Absorbed in the search; antimicrobial revelations from marine sponge ecosystems

Strains of bacteria are becoming more resistant to antibiotics; with many scientists warning our drugs could soon become ineffective against even the most basic of infections. On top of this the risk of viral epidemics has been increasing, many solutions are being explored and scientists are looking to marine fungi for potential sources of new antibiotic and antiviral drugs.

Bovio et al (2019) used PCR to identify marine fungi isolated from Atlantic sponge Grantia compressa, OSMAC revealed metabolic diversity in the isolate-Eurotium chevalieri MUT 2316, from which compounds were extracted, isolated, and characterised. Of these, Dihydroauroglaucin was shown to inhibit the replication of influenza A, with another compound-Isodihydroauroglaucin showing antibacterial activity against Escherichia coli ATCC 25922.

This paper is a good first step into looking at alternate sources of antibiotics and antiviral drugs, showing compounds that potentially could be used in the future. However long clinical trials would still be required before any of these compounds are usable. This paper is well written however some of the graphs are convoluted and hard to follow. Future research is needed into these novel compounds and their effects on additional pathogens to the ten presented here.

Bovio, E.; Garzoli, L.; Poli, A.; Luganini, A.; Villa, P.; Musumeci, R.; McCormack, G.P.; Cocuzza, C.E.; Gribaudo, G.; Mehiri, M.; Varese, G.C. Marine Fungi from the Sponge Grantia compressa: Biodiversity, Chemodiversity, and Biotechnological Potential. Mar. Drugs 2019, 17, 220.
https://www.mdpi.com/1660-3397/17/4/220

Are Microplastics Toxic to Microbes?

The effects of microplastics on the marine environment is a globally recognised issue. In this investigation the researchers wanted to test standard endpoints given by International Standard Organization (ISO) protocols. Using concentrations of microplastics well above environmentally relevant concentrations (25mg/L) they showed that there were no growth rate or toxicity effects of microplastics on the bacteria Vibrio fischeri and the diatom Phaeodactylum tricornutum.

Unfortunately, there were some inconsistencies in this investigation that are worth noting. The light to dark periods of the experiment are inconsistent ranging form 12-12h light dark to 16-8h light dark period. The mixing tourniquets and bottle types varied with treatment. These inconstancies and the lack of formatting make this a difficult paper to read. It is also strange that microplastics that are almost the size of or larger than the bacteria or algae used are being considered toxins. It is likely that chemicals on the surface of these plastics are more relevant.

Microplastics may not pose a threat to microbes in the ocean and more sensitive endpoints might need to be made for future investigation as highlighted in the study. I think a different approach to this problem would be more effective.

Gambardella, C., Piazza, V., Albentosa, M., Bebianno, M. J., Cardoso, C., Faimali, M., ... & Sendra, M. (2019). Microplastics do not affect standard ecotoxicological endpoints in marine unicellular organisms. Marine Pollution Bulletin, 143, 140-143.

10,000 marine fungi species waiting to be discovered!

This paper discusses the diversity of marine fungi. In the last 60 years, the number of identified marine fungi species has been multiplied by 5, and species are still being found on various substrata and unexplored habitats (particularly in the tropics). Various guesses on the number of marine fungi species are thought to be a gross underestimate, considering there are still unidentified species, endophytic and cryptic taxa. This review contains several fungal groups that have been poorly surveyed and therefore may be a potential source of more undiscovered marine species. Accounting for the potential sources, the number of marine fungi may in fact exceed 10,000 taxa.

The way that this paper was written made it difficult to comprehend in parts. Some of the sentence structure was hard to follow and other parts seemed to have no flow or direction, making for very wordy sentences that actually don’t say too much. I also found the tables to be a bit confusing, which they could have easily amended by using lined rows. Otherwise, an interesting review on marine fungi diversity and an eye-opening reminder of how little we truly know about marine microbiology.

Reference: Jones, E. (2011). Are there more marine fungi to be described?. Botanica Marina, 54(4).

Does aquaculture turn your stomach? Fish too!

This study focuses on the intestinal microbiota of the fine flounder (Paralichtys adspersus), a flatfish of commercial interest that is native to the Chilean coast. Intestinal microbiota is involved in a wide range of internal processes, such as modulating the immune system and providing nutrition. The societal value of the fine flounder has encouraged the development of aquaculture activities and stock enhancement, making it a species of interest when exploring . Knowledge of microbiota may aid in improving the cultivation of this species and so this study aimed to evaluate the intestinal microbiota community in farmed versus wild fishes.

Contents from the intestines of wild and reared fish were collected and DNA was extracted and then the V3-region of 16S rRNA was PCR amplified and sequenced using the Ion Torrent platform. The compositions of microbiota found in each group of specimens showed important distinctions between reared fish and wild fish. In wild flounder, the most abundant phylum was Proteobacteria which was found in far lower abundances in the reared flounder. Contrastingly, in the reared flounder, the most abundant phylum was Firmicutes, which was much less common in the wild flounder.

A total of four genera were identified between the two conditions and Bacillus and Pseudomonas being highly represented in the reared flounder and Athrobacter and Psychrobacter being highly represented in the wild flounder. These results show that, though in both cases, metabolic pathways indicated that the microbiota compositions found would have beneficial effects for the host, but wild flounder showed more remarkable pathways.

I personally found this paper to be very interesting, perhaps because it feels very current and important. There are mixed opinions on various aspects of aquaculture, such as the ethical treatment of livestock and thus the quality of the product, and the implications to the immediate and extended environment. This paper is one of the only studies I have come across where the actual individual organisms are assessed for the impact of aquaculture rather than looking at the bigger picture, showing that the effects of this type of agricultural practice has impacts on all scales. The only criticism I have is that it tends to get a little repetitive in parts. 

Reference: Ramírez, C. and Romero, J. (2017). Fine Flounder (Paralichthys adspersus) Microbiome Showed Important Differences between Wild and Reared Specimens. Frontiers in Microbiology, 08.

Synechoccocus and Cyanophage control phytoplankton?

This study focuses on unicellular cyanobacteria of the genus Synechococcus and its contribution to primary productivity in the oceans. The main findings support the hypothesis that a virus infection can play a substantial role in determining success of different Synechococcus genotypes and, in extension, seasonal succession.

The study took place in the Gulf of Aqaba, Red Sea, where nutrients levels are low. Here they observed a succession of Synechococcus genotypes over an annual cycle. Restriction fragment length polymorphism analysis of a 4403‐ bp rpoC1 gene fragment showed that there were large changes in genetic diversity. The abundance of co-occurring cyanophage capable of infecting marine Synechococcus was contingent on plaque assays, and their genetic diversity was determined by denaturing gradient gel electrophoresis analysis of a 118‐bp g20 gene fragment.

The results provide evidence that states both abundance and genetic diversity of cyanophage covaried with that of Synechococcus. Using multivariate statistical analyses, this indicated a significant relationship between cyanophage assemblage structure and that of Synechoccocus. These observations ring true to the ideology that cyanophage infection is a major defining factor in picophytoplankton succession.

This paper was very informative but I found that whilst reading it, I was having to research certain terms or methods used in order to understand. Although it is interesting and coherent, I would have appreciated a bit more explanation and descriptions of methods. Contrastingly, the figures were simple and clear which was useful.

Reference: Muhling, M., Fuller, N., Millard, A., Somerfield, P., Marie, D., Wilson, W., Scanlan, D., Post, A., Joint, I. and Mann, N. (2005). Genetic diversity of marine Synechococcus and co-occurring cyanophage communities: evidence for viral control of phytoplankton. Environmental Microbiology, 7(4), pp.499-508.

Biodiversity, Benthic Communities and Bioturbation

In this study, published in 2009 by Bertics and Ziebis, a combination of field and laboratory approaches were used in order to assess the effect of bioturbation on microbial diversity in a coastal lagoon (Catalina Harbor, Santa Catalina Island, CA, USA). The activity of two crustaceans, the ghost shrimp (Neotrypaea californiensis) and the fiddler crab (Uca crenulata) was assessed using detailed geochemical analyses, including oxygen microsensor measurements, to characterize environmental parameters. Furthermore, ARISA (amplified ribosomal intergenic spacer analysis) was used to compare the bacterial diversity along geochemical gradients and in relation to subsurface microniches.

One of the main aims of this study was to address whether burrows support similar or unique communities compared with the sediment surface by observing how varying environmental parameters affect benthic microbial communities. The results showed that microbial communities on the sediment surface are distinct from subsurface assemblages, and furthermore that different burrow types support diverse bacterial taxa. Comparisons drawn from the statistics indicate that availability of different oxidants are huge influencers of the presence and abundance of different taxa. When geochemical parameters were similar, the microbial communities affiliated with burrows were significantly similar to communities found on the sediment surface.

I found this paper to be a pleasant and simple read. It’s both concise and detailed which makes it very easy to follow and understand. The methods are the only part which I found to be a bit more difficult to comprehend and they seem to be unnecessarily long with many headings that I feel could have been condensed down further.

Reference: Bertics, V. and Ziebis, W. (2009). Biodiversity of benthic microbial communities in bioturbated coastal sediments is controlled by geochemical microniches. The ISME Journal, 3(11), pp.1269-1285

A Radically Adaptive Community

   Hydrothermal vent communities have been a scientific point of interest since their discovery, by and large due to their ability to thrive in such dynamic conditions. The environmental gradients and niches provided by hydrothermal vents give rise to a plethora of unique populations, making deep-sea hydrothermal fields a hugely diverse ecosystem.

   Yang et al. (2019) investigate the microbial communities that adapt to a range of changes that occur daily at the Southwest Indian Ridge. By extracting sediment cores from an inactive vent field, 16SrRNA high-throughput sequencing was used to examine the microbial composition of the area. Microbial communities were similar at the surface layer but began to distinguish unique functions at an increased depth. This reinforces the idea that hydrothermal vents expel reduced materials which are universally useful to members of microbial communities, but upon moving further from the surface, specialization is required.

   This study serves as a pioneer into the activity of the Southwest Indian Ridge. Whilst differences were observed in microbial communities, it is important to remember that over 80% of all detected OTUs were shared among different temperatures and sediment depths, suggesting that something connects distant hydrothermal habitats which could be the basis of future scientific study.

Yang, Z., Xiao, X., & Zhang, Y. (2019). Microbial diversity of sediments from an inactive hydrothermal vent field, Southwest Indian Ridge. Marine Life Science & Technology, 1-14.

Tolerant sponges might adapt using their microbiome

Increased carbon emissions have been associated with ocean acidification, which could be disastrous for many species. Botté et al take advantage of a natural CO2 seep to investigate the impacts of ocean acidification. They looked at two species of sponge; the more low-pH tolerant Coelocarteria singaporensis (more abundant at the seep site) and the more sensitive Stylissa flabelliformis (more abundant at the control site). The metagenome of samples taken from 3 individuals of each species from both the control and seep sites were sequenced; this was used to determine microbiome community structure and was also functionally annotated. They observed both differences in community structure and differences in functional genes between the 4 treatments. Bacteria associated with C singaporensis had an enhanced potential for efficient carbon and nitrogen metabolism, whereas those associated with S flabelliformis showed a loss of functional potential in more acidic waters. This suggests that the more tolerant C singaporensis makes use of microbiome mediated adaptation- a rapid technique which could help species in a changing climate. This also continues to demonstrate the importance of the microbiome to the health of the host. Overall, this is a useful study with important results that help to explain the ability of an organism to thrive where others do not. However, the use of two-species comparison could limit the scope of the results.

Reference: Botté E, Nielsen S, Wahab M, Webster J, Robbins S, Thomas T, Webster N, 2019, Changes in metabolic potential of the sponge microbiome under ocean acidification, nature communications (10:4134)

Black carbon’s colonisation by microbes

Black carbon is a pyrogenic material produced during the incomplete combustion of fossil fuels, bio-fuels and biomass. Its effects on the marine environment are understudied, particularly those on biogeochemical cycling. Black carbon particles are known to be reactive, due to their porous structure and external coverage of oxygen-containing functional groups. Other molecules react with these groups, (such as amino acids) resulting in adherence and aggregation. This study examines the way amino acid-amended black carbon is colonised by microbes. The researchers took SML samples, and added seawater and commercial black carbon. They then divided this sample into 15 bottles. 9 of these samples were amended with a 15N labelled algal amino acid mix, before being incubated for 12, 24 and 48 hours. 6 samples were used as controls, with 3 of them incubated for 48 hours and 3 used as “zero-hour” samples. The controls were not amended with the amino acid mix. The incubation was followed with nanoSIMS analysis. The results showed an increase in amino acid adsorption over time, leading to an increase in bacterial abundance in the experimental treatments. The researchers conclude that black carbon adsorption of amino acid molecules results in an increase in colonising bacteria on the particles. They discuss how this may be useful in remineralising the carbon, but also discuss how the “diversion” of the bacteria could disrupt the biological carbon pump, and how it is unclear whether remineralisation is actually occurring.

Benavides M, Chu Van T, Mari X, (2019), Amino acids promote black carbon aggregation and microbial colonisation in costal water off Vietnam, Science of the total environment, pp. 527-532

‘It’s complicated’ – seagrass and fungi

Fungi have significant positive and negative impacts on terrestrial angiosperms, however analogous marine relationships are poorly documented. This research aimed to characterise the mycobiome of Zostera marina using molecular methods including Sanger sequencing and phylogenetic reconstruction.

A noteworthy finding of this work was that fungal community structure varied both within and between plant parts –tissues hosted much different taxonomic orders, some of which were novel. They also found the mycobiome had relatively low diversity and put forward several hypotheses to postulate why, from high salinity, low oxygen, seasonality to antimicrobial compounds produced by Z. marina.  

Overall this work highlighted the complexities of studying marine fungi and its associations with angiosperms, though the blue sky nature of this work is important to progress knowledge in the field. Z. marina certainly host distinct fungal communities, the function and mechanisms of this relationship remain to be fully understood.

Ettinger, C.L., Eisen, J.A. (2019) Characterization of the mycobiome of the seagrass, Zostera marina, reveals putative associations with marine chytrids. Frontiers in Microbiology, 10(2476).