SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Bacterial diversity across a strong vertical contrast ecosystem; a salt wedge karstic estuary

Highly stratified karstic estuaries (salt-wedge estuaries) are characterized by a strong gradient of salinity and other environmental parameters. The bacterial diversity in many estuaries has been documented but no information is available about the diversity of bacteria in Mediterranean karstic estuaries. A combination of 454 pyrosequencing of the 16S rRNA gene and catalyzed reporter deposition-fluorescence in situ hybridization techniques were used to estimate the bacterial diversity across the karstic Krka River Estuary in February and July 2013. The bacterial community at the OTU level showed stronger seasonal, rather than spatial, variation that is caused by the phytoplankton bloom in February. The alphaproteobacterial SAR11 clade was an important group whose abundance showed a decrease toward the low salinity riverine water. Higher relative abundance of the SAR11 clade was detected in July when more oligotrophic conditions were observed. Roseobacter responded to the phytoplankton bloom in February increasing its abundance in the water layer with higher phytoplankton biomass. Cyanobacteria showed substantial seasonal change being an important primary producer in July during lower nutrient conditions. Actinobacteria and Betaproteobacteria were characteristic for the freshwaters layer of the estuary with Actinobacteria showing strong seasonal change and higher abundance in July. Bacteroidetes and Gammaproteobacteria also showed seasonal differences with higher abundances in February during the phytoplankton bloom in the inner part of the estuary. The bacterial community in the Krka River Estuary showed pronounced seasonal changes, due to the phytoplankton bloom observed in February, and vertical changes, as a result of a stable, sharp halocline that is characterizing this type of estuaries.

Biome: root:Environmental:Aquatic:Marine:Intertidal zone:Estuary
Metagenomic study of the microbial genes abundance in treated palm oil mill effluent

Metagenomic study of the microbial genes abundance in treated palm oil mill effluent

Biome: root:Engineered:Wastewater:Nutrient removal:Dissolved organics (anaerobic)
Ribosomal tag pyrosequencing of DNA and RNA reveals  'rare' taxa with high protein synthesis potential in the sediment of a hypersaline lake in Western Australia

Ribosomal tag pyrosequencing of DNA and RNA reveals  'rare' taxa with high protein synthesis potential in the sediment of a hypersaline lake in Western Australia

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Hypersaline:Sediment
DRY AND RAINY SEASONS REFLECT DIFFERENT SCENARIOS IN THE BACTERIAL COMMUNITY OF THE RHIZOSPHERE OF ENDEMIC CACTACEAE

We applied multiplexed barcoded 16S ribosomal RNA gene pyrosequencing to survey the diversity and distribution of bacteria of the rizhosphere of endemic cactaceae

Biome: root:Host-associated:Plants:Rhizosphere
Pyrosequencing of biofilm 16S ribosomal RNA (rRNA) supported on various materials with a wastewater inoculum.

The aim of this study was to provide new knowledge of bacterial community structure and composition found on various types of synthetic and natural support media used in the previous study. This was achieved by applying PCR based 454 pyrosequencing to bio?lm samples obtained from the media surfaces from laboratory scale, temperature-controlled experimental facility of the aerobic reactors. Then analyzed the sequences using bioinformatics tools. In particular we sought new understanding of the in?uence of different temperature conditions and media types on the bio?lm composition responsible for wastewater treatment. To the best of our knowledge, this study is the first application of pyrosequencing to characterize and compare biofilm samples on different types of media. Such information is important for the best operation and management of the FBRs in the future. It will prove very helpful in the selection of proper media having tendency of carrying diverse biofilm for respective wastewater treatment in the areas with extreme temperature conditions.

Biome: root:Engineered:Bioreactor:Continuous culture
Microbial diversity and community respiration in freshwater sediments influenced by artificial light at night

An increasing proportion of the Earth?s surface is illuminated at night. In aquatic ecosystems, artificial light at night (ALAN) may influence microbial communities living in the sediments. These communities are highly diverse and play an important role in the global carbon cycle. We combined field and laboratory experiments using sediments from an agricultural drainage system to examine how ALAN affects communities and alters carbon mineral- ization. Two identical light infrastructures were installed parallel to a drainage ditch before the start of the experiment. DNA metabarcoding indicated that both sediment communities were similar. After one was lit for five months (July?December 2012), we observed an increase in photoautotroph abundance (diatoms, Cyanobacteria) in ALAN-exposed sediments. In laboratory incubations mimicking summer and winter (six weeks each), communities in sediments that were exposed to ALAN for 1 year (July 2012?June 2013) showed less overall seasonal change compared with ALAN-naive sediments. Nocturnal community respiration was reduced in ALAN-exposed sedi- ments. In long-term exposed summer-sediments, we observed a shift from negative to positive net ecosystem production. Our results indicate ALAN may alter sediment communities over time, with implications for ecosystem- level functions. It may thus have the potential to transform inland waters to nocturnal carbon sinks.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
Microbial dynamics and biofouling in suspended and attached growth anaerobic membrane bioreactors treating low-strength synthetic wastewater

Two lab-scale anaerobic membrane bioreactors (AnMBRs), one up-flow attached-growth (UA) and another continuously stirred (CSTR), were operated under mesophilic conditions (35 ?C) while treating low-strength synthetic wastewater (800 mg/L COD). Each reactor was attached to both polyvinylidene fluoride (PVDF) and polyethersulfone (PES) microfiltration (MF) membranes concurrently in external cross-flow configuration. Both reactors were upstarted and run under the same operating conditions for multiple biofouling experiments. COD removal rates were similar for both reactors (90-96%). During the first fouling experiment conducted for the CSTR reactor, the PES membrane experienced an increase in transmembrane pressure (TMP) to above 60 kPa within the first 20 days of operation while all other membranes in both reactors experienced more gradual fouling rates. High performance liquid chromatography (HPLC) protein analysis of the soluble extracellular polymeric substances (EPS) of all biofilm samples showed a peak at retention time of 6 min that dominated in size when premature fouling was observed. This peak was also seen consistently in the soluble microbial products (SMP) of the retentate for both reactors. Microbial dynamics in reactor biomasses and in membrane biofilms were monitored using Ion Torrent sequencing targeting 16S rRNA genes. Results showed that presence of syntrophic bacteria and methanogens were higher in attached biomass as compared to suspended biomass while several dominant OTUs closest related to fermentative bacteria were dominant in the suspended biomass of the CSTR. Despite the UA reactors? inherent affinity for attached biomass, methane production rates were roughly 15% higher in the CSTR AnMBR than the UA. Furthermore, several groups of bacteria associates with the phylum Firmicutes were present in the CSTR suspended sludge at high relative abundances only in samples taken close to increases in TMP across the PES membrane, suggesting a possible connection with premature fouling.

Biome: root:Engineered:Bioreactor
MiDAS DNA Extraction and primer choice

Evaluation of the impact of DNA extraction and primer choice on the observed microbial community in activated sludge using 16S rRNA amplicon sequencing.

Biome: root:Engineered:Wastewater:Activated Sludge
MiDAS DNA Extraction metagenomics and metatranscriptomics

Evaluation of the impact of DNA extraction and primer choice on the observed microbial community in activated sludge using metagenomics and metatranscriptomics.

Biome: root:Engineered:Wastewater:Activated Sludge
Metaproteomics of aquatic microbial communities in a deep and stratified estuary

Here we harnessed the power of metaproteomics to assess the metabolic diversity and function of stratified aquatic microbial communities in the deep and expansive Lower St. Lawrence Estuary, located in Eastern Canada. Vertical profiling of the microbial communities through the stratified water column revealed differences in metabolic lifestyles and in carbon and nitrogen processing pathways. In productive surface waters, we identified heterotrophic populations involved in the processing of high and low molecular weight organic matter from both terrestrial (e.g. cellulose and xylose) and marine (e.g. organic compatible osmolytes) sources. In the less productive deep waters, chemosynthetic production coupled to nitrification by MG-I Thaumarchaeota and Nitrospina appeared to be a dominant metabolic strategy. Similar to other studies of the coastal ocean, we identified methanol oxidation proteins originating from the common OM43 marine clade. However, we also identified a novel lineage of methanol-oxidizers specifically in the particle rich bottom (i.e. nepheloid) layer. Membrane transport proteins assigned to the uncultivated MG-II Euryarchaeota were also specifically detected in the nepheloid layer. In total, these results revealed strong vertical structure of microbial taxa and metabolic activities, as well as the presence of specific ?nepheloid? taxa that may contribute significantly to coastal ocean nutrient cycling.

Biome: root:Environmental:Aquatic:Estuary
Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice

Antibiotics have long-lasting consequences on the gut microbiota with the potential to impact host physiology and health. However, little is known about the transgenerational impact of an antibiotic-perturbed microbiota. Here we demonstrated that adult pregnant female mice inoculated with a gut microbial community shaped by antibiotic exposure passed on their dysbiotic microbiota to their offspring. This dysbiotic microbiota remained distinct from controls for at least 5 months in the offspring without any continued exposure to antibiotics. By using IL-10 deficient mice, which are genetically susceptible to colitis, we showed mice that received an antibiotic-perturbed gut microbiota from their mothers had increased risk of colitis. Taken together, our findings indicate that the consequences of antibiotic exposure affecting the gut microbiota can extend to a second generation.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
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Biome: root:Environmental:Air
Molecular study on haloarchaea producing industerially important enzymes

Samples collected from soda lakes  in wadi al natrun ,egypt to study microbial diversity  and isolated DNA directly from environment to study molecular compositionof haloalkilophilic archaea producing important enzymes.

Biome: root:Environmental:Aquatic:Non-marine Saline and Alkaline:Alkaline
The first report of arbuscular mycorrhizal fungi in a New Zealand coastal dune reveals a diverse community

Arbuscular mycorrhizal fungi (AMF) are components of coastal dune ecosystems around the globe where they provide a range of benefits to plants. The diversity and structure of AMF communities within these ecosystems, however, are poorly known. This study presents the first report of an AMF community in a New Zealand dune. Root samples were collected from the grass Spinifex sericeus R. Br., which dominates dunes of the North Island of New Zealand, along a 90m transect. Spores were also collected. The AMF community within the roots was surveyed using 454 sequencing of the SSU gene region. The 22 operational taxonomic units recognised formed a phylogenetically diverse community, including at least 8 genera across the Glomerales and Diversisporales, with an additional genus detected by the spore investigation. Some root and spore derived sequences generated close BLAST matches to AMF from distant countries while others represent previously unknown biodiversity. Spore morphology also suggests undescribed AMF are present. The community was heavily dominated by the genera Rhizophagus and Racocetra, together with AMF from a clade with no matches to a described genus. Spatial heterogeneity was observed, with taxonomic composition changing over distances of only 30 m.

Biome: root:Host-associated:Plants:Rhizosphere
Ectomycorrhizal and fine root foraging across European forests: the concept of complementarity within 'root-mycorrhiza-bacteria' continuum

Ectomycorrhizal and fine root foraging across European forests: the concept of complementarity within 'root-mycorrhiza-bacteria' continuum

Biome: root:Host-associated:Plants:Rhizosphere:Forest soil
characterization of cervico-vaginal microbiota associated with HPV infection

Persistent high risk (HR)-HPV infection is a necessary condition for cervical cancer development. Lactobacillus depletion and increased bacterial diversity in vaginal microbiota facilitate HPV infection and persistence.Cervico-vaginal samples were obtained from samples collected within HPV screening programs for cervical cancer. One-year follow-up data were used to differentiate samples from patients developing persistent infection. Pyrosequencing of 16S rRNA was used to characterize the vaginal microbiota and to define community state type (CST) in each sample. Linear discriminant analysis effect size (LEfSe) was used to identify enriched taxa during HPV infection and persistence.

Biome: root:Host-associated:Human:Reproductive system:Female
Plants Assemble Species Specific Bacterial Communities From Common Core Taxa in Three Arcto-Alpine Climate Zones

Evidence for the pivotal role of plant-associated bacteria to plant health and productivity has accumulated rapidly in the last years. However, several key questions remain unanswered, among which is the impact of climate zones on the plant-associated microbiota. Importantly, plant-bacterial interactions in wild plants and in arcto-alpine biomes have not been well studied as compared to those in tropical and temperate biomes. We hypothesized that the bacterial communities associated with pioneer plants in the former regions have major roles in plant health support, and this would be reflected in the formation of climate and host plant specific endophytic communities. We also hypothesized that these endophytes would have a tight association with their respective host plants. To examine the drivers of the plant-associated bacterial communities, we compared the latter in the perennial plants Oxyria digyna and Saxifraga oppositifolia - naturally growing in three arcto-alpine regions [Mayrhofen, Austria - alpine, Kilpisj?rvi, Finland - low Arctic and Ny-?lesund, Svalbard -highArctic] - with those in the corresponding bulk soils. As expected, the bulk soil bacterial communities in the three regions were significantly different. The relative abundances of Proteobacteria decreased progressively from the alpine to the high-arctic soils, whereas those of Actinobacteria increased. The candidate division AD3 and Acidobacteria abounded in the low Arctic. With respect to the endophytic bacterial communities, plant species and geographic region were the major determinants of the community structures. The plants in the alpine region had higher relative abundances of Proteobacteria, as compared to the plants from the low- and high-arctic regions which were dominated by Firmicutes. A highly conserved shared set of omnipresent bacterial taxa was found to occur in the two plant species, here denoted as the ?tight? core bacteriome. Burkholderiales, Actinomycetales and Rhizobiales were common members of this core, and these taxa were the main contributors to the differences in the endophytic bacterial community structures across compartments as well as regions. We postulate that this tight core is due to selection by the two plants, concomitant with a highly efficient adaptation of such ?core bacteriome? to the plant-associated habitats.

Biome: root:Host-associated:Plants
Kelp forest microbial diversity

Kelp forest ecosystems are biodiversity hotspots, providing habitat for dense assemblages of marine organisms and an important source of energy and nutrients for both marine and terrestrial food webs. The surfaces of kelps support diverse microbial communities that are essential for the growth and development of their hosts, and for facilitating the transfer of carbon from algal primary production to higher trophic levels. We quantified the diversity and distribution of bacterial communities present on the surfaces of eight sympatric species of kelp from four sites on the central coast of British Columbia. Patterns of host-asscoiated microbial diversity were compared with samples collected from seawater and rocky substrate. This study is among the first to quantify the distribution of microbial diversity across sympatric species within kelp forests, providing an additional level of data towards a more comprehensive understanding of these ecologically important habitats.

Biome: root:Host-associated:Plants
System-level response to long-term irrigation in a drought-stressed pine forest

The impact of climate change on the soil microbiome potentially alters the biogeochemical cycle of terrestrial ecosystems. In semi-arid environments, water availability is a major constraint on biogeochemical cycles due to the combination of high summer temperatures and low rainfall. Here, we explored how ten years of irrigation of a water-limited pine forest in the central European Alps altered the soil microbiome and associated ecosystem functioning. A decade of irrigation stimulated tree growth, resulting in higher crown cover, larger yearly increments of tree biomass, increased litter fall, and greater root biomass. Greater amounts of plant-derived inputs associated with increased primary production in the irrigated forest stands stimulated soil microbial activity coupled to pronounced shifts in the microbiome from largely oligotrophic to more copiotrophic lifestyles. Microbial groups benefitting from increased resource availabilities (litter, rhizodeposits) thrived under irrigation, leading to enhanced soil organic matter mineralization. This unique long-term study provides new insights into the impact of precipitation changes on the soil microbiome and associated ecosystem functioning in a drought-prone pine forest ecosystem and improves our understanding of the persistency of long-term soil carbon stocks in a changing climate.

Biome: root:Host-associated:Plants:Rhizosphere:Forest soil
Effects of wood ash on forest soil microbial communities

Varying levels of wood ash were added to two Ontario forests and the effects of the organic layer soil microbial communities were assessed.

Biome: root:Host-associated:Plants:Rhizosphere:Forest soil
Transgenic banana plants expressing Xanthomonas wilt resistance genes revealed a stable non-target bacterial colonization structure

Africa is among the continents where the battle over genetically modified crops is currently being played out. The impact of GM in Africa could potentially be very positive. In Uganda, researchers have developed transgenic banana lines resistant to banana Xanthomonas wilt. The transgenic lines expressing hrap and pflp can provide a timely solution to the pandemic. However, the impact of the transgenes expression on non-target microorganisms has not yet been investigated. To study this effect, transgenic and control lines were grown under field conditions and their associated microbiome was investigated by 16S rRNA gene profiling combining amplicon sequencing and molecular fingerprinting. Three years after sucker planting, no statistically significant differences between transgenic lines and their non-modified predecessors were detected for their associated bacterial communities. The overall gammaproteobacterial rhizosphere microbiome was highly dominated by Xanthomonadales, while Pseudomonadales and Enterobacteriales were accumulated in the pseudostem. Shannon indices revealed much higher diversity in the rhizosphere than in the pseudostem endosphere. However, the expression of the transgenes did not result in changes in the diversity of Gammaproteobacteria, the closest relatives of the target pathogen. In this field experiment, the expression of the resistance genes appears to have no consequences for non-target rhizobacteria and endophytes.

Biome: root:Host-associated:Plants
Microbial diversity analysis of silage grass

Methane production via anaerobic fermentation of silaged energy grass, semiliquid, or solid municipal waste of complex composition by methanogenic microbial communities is a multistage process involving at least four groups of microorganisms. These are hydrolytic bacteria (polysaccharolytic, proteolytic, and lipolytic), fermentative bacteria, acetogenic bacteria (syntrophic, proton-reducing), and methanogenic archaea; complex trophic interactions exist between these groups.

Biome: root:Engineered:Food production:Silage fermentation
Analysing core microbiome of the Alpine bog vegetation

The current study address microbial diversity of Alpine bog vegetation using deep-sequencing of microbial 16S rRNA genes. Higher plant, bryophyte and lichen species were sampled from plots (1m2) in two Austrian bogs, Rotmoos and P?rgschachen Moor. The plots were dominated by Sphagnum magellanicum or Sphagnum angustifolium. Altogether, 46 plant and lichen samples of 24 species were collected. Amplicons were generated using 515F/806R (Caporaso et al. 2010 PNAS) and were sequenced using Illumina MiSeq v2 platform.

Biome: root:Environmental:Aquatic:Freshwater:Wetlands:Bog
Agroforestry leads to shifts within the gammaproteobacterial microbiome of banana plants cultivated in Central America

Bananas (Musa spp.) belong to the most important global food commodities, and their cultivation represents the world''s largest monoculture. Although the plant-associated microbiome has substantial influence on plant growth and health, there is a lack of knowledge of the banana microbiome and its influencing factors. We studied the impact of (i) biogeography, and (ii) agroforestry on the banana-associated gammaproteobacterial microbiome analyzing plants grown in smallholder farms in Nicaragua and Costa Rica. Profiles of 16S rRNA genes revealed high abundances of Pseudomonadales, Enterobacteriales, Xanthomonadales, and Legionellales. An extraordinary high diversity of the gammaproteobacterial microbiota was observed within the endophytic microenvironments (endorhiza and pseudostem), which was similar in both countries. Enterobacteria were identified as dominant group of above-ground plant parts (pseudostem and leaves). Neither biogeography nor agroforestry showed a statistically significant impact on the gammaproteobacterial banana microbiome in general. However, indicator species for each microenvironment and country, as well as for plants grown in Coffea intercropping systems with and without agri-silvicultural production of different Fabaceae trees (Inga spp. in Nicaragua and Erythrina poeppigiana in Costa Rica) could be identified. For example, banana plants grown in agroforestry systems were characterized by an increase of potential plant-beneficial bacteria, like Pseudomonas and Stenotrophomonas, and on the other side by a decrease of Erwinia. Hence, this study could show that as a result of legume-based agroforestry the indigenous banana-associated gammaproteobacterial community noticeably shifted.

Biome: root:Host-associated:Plants:Phylloplane:Endophytes