Should I burrow?

Marine sediments harbor an abundance of microbial communities and the credit for this, as well as facilitating their biogeochemical processes, goes to bioturbating fauna such as crustaceans, polychaetes, and bivalves that dominate infaunal assemblages (Woodin, 1974) and act as ‘ecosystem engineers’ (Taylor and Cunliffe, 2015). They also alter the geochemical properties of sediments and impact microbial populations. But what about the microbial community in the (neighbouring) sediment that is undisturbed?

Papers mentioned in Taylor and Cunliffe (2015) state that bacterial abundance is greater in burrows than in the surrounding unaffected sediment and the diversity between them is distinct. This is because they provide distinct microhabitats and are geochemically different in composition.

Hediste (Nereis) diversicolor, the model organism in this paper, has semi-permanent burrows that impact sediment geochemical properties by aiding oxygenation of water and mixing of the sediment. Therefore, this study compares the microbial (bacteria and eukarya) diversity between bioturbated sediment (which stimulates oil degradation) and un-bioturbated sediment.

DNA and RNA were extracted from the un-bioturbated sediment (without H. diversicolor) and burrow samples. To assess microbial activity and differences in community, RNA samples from both types of sediments were used for 16S rRNA and 18S rRNA Q-RT-PCR and were amplified. 16S rRNA genes from DNA samples from the two sediments were also amplified by PCR. An Ion Torrent was used for sequencing and the data was analysed using the an open-source bioinformatics software package. Using RISA, they assessed the effect of H. diversicolor on bacterial communities in oil-contaminated sediment. Using a combination of T-RFLP and clone libraries, they assessed the changes in structure of bacterial communities in polluted sediments.

The total eukaryotic and bacterial communities were more active in burrows (18S and 16S rRNA transcripts were significantly higher, respectively). When 18S (for eukarya) and 16S (for bacteria) rRNA transcript OTUs were analysed, the burrow population formed distinct clusters. In H. diversicolor burrows, the orders Alteromonadales, Methylococcales, Oceanospirillales and Thiotrichales were more abundant. According to 18S rRNA sequences, fungi (Basidiomycota) dominated both types of sediment. Through interactions with oil-degrading bacteria, fungi are known to directly degrade hydrocarbons. 

This paper also focused on relative abundance of obligate hydrocarbonoclastic bacteria (OHCB). From 16S rRNA sequences with DNA and RNA gene library analysis, Cycloclasticus were found in high abundance in burrows and were also present in unbioturbated sediment. Alcanivorax, Marinobacter and Oleibacter were also prevalent in the burrows and were either absent or present in low amounts in the unbioturbated sediment. Alcanivorax, Marinobacter and Cycloclasticus have been shown to possess oil degrading properties (Taylor and Cunliffe, 2015).

OHCB has shown to respond to changes, such as oil influx (Taylor and Cunliffe, 2015). Assessment of the impact of the Deepwater Horizon oil spill in the Gulf of Mexico using 18S rRNA gene pyrosequencing showed that fungi dominate post-spill communities too. In H. diversicolor burrows, Cycloclasticus, Alcanivorax and Deltaproteobacteria (major components after the Prestige oil spill) were less abundant and this is due to oxygenation of the burrows causing a switch in metabolism, resulting in more rapid hydrocarbon degradation (Taylor and Cunliffe, 2015). The potential for bacterial communities to remediate polluted sediments is reduced in the presence of bacterivorous meiofauna, which decrease mineralization rates and alter bacterial community structure (Näslund et al., 2010).

This paper provides a good understanding of the relationship between burrowing organisms and microbial abundance and diversity. It also highlights the importance of these microbial communities in natural remediation through the process of degradation of polluted (oil contaminated) sediments. This in turn, gives us an insight into the anthropogenic impacts on the sediment and how organisms that inhabit these sediment cope as a result. To gain a deeper perspective of this, the feature of the burrow (such as lining) and the host invertebrate’s characteristics is important to establish. Although this paper has touched upon some biological limiting factors and Woodin (1974) has demonstrated the importance of biological interactions to the determination of species abundance in sediment, it would be interesting to see the effect of physical limiting factors. Another concept to bear in mind would be the stability-time hypothesis to further explain patterns of diversity of the hosts as well as the microbes. 

Bibliography

Paper Reviewed -

Taylor and Cunliffe. (2015). Polychaete burrows harbour distinct microbial communities in oil-contaminated coastal sediments. Environmental Microbiology Reports, 7(4), 606–613.

Additional references - 

Woodin, S. A. (1974). Polychaete Abundance Patterns in a Marine Soft-Sediment Environment: The Importance of Biological Interactions. Ecological Monographs, 44(2), 171-187.

Johan Näslund, F. J. (2010, May 13). Meiofauna reduces bacterial mineralization of naphthalene in marine sediment. Retrieved from www.nature.com: http://www.nature.com/ismej/journal/v4/n11/full/ismej201063a.html

Charles C. Steward, S. C. (1996, March 28). Microbial biomass and community structures in the burrows of bromophenol producing and non-producing marine worms and surrounding sediments. MARINE ECOLOGY PROGRESS SERIES, 133, 149-165.

The fish gut microbiome under a fisheye lens

Ghanbari et al., (2015) portray how the development of Next Generation Sequencing (NGS) has been pivotal to our understanding of the fish gut microbiome. The relationship between gut microbiota and physiology is complex and influenced by lots of external factors affecting the host. Fish are an excellent model to study the factors affecting intestinal bacterial community due to the diversity of their physiology, ecology and natural history. It is important to understand the dynamics of microbial communities as they are so influential to the host’s physiology.  A comprehensive understanding of the fish gut microbiome will be beneficial for future aquaculture developments. This review highlights the need for a shift from taxonomic to functional profiling of microbial communities through the use of ‘meta’ data.

Recently, NGS technologies are being used for metabarcoding studies to characterize the fish gut – microbiome. This has paved the way for gut microbial analysis as the composition of densely populated microbial communities can be determined rapidly and at a low cost. However, NGS technologies are still limited; for instance, short reads can cause issues with assembling and mapping sequences however longer reads are prone to error readings which may overestimate richness estimates. The caveats listed in the review highlight the complexities of interpreting NGS data.

NGS based studies have used 16S rRNA sequencing to describe the diversity of bacterial taxa associated with the fish gut. Studies have demonstrated that despite high bacterial density, it has an unusually low diversity. This is due to the core gut microbiota concept; the presence of similar fish gut bacteria from different populations that are integral to gut functionality.

In addition to the core gut microbiota, other environmental and host related factors influence bacterial communities. The reviewed studies used a combination of pyrosequencing and metagenomics to assess the origin of bacteria and found that colonization from the surrounding water and sediment is a primary recruitment mechanism. However, other studies, again through 16S rRNA pyrosequencing, have revealed the presence of species-specific microbiota irrespective of environment and life history. These specialized bacteria are selected for by the host and retrieved sequences suggest they benefit the host via vitamin production and food digestion.

In addition, the interaction of feeding habit, diet and genetic factors can also impact bacterial composition. NGS based studies have revealed a trend in bacterial diversity between feeding strategies, as planktivorous fish were found to have a significantly higher diversity than that of omnivorous and herbivorous species. As well as this, diet composition and origin of ingredients were shown via pyrosequencing to significantly influence the abundance of specific taxa. Furthermore, the effect of diet on the abundance of OTUs was significantly different betwen male and female fish. Likewise, one study found an inverse and sex dependent relationship between the allelic diversity of an immune system related gene and bacterial diversity. Interestingly this study suggests that contrary to expectations adaptive immunity constrains bacterial communities.

Lastly, specific treatments can be applied to promote beneficial bacteria, for instance, probiotic and prebiotic supplements. One study demonstrated the use of a prebiotic carbohydrate significantly decreased bacterial diversity, but improved growth performance and boosted immune responses. These recent NGS tools have allowed the modification of diets and treatments to be utilised in aquaculture.

The reviewed studies have largely used 16S rRNA pyrosequencing to assess the effect of factors on the taxonomic profile of the microbial community and highlight the complex relationship between the host, gut microbiome and environment. Future studies should use meta-omic approaches in a high – throughput fashion to address issues regarding metabolic potential and functional impact. This review is important as despite advances in technology it is essential to simultaneously reflect on and develop the approaches being used.

Reviewed paper:

Ghanbari, M., Kneifel, W., & Domig, K. (2015). A new view of the fish gut microbiome: Advances from next-generation sequencing. Aquaculture, 448, 464-475.

http://dx.doi.org/10.1016/j.aquaculture.2015.06.033

Controlling Bacterial diseases in aquaculture

Antibiotics are widely used medicines for controlling diseases both for us and our food. Nowadays, studies worldwide show problems concerning a higher number of pathogenic bacteria strains becoming resistant, increasing health risks. We have high dependency on aquaculture, it is the fastest-growing food-producing business. However, it costs around several billion US$ per year to prevent disease outbreaks and denature those already occurring. Resistant pathogen studies are important in determining how resistance spreads. Defoirdt et al., (2011) states resistance genes, transferable plasmids and integrons are passed via horizontal gene transfer to bacteria, causing diseases such as Salmonella and Cholera. These studies are also important as diseases limit aquaculture development. As a high abundance of untreatable, harmful bacteria grow in waters around shoals, are consequently ingested by fish, they then become treatable. In the absence of diseases antibiotics are still used, causing resistance. Thailand’s 76 shrimp farms received daily doses of 10 antibiotics.

This is an easy to follow review paper detailing other methods, currently tested, for potentially replacing antibiotics. However, methods were not written but referenced other studies, this could have enhanced my understanding. Novel biocontrol strategies have reported success in certain fish and shrimp species, preventing disease. Defoirdt et al , (2011) critically details benefits and constraints of each technique.

1)    Killing one specific pathogen. Using antibacterial agents, bacteriophages specific to infecting target strains, results in decreased resistance and beneficial bacteria harm. Shivu isolated strain-specific phages from shrimp hatcheries and V. harveyi strains, he found lysed phages could not infect other Vibrio sp. Therefore, tiger shrimps (P. mondon) survival increased from 17-86%. However, virulence genes can transfer resistance to phage attachment. Vibrionaceae genomes contain rctB homologues, a perfect target for RctB to inhibit virulence gene replication.

2)    Growth inhibitors. Using short-chain fatty acids in animal diets controls Salmonella and Vibrio’s growth by decreasing intestinal pH, thus, increasing useful microbial communities. One limitation is excess leaching, therefore, high doses are needed. Recently, polyhydroxyalkanoates are added to gastrointestinal tracts producing similar effects, once degraded, to short-chain fatty acids, increasing survival rate.

3)    Inhibition of virulence gene expression. Beneficial as pathogen’s rate of developing resistance is extremely low, however, there is environmental selective pressure. Quarom sensing has two systems in Vibrio’s, first; use N-acylhomoserine lactones (AHLs) as signal molecules in the cytoplasm of Gram-negative bacteria. The second; multi-channel quorum sensing at the cell surface. Both systems regulate virulence gene expression, therefore, interfering with signal molecule detection is a focus. In turbot, lactonase enzymes in Bacillus sp inactivate AHLs. Halogenated furanones also disrupt gene expression preventing vibriosis. Reports however, show it is toxic in slightly higher concentrations than when effective, therefore, a food additive cinnamaldehyde is used. Other quarom sensing inhibiting compounds are produced by algae, corals, sponges, epidiotic bacteria and marine bacterial secondary metabolites. Antivirulence therapy also inhibit specific virulence factors. The cholera toxin in V. chloerae is controlled by the ToxR regulon, expression correlating to its harmfulness, reports of virstatin inhibits gene expression, yet, untested.

                    

This review, in my opinion, suggests antibiotics are becoming outdated. Further work is needed regarding combining new biocontrol strategies for disease prevention, as resistance development still occurs individually. This paper mainly focusses on shrimp aquaculture, including a wider range of species would have benefitted. Therefore, future aquaculture research on farmed species would aid disease prevention. Better or more biocontrol strategies could result, be combined, reducing antibiotic addiction. My knowledge was limited on aquaculture. Thus, novel biocontrol strategies, plus learning the molecular agents are obtained from aquatic organisms, attracted my interest as they link to modern day human medicinal research and species evolution.

Reference

Defoirdt, T., Sorgeloos, P., & Bossier, P. (2011). Alternatives to antibiotics for the control of bacterial disease in aquaculture. Current Opinion in Microbiology, 14(3), 251-258

https://s3.amazonaws.com/academia.edu.documents/45238802/Alternatives_to_antibiotics_for_the_cont20160430-7911-muvuev.pdf?AWSAccessKeyId=AKIAIWOWYYGZ2Y53UL3A&Expires=1508923193&Signature=4MphVgjkwT9GrJAJGCpYHTjsm%2BA%3D&response-content-disposition=inline%3B%20filename%3DAlternatives_to_antibiotics_for_the_cont.pdf