Microbes and Greenhouse Gases

The aim of this study was to characterise the composition of the microbial mats located at the Shanes seep within the coal oil point (COP) seep and investigate whether this contributes to methane oxidisation. The study used ex situ and in situ carbon 13 (¹³C) labelling of methane to monitor the methane uptake by the microbial mat. Also, parallel lipid and DNA analysis was used to look at the abundance and diversity of the mats.

The marine subsurface is a large reservoir for methane, which is important greenhouse gas as it warms the globe 25 times greater than carbon dioxide (Schneising et al., 2009). The micro-organisms, including methanotrophs and methylotrophs, in the water column and seabed utilise some of this methane, limiting the methane released from the sea to the atmosphere. Methanotrophs metabolise methane directly while methylotrophs use methanol and other partially oxidised methane metabolites. The presence of these microbes could be the basis of a food web, creating various niches that encourage a diverse community with important nutrient cycling roles. These microbial mat communities are often dominated by sulfur oxidising bacteria. There have been few studies investigating flow of methane as a carbon source through microbial mats, those that do often looked at dark or low oxygen environments. These studies suggested that the methanotrophy in these environments were mostly anaerobic. However, other studies have shown both anaerobic and aerobic methanotrophs co-occurring in sulfur-oxidising microbial mats, which suggests that shallow oxygen rich environments work in a different manner to the more rigorously researched deep low oxygen communities. To reverse this trend in the literature, this study investigated the microbial mats in COP, which is one of the largest hydrocarbon seeps and a relatively shallow oxygen rich environment (Leifer et al., 2006).

The initial observations showed there was a highly diverse microbial community both within and between mats. This suggests that there could be various metabolic pathways and niches within the community. The diversity of the communities was confirmed with 16S rRNA sequencing. Through assessing the interacting polar lipids (IPL), the study proposed that the mats were mostly bacterial.

To determine if the microbial mats could have an impact on the seeping methane, carbon 13 (¹³C) enriched methane was fed to the microbial mats in a lab setting. The results from this were then extrapolated to represent in situ conditions, and it was estimated that the microbial mats would consume 0.006% of the methane produced, yet it is suggested that the seep stimulates microbial growth as the mats are found within the seep and not outside it. Results from the IPL assessment of ¹³C treated samples suggests that the mats do harbour active methanotrophs as the samples were dominated by Methylcoccaceae, a family of aerobic methanotrophs. This was confirmed by DNA analysis of the samples. Interestingly, this analysis also showed there was diversity and abundance changes between the samples, showing that the microbial mats are complex and poorly understood communities that require further investigation for a deeper understanding of their mechanics.

The study then looked at the methane and CO₂ assimilation in situ by assessing the natural depletion of ¹³C methane and its natural enrichment of CO₂; it found that Methylcoccaceae actively converted the ¹³C methane to biomass within the microbial mats. The biomass was used as a basis for the food web in the mat community and led to a diverse array of organisms comparable to the lab experiment. Additionally, there was evidence of methylophylya activity probably from partially oxidised methane; this activity is caused by organisms indirectly oxidising methane by using methanol. This could increase the efficiency of the consumption of methane by the mat, but further investigation would be needed. Within the mat, further oxidised methane seemed to be used by sulfur-oxidising bacteria, which acquire their carbon from CO₂. They coexist with the methanotrophic/methylotrophic bacteria, and these interactions supplement their CO₂ uptake, which is important as 17% of the gas released by the seep is CO₂.

COP also releases oil and tar along with the gas. Alcanivoraceae, Petrobacter and Oleomonas taxa were found in the top 50 OTUs, suggesting there are various metabolic pathways to degrade ethanol, propanol and butanol, and oxidise aliphatic and aromatic hydrocarbons. This could provide a reasonable explanation to the diversity of the microbial mats, so there are various niches to exploit. There were other functions found within the mats. The abundance of Myxobacteria, characterised by gliding motility, swarming and biofilm development, in several samples suggests that they could drive the initial mat formation. Also, a small eukaryotic phytoplankton population was discovered, which could supply the oxygen for the aerobic activity in the microbial mat. Their growth is enabled by the seeps location within the euphotic zone and could explain the absence of aerobic methanotrophs at deeper seeps.

The study demonstrates the diverse mechanisms for hydrocarbon uptake in seep sediments and characterises a previously uncharacterised seep sediment type. It also shows that there is a huge range of unspecified diversity that, if investigated further, could lead to advances in understanding of microbial degradation of hydrocarbons. This could be used in the event of oil spills. Although the mats acted as a sink for a small fraction of carbon released by the sink, it has shown three main pathways for biomass productivity, which suggests that this is a robust community.

References

Schneising, O., Buchwitz, M., Burrows, J.P., Bovensmann, H., Bergamaschi, P. and Peters, W., 2009. Three years of greenhouse gas column-averaged dry air mole fractions retrieved from satellite–Part 2: Methane. Atmospheric chemistry and physics, 9(2), pp.443-465.

Leifer, I., Luyendyk, B. and Broderick, K., 2006. Tracking an oil slick from multiple natural sources, Coal Oil Point, California. Marine and Petroleum Geology, 23(5), pp.621-630.

Article Reviewed

Paul, B.G., Ding, H., Bagby, S.C., Kellermann, M.Y., Redmond, M.C., Andersen, G.L. and Valentine, D.L., 2017. Methane-Oxidizing Bacteria Shunt Carbon to Microbial Mats at a Marine Hydrocarbon Seep. Frontiers in Microbiology, 8.

Sponge microbial communities remain stable despite pollution

Marine sponges are known to have a symbiosis with diverse microbial communities. These communities have a significant role in host functioning but there is little previous literature regarding what effect anthropogenic disturbances, such as pollution, have on sponge-microbe reactions.

The sponge species, Crambe crambe, also known as the Oyster sponge and is an orange-red encrusting sponge. It is common in the Mediterranean Sea and has been found to accumulate heavy metals present in polluted harbours. The aim of the paper by Gantt et al. (2017) was to establish if the microbiome of C. crambe was different between the sponges found in the polluted harbour and sponges located 1 kilometre away in a natural habitat.

The study took place at Blanes harbour in Spain, which was chosen due to the high pollution, and the surrounding habitats in the area. Sponge samples and ambient seawater were collected in replicates of three from both the harbour and the natural habitat. 16S rRNA was used to determine the microbial composition of each sample using the Illumina Hi-Seq platform.  

The study found that there was no significant difference between the diversity of the microbial communities of the different sample sites in the C. crambe samples. There was also no significant difference in the community structures. However, there was a significant difference in the community structure of the seawater samples collected inside the harbour compared with outside. There was a clear difference between the microbiomes of C. crambe and that of the seawater microbes which are free living. The C. crambe microbiome was dominated by Proteobacteria across all site samples. Betaproteobacteria made up more than 86% of the community.

The results suggest that the microbiomes of these sponges have a higher pollution tolerance and greater stability than the free living microbes in the seawater as the presence of contaminants did not significantly alter the community composition of the microbiomes. The change in community of the ambient seawater had little effect on the sponges. 

The finding of this paper sheds a more positive outlook than most other pollution studies as the sponges were resilient to the effects of contamination in the harbour. It would appear that C. crambe can potentially mitigate the effects of pollution on their coastal marine communities.

Reviewed paper:

Gantt, S., López-Legentil, S., & Erwin, P. (2017). Stable microbial communities in the sponge Crambe crambe from inside and outside a polluted Mediterranean harbor. FEMS Microbiology Letters, 364(11). http://dx.doi.org/10.1093/femsle/fnx105

Seasonal shifts in the Marine Viruses of Goseong Bay, Korea.

Viruses are the most abundant biological entities in our oceans making up a sizeable proportion of genetic diversity in marine ecosystems. But considering this we know very little about their biodiversity and their role. In this study they look at the diversity of viruses found in Goseong Bay, as well as the effects of seasonal changes on the virus populations.

This study sampled sea water from 6 sites in Goseong Bay, Korea during each season of 2014. The study focused on how changes in temperature, salinity, dissolved oxygen and nutrient concentrations effected the biodiversity of viral populations. These variables were tested at the site when the sea water samples were taken. From this they found the only environmental variable that had a marked change with seasonality was temperature which ranged from as low as 8.95 °C in March to 26.4 °C in September. Once collected, the sea water samples were filtered and then sequenced using Illumina SBS sequencing. They then compared these results to a viral genomic sequence database. 

The results from this found there was 385,444 reads across all seasons with 77% of these being bacteriophages, 26% Algal viruses and 1% other viruses. The Pelagibacter phage was the most abundant making up 36% of this, but there was a total of 108 species present across the samples from all 4 seasons.

Regarding the 4 seasons, the authors found a clear difference between them, with viral abundance higher in March than in any other season. They also found that the dominant species changed with season with Pelagibacter phages dominating in September when it was hot and Roseobacter phages when it was cold in March.

 The four most common viruses identified overall were:

·         Pelagibacter ubique which feeds on dissolved organic carbon and nitrogen and can synthesize all amino acids.

·          Ostereococcus which infects algal plankton and is thought to shape communities by ‘killing the winner’.

·          Iridoviridae which infects invertebrates and vertebrates and is a lethal pathogen of fish. It has caused numerous economic losses across Asia due to the infection of aquaculture systems.

·         Poxvirus which infects marine mammals causing skin legions and may also cause disease in humans.

 These dominant viruses all have a clear impact on varying parts of the ecosystem, highlighting the positive but also the possibly damaging role viruses play in the marine environment. As well as this the presence/absence of certain viruses could act as indicators for risks to aquaculture and marine industry in this region.

Despite the clear importance of virus biodiversity there are very few studies about it. The authors suggest this is due to technical challenges generally based on limitations of resources. The authors also point out that even previous studies are not totally reliable, as although metagenomics is now well established, often the sample processing techniques are not and so can often leads to bias in the results.

 This study provides a useful foundation for future studies and for comparable analysis. As well as highlighting how, temperature can affect virus diversity which is more relevant than ever with the current threats from climate change.  The authors also suggest investigating the correlation between marine viruses and their hosts in future studies.

Paper reviewed

Hwang, J., Park, S., Park, M., Lee, S., & Lee, T. (2017). Seasonal Dynamics and Metagenomic Characterization of Marine Viruses in Goseong Bay, Korea. PLOS ONE, 12(1), e0169841. http://dx.doi.org/10.1371/journal.pone.0169841

Smoking Hot Marine Fungi: Deep sea vent marine fungi culturing and study

 Marine fungi are known to be well studied in accessible habitats such as tropical mangrove forest, estuarine or open ocean. Deep sea marine fungi on the other hand are not widely studied as they are challenging to sample from the deep sea due to cost and a lack of expedition expertise.

In previous years, scientists have assembled evidence of deep sea fungi communities and diversity and are also studying their ecological role in the environment. The role of marine fungi in brackish water, tidal zones and estuarine habitats is an agent of degrading organic matter such as micro and macro algae. The paper mentions that the role of marine algae seems to have been underestimated, perhaps overshadowed by other major degrading agents such as bacteria, E.huxleyi virus, etc.

There are several factors that makes deep-sea sampling challenging. As we know that the majority of organic matter from planktonic to hard multicellular living organisms sink to the bottom floor, finding its way to the deep sea.  It makes up the sample in the deep-sea ecosystem, so the deep sea habitat doesn’t necessarily consist its original sample. Many organic samples might come from a variety of different origin. As the result of this, deep sea fungi sample may contain sample the from upper layer. The paper mentions that decaying algae, higher plants and wood found in the deep sea may contain fungi from the previous habitats carried by attaching to the matter, in which case samples might not be endemic to the system. But so far Burgaud et.al (2009) mention that there are a scarce number of deep sea samples of marine Fungi and the sea Vent fungi sample is a novel sample.

Studies employed culture-independent methods combined with SSU rRNA to survey microeukaryotes diversity in extreme environments such as samples in acidic and iron river. This method reveals new fungal phylotypes with a fungal specific primer and reveals diversity of fungi in extreme environments, which can be applied to sample deep sea vent fungal diversity. Burgaud et.al (2009) collected samples of 210 fungal growth of which 42 samples yield to isolation of fungi. The hydrothermal samples gathered were mostly from shrimp and mussels with some from tubeworms, other animals and abiotic surfaces, for which 33% of the isolated strains belonged to new phylotypes. Burgaud et.al (2009) also mentions that there is no previous report of culturing filamentous fungi from deep-sea vent ecosystem.

Samples of filamentous fungi from the deep sea vent were cultured and observed to discriminate individuals of filamentous fungi for their ability to live in deep-sea hydrothermal ecosystems. The 18s rRNA sequence indicate the presence of Ascomycota and Basidiomycota in the culture collection which were represented by Pezyzomycotina subphylum (of Ascomycota) and Tilletiopsis pallescens (close to Basidomycota).

Little is known about deep sea marine fungi’s role in the ecosystem – there is one case of Carponia-like parasitic fungi in a mussel hill of Fiji basin reported, causing tissue deterioration on deep sea mussel (but this is a rare case). Mussel samples were relatively healthy despite the presence of fungi, which proves that they were not a strict saprophyte and that fungi may be a parasite or opportunistic pathogen.

This paper has an interesting and novel experiment (and observations) which could be considered a breakthrough when looking at deep sea fungal samples and culturing methods. Even though there is no independent method section, it seems that the method is merged with results and introduction, which gives a unique guideline while adding brief method in the result section. Though not all readers may enjoy this style I personally do and, overall, I feel it is a very interesting paper and an important read for marine fungi enthusiasts.

Reviewed paper:

Burgaud G et al.,(2009) “Diversity of culturable marine filamentous fungi from deep-sea hydrothermal vents”. Environ Microbiol. 2009 Jun;11(6):1588-600., Link https://www.ncbi.nlm.nih.gov/pubmed/19239486

bacteria and marine fungi, plastic degraders?

Polyethylene (PE) Is the most commonly produced plastic that is discarded after use. A large amount of plastic eventually ends up scattered throughout the oceans. Polymer type, environmental conditions and season can affect the composition of a microbial biofilm. Plastic debris has a hard, hydrophobic surface which is an ideal environment for settlers. It can take as little as one week for a biofilm to form on plastic debris with the biofilm community significantly differing from that of the surrounding the environment. The degradation of PD is extremely slow and it is thought that microorganisms may degrade PD in the environment. A few bacterial species have been identified as PE degraders and recently marine fungus have also been shown to have the potential to degrade PE.

Current studies on biofilm formation on plastics are short term studies that do not assess the bacterial communities present on the plastics. These studies are also carried out on random pieces of collected plastic of unknow origin.

Long term exposure experiments (44 weeks) were carried out in the Belgian part of the North Sea at two locations in the harbour of Ostend and offshore, at the Thornton windmill park. The Harbour is affected by land run-off, ship discharges and pollution through waste pipes while the off-shore site is affected by activities from a wind farm and Fisheries.

Two types of PE with different colours and shapes were chosen. Transparent plastic sheets and orange dolly ropes were used. Three pieces of each were attached to an anchor and sent to the seafloor in both locations and Samples were collected at different time points. Half of the plastic was used for DNA extraction and half used in biofilm assays. Samples of sea water and sediments were also collected at the same time.

From the first week, a coating containing a biofilm, sediment particles, algae and macro-fouling species could be observed on plastic sheets at the harbour. Bacterial and fungal communities were analysed through metabarcoding and sample richness was assessed using OTU’s. Both showed that the plastic sheets and dollies had similar assemblages of bacteria and fungi in the harbour. At each timepoint the bacterial richness of the plastics was higher than fungal richness.

The bacterial community in the harbour showed a gradual change in abundance of bacterial classes over time. Alpha- and Gammaproteobacterial are primary biofilm colonizers while Bacteroidetes are secondary biofilm colonizers. There was a gradual shift between the two types suggesting that there are time points in the development of biofilms. This was not however seen on the dolly ropes.

25 bacterial core OTUs were identified on both plastic types. These were then placed into 4 groups based on their core members. 1 – neutral, without a clear period of high abundance, 2- higher abundance in the beginning, 3- higher abundance in the middle and 4- OTUs with highest abundance at the end of the exposure period.

Most of the fungal communities on the plastics could not be assigned using the UNITE database. Some of the reads could be identified as fungi using BLAST. This showed that Ascomycota was highly abundant but there was no core group of fungal organisms showing that fungi had high variability over time.

Offshore plastics had biofilm formation but it was much less pronounced compared to the harbour. The amount of biofilm seen at 22 weeks on the offshore site was similar in amount to the harbour site after 1 week. Bacterial OTUs remained low in offshore compare to harbour up to week 18. Fungal OTUs were similar between the two sites. Offshore sites did not have a gradient of primary and secondary colonizers with levels remaining steady throughout.

10 OTUs were identified in the offshore sites which were dominated by Flavobacteria and Gammaproteobacteria. When assessing the fungal communities more of the offshore sequences were unassigned than in the harbour. Fungal communities were like harbour communities in that there were no core members and that Ascomycota and Basidiomycota dominated.

Overall three fungi identified to species level were found on the plastic samples. These were more abundant on the harbour site and have been previously identified as PE biodegraders. No previously identified bacterial PE biodegraders were found in any of the plastic samples. This study found that substrate degradation efficiency increased when a biofilm is formed on the substrate and microbial populations had a higher metabolic activity when in a biofilm compared to when in the planktonic form. Overall there was no significant increase in biodegradation of plastics by microorganisms.

This study was limited by the lack of knowledge of marine Fungi. Many marine fungi are not functionally characterized and little is known about their biological functions and so their role in biodegradation of plastics is little understood.

Temporal Dynamics of Bacterial and Fungal Colonization on Plastic Debris in the North Sea

Tender et al., (2017) ‘Temporal Dynamics of Bacterial and Fungal Colonization on Plastic Debris in the North Sea’, Environ. Sci. Technol 51, 7350−7360. DOI: 10.1021/acs.est.7b00697

Vitamin Sea: a review of the role of vitamins in marine biogeochemistry

A review by Sanudo-Wilhelmy et al. (2014) discusses the roles of soluble B vitamins in marine biogeochemistry, drawing upon a range of peer-reviewed literature. This blog aims to summarise the key points of this paper, especially those which are most relevant the material covered in the module.

Vitamins are small organic molecules that are required in both primary and secondary metabolism throughout all domains of life. Vitamins are vital for life and the name originates from “vital amine” (Funk, 1912) as it was initially believed that all vitamins were amines (but this was later proved not to be true). Vitamins are grouped by their solubility; B vitamins have several hydroxyl groups, meaning that they are soluble in water. Vitamins are commonly required growth factors and coenzymes for intermediary metabolism and have a role in many important metabolic pathways (Madigan & Martinko, 2005).

B vitamins have a central metabolic role in both marine phytoplankton and bacteria. Phytoplankton dynamics, particularly the succession of species, are greatly influenced by the availability of essential B vitamins and the different species-specific requirements for those growth factors. According to Carlucci & Bowes (1970a), some phytoplankton species excrete extracellular B vitamins and it was found that dissolved vitamins in high concentrations are linked to high phytoplankton biomass. The growth of certain organisms is influenced by other organisms that produce their required growth factors. Dominant phytoplankton species are affected by the depletion or enrichment of various B vitamins depending on their specific growth requirements. This is apparent in algal blooms; species-specific requirements cause species to flourish but this will deplete the water of a certain vitamin, allowing for the enrichment of a different vitamin and favouring the algal species with a suitable vitamin specifity to bloom (Provasoli, 1963).  

The study of B vitamins is important as many marine algae require them for growth (Provasoli & Carlucci, 1974). B vitamin auxotrophy (the inability of an organism to synthesize vitamin B which is required for its growth) was found to be common amongst phytoplankton and bacteria taxa (Croft et al., 2006). There is a nutritional relationship between auxotrophs and vitamin producers (Carlucci & Bowes, 1970b). Many eukaryotic phytoplankton cannot synthesize vitamin B12 from scratch which has lead to 70% of species becoming dependent on vitamin B12 being present in their environment. However, some species have overcome this limitation by adapting to use alternative enzymes. Vitamin auxotrophy in prokaryotes can be determined by testing for the presence or absence of vitamin synthesis pathways. Koch et al. (2012) noted that marine bacteria have to compete with the other organisms in their environment for the vitamins they require. A common misconception is that vitamins are only produced by prokaryotes, but vitamin-producing and consuming bacteria and algae are also present in the ocean.

This paper also looks at the distribution of vitamins throughout the oceans. Vitamin B12 was found in the highest concentrations in coastal waters and the lowest in open-ocean. The dissolved B12 was found to be highest at intermediate depth but was lower above and below. Sanudo-Wilhelmy et al. (2012) indicated that the distribution and concentration of vitamins is site specific and independent of each other. The cause of vitamin depletion has yet to be identified but it appears that vitamins are degraded by rise in water temperature and solar radiation (Carlucci et al., 1969); this could mean that climate change could reduce vitamin concentrations in the ocean.

Despite this comprehensive review which has compiled a lot of research regarding the current knowledge o f B vitamins in the ocean, there are still a lot of areas for expanded research. However, this will require improved methods according to the authors. A topic of particular interest to me is with regards to how the increasing sea temperatures will effect vitamin distributions on a global scale and the species that simply cannot grow or survive without these necessary growth factors.

Reviewed paper:

Sañudo-Wilhelmy, S., Gómez-Consarnau, L., Suffridge, C., & Webb, E. (2014). The Role of B Vitamins in Marine Biogeochemistry. Annual Review Of Marine Science, 6(1), 339-367. http://dx.doi.org/10.1146/annurev-marine-120710-100912

Other cited papers:

CarlucciAF,SilbernagelSB.1969a.Effectofvitaminconcentrationsongrowthanddevelopmentofvitaminrequiring algae. J. Phycol. 5:64–67

CarlucciAF,BowesPM.1970a.ProductionofvitaminB12,thiamine,andbiotinbyphytoplankton.J. Phycol. 6:351–57

Carlucci AF, Bowes PM. 1970b. Vitamin production and utilization by phytoplankton in mixed culture. J. Phycol. 6:393–400

Croft M, Warren MJ, Smith AG. 2006. Algae need their vitamins. Eukaryot. Cell 5:1175–8

Funk C. 1912. The etiology of the deficiency diseases. J. State Med. 20:341–68

Koch F, Hatten-Lehmann TK, Goleski JA, Sa˜nudo-Wilhelmy SA, Fisher NS, Gobler CJ. 2012. Vitamin B1 and B12 uptake and cycling by plankton communities in coastal ecosystems. Front. Microbiol. 3:363

MadiganMT,MartinkoJM,eds.2005.BrockBiologyofMicroorganisms.UpperSaddleRiver,NJ:PrenticeHall. 11th ed.

ProvasoliL.1963.Organicregulationofphytoplanktonfertility.InTheSea,Vol.2,CompositionofSea-Water, Comparative and Descriptive Oceanography, ed. MH Hill, pp. 165–219. New York: Interscience

ProvasoliL,CarlucciAF.1974.Vitaminsandgrowthregulators.InAlgalPhysiologyandBiochemistry,ed.WDP Steward, pp. 741–87. Berkeley: Univ. Calif. Press

Sanudo-Wilhelmy SA, Cutter LS, Durazo R, Smail EA, Gomez-Consarnau L, etal.2012.MultipleB-vitamin depletion in large areas of the coastal ocean. Proc. Natl. Acad. Sci. USA 109:14041–45

Icy Cold Marine Fungi – Domination of Cryptomycota and Chytridiomycota

With the help of high throughput sequencing, DNA analysis have opened doors to a vast diversity of fungi, but a number of aquatic fungi are still missing from the fungal lineage, namely Cryptomycota and Chytridiomycota (the early diverging lineages) (Rojas-Jimenez et al., 2017). Lepelletier et al (2014) mentions how only a few studies have reported Chydrids in the marine environment and a limited number of marine Chytrids have been properly identified. This has led to the understanding that the diversity of fungi is relatively higher in terrestrial systems compared to marine and freshwater systems.

Members of the basal phyla, Chytridiomycota and Cryptomycota, have mechanisms such as their mobile, parasitize and saprophytic capabilities that allow them to survive in aquatic environments. These fungi, along with Dikarya, contribute to the overall functioning of the ecosystem as they take part in the carbon and nutrient cycle (Rojas-Jimenez et al., 2017).

The sampling sites were five ice-covered lake basins in the McMurdo Dry Valleys, Antarctica - Lake Miers, Lake Fryxell, Lake Hoare, and the West and East lobes of Lake Bonney. Several environmental parameters were measured - temperature and conductivity, many ions, dissolved oxygen, DOC, bacterial production, PPP and chlorophyll concentrations. DNA and RNA extraction, and cDNA synthesis were undertaken following protocols/kits and V7 and V8 regions of the 18S rRNA gene were amplified using specific primers. The samples were sequenced on an Illumina MiSeq sequencer and were deposited into the NCBI Sequence Read Archive. The 18S rRNA gene sequences were quantified and were assigned to OTUs and each taxa were also assigned to OTUs. Finally, the BLAST tool was used to obtain an accurate taxonomic assignation of the eukaryotes. Statistical analysis was performed in R.

From 4.99 m sequences that were analysed, 787,937 were classified as fungi and the DNA and RNA derived suggests that the fungal communities were active. Cryptomycota and Chytridiomycota were the most abundant fungal taxa in the sites. With reference to fungal reads and OTUs; Cryptomycota represented 72% and 44%; and Chytridiomycota represented 26% and 40% respectively. There were significant differences in fungal richness and community composition among the five lakes, with Lake Miers exhibiting the highest in all the depth layers, due to the freshwater habitat, warmer temperatures, and location – being situated in a valley with a higher altitude. The interaction between salinity and depth is what shapes the communities and diversity in the area. Rojas-Jimenez et al (2017) observed that with an increase in depth there was a significant difference between the richness of both habitats. Deep waters that form the monimolimnia (non-mixing layer of the lake) had a higher proportion of fungi than the mixolimnia (mixing layer of the lake).

Freshwater contained a significantly higher proportion of fungi and higher species richness than brackish waters (but an unequal abundance distribution) and there was a clear separation between the populations, eg: Blastocladiomycota was only found in freshwaters. As there were differences in community composition between lakes, depths and habitats, it is safe to say that some fungal taxa have a preference for certain niches.

Using the network analysis technique strong positive relationships between Chytrids and Cryptophyta (the most abundant primary producer) were visualized. Chytrids also had associations with Prasinophytae, Basidiomycota, Rhizaria, Zygomycota, Chloropastida, Chlorophyta and Stramenopile.

Recent findings of Chytridiomycota dominating freshwater and marine communities led Rojas-Jimenez et al (2017) to believe that basal fungal communities dominate undisturbed aquatic systems, whereas higher fungal communities (Dikarya) dominate terrestrial systems as well as aquatic systems affected by terrestrial and anthropogenic input.

This study has many potential areas for further research such as understanding how parasitic fungi may play a crucial role in maintaining phytoplankton biomass (considering the lack of grazers in this habitat) and the role fungi plays in energy, nutrient and carbon transferring by exhibiting these relationships. Also, the sample sites used have microbes living in extreme conditions that have not had anthropogenic influence, which makes it a good model to understand how fungi are able to cope with lower temperatures, osmoregulation and high ion levels.

It is interesting to note that Rojas-Jimenez et al (2017) did not observe any associations between Chytrids and Antarctic diatoms or dinoflagellates, since Chytrids have known to infect freshwater diatoms (Bruning., 1991), marine diatoms (Scholz et al., 2014) and dinoflagellates (Lepelletier et al., 2014), and also Arctic diatoms (Hassett and Gradinger., 2016). As we are entering a world where more and more molecular tools are available, it would be beneficial to implement different tools to further understand these fungal groups, with respect to their biology and ecology. As this is the first study emphasizing the dominance of Cryptomycota, along with Chytridiomycota in an aquatic ecosystem, it does a good job highlighting the dynamics of the early diverging fungi.

Reference:

Rojas-Jimenez, K., Wurzbacher, C., Bourne, E., Chiuchiolo, A., Priscu, J. and Grossart, H. (2017). Early diverging lineages within Cryptomycota and Chytridiomycota dominate the fungal communities in ice-covered lakes of the McMurdo Dry Valleys, Antarctica. Scientific Reports, [online] 7(1). Available at: https://www.nature.com/articles/s41598-017-15598-w#article-comments [Accessed 6 Jan. 2018].

Additional references:

Lepelletier, F., Karpov, S., Alacid, E., Le Panse, S., Bigeard, E., Garcés, E., Jeanthon, C. and Guillou, L. (2014). Dinomyces arenysensis gen. et sp. nov. (Rhizophydiales, Dinomycetaceae fam. nov.), a Chytrid Infecting Marine Dinoflagellates. Protist, [online] 165(2), pp.230-244. Available at: http://www.sciencedirect.com/science/article/pii/S1434461014000170.

Bruning, K. (1991). Infection of the diatom Asterionella by a chytrid. II. Effects of light on survival and epidemic development of the parasite. Journal of Plankton Research, 13(1), pp.119-129.

Scholz, B., Küpper, F., Vyverman, W. and Karsten, U. (2014). Eukaryotic pathogens (Chytridiomycota and Oomycota) infecting marine microphytobenthic diatoms - a methodological comparison. Journal of Phycology, [online] 50(6), pp.1009-1019. Available at: http://onlinelibrary.wiley.com/doi/10.1111/jpy.12230/full.

Hassett, B. and Gradinger, R. (2016). Chytrids dominate arctic marine fungal communities. Environmental Microbiology, [online] 18(6), pp.2001-2009. Available at: http://onlinelibrary.wiley.com/store/10.1111/1462-2920.13216/asset/emi13216.pdf?v=1&t=jc4qdznz&s=e300e3f5d2e6413a73bf78d3832aba5ff1ae33ff.