Diuron and its effects on diatoms (jack tyler)

Anti-fouling agents have the ability to prevent the settlement and growth of marine organism in submerged habitats as well as impacting primary production levels. Both sinking rate and the physio-chemistry of marine diatoms are impacted on by the presence of diuron. Diuron is a photosystem II inhibitor which prevents electron transfer. 

Two species in particular were looked at, Thalassiosira pseudonana (single-celled species) and Skeletonema marinoi-dohrnii (complex chain forming species). Cultures were grown and maintained for both species and then used for various experiments. 

Sinking rates decreased significantly in both diatom species with exposure to diuron at 50% effective concentration for growth. Furthermore, photosynthetic performance of both diatoms also significantly decreased. Number of cells per chain of S.marinoi-dohrnii decreased significantly however T.pseudonana cell diameter remained constant. Lipid concentration increased in both species while water soluble protein concentration decreased in T.pseudonana after 72 hours. 

These observed changes in composition are suggested to be the reason why sinking speed is decreased. The roll-on impact of the decreased sinking speed may in fact increase risk of diuron exposure and therefore exacerbate the problem even further. Furthermore, many diatom species have a resting stage cell under unfavorable environmental conditions. Reduced sinking rate will possibly prevent diatoms reaching this stage in time and negatively impacting upon the groth of the diatom. Previous studies have found that when photosystem II is impaired, the products of photosynthesis are not taken up as normal, and instead deposited as lipids. Therefore, higher neutral lipid levels may be a biological reaction to physiological stress. It was found that the correlation between the number of cells per chain and photosynthetic parameters in chain-forming diatoms suggest that there is an obligate reliance between chain length and sinking rate whereas single-celled diatoms sinking rate was determined by its biochemical composition. 

paper reviewed:

Saranya, K., Sundaramanickam, A., Shekhar, S., Meena, M., Sathishkumar, R. S., & Balasubramanian, T. (2018). Biosorption of multi-heavy metals by coral associated phosphate solubilising bacteria Cronobacter muytjensii KSCAS2. Journal of Environmental Management, 222, 396-401. doi:10.1016/j.jenvman.2018.05.083

coral bacteria used in agriculture (jack tyler)

Heavy metal contamination is a big problem for agricultural businesses due to the fact that heavy metals decrease in microbial activity and productivity of the crops. These heavy metals are essential to life at low concentrations however are poisonous at higher concentrations as well as to top consumers in the food chain via bioaccumulation, including humans. Bacteria have been identified as the most important biosorbents used for metal detoxification.  

This study examines potential detoxification efficiency of heavy metals by phosphate solubilizing bacteria isolated from coral, sea grass and mangrove environment. Out of 42 strains found, 4 were selected based on solubilization index for metal tolerance test. KSCAS2 exhibited maximum tolerance to heavy metal due to the fact that it has extracellular metal ions in amorphous. Percentages of metal removal varied depending on the metal in question (55%-77%). When initial concentration was doubled, removal capacity decreased (44%-67%). KSCAS2 showed tolerance up to 500 mg/L for individual metals and up to 200 mg/L in combination metals. Bioabsorption capacity supported by SEM and FTIR 

KSCAS2 was suggested to be Cronobacter muytjensii due to the low growth inhibition, high metal tolerance and good phosphate solubilising capability as well as molecular analysis of 16S rRna sequencing. No previous study on the heavy metal resistance of this bacterium has been carried out. It is believed to be an opportunistic pathogen, however the results of this study would suggest that it would be an efficient method of cleaning agricultural soil of heavy metals due to its strong ability to absorb these heavy metals as well as being easy to culture, enabling a great quantity of them to be produced and for relatively cheap. 

This study is interesting because it shows how the marine environment can be useful in finding novel ways to make human life more efficient. As so much of the marine environment is undiscovered or still a mystery, the potential for there to be useful bacteria is endless. 

Paper reviwed: 

Saranya, K., Sundaramanickam, A., Shekhar, S., Meena, M., Sathishkumar, R. S., & Balasubramanian, T. (2018). Biosorption of multi-heavy metals by coral associated phosphate solubilising bacteria Cronobacter muytjensii KSCAS2. Journal of Environmental Management,222, 396-401. doi:10.1016/j.jenvman.2018.05.083 

Fighting the DWH oil spill with exopolymers

The Deepwater Horizon (DWH) incident is one of the most tragic man-made disasters, which provoked major outcry from the public and the scientific community. Since then there has been a lot of research being done on the bacterial community involved in the oil degradation. One of the major processes that lead to the sedimentation of the oil to the seafloor was marine oil snow formation - oil droplets coagulated with transparent exopolymer particles into aggregates on the sea surface, which then rapidly sink to the ocean floor. The exopolymers, or extracellular polymeric substances (EPS), are biopolymers of high molecular weight secreted by microorganisms, which are primarily composed of proteins and carbohydrates (Passow et al. 2012). They have diverse functions for bacteria, and have recently being given major credit for influencing the fate of oil and chemical dispersants in the ocean.

Bacosa et al. (2018) researched into the identity of the key species involved in EPS production and oil degradation, and into the interacting factors in marine snow production. They succeeded in isolating nine bacterial strains, all belonging to the phylum Proteobacteria, which produce ETS in the presence of oil or Corexit as carbon sources. Six of the isolates were identified as members of the genus Alteromonas and the other three isolates were Thalassospira, Aestuariibacter, and Escherichia, with the last two not previously reported to be associated with oiled samples from the Gulf of Mexico following the DWH spill. Aggregate production varied with treatments and isolates, and the protein and carbohydrate content of the EPS differed across treatment and strain. The study showed that the presence of oil and Corexit generally increase the protein (but not the carbohydrate) content of EPS produced by bacteria. They displayed astounding results with one of the Alteromonas stains (W14) having an increase in protein content of EPS by 550-fold after the addition of Corexit. This suggests that the role of high protein is linked to boosted aggregation probably to protect the cells in disadvantageous conditions. The research also looked into the extracellular enzyme activity of the strains, reporting an enhanced activity in leucine amino-peptidase and alkaline phosphatase, when Corexit was added. A relationship between enhanced peptidase activity and the previously reported higher protein content of the EPS has been dismissed, because of the lack of increase in peptidase in some of the strains with enhanced protein content, including the W14 one. The study showed a typical oil degradation pattern with alkanes preferably degraded over the PAHs and managed to unravel the role of the Thalassopira in the picture, as evidence of their ability to degrade both alkanes and PAHs (2 and 3 rings) has been presented.  

The study of Bacosa et al. (2018) has introduced some new data on the bacterial community involved in oil degradation, and has brilliantly displayed the importance of EPS in the sedimentation of oil in the deep sea. Exopolymers are currently one of the hottest fields for research in marine microbiology, as impending findings on the tiny ecological niches of biofilms and aggregates require a broader understanding of the marine microworld.

Reviewed article:

Bacosa, H., Kamalanathan, M., Chiu, M., Tsai, S., Sun, L., Labonté, J., Schwehr, K., Hala, D., Santschi, P., Chin, W., Quigg, A. 2018. Extracellular polymeric substances (EPS) producing and oil degrading bacteria isolated from the northern Gulf of Mexico PLoS ONE 13(12): e0208406. https://doi.org/10.1371/journal. pone.0208406

References:

Passow, U., Ziervogel, K., Asper, V., Dierks, A. 2012. Marine snow formation in the aftermath of the Deepwater Horizon oil spill in the Gulf of Mexico. Environ. Res. Lett., 7 (2012), p. 11, 10.1088/1748-9326/7/3/035301

It's in the Genes: Host Genetics and Microbiomes

The microbiomes of teleosts have been identified to play important roles in host disease immunity by excluding pathogens within mucus coatings and helping to develop immune responses. These microbiomes are developed early in a fish’s life and the communities often differ depending on diet, the external environment and the ability of microbes to outcompete others within the community. However, one somewhat understudied mechanism for the development of distinct microbiome communities in fish is the contribution of host genetics. Can genetics change the microbiome communities and increase resistance to disease?

Flavobacterium psychrophilum is a pathogenic bacteria and the causative agent of the Bacterial Cold Water Disease which wreaks havoc within Salmonid fish stocks. The disease causes caudal fin necrosis, skin lesions, and mortality and there is no commercially available vaccine to combat the infection. Therefore, it is imperative that we understand and characterize mechanisms, such as microbiome compositions and genetics, that increase resistance to this disease. The aims of the study presented here were to: investigate whether F. psychrophilum resistant and susceptible rainbow trout have bacterial assemblages associated with gut and gills, and, to investigate if host genetics and tank conditions also changed these assemblages.

Trout were selectively bred to produce F. psychrophilum resistant and susceptible lines and each line was placed into either high- or low-density holding tanks and left to grow. Disease resistance was tested on healthy fish from each line by injecting them with an F. psychrophilum strain and survival was recorded over 21 days. Community analysis was carried out by extracting genomic DNA from the gills and mid-guts of each line from the different holding densities. 16S rRNA was PCR amplified and sequenced on Illumina MiSeq high-throughput platform, microbiome community compositions and diversity indices were then calculated from these sequences.

Firstly, and rather unsurprisingly, the resistant trout line had much higher survival to infection (3% mortality) compared to the susceptible line (69% mortality), validating the resistance/susceptible phenotypes. Eight phyla were identified in the mid-guts from both lines with Tenericutes beginning the most abundant. The genus Mycoplasma made up almost all the Tenericutes but were found in lower abundance in susceptible fish. Perhaps a low Mycoplasma abundance is associated with disease susceptibility and that Mycoplasma could outcompete pathogens in the gut. At the gills, 9 phyla were found with Proteobacteria being the most abundant. Also, trace amounts of Flavobacteria sp. were detected at the gills. Flavobacteria infection may not be due to its abundance but its ability to displace other microbes within the community. Stock density and genetics did alter gut microbiome community structures, with high-density and low-density susceptible trout distinctly clustering from one another. Housing density had no effect on resistant fish gut community clustering, but the microbial diversities were much lower than susceptible fish. Resilience, therefore, may be associated with a less diverse microbiome.

This study does look to suggest that host genetics and the environment can have an influence over the mid-gut communities but not gill communities. Host genetics coupled with the external environment can select for distinct gut microbial communities and, in turn, determine an animal’s resilience to infection.

Paper reviewed:

Brown, R.M., Wiens, G.D., & Salinas, I. (2019). Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss). Fish and Shellfish Immunology, 86, 497-506.

A Toxic Relationship

Phytoplankton blooms are a naturally occurring phenomenon along coastlines worldwide. Large accumulations of certain hazardous phytoplankton species can have detrimental effects on marine wildlife as well as on human health and local economies. Numerous species of dinoflagellates, diatoms and cyanobacteria are known to release harmful ‘phytotoxins’ into the environment during these events, which are commonly referred to as harmful algal blooms (HABs).

 In order to mitigate related health epidemics, coastal waters can be monitored for HAB species along with their toxic exudates. However, identifying the mechanisms which cause HABs to arise in the first place may prove to be a more effective management strategy, perhaps allowing preventative measures to be implemented. There is continuing debate amongst the scientific community as to whether HABs are increasing due to anthropogenic activity or if they are predominantly naturally occurring events that we’ve simply become better at detecting.     

 Whilst the potential causes of HABs have received considerable attention from researchers, until recently, few studies had addressed the possible contributing roles of interactions between phytoplankton and co-occurring bacterioplankton. These interactions are most likely based upon the exchange of nutrients, for example, it has emerged that specific bacteria could modulate algal growth and bloom dynamics via the provision of iron. Iron is vital to all life on Earth, playing key roles in respiration and photosynthesis. Yet, its bioavailability within the marine environment can be poor due to its low solubility in seawater. Consequently, marine bacteria have developed complex systems to generate high-affinity iron-chelating compounds called siderophores to acquire, transform and process this fundamental element. Although iron acquisition by marine bacteria is reasonably well understood, much less is known about iron acquisition from low iron concentration marine environments by phytoplankton. Accordingly, one recent study investigated whether the growth of Lingulodinium polyedrum, a HAB associated dinoflagellate, is affected by the presence of siderophores, a potential bioavailable form of iron provided by bacteria.

 Having previously studied blooms of L. polyedrum in the field, Yarimizu et al., identified that populations of L. polyedrum and bacterial siderophore producers fluctuated in synchrony with one another. Consequently, subsequent lab study endeavoured to confirm a mutualistic relationship between L. polyedrum and the vibrioferrin siderophore producing bacterium Marinobacter algicola DG893, via culture-based techniques. For comparative study, a mutant form of DG893 without siderophore biosynthesis genes was generated.

 As expected, iron was found to be growth limiting to L. polyedrum in axenic culture. Furthermore, in concordance with patterns observed in the field, L. polyedrum growth was enhanced when cultured together with DG893. Although growth was also promoted by the mutant form of DG893, algal growth was most significantly improved by non-mutant DG893, highlighting the importance of siderophore vibrioferrin as a source of iron for the dinoflagellate. Growth enhancement by the mutant DG893 suggests that the bacteria may be offering further benefits to co-occurring algae, such as the provision of vital B vitamins.

 Furthermore, the findings of this study highlight the mutually beneficial nature of the relationship between L. polyedrum and DG893. Without the addition of an artificial carbon source, DG893 was incapable of growth in axenic culture. However, when cultured alongside L. polyedrum, DG893 grew well without requiring the addition of artificial carbon, indicating that the dinoflagellate provided an adequate reservoir dissolved organic carbon.

 Ultimately, Yarimizu et al. have made a noteworthy contribution to our understanding of potential HAB facilitation through effective demonstration of this algae-bacterium mutualism. Nevertheless, more data is needed from the field to understand how such mechanisms may operate in the natural environment. Likewise, investigating how humans may be influencing the dynamics of such mutualisms through processes such as eutrophication and overfishing could yield some interesting results.           

Reviewed Paper:

Yarimizu, K., Cruz-López, R. & Carrano, C. J. (2018). Iron and Harmful Algae Blooms: Potential Algal-Bacterial Mutualism Between Linguldinium polyedrum and Marinobacter algicola. Frontiers in Marine Science, 5: 180

The importance of being temperate when it comes to extremes: marine viruses in the Southern ocean

Viruses have a substantial role in the ocean as they shape the microbial ecosystem and have the potential to affect the flow of energy and matter in the marine environment. Viral infections resulting in cell lysis lead to a “short circuit” in the microbial loop, as bacterial production is being fueled by recycling and respiration and the amount of organic matter available to macroorganisms is being reduced (Fuhrman 2000). Viruses use different replication strategies and grasping the “why” and the “how” behind those is critical to understanding viral ecology. Let’s start with the “how”.

Viral infections can be lytic: the viral DNA replicates independently from the host, which results in lysis of the cell (Miller and Day, 2008). Phages relying solely on this strategy are called virulent. In the lysogenic virus infections the viral DNA is maintained within the host as a prophage, where it’s being copied alongside the host’s DNA when the infected cell replicates, until induced to replicate lytically (Miller and Day, 2008). Viruses using both the lysogenic and the lytic cycle are called temperate. A great amount of studies examining the correlation between virus replication strategy and bacterial abundance and production have been rather inconclusive. Here Brum et al. 2015 demonstrate that temperate viruses dominate the dsDNA viral assemblage of the western Antarctic Peninsula (WAP) in the Southern ocean, and manage to gain insight into the strategy behind it.

According to the study temperate viruses dominate the WAP dsDNA viral assemblage primarily using lysogeny when bacterial production is low (in the spring) and switching to lytic replication in response to increased bacterial abundance and productivity (in the summer). Moreover, comparative analysis of viromes revealed that the taxonomic composition of the sequences unique to temperate and lytic viruses in the WAP was different. Namely, myoviruses were more abundant in the lytic-enriched virome and podoviruses were more abundant in temperate-enriched viromes. However, we can’t really talk about dominant sequences, as 93–95% of the reads remained taxonomically unassigned. Comparing this research with other studies of viral communities from lower-latitude marine ecosystems exhibits a difference in the trend in lysogeny. Higher-latitude environments display strong seasonality in percent lysogeny, with the highest values in winter and spring, in contrast to lower-latitude environments where lysogeny is sporadically detected. These trends with latitude might be explained by the relative abundance of temperate viruses, which dominate polar aquatic systems, probably because the intense seasonal variations in productivity in these regions favor viruses capable of switching replication strategies in response to changes in host productivity. However, it is important to say that because of the usage of quantitative dsDNA virome construction and comparison as a main research method this paper does not provide any data on single-stranded DNA or RNA viruses. Even though this study is a stepping stone in the understanding of polar viral-ecology, it is still a baby step in this very wide and unexplored field.

Reviewed paper:

Brum, J., Hurwitz, B., Schofield, O., Ducklow, H., Sullivan, M. (2015). Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics. In: The ISME Journal (2015), 1–13. doi: 10.1038/ismej.2015.125 

References:

Fuhrman, J. (2000). Impact of viruses on bacterial processes. In: Kirchman DL (ed) Microbial Ecology of the Oceans. Wiley-Liss, Inc.: New York, NY, USA, pp 327–350.

Miller RV, Day MJ. (2008). Contribution of lysogeny, pseudolysogeny, and starvation to phage ecology. In: Abedon ST (ed) Bacteriophage Ecology: Population Growth, Evolution, and Impact of Bacterial Viruses. Cambridge University Press: Cambridge, UK, pp 114–143.

Understanding the roles of bacterial communities- 3 months after DWH

The role of sediment-dwelling marine bacteria is poorly understood. The Deepwater Horizon oil spill in New Mexico in 2010 provided an opportunity to study the bacterial communities’ response to the oil. After the wellhead was capped the role of hydrocarbon degradation was predominantly undertaken by bacteria. Using metagenome analysis of communities from 13 samples of sediment along a transect up to 60 km away from the capped wellhead, the bacterial genomes were reconstructed and grouped according to taxa. Majority of the reads were associated with Gammaproteobacteria (66% or 119 Mbp). The same genomes, comprising of six Gammaproteobacteria and two Bacteriodites genome bins were found at all near well sites, at many less impacted or unimpacted distant locations. Depicting a uniform community across the transect.

The metabolic pathways of the community were established from the genes present comparing the sequences to library databases and measuring the abundances in proximal sites and distal sites. 

Genes coding for alkane-degrading pathways were abundant across the transect indicating a selection for alkane degradation in bacteria across the seabed. Enrichment occurring in proximal sites.

The paper explores the roles of the bacterial communities in the sediment in New Mexico, the changes in abundances and reveals the potential of a uniform community in an area with natural hydrocarbon seeps suggesting the retention of Alkane degrading pathways over many generations of bacteria.

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Article reviewed

Handley, K. M., Piceno, Y. M., Hu, P., Tom, L. M., Mason, O. U., Andersen, G. L., ... & Gilbert, J. A. (2017). Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill. The ISME journal, 11(11), 2569.

Available at: https://www.nature.com/articles/ismej2017110