Something smells fishy…

The skin of marine animals is covered in a diverse range of microbial communities. These microbiomes are fundamental to the fitness of the host as they regulate metabolism/ immune system, enhance nutrients absorption and protect against pathogens. Previously, the composition and diversity of these microbiomes have been largely neglected.Chiarello et al. (2018) investigated the diversity, variability and their drivers of these microbiomes of several coral reef fish species using metabarcoding of 16S rRNA V4 region. The findings of this paper allow diverse predictions about potential anthropogenic impacts on coral reef inhabitants.
Prokaryotic communities on the skin of individuals were highly diverse with the composition of microbiomes varying greatly Intra- and inter-individually. The community variation across species was dependent on the genetic similarities of the species of the host and the differences in its ecological traits. It was also highlighted that the differences between species are the variances in immune systems.The results of this study were limited by the lack of specific primers available to explore the archaeal diversity. Despite this it the paper managed to highlight that the microbiome diversity of coral reef fish skin was much higher than previously realised this exemplified that a loss of micro-organism diversity would also negatively impact microbial communities. Furthermore, anthropogenic impacts will lead to a loss of untapped potential of host-associated organisms for medical purposes.

Chiarello, M., Auguet, J., Bettarel, Y., Bouvier, C., Claverie, T., Graham, N., Rieuvilleneuve, F., Sucré, E., Bouvier, T. and Villéger, S. (2018). Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet. Microbiome

The crude control oil has over gut microbiomes

 PAHs (polycyclic aromatic hydrocarbons) are components of crude oil which are released into the marine environment from anthropogenic contamination. These have strong cardiotoxicity effects in fish and can induce immunosuppression. 

Walter et al. (2019) used high-throughput illumine sequencing of the 16s rRNA V4 region to look at the gut microbiome of Gadus morhua (Atlantic cod) from two different locations along Norway: the south where, due to high levels of anthropogenic activities there is expected to be greater amounts of PAHs and from the northern waters which should be pristine in comparison. The bacterial taxa present can be used as a novel indicator of PAH contamination as pollutants are a controlling factor that shapes the gastrointestinal microbiome. 

Several groups of PAH-degrading bacteria were found only in the fish from the southern region including Deferribacteraceae a family which are biomarkers of oil pollution along with many OTUs that represent additional hydrocarbon-degrading bacteria. Comparison of the gut microbiomes suggests that cod from the southern region have a higher exposure to PAHs and therefore require an altered microbiome to breakdown these pollutants. The importance of looking at the functional aspect of the microbiome is highlighted in this paper as the change in pollutants has direct control of the microbiome and the fishes' ability to adapt to the pollutants they encounter. 

Walter, J. M., Bagi, A., & Pampanin, D. M. (2019). Insights into the Potential of the Atlantic Cod Gut Microbiome as Biomarker of Oil Contamination in the Marine Environment. Microorganisms, 7(7), 209.

Life on plastic, it’s fantastic

Plastic is readily colonised by a microbial biofilm and a leading hypothesis states that all plastics possess the same microbial community. In a field incubation experiment, Pinto et al. (2019) rejected this hypothesis. Most plastics had a bacterial community structure that was only marginally different to that on glass. However, polyvinyl chloride (PVC) was colonised by a strikingly different community, with dominance of the families Alteromonadaceae and Oceanospirillaceae in ambient and shaded light conditions, respectively. Bacterial clades were identified using the 16S rRNA V3-V4 hypervariable region.

The study suggests that each polymer type supports a distinct bacterial community, potentially driven by differential adsorption of organic compounds. Furthermore, the uniqueness of the PVC community is likely due to the presence of phthalates, which can be utilised by Alteromonadaceae and Oceanospirillaceae. Some members of these families are also known to degrade hydrocarbons and thrive in oil spills. Although current research is suggesting that such bacteria degrade plastic, there is no direct evidence for plastic-derived carbon in bacterial cells (Pinto, personal communication). We are certainly a long way from finding a bacterium that can help clean up our mess! And if we could find such an organism, would that really improve our situation?

Pinto, M., Langer, T. M., Hüffer, T., Hofmann, T., & Herndl, G. J. (2019). The composition of bacterial communities associated with plastic biofilms differs between different polymers and stages of biofilm succession. PLoS One, 14(6), e0217165.

Some bacteria may find plastic yummy

Plastic is an increasingly ubiquitous substratum in the marine environment. Consequently, it is critical to understand its effect on the microbiome. In a series of incubation experiments, Romera-Castillo et al. (2018) found that four widely used plastic types leach dissolved organic carbon (DOC) when exposed to seawater. This plastic-derived DOC may be used by bacteria from Adriatic surface waters, as evidenced by a positive linear relationship between leached DOC and consumed DOC. Importantly, artificial solar radiation decreased the bioavailability of plastic-derived DOC, as indicated by lower bacterial growth and protein synthesis. This is likely due to deleterious free radicals, produced during photodegradation of plastic.

These findings suggest that plastic could be a novel oceanic carbon source, which may alter food-web and carbon cycling dynamics. One shortcoming of this study is the unknown identity of bacterial clades. Moreover, the effect of insolation generally seems more important than that of plastic on bacterial activity, which was only rarely higher in irradiated plastic compared to control treatments. Perhaps plastic is only a meaningful carbon source in the deep sea and its usage by the respective microbiome should be investigated. Finally, the capacity to infer global trends from laboratory experimentation is limited. 

Romera-Castillo, C., Pinto, M., Langer, T. M., Álvarez-Salgado, X. A., & Herndl, G. J. (2018). Dissolved organic carbon leaching from plastics stimulates microbial activity in the ocean. Nature Communications, 9(1), 1430.

Is it just a phage? Autochthonous bacteriophages and its importance in the microbial loop

The microbial loop is an important component of planktonic communities and is an intermediate element of organic-matter transformation. Lake Baikal is an ancient, oligotrophic lake with high scientific and practical significance. The Autochthonous bacteriophages found in the lake are a previously unknown element in the microbial loop in Lake Baikal. 

Drucker et al. (2019) used transmission electron microscopy to observe bacteriophage samples collected in littoral and pelagic areas of Lake Baikal. Morphological diversity of phages were identified and the total number of bacteria was measured on polycarbonate filters. Many of the morphotypes identified are not present in the International Committee on Taxonomy of Viruses (ICTV) and have not yet been described. This study highlighted the high taxonomic diversity of bacteriophages. This is not surprising considering its long period of existence which resulted in the formation of a unique freshwater biota. Phage purification and DNA isolation were performed and high-throughput sequencing was used to sequence and assemble the genomes of phages PaBG and MD8. The genome analysis of MD8 revealed a cluster of genes which determined its ecological significance depending on the state of biofilm. This sheds a light on the importance of the chemical and physical factors of the environment which needs further investigating.

Drucker, V.V., Belykh, O.I., Gorshkova, A.S., Bondar, A.A. and Sykilinda, N.N., 2019. Autochthonous Bacteriophages in the Microbial Loop Structure of Different Biotopes of Lake Baikal. Contemporary Problems of Ecology, 12(2), pp.143-154.

A bloomin' timeline for HABs ?

Besides better detection methods and increasing scientific awareness, frequencies and severity of harmful algal blooms (HABs) have increased over the years. This study emphasises the importance of establishing a historical baseline for HAB distributions in order to understand the future direction of HABs and their impact on coastal ecosystems. Using an eDNA metabarcoding approach, historical baseline data was established for HAB distributions around the Australian coast involving sediment samples dating from 1987-2014. 

Taxonomic identification revealed 14 different genera which identified as HAB-associated taxa. Changes in the diversity and distribution of HAB taxa over 30 years were revealed and the original sources of invasive species could be sourced. Here, Shaw et al. (2019) show historical samples to be a useful tool for retrospective biomapping of HAB species, providing insights into past HAB distributions and their effect on ecosystems, moreover this study emphasises how the shipping industry has contributed to the spread of invasive species over the years. 

This study relies on the persistence of eDNA, which degrades over time. Interpretations of these results should therefore be cautious, as observed changes in diversity could be due to the loss of eDNA in older samples. 

Reviewed paper: Shaw, J., Weyrich, L., Hallegraeff, G., & Cooper, A. (2019).  Retrospective eDNA assessment of harmful algae in historical ship ballast tank and marine port sediments. Molecular Ecology,  28, 2476– 2485.

More than just a fungi? Novel secondary metabolites from marine fungi

Microbes are a rich source of therapeutically useful secondary metabolites. Recently, natural products research was revolutionised by novel techniques combining well-known screening methods with life science informatics strategies. However, this research has primarily focused on terrestrial and marine bacteria, whereas marine fungi have largely been neglected. 

Kumar et al. (2018) applied high-throughput methods to two parasitic fungal isolates, Calcarisporium sp. KF525 and Pestalotiopsis sp. KF079. They sequenced and assembled both genomes, before using bioinformatics tools for genome mining of biosynthetic gene clusters (BGCs). Critically, 98% of the detected BGCs in Calcarisporium sp. and 97% in Pestalotiopsis sp. have no homologous clusters in the relevant database of known BGCs, making them by definition ‘novel’. Some of these BGCs share characteristics with unidentified, bacterial BGCs. This might be due to the fact that the database consists primarily of BGCs found in non-fungal organisms. Although few novel BGCs were expressed in culture, genome mining tools still allowed the authors to make inferences on how the species manage to survive in their host’s environment and how they have specialized for host degradation. However, more importantly, the study emphasizes how little is yet known about BGCs and secondary metabolite biosynthesis in marine fungi and stresses the potential importance of marine fungi in the discovery of novel secondary metabolites and future therapeutic agents.

Kumar, A., Sørensen, J. L., Hansen, F. T., Arvas, M., Syed, M. F., Hassan, L., … Kempken, F. (2018). Genome Sequencing and analyses of Two Marine Fungi from the North Sea Unraveled a Plethora of Novel Biosynthetic Gene Clusters. Scientific Reports, 8(1), 10187. doi: 10.1038/s41598-018-28473-z