It’s complicated – microbial hydrocarbon degradation in sandy soils based on contamination history

Anthropogenic chemicals like polycyclic aromatic hydrocarbons (PAH) require quick removal from contaminated ecosystems. Therefore, it is crucial to investigate microbial community compositions of contaminated ecosystems to identify microbes with biodegrading capabilities for bioremediation.

Schwarz et al. (2018) predicted contamination responsiveness based on community structure in (shallow/deep) pristine and previously contaminated soil before adding phenanthrene as a proxy for PAH contamination. DNA and RNA stable isotope probing (SIP) was used in combination with temperature gradient electrophoresis to identify hydrocarbon-degrading microbes and assess community structures based on the 16S rRNA gene and the fungal ITS region. 

Fungal and bacterial baseline communities were similar across all sample types and included prominent hydrocarbon-degrading species in both soil types. Incubation with phenanthrene caused a decrease in fungal and bacterial diversity and evenness, leading to increased functional organisation. As expected, SIP identified several bacterial Gammaproteobacteria and fungal Basidiomycota as key degraders. Additionally, fungal community profiles of the samples with the highest degradation rates, deep pristine and shallow contaminated, were very similar in contrast to bacterial communities. Therefore, high degradation seemed to be neither related to contamination history, nor sample depth, indicating a more complex underlying causality than just microbial community structure, including an adaptable fungal community.

Schwarz, A., Adetutu, E. M., Juhasz, A. L., Aburto-Medina, A., Ball, A. S., & Shahsavari, E. (2018). Microbial Degradation of Phenanthrene in Pristine and Contaminated Sandy Soils. Microbial Ecology, 75(4), 888–902. https://doi.org/10.1007/s00248-017-1094-8

Host-specific and environmental influences of the gill microbiome.

The Teleost gill is an important colonising site for microbial organisms. However, little is understood about these communities and how host and environmental factors influence their structure and diversity.

Pratte et al. (2018) assessed similarities and variations in gill microbiome between host and environmental microbiomes across 15 fish families with varying diets and age. The study sequenced the V3-V4 region of the 16S rRNA gene before PCR amplification, clustering all microbiome sequences into OTU’s of 97% similarity.

The study highlighted evidence of Gill microbiomes jointly influenced by environmental microbes and host-specific factors. Environmental samples accounted for 75% of the gill microbiome OTU structure with few gill niche-specific bacterial genera Shewanella and family endozoicimonaceae. Host-specific analysis revealed a shared organising factor between individuals gill and intestine microbiomes and variations in microbiome compositions with host diet and age.

Overall, whilst the study gave evidence of factors influencing the gill microbiome of reef fish, building on an area of poor understanding, it seems to question why such factors would influence the gill microbiome, delving beyond the studies’ reach. Finally, I believe future studies could look further into the residency and characterisation of these host-specific and environmental microbes in the gill microbiome.

Pratte, Z. A., Besson, M., Hollman, R. D., & Stewart, F. J. (2018). The gills of reef fish support a distinct microbiome influenced by host-specific factors. Applied and Environmental Microbiology., 84(9), e00063-18.

Is jellyfish mucus spreading pathogenic disease?

The warmer waters during summer allow jellyfish populations to bloom, and with them may come a greater risk of disease. Through a combination of culture-based and molecular techniques Basso, et al. (2019) investigated the microbiome within various regions; mucus secretion, umbrella and arms, of the jellyfish species, Rhizostoma pulmo. This paper highlighted that each region has its own bacterial community. Notably, the mucus provides a substrate for a particularly diverse and rich array of bacteria. However, within these communities several pathogenic genera of bacteria were found, including Vibrio, Coxiella and Tenacibaculum.

As a planktonic species, R. pulmo secrete mucus whilst they passively drift through their surroundings. This means they can potentially inoculate large areas of water, acting as mobile vectors for bacterial pathogens. With climate change leading to rising water temperatures, could a resulting increase in jellyfish populations lead to greater outbreaks of disease?

Furthermore, whilst the study focuses on the potential hazard this poses, I feel it also calls into question whether other cnidarian species, with different mucus compositions, harbour their own unique microbiomes. If this is the case, then outbreaks of certain species could potentially act as indicators for the increased presence of certain pathogens within the environment.

Basso, L., Rizzo, L. , Marzano, M., Intranuovo, M., Fosso, B., Pesole, G., Piraino, S.,  Stabili, L. (2019). Jellyfish summer outbreaks as bacterial vectors and potential hazards for marine animals and humans health? The case of Rhizostoma pulmo (Scyphozoa, Cnidaria). Science of the Total Environment, 692, 305–318.

What lurks in ships’ ballast?

Plastics and microplastics are ubiquitous in the oceans and provide both a substratum and

substrate for microbes.  Plastics adsorb and concentrate metals and toxic chemicals

(including antibiotics) by a factor up to 10⁶.  It has been shown that co- and cross-resistance

result in co-selection, meaning that exposure to one metal/toxin/antibiotic can result in the rapid evolution of microbial tolerance or resistance to multiple others.

This review highlights microplastics in ballast water as a source and vector for toxic compounds.  The transport of pathogens between continents is concerning and we know, for example, that Vibrio cholerae was dispersed in ballast water from Asia to Latin America. Biofilm formers do well on internal tank surfaces so it is reasonable to propose that may also be true for microplastic particles.  Ships’ ballast tanks are closed systems within which microbes are exposed to a cocktail of toxic compounds and it is plausible that this environment could significantly increase pathogen virulence. 

However, the key limitation in the paper is that we do not yet have evidence to show that microplastics in ballast increase microbial virulence.  Therefore the authors’ call to amend the Ballast Water Management Convention seems premature, but certainly more urgent research is needed.  

NAIK, R. K. et al. 2019. Microplastics in ballast water as an emerging source and vector for harmful chemicals, antibiotics, metals, bacterial pathogens and HAB species: A potential risk to the marine environment and human health. Marine pollution bulletin, 149, 110525.

The microbiomes of hungry perch

Microbes within the gut help with digestion, metabolism and defending against pathogens.  Fish are no exceptions when it comes to gut microbiomes however compared to humans, ruminants and arthropods they are relatively understudied.  In other organism’s stress has been shown to change gut microbial composition so Zha et al. (2018) set out to look at the changes in Eurasian perch, when predators are present and when food is scares. 

Fish were given varying quantities of food and were separated into tanks with the presence of predator behind a barrier or without.  The V4 region of the 16S rRNA was amplified from the entire intestine using PCR then sequenced and grouped into OUT’s of >97% similarity.

The presence of pike did not affect most of the microbes found but instead food stress was the important factor.  The microbes showing the most difference are Tenericutes and Fusobacteria with an increase and decrease respectively as food levels increase. This suggests that Fusobacteria may be used as an indicator for individuals under stress as they have significantly lower levels.  Further studies could look at the effect that Fusobacteria has on the individual and why levels decrease in times of food stress.

Zha, Y., Eiler, S., Johansson, F., Svanbak, R. (2018). Effects of predation stress and food ration on perch gut microbiota. Microbiome, 6.

https://doi.org/10.1186/s40168-018-0400-0

Plastic debris is creating superbugs!

Microplastics, metals and antibiotics are ubiquitous, accumulating contaminants inflicting adverse impacts on aquatic ecosystems. But how do these pollutants all link? Yang et al. (2019) proposed that the marine plastics act as a reservoir for metal resistance genes (MRGs) and antibiotic resistance genes (ARGs), as they become vectors for pollutants and bacteria, promoting resistance and increasing the exchange of genes. 

Using metagenomic data for microbial communities on plastic debris found in the North Pacific Gyre, the abundance and diversity of ARGs and MRGs in bacterial taxa on plastics was determined. The presence of ARGs and MRGs occurred on all plastic samples, with greater diversity of ARG and MRG subtypes in the plastic biota. The genes identified provided resistance to 13 different antibiotics and 11 metals, far fewer subtypes were found in seawater controls. Non-random co-occurrence patterns of resistance genes was observed, MRGs and ARGs are co-selected as they share regulation factors and can be co-transferred. 

This paper highlights the contribution of marine plastic pollution to increasing the occurrence, diversity and spread of antibiotic resistance, the wider significance being that anthropogenic pollution is promoting the spread of multi-drug resistance amongst bacteria, hence will inevitably accelerate the day when antibiotics become ineffective.

Yang, Y., Liu, G., Song, W., Ye, C., Lin, H., Li, Z., & Liu, W. (2019). Plastics in the marine environment are reservoirs for antibiotic and metal resistance genes. Environment international, 123, 79-86.

Oil dispersant, too good to be true?

Effects of oil spills and chemical dispersant on deep-water shipwrecks and their associated microorganisms are largely unknown. Salerno et al. (2018) investigated this by using bioinformatic analysis of sequenced 16S rRNA gene amplicons to study biofilm growth on Carbon steel disks (CSD).  Investigating the impacts of oil and dispersant when present. Metal corrosion of these disks was characterised using ESEM and EDS. Oil-dispersant and oil treated CSDs were shown to have roughly twice the number of hydrocarbon-degraders compared to the control. Corrosion in these treatments was also greater due to presence of bacteria used in bioremediation from the Pseudomonas genus which can also produce hydrogen sulfide.

Other studies have shown that biofilms in the presence of dispersed oil have elevated amounts of stress response genes and greater growth rates. This indicates a community response under adverse conditions causing biofilms to thrive. However, this study shows although there may be proliferation of biofilms, residue oil effects are severe compromising shipwrecks as habitats due to increased corrosion, and disrupting community compositions, putting into question the effectiveness of dispersants. One criticism of this study is their use of only one metal alloy as an artificial habitat as different shipwrecks can be made of varying metals so levels of corrosion and colonisation may vary.

Salerno J.L., Little B., Lee J., Hamdan J.L., (2018) Exposure to Crude Oil and Chemical Dispersant May Impact Marine Microbial Biofilm Composition and Steel Corrosion.  Frontiers in Marine Science.5. doi:10.3389/fmars.2018.00196

The curious diet of deep sea archaea

Hydrocarbon gas seeps on the ocean floor release several alkane gases, amongst these is ethane. This gas can contribute to the greenhouse effect but only a small proportion released reaches the atmosphere due to consumption by microorganisms. Little is understood about the deep sea microorganisms which catalyse the breakdown and consumption of this gas or how by the process of anaerobic oxidation this reaction occurs.

Chen et al. (2019) conducted a 10-year study to investigate the microorganisms capable of processing and consuming ethane. In doing so, a vast array of molecular analysis was used (including CARD-FISH and nanoSIMS) to determine the species responsible for the process. They discovered and identified a new species of anaerobic methanotrophic archaea which they called Candidatus Argoarchaeum ethanivorans. This archaea species works in a syntrophic relationship with sulphate reducing Deltaproteobacteria to consume the ethane.

In this study, they did not culture the archaea which proved the ability to study in-depth microbes without the need to culture them. Additionally, this study echoes the importance of understanding the processes of the deep ocean as these microbes reduce the potential effect of this greenhouse gas which can become an asset to use in the future.

Chen, S.C., Musat, N., Lechtenfeld, O.J., Paschke, H., Schmidt, M., Said, N., Popp, D., Calabrese, F., Stryhanyuk, H., Jaekel, U. and Zhu, Y.G. (2019). Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep. Nature, 568(7750), 108.

A look into the future- how increasing temperatures could affect organisms

The marine Roseobacter clade is an abundant heterotrophic bacterial group and plays an important role in marine communities. Kent et al. (2018) used Roseovarius sp. strain TM1035 and looked at the capacity and ecological implications of adaption to warmer ocean environments. This was done by running fitness and physiological assays to look at how stressful, high-temperature regimes would affect 500 generations of this strain. 

This study found that isolates which adapted to the high-temperature significantly improved their fitness and increased biofilm formation. Through extracting and sequencing the DNA, they identified genomic variation underlying high-temperature adaptation with more mutations occurring in the high versus low temperature lines. Results show a clear capacity for rapid adaption to elevated temperature through a significant lifestyle change. It would be interesting to see how the short-term rapid adaptive changes may differ from long-term establishments of distinct ecotypes adapted to higher temperatures. These changes may be different from the predictions assumed in this paper so would be interesting to look at. Overall, this study has helped us understand how increasing future temperatures could affect organismal physiology and how it could lead to an alteration in microbial lifestyle.

Kent, A.G., Garcia, C.A. and Martiny, A.C., 2018. Increased biofilm formation due to high-temperature adaptation in marine Roseobacter. Nature microbiology, 3(9), p.989.

Can microbes fly? Experimental viral and bacterial aerosolization

Bacterial and viral aerosolization influences atmospheric processes and the spread of harmful microbes. Sea spray aerosol (SSA) contributes to microbial aerosolization through bubble bursting in the sea surface microlayer (SML). However, taxa with the ability to become airborne as well as their environmental influence factors have not accurately been identified so far.

Michaud et al. (2018) addressed this gap by using a custom ocean-atmosphere facility simulating a natural ecosystem. They assessed viral and bacterial abundance and community structures in subsurface water, SML and SSA using metagenomic approaches during an induced phytoplankton bloom. They identified several bacterial taxa with high aerosolization ability and a conservation of this ability within taxonomic orders and classes. In contrast, viruses were less able to aerosolize and highly influenced by changing environmental factors. In both, bacteria and viruses, they also found several mechanisms promoting aerosolization, many of which involved increased hydrophobicity. Even though the experimental setup is still limited due to the absence of several abiotic and biotic factors, like diurnal light conditions and predation, and sampling difficulties in the SSA, it is still unprecedented in its accuracy of the simulation of this unique ecosystem and forms a baseline that future studies can build on.

Michaud, J. M., Thompson, L. R., Kaul, D., Espinoza, J. L., Alexander Richter, R., Xu, Z. Z., … Prather, K. A. (2018). Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm. Nature Communications, Vol. 9. https://doi.org/10.1038/s41467-018-04409-z

The Advantageous Microbiome of a Celebrity Cichlid

Access to resources enjoyed by dominant animals within a social hierarchy leads to distinct behavioural and physiological changes. This induces dynamic, population-level shifts in microbiome composition, mediated by the presence of certain bacterial clades. Singh et al. (2019) performed bioinformatic analysis of 16S rDNA sequences from faecal samples to examine if the social hierarchy in the cichlid fish, Astatotilapia burtoni, influences their gut microbiome. At high social rank, gut microbial diversity and the abundance of beneficial microbial clades increased, stabilizing the community by broadening available niche space. In subordinate animals, an increase in pathogen load, specifically Enterobacteriaceae, was seen, resulting in a loss of microbial community diversity.

The fish microbiome has been shown to direct the development and function of host neural, endocrine and immune systems and is considered vital to maintaining host physiological and metabolic homeostasis, highlighting the importance to integrate microbiome derived physiological effects into future studies of behaviour. In this study, the OTU number was lower than those in similar studies that directly sampled gut tissue, indicating that non-invasive faecal samples cannot provide a complete synopsis of gut microbiota. This may explain why Firmicutesand Verrucomicrobia were absent here, yet found to be part of the core gut microbiome in similar cichlid studies.

Singh, A., Hammond, J. J. F., O'Rourke, C. F., & Renn, S. C. (2019). Gut microbial diversity increases with social rank in the African cichlid fish, Astatotilapia burtoni. Animal Behaviour, 152, 79-91. This article can be found at: https://www.sciencedirect.com/science/article/pii/S0003347219301125

Carnivorous plants of the deep

The discovery of living phytoplankton at 4000 m depth during the Malaspina expedition raised new questions about phytoplankton ecology. Guo et al. (2018) found some answers by literally digging deeper: they sampled pico- and nanophytoplankton (PN) from the Mariana Trench up to a depth of 8320 m. PN were identified using the V1-V3 region of the 18S rRNA gene (for eukaryotes) and the plastid 23S rRNA gene (mainly for bacteria). Overall PN diversity was virtually constant between 4 and 8320 m. Dominant OTUs across all depths belonged to the phylum Dinoflagellata and family Prochloraceae. Interestingly, dominant eukaryotic PN at 8320 m belonged to the classes Chrysophyceae and Eustigmatophyceae, which are known to be capable of heterotrophy.

This study significantly increased our knowledge on deep sea plant communities. Nonetheless, it remains to be seen whether the main metabolic pathway of deep PN is heterotrophy. Other explanations for deep PN may be that they survive as resting cysts or sink more quickly than previously thought. However, the latter is unlikely because Guo et al. (2018) showed that there are characteristic deep PN communities. Either way, future research in this field will have profound implications for our understanding of the oceanic carbon cycle!

Guo, R., Liang, Y., Xin, Y., Wang, L., Cao, C., Xie, R., Zhang, C., Tian, J. & Zhang, Y. (2018). Insight into the pico- and nano-phytoplankton communities in the deepest biosphere, the Mariana Trench. Frontiers in Microbiology, 9, 2289.

Are fish and bacteria like Fred and Barney?

Dissolved organic carbon (DOC) is receiving increasing research interest because of its contribution to carbon sequestration (CS). Microbes enhance CS through primary production and the microbial carbon pump (i.e. transformation of bioavailable into persistent DOC). In a mesocosm experiment, Limberger et al. (2019) found that sticklebacks increase microbial production and reprocessing of DOC. This idea was supported by positive effects on the biomass of phytoplankton and the bacterial classes Cytophagia and Alphaproteobacteria, which are competent degraders. Chlorophyll-a was used as a proxy for phytoplankton biomass. Bacteria were counted using flowcytometry and identified through Illumina sequencing of the 16S rRNA gene’s V3 region. Freshness of DOC was estimated using spectrophotometry.

This research presents the possibility for trophic cascades to increase microbial biomass, which in turn affects the composition of the DOC pool. In other words, predation may be important in the global carbon cycle. However, it is questionable whether the results are meaningful for global CS. Firstly, Limberger et al. (2019) only studied one species, from which it is difficult to make predictions about fish in general. Secondly, there was actually no measurable increase in DOC in the presence of fish (only the freshness of DOC was significantly higher)!  

Limberger, R., Birtel, J., Peter, H., Catalán, N., da Silva Farias, D., Best, R. J., Brodersen, J., Bürgmann, H. & Matthews, B. (2019). Predator‐induced changes in dissolved organic carbon dynamics. Oikos, 128(3), 430-440.

Microplastic-colonizing communities like everything to be just right, when deciding to settle down

The global distribution of microplastics in the marine environment has been of popular interest to the scientific community recently and it is now apparent that biogeography plays an important role for the composition of microplastic colonizing communities. In a two week, in situ incubation experiment, Oberbeckmann et al. (2018) investigated how the composition and specificity of bacterial communities that colonise on natural and synthetic substances differ along an environmental gradient in the Baltic Sea. Plastic-specific assemblages were found via high-throughput sequencing, developing solely under certain conditions, including lower nutrient concentrations and higher salinities. One genus that was more abundant on plastic in areas of increased nutrients than on any other material tested was Sphingomonadaceae, which is known to be a reservoir for antibiotic-resistance. 

This study provides evidence that microplastic specific marine microbiomes exist and are dependent on ambient environmental conditions. This has ecological significance, particularly in microplastic-associated bacterial populations in plastic accumulation zones, as the potential for microplastics to be a hotspot for the transport and transfer of antibiotic resistance has not been investigated as of yet, and may be of great importance. One shortcoming of this study was that data to assess both communities (free living and attached) was only collected at a two-week timepoint; there was no measure of what happened during the initial few hours or days, which previous research suggests it is important in subsequent community recruitment.

Oberbeckmann, S., Kreikemeyer, B., & Labrenz, M. (2018). Environmental factors support the formation of specific bacterial assemblages on microplastics. Frontiers in microbiology, 8, 2709. This article can be found at: https://www.frontiersin.org/articles/10.3389/fmicb.2017.02709/full

I like you but not you – The microbiome of Ircinia campana

Sponges such as Ircinia campana are hosts to large communities of microorganisms that influence and maintain the hosts health, physiology and development. The microbiome of a sponge is complex and numerous with most containing around 52 bacterial phyla alone. 

The study by Griffiths et al. (2019) focused on how the genotype and location of I. campana effects their microbiome, by assigning OTUs following a PCR.

Results showed, that individuals had several thousand OTUs, with a significant difference in microbiome by location and individuals’ genetic distance.

Two transmission methods are hypothesised to be the reason, one parentally passed on microbes, the other taking up the community directly from the surrounding seawater. 

The study provides interesting insights into the conservation efforts necessary and gives a baseline for further studies, especially ones to assist in the dealing with climate change. Different microbial communities could assist in better adaptation for future conditions such as increased temperature and ocean acidification. Additionally, the sponge microbiome can be useful to us humans too. Some microbes produce secondary metabolites that can be used in pharmaceuticals, by understanding which microbes have which role in the complex system scientist could use it to provide a better medical care. 

Grittiths, S., Antwis R., Lenzi, L., Lucaci, A., Behringer, D., Butler IV, Mark., Preziosi, R. (2019) Host genetics and geography influence microbiome composition in the sponge Ircinia campana. Journal of Animal Ecology  

Karenia brevis: marine microbes to the rescue?

Colloquially referred to as “red tides”, Karenia brevis is a harmful dinoflagellate whose blooms contain brevetoxin. Brevetoxin disrupts sodium channels and affects neurotransmission, it is powerful enough to cause serious symptoms in humans.

Three fluorescently labelled conjugates of brevetoxin were used to study how the toxin was taken up by various microbial groups. Successful uptake of conjugates was demonstrated by intracellular fluorescence in a diverse array of microbes; diatoms, dinoflagellates, haptophytes, rotifers, cryptophytes and ciliates.

This study is unique in its attempt to ascertain whether specific microbial species’ could be utilised during Karenia brevis blooms to act as a biological sink for the algal toxin. As the work is the first of its kind it must serve as a building block for any future study, the conjugates they used were modified and results cannot be fully recognised to work for parent metabolites in the field until more research is completed. Future studies would do well to elucidate which microbes are best suited as biological sinks, as sequestration mechanisms had much variation. Whilst microbes are seemingly capable of taking up brevetoxin, questions remain about the long-term implications regarding the bioaccumulation of toxins as a result.

Kramer, B.J., Bourdelais, A.J., Kitchen, S.A., Taylor, A.R. (2019) Uptake and localization of fluorescently-labelled Karenia brevis metabolites in non-toxic marine microbial taxa. Phycological Society of America, 55, 47-59.
https://onlinelibrary.wiley.com/doi/full/10.1111/jpy.12787

Conforming corals and their cantankerous cousins

This study builds on the idea of a coral holobiont, and suggests that some species of coral may display a type of plasticity to environmental changes by modifying their microbiome; this could be beneficial to survival faced with anthropogenic pressure.

The microbiomes of two species of coral (Acropora hemprichii and Pocillopora verrucosa) were sequenced during a reciprocal transplantation experiment across 5 sites with varying levels of anthropogenic impact. P. verrucosa showed a fairly consistent microbiome, whereas A. hemprichii showed variation. This lead to the proposal of microbiome “conformers and regulators”. Conformers change their microbiome with their environment, whereas regulators maintain their microbiome regardless of their environment.

This paper concludes by suggesting conformers like A. hemprichii will be better able to cope with environmental change. Whilst it acknowledges that more research is required to confirm this, I am not convinced by this conclusions validity.

Whilst the paper mentions that A. hemprichii had more microbes associated with disease, it does not discuss how, by taking up different microbes, conformers could be increasing their risk of disease, which could negate any benefits their ability to adjust to environmental change might have. The conclusions would have been more robust if some measure of mortality of the two species was included.

Reference: Ziegler M, Grupstra C, Barreto M, Eaton M, BaOmar J, Zubier K, Al-Sofyani A, Turki A,Ormond R, Voolstra C, (2019), Coral bacterial community structure responds to environmental change in a host-specific manner, nature communications, https://doi.org/10.1038/s41467-019-10969-5

Polar microbial responses to man-made DOC.

Anthropogenic dissolved organic carbon (ADOC) is composed of thousands of organic pollutants from hydrocarbon emissions and synthetic compounds. Yet its effects on marine microbial communities has barely been assessed.

The study investigated responses in Arctic and Antarctic coastal bacterial communities to ADOC concentrations over a 24hr period. Using methods such as CARD-FISH, Flow cytometry, High-throughput sequencing and Bioinformatics, Cerro-Gálvez et al (2019) assessed cell abundance, community composition, gene frequencies and transcriptional responses to ADOC exposures.

ADOC had no effect on community structure however, increased the abundance of rare biosphere bacteria, such as Nocardioides sp. (Arctic), Psuedomonas sp. (Antarctica) associated with hydrocarbon degradation. Gene frequencies and transcriptional activity revealed increased transcriptional activity of ubiquitous Flavobacteria in both communities to ADOC. ADOC further enriched Transcripts in cell function and protein coding, differing between polar communities. Gene expressions, revealed cellular adaptations and detoxifying mechanisms in some bacterial communities, assumed to detoxify ADOC concentrations.

The paper highlights change in community composition, transcriptional response and detoxifying mechanisms under ADOC. However, it gives an important contribution to the responses and impacts associated with ADOC expressing changes in polar bacterial communities, before emphasising the importance for further studies of ADOC on microbial communities in oceanic ecosystems.

Cerro‐Gálvez, E., Casal, P., Lundin, D., Piña, B., Pinhassi, J., Dachs, J., & Vila‐Costa, M. (2019). Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters. Environmental microbiology, 21(4), 1466-1481.

Poorly protists and their viral infections

Little was known about marine viruses until the last decade as viral metagenomics improved allowing us to study their diversity and biogeography. However, the interaction between host and virus is still under studied, especially the interaction of viral infections on protists.  Using single cell genomics Castillo Y.M. et al. (2019) used un-cultured stramenopiles, collected by the Tara Oceans expedition, to carry out viral sequencing and analyse the virophages found.

Around 1-3 viral contigs were found in 37 of the 64 cells sequenced, showing that protists cells do contain viruses but the association between the host cell and virus was unable to be identified.  These viruses may have been engulfed by the cell, permanently part of the genome or be replicating within the cell.  >95% of viral sequences identified were found in only one stramenopile lineage with only 3 shared between lineages.  This suggests that viruses infecting protists are more specialist than those infecting eukaryotes when you compare with previous studies.

I think this study gives an important stepping-stone into viral-protist relationships and creates some base knowledge for further research on the interactions and importance of viruses within protist cells.

Castillo, Y. M., Mangot, J.F., Benites, L.F., Logares, R., Kuronishi, M., Ogata, H., Jaillon, O., Massana, R., Sebastian, M., Vaque, D. (2019). Assessing the viral content of uncultured picoeukaryotes in the global-ocean by single cell genomics. Molecular ecology, 28(28), 4272-4289

https://doi.org/10.1111/mec.15210 

The effect of stress on survival and bioluminescence

This study investigates how increased stress affects the fitness of free-living microorganisms and the knock-on effect as they colonise and perform in a host. Vibrionaceae were tested as they are interesting within the context of climate change as they are sensitive to temperature changes, and are able to invade harsh environments, both features connected with climate change.

Cohen et al (2018) used the same strain of marine bioluminescent bacterium Vibrio fischeri (ET00-7-1) to investigate this question exposing Vibrio fischeri to either different or fluctuating temperatures. Strain fitness was compared to ancestors (un-evolved line), distinguishing the two with the use of “neutral markers”. In both free-living (fitness) and host-associated life (bioluminescence and ability to colonise) there were significant increases in ability under stress (heat specialists>temp generalists>cold specialists>ancestors).

This is interesting as many species of Vibrionaceae are pathogenic such as Vibrio cholerae, so temperature increase may not only increase their spread and ability to colonise but also increase their virulence. However, there has been evidence that extreme temperatures effect the ability of microorganisms to engage with hosts, partially because of the effect on gene expression so this may lead to reduction in ability to colonise a host.

Cohen L.M., Mashanova V.E., Rosen M.N., Soto W. (2019) Adaptation to temperature stress by Vibrio fischeri facilitates this microbe’s symbiosis with the Hawaiian bobtail squid (Euprymna scolopes). EVOLUTION. 73, 1885-1897.

Can picky protists help control an algal bloom?

Mixotrophic dinoflagellates (MTDs) are a major constituent of the microbial food web, but also play a huge role in the outbreak of red-tide events. Our understanding of the microbial mechanisms behind these red-tide outbreaks can be aided by studying top-down feeding on MTDs by their predators.


The growth rate and feeding preferences of Favella ehrenbergii, a Tintinnid ciliate, were studied by Yang et al. (2019) in both single and mixed prey conditions. Two MTDs; Scrippsiella trochoidea and Heterocapsa triquetra, were used as prey in the lab over 48hrs. No flashy, modern molecular techniques here- a seemingly well thought out methodology, microscopy work and mathematics enabled the estimation of growth rates, and subsequently prey preferences.


In short, Tintinnids achieve a higher growth rate when fed mixed diets compared to a monodiet and switch their feeding preferences to other species when mixed prey is available. This is likely due to their desire to consume fatty acids available from different MTDs and will undoubtedly affect the top-down control of MTDs.


Relevant to microbial trophic ecology, Yang and colleagues highlight an important link to potentially harmful red-tide events. Despite this, I do wonder how a small scale lab experiment can be applied to such a large scale phenomenon, making me think the authors’ claims that this research could help ‘predict’ red-tide outbreaks seems a bit far-fetched! No doubt though that this work will contribute to the understanding of red-tide MTD ecology and provide further knowledge of important microbial food webs.



Yang, J., Löder, M. G. J., Jiang, Y., & Wiltshire, K. H. (2019). Are tintinnids picky grazers: Feeding experiments on a mixture of mixotrophic dinoflagellates and implications for red tide dynamics. Marine pollution bulletin, 149, 110488.

Deep sea microbial variety, litterally

What microbial assemblages exist on deep sea anthropogenic litter?  This study collected 12 items and two sediment cores in the equatorial Atlantic including plastic, fabric, glass, rubber and metal.  Some 30,000 bacterial and archaeal 16S rRNA V4 sequences were identified and communities compared using PRIMER.

Each type of material showed that a large number of taxa were unique to that material, with only 3% of OTUs common to all. This suggests that each material type has different assemblages.  The diversity of prokaryotes on the metal substratum was much lower than other material and specialist iron-oxidising Zetaproteobacteria were present, a finding mirrored in studies of ferromanganese nodules. Length of time on the seabed and history since release were not known and could equally contribute to differences in biofilm community composition.

All litter types were colonised suggesting that the notion of a Plastisphere can be extended to a Litterosphere.  This is interesting work being the first attempt to answer this question. The inherent difficulty of sampling at deep remote locations means we will need more replication and samples to understand deep sea biofilms and the effect we are having on ecosystem processes.

Woodall L.C. et al. (2019). Deep-sea anthropogenic macrodebris harbours rich and diverse communities of bacteria and archaea. PLos One 13 (11), e0206220

Does the Plastisphere have a core?

Previous studies show that biofilm microbial communities are different to open seawater but do biofilm communities on different types of plastic differ from each other?  This study placed 9 types of plastic in dark, flowing seawater for 15 months then studied the results with SEM and 16S/18S sequencing. 

Prokaryote plastic communities were overall distinct from that in a glass control but were very similar to each other. However, the make-up of plastic communities were different enough to be significant, in most cases differing by just a handful of OTUs. The eukaryote plastic communities differed to a greater extent but this may reflect inherent heterogeneity rather than the physicochemical properties of each plastic, so the jury’s still out on eukaryotes. As the prokaryote sequence library only covered 86% of taxa it’s still possible that rare taxa exist which are specific to particular synthetic polymers, potentially including pathogens or potential plastic-destroyers.

So yes, this study supports the view that there is a core prokaryote plastic community, at least in mature, sheltered, dark conditions.  It would be interesting to know more about communities and succession in more energetic, irradiated ocean surface conditions where the life of most ocean plastic begins.

Kirstein, I. V., Wichels, A., Krohne, G., & Gerdts, G. (2018). Mature biofilm communities on synthetic polymers in seawater - Specific or general? Marine Environmental Research, 142, 147-154. doi:10.1016/j.marenvres.2018.09.028