Why might you want fungus in your skeleton?

Fungi grow epi- and endo-biontically in reef corals and some even bore into coral skeleton.  Goés-Neto et al. used 18S rRNA metabarcoding to identify endolithic fungi from 11 coral genera from around Australia and PNG.  At 97% similarity over 90% of OTUs were matched to reference sequences and FunGuild was used to classify OTUs by broad trophic mode.

Most OTUs were Ascomycota or Basidiomycota, a few of which had never been associated with corals before, and at least some of the 8% unassigned OTUs may be new to science. There was great diversity in fungal communities between coral taxa with Porites showing most fungal genera. Most fungal OTUs were, unsurprisingly, classed as saprotrophs, including the most common genera, Lulworthia and Lulwoana, which occur across a wide geographical range.  

This paper is valuable in revealing the fungi present within coral.  Sampling was, however, skewed towards Porites (17 of 25 samples); more balanced sampling may show greater diversity in other coral genera which were limited to one individual.  Other research has found fungal genes which reduce nitrate and assimilate ammonia suggesting fungi may have important nutrient recycling roles in oligotrophic oceans.  Further Metagenome/transcriptone work would be needed to illuminate detailed fungal functions.

GOÉS-NETO, A., MARCELINO, V. R., VERBRUGGEN, H., DA SILVA, F. F. & BADOTTI, F. Biodiversity of endolithic fungi in coral skeletons and other reef substrates revealed with 18S rDNA metabarcoding. Coral Reefs.

Lazy but efficient

According to the Black Queen Hypothesis (BQH), functions, which are essential, costly and leaky, bring about organisms that lose the encoding genes and profit from the work of others. To test whether the BQH applies to pesticide degradation, Billet et al. (2019) chose four genera of bacteria involved in atrazine degradation. The authors decided to perform culture-based experiments in addition to multiplex PCR. The loss of atrazine degrading genes after ~100 generations in cultures without atrazine established the high cost of expressing this function. In cultures with atrazine as the only nitrogen source, atrazine mineralisation became more efficient. Quantification of colony forming units in all possible combinations of co- and monocultures revealed strong dependence of three species on the fourth. Multiplex PCR further evidenced a loss of key genes in these species. Interestingly, one of the dependent species slightly buffered the negative impact on the public goods provider.

This study provides remarkable insight into microbial evolution and ecology within the conceptual framework of the BQH. The results suggest that microbial assemblages are more effective at degrading pesticides, even though one microbe does the bulk of the work. This insight has implications for the usage of microbes in bioremediation projects.

Billet, L., Devers, M., Rouard, N., Martin-Laurent, F. & Spor, A. (2019). Labour sharing promotes coexistence in atrazine degrading bacterial communities. Scientific Reports, 9(1), 18363.

Horizontally transmitted symbionts are also loyal partners

Because they are retained over several host generations, vertically transmitted symbionts are traditionally thought to be more genetically isolated than horizontally transmitted ones. Using metagenome sequencing, Romero Picazo et al. (2019) provided evidence for high genetic isolation between populations of sulfur- and methane-oxidising symbionts of Bathymodiolus brooksi living at cold seeps. Although both symbiont types are horizontally transferred, nucleotide diversity (π) and ɑ-diversity were found to be low. Furthermore, population isolation (F_ST) and β-diversity were high between mussel individuals. Where 1 indicates complete isolation, F_ST equalled 0.6 and 0.5 for sulfur- and methane-oxidising symbionts, respectively. Host and symbiont F_ST values were not correlated and neither were symbiont F_ST and geographical location. Consequently, these factors do not contribute to the observed genetic isolation.

This research suggests the possibility of marked population isolation in horizontally transmitted symbionts. The authors suggest that genetic isolation is maintained through self-infection of mussel individuals with symbionts. Faced with evidence of high symbiont geneflow in other Bathymodiolus spp. from hydrothermal vents, Romero Picazo et al. (2019) point towards the relatively low concentrations of symbionts in seawater at cold seeps. It seems that the spectrum of genetic isolation in horizontally transmitted symbiont populations is larger than previously thought.

Romero Picazo, D., Dagan, T., Ansorge, R., Petersen, J. N., Dubilier, N. & Kupczok, A. (2019). Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated. The ISME Journal, 13(12), 2954–2968.

Diverse symbionts may enhance survival in the deep sea

Symbiont intraspecific diversity is thought to be restricted in nature because hosts tend to select an optimal symbiont. Ansorge et al. (2019) showed that this does not hold true for Bathymodiolus spp. and their sulfur-oxidising symbionts at Mid-Atlantic Ridge hydrothermal vents. Metagenome sequencing revealed a high frequency of symbiont SNPs (5-11 per kilobase pair). More specifically, up to 16 strains were estimated per host. Intra- and interhost nucleotide diversity (π) was high but similar for each vent site. In addition to low within-site population isolation (F_ST) this indicated intermixing of symbiont strains between hosts. Metatranscriptome sequencing and direct-geneFISH revealed that only some strains, clustered in specific bacteriocytes, were able to perform hydrogen oxidation. Furthermore, the large variation in the ability to perform the various steps of nitrate respiration suggests labour division among strains.

This study infers that symbiont strain diversity may be widespread in nature, at least in low-cost associations where symbionts harvest energy from the environment. Benefits of high and intermixed strain diversity are (i) optimally adapted symbionts through natural selection, (ii) faster adaptation to new environments, (iii) labour division and (iv) resilience to disease. Perhaps the ecological meaning of host and ecosystem biodiversity is more similar after all?

Ansorge, R., Romano, S., Sayavedra, L., Porras, M. Á. G., Kupczok, A., Tegetmeyer, H. E., Dubilier, N. & Petersen, J. (2019). Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels. Nature Microbiology, 4(12), 2487-2497.

Backseat drivers: A symbiosis between magnetotactic bacteria and protists

Currently, no study has yet shown that microbial eukaryotes possess magnetotactic mechanisms. However, Monteil et al. (2019) revealed that, through a fascinating symbiosis, some protists are capable of indirectly utilising this ability.

Anoxic marine sediment samples taken from the Mediterranean, San Francisco Bay and New Zealand underwent magnetic enrichment. This resulted in the attraction of a group of flagellated protozoans, identified as Symbiontida. Upon closer inspection, their surfaces were found to be covered with magnetosome-containing Deltaproteobacteria – known as magnetotactic bacteria. Whilst magnetotactic bacteria are often classified as being motile, genomic analysis revealed that these lack genes coding for flagellar proteins or chemotaxis. A further phylogenetic tree analysis indicates that these two species have a congruent evolution and diversification. Through this coevolution and resulting mutualistic symbiosis, it seems that the bacteria have lost their own motility, with this instead being provided by the flagellated host protist. In turn, the protist ‘gains’ magnetotaxis from the ectosymbiotic bacteria, potentially improving their navigational abilities. Furthermore, they may benefit from syntrophy, transferring hydrogen-based products amongst themselves. This is an exceptional case of symbiosis allowing for eukaryotic magnetoreception, however, the mechanisms through which this occurs, and its potential benefits, remains to be explored in depth.

Monteil, C., Vallenet, D., Menguy, N., Benzerara, K., Barbe, V., Fouteau, S., & Cruaud, C., & Floriani, M., Viollier, E., Adryanczyk, G., Leonhardt, N., Faivre, D., Pignol, D., Lopez-Garcia, P., Weld, R., & Lefèvre, C. (2019). Ectosymbiotic bacteria at the origin of magnetoreception in a marine protist. Nature Microbiology, 4, 1088–1095.

Chytrids and what effects their transmission sucess

The understanding of parasite characteristics, their contribution to overall fitness and the influence of both the external and host environment is a poorly studied area but could play a dynamic role in predicting disease outcome. Agha et al., 2018, used transmission success as a proxy for fitness while studying the influence of life-history traits on the of chytrid parasites during infection of the cyanobacterium Planktothrix spp. Interestingly, due to the positive correlations between sporangial size and the numbers of contained zoospores,  was noted that chytrids are potentially able to exploit trade-offs between reproductive output and propagule longevity depending on the environment to maximise fitness. Overall the study found that transmission success in chytrids is the result of an interaction between individual traits and the host environment individually or connected with the external environment. Successful evasion of host barrier defences appears to be driven purely by the host environment. Alternatively, parasite fitness traits related to the efficiency of the extraction of nutrients are influenced by both the host environment and environmental interactions. In future, an understanding of these traits will lead to the development of a better understanding of individual infection mechanisms. 

Agha, R., Gross, A., Gerphagnon, M., Rohrlack, T. and Wolinska, J. (2018). Fitness and eco-physiological response of a chytrid fungal parasite infecting planktonic cyanobacteria to thermal and host genotype variation. Parasitology, 145(10), pp.1279-1286.

Gutless flatworm host unique chemosynthetic bacteria

The marine flatworm Paracatenula has an obligate symbiosis with Candidatus Riegeria, a chemoautotrophic bacterium, due to its lack of mouth and gut. Paracatenula is completely dependent on its intracellular endosymbiont for nutrition, this symbiosis has been vertically transmitted for around 500 million years resulting in a highly specialised relationship.

Using techniques including CARD-FISH, gene expression and image analysis, this study investigated the genome and mechanisms of Ca. Riegeria to elucidate the physiology and evolution of the symbiosis.

They found that Ca. R. has a genome about a third of the size of its free living relatives, this reduced genome included specialised energy efficient pathways for essential functions such as sulphide and carbon fixation which were linked to its Rhodospirillaceae ancestry. Ca. R. provides energy storage for the host flatworm, accounting for up to a third to half of Paracatenula’s biomass, unusually for a chemosynthetic symbiosis, nutrition is secreted to the host via outer membrane vesicle (OMV). 

This paper intricately and eloquently examined the relationship between Paracatenula and Ca. R., their findings were complex and interesting. Combining the results and discussion helped breakdown key findings and comment on individual facets of their work.

Jäckle, O., Seah, B.K.B., Tietjen, M., Leisch, N., Liebeke, M., Kleiner, M., Berg, J.S., Gruber-Vodicka, H.R. (2019) Chemosynthetic symbiont with a drastically reduced genome serves as primary energy storage in the marine flatworm Paracatenula. Proceedings of the National Academy of Sciences, 116(7), pp 8505-8514.

Glacier milk – fine sediment as bad news for virus community

Suspended sediment from melting glaciers in Arctic waters can overlap with phytoplankton, bacteria and viruses which can have consequences for trophic transfers and biogeochemical cycles. Through the increased turbidity, primary production can be reduced and grazing decreased due to ingestion of particles.

By taking sea water samples across 3 transects towards different glaciers Maat et al. (2019) investigated the effects of fine sediments on the microbial community. Increased sediment presence altered the turbidity and salinity thus negatively affecting phytoplankton growth, decreasing virus-bacteria interaction as well as the virus community, reducing host mortality. 

It is hypothesised that the reduced virus effect could stimulate trophic transfers and carbon export, however even the abundance of phytoplankton and bacteria decreased towards the glaciers.

Effects from the change in abundance are unstudied. An increase in carbon export could lead to higher carbon availability throughout the water column, the effect this might have on atmospheric carbon and climate change is however unknown. Additionally, the uncontrolled growth of phytoplankton and bacteria could lead to harmful blooms and bring risks to the wider food web and ecosystem balance. Further study is required to understand the impact of glacier melt on the microbial community and its wider reach.

Maat, D., Visser, R., Brussaard, C. (2019) Virus removal by glacier-derived suspended fine sediment in the Arctic. Journal of Experimental Marine Biology and Ecology, Vol. 521

Accessible through: https://doi.org/10.1016/j.jembe.2019.151227

Ignorantly ignoring bacterial biofilms

TARA oceans provided cutting edge open ocean (OO) microbial diversity data but ignores microbial biofilm diversity. To identify currently undetected members of the ocean microbiome and decipher their putative functions, Zhang et al. stimulated biofilm growth on artificial substrates at globally distributed locations and compared the 16S rRNA within the metagenomes of these to TARA OO metagenomes. Using artificial surfaces seems peculiar as these are unnatural in the ocean, and their justification for using these seems unclear. Despite this, they still identify a huge 6411 abundant biofilm specific OTUs (mostly bacteria), independent in taxonomy, and potentially their function, to OO OTUs. Conserved functional cores were apparent across all biofilms, potentially illustrating coordination of stress responses and microbe-microbe interactions. It would be interesting to investigate this further- do they play a role in functions such as quorum sensing or nutrient/vitamin provisioning?

 Generally, results highlight the importance of studying microbial communities of habitats aside from those in the OO. This is highlighted by a 20% increase in known microbial diversity resultant from this study alone. This will allow the creation of a genomic database far larger than previously considered, and really enhance our understanding of microbial life and diversity in all ocean habitats.



Zhang, W., Ding, W., Li, Y. X., Tam, C., Bougouffa, S., Wang, R., ... & Sun, J. (2019). Marine biofilms constitute a bank of hidden microbial diversity and functional potential. Nature communications, 10(1), 517.

Step back Vibrio: These shrimp have a fungal bodyguard.

With antibiotic use strife in aquaculture, Soowannayan et al. (2019) strives to find a more sustainable solution for tackling Vibrio infection in shrimp, through fungi. The study starts optimistically, with 25 of the 39 fungal isolates used displaying an ability to inhibit biofilm formation for all 7 Vibrio isolates tested against, under lab conditions. However, when supplemented into feed, only one fungal isolate, MCR55 from Oceanitis cincinnatula, provided shrimp with protection from necrosis disease (AHPND) caused by an isolate of V. parahaemolytious. This showed great success, resulting in a mean survival rate similar to those of unchallenged shrimp, highlighting the potential of this avenue.

This early screening has identified the antagonistic properties of O. cincinnatula. However, the mechanism by which this occurs remains unknown although they theorize it may be the result of disruption of bacterial quorum sensing, preventing formation of Vibrio biofilms within the shrimp’s stomach. It’s clear more research is needed to isolate and identify the key substance(s) involved in Vibrio inhibition, and whether this could provide a commercially viable alternative. This study really illustrates the potential for fungi as sources for antimicrobial products, which should be explored in greater depth.

Soowannayan, C., Chandra Teja, D.N., Yatip, P., Mazumder, F.Y., Krataitong, K., Unagul, P., Suetrong, S., Preedanon, S., Klaysuban, A., Sakayaroj, J., Sangtiean, T. (2019). Vibrio biofilm inhibitors screened from marine fungi protect shrimp against acute hepatopancreatic necrosis disease (AHPND). Aquaculture, 499, 1-8.

Microbial community structure of the coastal SSA

The sea spray aerosol (SSA) is a well described, abundant habitat in open oceans. Yet little is known about their microbial composition, abundance and connectivity in coastal regions.

Narrowing this gap, Graham et al (2018) characterised and compared the SSA microbial composition between sand and water compositions across three physically varying Californian beaches. SSA, sand and water were sampled contemporaneously, followed by next generation sequencing to characterise microbes.

SSA and sand bacterial 16s rRNA concentrations varied amongst beaches. Bacterial diversity was similar between the SSA, sand and water across beaches. Beach SSA communities were all similar except one beach (Baker beach). SSA characterisation identified shared Operational taxonomic units (OTU) associated with biogeochemical cycling Planctomyces and pathogenic bacteria such as Enterococcus between beaches and water samples.

By comparing the coastal SSA among beaches, sand and water samples, the paper gives an insight into its connectivity. The characterisation of shared OUT’s further contributes in understanding the SSA ecological roles. Interactions between the coastal SSA, sand and water further support the model of SSA generation by breaking waves. However, interactions between the SSA and water could be compromised as the sea surface microlayer wasn’t sampled, which is strongly associated with SSA communities.

Graham, K. E., Prussin, A. J., Marr, L. C., Sassoubre, L. M., & Boehm, A. B. (2018). Microbial community structure of sea spray aerosols at three California beaches. FEMS microbiology ecology, 94(3), fiy005.

The gut feeling – phage vs antibiotic therapy

Endangered green turtles, C. mydas, are routinely rehabilitated from bacterial disease using antibiotics, however this can cause long-term gut-related dysbiosis in these herbivores. Ahasan et al. (2019) investigated the ability for phage treatment to eliminate targeted bacteria in captive green turtles. Using 16SrRNA sequencing of bacterial communities in faecal samples, gut microbiome community changes were assessed in turtles either given an oral dose of antibiotic, Acinetobacter venetianus-specific phage cocktail, or a control. Antibiotic and phage treatments significantly lowered the abundance of target Acinetobacter, phage treatment did not permanently alter gut bacterial community composition, unlike the antibiotic.

Ahasan conveys the difficulty in diagnosing disease in C. mydas, it would therefore prove difficult to apply these results to develop phage therapy when the target bacteria are unknown. Additionally, Acinetobacter are not C. mydas pathogens, healthy turtles were used and remained unexposed to a pathogen, so the effect of phage therapy in treating a pathogenic disease in vivo remains unspecified. Despite its flaws, this study demonstrates the ability for phages to eliminate selective bacteria in green turtles, without deleterious effects. Working antibiotics are becoming limited, these results emphasise the potential for phage therapy to replace larger scale antibiotic use such as in aquaculture.

Ahasan, M. S., Kinobe, R., Elliott, L., Owens, L., Scott, J., Picard, J., Huerlimann, R. & Ariel, E. (2019). Bacteriophage versus antibiotic therapy on gut bacterial communities of juvenile green turtle, Chelonia mydas. Environmental microbiology.

A blooming disputing: green energy in the oligotrophic ocean

Ocean Thermal Energy Conversion (OTEC) produces electricity using the temperature difference between deep ocean waters and tropical surface waters and is considered a clean energy source. However, effects on microorganisms of OTEC discharging cold nutrient rich water within warm oligotrophic surface water is relatively unknown.

Giraud et al (2019) investigated this, using in situ microcosm incubations of various seawater depth mixes, simulating deep-sea water discharge. Carbon and Nitrate uptake was measured using 13C/15N isotopic label technique. Microbial effects were limited with 2% deep water addition and negligible with discharge at the bottom of euphotic zone. However, a shift in assemblage to larger phytoplankton with 10% addition at the DCM was shown due to inputs of PO₄³⁻ and NO₃­­­^-.   

This change to a more nutrient rich environment with a higher light exposure has shown to cause shifts in assemblage potentially elevating risks of eutrophication, harming surrounding communities. This puts into question the effectiveness of this green energy source and its effects on microbial communities. A weakness of this paper is its lack of scope, only looking at the changes over 6-days periods, if the study had been carried out for a longer period the results would be more convincing.

Giraud, M., Garçon, V., de la Broise, D., L’Helguen, S., Sudre, J., & Boye, M. (2019). Potential effects of deep seawater discharge by an Ocean Thermal Energy Conversion plant on the marine microorganisms in oligotrophic waters. Science of The Total Environment, 693, 133491.

Harnessing the power of microbes, Part 2 The Bio-battery

Sediment microbial fuel cells (SMFCs) are bioelectrochemical systems similar to Microbial fuel cells (MFCs) which generate electrical current using microbes. However, SMFCs use electrochemically active bacteria (EAB) found in marine sediments. In MFCs sediment is the limiting factor but for in situ SMFCs, this limitation is removed allowing for a theoretical continuous generation of electricity. Additionally, an electrical charge can be stored within the anode in these systems and can be released when needed producing bio-batteries.

Sudirjo et al (2019) studied the long term use and storage capacity of these SMFCs to create rechargeable bio-batteries. The key component was the use of activated carbon which offers itself a successful anode material that allows bacteria to grow within the porous structure and form biofilms as well as having the capacity to store electrons and thus enable the electrical power to be stored and released later. This paper offers a look into the use of these systems over long periods and theoretical use of these systems as ex-situ bio-batteries to store electricity and use them for off-grid purposes. Through the testing conducted it was calculated that this bio-battery would run for up to 21 years with minimal maintenance 

  

Strik, D., Buisman, C. J., & Sudirjo, E. (2019). Marine sediment mixed with activated carbon allows electricity production and storage from internal and external energy sources: a new rechargeable bio-battery with bi-directional electron transfer properties. Frontiers in microbiology, 10, 934.

Oil formations take toll on microbes

Oil compounds are found in surface slick, droplet, and dissolved forms after spill events. Combinations of these forms influence the variability of microbial responses to oil aggregations. Researchers can create environments knows as ‘WAF’s, where oil is present in all forms mentioned above, and ‘WSF’s, with oil in a dissolved form only. In an interesting and thorough study, Bera et al. (2019) use these two environments in mesocosm set-ups to identify the impact different oil aggregations have on bacterial community composition, phytoplankton productivity, and the abundance of exopolymer particles.

16S rRNA sequencing revealed differential bacterial community structures between WAF and WSF treatments, with different OTUs enriched in each treatment. This may be explained by hydrocarbon-degrading bacteria preferring readily available oil droplets (for faster biofilm formation) in the WAF treatment, which aren’t present in WSF. Analysis of chlorophyll α fluorescence shows consistent phytoplankton communities across both treatments. Reduced electron transport and growth rates in the WSF treatment, however, indicate dissolved PAHs have a damaging effect on phytoplankton photosystems. TEP production was higher in WSF compared to WAF, potentially due to phytoplankton increasing polysaccharide-rich substance release in times of stress. The information provided above is just a snapshot of the knowledge gained from this study, and I imagine it will be extremely high impact.

Bera, G., Doyle, S., Passow, U., Kamalanathan, M., Wade, T. L., Sylvan, J. B., ... & Knap, A. H. (2019). Biological response to dissolved versus dispersed oil. Marine pollution bulletin, 110713.
https://www.sciencedirect.com/science/article/pii/S0025326X19308690

Seagrass- Microbial Friend or Foe?

   Seagrass meadows are hugely important ecosystems which require a delicate balance of nutrients in order to provide habitats for a multitude of organisms worldwide. Shark Bay features some of the largest meadows in the world, yet its waters are categorized as highly oligotrophic. This bay is characterized by a natural salinity and phosphate gradient which is amplified by the presence of seagrass, which acts as a natural barrier to water circulation, giving rise to different environmental conditions and therefore different microbial communities. Fraser et al. (2018) aimed to investigate the different microbes present within different conditions, as it was hypothesized that different genes which alter nutrient uptake would be up regulated depending on their position along the gradient.

   Metagenomic sequencing provided an image as to what functional and taxonomic changes were present between different microbial communities. It was observed that there were distinct shifts in both functional and taxonomic structure of communities along the saline/phosphate gradient, which also impacts seagrass activity and configuration. This information could prove essential with respect to our understanding of the interactions between seagrasses and their microbial community composition within a changing environment, a topic becoming increasingly important as our climate continues to verge toward extremes.

Fraser, M. W., Gleeson, D., Grierson, P. F., Laverock, B., & Kendrick, G. A. (2018). Metagenomic evidence of microbial community responsiveness to phosphorus and salinity gradients in seagrass sediments. Frontiers in microbiology, 9, 1703.

Fe Fi Fo Fum iron sensing in Trichodesmium?

Trichodesmium is integral to the global microbiome and carbon sequestration which makes it increasingly relevant to study. They use Nitrogenase to fix N₂ but this has high iron (Fe) requirements which in the open ocen is often in low supply.

Researchers tested wild Trichodesmium reaction to natural, Fe-coated and Fe-less dust. Trichodesmium showed a higher short-term interaction, cantering and long-term interaction of natural and Fe-coated dust. They also did a ⁵⁷Fe tracer experiment using submicron scale surface imaging with NanoSIMS and found ⁵⁷Fe in the colony core.

I agree with the researchers that this study provides evidence for the selective collection of dust and Fe-rich particles and the disposal of Fe-free particles. To say this proves Fe sensing I think is an overstep. Trichodesmium interacted more with natural dust which to me suggests a more indiscriminate sensing mechanism, that may be related to particle charge. Also, the retention of the dust could relate to time taken to incorporate particles as Fe-free would have less to incorporate. The researchers may have considered these factors making them irrelevant but the mechanism could be more complicated so future research could provide further insight.  

Kessler, N., Armoza-Zvuloni, R., Wang, S., Basu, S., Weber, P. K., Stuart, R. K., & Shaked, Y. (2019). Selective collection of iron-rich dust particles by natural Trichodesmium colonies. The ISME journal, 1-13.