| Marine microbial symbionts - Corals | Symbiosis of the coral polyp and a dinoflagellate called zooxanthellae. Primarily consisting of the genus Symbiodinium. These zooxanthellae in combination with pigments, give the coral its colour. The zooxanthellae provide the coral with energy via photosynthesis and the coral polyp provides the zooxanthellae with an environment with high light availability, CO2 and nutrients. Up to 90% of the corals energy requirements is obtained through photosynthesis. |
| Island Mass Effect | Increased nutrient concentrations may result from N2 fixation, decomposition, animal waste products. Current-bathymetric interactions - drive vertical transport of water masses via upwelling, downstream mixing and eddies, and internal waves. Island-associated inputs. |
| Marine microbial symbionts - Sponges | Sponges host diverse microbial symbiont communities that contribute to digestion and nutrient release from the filtered organics. In some species cyanobacterial (or dinoflagellate) endosymbionts can supply fresh photosynthate to meet a substantial fraction of the sponge energy requirements. N fixation, denitrification, and annamox are also known to occur
Sponges contribute to explain Darwin’s paradox through the generation of inorganic nutrients for the reef. |
| Generalist vs Specialist | Generalists - Environment changes, different pathway, regulated systems. Specialists - Core-proteome, essential proteins, stable env. conditions, difficult to culture. |
| Evolution to oligotrophy | Limiting nutrients in primary production: P, N and Fe. 1. Increase the: -surface area to volume ratio, -number and affinity of active membrane transporters, -diversity of available nutrient forms. 2. Decrease the demand: -Streamline genome, -Decrease the DNA G-C content, -Change phospholipids for others non-P containing lipids in the membrane, -Use enzymes with lower metal demands, -Use catabolic pathways with less costly enzymes, -Eliminate costly processes that can be ‘outsourced. |
| Ecological theories - Black Queen Hypothesis | 1. Many biological processes are ‘leaky’ and, hence, become what is known as common goods.
2. Species specialize in the consumption of a common good (loss of function due to genome streamlining) escape competition and therefore favour coexistence. 3. Dependency transforms interactions to novel long-lasting cooperative interactions. |
| Evolutionary arms race | Evolutionary arms race is an evolutionary struggle between competing sets of co-evolving genes, traits, or species, that develop adaptations and counter-adaptations against each other. Generally applied in marine microbes in the host-virus co-evolution but also applicable to grazer-prey and competing interactions. The evolution usually comes at a fitness cost. |
| Increasing CO2 emissions | 1. The buffering effect of oceans - Oceans absorb CO2 in equilibrium with atmospheric increase, Biological activity precipitates CO2 in the form of CaCO3 but with pH decrease, Biological activity is known to produce RDOM (and POM) that draws carbon from the surface and sinks to the bottom of the oceans where it can remain for centuries. 2. Ocean acidification - change in pH = 30% increase in H+ ions, Drop in limestone formation, Reef decline and Increasing wave energy on shorelines. 3. Temperature increase |
| Temperature increase effects | 1. Sea ice loss - Loss of habitat, Unpredictable consequences. 2. Sea Level Rise. 3. Higher stratification - Higher temperatures in surface seawater enhances the thermocline and hence, less nutrient upwelling… decrease in primary productivity in certain areas of the ocean. 4. Changes in currents. 5. Heat content - Total ocean heat content rising - 2 consequences: Warming in irregular patches, species shift pole-wards, Rising Accumulated Cyclone Energy. 6. Spawning errors (asynchrony). 7. Marine diseases |
| Increasing use of fertilisers and untreated sewage | 1. Eutrophication. 2. Harmful algal blooms: occur when colonies of algae grow out of control while producing toxic or harmful effects on people etc. |
| Overfishing | Increasing fishing efforts over the last 50 years as well as unsustainable fishing practices are pushing many fish stocks to the point of collapse. 85% of the world's fisheries have been pushed to or beyond their biological limits and are in need of strict management plans to restore them. |
| Pollution | Pollution is anything that causes harmful, or potentially harmful, effects. Ocean are ‘good at making pollutants disappear’...not for: Radioactive waste, Heavy metals, Oil spills, Noise, Plastic marine debris |
| Limulus circulatory system | Limulus made circulatory defence involves amoebocytes. Obloid in the blood stream and performs most of the normal functions associated with blood cells, engulfing foreign or dead cells, transport etc. Packed with small granules. Granules contain a clotting factor called coagulogen. When the cell detects bacterial endotoxin, coagulogen is released from granules and clots |
| Molecular cloning of GFP | In 1992, Douglas Prasher reports the cloning of the gene encoding avGFP into E.coli. Quickly realises the protein can work in many species and is independent of co-factors. Prasher suggests using GFP as a reporter molecule in diverse cells, for both gene expression studies and protein fusion. Before leaving, passed his cDNA clone of avGFP to Martin Chalfie and Roger Tsien |
| Impact of GFP on biotechnology | Enabling technology for medical biotechnology. Enables us to study and understand disease .Enabled the development and testing of drugs and pharmaceuticals |
| Rhodopsins and optogenetics | Rhodopsins are light-sensitive receptor proteins involved in signal transduction. All rhodopsins bind retinal as the chromophore. The best known rhodposins are the light sensitive pigments within the rods of our eyes. In microbes, rhodopsins can act as receptors that change conformation in
response to light to trigger intracellular signalling, as pumps that drive protons or chloride ions across the cell membrane, or as non-specific cation channels. |
| Optogenetics in neurobiology | Optogenetics refers to the ability to control or monitor cellular activities with light (‘opto’) using genetically encoded machinery. In the case of channelrhodopsins (ChR): When expressed in neuronal cells, the application of light can stimulate cations into the cell, thus depolarising it, and stimulating action potentials. Conversely: proton and chloride-pumping rhodopsins can be used to selectively hyperpolarize the cell and inhibit action potentials through either pumping protons out or pumping chloride into the cell. |
| Types of Aquaculture (Offshore vs Onshore) | Offshore: No control over environmental conditions, Difficult to control release of contaminated
waste, Subject to pathogens and parasites from the environment, Relatively cheap. Onshore: Conditions can be optimised, Stocking densities often increased leading to stress and disease, Initial outlay expensive |
| Stakeholders and Regulators | Policy makers: Introduce legislation and require reporting.
Statutory bodies: Enact and Enforce legislation.
Beneficiaries: Fishermen and public. |
| Key concepts in fisheries management | Gear selection (e.g. EU ban on pulse trawling). Fishing effort. Quotas (set by ICES based on historical species specific catches and current spawning stock data – MSY etc.). Fisheries closures. Transient fisheries closures (Pulse fishing) → Large scale fisheries closures (North Atlantic
Cod). |
| Marine Protected Areas - What are they? | No real definition (a ‘catch all’ term) – aka marine reserves, marine conservation zones. Cover many aspects of conservation from protection of individual species to a no take zone. Criticised as ‘Paper parks’. A legal framework to mange marine resources. This includes regulation, policing and monitoring. Spatially variable. We are at the start of the process |
| Meta-analyses of MPA effectiveness | 87 MPAs (964 sites) investigated worldwide. Studied effectiveness with reference to 5 key management practices: 1) degree of fishing permitted within MPAs 2) level of enforcement;
3) MPA age 4) MPA size 5) presence of continuous habitat allowing unconstrained movement of fish across MPA boundaries. |
| The ‘Great Plate Count Anomaly’ | The number of bacteria that can be grown using standard plating methods is frequently 1-4 orders of magnitude fewer than the number of cells observed by direct microscope count. Oligotrophs: adapted to low nutrient concentrations. Copiotrophs: needing high nutrient concentrations, but possessing various adaptations to survive periods of low nutrients. Opportunitroph: equipped to take advantage of transient occurrences of high-nutrient niches within a bulk low nutrient environment. |
| Studying the phylogenetic relationships among organisms within natural communities using rRNA sequences | rRNAs - specify structural RNA products of ribosomes. Bacterial ribosomes comprise 3 rRNAs : 23S (~ 2.4 kb) 16S (1.5 kb) & 5S (0.12 kb). Most conserved & widely used is the 16S rRNA : databases currently contain 2,500 sequences (cultured bacteria number 2,600). |
| Use of 16S rRNA sequences | It’s a universal marker which comprises both variable and conserved regions; - variable regions can be used to derive relatedness, and serve as phylogenetic chronometers. It can be selectively amplified depending on the taxonomic resolution needed. It constitutes more than 95% of the total cellular RNA content and possesses a rather large size (1.5 kb). This molecule is also ecologically relevant since the cell content of rRNA, which can be quantified using in situ hybridization, provides an index of the metabolic activity and growth rate of a population |
| 16S rRNA sequences & the marine environment | i) Obtain 16S rRNA sequences. ii) Compare gene sequences with large collection of sequences in the database. iii) Can then design oligonucleoides which are specific to different constituents of the community. iv) Oligonucleotide probes can be used to quantify distributions & identify cell types. |
| Results of 16S rRNA analysis | Of the 14 different lineages in SAR & ALO 6 were found in both libraries, & several genes cloned from the Sargasso were nearly identical to genes cloned from the Pacific population suggesting such uncultured groups are widely distributed in surface waters of subtropical oceans. a- proteobacteria: SAR1. γ-proteobacteria: SAR86. A remarkable discovery was the identification of Archaea as important members of the marine bacterioplankton community. |
| Cultivation of the ubiquitous SAR11 marine bacterioplankton clade in 2002 | Group accounts for 26% of all ribosomal RNA sequences that have been identified in seawater
Cultures obtained by high-throughput procedures for isolating cell cultures through the dilution of natural microbial communities into very low nutrient media. Volume of cells is 0.01 μm3 – amongst the smallest free-living cells in culture. Cells are crescent-shaped, 0.37-0.89 μm in length with average cell diameter of 0.12-0.2 μm. Genome size estimated to be 1.54 Mb |
| The SAR11 clade dominates ocean surface bacterioplankton communities | On average SAR11 accounts for a third of the cells present in surface waters and nearly a fifth of the cells present in the mesopelagic zone. In some regions members of the SAR11 clade represent as much as 50% of the total surface microbial community and 25% of the sub-euphotic microbial community. It is estimated that globally there are 2.4x10^28 SAR11 cells in the oceans, half of which are located in the euphotic zone. This suggests that this microbial group is among the most successful organisms on Earth – even though the biogeochemical role of the SAR11 clade is unknown. |
| Are there any problems associated with these molecular approaches? | i) bias in cloning : extraction of DNA; genome size; no. of rRNA genes; unclonable fragments.
ii) Coverage of clone libraries - Coverage C= 1 – (n1/N). Coverage is the portion of a clone library of infinite size that would be sampled by an actual clone library. |
