Bloom or bust

It is commonly known that viral lysis of marine organisms, such as microalgae and plankton, is an important source of carbon and nutrients such as nitrogen for bacteria in the oceans. This influx of organic matter fuels bacterial growth and shapes the way their communities form. In turn this has an effect on microbial loop processes and therefore marine food webs.

While most studies focus on post-lysis effects, a recent study by Sheik et al. (2013) looks at exactly how viral infection of the unicellular algae Phaeocystis globosa (which often form large blooms in polar regions), affects surrounding bacterial populations from the moment of infection to post-lysis stages.

To measure the bacterial communities surrounding P. globosa cells, a method called CARD-FISH (catalysed reporter deposition-fluorescence in-situ hybridization) was used. Measurements of the bacteria were taken at regular intervals, and this was able to provide evidence of increasing population numbers, especially of the gammaproteobacteria Alteromonas, just 5 – 8 hours after viral infection of P. globosa cells, before cell lysis at ~12 hours.

A combination of HISH and nanoSIMS was used to measure how much carbon and nitrogen was assimilated by the bacterial populations. This showed that ~20% of the measured C and N were leaked during early viral infection.

The leakage of organic matter from the infected but still intact cells resulted in colonization of the infected algae by bacteria. I think this is potentially due to the creation of a chemotactic gradient which attracts the bacteria towards the source of the organic matter, similar to how bacteria find sinking marine snow particles and plumes.

I believe this work is a step forward in understanding the degree to which viruses impact bacterial communities in the ocean. It is a detailed expansion of work already done on the effect of viral lysis on carbon and nitrogen cycling by bacteria. It not only manages to quantify the bacterial communities utilizing carbon and nitrogen released from infected algal particles, but also provides us with a new niche to study by looking at the bacteria which colonize infected algal particles. I think this paper can be used as a good base for better understanding the processes behind algal blooms and their effects on oceanic microbial processes.

Abdul R Sheik, C. P. (2013). Responses of the coastal bacterial community to viral infection of the algae Phaeocystis globosa. Multidisciplinary Journal of Microbial Ecology, 8, 212 - 225.

Deadly winds – Death comes from above

Marine viruses are a key participant in global ocean processes. Viruses are known to infect all forms of cellular life. Hence, they have a significant impact on oceanic nutrient cycles.

The study by Sharoni et al. (2015) focuses on the link between the Emiliania huxleyi virus (EhV) and the common, bloom-forming phytoplankton E. huxleyi in the North Atlantic. Furthermore it examines the dispersal mechanisms. It is shown that aerosolized EhV can be carried on the wind and still be infective.

It is known that virus dispersal can occur in different ways, such as diffusion, mixing, advection, currents and throughout the food web. This paper proves the hypothesis that virus dispersal is not limited to the water body only.

To proof that hypothesis, an aerosolization by wind-induced bubble bursting was simulated in the laboratory. In the first step E. huxleyi was cultivated and infected with EhV. Measuring the concentration of EhV in the air showed that the distribution of EhV in the air grew proportional with the viral production in the water.

To verify that the EhV is still infective, the outflow of the system was linked to another set up with a susceptible strain and a resistant strain of E. huxleyi. As expected, the resistant strain showed no infection whilst the susceptible strain showed viral infection.

In the next step the decay rate of airborne EhV was tested. Using a probable number method (MPN) for calculations of viral infectivity and comparing it to previous studies about the decay rate of viruses it became apparent that EhV can remain infective for several hours.

To compare the results of the laboratory experiment with the natural events, aerosol samples were collected during the E. huxleyi spring bloom in the North Atlantic. Analysis of collected aerosol samples contained virus like particles. Further examination of the DNA signature verified the presumption that the virus like particles was the EhV.

In my opinion the work of Sharoni et al. (2015) contributes to a better understanding of the marine viral dispersal and its impact on oceanic processes. Even though it is known that natural aerosol transmission of viruses is natural, this paper gives a new insight into viral infection and dispersal in the marine environment. For instance to understand the extent of the collapse of E. huxleyi blooms caused by EhV, it is important to know how viral dispersal is working. Not only chemical, physical or biological processes in the water body play a role in the understanding of phytoplankton blooms and their consequences, such as DMSP release caused by viral lysis. Additionally meterological processes and regional climate impacts must be considered for further studies.

Shlomit Sharoni, Miri Trainic, Daniella Schatz, Yoav Lehahn, Michel J. Flores, Kay D. Bidle, Shifra Ben-Dor, Yinon Rudich, Ilan Koren, and Assaf Vardi (2015)

Infection of phytoplankton by aerosolized marine viruses

PNAS 2015 112 (21) 6643-6647;doi:10.1073/pnas.1423667112

http://www.pnas.org/content/112/21/6643.full

Welcome to the 2015 blog

Most of your learning about recent developments will come from reading and evaluating the latest research papers. The coursework mark (which is 50% of the module mark) will be derived from tutor assessment of your online postings to the blog site, which should show evidence of current awareness of the scientific rationale and potential applications of recent research findings relevant to the module content. The assessment will be based on the frequency and — most importantly — the quality of your contributions (both your own reviews and the comments on other people’s contributions). 

The idea is that all members of the class post short items interpreting the key elements of  research papers you have read. Other members can also read these and comment on the posts. In this way, we will build up an exciting picture of the latest developments in this fast-moving subject. If everyone contributes and follows the blog regularly, we will have a great resource to supplement the lectures. Although it requires quite a lot of work and regular inputs (for me as well as you!), this collaborative effort will be a great revision aid for the exams too.  The students in the past four years gave very positive feedback and I hope that you also find this an enjoyable way of learning!  

Please check the module guidance on the Moodle Site for more information about how to create your posts and the assessment criteria used.

Group post: Tracing the carbon flow from diatoms to bacteria in a benthic biofilm

The microphytobenthic community provides a vital carbon source for higher trophic levels in coastal ecosystems. In addition, through the formation of a biofilm the microphytobenthos –typically dominated by benthic diatoms- stabilises soft sediments and provides settlement cues for intertidal organisms. Low molecular weight exudates released by diatoms may be directly utilised by bacteria, whereas high molecular weight compounds such as extracellular polymeric substances (EPS) may need to be hydrolysed by extracellular enzymes.

Miyatake et al. (2014), traced the in situ carbon flow from benthic diatoms through heterotrophic bacteria in an intertidal sediment over 5 days using a pulse-chase method, advantageous over laboratory based techniques by preserving environmental variables such as wave, sediment, and pore water dynamics. The study was conducted on an intertidal flat covered by a diatom mat in The Netherlands, 0.15 m below the mean tidal level. Two 50 x 50 cm frames were inserted into the sediment to a depth of 8 cm to contain the carbon flow. ¹³C Sodium bicarbonate was sprayed onto the sediment to a final concentration of 1 g [¹³C] sodium bicarbonate m². The first sampling occurred after 4 hours (pulse period) and subsequent sampling at 12 h, 1 d, 2 d, 3 d, and 5 d (chase period). 16S rRNA (Mag-SIP) and phospholipid derived fatty acid (PLFA) biomarkers were used for the identification of the major active microbial groups. A wide range of oligonucleotide probes was used to generate clone libraries for Mag-SIP bacterial analysis derived from total RNA and captured 16S rRNA. Water extractable carbohydrates were extracted to identify the intermediate compounds produced by the diatoms and those bacterial groups which assimilated them.

Out of the primary producers; diatoms were predominant with Gammaproteobacteria, Bacteroidetes, and Deltaproteobacteria being the main heterotrophic bacterial groups. Data from both ¹³C-PLFA and ¹³C-rRNA suggest a fast transfer of label from diatoms (60 nmol ¹³C g^-1 dry weight [dry wt]) to bacteria (7 nmol ¹³C g^-1 [dry wt]) during the first twenty-four hours, which suggests an exudation of low-molecular-weight organic compounds by diatoms that could be directly utilised by bacteria. Following this initial fast transfer, labelling of bacteria continued at a slower rate (13 nmol ¹³C g^-1 [dry wt]), which coincided with the degradation of carbohydrates in water-extractable extracellular polymeric substances (EPS) initially produced by the diatoms.

Unexpectedly, secondary labelling was also discovered for the diatoms. They may have used the EPS as external storage of carbon since the DIC was low.  On the other hand it is possible that the diatoms gradually reincorporated a variety of EPS and although this wasn’t the focus of the study, there are papers supporting this theory such as Smith and Underwood 2000 which showed that reserve compounds were used in the dark.  It was expected that there would be some specialized bacterial groups associated with the mat fulfilling different nutrient niches. However, the results suggest that the heterotrophic bacterial community equally shared the diatom organic matter. This study demonstrates the close nutrient coupling between benthic diatoms and heterotrophic bacteria. This study didn’t consider the action of macrofauna on the nutrient pathway concerned. Considering the open nature of this in vivo experiment. Burrowing organisms may have caused bioturbation within the sediment, or molluscan grazing upon the biofilm may have occurred. Considering the importance of benthic biofilms as a carbon source for higher trophic levels it is important to consider these processes.

Reference:
Miyatake, T., Moerdijk-Poortvliet, T. C., Stal, L. J., & Boschker, H. T. (2014). Tracing carbon flow from microphytobenthos to major bacterial groups in an intertidal marine sediment by using an in situ 13C pulse‐chase method.Limnology and Oceanography, 59(4), 1275-1287.

Protozoan parasites threaten tropical bathing waters

Pollution in the form of sewage is a major contributor to the fouling of shallow tropical coastal waters. These warm coastal water can harbour various pathogenic microbes, capable of causing harm to human health. This study looks specifically at two protozoan intestinal parasites, Giardia duodenalis and Cryptosporidium parvum, both environmentally robust in their cyst stages allowing prevalence in sewage waste waters entering the marine environment. In recreational coastal areas, the likelihood of these pathogens causing harm is increased by activities such as swimming and water sport activities. However, in the tropics the levels of this harm have not yet been estimated. Tropical areas are of particular interest in terms of harbouring pathogens as temperature and sunlight irradiation may increase their survival. This combined with the posing threat of climate change and increasing population densities in coastal areas is cause of significant concern for human health in bathing waters.

In this study, the potential risks were assessed in Venezuela’s central coast, an area of high intensity recreation usage. They used SYBR green I real time PCR to look for genetic markers of Cryptosporidium and Giardia cysts specifically and traditional culture methods to assess for faecal indicator bacteria FIB) and water quality deterioration. Risk of each species was determined by the level of cysts found in the areas using a dose response model, showing that Cryptosporidium has a risk value of 0.026 and Giardia has a a risk value of 0.00572, equating to a 39 and 50% chance of rate becoming ill once infected, respectively. Both of these were below the U.S. EPA upper bound on recreational risk of 0.036 however, 95th percentile estimates for Giardiasis for children exceeded the 0.036 level, suggesting levels of contamination may not be completely safe. A Monte Carlo uncertainty analysis was performed in order to determine the probability distribution of risks. 35% of the sites were shown to harbour Giardia cysts while Cryptosporidium were only detected in 14%. This level increased with the extent of sewage pollution and bather density during collection based on FIB levels. Giardia is the most common protozoan parasite found in human faecal samples in clinical laboratories for parasitic examination, explaining its widespread occurrence in the tested bating waters.

This study highlights the importance of pathogen specific detection for detection of disease risk in specific geographical areas. It shows how the risks of parasitic diseases acquired whilst undertaking recreation activity in tropical waters can be estimated using quantitative microbial risk assessment. Future research is needed into understanding fully the relationship between sewage pathogens and surrogate indicators in tropical waters, however this research highlights the advantages of using microbial tracking to identify sewage pollution. I think that issues such as sewage pollution are increasingly needed with the changing climate, as research into more tropical parasitic microbes will need to be applied to more temperate regions as temperatures increase and species distributions change with the climate. It is important that reliable detection methods are implemented soon.

Betancourt, W., Duarte, D., Vásquez, R. and Gurian, P. (2014). Cryptosporidium and Giardia in tropical recreational marine waters contaminated with domestic sewage: Estimation of bathing-associated disease risks. Marine Pollution Bulletin, 85(1), pp.268-273.

Papers for revision

As previously discussed in the final workshop for the module, I have included below the web addresses for the Ocean Acidification and Biofilm papers which Anita and I read for our global change project. I hope they are of use.

Intertidal epilithic bacteria diversity changes along a naturally occurring carbon dioxide and pH gradient. 

http://onlinelibrary.wiley.com.plymouth.idm.oclc.org/doi/10.1111/1574-6941.12368/epdf

Microbial biofilms in intertidal systems: an overview.

http://www.sciencedirect.com.plymouth.idm.oclc.org/science/article/pii/S0278434300000224

This paper addresses microbial biofilms in general, however, this does include some information on pH reduction effects on biofilm structure and associated microbes.  

My final blog post-I'll sign off with some gastrointestinal bacteria from turbot, lovely.

The gastrointestinal (GI) tract of fish is very complex, containing up to 107-108 colony-forming units (A unit used to measure the number of viable bacteria). The GI tract composition for farmed adult turbot Scophthalmus maximus hasn’t been previously studied using metagenomics (Xing et al., 2013). Xing et al., (2013) therefore looked into this, using metagenomics alongside 16S rRNA analysis, aiming to characterize taxonomic distribution and metabolic potential of the S.maximus microbiome, assess the bacterial diversity and see how the microbiome is related to the environment.

Xing et al., (2013) used 10 adult S.maximus alongside water samples from China. The GI tract of each fish was removed, and the contents squeezed out. The mucus was also collected, along with the bacteria present in the seawater. The genomic DNA was extracted and metagenomics and 16S rRNA were carried out to assess the taxonomic composition and functional diversity of the microbiome.

They found that both the GI tract and mucus samples of the fish were largely made up of Protebacteria (a major bacterial group) and Firmicutes. It was also found that the GI tract might possess bacteria that are initially associated with the seaewater. Both quorum sensing and biofilm formation were found to be overabundant when compared to other metagenomes. The genes associated with these were found to be mainly in species within the group Vibrio. The species also showed an overrepresentation of the systems associated with protein folding and stress responses. Alongside this, the genes related to human activity, such as antibiotic and heavy metal resistance were also detected. Therefore, it can be inferred that humans are affecting the GI microbiome in marine aquaculture species. (Xing et al., 2013)

Being one of the very early pieces of research using metagenomics on a farmed species, I feel this study is clearly of huge importance both in the present and for the future of aquaculture. It gives a clear idea of the bacteria that are associated with the fish, in this case, a high level of Vibrio. Also showing a detection of the genes associated with antibiotic resistance shows that the fish microbiome in aquaculture is being compromised by humans. Xing et al., (2013) suggest that aquaculture may effect the microbiome of the fish. Finding this out has huge implications in terms of being able to manage aquaculture to give the healthiest fish and the best yield. I feel using metagenomic profiling in the GI tract of fish holds potential for giving an insight into the bacteria associated with it and so may be of great use in the future of aquaculture. However, the number of samples and species that this is conducted on needs to be hugely increased in order to give broader, more applicable results.

Reference:

Xing, M., Hou, Z., Yuan, J., Liu, Y., Qu, Y., Liu, B. (2013). Taxonomic and functional metagenomic profiling of gastrointestinal tract microbiome of the farmed adult turbot (Scophthalmus maximus). FEMS Microbiology Ecology. 86, 432-443.