Complex Interactions Within Microbial Communities

Interactions between micro-organisms are an important feature of marine environments, and have a significant role in shaping communities and ecosystems. Previous studies have revealed some of the mechanisms of these interactions, which include the facilitation of vitamin and mineral uptake, inter- and intra-specific communication and allelopathy. Results have shown that heterotrophic bacteria can have a positive or negative effect on growth of algae and cyanobacteria, and more recent studies have investigated the effects of heterotrophic bacteria on one of the most abundant phototrophs in temperate and tropical oceans, Prochlorococcus.

The paper expands upon this previous work, and details the effects of 344 strains of heterotrophic bacteria on the growth of two Prochlorococcus strains; a low light adapted strain (MIT9313) isolated from the Gulf Stream and a high light adapted strain (MED4) isolated from the Mediterranean Sea. Two ecologically distinct strains were chosen in order to determine whether the same heterotroph would have different effects on each strain. The heterotrophic bacteria, consisting of gamma-proteobacteria and alpha-proteobacteria, were isolated from the Hawaii Ocean Time Series (HOT) station ALOHA, which has an extensively studied Prochlorococcus-dominated community.

The heterotrophs and the Prochlorococcus strains were co-cultured in 96-well plates on Pro99 media with pyruvate, acetate, lactate, glycerol and a vitamin mix added. Plates were kept at 20°C and 27µE constant cold white illumination for 42 days, and almost every day a reading of the bulk chlorophyll fluorescence (FL) was taken to produce a growth curve for each strain.

The authors discovered that the growth of strain MIT9313 was affected more than that of strain MED4, with ninety-eight per cent of the heterotrophs having no clear effect on MED4, compared to only 6% which had no effect on MIT9313. Other heterotrophs caused the MIT9313 strain to enter exponential growth earlier or later, or caused growth to arrest early. Partial 16S ribosomal sequencing was used to define closely related bacteria to determine whether they had similar effects on the growth of the strains. The results revealed that bacteria whose sequences differed by 1-2% did have similar effects on MIT9313.

The authors also sought to find out whether the interactions required cell-to-cell contact, by co-culturing MIT9313 with five bacterial strains from different clades, and separating them with a 0.4 µm membrane. Those heterotrophs which caused early exponential growth of strain MIT9313 in the original experiment had the same effect when separated by the membrane, indicating that diffusible soluble compounds mediated this response. Interestingly, Alteromonas strain HOTo1A3 only caused late growth when mixed with MIT9313, and not when separated by the membrane.

The relevance of this study could be called into question as the authors were unable to replicate the natural environment of Prochlorococcus, and did not isolate the strains from the same location as the heterotrophs. However the paper does lay the foundations for further research to take place, involving a more diverse range of bacteria, to further our understanding of these complex interactions which are so important within communities.

A review of: Sher, D., Thompson, J.W., Kashtan, N., Croal, L. and Chisholm, S.W. (2011) Response of Prochlorococcus ecotypes to co-culture with diverse marine bacteria, The ISME Journal, 5, 1125-1132.

Infecting Infections: The Use of Phage to Tackle Coral Bleaching Diseases.

Corals throughout the world are in decline for a number of reasons including microbial disease and environmental pressures. Different methods that have been proposed in recent years include those such as antibiotic treatment and immunisation. However, due to the quantities of antibiotics needed to treat a whole reef, the effects of antibiotics on non-pathogenic species and the lack of an adaptive immune system with regards to immunisation, these methods are not viable for effective coral disease management. This paper explores the idea of phage therapy as a treatment of pathogens associated with coral bleaching. Recent research by the authors indicated that coral pathogen specific phage effectively inhibits coral disease and, therefore, this paper further explores whether this theory can be scaled up and still remain relevant. The research investigates the relationship between the Red Sea coral Favia favus, the causative agent of white plague like disease (γ-proteobacterium Thalassomonas loyana) and the bacteriophage BA3.

To determine phage adsorption starved Thalassomonas loyana were taken and added at different concentrations to different concentrations of phage. Samples were taken at different time intervals and plaque assayed with the results used to determine a rate of adsorption of 1.0x10-6 phage per ml per min. This shows that when higher concentrations of T.loyana than phage are present there is less free phage in the water and shows that the starved bacteria do not down regulate viral receptors during nutrient stress.

The effects of inoculating healthy coral with T.loyana contaminated water and the subsequent protection provided after addition of phage at different stages of infection were then studied. The results showed the white plague like disease progressed rapidly leading to tissue lysis after 4-6 days in coral that had not been treated with phage and in coral where phage had been added 2 days post infection. However, these effects were prevented if the phage was added to the coral 24 hours after the initial inoculation and where phage was added as soon as the pathogen was introduced to the aquaria.

Finally, coral to coral transmission of disease was explored by adding healthy coral to an aquarium containing diseased coral. Once more, when phage was not added to the aquarium within one day the corals showed signs of the disease and died within two weeks. When the phage was added to the healthy coral within one day then transmission of the disease was inhibited.

This paper shows that phage treatment could only be effectively used to prevent and control the transmission of coral diseases locally as, if not noticed within 24hrs, any addition of phage would be ineffective as the coral’s fate has already been decided.

Previous studies by the authors also suggests that the fast mutation rate of T.loyana (3.7 x 10-6 per generation) conferring resistance to phage-receptor binding would , therefore, require the use of other T.loyana specific phage to be used in conjunction with BA3 treatment.

This paper shows that things aren’t as simple as they first appear and that more field work needs to be carried out to determine the overall effects of phage treatment on the management and conservation of the world’s endangered coral ecosystems.

A review of - Efrony, R; Atad, I; Rosenberg, E. Phage Therapy of Coral White Plague Disease: Properties of Phage BA3. 2009. curr. micro. 58:139-145.

The great diversity of microbial assemblages

A Review of: J A Gilbert, et al. (2011). Defining seasonal
marine microbial community dynamics. The ISME Journal.

This paper explores the seasonal variability of microbial assemblages, focusing on the environmental factors which influence their varying diversity. The study summarises a 6-year time series of 16S rRNA tag pyrosequencing of samples taken from the English Channel. This topic has been widely researched before now where previous researchers have mainly focused on the importance of temperature and nutrient concentrations, and have rarely collected samples over such a long period. The introduction to this paper suggests that only very recently have molecular techniques been useful descriptions of these microbial assemblages. These techniques are also constantly being developed and improved in order to better map microbial communities.

It was recently shown in a previous 1-year study by Gilbert et al (2009) that bacterioplankton diversity followed a latitudinal gradient, with maximum potential richness being primarily fuelled by temperature. The main aim of the study is to expand on this discovery, by further characterising the potential drivers of seasonal patterns of bacterioplankton diversity in the Western English Channel. Three factors were chosen to be analysed for potential correlations with the observed seasonal patterns. These were varying concentrations of inorganic nutrients, annual water-temperature cycle, and the population structure of the eukaryotic phytoplankton and zooplankton. In order to test their theories samples were collected on 72 instances between January 2003 and December 2008 from the same site. Bacterial diversity was examined from each sample which included assessing a wide range of variables. These variables include phytoplankton and zooplankton species abundance, the concentrations of ammonia, nitrate and nitrite, phosphate, silicate, total organic carbon and nitrogen, salinity, chlorophyll, photosynthetically active radiation, North Atlantic Oscillation data, day length, primary productivity and temperature.

Bacterioplankton was found to be very diverse at the chosen sample site with a total of 8794 different OTUs (operational taxonomic units) found over the 6-year series. While this shows great diversity at this location, a common problem associated with studies of natural assemblages was faced – identifying sequences to species level. The taxonomic levels that were achieved for the remaining OTUs are as follows – Phylum (9%), Class (32%), Order (10%), Family (26%), Genus (21%). The study showed significant seasonal variations in OTU frequency throughout the 6-year period, but also strong repeating patterns. The Alphaproteobacteria were the most abundant Class, which was expected. OTUs most frequently recorded were of the Ricketsiales and Rhodobacteriales. Flavobacteriales were also found in high frequency.

Alpha diversity was relatively constant across the 6-year series, but showed distinct cyclical patterns with a maximum in winter and minimum in summer. This pattern was further confirmed by analysis of variance for all taxa. It is suggested that this seasonal cycle was also consistent across the 6-year series. Seasonal trends in the most abundant bacteria were very interesting, and also gave consistency to what is already known from single-strain-level studies. One of the most abundant Orders, Rickettsiales, tended to peak in winter, favouring low levels of light and primary production, but maximum concentrations of inorganic nutrients. In contrast, Rhodobacterales peaked in spring and autumn, where nutrient concentrations are lower, but primary production is higher.

Another interesting part of the study which I would have liked to see in more depth was the mention of bacterial ‘blooms’. At one stage during the study a single Vibrio species accounted for 54% of the sequences. However, at all other times, this taxon was rare, with an abundance of 0-2%. The peak also correlated with an increased abundance of the diatom, Chaetoceros compressus, which at all other times had a similarly low abundance. The study does not look at this in more depth, but it could be of interest to analyse the relationship.

This study has shown that strong seasonal patterns exist in this surface water microbial community. The patterns of most abundant, common and variable OTUs are also consistent with other reports. This suggests that seasonal succession patterns of marine surface water bacterial communities in temperate regions may be sustained across different regions also. The study has also identified key drivers of the communities varying diversity. Day length has proven to be an important factor for describing temporal community structure, being the variable which best supports overall bacterial richness. The taxa identified also present different seasonal cycles, relying on varying concentrations of inorganic nutrients. Also, blooms of rare OTUs may be linked to changes in population structure of eukaryotic species and environmental variables. The techniques used to monitor such driving forces still need to be greatly improved in order to better identify patterns in microbial community composition. Monitoring these patterns over a greater time scale is also important to confirm persistence. Despite this, the study has successfully highlighted the factors which influence the varying diversity in microbial assemblages. It is however important to consider that microbial communities are very diverse, fast-growing and dependent on local environmental conditions. These highly sensitive communities can be a great measure of the state of the microbial food web and are important to consider when looking at the bigger picture – they may well serve as important indicators, being the first reactors to the biologically critical effects of anthropogenic activities and global climate change.

How environmental conditions cause the formation of different Flavobacteria communities in the North Atlantic Ocean

A review of Gómez-Pereira, R. P. et al (2010) Distinct Flavobacterial communities in contrasting water masses of North Atlantic Ocean, The ISME Journal. 4, 472-487.

Flavobacteria are one of the most abundant groups of picoplankton found in the marine environment, yet quantitative research about the population of the numerous clades and their distribution patterns is still very much unknown. These microbes have been found to occupy a variety of marine systems, including open ocean waters as well as coastal sediments and hydrothermal vents and are thought to thrive in more productive conditions such as in areas where phytoplankton and algal blooms are high. However, they have also been found in oligotrophic marine surface waters, which also suggests their capability to adapt to various conditions even those where there is minimal life and nutrients. Sequence-based studies have shown the presence of different clades, for example some that are dominant during an algal bloom and others which dominate the area before or after the bloom. Findings like these stress the importance for further research to be done to found out about the clades, their population, distribution patterns and also the association and dynamics between Flavobacterial and phytoplankton communities.

This study intends to further the understanding of these microbes by conducting quantitative analysis in an area where algal blooms are present, specifically in the North Antlantic ocean, between the east Greenland current where there is a high concentration of chlorophyll a and the North Atlantic subtropical gyre (NAST), which in contrast is an oligotrophic area with little primary production. These two strong gradients will act as environmental barriers and will influence the distribution of the picoplankton groups, particularly different clades of flavobacteria and will allow for good analysis of their distribution.

A transect was formed encompassing 9 water masses and each station was sampled at 12 depths, from 10m to 250m or 500m. It measured the chlorophyll a, total picoplankton, analysed the nutrients present and observed the thermal and optical properties. 16s rRNA gene libraries were also constructed from the 20m samples and specific primers were used to help identify the different phylotypes.

It was predicted that from the transect laid out, common Flavobacteria would be present in each, however individual clades will prevail in each of the areas, and that there will be a higher abundance in the northern areas due to the lower temperature and high nutrient and phytoplankton levels, which will allow them to thrive.

The results found that as predicted, flavobacteria favoured colder, nutrient rich areas, but that clades had been found which preferred the oligotrophic conditions in warmer waters such as in the NAST area. Cluster analysis of clade abundance showed flavobacterial communities were generally homogeneous within the specific water masses but varied between them. Furthermore, 16s rRNA analysis confirmed only little overlap (2-5%) between the bodies of water where characteristics such as nutrient level and temperature varied greatly and larger overlaps of phylotypes (25-40%) in areas where these characteristics were a lot more similar.

Chlorophyll a was also found to be a factor in the diversity of clades, as through CARD-FISH quantification, it was found that in areas were sharp decreases in chlorophyll a were detected, reduction in specific populations of Flavobacteria (VIS3, VIS4 and VIS6) were also found. Rare clades, such as VIS1 and VIS2 were only found in low frequencies (<0.5% relative abundance) and all showed preferences to different enviormenatl conditions, such as iron-fertilised waters or temprerature. Due to their low numbers in all the areas, it has still not been established what role they play in the ecological function in the marine environment.

Considering the results, and in addition to previous studies concerning Flavobacteria distribution, it can be seen that picoplankton, and thus Flavobacteria populations have pronounced seasonal, latitudinal and depth distribution patterns, therefore also showing differential distribution patterns.

The study has provided quite specific results for many of the clades found in the samples, adding to the limited data and helping establish the various adaptions, environmental preferences and roles of the different clades found, thus furthering our knowledge of the distribution and biogeography of flavobacteria in the North Atlantic.

However, apart from the previous studies which were used to provide further data, the study was conducted only throughout September. To further their work, the populations could be sampled repeatedly across the year, for example every month or season. Conditions throughout the transect will change throughout the year and this can have a big impact on the populations and distributions of the clades. By looking at more samples, the data will be more representative of the flavobacterial phylotypes and could provide interesting correlations between populations and environmental changes. It would also allow more research to be done concerning the rare clades, as it would be possible to look at how the population size varies throughout each season, to establish whether they always remain small in number or whether preferred conditions and thus populations blooms occur periodically and how this would affect their role in their ecosystem.

What drives virioplankton dynamics in the north-western Sargasso Sea?

An estimated 10³⁰ virioplankton (viruses) are present in the world’s oceans, the majority of which are phages. These virioplankton are dynamic members of the community which have been shown to have significant influence on prokaryotic abundance, community structure, genetic exchange and global biochemical cycles, as well as being a vital genetic resource. They are also incredibly abundant with concentrations of 10⁷ viruses ml^-1 and an average ratio of 10 viruses to every bacteria. This abundance is typically highest in coastal regions and in the euphotic zone, which is thought to reflect the decrease in host abundance towards the deeper, more oceanic waters. Here, the dynamics of virioplankton are less well understood and so this study presents the first depth-resolved (300m) multi-year time series of oceanic virioplankton abundance and explains the dynamics in the context of water column stability, and bacterioplankton abundance and community composition.

Data were collected over a 10 year period as part of the Bermuda Atlantic Time-Series (BATS) program. The site was sampled for virio- and bacterioplankton monthly, and also biweekly between February and April, at a range of depths from 0-300m between January 2000 and December 2009. These samples were then fixed with formalin and gluteraldehyde, respectively, and stored until processing. Picophytoplankton samples were also taken, however only for the depths up to 250m. The mixed layer depth (MLD) was also determined. This is the depth of the largely homogenous layer of water found in seasonal systems caused by turbulent mixing.

The virioplankton samples were filtered then stained with SYBR Green I and enumerated using epifluorescence microscopy. A similar procedure was adopted for the bacterioplankton samples, although a 4’, 6-diamidino-2-phenylindole dihydrochloride stain was used. Flow cytometry was used to enumerate Prochlorococcus and Synecococcus samples; and to quantify the abundance of the SAR11 and Rhodobacteraceae clades.

The study reveals recurring annual patterns in virioplankton abundance which coincide with patterns in water column stability, represented by the MLD. The MLD reached depths of 150-300m in late winter/early spring due to mixing, followed by summer stratification events resulting in a low MLD (<50m). During such stratification events virioplankton abundance accumulated below the MLD and surface abundances were at minimal values, possibly due to high levels of ultraviolet radiation exposure to the hosts or to the viruses themselves. However from July to December, during convective mixing, virioplankton abundances initially increased, potentially due to redistribution and enhanced mixing with hosts, but subsequently fell within the upper 300m. This implies that convective mixing cannot be the only driver of virioplankton dynamics.

Trends in bacterioplankton abundances were also found to be apparent and some held a correlation with those of the virioplankton community. In terms of total abundances, both virio- and bacterioplankton reached maxima below the MLD during stratification events; however, they did not coincide temporally or with depth. Although, when only data from the depth region of the virioplankton maxima (60-100m) were considered; a slow accumulation of bacterioplankton was found between January and July, followed by a decrease between July and December. This decrease coincided with the continual increase in virioplankton abundance from July to December and seemed to be consistent with the Lotka-Volterra model of predator-prey relationships. Consequently, it seemed to be a ‘kill the winner’ scenario.

However, the lack of any real correlation was unmistakeable and unsurprising given that many viruses are host-specific. Therefore it seemed more likely that virioplankton dynamics would be more strongly correlated to specific lineages within the bacterioplankton. The SAR11 clade, although one of the most ubiquitous eukaryotic groups in open ocean systems, showed little correlation with the virioplankton dynamics. A weak, negative correlation was found with the mean depth horizon (60-100m) but the virioplankton-to-SAR11 ratio was consistently within a narrow range and varied little according to season and the MLD, suggesting no real relationship between the SAR11 clade and virioplankton abundances. This may be due to SAR11 being a defence specialist or its being a suboptimal host due to its k-selected life history strategy.

Synecococcus was also considered to be an unlikely driver of virioplankton abundance dynamics as they were completely decoupled from those of the virioplankton both temporally and with depth. Although the abundances were inversely correlated, suggesting a ‘kill the winner’ scenario, calculations showed that the predator-prey period ought to be shorter than observed. Furthermore, the virioplankton-to-Synecococcus ratio was very high and variable (1000- >2000) at the depth horizon between July and December; values which vastly exceed the burst size of lab cultured cyanophages which infect Synecococcus.

Conversely, Prochlorococcus was found to be very tightly coupled with virioplankton dynamics. Regular annual patterns demonstrated by the Prochlorococcus were very similar to those of the virioplankton including the annual maxima developing in the depth horizon of 60-100m and the variability of surface layer maxima during stratification events. Thus the two were highly correlated, with 44% of variance in virioplankton dynamics explained by those of Prochlorococcus. Also, in years when Prochlorococcus abundances were low, so too were those of the virioplankton. Although the link between these two groups is purely correlative, it seems highly likely that Prochlorococcus could be the driving force behind the oceanic abundance variations in the virioplankton at BATS, and that therefore the majority of the virioplankton community could be cyanophages.

Results for the Rhodobacteraceae clade also showed correlative evidence for potentially being the driver of virioplankton dynamics as it too had its annual maxima occurring within the 60-100m depth horizon and explained 23% of virioplankton variance in the data. However, members of the Rhodobacteraceae are typically found at low abundances in oligotrophic waters such as those at BATS and even with their r-selected strategy would not produce burst sizes large enough to carry the virioplankton dynamics found in the study. Therefore it is unlikely that the Rhodobacteraceae have much real influence on the virioplankton abundance dynamics.

As a consequence of these results, it is probable that virioplankton dynamics at BATS are influenced mostly by host availability and that the host appears to be Prochlorococcus. This availability is however, influenced by the seasonal mixing cycles found within the BATS area and so I think that further research ought to be done here to confirm the ecological processes at work. Having said that, this paper alone does give a good insight into the ecological role that viruses play within oceanic systems; which was a previous unknown for the area.

A review of:

Rachel J. Parsons, Mya Breitbart, Michael W. Lomas and Craig A. Carlson (2011) Ocean time-series reveals recurring patterns of virioplankton dynamics in the northwestern Sargasso Sea; The ISME Journal [online] doi:10.1038/ismej.2011.101

A STORY OF SUCCESSION: BLACK BAND DISEASE

It has long been known that black band disease (BBD) is a poly-microbial disease which affects corals, characterised by a darkly pigment microbial mat, leading tissue loss and necrosis. However, what is currently unknown is how these microbes cause the cause the black bands or how changes in the microbial communities lead to the onset of BBD.
In has been noted in previous research that distinctly different cyanobacterium patches (CP) sometimes developed into BBD.
With the threat of BBD only likely to increase over time, with the predicted trends in global warming, it is worthwhile knowing BBD transmission modes and the early developmental stages to help the advance of reef management strategies to mitigate the impacts of this disease.

In this paper the authors studied an inshore Montipora reef at Pelorus Island in the central Great Barrier Reef (GBR) between September 2006 and January 2009. CP infected colonies were individually tagged and monitored approximately monthly to determine if the CP lesions developed into BBD.

Not all CP lead to BBD, and not all BBD is derived from CP, as demonstrated by the findings that 18.7% of the 262 CP lesions recorded on Montipora developed into the visually characteristic BBD lesions, with the remaining 81.3% of CP lesions disappearing, but leaving behind exposed coral skeleton. Of the 263 BBD cases observed on Montipora 18.6% were derived from the CP, sources for the remaining BBD lesions are not known.
16S rRNA clone libraries showed distinct differences between CP and BBD lesions and terminal restriction fragment length polymorphism analysis revealed a shift in bacterial ribotypes during transitions from CP to BBD.
CP clone libraries were dominated with Alphaproteobacteria-affiliated sequences in comparison to BBD clone libraries which were dominated by Gammaproteobacteria-affiliated sequences. The percentage of cyanobacterial-affiliated sequences increased in the transition from CP to BBD, contributing to only 7.3% of the CP clone library at an intermediate stage compared to 42.6% at an advanced stage of BBD.
The maximum prevalence of CP was between November and December, with the maximum prevalence of BBD 40-50 days after, this, together with the fact 40-50days is the average recorded time for CP to develop into BBD, delivers evidence that CP can be an early successional stage for BBD.
The authors believe Trichodesmium species (the dominant cyanobacteria in CP) act in the same way as Hydrocoleum ssp. in that they are a huge contributor of nitrogen fixation. The authors therefore believe Trichodesmium spp. have a huge part in the successional changes from CP to BBD because they create new niches for others microbes.

The authors point out that further research which would help to discover which microbes are the key players in the BBD pathogenesis development is needed. This would involve key functional genes and their expressions at different stages in the CP-BBD development.

This paper was an interesting read; it offers a good insight into one way BBD develops i.e. through successional changes. However, as already mentioned above BBD does not only develop from CP, the other ways remain unknown. It offers an explanation on how the microbial community changes, but does not offer any way to stop these changes, meaning that in terms of reef management more needs to be done to stop corals reefs dying. I believe this paper is impourtant in its area and acts as a good stepping stone for further research to be carried out.

A review of;
Sato Y, Willis BL and Bourne DG (2010) Successional changes in bacterial communities during the development of black band disease on the reef coral, Montipora hispida. The ISME Journal. 4, 203-214.

Virus-host interactions review

Although viruses are the most abundant and the most highly diverse “biological entity” within the marine environment, and in fact the world in general it has only been recently that the roles they play within marine systems are beginning to become understood. It wasn’t until Proctor and Fuhrman (1991) that viral lysis of bacteria was first recognized to be an important marine process. Viral lysis creates dissolved organic matter (DOM), which becomes a source of nutrients and the cycling of carbon in marine systems.

This review by Sandaa (2008) examines virus-host interactions. Due to prokaryotes (bacteria and archaea) being the most abundant host type it assumed that the majority of the viruses are bacteriophages. The review goes on to explain that in marine environments double stranded DNA (dsDNA) has a genome size range of 15 to 630 kb and that in order of highest abundance, small genome-viruses (SGV) 20 to 80 kb are top, with middle genome-sized viruses (MGV) 80 to 280 kb being less abundant and large genome-sized viruses (LGV) 280 to 500 kb are the least abundant. And that the genomic size range of marine bacteriophages, which as explained above are thought to be the most abundant marine viruses is 39 to 243 kb. Bacteriophages then fit into the SGV and MGV genomic size range, which makes sense, as they are the most dominant size ranges. Also the bacteriophage thought to be the most numerous group Podoviridae has a genomic size range of 39 to 60 kb and so falls under the category SGV, the most abundant marine genome viral size.

As well as the idea stated above that viruses are important because they release DOM into the environment, it is also suggested that they may play an important role in regulating populations of host bacteria. One mechanism that is given as a potential explanation for this a top-down model labeled “killing the winner”. The role of the virus in this model is to restrict the dominance of a certain bacterial species. The implications are that bacteriophages control the most abundant or competitively superior bacterial populations and therefore allow less abundant or inferior competitively populations to co-exist, rather than be excluded. This allows a higher biodiversity than if a dominant population was left to dominate. Disturbance. Given as an example of evidence that supports this idea comes from a mesocosm study in which the termination of a bloom of the coccolithophorid Emiliania huxleyi was followed by an increase in the specific virus E. huxleyi (EhV). The review does concede however that studies on these ideas have been contradictory in their findings, with some studies suggesting a limited ability of viruses to control hosts’ populations and others suggesting an element of control is visible. It has even been proposed that the most dominant hosts are the least likely to suffer from viral lysis.

The final way that the review exams how viruses may affect their hosts is by horizontal gene transfer. New genetic traits may be introduced from one organism to another from viruses by horizontal gene transfer, e.g. from one bacteria to another. Viruses then are altering the genetics of other organisms, which of course has huge evolutionary implications. This gene transfer can clearly be beneficial to the hosts, given as an example are photosynthetic genes, which code for functional properties and may be beneficial for the host have been uncovered in the viral genome. Gene transfer may lead to metabolic benefits and also as a potential result an increase in fitness of the host.

The author’s conclusion to the question of whether virus-host interactions in the marine environment are a burden or benefit to the host population is favoured on the beneficial side. Although noted that there may be an energy cost from the hosts for carrying the viral genetic material, this is outweighed by the befits of increased fitness from gene transfer as beneficial genes spread through populations, with the virus-host relationship being described as irreplaceable for driving microbial evolution by the author. It is also clear that their is a lot left to discover.

Sandaa (2008) Burden or benefit? Virus-host interactions in the marine environment. Research in Microbiology 159 (2008) 374e381

Climate change, Marine mucilage and Microbial Pathogens

A Review of: Roberto Danovaro, Serena Fonda Umani and Antonio Pusceddu (2009). Climate Change and the Potential Spreading of Marine Mucilage and Microbial Pathogens in the Mediterranean Sea. PLoS ONE 4(9).

Marine snow is ubiquitous in the oceans of the world. During summer, water column stratification can promote the coalescence of small sized aggregates into large massive sheets, thin layers, flocs and clouds, know collectively as marine mucilage. Mucilage is a gelatinous evolving stage of marine snow which can reach huge dimensions and cover areas of hundreds of kilometres of coastline.

There are many theories as to what triggers marine mucilage formation and this phenomenon has created increasing concern in coastal areas due to its socio-economical consequences. The Mediterranean basin is one of the most severely affected areas by marine mucilage. Once the mucilage sinks and settles on the sediment it causes yet more problems in it subsequent suffocation of benthic organisms, including bottom dwelling nekton, provoking serious economical damage.

Mucilage is able to entrap high abundances of a wide range of organisms from small phytoplankton to large zooplankton. It is also a major repository for prokaryotes and viruses. Fingerprint techniques such as ARISA provided evidence that mucilage aggregates not only entrap prokaryotes present in the water column but also contained bacterial species which were absent in the surrounding seawater - The study found that more than 90% of the bacterial taxa encountered in the mucilage were not found in the surrounding seawater. It also appears to be somewhat of a bacterial hotspot as the number of ribotypes in the mucilage was ca 65% higher than in the water.

FISH analysis revealed that mucilage contained large numbers of pathogenic bacteria such as Vibrio harveyi that has the potential to infect a wide range of organisms. Although the mechanisms by which the mucilage hosts large numbers of pathogens is not clear, the authors hypothesised that the complex organic matrix of the mucilage offers micro-niches to pathogens with favourable conditions for colonisation and survival.

Analysis of historical reports indicates that the frequency of mucilage has increased almost exponentially in the last two decades in the Mediterranean although these outbreaks do not result from increased primary production of the system.

The authors have evidence to support that with an increase in temperature there is also an increase in mucilage incidents but that temperature alone cannot be used to predict mucilage occurrences at a basin scale because several other factors may also promote mucilage formation and/ or increases the magnitude of this phenomenon including hydrodynamic regime (current speed and water mass turnover), oxygen availability and other factors.

Coastal areas repeatedly affected by mucilage outbreaks share many common environmental problems such as a long history of human exploitation, including over-fishing which can be responsible for the alteration of the benthic biogeochemical cycles, and the presence of macro- and micro-pollutants, which can have a strong influence on microbial-loop functioning and cause an increase in viral infection.

This study highlights the growing importance of marine mucilage. In conclusion the authors point out that if the frequency and persistence of marine mucilage continues to increase, an increased frequency and extension of some marine diseases may result in potential consequences to human health. Their effect on other marine organisms is huge not only when it settles on the sediment but floating in or on the surface of the water column also. More research is needed to fully understand the damaging potential of marine mucilage and also to work out how we can prevent occurrences, especially now that there is evidence that climate change may be a prominent controlling factor. I think this work is very important especially now that it is affecting more and more organisms and because we just don’t know how much potential marine mucilage has to change marine ecosystems.

Roles of free-living and particle attached bacteria in subarctic estuarine systems.

In particle rich subarctic estuarine systems, like the Hudson Bay, free living and particle-attached bacteria play an integral role in recycling and exportation of particulate organic matter. To help us to understand the global carbon cycle and estimate biological pump efficiency we need to develop our knowledge of the transfer of particulate organic matter within the food web, its movement through the water column and the processes involved with recycling it

Particle attached bacteria are often larger then free living bacteria so it is assumed that their metabolic activity is believed to be more active on a per cell basis, however the opposite has been observed. In particle rich estuarine systems particle attached bacteria may reach more than 60% of the total bacterial abundance. As a result of this dominance they have been shown break down a larger fraction of the organic matter associated with sinking particles then free living however as a result of a discrepancy called “particle decomposition paradox” particle attached bacteria hydrolyse organic much faster compared to their uptake of the end product. So only a small portion is of POC is respired by particle attached. Making the free living bacteria are the main recyclers during sedimentation.

The objectives of the study were first to determine abundance, cell size, sinking velocity of particle attached and free living bacteria and their relationship with environmental conditions. The second to develop a carbon budget to consider the potential contribution of particle attached bacteria to total POC sinking export and to total carbon loss through bacterial respiration. They predicted that particle attached bacteria will have sinking velocities higher than predicted by Stoke’s law therefore can potentially contribute to POC sinking flux. Also that particle attached would dominate bacterial abundance.

The results showed that particle attached bacteria are dependent on the number and or size of particles available for attachment this was demonstrated by the positive relationships between bacterial biomass and POC concentration. They did not observe any significant difference between sampling depths, 50% of surface irradiance and the deepchlorophyll a maximum, despite large differences in the environmental conditions. This is likely to be the result of a balance between bacterial growth rates and grazing pressure.

This study is an important contribution to our understanding of these systems as to the author’s knowledge no other study has addressed these bacteria’s dual role in recycling and exporting of POM. This study for the first time combines the settling column method with flow cytometry which allows them to simultaneously determine: characteristics, abundance and sinking velocities of the target bacteria. Particles called Microaggregates (marine snow) have been studied extensively while they have taken a different approach and focused on the bacteria attached to them and most notably on the protist cells. It is integral for us to develop our understanding of these relationships because as climate change causes permafrost to melt there will be an increase in particle load into the estuarine systems like The Hudson Bay. This will lead to a massive increase in the abundance of particle attached bacteria meaning they will play an even larger role in the organic carbon cycling process

A review of: A. Lapoussiere et al Role of free-living and particle-attached bacteria in the recycling and export of organic material in the Hudson Bay system. Journal of Marine systems 88 (2011) 434-445

Microbial Biodegradation of PAH Pollution

A review of: Wang, Y.F and Tam, N.F.Y. (2011) Microbial community dynamics and biodegradation of polycyclic aromatic hydrocarbons in polluted marine sediments in Hong Kong. Marine Pollution Bulletin. 63, 424-430

Pollutants are a significant environmental concern, particularly in marine environments where they can become ubiquitous. They can cause significant shifts in community structures and the example used in this paper are PAHs, polycyclic aromatic hydrocarbons. These are hydrocarbons with two or more fused hydrocarbon rings formed during incomplete combustion of organic materials and are often pollutants as a result of oil spills and leakages. The concerns over PAHs are due to their tendency to be both carcinogens and mutagens, particularly those that have a high molecular weight. Fortunately, some microbial communities found in marine sediments are resistant to and are even able to degrade PAHs.

This study explores the dynamics of microbial populations during PAH biodegradation and investigates how different levels of contamination affect the microbial community structure by artificially spiking samples of marine sediment with a mixture of PAHs (fluorene, phenanthrene, fluoranthene and pyrene) at three different levels (P1 - P3, where P3 is the highest). To achieve this, the population sizes of THB (total heterotrophic bacteria) and PDB (PAH degrading bacteria) were counted using the most probable number method and analysis of ester-linked fatty acid methyl esters (EL-FAME) and DGGE (denaturing gradient gel electrophoresis) were used to look at phenotypic and genotypic succession in the microbial community.

The numbers of THB were highest in the control and lowest in the high level (P3) treatment while the numbers of PDB were highest in the P3 treatment. The proportion of PDB to THB in the mid and high level treatments (P2 and P3) significantly increased with time indicating the predominance of PDB at high stress.

Analysis of DGGE found significantly lower diversity in the high level treatments compared to any of the others, which was not found in the EL-FAME analysis suggesting that the responses of the microbial community to environmental stresses takes place at different levels and that adaptations to the phenotype comes after genotypic selection under extreme environmental stresses.

At high PAH concentration, the PAH resistant or degrading bacteria survive, become dominant and begin biodegradation of PAH. But once the levels gradually decrease with degradation, the non-PAH degraders start to recover and feed on the PAH intermediates. Further supported by the PDB/THB ratio which was found to increase three days after spiking (PDB required time to adapt before biodegradation could take place), reach a peak in the middle of the experiment and start to decline toward the end, suggesting a recovery of the microbial diversity.

EL-FAME illustrated that the ratio of branched fatty acids to MUFA (mono-unsaturated fatty acids) decreased significantly in all level treatments toward the middle of the experiment, as PAH concentrations began to accumulate in the sediment. Branched fatty acids and MUFA are generally considered as biomarkers for gram-positive and gram-negative bacteria respectively so the shift to increased MUFA suggests a shift to gram negative bacteria.

Previous studies had shown that gram-negative bacteria were more frequently selected with low molecular weight (LMW) PAHs and the relative abundance of fatty acids in strains that were capable of degrading PAHs confirm that gram-negative strains have highly abundant MUFA. This shift in the ratio of branched to MUFA could also suggest a bacterial adaptation or response to environmental stress because the decrease in the ratio could help to increase the fluidity of the cell membranes and therefore facilitate the uptake of LMW PAHs.

The authors note in this study about the significantly increased sensitivity of the DGGE method in comparison to EL-FAME and the study in general illustrates the applications of these methods in marine microbiology. I thought this paper had some similarities with what were aiming to achieve in the practical sessions with regard to exploring the effect of sediment contamination on microbial communities and therefore I thought it might be useful to see examples of similar studies. I also found that it was interesting to see how marine microbes were able to adapt to anthropogenic stresses.

The microbial loop – 25 years later

Tom Fenchel 2008

This review talks of the development of our knowledge of nutrient cycling in the water column since the paper in 1983, that the author also wrote, that coined the term 'microbial loop'.

The paper acknowledges the previous findings and then goes through some of the major developments such as improvements in techniques for counting bacteria. This combined with the use of 14 C-labelled substrates showed microbes were very active and play a major role in the transformation of matter and energy in the plankton.

It turns out that the microbial loop dominates primary produced carbon cycling and the classical plankton food chain only dominates when there is a rich supply of nutrients in up-welling areas, for example. The competition for dissolved mineral nutrients favours small organisms. New techniques have also found that unicellular photosynthetic prokaryotes such as ubiquitous Synechococcus and Prochlorophytes are major primary producers. Other novel and maybe important energy inputs into the microbial loop include Rosebactor and relatives that are aerobic photoheterotrophs that can generate ATP from light. Mixotrophy represent another complexity that was later added to the microbial loop.

However the most important new functional group is constituted by viruses. Mortality caused by viruses is of a similar magnitude as protozoan grazing; however, the fact that virus – in contrast to protozoan grazing- is highly host-specific means that the effect is different. Viruses drive successional changes of the bacterial biota and perhaps viruses sustain higher bacterial species diversity because the most numerous types of bacteria are the most susceptible.

Despite insight deriving from methods of molecular genetics it will be important to develop methods for growing organisms in the laboratory in order to unravel their
functional properties. It is not known to what extent genetic distances actually correlate with phenotypic differentiation and much genetic variation is likely to be selectively neutral. Also, isolated DNA strands deriving from lysed cells may float around in the environment. Therefore DNA -extraction and subsequent multiplying and sequencing RNA-genes may provide a rather misleading picture of the microbial diversity in terms of the number of organisms that actually play a role at a particular place and time. This problem gets worse with PCR and low copy number techniques. Detection of the presence of gene families involved in metabolic traits may provide more information. Methods such as FISH may then establish the in situ quantitative role of the different strains.

The paper then discusses the spatial heterogeneity of plankton. Evidence indicates that a large fraction of the microbial activity in the water column takes place on suspended particles such as marine snow that may also serve as food for zooplankton such as copepods. Modelling studies have suggested that bacterial chemotaxis may roughly double the rate of mineralisation in seawater relative to the situation in which bacteria are immobile. The water column cannot therefore be considered as a completely mixed system in which encounters between interacting organisms are entirely random. Rather, plankton is to some extent spatially organised on a small scale and this affects biologically-mediated transfer of matter and energy.

In conclusion the paper discusses the impact of the name ‘microbial loop’.
Before Azam et al 1983, Keys et al. (1935) showed that dissolved organic matter in seawater is mineralised exclusively by bacteria and that paper also discussed whether protozoa control bacterial population size and so anticipated the microbial loop by half a century. Just the couple of words: “microbial loop” described that plankton food chains are more complex and that microbes play a much greater role in them than had been acknowledged than how marine plankton food chains were
presented in textbooks of the day.

The paper is very relevant to the module.

A chemical arms race….

A review of: Kay D Bidle and Assaf Vardi. (2011). A chemical arms race at sea mediates algal host-virus interactions. Current Opinion in Microbiology. 14, 449-457.

As we delve deeper into the study of marine microbiology we are becoming increasingly aware the importance of viruses and their interactions on microbial populations in the oceans and the ocean processes. Some of you have already posted on viruses and how they shape the microbial communities which in turn affects productivity, either helping or hindering.

This paper is a literature review as opposed to an experimental report. The focus of this review is the recent work in algal host-virus systems and the elegant strategies of viral infection. In this paper the authors refer to metagenomic approaches and the important role these play in understanding the diversity, lateral gene transfer (LGT) and metabolic rewiring. LGT is important for viruses because this “mechanism allows the virus to manipulate and ‘rewire’ host metabolic pathways for their replication”. The authors use an example of the Coccolithoviruses and how they infect an annual algal bloom of Emiliania huxleyi (E.huxleyi) which is the most abundant coccolithophore globally. This example explains how the coccolithovirus uses a co-evolutionary biochemical ‘arms race’ to manipulate metabolic pathways and regulates cell fate via programmed cell death (PCD). Virally encoded-glycosphingolipids (vGSLs) seem to be another focus within the review. It states that vGSLs critically control the host-viral interactions in E.huxleyi and this lipid based host virus plays a major role in regulating viral infections of natural populations.

Two further topics within the review talk about functional conservation and diversity of viruses where they explain about biochemical, molecular and physiological markers and how these show a mechanistic link between PCD and viral infection using an example of the newly discovered picornaviruses which infect both diatoms and dinoflagellates. The other talking about mechanisms of resistance and how the evidence gathered can actually bring new thinking into the mechanisms of resistance to viral infection.

This review talks about some very interesting areas of science which we are only uncovering now but it does relate the importance of virus-host interactions and how metagenomic approaches can help understand viruses further. It also has some very interesting figures which do help to understand some of the concepts the authors are trying to portray. As this is a literature review In the last paragraph the authors talk about using the subcellular approaches reviewed to give insight to viral infection over different spatial scales including the effects of climate change looking at prior and post, so look out for a paper in the next couple of years by these authors as they might be able to tells us more…?

Can coral change their zooxanthellae to overcome thermal stress?

Zooxanthellae provide an extremely efficient source of nutrients for their coral symbionts, meeting up to 90% of their requirements. This symbiosis is under threat due to rising sea temperatures caused my global warming, and coral, along with their zooxanthellae will need to be able to adapt well to prevent widespread dieback. It seems that some coral types can associate with a variety of zooxanthellae symbionts as oppose to just one, possibly making these species more able to cope with the selective pressures that rising sea temperatures will cause. Evidence shows that coral harbouring a larger proportion of D-type symbionts are likely to be more heat resistant than those with other types and those coral reefs that have been subject to repeated bleaching periods are more likely to be harbouring those heat resistant strains.

This paper looks into the possible ability of some coral species to change the zooxanthellae that they form a symbiosis with in order to overcome the stresses caused increased sea temperatures brought about global warming. Colonies of an indo-pacific coral species were transplanted from two areas of cool water into an area of warmer water, already containing a colony of the same species (A. Millepora). Colonies were also tested in their original cooler areas as a control. The zooxanthellae genotypes were tested before transplantation to ascertain which types were present within the coral (all contained less thermally efficient type C2 zooxanthellae while some from one colony were found to also contain more thermally efficient type D zooxanthellae). After a period of 14 months, 12 nubbins of 3-5cm were taken from the transplanted and control samples. These were then placed in tanks and tested for thermal resistance at 27.5 (control), 30, 31 and 32 ^oC.

The authors found that in one of the transplanted colonies (with D type already present), the zooxanthellae type had switched from type C2 and type D to type D only after thermally induced bleaching. Corals from the other transplanted colony however, were found to recover from bleaching with only the original type C2 zooxanthellae. It was said to be unclear whether the switching of zooxanthellae recorded was due to the presence of the D type before treatment, or whether more of the thermally efficient type was taken in by the coral from the environment.

Type D zooxanthellae were found to have a thermal tolerance of only 1-1.5^oC higher than that of type C2. The authors infer that this difference could have huge ecological benefits; however, due to the predicted average rise in tropical sea temperatures (1-3^oC) over the next 100 years, it is not thought that this will be enough to save many coral species.

I think this paper provides a good insight into ways coral zooxanthellae can possibly change to cope with rises in sea temperatures. If used effectively, some of the data from this investigation could buy us some time so that we can continue to combat global warming. Naturally, further investigation would need to be conducted, especially because the results from this paper were found to be inconclusive. Further study could possibly include a wider range of coral species to see whether results vary between them, and whether there are many that could make use of more thermally resistant symbionts.

Reference:

Berkelmans, R., van Oppen, M.J.H. (2006) The role of zooxanthellae in the thermal tolerance of corals: a ‘nugget of hope’ for coral reefs in an era of climate change, proceedings of the royal society, 273, 2305-2312

Annual changes in Prochlorococcus populations and why it is important

For many years it has been understood that marine microbes play a vital role in the oceans food webs. Probably the most important role is carried out by the photoautotrophic primary producers. These microbes use the energy from the sun and CO2 to produce organic molecules that are essential for life. Other marine microbes may either feed on these organisms or on dissolved organic molecules (DOM) that have found their way into the water column from these cells. The largest contributors to primary production are two genera of Cyanobacteria called Synechococcus and Prochlorococcus which are found throughout the world’s oceans.

It is easy to think of the marine food web as never changing and being a constant loop. The truth is that many things can have an impact on the way an ecosystem works. Any change in the dynamics or abundance of a primary producer like Prochlorococcus could change the whole microbial community found in that area. This in turn could affect larger organisms and continue up the food web.

In this paper the authors studied the temporal and spatial dynamics of several Prochloroccus clades, referred to in this study as ecotypes, in the Atlantic and Pacific oceans near the islands of Bermuda and Hawaii respectively. This was done in order to explore whether normal changes in environmental factors could have a significant effect on which ecotype is dominant. Samples were collected continuously over a 5 year period at depths ranging between 1 and 200m. PCR and flow cytometry were used for species identification and measure of abundance. Measurements in light, temperature and mixing of the water column were also taken to investigate environmental changes.

This study found that there seems to be a strong annual pattern of ecotype abundance and succession of which ecotype was dominant throughout the year. Two ecotypes that live close to the ocean surface that require high light levels peaked in the spring months and droped again in the winter, a third high light ecotype did not not peak until October when the other two clades had decreased in abundance and light levels were lower. Two other ecotypes that live in the lower end of the euphotic zone where light levels are already very low also peaked in the autumn. These two ecotypes are obviously very sensitive to higher irradiances as they could not be detected anywhere near the surface. These trends were repeated every year, throughout the five-year study although the Atlantic populations showed stronger trends compared to the Pacific.

I think this paper gives a good indication into the dynamics of a very important genus of Cyanobacteria. The next stage would be to study how Prochloroccus ecotypes differ in their production of DOM and the other roles they play in the marine microbial food web and how having different ecotypes dominant at different times of the year might affect these things. Undoubtedly, this would be a major task. I also think that it should be noted that this study concentrated on Prochloroccus and not Synechococcus. Synechococcus tend to be more abundant in cooler waters and it would be interesting to see whether they follow the same patterns as Prochloroccus. Especially when we consider the fact that Synechococcus tends to be concentrated more at the surface compared to Prochloroccus.

A review of:
R, Malmstrom. A, Coe. G, Kettler. A, Martiny.J, Frias-Lopez. E, Zinser and S, Chisholm. (2010) Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific. The ISME Journal. 4, 1252-1264.

Genomic features in relation to trophic strategy

A review of: Lauro, FM. McDougald, D. Thomas, T. et al (2009) The genomic basis of trophic strategy in marine bacteria. Proceedings of the National Academy of Sciences, Vol. 106 (37) 155527-33.

The marine environment is known for being one of the largest on the planet, but it is also one of the most productive. It is saturated with microorganisms, and it is the bacteria (along with Archaea), which play important roles in biogeochemical processes and are responsible for cycling the largest pool of organic carbon on the planet. As well as being one of the largest environments it is also one of the harshest with conditions varying dramatically and ranging from nutrient rich (copiotrophic) to nutrient poor (oligotrophic).

This study investigates two types of marine bacteria which have adapted to the selective pressures of these extreme conditions, photobacterium angustum S14 (copiotroph) and sphingopyxis alaskensis RB2256 (oligotroph). The aim of the study was to show that the trophic strategy behind these marine bacteria was reflected in their genomics, by sequencing their genomes to understand the molecular basis behind their adaptations. This information would be invaluable as it will allow for ecological characteristics of unculturable microorganisms to be determined.

To ensure that there was a stronger basis than just the comparison of the two bacteria, the genetic markers derived were validated by searching for 32 additional genome sequences which represented relating species. In total 43 genetic markers were accurately identified which predict trophic strategy. These were also consistent with physiological adaptations for enhancing microbial reproduction under specific nutrient regimes.

The comparisons between the two bacteria allowed a set of discriminative genomic features of trophic lifestyles to be defined. Genomic markers were applied to a clustering method along with 92 additional genomes of marine bacteria, which made it possible to detect more subtle variations in trophic strategy across the full range of genomes used. A model was produced which was able to predict the trophic strategy of an organism from genomic data. This was tested using genomic sequences with metagenomic datasets to allow for the trophic strategies of dominant micro-organisms in whole environmental samples to be derived. Even after reducing the number of core characteristics in the study there was little effect on the predicted outcomes indicating that this model is robust and will be a useful application to a wide range of data sets.

The importance of sequencing the genome of an organism is something of common knowledge; this paper shows the implications of sequencing in understanding bacterial evolution. It can show how bacteria have evolved to inhabit different niches and may indicate previously unknown relationships in communities. It could be used to predict how bacteria will cope or adapt to changes, this could be an important tool for ecotoxicologists.

Will ocean acidification affect marine microbes?

Since the beginning of the industrial revolution, as a result of anthropogenic CO₂ emissions in the atmosphere, ocean pH has already decreased by about 0.1 units. If the emissions will continue at the present rate, by the end of this century it is projected to fall a further 0.3-0.4 pH units, a rate of change that has not been experienced by our planet, for at least 400,000 years.

This fundamental alteration in basic ocean chemistry is likely to have wide and severe implications for all ocean life. Several detailed studies have already demonstrated various adverse effects of ocean acidification in a large number of marine organisms. However, to date, it is still not clear how marine microbes will respond to changes in pCO₂-pH in the ocean and the results of the experiments carried out so far are often inconsistent and at times conflicting.

For example, altough numerous studies suggest a negative effect of acidification on coccolithophores, at least two studies indicate enhanced calcification under elevated pCO₂.

The same conflicting results were obtained for cyanobacteria (increasing photosynthesis with elevated CO₂ is generally observed in Synechococcus but not in Prochlorococcus) and for many others eukaryotic phytoplankton species (e.g. Diatoms) which have carbon concentrating mechanisms that considerably diminish the sensitivity of photosynthesis to CO₂ variations.

Microbes are involved in the most important biogeochemical processes of our planet and it's clear that assessing if and how they will respond or adapt to ocean acification is of crucial importance for predicting the global consequences of climate changes.

Will variations in external pH affect the cell surface chemical and protonic equilibria? Will microbial communities continue to function at a lower pH? Do they have the metabolic and genetic plasticity to acclimatize in a rapidly changing sea? How microbes will react to the synergistic or antagonistic effects of global warming? We urgently need answers to these questions, because to date unfortunately, we don't have any reliable estimates on how microbial physiology will be affected by ocean acidification and even less information is available about how primary productivity, microbial communities composition and biogeochemical cycles will change in a more acidic sea.

More ecological, multifactorial, physiological and genomic studies are needed as well as microcosm/mesocosm comparative perturbation experiments and large-scale, long-term surveys are strongly required before we can try to predict how marine microorganism will react to ocean acidification.

The autors points out that, in reality, pH and CO₂ in the ocean are not constant at all, and in many acquatic habitats such as freshwater lakes (diel variations of 2-3 pH units), deep oceans (water below 350m has a pH less than 7.8), estuaries and coastal regions, microbes already experience remarkable short-term, local and seasonal changes in pH that are often many times greater than those projected for the end of this century and yet, they are still there.

In these environments infact, most of the pH variability is a consequence of microbial activity in it-self, such as respiration or photosynthesis and often phytoplankton blooms can locally and rapidly reduce pCO2, with a concomitant increase in pH. Thus the authors conclude that marine microorganisms somehow, must be already capable of accomodating rapid and sometimes large changes in pH and with some exception, the microbial community and the biogeochemical cycles should not be assumed to be at risk until more detailed studies will prove the contrary.

Reference:

Joint, I., Doney, S. C., & Karl, D. M. (2011). "Will ocean acidification affect marine microbes?" The ISME Journal. 5 (1): 1-7.

Marine virus commandeers cell cycle. A possible novel strategy for future cancer therapy?

A review of: Lui J. et al (2011) Virus infection disturbs cyclin expression, leading to cell cycle arrest in the unicellular marine algae Emiliania huxleyi and Chrysochromulina ericina. African Journal of Microbiology Research, Vol. 5 (14). P1801-1807.

Viral infections are significant in shaping marine environments by regulating succession and composition of phytoplankton communities, and crucial in their role in releasing dissolved organic matter into seawater. The importance of viruses is further emphasized by their sheer abundance suggesting a critical part in oceanic processes. Some viruses depend on the cell cycle of the host while others do not. Lui, J. et al (2001) believe that understanding the mechanisms of cell cycle arrest induced by viruses in phytoplankton hosts can help explain host-virus interactions as well as describe how viral activity is regulated in natural ecosystems.

Emiliania huxleyi is ubiquitous in the marine environment and can form blooms in coastal and oceanic waters while Chrysochromulina ericina can be found in much lower densities. Large double stranded viruses specific to E. huxleyi (EhV) and C. ericina (CeV) have been shown to cause cell cycle arrest and delay in mitosis (M phase) entry.

EhV was shown to inhibit the CDC2/cyclin B complex by phosphorylating Y15 (tyrosine in 15^th position in the amino acid secondary structure)thus blocking the active site of the mitogen promoting factor complex (MPF). There is also evidence of phosphorylation of other amino acids close to Y15. In sequence, WEE1 and CAK1 (seriously) phosphorylates Y15 and T161 (threonine at position 161) respectively. CDC25 then dephosphorylates Y15, resulting in the activation of CDC2/Cyclin B complex and subsequent progression through the G₂/M checkpoint. An increase in WEE1 proteins and deactivation of CDC25 was detected in the EhV infected cells but not in the control. The authors hypothesise that cell cycle arrest in EhV infection is to maximize viral progeny output, and in order to exert control it is necessary for the virus to block host cell cycle control mechanisms.

CeV infection decreased CDC2/cyclin B complex formation by reducing cyclin B levels while over-expressing CDC2, causing G₂ cell cycle delay. Active CDC2 was only detected late in the cell cycle of control samples, while active CDC2 was detected throughout the cell cycle in infected cells. A decrease in WEE1 protein levels was also detected. An active CDC2 and no detectable cyclin B in CeV infection suggests CDC2 (modified or unmodified) had acquired a partner protein, possibly of viral origin. The authors theorize that CeV has adopted a strategy of early cellular activation in order to facilitate viral replication at the expense of host DNA replication.

Algal host-virus interactions regulate growth dynamics of primary producers and differences in cell cycle manipulation in response to viral infection may be related to ecological strategies of the host, the virus, or both. Furthermore, it is unclear whether it is the host ecology (abundance, growth rate etc.) that dictates the interaction or whether it is the virus that determines host ecology. The authors conclude that the results indicate interactions between host and virus is optimized to maintain sustainable populations of both host and virus while avoiding extinction.

Proteins associated with cell cycle progression have been thoroughly studied in phytoplankton, showing homology and highly conserved functional domains to counterparts in other organisms. This was further reinforced by the use of commercially available antibodies for the detection of G₂/M regulatory proteins, indicating similar mechanisms between the phytoplankton and in higher eukaryotes.

In cancer studies, the defining characteristic of the p53 tumour suppressor protein (‘guardian of the genome’) is to arrest/delay the cell cycle at checkpoints during abnormal cell proliferation, which when rendered non-functional, has been implicated in over 50% of cancer cases in humans. The strategies used by EhV and CeV are similar in effect to p53 but most likely through a completely different cellular process. Cancer cells are defined by unregulated cell proliferation and a greater understanding of the molecular mechanisms behind viral induced cell cycle disruption by EhV and CeV may provide a novel strategy for tumour site directed cancer therapy in the future.