SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Coral-associated bacteria demonstrate phylosymbiosis and cophylogeny

Scleractinian corals’ microbial symbionts influence host health, yet how these coral microbiomes assembled over evolution is not well understood. We survey bacterial and archaeal communities in phylogenetically diverse Australian corals representing more than 425 million years of diversification. We show that corals exhibit anatomical compartmentalization of the microbiome such that the coral surface mucus layer, tissue, and skeleton microbiomes show distinct modern microbial ecology and evolutionary assembly. In corals, these compartments differ greatly in microbial community composition, richness, and response to host vs. environmental drivers. We also find evidence of coral-microbe phylosymbiosis, in which coral microbiome composition and richness reflects coral phylogeny. Surprisingly, the coral skeleton represents the most biodiverse coral microbiome, and also shows the strongest evidence of phylosymbiosis. Together these results trace microbial symbiosis across anatomy during the evolution of a basal animal lineage.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Coral reef
Human gut microbiome viewed across age and geography

Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.

Biome: root:Host-associated:Human:Digestive system:Large intestine
Characterization of bacterial communities in soil under no-tillage practices with contrasting fertilization strategies

Long term experiment in Argentina.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
16S rRNA gene-based analysis of soil prokaryotic communities inhabiting fields of the Mezquital Valley, Mexico

Central objective of this study is to analyze the diversity and composition of prokaryotic communities present in fields of the Mezquital Valley, Mexico.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Natural saline soil, Sicily (Italy) Targeted Locus (Loci)

16S rRNA analysis to inspect distribution of different bacterial groups as a function of spatial gradients of soil salinity and pH

Biome: root:Environmental:Terrestrial:Soil
Northern Gulf of Mexico Hypoxia can Alter Sediment Communities of Nitrifying Archaea

The sediments were obtained from station Z02 located at the 20 m isobath south of Terrebonne Bay in the northern Gulf of Mexico (latitude 28.875oN; longitude 90.428oW). The cores were collected in April and September 2006.

Biome: root:Environmental:Aquatic:Marine:Sediment
Forest Soil Metagenome - Eucalyptus urograndis and Acacia mangium

Forest soil under three different compositions: 1 - Eucalyptus urograndis monoculture 2 - Acacia mangium monoculture 3 - Mixed plantation

Biome: root:Environmental:Terrestrial:Soil
22V-SMAR-TVG10 Targeted Locus (Loci)

Bacterial Diversity of Deep-sea Environment

Biome: root:Environmental:Aquatic:Marine:Sediment
Ocean Targeted Locus (Loci)

The cyanobacteria Prochlorococcus and Synechococcus are important marine primary producers. We explored their distributions and co-variance along a physico-chemical gradient from coastal to open ocean waters in the Northeastern Pacific Ocean. Based on 16S rRNA gene sequencing we identified two new clades of Synechococcus, EPC1 and EPC2, and delineated an interannual pattern in a dynamic transition zone where upwelled and eastern boundary current waters mix. In years when more oligotrophic water intrudes further inshore Prochlorococcus HLI and LLI are more abundant, while under stronger upwelling Synechococcus I and IV dominate. However, contributions of some cyanobacterial clades are proportionally relatively constant, e.g., Synechococcus EPC2. In addition to supporting observations that Prochlorococcus LLI thrive at higher irradiances than other LL taxa, the results suggest LLI tolerate lower temperatures than reported. The phylogenetic precision of our analytical approach and depth of barcoded pyrosequencing also allowed us to detect clades at low abundance in unexpected places. For example, Prochlorococcus at the coast, and sequences related to freshwater Cyanobium spp. in the open ocean, although it remains unclear whether these come from resident or advected cells. Our study enhances understanding of cyanobacterial distributions by applying state-of-the-art phylogenetic analysis tools to an ecologically important eastern boundary system.

Biome: root:Environmental:Aquatic:Marine
EMG produced TPA metagenomics assembly of PRJEB62473 data set (The INTEGRATE project).

The Third Party Annotation (TPA)  assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB62473, and was assembled with metaspades v3.15.3. This project includes samples from the following biomes: root:Host-associated:Human:Digestive system:Large intestine:Fecal.

Biome: root:Host-associated:Human:Digestive system:Large intestine:Fecal
ADDOMEx Tier 3 Experiments: Mesocosm Si with Gulf of Mexico coastal waters

Here we describe microbial community dynamics in the Mesocosm-Si experiment. Using 16S rRNA gene sequencing of filtered water samples collected every 24 hours from the mesocosm treatments, we characterized community membership and structure to determine how the mesocosm communities responded to a passively dosed (via silicone tubing) water accomdated fraction of oil.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Oil-contaminated
Complex Heteropolysaccharide Enriched Soils Targeted Locus (Loci)

Stable-isotope-probing of two soils using two complex heteropolysaccharides as a substrate.

Biome: root:Environmental:Terrestrial:Soil
Otumba arable soil Metagenome

Soil microbial biomass has been determined since the mid 1970’s by the chloroform fumigation incubation technique as proposed by Jenkinson and Powlson (1976). The microbial biomass C can be determined by subtracting the CO2 emitted from an unfumigated soil (mineralization of soil organic matter) from that emitted from a chloroform fumigated inoculated soil (mineralization of soil organic matter and killed soil microorganisms) and dividing the difference by a proportionality factor (kC 1⁄4 0.45). The question remained which microorganisms recolonized a fumigated soil. An arable soil was fumigated for one day with ethanol-free chloroform or left unfumigated and incubated aerobically after removal of the chloroform for 10 days. The bacterial population structures were determined in the fumigated and unfumigated soil after 0, 1, 5 and 10 days by means of 454 pyrosequencing of the 16S rRNA gene.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Haerbin black soil Genome sequencing

Black soil different fertilizer

Biome: root:Environmental:Terrestrial:Soil
Plasma soil pretreatment trail

Plasma is the fourth state of matter and it can be generated by coupling sufficient quantities of energy to a gas to induce ionization. Plasma treatment is known for its antimicrobial properties by generating agents such as reactive oxygen and nitrogen species to kill and reduce proliferation of various microorganisms. Here, we examine an effect of plasma exposure on soil samples. Various exposure times and plasma properties were tested. Microbial communities of soil samples were examined by sequencing ribosomal 16S gene and comparing abundance of different microbial groups in treated and non-treated samples.

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Standard filtration practices significantly distort planktonic microbial diversity estimates

Filtration is the standard method for isolating planktonic microbial biomass for analysis. It is unclear how the taxonomic composition of biomass on a filter changes as a function of filtered water volume, potentially due to filter clogging. Using seawater from a marine oxygen minimum zone, we conducted experiments to quantify the 16S rRNA gene composition of biomass on a prefilter (GF/A, 1.6 um pore size) and a downstream collection filter (Sterivex, 0.2 um) over a range of typical collection volumes, from 50 to 5000 ml. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences affiliated with Vibrionales decreased from ~40-60% of the prefilter datasets at low volumes (50-500 ml) to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Taxa shown previously to be associated with marine particles, including diverse members of the Deltaproteobacteria, Planctomycetes and Bacteroidetes, were among those showing the greatest increase with filter volume (4 to 27-fold). Metrics of taxon richness (97% sequence clusters) also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise serious concerns for studies using filter fractionation to separate biomass for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.

Biome: root:Environmental:Aquatic:Marine
Bacterial diversity in agricultural soils

Barcoded amplicon sequencing targeting V4 regions of 16S gene from uncultured soil bacteria.

Biome: root:Environmental:Terrestrial:Soil
Marine metagenome ICM_BSP

Seasonal dynamics of bacterioplankton communities in the Baltic Sea Proper.

Biome: root:Environmental:Aquatic:Marine
Marine metagenome ICM_ABR

Diversity of active microbial communities in surface seawaters along a north-south transect in the South Pacific Ocean.

Biome: root:Environmental:Aquatic:Marine
Prokaryotic community structure in the deep Southwest Indian Ocean with an emphasis on actinobacteria Targeted Locus (Loci)

Knowledge about the biodiversity extent and biogeography of deep-sea microorganisms is far from adequate. Due to its remote location, the related investigations of the Southwest Indian Ocean (SWIR) remaine extremely difficult and the microbial diversity at the SWIR has rarely been studied. Only two studies got limited numbers of 16S rRNA gene sequences, and much more in-depth sequencing efforts to evaluate the abundance and diversity of prokaryotes at the SWIR are still needed. In this study, pyrosequencing was used to investigate the community structure and biogeography of prokaryotes, especially actinobacteria, in the deep SWIR. It also identified the factors in contributing to the distribution of the prokaryotes and actinobacteria, the historical contingencies, contemporary environmental factors, or both? The results would provide further insights on the prokaryotic, especially actinobacterial community structure at the SWIR and help to understand the underling mechanisms of the microbial distribution in the deep ocean. To our knowledge, this is the first report on the biodiversity and biogeography of actinobacteria at the SWIR.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Sediment
Soil bacterial diversity is associated with human population density in urban greenspaces

Urban greenspaces form a vital part of the urban ecosystem and provide an extensive array of ecosystem services, including pollutant degradation, water management, carbon maintenance, and nutrient cycling. However, while the soil microbiota in these ecosystems are essential to these services they remain under-characterized. Here we aimed to determine whether turf grass soil bacterial communities were associated with human population density across a range of greenspaces in parks, streets, and residential areas across a major urban area. Results showed that bacterial diversity was significantly positively correlated with population density within the immediate vicinity of the sampled areas; and species diversity was greater in park and street soils, when compared with residential zones. Population density and greenspace type (park vs street vs residential area) also associated with the composition and structure of the bacterial community. Edaphic properties, including pH, moisture and texture, were also significantly correlated with microbial composition and structure. Co-occurrence network analysis revealed that microbial guilds in urban soils were well connected. Soil moisture and texture together with population density and greenspace type showed strong correlations with several network topological features including assortativity degree, edge density, average path, average betweenness and closeness. These results indicate that changes in urban demographics, as well as the changes in land-use may influence the diversity and structure of urban soil microbial communities. As urbanization is rapidly growing across the planet, understanding the consequences of different urban zoning on soil microbiota represents an unmet need.

Biome: root:Environmental:Terrestrial:Soil
Colonization patterns of soil microbial communities in the Atacama Desert

The Atacama Desert is one of the driest deserts in the world and its soil characterized by extremely low moisture, organic carbon content, and oxidizing conditions has been considered to be at the dry limit for life. We collected soil samples from 3 geographic locations in the hyper-arid zone of the Atacama Desert, and from 3 locations along a North-South transect of increasing rainfall, to identify what factors might shape the diversity of its soil microbiome. Analyses of non-culture based, high throughput DNA sequence data revealed that communities from the 6 geographic locations were structurally and phylogenetically distinct (ANOVA test for observed OTU0.03, p<0.001; UniFrac distances) and that communities from locations in the hyper-arid zone displayed the lowest levels of diversity. We found bacterial taxa similar to those found in other arid soil communities with an abundance of Rubrobacterales, Actinomycetales, Acidimicrobiales, and a number of families from the Thermoleophilia. The extremely low abundance of Firmicutes, the phylum that comprises most sporulating bacteria, indicated that most bacteria in the soil were in the form of vegetative cells. No archaea were found in an of the soil samples. Integrating molecular data with climate and soil geochemistry, we found that air relative humidity (RH) and soil conductivity significantly correlated with microbial communities diversity metrics (least square linear regression for observed OTU0.03 and air RH and soil conductivity, p<0.001; UniFrac PCoA spearman’s correlation for air RH and soil conductivity, p<0.0001), indicating that water availability and salt content are key factors in shaping the Atacama soil microbiome. Mineralization studies showed communities actively metabolizing in all soil samples with increased rates in soils from the southern locations. These findings suggest that over geological time, and due to rare rain events, physicochemical factors potentially played a major role in selecting microorganisms that are most adapted to extreme desiccating conditions.

Biome: root:Environmental:Terrestrial:Soil:Desert
Archaeal diversity of surface seawater (A3,A5,G3,G5) Targeted Locus (Loci)

To investigate the archaeal diversity of sea water from Greatwall cove and Ardley cove, Fildes Peninsula, four surface water samples were collected during the 29th Chinese Antarctic scientific expedition in 2013.

Biome: root:Environmental:Aquatic:Marine
16S amplicon based soil and leaf microbiome survey in Hungarian vineyards

Seven Hungarian wine regions have been sampled for leaf and 20cm deep soil samples from the same plants. All vineyards are of different soil types and grape cultivars. Total DNA has been extracted and 16S amplicon sequencing has been applied to the samples.

Biome: root:Host-associated:Plants
Southern Ocean

Southern Ocean bacterioplankton community

Biome: root:Environmental:Aquatic:Marine:Oceanic
Investigation of the suitability of Remane’s species minimum concept in a Mediterranean transitional waters ecosystem

The aim of the present study was to investigate the sediment bacterial diversity of a transect river-lagoon-open sea, i.e. from freshwater to marine, occurring at Amvrakikos Gulf (Ionian Sea, Western Greece) and to test whether it follows the Remane's concept, both in terms of species composition but also of functionality. Remane’s Artenminimum (“species minimum”) concept was developed for the Baltic Sea, the world’s largest semi-enclosed brackish water body with a unique permanent salinity gradient. It argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum, which occurs at salinity 5 to 8, because the number of brackish specialists does not compensate for the decline in marine and freshwater diversity. DNA was extracted from sediment samples collected in situ from six stations along the aforementioned transect and sequenced for the 16S rRNA gene.

Biome: root:Environmental:Aquatic:Marine:Oceanic:Benthic
Composition and Genetic Diversity of Microbial Communities in Subtropical Coastal Wetland Sediments

This study aimed to examine the composition and genetic diversity of bacterial, archaeal and fungal communities in surface sediments of a subtropical coastal wetland.

Biome: root:Environmental:Aquatic:Freshwater:Wetlands:Sediment
CARBOM cruise 2013 flow cytometry sorted phytoplankton


Biome: root:Environmental:Aquatic:Marine
Dorrestein_3D_metabolic_map

Skin samples from human 3D metabolic map

Biome: root:Host-associated:Human:Skin
Bacterial community composition of divergent soil habitats in a polar desert Metagenome

A 16S rDNA sequencing approach was used to examine the differences in diversity and community composition between three divergent soil habitats of the McMurdo Dry Valleys, Antarctica.

Biome: root:Environmental:Terrestrial:Soil:Desert
Microbial communities associated with Juncus roemerianus and Spartina alterniflora vegetated sediments in Louisiana saltmarshes

"Saltmarshes are typically dominated by perennial grasses with large underground rhizome systems that can change local sediment conditions and be important in shaping the sediment microbial community. Factors that control plant zonation in saltmarshes (e.g. salinity) are also likely to influence the microbial community, but little is known as to whether microbial communities share distribution patterns with plants in these systems. To determine the extent to which microbial assemblages are influenced by saltmarsh plant communities, as well as to examine patterns in microbial community structure at local and regional scales, we sampled sediments at three saltmarshes in Louisiana, USA. All three systems exhibit a patchy distribution of Juncus roemerianus stands within a Spartina alterniflora marsh. Sediment samples were collected from the interior of several J. roemerianus stands as well as from the S. alterniflora matrix. Samples were assayed for extracellular enzyme activity and DNA extracted to determine microbial community composition. Denaturing gradient gel electrophoresis of rRNA gene fragments was used to determine regional patterns in bacterial, archaeal, and fungal assemblages, while Illumina sequencing was used to examine local, vegetation-driven, patterns in community structure at one site. Both enzyme activity and microbial community structure were primarily influenced by regional site. Within individual saltmarshes, bacterial and archaeal communities differed between J. roemerianus and S. alterniflora vegetated sediments, while fungal communities did not. These results highlight the importance of the plant community in shaping the sediment microbial community in saltmarshes, but also demonstrate that regional scale factors are at least as important."

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Salt marsh
Marine metagenome ICM_WBS

Pyrosequencing as a paleometagenomical tool offers a window into Holocene plankton, littoral fauna, and terrestrial vegetation in the Black Sea.

Biome: root:Environmental:Aquatic:Marine
Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing
                in Naples Bay

Haptophytes are a key phylum of marine protists, including ~300
                described morphospecies and 80 morphogenera. We used 454-pyrosequencing on large
                subunit ribosomal DNA (LSU rDNA) fragments to assess the diversity from size
                fractioned plankton samples collected in the Bay of Naples. One group-specific
                primer set targeting an overlapping region of the LSU rDNA D1/D2 region was used to
                amplify Haptophyte sequences from nucleic acid extracts (total DNA or RNA) of two
                size fractions (0.8-3 or 3-20 μm) and two sampling depths (subsurface, at 1m, or
                deep-chlorophyll-maximum (DCM) at 23m).

Biome: root:Environmental:Aquatic:Marine:Coastal
Soil microbiome CENEB Metagenome

This project investigated three agricultural practices, i.e. different raised bed planting systems (tilled raised beds vs permanent raised beds), different levels of residue retention (full, partial and no retention of crop residue) and two application rates of inorganic N fertilizer (0 or 300 kg N ha-1), at a 20-year long-term field experiment cultivated with wheat (Triticum spp. L.) and maize (Zea mays L.). This study included also the effect of residue burning

Biome: root:Environmental:Terrestrial:Soil:Agricultural
Plant niche rather than soil or species shapes the microbiota

Plant niche rather than soil or species shapes the microbiota. Plants are colonised in 2 weeks time and this process is continuous.

Biome: root:Environmental:Terrestrial:Soil
Soil bacteria on root-knot nematodes and in bulk soil, 16S rRNA genes

Bacterial communities associated with juveniles of the plant-parasitic nematode Meloidogyne hapla in three arable soils of differing supressiveness

Biome: root:Host-associated
Bacterial community during the Austral summer in the Amundsen Sea Polynya, Antarctica

454-pyrosequencing (16S rDNA) dataset of bacterial community in the Amundsen Sea Polynya from the ASPIRE research expedition in Antarctica during the Austral summer 2010-2011.  In situ and experimental incubation samples are included in this dataset.

Biome: root:Environmental:Aquatic:Marine
Bacterial Biogeography of Coastal Water in the Northern East China Sea

The Northern East China Sea is a unique marine ecosystem with multiple environmental gradients (e.g. salinity, pH, and nutrients) along northwest to southeast, forming a horn-shaped pattern with Hangzhou Bay as the tip. This study applied 16S amplicon high-throughput sequencing with Illumina MiSeq technique and multiple statistical analyses to quantitatively reveal the relative contributions of local environmental conditions and regional spatial factors in shaping bacterial biogeographic pattern of coastal water using 95 surface water samples collected from 95 sites across 8 coastal zones, from Hangzhou Bay (northwest) to outside of Sanmen Bay (southeast), in the Northern East China Sea across a > 200 km scale.

Biome: root:Environmental:Aquatic:Marine:Coastal
Red Sea microbial plankton Raw sequence reads

To examine the diversity of the microbial plankton in the northern and southern extremes of the Red Sea.

Biome: root:Environmental:Aquatic:Marine