Coral reefs: ship-wrecked?

A review of Kelly, L.W et al (2011) Black reefs: iron induced phase shifts on coral reefs, The ISME Journal.

Several pristine coral reefs, isolated from pollution and human activity, lie in the central Pacific surrounded by the Line Islands (LI). The reefs have flourished due to the rich supply of calcium carbonate and also the lack of iron. However, black reefs, characterised by high abundance of algae, cyanobacteria and corallimorphs, a significant loss of corals and crustose coralline algae (CCA) have increased around the islands and researchers have linked these to shipwrecks reported in the area, which release iron-rich debris, polluting the reefs. Similar phase shifts, where conditions favour algal growth in normally coral-dominated ecosystems, have been documented on the Phoenix Islands and were also found offshore of Sumatra, where wildfires caused iron-rich ash deposits on the surrounding reefs and killed nearly 100% of corals. However, few studies have measured the iron availability to benthic organisms in reefs and therefore are unable to directly link wreck debris to the formation and maintenance of black reefs.

This study aims to show the detrimental impact of iron enrichment on reefs in normally iron-depleted oceans such as the LI. Research was focused on 3 black reefs, Millenium atoll, Tabuaeran and Kingman. Chemical analysis and iron concentrations from the reef algae and rubble were measured, the effects on coral, algae and associated microbes were documented and the microbial communities were identified to the lowest taxonomic level possible using metagenomics and counted using epifluorescence microscopy.

Looking at the natural history of the black reefs, researchers concluded that they (1) are always congruent with sources of iron, such as wrecks; (2) develop quickly, such as at Kingman, which harboured the second highest coral diversity in the central Pacific and in less than 3 years the CCA cover alone had declined to <10% and D.teniussima, a green algae had increased to 80%; (3) persist for decades, such as at Tabuaeran, where effects are persistent after 40years and there is little coral recovery, and (4) have similar biotic composition, in terms of turf algae, cyanobacterial mats and corallimorphs. Millennium atoll, for example, was characterised by a high abundance corals, CCA and low abundance of benthic algae prior to the 1993 shipwreck. After, turf algae and cyanobacterial mats formed and benthic coral cover was 16.7% compared to 65.9% on surrounding reference sites.

Iron concentrations also increased at the sites, specifically 6 times higher at the millennium site (~663μmol) in comparison to reference site samples (~105μmol), showing that iron is being recycled and accumulating in the algae, allowing it to spread kilometres away from the wrecks, carrying iron with them.

These findings are also supported by Martin et al (1994) who determined that low primary production despite the low-chlorophyll and high nutrient, phosphorous and nitrogen in the LI, is due to the limited iron levels, as after iron addition, there is rapid increase in primary production.

Furthermore, P.meandrina coral collected from a reference site was incubated in the presence or absence of ferric chloride and algal-covered rubble from the black reef. Results showed that coral incubated in both iron and rubble had the largest mortality (50% dead, 20%dying) and when using antibiotics to modulate the microbes, the mortality rate decreased, determining the detrimental effect of reef-associated microbes on coral.

Microbial communities also differed significantly between the black reefs and healthy reference sites. The black reef microbial abundance was three times higher and 10-fold more heterotrophic microbes as well as 2- to 10-fold more opportunistic coral pathogens and iron-associated virulence factor genes were present, suggesting that iron promotes subsets of virulent microbes which import iron to flourish.

Due to the results and background support, the researchers have concluded that large-scale algal overgrowth on at black reefs is due to iron supplementation.

This study has helped to confirm the links between iron-enrichment and the destruction of coral reefs. They also extended the experiment by looking at other variables such as algal mats and how they damages, spread over large areas and prevent coral recovery even without the presence of iron. This emphasises the major impact that abandoned wrecks are having on marine ecosystems and that simply attempting to remove the iron is just not enough. Much emphasis has gone onto global warming and its effect on reefs , but perhaps more focus needs to be put on other contributory factors, like these wrecks and other man-made debris, that are left abandoned in the sea, damaging the decreasing, sensitive, pristine coral reefs.

Other references: Martin, J.H et al (1994), Testing the iron hypothesis in ecosystems of the equatorial Pacific-Ocean, Nature 371: 123-129

Shipwrecked? Have no fear ‘Black Reef’ microbial community shunts will engulf you!

Black reefs: iron-induced phase shifts on coral reefs.

L W Kelly, K L Barott, E Dinsdale, A M Friedlander, B Nosrat, D Obura, E Sala, S A Sandin, J E Smith, Mark J A Vermeij, G J Williams, D Willner, F Rohwer (2011)

The ISME journal p. 1-12

The Line Islands are calcium carbonate coral reefs >0.75km² in size. These reefs are situated in iron poor regions of the central pacific. These islands are uninhabited and are not exposed to point sources of pollution, apart from shipwrecks, which have been documented on several of the line islands and surrounding reefs. There are also shipwrecks on carbonate atolls throughout the pacific.

In the Line islands, areas surrounding the shipwrecks become Black Reefs. They were noted by Kelly et al. 20011, to be characterized by high levels of turf and macroalgae, cyanobacterial mats, corallimorphs and an extensive loss of corals and crustose coralline algae. It was noted by the authors that similar community phase shifts in response to shipwrecks have been documented on other coral reefs. Literature flags up Rhodactis howesii has spread over coral reef terrace on Palmyra atoll, which also had a shipwreck (work et al., 2008). Authors referenced several cases of community phase shifts hypothesised to occur as a result of shipwrecks. It was also documented in the introduction that iron fertilization from the aftermath of wildfires in Indonesia (iron rich ash) enriched the coastal waters, which led to an explosion of dinoflagellates that suffocated and killed 100% of corals. Perhaps due to these literature insights and the fact that iron concentration is extremely limited in the Line Islands the authors hypothesised that: 1) Iron limits primary production of algae and cyanobacteria on central pacific coral atolls where there are no emergent basaltic rocks; 2) on these atolls shipwrecks associated iron release, releases these primary producers from bottom up control and 3) the resulting communities of fleshy algae cyanobacteria either directly compete with the coral or they promote bacteria that kill corals.

Kelly et al. used a combination of benthic surveys, chemistry, metagenomics and ex-situ microcosm experiments to investigate their hypotheses of shipwrecks potentially initiating and perpetuating Black Reefs.

Their research found that live coral cover was reduced from 60% to <10% on several of the Black Reef sites. There were increased abundances of turf algae, macroalgae, pathogen-like microbes and virulence factor genes (when compared to a virulence factor database) and corallimorphs in the Black Reefs when compared to the control sites. The water surrounding the polluted sites was found to be cloudy with elevated concentrations of organic matter. They provided evidence that the phase shifts occur rapidly as a result of studying and documenting the natural history of the Black Reefs. Iron concentrations from algae tissues were discovered to be six times higher than in algae collected from reference sites. Ex-situ experiments demonstrated that corals were killed by black reef rubble from microbial activity.

The authors suggest that benthic algal overgrowth combined with iron enrichment is a mechanistic stimulation of heterotrophic microbes, as result of organic carbon being released by benthic algae. Which in turn leads to asphyxiation of the coral. They also infer from their mesocosm experiments that Black Reefs rubble algae were lethal to corals without iron enrichment, which they suggest is a prediction (indicator) of the long term consequences of these phase shifts after the removal of iron.

Kelly et al. conclude with the following main points:

1. Due to the remote location data sets for analysis were incomplete for all the study sites. 2. Further metagenomics analysis of microbial communities would reveal more about the pathogenic bacteria. 3.comparasons of iron concentrations between reference sites and Black Reefs sites were not carried out on the same species. 4. The spreading pattern of the Black Reefs adopts a ‘ratchet like mechanism’; allowing the Black Reef to crawl along, as a result of a re-mineralization process were upon the death of the polluted microbial algal mats, the iron is made available to further the Black Coral. 6.That the new pathogenic microbial community phase shift is maintained following a shipwreck by self-reinforcing feedback mechanisms.

Their evidence provides significant results that shipwrecks detrimentally impact corals and associated algae in iron-limited regions. The evidence is amassed from a variety of techniques , microbial abundance counts to virulent gene comparisons . This use of multiple investigating strategies lead to a variety of findings that supported their hypotheses. The paper contains various grammatical errors, which confused me as to exactly what their findings were e.g. in the abstract. As they suggested themselves further metagenomics analysis of the microbial community would have been interesting. The further application of molecular techniques (FISH and DGGE) would have potentially revealed more about the pathogenic bacteria thought to be involved in the coral death. To conclude their research held substantial weight that shipwrecks cause iron induced phase shifts! The final recommendation was to remove the shipwrecks before detrimental ecological impact sets in. This concluding recommendation seems rather difficult to reinforce and would incur considerable cost, which in my opinion the merchant navy responsible for the vessel should take the damage not the corals. Perhaps call me idealistic but to me it seems a feasible responsibility of a ‘commendable’ company. After all if you break down on motorway or any road in fact you don’t just get out and leave you car for good, unless you’re a proper w*****. I’m a strong believer in a low footprint mentality, evidence like this reaffirms my conviction.

The Viral Shunt and the Deep-Sea Paradox

Deep-sea ecosystems cover about 65% of the Earth’s surface and therefore they play a fundamental role in the global biogeochemical cycles and biomass production. This vast, extreme and dark ecosystem frequently experiences organic nutrient limitation because it lacks photosynthetic primary production and thus it mainly depends on the carbon export from the sea surface. Despite this, the prokaryotic biomass in the top 10cm of deep-sea sediments, is surprisingly high (approximately 160 Pg) and even though in situ experiments suggest that procariotes do not significantly contribute to the food requirements of higher trophic levels, it represents a potentially enormous food source for deep-sea benthic consumers. The high prokaryotic biomass in a food-limited ecosystem and the non-use of this component by benthic fauna represents currently, the two unsolved paradoxes of the deep oceans, which could be partially explained, according to the authors, through the deep 'viral shunt'.

Analyzing 232 deep-sea sediment samples coming from all over the world and from all depths from 165m to 5,571m, the authors shows that viriobenthos is a highly dynamic and active component of deep-sea ecosystems and by far, is probably the most abundant ‘life form’ in the world’s oceans.

They found that:

• Viral production and abundance are consistently high in surface sediments (top 1-cm) at all depths worldwide, with values similar to those reported for coastal sediments.

• Viruses are responsible for the abatement of 80% of the total prokaryotic production in deep-sea sediments.

• Virus-induced prokaryotic mortality increases significantly with water depth (from 16% in coastal sediments to 89% in sediments beneath 1,000m depth).

The intracellular material released by viral lysis of infected microbes has two main effects: It drastically reduce the microbial biomass potentially available to higher trophic levels and it provides an important bioavailable organic source to non-infected prokaryotes; balancing in this way the low and often limiting amount of organic detritus available in deep sediments.

In other words viruses kills an important fraction of benthic prokaryotes reducing the competition for resources (top down, predatory control) and generating labile organic material that stimulates the metabolism of others uninfected deep-sea prokaryotes (bottom-up mechanism). The significant and positive relationship between viral and prokaryotic production and between the release of carbon from viral lysis and prokaryotic turnover, demonstrate that in deep environments a stronger viral shunt is required for high prokaryotic growth rates. The viral shunt thus, can help us to better understand the paradox of a fast prokaryotic turnover in a food-limited deep-sea ecosystem.

This shunt of most of the prokaryotic carbon production into organic detritus has also important implications for nutrient cycling on a global scale. Organic carbon supplied by viral lysis promotes the microbial turnover and thus the recycling of most key elements (including nitrogen and phosphorus). The viral infection has therefore, an important role in the functioning of the largest ecosystem of the biosphere and the integration of the viral component into biogeochemical models is of primary importance for an improved understanding of global oceanic processes.

Reference:

Danovaro R, Dell'Anno A, Corinaldesi C, Magagnini M, Noble R, Tamburini C, Weinbauer M, (2008): Major viral impact on the functioning of benthic deep-sea ecosystems. Nature, 454:1084-1087.

Exploring the Deep

A review of: De Corte, D. et al (2010) Links between viral and prokaryotic communities throughout the water column in the (sub)tropical Atlantic Ocean, The ISME Journal, 4, 1431-1442.

Marine viruses have a number of important roles within ocean processes; this paper investigates the effects of viruses on the abundance, production and diversity of prokaryotes, with a particular focus on changes in the relation between these two micro-organisms throughout the water column.

The (sub)tropical Atlantic Ocean was the chosen study site. Samples were taken from 37 stations from the epi- to the abyssopelagic layer (from depths of approximately 100 to 7000 m). Flow cytometry was used to determine prokaryotic and viral abundance, and viral, archaeal and bacterial community composition were analysed using randomly amplified polymorphic DNA-PCR (RAPD-PCR), terminal restriction fragment length polymorphism (T-RFLP) and automated ribosomal intergenic spacer analysis (ARISA), respectively. Heterotrophic prokaryotic activity and viral production were also measured.

Results showed that viral abundance was significantly related to both prokaryotic abundance and heterotrophic activity; all decreased with depth with prokaryotic abundance decreasing exponentially. The virus-to-prokaryote abundance ratio saw a linear increase with depth. The authors inferred that the viral abundance decreases at a lesser extent than prokaryotic abundance because viruses take longer to decay in deeper waters than in near-surface waters.

Two types of viral production were analysed; lytic viral production decreased linearly with depth whereas lysogenic viral production showed no clear trend. It is suggested that a shift from a lytic life cycle to a lysogenic life cycle could occur as a result of a decrease in host abundance, although the authors point out that the lack of a pattern in lysogenic viral production indicates inconsistent virus-prokaryote interactions in deep waters.

A total of 24 operational taxonomic units (OTUs) were determined in the viral community, with a cluster found in the bathy- abyssopelagic layer. Within the bacterial community a total of 142 OTUs were found with clusters at the epi- mesopelagic and bathy- abyssopelagic layers. Ten OTUs on the 16s rDNA level were found within the archaeal community, with clusters at the meso- upper bathypelagic and bathy-abyssopelagic layer.

Covariance was seen between the number of OTUs of archaea and viruses. Both initially decreased with depth, remaining constant from the mesopelagic to a depth of 3000 - 4000m, before decreasing again. In contrast the number of bacterial OTUs increased twofold between depths of 3000 – 5200m. This could be because different methods were used to identify the numbers of OTUs, but the authors suggest it is more likely that viruses at these depths have a wider host range than viruses nearer the surface.

Previous studies on interactions between viruses and prokaryotes have mainly taken place in surface waters. This paper, although not very extensive, details many results and observations. The general conclusion reached is that the deep Atlantic is more heterogeneous than previously thought. The strong link between viral abundance and heterotrophic activity observed within both surface and deeper waters suggests that dynamic systems are found throughout the water column, from the lower epi- to the abyssopelagic layer.

Black Smokers.....Isolation of two novel piezophiles.

A review of:
Ken Takai, Massayuki Miyazaki, Hisako Hirayama, Satoshi Nakagawa, Joel Querellou and Anne Godfroy. (2009). Isolation and physiological characterization of two novel, piezophilic, thermophilic chemolithoautotrophs from a deep-sea hydrothermal vent chimney.Environmental Microbiology. 11(8), 1983-1997.

In 1957 there was some pioneer research by Zobell and Morita on deep-sea piezophiles, since then there has been half a century of research yet still we are not fully aware of which microorganisms thrive in these deep sea vents. This is due to a number of reasons but typically when there have been samples collected at high expense these microorganisms cannot be cultured successfully. In this paper the authors have successfully cultivated and isolated two novel thermophilic piezophiles which are capable of chemolithoautotrophic growth from a black smoker chimney at the TAG field in the Mid-Atlantic Ridge.

The two strains (strains 106 and 108) were cultivated using a liquid serial dilution culture and a piezophilic cultivation technique. Liquid serial dilution cultures were made to estimate the abundance of culturable microorganisms (viable counts). Serial dilutions were carried out from the chimney sub samples under various cultivation conditions. The piezophilic cultivation techniques were where the enrichment and purification of the strains occurred after a 2 week incubation period. During the two week incubation period the strains were inoculated in test tubes containing MMJHS medium (1g of NaNO3, 1g of Na2S2O3 .5H2O, 1g of NaHCO3, 30g of elemental sulphur and 10ml of vitamin solution per litre of synthetic seawater. Takai et al. 2003) under a gas phase of 80% H2 + 20% CO2 (0.2 MPa) at 50°C. It must be noted that these were only two fragments from a very complex method where they also looked at the morphology, total direct cell counts, fluid chemistry, growth characteristics, energy and carbon sources, cellular fatty acid composition, nucleic acid analyses and whole-cell FISH analysis to help characterise each strain.

The results section describes the two strains morphological, physiological and metabolic properties. The authors found that strain 106 was a motile thin spiral that was 6-20µm long and 0.4-0.6µm wide with polar flagellum under piezophilic cultivation conditions but under conventional gas pressures were shorter, up to 4µm long. Strain 106 also uses reduced sulphur compounds as the electron donors, with nitrate and O2 as the electron acceptors. Cells of strain 108 were non-motile, short and oval, approximately 1-1.5µm long and 0.6-0.7µm wide with no flagellum observed. It is also a facultative chemoautotroph, capable of both chemolithoautotrophic growth with H2 and S oxidations and organotrophic growth with complex organics or organic acids using nitrate and O2 as the electron acceptors.

This paper was an interesting read with new methods in cultivation being utilised. The amount of methods used help to describe most of the characteristics of both strains and indeed required. The only criticism I would have is the order in which they displayed the paper with experimental methods being displayed after the results and discussion, I believe it would have made the results a little clearer when reading if you knew the exact methods they used before reading.

Additional reference: Takai et al., (2003) Isolation and phylogenetic diversity of members of previously uncultivated epsilon-Proteobacteria in deep-sea hydrothermal fields. FEMS Microbiol Lett. 218, 167-174

Discovering OHCBs ...

A review of Obligate oil-degrading marine bacteria Current Opinion in Biotechnology, Volume 18, Issue 3, June 2007, Pages 257-266 Michail M Yakimov, Kenneth N Timmis, Peter N Golyshin

Obligate hydrocarbonoclastic bacteria ( OHCB ) has recently been detected in marine water, where they play an important role in biomerediation processes.

In this paper, authors review latest results pertaining to the biogeography, ecophysiology, genomics and potential for biotechnological applications of OHCB.

Hydrocarbon degrading bacteria are found everywhere, both in marine and terrestrial environments. We should not be surprised by this : hydrocarbons and their derivates existing in different forms ( solid, liquid and gaseous fossil carbon deposits, lipids and fatty acids ... ) are ubiquitous in the biosphere and have high carbon content available for biomass.

In contrast to terrestrial hydrocarbon degraders which tend to be metabolically versatile, marine degraders are mostly highly specialized obligate hydrocarbon utilizers, so they are referred as OHCB. Their growth occurs only on substrates containing long-chain alkyl moieties, so they have a highly specialized substrate specifity.

Few OHCB have been isolated from different sites.

Alcanivorax borkumensis has been detected in all types of marine environments: water at all levels and depth, hydrotermal vents and mud vulcanoes, whale carcass, marine invertebrates and algae. This ubiquity is due to its ability to grow on many saturated petroleum fraction constituents and on biogenic hydrocarbon.

Marinobacter species are important marine hydrocarbon degraders that are metabolically more versatile than Alcanivorax, because of the 1500 additional genes that Alcanivorax lacks.

T. oleivorans and Cycloclasticus spp. are also widely distributed, but they have mostly been found in the Northern hemisphere.

Oleiphilus messinensis, initially isolated from harbor sediments ( Messina, Italy ) seems to thrive elsewhere as a sponge symbiont.

In contrast to the cosmopolitan OHCBs discussed above, Oleispira antarctica inhabits only cold waters at high latitudes.

What makes OHCBs so different and let them to take more advantage than other bacteria living in the same environment?

OHCBs exhibit features typical of oligotrophic bacteria.

Remarkably, most of these organisms have an outer cellular membrane enriched for a wide range of transport system for the capture of nutrients ( nitrate especially ) and oligo-elements ( Mg, Mo, Zn, Co ) from the generally nutrient-poor marine environment.

No genes for either passive or active carbohydrate transporters, wich are usually present in other bacteria, were identified in the genome. This observation is consistent with the inability to use monomeric sugars as growth substrates.

When OHCBs show their presence in the environment?

Several microcosms studies have shown that an influx of oil in a marine site causes population densities of OHCB increase up to 90% of the total microbial community, causing a shift in community balance.

A temporal succession of different genera occuring in the bloom has been described : aliphatic hydrocarbon-degraders, in particula Alcanivorax, are the first to bloom and are succeded by microbes such as Cyclocasticus specialized for the remaining compounds that are more difficult to degrade.

Authors point out that, although revealing, such microcosm studies are reductionist and artificial, and they lack of the complexity, diversity and dynamics of natural inputs ( mineral nitrogen and phosphorous ), exports ( cellular metabolites ) and predator grazing.

Further, some studies used tecniques unable to establish the causality between an organism and its physiology/environmental role. For istance, numerous isolates of T. oleivorans obtained from the Polar coastal area of Russia, from the Mediterranean sea and from the North sea, were identical in terms of their small subunit rRNA gene sequences, but exhibit distinct substrate preferences and temperature requirements. This aspect must be considered when developing potential mitigation strategies to combat oil pollution in marine water.

The key role of OHCB in bioremediation processes is well-known, but we must also think about other potential applications of these bacteria.

Recent studies resulted in the identification of novel enzymes : 5 groups of carboxylesterases were biochemically characterised and exhibited good potential for biosynthetic applications.

Moreover, future studies should investigate the role of predators and grazers ( viruses, procariotes, eucariotes ) on the composition, population dynamics and ecophysiological functioning of marine oil-degrading communities.

Microbes to the rescue the war against harmful algal blooms.

This paper discusses the dangers associated with harmful algal blooms (HABs) and the use of biological control as the most promising method to control and prevent these blooms. Harmful algal blooms are commonly found in eutrophic water bodies. Understanding these blooms and developing techniques used to control them is vital as they pose a serious health risks to all forms of life. They reduce water quality, they have serious negative effects on lake ecology and current methods of control are inefficient in terms of time and money. As pollution to our water sources is increasing we will see more and more harmful algal blooms worldwide the problems are becoming more relevant and so development of new methods of control is becoming vital.

We already use a number of different methods to control blooms however they generally have adverse effects on ecology, are costly and time consuming. The use of algicides such as harmful chemicals like copper are used to induce cell lysis releasing toxic chemical into the surrounding waters. The toxins do eventually degrade however long waiting periods are necessary. Microsystins are susceptible to breakdown by aquatic bacteria. These microbes are found naturally in rivers and reservoirs. Although these bacteria are indigenous to the lakes; blooms still occur. This is because the concentration of predatory bacteria is often not sufficient enough to cause lysis when there are enough hosts, and then lysis will occur.
Criteria for a good biological control agent are: high tolerance to a variation on conditions, ability to survive low prey densities, should be indigenous to limit environmental impact (not genetically modified). There is a fear that bacteria might switch hosts and have serious impact on other important crops or organisms. Viral pathogens would be ideal as biocontrol agents as they are target selective and specific for nuisance cyanobacteria. Despite this bacterial agents are considered more promising as they can survive on alternate food sources during non-bloom periods. This would mean they would be more likely to survive for extended periods of time and so would be needed to be reapplied less often.
Many trials have been carried out with success, Bourne et al. (1996) isolated a bacterium which is thought to be able to remove 90% of toxins in 2 to 10 days also Nakamura et al in 2003 immobilised Bacilus cereus. Placed in floating biodegradable plastic carriers they used them to control microcystis blooms successful eliminating 99% of the bloom in 4 days. The bacteria utilised the starch as a nutrient source and the floating carrier enabled immobilized bacteria to be directed to floating cyanobacteria blooms.
More research is needed in this field as the mechanisms involved in cyanobacterial lysis are poorly understood. Studies on application of biocontrol agents are rather limited. Most studies have been limited to lysis of laboratory cultured bacteria. Much more testing is need before further tests can be carried out on our freshwater systems. We need to learn more about anti algal activity and the effects of bacteria on other organisms
This is an extremely interesting area of research which is going to become more important as blooms become more common. The risks of control through predatory bacteria needs to be better understood however it appears to be an encouraging step forward in the management of toxins.


A review of: R. Jabulani Gumbo et al. Biological control of Mircocystis dominated harmful algal blooms African Journal of Biotechnology Vol. 7 (25), pp. 4765-4773, 29 December, 2008