DNA barcoding of consumer-relevant mushrooms

The dietary supplement industry has grown from $4 billion in 1994 to an estimated value of $35 billion in 2015 in the United States, and many “mushroom” containing dietary supplements are formulated with one to several fungal species. The world production of mushrooms for this industry has been estimated to be around $18 billion, and their trade has been compared to the value of coffee sales worldwide. In 2002, the global market value of mushrooms in dietary supplement was approximated to range from $5-6 billion.

However, the industry is facing the challenge of ensuring reliable species identifications for process material. A multitude of modifications along a multilevel supply chain makes it particilar difficult for samples containing fungal mycelia. Processes such as milling, drying, and extraction usually destroy important morphological characters and as a consequence species identification based on such methods is out of the question.

A group of US researchers has now successfully demonstrated the utility of the DNA barcode standard marker ITS to provide reliable species IDs for all sorts of fungi found in the food and dietary supplement products. Their results confirm - not unexpected - that barcoding works quite well and, if properly executed, could enrich the tool set available to regulators and researchers.

Barcoding methods highlighted here could ensure the industry of product reliability, thereby ensuring both consumer safety and product integrity. Even when morphology can be discerned, for example in culinary mushrooms, we have revealed that a sample labeled as B. edulis and sold in a U.S. grocery store was actually a new species that was recently reported from grocery stores in the UK. We have also demonstrated that some fungal containing products sold commercially as dietary supplement are not entirely accurate in terms of the scientific names that were displayed on the product label.

eDNA to detect largetooth sawfish

Sawfishes (Family Pristidae) are the most threatened family of elasmobranch (sharks and rays), with all 5 species listed on the IUCN Red List of Threatened Species as either Critically Endangered or Endangered. Limited observational data and expert opinion suggest that sawfish species are now extinct in at least 20 countries within their former distribution, and are possibly extinct in many more.

A lack of understanding the remaining extant range of sawfish due to their rarity and scattered occurence in remote regions has hampered our ability to implement recovery strategies. Researchers from James Cook University and Charles Darwin University have tested the utility of DNA barcodes obtained from environmental DNA (eDNA) to find the freshwater largetooth sawfish (Pristis microdon) in remote northern Australia.

Before trying the technique in the wild some initial tests were done on water samples from different aquaria and the colleagues were able to correctly tell which contained largetooth sawfish. Traditional methods to search for sawfish, such as fishing surveys, can be expensive and time-consuming. To test the approach in the wild, the research team sampled known largetooth sawfish habitats in the Daly River, Northern Territory. They partnered with indigenous owners and rangers. 

The method was mostly accurate in waterholes but not as good in flowing rivers likely the result of the high water flow and the associated turnover rates . This is not a big problem, this is very much a trial phase and it will be solved quite easily given some more time. Within five to ten years it's hoped that all eDNA analysis will be able to be completed in the field, with no need to take samples back to the lab.

What snow leopards really eat

Declining prey populations are widely recognized as a primary threat to snow leopard (Panthera uncia) populations throughout their range. Effective snow leopard conservation will depend upon reliable knowledge of food habits. Unfortunately, past food-habit studies may be biased by inclusion of nontarget species in fecal analysis, potentially misinforming managers about snow leopard prey requirements.

It was estimated that there are only 4,500–7,500 snow leopards left in the wild and consequently the species is listed in CITES Appendix I. Knowledge of their dietary habits is a life-history parameter needed for effective conservation but it seems that as a result of the inclusion of non-target species samples in past studies, our understanding of the snow leopard has been biased to say the least. The issue with collecting and identifying scat in the field is that researchers mostly rely on morphological characteristics such as shape, size or associated signs of snow leopards, and since scat from different species can look similar, this can lead to misrepresented population estimates and errors in reporting what the snow leopards are actually eating.

It has been thought that they consume great numbers of small mammals such as marmots, hares and pika, as well as wild ungulates, such as ibex. Older estimates of the amount of small mammals snow leopards consume may have been overstated, and the importance of large ungulate populations to the snow leopard's diets may have been understated, as a new study suggests. Stable snow leopard populations are possibly more reliant upon large ungulate prey than previously understood.

This can affect conservation plans because if snow leopards are eating more large ungulates, we need to make sure we're maintaining those large ungulate populations. Otherwise, a population of snow leopards might not survive because there's not enough prey, or they may start eating more domestic livestock, which can cause problems with local human populations. That could result in people going out and killing snow leopards in retribution.

The colleagues analyzed 199 suspected snow leopard scat samples collected from two study sites in Tajikistan and from two study sites in Kyrgyzstan utilizing mitochondrial genetic markers. Overall, only about a third of collected scats thought to be from snow leopards were confirmed as snow leopard, many turned out to be from red fox . The snow leopard samples were most often confused with red fox (Vulpes vulpes) scat, which comprised almost 40% of collected samples.

We don't want to overstate our results because this was just one study, but we did notice that if we were using the blind approach, we definitely had a lot more small mammal occurrence in those scats. When we used genetics to pre-screen the scat and find out which ones were actually snow leopard, there were many fewer small mammals in those scats. It's a little bit of conjecture, but our thought is that a lot of food habit studies that have not been able to verify that their scat is actually from the species that they're studying probably do have this bias soaking in from other species.

The microbiome of wine

Source: cupegraf

Culture-independent methods of microbial identification have been developed, which allow for DNA extraction directly from environmental samples without subjecting microbes to growth on nutrient media. These methods often involve next generation DNA sequencing (NGS) for identifying microbes and qPCR for quantifying them. Despite the benefits of extracting all DNA from the sample, results may be compromised by amplifying DNA from dead cells. 

In a recent study, researchers of the University of British Columbia developed a technique that combines a process to identify the full spectrum of DNA in yeast and bacteria samples with a technique that distinguishes between live and dead micro-organisms. Key in the development of their method was the use of a light-sensitive dye, propidium monoazide, which deactivates DNA in non-viable cells and thereby prevents it from being detected. The colleagues tried to identifying the yeast and bacterial diversity of wines.

Since only live micro-organisms are relevant in the various stages of fermentation as they relate to the senses, this study provides some of the important tools that will be necessary to determine why different types of wine taste and smell as they do. While more research needs to be conducted, these findings could also lead to the identification and elimination of micro-organisms that are responsible for spoilage.

The new technique allows for a much faster and more accurate assessment. What previously could have taken multiple experiments and months of trial and error, can now be done in a single experiment. 

The next stages of research will focus this technique on different types of wine making methods to see how they change micro-organisms that affect the final wine product.

DNA barcoding of frugivorous bird diets

Eurasian Blackcap (Sylvia atricapilla)

Frugivores are critical components of restoration programs because they are seed dispersers. Thus, knowledge about bird–plant trophic relationships is essential in the evaluation of the efficacy of restoration processes. 

The traditional approach to the analysis of the diet of frugivore birds is the morphological identification of plant residues in droppings. Unfortunately, this is time-consuming, requires expert botanical knowledge, and cannot be used for fragments lacking any visible morphological characteristics. It seems obvious that molecular approaches such as DNA barcoding could instead be used as a universal tool to rapidly characterize the diet of a frugivorous bird or any other bird for that matter.

A group of Italian researchers was interested in using frugivorous birds as bioindicators of the efficacy of restoration at a site of community importance in Italy (Pusiano Lake in the North of the country). Over 3 years the team collected 642 Eurasian Blackcap (Sylvia atricapilla) droppings at the site during the autumn migration. Intact seeds and fragmented plant material were analyzed at two plastid loci (the barcode region rbcL and trnH-psbA), and the resulting plant identifications were validated by comparison with a reference molecular data set of the local flora.

The colleagues were able to find at least 17 plant species, including 7 of 11 newly transplanted taxa. Remarkably, 188 samples contained exclusively fragmented plant material unidentifiable with morphological methods. On the other hand it wasn't difficult to find sufficient DNA in all of their samples which shows the superiority of the method. Identification success was also exceptionally high which led to the summary:

Our results demonstrate the potential for DNA barcoding to be used to monitor the effectiveness of restoration plantings and to obtain information about fruit consumption and dispersal of invasive or unexpected plant species. Such an approach provides valuable information that could be used to study local plant biodiversity and to survey its evolution over time.

Plant species diversity for soil health

Plant diversity loss impairs ecosystem functioning, including important effects on soil. Most studies that have explored plant diversity effects belowground, however, have largely focused on biological processes. As such, our understanding of how plant diversity impacts the soil physical environment remains limited, despite the fundamental role soil physical structure plays in ensuring soil function and ecosystem service provision.

As a result of changing land use to feed a growing population, climate change, and contamination of land with toxic chemicals, our soil resources are deteriorating, posing a serious threat to food security.

Plant roots play a key part in keeping soil together, making it resistant to erosion and helping water flow through the soil, which can help to prevent floods. But until now little was understood about how roots of different plant communities affect the physical condition of the soil. A team of researchers from the UK, Netherlands and Germany presented new evidence that an increase in plant species diversity can protect soil in grasslands by improving soil structure.

In a series of experiments in field sites in the UK (plant manipulation experiment conducted at the Lancaster University Field Station) and Germany (large scale plot experiment in Jena), the researchers tested the soil's structural stability when planted with a variety of different grasses, herbs and legumes. They found that soil structure improved with higher plant diversity and that the diverse properties of different plant roots were the key factor in keeping soil healthy.

For example legumes are better at getting water into the soil more quickly and maintaining root-soil strength. Grasses, however, have fine rooting systems that enhance the stability of soil making it more resistant to erosion. Combining these effects enhances the benefits for the soil. 

We only need to look at historical examples such the American Dust Bowl of the 1930s to see that globally, the physical degradation of our soil presents a serious threat to human well-being. This study offers clear evidence that by increasing species richness we can not only increase ecological value, but also provide a degree of protection to our soil which is good news for the future.

Soils are severely degraded in many parts of the world and these findings suggest that enhancing plant diversity could be an important way of speeding up their restoration to bring back fertility. It is almost like different combinations of roots can be used to engineer the soil, working to enhance its physical structure which is key to soil health.

From DNA barcodes to biomes

Today is a public holiday in Canada, so I'll keep posting to a minimum. However, I don't want to miss the opportunity to announce a special them issue of the Philosophical Transactions of the Royal Society. The issue comprises of contributions derived from presentations at the 6th International Barcode of Life conference. There is even one with me as co-author. All of them are Open Access. Enjoy reading:

Introduction: From writing to reading the encyclopedia of life

Paul D. N. Hebert, Peter M. Hollingsworth, and Mehrdad Hajibabaei

Opinion piece: DNA barcoding and taxonomy: dark taxa and dark texts

Roderic D. M. Page

Opinion piece: Imagining Sisyphus happy: DNA barcoding and the unnamed majority

Mark Blaxter

Review article: Advancing taxonomy and bioinventories with DNA barcodes

Scott E. Miller, Axel Hausmann, Winnie Hallwachs, and Daniel H. Janzen

Opinion piece: Biodiversity analysis in the digital era

John La Salle, Kristen J. Williams, and Craig Moritz

Research article: Counting animal species with DNA barcodes: Canadian insects

Paul D. N. Hebert, Sujeevan Ratnasingham, Evgeny V. Zakharov, Angela C. Telfer, Valerie Levesque-Beaudin, Megan A. Milton, Stephanie Pedersen, Paul Jannetta, and Jeremy R. deWaard

Opinion piece: Telling plant species apart with DNA: from barcodes to genomes

Peter M. Hollingsworth, De-Zhu Li, Michelle van der Bank, and Alex D. Twyford

Review article: Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches

Rebecca Yahr, Conrad L. Schoch, and Bryn T. M. Dentinger

Review article: Censusing marine eukaryotic diversity in the twenty-first century

Matthieu Leray and Nancy Knowlton

Review article: Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans

Camilla Speller, Youri van den Hurk, Anne Charpentier, Ana Rodrigues, Armelle Gardeisen, Barbara Wilkens, Krista McGrath, Keri Rowsell, Luke Spindler, Matthew Collins, and Michael Hofreiter

Review article: DNA barcoding in diverse educational settings: five case studies

Heather J. Henter, Ralph Imondi, Karen James, Diana Spencer, and Dirk Steinke

Research article: The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life

Xin Zhou, Paul B. Frandsen, Ralph W. Holzenthal, Clare R. Beet, Kristi R. Bennett, Roger J. Blahnik, Núria Bonada, David Cartwright, Suvdtsetseg Chuluunbat, Graeme V. Cocks, Gemma E. Collins, Jeremy deWaard, John Dean, Oliver S. Flint, Jr, Axel Hausmann, Lars Hendrich, Monika Hess, Ian D. Hogg, Boris C. Kondratieff, Hans Malicky, Megan A. Milton, Jérôme Morinière, John C. Morse, François Ngera Mwangi, Steffen U. Pauls, María Razo Gonzalez, Aki Rinne, Jason L. Robinson, Juha Salokannel, Michael Shackleton, Brian Smith, Alexandros Stamatakis, Ros StClair, Jessica A. Thomas, Carmen Zamora-Muñoz, Tanja Ziesmann, and Karl M. Kjer

Review article: Dissecting host-associated communities with DNA barcodes

Christopher C. M. Baker, Leonora S. Bittleston, Jon G. Sanders, and Naomi E. Pierce

Review article: Insect symbionts in food webs

Ailsa H. C. McLean, Benjamin J. Parker, Jan Hrček, Lee M. Henry, and H. Charles J. Godfray

Opinion piece: A new way to contemplate Darwin's tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring

Mehrdad Hajibabaei, Donald J. Baird, Nicole A. Fahner, Robert Beiko, and G. Brian Golding

Review article: Multilocus inference of species trees and DNA barcoding

Diego Mallo and David Posada