What's in the Neuston- the Biology of the Western Mediterranean and the South Adriatic Sea.

Neuston, the content of the Sea surface Microlayer, defined as the top 1 cm of the sea surface is the interface between water and air. The Sea surface microlayer (SSML) may play an important role in biogeochemical processes. The SSML plays host to a wide-ranging biological diversity and is threatened by microplastic debris. More research is being undertaken to identify the effect of plastic debris than focusing on the biological and diversity element of the Neuston.

In this paper, the Authors focus on the community composition, abundance and biodiversity of the Western Mediterranean and the Adriatic Sea. Using a neuston net Samples of the neuston were taken from 59 stations around the South Adriatic Sea and the West Mediterranean on a cruise in 2013. A second cruise in 2015 undertaken in the South Adriatic to assess changes in distribution in time. With 21 stations being sampled on this occasion, 13 of which were in the same location as 2013. The individuals were identified using a compound light microscope and classified to family level for determination of the community composition.

In 2013 and 2015, In total 112 taxa belonging to 19 Phyla were sampled across all stations in the western Mediterranean and the South Adriatic Sea. In 2013 101 taxa were found, with the most abundant phylum being Arthropoda consisting of 60 taxa. With 57 taxa related to the Crustacea. Only 5 truly neuston taxa were present Porpitidae, Velellidae, Janthinidae, Pontellidae and Idotheidae. Pontellidae and Idotheidae were the two most abundant eu-neustonian taxa found in 36 and 31 stations respectively.

Using diversity analyses, there was higher diversity and taxonomic richness in the Southern Adriatic Sea than the Mediterranean however, there was higher Abundances in the Western Mediterranean. Negligible differences were uncovered between 2013 and 2015 samples in the South Adriatic sea despite sampling in different seasons and spaces.

The results presented were in accordance with previous studies of the neuston in terms of community composition with a higher abundance of mero neuston (105 taxa) than eu- and epi- neuston (5 and 2 taxa respectively). Spatial distribution was present In the South Adriatic but not in the Western Mediterranean. Due to the lack of studies in the Adriatic Sea comparisons could not be made between work.

The demonstration of Biological diversity in the neuston shows domination of Crustacea (Copepoda in every sample taken) and very little representation of purely neuston dwelling organisms. Suggesting that organisms only spend limited periods of their lives in the Neuston.

------------
Liparoto, A., Mancinelli, G., & Belmonte, G. (2017). Spatial variation in biodiversity patterns of neuston in the Western Mediterranean and Southern Adriatic Seas. Journal of Sea Research, 129, 12-21.

Accsess https://www.sciencedirect.com/science/article/abs/pii/S1385110116301769

Aquatic Fungi: Overlooked No More

 Although fungi are recognised for their ecological importance within terrestrial environments, comparatively little is understood about their functions within aquatic environments. Aquatic fungi comprise only a tiny fraction of identified marine clones, which is probably why they have been somewhat overlooked by microbiologists. However, researchers are beginning to uncover that fungi contribute more to aquatic ecology than once thought, especially with regard to the oceans. Recent studies utilising modern high-throughput sequencing techniques have demonstrated larger proportions, as well as greater taxonomic diversity, of marine fungi than previously described. Consequently, the field is of growing interest to researchers.          

 The fungal group Chytridiomycota is acknowledged as ecologically significant in freshwater systems. They are well known as facilitators of the transfer of organic carbon from phytoplankton into zooplankton, through saprophytic and parasitic activity. Yet, these important decomposers have been seldom reported within marine studies. The findings of one recent study however, found Chytridiomycota-like sequences to dominate samples from a diverse range of aquatic environments, including marine!  

 Comeau et al. performed a broad analysis of fungal diversity within marine and freshwater systems across both Arctic and temperate climates. Samples of sea-ice were also acquired from locations within the Arctic. A total of 319 samples were collected from 103 sites, between 2003 and 2011, generating an extensive database of more than 3.6 million sequences. Fungal diversity was then assessed by examining the V4 region of 18S rRNA (DNA and RNA).

 Data analysis revealed all samples to contain fungal sequences. A total of 44 fungal genera were identified, portraying a great richness in fungal diversity. Whilst there were no significant correlations between the different fungal taxa and factors such as season, depth, or salinity, fungal abundance was found to be slightly higher within warmer regions, indicating a preference for higher temperatures. Appraisal of fungal diversity was conducted by clustering fungal sequences into Operational Taxonomic Units (OTUs) at 98% shared identity. Clustering of OTUs revealed minimal overlap between environmental niches (freshwater, marine and sea-ice) demonstrating a strong degree of environmental specificity.    
   

 The most notable outcome of this study was the aforementioned dominance of Chytridiomycota-like sequences within almost all samples, including marine where they have been previously reported in much lower abundance. Within this group, the dominating sequences were closely matched to an uncultured clone, CFL161DB09, which originates from an Arctic seawater sample. Whilst these sequences are grouped together with the Chytridiomycota within this study, they actually represent novel lineages of chytrid. Moreover, Comeau et al. were able to show that there were significant positive correlations between the yield of Chytridiomycota-like sequences within samples, and both chlorophyll a concentration and yield of diatom sequences. Whilst the ecological functions performed by these novel chytrid lineages are still undetermined, these findings suggest that they probably act as algal parasites, akin to previously studied freshwater chytrids.

 Overall, this study works to highlight the requirement for more extensive investigation of aquatic fungi, especially within marine environments. Long overlooked, it is emerging that this fraction of the microbial eukarya contribute far more to the ecology of aquatic environments than traditionally believed, with possible key roles as decomposers and nutrient cyclers. In order to gain understanding of these potential roles, physiological and ecological studies of novel chytrids should be pursued.                                 

Reviewed Paper:

Comeau, A. M., Vincent, W. F., Bernier, L. & Lovejoy, C. (2016). Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats. Scientific Reports, 6: 30120

Anna Karenina meets Spongebob's microbiome

“All happy families are alike; each unhappy family is unhappy in its own way.” In other words, we tend to differentiate people in their misery. And not only people. A very important part of research is understanding how organisms respond to unfavourable conditions. This has evolved from running around and poking them with a stick to putting their whole environment under stress. The quote from the renowned Anna Karenina is now being transferred to Biology books: the Anna Karenina principle predicts that in a host-associated microbiome certain stressors have stochastic rather than deterministic effects on community composition. Translating Tolstoy in Microbiology: “all healthy microbiomes are similar; each dysbiotic microbiome is dysbiotic in its own way” (Zaneveld et al. 2017). As ecologically important filter feeders with well-established microbial partnerships, sponges are a relevant target for microbial based monitoring studies.

Glasl et al. (2018) investigated how the diversity of the sponge microbiome influences community stability upon acute salinity fluctuations (ranging from 36 psu to 25 psu) under controlled experimental conditions. They used sponges with high and with low microbial abundance, testing the general ecological principle that increased biodiversity enhances the stability of an ecosystem (the stability-diversity concept). The sponges were highly tolerant of short-term acute salinity fluctuations, as they exhibited no signs of stress following salinity amendments. The microbiomes showed compositional resistance irrespective of their microbial diversity, as there was no shift in the compositional stability of the microbiome for both high and low diversity species. This lead to the conclusion that the stability-diversity concept does not apply to sponge microbiomes. The Anna Karenina principle also didn’t appear to hold here, as the dispersion of microbial communities remained consistent across both high and low diversity species, irrespective of experimental treatment. The study provides further evidence that sponge microbiomes exhibit strong genotype-specificity, suggesting that genotype-specific microbiome variations shoud be taken into account in future research. The high stability of the sponge holobiont upon salinity fluctuations and the resistance of sponge microbiomes against stressors support the evidence for the widely recognized environmental tolerance of sponges.

Reviewed article:

Glasl, B., Smith, C. E., Bourne, D. G. & Webster, N. S. (2018). Exploring the diversity-stability paradigm using sponge microbial communities. Sci. Rep.8, 1–9. doi: 10.1038/s41598-018-26641-9

References:

Zaneveld, J., Mcminds, R., Vega, R. (2017). Stress and stability: applying the Anna Karenina principle to animal microbiomes. Nature Microbiology, 2(9), 17121. doi: 10.1038/nmicrobiol.2017.121

What's for Dinner Mum? Microbial Fish Soup.

Through excessive demand on sea food with population growth, aquaculture has become a necessity for the sustainability of the seafood industry. Fish farming must be maintained at a high level of maintenance, however even with safety measures and precautions set up farmed fish are still easily subjected to pathogens. This research was undertaken to gain a better understanding of the gut microbial composition. This study will provide a good foundation for further analysis on the health of farmed fish as well as other forms of aquaculture. It will also allow us to determine the most dominate phylum of bacteria found within a fishes digestive system and allow for better detection of potential pathogens.

3 common species of commonly used cage fish were chosen for this analysis, Cobia, Pompano and Milkfish. Each fish was reared and kept on a specific diet for the purpose of understanding gut microbiota and how this can differ between species with similar/dissimilar diets. Each species was reared in fish cages for a month and fed a slow sinking pellet for the first 40 days, twice a day. Once fish had reached a certain weight (around 30g) they were moved into different (HDPE) tanks, this also meant a change to the type of diet each fish had.

Cobia were kept on a diet of low-priced sardines whereas the milkfish and pompano were fed 9–13mm commercial pellet which was made of 40% crude protein 15% crude fat, 9% ash, 2.4% crude fibre. This was kept up for 8 months before 5 fish of each species were taken for microbial analysis. Fish were euthanized, and gut samples were taken from the lower intestine of each fish for analysis, the DNA was extracted via the use of DNeasy blood and tissue kit. Bacterial composition analysis was achieved via a large-scale sequencing,

Identification of the microbes sampled was performed via High-throughput sequencing of V3-V4 hyper variable regions of 16S rDNA on Illumina MiSeq platform. This went on to show that this particular coastline is highly abundant in microbial diversity, with an analysis of  1.3 million quality-filtered sequences.

Results showed the marine gut microbes main species found within Cobia and Pompano were the Vibrio and Photobacterium spp (Gammaproteobacteria). With Pelomonas and Fuscobacterium  (proteobacteria) dominating the milkfish quantity of microbes. All species shared 96 OUT’s while still having their own unique gut microbes. Pompano showed to have the highest number of OTUs with 10,537 unique clusters, milkfish showed to lowest amount with 2799 clusters. Whilst cobia showed to have, 10,435 clusters analysed.

It is believed that these differences are due to the gut morphology of the different species as well as the physiological behaviour and specificity of each fish to be dissimilar. Further research into morphology and physiological behaviour of these species would provide insight.





Original Paper: Comparative profiling of microbial community of three economically important fishes reared in sea cages under tropical offshore environment
M.K. Rasheeda  , Vijaya Raghavan Rangamaran  , Senthilkumar Srinivasan, Sendhil Kumar Ramaiah, Rajaprabhu Gunasekaran, Santhanakumar Jaypal, Dharani Gopal, Kirubagaran Ramalingam

Microbes in the Red Sea

This research was undertaken to assess the effects of the growing industrialisation on the microbes found within the waters of the Egyptian coast. The Red Sea is home to a unique and diverse ecological systems. With industrialisation still growing at a steady pace, pollution from this is also steadily growing. Effects of shipping, the fishing market, marine traffic and petroleum industries alone leak high amounts of oil pollution into the oceans, this alongside shore run off and atmospheric pollution combined undoubtedly have an effect on the biological life of the oceans natural ecosystems. As the Red Sea is home to more than one ecosystem, it has meant that a study such as this is more beneficial on a wider scale as it gives us the chance to understand how different ecosystems are able to adapt and survive when placed under the same stress.

For this experiment 8 coastal sites and 2 lakes were chosen for sampling based on the industrial impacts that affected each area, all sites can be found along the Red Sea Egyptian coast.

Sediment samples were taken from each site with the use of a homemade stainless-steel core. 5g of each of the sample sediments were then placed into inoculation for bacterial culturing to perform a DNA extraction, which was done via the use of a QIAamp® DNA Blood Mini Kit. DNA sequencing was then followed after extraction via 16S rDNA pyrosequencing of hyper-variable regions V6 and V4as. From this analysis 131,402 significant reads of major bacterial taxa exposed there to be five main bacterial phyla dominating the sites: Proteobacteria (68%), Firmicutes (13%), Fusobacteria (12%), Bacteriodetes (6%), and Spirochetes (0.03%). When this was further studied it revealed a distinct group of bacteria mainly including marine vibrio spp, human pathogens and oil-degrading bacteria.

This suggested a ‘marine vibrio phenomena’ – high amounts of bacteria growth that can be harmful pathogens to humans and marine life alike. One of the vibrio spp, V. shilonii,  V. fortis and V. harveyi are known to have the potential to cause coral bleaching, posing a risk to the corals in the surrounding waters.  Each of these vibrio spp. are recorded as bacteria capable or surviving under harsh conditions like the ones currently being experienced. This shows that with the increase in unfavourable conditions due to a rise in pollution the abundancy of  marine life will decrease while the bacteria numbers will increase and adapt alongside the industrialisation. This could prove fatal to humans and land wildlife in the long run with an increase in pathogens being present in the environment.

The lakes surveyed showed 2 different groups, either human pathogens or no pathogens. One of the lakes used for sampling that was under a ‘protected’ site showed to have no pathogen or vibrio found within sediment analysis, this is a significant contrast in comparison to the other sample sites which all had some from of pathogenic bacteria present.

The results of this research prove that there are significant effects of pollution on the microbial community within the red sea. This study alone should encourage others to undergo further analysis to enable our future leaders to create a more sustainable way of life for generations to come and to enable current global leaders to start making more efficient methods of pollution reduction within the environments.

Original Paper: Egypt’s Red Sea coast: phylogenetic analysis of cultured microbial consortia in industrialized sites                                                                                                                                Ghada A. Mustafa, Amr Abd-Elgawad, Alyaa M. Abdel-Haleem and Rania Siam

Sulfur Eating Party down in the SSCS... Bacis only.

Marine microbes have been within the earth’s oceans for billions of years. With the oceans spanning over 70% of the earth’s surface, most areas remain unstudied, despite the many forms of transportation and equipment now within our grasp. Studies of marine microbes have been evident in demonstrating vital roles in regulating ecological processes. This knowledge has proved critical as it has furthered our understanding of ocean mechanisms as well as insights to the behaviours of marine life. 

This research was undertaken to get a better understanding of the bacterial community within Malaysian Waters. It was performed within the benthic region of the Off-Terengganu Coastline of the Southern South China Sea, which previously had not been studied. This coastline in particular is heavily anthropogenically polluted due to the consistent commercial shipping. It is also home to a large breakwater structure used for coastal defences, further changing the diversity of species found. The breakwater structure creates a trapping effect on any run off within the sediment, effectively further polluting the harbour.

This research was conducted on the Terengganu Coastline, home to the largest shipping post in the world, due to this and industrialisation land run off the coastline is surrounded by high-quality crude oil clusters.  Despite this the Terengganu coastline has a shallow, ±50 m neritic epipelagic seabed, with a diverse abundance of tropical marine life forms.

Research Sampling commenced on the 30^th November 2014 via a Smith McIntre grab. Samples of subsurface bacteria were taken at random from 2 separate sites. Samples were kept in double layered polyethylene bags placed in -25ᵒc to be analysed via 16S rDNA V3-V4 marker gene on the Illumina™ Miseq platform. Area 1 showed a higher species richness than Area 2 by 70%. This is assumed to be due to the higher abundance of seagrass that contributes to the amount of organic matter in the water column. This is further illustrated by the diversity and abundance of microbes that also changes with depth, for Area 1 an increase in depth meant going deeper than that of seagrass abundance. Physiochemical parameters of the sediment showed inadequate results for hydrothermal vents within sample areas, although high traces of hydrocarbon pollutants such as gasoline, diesel and mineral oil were found.

  

Epsilonproteobacteria was the most dominant phylum with 60% (Area 1) and 88% (Area 2) followed by Gammaproteobacteria, Deltaproteobacteria and finally Alphaproteobacteria.  Sulfurovum sp., of Epsilonproteobacteria, predominated the overall bacterial community found, however several other sulphur oxidizing bacteria found however from the Gammaproteobacteria genus. This shows the potential for high rates adaptability for survival within as more then one phylum was discovered, pressing for further research based on bacterium metabolic adaptations to be performed. Sulvurofum sp. is an innate bacterium found generally within volcanic regions and deep hydrothermal vents, neither of which was found during the initial physiochemical parameters’ measurement. Metabolic adaptations have come into questioning, with the potential of this being an important role in regulating hydrocarbon pollutants for survival. This however requires further study, as well as future study on Sulvurofum sp. flexibility.

Overall it would seem that the pollution and breakwater structure combined have had a large effect on the ecosystem of the Terengganu Coastline. I believe further research is crucial to understand more about the adaptability of the microbes within this area as they play a vital roles within the regulation of the oceans ecological processes.   

Paper Origin: Abundance of sulfur-degrading bacteria in a benthic bacterial community of shallow sea sediment in the off-Terengganu coast of the South China Sea

 Zahar Marziah, Akbariah Mahdzir, Md. Nor Musa, Abu Bakar Jaafar, Azran Azhim & Hirofumi Hara

microbial fauna of deep sea vent crab species in comparison to shallow water counterparts (jack tyler)

Deep sea hydrothermal vents are majorly variable ecosystems with the fauna inhabiting the requiring highly niche adaptations. As well as the, symbiosis is rife, with bacteria aiding larger organisms to take up more oxygen or obtain the necessary nutrients that they need. Decapod crustaceans usually have a diverse range of bacteria associated with them.Epibiotic bacteria have been found on crabs before, however the gills and the intestines have been looked at very little.  

High-throughput sequencing of 16S rDNA allows a wider picture of the diversity of the microbial fauna present in a sample. For this study, Austinograea sp (deep sea vent), Eriocheir sinensis (fresh water but mates and spawns in saline water) and Portunus trituberculatus (salt water) were looked at to provide a wide picture of the diversity in the microbial communities within the gills of crabs.  

The highest and lowest diversity in bacterial communities were observed in the gill and intestines of Austinograea sp respectively. Through non-metric multidimensional scaling analysis, it was found that the bacterial community in Austiongraea sp was highly distinctive. Of the OUTs found, Leucothrix, Sulfurospirillum and Arcobacter may be involved in oxidizing reduced sulfur compounds and sulfur metabolism. Marinomonas and polaribacter are adapted to low temperature while Fusibacter and Psychrilyobacter may survive well under hypoxic conditions. Furthermore, bacteria commonly found in seawater were dominant in the gill, which is to be expected due to the fact that the gills filter water, but anaerobic bacteria showed high abundance in the intestines.  

The study shows that there is indeed a difference between the deep sea vent species and the two shallow water species when it came to microbiota. This is most likely due to the difference in habitat and food sources of the species. The deep sea species lives in an environment which is a lot harsher than that of the shallow water species, therefore, these novel species found are likely to aid the crab in surviving. whether that is uptake of nutrients in the gut or improved absorption of oxygen in the gills. Further to this the study provides evidence for tissue specific bacteria. 

Paper reviewed: 

Zhang, N., Song, C., Wang, M., Liu, Y., Hui, M., & Cui, Z. (2017). Diversity and characterization of bacteria associated with the deep-sea hydrothermal vent crab Austinograea sp. comparing with those of two shallow-water crabs by 16S ribosomal DNA analysis. PLOS ONE, 12(11), e0187842. doi:10.1371/journal.pone.0187842