SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Effect of suspended sediments on the sponge holobiont

Dredging can cause high suspended sediment concentrations (SSC) in the water column, posing risks to filter feeding organisms like sponges as sediment may clog their aquiferous systems and reduce feeding. In order to provide pressure:response values for sponges to SSC and tease apart the cause:effect pathways of dredging pressures, five heterotrophic and phototrophic species were experimentally exposed to a range of dredging-relevant SSC of up to 100 mg L-1, with light compensation across treatments to ensure that SSC was the primary physical parameter. This study shows that some sponge species exposed to high SSC (=23 mg L-1) for extended periods (28 d) have lower survival, increased necrosis, and reduced feeding ability with an associated depletion of energy reserves. In contrast, SSC of =10 mg L-1 causes few if any negative effects for most species and is thus suggested as a reasonable sub-lethal threshold for sponges. Microbial communities did not change significantly among SSC treatments, although nutritional shift from mixotrophy towards increased phototrophy was detected for some sponge species exposed to high SSC. However, it is expected that the combined effect of SSC with low light availability and sediment smothering will increase the negative effects on sponges.

Biome: root:Host-associated:Porifera
Deep Sea Sponge and Seawater Targeted Locus (Loci)

The microbiota of four individual deep water sponges, Lissodendoryx diversichela, Poecillastra compressa, Inflatella pellicula, and Stelletta normani, together with surrounding seawater were analysed by pyrosequencing of a region of the 16S rRNA gene common to Bacteria and Archaea. The microbial communities of L. diversichela, P. compressa and I. pellicula were typical of low microbial abundance (LMA) sponges while S. normani was found to have a community more typical of high microbial abundance (HMA) sponges. Analysis of the deep sea sponge microbiota revealed that the three LMA-like sponges shared a set of abundant OTUs that were distinct from those associated with sponges from shallow waters.

Biome: root:Environmental:Aquatic:Marine
Sponge Raw sequence reads

Describe the microbiome of Mediterranean sponges

Biome: root:Host-associated:Porifera
16S Miseq Illumina sequences from sponge associated with sponges in Vietnam

Analysis of microbial communities associated with sponges in Vietnam

Biome: root:Host-associated:Porifera
Microbial diversity associated with South African marine Latrunculid sponges

This study investigates the microbial communities associated with indigenous Latrunculid sponges found in South African coastal waters. The study aims to identify dominant bacteria associated with the Latrunculid sponges in order to assess the possible interactions between sponge hosts and their harboured symbionts. Latrunculid sponges are well known producers of secondary metabolites including discorhabdins, makaluvamines and tsitsikammamines which have anti-cancer, anti-microbial and anti-malarial activity. Associated microbial symbionts may aid in, or be responsible for the production of these secondary metabolites.

Biome: root:Host-associated:Porifera
Microbial Diversity in Antarctic Shelf Sponges

Investigation of the microbial diversity in Antarctic shelf sponges

Biome: root:Host-associated:Porifera
Microbiota composition and metabolomic profiles of the deep sea sponges Weberella bursa, Stryphnus fortis and Geodia barretti along a depth gradient

In this study we assessed prokaryotic community and metabolite profiles of the three deep sea sponges: W. bursa, S. fortis and G. barretti collected at the Davis Strait at depth range of 200 - 1400 m. Microbial composition was investigated using 16S rRNA gene amplicon sequencing by applying the Illumina MiSeq technology and metabolomic profiles were screened using UPLC-QTOF mass spectrometry. The overall aim of this study is to investigate to what extend depth influences microbial composition and metabolite profiles of the deep sea sponges.

Biome: root:Host-associated:Porifera
Xestospongia muta Raw sequence reads

The giant barrel sponge, Xestospongia muta represents a foundation and ecologically important species of Caribbean coral reefs. In April 2012 an outbreak of Sponge Orange Band (SOB) Disease occurred in Southeast Florida, USA. This study provides one of the most extensive profiles of healthy and SOB-associated microbial communities within Xestospongia muta to date with implications of a possible polymicrobial origin for SOB.

Biome: root:Host-associated:Porifera
Prokaryotic community analysis of the marine sponges Xestospongia muta and Agelas sventres along a depth gradient

In this study we investigated prokaryotic community of marine sponges Xestospongia muta and Agelas sventres along a depth gradient. We employed 16S rRNA gene amplicon sequencing from sponge''s tissue and their cultivable microbial fractions by using the Illumina MiSeq technology.

Biome: root:Host-associated:Porifera
Coral Reef Biotopes Metagenome_M

In the present study, microbial communities of sponges, Sediments and Seawater inhabiting coral reef ecosystems were investigated using barcoded pyrosequencing of 16S rRNA gene amplicons. Our main goals were to compare the bacterial and archaeal richness and composition of two sponge species, sediment and seawater inhabiting coral reef systems. FLX 454 titanium pyrosequencing study. Note that the sequences submitted are raw sequences prior to any analysis and thus contain short sequences, poor quality sequences and chimera. These will need to be filtered out using, e.g., using qiime scripts such as split_libraries and pick_otus with the usearch_ref argument, which will provide a chimera check and filter out poor quality sequences..

Biome: root:Host-associated:Porifera
Bacterial community diversity associated with apple replant diseases

To investigate the effects of soil disinfection treatments on the bacterial community composition and diversity adhering to the apple roots

Biome: root:Host-associated:Plants:Root
Potato rhizosphere Metagenome

The goal is to study the diversity of potato-associated bacteria in the Central Andean Highlands

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Root microbiome Targeted Locus (Loci)

Procaryotes are known to have a role in the establishment of ectomycorrhizal symbiosis. Our goal was to decribe the structure of fungal and bacterial communities associated to ectomycorrhizosphere/rhizosphere and the surrounding bulk soil of truffle-inoculated seedlings.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Mulberry surface soil Targeted Locus (Loci)

A survey of bacterial community in mulberry surface soil

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Soil sample

A field study was conducted to compare bacterial communities of rhizosheaths of wheat grown under wheat-cotton and wheat-rice rotation and to study the effects of PGPB inoculation.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Apple rhizosphere soil Metagenome

Pyrosequencing was used to charicterize the bacteria community change of apple rhizosphere under replant and new plant condition to reveal the mechanism of apple replant disease in Beijing.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Rhizosphere soil Metagenome

Healthy and bacterial wilted tomato plants rhizosphere soil

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Sugar beet rhizosphere microbiome Targeted Locus (Loci)

Study to reveal the diversity of bacteria in the rhizosphere of wild sugar beets in their natural habitat and of commercial sugar beet cultivars in natural and standard soil

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Bamboo soil bacterial community with different elevation Metagenome

To understand what trend of bacterial structure and diversity in bamboo soils across elevations

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Rhizosphere soil sample Targeted Locus (Loci)

Comparing microbial Communities in the Soil Rhizosphere of Six Plant Species in an Alpine Meadow on the Qinghai-Tibet Plateau

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Water melon soil Targeted Locus (Loci)

Microbial community in water melon rhizosphere after grafting

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Soils planted Panax notoginseng

To study on the role of microorganisms in soils to the replant disease of Panax notoginseng.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Plant root microbiome

Due to the long durations spent inside by many humans, indoor air quality has become a growing concern. Biofiltration has emerged as a potential mechanism to clean the indoor air of harmful volatile organic compounds (VOCs), which are usually at higher concentrations indoors than outdoors. Root-associated microbes are thought to drive the functioning of plant-based biofilters, or biowalls, converting VOCs into biomass, energy, and carbon dioxide. But little is known about the root communities of such artificially grown plants, how or whether they differ from those grown in soil, and whether any changes in composition are driven by VOCs. In this study, we investigate how bacterial communities on biofilter plant roots change over time and in response to VOC exposure. Through analyses of 16S rRNA amplicon sequence libraries, we compare root communities from soil-grown plants versus those from two biowalls, while also comparing communities from roots exposed to clean- versus VOC-laden- air in a laboratory biofiltration system. Results show differences in bacterial communities between soil- versus biowall-grown plants, and between those from between clean air versus VOC exposed plant roots. Biowall-grown and VOC-exposed roots both harbored enriched levels of bacteria from the genus Hyphomicrobium. Given their known capacities to break down aromatic and halogenated compounds, we hypothesize these bacteria to be important VOC-degraders. While different strains of Hyphomicrobium proliferated in the two studied biowalls and our lab experiment, strains were shared across plant species suggesting that a wide range of ornamental houseplants harbor similar microbes of potential use in living biofilters.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
SEPTANTE Targeted Locus (Loci)

The consequences of a variable carbon bias on soil bacterial populations were investigated in artificial exudation system. An artificial exudation system was set up in which octopine was brought along with other carbon compounds at four different ratios. rrs-amplicon pyrosequencing analyses were performed to reveal the impact on the structure and diversity of bacterial community.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Banana rhizosphere soil Targeted Locus (Loci)

16S rRNA amplicons of diseased and disease suppressive soil and soil after biological remediation.

Biome: root:Host-associated:Plants:Rhizosphere:Soil
paddy soil Genome sequencing

Paddy soil Genome sequencing

Biome: root:Host-associated:Plants:Rhizosphere:Soil
Rhizobiome of Northeastern Atlantic seagrasses

This project aimed at revealing the microbial diversity associated with the rhizosphere of the seagrasses Zostera marina, Z. noltii and Cymodocea nodosa, through the sequencing of 16S rRNA amplicons using Illumina Miseq-platform. The rhizobiomes of these seagrasses were compared within one sampling site, and between two different geographical locations  Portugal and France. Besides, we evaluated differences between the rhizobiomes and their surrounding environment (i.e., bulk sediments and seawater). This study improves the understanding of microbial processes in the rhizosphere of seagrasses, highlighting the importance of bacteria involved in the sulfur cycle for the fitness of the plants.

Biome: root:Host-associated:Plants:Rhizosphere
Soil Metagenome

A high-protein soybean cultivar was grown in three different fields that were continuously cropped for 1, 2, and 3 years. By analyzing the diversity of fungi in rhizosphere soil during the branching period of soybeans planted in these three fields, and comparing the diversity of fungi in rhizosphere soil during periods of high incidence of root rot disease, the dominant fungi responsible for soybean root rot disease could be identified.

Biome: root:Host-associated:Plants:Rhizosphere
willow rhizosphere Metagenome

Plants interact closely with microbes, which are partly responsible for plant growth, health and adaptation to stressful environments. Engineering the plant-associated microbiome could improve plants survival and performance in stressful environments such as contaminated soils. Here, willow cuttings were planted into highly petroleum-contaminated soils that had been gamma-irradiated and subjected to one of four treatments: inoculation with rhizosphere soil from a willow that grew well (LA) or sub-optimally (SM) in highly contaminated soils or with bulk soil in which the planted willow had died (DE) or no inoculation (CO). Samples were taken from the starting inoculum, at the beginning of the experiment (T0) and after 100 days of growth (TF). Short hypervariable regions of archaeal/bacterial 16S rRNA genes and the fungal ITS region were amplified from soil DNA extracts and sequenced on the Illumina MiSeq. Willow growth was monitored throughout the experiment, and plant biomass was measured at TF. CO willows were significantly smaller throughout the experiment, while DE willows were the largest at TF. Microbiomes of different treatments was divergent at T0, but for most samples, had converged on highly similar communities by TF. Willow biomass was more strongly linked to overall microbial community structure at T0 than to microbial community structure at TF, and the relative abundance of many genera at T0 was significantly correlated to final willow root and shoot biomass. Although microbial communities had mostly converged at TF, lasting differences in willow growth were observed, probably linked to differences in T0 microbial communities.

Biome: root:Host-associated:Plants:Rhizosphere
rhizosphere soil named MPt17+Pt2, MPt17, Pt2 and CK Metagenome

A 454 pyrosequencing analysis on the bacterial communities from four selected soils was presented. The results showed that the dominant bacterial communities of the soil samples were similar. A total of 11,911 OTUs with 80,772 valid reads were identified, which could be assigned into 29 different phyla, 147 families and 279 genera.

Biome: root:Host-associated:Plants:Rhizosphere
Monsoon bacterial diversity of pneumatophore-rhizosphere of Avicennia Marina in vellar estuarine Metagenome

Pneumatophore-rhizosphere soil of Avicennia Marina in vellar estuarine

Biome: root:Host-associated:Plants:Rhizosphere
Wetland peat Targeted Locus (Loci)

Restoration of wetlands has a great potential to reverse land subsidence on peat islands previously drained for agriculture, thereby reducing risk of levee failure. In addition, the high primary production and slow decomposition rates found in restored wetlands may result in a net atmospheric CO2 sequestration. However, one major concern is the emission of CH4 that could potentially offset the carbon captured due to primary production. In wetland ecosystems, microorganisms play key roles in governing greenhouse gas flux. In this study, we collected belowground samples from a restored wetland largely vegetated with cattails and tules from a pilot-scale restoration project. We selected sites that exhibited gradients in physicochemical conditions, peat accretion rates and CH4 emission. From each site, we collected samples from the bulk peat, cattail rhizomes and tule rhizomes. Pyrosequencing of amplified V8 regions of 16S rRNA genes was used to generate microbial community profiles in order to to identify community patterns and indicator species that are associated with biogeochemistry and CH4 emission along the gradients.

Biome: root:Host-associated:Plants:Rhizosphere
Soil Metagenome

Mechanisms of microbes-mediated carbon and nitrogen cycles in the rhizosphere soil under long-term fertilization practices

Biome: root:Host-associated:Plants:Rhizosphere
Microbial diversity in rhizosphere soil

Thanks to next generation sequencing techniques such as amplicon pyrosequencing, microbial diversity can be studied to an unprecedented degree. Given the importance of soil and especially of the rhizosphere for plant growth and biogeochemical cycles, the aim of the study is to determine the microbial diversity present in rhizosphere soil.  Rhizosphere soil associated with Thymus zygis plants from the Sierra Nevada National Park in Southern Spain.

Biome: root:Host-associated:Plants:Rhizosphere
Apple rhizosphere soil Metagenome

Application of compost at different rates on apple rhizosphere soil was studied, and pyrosequencing was employed to characterize the bacterial community structure.

Biome: root:Host-associated:Plants:Rhizosphere
Bacterial community of rhizosphere soil in Longgang Longterm Fertilization Metagenome

Bacterial community of rhizosphere soil in 9 different fertilization treatments for 5 years was measured with 454-sequencing.

Biome: root:Host-associated:Plants:Rhizosphere
Rhizosphere bacterial community 16S sequencing from field grown wheat

We sequenced bacterial communities both loosely and tightly bound to wheat roots growing in the field. We studied changes in community compostition over different plant stages, soil types, genotypes and rotations. Plasticity in the rhizosphere microbiome offers promise for beneficially manipulating the soil ecology of intense cereal systems.

Biome: root:Host-associated:Plants:Rhizosphere
Sansui tobacco rhizosphere Metagenome

Bacterial community from tobacco rhizosphere soil in Sansui.  Tobacco rhizosphere soil were collected in 2011 at Sansui county.

Biome: root:Host-associated:Plants:Rhizosphere
Laguna Brava Targeted Locus (Loci)

To study the diversity of AM fungal associated to vegetation adapted to extreme environmental conditions in high Andean wetlands.  AMF from rhizospheric soil and alophyte plants.

Biome: root:Host-associated:Plants:Rhizosphere
Pampa ondulada Targeted Locus (Loci)

Impact of agronomic management of soil on arbuscular mycorrhizal fungal diversity.  Pampa ondulada soybean rhzosphere AMF.

Biome: root:Host-associated:Plants:Rhizosphere
wheat associated microbiome Raw sequence reads

This study is about testing an artificially elevated JA signalling on the wheat associated microbial community structure

Biome: root:Host-associated:Plants
Tomato phyllosphere Metagenome

Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato).  Targeted and whole metagenomes from different organs of the tomato plant.

Biome: root:Host-associated:Plants:Phylloplane
Phyllosphere bacterial community of Wolffia australiana Targeted Locus (Loci)

We aimed at analyzing the composition and structure of the phyllosphere bacterial communities of W. australiana and addressed two major questions: (1) what is the specialty of the bacterial community in the phyllosphere of floating macrophytes; (2) what controls the bacterial communities of the macrophyte phyllosphere in paddy soils.  16S rDNA V3 section of bacteria associated with phyllosphere of Wolffia australiana, water, and soil in paddy-soil ecosystem.

Biome: root:Host-associated:Plants
oyster metagenome Targeted loci environmental

We studied microbial communities related to Pacific oysters in Puget Sound estuarine of Washington State, USA.

Biome: root:Host-associated:Mollusca
Identification of bovine respiratory disease complex associated bacteria using a 16S rRNA gene amplicon sequencing assay

Bacteria, many of which are normal flora of the bovine upper respiratory tract, can cause and exacerbate virus or stess induced bovine respiratory disease complex (BRDC). The objective of this study was to develop a single universal assay, based on high throughput phylogenetic (16S ribosomal RNA (rRNA) gene) PCR amplicon sequencing, with potential to accurately identify and differentiate bacteria in post-mortem tissue samples harvested from fatal BRDC cases.

Biome: root:Host-associated:Mammals:Respiratory system:Pulmonary system
Bos taurus breed:Angus Hereford Targeted Locus (Loci)

Nasopharyngeal microbiota of feedlot cattle exposed to commingling and auction market stress.

Biome: root:Host-associated:Mammals:Respiratory system:Nasopharyngeal
Bos taurus Targeted Locus (Loci)

Monitoring the nasopharyngeal microbiota in feedlot cattle from entry to exit

Biome: root:Host-associated:Mammals:Respiratory system:Nasopharyngeal
Characterization of the nasopharyngeal microbiota in naturally occurring respiratory disease in feedlot cattle

Bovine respiratory disease (BRD) is a major cause of morbidity, mortality and economic loss in the US cattle industry. In view of the importance of this disease complex, and the need to reduce antimicrobial use in food producing animals, there is growing interest in developing novel strategies to enhance host immune defenses against respiratory pathogens. The cooperative interactions between microbes and their hosts have been recognized for years, and there is increasing evidence that mucosal bacterial populations act, not only as a reservoir of potential pathogens, but also in regulating local and systemic immune homeostasis through a complex cross talk with the epithelium, local immune system and mucosal neuronal pathways. In this study we used culture-independent techniques to characterize the nasopharyngeal microbiome of cattle during the initial processing phase in the commercial feedlot. In addition, we compared the dynamics of change in these microbial communities, between clinically healthy calves and those that develop BRD within the first month of entry in to the feedlot.

Biome: root:Host-associated:Mammals:Respiratory system:Nasopharyngeal
Characterization of nasopharyngeal microbiotas as the source of lung microbiotas in clinically healthy feedlot cattle

Efficient characterization of airway microbiota is expected to provide insights into the pathophysiology of respiratory diseases. No studies have examined the relationships between bacterial communities along the upper and lower respiratory tract in clinically healthy feedlot cattle using next generation sequencing. Therefore, our objective was to characterize the composition and structure of the nasopharyngeal microbiota as the source of lung microbiotas in clinically healthy feedlot cattle.

Biome: root:Host-associated:Mammals:Respiratory system:Nasopharyngeal
Respiratory microbiome in feedlot cattle Raw sequence reads

The primary objective of this study was to apply next generation techniques to characterize the composition and structure of the respiratory tract microbial communities in clinically healthy feedlot cattle.

Biome: root:Host-associated:Mammals:Respiratory system
Mesocricetus auratus Metagenome

Intestinal and biliary microbiome of the hamster (Syrian Golden Hamster) infected with the liver fluke, Opisthorchis viverrini.

Biome: root:Host-associated:Mammals:Gastrointestinal tract:Intestine
Sheep rumen microbiome

Rumen metagenome and metatranscriptome sequencing from low and high methane producing sheep.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Metagonimus yokogawai infected mouse cecal microbiome

We performed a 16S rRNA amplicon analysis to investigate changes in the gut microbiome due to M. yokogawai infection in ICR mice using high-throughput sequencing technology.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
The Caprine Abomasal Microbiome

Haemonchus contortus is one of the most injurious helminth parasite for small ruminants. In this study, we characterized the impact of H. contortus infection on the caprine abomasal microbiome.

Biome: root:Host-associated:Mammals:Digestive system
Gut microbiome in rats treated with [saline or helminths], [PBS or E. coli], and [PBS or LPS]

We need a description here.

Biome: root:Host-associated:Mammals:Digestive system
invertebrate gut metagenome Raw sequence reads

comparison of intestinal microbiota composition of sea cucumber in two habitats

Biome: root:Host-associated:Invertebrates:Echinodermata