SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Meterosideros Flower Microbiota

Eukaryote-associated microbiomes interact with their hosts in multiple manners, thereby affecting the hosts? phenotype, physical condition and behaviour. In plants, bacteria have numerous functions, with variable net effects, both in natural and agricultural systems. However, information about the composition and diversity of the bacterial communities associated with different aboveground plant organs, particularly flowers, is lacking. In addition, the relative effects of microhabitat and environmental conditions on community establishment require further attention. Here, using culture-independent methods, we determine that leaves and three floral microhabitats of Metrosideros polymorpha (Myrtaceae), a tree endemic to Hawai?i, host unique indicator communities composed of relatively abundant bacterial taxa. These indicator communities are accompanied by a large number of ubiquitous or rare bacteria with lower abundances. In our study system, the strong effect of microhabitat filtering on plant-associated community composition and bacterial richness and diversity strongly exceeds the influence of environmental effects such as precipitation, altitude, substrate age and geographic distance. Thus, the bacterial richness of aboveground plant organs is strongly underestimated when only one microhabitat, e.g., leaves, is considered. Our study represents a first step towards a comprehensive characterisation of the distribution, composition, and underlying factors, of plant bacterial communities, with implications for future basic and applied research on plant health, pollination and reproduction.

Biome: root:Host-associated:Plants:Phylloplane
Response of plant-associated bacterial community to simulated climate changes

The microorganisms inhabiting plant, such as leaf and root play important roles in plant growth. However, the microbial community structure and their response to climate changes are poorly understood. The objective was to survey the composition of microbial communities from root and clarify the response of bacterial communities to elevated CO2 and/or soil temperature.

Biome: root:Host-associated:Plants
The bacteria and fungi associated with the leaves of Arabidopsis thaliana

Identifying the factors that influence the outcome of host-microbial interactions is critical to protecting biodiversity, minimizing agricultural losses, and improving human health. A few genes that determine symbiosis or resistance to infectious disease have been identified in model species, but a comprehensive examination of how a host''s genotype influences the structure of its microbial community is lacking. We conducted a field experiment using Arabidopsis thaliana to determine if host-genetic variation shapes the composition of its leaf bacterial and fungal community.

Biome: root:Host-associated:Plants:Phylloplane
Microbiome and metagenome of forest biochar

We analyzed taxonomic marker gene amplicons from microbial communities in four-year-old biochar particles and in adjacent soils across three forest environments.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils

Forest ecosystems need to be sustainably managed, as they are major reservoirs of biodiversity, provide important economic resources and modulate global climate. We have a poor knowledge of populations responsible for key biomass degradation processes in forest soils and the effects of forest harvesting on these populations. Here we investigated the effects of three timber harvesting methods, varying in the degree of organic matter removal, on hemicellulolytic bacterial and fungal populations ten to sixteen years after harvesting and replanting. We used stable-isotope probing to identify populations that incorporated 13C-labeled hemicellulose, analyzing 13C-enriched phospholipid fatty acids, bacterial 16S rRNA genes and fungal ITS regions. In soil microcosms, we identified 104 bacterial and 52 fungal hemicellulolytic operational taxonomic units (OTUs). Several of these OTUs are affiliated with taxa not previously reported to degrade hemicellulose, including the bacterial genera Methylibium, Pelomonas and Rhodoferax, and the fungal genera Cladosporium, Pseudeurotiaceae, Capronia, Xenopolyscytalum and Venturia. The effect of harvesting on hemicellulolytic populations was evaluated based on in situ bacterial and fungal OTUs. Harvesting treatments had significant but modest long-term effects on relative abundances of hemicellulolytic populations, which differed in strength between two ecozones and between soil layers. For soils incubated in microcosms, prior harvesting treatments did not affect the rate of incorporation of hemicellulose carbon into microbial biomass. In six ecozones across North America, distributions of the bacterial hemicellulolytic OTUs were similar, while distributions of fungal ones differed. Our work demonstrates that diverse taxa in soil are hemicellulolytic, many of which are differentially affected by the impact of harvesting on environmental conditions. However, the hemicellulolytic capacity of soil communities appears resilient.

Biome: root:Environmental:Terrestrial:Soil:Forest soil
Soil microbiome responses to the short-term effects of Amazonian deforestation

Slash-and-burning forest clearing is a common practice in the Amazon region. In order to understand to what extent this may change the basic mechanisms of soil fertility, we analyzed the structure of the microbial community in forest and deforested soils and relate these to changes in soil chemical factors. Deforestation decreased soil organic matter (OM) content and factors linked to soil acidity, and raised soil pH, base saturation, and the concentration of exchangeable bases. Concomitantly to expected changes in soil chemical factors, we observed an increase in the alpha diversity of the bacterial microbiota and relative abundance of putative copiotrophic microbes such as Actinobacteria, and a decrease in the relative abundance of bacteria such as Chlamydiae, Planctomycetes and Verrucomicrobia in the deforested soils. We did not observe an increase in genes related to microbial nutrient metabolism in deforested soils; however we did observe changes in community functions, which included increases in DNA repair, protein processing, modification, degradation and folding functions. In addition there were changes in composition of the bacterial groups associated with metabolism-related functions. Co-occurrence microbial network structures identified distinct phylogenetic pattern for forest and deforested soils and opened the possibilities to investigate relationships between Planctomycetes and Al content, and Actinobacteria and nitrogen sources in Amazon soils. The results support taxonomical and functional adaptations in the soil bacterial community following deforestation. We hypothesize that these microbial adaptations may serve as a buffer to drastic changes in soil fertility after slash-and-burning deforestation in the Amazon region.

Biome: root:Environmental:Terrestrial:Soil:Tropical rainforest
Rhizosphere microbial community composition affects cadmium and zinc uptake of the metal-hyperaccumulating plant Arabidopsis halleri

The remediation of metal-contaminated soils by phytoextraction depends on plant growth and plant metal accessibility. Soil microorganisms can affect the accumulation of metals by plants by either directly or indirectly stimulating plant growth and activity or by (im)mobilizing and/or complexing metals. Understanding the intricate interplay of metal-accumulating plants with their rhizosphere microbiome is an important step towards the application and optimization of phytoremediation. We studied the effect of a ?native? compared to a strongly disturbed (gamma-irradiated) soil microbial community on cadmium and zinc accumulation by the plant Arabidopsis halleri in soil microcosm experiments. A. halleri accumulated 100% more cadmium and 15% more zinc when grown on the untreated compared to the gamma-irradiated soil. Gamma-irradiation did not affect soil metal bioavailability or plant growth. However, it strongly altered soil microbial community composition and overall cell numbers. Pyrosequencing of 16S rRNA gene amplicons of DNA extracted from rhizosphere samples of A. halleri revealed distinct differences in microbial community richness and evenness between the untreated and gamma-irradiated soil. Classification and comparative sequence analysis allowed the identification of microbial taxa (Lysobacter, Streptomyces, and Agromyces) that might have enhanced the accumulation of Cd and Zn by A. halleri in the microcosms with the untreated soil. We discuss different mechanisms of interaction of A. halleri with its rhizosphere microbiome that might have directly or indirectly affected plant metal accumulation. Deciphering the complex interplay between A. halleri and individual microbial taxa will help to further develop soil metal phytoextraction strategies as efficient and sustainable remediation procedure.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Analysis of microbial communities in leafy greens using Illumina MiSeq

Our work provides the first microbial profiling of leafy green phyllosphere in Europe and contributes to the questions on how the community structure changes on different types of leafy greens and at different time points within one planting.

Biome: root:Host-associated:Plants:Phylloplane
Arabidopsis thaliana culture collections of leaf- and root-associated bacteria  (Synthetic Communities 16S rRNA data)

Roots and leaves of healthy plants host taxonomically structured bacterial assemblies, and members of these communities contribute to plant growth and health. We established Arabidopsis leaf- and root-derived microbiota culture collections representing the majority of bacterial species that are reproducibly detectable by culture-independent community sequencing. We found an extensive taxonomic overlap between the leaf and root microbiotas. Genome drafts of 400 isolates revealed a large overlap of genome-encoded functional capabilities between leaf and root-derived bacteria with few significant differences at the level of individual functional categories. Using defined bacterial communities and a gnotobiotic Arabidopsis plant system we show that the isolates form assemblies resembling natural microbiotas on their cognate host organs, but are also capable of ectopic leaf or root colonization. Whilst this raises the possibility of reciprocal relocation between root and leaf microbiota members, genome information and recolonization experiments also provide evidence for microbiota specialization to their respective niche.

Biome: root:Host-associated:Plants
Metagenome of the culturable bacterial endophytes of Palm Oil Fruit

The bacterial endophytes within the palm oil fruit (Elaeis guineensis) were cultured using a palm-oil enriched medium and the bacterial cells present in the microcosm were separated by filtration through a 14 micrometer pore filter. The DNA obltained by these cells was then sequenced using 454 pyrosequencing technology on the 454 GS FLX platform. A single fragment (shotgun) library was sequenced in two separate runs.

Biome: root:Host-associated:Plants:Rhizoplane:Endophytes
Ileum content of female broilers belonging to different genetics

Ileum content of female broilers belonging to different genetics

Biome: root:Host-associated:Birds:Digestive system:Digestive tube
Total metagenomic analysis

Comparison between samples obtained from tucurui reservoir

Biome: root:Environmental:Aquatic:Freshwater:Lake
Taxonomic and functional diversity of the virus community from a South African thermal spring

The virus community composition and functional gene content from a South African hot spring (Brandvlei)was analyzed through a shotgun metagenomics approach.

Biome: root:Environmental:Aquatic:Thermal springs:Hot (42-90C)
Estimation of variability in the gut microbiota resistome of the Russian citizens aimed at identification of pathways for transmission and spread of antibiotic resistance.

A problem of antibiotic resistance emergence in microbiome will be investigated in the research. To date, gut microbiome (as well as soil microbiome) is considered to be antibiotic resistance reservoir. The resistance can accumulate in the microbiome after antibiotic treatment against infectious agents, and it can be passed to pathogenic bacteria during further infections, even though absence of the target infection is checked after each therapy. Moreover, use of antibiotics in agriculture and every day life (without doctor’s recommendations) creates an environment for antibiotic resistance transfer between microbiomes, as there is always a selective pressure for it. That is a quite dangerous situation, as there is a permanent ubiquitous antibiotic resistance (AR) background. In the framework of the research available data on Russian and worldwide microbiomes (more than 2000 by 2015 year) will be analyzed and groups of patients who passed antibiotic treatment will be studied. Using obtained results a map of antibiotic resistance expansion will be created, dominating mechanisms of the resistance transfer and AR genes hosts will be revealed. Additionally, laboratory methods and mathematical analysis for genes’ and mechanisms’ screening will be developed. The developed models AR transfer will make possible modeling of various methods for AR transfer prevention, or, alternatively, modeling of consequences of different antibiotics’ use. Concluding, basic mechanisms of AR emergence will be described (6-1-3) and new methods of screening will be proposed. Furthermore, principle of the screening operation will be demonstrated on available data on AR, as well as on chosen clinical groups.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
Root microbiome in phytohormone mutants.

The root bacterial microbiome of Arabidopsis thaliana was profiled, via 16S rRNA gene sequencing. Roots of wild-type plants and isogenic mutants in biosynthesis/signaling of salicylic acid, jasmonic acid and ethylene were profiled. Endophytic compartment and rhizosphere were independently profiled from each plant, as well as bulk soil controls.

Biome: root:Host-associated:Plants:Rhizosphere
Extensive overlap of tropical rainforest bacterial endophytes between soil, plant parts and plant species.

The extent to which distinct bacterial endophyte communities occur between different plant organs and species is unclear, and has implications for bioprospecting efforts. Using V3 region of bacterial 16S rRNA gene, we investigated the diversity patterns in total, uncultured bacterial endophyte communities of three rainforest plant species, comparing leaf, stem, and root endophytes, plus rhizosphere soil community employing MiSeq. There was extensive overlap in bacterial communities between plant organs, between replicate plants of the same species, between plant species, and between plant organ and rhizosphere soil, with no consistent clustering by compartment or host plant species. Both the lack of clustering in an NMDS ordination and an NMTD analysis suggested that bacterial endophyte OTUs were stochastically distributed amongst plant species and organs, and rhizosphere soil. Percentage turnover of OTUs samples was similar for plant individuals of the same species and of different species, at around 80-90%. Our results suggest that sampling of extra individuals, extra plant organs, extra species, or use of rhizosphere soil, might be about equally effective for obtaining new OTUs for culture. Our observations suggest that the plant endophyte community may be much more diverse, but less predictable, than would be expected from culturing efforts alone.

Biome: root:Host-associated:Plants:Rhizosphere:Epiphytes
Root microbiome of phytohormone mutants in synthetic recolonization experiments.

The root bacterial microbiome of Arabidopsis thaliana was profiled, via 16S rRNA gene sequencing. Plants were grown in a sterilized calcined clay substrate inoculated with 37 root isolates plus E. coli. Root endophytic comparment of wild-type plants and isogenic mutants in biosynthesis/signaling of salicylic acid, jasmonic acid and ethylene were profiled. A subset of the plants revceived exogenous aplication of salicylic acid on the leaves.

Biome: root:Host-associated:Plants:Rhizome
Community profile of winery wastewater treatment plant

Here we investigated the community profile of a winery wastewater treatment plant dominated by glycogen accumulating organisms.

Biome: root:Engineered:Wastewater:Industrial wastewater
Effects of crown gall disease on natural microbiota of Vitis vinifera

The crown gall disease in grapevine is mediated by Agrobacterium vitis and results in tumorous growth. The tumor offers an ecological niche for the pathogen and eventually for other bacteria as well. We wanted to know if the crown gall disease affects the bacterial community of the grapevine plant. Using next generation sequencing of the V4 region of 16S rDNA amplicons we recorded the microbiota from galled and non-galled grapevine plants as well as of the soil at three seasons of the year. The root, trunk, one-year-old cane and the soil hosted distinct microbiota, which differed according to spring, summer, and autumn. However, the crown gall disease influenced the structure of the microbiota only in grapevine trunks. There the bacterial richness was higher and comprised for example exclusively the plant pathogens Xanthomonas sp., Sodalis sp., and an unknown Gammaproteobacterium. The seasons additionally affected the microbiota in the trunks with and without a crown gall differently. A. vitis, Pseudomonas sp. and Enterobacteriaceae sp. were the most abundant sequences in crown galls at each season. In contrast, in healthy trunks (=non-galled) the microbial composition changed from season to season. Altogether, twenty-two operational taxonomic units, representing bacterial species, were significantly enriched in crown galls and only three in healthy trunks. Our results support the idea that other bacteria than the pathogen A. vitis can adapt to the crown gall environment. How these profit from the new environment and if they influence crown gall development will be the subject of future work.

Biome: root:Host-associated:Plants
Effects of organic matter manipulation on bacterial community diversity and function

Lake ecosystems provide important services including their ability to support complex food webs, and their connection to the global carbon cycle. These services are dependent on how microorganisms interact with available organic matter (OM), both dissolved and particulate. Therefore, in order to manage these important ecosystems and their services successfully, it is necessary to understand how the quality and quantity of DOM affects microbial communities. Linking DOM quality and quantity to microbial community complexity and function are crucial steps toward a mechanistic understanding of freshwater ecosystems. Understanding these relationships at the microbial scale will enable us to make predictions about landscape-scale environmental change and its effect on aquatic carbon cycling and food web processes. In this study, I aim to investigate the effect of organic matter manipulation on the molecular structure of DOM and the microbial community composition and function in freshwater boreal lakes.

Biome: root:Environmental:Aquatic:Freshwater:Lake
A diverse array of bacteria that inhabit the rhizosphere and different plant organs play a crucial role in plant health and growth.

This study addressed two fundamental questions: (1)How does the bacterial community structure differ between the different organs of Lepidium perfoliatum L.?(2) Do different tissues have thepotential to influence the structure of bacterial communities?

Biome: root:Host-associated:Plants
Accessing and Identification of Novel Environmental Alleles of the ACC Deaminase Domain Region through a Competition Assay

Rhizosphere soil samples from four Maize inbred lines (Oh43, MS71, M37W, and NC358) were collected from a field in Missouri, USA, in 2010. PCR reactions, pooled DNA extracted from all four lines, used custom primers a2F 5'- GSAACAAGACGCGCAAG-3' and a2R 5'-CACSAGCACGCACTTCATG-3', to amplify a 37 amino acid region from the full-length accD gene. These degenerate primers were designed using an alignment of bacterial accD genes obtained from public databases.

Biome: root:Host-associated:Plants:Rhizosphere
tes

test 2

Biome: root:Host-associated:Plants:Phylloplane
Class project on metagenomics using samples from soil.

Class project to get a hand on exercise on metagenomics. Samples were collected from soil and sequenced in Ion torrent PGM.

Biome: root:Environmental:Terrestrial:Soil
Soils collected from a petroleum hydrocarbon contaminated site in Greenland.

Soils collected from a petroleum hydrocarbon contaminated site in Greenland.

Biome: root:Environmental:Terrestrial:Soil:Oil-contaminated
Root microbiome of Arabidopsis plants with altered phosphate starvation response

The root bacterial microbiome of Arabidopsis thaliana was profiled, via 16S rRNA gene sequencing. Plants were grown in either a previouly characterizes wiled soil or in gnotobiotic plate conditions with a 35 bacteria synthetic community. Root endophytic comparment of wild-type plants and isogenic mutants was charachterized. For the synthetic community experiments, different phosphate levels in the media were used.

Biome: root:Host-associated:Plants:Rhizosphere
Environmental soil samples from a gasoline contaminated site in Meadow Lake, Saskatchewan, Canada.

A gasoline contaminated site in Meadow Lake, Saskatchewan was monitored for hydrocarbon degradation. Different types of biochar and forms of phosphate were tested to track optimal degradation of gasoline at the site.

Biome: root:Environmental:Terrestrial:Soil:Oil-contaminated
Yeast diversity during the fermentation of Andean chicha: a comparison between high-throughput sequencing and culture-dependent approaches.

The diversity and dynamics of yeasts associated with the fermentation of Argentinian maize-based beverage chicha was investigated. Samples taken at different stages from two chicha productions were analyzed by culture-dependent and culture-independent methods. Classical microbiological methods allowed isolation of five hundred eighty-two yeasts identified into 16 species by RFLPs and sequencing of D1/D2 26S rRNA gene. Genetic typing of isolates from the dominant species, Saccharomyces cerevisiae, by PCR of delta elements revealed up to 42 different patterns. High-throughput sequencing of D1/D2 26S rRNA gene amplicons from chicha samples allowed detection of more than one hundred yeast species and almost fifty filamentous fungi taxa. Analysis of the data revealed that yeasts dominated the fermentation, although, a significant percentage of filamentous fungi appeared in the first step of the process. Statistical examination of results showed that very few taxa were represented by more than 1% of the reads per sample at any step of the process. S. cerevisiae represented more than 90% of the reads in the fermentative samples. Other yeast species, different from S. cerevisiae, dominated the pre-fermentative steps and abounded in fermentative samples when S. cerevisiae was in percentages below 90%. Most yeasts species detected by pyrosequencing were not recovered by cultivation. In contrast, the cultivation-based methodology detected very few yeast taxa, and most of them corresponded with none or very few reads in the pyrosequencing analysis.

Biome: root:Engineered:Food production:Fermented beverages