Tuesday, 31 December 2013

Microbial distributions across methane-associated geochemical zones in marine sediments

In deep marine sediments along continental margins, methane is one of the dominant features that determine the microbial community. Sediments containing methane are spilt into three separate geochemical zones according to methane concentration and gas hydrate stability. The uppermost zone in the sediment, sulphate methane transition zone (SMTZ), is where minimal levels of methane merge with sulphate from overlying water. Below the SMTZ, gas hydrate (methane ice) is formed, creating the gas hydrate stability zone (GHSZ) and beneath this is the free gas zone (FGZ). Methane gas is present here as the methane concentration exceeds its solubility.

Microbial communities in the SMTZ are globally important as they perform anaerobic oxidation of methane, consuming nearly 90% of all methane produced in deeper sediments. This layer of sediment contains a distinct community of Deltaproteobacteria and anaerobic methanotrophs (ANME).

The objective of this study was to investigate the microbial community composition in different geochemical zones in relation to methane and other abiotic factors of the sediment. Cores were taken from two different sites from the Ulleung Basin. DNA was extracted and a PhyloChip micro-assay and a terminal restriction fragment length polymorphism (T-RFLP) was used to assess the microbial community structure.

It was concluded that the three different geochemical zones are significantly different in terms of the microbial community however there was some overlap in community structure. From the PhyloChip analysis, SMTZ was found to have 74 taxa related to Deltaproteobacteria and the archaeal taxa detected was related to Thermoplasmata. In the GHSZ a lower diversity of 65 taxa were found related to Vibrio-like taxa. Little DNA was extracted from FGZ samples and therefore analysis was very limited.

Archaeal genes were not found below the SMTZ which was unusual as archaeal methanogens were expected as the production of methane was present in the sediment but there could have been possible complications with detecting the archaea. Another possibility is that the methanogenic zone was not sampled, as it usually occurs below the SMTZ but in the upper 50 metres below the seafloor.

ANME are commonly associated with the SMTZ but was not found in the Ulleung Basin, but the Marine Benthic Group-B was detected instead which suggests that other microbial groups are involved in the oxidation of methane. Another explanation would be that the samples missed the area of high ANME abundance.

From the GHSZ, two distinct microbial groups were discovered, separated along the hydrate saturation of the nearest hydrate layer vector. The presence or physical properties associated with hydrate was thought to affect microbial distributions at varying distances from the source. Vibrio-types are one of the species that prefer sediments closer to the hydrate containing sediment.

Applying these significant patterns to other sedimentary environments will be very difficult as the microbial community can vary greatly according to location therefore assumptions should not be made on the basis of previous studies.
Briggs, B.R., Graw, M., Brodie, E.L., Bahk, J., Kim, S., Hyun, J., Kim, J., Torres, M. and Colwell, F.S. (2013) Microbial distributions detected by an oligonucleotide microarray across geochemical zones associated with methane in marine sediments from the Ulleung Basin. Marine and Petroleum Geology. 47: 147-154

Vibrio are a genus of gram-negative, rod-shaped bacteria belonging to the class Gammaproteobacteria. This abundant taxa is responsible for causing some well-known diseases within the human population.  These include Vibrio cholera; responsible for cholera epidemics, Vibrio vulnificus; known to be the origin of septicaemia and shellfish associated death, and Vibrio parahaemolyticus; the cause of seafood gastroenteritis. However, it should be noted that there are a multitude of other Vibrio taxa that do not have a negative effect upon the human population, such as Vibrio fischeri and Vibrio harveyi.

It is well-known that Vibrio are thermo-dependant organisms and are more common in warmer climes, but there has been evidence to suggest that the reservoir of this genus is increasing due to a rise in global sea surface temperatures (SST). A paper by Pascual et al. (2000) documented that El Niño events, leading to a warmer climate, were correlated with abundant cholera outbreaks in Asia and South America. It has also been found that during the recent spate of warmer weather in Europe, an increase in reported wound infections {possibly from Vibrio vulnificus} has occurred in the North and Baltic seas. Other papers have also linked the mass mortality of marine organisms to an increase in abundance of Vibrio-based infections.

The aim of this investigation was to provide evidence that Vibrio has increased in dominance within the plankton-associated bacterial community of the North Sea over the last 44 years, and that this is significantly correlated with increasing sea surface temperature.

The samples used were preserved in formalin and collected from the Rhine and Humber estuaries; dating from August 1961-2005. These samples were collected via the Continuous Plankton Reader Survey. Small flecks were cut from these samples and were centrifuged before DNA extraction was conducted. The amount of DNA extracted was determined by using Pico Green fluorescence and real time PCR was used to amplify the DNA. Primers were then added to locate the V6 (hyper-variable) region, specific to the genus Vibrio. This DNA was then pyrosequenced and BLASTed against a reference data base to assess taxonomic diversity. The average sea surface temperature, phytoplankton colour index and total copepod abundance were taken by the Continuous Plankton Recorder at the time of acquiring the samples.

A positive, significant correlation was found between SST and an increase in Vibrio abundance in the Rhine estuary but not the Humber. This is thought to be due to higher SST in the Rhine estuary. However, other variables such as salinity, nitrate and phosphorus content of the estuaries were not measured but may have also caused the recorded increase in the genus. The variability in Vibrio abundance was calculated to be 45% due to SST, 50% including the total copepod abundance and phytoplankton colour, but there was no explanation for the other 50% of variability found. Pyrosequencing has suggested that Vibrio have not only increased in the abundance but also become dominant in the plankton-associated bacterial community, implying that a major shift has occurred. This statement seems particularly strong as other bacterial communities not associated with Gammaproteobacteria were not extensively discussed.
An ecological regime shift in the late 1980's was considered as being partially responsible for the bacterial community shift as it caused an increased incursion of warm oceanic water in the North Sea. This shift was known to affect all marine life.

We found this research crucial as it has implications to human health, crashes in marine mammal populations and also a threat to oceanic aquaculture. However it should be noted that only estuaries were tested and there could be many other factors affecting the increase in Vibrio abundance. These include human waste and pollution; and high nutrient levels. Also the Vibrio discussed are associated with brackish and estuarine waters and therefore we agree that they may not greatly affect the ocean as suggested. Lastly it has been suggested by other papers that the V3 region on the gene was a lot more reliable than the V6 region at detecting Vibrio species.   

Vezzulli L, Brettar I, Pezzati E, Reid P.C, Colwell R.R, Hofle M.G and Pruzzo C. 2012. Long-term effects of ocean warming on the prokaryote community: evidence from the Vibrios. ISME Journal. 6 : 21-30.

Written by Georgia Hall and Rachel Bransgrove

Evidence of a shift in bacterial community structure from healthy to diseased corals, maintained across species

Evidence of a shift in bacterial community structure from healthy to diseased corals, maintained across species

White Plague Disease (WPD), investigated here, has been linked to coral reef declines globally however it is largely unclear whether a) the disease reported is actually WPD or an alternative disease with similar phenotypic characteristics or b) whether there is a definitive causative agent.   Thalassomonas loyana has been proposed as the pathogen causing WPD (or White Plague-like disease – WPL) in the red sea and Auranimonas coralicida the causative agent in the Caribbean, however neither of these species has been identified in many subsequent studies, including this focal study.  It is now thought unlikely that one single cause can be identified, but more a shift in community likely due to environmental or host condition, providing a niche for opportunistic pathogens.  This study sought to compare bacterial assemblages associated with two species of coral displaying WPL disease, in both diseased and healthy samples, to assess bacterial community changes.

The corals were collected from the same reef (Gulf of Thailand) to minimise any environmental effect and 16s rRNA gene microarrays (PhyloChip G3) were used to ascertain Operational Taxonomic Units (OTUs) in each sample.  Additionally, 16s rRNA gene sequences were used to conduct a search of comparisons with clone libraries.  Overall, analyses found the bacterial assemblages were species specific but also distinct in both diseased and healthy corals of both species.  The results indicate a differentiated pattern of community structure in diseased and healthy corals that is maintained inter-species, with a higher abundance of taxa that have known coral pathogens including Pseudomonadaceae, Rhodobacteraceae, Vibrionaceae and Alteromonadaceae , found in diseased corals.

Additionally, the results show a marked increase in bacterial diversity in diseased corals of both species, which reportedly corroborates findings in other similar studies.  This however, is in contrast to another recent study using the same PhyloChip G3 techniques (Kellog et al., 2013) looking at WPL in a coral species from two Caribbean locations, which found the complete opposite, even after applying analyses comparative to this focal study.  Why would this be?  As addressed in the lectures, many diseases displaying phenotypic characteristics akin to WPD, may be one of a variety of diseases, including WPD Type I, II & III.  It is possible that each ‘strain’ of disease harbours a unique bacterial assemblage that may explain the differences in diversity associated with diseased corals between studies.  Furthermore,  Kellog et al., (2013) argue that many clone libraries are biased toward Gram negative sequences, which would naturally exclude many Gram positive bacteria that may be associated with the coral microbiota.  There was no mention of either Gram negative or Gram positive gene sequences by Roder et al., which may affect the assemblages found in this study.  Clarification of this point is necessary to speculate further.   

Nevertheless, irrespective of whether the there is an increased or decreased abundance in bacterial diversity, it is apparent there is a distinct shift in community structure from a healthy to diseased state in corals, which appears to be common across species (Roder et al., 2014) and habitats (Kellog et al., 2013).   The PhyloChip  G3 may be effective in assessing coral health states in providing a more detailed picture of the bacterial community than has been previously possible, however it is clear that further clarification and research must be attained to provide a framework for assessment.

Roder, C., Arif, C., Bayer, T., Aranda, M., Daniels, C., Shibl, A., Chavanich, S. & Voolstra, C. R. (2014). Bacterial profiling of white plague disease in a comparative coral species framework. The ISME journal. 8, 31-39

Kellogg, C. A., Piceno, Y. M., Tom, L. M., DeSantis, T. Z., Gray, M. A., Zawada, D. G., & Andersen, G. L. (2013). Comparing Bacterial Community Composition between Healthy and White Plague-Like Disease States in Orbicella annularis Using PhyloChip™ G3 Microarrays. PloS one, 8(11), e79801.

Monday, 30 December 2013


White plague (WP)–like disease is one of the ecologically significant coral diseases. It causes tissue loss and affects many species from Caribbean Sea and other locations. This disease has been classified in three types, based on the rate of progression of tissue loss. A bacterium, Aurantimonas coralicida was proposed as a causative agent; but this view is challenged as A. coralicida has not always found to be associated with WP diseased coral colonies. There is lot of confusion about WP disease in corals; about its causative agent and also whether three types of WP are in fact, one disease or it represents different diseases.
          This study investigated an outbreak of WP type l –like disease occurred in the US Virgin Islands in 2010, looking at totally different hypothesis of viruses as the causative agent of WP. Though, viruses have been characterized from healthy and stressed corals and also their symbiont zooxanthellae; very little is known about their role in coral diseases. The suspicion is on four main groups of viruses – bacteriophages (infecting coral associated microbes and not the corals), enveloped herpes-like viruses, nucleocytoplasmic large DNA viruses and single stranded DNA (ssDNA) viruses. Transmission electron microscopy was used to see if viruses are involved in bleaching and WP disease whereas replicated metagenomics was used to characterize viruses associated with the healthy, bleached and WP diseased corals.
          Interestingly, in contrary to previous belief, bacterial pathogens were not found to be associated with WP samples rather; novel types of single stranded DNA viruses were shown as causative agents of WP. Likely host of this type of viruses appears to be coral animal itself. Higher number of these viruses was found in samples of diseased coral compared to healthy ones. Additionally, the viral community of this type of viruses associated with WP diseased samples was unique and different from same type of viruses collected from water column. Based on previous studies, the authors linked outbreaks of this type of viruses to anthropogenic environmental degradation and pollution.
The other group of DNA viruses – nucleocytoplasmic large DNA viruses were noted in abundance on samples of bleached corals, compared to non-bleached ones. This finding supports the possibility that this type of viruses infects algal symbionts (zooxanthellae) and hence may be involved in thermal stress-induced bleaching response.
          Herpes viruses appeared to be common associates of corals, as the authors noted that this type of viruses dominated samples of healthy corals. Significant number of bacteriophages was also found from all coral and seawater samples.
In conclusion, various health states of coral (i.e. healthy, bleached and diseased) have different viral communities. WP diseased corals harbour highest diversity of eukaryotic viruses; bleached corals have intermediate viral diversity whereas healthy corals have the lowest viral diversity. Greater viral diversity of WP samples compared to healthy ones is not related to symbiont densities of both healthy and diseased samples.
This study made me think about mysterious nature of coral diseases. Just few days ago, I reviewed a paper (by Atad et al. 2012, and published the post on blog on 18 December 2013), which experimentally proved that a bacterial pathogen is behind the WP coral disease in the Red Sea. In the Caribbean, completely different bacterium was hypothesized as a causative agent of the same disease and this paper showed single stranded DNA viruses as the causative agent of the same disease! How can there be more than one type of causative agents behind single/same disease? How can there be variability among causative agents of the same disease in relation to geographic location? Or as the authors said WP represents more than one disease? This situation typically reflects etiologically complex nature of coral diseases and need for further research with more robust methodologies for better understanding of coral diseases.

Soffer, N., Brandt, M. E., Correa, A. M., Smith, T. B., & Thurber, R. V. (2013). Potential role of viruses in white plague coral disease. The ISME journal 1-13. doi:10.1038/ismej.2013.137.

Transient Shifts in Bacterial Communities Associated with the Temperate Gorgonian Paramuricea clavata in the Northwestern Mediterranean Sea

To follow one of the main topics of the blog (bacteria-coral relationship), I review this article on bacterial communities associated with a Mediterranean gorgonian coral, Paramuricea clavata. This species is considered a key species for coralligenous assemblages and his presence and abundance is also considered as bio-indicator of high environmental quality. Together with Posidonia oceanica seagrass meadow, coralligenous accretions are the higher biodiversity environments in the Mediterranean Sea. P. clavata is a long-lived aposymbiotic colonial octocoral with long branches and bushy colonies that also contribute to improve environmental eterogenity of corralligenous accretions.
                                            (picture from google)

Authors in this article present a spatial and temporal study of bacterial diversity associated with this octocoral. They also underline that it represent a pioneer baseline work because there is a lack of informations on bacterial communities associated with temperate water octocoral with respect to scleractinian reef-forming corals. They collected 4 years (2007–2010) seasonal sampling in 3 distinct sites in NW Mediterranean Sea, separated by hundreds of kilometers (Provence, Corsican and Catalan coasts), and also exposed to different grade of anthropogenic stressors.
To evaluate which bacteria might be conserved across geographically remote P. clavata populations, authors use three molecular culture-independent approaches (denaturing gradient gel electrophoresis (DGGE), terminal-restriction fragment length polymorphism (T-RFLP) and 16S RNA gene clones library construction).

One of the first presented result is the high grade of consistency between 16S rDNA DGGE banding profiles from all the samples indicating high similarity in bacterial composition between 3 sites. This broadly similar bacterial composition suggest that it might be not driven by local environmental and single colony-related factors. Extracting and sequencing this DNA and relating it to a correspondent ribotype, they found these bacteria belonging to Hahellaceae family within Oceanospirillales order (class Gammaproteobacteria). They note also that this Oceanospirillales-affiliated sequences is the most frequent ribotype found in healthy hexacorals suggesting a specific cnidarian symbiotic complex but with a different host selective control among hexa- and octocoral. In Hahellaceae family, authors also were able to detect Endozoicomonas- (96% similar to bacteria found in tropical gorgonian Gorgonia ventalina) and Spongiobacter-related ribotype. Spongiobacter-related metabolize DMSP in A. millepora (hexacoral) but the potential functioning in gorgonian holobiont are unknow for the moment. Authors also suppose other fisiological roles for Oceanospirillales as the production of extracellular hydrolytic enzymes maybe usefull for trophic relationship among host and symbiont.

Another result presented was a transient compositional community shift during summer 2007 in all 3 sites. Combination of bacteria was different and ribotypes show a higher diversity distributed among 5 bacterial phila: Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes and Cyanobacteria. Belonging to the first two group respectively, they report prominent Paenibacillus- and Propionibacterium-related sequences (found also in low abundance in healty and/or bleached colonies of cold-water and tropical scleractinian corals). Because authors found this change in microbiota composition only during 1 sampling period they present it like a disruption (without any visible signs of desease of P. clavata colonies) of normal Hahellaceae association. The situation shift back in the following winter sampling with again Hahellaceae dominated community allowing authors to suppose this as normal symbiont for P. clavata. Causes of this transient shift in 3 geographically distant population during 2007 summer are not clear but authors link it to altered physiological state of the holobiont during stress conditions. Interestingly they didn’t find Vibrio coralliilyticus in Paenibacillus-dominated summer 2007 clone libraries, although this Vibrio and other has been implicated in recent disease outbreaks and tissue necrosis in P. clavata populations during climatic anomalies in Mediterranean Sea. Authors didn’t ruled-out hypothesis like anthropogenic and abiotic stressor or bacteriophage infection targeting Hahellaceae.

In conclusion this study was the first on Mediterranean octocoral-associated microbiota and should be very interesting understand something more on the in-situ location of these bacteria within gorgonian tissue and also something more on possible physiologic functions of symbionts. 

La Rivière, M., Roumagnac, M., Garrabou, J., & Bally, M. (2013). Transient Shifts in Bacterial Communities Associated with the Temperate Gorgonian Paramuricea clavata in the Northwestern Mediterranean Sea. PloS one8(2), e57385.

Sunday, 29 December 2013

The Shifts in the Bacterial and Fungal Communities Associated with Dark Spot Syndrome in the Coral Stephanocoenia intersepta

Dark Spot Syndrome (DSS) is thought to be one of the most widespread coral diseases and/ or syndromes in the whole of the Caribbean, and can be seen as dark spots on the corals’ surface in varying colours and sizes.  The lesions that subsequently form become depressed into the skeleton, and the subsequent loss of tissue can lead to the successional colonisation by algae and/ or boring sponges. It has been suggested that communities of fungi and bacteria, rather than one single bacterium, may contribute to infection, particularly in the coral species Stephanocoenia intersepta, Stephanocoenia siderea and Montastraea annularis. However previous reports have indicated that many other coral species can also be affected, so it has significant implications for coral ecology and population biology within the Caribbean. 

Other studies have attempted to isolate one sole bacterium that causes a certain disease, and only use culture-dependent techniques, whereas this study undertakes culture-independent molecular analyses of both bacterial and fungal communities that are present, and so possibly associated with DSS, to determine any shifts in these communities. In addition, they compare the communities in different types of tissue in S. intersepta (healthy tissue with no signs of DSS (H); apparently healthy tissue >5cm from the lesion on a coral showing signs of DSS (AH); and the different sized lesions for DSS itself. This study has also attempted to determine the temporal changes of assemblages as the disease and/ or syndrome persists by comparing the different sizes of the lesions. The authors used three different sizes (Small, S-DL; Medium, M-DL; and Large, L-DL) of spots as they are thought to be an indicator for the age of infection, due to the fact that they progress ~3 mm per month. 

The 16S rRNA gene bacterial diversity of H, AH and the three different sizes of disease lesions (S-DL, M-DL and L-DL) varied significantly. Four ribotypes related to Corynebacterium sp., Acinetobacter sp., Parvularculaceae sp., and Oscillatoria sp. (also the causal agent of Black Band Disease (BBD)) matched the patterns expected from the potential pathogens, as they were absent from H, increased in abundance with AH, and were dominant in the disease lesions. Two Vibrio species were also dominant in the lesions only, although other conflicting results showed that other species of the same genus (i.e. V. harveyi and V. carchariae) were present in all/ most samples, which implied that some potential coral pathogens may exist in healthy tissues. In comparison, the fungal diversity was much lower, but one particular pathogen which showed the most significant difference between healthy and diseased tissues was the newly-identified strain of the ribotype, Rhytisma acerinum, which is a known causal agent of tar spot on terrestrial tree leaves. 

The authors therefore suggest that the darker pigmented state of the zooxanthellae caused by DSS is predominantly down to R. acerinum and the bacteria Oscillatoria, as similar previous results for BBD imply that bacterial communities vary with lesion size, so it is likely to be linked to the age of infection, as predicted. 

I particularly liked this paper because it focuses on the microbial community and which pathogens are involved, but is also able to indicate which microorganisms contribute more to the infection and the manifestation of DSS than others in this assemblage, such as R. acerinum and the bacterium Oscillatoria. It is by no means a holistic view of the cause of the disease however, particularly due to the fact that they are unable to establish whether DSS is actually a disease or if it is a syndrome, so it is clear that there is a paucity of knowledge and understanding concerning Dark Spot Syndrome. As they mentioned the three coral species that are normally affected in the introduction of the paper, I felt that they could have expanded this study out to compare the microbial communities in both healthy and diseased tissues between the different species. 
Sweet, M., Burn, D., Croquer, A., and Leary P. (2013) Characterisation of the bacterial and fungal communities associated with different lesion sizes of Dark Spot Syndrome occurring in the coral Stephanocoenia intersepta. PLoS ONE, 8(4): e62580. doi:10.1371/journal.pone.0062580

Thursday, 26 December 2013

Hydrogen as an energy source for hydrothermal vent symbioses

Both reduced sulphur and methane have previously been described as energy sources for symbiotic bacteria in marine chemosynthetic ecosystems. Though many other potential chemosynthetic sources are available, none have previously been shown to be utilised by such bacteria.  The interaction between mantle-derived ultramafic rocks and seawater at some hydrothermal vents produces fluids characterised by high hydrogen concentrations. With an energy yield from hydrogen oxidation providing 7 times and 18 times more energy kg¯¹ vent fluid than methane oxidation and sulphide oxidation respectively, hydrogen would be a favourable energy source for chemosynthetic microbes.

Mussels, Bathymodiolus puteoserpentis, are the most abundant macrofauna at the Logatchev vent field on the Mid-Atlantic Ridge, characterised by ultramafic outcrops. The gills of these mussels play host to methane and sulphur oxidising bacteria which allows them to dominate such an environment. Such bacteria have shown a genetic potential for hydrogen uptake and oxidation. Membrane-bound respiratory enzymes, NiFe hydrogenases, are key to hydrogen metabolism. The hupL gene, responsible for encoding NiFe hydrogenases, was found in gill tissues containing bacterial symbionts.  The presence of this gene was not limited to mussel symbionts at high hydrogen concentration vents however, with other vent mussels containing symbionts with hydrogen uptake properties. 

Upon incubation of B. puteoserpentis gill tissues with hydrogen, rapid-uptake of hydrogen was observed. Subsequent incubation with both hydrogen and CO₂ together determined that carbon uptake and fixation rates were comparable to fixation rates concurrent with sulphide, suggesting that carbon autotrophy could be fuelled by sulphide and hydrogen to the same extent. Utilisation of hydrogen as an additional energy source was also feasible though less efficient at low hydrogen venting systems with symbionts of mussels from such sites having the capacity to uptake hydrogen at a rate correlated with ambient concentration.

Of the two chemosynthetic gammaproteobacteria hosted in B. puteoserpentis gills, sulphur-oxidising and methane-oxidising, it was found that hydrogen is utilised by sulphur-oxidizing bacteria. Genome sequencing, hupL gene FISH and immunohistochemistry in conjunction with 16S rRNA FISH all inferred a link between hydrogen uptake and utilisation by sulphur-oxidising bacteria for energy.

To account for uncertainties in extrapolating data from laboratory-based manipulation experiments an in situ mass spectrometer was deployed to simultaneously measure hydrogen concentrations and temperature in two areas around vents: directly at the source of fluid emissions from the seafloor and an area where fluids had been exposed to a B. puteoserpentis mussel bed. Significant hydrogen depletion was measured around mussel beds in comparison to source fluid confirming a high consumption of hydrogen by mussel beds, probably by sulphur-oxidising bacteria. This trend was also true of methane.

It makes sense that with high hydrogen availability having the capacity to utilise hydrogen as a source of energy provides a competitive edge, and allows the occupancy of a different niche. Though not observed for methane symbionts in B. puteoserpentis, there is the potential for the utilisation hydrogen as energy source to be prevalent amongst other vents mussels and other symbiotic bacteria for chemosynthesis. If so, it could prove to be of huge environmental importance as a hydrogen sink.  

Petersen J., Zielinski F., Pape T., Sierfert R., Moraru C., Amann R., Hourdez S., Girguis P., Wankel S., Barbe V., Pelletier E., Fink D., Borowski C., Bach W. and Dubilier N. (2011) Hydrogen as an energy source for hydrothermal vent symbioses. Nature, 476, 176-180

Tuesday, 24 December 2013

Levels of immunity parameters underpin bleaching and disease susceptibility of reef corals.

Since our lecture on coral diseases, I was curious about the coral immune system. This paper focused on variables commonly associated with invertebrate immunity and investigated their relationship with regards to coral susceptibility (bleaching and disease) with both hard (Scleractinia) and soft (Alcyonacea) corals spanning 10 families from the Great Barrier Reef. Whilst this paper mainly focuses on coral bleaching, it mentioned several times how the mechanisms of defence against coral bleaching are similar to the defence strategies employed during infection.

This paper regarded four main variables, which were used to make up a Constituent immunity number. These variables were presence/frequency of melanin, size of melanin containing granular cells, phenoloxidase (PO) activity, and concentrations of fluorescent proteins (FPs.)

  •         Presence/frequency of melanin
  •         Size of melanin containing granular cells

The melanin-synthesis pathway is a key invertebrate defence mechanism, triggered by physical injury or invasion by foreign organisms. When activated, it enables the deposition of encapsulating melanins and produces highly cytotoxic intermediates such as reactive oxygen species (ROS).

The 15 species investigated all contained melanin-containing granular cells in the free body wall tissue, however the distribution and density of melanin containing granular cells varies within species. Melanin frequency was negatively correlated with disease susceptibility (deducted from field studies of disease prevalence) – ergo corals with the lowest melanin frequency showed the highest disease prevalence. The spatial distribution of melanin is also important in the effectiveness of coral defence e.g. having UV- and visible-light-absorbing melanain in epidermal cell layers may protect zooxanthellae from excess UV/light in the environment.

It has been proposed melanin-containing granular cells are potential amebocytes, a mobile possible phagocytic defence mechanism which characteristically aggregate in area of injury or invasion. A mobile defence mechanism is further beneficial as entry points of attack are unpredictable.

  •        Phenoloxidase (PO) activity – which indicates melanin pathway activity.

This is another indication of melanin pathway activity, and once again was present in all coral families, while showing a significant variation of activity dependent on species.

  •         Concentrations of fluorescent proteins (FPs)

Known to remit light at different wavelengths, the biological role of FPs is still not fully understood, however they do show reactive oxygen scavenging properties which would provide protection during high oxidise stress conditions such as coral bleaching and pathogen invasion. FPs are present in unbleached but still compromised tissues suggests that they are involved in immunity against not just coral bleaching, but also infection. Like other variables investigated, concentrations varied significantly among coral families.


Immunity parameters were strongly interdependent with size of melanin-containing granular cells, PO activity and FP concentrations. There was a significant positive correlation between Constituent immunity and both bleaching and disease susceptibility.

Consistent differences in disease susceptibility across families suggest taxa-specific levels of disease resistance and investment in immunity mechanisms. Immunity was found to explain over 78% of interfamily variation in bleaching susceptibility, and 83% of disease susceptibility, providing evidence that the coral host itself plays a major role in pathogen and bleaching resistance.

Another interesting point raised by the paper, is the idea that Immunity varies among individuals due to species specific differences in allocation of energy to certain traits. This paper uses life history theory to predict the species which have higher immune functions, will have allocated less energy into growth and/or reproduction. This idea was backed up by the fact that the fast growing/branching species of Acropora (which requires a vast amount of energy to promote rapid colonial growth) was seen to demonstrate the lowest immune rank, which in turn contributed to a high susceptibility to bleaching and disease.

The paper also mentioned the necessity of a holist approach in understanding bleaching and disease with regards to corals – due to the combined effects of several base defence mechanisms in these species: which I though was a point that needed reiterating, as often we get so focused in science we find ourselves drawing conclusions between A and B – without taking into consideration the whole network of mechanisms which are going on in the microscopic world!

Palmer, C. V., Bythell, J. C., & Willis, B. L. (2010). Levels of immunity parameters underpin bleaching and disease susceptibility of reef corals. The FASEB Journal, 24(6), 1935-1946.

Monday, 23 December 2013

Marine Sediment Bacteria Harbour a Pool of Antibiotic Resistance Genes similar to Human Pathogens

Bacterial resistance to antibiotics is an increasing and serious problem for disease control, especially for public health since the common antibiotics are becoming less effective and only a few new drugs are under investigation. Due to the use of antibiotics in aquaculture, many compounds accumulate in the oceans and various bacterial species have developed resistance. The resistance genes are commonly associated with mobile plasmids within the bacteria and genetic exchange between bacteria via horizontal gene transfer (HGT) often involves these parts of genetic information. The total gene pool for antibiotic resistance of pathogenic and non-pathogenic bacteria is referred to as the resistome, which has not been well studied for marine bacteria.

This study aimed to investigate the bacterial resistome of marine fish farm sediment and further examined the relationship between the ocean resistome and the pathogenic resistome in order to establish its clinical importance. Marine sediment was sampled and plasmids were metagenomically analysed to identify the resistance genes. Results showed that the majority of collected plasmid DNA came from Proteobacteria hosts (82 %) of which 54 % belonged to the Gammaproteobacteria. 58 resistance genes with high homology (≥ 80 % identity) were found as well as numerous ones with an overlap of 40 – 80 % of resistance genes from the databank which suggests an occurrence of yet unknown genes from the marine sediment.

The 58 resistance genes with high identity were associated with 11 classes of antibiotics and the distribution of these genes is shown in the figure below and it becomes obvious that the marine sediment is a reservoir of a variety of antibiotic resistance genes.

                                      The diversity of antibiotics identified from the 58 highly homologous resistance genes.

In addition to this, around 10 % of all reads were linked to a gene which encodes an antibiotic resistance compound in the human pathogen Salmonella enterica that causes gastroenteritis. Altogether, six contigs (overlapping DNA segments/reads) with antibiotic resistance genes from human pathogens were found in the marine samples with more than 90 % identity. Among the six, contig891 shared 99 % overlap with several human pathogen species such as Yersinia ruckeri and has also been detected in the fish pathogenic bacterium Aeromonas salmonicida.

This study confirmed that plasmids are the key carriers of antibiotic resistance genes and added knowledge to the diversity of antibiotics present in the marine environment; so far only tetracycline and few others had been identified. Moreover it was uncovered that many marine bacteria in the sediment harbour antibiotic resistance genes highly similar to the ones found in human pathogens and it can be concluded that these bacteria acquired their resistance through HGT from the human pathogens that are continuously released into the oceans. Since many antibiotics are introduced into the ocean through aquaculture, many bacteria also had the opportunity to develop resistance. The fish farm sediment bacteria are in constant contact with the fish and thus, these bacteria can have a great impact on the global spread of antibiotic resistance genes.
Yang, et al. (2013) Marine Sediment Bacteria Harbour Antibiotic Resistance Genes Highly Similar To Those Found in Human Pathogens. Microbiology of Aquatic Systems