The Path of Least Resistance

Microbes that cause us health problems and considerable expense often live in a biofilm. Inside a biofilm microbes become highly resistant to antibiotics and other methods of eradication – solving this issue is of paramount importance to the healthcare sector…

Microbes are often thought of as free floating, singular, life forms, devoid of senses and very much alone in life. The vast majority of bacteria actually exist in biofilms; which in the simplest definition is the point at which a free-floating bacterium attaches to a surface and starts multiplying. Within biofilms, micro-organisms relay signals that create parts of the biofilm – structures such as water channels and the slime it is protected by. These highly specialised and complex biological systems have been identified in 3.2-billion-year-old rocks in Pilbara Craton, Australia. This early appearance in nature exhibits how integral biofilm production is to microbial organisms. It is not exaggerating to suggest that the biofilm mode of life is the most successful biological system on the planet.

The matrix of slime that the bacteria surround themselves in is composed of carbohydrates, fats, proteins, DNA and other small compounds. This slime protects bacteria from the environment, attaches them to surfaces, allows digestion inside the biofilm and connects cells to one another. It is not surprising that the sticky matrix can constitute up to 90% of biofilm dry mass – it is vitally important to the microbes that live in a biofilm. The components of this slime vary depending on the microbes that are present. Currently our knowledge of the slime matrix is poor; its complexity and the difficulty of measuring substances have caused this.

A fungal biofilm living on a surface.

Biofilms are highly resistant to the immune system, viral attack, UV radiation, physical forces, water loss, biocides, and antibiotics. Increased resistance to the drugs used in hospitals is due to many factors: 1) restricted penetration of the drugs through the slime, 2) slow growth of bacteria (most antibiotics work on microbes that are multiplying), 3) resistant microbes (super bugs), and 4) altered chemical microenvironments. The bacteria within a biofilm can exhibit extremely complex and coordinated behaviour. Cell signalling and quorum sensing, a way of bacterial communication, allows the microbes to sense and respond to the local environment, thereby increasing survival chances. High levels of resistance are therefore related to three major factors – the slime “wall”, bacterial behaviour, and the communities within the matrix. Complexity means the biofilm is extraordinarily resistant to severe conditions.

A biofilm is a major obstacle - defended by its slime "wall".

Bacterial biofilms often form on living tissues (like a sinus cavity or open wound) or on the inert surfaces of medical devices (like pacemakers or replacement hips). A common example of this would be the plaque that is forming on your teeth this very minute – a biofilm that is only kept in check by the mechanical action of a toothbrush. Of the bacterial infections treated by physicians, some 60% are thought to be biofilm related. Conventional medicine treats planktonic bacteria well but traditional therapy can have little effect on biofilms; it is not surprising that after billions of years of adaptation that the biofilm manner of life is resistant to many deleterious agents. Typically chronic diseases arise from biofilm infections; they remain hard to treat, costing health services time and money whilst reducing patient quality of life.

So as mentioned, biofilms cause a variety of infectious diseases and are resistant to conventional healthcare therapy – to solve this problem we need novel ideas. One such promising idea actually hopes to turn the biofilm microbes against themselves. It makes sense that the microbes that form biofilms should have a means of escape, either for spreading to a new location or running from environmental problems. The release of cells requires modification of the slime, usually by enzymes produced from the microbes living inside the biofilm. These enzymes break apart the carbohydrates or proteins that form the sticky, impenetrable slime – thus dissolving it and thereby releasing the microbes from within. Recently scientists have begun to take these enzymes and use them against biofilms, biofilm warfare of the 21st century kind – this appears to be the most promising avenue in the treatment of biofilm infections.

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Ghosts in Tropical Waters

Warm water corals live in association with algal partners (zooanthellae), if these algae leave the consequences for the coral are stark – death or years of vulnerability. Globally such events, known as coral bleaching (because the corals go transparent after algae loss) are increasing in frequency and severity. It’s even been mentioned on Neighbours – why do corals lose their algae?..

The way in which corals and zooanthellae live together, sharing resources, is known as a symbiosis. The algae live inside the coral, sheltered from predators in the water, gaining phosphorus, nitrogen waste and carbon dioxide from its partner whilst giving its host the product of photosynthesis – energy. As such both gain from each other, primarily acquiring increased rates of growth and regeneration – a reason for its evolution. However this relationship is fragile, the algae live life in the fast lane whereas the coral are slow movers, growing over decades and centuries – or in scientific terms, algae have high metabolic rates  (the speed of energy use) and coral have low ones. A way in which the host corals get round this is to increase its own uptake of energy and also try and decrease the photosynthetic output of its zooanthellae helpers. Nevertheless there remains, for all these symbiotic interactions an upper and lower limit within they can occur.

The brown colouration is the zooanthellae inside the coral polyp.

Coral bleaching is a sign that metabolic rates have been changed – and the triggers for this are many: increased/decreased sea surface temperatures, changes in salinity and nitrogen levels, disease, increased sun radiation and others. Most have been caused by a combination of increased water temperatures and sun radiation – during periods of extreme warmth. The last major global bleaching episode was during the El Nino of 1997-1998, a period of unrivalled sea warmth. Since then these events are becoming all too often; this year 90% of Thailand corals have bleached and an alarming 20% have died. Whilst the El Nino of 13 years ago was a freak the rise in sea surface temperatures of the last decade can, in large part, be placed on global warming (be it man-made or a cycle). Corals and the amazing abundance of life that survives nearby is under stress because of this.

To be clear, there is no coherent explanation of why the symbiosis breaks down during warmth. They have always bleached on seasonal variations – but mass bleaching events of late are undoubtedly anthropogenic (man-made) in origin. The triggers are well known but the mechanism of algal expulsion and why the algae relocate is the debate of many a coral reef scientist. One of the most coherent explanations is that it’s a mechanism in which to reduce stress – it is also, the last line of defence against extreme temperatures, usually occurring at 1-2 degrees Celsius above the ambient conditions. Before this coral and algae reduce mortality using fluorescent proteins to scatter light, proteins that absorb ultraviolet radiation, heat shock proteins, a system of oxidant removal (as photosynthesis rates increase oxidants do to, leading to cell damage) and lastly the coral start sustaining themselves through filter feeding as best they can. This happens seasonally, and doesn’t cause long term damage but periods of extreme, or extraordinary, warmth causes a major shift in metabolic rates and a communication breakdown between the partners – zooanthellae are expelled rapidly by the coral. The limits in which a symbiosis can occur has been broken – photosynthesis occurs too rapidly at high temperatures, the host coral cannot cope with the abundance of energy; loss of zooanthellae reduces stress. A large loss of zooanthellae leads to the discolouration of the host and a terminal decline as its own feeding cannot sustain it.

Ghostly white corals litter the sea.

Other scientists think that the bleaching process is actually a way in which to facilitate adaptation to climate change. Ejecting algae that survive best in less warm seas so that new algae can take their place, these ones able survive in extreme warmth. This “Adaptive Bleaching Hypothesis” has gained favour amongst scientists but relies on 5 major assumptions – the main one being that many types of zooanthellae actually exist in one area of coral.

It is important to discover the true reason for loss of algae in corals, although it certainly appears the trigger is increased sea temperatures. The reefs that warm water corals build are extremely important and we must learn more about them – we must protect them.

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Turning Water Into Vinegar

Scientific consensus suggests that as a result of mans CO2 emissions the oceanic carbonate system is changing – lowering the pH of these precious waters, creating a more acid environment. This profoundly changing chemistry could have a major effect on oceanic biology in the near future…

Most people agree that since the industrial revolution began and human society started mass use of fossil fuels, CO2 levels have risen in the atmosphere – at no point in the last 650 thousand years has CO2 existed in such large amounts. In more recent times scientists have discovered that whilst 50% of the CO2 released goes into the atmosphere and warms the planet up, a further 30% of the total amount is absorbed by the seas. This uptake of CO2 has decreased the pH of the oceans by 0.1 units in 250 years, a 25% increase in H+ ions as the scale is logarithmic (although the seas will not be vinegar just yet!). Over the last 20 million years there has not been a sharper change in ocean chemistry – worryingly evidence suggests that the ocean system is at risk from such a transformation.

Organisms are adapted to the conditions they live in at the present, if the environment changes slowly, because of natural selection, there will be few consequences for overall species abundance – what is unknown is how a rapid change will affect an ecosystem. The previous major episode of CO2 increase was 55 million years ago, at a point known as the Paleocene-Eocene Thermal Maximum (PETM). During the PETM temperatures rose by 6 degrees Celsius, and because of the more acid seas led to a widespread extinction of foraminifera; small plankton that typically employ calcium carbonate (CaCO3) shells as a means of housing. Interestingly this period gave rise to a major and Earth history defining proliferation in mammalian species but for this article I am concentrating on the seas. The PETM and recent anthropogenic (man-made) release of CO2 have alarming parallels, and it may give a hint to the future of our seas.


More CO2 in the waters leads to a reduction in available calcium carbonate ions (CO32-) making it harder and more energetically expensive to deposit CaCO3 as a shell. Many of the oceans organisms rely on CaCO3 shells: cold and warm water corals, large algae’s, invertebrates like oysters, and plankton. All species are important in an ecosystem but some are particularly vital to the environmental health of an area – the reef building corals of tropical and cold waters are such organisms. Currently 95% of warm water corals live in areas where dissolution of CaCO3 is not a risk but by 2100 70% could live in corrosive waters – this would lead to a loss of habitat stability and with it most of the fish/invertebrates that shelter in such systems; this would ravage regions. The plankton groups of coccolithophores, foraminifera and pteropods are also globally important calcium carbonate users; pteropods are most at danger, given that they survive in cold waters where the change in pH has a bigger effect. However current science suggests there will be both winners and losers here and nothing is certain.

The last point is an important one; obviously changes in ocean chemistry will not harm all species, it’s important not to loose sight of that. Seagrasses could be the biggest winners with more CO2 in the water leading to increased photosynthesis. Zostera marina, a common seagrass, provides habitats for juvenile fish and therefore an indirect effect of increased seagrass abundance may be more adult fish. Photosynthesis rates have also been shown to increase in some species of plankton and jellyfish are already increasing in abundance in the North Sea due to ocean changes – with a possible threat to other forms of life. What emerges is that the ocean ecosystem is complex, far beyond that of any terrestrial environment and knowing the consequences of anything, from an oil spill to changes in chemistry is very hard to infer from experimentation or computer models.


Seagrass beds could dominate future ocean ecosystems.

Ultimately there is still a need for scientific literature. What we know now is that a change is occurring, some species will become extinct, and others will thrive in a new set of conditions – what we don’t know is how this will affect us over the long term, good or bad.

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Ocean Fertilization – Can Iron Save the Planet?

Does the Southern Ocean hold the key to halting climate change?

Does the Southern Ocean hold the key to halting climate change?

Oceanic iron fertilization is regarded by many as a possible solution to modern climate change. Recent findings presented by Raymond Pollard and colleagues, in the journal Nature, has called this into question; the carbon capturing ability of oceans may be some 15-50 times less effective than previously thought…

John Martin, the late originator of the iron fertilisation idea, once jokingly said “give me half a tanker of iron, and I’ll give you an ice age”; he adamantly believed iron could be used to cool the Earth. Since those words in the 1980s vast areas of the world’s oceans have been classified as lacking adequate iron to fuel plankton growth, so-called high nutrient-low chlorophyll (HNLC) waters. The iron fertilisation theory suggests that artificial addition of iron into these areas could create blooms of algae that would remove excess CO2 from the atmosphere because during photosynthesis this compound is used and integrated into the animals themselves. This CO2 also becomes a part of those that graze from the plankton thus filtering through the food web. Eventually the waste products and dead parts of these “carbon collectors” falls to the seafloor as marine snow and becomes ‘locked’ in the sediments. So this theory if viable in practice, would lead to blooms of phytoplankton and atmospheric carbon removed into ocean floors.

The Southern Ocean is an area that lacks bio-available iron, creating an ecosystem where rates of photosynthesis and carbon export are low. As this ocean covers a large area and has abundant nutrients it is viewed by some as a particularly important potential CO2 sink. A number of recent artificial iron enrichment experiments have been carried out in the Southern Ocean but despite these tests the ability of this ocean to lock carbon away remained poorly understood until the work by Pollard’s team. An alternative to artificial experiments is to study the role of iron in natural areas and the recently conducted research programme, known as CROZEX, during the austral summer of 2004/05 near the Crozet Islands was one such opportunity. The productivity near the two islands is highly affected by the oceanic currents that flow past it and as a result HNLC areas exist, some of which undergo iron fertilisation during the light-limited winter (areas with abundant iron), and others that do not (these areas lack iron).

The CROZEX research team found that plankton blooms at the two regions were markedly different; the one observed in the iron abundant region lasting longer, of a greater magnitude and compromising of different species of phytoplankton to the iron limited area. As a consequence the amount of carbon falling from the surface waters to the seabed was 2 to 3 times higher in the enriched area. Whilst these results support the original hypothesis of John Martin and gave carbon sequestration some 18 times greater than that found during an artificial experiment (SERIES) it was also 77 times less than another bloom that occurred from natural iron fertilisation. Applied on a global scale the findings are short of other geo-engineering estimates by 15 to 50 times.

So the work by Raymond Pollard and others has significant implications for the earlier proposals of climate change mitigation by iron fertilisation, leading some to call this form of geo-engineering “dead in the water”. Certainly more research is required, especially into the indirect effects of fertilisation – how will ecosystems react to phytoplankton blooms in previously barren environments? With commercial groups, governments, lawyers, and environmentalists ready to ‘jump’ on to the idea a clear set of regulations and directions is needed to safeguard the future; the last thing we need is an iron experiment after the carbon experiment.


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