Plastic degradation and biofilm formation

Plastic became an omnipresent material in the everyday life these days and one has to deal with the waste. A lot of plastic is not recycled, therefore, a lot of plastic occurs in the environment, also in the ocean waters (like in the Great Pacific Garbage Patch). Plastic and its particles can be ingested by animals or can be incorporated in the sediments. Consequently, plastic debris is a significant problem in environmental pollution and can also be ingested by humans who consume e.g. fish that on its part has ingested plastic particles.

Normally, plastic is positively buoyant and floats at the seawater-air interface. As a result of fouling processes and degradation it can lose its buoyancy and start sinking and therefore e.g. can be incorporated in the sediments. Attaching algae to the plastic and other organisms can increase the degradation process and make the plastic neutrally buoyant. The attaching organisms can form biofilms, whereby firstly bacteria will attach to the plastic, followed by unicellular eukaryotes, larvae and spores.

The study by Lobelle & Cunliffe (2011) aimed to examine the early biofilm formation on plastic debris to get a better understanding of the mechanisms of the behaviour of plastic in the oceans.

For that reason, plastic food bags (polyethylene) were secured to boards and brought into the coastal waters in Plymouth, UK at 2 m depth for a duration of 3 weeks in summer. The plastic bags were sampled weekly and brought to the laboratory. Lobelle & Cunliffe used crystal violet to dye the samples and to make the attached biofilm visible. The stained plastic samples were incubated in ethanol, which was then transferred into a cuvette and its optical density at 595 nm was measured. Buoyancy was measured by placing the washed plastic samples in sterile seawater and noting its position after 10 min. Furthermore, the hydrophobicity was measured and the attached biofilm was diluted and plated out on Marine Agar 2216 (Difco) and polyethylene marine agar plates and incubated for 3 weeks to determine the number of culturable bacteria on the plastic samples.

After the first week of the experiment a visible biofilm has started to form and significantly increased during the 3 weeks. Coinciding with this, a decrease in hydrophobicity as well as an increase in hydrophilicity after 2 weeks were detected. Additionally, the plastic lost its positive buoyancy after about 2 weeks and floated below the seawater-air interface when tested in the laboratory and showed neutral buoyancy in week 3.

Apparently, the plastic samples were positively buoyant again and floated at the seawater-air interface as the control plastic in week 3, which is contradictory to the finding presented above. The authors mention that physicochemical effects of biofilm can be reversible and plastic can be positively buoyant when rapidly defouled, but do not really explain the finding and it remains unclear.

Over the duration of the experiment an increasing number of culturable bacteria has been found but no polyethylene-degrading bacteria were detected. Previous studies have shown that plastic-degrading bacteria like Pseudomonas or Arthrobacter have only been isolated from plastic after 12 weeks. Consequently, it takes longer to “infect” plastic with plastic-degrading bacteria.

The paper by Lobelle & Cunliffe is a bit hard to follow because it has no subheadings to structure it more. Moreover, it lacks some information to clarify the results. It is not clear, why the plastic was placed at 2 m depth. I think that, firstly, the plastic would float in the SML and would start to sink after a while. I think that the composition of the bacterial communities differs between the SML and at 2 m depth, so it would appear more logic to me to place the plastic bags directly at the surface, because plastic-degrading bacteria may be more abundant in the SML. A possible reason for the placement could be that the plastic cannot be ingested by e.g. birds during the duration of the experiment. Additionally, I have not found the results of the optical density measurements. In some points the study seems to be incomplete or some parts were not chosen to be published in this 4 page long paper.

All in all, this study provides a good base for understanding the influencing factors on plastic debris behaviour. It has been cited nearly 100 times since its publication and shows that plastic-degradation may start after more than 3 weeks and is a long process that includes different factors. It would be interesting to see how the results change when the study is conducted with the plastic floating directly at the seawater-air interface and with a different kind of plastic. 

Reviewed paper:

Lobelle, D., & Cunliffe, M. (2011). Early microbial biofilm formation on marine plastic debris. Marine Pollution Bulletin, 62(1), 197-200.

http://ac.els-cdn.com/S0025326X1000473X/1-s2.0-S0025326X1000473X-main.pdf?_tid=e830865e-b55f-11e6-b984-00000aab0f27&acdnat=1480333600_8074b98c59785186b7da541593992c3d

The Time Traveller’s Guide to the Salt Marsh: Marine to terrestrial shifts in fungal communities

Temperate salt marshes are characterised by halophilic angiosperms diurnally subjected to tidal inundation. As habitats, they represent areas of high productivity and carbon sequestration. Previous studies have shown fungi to play an integral role in terrestrial biogeochemical cycling by positively (or negatively) interacting with carbon cycling in associated plants. It is relatively unknown whether fungi play an analogous role in salt marsh ecosystems and how such fungal communities are established. Therefore, Dini-Andreote and colleagues (2016) investigated large-scale fungal community succession in an ambitious salt marsh survey.

Sediment deposition has gradually extended the Dutch island of Schiermonnikoog eastwards, creating a temporally younger salt marsh habitat than that in the West. Such environments are ecologically designated as ‘chronosequences’ -  habitats where the only assumed variable across the study area is age. The ~8km cline at Schiermonnikoog represents a temporal gradient of over 105 year and was thus selected for investigation in this study. Sediment samples were collected along the temporal gradient and fungal ITS regions were sequenced using Illumina Mi-Seq to characterise the fungal community. Bioinformatic analysis identified 917 total OTU’s across 16 classes, mostly belonging to the Dikarya. Contrary to the authors’ initial hypotheses, the β-diversity of early-successional communities was comparable to older samples (although fungal abundance was up to 100x lower). The earlier communities were, however, considerably more dynamic and fluctuated at small spatiotemporal scales relative to older samples, suggesting stable assemblages had not yet been established.

Most fascinatingly, OTU’s from earlier, more tidally-inundated sites were mostly composed of unidentified aquatic taxa (20.7% of which belonged to the parasitic Rozellomycota) with few Dikarya while mature communities showed filamentous and edaphic (soil-associated) characteristics. Distance-based linear modelling suggested that the predicting factors of fungal community structure were organic matter (OM) concentration and soil structure. This lead the authors to conclude that salt marsh fungal communities are established from dynamic marine consortia, which evolve into stable terrestrial assemblages as soil structure and angiosperm enrichment becomes established.

As with any large metabarcoding study, artefacts were present. The authors humbly acknowledge that the ITS primers employed were biased against chytrid-like signatures, which may explain their under-representation in this study. As well as this, abundance was enumerated using ITS signature quantification, which may have been obscured by fungal taxa with multiple gene copies - perhaps a problem that could be overcome in further studies using FISH coupled to flow cytometry.

In regards to further research, the authors’ conclusion that OM and soil structure were predictors of community identity warrants further investigation into the physiochemical modelling of angiosperm colonisation and their fungal symbionts. Multivariate changes in habitat over time may very well be attributed to chemical and structural niche creation by pioneer angiosperms, which may themselves be the drivers of fungal change. I would also be keen to see this phenomenon investigated in reverse, should an appropriate chronosequence be identified. Anthropogenic sea level rise is predicted to encroach into tidal wetlands (Galbraith et al, 2002) and studying the response of salt marsh fungal communities to salinization may show this succession in reverse.

In conclusion, this study is the first large-scale and high-resolution survey of fungal community succession in salt marsh soils and provides an impressive and comprehensive basis for further study.

Reviewed Paper: Dini-Andreote, F., Pylro, V. S., Baldrian, P., van Elsas, J. D., & Salles, J. F. (2016). Ecological succession reveals potential signatures of marine–terrestrial transition in salt marsh fungal communities. The ISME journal. http://www.nature.com/ismej/journal/v10/n8/full/ismej2015254a.html

Wetland Inundation: Galbraith, H., Jones, R., Park, R., Clough, J., Herrod-Julius, S., Harrington, B., & Page, G. (2002). Global climate change and sea level rise: potential losses of intertidal habitat for shorebirds. Waterbirds, 25(2), 173-183.  http://www.bioone.org/doi/abs/10.1675/1524-4695(2002)025%5B0173:GCCASL%5D2.0.CO%3B2

Synergy as the key to bioremediating oil pollution

A lot of research has been done on the possibilities of using microbes to decontaminate the marine pollution after an oil spill. Bioremediation appears to be no only an efficient, but also an economically beneficial technique. This depends however, on the bacteria used and the composition of compounds in the oil. Often, the bacteria used are indigenous to the site of pollution and in combination with each other instead of using single bacteria strains. Also, four main fractions of oil can be distinguished regarding polarizability and polarity: saturated alkanes, aromatics, resins and asphaltenes.  Li et al. (2016) researched what bacterial consortium would have the best biodegradation results in the Bohai Bay in Chine, where a serious spill of crude oil occurred in 2011.

The study consists of three main parts. First, oil-degrading bacteria are isolated and identified from Bohai Bay. The identification was executed using 16s rRNA sequences of the isolated strains. Five bacteria showed a significant contribution to degrading the crude oil and were eventually used for further research. They were named TBOC-1, TBOC-2, TBOC-3 and TBOC-4 and TBOC-5. Secondly, the biodegradation of the hydrocarbons by the bacteria was analysed and the five different strains were compiled into three consortia, of which the remediation effectiveness was assessed in the last part. Consortium A consisted of TBOC-4 and TBOC-5 on a 1:1 ratio, since these strains performed better on biodegradation of saturated alkanes and because TBOC-5 degraded aromatics more effectively compared to the other bacteria. (There was no significant degradation shown for resins and asphaltenes.) Consortium A was therefore expected to have complementary benefits. However, in the results it is shown that TCOB-2 has the highest value for oil biodegradation of saturates, but it isn’t used in any of the consortia. There is no reason mentioned for this, but it would be interesting to get further details on this. Consortium B and Consortium C functioned as comparisons and consisted of TCOB-1, TCOB-4, TCOB-5 and TCOB-1, TCOB-5, respectively. Again, no reason was mentioned for using TCOB-1 in these comparative consortia instead of one of the other three remaining strains.

The degradation rates for consortia A, B and C, respectively, were 51.87%, 35.29%and 21.39% after one week of incubation. The study shows an increase of 47.45% in the degradation  rate comparing bioremediation using a single strain and consortium A, which implies synergy between TCOB-4 and TCOB-5. What single bacterium they made this comparison with is not mentioned however. The authors further compare their own findings to several other studies, with the side note that the outcomes can not be compared directly, since the parameters in the experimental set up differ per study. It might have been interesting to show all these parameters and results per study in a table for a more detailed comparison. Looking at the results of consortia B and C, it is concluded that (1) it’s important to choose the most effective bacterial strains in order to reach the highest possible degradation rate and that (2) one should consider the possibility of bacteria strains limiting each other and thereby reducing the growth of the most efficient oil degrading bacteria and the overall biodegradation efficiency. In other words, using more strains of bacteria would increase the chance of having the more effective ones amongst them, but a higher amount of different bacteria increases the possibility of competition to occur as well.

This study gives an example of finding an effective construction for a bioremediating bacterial consortium and highlight the necessity to focus on complementary advantages. The main outcome is that the key to constructing these consortia is not the amount of bacteria species used, but to use bacteria that show synergetic bioremediation results. However, this statement seems contradictory to the outcome formulated in the discussion part, where the quantity of bacteria did seem to matter. The paper contains more of these obscurities, which gives a rather unreliable appearance to it. Also, the findings don’t seem to be innovative and it’s not clear how this research contributes to the scientific context. Especially since a lot of similar research has already been done on this subject. The authors do state however, that they’ve found a particularly interesting combination of oil degrading bacteria with consortia A. Since it only consists of two bacteria, it should be more economic and less ecologically complex compared to earlier researched consortia consisting of more different bacterial strains. All in all, I think this paper was an easy to read piece for people who want more background knowledge on this subject, despite the sometimes confusing or contradicting way in which some details are presented.

Article reviewed:
Adam, M. (2016). Biodegradation of marine crude oil pollution using a salt-tolerant bacterial consortium isolated from Bohai Bay, China. Marine pollution bulletin, 105(1), 43-50.

Ocean Acidification means more fun for fungi

When one thinks of ocean acidification; it’s rare that we think of marine organisms thriving.  However, a paper by Krause et al.,(2016) suggests that a group of previously neglected marine fungi, prefer low pH levels, and therefore may play an important role in our increasingly acidic oceans. Due to the ability of fungi to degrade complex substrates (lignocellulose and calcareous structure), they are important decomposers in the ocean and are able to fulfil a niche which previously had been thought unfulfilled.

Water was collected from Helgoland Roads Station on the 24^th of April 2011, and the 3^rd of May 2012. Sea water samples were either incubated at the in situ pH (8.10 in 2011 and 8.26 in 2012) or adjusted to pH 7.82 and 7.67.  20 replicates were incubated for each pH treatment (microcosm), and incubated in the dark for a period of 4 weeks, at the temperature of the in-situ samples (7 °C for 2011 & 8 °C for 2012), with Jars mixed daily by inversion. Fungal abundance (cfu) was determined at 7 °C to 8 °C (mean of the upper 10% of temperatures recorded from the study site from 2000-2010). These temperatures were chosen to determine whether different fungal groups (cold-adapted versus warm-adapted) were present and reacted differently to pH. Samples were filtered through nitrocellulose filters, and placed onto Wickerham’s YM agar, prepared with sea water from the sampling site. All filamentous and yeast-like colonies were counted by eye. F-ARISA analysis was used (culture-independent), and mechanical lysis was performed. To determine whether the different incubation temperatures selected for different fungal populations, DNA from bulk cfu filters with mycel was extracted and analysed using F-ARISA. Amplification using specific primers and reverse primers was used, labelled with infrared dye, and analysed based on the Jaccard coefficient. To avoid bias from the lack of data from 2011, statistical analysis was conducted separately for 2011 & 2012.  The surface pH at Helgoland was determined by sampling 5 times a week from September 2011-2012, with samples taken between 06:00 and 10:00h. Samples were immediately taken to the lab and measured.

In the sea water samples, 88 +-cfu 1^-1 In Spring 2011, and 34+-5cfu 1^-1 in spring 2012 were observed. Higher abundances in 2011 may be explained by the higher overall phytoplankton abundance on the sampling days (8.5x10⁶ cells 1^-1 versus 2.4 x10⁶ cells 1^-1 in 2012).  Fungal spores from terrestrial origin, likely introduced by water runoffs or wind, were found on agar plates, but were not actively growing within the sea water. During the experiment, fungal number increased greatly, indicating active growth. A strong influence of pH was also observed. Up to 1.2 x 10³ cfu 1^-1 at pH in-situ, 1.6 x 10⁴ cfu 1^-1 at pH 7.82 and up to 9.0 x 10⁵ cfu 1^-1 at pH 7.67. Factorial ANOVA’s showed that pH significantly influenced cfu 1^-1in both 2011 and 2012. Temperature also had a significant effect on community structure on bulk cfu filters with mycelium, and the pH effect on abundance for both groups was comparable, because, for both temperatures, cfu 1^-1 were always significantly higher at 7.82 and 7.67 than in-situ. Cfu 1^-1 were 8 to 9 times higher at pH 7.82 and 34 times higher at pH 7.67, compared to in-situ. Results from this experiment indicate that even moderate acidification may lead to an increase in fungal abundance. Different fungal communities were present between the 2 years; with the community structures of both significantly influenced by pH – the most significant being between pH 7.82 and in-situ.

The authors emphasise that microbes already experience large natural fluctuations in pH, due to depth of phytoplankton blooms, thus, it is important to take into account the natural variability of the study site. An average pH_NBS of >8.1 was determined, but higher values were observed which correlated with the spring blooming events, and values <8.0 do not occur at present. Therefore, it is probable that fungal responses may differ in regions which experience lower pH values. None the less, the results indicate that pH observed are of a general nature, and although different fungal communities developed in the 2 year study, with different temperatures hinting at the presence of fungi occupying different fundamental niches, the direct pH effect on fungal numbers remained consistent (The authors have made plans to identify the fungi)

The paper concludes with a section named  ‘Ecological implications’, summarising how OA may lead to: increased importance of fungi in microbial food webs, increased nutrient availability, rising threats of marine fungal parasites and pathogens, and an increase in the abundance of fungi in our oceans. The paper highlights how marine fungi have, up until now, been neglected – and the authors suggest a strong role of fungi in the microbial loop, which is likely to increase with increasing acidity. However, the authors are aware of the limitations of their work, and suggest that future research into the role of fungi in marine environments is “urgently needed”, with their own plans already made to identify fungal species found within samples in a future paper.

Reviewed paper:  Krause, E., Wichels, A., Giménez, L. and Gerdts, G., 2013. Marine fungi may benefit from ocean acidification. Aquatic Microbial Ecology, 69(1), pp.59-67.

Microbial sediment community shifts in response to the DWH oil spill

The Deepwater horizon oil spill in 2010 cause catastrophic damage to the marine environment, and will take many years the previous communities to present again.

78% of the oil spilt was managed to be deleted by natural means or human intervention by August 2010 the remaining oil most probably found its way in to the marine sediments. Kimes et al, aimed to assess which microbial communities were present in the sediments around the oil spill and determine their metabolic capabilities.

Deep-sea sediment cores were collected between September and October 2010, from sites close to the DWH site and sites further away to be used as control groups. The metagenome of each sample was determined, followed by PCR of function genes including genes coding for; the catalytic subunit of the anaerobic glycyl radical enzyme (assA and bssA), alkylsuccinate synthase and Benzylsuccinate synthases. Finally, phylum level classifications were made from each metagenome, and differences in the Proteobacteria at the class and order level, as this group showed great differences between the sites.

This paper presents three new metagenomics data sets from deep sea sediments following DWH oil spill, when looking at this data along with previous data sets from the DWH oil spill site there is clear distinctions in the microbial communities between the sites in the Gulf of Mexico and the ‘control’ site; Peru Margin.  Oceanospirillales was previously shown to be a dominant bacterial order in the deep water oil plume associated with the DWH event (Hazen et al., 2010). The Kimes et al study did find bacteria in the Oceanospirillales order with many sequences in the meta genome related to Alcanivorax borkumensis. Over all there was a similar abundance of Oceanospirillales sequences found at all 3 sites, and in general a similar abundance of Gammaproteobacteria.

There were higher levels of Deltaproteobacteria in sediment cores closest to the DWH site, where levels of PAH’s were at their highest. Clone libraries support of assA and bssA support the metagenomics analysis with but being found at the site near the DWH and not at the control, unimpacted site showing the potential for aliphatic and aromatic hydrocarbon degradation.

A main conclusion in this paper is that the lack of distinctions within the 3 samples maybe caused by a quick degradation of the oil in the water column, previous papers showed increased levels of oil degrading bacteria in the water column, and in turn the amount of hydrocarbon loading that occurred in the deep-sea sediments was not significant enough to promote microbial growth.

The Authors accept some major downfalls of this study which may impact on the reliability of the results, including the low replication number, but it was noted that it was limited due to political and logistical reasons. A well as this study only revealing a snapshot in time, which may be at a time when the community was beginning to shift to reflect the increasing importance of anaerobic microbes. The best way to over-come this is by preforming a time series study.

I think the strength of this study lies in the interdisciplinary approach it takes to assess the phylogenetic comparisons and functional potential of the microbial communities which were effect by the DWH oil spill. This data as well as previous data suggests that the presence of PAH’s, alkanes and alkenes may influence the microbial communities which are exposed to anthropogenic hydrocarbons.  

Reviewed paper: 

Kimes, N. E., Callaghan, A. V., Aktas, D. F., Smith, W. L., Sunner, J., Golding, B., … Morris, P. J. (2013). Metagenomic analysis and metabolite profiling of deep–sea sediments from the gulf of Mexico following the Deepwater horizon oil spill. Frontiers in Microbiology, 4, . doi:10.3389/fmicb.2013.00050 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3598227/

Hazen, T. C., Dubinsky, E. A., DeSantis, T. Z., Andersen, G. L., Piceno, Y. M., Singh, N., … Mason, O. U. (2010). Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science, 330(6001), 204–208. doi:10.1126/science.1195979 http://science.sciencemag.org/content/330/6001/204

Marine fungi as a source of new hydrophobins?

Fungi are a monophyletic group that has been found across all parts of the world. These fungi are very diverse, some being filamentous and containing structures known as hyphae, whilst other fungi are single celled with no hyphae. Many of these filamentous fungi produce hydrophobins - small proteins of about 100 amino acids that are the most powerful surface-active proteins to our current knowledge. Hydrophobins have an amphiphilic structure, with their hydrophobic aliphatic side chains able to create a coating on the surface of an object. These properties have been shown to have uses in coating of spores, which allows the fungus to move about and to attach to different surfaces.

Cicatiello et al (2016) aimed to identify marine fungi as a source of hydrophobins. Hydrophobins were split into Class I and Class II, depending on their properties. Class I form highly stable, highly insoluble aggregates and have distinct rodlets, whereas Class II are less stable and lack the ability to form rodlets.

Marine fungi was isolated from the seagrass Posidonia oceanica, the green alga Flabellia petiolata and the brown alga Padina pavonica near Elba island in the Mediterranean sea. Each marine fungal strain was maintained on an agar plate at 20^OC. To extract Class I and Class II hydrophobins from the culture broth, proteins were aggregated by bubbling air using a Waring blend, and the foam was collected and treated with 20% trichloroacetic acid.

To extract Class II hydrophobins from the mycelium, mycelia were washed with water and proteins were extracted using 60% ethanol in a bath sonicator. Class I hydrophobins were extracted using 2% sodium dodecyl sulphate, water, 60% ethanol and trifluoroacetic acid.

The results showed that 23 out of the 100 strains of marine fungi were chosen due to their foam producing capabilities in shaken cultures, thus showing the production of biosurfactants. The isolation of Class I and Class II hydrophobins from the culture broth and the mycelium allowed the identification of 6 new putative hydrophobins that could be used in biotechnological instances in the future.

This study provided evidence for marine fungi as sources of hydrophobins, and seemed to go beyond the aims they set by trying to look at the functions of the identified hydrophobins. Whilst this is a good thing, it did seem to get confusing at times as to what they were trying to achieve. The way it was written was also confusing at times as the parts of the methods seemed to appear in the results and discussion sections. This paper could be more clear and concise on just what it was trying to show, and could be written better, but I think the overall conclusion and results seemed to show that the study was successful in reaching its aim.

Reviewed paper: Cicatiello, Paola., Gravagnuolo, Alfredo. Maria., Gnavi, Giorgio., Varese, Giovanna. Cristina., and Giardina, Paola. (2016). Marine fungi as a source of new hydrophobins. International journal of biological macromolecules. 92: 1229-1233. http://www.sciencedirect.com/science/article/pii/S0141813016311928  

Picomanaging – Fungi as possible parasites of photosynthetic picoeukaryotes

Photosynthetic picoeukaryotes (PPE) are major contributors to CO₂-fixation in marine ecosystems. These small organisms (here defined as < 5µm in diameter) not only fix carbon but some mixotrophic species also help regulate bacterioplankton abundance. While the molecular diversity of PPEs is relatively well known, the factors controlling their abundance are not. However, recent studies suggest a top-down regulation instead of other limiting factors such as nutrient abundance. One possible regulating mechanism might be eukaryotic parasites. In addition to members of the Alveolata clade, marine fungi are well-known eukaryotic parasites. In their paper, Lepère et al. (2015) examined the effect of eukaryotic parasitism on PPEs in the marine environment.  

Water samples were taken from 0-88 m depth along the AMT19 transect in the Southern Atlantic Ocean, including the southern subtropical gyre (SG) and the southern temperate region (ST) off the coast of South America. The abundance and distribution of free-living Syndiniales (an order of dinoflagellates), Perkinsozoa (protists) and fungi were investigated using filtered samples. Additionally, the PPEs were divided into small (Plast-S) and large fractions (Plast-L) and the interactions between PPEs and putative parasites were analysed using flow-cytometric cell sorting, tyramide signal amplification - FISH (TSA-FISH) and wheat germ agglutinin (WGA) chitin staining.

The analysis of PPE community structure along AMT19, yielded similar findings to previous studies. Prymnesiophycae (48%) dominated the Plast-L populations, while Pelagophyceae (30%) and Chrysophyceae (20%) made up the majority of the Plast-S populations.
Syndiniales were only detected at low abundance, albeit with high variation between sites. As expected, Perkinsozoa were generally absent from the sea-water, as they are preferentially found in sediments. In order to avoid 18S rRNA copy number bias, the authors examined free-living fungi with three specific FISH probes, specifically targeting different fungal sequences. The average abundance of free-living fungi was 9.3% of the total Eukarya, most of which were zoospores. The highest abundance of fungi was detected in the ST region (14%). Generally, Chytridiales accounted for 3.5% of the total eukaryote community. In contrast, no positive signals were detected for Cryptomyocota and the clade doesn’t appear to be abundant in surface sea-water. 

Dual labelling TSA-FISH showed no association between PPEs and Syndiniales dinospores and they are generally found to parasitize larger organisms e.g. other dinoflagellates. The authors were able to demonstrate associations between fungi and PPEs, in which sporangia seemed to be attached to the surface of the algae. Targeting of rRNA showed the algal cells to be active and not under saprotrophic feeding by the fungi. However, these interactions were only detected in Plast-L populations, where. 3% of the Prymnesiophyceae and 6.4% of the Chrysophyceae had fungi attached to their surfaces. These interactions were observed in both the ST and SG. Moreover, the authors identified possible different stages of fungal infection. 

Lepère et al. are the first to demonstrate presumable parasitic fungi and their impact on PPEs. In addition to grazing, picophytoplankton abundance might therefore also be regulated by parasitism. However, this study merely suggests a possibility and the authors acknowledge some limitations in their study e.g. the availability of suitable oligonucleotide sequences. Nevertheless, the authors don’t mention why they deviated from the general size classification of picoplankton (0.2 - 2 µm instead of < 5 µm), or why six years passed between the sampling in 2009 and publishing in 2015. 

Reviewed Paper:

Lepère, C., Ostrowski, M., Hartmann, M., Zubkov, M. V., & Scanlan, D. J. (2015). In situ associations between marine photosynthetic picoeukaryotes and potential parasites–a role for fungi?. Environmental microbiology reports. Link: http://onlinelibrary.wiley.com/doi/10.1111/1758-2229.12339/abstract

Bioturbation and increasing temperature in shallow-lake sediments; is there an effect?

 Although Lakes only occupy 2% of the Earth’s surface (a meagre percentage when compared to the 70% covered by oceans); they still play substantial roles in global biogeochemical cycles. Shallow lakes are important carbon metabolism sites, with aerobic respiration being an important meahcniams in the carbon metabolism of lakes. Bioturbation is impacted by benthic animals, which re-work the sediment matrix; and their impact has been underestimated until now. Seasonal variation plays an important role in biological activity, and this experiment uses microcosm experiments to investigate how the impact of biurtabation on lake sediment respiration changes with increasing temperatures.

The bioturbator used for these microcosm experiments is Chironomidae larvae (Diptera), a species which dominates fresh waters and is considered highly important in aquatic bioturbation. Resazurin is a bioreactive tracer, and its decay is proportional to aerobic respiration within the system; thus it can be used to assess the temperature-dependent differences in sediment respiration. Resazurin is not susceptible to respiration of apneustic aquatic animals; therefore its use enables the independent quantification of sediment respiration impacts of chironomid bioturbation, from their own respiration.

Experiments used glass cylindrical mesocosms with a volume of 566ml; containing 200g of sediment from Lake Muggelsee (Berlin, Germany), with known nutrient levels. Bank filtrate water (250ml) was used in the mesocosm, and was constantly aerated to assure homogenous mixing and continuous oxic conditions in the water overlying the sediment. All animals used in the experiment were of similar ages and comparable sizes. They were used in 3 different densities which corresponded to in situ analysis of the source lake; using a range of 0, 1000 and 2000m^-2 in the experiment compared to 500- 2000 per m ² in situ.  Animals were acclimatised to each respective temperature (5, 10, 15, 20 and 30 ° C) 5 days prior to the experiment, and stable redox conditions were established in the sediment before commencing. Oxic interfaces were visible as ‘light-reddish brown’ patches in sediments and usually appeared between 24 and 36h, indicating that the 5-day long pre-experimental acclimatisation phase was sufficient. Four replicates (at each temperature) for each larval density were conducted. Aerobic respiration was quantified by measuring fluorescence of resazurin (because resazurin decay is proportional to aerobic respiration in the system (average r² =0.986), thus acting as a proxy for 0₂ consumption.

The microcosm experiments revealed respiration differences between bioturbated and non-bioturbated sediments, showing an increase of respiration with rising temperatures. At 5 °C, the difference in sediment respiration between bioturbated and non-bioturbated respiration was statistically not significant.  Whilst at 10°C and above, respiration differences between non-bioturbated and chironomid-bioturbated sediments were statistically significant, and increased with rising temperature. The largest difference was seen in the 30°C microcosm experiment, with respiration in microcosms containing 1000 larvae m^-2 being 4.4 x higher than in non-bioturbated sediments, and those containing 2000 larvae m^-2 exceeded non-bioturbated sediments by six times. Temperature dependent respiration was only highly significant in microcosms containing 1000-2000 larvae m^-2, and was not statistically significant in the non-bioturbated microcosms.

This paper, for the first time, has enabled the measurement of respiration not affected by the respiration of chironomids’; therefore showing that the increased respiration rates in this study, to be solely attributed by the bioirrigation-impacted sediment respiration. It was proven that increasing temperature significantly enhances the impact of chironomid bioturbation on sediment respiration (i.e.  Strong seasonal changes of sediment respiration sue to seasonal changes of lake). This paper shows that increasing global temperatures impact the sediment - microbial communities within lakes, and that even an increase of a few degrees may be sufficient to increase respiration rates within sediment. None the less, they still believe that more research is needed in this area; as already mentioned in the beginning - it is a heavily under explored area of microbiology.


I would highly recommend looking at the graphs in the paper, as they really help to explain the linear relationships between temperature and respiration. 

http://rsbl.royalsocietypublishing.org/content/roybiolett/12/8/20160448.full.pdf

Reviewed paper : Baranov, V., Lewandowski, J. and Krause, S., 2016. Bioturbation enhances the aerobic respiration of lake sediments in warming lakes. Biology Letters, 12(8), p.20160448.