SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Halophilic Communities as a Source for Novel Lignocellulolytic Enzymes

The goal of my project has been to identify microbes and enzymes tolerant of varying levels of salinity. The driving hypothesis for this work is that salt tolerance correlates with ionic liquid tolerance. Ionic liquids are presently the best means of pretreating lignocellulosic biomass to better enable its biological conversion into useful products at biorefineries. Ionic liquid tolerance enzymes and microbes with help consolidate the various steps in the production of biofuels and reduce the impact of residual ionic liquids in feedstock materials, thereby reducing processing costs. We have collected samples from Puerto Rico and the San Francisco Bay in California from environments representing a gradient of salinities. Both sediment-associated and planctonic microbial community samples were collected and enrichments have been prepared from some of the samples. Each of the environments samples are also of great interest to the broader environmental microbiology scientific community including planctonic samples from the Bioluminescent Bay near La Parguera, PR and sediment samples from Thalassia testudinum beds near the bay.

Biome: root:Mixed
Distinct microbial communities associated with buried soils in the Siberian tundra.

Around 1700 Gt carbon are stored in the Northern latitude permafrost regions (Schuur et al, BioScience 2008). This is more than double the size of the atmospheric carbon pool but the estimates are still quite uncertain and might be even higher. It is however estimated that 25 percent of this large carbon pool in Arctic soils will be lost by the end of the 21st century and will be released to the atmosphere as CO2 (Gruber et al., 2004). The subduction of organic-rich material from the surface to deeper layers caused by repeated freezing and thawing of the active layer during Arctic summer is assumed to be a major mechanism of carbon storage in the Arctic. These cryoturbations are spatially widely distributed and store high amounts of soil organic carbon (SOC). Decomposition of recent cryoturbated carbon is strongly retarded thereby essentially taking out this fraction of SOC from the current carbon cycle. Todays primary concern and research focus is the vulnerability of cryoturbated SOC due to global warming which is predicted to lead to intensified decomposition and elevated greenhouse gas emissions. Here we present a study that aims to provide a comprehensive picture of the microbial community structure of permafrost-affected and cryoturbated soils of different Northern latitude permafrost regions in Siberia and Greenland. For this purpose, soil samples were collected in northeast Siberia in a transect along the upper Kolyma river, and in the Zackenberg region, Greenland. The sampling scheme covered several bioclimatic subzones and vegetation types. We are currently analysing data retrieved from SSU amplicon sequencing, the quantification of several functional groups involved in carbon cycling and physico-chemical analyses in order to predict potential microbial regulators in SOC storage. This study is part of the multinational CryoCARB project (for further information, see: www.cryocarb.net).

Biome: root:Environmental:Terrestrial:Soil
Brazilian Antarctic cleanup 16S

Contaminated soil collected near from Brazilian Antarctic Station Comandante Ferrar after fire led to an explosion with diesel contamination of soil/tundra in February 2012

Biome: root:Environmental:Terrestrial:Soil
Defining seasonal marine microbial community dynamics

In order to facilitate conservation of biological diversity we require comprehensive knowledge of the microbial ecology of an ecosystem. As the vast majority of microbes are not readily culturable, we must use molecular tools to investigate their diversity and function in marine ecosystem. However, it is still difficult to understand their role in ecological processes. Here we present a study to characterize changes in the diversity and metabolic activity of the heterotrophic bacterial community over an annual cycle in the Western English Channel. For this purpose, surface water samples were collected from the sampling station, L4, every week for a year. The respiration rate of the heterotrophic microbial community was determined from the decrease in dissolved oxygen content of the less than 0.8m size-fraction of the sea water. We are currently analyzing captured DNA using 16S rRNA amplicon and shotgun metagenomic pyrosequencing to determine the diversity and functional profile of the active bacteria in order to characterize annual changes in the active bacterial community. This dataset sits within the larger framework of the Western English Channel bacterial diversity time series (2003-2009) and the seasonal metagenomic and metatranscriptomic studies associated with this site. We demonstrate that respiration rates are characterized by specific microbial diversity and function at different times of year, highlighting seasonal fluctuation in this ecosystem.

Biome: root:Environmental:Aquatic:Marine
Song Colorado freshwater fish

Microbiota of slime and gut samples from different species of freshwater fish from the Colorado River.

Biome: root:Mixed
Microbial Community and Ovine Host Responses to Early and Late Haemonchus contortus Infection

This work seeks to explore the impact of early and late Haemonchus infection on abomasal and ruminal microbial community, and ovine host. Overall, these results indicate that Haemonchus infection plays a crucial role for shaping abomasal and ruminal microbial community composition, and diversity.

Biome: root:Host-associated:Mammals:Digestive system:Stomach
Migratory locust

Migratory locust gut microbiome isolated from Saudia Arabia

Biome: root:Host-associated:Insecta:Digestive system
Single Batch Fermentation System Simulating Human Colonic Microbiota_Ulcerative colitis

KUHIMM

Biome: root:Engineered:Lab enrichment
Gut microbiome response to short term dietary intervention in reactive hypoglycemia subjects

Gut microbiome response to short term dietary intervention in reactive hypoglycemia subjects

Biome: root:Host-associated:Human:Digestive system:Intestine
YWI microbiome study

Anaerobic digestion process in waste water treatment plants is a well-established method of converting organic material to a biogas. However, the microbiomes involved in AD are not fully understood highlighting the importance of community profiling study for getting essential information on how the communities are structured. Here, we profiled microbial communities of fifteen full-scale anaerobic digesters operated by regional waste water treatment company. Using amplicon 16S sequencing of V4 regions, we observed a presence of highly diverse microbiomes and differences between samples associated with digesters operational status and feedstock pre-treatment. Most abundant phyla and their members were revealed showing the presence of a core microbiome in these reactors.

Biome: root:Engineered:Wastewater:Water and sludge
Research on Airborne Ice Nucleating Species

Research on Airborne Ice Nucleating Species

Biome: root:Environmental:Air
The study aims to study the transcriptional response of soil communities to the artificial pollution with toluene

This study project for a complete characterization and interpretation of the functional response of local microbial communities present in different type soils upon contamination of toluene.

Biome: root:Environmental:Terrestrial:Soil:Clay
Core MV1012-46.9-JPC2 aDNA metagenomes and negative control

Illumina 4000 sequencing of MV1012-46.9-JPC2 sediment core

Biome: root:Environmental:Aquatic:Marine:Sediment
Resistflow-WWTPs-16S DNA data (unpublished)

This is unpublished data. Any use of the data in a publication, meta-analysis, or global survey should get the approval from the corresponding author (helmut.buergmann@eawag.ch). RESIST-Flow: Understanding resistance gene flow during passage of wastewater treatment

Biome: root:Engineered:Wastewater
photoautotrophic_biofilm

Samples of this study were collected of a super-intensive shrimp culture using photoautotrophic biofilm as complementary aquafeed

Biome: root:Environmental:Aquatic
Microbial community response to different substrates during anaerobic digestion

This study investigated the changes of microbial community response to anaerobic digestion of pig manure, chicken manure, sewage sludge, sterilized pig manure, sterilized chicken manure and sterilized sewage sludge. The authors tried to clarify the role of the substrate microbial community on the fate of ARGs during anaerobic digestion.

Biome: root:Engineered:Wastewater:Water and sludge
Lane 6 Analysis

Negative control lane for ancient DNA taken from core MV1012 46.9

Biome: root:Environmental:Aquatic:Marine:Coastal:Sediment
LogMPIE: Landscape Of Gut Microbiome - Pan India Exploration

LogMPIE is an observational, multi-center, cross geography and age-group study. The primary objective of the study was to report the microbiome baseline across India. The study reported data from over 1000 subjects. Additionally, for individual subjects, factors such as BMI, lifestyle, dietary habits and gender were recorded.  The study was conducted by Tata Chemicals Limited.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
The fecal microbiota in L-DOPA naive PD patients

Parkinson's disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both, the enteric and the central nervous system, possibly spreading from one to another via the vagus nerves. As gastrointestinal dysfunction often precedes or parallels motor symptoms, the enteric system with its vast diversity of microorganisms may be involved in PD pathogenesis. Alterations in the enteric microbial taxonomic level of L-DOPA-naïve PD patients might also serve as a biomarker.We thus compared the fecal microbiomes of 31 early stage, L-DOPA-naive PD subjects to 28 age matched controls by metagenomic analysis.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Ammonia effect on food waste anaerobic digestion

Food waste has high organic content that enables it to become an attractive feedstock for anaerobic digestion. However, food waste anaerobic digestion often suffers from a poor performance and instability caused by a high ammonium concentration resulted from a high nitrogen content in the feedstock. This study aimed to trace dynamic changes in microbial populations during food waste digestion adapted to increasing ammonium concentration, using both biofunctional information obtained from radioactive isotope tracer technique, analysis of 16S rRNA amplicons and fluorescence in situ hybridisation.

Biome: root:Engineered:Wastewater:Water and sludge
Catchment sources of microbes

We will undertake the first ever large-scale microbiome exploration in Melbourne water catchments to provide a baseline dataset on the composition of microbial communities in animals, water and the environment to underpin drinking water quality management.

Biome: root:Host-associated:Mammals:Digestive system
Puerto Rico and Plantanal

Part of the Western acculturation project - Plantanal and D1-30 longitudinal babies from PR

Biome: root:Host-associated:Mammals
Peralta starlings

We explored how experimental changes in humidity and temperature affect female incubation performance and nest environment and bacterial community on eggshells. We also explored the relationship between bird ectoparasites and egg colour, with bacterial load on eggshells and hatching success.

Biome: root:Host-associated:Birds
Microbiome of honey bees from Puerto Rico

Samples of bees, royal jelly from honey bees (Apis mellifera) in Puerto Rico. Includes whole head, whole larva, whole pupa, whole gut and royal jelly. Effect of Tetracycline application.

Biome: root:Host-associated:Insecta
Effect of natural additives on the rumen microbiome following feeding of beef cattle with a blend of natural additives

The indiscriminate use of antibiotics in animal production and human consumption is related to the increase of microorganisms resistant to a wide class of chemical compounds. Thus, alternatives are sought for the use of growth promoters and antimicrobials in animal production. Recent research demonstrates the potential of applying essential oils (OEs) in several areas as potential substitutes for antibiotics. This is because they have characteristics similar to these products. However, there are few data in the literature regarding the actions of OEs in axenic cultures of anaerobic ruminal microorganisms. Thus, a project is proposed to: evaluate the efficacy of essential oils from the sequencing of rumen microorganisms of finished cattle in confinement; determine the genes expressed by the ruminal microbiota; identify pure cultures affected by the presence of OEs; to observe the effect of OEs on ruminal bacteria by electron microscopy; to evaluate the microbial resistance of OEs in ruminal bacteria; and evaluate the metatranscriptome of axenic culture of ruminal bacteria cultured with OEs. It is expected to identify species strongly affected by OEs and metabolic routes and mechanisms used by ruminal microorganisms to deal with the presence of OEs and their active compounds. Queen's University of Belfast is part of the Russel Group, which contains the 24 best institutions in the UK. An important part of Queen's University's research is related to food safety. Thus, the university has highly qualified equipment and technical staff for research related to the entire food production chain.

Biome: root:Host-associated:Animal:Digestive system
Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau

Continent-scale biogeography has been extensively studied in soils and marine systems, but little is known about biogeographical patterns in non-marine sediments. We used barcode pyrosequencing to quantify the effects of local geochemical properties and geographic distance for bacterial community structure and membership, using sediment samples from 15 lakes on the Tibetan Plateau (4–1670 km apart). Bacterial communities were surprisingly diverse, and distinct from soil communities. Four of 26 phyla detected were dominant: Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria, albeit 20.2% of sequences were unclassified at the phylum level. As previously observed in acidic soil, pH was the dominant factor influencing alkaline sediment community structure, phylotype richness and phylogenetic diversity. In contrast, archaeal communities were less affected by pH. More geographically distant sites had more dissimilar communities (r = 0.443, P = 0.030). Variance partitioning analysis showed that geographic distance (historical contingencies) contributed more to bacterial community variation (12.2%) than any other factor, although the environmental factors explained more variance when combined (28.9%). Together, our results show that pH is the best predictor of bacterial community structure in alkaline sediments, and confirm that both geographic distance and chemical factors govern bacterial biogeography in lake sediments.

Biome: root:Environmental:Aquatic:Sediment
Hawaii Kohala Volcanic Soils

We are studying a network of sites along an extreme rainfall gradient that ranges from 200 mm to 3500 mm/year over a short distance of 12 km due to orographic moisture interception by Kohala Mountain in Hawaii. This climate sequence is ideal for studying soil development because the effects of rainfall on soil properties can be isolated from other environmental factors. Unlike most gradients that span arid to wet tropical climates, soil forming factors other than rainfall vary minimally across these sites: Parent material and topography are constant and there is minimal variation in vegetation and climate factors other than rainfall. These unique circumstances make this gradient a powerful model field system to understand the effects of rainfall variation on soil development and ecosystem biogeochemistry, as demonstrated by the seminal work done in these areas by our collaborators Peter Vitousek (Stanford) and Oliver Chadwick (UCSB). In spite of the wealth of ecosystem and soils research conducted at these sites, there is little known about soil microorganisms in these soils and no community characterization using DNA sequencing. We will sequence soil 16S rRNA genes from 13 different locations along the gradient. At each location we have samples from each of three depths (0-15 15-30, 30-50 cm) and four field replicates for each depth at most locations.

Biome: root:Mixed
Long Term Soil Productivity project

The Long-Term Soil Productivity (LTSP) study was established to demonstrate how alteration of soil porosity and organic matter (two of the more alterable soil properties) would affect soil processes and site productivity throughout forest lands of North America. The experimental design is a 3 x 3 factorial with 3 levels of organic matter loss and 3 levels of soil compaction. The organic matter (OM) treatments include stem-only harvest, whole-tree harvest, and forest floor displacement to mineral soil. The compaction treatments include no compaction, light compaction (2 cm impression), and heavy compaction (4 cm impression). In BC, we have three replicate blocks in the Sub-Boreal Spruce (SBS) biogeoclimatic zone, three in the Boreal White and Black Spruce (BWBS) biogeoclimatic zone, three in the Interior Douglas-fir (IDF) biogeoclimatic zone on common, acidic forest soil, three in the IDF on sensitive calcareous soils, and two replicates have been installed in the Interior Cedar Hemlock (ICH) biogeoclimatic zone that complete an installation initiated by the USDA Forest Service in Idaho.

Biome: root:Environmental:Terrestrial:Soil
Myrold Oregon transect

OTTER. The Oregon transect consists of sites that follow a gradient of net primary productivity from the highest productivity forests in the world (coastal Sitka spruce) to semi-arid juniper woodlands (Fig. 1). This gradient represents the range of net primary productivity found in North America (Runyan et al., 1994). In addition to differences in productivity and vegetation composition, these sites also display a range of soil types. Extensive metadata are available for these sites (Gholz, 1982; Myrold et al., 1989; Runyan et al., 1994; Stark and Hart, 1997; daac.ornl.gov), but no information is available on the microbial communities of these soils. A total of 6 sites will be studied, with 3, 30-by-30 m plots established at each site to provide some information about within site variability, which will result in 18 samples for analysis.

Biome: root:Environmental:Terrestrial:Soil
Biodiversity and Functional Patterns of Microbial Assemblages in Postglacial Pond Sediment Profiles

The purpose of this project is to characterize biodiversity and functional patterns of microbial assemblages in sediment profiles of postglacial ponds that have experienced different histories of human land-use change, and to compare these patterns with a suite of temporal, biological and geochemical markers.

Biome: root:Environmental:Aquatic:Sediment
Spirito monensin cow hindgut

This study aims to investigate the effect of monensin (Rumensin, Elanco-Eli Lilly Co.) on the microbial community structure of the cow hindgut. Monensin is an ionophore antibiotic administered to cattle and dairy cows to increase their feed efficiency by altering rumen fermentation. Monensin acts by changing the activity of specific metabolic pathways, leading to an increase in propionate concentrations and a decrease in acetate and butyrate concentrations in the cow rumen. Previous studies conducted on the effect of monensin on rumen microbial community structure have led to differing conclusions. In addition, few studies have been conducted to assess the effect of monensin on the microbial community structure elsewhere in the cow digestive tract, such as in the cow hindgut. For the current study, manure was collected, over a period of three months, from eight dairy cows housed at the Teaching and Research Center at Cornell University. Four of the cows were fed a control diet containing no monensin. The other four cows were fed a diet with measured incrementally increasing amounts of monensin. To investigate the effect of monensin on the microbial community composition of the cow hindgut, a total of 184 rectal grab samples were collected from the eight cows over the three month period. Once collected, the samples were processed and stored in a -80degreeC freezer for later microbial community composition analysis. The samples were then extracted using the MO BIO Powersoil-htp 96 Well Soil DNA Isolation Kit and frozen at -80degreeC until they could be sent for further processing and sequencing.

Biome: root:Host-associated:Animal:Digestive system:Fecal
Garcia bird gut microbiome

Characterization of bird gut microbiome - gizzard, upper intestine, lower intestine from birds in Venezuela. With Maria -Gloria Dominguez Bello

Biome: root:Host-associated:Birds:Digestive system
Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography

Interactions between hosts and associated microbial communities can fundamentally shape the development and ecology of 'holobionts', from humans to marine habitat-forming organisms such as seaweeds. In marine systems, planktonic microbial community structure is mainly driven by geography and related environmental factors, but the large-scale drivers of host-associated microbial communities are largely unknown. Using 16S-rRNA gene sequencing, we characterized 260 seaweed-associated bacterial and archaeal communities on the kelp Ecklonia radiata from three biogeographical provinces spanning 10° of latitude and 35° of longitude across the Australian continent. These phylogenetically and taxonomically diverse communities were more strongly and consistently associated with host condition than geographical location or environmental variables, and a 'core' microbial community characteristic of healthy kelps appears to be lost when hosts become stressed. Microbial communities on stressed individuals were more similar to each other among locations than those on healthy hosts. In contrast to biogeographical patterns of planktonic marine microbial communities, host traits emerge as critical determinants of associated microbial community structure of these holobionts, even at a continental scale.

Biome: root:Host-associated:Plants
Growth phase-associated changes in the transcriptome of Pseudomonas veronii 1YdBTEX2 in minimal media with toluene.

To study which genes are specifically induced during the different growth phases in toluene, which could indicate the changes in BTEX metabolism as well as the biological processes affected during the different growth phases, a controlled RNA-seq transcriptome analysis was carried out. Gene expression levels were analyzed from cultures upon inoculation (T0), after 4(T4) and 24(T24) hours after inoculation in minimal medium with toluene.

Biome: root:Engineered:Modeled:Simulated communities (microbial mixture)
Microbial community of the bulk soil and rhizosphere of rice plants over its lifecycle

Soil and rhizosphere samples from 4 cultivars of Japanese rice from planting to harvest

Biome: root:Mixed
Ezenwa Cape Buffalo

Cape Buffalo in South Africa were sampled (fecal) in 2011

Biome: root:Host-associated:Mammals:Digestive system
AD-culturomics

Metagenomic studies on microbial ecosystems provide in silico confirmation that these communities consist of thousands of microbial species of which the majority remains poorly characterised and/or uncultured. Specifically, in anaerobic microbial communities that govern conversion of organic matter to biogas, isolation approaches are limited. Following this notion, the project proposes to isolate, identify and archive novel microorganisms from anaerobic digesters (AD) using the isolation chips technique. “Artificial” seed communities could then be created to enhance energy recovery from AD systems by increasing production of biogas.

Biome: root:Engineered:Wastewater:Water and sludge