Bioluminescent species are part of the oceans ecosystems in much the same way as any other species of deep-sea fish; as a result are exposed to the same threats as the non luminescing organisms they share their habitats with. Current threats to the organisms in the deep sea are similar to those of coastal and pelagic organisms in respect to over fishing, climate change and ocean acidification.

The difference between fishing in coastal waters and that of the deep sea is the number of laws in place to prevent overfishing. The deep sea is outside of any countries boundaries and therefore there are no regulations controlling what and how much of a resource is taken; therefore there is a high risk of exploiting many species (Davies et al. 2007).

The life history of many deep-sea species means that a small change to the population size could have a large effect in the long term. Many species have high longevity, grow slowly, reach maturity at a late age and have low fecundity (Davies et al. 2007). Over the last 50 years there has been an observed shift in fishing areas to deeper water (Rhul & Smith 2004), which is increasing the risk of exploitation of already vulnerable species in these areas. Direct results of climate change such as change in ocean currents have also been seen to have an impact on reproduction, oxygen consumption and growth rates in the deep sea (Davies et al. 2007).

Ocean acidification also is at risk of changing the balance in the deep sea, as it is known to reduce the productivity and therefore plankton abundance (Raven et al. 2005). A reduction in the productivity may result in reduced food sources for both benthic and pelagic organisms. Usually 2-4% of the spring bloom will reach the sea floor (Gooday 2002), providing benthic organisms with a regular food supply which would be significantly reduced with a decrease in surface productivity.  Many pelagic species undergo large diel migrations in order to feed on the produce of the surface waters (Widder 2002). These organisms would also be heavily affected should this food source become depleted.

Our understanding of the organisms of the deep sea, bioluminescent organisms in particular, is still very limited. As a result the exact consequences of anthropogenic activities on such species are unknown. In light of this we need to take extra care around these areas to ensure that these species and the ecosystems they are part of are preserved. One way of ensuring this happens is to create marine protected areas which are carefully controlled and managed (Davies et al. 2007) with suitable consequences for those who do not abide by the laws of theses areas.

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