Diatom Bowler Paper

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Notes on the paper, as you see there is a lot of content about diatoms.

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• Diatoms in the Modern Ocean

  • Diatoms are the leading group of eukaryotic phytoplankton.
  • They achieved dominance in the last 100 million years.

• Genomic Revelations

  • Whole-genome sequencing of Thalassiosira pseudonana and Phaeodactylum tricornutum.
  • Genes acquired from:
  • Endosymbiotic ancestors.
  • Horizontal gene transfer from marine bacteria.

• Unique Metabolic Capabilities

  • Integration of a urea cycle within photosynthetic cells.

• Genomic Approaches

  • Shedding light on oceanographic and biogeochemical processes.
  • Insights into nutrient assimilation and diatom life histories.

• Climate Change Concerns

  • Potential impacts on diatom physiology.
  • Effects on broader oceanic processes.

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Importance of Diatoms

1. Primary Producers:

   • Diatoms contribute to a significant portion of primary production in aquatic ecosystems, accounting for approximately 20% of global photosynthetic carbon fixation in marine environments.

2. Biodiversity:

   • Diatoms are incredibly diverse, with an estimated 100,000 species. This diversity makes them one of the most abundant and varied groups of phytoplankton.

3. Oxygen Production:

   • Diatoms produce approximately 20-25% of the world's oxygen, making them a crucial contributor to the Earth's oxygen supply.

4. Carbon Sequestration:

   • Diatoms play a role in sequestering carbon in the ocean. They are responsible for the burial of up to 10 Gt (gigatons) of carbon annually in marine sediments.

5. Nutrient Cycling:

   • Diatoms are significant in nutrient cycling, particularly in marine ecosystems. They are responsible for a large portion of silica and carbon uptake in marine waters.

6. Indicator Species:

   • Diatoms are commonly used as bioindicators in environmental monitoring. Changes in diatom communities can indicate shifts in water quality and ecosystem health.

7. Economic Importance:

   • Diatoms have commercial value. The diatomaceous earth, derived from fossilized diatoms, is used in various industries, including filtration, agriculture, and pharmaceuticals.

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Diatoms' Importance in Marine Ecosystems

• Diatoms' Ecosystem Services:

  • Serve as the foundation of marine food chains.
  • Support higher trophic levels, promoting energy-efficient food webs.

• Role in Coastal Fisheries:

  • Critical for sustaining large-scale coastal fisheries, such as anchovies in the Peruvian upwelling.

• Biological Carbon Pump:

  • Heavy siliceous walls of diatoms contribute to the downward flux of carbon in the ocean.
  • Dead and dying diatoms facilitate the transfer of energy, electrons, and carbon to the deep sea.
  • Contribute to the long-term storage of carbon in marine sediments.

• Global Silica Cycle:

  • Influence the availability and cycling of silica in marine ecosystems.
  • Vital for the growth and health of marine organisms, including diatoms.

• Peruvian Upwelling:

  • An important oceanic phenomenon off the coast of Peru where nutrient-rich deep waters rise to the surface.
  • Supports a highly productive marine ecosystem, with diatoms playing a crucial role in sustaining fisheries like anchovies.

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Genome Sequencing and Insights in Diatoms

• Genome Sequences:

  • Complete genome sequences reported for two diatoms:
  • Thalassiosira pseudonana (Reference: Armbrust et al. 2004)
  • Phaeodactylum tricornutum (Reference: Bowler et al. 2008)
  • Chosen for their small genome sizes:
  • T. pseudonana: 32.4 Megabases (Mb)
  • P. tricornutum: 27.4 Mb
  • T. pseudonana: Representative of centric diatoms
  • P. tricornutum: A pennate diatom

• Genomic Information:

  • Both diatom genomes contain between 10,000 and 14,000 genes.
  • Approximately 50% of genes have a known function based on current knowledge.
  • Around 35% of genes are specific to each diatom.

• Phylogenomic Insights:

  • Diatom origins linked to a secondary endosymbiotic event.
  • Originated from a red alga associating with a heterotrophic eukaryote.
  • Diatom genomes contain traces of both endosymbiotic partners.
  • Diatom genomes differ in gene repertoires from green algae and higher plants.

• Novel Metabolic Insights:

  • Diatom genomes incorporate genes for novel metabolisms.
  • Examples include mitochondrial fatty acid oxidation pathways and a urea cycle within a photosynthetic cell (Reference: Allen et al. 2006).

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Insights from Diatom Genome Sequences

• Red Algal Origins:

  • Initial findings supported a red algal endosymbiont with approximately 170 genes of red algal origins.
  • Many more genes (over 1700) showed traces of green algal origins, suggesting a preceding green algal endosymbiont.
  • Plastid-localized proteins from the green alga incorporated into the red algal endosymbiont, leading to the diatom plastid.

• Serial Secondary Endosymbiosis:

  • Diatoms likely derived from a serial secondary endosymbiosis, as first proposed by Sanchez-Puerta & Delwiche (2008).

• Bacterial Gene Presence:

  • Diatom genomes contain bacterial genes, with P. tricornutum having at least 587 such genes, constituting at least 5% of total gene content.
  • Over half of these bacterial genes are also shared with T. pseudonana.
  • Diatoms exhibit a unique pattern of horizontal gene transfer, potentially due to their associations with bacteria.

• Diatom Genomic Complexity:

  • Diatom genomes combine genes from various origins, encoding unique pathways for nutrient assimilation and metabolite management.
  • These genomic features have profound implications for understanding diatoms' roles in biogeochemical cycles.

• Challenges in Functional Assignment:

  • Most diatom genes with assigned functions are based on extrapolations from model organisms like yeast and Arabidopsis.
  • Limited knowledge exists for diatom-specific genes and their functions.
  • Studying gene expression in response to ecological stimuli is a promising approach to understand diatom-specific adaptations.

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The passage discusses the challenges and advancements in assigning specific functions to genes, particularly in diatoms. Here's a breakdown of what it's saying:

1. Assigning Function to Genes: The goal is to determine what each gene does or its specific role in an organism.

2. Challenges with Correlations: Simply observing correlations between genes and certain traits doesn't provide definitive proof of a gene's function.

3. Gold Standard in Biology: The most definitive way to understand a gene's function is to "knock out" or deactivate the gene and observe the resulting effects on the organism. If the organism shows a specific change (perturbation), it suggests the gene was responsible for that function.

4. Advancements in Diatom Research:

   • Techniques for genetic transformation (altering genes) in diatoms have been developed and reported.
   • Techniques are particularly advanced for a specific diatom species, P. tricornutum.
   • A method called RNA interference (RNAi) has been described. This technique can be used to deactivate or "silence" specific genes, allowing researchers to study their functions.

5. Demonstration of the Technique's Utility: The RNAi technique was used to deactivate a gene involved in DNA repair. When this gene was silenced, the cells became more sensitive to UV irradiation (a type of DNA-damaging radiation). This demonstrated the gene's role in DNA repair.

6. Conclusion: With these advanced techniques, particularly RNAi, there are no longer technical obstacles preventing scientists from determining the function of uncharacterized genes in diatoms.

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• Silica Frustule Preservation:

  • The silica frustule of diatoms is well-preserved over geological timescales.
  • The fossil record of diatoms is extensive, with notable deposits like diatomaceous earth and cherts that can be over 1 km thick in some places.

• Biochemical Markers:

  • Certain biochemical markers, such as C25 heavily branched isoprenoid alkenes and 24-nor/27-nor-diacholestanes in crude oil, serve as proxies for diatom abundance.

• Evolutionary History:

  • The evolutionary history of diatoms has been reconstructed, linking their development to major Earth events.
  • Fossil records indicate that centric diatoms emerged first, followed by pennate diatoms. This evolutionary sequence aligns with molecular phylogenies, although there are discrepancies in timing.

• Diatom Fossil Records:

  • Molecular clocks suggest a diatom origin around 250 Mya, but the oldest confirmed diatom fossils date back to 180 Mya.
  • Centric diatom fossils from the Jurassic Period are limited, with more abundant fossils appearing in the Cretaceous period.

• Planktonic Diatom Diversity:

  • A significant shift in diatom diversity occurred around the Eocene-Oligocene boundary, leading to the appearance of many modern diatom genera.

• Modern Phytoplankton Lineages:

  • Before the Mesozoic era, phytoplankton primarily consisted of cyanobacteria and acritarchs.
  • Modern phytoplankton lineages introduced heavy cell walls, contributing to enhanced carbon sequestration and creating petroleum reserves.

• Cretaceous-Tertiary Mass Extinction:

  • Diatoms survived relatively well during this mass extinction and began colonizing the open ocean.
  • Planktonic diatom diversity peaked during the Eocene but declined afterward.

• Oligocene Events:

  • The Oligocene was marked by significant global events, including increased ice volume and Antarctic ice cap formation.
  • The Antarctic Circumpolar Current became established, which is now a major region of diatom-based carbon export.

• Evolutionary Innovations in Diatoms:

  • Silica mobilization for building cell walls was a critical evolutionary innovation in diatoms.
  • The ability to use silicon more efficiently allowed diatoms to expand into open ocean environments.

• Survival of Diatoms:

  • The reasons for diatoms' relative survival during the end-Cretaceous mass extinction remain unclear.

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• Role of the Raphe:

  • The raphe, a slit along the frustule of diatoms, facilitates movement through the secretion of polysaccharides.
  • Initially evolved for surface gliding in benthic diatoms, raphid pennate diatoms now exploit this for movement in planktonic environments.
  • Active gliding in water allows them to utilize thin layers of physical discontinuity for reproduction and bloom formation.

• Evolutionary Origins of the Raphe:

  • Genome sequences haven't yet revealed the origins of the raphe.
  • Potential genes involved in raphe construction include myosins, some of which play roles in alveolates.
  • P. tricornutum has genes related to raphe construction, while T. pseudonana lacks them.

• Innovations and Adaptations:

  • Diatom genes and potential gene incorporations from bacteria played roles in major innovations.
  • Polysaccharide biosynthesis genes from bacteria might have helped diatoms expand into open ocean environments.
  • Buoyancy control, lipid content, and the evolution of structures like spines were central for diatom invasion into pelagic environments.

• Diatom Genome Diversification:

  • Analysis of diatom genomes showed rapid diversification rates for diatom-specific genes.
  • T. pseudonana and P. tricornutum, despite diverging around 90 Mya, have evolved as much as metazoans in 550 million years.
  • The cause of rapid diversification remains uncertain; it's unlikely due to genome duplication events but may involve diatom-specific mobile genetic elements like transposons.
  • Copia-like retrotransposons in diatoms, especially in P. tricornutum, could promote genome rearrangements, leading to diversification.
  • Some of these transposons activate in response to stress, potentially facilitating genome rearrangements for diatom diversification.

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Climate Change Impact on Diatoms

• Human Activities & CO2 Emissions:

  • Human activities have disrupted global equilibria, primarily due to CO2 and greenhouse gas emissions.
  • Approximately 79 million tons of CO2 are released daily from fossil fuel burning, deforestation, and cement production.
  • Since the industrial era, a third of this CO2 has been absorbed by oceans, leading to changes in seawater chemistry.

• Seawater Chemistry & pH Levels:

  • CO2 absorption in oceans forms carbonic acid, increasing H+ ions and reducing seawater pH.
  • Current surface waters have an average pH of 8.1, down by 0.1 units from preindustrial times.
  • Predictions suggest ocean pH could drop to 7.8 by the end of the century, unprecedented in millions of years.

• Impacts on Phytoplankton & Diatoms:

  • Rising temperatures may increase vertical stratification in water columns, potentially depriving phytoplankton of essential nutrients.
  • Diatoms, which prefer cooler waters, may face challenges, but their silicification processes might be less affected by pH changes compared to other organisms.
  • Diatom abundance might increase due to higher bicarbonate availability, potentially affecting coccolithophorids. However, evidence from the past doesn't support this.

• Understanding Ocean Acidification:

  • Essential to understand the consequences of ocean acidification on various organisms.
  • Studies using genomics can help identify key genes and evolutionary responses to adaptation in changing conditions.

• Other Climate Change Impacts:

  • Climate change may lead to increased size of oligotrophic gyres and expansion of oxygen minimum zones.
  • Changing thermal windows may result in shifts in species interactions, affecting community compositions and food web structures.
  • This could favor generalist species over specialists, leading to a potential loss in biodiversity and reducing the resilience of ocean ecosystems.

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Carbon

• Half of Earth's annual organic production is in the ocean's photic zone.
• The ocean plays a key role in the global carbon cycle.
• Diatoms are prominent in today's oceans.
• Every fifth breath's oxygen comes from diatoms.
• Diatoms contribute to the biological carbon pump.
• They help transfer carbon to the deep ocean.
• This aids in long-term removal of atmospheric CO2.

Carbon Continue

Inorganic Carbon Metabolism in Diatoms:

• Diatoms face challenges related to how they process inorganic carbon.
• CO2 levels in water can be low, affecting photosynthesis.
• Rubisco, an enzyme central to photosynthesis, can also perform an oxygenation reaction under low CO2, leading to inefficiencies.
• Rubisco (Ribulose-1,5-bisphosphate carboxylase/oxygenase) is the primary enzyme responsible for carbon fixation during photosynthesis. Its primary role is to catalyze the carboxylation of ribulose-1,5-bisphosphate (RuBP) with CO2, producing two molecules of 3-phosphoglycerate, which then enter the Calvin cycle to produce sugars.
• However, Rubisco can also react with oxygen (O2) instead of CO2, leading to an oxygenation reaction. This reaction produces one molecule of 3-phosphoglycerate and one molecule of a two-carbon compound (2-phosphoglycolate) in a process known as photorespiration. Unlike the Calvin cycle, which is part of the productive pathway of photosynthesis, the photorespiration process doesn't produce useful organic molecules and can be considered wasteful in terms of energy and resources for the plant.
• Rubisco is another key enzyme in photosynthesis that takes CO2 from the environment and uses it to produce sugars.
• The oxaloacetate produced by PEPC serves as a concentrated source of CO2 for Rubisco, making the carbon-fixing process more efficient for diatoms.

Diatom Genome and HCO3 Uptake:

• Diatom DNA sequences indicate specialized mechanisms to absorb bicarbonate (HCO3), an alternative form of carbon.
• Many of these mechanisms resemble those found in more complex organisms like metazoans.
• P. tricornutum, a specific diatom, possesses transporters and enzymes specialized for HCO3 uptake, ensuring a steady supply of carbon for photosynthesis.

Diatom Photosynthesis Mechanisms:

• There's a hypothesis that diatoms may use a biochemical pathway similar to C4 plants for photosynthesis, a more efficient method in certain conditions.
• Some experiments suggest variations between different diatom species in how they perform photosynthesis.
• An interesting finding is the presence of significant photorespiration in diatoms, suggesting they might have backup mechanisms to deal with inefficiencies in photosynthesis.
• the "C4" referred to in the context of photosynthesis is not related to methane. In biology, the terms C3, C4, and CAM (Crassulacean Acid Metabolism) are used to describe different pathways plants use to fix carbon dioxide during photosynthesis.
• C3 Photosynthesis: Most plants use this pathway. In the first step of photosynthesis, a three-carbon compound (3-phosphoglycerate, or 3-PGA) is produced. This process occurs in mesophyll cells.
• C4 Photosynthesis: In some plants, especially those adapted to hot and dry environments, an initial step captures CO2 into a four-carbon compound (oxaloacetate) in mesophyll cells. This four-carbon compound is then shuttled to bundle sheath cells, where it releases CO2 for the Calvin cycle. This separation in cells is why it's called "C4" photosynthesis.
• CAM Photosynthesis: Some succulent plants, like cacti, use a variant of C4 photosynthesis called CAM. They open their stomata at night to take in CO2 and fix it into organic acids. During the day, when it's hot and dry, they close their stomata to reduce water loss. The CO2 stored as organic acids is then released and used in the Calvin cycle.

PEPC and Diatom Photosynthesis:

• Inhibiting certain enzymes, like PEPC, can significantly hinder photosynthesis in some diatoms.
• This enzyme plays a role in a proposed C4-like pathway in diatoms, where a compound called oxaloacetate is converted to provide concentrated CO2 for Rubisco.

Diatom Cellular Processes:

• Diatoms seem to have evolved mechanisms that allow them to efficiently capture and utilize inorganic carbon.
• While genome data suggests some pathways, actual experimental evidence sometimes contradicts these predictions, indicating gaps in our understanding.
• Certain metabolic reactions, crucial for efficient carbon utilization, might be occurring in unexpected places like the mitochondria within diatom cells.

Role of Mitochondria in Diatoms:

• Mitochondria, traditionally known as the energy powerhouse of cells, have been found to play a central role in carbon and nitrogen processing in diatoms.
• Diatoms might have unique ways of storing and utilizing energy, possibly explaining their resilience and ability to thrive in varied conditions.
• Evolutionary events have introduced new genes and processes into diatoms, further enriching their cellular machinery.

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What is one thing you thought was interesting.

I found the article amazing, it made me really want to work with diatoms.

I guess to bring up a conversation, we study bacterial strains. In these strain we have these genomes that allow us to see the mechanisms that happen within these organisms. Which so happens diatoms also have genomic code on which we can look into the same way.

Now the way I am thinking about it is the level of being a bioindicator.

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How do bacteria and diatoms differ in their roles as bioindicators?

Bacteria as Bioindicators:

1. Composition-Based Assessment: By examining the types and relative abundance of bacterial species present in a sample, scientists can infer specific environmental conditions. Different bacteria thrive under different conditions, so their presence or absence can provide clues about factors like pH, nutrient levels, salinity, and more.

2. Physiological Reactions: Bacteria are sensitive to changes in their environment. For instance, the presence of specific bacterial species might indicate pollution or other environmental disturbances. Some bacteria are known to metabolize specific pollutants, and their abundance might suggest contamination.

3. Rapid Response: Bacterial populations can change relatively quickly in response to environmental changes, making them valuable for detecting recent disturbances or changes in environmental conditions.

Diatoms as Bioindicators:

1. Quality-Based Assessment: Diatoms are single-celled algae with unique silica shells. The species composition and morphology of diatoms can indicate water quality, salinity, pH, and other environmental parameters. Certain species of diatoms are associated with specific water quality conditions.

2. Production Metrics: Diatoms produce organic matter through photosynthesis. By assessing factors like diatom biomass or productivity, scientists can gain insights into nutrient availability, light conditions, and overall water quality. Changes in diatom productivity might indicate nutrient enrichment (eutrophication) or other disturbances.

3. Indicators of Past Conditions: Diatom fossils (diatomaceous earth) have been used to reconstruct past environmental conditions. The species composition of fossilized diatoms in sediment layers can provide historical insights into environmental changes over time.

In summary, while both bacteria and diatoms can serve as bioindicators, they offer different types of information. Bacterial communities provide insights into current environmental conditions based on their composition and physiological reactions. In contrast, diatoms offer information about both current conditions (through species composition and productivity) and historical environmental changes (through fossilized remains).

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Bacterial (Prokaryotic) Characteristics:

1. Genetic Material:

   • Location: Singular, circular chromosome in the nucleoid.
   • Organization: Lacks histones; no splicing.

2. Cellular Structure:

   • Organelles: No membrane-bound organelles.
   • Ribosomes: 70S.

3. Cell Wall:

   • Contains peptidoglycan.
   • Some have an outer membrane (e.g., Gram-negative).

4. Reproduction:

   • Asexual reproduction via binary fission.
   • Genetic material exchange: conjugation, transformation, transduction.

5. Size: 0.5 to 5 micrometers.

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Eukaryotic Characteristics:

1. Genetic Material:

   • Location: Enclosed within the nuclear membrane.
   • Organization: Multiple linear chromosomes with histones; splicing occurs.

2. Cellular Structure:

   • Organelles: Membrane-bound organelles present.
   • Ribosomes: 80S, both free and bound.

3. Cell Wall:

   • Present in some (e.g., plants, fungi) but varies in composition.

4. Reproduction:

   • Asexual (e.g., mitosis) and sexual (e.g., meiosis, fertilization).

5. Size: 10 to 100 micrometers.

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Differences in Histone Presence Between Bacteria and Eukaryotes:

Eukaryotes:

1. Genome Size and Organization:

   • Typically larger and more complex.
   • DNA organized into multiple linear chromosomes.

2. Packaging Requirement:

   • DNA needs to be tightly packed due to its complexity.
   • Histones play a role in this packaging, forming nucleosomes.

3. DNA Compaction:

   • Histones wrap DNA, facilitating condensation and efficient storage.

4. Regulation of Gene Expression:

   • Histone modifications (e.g., acetylation, methylation) influence DNA accessibility.
   • Complex mechanisms for transcriptional regulation.

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Bacteria:

1. Genome Size and Organization:

   • Generally smaller and more compact.
   • DNA is usually a singular, circular chromosome in the nucleoid.

2. No Need for Compaction:

   • Bacterial DNA's compact nature reduces the need for extensive packaging.

3. Direct Regulation:

   • Bacteria regulate gene expression more directly without histone-mediated processes.

In summary, while eukaryotes utilize histones for DNA packaging and regulation due to their complex genomes, bacteria have evolved alternative mechanisms suited to their simpler genomic organization.