability of iron prompts phytoplankton bloom which use CO2 to grow -> Phytoplankton die and fall to the ocean floor where CO2 is held for centuries....