User:Migdesmarais/sandbox

Article Evaluation
Cyanobacteria

Overall, the article seems to touch on key aspects of Cyanobacteria but is not exhaustive. Parts of the article seem disjointed and would need to be improved upon. Some text from citations has been copied word for word into the article and is not necessarily important or relevant. According to previous training, this should not be done in a Wikipedia article.


 * Is everything in the article relevant to the article topic? Is there anything that distracted you?

All the information presented in this article is relevant to the topic. The lead section could be improved since it includes facts about Cyanobacteria which are not necessarily part of major aspects of the topic. They are redundant and are repeated later in the article.


 * Is the article neutral? Are there any claims, or frames, that appear heavily biased toward a particular position?

The article is generally neutral. There are no major claims or frames that appear heavily biased toward a particular position.


 * Are there viewpoints that are overrepresented, or underrepresented?

Some part of the "Biotechnology" section may be overrepresented and biased towards recent commercial studies from a company called Algenol. This company claims to successfully use Cyanobacteria as a sustainable energy and food source.

The "Photosynthesis" section of this article is quite elaborate and may be overrepresented. Details such as the electron transport mechanism in Cyanobacteria could have been included as a link directing to other Wikipedia pages on the topic.

Their role in the nitrogen cycle (nitrogen fixation) and the carbon cycle (carbon fixation) may be underrepresented in this article compared to other less important or studied aspects.


 * Check a few citations. Do the links work? Does the source support the claims in the article?

The citations links are in working order. The sources linked to this article support the claims and are extensive.


 * Is each fact referenced with an appropriate, reliable reference? Where does the information come from? Are these neutral sources? If biased, is that bias noted?

The facts presented in this article are referenced with appropriate and reliable references. The information comes from reputable scientific journals and publications. The sources are mostly neutral, and therefore should not be biased.


 * Is any information out of date? Is anything missing that could be added?

The information presented is relevant but does not seem up to date for all sections. Links to important species of Cyanobacteria, their role in the open ocean and characteristics could be added to the "Ecology" section. This could add to the readers understanding of how complex Cyanobacteria are and how important they are to biogeochemical cycles and the environment in general.


 * Check out the Talk page of the article. What kinds of conversations, if any, are going on behind the scenes about how to represent this topic?

The Talk page of the article is highly extensive and deals with different aspects, recent studies and conflicts related to Cyanobacteria such as Orders, Microfossils, Recent changes, Satellite images, etc. The Talk page seems very constructive and is a good way to build on other users knowledge to publish the most accurate information about the topic.


 * How is the article rated? Is it a part of any WikiProjects?

The article is rated as a C-Class Wikipedia Article which is an average rating for a Wikipedia page. The article could be improved. The article is part of three WikiPorjects: Microbiology, Algae and Palaeontology.


 * How does the way Wikipedia discusses this topic differ from the way we've talked about it in class?

This Wikipedia page describes the topic in a general way and does touch key aspects. However, it does provide an exhaustive and highly scientific approach to the subject like we do in class (ex.: distribution, clades, abundance, methods, etc.).

Potential Topics
 SAR supergroup : adding to 

Links to Wikipedia pages on the topic of different SAR supergroup members (SAR11, SAR324, SAR202, etc.) could be added.

A section about their different environment and ecology would be a great addition.

A note about the origin of their names (SARgasso Sea) could be interesting.

A lot of research papers exist on the SAR supergroup and therefore this article could be expanded greatly.

 Oxygen minimum zone : adding to 

The role of OMZs in biogeochemical processes and redox states could be added to this article.

Links to different OMZs around the world, or simply describing important and well-studied OMZs would be interesting.

Microbes are a major part of OMZs and should have a section.

 Sea ice microbial communities (SIMCO) : new article 

Spatial and temporal distribution

Diversity (taxonomy)

Metabolic pathways

Role in microbial loop and in the food chain

Sea Ice Microbial Communities (SIMCO)
Article: Sea ice microbial communities (SIMCO)

This Wikipedia article will review the spatial and temporal distribution of Sea Ice Microbial Communities (SIMCO) around the world in general and in response to seasonal changes (sea ice melting, light availability, nutrients, etc.), their diversity and community composition, and their role in the microbial loop and te food chain in general. Other points will include their relevance to biogeochemical cycles at a small scale but also at the planetary scale. It will cover their significance and importance in the environment. Submitted and approved.

Workload:
- wiki intro: Shannon

- physical environment (sea ice) Miguel

- spatial and temporal distribution: Scarlett

- microbial community diversity - Arctic: Shannon - Antarctic: Miguel

- adaptation: Miguel

- role in microbial loop/biogeochemistry/nutrient cycles: Scarlett

- nitrogen/phosphorus: Edwin

Introduction
Sea ice microbial communities (SIMCO) refer to groups of microorganisms living within and at the interfaces of sea ice at the poles. The ice matrix they inhabit has strong vertical gradients of salinity, light, temperature and nutrients. Sea ice chemistry is most influenced by the salinity of the brine which affects the pH and the concentration of dissolved nutrients and gases. The brine formed during the melting sea ice creates pores and channels in the sea ice in which these microbes can live. As a result of these gradients and dynamic conditions, a higher abundance of microbes are found in the lower layer of the ice, although some are found in the middle and upper layers. Despite this extreme variability in environmental conditions, the taxonomical community composition tends to remain consistent throughout the year, until the ice melts.

Much of the knowledge concerning the community diversity of the sea ice is known through genetic analyses and next-generation sequencing. In both the Arctic and Antarctic, Alphaproteobacteria, Gammaproteobacteria and Flavobacteriia are the common bacterial classes found. Most sea ice Archaea belong to the phylum Thaumarchaeota while most of the protists belong to one of 3 supergroups: Alveolata, Stramenophile and Rhizaria. The abundance of living cells within and on sea ice ranges from 104-108 cells/mL. These microbial communities play a significant role in the microbial loop as well as in global biogeochemical cycles. Sea ice communities are important because they provide an energy source for higher trophic levels, they contribute to primary production and they provide a net influx of Carbon in the oceans at the poles.

Sea ice formation and physical properties
The autumnal decrease in atmospheric temperatures in the Arctic and Antarctic leads to the formation of a surface layer of ice crystals called frazil ice. A mixture of salts, nutrients and dissolved organic matter (DOM) known as brine is expelled when frazil ice solidifies to form sea ice. Brine permeates through the ice cover and creates a network of channels and pores. This process forms an initial semisolid matrix of approximately 1 meter in thickness with strong temperature, salinity, light and nutrient gradients.

Since thickening of the sea ice during winter months results in more salts being expelled from the frazil ice, atmospheric temperatures are strongly and negatively correlated to brine salinity. The sea ice-seawater interface temperature is maintained at the freezing point of seawater (~1.8°C) while the sea ice-air interface reflects more the current atmospheric temperature. Brine salinity can increase to as much as 100 PSU when sea ice temperature reaches ~3°C below the freezing point of seawater. Brine temperature typically ranges from -1.9 to -6.7 °C in the winter. Sea ice temperatures fluctuate in response to irradiance and atmospheric temperatures, but also change in response to the volume of snowfall. Accumulating snow on the ice cover combined with harsh atmospheric conditions can lead to the formation of a snowpack layer that absorbs UV radiations and provides insulation to the bottom ice layer. The fraction of irradiance reaching the sea ice matrix is thus also controlled by the amount of snowfall and varies from <0.01% to 5% depending on the thickness and density of the snowpack.

The surface of sea ice also allows the formation of frost flowers, which have their own unique microbial communities.

Carbon species, nutrients and gases
The fluctuation of brine salinity, which is controlled by atmospheric temperatures, is the single-most influential factor on the chemistry of the sea ice matrix. The solubility of carbon dioxide and oxygen, two biologically essential gases, decreases in higher salinity solutions. This can result in hypoxia within high heterotrophic activity regions of the sea ice matrix. Regions of high photosynthetic activity often exhibit internal depletion of inorganic carbon compound and hyperoxia. These conditions have the potential to elevate brine pH and to further contribute to the creation of an extreme environment. In these conditions, high concentrations of DOM and ammonia and low concentrations of nutrients often characterize the ice matrix.

High brine salinity combined with an elevated pH reduces the rate at which gases and inorganic nutrients diffuse into the ice matrix. The concentration of nutrients such as nitrate, phosphate and silicate inside the sea ice matrix relies largely on the diffusive influx from the sea ice-water interface and to some extent on the atmospheric deposits on the sea ice-air interface. Iron concentrations in the Southern Ocean ice cover are thought to be regulated by the amount of new iron supply at the time of ice formation and were shown to be reduced during late winter.

The chemical properties of the sea ice matrix are highly complex and depend on the interaction between the internal sea ice biological assemblage as well as external physical factors. Winters are typically characterized by moderate oxygen levels that are accompanied by nutrient and inorganic carbon concentrations that are not growth limiting to phytoplankton. Summers are typically characterized by high oxygen levels that are accompanied by a depletion of nutrients and inorganic carbon. Because of its diffusive interaction with seawater, the lower part of the sea ice matrix is typically characterized by higher nutrient concentrations.

Colonization
Microorganisms present in the surface seawater during fall are integrated in the brine solution during ice formation. A small proportion of the initial microbial population colonizes the ice matrix while the rest is expelled with brine. Studies have shown that sea ice microbial retention can be enhanced by the presence of extracellular polymeric substance/polysaccharides (EPS) on the walls of the brine channels. EPS are proteins expressed on the cell walls of microorganism such as algae. They improve the cell adherence to surfaces and when found in sufficient concentration, are thought to play a role in recruiting other organisms such as microbes.

Airborne microorganisms make up a significant proportion of the microbial input to the ice matrix. Microorganisms located in the sea or in the ice matrix brine can be incorporated in falling snow or in aerosols, and subsequently transported by strong winds such as the West Wind Drift that causes the Antarctic Circumpolar Current. These airborne microorganisms can originate from terrestrial environment and marine environment, thus contributing to the diversity of the SIMCO.

Spatial Distribution
Microbes colonizing the Antarctic sea ice are eventually incorporated in the pore spaces and brine channels of the ice matrix, but can also inhabit the ice-seawater interface. Pore spaces in the matrix lose their ability to exchange nutrients, DOM and microorganisms with brine at approximately -5°C. This suggests that the Antarctic microbial community is fluid along the ice matrix during fall and spring and that it is restricted during winter.

In the Arctic, brine channels are also inhabited by bacteria. Channels as small as ≤200 μm offer a spatial refuge with microbial community concentrations of 1-2 orders of magnitude higher than in the remaining channel network.

Both the Antarctic and Arctic sea ice environments present strong vertical gradients of salinity, temperature, light, nutrients and DOM. These gradients were shown to induce strong vertical stratification in bacterial communities throughout the ice layer. Microbial abundance declines significantly with depth in the upper and middle ice, but not in the lowest, suggesting that much of the prokaryotic bacterial community is resistant to extreme environmental conditions. Heterotrophic bacteria were also shown to be more abundant at the bottom of the ice layer in zones of greater algae concentration, which characterized by higher DOM and nutrient concentrations.

Temporal Distribution
The temporal distribution of microbial community composition in the Antarctic and Arctic sea ice does not present significant seasonal variability, despite extremes in environmental conditions. Previous studies of sea ice habitats have shown that the composition of SIMCO in early fall is identical to the source seawater community. The microbial community composition does not seem to change significantly in fall and winter, despite the extreme variability in irradiance, temperature, salinity and nutrient concentrations. In contrast, the abundance within the SIMCO is reduced throughout the winter as resources become limiting. Studies have shown that sea ice microalgae provide a platform and organic nutrient source for bacterial growth, therefore increasing community diversity and abundance. It has also been proven that microbes produce extracellular polymeric substances (EPS) to help retain nutrients and survive under high salinity and low temperature conditions.

The increase in irradiance levels in late spring promotes ice algal photosynthesis which in turn affects the microbial community abundance and composition. While most of the sea ice cover melts in late spring in the Antarctic and Arctic, multiyear sea ice occasionally persists when late spring and summer temperatures are lower than average. This suggests that certain microbial lineages may have adapted more efficiently to the extreme conditions of sea ice environments. Temporal abundance can also be affected by the thickness of the annual ice cover and seasonal temperature variations. The ice cover thickness was shown to regulate microbial production and the temperature of the ice matrix through layer insulation.

Community composition
A majority of the information on sea ice microbial community composition comes from 16S ribosomal RNA taxonomic marker genes and metagenomic analyses. Next-generation sequencing has allowed researcher to identify and quantify microbial communities, and to gain a more complete understanding of its structure.

Arctic
Metagenomic studies of Arctic sea ice show classes Alphaproteobacteria, Gammaproteobacteria and Flavobacteria. Within the Flavobacteriia class the genera Polaribacter, Psychrobacter, Psychroflexus, and Flavobacterium are the most common. Within Gammaproteobacteria the genera Glaciecola and Colwellia are the most common. Also found in Arctic sea ice samples were bacteria of the following classes and phylums: Opitutae, Bacilli, Cyanobacteria, Betaproteobacteria, Sphingobacteria, and Aquificae.

Antarctic
Metagenomic studies of the Ross Sea illustrate the high abundance of aerobic anoxygenic phototrophic bacteria in sea ice environments. These specialists were shown to mostly belong to the Alphaproteobacteria class. Genera of the Alphaproteobacteria class were shown to include Loktanella, Octadecabacter, Roseobacter, Sulfitobacter and Methylobacterium and to agree with previous phylogenetic analyses of sea ice around the Antarctic. A study of the SIMCO 16S ribosomal RNA at Cape Hallett in the Antarctic has shown that aerobic oxygenic phototrophic bacteria may be equally abundant.

Members of the Gammaproteobacteria and Flaviobacteria classes were also shown to be abundant within the ice matrix, and thus to be adapted to the sea ice conditions. Genera of the Gammaproteobacteria class found in the Ross Sea and around the Antarctic waters include Colwellia, Marionomonas, Pseudoalteromonas and Psychrobacter. The orders Chlamydiales and Verrucomicrobiales were also found in the sea ice microbial assemblage of these locations. The predominance of Gammaproteobacteria in sea ice around the globe have been reported by many studies. A large proportion of the identified SIMCO in these studies were shown to belong to phylotypes associated with heterotrophic taxa.

While this gives researchers an insight into the microbial community composition of the Antarctic sea ice, there are clear shifts between locations in the Southern Ocean. These shifts are attributed to biological and physical forcing factors. These factors include the composition of the microbial communities in place at the moment of sea ice formation, and the regional weather and wind patterns affecting the transport of snow and aerosols.

Archaea
Studies of the 16s ribosomal RNA subunits found in the sea ice cover of Terra Nova Bay have shown that archaea consist of ≤ 6.6% of the total prokaryotic community in this environment. 90.8% of this archaeal community belonged to the phylum Thaumarchaeota, a close parent to marine ammonia-oxidizing bacteria, while Euryarchaeota made up the rest of the community. Other molecular phylogenetic analyses of the SIMCO have detected no trace of the archaeal domain.

Protists
Metagenomic studies of Arctic sea ice using 454 sequencing of 18S rDNA and 18S rRNA. These studies showed dominance of three supergroups: Alveolata, Stramenophile, and Rhizaria. Within the Alveolates most common were Ciliates, and Dinoflagellates. Within the Stramenophile group most organisms were classified as Bacillariophyceae. Finally most of the Rhizarians were classified as from Thecofilosea.

Adaptation
Studies have shown that high concentrations of microbial cryoprotective exopolymer (EPS) were found in the sea ice brine. These EPS were shown to correlate with a stable microbial community composition throughout the winter season. They are thought to play an important role in sea ice environments where they act as a buffer and cryoprotectant against high salinity and ice-crystal damage. These exopolymers are believed to constitute a microbial adaptation to low temperatures in extreme environments.

Sea ice microbes have also developed anti-freeze protein s, which prevent the formation of ice crystals that could damage bacterial membranes. It is common for these proteins to be rich in beta-sheets as they prevent the formation of ice crystals.

Role in the Microbial Loop
Bacteria in all environments contribute to the microbial loop, but the roles of sea ice microbial communities in the microbial loop differ due to the rapidly changing environmental conditions found in the Arctic and Antarctic. Sea ice algae contribute 10%–28% of the total primary production in ice-covered regions of the Antarctic. Microalgae provide a vital source of nutrition for juvenile zooplankton such as the Antarctic krill Euphausia superba in the winter. DOM derived from phototrophic microalgae is crucial to the microbial loop, by serving as a growth substrate for heterotrophic bacteria.

The microbial loop functions differently in sea ice, as compared to oligotrophic or temperate waters. Animals found in the extreme polar environments depend on the high bacterial production as a food source, despite the slow turnover of DOM. The microbial production of ammonium in nitrate-rich Antarctic waters may provide the necessary reductants for nitrogen fixation, increasing primary productivity of light-limited phytoplankton. Phytoflagellates and diatoms found in the Antarctic pelagic environment are directly digestible by metozoan herbivores.

Biogeochemical cycles
Biochemical cycle contributes the movement of elements between organisms and the environment. In order to maintain ecosystem function properly, all those elements must be cycled continuously in forms from nonliving components to the living. Nitrogen and phosphorus are essential elements for marine ecosystem biomass growth, and under ideal growth conditions, nitrogen and phosphorus ratio is usually within predictable stoichiometry. The Sea Ice of Antarctic continent contributes to not only climate control, but also does the significant role as a reservoir of microorganisms and nutrients, and regulating global biogeochemical cycles such as nitrogen and phosphorus cycling. Sea ice does the important role of providing habitats for microorganisms and food webs globally, and the sea ice microbial community is well adapted in response to the nitrogen and phosphorus-poor environment

Nitrogen
Nitrogen fixation does the important source of supporting biological production in the ocean marine environment. Dissolved organic nitrogen is uniformly distributed in the water column with higher in surface than the depth, and gradually increasing dissolved organic nitrogen towards coastal areas and estuaries.

Generally, nitrogen fixation process occurs in warmer seawater area such as subtropical oligotrophic gyre and tropical area; however, the nitrogen fixation can occur at the lower temperature such as artic area where nitrogen is not limiting. Dissolved organic nitrogen concentration in Sea ice is lower than the concentrations in the oligotrophic area. Dissolved organic nitrogen is not produced efficiently from photosynthesis by phytoplankton blooms in Arctic waters for the bacterial uptake. Within the sea ice, recycling of organic compounds dominates over fixation of nitrogen because of lower temperature isolating ice from nitrogen deposition, which suggest that the nitrogen input is not enough to sustain microbial growth. Therefore, nitrogen-fixing bacteria does the important source of microbial assemblages in artic area.

The nitrogen presents in the ice sheet in two phases. The sea ice contains nitrogen as aerosol from the gas forms onto the ice surface, and air pockets between the ice molecules from the 78% of the atmosphere enclosed by the ice molecules. Generally, the sea ice contains nitrogen in forms of two main compounds nitrate and ammonium, and the nitrate is the dominant compound in the sea ice. The rate of microbial processes increased nitrate production by oxidation of ammonium and mineralization of organic nitrogen within the ice column. The ammonium is deposited within the ice sheet as aerosol irreversible way, while the nitrate can be exchanged between the ice sheet and the atmosphere by evaporation of nitric acid through photolysis. During algal bloom, low concentration of nitrate (high consumption of nitrate) causes a high rate of nitrogen remineralization by accumulation of ammonia and nitrite in the sea ice. Hence, denitrification by bacteria dominates with high nitrite concentrations in sea ice.

Phosphorus
Similarly to nitrogen, the phosphorus cycle has a great influence on ocean ecosystems. Phosphorus is an essential nutrient for the marine ecosystem, and it plays a critical role in cell development, and which its availability does huge impact on primary production in marine environments. The biogeochemical cycling of phosphorus in the ocean does determinant of marine ecosystem structure and function. Phosphorus is usually stored in sediments and rocks in forms of inorganic matter, which is not accessible marine organisms, therefore bacteria does important role of converting inorganic phosphorus into organic forms.

In fact, there are relatively large concentrations of dissolved organic phosphorus in the ocean, but in order to enzyme access this phosphorus source, they require zinc(Zn) and iron(Fe). Dissolved organic phosphorus pool plays a critical role in driving growth, metabolism of the marine ecosystem. From the study, the bacterial activity in the sea ice is mainly limited by phosphorus. The additional input of phosphorus stimulates bacterial production while additional nitrogen does not trigger.