Wednesday, October 26, 2016

Microbial soil live

A new study sheds light on one of Earth's most important and least understood realms of life. The subterranean world hosts up to one-fifth of all biomass, but it remains a mystery. Little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. 

The new research is part of a project called Sustainable Systems Scientific Focus Area 2.0 (did I mention that I hate these 2.0 references?) , which is developing a predictive understanding of terrestrial environments from the genome to the watershed scale. The project's field research takes place at a research site near the town of Rifle, Colorado, where for the past several years scientists have conducted experiments designed to stimulate populations of subterranean microbes that are naturally present in very low numbers. Researchers reconstructed the genomes of more than 2,500 microbes from sediment and groundwater samples collected at an aquifer in Colorado.These represent about 80 % of all known bacterial phyla, a remarkable degree of biodiversity at one location. They also discovered 47 new phylum-level bacterial groups, naming many of them after influential microbiologists and other scientists. And they learned new insights about how microbial communities work together to drive processes that are critical to the planet's climate and life everywhere, such as the carbon and nitrogen cycles.

Soil and water samples were subjected to so-called terabase metagenomic sequencing. This high-throughput method isolates and purifies DNA from environmental samples, and then sequences at least one trillion base pairs of DNA at a time. Warning - don't try this at home as the bioinformatics for this amount of data is - to say the least - challenging.

Their approach has redrawn the bacterial tree of life. Between the 47 new bacterial groups reported in this work, and 35 new groups published last year (also found at the Rifle site), the colleagues have doubled the number of known bacterial groups.

We didn't expect to find this incredible microbial diversity. But then again, we know little about the roles of subsurface microbes in biogeochemical processes, and more broadly, we don't really know what's down there.

The scientists also conducted metabolic analyses of 36% of the organisms detected in the aquifer system. They focused on a phenomenon called metabolic handoff, which essentially means one microbe's waste is another microbe's food. It's known from lab studies that handoffs are needed in certain reactions, but these interconnected networks are widespread and vastly more complex in the real world. Carbon, hydrogen, nitrogen, and sulfur cycles are all driven by metabolic handoffs that require an unexpectedly high degree of interdependence among microbes. The vast majority of microorganisms can't fully reduce a compound on their own. It takes a team. There are also backup species ready to perform a handoff if first-string microbes are unavailable.

The combination of high microbial diversity and interconnections through metabolic handoffs likely results in high ecosystem resilience.

Friday, October 21, 2016

A DNA barcode for an extinct species

The sunset moth (Urania sloanus) from Jamaica has been last seen around 1895. This spectacular moths went extinct in the mid-1890s or the very early 1900s.  It was first described by Pieter Cramer, a Dutch merchant and entomologist in 1779. The species name honours Sir Hans Sloane (1660–1753), who served as physician to Jamaica's Lieutenant Governor in 1687-88 and whose collection of plant and animal specimens became the foundation of the British Museum. The genus name Urania derives from Ancient Greek Ουρανία, one of the Muses, and means literally 'The Heavenly One'.

There are only a few specimens preserved in the most prestigious world collections, and there was one offered on eBay a few years ago and a former colleague of mine actually bought it with the help of the entire Augusta campus of the University of Alberta.

What we did not have so far was a DNA barcode of this species but that has changed now. Using High-throughput sequencing (HTS) technology colleagues from our institute and the Canadian National Collection of Insects were able to provide a full-length barcode sequence for this extinct beauty. They used a HTS protocol developed specifically for museum type specimens. This new sequence allowed them to make a phylogenetic placement of the species and this in turn has some important implications which the authors explain in their conclusion:

Despite the complex and much debated geological history of the Caribbean, the evolution of Urania in the region seems relatively recent and mostly based on dispersal and subsequent isolation. Island biogeographic theory predicts that most island species are likely to be recent derivatives from mainland populations, and with some exceptions, islands (particularly small islands, here not the case for Cuba) tend to be home not to ancient endemics, but rather to recent offshoots from mainland progenitors. This has important implications for conservation biology, considering that many island populations are threatened.While the loss of island lineages is regrettable, it is important to recognize that closely allied populations often occur on neighbouring mainlands. Understanding the evolutionary relationships between island species and their mainland counterparts is thus a key consideration in island conservation efforts.

Thursday, October 20, 2016

The 'Higgs Bison'

The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (<11.7 thousand years ago) remains a mystery. 

More than 15,000 years ago.Ice Age cave artists recorded ancestral bison and cattle species. Bovids in Europe at this time consisted of two forms: the Aurochs (Bos primigenius), ancestor of modern cattle, and Steppe bison (Bison priscus). Interestingly , the cave paintings depict bison with either long horns and large forequarters (more like the American bison, which is descended from the Steppe bison) or with shorter horns and small humps, more similar to the wisent. It turns out the artists had also recorded a hybrid species. This mysterious new species, known affectionately by the researchers as the Higgs Bison because of its elusive nature, originated over 120,000 years ago through the hybridisation of the Aurochs  and the Steppe Bison. 

Ancient DNA research by an international team has revealed that the Higgs Bison eventually became the ancestor of the modern wisent, which today survives in protected reserves such as the Białowieża forest between Poland and Belarus. The team studied ancient DNA extracted from radiocarbon-dated bones and teeth found in caves across Europe, the Urals, and the Caucasus to trace the genetic history of the populations. Radiocarbon dating showed that the Higgs Bison dominated the European record for thousands of years at several points, but alternated over time with the Steppe bison, which had previously been considered the only bison species present in Late Ice Age Europe.

Once formed, the new hybrid species seems to have successfully carved out a niche on the landscape, and kept to itself genetically. It dominated during colder tundra-like periods, without warm summers, and was the largest European species to survive the megafaunal extinctions. However, the modern European bison looks genetically quite different as it went through a genetic bottleneck of only 12 individuals in the 1920s, when it almost became extinct. That's why the ancient form looked so much like a new species.

Wednesday, October 19, 2016

Climate change monitors

Losing mussel beds is essentially like clearing a forest. If they go, everything that's living in them will go. They are a major food supply for many species, including lobsters and crabs. They also function as filters along near-​​shore waters, clearing huge amounts of particulates. So losing them can affect everything from the growth of species we care about because we want to eat them to water clarity to biodiversity of all the tiny animals that live on the insides of the beds.

One direct impact of global climate change is the change in body temperature in ecothermic organisms. Especially species that are exposed to direct solar radiation can exhibit much higher internal temperatures that the medium around them with profound impact on their physiology. 

In this regard mussels can act as a barometer of climate change. That's because they rely on external sources of heat such as air temperature and sun exposure for their body heat and thrive, or not, depending on those conditions. For the past 18 years, every 10 to 15 minutes, a global research team used biomimetic sensors - which they called robomussels - to track internal body temperature, which is determined by the temperature of the surrounding air or water, and the amount of solar radiation the devices absorb. They placed the devices inside mussel beds in oceans around the globe and recorded temperatures. The researchers have built a database of nearly two decades worth of data enabling them to pinpoint areas of unusual warming, intervene to help curb damage to vital marine ecosystems, and develop strategies that could prevent extinction of certain species. Using this kind of fieldwork along with mathematical and computational models, they can forecast patterns of growth, reproduction, and survival of mussels in intertidal zones.

These datasets tell us when and where to look for the effects of climate change. Without them we could miss early warning signs of trouble. The robomussels' near-​​continuous measurements serve as an early warning system. If we start to see sites where the animals are regularly getting to temperatures that are right below what kills them, we know that any slight increase is likely to send them over the edge, and we can act.

Tuesday, October 11, 2016

From the inbox: PhD position, University of Eastern Finland

PhD student position in Ecological genomics of rapid radiations in plant-feeding insects
University of Eastern Finland, Department of Environmental and Biological Sciences (Joensuu campus)

We are looking for a highly motivated person to perform research on the biotic and abiotic drivers of diversification in young but species-rich groups of sawflies (order Hymenoptera). In many of these plant-feeding groups, speciation may be facilitated by specialization into using alternative host plants or other feeding niches, or by simple geographic isolation. In general terms, the project aims at explaining the origin of niche and species diversity in species-rich and widely distributed resource-consumer communities.

The focus will be on ecologically diverse sawfly groups containing numerous closely-related species that cannot be separated using standard morphological and population-genetic methods. New population-genomic approaches based on genotyping by next-generation sequencing (NGS) provide a means for studying the species status of closely-related lineages feeding on different host plants or inhabiting different geographic regions, and to estimate the level of gene flow across species boundaries.

The work will be performed mainly in the Joensuu Molecular Ecology Group, which is led by Associate Professor Tommi Nyman, and operates at the Department of Environmental and Biological Sciences of the University of Eastern Finland. In addition to Tommi Nyman, the work will be supervised by Senior Curator Marko Mutanen (University of Oulu, Finland) and Curator Stefan Schmidt (Zoologische Staatssammlung München, Germany). Part of the laboratory work will be done during extended visits to the laboratories of the external co-supervisors. The project, which is funded by the Academy of Finland, also includes extensive collaboration with an international network of experts on sawfly taxonomy, biogeography, and ecology. 


During the project, the PhD student will tackle central eco-evolutionary questions based on research on several taxonomically complex but evolutionarily highly interesting sawfly groups. Analyses will be based on specimen-level genotypic data obtained using reduced-representation NGS methods (including ddRADseq). The work requires very diverse skills, including field sampling, laboratory work, use of bioinformatic pipelines, population-genetic analyses, and writing research papers. Many of these skills will be learned during the project, but applicants should have a strong background in population genetics or related fields.

The PhD student positions may be applied for by persons who according to the Universities Act of Finland (558/2009, Chapter 5, Section 37) are eligible for studies leading to a scientific postgraduate degree. Persons graduating in the near future are also encouraged to apply. However, they are expected to hold a relevant MSc degree (or equivalent) by the starting date of the Early Stage Researcher position.


The position will first be filled for 24 months, with a possibility for prolongation for six months. The continuation of the position will be agreed separately. The current funding covers the first 2.5 years of the PhD project, but the chances of obtaining further funding should be good if things proceed as planned. The start date of the position is 1 January 2017 or as agreed. Positions of early stage researchers shall always be filled for a fixed term (UEF Administrative Regulations, Section 30). A probationary period is applied to all new members of the staff.

The salary of the position is determined in accordance with the salary system of Finnish universities and is based on levels 2-4 of the job requirement level chart for teaching and research staff (euro 1,986 - 2,475 / month). In addition to the job requirement component, the salary includes a personal performance component, which may be a maximum of 46.3% of the job requirement component. In practice, the salary will be circa euro 2,320 / month at the start of the project.


The University of Eastern Finland, UEF, is one of the largest multidisciplinary universities in Finland. We offer education in nearly one hundred major subjects, and are home to approximately 15,000 students and 2,800 members of staff. We operate on three campuses in Joensuu, Kuopio and Savonlinna. In international rankings, we are ranked among the leading 300 universities in the world.

The Faculty of Science and Forestry operates on the Kuopio and Joensuu campuses of the University of Eastern Finland. The mission of the faculty is to carry out internationally recognised scientific research and to offer research-education in the fields of natural sciences and forest sciences. The faculty invests in all of the strategic research areas of the university. The faculty's environments for research and learning are international, modern and multidisciplinary.  The faculty has approximately 3,800 Bachelor's and Master's degree students and some 490 postgraduate students. The number of staff amounts to 560. 


For further information on the position, please contact Associate professor Tommi Nyman, tel. +358 40 5206540. For further information on the application procedure, please contact Executive Head of Administration Arja Hirvonen, tel. +358 44 716 3422. 


The electronic application should contain the following appendices:
- a resume or CV, including contact information of two referees
- a list of publications (if applicable)
- copies of the applicant's academic degree certificates/ diplomas, and copies of certificates /
  diplomas relating to the applicant's  language proficiency, if not indicated in the academic degree
- cover letter explaining possible past research experience, future interests, and motivation for    
  applying for the position (max 2 pages)

 The application needs to be submitted no later than October 31, 2016 (by 24.00 hours Finnish time) by using the electronic application form

Tuesday, October 4, 2016

Global costs of invasive insects

Tetropium fuscum
For thousands of years, insects have been responsible for the spread of diseases in humans and livestock. They caused considerable damage on many levels: from attacks on crops and stocks, through the destruction of infrastructure, to the devastation of forests, thereby altering and weakening ecosystems. Among all living things, insects alone are probably the group responsible for the greatest costs. In addition, they are among the most aggressive invasive species. About 87% of 2500 terrestrial invertebrates that have colonized new territories are in fact insects.

The question remains - just how big is the economic damage insects are currently causing? In an attempt to answer this question an international team of researchers build a comprehensive database on economic damage attributable to invasive insects worldwide. Their data covered damage to goods and services, health care costs and agricultural losses and although we are looking at invasive species alone the authors came up with an estimated minimum economic damage of US$70 billion per year. 

Globally insects are taking a heavy toll on agriculture by consuming 40% of the harvest which would be enough to feed one billion people. 

Total health care costs attributable to invasive insects exceed US$6.9 billion (without counting malaria, Zika, or economic impacts on tourism or productivity, etc.). Among the diseases that have the greatest economic impact, dengue fever ranks first with costs accounting for 84% of the total.

Of the insects studied by the colleagues, the Formosan termite (Coptotermes formosanus) ranks as the most destructive, allegedly causing over US$30.2 billion of damage per year in the world. However, according to the research group, this estimate is based on a study that was insufficiently documented. Studies that were based on more sound data show other species at the top, e.g. the cabbage moth (Plutella xylostella), with a cost of US$4.1 billion per year, and the brown spruce longhorn beetle (Tetropium fuscum), which annually costs US$4 billion in Canada alone.

According to this study, North America suffers the largest financial losses, at US$27.3 billion annually, while Europe is currently listed at only US$3.6 billion per year. This difference, however, can be explained rather by the lack of evaluation sources than by a difference in exposure to these dangers. Thus, the total annual cost estimation is a real minimum likely representing a large underestimate of the real costs. Many parts of the world do not offer enough economic data to produce an accurate estimate. In addition, the research team focused on the study of the ten most costly invasive species, not counting the very large number that cause less damage. Finally, considering the estimated values of ecosystem services on a global scale (hundreds of billions of dollars for crop pollination alone), the disruption caused by invasive insects could reach a level far beyond the current estimate.

Some very scary numbers indeed. Keep in mind we are looking at lowest estimates using the most conservative approach to extrapolate them. I am not saying that DNA barcoding would be the ultimate solution to the problem of invasive species but it would certainly make a big contribution by helping to identify potential invaders early enough. Given the immense sums I was just talking about it seems rather modest if somebody asks for $2 billion to barcode all species (not only insects) of planet Earth.