In situ grazing experiments on Deep Sea microbial food webs

Protists interact in several ways with bacterial and archaeal populations which has the effect of substantially shaping the structure of these communities within the marine environment.

Protists graze using a mode of nutrition called phagotrophy. This method of grazing can affect the activity, quantity and physiological state of the prey organisms, these factors can lead to protists exhibiting prey preferences. An assemblage of protists feeding in this manner may graze on anything from 25% to >100% of the daily production of prokaryote plankton.

A study carried out by Pachiadaki et al (2014) looks at the grazing activities of phagotrophic protists in the Eastern Mediterranean Sea at depths ranging from 40m down to 3540m at the redoxcline in the Urania basin. The Authors of this paper carried out the first in situ incubation of samples and due to the fact that the sample was being suspended at depths of 40 - 3540m for periods of time extending from 4 – 16h they were not able to carry out replicates of the full experiment and only managed to replicate the counts of the organisms in each treatment. Two variations of the experiment were carried out. Both experiments used fluorescently labelled prokaryotes (FLPs) to track the grazing impact of the protistan communities. The experiments differed in the length of incubation. The shorter incubation experiments were used to trace the ingested FLPs; the longer incubation times were used to estimate the rate of disappearance of the FLPs.

The study found that both prokaryotic and Protistan abundance fell between the euphotic zone and mesopelagic zone. The difference came when the abundance of prokaryotic cells stabilised the deeper the sampling went into the mesopelagic layer whereas the protistan abundance continued to fall with depth. The samples at the greatest depths of 3000m and 3540m showed an increase in not only prokaryotic and protistan abundance but also showed elevated rates of daily prokaryotic turnover. This was especially noticeable at the Urania interface where the turnover rate was greater than that measured in the photic zone at 40m. The increased abundance of both prokaryotic and protistan cells was in conflict with previous counts but this unusual increase in abundance was put down to a resent eruption of a mud volcano in the vicinity of the test area.

This study provided a good insight to the microbial assemblages at varying depths and the effects of protistan grazing on the prokaryotic communities present. It also proved that in situ incubation and sampling of cultures is possible although the technology does need some improvement to be able to replicate the whole experiment to increase the reliability of future experiments.

Pachiadaki, M. G., Taylor, C., Oikonomou, A., Yakimov, M. M., Stoeck, T., & Edgcomb, V. (2014). In situ grazing experiments apply new technology to gain insights into deep-sea microbial food webs. Deep Sea Research Part II: Topical Studies in Oceanography.

From Microcosm to the Ocean

Protists have long been used as model species in various biological disciplines from cell to molecular biology. However, to this day they aren’t commonly used in marine ecology.

Protists are found in all marine habitats and are important components of all processes and food webs. They occupy every position from primary producers to parasites. Moreover, they are generally easy to cultivate and new molecular methods ease the in depth study of protists. Yet, most studies focus on bacteria to study macro ecological theories on microbes. In their review based on presentations at the VII ECOP/ISOP meeting in 2015, Weisse et al. (2016) outline the framework and methods for macro ecological studies on protists and advocate to revive aquatic protists as model organisms in conceptual studies. 

The focus of the review lies on functional ecology of aquatic phagotrophic protists, both heterotrophic and mixotrophic. Weisse et al. define functional ecology as the functions of a species in an ecosystem or community and the application of ecological models from the organism to whole ecosystems. As protists are important grazers in aquatic environments, their study is vital to understand the impact of various intensities of grazing due to seasonal, horizontal and vertical variability. Nevertheless, the transfer from laboratory to the ocean is very challenging. Research is usually carried out under controlled and very specific conditions, using one species in a microcosm. This approach is problematic in as it selects for species which are able to survive in specific environments and in situ conditions are notoriously difficult to mimic. Furthermore, prolonged captivity is shown to cause changes in feeding rhythms and in behaviour under stress. Also, single strain cultures eliminate intra- and interspecific interactions. Weisse at al. stress the importance for more detailed data on phagotrophic protists and outline possible methods to standardize future research.

While the review is said to focus on phagotrophic protists, Weisse et al. often use more general descriptors such as heterotrophic, autotrophic and mixotrophic. Thus most of the review could presumably also be applied to other types of protists. Interestingly, Weisse et al. refer to an online repository on methods for conceptual studies on protists (Altermatt et al. (2015)), but only to acknowledge that interest in protists as model organisms in ecology has been revived recently. Even though they strongly encourage fellow scientists to expand their research on protists, they do not further refer to the open access archive on various methods.

Reviewed Paper:

Weisse, T., Anderson, R., Arndt, H., Calbet, A., Hansen, P. J., & Montagnes, D. J. (2016). Functional ecology of aquatic phagotrophic protists–Concepts, limitations, and perspectives. European journal of protistology. Link: http://www.sciencedirect.com/science/article/pii/S0932473916300189

Further Reading:

Altermatt, F., Fronhofer, E. A., Garnier, A., Giometto, A., Hammes, F., Klecka, J., ... & Plebani, M. (2015). Big answers from small worlds: a user's guide for protist microcosms as a model system in ecology and evolution. Methods in Ecology and Evolution, 6(2), 218-231. Link: http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12312/full

Schmoker, C., Hernández-León, S., & Calbet, A. (2013). Microzooplankton grazing in the oceans: impacts, data variability, knowledge gaps and future directions. Journal of Plankton Research, 35(4), 691-706. Link: http://plankt.oxfordjournals.org/content/35/4/691.full.pdf+html

Death by grazing or viral lysis?

Before Proctor and Fuhrman (1991) started to research viral infection and mortality of cyanobacteria, protozoan grazing was considered the main cause of cyanobacteria mortality, although the mechanisms of this were poorly understood. Their findings in this paper showed uncertain results as to just how much mortality viruses were responsible for, due to the difficulty in differentiating between viruses simply being attached to the hosts, or viruses infecting their hosts via the lytic cycle. Due to this, many scientists have used this paper as a basis to try and find out just how many microbes are killed via viral lysis or grazing.

One such paper published by Tsai, Gong and Chao (2016) looked at nanoflagellate grazing and viral lysis on bacterial mortality in the Subtropical Western Pacific. Using two different depths and a modified dilution technique, their results showed that nanoflagellate grazing was the highest cause of bacterial mortality at the shallowest depth (81-87%), whereas viral lysis was the highest cause of bacterial mortality at the deepest depth (67-75%). 

Whilst this study was successful in identifying the percentages of bacterial mortality due to viral lysis and nanoflagellate grazing, and therefore how the nutrients are flowing within the food web, it only gives an image of what is happening at the two depths that were studied in the one specific area of the subtropical western pacific. Whilst other studies have been conducted to look at how this changes due to season, host organism and environmental conditions, these factors are still poorly understood, particularly in this region. This suggests that this study is a good starting point in determining how nutrients enter the food web at the different depths, as many of the previous studies to date have focused on shallow waters. However, further study is needed to understand the carbon cycling under these different conditions, and also on a global scale. It seems there are a lot of factors to consider when researching this topic, and so there is a lot of room to experiment. It will be interesting to see whether grazing or viral lysis is responsible for the most bacterial mortality when tested under other conditions, especially in deeper waters.

Proctor, Lita. M., and Fuhrman, Jed. A. (1990). Viral Mortality of Marine Bacteria and Cyanobacteria. Nature, 343: 60-62 http://www.nature.com/nature/journal/v343/n6253/pdf/343060a0.pdf

Reviewed Paper: Tsai, A., Gong, G. and Chao, C. F. (2016). Contribution of Viral Lysis and Nanoflagellate Grazing to Bacterial Mortality at Surface Waters and Deeper Depths in the Coastal Ecosystem of Subtropical Western Pacific. Estuaries and Coasts, 39(5): 1357-1366 http://link.springer.com/article/10.1007/s12237-016-0098-9