SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Anaerobic ammonium-oxidizing bacteria in marine environments: widespread occurrence but low diversity

The respiratory reduction of nitrate (denitrification) is acknowledged as the most important process that converts biologically available nitrogen to gaseous dinitrogen (N2) in marine ecosystems. Observations during the last decade, however, indicate that anaerobic ammonium oxidation by nitrite (anammox) may be an important pathway for N2 formation and N removal in coastal marine sediments and in anoxic water columns of the oceans (e.g. Hulth et al., 2005). For about a decade we have explored this mechanism during N mineralization by a wide range of biogeochemical and molecular tools including e.g. benthic flux measurements and high resolution imaging of solute distributions, 15N amendments (single and coupled additions of 15NH4+, 14NO3- and 15NO3-), polymerase chain reaction (PCR), and qualitative and quantitative fluorescence in situ hybridization (FISH) (e.g. Brandsma et al., 2011; Schmid et al., 2007; Engstrom et al., 2005; Jetten et al., 2003). The present study focuses on benthic N-cycling in the deepest trough of a Swedish fjord where the anammox reaction contributes up to 79% of total N2 production. The relative importance of anammox for N2 release was directly correlated with a variety of biogeochemical parameters. The observed correlations indicated a competition between reductants for pore water nitrite during early diagenesis, and that additional factors (e.g. availability of Mn-oxides), superimposed on overall patterns of diagenetic activity, are important for determining absolute and relative rates of anammox in coastal marine sediments. Insight in the metagenome of the microbial community in this complex benthic environment would provide complementary and critical information to further understand N cycling in marine environments.

Biome: root:Environmental:Aquatic:Marine:Sediment
Kilauea geothermal soils and biofilms

Examination of geothermal sites on Kilauea. One site involves a steaming tumulus that supports a stratified biofilm at about 50 C. The site other involves a forest that was destroyed by sub-surface heating. What exists at present are heated soils and biofilms that develop on steaming tree trunks. The latter include anoxygenic chloroflexi plus a variety of CO oxidizers.

Biome: root:Mixed
magnificent mongolian microbes

How the microbial ecology of the Mongolian Steppe shifts with climate change is a central question under investigation in the five-year PIRE Mongolia Project (Partnerships in International Research and Education, mongolia.bio.upenn.edu). Through this project, plant ecologists, biogeochemists, soil scientists, and climate modelers, are empirically documenting the effects of climate and land-use change on this arid ecosystem. Though many global change studies strive to link ecosystem shifts to microbial mechanisms, few have integrated edaphic, floristic and climatic data with microbial community data produced by Next-Generation Sequencing techniques, as is being done in the PIRE Mongolia Project. Moreover, the experimental design is comparable to numerous other climate change studies, allowing for the production of globally relevant data. Presently, 16S pyrosequencing data is being analyzed from the soil microbial community of this well replicated, multi-factorial experiment, which includes warming, watering, grazing and topography treatments. The average annual temperature at the Lake Hvsgl Long-Term Ecological Research (LTER) site has increased by 1.7C since 1963, and some of the greatest projected increases in temperature are associated with northern Mongolia. Hence, this site is therefore ideally suited for studying ecological shifts driven by climate change. One of the initial hypotheses in this moisture-limited system is that microbial diversity will decrease with warming and increase with watering. In order to unravel the microbial community composition of the system, 16S data will be integrated with spatial and temporal data that includes information on carbon and nitrogen fluxes, changes in plant phenology and shifts in climate.

Biome: root:Environmental:Terrestrial:Soil
Examination of Microbial Communities through a Freshwater/saltwater Transition Zone in Cenotes, Yucatan, Mexico

We have groundwater samples from karst sinkholes (cenotes) from Yucatan Peninsula, Mexico. Since the groundwater is permanently stratified, we have samples from fresh water, saline water, and the fresh-saline water interfaces from three different cenotes plus a control site that is an abandoned drinking water well at a hotel territory. Our three cenotes differ by depth (20-150 m), the amount carbon input from organic matter, light input, and proximity to the coast (increased influence from marine as well as anthropogenic sources). We have samples from the cenotes Xcolac, Calica and the hotel well from both dry and rainy seasons. In addition, we have dry season sediment samples from cenotes Xcolac and Calica.

Biome: root:Environmental:Aquatic
Gibbons tongue river 16S

The samples are river sediment particles (1.75-2.36 mm in diameter) taken from the top 20 cm of the river bed. For each sampling, we measured the coordinates, water temp, pH, dissolved oxygen percent, conductivity, whether the water was upwelling or downwelling.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Prokaryote populations of extant microbialites along a depth gradient in Pavilion Lake, British Columbia, Canada

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 both Pavilion and Kelly lakes have provided a new environment for the scientific community to study. These lakes demonstrate that large and uniquely shaped structures can also occur in non-extreme environments that also support fish, plants and other species. The microbialites of these modern lakes are relevant to our understanding of ancient microbiaites 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 PLRP was founded in 2004, and has grown in exciting new directions ever since. During the 2004 field season, PLRP scientists discovered microbialites in Kelly Lake, which is approximately 20 km NW from Pavilion Lake. The PLRP team will be taking their DeepWorker Science and Exploration (DSE) program to Kelly Lake in 2011. These research activities complement those that have taken place at Pavilion Lake since 2008, and will help to broaden our understanding of modern microbialite-rich environments. Further to these science activities, the PLRP supports a thriving human exploration research component. The focus of this program element is the development of operational technologies and strategies that facilitate scientific productivity and efficiency for future human scientific exploration of our Solar System.

Biome: root:Environmental:Aquatic:Freshwater:Lake
NEON: Directions and resources for long-term monitoring in soil microbial ecology

The EMP_Pilot represents a subset of soil samples from the National Ecological Observatory Network (NEON) microbe prototype project. The EMP_Pilot was designed as a cross-facility comparison to quantify variation in sample processing and outputs from two sequencing facilities (Argonne National Labs, Lawrence Berkeley Labs) for quality assurance. The twelve soil samples that comprise the EMP-Pilot were collected in 2009 from four NEON core domain sites in Alaska, Florida,Utah, and Hawaii and represent gradients in ecosystem and soil properties. Information regarding the NEON Domain sites can be found at www.neoninc.org/science/domains. In 2013, soil biochemical, phospholipid fatty acid (PLFA), and targeted gene sequence data associated with the EMP-Pilot samples will be available through NEON's data sharing system.

Biome: root:Environmental:Terrestrial:Soil
Jurelivicius Antarctic cleanup

Antarctic Clean Up Project. Microcosms constructed at Brazilian Antarctic Station. Comandante Ferraz using diesel-oil contaminated soil. The contamination was caused by a blast and fire at the station in Ferbruary of 2012

Biome: root:Environmental:Terrestrial:Soil:Sand:Oil-contaminated
Replicating the microbial community and water quality performance of full-scale slow sand filters in laboratory-scale filters.

Temporal and spatial variation of samples from a slow sand filter water purification system. This is illumina repeat of 454 data

Biome: root:Mixed
Diversity of carbonate deposits and basement rocks in continental and marine serpentinite seeps.

Biogeography of serpentinite-hosted microbial communities Microbial habitats hosted in ultramafic rocks constitute substantial, globally-distributed portions of the subsurface biosphere, occurring both on the continents and beneath the seafloor. The aqueous alteration of ultramafics, in a process known as serpentinization, creates energy rich, high pH conditions, with low concentrations of inorganic carbon which place fundamental constraints upon microbial metabolism and physiology. Despite their importance, very few studies have attempted to directly access and quantify microbial activities and distributions in the serpentinite-hosted ecosystems. We have initiated microbiological studies of alkaline springs and their associated carbonate deposits at three separate continental sites of serpentinization in Newfoundland, Italy, and California, and we are comparing these results to previous analyses of the Lost City hydrothermal field, near the Mid-Atlantic Ridge. We anticipate that the data from these samples will yield insight into the biogeography of serpentinite-hosted microbial communities and provide targets for further investigation of important biogeochemical processes.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
Bioturbating shrimp alter the structure and diversity of bacterial communities in coastal marine sediments

Investigation into the effects of ocean acidification on microbial community structure and diversity in bioturbated coastal marine sediments. Samples taken from surface sediments and sediment from the burrow walls of Upogebia deltaura, a bioturbating shrimp species. Sediments were subjected to 5 different pH levels over a 14-week exposure period. Bacterial and archaeal 16S genes were sequenced.

Biome: root:Environmental:Aquatic:Marine:Sediment
The role of macrobiota in structuring microbial communities along rocky shores

I hypothesize that microbial populations of the rocky intertidal of the northeast Pacific should be related to the nitrogen sources available to them, particularly the presence of animals and gradients in animals abundance. I thus have 48 collections for 16s analyses through the EMP at Argonne Labs (Gilbert Lab) designed to test whether microbial diversity increases in proximity to ammonium-excreting animals and whether the presence and absence of the abundant California mussel is a determinant of microbial diversity. All samples come from the coast of Washington state in 2009 and 2010, including 2 locales: Tatoosh Island and Second Beach. Microbial populations of the rocky intertidal areas of the northeast Pacific are little described compared to their open ocean counterparts. Thus, the work will be a novel investigation into diversity of this area as well as determinants of diversity.

Biome: root:Mixed
Canadian MetaMicroBiome Initiative samples from

Microbial communities harbor immense genetic diversity with enormous promise for applications in bioproduct synthesis and green chemistry. Metagenomic libraries provide a window into this largely untapped reservoir of nucleic acid diversity and individual libraries have been generated from a variety of terrestrial and aquatic environments. A limitation is that metagenomic libraries are typically project-specific and maintained in isolation. In an effort to enable the sharing of genetic material from environmental samples for the benefit of the scientific community, we are establishing the Canadian MetaMicroBiome Library. This repository will house composite soil samples that are characterized by extensive 16S rRNA gene and whole-genome sequencing, generating taxonomic profiles and metabolic pathway reconstructions for each sample. The sequence data will be submitted to existing public databases and linked with detailed physical, chemical and geographic characterization of the samples according to established metagenomic standards. Sample DNA will be used to construct high quality libraries in cosmid vectors, allowing for phenotypic screening in a broad range of microbial surrogate hosts. Phenotypic screening of metagenomic libraries provides access to truly novel functions that would otherwise be missed by sequence-based surveys of bulk community DNA or metagenomic libraries. MetaMicroBiome is being initiated with soil samples collected from across Canada, and initial libraries are being screened for novel glycoside hydrolase activities in multiple surrogate hosts. Once MetaMicroBiome is established, contributions of samples from other environments will be accepted for inclusion. The resulting resource will provide the international scientific community with access to a common collection of thoroughly characterized community-contributed genetic material in clone library format for custom phenotypic screens.

Biome: root:Environmental:Terrestrial:Soil
Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin

The Ocean Drilling Program (ODP) was funded by the U.S. National Science Foundation and 22 international partners (JOIDES) to conduct basic research into the history of the ocean basins and the overall nature of the crust beneath the ocean floor using the scientific drill ship JOIDES Resolution. Joint Oceanographic Institutions, Inc. (JOI), a group of 18 U.S. institutions, was the Program Manager. Texas A&amp;M University, College of Geosciences was the Science Operator. Columbia University, Lamont-Doherty Earth Observatory provided Logging Services and administered the Site Survey Data Bank. Any opinions, findings, and conclusions or recommendations expressed in these documents are those of the author(s) and do not necessarily reflect the views of the National Science Foundation, the participating agencies, Joint Oceanographic Institutions, Inc., Texas A&amp;M University, or Texas A&amp;M Research Foundation.Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100 to 2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
Dominguez sleep deprived flies

The sleep deprivation experiment was done in wild flies or in pumilio knockdown expression (using RNA interference). Pumilio seems critical for the homeostatic response to sleep deprivation.When wild flies are sleep deprived, they respond by sleeping more after the deprivation stimulus is removed. Pumilio RNAi (expression knockdown) sleep less after sleep deprivation. Analyzing these samples, we can see if sleep deprivation leads to the disregulation of intestinal microbes, and if pumilio plays a role on this regulation.

Biome: root:Host-associated:Insecta
The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys (NZTABS)

Terrestrial Antarctic Biocomplexity Survey. The New Zealand Terrestrial Antarctic Biocomplexity survey (NZTABS) is the largest and most comprehensive landscape scale biological study ever undertaken. The Antarctic Dry Valley system offers unprecedented access to a trophically simple biological system that appears to be solely structured by abiotic environmental drivers. The primary biology in this system is microbial. Linking a range of high-resolution remote sensing data with over 600 person days in the field, the 220 km2 3 valley NZTABS survey now includes over 650 spatially strategic soil samples targeting the diversity habitats in the system. Each sample and site has been analyzed for a range of geochemistry as well as a comprehensive survey of biology (all visible vegetation, insects, all infauna and flora (nematodes, rotifers, tartigrades), and microbiology). The initial microbial surveys (Bacteria, Cyanobacteria, fungi) were carried only using DNA fingerprinting analysis. All of the information has been placed into and interactive GIS framework allowing direct relationships between all parameters to be queried. The central objective of the survey is to determine the primary environmental drivers for structuring the biology to enable us to develop a model that can predict the distribution of biology across the entire Dry Valley system (6500 km2) using only remote sensing. Ultimately we hope that the model will be able to identify areas of sensitivity or unusual complexity that should be protected.

Biome: root:Mixed
McGuire Nicaragua coffee soil

Coffee plantations in northern Latin America coincide with areas of extremely rich biodiversity. Recent advances by fair trade organizations have stimulated sustainable agriculture in the form of shade coffee plantations as a way of reconciling economic and conservation targets; however, the shade management techniques vary between sites and result in different canopy assemblies across farms over time. The effect of differing canopy regimes on microbial communities are poorly understood but guide nutrient cycling, crucial for both agriculture and the maintenance of ecosystem diversity. The goal of this project is to explore the relationship between managed canopies, land use history, and soil microbial communities in Nicaraguan shade-coffee plantations, and use this information to develop a set of guidelines for soil management to improve soil quality.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Environmental metagenomic interrogation of Thar desert microbial communities

Interrogation soil microbial community from arid and semiarid regions of the Thar Desert is essential. Until recently the studies on Thar desert soil microbes mostly focused on cultivation alone. Here we use culture independent approach. T-RFLP result shows that there is a significant difference among arid and semiarid soil bacterial communities, they clustered according to the sample type arid-soil, semi-arid soil, sand dune. Our clone library showed difference in the bacterial communities among arid-soil, semi-arid soil, sand dune respectively.

Biome: root:Environmental:Terrestrial:Soil:Desert
Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm.

Soil pH effect on soil metagenome Craibstone, Scotland soil maintained at different pH levels (4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5) and harvested in 2006 and 2007

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Protist diversity in a permanently ice-covered Antarctic Lake during the polar night transition

The McMurdo Dry Valleys of Antarctica harbor numerous permanently ice-covered lakes, which provide a year-round oasis for microbial life. Microbial eukaryotes in these lakes occupy a variety of trophic levels within the simple aquatic food web ranging from primary producers to tertiary predators. Here, we report the first molecular study to describe the vertical distribution of the eukaryotic community residing in the photic zone of the east lobe (ELB) and west lobe (WLB) of the chemically stratified Lake Bonney. The 18S ribosomal RNA (rRNA) libraries revealed vertically stratified populations dominated by photosynthetic protists, with a cryptophyte dominating shallow populations (ELB-6m; WLB-10m), a haptophyte occupying mid-depths (both lobes 13m) and chlorophytes residing in the deepest layers (ELB-18 and 20m; WLB-15 and 20m) of the photic zone. A previously undetected stramenopile occurred throughout the water column of both lobes. Temporal variation in the eukaryotic populations was examined during the transition from Antarctic summer (24-h sunlight) to polar night (complete dark). Protist diversity was similar between the two lobes of Lake Bonney due to exchange between the photic zones of the two basins via a narrow bedrock sill. However, vertical and temporal variation in protist distribution occurred, indicating the influence of the unique water chemistry on the biology of the two dry valley watersheds.

Biome: root:Environmental:Aquatic:Freshwater:Ice:Glacial lake
Catlin Arctic Survey 2010 L3

The Catlin Arctic Surveys deployed an Explorer Team (years 2009, 2010, 2011) and Ice Base (years 2010, 2011), to examine sea ice thickness (addressing the rate of loss), and the phenomena of ocean acidification and thermohaline destabilisation (two key consequences of sea ice loss). The climate change-driven themes of the Catlin Arctic Surveys introduced each year (sea-ice loss, 2009, ocean acidification, 2010, thermohaline destabilisation, 2011) are inter-related, with potential global effects. These samples are from the 2010 expedition.

Biome: root:Environmental:Aquatic:Marine
Rees Vulcano island MedSea

A survey was performed in nearshore waters of the Island of Vulcano, Italy during May 2011 to investigate the impact of elevated CO2 from volcanic vents on the phytoplankton in local seawater populations. Samples were collected onto sterivex filters on two days at a range of 4 pH levels on each day.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents
New Zealand Free Air Carbon dioxide Enrichment soil samples

Rhizosphere soil samples from Rings 1-6 of NZ FACE (New Zealand Free Air Carbon Dioxide Enrichment) experiment. Each ring pasture has an atmosphere that is either enriched with 475 ppm CO2 or ambient atmospheric CO2 throughout the photoperiod and throughout the photoperiod since 1997. Each sample also comes from either an area exposed to warming treatment since 2009 or an area with no warming treatment.

Biome: root:Environmental:Terrestrial:Soil
Chu Changbai mountain soil

We have collected 24 soil samples in different elevations in Changbai Mountain, northeastern China, and investigated the distributions of microbial communities and functions along elevation. Climate warming often results in increased forest fire. We have collected 60 soil samples in Greater Khingan Mountains, northern China, and investigated microbial response to forest fire and microbial succession after post-fire.

Biome: root:Environmental:Terrestrial:Soil