Posts Tagged ‘Environment’

How to stop the bugs eating your lunch

Tuesday, March 26th, 2013

Nepenthes gracilis Like other carnivorous plants, Nepenthes species grow on poor soil. They need to complement their mineral nutrients – primarily with nitrogen and phosphorus – from caught and digested prey. When visiting the pitfall traps, the attracted prey, mainly arthropods, falls into the trap, drowns and is digested by the enzyme cocktail of the pitcher fluid.

Due to the fact that closed Nepenthes pitchers have no direct contact with the environment, it has been widely claimed that their pitcher fluid is sterile and that all proteins and compounds identified in this pitcher fluid are solely plant-derived. But only two experiments had been conducted to demonstrate the sterility of pitcher liquid: fluid taken from a closed pitcher was plated either on plain nutrient agar (Hepburn, 1918) or on meat agar plates (Lüttge, 1964) and incubated for several days. In no case were any bacterial colonies detected and the authors concluded that the pitcher fluid is sterile. However, the presence of microbes cannot be excluded by such simple experiments because most micro-organisms cannot be grown in culture.

Researchers have now analysed the composition of Nepenthes digestive fluid from closed pitchers to reveal whether or not pitchers are really sterile inside and how these plants manage to keep microbial growth under control. Thecontent of proteins, inorganic ion compositions and secondary metabolites were studied. In addition, the effect of pitcher fluid on microbial growth was investigated. The results reveal that the fluid of closed Nepenthes pitchers is composed provides anti-microbial conditions. Thus these plants can avoid, at least to some extent, the growth of microbes that compete with the plant for the prey-derived nutrients available in the pitcher.

 

Secreted pitfall-trap fluid of carnivorous Nepenthes plants is unsuitable for microbial growth. (2013) Annals of Botany 111 (3): 375-383

 

Microbial Bebop 

Thursday, March 7th, 2013
“Microbial bebop” is created using five years’ worth of consecutive measurements of ocean microbial life and environmental factors like temperature, dissolved salts and chlorophyll concentrations. How? See: http://goo.gl/HJTec

Listen to the oceans here: https://soundcloud.com/plos-one-media/sets/microbial-bebop

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Are we missing half of the viruses in the ocean?

Wednesday, March 6th, 2013

Wave Microbial ecologists have devoted considerable effort to understanding the nature of the viruses in seawater, because viruses have key roles in the evolution, ecology and mortality of marine plankton. For at least the past two decades, researchers have assumed that the pool of viruses in the ocean is dominated by bacteriophages with DNA genomes. Perhaps as a consequence, studies of the molecular diversity of marine viruses have most commonly focused on DNA viruses. However, evidence that RNA viruses are important contributors to marine plankton ecology has been steadily accumulating.

A recent paper shows that there are a large number of RNA viruses in surface ocean waters, and concludes that RNA viruses made up between 38 and 63% of the viruses in the sea water. In other words, about half of the viruses in the ocean (or at least, off Hawaii, where such fieldwork is most fun) are RNA viruses, suggesting that our current guess at the total number of viruses on earth, 1031, could be a major under estimate.

 

Are we missing half of the viruses in the ocean? (2013) ISME Journal 7, 672–679 doi: 10.1038/ismej.2012.121
Viruses are abundant in the ocean and a major driving force in plankton ecology and evolution. It has been assumed that most of the viruses in seawater contain DNA and infect bacteria, but RNA-containing viruses in the ocean, which almost exclusively infect eukaryotes, have never been quantified. We compared the total mass of RNA and DNA in the viral fraction harvested from seawater and using data on the mass of nucleic acid per RNA- or DNA-containing virion, estimated the abundances of each. Our data suggest that the abundance of RNA viruses rivaled or exceeded that of DNA viruses in samples of coastal seawater. The dominant RNA viruses in the samples were marine picorna-like viruses, which have small genomes and are at or below the detection limit of common fluorescence-based counting methods. If our results are typical, this means that counts of viruses and the rate measurements that depend on them, such as viral production, are significantly underestimated by current practices. As these RNA viruses infect eukaryotes, our data imply that protists contribute more to marine viral dynamics than one might expect based on their relatively low abundance. This conclusion is a departure from the prevailing view of viruses in the ocean, but is consistent with earlier theoretical predictions.

What is the commonest living thing on Earth? 

Thursday, February 14th, 2013

Pelagibacter ubique is the most successful member of a group of bacteria called SAR11, that jointly constitute about a third of the single-celled organisms in the ocean. But this is not P. ubique’s only claim to fame, for unlike almost every other known cellular creature, it and its relatives have seemed to be untroubled by viruses. But four viruses that parasitise P. ubique have now neen found, and one called HTVC010P was the commonest. It thus displaces its host as the likely winner of the most-common-living-thing prize.

Abundant SAR11 viruses in the ocean. (2013) Nature. doi: 10.1038/nature11921 http://goo.gl/iXVyF

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Phage-bacteria infection networks

Wednesday, January 23rd, 2013

Bacteriophage Phage and their bacterial hosts are the most abundant and genetically diverse group of organisms on the planet. Given their dominance, it is no wonder that many recent studies have found that phage-bacteria interactions strongly influence global biogeochemical cycles, incidence of human diseases, productivity of industrial microbial commodities, and patterns of microbial genome diversity. Unfortunately, given the extreme diversity and complexity of microbial communities, traditional analyses fail to characterize interaction patterns and underlying processes.

Despite increasing recognition that phages play a significant role in shaping microbial ecosystems, fundamental questions remain unanswered. Quantifying who infects whom is essential to understand how infections at the cellular level (such as changes to metabolic rates, gene transfer, and the fate of cells) scale-up to influence ecosystem function in complex environments. This paper reviews systems approaches that combine empirical data with rigorous theoretical analysis to study phage-bacterial interactions as networks rather than as coupled interactions in isolation, and highlights the ways in which a better understanding of phage–bacteria infection networks will aid predictive models of viral effects on microbial communities, from microbiomes to the whole Earth.

 

Phage-bacteria infection networks. (2012) Trends Microbiol. doi: 10.1016/j.tim.2012.11.003

Peptidoglycan: a post-genomic analysis

Monday, January 21st, 2013

Peptidoglycan Peptidoglycan (PG) is a component of the bacterial cell wall that participates in withstanding osmotic pressure, maintaining the cell shape and anchoring other cell envelope components. PG is composed of linear glycan strands cross-linked by short peptides, with glycan strands of alternating N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) residues linked by β-1→4 bonds. The presence of PG is the basis of the first classification of bacteria using the staining procedure developed by Hans Christian Joachim Gram in 1884.

PG biosynthesis is a dynamic complex process involving 20 enzymatic reactions. To be able to synthesize and to degrade PG, an organism needs a minimal set of three genes, comprising one GT28 gene, one GT51 gene and at least one gene of five GH families. This paper examines 1,644 genomes for the presence of a minimal 3-gene set necessary for PG metabolism. None of the 103 Viruses or 101 Archaea examined possessed the minimal 3-gene set, but the set was detected in 1/42 of the Eukarya members and in 90.1% of Bacteria.

 

Peptidoglycan: a post-genomic analysis. (2012) BMC Microbiology 12, 294. doi:10.1186/1471-2180-12-294
To derive post-genomic, neutral insight into the peptidoglycan (PG) distribution among organisms, we mined 1,644 genomes listed in the Carbohydrate-Active Enzymes database for the presence of a minimal 3-gene set that is necessary for PG metabolism. This gene set consists of one gene from the glycosyltransferase family GT28, one from family GT51 and at least one gene belonging to one of five glycoside hydrolase families (GH23, GH73, GH102, GH103 and GH104). None of the 103 Viruses or 101 Archaea examined possessed the minimal 3-gene set, but this set was detected in 1/42 of the Eukarya members (Micromonas sp., coding for GT28, GT51 and GH103) and in 1,260/1,398 (90.1%) of Bacteria, with a 100% positive predictive value for the presence of PG. Pearson correlation test showed that GT51 family genes were significantly associated with PG with a value of 0.963 and a p value less than 10-3. This result was confirmed by a phylogenetic comparative analysis showing that the GT51-encoding gene was significantly associated with PG with a Pagel’s score of 60 and 51 (percentage of error close to 0%). Phylogenetic analysis indicated that the GT51 gene history comprised eight loss and one gain events, and suggested a dynamic on-going process. Genome analysis is a neutral approach to explore prospectively the presence of PG in uncultured, sequenced organisms with high predictive values.

Microbiology of Clouds 

Saturday, December 22nd, 2012

Within clouds, microorganisms are metabolically active. This article investigates the interactions between microorganisms and the reactive oxygenated species that are present in cloud water because these chemical compounds drive the oxidant capacity of the cloud system.
PNAS: http://www.pnas.org/content/early/2012/12/20/1205743110.short

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Is this research a turkey 

Friday, November 30th, 2012

No, it’s a guineafowl! Turkey raises and releases thousands of non-native guineafowl to eat ticks that carry the deadly Crimean-Congo hemorrhagic fever virus. Yet research suggests guineafowl eat few ticks, but carry the parasites on their feathers, possibly spreading the disease they were meant to stop.

Crimean-Congo hemorrhagic fever was identified as an emerging disease in Turkey in 2002. Initial symptoms include high fever, headache, back pain, joint pain, stomach pain and vomiting. Common symptoms include red eyes, a flushed face, a red throat and red spots on the palate. More severe symptoms include jaundice and mood and sensory perception changes. From about day four and for two weeks, patients have large bruised areas and serious nosebleeds. Recovery is slow; the existence of long-term complications is uncertain. Outbreaks of the viral disease have led to death rates ranging from 9 percent to 50 percent among hospitalized patients.

Between 2002 and last May, the tick-borne virus infected 6,392 people in Turkey and killed 322 of them. The virus was first identified in Crimea in 1944 and then in the Congo in 1969, and now it is found in Eastern and Southern Europe, the Mediterranean region, the Middle East, northwest China, central Asia and the Indian subcontinent.
Crimean-Congo hemorrhagic fever in Turkey has been attributed to several possible causes, including changes in land use and hunting practices, movement of livestock, climate change, migratory birds and fragmentation of habitat caused by a decline in agriculture and resulting increase in forest, creating habitats for both domestic and wild animals that carry ticks. See: http://goo.gl/QCfTx

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Life abounds in Antarctic lake sealed under ice 

Tuesday, November 27th, 2012

It is permanently covered by a massive cap of ice up to 27 metres thick, is six times saltier than normal sea water, and at −13 °C is one of the coldest aquatic environments on Earth – yet Lake Vida in Antarctica teems with life. Scientists drilling into the lake have found abundant and diverse bacteria. Water samples from both trips yielded around one-tenth of the abundance of cells usually found in freshwater lakes in moderate climate zones. Some of the cells measured up to 1 micrometre in diameter – about normal for microbes – but the samples contained many more particles that were around 0.2 micrometres in diameter. Neither of these cell types represents a previously unknown life form. However, one abundant bacterium of normal size seems to have no close relatives among cultivated bacteria, and so may represent a new phylum. Nature news: http://goo.gl/UFJSW

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