Microbes munching on microplastics in mangrove mud

Microplastic pollution in marine ecosystems is a contemporary issue that has been at the forefront of environmental research and the media in recent years. Roughly 4.8 million tonnes of plastic enter the marine environment every year with microplastics constituting 92.4% of this waste. Microplastics are often made deliberately for use in cosmetics that then pass through wastewater treatment or by the weathering and breakdown of large plastic debris.

Microplastics have a global ocean distribution and we are still only just beginning to discover the ill effects that they cause to marine animals and environments. Microplastics are often found within filter feeding invertebrates, marine mammals and seabirds causing pathological stress, stunted growth, and false satiation and even facilitate the accumulation of heavy metals in marine sediments. Even with ever-increasing evidence of the damage to marine life microplastics cause, less attention is given to strategies for environmental remediation. Mangrove forests support a high diversity of microbes and are often subjected to high plastic pollution, could members of these microbial communities be a solution to our growing plastic problem?

The aims of the reviewed study were to provide a remediation solution to microplastic polluted environments, using bacterial isolates, and to evaluate the potential of marine bacteria to degrade microplastics.

Microplastic polyethylene, Polypropylene (PP), Polystyrene and Polyethylene terephthalate were collected and treated with UV-radiation. Sediment samples were taken from the top 4 cm from six mangrove forests around the Peninsular Malaysia from which bacteria were isolated, plated onto nutrient agar (NA) and incubated. Pure cultures were obtained after incubation for species identification and plating onto a mineral salt medium (MSM) with the UV-treated microplastics as the only carbon source. Species that could grow on the MSM were inoculated into an MSM broth containing one of the four microplastics and incubated for 40 days. Cell growth was monitored every 10 days and after 40 days microplastic weight loss, the rate of degradation and half-life was calculated. Changes in the plastic structure were assessed by Fourier transform infrared and scanning electron microscopy (SEM).

Only two isolates obtained from incubation could grow in the presence of plastics, these were Bacillus cereus and Bacillus gottheilii. Both species showed similar growth patterns over the 40-day incubations with exponential growth between day 0 and 20 followed by a die off. However, B. gottheilii could grow in the presence of PP where B. cereus could not. B. gottheilii shows a wider capacity to degrade microplastics than B. cereus while also degrading plastics at a higher rate. Microplastics were also shown to be oxidised when inoculated, these bacterial species are able to alter the chemical structure of plastic polymers to make them easier to adhere to and degrade. SEM observations also revealed that plastics inoculated with B. cereus and B. gottheilii had much rougher surfaces and bore crevices and holes.

This study has revealed two bacterial species with a capacity to degrade plastic and could serve as a solution to boost remediation of polluted mangrove sediments. Adding bacteria to sediments may be an “environmentally safe” method of plastic clean-up, but future work should focus on what effect if any, adding these microbes has on the community dynamics of the sediment. Also, subsequent work should try to establish the molecular and genetic pathways these microbes possess that are involved in microplastic degradation.

Paper reviewed:

Auta, H.S., Emenike, C.U., & Fauziah, S.H. (2017). Screening of Bacillus strains isolated from mangrove ecosystems in Peninsular Malaysia for microplastic degradation. Environmental pollution, 231, 1552-1559.

Reef Fish Farming Behaviour May Be Promoting Coral Disease

 Anthropogenic driven environmental change has led to the severe degradation of coral reefs worldwide. The occurrence of coral disease has increased significantly in recent years, resulting in mass coral mortality and subsequent habitat loss for countless species. Whilst the exact causes of coral disease continue to elude researchers, well studied coral diseases such as black band disease (BBD) are associated with a consortium of pathogenic microbes infecting the host. As such, gaining a more comprehensive understanding of the processes influencing microbial community structure and disease ecology within coral reef ecosystems is paramount to the efficacy of future conservation efforts.

 Previous research has emphasised the significance of coral-algae interactions in configuring reef microbial communities, yet few studies have addressed the roles that fish may play in mediating these interactions. Consequently, one recent study endeavoured to examine how the grazing activities of territorial damselfish may indirectly alter benthic microbial populations, potentially influencing the prevalence of coral disease.  

 In order to cultivate patches of palatable filamentous algae, damselfish farm the reef benthos, weeding out unfavourable algal species. Accordingly, damselfish engineer reef ecosystems, promoting a large biomass of low-diversity turf algae. However, previous work has illustrated turf algae to be detrimental to coral health, accommodating potentially coral-pathogenic bacteria as well as releasing harmful dissolved compounds. Therefore, it is possible that damselfish farming behaviour could prove damaging to reef health.     

 Casey et al. investigated the benthic microbial communities of shallow reefs surrounding Lizard Island, situated in the northern Great Barrier Reef. Sampling was carried out within the territories of two damselfish species, Stegastes nigricans and Stegastes apicalis, as well as within control plots devoid of territorial grazers. Initially, algal compositions were characterised inside the territories of both species, revealing assemblages dominated by rhodophytes (over 50% coverage from Polysiphonia sp.) with almost all macroalgae eliminated.

 Benthic microbial communities were subsequently characterised by analysing samples of epilithic algal matrix (EAM). EAM is the overriding component of benthos within damselfish territories and is made up largely of turf algae, detritus, and an array of associated microbes. Bacterial assemblages within EAM samples were characterised by 16S rDNA sequencing, revealing that damselfish territories have microbial communities distinct from control plots. EAM microbial communities within S. nigricans and S. apicalis territories, whilst distinct from one another displayed some similarities, probably due to the dominance of Polysiphonia sp. cultivated by both species. Similarly, overlaps were found between EAM microbial communities in S. apicalis territories and control samples. S. apicalis tend to select plots on more flattened areas of benthos, comparable to control plots, likely accounting for these overlaps. In contrast, S. nigricans cultivates algae on the branches of acroporid coral.  

 Analysis of bacterial phylotypes within samples revealed that damselfish territories contained two to three times more potential coral pathogens than control samples. These potential pathogens are cyanobacteria belonging to generas Leptolyngbya and Oscillatoria and have been previously connected to the pathogenicity of BBD. Furthermore, coral disease surveys found that staghorn coral, Acropora muricata, was significantly more likely to be afflicted with BBD within territories of S. nigricans than within control plots. Together, these findings stress the link between damselfish grazing activities altering reef benthos and increased prevalence of microbes associated with coral disease.     

 As damselfish abundance appears to be increasing as an indirect consequence of overfishing, we may expect to see a proliferation in benthos sculpted by their farming behaviours. This study effectively demonstrates the potential adverse consequences for coral reef health associated with such ecosystem alteration, making a valuable contribution to the current understanding of coral reef disease ecology. Nevertheless, research is required to gain a clearer understanding of the mechanisms underpinning such shifts in benthic microbial communities, perhaps also factoring in abiotic variables such as water temperature, known to strongly influence coral disease occurrence.  

Reviewed Paper:

Casey, J. M., Ainsworth, T. D., Choat, J. M. & Connolly, S. R. (2014). Farming behavior of reef fishes increases the prevalence of coral disease associated microbes and black band disease. Proceedings of the Royal Society, 281: 20141032.

Has it always been like this, or is it just a phage? Lysogenic viruses found associated to high host abundances.

There are different ecological consequences from lytic and lysogenic strategies of viruses. Lytic cycles generally remove genetic material and energy from the food chain. Conversely, lysogenic cycles can cause transfer of genetic material between host bacteria (transduction) and may allow for increased bacterial survivorship. Therefore, it is important to understand these strategies and their impacts on marine ecosystems. But first, what do we know... 

Viral reproduction has two cycles: lytic and lysogenic. In the lytic cycle, a bacteriophage injects viral DNA through the cell wall of the host. Next, biosynthesis occurs until progeny phages are matured. The progeny phages then burst out of the membrane and are released to the environment. For the lysogenic cycle, viral DNA is injected into the genome of the host and the DNA becomes part of the chromosome. As the bacterial host divides, the viral DNA becomes part of the daughter cells. The viral DNA remains dormant until a stimulus (e.g. ultraviolet light) excides the viral DNA. Next follows biosynthesis, maturation, and finally the progeny phages burst and are released. 

Viruses, like many other strong competitors and predators, have an evolutionary dilemma: they must be successful, but not too successful so that they drive their hosts to extinction. It has been thought that lysogeny is a technique designed to ensure this; lysogeny allows the phage to survive, without killing the hosts when host numbers are few. Lysogeny also means that the phage is in the same place as the host when growth conditions improve. Generally, lysogeny would be more common in oligotrophic waters.  

When host abundance is high, there is an increased likeliness of virus-host collisions and opportunities for lytic viruses – this would show a higher virus-to-microbe ratio. However, a study by Knowles et al. (2016) found the opposite. The study conducted meta-analysis approach including: (1) experimental manipulations (2) literature meta-analyses, (3) direct counts, and (4) a personal study of 24 coral reef viral metagenomics. Authors found that there was a decrease in virus-to-microbe abundance as microbe abundance increased. Authors explain that this was caused by increased lysogeny at higher abundances – results showed that as microbe abundance increased, genes that are associated with integration and excision of lysogenic viruses increased as well. But why?  

Authors investigated alternate hypotheses and the leading explanation was the defense hypothesis: that the high abundance host communities were dominated by defensive, slow-growing strains of hosts, associated with low virus production. Therefore, viruses would mainly infect the more-competitive and faster-growing strains of hosts which had lower abundances. Despite this, metagenomic data showed that there was no correlation between viral-defense genes and microbe abundance.  

The final explanation was the Piggyback-the-Winner hypothesis, rather than Kill-the-Winner models. This implies that viruses exploit their hosts for a more prolonged period, rather than killing them. Under the Piggyback-the-Winner dynamics, there is likely more virulence content in microbial communities than previously thought – Authors claim that this data suggests facilitation for microbialisation. 

Overall, virus-host community structure may be less known than previously thought – the rules behind lysogeny and lytic strategies remain uncertain however, research shows complex virus-host interactions, from an evolutionary perspective. Research on this topic could have huge consequences to help understand virome interactions. So, more microbes... less viruses? 

Reviewed paper:

Knowles, B., Silveira, C.B., Bailey, B.A., Barott, K., Cantu, V.A., Cobián-Güemes, A.G., Coutinho, F.H., Dinsdale, E.A., Felts, B., Furby, K.A. and George, E.E., 2016. Lytic to temperate switching of viral communities. Nature, 531(7595), p.466. 

Fish guts are going viral!

The gastro-intestinal microbiome of organisms is multi-faceted, and consists of a plethora of bacteria, viruses, fungi and archaea that co-evolved with their host. For years, human bacterial gut community have dominated research focus, but recently bacteriophages (viruses infecting bacteria) have been shown to play a vital role in whole community interaction and control. We currently have scant knowledge of the composition or life histories of this portion of the microbiota, especially in non-human organisms. Despite the high ecological and socio-economic value of fish, their gastro-intestinal microbiota, vital to the healthy function of the organism, has received relatively little research interest. Bettarel et al. (2018) aimed to change this, and set out to examine the ecological features of viruses present in the gut microbiome of an extreme euryhaline Tilapia: Sarotherodon melanotheron. 

Adult Tilapia were sampled from sites with a range of pollutant concentrations in Senegal, and gut contents were collected. Epifluorescence microscopy was used to quantify bacteria and viruses present; this was compared to numbers in the environment. Viral morphotypes were observed using transmission electron microscopy. The proportion of lysogenic bacteria was also evaluated using a method that manually initiates prophage induction and thus the bacterial lytic cycle, though addition of Mitomycin C (Jiang and Paul, 1996).

This study was the first to report viral abundances in the fish gut, and indeed the community was diverse, abundant (0.2–10.7 x 10⁹ viruses ml^-1), and comparable to the human gut. The positive correlation between bacterial and viral abundance suggests viral community was dominated by phages, with an association with the dominant bacterial groups present: Firmicutes, Proteobacteria, and Bacteriodetes. These major members are similar to the human gut microbiome, supporting the paradigm that a core community is needed to ensure efficiency of primary gut function. The rest of the microbiome may be more species-specific to cope with variable diet. 

A large proportion (8.1%-33%) of the gut samples consisted of lysogenised bacterial cells (bacterial cells with an integrated viral prophage in the genome), significantly higher than the environmental counterparts. Lysogeny, the non-destructive method of viral reproduction, is usually considered a refuge strategy for viruses in suboptimal environments; for example, when bacterial abundance is low or has compromised metabolism. However, the environment here had a relatively low bacteria : virus ratio due to quickly proliferating bacterial cells, suggesting that a new model, “piggybacking-the-winner”, may be more apt. In this, lysogeny is an advantageous strategy: it can provide immunity against viral sub-infections and improve acquisition of optimal survival genes. Bacterial homeostasis in the gut community is likely to be maintained by having a temperate phageome.

Pollutant concentrations were correlated with the fraction of lysogenised cells, showing that pollutants may be significant in governing the internal microbe-microbe interactions, and so the health of the organism. The physiological stress of their presence could have triggered lysogenic pathways, affecting the balance of temperate and virulent viruses in the gut microbiome, compromising the carefully balanced equilibrium.

This study not only sheds light on a little known portion of an important microbial system, but also provides further stock to the “piggybacking-the-winner” strategy. The notion that processes can have multiple uses within different ecological contexts is an important one, and one which incurs curiosity in every instance: more research into this will undoubtedly lead to exciting discoveries!

Reviewed paper: 

Bettarel, Y., Combe, M., Adingra, A., Ndiaye, A., Bouvier, T., Panfili, J., & Durand, J. D. (2018). Hordes of Phages in the Gut of the Tilapia Sarotherodon melanotheron. Scientific reports, 8. 

Referenced paper:

Jiang, S. C., & Paul, J. H. (1996). Occurrence of lysogenic bacteria in marine microbial communities as determined by prophage induction. Marine Ecology Progress Series, 142, 27-38.

Marine Biofilms – platforms on a give-and take basis

Over the past years an important focus in the field of marine microbial ecology has been the study of marine biofilms. These multi-cultural communities adhered to surfaces are beneficial for their members. Embedded in a self-produced matrix consisting of extracellular polymeric substances the microbes profit from a stable and more stress-resistant environment (Xavier and Foster, 2007).

In 2018 an article was published by a group of French marine microbiologists. The main aim of the study was to get a better insight in marine biofilms. They wanted to distinguish the key members of these communities, their interactions and any dynamical changes regarding the composition and abundance.

The study was conducted in a Mediterranean bay in France over a period of 75 days.

Plastic panels were used as substrates. You may wonder why scientists would do research on biofilms? Throughout your course of studies you probably have learned about this topic. But the scientist questioned previous studies. Earlier investigations do not show the actual diversity of the marine microbial communities because of the chosen primers. Previous primer sets exhibit small coverage ranges for bacterial communities and even smaller or no coverage for Archaea. So in fact little is known about the true life of these communities.

The researches underline that the choice of primers should not be underestimated. To obtain correct data with high resolution and high accuracy, suitable primer sets should be used.

The study stands out by a multiple use of scientific approaches. With the help of computer software the most suitable primer was found, covering 88% of main bacterial groups and 83% of main Archaea groups. 16S rRNA sequence analyses were undertaken with the generalist primer. Additionally flow cytometry, network and cluster testing was applied. The gene comparisons allowed the researches to identify 7012 OTUs in total indicating the impressive diversity of biofilms. The pioneer communities, so the first microbes growing on the plastic panel, were mainly Gamma-proteobacteria. Archaea did not really grow in these microbial communities (only <0.4%).

With the most abundant OTUs cluster analyses were conducted showing strong changes in the composition of the communities. Biofilms are highly dynamic, expressed by rapid changes in the abundance of bacterial taxa. 90 % of the taxonomic units were short lived. Alpha-proteobacteria and Flavobacteriia dominated the pioneer communities rapidly. Interesting is that even if there are some negative interactions, biofilms do not exist because of competitive reasons between microbes but mainly because of intra-and interspecific cooperation. I would describe it as a platform on a give-and take basis, where everyone can share and provide something and profit in return by others. Another key finding of the study was that environmental conditions influence the dynamics in biofilms more than previously thought. Temperature as a physical variable has the strongest impact, silicate the lowest. 

Conclusion

The presented study gave a new insight in the world of marine microbial communities showing that things aren’t always as simple as we might think. The level of diversity and interactions hardly can be imagined in its entirety. An important head finding is that Flavobacteriia might play one of the main roles in the functioning of these marine ecosystems.

Article Reviewed:

Pollet, T., Berdjeb, L., Garnier, C., Durrieu, G., Le Poupon, C., Misson, B., & Jean-François, B. (2018). Prokaryotic community successions and interactions in marine biofilms: the key role of Flavobacteriia. FEMS microbiology ecology, 94(6), fiy083.

Reference: 
Xavier, J. B., & Foster, K. R. (2007). Cooperation and conflict in microbial biofilms. Proceedings of the National Academy of Sciences, 104(3), 876-881.