Glowing guts?- The intestinal microbiome of Atlantic cod

The fish intestinal microbiome contains a complex and specialised gut bacterial community which is important for multiple functions, including metabolism, growth and development. Riiser et al., (2018) identified a gap in the research comparing healthy wild fish from the same species living in different habitats. Atlantic cod are an economically and ecologically important species in the North Atlantic Ocean. Their ability to exploit a wide range of ecological niches may influence the composition of its intestinal microbiome; this makes it an interesting model species to look at.

In this study, they used metagenomic shotgun sequencing to explore the intestinal microbiome of 19 adult Atlantic cod individuals from two study sites. Overall no significant differences in microbiome composition were found in species from both study sites. However, results identified two abundant species, Photobacterium kishitanii and Photobacterium iliopiscarium in individuals from both study sites. P kishitanii can generate bioluminescence which may suggest that fish intestines form a niche for bioluminescent bacteria.

It is still unclear of the functional role of both Photobacterium in the Atlantic cod intestines; further research needs to be done to explore this as well as the reasoning behind their high abundance.

Riiser, E., Haverkamp, T., Varadharajan, S., Borgan, Ø., Jakobsen, K., Jentoft, S. and Star, B. (2019). Switching on the light: using metagenomic shotgun sequencing to characterize the intestinal microbiome of Atlantic cod. Environmental Microbiology, 21(7), pp.2576-2594.

DMSP signals the end for E.hux?

Roseobacter interactions with phytoplankton blooms range from cooperative to pathogenic and are probably mediated by info-chemicals.  Dimethylsulphoniopropionate (DMSP) and its breakdown products generate cloud condensation nuclei, act as a chemoattractant for seabirds and potentially also for bacteria seeking sulphur and carbon sources.  Emiliania huxleyi (E.hux) forms massive blooms and is a significant producer of DMSP which is consumed by co-occurring Sulfitobacter.  

E.hux blooms are known to be mitigated through viral lysis and grazing but Barak-Gavish et al. (2018) postulated that bacteria may also have a role.  They showed that E.hux populations were indeed decimated when cocultured with Sulfitobacter D7.  However, E.hux monocultures and cocultures with the co-occurring Marinobacter D6 were unaffected.  Resistant E.hux strains became more susceptible when DMSP was added to Sulfitobacter cocultures showing that bacterial growth and algicidal interaction appear to be mediated by DMSP concentration.

It is valuable to reveal a potential new player in bloom mediation but, given a 40% mortality in the control sample, it is possible that other pathogens were at work such as viruses which passed through cell sorting as endosymbionts. Given the importance of E.hux to the carbon-sink process more work is needed to understand how Sulfitobacter, and other pathogens, interact in bloom communities and the signal molecules involved. 

BARAK-GAVISH, N., FRADA, M. J., KU, C., LEE, P. A., DITULLIO, G. R., MALITSKY, S., AHARONI, A., GREEN, S. J., ROTKOPF, R., KARTVELISHVILY, E., SHEYN, U., SCHATZ, D. & VARDI, A. 2018. Bacterial virulence against an oceanic bloom-forming phytoplankter is mediated by algal DMSP. Science Advances, 4.

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Sponge microbiomes – are they affected by pollution?

Microbes account for a large proportion of the biomass of marine sponges. The microbial assemblages in marine sponges have been shown to be affected by factors such as temperature extremes, disease and heavy metal pollution.

Gantt et al. (2017) conducted a study where they sampled microbes associated with the sponge Crambe crambe and from the ambient seawater in 2 locations: a polluted harbour in Blanes, Spain and a nearby natural environment. They hypothesized that the microbiomes of the sponge would differ in the polluted and unpolluted area.

16S rRNA sequences were amplified and sequenced using Illumina and no difference in microbial community structure in sponges between the sample sites was found; whereas there was a difference between ambient sea water at the two sites. The microbial community in the sponges differed from the ambient sea water at both locations.

It was suggested that the results may indicate that sponge microbiomes are much more stable and pollutant-tolerant than previously thought. However, other similar studies on other species of sponge have found the microbiomes to be affected by pollution so to further this study I would suggest sampling from multiple polluted sites in the area to see if the trend found still stands.

Gantt, S., López-Legentil, S., Erwin, P. (2017). Stable microbial communities in the sponge Crambe crambe from inside and outside a polluted Mediterranean harbor. FEMS Microbiology Letters, 364(11).

Gut microbiome to keep a crab healthy

Previously relatively unstudied the microbiome and how it is derived within S. paramamosain’s open circulatory system can be important for aquaculture and further reaching human health. 

Zhang et al. (2019) extracted DNA from 12, in isolation kept, crab gills, midgut, hepatopancreas and haemolymph, to sequence and identify the bacterial community present. Significant differences between male and females were found in most areas with greatest abundance found in the midgut. SourceTracker analysis showed that the microbiome of the haemolymph was derived from the midgut and hepatopancreas. 

Confirming the hypothesis that the microorganisms in the haemolymph are derived from the gut due to the crabs open circulatory system. 

Overall, a variety of different microorganisms were found, some pathogenic and of potential risk to consumers. Healthy crabs are able to maintain and regulate their community well. Some stimulate immune molecules giving the microbiome a role within the crab immune system. Rapid proliferation of haemolymph biota may therefore lead to host disease. 

The paper makes promises on further reach without proper conclusion, resulting in a speculative discussion not always backed by results. As an explorative study this paper provides a baseline for further research, that could answer the wider significance on human health.

Zhang, X., Zhang, M., Zheng, H., Ye, H., Zhang, X., Li, S. (2019) Source of hemolymph microbiota and their roles in the immune system of mud crab. Development and Comparative Immunology, Vol. 102

Accessible through: https://doi.org/10.1016/j.dci.2019.103470

Molluscan mutilation modifies mutualists microbiome

Corallivores have been shown to be associated with the spread of disease that can devastate coral habitats. This may be due to dysbiosis that reduces mutualistic microbes and allows pathogens to dominate. Understanding the complexity of these relationships could prove vital for conservation efforts.

This investigation examined coral mucus from un-grazed and Drupella-grazed Acroporids to assess if bacteromes and viromes would change. They found higher abundance and activity of bacteria and viruses in grazed, with bacterial pathogens dominating and viruses showed a shift from lysogenic to lytic pathways.

For bacterial community analysis simultaneous 16 ribosomal DNA barcoding was used for the first time in the context of corallivory. Virome analysis was less reliable as they used outdated metrics, but novel CRESS-DNA viruses were detected that have potential for further study. It remains vital that further study of this area continues as the pathways of disease are not yet fully recognised. To prevent disease and coral habitat loss a full understanding of the coral microbiome and its interactions with predators and the environment is required. As shown in this paper coral health may depend on associated microbes but if the balance tipped corrals may be lost.  

Bettarel, Yvan, et al. "Corallivory and the microbial debacle in two branching scleractinians." The ISME journal 12.4 (2018): 1109.

Having a gut feeling? Diet influences fish microbiomes and the immune system

Nutrients have diverse effects on an organism’s microbiome, which in turn influences the host’s immune system. So far, the relationship between diet, microbiome and immune response has only been studied extensively in mammals in controlled environments. 

Therefore, Friberg et al. (2019) aimed to explore this relationship in three-spined sticklebacks combining field and laboratory observations. In wild fish, they tested for gene expression profiles in different seasons. To identify diet as the driver for microbiome and gene expression alterations, experimental fish were fed a season-specific diet (summer-like/winter-like). They then created expression profiles of genes involved in seasonal immunoregulation and performed 16S rRNA sequencing on gut and gill microbiomes. 

In wild fish, season altered bacterial community structure and gene expression. In experimental fish, summer-biased genes were up-regulated during the summer-like diet and vice versa. Moreover, diet significantly influenced gut and gill microbiome compositions, with the latter being more strongly associated with immunoregulation. Particularly, they reported increased presence of pathogenic Corynebacteriales under the summer-like conditions. 

The study stresses the effect of diet on microbiome composition and immunophenotype in wild and experimental fish, whilst also addressing the issue of making inferences about mechanisms in the natural environment based on results from controlled experimental conditions. 

Friberg, I. M., Taylor, J. D., & Jackson, J. A. (2019). Diet in the Driving Seat: Natural Diet-Immunity-Microbiome Interactions in Wild Fish. Frontiers in Immunology, 10, 243. https://doi.org/10.3389/fimmu.2019.00243

Too cold to fix?

Biological N₂ fixation is an important source of nitrogen (N) in tropical and subtropical oceans relatively poor in nutrients. Previous research on N₂ fixation has focused on the well-known cyanobacterium Trichodesmium and the diatom symbiont Richelia, which are found in warm waters (>20 °c) with low concentrations of fixed N. However, not a lot of research has been done in waters with lower temperatures and higher concentrations of fixed inorganic nitrogen. This paper by Harding et al., (2018) looked at the cyanobacterial symbiont UCYN-A and how it fixed N₂ in these conditions.

The nifH gene, which is a widely-used proxy for N2-fixing microorganisms was sequenced to identify UCYN-A haptophytes. CARD-FISH and nanoscale secondary ion mass spectrometry was used to measure 13N2 uptake into unicellular cyanobacterial symbionts. It showed that the UCYN-A symbiosis was actively fixing N2. Results showed that low temperatures in polar waters does not limit the distribution or activity of N2-fixing cyanobacteria. 

This paper is interesting as it challenges commonly held ideas about global marine N2 fixation. This research will be useful in understanding and predicting global patterns of N2 fixation. One limitation of this study is that more research is needed to determine the quantitative significance of N₂ fixation by UCYN-A.

Harding, K., Turk-Kubo, K., Sipler, R., Mills, M., Bronk, D. and Zehr, J. (2018). Symbiotic unicellular cyanobacteria fix nitrogen in the Arctic Ocean. Proceedings of the National Academy of Sciences, 115(52), pp.13371-13375.

How to name a Chytrid: the identification and characterisation of an unknown marine Chytrid.

The identification and characterisation of marine Chytrids has long been considered a grey area of marine fungi understanding, with hazy knowledge linking function and taxonomy.

Garvetto et al. (2019) investigated the morphology, global distribution and phylogeny of an unknown Chytrid infecting the marine Diatom Skeletonema. By collecting and isolating the Chytrid from Skeletonema, the study used a combination of microscopy and molecular tools (Phylogenetic tree construction and Metabarcoding), followed by accessing Ocean sampling day (OSD) data.

Microscopy revealed a zoospore thallus and observations of mature sporangia cell wall thickening, characteristic of the order Rhizophydiales morphology. Phylogeny supported microscopy observations as the unknown Chytrid belongs to the Rhizophydiales. Yet the Chytrid didn’t belong to either family of the order, thus giving the temporary name SKCyt. In terms of distribution, Metabarcoding and OSD data identified similar isolates distributed on each North Atlantic coastline.

In summary, this paper gives an example of what molecular and microscopy tool combinations can achieve, contributing to our understanding of marine Chytrid morphology, distribution and taxonomy. However, this paper leaves you with little discussion into SKCyt’s form and function. For future studies I would suggest further investigations into form, function and interactions of SKCyt and other unknown Chytrids.

Garvetto, A., Badis, Y., Perrineau, M. M., Rad-Menéndez, C., Bresnan, E., & Gachon, C. M. (2019). Chytrid infecting the bloom-forming marine diatom Skeletonema sp.: Morphology, phylogeny and distribution of a novel species within the Rhizophydiales. Fungal biology, 123(6), 471-480.

Black carbon. It's a bit different from blue steel!

The coastal environment is where land, sea and air meet making it one of the most biogeochemically active parts of the ocean but also exposes it to many anthropogenic threats, one of these being ‘black carbon’.  This is the aerosols/soot that result from the incomplete combustion of fossil fuels creating carbon-rich compounds which enter the sea through the atmosphere or land runoff.

Paradeep Ram et al. (2018) sampled the surface microlayer and at 1.5m depth in Haloing Bay, Vietnam, Known for its high atmospheric BC levels.  They used solid-phase extraction to measure BC levels and counted abundances of bacteria and virus’ using stains.  Their results showed that the surface layer is significantly more enriched with BC by a factor of 105, and the abundance is significantly higher and more variable of bacteria and virus’.  The virus-to-bacteria ratio was also much higher which suggests that the bacteria may be the main host for these virus’.

The percentage of carbon found to be BC here was the highest reported (32-97%) and the elevated levels in the surface suggested a high holding period here before sampling, which may be attributed to low wind speeds. However, the bacterial and viral elevations were minimal compared to other studies which they put down to potentially being their sampling method as the type of sampler used for the SML greatly effects results.  Despite this the results shed light on a different kind of damage burning of fossil fuels is doing and opens up many more questions for future study.

Pradeep Ram, A.S., Mari, X., Brune, J., Torreton, J.p., Chu, V.T., Raimbault, P., Niggemann, J., Sime-Ngando, T. (2018) Bacterial-viral interactions in the sea surface microlayer of a black carbon-dominated tropical coastal ecosystem (Halong Bay, Vietnam). Elem Sci Anth. (6):13.

Distinct microbial communities at hydrothermal vents

Microbial communities at deep-sea hydrothermal vents were investigated using molecular and geochemical analysis, elucidating patterns over temporal and spatial scales. Differences in micobial composition were found between sites, as well as less pronounced differences within sites over time. Key populations which manage carbon, sulphur, hydrogen and nitrogen levels were identified such as SUP05 at ‘Anemone’ site and methanogenic Archaea at ‘Marker 113’ site.

Findings focussed on microbial population dynamics over time, including their ability to maintain distinct communities, demonstrated by a vent eruption between sampling; many geophysical changes occurred but microbial structure remained stable. Seafloor sampling was interesting, revealing the substrate may act as a microbial ‘bank’.

Relationships between microbial communities and environmental factors were suggested, however these links must be treated with caution. Better communication of the statistical analysis about the differences would have helped highlight where major differences in microbial structure are found and inferences could have been made into why this is the case.

Deep-sea hydrothermal vents microbiomes are complex, this work highlights the variability that can be found, as sampling only took place once a year for three years per site, more regular sampling would be interesting to understand the dynamism of these unique communities.

Fortunato, C.S., Larson, B., Butterfield, D.A., Huber, J.A. (2018) Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent fluids. Environmental Microbiology, 20(2), 769-784. doi:10.1111/1462-2920.14011