Princeton University Professor Tullis Onstott and his team used the MO BIO UltraClean® Mega Soil DNA Isolation Kit to remove bulk DNA from filtered fracture water for downstream metagenomic analyses. The water was collected from South African gold mines that stretch nearly a mile below the earth. A large scale DNA isolation kit was required for this project because of the enormous volume of water required for a complete metagenome – up to 8000 liters! While hot, salty water samples were collected from multiple boreholes, one specimen collected from a 2.8 km borehole yielded remarkable results. Using the16S rRNA gene to examine the biodiversity present in the fracture water, Tullis’ group discovered that 99.9% of the sample was comprised of a single bacteria. The chromosomal genome of this extraordinary microorganism revealed that it is a motile, sporulating, sulfate reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon using machinery shared with archaea. The team proposed a name of Candidatus Desulforudis audaxviator, which aptly describes a microbe that is capable of an independent lifestyle well suited to long-term seclusion from the photosphere. This fascinating microorganism manages to survive deep within the Earth’s crust, and provides the first example of a natural ecosystem that appears to have its biological component entirely encoded within a single genome. These exciting discoveries were recently published in Science, 322:275-278, "Environmental genomics reveals a single species ecosystem deep within the Earth".
The group has no plans to stop their search for undiscovered microorganisms. They are already making preparations for their next trip to collect samples in the Witwatersrand Basin to look for microorganisms similar to Candidatus Desulforudis audaxviator. Additionally, the group kicked off another new project earlier this year with a conference on subsurface microorganisms and inauguration of the Network of Inner Space Observatories (NISO), an international research network dedicated to the development of underground laboratories and mines for microbial studies. During this interactive conference, scientists had the opportunity to travel underground to collect samples from several different high pressure boreholes to test different types of filtration devices. The results of these studies are expected to reveal the presence of additional types of mysterious microorganisms.
Thulani Makhalanyane, PhD candidate at the Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, South Africa, along with Professor Donald Cowan, recently took a trip to the Namib Desert, to conduct research focused on understanding the microbiology of hyperarid desert microbial communities, particularly, the hypolithic communities. Hypoliths, which are microbes found underneath translucent rocks, are particularly exciting microbial niche communities. "We are interested in understanding the composition and community dynamics of hypoliths. This involves the analysis of microbial (prokaryote and eukaryote) diversity, and building a relationship between community composition and local physiochemical properties such as pH, relative humidity and temperature. One of the microenvironmental dynamics which is particularly exciting is water relations - we would like to understand the relative contributions of rain, fog (condensation) and ground water."
To successfully isolate community DNA from these difficult samples, Thulani relied on the MO BIO PowerSoil® DNA Isolation Kit. This allowed them to determine the members comprising the hypolithons through amplification and subsequent cloning of 16S rRNA gene amplicons. The next step was to determine which members of these communities are active through metatranscriptomic analysis. This involved RNA extractions, using the RNA PowerSoil® Total RNA Isolation Kit, from samples stored with Lifeguard Soil Preservation Solution.
"MO BIO Kits (such as the DNA and RNA extractions kits) have been very useful in obtaining metagenomic nucleic acid preparations from low biomass samples such as the Namibian hypolithons. We are often unable to carry out extractions immediately in the field, so being able to preserve samples in Lifeguard Soil Preservation Solution gives us the flexibility of carrying out extractions in the lab."
At the southernmost-tip of the East African Rift Valley in Kenya, lies a, at times, virtual pool of sodium carbonate, the Lake Magadi. This lake is replenished primarily by surrounding saline hot springs, setting the scene for an extremely challenging environment for life of any form. With soda covering around 80% of the lake surface in the dry season, and areas within the lake containing salt up to 40 meters thick, there is only one surviving species of fish withstanding the conditions.
However, when it comes to survival in strange and difficult conditions, extremophile microbes are up for the challenge. And where there are unusual microbes to be found, equally determined and inquisitive scientists will follow. In this difficult environment, a collaborative project between Don Cowan, Director of the Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape town, SA and Prof Hamadi Boga, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya delves into the lives and livelihoods of these incredible microorganisms.
The project, funded jointly by the National Research Foundation of South Africa and the Kenyan National Council for Science and Technology aims to investigate the microbial diversity of different biotopes of Lake Magadi. Many of these lakes are characterised by high salinity and pH and, due to their tectonic origins, some also exhibit hydrothermal sources sited close to the lake margins. The researchers principally will both use modern metagenomic and phylogenetic methods, in conjunction with the PowerWater® DNA Isolation Kit, to assess the diversity of different groups of microorganisms, linking community fingerprints to the physicochemical characteristics of the sites. Specific surveys of actinobacterial diversity will be supported by culture-dependent studies.
Holly Ganz, Ph. D. in the Department of Environmental Science, Policy & Management at UC Berkeley and her research team are working in collaboration with the Etosha Ecological Institute in Namibia to investigate the role scavengers, such as the lappet-faced vultures pictured below, may play in the regular anthrax outbreaks in herbivorous mammal populations in the area.
In Etosha National Park, every year herbivorous populations such as the zebra, springbok and wildebeest encounter anthrax outbreaks. The bodies of animals deceased due to infection become prey for a number of scavengers in the region. Vultures are among the most abundant scavengers here and they may play a role in the distribution of Bacillus anthracis endospores. However, this role has not been quantified, and a misguided belief that vultures transmit disease over long distances has led to an extreme decline in numbers. Dr. Ganz informed us that both of their study species, lappet-faced vultures (Torgos tracheliotos) and white-backed vultures (Gyps africanus), are currently listed as threatened species. Their research, then, not only seeks to better understand population disease transmission, but also seeks to strengthen coonservation efforts.
The research team is measuring B. anthracis DNA concentrations near vulture nests and roosts using nested PCR and the PhyloChip. "We are big users and fans of the PowerMax® Soil DNA Isolation Kit," says Dr. Ganz. Master's students Laimy and Dudu from the University of Namibia, are shown in the right column, using the PowerMax® kits in the laboratory at the Etosha Ecological Institute.
Alexandre de Kochko from the “Centre IRD” in Montpellier (France) is working in collaboration
with two Malagasy Colleagues, Jean-Jacques Rakotomalala and Josiane Razafinarivo, (pictured above) on the evolution of Malagasy Coffea species. Coffea (coffee) is a large genus (containing more than 90 species) of flowering plants in the family Rubiaceae.
|Madagascar is a very important secondary center of diversification of Coffea species. Among the 103 species so far described, over 50 are endemic to Madagascar. Up to now, these species have been poorly studied, but it is primordial to describe precisely the genetic diversity present on the island.|
According to them, it would be quite interesting to get more information on how such diversity arises on the Big Island. This is why the FOFIFA (FOibe Fikarohana ampiharina amin'ny Fampandrosoana ny eny Ambanivohitra), and the IRD (Institut de Recherche pour le Développement) use MO BIO PowerPlant® DNA Isolation Kit in their joined research project to better understand the axis of evolution of Malagasy Coffee species. Work is mainly pursued in Antananarivo, location of the FOFIFA facilities, and in Kianjavata, where the Coffea collection is maintained.
Dr. Laurie Casalot, from the French Research Institute for Development (Marseilles, France), Department of Microbiology and Biotechnology of Hot Climates, extracts really complex samples from a settling tank at a semi-industrial olive oil factory in Morocco. The samples were collected at two different periods: 2 weeks after the oil-production campaign and 7 months after this campaign. In the meantime, the outside temperature reached more than 40ºC and the water evaporated leaving only an extremely viscous solution (see picture below), making the samples quite challenging for extracting DNA.
To test the performance of the PowerClean® DNA Clean-Up Kit, Dr. Casalot and her team did different experiments. They took their samples and isolated the DNA with various methods including the PowerSoil® DNA Isolation Kit.
They did a series of PCR amplifications on their isolated DNA before and after using the PowerClean® DNA Clean-Up Kit. In addition, they took an archived sample that they were previously unable to amplify under any conditions. The archived sample was purified with PowerClean DNA® Clean-Up Kit and the same amplifications were performed.
Dr. Casalot said: "We were quite satisfied with the results since we obtained amplifications with all the samples, including the archived one that we were previously unable to amplify. The amplifications were quite strong in comparison with the ones obtained before purification." An extremely good result was obtained with three of the samples that were very challenging.
Finally, while not every sample required an additional clean up step for successful PCR, Dr. Casalot emphasizes that she would recommend the PowerClean® DNA Clean-Up Kit to any person working with challenging samples like hers.