Phytoplankton Numbers Plummet due to Global Warming

A review of: Boyce, D. G., Lewis, M. R., and Worm, B. (2010) Global phytoplankton decline over the past century. Nature 466: 591-596

Recent research has suggested that phytoplankton numbers are plummeting. Marine phytoplankton are important marine organisms, strongly influential in major climatic process and biogeochemical cycles as well as being responsible for over half of global primary production. A decline in phytoplankton numbers does not just threaten ocean processes and diversity. Three billion people depend on seafood as part of their diet and nearly one tenth of the world’s population depend on the fisheries industry.

Perhaps the most obvious suggestion for this decline can be found in global warming. More than 90% of the heat retained by the Earth due to greenhouse gases end up in the sea. This causes surface waters to warm and as they do so, become less dense, preventing colder nutrient-filled waters to rise to the surface. This, in turn prevents the waters mixing and so, the phytoplankton in the warmer waters run out of nutrients required for growth. In this article, the authors compile and analyse in-situ chlorophyll (Chl) and ocean transparency measurements collected over the last century, to investigate the changes in phytoplankton biomass and to see whether this is in fact happening.

The authors found that in 59% of the data used, there was a decline in phytoplankton numbers. It was also observed that Chl declined more rapidly, the further the distance from land. They suggest this may be due to an increasing intensity of vertical stratification and ocean warming. The global oceans were then split into ten regions in which to evaluate regional trends and found that there was phytoplankton decline in 8 of the 10 regions. The largest declines were found in the South and equatorial Atlantic regions.

All in all, the analysis suggested that global Chl concentration and therefore phytoplankton biomass had declined over the last century, and has declined by almost 40% since the 1940s. Evidence from the analysis related primarily to climate variation, particularly to rising sea surface temperatures. These results are therefore consistent with the hypothesis that increasing ocean warming is changing the marine ecosystem with implications for both biogeochemical cycling and population numbers. The authors hope that this study provides an incentive for greater observation and remedial action.

Additional reference: Holmes, B. (2012) Too-blue oceans: The invisible famine. New Scientist 2859

Plenty of extracellular DNA makes your community stronger

Biofilms are formed by aggregates of bacteria and are held together by extracellular polymeric substances (which consists of a mixture of substrates of bacterially produced polymers), one of these constituents is extracellular DNA (eDNA), it's role is not clearly understood. The advantages of biofilms are thought to be: protection against desiccation, mechanical sheer strength and chemical toxins. The composition of EPS is varied and is dependent on the species present in the biofilm and the growth conditions. Generally speaking it mainly consists of three compounds: polysaccharides, proteins and extracellular DNA. Recent research indicated eDNA is frequently a component of many biofilms. Documented species that produce eDNA are: Pseudomonas aeruginosa, Neisseria gonorrhoeae, Staphyloccocus epidermidis, Shewanella sp., Acinetobacter calcoaceticus and Bacillus subtilus. eDNA is present in both natural and synthetic environments and comprises of up to 70% of total DNA pool in a biofilm and typically ranges from 2 mg g^-1 to 300 mg g^-1. It is thought to originate from either cell lysis or be secreted from live cells. The production of eDNA in P.aeruginosa have been linked to quorum sensing. Research indicates eDNA has several roles: a nutrient source during low nutrient conditions, phosphorus cycling in sea sediments, horizontal gene transfer, and structural strength. The abundance and importance of eDNA in bacterial complexes is not well documented, the authors attribute this to a lack of stable methods for quantitative in situ studies. Methods that are used are qPCR, spectrophotometric detection, DAPI, SYTO, DDAO and PI stains. The aim of Dominiek et al.'s research was to further develop in situ techniques for quantitative analysis of eDNA in mixed biofilms and activated sludge flocks. Their technique was simplistic and combined refining staining methods with in situ hybridisation (fish) for the identification of microbes.

Their staining results indicate that most of the eDNA was found around living cells, more specifically there was increased abundance around microcolonies of certain species of bacteria, which suggests there is variation in the production of eDNA among species. This supports the hypothesis that eDNA originates from live cells, however, it is also suggested that it may provide evidence that sub microcolonies are releasing eDNA during lysis. Confocal FISH images of extracellular floc before and after a 60 minute DNase 1 incubation, showed there was a loss in eDNA as a result of its degradation. Their quantitative results indicate eDNA ranges from 50 to 300 mg g^-1. Fish results reveal that some species in particular produce high levels of floc eDNA: Curvibacter, Thauera, Nitrospira, Accamulibacter and Campetibacter. These were found in three Danish waste water treatments. Results also demonstrated that eDNA provided structural integrity for the biofilms.

The main discussion points are: 1. eDNA is an important component of ESP. 2. The different contents of eDNA in activated sludge in different tested treatment plants is most likely due to different microbial populations. 3. Most eDNA was found around living cells, suggesting active production of this polymer. 4. DNase 1 had substantial defloculating effects on the entire biofilm floc and also indicated low levels of eDNA impacted the EPS matrix and had consequences to floc strength. 5. Structural biofilm strength resulted in better performance in pressure dewatering conditions and gravity drainage, finally 6. The species composition influences the properties of the EPS and thus its function.

The methods they developed to quantify the abundance of eDNA proved effective. New evidence was gathered about particular bacteria that are strong floc producers. This research presents further detailed insight into the structure of constituent parts of biofilms. What I found surprising is that DNA holds a key structural role, I would have thought that cheaper to produce macromolecules would have been used. This leads me to postulate that eDNA plays other roles within biofilms e.g. transformation and nutrient cycling and cellular communication.

Dominiak, D. M., Nielsen, J. L., Nielsen, Per H., (2011) Extracellular DNA is abundant and important for microcolony strength in mixed microbial biofilms. Environmental Microbiology 13(3), 710-721

Oil Bioremediation

A review of: Lü, J. C., Li, Z. T., Hussain, K., and Yang, G. K. (2011) Bioremediation: The New Directions of Oil Spill Cleanup. Middle-East Journal of Scientific Research 7(5): 738-740

Oil pollution is an increasing concern, particularly with the ever increasing demand. With this increasing level of pollution, an effective solution for the environment is required; bioremediation is one such effective method. This paper looks at current knowledge in bioremediation including its techniques, advantages and disadvantages, particularly as a pollution control mechanism.

Bioremediation is the breakdown of dangerous or hazardous chemical and contaminants using microorganisms to break down and detoxify by transforming them into less harmful substances. This can take advantage of a naturally occurring metabolic pathway or through the genetic modification of the microorganism. Bioremediation can be used both in marine and terrestrial pollution and can take place in-situ (treated at the site of contamination) or ex-situ (the contaminated material is removed for treatment elsewhere). For marine environments, in-situ treatment is the only really viable option in most circumstances. Bioremediation can also be done both aerobically (through the addition of oxygen either by injection or the addition of nutrients) and anaerobically. Techniques outlined in this paper include; bioangmentation (involves the addition of microorganisms that can degrade a particular contaminant, biostimulation (the addition of nutrients to increase the level of activity) and bioventing (the addition of oxygen).

The advantages of bioremediation generally outweigh the disadvantages. The authors state that bioremediation is generally more economical than using other methods of treatment since it can be performed in situ and, in marine environments, there are plenty of microorganisms present for bioremediation to occur. It also has the advantage of being a natural process and therefore is expected to have minimal environmental impact. However, bioremediation may not be an instantaneous process, mostly it isn’t. It can take weeks or months depending on the amount of pollution and additional nutrients and/or microorganisms may be required for this method to be effective. As well as this, some contaminants may not be biodegradable, limiting the practical uses of this method.

Bioremediation is therefore an effective, low cost, naturally occurring method that can be of particular use in certain circumstances of pollution, such as in the marine environment. However, its scope of use is limited and so can only really be used for certain types of contaminants, such as oil pollution. The authors mention the use of microorganisms to degrade metals and research on this would certainly be valuable to increase the usefulness of this method and to help introduce methods of pollution control that are ‘environmentally friendly’.

Marine isoprene-degrading bacteria

A review of: Alvarez, L.A., Exton, D.A., Timmis, K.N., Suggett, D.J. & McGenity, T.J., (2009), Characterisation of marine isoprene-degrading communities, Environmental Biology, 11(12): 3280-3291

Isoprene is the second most abundant natural hydrocarbon in the atmosphere. It is volatile and can result in the formation of tropospheric ozone, the third most powerful greenhouse gas. Marine algae are known as a significant source of isoprene, whilst some freshwater bacteria are able to degrade the compound. Despite its high energy content, only hints of isoprene degradation in marine and coastal environments have been observed. Significant proportions of gases like methane are oxidised before they can enter the atmosphere and models of marine isoprene flux assume a bacterial sink, however clear evidence is still lacking. This study aims to determine the extent of isoprene degradation in marine environments, whilst identifying the organisms responsible and their relationship with the microalgae.

All samples were taken from various points in an estuary. Isoprene-degrading bacteria obtained from the samples were cultured on agar in isoprene-saturated atmosphere and analysed by DGGE and pyrosequencing of the 16s rRNA genes. Some were also incubated with phytoplankton species to analyse their relationship.

They found that Isoprene concentrations decreased from the head of the estuary to the mouth. They noted that the higher nutrient levels at the head of the estuary elevated microalgal production in the water column which may have led to the higher levels. Isoprene added to the samples of the marine and estuarine water and sediment slurry was significantly degraded, with degradation at least an order of magnitude faster in sediments then water samples and the onset and rate of biodegradation being more rapid at the head of the estuary then at the mouth. Also interestingly, biodegradation was more than 10-fold faster in all samples when isoprene was added at 0.001% than when added at 0.1% v/v, suggesting that degradation is favoured at lower concentrations. It could also be that the high concentrations may have killed the degraders, as isoprene and its degradation products can be toxic.

The degrading bacteria were mainly Actinobacteria, such as Rhodococcus, which were found in all samples and seem to be the main organism responsible for isoprene degradation in coastal samples. Bacteroidetes and Psuedomonas were also present, which were not previously known as isoprene-degraders. Studies generally suggest that Bacteriodetes benefit from the extracellular polymeric substances produced by algae, however this study explains that isoprene is also an important algal product that supports bacterial growth.

They also found that isolated isoprene-degrading bacteria are nutritionally versatile and most degrade n-alkanes for carbon and energy. They explain that isoprene-degrading capacity is widespread in diverse phyla, questioning whether such microbes are specialist isoprene degraders or generalists. In contrast to specialist methane-oxidizing microbes and many coastal microorganisms, these degraders opportunistically utilize a wide range of compounds from the dissolved organic carbon pool. Suggesting that, in the absence of spilled petroleum hydrocarbons, algal production of isoprene could maintain viable populations of hydrocarbon-degrading microbes.

This study confirms that Isoprene-producing algae support the growth of a mixture of isolates which utilise the carbon source and act as marine isoprene-sinks, overall providing a clearer picture of the relationship between consuming bacteria and producing algae and how this affects the isoprene flux and the proportion emitted into the atmosphere.

Silver nanoparticles as a cause of oxidative stress in microalgae

            Silver nanoparticles (AgNPs) are one of the most widely used nanomaterials in products across industries. They are often used for their antimicrobial activity in medicine and are also often found in detergents. Unfortunately these nanoparticles are highly mobile and easily transported into aquatic systems and although AgNPs are beneficial to us, in the products previously discussed, they have been shown to have a negative impact on marine ecosystems, the extent of which is not yet known. As the nanoparticles have such a large surface area to volume ratio it is thought that AgNP react strongly with compartments within and outside of the cell which may cause problems such as an increase in free radical production, causing oxidative stress, which may fatally damage the cells

            This paper investigates the detrimental effects of AgNPs on two species of microalgae; Chlorella vulgaris, a freshwater species, and Dunaliella tertiolecta, a marine species. The two species of algae were exposed to varying concentrations of AgNPs (0 mg/l, 0.01 mg/l, 0.1 mg/l, 1 mg/l and 10 mg/l) for 24 hours. They investigated the damage done to the different algae and different exposures using a number of methods. Any morphological changes between the different exposures were recorded. As well as this the total chlorophyll, amount of viable cells, amount of reactive oxygen species (ROS) formation and amount of lipid peroxidation were measured.

            It was found that both algal species showed cell aggregate formation (at 0.1 mg/l AgNPs) compared to the control (o mg/l) and it was also found that at 10 mg/l AgNPs C. vulgaris formed large aggregates. It was also found that the total chlorophyll count decreased with increasing concentrations of AgNPs in both species of algae. The total chlorophyll in D. tertiolecta was 75% (of the total chlorophyll in the control) at 10 mg/l in comparison to 50% in C. vulgaris. The number of viable cells also decreased with increasing AgNP concentration and there was a drastic decrease in viable cells at 10 mg/l with 4% (of the viable cells in the control) in D. tertiolecta and a 12% in C. vulgaris. The amount of lipid peroxidation and ROS levels (both per viable cells) increased with increasing concentration. It was also found that the amount of lipid peroxidation and ROS levels in D. tertiolecta were much higher than those in C. vulgaris.

            The results of this paper clearly indicate that both of the species of algae are badly affected by the presence of AgNPs at concentrations as low as 0.01 mg/l and that at 10 mg/l the production of ROS increases dramatically.  D. tertiolecta, the marine species, is more severely affected by AgNPs, It is however thought that this may be because more chloride is present in the seawater growth medium, in comparison to the freshwater growth medium, and that this chloride augments the toxic effects of silver. As algae play a vital role in oxygen production and are involved in the food chain the presence of AgNPs may have a huge effect on the wider aquatic community and it is therefore clear that something needs to be done to reduce the amount of AgNPs being leaked into the environment.

Reference: Oukarroum, A., Bras, S., Perreault, F., & Popovic, R. (2012). Inhibitory effects of silver nanoparticles in two green algae, Chlorella vulgaris and Dunaliella tertiolecta. Ecotoxicology and Environmental Safety, 78, 80-85.

The impact of silver nanoparticles of marine biofilms

Nanoparticles are particles with at least one dimension between 1-100nm, the use of silver nanoparticles in industry has increased over recent years due to the bactericidal capacity, low cost and ease of handling. Silver nanoparticles (AgNPs) are used in products such as cosmetics, plastics and clothing. Due to the increase in their use the potential for their release and accumulation into the environment has also increased. The environmental risk of AgNPs is not yet understood, some studies suggest that there is limited environmental risk, however due to the antibacterial properties of AgNPs there is potential for them to have detrimental effects on natural bacterial communities. Bacteria are primarily found in the marine environment as biofilms, and understanding the effect of AgNPs on bacteria is extremely important because biofilms are primary producers in many ecosystems and also they are responsible for environmental processes such as biogeochemical cycling. Furthermore there may be adverse effects as a result of AgNP exposure on wastewater microorganisms; this may result in the decrease in the effectiveness of contaminant removal in biological treatment processes.

The aim of the study was to assess the impact of AgNPs on waste water biofilms microbial community structure. The author hypothesised that the impact of AgNPs would be dependent on the strain of bacteria and also the impact would differ between planktonic cells and those in a biofilm. To assess their hypotheses, both original wastewater biofilms and isolated planktonic pure culture bacteria from the biofilms were exposed to AgNPs. Possible protective mechanisms in the biofilm were investigated, such as physical exclusion due to the effects of EPS. The role of community interactions was also studied using an artificially mixed community to verify any effect on the community interaction. To analyse community shift after AgNP exposure PCR-DGGE was used. Three terms were proposed to suggest the response of the microbes after AgNP exposure. Tolerance was where the sample survived under the AgNP treatment, susceptibility and sensitivity were used to describe their ability to react to AgNP exposure.

The study found that bacterial biofilms are highly tolerant to AgNP exposure, after 24 hours of 200 mg/l exposure the heterotrophic plate counts were insignificant. However if the Extracellular polymeric substances were removed the bacteria became highly susceptible under the same conditions. Furthermore if bacteria from the biofilm were treated as planktonic cells they were highly sensitive to AgNP exposure with most cells dying after 1 hour of 1mg/l exposure. These results suggest that the EPS and the microbial community interactions play an important role in effect the way AgNP exposure effect the bacterial cells. The study also found that slower growing strains WWBF-3 (CFB group bacterium) and WWBF-5 (Microbacterium oxydans) were more tolerant to AgNPs than the faster growing strains, previous studies have also documented the fact slower growing bacteria are more resistant to antibiotics. Although the reason has not been highlighted in the paper, it can be speculated the reason for this is that if the antibiotics are a β-lactam antibiotics, which only lyse growing cells, a slower growing community would have less chance for cells to be lysed and hence the lower effect of antibiotics on these strains.

In the paper it is outlined that during the study the AgNPs were found to be sorbed to biofilm matrix, indicating a removal of NPs from wastewater into the biofilm. This finding I feel is extremely important, as biofilms are a primary food source in many ecosystems incorporations of NPs in the biofilm may result in transfer of NPs through the food chain.

A review of : Sheng, Z., Lui, Y. 2011. Effects of silver nanoparticles on wastewater biofilms. Water Research. 45 (18), 6039-6050.

Efficacy of in-feed probiotics vs. skin infections for the rainbow trout.

A review of: Pieters, N., Brunt, J., Austin, B., & Lyndon, a R. (2008). Efficacy of in-feed probiotics against Aeromonas bestiarum and Ichthyophthirius multifiliis skin infections in rainbow trout (Oncorhynchus mykiss, Walbaum). Journal of applied microbiology, 105(3), 723-32.

Aquaculture has been a rapidly growing industry for a few decades now and there have been some problems involved with growing fish outside of their natural habitat. Disease, parasites and welfare/ stress of the fish have been common issues within aquaculture and the introduction of probiotics has helped to relieve the pressures of some individual cases as shown by Ferguson et al, (2010), where his investigation found that oral supplementation of Pediococcus acidilactici stimulated some aspects of immune response of the red tilapia (Oreochromis niloticus).

In this study the authors investigated the efficacy of in-feed probiotics against skin infections caused by Aeromonas bestiarum (A. bestiarum) and Ichthyophthirius multifiliis (Ich) in the rainbow trout (Oncorhynchus mykiss, Walbaum). They did this by inducing both of the skin infections by intradermal injections directly into the dorsal fin base, each of the probiotics were administered orally (108 cells per g feed for GC2 [Aeromonas sobria] and 1010 cells per g feed for BA211 [Brochothrix thermosphacta]) for two weeks. At the end of the feed trial the trout were dissected aseptically and blood and kidney samples were taken. The authors then counted blood cells and used several assays to look at the pinocytic, chemotactic, alternative complement pathway (ACP), serum lysozyme and epidermal mucus lysozyme activities the authors also looked into intracellular respiratory burst assay and Epidermal mucus total protein concentration.

The results showed for skin infection A. bestiarum probiotic GC2 led to 76% survival and BA211 led to 88% survival compared to the control which only had a 22% survival rate. For the infection Ich the probiotic GC2 led to 100% survival BA211 led to 2% survival and the controls had a survival rate of 0%. The analysis of innate immune responses showed that probiotic GC2 resulted in higher phagocytic activity, whereas probiotic BA211 showed enhanced respiratory burst activity.

The authors conclude that GC2 was the more effective probiotic although both probiotics stimulated different pathways in the innate immune response system. This study is of great significance as it was the first to show that probiotics could be used to treat epidermal skin infections which can be applied in aquaculture of rainbow trout.

Reference: Ferguson, R. M. W., Merrifield, D. L., Harper, G. M., Rawling, M. D., Mustafa, S., Picchietti, S., Balcázar, J. L., et al. (2010). The effect of Pediococcus acidilactici on the gut microbiota and immune status of on-growing red tilapia (Oreochromis niloticus). Journal of applied microbiology, 109(3), 851-62.