SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample - 3 prime

The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.

Biome: root:Mixed
EMG produced TPA metagenomics assembly of the EMOSE (2017) Inter-Comparison of Marine Plankton Metagenome Analysis Methods (BZZ_CAA_CAN) data set.

The BZZ_CAA_CAN Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB87662.  This project includes samples from the following biomes: Environmental, Aquatic, Marine.

Biome: root:Environmental:Aquatic:Marine
Song whitehead bats

Seba's short-tailed bat, Carollia perspicillata, is a frugivorous bat that feeds mainly on the fruits of plants of the genus Piper, serving as important dispersers of their seeds. However, Piper species are known to contain secondary metabolites that are often toxic or distasteful to some consumers and also function to protect the plant from attack by microbes and insects. Piperine is one such metabolite (an alkaloid) found in Piper species that has been shown to have both antibacterial and antifungal activity. One study showed that supplementation of fruit with piperine resulted in decreased consumption by C. perspicillata. These studies suggest that a tradeoff may exist between the potential benefits and disadvantages to the host of consuming such metabolites. We propose to determine whether piperine consumption affects the composition of the microbial communities that inhabit the gut of this bat species.

Biome: root:Host-associated:Mammals
Gut microbiome of hibernating bears

I hypothesize that the colon microbiome of the hibernating black bears is a unique assemblage of bacteria that performs functions vital for hibernation, giving bears the unique ability to survive for months without eating or urinating. The first step in studying this phenomenon is to identify the bacteria that comprise this microbiome using 16S amplicon data. My colleagues and I have collected samples from the colons of 17 hibernating American black bears (Ursus americanus) in Minnesota, USA. We used three methods of collection that sampled from 10.5cm to 40cm proximal to the anus, for a total of 49 samples. DNA has been extracted, using EMP standard protocols, at the Biofrontiers Institute, Knight lab, in Boulder, Colorado.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
The gut microbiota distinguishes GI-healthy and -unhealthy captive colobineprimates - Hale folivorous primates (MiSeq)

I currently have a total of 160 DNA samples (from feces) that represent the following species: wild Rhinopithecus brelichi (Guizhou snub nosed monkey, 3 wild Macaca thibetana (Tibetan macaque),10 captive Rhinopithecus brelichi (Guizhou snub nosed monkey),3 captive Rhinopithecus roxellana (Sichuan snub nosed monkey, 2 captive Colobus guereza (Eastern black and white colubus monkey),16 captive Nasalis larvatus (Proboscis monkey);-8 captive Pygathrix nemaeus nemaeus (Red shanked douc langur), 11 captive Trachyipthecus auratus (Javan langur), 3 captive Trachypithecus vetulus vatulus/nestor (Purple faced langurs), 1 pooled sample from Ateles geoffroyi (Spider monkeys). These samples were collected by Chia Tan (San Diego Zoo) and myself from the Fanjingshan National Nature Reserve (Guizhou, China), the Panxi Breeding Center (Guizhou, China), the Singapore Zoo (Singapore), and the Columbian Park Zoo (Lafayette, Indiana, USA). All samples amplified on a gel after performing PCR with 16srRNA primers. MiSeq data trimmed to 100bp in the study)

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Seyler North Atlantic water column

CLIVAR (Climate Variability and Predictability) is a core component of the World Climate Research Program (WCRP). CLIVAR's objective, as stated on their website (www.clivar.org) is to describe and understand the ocean-atmosphere processes responsible for climate variability and predictability on seasonal, interannual, decadal, and centennial time-scales, through the collection and analysis of observations and the development and application of models of the coupled climate system, in cooperation with other relevant climate-research and observing activities. In April-May 2012, we participated in a research cruise as part of the US CLIVAR/CO2 Repeat Hydrography program, onboard the UNOLS ships R/V Atlantis. The cruise was a repeat of World Ocean Circulation Experiment (WOCE) line A20 (longitude 52W), previously conducted in 2003. 10-L water samples were collected at a total of 83 stations at varying depth intervals, using a 36-Niskin bottle rosette. We took 0.5-1.0 L samples from the rosette roughly once per day at 16 stations throughout the cruise. At each station, water was taken from at least three distinct zones in the water column, based on data from the CTD: the middle of the mixed layer, the local oxygen minimum, and the middle of the bathypelagic zone. At 7 stations, samples were also drawn from the bottom-most bottle. Biomass was immediately collected on 0.2 um filters under vacuum filtration. SIP microcosms were set up at 13 stations using 13C sodium acetate, 13C urea, 13C sodium bicarbonate, 13C algal lipid/pigment extract, and 15N algal protein extract. The samples submitted to the Earth Microbiome Project represent T=0 time points for the SIP microcosms (before amendment) and extra samples taken for RNA/DNA analysis. Results from SIP are currently being processed.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Metagenomic analysis of some key samples from anaerobic digestion of high salt and sulphate waste.

The waste stream generated by our industrial partner, MARA/AO3, during the production of omega3 fatty acids from marine algae is very large and still rich in nutrients and solid cellular material.The generated wastewater contains amino acids, metals, sulphate and high salt concentration. Discharge or treatment of this waste has an associated cost, both fiscal and environmental. Anaerobic digestion of this waste has the potential to reduce costs, recover value and resources and reduce environmental impact. This project explored whether a salt-tolerant microbial community can carry out effective anaerobic digestion of this high-salt waste stream. We additionally investigated whether the used of molybdate as an inhibitor of sulphate reduction can increase the methane production potential of the sulphate-rich AO3 waste.

Biome: root:Engineered:Bioreactor
Acidobacterial EPS degraders uraveled by stable isotope probing - Shotgun Metagenomics sequencing

Stable isotope probing was used to evaluate which microorganisms, bacteria and fungi, were involved in the assimilation of an exopolysaccharide (EPS) produced by the acidobacterial strain Granulicella WH15. The strain was grown in culture medium with labeled glucose, in order to produce labeled EPS. The EPS was extracted, the polysaccharide purified and incubated with soil. This is the shotgun metagenomics data derived from this study

Biome: root:Engineered:Solid waste:Composting
Caprobiome_2

Samples come from inoculum (anaerobic sludge) and UASB reactor fed with acid whey containing mostly ethanol or lactate.

Biome: root:Engineered:Wastewater
Microbial diversity in arctic freshwaters is structured by inoculation of microbes from soils

A 12-year sample archive of DNA from Alaskan arctic tundra ecosystems are available to the Earth Microbiome Project for comparison of microbial diversity across a range of arctic environments from soils to water to sediments. These samples were preserved and extracted using a method that differs from that of the EMP. Therefore, we must test how the extraction method used to extract our archived samples compares with those methods used by the EMP. The samples for this test were collected during the summer of 2011 at the Toolik Field Station. Each site was sampled in triplicate and samples were divided and preserved for extraction using our standard protocol (three replicates), and for extraction using the EMP protocol (three replicates). Half of the samples are from the epilimnion and hypolimnion of ultra-oligotrophic Toolik Lake collected over the course of the summer, and the rest are from different environments associated with a headwater stream that lies upslope of Toolik Lake. The data from these samples will allow us to test whether our extraction protocol yields results that are similar to the EMP extraction protocol, to investigate how replicates compare, and to determine how the microbial community and its metagenome changes over the course of the summer in Arctic tundra waters. LTRB, Long Term Ecological Research. The samples from this study were provided to the EMP for amplification with the EMP protocols

Biome: root:Mixed
Impact of Plant Development on Structure and Function of Rhizosphere Microbial Community associated with Groundnut (Arachis hypogaea L.)

Impact of Plant Development on Structure and Function of Rhizosphere Microbial Community associated with Groundnut (Arachis hypogaea L.).Present study investigates changes in microbiome of Groundnut rhizosphere throughout the development of plant from pre-sowing to post-harvest.

Biome: root:Environmental:Terrestrial:Soil
IBK Shotgun Metagenomics Analysis Sample A3

IBK Shotgun Metagenomics Analysis Sample A3

Biome: root:Host-associated:Mammals
Knight skin biogeography comparison

Knight_skin_biogeography - Comparison of skin samples from a rat (mammal), cyclostomid (fish), iguana (reptile), bull frog (amphibian) and a bird (pigeon) to determine if the site chosen to sample on different animals are dependent on site selection.

Biome: root:Host-associated:Animal
The oral and skin microbiomes of captive Komodo Dragons are significantly shared with their habitat.

Here we collect saliva, skin, and fecal samples from captive Komodo dragons (V. komodoensis) and other captive varanids (V. olivaceus, V. indicus, V. rudicollis) in the first-ever culture-independent assessment of the varanid microbiome. Environmental samples were also collected to characterize host-environment microbiome sharing. This study adds crucial information to our understanding of captive Komodo dragon microbial ecology.

Biome: root:Mixed
Gut microbiota of phyllostomid bats that span a breadth of diets

The microbial communities that inhabit the gut of animals play essential roles in host biology including nutrient provisioning, regulation of tissue development, and immune system development. Both ecological and evolutionary forces are thought to have shaped these communities. However, previous efforts to quantify the extent to which different factors contribute to the structure of gut bacterial communities have targeted either a range of host diversity too narrow to analyze ecological drivers of community structure, or so wide that diet and phylogeny are tightly correlated, and thus difficult to disentangle. In order to assess the relative contribution of host ecology (including dietary specializations) and evolution (phylogenetic relationships) in shaping gut microbiome diversity we have chosen to study the phyllostomid bats (Chiroptera: Phyllostomidae). Phyllostomid bats span almost the entire dietary diversity known for terrestrial mammals, with omnivorous, insectivorous, carnivorous, hematophagous, nectarivorous, and frugivorous species. Crucially, there is a robust phylogenetic framework for this group that indicates dietary specialization has evolved multiple times from insect-feeding ancestors. Nectar feeding and carnivory have each evolved twice, the inclusion of some fruit in the diet has evolved 5 times, and blood-feeding and extreme frugivory have evolved one time each. Repeated instances of the evolution of dietary specializations enable analyses that separate host diet and environment from phylogeny as drivers of bacterial community structure. To date, we have collected 96 fecal samples for 38 species that span the dietary diversity of the clade. All of these samples were collected in the field in Belize and Ecuador, and thus represent the microbiome of these bats in their natural habitat. We would like to generate 16S and shotgun metagenomic sequences for these samples to assess community membership and function. This project represents a significant step forward in the characterization of vertebrate microbiome because it enables hypotheses on the relative importance of different factors in structuring bacterial communities to be explicitly tested. These data will also provide insight into the role the gut microbial community plays in adaptation to novel diets.

Biome: root:Host-associated:Mammals:Digestive system
A combination of biochar-mineral complexes and compost improves soil bacterial processes, soil quality, and plant properties

Biochar is derived from the oxygen-limited pyrolysis of organic matter (e.g. agricultural or municipal waste) and constitutes for complex structure of recalcitrant, porous carbon and well as mobile minerals and nutrients. Several studies have shown that the addition of biochar improves agricultural yields and performance in a way comparable to classical NPK or urea-based fertilisers. Biochar is therefore an emerging and attractive replacement for classical farming practices with the additional benefit of sequestering carbon that would otherwise be burnt or composted. The mechanisms behind the beneficial properties of biochar are not well understood, but initial work has shown that its amendment to soil impacts on microbial community composition. To better understand these processes, this project will obtain a comprehensive picture of the microbial community in bulk soil, roots and biochar particles in agricultural soils that were supplemented with various amounts of biochar as part of a field trial executed by the New South Wales Department of Primary Industries (DPI). A total of 253 samples will be analysed, that constitute a design that will allow us to understand where the most pronounced microbial changes occur (e.g. biochar particle versus soil) and what changes in the microbial communities occur over time.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Agricultural intensification and the functional capacity of soil microbes on smallholder African farms -swkenya

Since 2005, the Africa Green Revolution has aimed to increase crop yields on small-scale farms in sub-Saharan Africa by promoting the increased use of mineral fertilizers. Microbial ecologists have begun to understand the relationship between nutrient enrichment and bacterial community composition but little-to-no work has been done to understand the effects of different agricultural management practices on microbial diversity and function in tropical systems. For this study, we collected soil samples from 21 farms of three management types, high mineral fertilizer use, low mineral fertilizer use, and improved fallow.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Panama Precip Grad Soil

The effect of precipitation in structuring soil microbial communities has not been extensively explored in lowland tropical rain forests. Across the Isthmus of Panama, there is a precipitation gradient ranging from 1600 mm MAP to less than 3000 mm MAP with several other biotic and abiotic factors found to co-vary with MAP. The Smithsonian Tropical Research Institute has established more than 40 plots (1 ha each) in which all trees 10cm dbh have been identified to species and mapped.

Biome: root:Environmental:Terrestrial:Soil
Malaysia Pasoh Landuse Logged Forest

In Malaysia and much of Southeast Asia the major drivers of deforestation are logging and expansion of oil palm agriculture. Forests regenerating from logging have been found to support relatively high levels of biodiversity for some larger taxa, while oil palm plantations have been shown to harbor a very small fraction of biodiversity that would otherwise be observed in primary forest. However, no studies have evaluated the belowground communities in these mosaics across the tropical landscape.

Biome: root:Environmental:Terrestrial:Soil:Tropical rainforest
Malaysia Lambir Soils

Lambir Hills National Park is located in Sarawak, Malaysia on the island of Borneo. The Center for Tropical Forest Science (http://www.ctfs.si.edu/) established a permanent 52-ha research plot at this site in 1991 and mapped, tagged, and identified all trees 1cm dbh (recensuses occur every 5 years). Of all the CTFS plots established to date (&gt;40 across the world), Lambir Hills is the most diverse in terms of tree species with &gt;1000 species found to be coexisting. One of the major drivers of high tree diversity at this site is thought to be the soil heterogeneity. There are four distinct soil types at this site ranging from low to high fertility.

Biome: root:Environmental:Terrestrial:Soil:Tropical rainforest
Agricultural intensification and the functional capacity of soil microbes on smallholder African farms - kakamenga

For the previous 2-3 years, soils from a chronosequence of farms along the edge of the Kakamega forest in Kenya along with soils from adjacent forested plots were sampled for trace gas fluxes and nitrogen cycling processes. This project sampled soils from the same plots to evaluate the effects of land use change and farm age on the bacteria responsible for key nitrogen cycling processes.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Friedman Alaska peat soils

The samples are from Cornell University in the lab of Lars Angenent, and are soils and biofilms from tundra ecosystems outside Barrow, AK.

Biome: root:Environmental:Terrestrial:Soil
Urban stress is associated with variation in microbial species composition, but not richness, in Manhattan

Green roof and city park samples. In urban environments, green roofs provide a number of potential benefits, including decreases in urban heat island effects and reduced energy costs for buildings. However, they may also serve as habitat islands for maintaining biodiversity across the landscape, similarly to city parks. In this project, eleven experimental green roofs were sampled in addition to five city parks. The green roofs were spread across all five boroughs of New York City and were established in 2010 on top of select recreation centers run by the New York City Department of Parks and Recreation. All experimental green roofs were planted with the same density of native plant communities from the greater New York area and had identical soil substrate and planting box dimensions. The five city parks chosen for sampling included Central Park, the largest park in New York City, and the High Line, which is the newest large park established in the city. From each green roof, six composite soil cores (0-10 cm) were taken from six planting boxes (each box 4 m X 2 m) for a total of six representative samples per green roof. On three of the green roofs, we sampled in a spatially-explicit manner to capture fine-scale heterogeneity in microbial composition. For these samples, 10 individual soil cores were collected from three planting boxes for a total of 30 soil cores per roof. From each city park, three plots (20 m X 20 m) were sampled and five soil cores (0 to 10 cm) were composited as a representative sample for each plot. In Central Park, five plots were sampled rather than three plots due to the larger size of the park. Research questions: Do green roofs planted with native plants in New York City function as biodiversity reservoirs for bacteria, is there significant heterogeneity in microbial community composition at fine spatial scales within individual green roofs, based on the fine-scale spatial heterogeneity of green roof soil bacteria, how many samples are necessary to collect as a representative sample for each green roof, how much overlap is there in microbial community composition of the green roof substrates and city park soils and is there evidence for biogeographical structuring of green roof microbial communities across New York City.

Biome: root:Environmental:Terrestrial:Soil
Mission Bay Sediment Viromes

Mission Bay Sediment Viromes

Biome: root:Environmental:Aquatic:Marine:Sediment
Marine mammal skin microbiomes

Skin samples from 139 animals, encompassing 12 species, have already been collected in collaboration with marine mammal scientists. These samples include skin biopsies from free-ranging animals from offshore Hawaii, field-captured and released animals from coastal Massachusetts and stranded and by-caught animals, primarily from Cape Cod. Samples are from the following species are currently stored in my lab at -80C: short-beaked common dolphin (Delphinus delphis), Atlantic white-sided dolphin (Lagenorphynchus acutus), rough-toothed dolphin (Steno bredanensis), bottlenose dolphin (Tursiops truncates), pantropical spotted dolphin (Stenella attenuata), harbor porpoise (Phocoena phocoena), short-finned pilot whale (Globicephala macrorhynchus), sperm whale (Physeter macrocephalus), melon headed whale (Peponocephala electra), minke whale (Balaenoptera acutorostrata), harbor seal (Phoca vitulina), and grey seal (Halichoerus grypus). Additionally, skin samples have been committed to me from 3 other species: fin whales (Balaenoptera physalus) and sei whales (Balaenoptera borealis) from offshore Massachusettes, and free-ranging beluga whales (Delphinapterus leucas) from Alaska. The skin samples were obtained from free-ranging, beach stranded, or recently deceased animals. The majority of the free-ranging animals were observed to be in apparently good health condition, while those stranded on the beach (samples obtained from both live and dead animals) are considered to be health-compromised.

Biome: root:Host-associated:Mammals:Skin
Recovery of biological soil crust-like microbial communities in previously submerged soils of Glen canyon

In 1963 the Glen Canyon Dam was completed and Lake Powell began to fill. After recent, successive years of drought in the Colorado River upper basin the water level in Lake Powell has been steadily declining, and is now approximately 100 ft below the high water line. Here we present a survey of soil microbial communities at three sites in Glen Canyon, each spanning a transect from just below the current water level to above the high water line in steps of 10 vertical feet. Approximately 100 samples were collected, and archaeal and bacterial 16S rRNA was sequenced on the Illumina HiSeq2000 platform to a median sampling depth of approximately 81,000 sequences per sample. We show that the phylogenetic composition of the submerged and exposed soil microbial communities are distinct, and that with time since reemergence microbial communities of exposed soils have become more similar to those of biological soil crusts, which typify undisturbed soils of the area. Our results suggest that as the water level of Lake Powell recedes, the microbial communities of Glen Canyon soils are dynamically recovering from flood disturbance.

Biome: root:Environmental:Terrestrial:Soil