Free genomic sequencing of Bacterial and Archaeal type strains

The Community Sequencing Program (CSP) Quarterly Microbial call of the DOE Joint Genomes Institute provides a great opportunity to obtain draft genomic sequences of the type strains of bacterial and archaeal species. The type strains may also include proposed species prior to publication. Type strains must be relevant to DOE mission areas, such as bioenergy, biogeochemistry, bioremediation, carbon cycling, and phylogenetic diversity. However, strains of human pathogens and human associated species are not eligible. Proposals for genome sequencing of type strains can be submitted through the CSP Quarterly Microbial call, whose deadline is December 17, 2012, with approval usually being completed within one month. Up to 12 strains can be included in each proposal. Proposals for larger numbers of strains need to be submitted to the CSP annual call in the spring. If you cannot make the December call, Quarterly calls are also scheduled for March 25, June 17, and September 23, 2013.

Proposals may be completed on-line at: http://proposals.jgi-psf.org/proposals. You will need to register and sign in to this server. Once on the server, follow the links to the “CSP Quarterly Microbial/Metagenome”. All strains will have to have been deposited in a culture collection, including proposed type strains prior to publication. If a culture collection ID is not available, you can attach a copy of the Certification of Availability. Once approved, you will need to provide 5-10 µg of high molecular weight DNA.

For questions, contact Barny Whitman, University of Georgia (whitman@uga.edu).

Waste water and insect life… or better… insect death!

Neonicotinoids are neuro-active insecticides which derive their toxicity to target species from acting mainly agonistically on nicotinic acetylcholine receptors (nAChRs) on the post-synaptic membrane. This means that normal nerve impulses become impaired. Among neonicotinoids, imidacloprid shows a selective toxicity for insects or at least it should!

An interesting research, published by Tessa C. Van Dijk, Marja A. Van Staalduinen and Jeroen P. Van der Sluijs in the  journal PLoS One, found that 70% less invertebrate species were found in water polluted with the insecticide imidacloprid compared to clean water. There were also far fewer individuals of each species in the polluted water so that this is the first study showing a clear effect in the field.

According to Van Dijk and colleagues:

Our regression analysis showed a significant negative relationship (P<0.001) between macro-invertebrate abundance and imidacloprid concentration for all species pooled. A significant negative relationship was also found for the orders Amphipoda, Basommatophora, Diptera, Ephemeroptera and Isopoda, and for several species separately. The order Odonata had a negative relationship very close to the significance threshold of 0.05 (P = 0.051). However, in accordance with previous research, a positive relationship was found for the order Actinedida.

… that means that this comound is killing mayflies, midges and molluscs and we can not exclude that the pollution could have a knock-on effect on birds such as swallows that rely on flying insects for food.

In an interview to The Guardian, Julian Little, spokesman for Bayer Cropscience, which manufactures imidacloprid, said that “There doesn’t appear to be anything hugely surprising in this article. It shows the presence of high levels of insecticide in water can have effects on aquatic insects and other invertebrates. Should we have strong stewardship of insecticides to minimise any contamination of water? Yes we should and yes we do.”

It is true that the problem is not the molecule itself, but its use or better its abuse, but we have to understand what is happening in the several reported cases of extreme pollution, with imidacloprid levels 25,000 times the limit where the water contained so much insecticide that it could actually be used directly as a lice-control pesticide!

Van Dijk, T., Van Staalduinen, M., & Van der Sluijs, J. (2013). Macro-invertebrate decline in surface water polluted with Imidacloprid PLoS ONE, 8 (5) DOI: 10.1371/journal.pone.0062374

Replacing bacterial symbionts with a fungal symbiont… unusual changes in aphids!

Current models of bacterial genome evolution suggest that in small populations a burst of transposable element activity may lead to inactivation of non-essential genes and large deletions, followed by erosion of the pseudogenes resulting in genome reduction. Due to this process, the smallest sequenced cellular genomes are all obligate intracellular symbionts of insects. Interestingly, it seems that the presence of symbionts in small populations within each host reduces the efficacy of the purifying selection increasing the genetic drift that increase the fixation of deleterious mutations.

The evolutionary scenarios seem to be quite different for eukaryotic symbionts since they have different evolutionary patterns of their genomes and it has been reported the gain of mobile genetic elements and intronic sequences resulting in larger genomes.

A recent paper by Kevin J. Vogel and Nancy A. Moran compared the evolution of symbiont analyzing a monophyletic group of aphids within the subfamily Cerataphidinae that have lost the bacterial symbiont common to all other Aphididae (Buchnera aphidicola), which have been replaced by a eukaryotic one, the Yeast-Like Symbiont (YLS). In particular, Vogel and Moran used this system as a model to test the hypothesis that chronically high levels of genetic drift will result in an increase in size of a eukaryotic symbiont genome.

Sequencing of the Yeast-Like Symbiont genome revealed, unlike the obligate bacterial symbionts that lost several genes for DNA repair and recombination, the YLS appears to have fully functional recombinational machinery, including the full suite of genes necessary for meiotic division. Furthermore, the YLS’s genome reveals a diverse suite of metabolic abilities unlike the streamlined metabolism of the obligate bacterial symbionts of insects, though it has lost many genes found in related fungi. At this regards, like Buchnera, the YLS encodes the full biosynthesis pathways for essential amino acids, though it can also produce the non-essential amino acids, which Buchnera mostly receives from the host. The ability of the YLS to produce essential amino acids supports the hypothesis that the YLS has replaced Buchnera’s functional role in these aphids.

The genome of the YLS resulted enriched in introns and presented an elevated rates of amino acid substitution but no burst in mobile DNAs has been observed so that the YLS genome do not support the hypothesis of rampant genome expansion observed in fungi such as Tuber melanosporum. The high gene density and small intergenic spacers suggest that YLS may reside in a range of population size and genome size that allow for expansion of introns but limit the rampant proliferation of mobile genetic elements.

As a whole, the patterns observed in the YLS genome suggest that its symbiotic lifestyle is permissive to intron proliferation and accelerated sequence evolution, though other factors appear to limit its overall genome expansion. This result could suggest the intron and mobile DNA gains occur in different times, but the Buchnera-aphid symbiosis is much older, and is thought to originate at least 200 mya so that the relatively young association of YLS with hosts may not have permitted sufficient time to allow for genome expansion.

Vogel KJ, & Moran NA (2013). Functional and evolutionary analysis of the genome of an obligate fungal symbiont. Genome biology and evolution PMID: 23563967

Leave aphids on your plants to preserve your children!

Aphids are frequently controlled by chemical compounds so that it could be not so unusual that you may interact with insecticides, for instance, after a general treatment of your home for spiders, insects or termites.

A new study published by Elizabeth Milne et al. in the journal Cancer Causes & Control  reveals that women exposed within a year of pregnancy are almost twice as likely to have a child that develops a brain tumor. Interestingly this result is not due to household applications of insecticides by homeowners, but the study examines the role of pesticides applied by professional pest control applicators that use insecticides in proper amounts and protocols.

This study reports data from more than 3 hundred of families in  Australia and it clearly shows that, for instance, termites treatment by professional applicators brings to a 50% greater risk if mothers and fathers are exposed either in the year before or during pregnancy.

Surprisingly, this effect is not related only to mother’s exposure, but also to father’s exposure to chemicals. If previous studies showed that insecticide treatments were linked to childhood brain tumors and childhood leukemia, here we have evidence that home exposure to insecticides can be as much as dangerous than occupational exposures. Therefore, preconception pesticide exposure, and possibly exposure during pregnancy, is associated with an increased CBT risk and it may be advisable for both parents to avoid pesticide exposure during this time.

As reported in the website Beyond Pesticides, a 2009 study from the U.S Environmental Protection Agency and the U.S Department of Housing and Urban Development found the pesticide permethrin in 89% of the 500 homes randomly selected for sampling, whereas other studies found at least five pesticides in the air of 60% of 29 homes occupied by pregnant Hispanic women and the presence of piperonyl butoxide (PBO,  an organic compound used as pesticide synergist) in 75% of homes occupied by pregnant women in inner-city New York.

At the same time, a further study links chemicals used in some lice treatment products and pet collars to childhood brain tumors. In particular, scientists correlated the exposure to organophosphorus- and carbamate-type insecticides to a child’s gene variations that might alter the way the child breaks down pesticides in the body. While general insecticide exposure increased the risk of tumors, if a child was not able to neutralize AChE inhibitors (nerve-damaging organophosphorus insecticides are AChE inhibitors) due to a genetic trait, they were even more likely to develop brain tumors. Researchers found that a child’s genetic variations did not seem to increase the risk of childhood brain tumors independently, but when coupled with exposure to organophosphorus insecticides, and possibly carbamate insecticides, the risks increased significantly.

Try to avoid insecticide exposure in your community taking into account that the presence of some insects in your home and garden is not so dangerous as some insecticides could be for your children.

Greenop KR, Peters S, Bailey HD, Fritschi L, Attia J, Scott RJ, Glass DC, de Klerk NH, Alvaro F, Armstrong BK, & Milne E (2013). Exposure to pesticides and the risk of childhood brain tumors. Cancer causes & control : CCC PMID: 23558445

Unexpected bites.. from aphids!

When I was a student working on my lab project for the thesis in biological sciences, I performed some experiments with a student who was in my course. Once she told me that she was worried that aphids could bite her, since she had an itchy rash after putting new plants in our insectary with the aphid Megoura viciae (in the photo). Of course I told her that she was crazy, but now I’m not sure since this afternoon I read a nice post from the blog Don’t forget the Roundabouts, where Simon Leather report that there are in literature some aphid species that could bite you, including a species that is well-known to attack people who stand or sit underneath “their” tree.

At the same time, Leather in the post entitled “Tinker, Tailor, Soldier Aphid!” reported that in some species, aphid soldiers don’t just fight other aphids, but actually defend their siblings against predators, even being able to kill lacewing larvae so that it should thus not come as a surprise to find that not all aphids are vegans (according to the title of the Leather’s post).

Are you looking for unsually long insect mouthparts? Take a glance at aphids!

Today I was looking some photos of aphids in the twitter page of Professor Simon Leather (Harper Adams University), when I found his photo on the left of the aphid Stomaphis graffii. As you can see, the rostrum of this aphid is abnormally long. Other species of the same genus (such as Stomaphis mordvilkoi) have a long rostrum as you can see in the photography at right (by Haltrich Attila, associate professor at the St. Stephen University, Budapest).

This development is most remarkably seen in the rare species Stomaphis quercus which exhibits the organ more than twice and a half the total length of the body. Considered as a proboscis, these aphids have proportionally one of the longest of all known animals!!!

So that if you are looking for insects with unusual mouthparts you can cite not only Xanthopan morgani praedicta, which has a proboscis about 20 cm, but also aphids of the genus Stomaphis. Actually, as reported by David Grimaldi and Michael S. Engel in their comprehensive book “Evolution of the Insects” (pag. 521), the insect species with the longest proboscis is Moegistorrhynchus longirostris whose proboscis is 10 times longer than body.

Aphids are indicators of an healthy garden

Reading some posts in the blog Gardening in tune with nature, I found a nice text written by Reeser Manley suggesting that aphids are evidence of an healthy garden ecosystem. This is absolutely true!!! Even if aphids may damage plants of agricultural interest, they rarelly damage plants in a garden to warrant intervention by the gardener.  Moreover, in exceptional situations, when predators cannot keep up with a heavy infestation on your plants, mechanical controls will work so that you can dislodge aphids with a strong stream of water since, once knocked to the ground, aphids have a difficult time climbing back up to the stem tip. As Manley wrote:

In the past, I have known otherwise rational gardeners that would bring out the big guns from the chemical shelf of the tool shed when they spotted a single aphid.  Some of the most toxic insecticides, including nicotine sulfate, malathion, diazinon, and dimethoate have been used to kill aphids along with beneficial insects and other forms of garden life.

If you have a garden, in place of chemicals, ask for the help of ladybugs, lacewings, parasitic wasps, and syrphid flies to control aphids and you can also buy some boxes with ladybugs for you garden.

I have some plants of Ibiscus with aphids on my balcony, but no chemicals have been used since several years and I still have the same plants. Moreover, if you look at aphids on your plants you can have some intriguing lessons of garden ecology. You will see ants breeding aphids and fighting ladybugs, wasps putting their eggs within the aphid bodies, we will bread ladybugs from larvae to adults and so on… simply looking at your plants in place of spraying chemicals on them.