Forest fragmentation has been a prominent threat to the conservation of biodiversity, especially in tropical habitats. Costa Rica, nestled in the Central American isthmus, houses an extensive amount of biodiversity, and so is an area where crucial examination and careful monitoring of land fragmentation and its effects are pertinent. The Organization for Tropical Studies (OTS), in Costa Rica, takes a large part in this very important role. OTS is a nonprofit organization that brings together 63 research institutions in the United States, Latin America and Australia to "provide leadership in education, research and the responsible use of natural resources in the tropics."
Natalie Sánchez, master’s student at the Universidad Nacional in San Jose, Costa Rica, and her colleagues at the OTS are studying the diversity and structure of the soil microbial communities in one of the most deforested counties in Costa Rica. The land has undergone heavy fragmentation, resulting in a mosaic of agricultural lands for multiple uses. This region used to be an important ground for the production of coffee but, due to the decrease of the coffee price worldwide, most of the land has been converted to pasture in the last decade.
Natalie and her colleagues used the PowerSoil® DNA Isolation Kit to extract genomic DNA from the microbial mat across different land use types, including recently abandoned castle pastures, restoration plots and advanced secondary forests. “We had great success using this kit with our environmental samples and we have been able to successfully amplify all extracted DNA," said Natalie. The original goal of this project was to identify the microbial communities present in the soil to study the effects of forest fragmentation and isolation on plant and animal communities, but they are also currently able to conduct research, additionally, on biological corridors and restoration ecology.
Deep, deep below the surface, at 2000m depth in the Gulf of California, lies an intriguing and unique hydrothermal vent system of microbial wonder. This system is unlike any other in that this hydrothermal fluid does not erupt through black smokers, but instead, slowly percolates upward through a layer of organic-rich thick sediment. A collaborative team of researchers from around the globe, including a group from UNC Chapel Hill led by chief scientist Andreas Teske, make up a multidisciplinary team, aboard the Guaymas Expedition- 2009, analyzing the geochemistry and microbiology of Guaymas hydrothermal seeps. These studies notably include analysis of the mats of Beggiatoa organisms that often form on top of active hot areas of fluid escape.
"This is a follow up expedition from last year - the sediments we collected last year yielded some interesting things. Right now one of the biggest is the discovery of the microbial process of anaerobic methane oxidation happening at 3 very different temperature regimes. Anaerobic methane oxidation hasn't been well studied at high temperatures, and using the MO BIO PowerSoil® DNA and RNA PowerSoil® Total RNA isolation kits, we found that active suspected methane oxidizers present at both high and lower temperatures in Guaymas are from the same phylogenetic groups," stated Jennifer Biddle, Ph.D., UNC Chapel Hill (shown at right).
Jennifer Kerekes is currently a Ph.D. student in the Department of Plant and Microbial Biology at the University of California, Berkeley. Her recent work at the Barro Colorado Nature Monument in Panama focused on the effect of repeated and long-term exposure of macronutrients and micronutrients on saprotrophic fungal diversity. She used the PowerSoil® DNA Isolation Kit for total genomic DNA extraction from soil and leaf litter environmental samples. “The PowerSoil DNA Isolation Kit has been very useful for isolating total genomic DNA and has had great results in amplifying microbial DNA,” said Jennifer. She also had positive results with the PowerSoil DNA Isolation Kit in El Salvador at the Walter Thilo Deininger Park where, where in collaboration with the Instituto Salvadoreño de Turismo and the local community, she is studying the diversity and community structure of soil fungi in a dry tropical forest.
Water up to 400°C shoots skyward carrying hoards of toxic chemicals from cracks in the earth's crust at the depths of our seas! Aspects of the newly explored deep-sea hydrothermal vents are nothing short of absolutely captivating. Previous expeditions to these vents have identified strange and exotic sea floor dwellers, but the National Science Foundation's "Extreme 2008: A Deep-Sea Adventure" was the first to investigate the viral and protozoan extremophiles that play a vital role in vent ecosystem balance. Led by University of Delaware marine scientist, Craig Cary, this international research team set sail aboard the R/V Atlantis to the Pacific and Sea of Cortés, to explore this foreign and extreme environment.
Dr. Eric Wommack, associate professor at the University of Delaware, headed the capture of marine viruses for analysis in the shipboard lab. Dr. David Caron, professor at the Wrigley Institute for Environmental Studies at the University of Southern California studied the deep-sea protozoa. These two previously overlooked groups are closely related to, and drastically affect the bacterial populations that form the basis of the vent food chain. The team, including scientists and graduate students from universities in the states, Mexico, and New Zealand, carried out ground breaking research that may offer great insight into this complex and unfamiliar ecosystem.
Milagro Fernández (see right picture) is currently a Ph.D. student in Biological Sciences at Simon Bolivar University, Venezuela. Her Ph.D. thesis subject is on detection and isolation of Vibrios in a marine coastal environment of Venezuela. She uses our UltraClean® Microbial DNA Isolation Kit for DNA extraction of Vibrio cultures from seawater, plankton, and oyster tissue.
The aim of her research is to detect and isolate pathogenic Vibrio spp. from seawater, plankton, and mollusks in a touristic area of Venezuela exposed to fecal contamination. These samples are analyzed by culture techniques, PCR and 16S rRNA gene sequencing. Milagro Fernandez quoted that "For total genomic DNA extraction from bacterial cultures, the UltraClean® Microbial DNA Isolation Kit has been very useful"
She is now using the UltraClean® Water DNA Isolation Kit for the direct detection of these bacteria in the environmental samples, whose presence is a public health concern.
Dr. Maria A. García-Amado, Researcher from Laboratorio de Fisiología Gastrointestinal (Centro de Biofísica y Bioquímica, Instituto Venezolano de Investigaciones Científicas (IVIC), Mrs Sanz posdoctoral student from Centro de Ecologia (IVIC), both from Venezuela and Mrs Rodríguez-Ferraro, doctoral student from the Department of Biology, University of Missouri-St. Louis (USA) work in Venezuela in the detection of the Helicobacter genus in feces of wild birds.
They isolate DNA of bacteria from the fecal samples using UltraClean® Microbial DNA Isolation Kit. Dr. Garcia-Amado quoted: “This kit is easy to use and we have excellent results!”The wild birds are caught with mist nets, Dr. Garcia-Amado and her colleagues took morphometric measurement and collected the feces, and then the birds are liberated.” (No harm is done to the birds during the process)
The aim of their study is to evaluate the prevalence of Helicobacter species in wild birds from Venezuela and to determine if these Helicobacter species may pose a risk to humans. (Mrs Sanz and Mrs Rodriguez Ferraro are both shown in the pictures)
Helicobacter spp. are gram negative, curved, S-shaped or spiral shaped bacteria. The specie more studied is Helicobacter pylori, it is a gastrointestinal pathogen that causes chronic superficial gastritis and gastric ulcers in humans. Only 5 Helicobacter species (H. pullorum, H. pametesis, H. canadensis, H. anseris and H. brantae) use birds as natural reservoirs and two of them (H. pullorum and H. canadensis) has been associated with gastroenteritis in humans, suggesting that birds are a vector for transmission of Helicobacter.
Nevertheless, Dr. Garcia- Amado mentioned that only a few studies have reported Helicobacter infection in wild birds.