Microbial vintage

It always has been a very important questions to some - What makes a great wine? Answers to this question have been - to say the least - diverse: the right soil, a good grape, a competent winegrower, etc. Well, it looks like we have to add one more item to the list - good bacteria.

On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone.

Researchers from the University of California, Davis, analyzed grape samples from eight California wineries and found that microbes factor into the way wines taste from region to region. In total they collected 273 grape must samples. Must is actually a term for wine grapes that have been plucked from the stem and crushed together. The reason why the researchers decided to use must, and not just individual grapes, was because individual grapes - even from the same vineyard - can have different microbial communities on them. Using must was a rather simple way of pooling the samples.

The study used a high-throughput, short-amplicon sequencing approach (Illumina platform) with primers for the V4 domain of bacterial 16S rRNA and the internal transcribed spacer (ITS) DNA Barcode to identify the types of bacterial and fungal species in each set of must. 

They found that different bacterial compositions were present in different regions, potentially giving grapes a distinctive taste or in the worst case - ruining them. Lactic acid bacteria, for instance, were found to be common in the Napa Valley. Lactic acid bacteria can lead to the spoiling of wine, but they are also capable to turn malic acid into lactic acid, which gives a Zinfandel wine a distinct taste. Species composition differences between regions might also contribute to differences of taste between two Zinfandel wines.    

This metabarcoding approach makes it possible to ascertain which specific microbes and combinations of microbes are more or less important for the quality of a given wine in a given vineyard over time. The consistency of the microbial diversity over time may ultimately contribute to the quality of a wine and the reputation of vineyards. However, whether these regionally different microbiota actually directly modulate wine sensory qualities must be experimentally tested, as do pretty much all putative features of wine terroir.

We demonstrate that grape-associated microbial biogeography is nonrandomly associated with regional, varietal, and climatic factors across multiscale viticultural zones. This poses a paradigm shift in our understanding of food and agricultural systems beyond grape and wine production, wherein patterning of whole microbial communities associated with agricultural products may associate with downstream quality characteristics. Elucidating the relationship between production region, climate, and microbial patterns may enhance biological control within these systems, improving the supply, consumer acceptance, and economic value of important agricultural commodities.

Dog parasites

The Chinese province of Qinghai on the Qinghai-Tibetan Plateau is one of the most highly endemic areas for Echinococcus parasites. Nomadism of high-altitude adaptive animals,  such as yak and sheep, is very popular, and most farmers keep dogs for protection and for herding.  Together, these conditions favor both endemism and the lifecycle of taeniid cestodes. Dogs are also infected with parasites by eating rodents in the pasture. The prevalence of Echinococcus in humans was determined at 6.1% for Echinococcus granulosus and 5.1% for Echinococcus multilocularis in the Qinghai Province. The prevalence in domestic animals was very high with the reported values reaching over 50 % for Echinococcus granulosus in dogs, yaks and sheep. Dogs also serve as the definitive host for Taenia species which also can infect other domestic animals, such as yaks and sheep, and thus would reduce animal health and affect meat quality. The life cycle of the parasites connects both dogs and livestock (see figure above). 

A variety of methods have been used to diagnose taeniid infection in dogs. One common method for diagnosis in live dogs is the examination of fecal eggs. While this has been difficult in the past as eggs don't show a lot of species specific features DNA Barcoding is used in more recent studies. For a new study, researchers collected dog feces before and after deworming at a pilot site in the Qinghai Province and thereby determined an optimal sampling schedule for egg examination. By using this method, they were able to evaluate the prevalence of taeniid cestodes in dogs at different sites in the Province. Subsequently one site was selected and the team conducted a control trial of taeniid infection in dogs with periodic deworming treatment. 

Analysis of 277 dog feces revealed that taeniid cestodes, including Taenia species and Echinococcus granulosus, were e.g. highly prevalent in one region (34.4%), but no eggs were found in a region where a control trial on canine echinococcosis had been conducted 20 years ago. The first region was chosen for the control trial with the result that he prevalence of taeniid cestodes in the dogs was reduced to 9.6% and 4.9% after one and two years, respectively,  indicating that some dogs did not receive proper treatment. The researchers went back and conducted a survey among the farmers which revealed that most farmers were not familiar with echinococcosis or the transmission route of the disease. All these findings imply that DNA Barcoding utilized for species identification and a program for educating local farmers will greatly improve infection control.

Black flies

Black flies are members of the fly family Simuliidae. To date over 1,800 species of black flies are known. Most species belong to the large genus Simulium. Most black flies feed on the blood of mammals, including humans, although the males feed mainly on nectar. The ones feeding on human blood are a nuisance as the insects use their very short mouthparts that are sharp enough to cut into the flesh of their victim and lick the blood that comes out. A blood meal lasts about 3-6 minutes and can even go to 15 minutes. During this meal, a female eats as much blood as its own weight. In order to make the process more effective the insect injects saliva and an anticoagulant. The latter causes swelling and itching, and I can attest that the latter is really a nuisance. Also unlike the mosquito, black flies attack in silence without a distinct buzz.

Black flies are small insects, black or gray, with short legs, and antennae. They are known to spread several diseases, including river blindness in Africa and the (Central and South ) Americas.

Black flies are a nightmare for traditional taxonomy because of their small size and structural homogeneity. Banding patterns of the polytene chromosomes (cytotypes) have been the standard in addressing this challenge, but require experienced people to interpret them and typically are workable only for certain larva stages. 

Two researchers have now examined the efficiency of DNA Barcoding for differentiating morphospecies and cytoforms of species complexes occurring in Thailand:

A total of 351 cytochrome c oxidase subunit 1 sequences were obtained from 41 species in six subgenera of the genus Simulium in Thailand. Despite high intraspecific genetic divergence (mean = 2.00%, maximum = 9.27%), DNA barcodes provided 96% correct identification. Barcodes also differentiated cytoforms of selected species complexes, albeit with varying levels of success. Perfect differentiation was achieved for two cytoforms of Simulium feuerborni, and 91% correct identification was obtained for the Simulium angulistylum complex. Low success (33%), however, was obtained for the Simulium siamense complex. The differential efficiency of DNA barcodes to discriminate cytoforms was attributed to different levels of genetic structure and demographic histories of the taxa. DNA barcode trees were largely congruent with phylogenies based on previous molecular, chromosomal and morphological analyses, but revealed inconsistencies that will require further evaluation.

BIO image of the day

Our BIO image of the day got even better. By using some new mapping tools on Pinterest specimens presented come with more geographical information. For everyone interested in more detail there are always links to the specimen on BOLD and to its BIN page. 

Farewell Frederick Sanger

Frederick Sanger passed away yesterday at the age of 95.

Especially as DNA barcoders we have to give kudos to him as he was the pioneer that developed DNA sequencing, and most of the time we refer to the classical chain-termination method of DNA sequencing as Sanger-sequencing.

His group was actually the first that produced a whole genome sequence, made up of more than 5,000 basepairs, in a virus. Sanger was the only scientist to have been awarded the Nobel prize for Chemistry twice. The first one he received in 1958 for developing techniques to work out the precise chemical structure of proteins especially the one for insulin. The second prize he received together with Walter Gilbert and Paul Berg in 1980 for developing the chain-termination method to determine the nucleotide sequence of DNA. This invention represents the beginning of modern genetics with all the genome sequencing projects and - DNA Barcoding which despite newly developed sequencing technologies still is the method of choice for any sequence library building effort, e.g. all of 2.6 Million barcode sequences on BOLD are the result of Sanger sequencing.

A great scientist left us yesterday and one of his many qualities was modesty:

I was just a chap who messed about in his lab.

Yesterday's fun - Santa Claus Parade in Guelph

Effective Biodiversity Conservation

Although protected areas (PAs) cover 13% of Earth's land, substantial gaps remain in their coverage of global biodiversity. Thus, there has been emphasis on strategic expansion of the global PA network. However, because PAs are often understaffed, underfunded, and beleaguered in the face of external threats, efforts to expand PA coverage should be complemented by appropriate management of existing PAs. Previous calls for enhancing PA management have focused on improving operational effectiveness of each PA [e.g., staffing and budgets]. Little guidance has been offered on how to improve collective effectiveness for meeting global biodiversity conservation goals. We provide guidance for strategically allocating management efforts among and within existing PAs to strengthen their collective contribution toward preventing global species extinctions.

This is the first paragraph of a new study just published in Science in which colleagues identified the protected areas most critical to preventing extinctions of the world's mammals, birds and amphibians. Resulting from an international collaboration, this analysis provides practical advice for improving the effectiveness of protected areas in conserving global biodiversity.

The researchers calculated what they called 'irreplaceability' of individual protected areas, based on data on some 173,000 terrestrial protected areas and assessments of 21,500 species on the IUCN Red List. Their analysis looks at the contribution each protected area makes to the long-term survival of species.

Figure taken from Le Saout et. al. 2013

As a result, 78 sites have been identified as exceptionally irreplaceable. Together, they harbor the majority of the populations of more than 600 birds, amphibians, and mammals, half of which are considered globally threatened. In many cases these areas protect species that cannot be found anywhere else. Many are already designated as being of 'Outstanding Universal Value' under the UNESCO World Heritage Convention. These sites include the Galápagos Islands, the Manú National Park in Peru, and the Western Ghats in India. However, half of the land covered by these areas does not have World Heritage recognition. This includes for example the Udzungwa Mountains National Park in Tanzania, the Ciénaga de Zapata Wetland of International Importance in Cuba, and -- the most irreplaceable site in the world for threatened species -- the Sierra Nevada de Santa Marta Natural National Park in Colombia.

One needs to keep in mind that such a study can only be the beginning. All analyses focused on three groups representing the world's terrestrial vertebrate diversity. The advantage is the amount of data available for those animals but there is also a very practical reason to look at them first:

Local management plans often focus on charismatic species, and management decisions favoring these (e.g., habitat protection) will often benefit a whole set of species. However, management objectives established for particular species sometimes deliver no benefits to, or can even jeopardize the persistence of, other species. In such cases, we propose that species for which a PA has the highest conservation responsibility should be the first consideration for management and monitoring.

I guess we should be thinking of doing similar assessments for marine areas and of course for all other life on earth as: 

PAs are our main hope for meeting ambitious global conservation targets, such as preventing species extinctions, but the costs of ensuring their effective management are substantial, albeit affordable. We hope that the conceptual guidance and specific data provided here will support strategic reinforcement of the world's existing PAs, to improve their individual and collective effectiveness for conserving global biodiversity.

Gleanings from the Kunming conference - Underground trees

In South Africa's coastal grasslands, you can explore a forest by literally walking along its canopy. It is home to some extraordinary tree species which are called underground trees. Only the uppermost leaves and branches of the tree are visible. The rest of the tree is submerged below the deep sandy soil, creating a clonal network of underground forests.

Prof. Braam van Wyk, plant taxonomist from the University of Pretoria explains those specialized plants (the correct scientific term is pyrogenic geoxylic suffrutices):

It is a very peculiar growth form that is associated with our grasslands, and it is very much a type of growth form in Africa. It is not found in significant numbers anywhere else in the world, except perhaps to a limited degree in South America. It is a growth form where you get plants, woody plants that can be compared to underground trees, and all that you see are these green twigs which can be compared with a canopy of the tree. And this is probably one plant sitting here, or maybe even this whole area may be one plant, and it’s the canopy that just sticks out, the tips of the branches above ground. These tips may burn down every year, but the rest of the tree stays untouched underground. Why they have adopted this strategy… it is a very interesting challenge to come up with reasons. Fire, frost, a shallow water table and grazing have all been considered. There are lots of interesting things we can say about the reasons why plants have adopted this strategy and why it mainly evolved in Africa. They are called clones, and are essentially immortal, nothing can kill them, except for habitat destruction. Grazers can not kill them, fire can not kill them and they are drought resistant. They grow extremely slowly, and if you look at the diameter of some of these clones, they must be the oldest inhabitants of our grasslands. I would say easily more than a thousand years for many of these clones since the first seed arrived for that particular species. But I would not be surprised if some of them are one day shown to be perhaps more than 10 000 years old, amongst the oldest plants in the world, much older than any tree that you are going to see. They are very peculiar plants and we have quite a number of these species in our grasslands.

It was during Michelle Van der Bank's (University of Johannesburg) talk at the conference in Kunming that I first learned about these extraordinary trees. Michele was reporting on results of the TreeBOL Africa project. They have cataloged and barcoded over 50% of the estimated 2,486 woody shrub and tree species in southern Africa. The underground tree species were one example of how this dataset was used to address questions across disciplines including ecology, conservation biology, and taxonomy.

Gleanings from the Kunming conference - frosty springtails

Ask anyone to name an Antarctic land animal, the response most likely will be, "penguin." However, most of the usual suspects — penguins, seals — don't actually live on the continent. They just visit. With the exception of the emperor penguin all species spend most of their lives at sea. Actually, in order to see Antarctica's resident land animals, you have to look through a microscope. The animals that rule Antarctica are rotifers, tardigrades, mites, and springtails possessing a bizarre array of physiological tools and strategies to survive on the coldest, windiest, highest and driest continent on Earth.

Springtails for example are found all over the planet, but those that live in Antarctica have a few tricks to survive the harsh conditions. They can slow down their metabolism to save energy, and shortly before winter, they start to produce glycerol - the very same substance we use in our cars to prevent cooling water from freezing.

Ian Hogg and his team at the University of Waikato have been studying springtails in Antarctica for quite some time and some of their research was presented in Kunming.

They used DNA Barcodes to examine levels of genetic variability within and among populations of five endemic springtail species along a latitudinal gradient in the Ross Sea region of Antarctica. This work represents the first re-evaluation of several areas, including the central and southern Transantarctic Mountains, in almost 50 years. Three of the five species showed high levels of divergence at both small (<15km) and large (>300km) spatial scales. For example, Gomphiocephalus hodgsoni, a widespread and common species showed 7.6% sequence divergence on opposite sides of the Mackay Glacier and >8% when compared with sites near another glacier. The other two species (Neocryptopygus nivicolus and Antarctophorus subpolaris) also showed high levels of sequence divergences despite being more range-restricted. 

What are the potential reasons for such high barcode divergences? The colleagues conclude in their abstract:

... glaciation in Antarctica has promoted and maintained the levels of diversity observed among populations of springtails and that isolation has occurred even on relatively small spatial scales. Levels of divergence are likely to reflect the presence of previously unknown or cryptic species and conservation efforts should be directed towards protecting and preserving the biotic integrity of fragmented landscapes in Antarctica.

Gleanings from the Kunming conference - ECO-TROP

I've promised some posts about what I learned in Kunming during the International Barcode of Life Conference. Lot's of exciting new research ideas, interesting projects and astonishing results.

Let's start with a field school that integrates DNA Barcoding into an educational program that develops a census of invertebrate diversity in a National Park in Gabon.

Gabon is considered one of the world's major biodiversity hotspots. The forests and savannas covering most of the country are popular for their enigmatic species of vertebrates and higher plants. However, as usual, 

invertebrates are poorly known and as a consequence generally absent from conservation plans and strategies. DNA Barcoding seems to be the ideal tool to help with documenting basic descriptive metrics of invertebrate diversity (e.g. species richness, spatial or temporal turnover). 

Back in 2011, the first edition of the “field school in tropical ecology and palaeoecology” (ECO-TROP) was organized  in the National Park La Lopé (Ogoué Ivindo region) with the participation of several institutions from France*. 

The organizers think that DNA Barcoding is an unique educational tool to raise students’ awareness that can also assist and hopefully promote the future census and description of the local diversity. DNA Barcoding represents a central theme of this successful training program, strongly emphasizing its potential for the documentation of biodiversity in poorly known and hyperdiverse groups of invertebrates. 

Undergraduate students students from universities in France and Gabon are introduced to common invertebrate sampling methods which are routinely used in studies on biodiversity, ecology and palaeoecology in intertropical environments. The field course takes into account the lack of taxonomic information for these organisms and illustrates – both in the field, during short seminars and lab work sessions – the strength of an integrative approach to taxonomy (morphology and DNA), but also the value of a multidisciplinary approach by integrating ecological observations and measurements (e.g. soil profiles, vegetation structure), geographical factors at various scales (through aerial and satellite image analyses). Students also learn about the influence of past human occupation in these areas and their impact on the environment.

The ECO-TROP field school runs annually, with the prospect of moving to other National Parks of the country. The expectation is that all editions of ECO-TROP will significantly contribute to the knowledge of Gabon’s invertebrate biodiversity and, more importantly, to equip young field biologists with a solid understanding of ecological and conservational issues in relation to biological diversity, and in particular on the importance of invertebrates in ecosystems. 

h/t Thibaud Decaens



*Université de Rouen, Institut pour la Recherche et le Développement (IRD), Université de Rennes, Centre National de la Recherche Scientifique (CNRS) – and Gabon – Agence Nationale de Parc Nationaux (ANPN), Université de Masuku (USTM), World Conservation Society (WCS), Complexe Educatif Docteur Alphonse Mackanga Missandzou (CEDAMM), Institut de Recherche en Agronomie Forestière (CENAREST–IRAF)

Phylloxera

The hemipteran Phylloxera (Daktulosphaira vitifoliae) is a pest of commercial grapevines worldwide, originally native to eastern North America. These tiny insects, related to aphids, feed on the roots and leaves of grapevines which results in root deformations and secondary fungal infections. Juveniles also form protective galls on the undersides of grapevine leaves of some vine species.

The species has already spread and is found around most of the world's vineyards. One of Australia's primer vine regions - South Australia is home to the Phylloxera and Grape Industry Board of South Australia which is committed to minimising the risk of pests and diseases in particular Phylloxera in South Australian vineyards. The organisation has been spearheading research that resulted in the development of DNA tests (DNA Barcoding, eDNA analysis with taqMan probes). In order to support these efforts the South Australian Government has decided to spend $500,000 to speed up commercialisation of this new method of testing for phylloxera.

Traditional testing methods rely on digging around grapevines followed by visual inspection to see if the insect is living on the roots. If done comprehensively this method is extremely costly and the new DNA-based analysis could save the industry millions of dollars. Trials were already conducted in New South Wales and France and researchers are now looking into refinement of sampling protocol the need to establish the best location and depth to take a sample from, and how long it will take and at what temperatures before the DNA degrades’.

Save the vine!

Friday fun

Almost dark humor that is..

Carnival of Evolution #65

... and yet another carnival, this time with an eclectic mix of horror stories at PZ Myers' Pharyngula.

The cave cyber-centipede

A description of a new centipede species went through the press last week. Not so much because of the fact that it represents a very exotic find or bears a particular interesting name but rather because of the amount of additional information provided in addition to the usual data:

We demonstrate how a classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. A cave-dwelling centipede, Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae),  found in a remote karst region in Knin, Croatia, is the first eukaryotic species for which, in addition to the traditional morphological description, we provide a fully sequenced transcriptome, a DNA barcode, detailed anatomical X-ray microtomography (micro-CT) scans, and a movie of the living specimen to document important traits of its ex-situ behaviour....

...This pilot project illustrates a workflow of producing, storing, publishing and disseminating large data sets associated with a description of a new taxon. All data have been deposited in publicly accessible repositories, such as GigaScience GigaDB, NCBI, BOLD, Morphbank and Morphosource, and the respective open licenses used ensure their accessibility and re-usability.

Well, this is certainly not meant as a contribution to more faster descriptions (turbo-taxonomy). The international team of researchers sees it rather as a way to describe species in the future with as much information as possible. It also represents a rare type of collaboration between scientists, publishers (GigaScience, Pensoft) and genomic institutions (China National GeneBank, BGI-Shenzhen). 

Frankly, I am not sure what to make of this project. More data sounds great and more comprehensive descriptions of organisms are certainly very attractive. However, I strongly believe we do need to focus more on changing our ways to register and describe species as we seriously fall behind in our efforts to catalog biodiversity before it is wiped out by humanity. For this reason I do think the conclusion of the publication is perhaps a bit too enthusiastic although the point they make about standardization is one I do support:

Taxonomy is at a turning point in its history. New technologies allow for creation of new types of information at high speed and in gigantic volumes, but without clear rules for communication standards, we will not be able to exploit their full potential. We need to focus our efforts on linking these bits and pieces together, by documenting them, by standardising them and by making them retrievable. If such an infrastructure is in place, unforeseen analytical powers can be unleashed upon these data, creating a revolution in our abilities to understand and model the biosphere.

BIO's Daily Image

I am slowly catching up on my email and marking of course assignments. There is a lot left to report on the Kunming conference. Unfortunately, the connection at the site was not good enough (let alone the problem of blocked sites such as blogger) to provide proper updates. I will make up for that in the days to come.

Another thing that perhaps went largely unnoticed is a new feature we started about a week ago:

BIO's Daily Image

Our collections unit is also responsible for proper imaging of all specimens that go through our pipeline. Any specimen that arrives here will be photographed before tissue samples are taken and passed on to the lab for sequencing. As you can imagine over the years we have been amassing quite a few images of beautiful critters and every day we keep adding new ones. All of the images are uploaded to BOLD together with all other data associated with a specimen but we thought it would be a great idea to share some of them through another outlet on a daily basis. We chose Pinterest for that as it is most convenient and up-to-date. Furthermore, we can use widgets for our websites. I've added one to this blog (you should be able to see it in the column on the right). Enjoy!