Sierra Nevada Mountain Range, California, USA
The SDSU Plant Systematics Lab is working on the phylogenetic relationships of the plant family Boraginaceae, subtribe Cryptanthinae Brand and the anticipate a number of nomenclatural changes in the future.
Lee Ripma ( Graduate Student) : The objective of my master’s thesis research project is to elucidate the evolutionary relationships within the genus Oreocarya (Boraginaceae). Oreocarya has long been treated as a subgenus of Cryptantha and defined by perennial (or biennial) duration and production of only chasmogamous flowers. Past treatments by Payson and Higgins treated Oreocarya as a generic section or subgenus. A forethcoming paper by Hasenstab and Simpson recovers Oreocarya as a monophyletic clade and resurects the group to genus level. Their molecular phylogeny of Cryptantha s.l. finds that the genus as currently treated is polyphyletic and warrants a split into 5 genera. The group will be split into Cryptantha s.s., Oreocarya, Eremocarya, Greeneocharis and Johnstonella.
The research also supports the existence of the subtribe Cryptanthinae which also contains the genera Plagiobothrys, Pectocarya and Amsknkia. The evolutionary relationships within the Cryptanthinae subtribe have been the subject of much debate and research. The sampling of Oreocarya by Hasenstab and Simpson is preliminary as it only contains sequence data from eight of the 62 species of Oreocarya found in North America. My research aims to create a complete molecular phylogeny with all 62 species in Oreocarya. The phylogeny will be based upon molecular sequence data from both nuclear ribosomal (ITS and ETS) and chloroplast (matK, trnH-psbA and rpl16) gene regions of species in Oreocarya and several outgroup taxa. To procure DNA for phylogenetic analysis I collect vouchered herbarium specimens for all species in the field. Field collections are made throughout the range of the species. Missing samples will be obtained from recently (<20 years) collected herbarium material. Collections will include preserving leaf material in silica gel. From leaf material, DNA is extracted using the MoBio Plant Pro DNA isolation kit, amplified using PCR, and sequenced by standard techniques. DNA sequence data are aligned and cladograms constructed using parsimony and Bayesian phylogenetic inference. The resulting phylogeny will test the monophyly of the group and trace character evolution.
The resulting phylogeny can also be employed to revise past classifications proposed for the Oreocarya group. In addition to the molecular phylogeny I will conduct morphometric analysis of seven species in the Oreocarya nubigena group. The group was described based on morphological features by Higgins in 1971. His treatment of the group contained four species that were morphologically very similar but he felt deserved separation due to slight morphological differences and geographical isolation. The group now includes a recently described species, Oreocarya schoolcraftii and two novel species in the process of being described, O. howellii and O. ursina. The morphometric analysis will reveal consistent statistically significant morphological characters that separate the species within this group. A possible outcome of the analysis is that the species are not morphological differentiated and should not be treated at the species level. The molecular phylogeny of Oreocarya will inform our understanding of the evolutionary history of a genus of plants endemic to North America. It will test species boundaries in the closely related Oreocarya nubigena group. My research will provide a foundation for further molecular phylogenetic study in the subtribe Cryptanthinae.
The US viticulture industry generates >$30 billion revenue each year and employs more than 24,000 people. It is also a growth industry, but one that is highly susceptible to the vagaries of climate and changing weather patterns. There is exceptional merit in exploring the “quality” of soil and the vine microbiome when growing wine as there is a fundamental link between plant health and productivity and the microbial dynamics in the biogeochemical cycling nutrients.
The present study aims to classify the microbial diversity associated with the bulk soil, rhizosphere, roots, leaves, flowers (in the spring) and grapes (in the fall) from 4 Merlot vine clonal varieties, found in 2 different soil types, in 5 different wineries, in 3 different seasons over 2 years in the North Fork region of Long Island. We are attempting to determine the microbial community structure associated with the vines (endophytic and epiphytic) and to explore the factors which influence the community structure, e.g. host variety, soil type, geolocation, etc. Ultimately we will examine both the 16S rRNA community structure and the shotgun metagenomic functional characteristics to determine whether microbial community structure and function influence the health and productivity of the vines. In summary, by characterizing and defining the relationship between microbiota of the vines and soil, and the productivity and quality of the vines and wines, it will be possible to explore mitigation strategies that could prevent “bad years” in wine production.
We are using several MO BIO products in different stages of our laboratory pipeline because the MO BIO kits turned out to be the most reliable products to fulfill our needs. We use PowerSoil®-htp 96 Well Soil DNA Isolation Kit for DNA extraction in different samples types (bulk soil, rhizosphere, roots, leaves, flowers and grapes) obtaining good quality DNA. In addition, MO BIO’s UltraClean PCR Clean-up kit is an easy and fast way to clean PCR amplicons.
The project is called the Merlot Microbiome Project and is embedded in the Earth Microbiome Project. It is a collaborative study between Argonne National Laboratory/University of Chicago and The Research Triangle Institute (RTI) International in North Carolina. PIs are Jack Gilbert, Niels van der Lelie and Safiyh Taghavi . People involved in the study are Sarah Owens (Argonne National Laboratory), Iratxe Zarraonaindia (Argonne National Laboratory) and Kristin West (RTI International).
Anchialine habitats are defined as coastal ponds and pools that lack surface connections to the open ocean, but are influenced by both seawater and freshwater sources via subterranean connections to the ocean and underlying freshwater aquifers. Habitats fitting this definition are found worldwide, but are concentrated in the Hawaiian Islands, with 600 of the world’s ~1000 habitats. These Hawaiian anchialine habitats host diverse and often endemic macro- and microbiotic communities. Unfortunately, anchialine habitats in Hawaii are threatened by habitat destruction and alteration due to coastal development and invasive species.
Our laboratory at Auburn University, led by Dr. Scott Santos, has been studying the ecology and evolution of organisms in anchialine habitats for the last several years, and we have recently started to investigate the microbial component of these habitats. One area of interest is the distinct orange cyanobacterial crust found in some habitats on the islands of Maui and Hawaii. Due to wide fluctuations in salinity, water levels, and light exposure in Hawaiian anchialine habitats, the microbes composing this crust might warrant a more in-depth examination. As Dr. Santos explains in a feature for NSF’s Science Nation, “Anchialine habitats are considered extreme environments and there has been a lot of interest in looking at things like microbes from extreme environments, because they might hold potential applied value to human welfare” (more info). In this context, the National Science Foundation has generously funded the Santos Lab for 3 years to examine the microbial communities of Hawaii’s anchialine habitats (NSF-DEB #0949855). We are using high-throughput microbiome profiling by Illumina sequencing of 16S/18S-rDNA "tags" in conjunction with environmental data to identify factors influencing microbial community composition across space, investigate temporal dynamics in community composition, and quantify changes in community composition of habitats impacted by environmental perturbation.
We have been using the PowerSoil® and UltraClean® Soil DNA Isolation Kits to extract DNA from a wide range of samples, including sediments and mud from anchialine substrates, algal growths on anchialine rocks, and pieces of the orange cyanobacterial crust. Kiley Seitz, an undergraduate researcher in the lab, has quickly learned her way around these kits and remarks that they are “straightforward, easy to use, and highly efficient”. The microbial communities in the water column of anchialine habitats also interest us, but extractions have been problematic because of low yields from our Sterivex filters. We are therefore very anxious to try the new PowerWater® Sterivex DNA Isolation Kit and see how its yields compare to our current procedures.
We hope this research will ultimately further our limited understanding of microbial ecology in anchialine environments as well as develop a foundation for testing specific hypotheses on the ecological, biogeochemical, and metabolic roles microbes play in this vanishing ecosystem. Regrettably, continued human-mediated habitat alteration and destruction have drastically reduced the number of pristine anchialine habitats, by as much as 90% in some areas during the last ~30 years. As Santos says, “It’s a race against the clock to identify and study the organisms that manage to survive in this environment, before they’re gone.”
Ryan Adams, Greg Barnes, and Taylor Foulger, of Southern Utah University, in collaboration with mentors Terri Hildebrand and Paul Spruell, are wading their way into utilizing DNA analysis to describe irrigation water bacterial communities. They state, "access to clean water is essential to life. Around the world, water is used for both drinking and agricultural purposes; therefore, pathogen free water is paramount to healthy living. Methods that test for specific pathogenic bacteria in water samples have been developed. However, these approaches are limited in scope and do not detect non-pathogenic or atypical bacteria. Our research seeks to describe the bacterial communities of irrigation water found in Iron County, Utah using DNA sequencing analysis. During the course of this research bacterial DNA has been isolated, using the UltraClean® Water DNA Isolation Kit, from three irrigation water samples and methodology verified using negative and positive controls. Using the polymerase chain reaction we’ve amplified the 16s rRNA region. Additional analysis will target DNA sequence data from an array of microbial species, e.g. fungi and archae. Further testing will use additional DNA sequences to detect a wider variety of bacterial species. Bacterial fitness increases under specific environmental conditions, and results from this research provide a starting point in the understanding of composition in freshwater microbial communities. Based on these results, future research will focus on manipulating water chemistry to alter community-level interactions, potentially reducing the prevalence of pathogenic bacteria."
"How many organisms live on a square centimeter of your skin? What do they do, and how do they differ from those of your neighbor? Each person’s microbial jungle is so rich, colorful, and dynamic that in all likelihood your body hosts species that no scientist has ever studied. Your navel may very well be one of the last biological frontiers. It is time to explore!" proposes Jiri Hulcr, PhD, of the Belly Button Biodiversity project.
This group of biologists and science communicators from North Carolina State University simply want to know who our navel-dwelling neighbours are. Jiri explains, "this project is as much about learning as it is about teaching. We want to share the joy of discovering the fascinating diversity of our microbial symbionts, one body part at a time, starting with the well-protected belly button. You give us a sample, we will grow and identify the bacteria, and you get the results. Meet your personal ecosystem, in color!" The team uses MO BIO's PowerSoil® DNA and UltraClean® Microbial DNA Isolation Kits to tackle these challenging and diverse samples. For more information, visit www.wildlifeofyourbody.org.
Partners: NC Museum of Natural Sciences - MO BIO - GENEWIZ - Howard Hughes Medical Institute
The infamous LA river winds through the center of Los Angeles, heavily polluted with waste from the city. It may not quality as a southern California scenic destination, but as far as bioremediation projects go, this locale is ideal! The river provides a fertile source of microorganisms accustomed to living with and degrading pollutants. Nikki Thadani and a team of fellow California Institute of Technology (Caltech) undergraduates have chosen this urban river as their site of choice for the iGEM synthetic biology competition. They hope to produce a bioremediation system for endocrine disruptors. Endocrine disruptors such as DDT and BPA have a significant detrimental impact on the reproductive systems of organisms living in water systems such as lakes, rivers, and ponds. To determine a degradation pathway for these persistent environmental toxins, they collected soil samples from the LA river and extracted DNA from these samples using the MO BIO PowerMax® Soil DNA Isolation Kit. They are now in the process of creating a fosmid library from this DNA so they can test genes in the library for their ability to degrade endocrine disruptors, and thus isolate a degradation pathway for these pollutants.
Led by Dr. Chinh Doa, undergraduates of Drake University are delving into a project to assess microbial ecosystems within the prairies and waterways of central Iowa through molecular fingerprinting. The major goals of this project are to measure the changes in microbial diversity over time in a given water or soil microenvironment, quantify the fluctuations, and determine how sensitive microbial communities are to ‘normal’ changes in their environment. These students sampled the state parks and two rivers in the Des Moines area, the Des Moines River and the Raccoon River, as well as an area near the city dump. The overarching theme of this project is to determine if microbial diversity can be utilized as a metric for assessing the status or ‘health’ of an ecosystem.
Water and soil samples were collected from select sources located in Central Iowa, taking care to avoid areas that will be influenced by human activity. Students carefully recorded the conditions under which samples were gathered, including time, date, GPS/GIS location, and weather conditions. DNA was isolated from soil and water samples, microbes were cultured from these samples, and select samples were analyzed for chemical content. Students monitored water and soil in this manner over several weeks and in some cases over the course of the entire semester. Microbial fingerprinting involved amplifying an approximately 1 kb fragment of the small rRNA subunit, digesting this fragment with a panel of restriction enzymes, and analysis by tRFLP. The research team trusted MO BIO PowerSoil® DNA Isolation Kits as well as PowerWater® DNA Isolation Kits for optimized results. Genotyping was then performed at the core nucleic acid facility at Iowa State University.
To assess the results of their study, students will determine if bacterial diversity varies as a function of relative distance, with the depth that samples are taken, with weather conditions, season, and with time. They will also determine if t-RFLP can reproduce some of the bacteria identified by classical microbiological methods
A group of 33 people including Emelia DeForce (shown at right), a graduate student from University of Massachusetts Boston, sailed the tall ship SSV Corwith Cramer to collect and study plastics in the North Atlantic subtropical gyre. The research and teaching vessel of Sea Education Association in Woods Hole, MA left out of Bermuda and covered over 3800 nautical miles going east passing over the mid Atlantic Ridge on a 34 day journey. This was a follow-up cruise to sample an area that had not been surveyed for plastics. To collect the tiny pieces of plastic, mostly millimeters in size, they towed a neuston net several times a day overboard then sieved and counted over 48,000 tiny plastic pieces by hand! Emelia and other microbial ecologists on board also preserved pieces of plastic for further investigation back in the labs at Woods Hole Oceanographic Institution and Marine Biological Laboratories. Back on land, the microbes living on the plastic will be studied through DNA analysis, microscopy, and growth experiments. By extracting the DNA present on the plastics found floating at sea, molecular techniques will be used to answer questions about what species of microbes are living on the plastic and also how many of them are living there. Further investigations will reveal whether different types of plastic harbor different microbial communities and if those communities are different from planktonic cells in the open ocean.
A recent paper in Science from the Sea Education Association group was published and includes a data set of over 25 years of collecting and enumerating pieces of plastic from over 6500 net tows. The data shows that there has been no increase in the abundance of the plastic over time although there has indeed been an increase in plastics production. This has posed questions about the role that microbes are playing in the potential decomposition of plastics in the Atlantic Ocean. Emelia and researchers trusted MO BIO's PowerBiofilm™ DNA Isolation Kit and PowerBiofilm™ RNA Isolation Kit with their collected samples. Emelia relayed, "I am very excited about the PowerBiofilm kits... they will be perfect for this cruise as we will actively be looking for plastic degraders on the biofilms of plastics." The results from this work will provide data that will be fundamental to further the investigation of the fate of plastics at sea.
Pavilion Lake, in northern British Columbia, holds a uniquely diverse array of microbialites that may offer information for equally diverse applications, spanning from the ancient past to vitality at the far reaches of our solar system! PhD Student Rick White, along with the Suttle Lab at the University of British Columbia, describes his research endeavors at this exciting site. 'The Pavilion Lake Research Project (PLRP) is an international, multi-disciplinary, science and exploration effort to explain the origin of freshwater microbialites in Pavilion Lake, British Columbia, Canada. Fossil microbialites represent some of the earliest remnants of life on ancient Earth, and were common from ~2.5 billion to 540 million years ago. Today, microbialites are found in environments where conditions are often too harsh for most organisms. However, the microbialites in Pavilion Lake have provided a new environment for the scientific community to study that demonstrates that large, and uniquely shaped structures can also occur in non-extreme environments that support fish, plants and other species.
The microbialites of Pavilion Lake are relevant to our understanding of ancient microbialites that were once common and diverse on early Earth. As such, Pavilion Lake has become an exciting field site for Earth scientists and astrobiologists who are interested in the application of the PLRP research to the search for life in our solar system and beyond. The project began in 2004, and has grown in exciting new directions ever since. Microbialites are carbonate structures that form in water with the help of microorganisms. Commonly we see carbonates as limestone, but in certain special cases – often when life is involved – the carbonate precipitates to form some very unique structures. These microbialites are interesting because they can help us understand the types of structures that microorganisms form and the biological signatures they leave behind. We can then use this information to study similar structures from over 2.5 billion years ago.
Microbialites are present in a number of lakes around the world, but what makes Pavilion Lake so special is the remarkable diversity! Not only is the lake full of microbialites, but the structures range in size, morphology, and depth. As the lake was explored, the diversity of microbialites fell into four general morphological categories: cauliflower, chimney, artichoke, and coral. From the four locations around the lake that were initially studied intensely, these morphology types seem to correlate with depth. The bulbous structures occur in the shallows, with chimneys, artichokes, and coral-like structures at increasing depths. Next year the team will be diving into a lake called Kelly Lake, and potentially Pavilion Lake at the same time. This creates a challenge for the communications team. Both sites must have broadband access to the Space Network Research Federation (SNRF) and the Internet, and be able to communicate from site to site at all times. We are using the MO BIO PowerSoil® DNA Isolation Kit and RNA Powersoil® Total RNA Isolation Kit in the field for isolation of RNA and DNA from modern microbialites as part of a CSA/NASA MARS-analog project named MARSLIFE. The kits allow us to extract nucleic acids directly from the microbialites and their associated biofilms which is crucial to our studies of virus and microbe diversity.' www.pavilionlake.com
Dr.Jenny Baeseman has trusted MO BIO kits for many years to isolate DNA from elements in extreme environments. She was one of MO BIO’s PowerSoil® DNA Isolation Kit's greatest fans when she was a professor at Princeton University, studying the bacteria that inhabit the streams of McMurdo Valley, Antarctica. She is now the Director of a new organization called APECS - the Association of Polar Early Career Scientists. APECS is an international and interdisciplinary organization for undergraduate and graduate students, postdoctoral researchers, early faculty members, educators and others with interests in Polar Regions and the wider cryosphere.
Her aims, as the APECS director, are to stimulate interdisciplinary and international research collaborations, and develop effective future leaders in polar research, education and outreach. It is quite a big task, as she mentions, that there are many skills early career polar researchers require for the basis of a strong career. In order to help address this, the Association of Polar Early Career Scientists (APECS), together with the ArcticNet Student Association, and the Northern Research Forum held the IPY International Early Career Researcher Symposium.
Understanding the importance of this kind of meeting and how it can help the research community in the future, MO BIO Laboratories proudly became one of the sponsors of the symposium that was held in Victoria, B.C, Canada from December 4-8. The Symposium brought together early career polar researchers from 14 different countries and a wide range of disciplines for a series of training sessions to develop professional skills, work with senior mentors, and develop international and interdisciplinary collaborations. You can find all the recording of the plenary talks and breakout sessions on the APECS website. The outcome of this meeting was very positive. As a result, participants of the workshop said that less than 20% of what they learned from the three days together had been taught in their graduate programs and all stated the need for more events like this on an international and interdisciplinary level.
MO BIO believes in giving back to the scientific community, with great hope for its impact on the future generation of researchers (not to mention their impact on the world we live in, itself), and is proud to support functions like this symposium.
For more information: www.apecs.is
Every year, Dr. Lyle Whyte’s research team travel to the McGill Arctic Research Station (MARS) located in the Canadian High Arctic on Axel Heiberg Island (nearly 80° north). Celebrating its 50th year (1960-2010), the MARS provides access to several unique sites for studying microbial biodiversity and ecology in subzero environments but are particular interest as analogs for Martian habitats. The habitats include unique perennial cold saline springs, permafrost and ground ice, and ice shelf microbial matt communities. The team's research aims to better understand the diversity of the microbial communities, their ability to grow at subzero temperatures, their activity in situ, and the impact of such activity on biogeochemical cycling.
"Much of the work is conducted in the laboratory, but relies heavily on good sample collection, preservation and handling says Dr. Nadia Mykytczuk (post-doctoral fellow pictured with Dr. Lyle Whyte above). Not only is the sample collection challenging in weather conditions that can range from - 40°C to beautifully sunny days with temperatures reaching 15°C, but the samples themselves can present quite a challenge for downstream processing. Low microbial biomass (103 to 105 cells/g sediment) and high salinity (7.5 to 25 % NaCl) make DNA extraction difficult. We’ve come to rely on the MO BIO UltraClean® Soil DNA and PowerMax® Soil DNA Isolation kits to extract DNA from these various sample substrates and to date have had high yields and excellent DNA quality. This year’s expedition team was also keen on trying the new Lifeguard™ Soil Preservation Solution to help in our recovery of RNA using the RNA PowerSoil® Total RNA Isolation Kit for transcriptome analyses from the cold spring biofilms and sediment microbial communities. Where every sample is precious, the reliability and excellent recovery potential of MO BIO kits has allowed us to hunt for what life might look like on Mars by studying the microbes at MARS."
Photo credits: Dr. Lori Ziolkowski and Dr. Nadia Mykytczuk
Many of us are familiar with the debilitating, even immobilizing, effects of foot pain. Yet, we cannot begin to relate to the detrimental and possibly fatal "foot" ailment common to horses. For centuries, the painful vascular disease equine laminitis has been recorded as commonly occurring, and remains without established proper treatment or method of prevention. This condition results from the inflammation of layers of laminae within the hoof, which can cause detachment of the pedal bone from the hoof wall. In extreme cases, the bone may even puncture through the hoof, often requiring euthanasia. Virginia Tech Department of Animal and Poultry Science PhD Candidate Jessica Suagee (pictured in right column and above on right), with the assistance of Middleburg Agricultural Research and Extension Center (MARE Center) intern Candace Flinn (above center) and Lab Tech Tracy Smith (above left), has been researching the effects of diet on susceptibility to and development of laminitis in horses. Jessica informed us that "high starch and sugar diets can lead to the development of insulin resistance- a condition that predisposes the horse to laminitis." Through glycemic response testing in blood sampling, she is looking at peak insulin response as it corresponds with adaptation to feed.
"Where MO BIO comes in is that I'm also looking at markers of systemic inflammation, because we think that the development of low grade chronic inflammation plays a role in the development of insulin resistance." Jessica has chosen the BiOstic™ Stabilized Blood RNA Isolation Kit to measure cytokines as inflammatory markers in whole blood RNA. They are currently about 30 days into the 90 day feed treatment, with exciting insight yet to come.
To many, soil samples dating back 4,000 years sound incredibly ancient. However, Dr. Janghid, an experienced specialist in soil DNA, barely blinked an eye at it, stating, “While this 4,000 year old soil is not too old, our other site in Altamaha, GA has soils as old as 500,000 years!”
When it comes to isolating DNA from his precious and rare soil samples, Dr Janghid trusts the PowerMax® Soil DNA Isolation Kit. The low biomass and humic acids contained in these samples are an issue for DNA extraction and amplification. However, with the combination of a large amount of starting material (up to 10 grams of soil) and MO BIO's patented Inhibitor Removal Technology® (included in this kit), Dr. Janghid has achieved 100% success in DNA isolation from his challenging samples up to date.
Classifying deep sub-seafloor microorganisms:
Under the auspices of the NSF, Sean Jungbluth, a graduate student at the University of Hawaii, Dr Mike Rappéan, and an interdisciplinary team of researchers across the nation, are attempting to characterize the microbial community inhabiting the sediment-covered seafloor basement. On the Juan de Fuca plate off the coast of the Pacific Northwest, holes are drilled into the bottom of the ocean 2,500+ meters deep. The HOV Alvin has been outfitted with technology that allows for uncontaminated sampling of fluids from deep below the seafloor, and using custom-built fluid sampling devices, collects and transports the samples to the surface for analysis. The microbial community in this environment will be better identified using 16S rRNA sequencing.
Bad bugs, good bugs! Soil-borne plant pathogens are a constant threat to crop health. Beneficial microbes can keep these pathogens in check in natural soils, as well as in soil-less potting mixes used for greenhouse and nursery production. Specific beneficial microbes have been isolated and are used as inoculants to suppress pathogens. Graduate student Anuthep Pasura, working under the direction of Dr. George Elliott in the Department of Plant Science at the University of Connecticut in Storrs, CT, has developed real-time PCR assays for several beneficial microbes and a soil-borne pathogen. He is using the PCR assays to follow population dynamics of microbial inoculants and the pathogen in different soil-less potting mixes. A key to success in this project is the PowerSoil® DNA Isolation Kit. According to Anuthep, using this kit has made it possible to extract good quality inhibitor-free microbial DNA from potting mixes that contain 75 to 85% organic matter.