Posts Tagged ‘Environment’

Virus ecology

Thursday, June 5th, 2014

Viruses Nothing wildly new here, but rather a nice overview of viruses from an ecological rather than a disease perspective.

What Ecologists Can Tell Virologists. Annual Review of Microbiology, first posted online on May 16, 2014. doi: 10.1146/annurev-micro-091313-103436

I pictured myself as a virus…and tried to sense what it would be like. — Jonas Salk

Ecology as a science evolved from natural history, the observational study of the interactions of plants and animals with each other and their environments. As natural history matured, it became increasingly quantitative, experimental, and taxonomically broad. Focus diversified beyond the Eukarya to include the hidden world of microbial life. Microbes, particularly viruses, were shown to exist in unfathomable numbers, affecting every living organism. Slowly viruses came to be viewed in an ecological context rather than as abstract, disease-causing agents. This shift is exemplified by an increasing tendency to refer to viruses as living organisms instead of inert particles. In recent years, researchers have recognized the critical contributions of viruses to fundamental ecological processes such as biogeochemical cycling, competition, community structuring, and horizontal gene transfer. This review describes virus ecology from a virus’s perspective. If we are, like Jonas Salk, to imagine ourselves as a virus, what kind of world would we experience?



Antibiotics – let’s clean up our act

Tuesday, May 27th, 2014
East Penobscot Bay, Maine by Jason Mrachina

Beautiful Penobscot Bay

Last week I wrote about a new type of antibiotic which targets bacteria in biiofilms. Ron Huber (Friends of Penobscot Bay) left an interesting comment:

“Of concern to us as … conservationists is whether these broad spectrum peptide antibiotics are digested by standard sewage treatment plant technology or pass essentially unscathed through the patient and the wastewater treatment facility and into the receiving waters. We want and absolutely need vigorous marine biofilms, an at a variety of scales and species mixes, if we are to have mussels, lobsters, clams, oysters and other organisms at all… Sewage plants are adaptable; can something be added that would bind with the antibiotic or otherwise render it harmless before discharge We would really like to know!” (full comment)

There has been much discussion about the misuse of antibiotics in agriculture and the impact of such careless use on human health. There has been rather less public discuss on on the environmental impact of antibiotic resides in sewage effluent. So apart from the environment, do antibiotic residues which survive sewage pose a risk to human health?

Yes they do (Selective pressure of antibiotic pollution on bacteria of importance to public health. (2012) Environmental health perspectives, 120(8), 1100). Consequently, there is a fair amount of research being carried out in this area – it just doesn’t make it into the press. Standard sewage treatment processes reduce but don’t eliminate antibiotics in sewage and these can contribute to the evolution and persistence of resistant pathogens in the environment (The effectiveness of sewage treatment processes to remove faecal pathogens and antibiotic residues. (2012) Journal of Environmental Science and Health, Part A, 47(2), 289-297). This paper shows that more advanced treatments such as membrane bioreactor technology reduce antibiotic resides more than the conventional activated sludge process, but still do not eliminate them completely from the wastewater.

What effect do these residues have on the environment? We really don’t know, but it seems likely that legislators are more likely to respond to the costs involved in improving sewage treatment via the human health argument rather than the environmental argument. Sad, but that’s how it is. As far as the new peptide antibiotic I wrote about last week is concerned, we simply don’t know yet how it will be affected by sewage treatment processes. But should we be worried about such criteria when introducing new compounds for therapeutic use? Yes we should. Of course, it’s not just antibiotics we have to worry about.


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:

Listen to the oceans here:


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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


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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.


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