SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 sequencing-by-synthesis

Information on genetic diversity of picoeukaryotes (<2 to 3 µm) comes mainly from traditional gene cloning and sequencing. However, the method suffers from cloning biases and limited throughput. We studied the composition and genetic diversity of picoeukaryotes off the subtropical western Pacific coast using cloning-independent and massively parallel 454 pyrosequencing of the hypervariable V4 region of the 18S rRNA gene. The approach gave a high coverage of the community at genetic difference >=5% but still underestimated the total diversity at genetic difference <=2%. Picoeukaryotic assemblage in the eutrophic site was less diverse than that with low chlorophyll a biomass. Stramenopiles, dinoflagellates, ciliates and prasinophytes were the dominant groups, comprising approximately 29, 19, 11 and 11% of the picoeukaryotes respectively. A differential spatial distribution of high-level taxonomic groups and phylotype OTUs of picoeukaryotes was observed between samples. Our study represents the most comprehensive examination of marine picoeukaryotic diversity to date, using the 454 sequencing-by-synthesis technology for the first time.

Biome: root:Environmental:Aquatic:Marine
MiSeq 16S rRNA gene (archaeal 16S rRNA gene) sequences of 4 SCS sediments

DNA from 4 SCS sediments have been extracted and amplified by 21f/958r & Arch347F/Arch806R primer pairs (for archaeal 16S rRNA gene). The archaeal communities of these 4 samples were obtained.

Biome: root:Environmental:Aquatic:Marine:Sediment
Identification and activity of acetate-assimilating microorganisms in diffuse hydrothermal fluids

In diffuse hydrothermal fluids concentrations of organic compounds such as acetate can be significant. To date knowledge about mixo- and heterotrophic microorganisms in hydrothermal systems is derived from pure cultures only. We set out to identify acetate-consuming microorganisms in diffuse fluids from two distinct hydrothermal systems using cultivation-independent approaches. For this purpose we combined a characterization of the microbial community in fluids with short-term incubations (8-12 h) using 13C-labeled acetate at low concentrations (10 or 30 µM). We followed cell growth and assimilation of 13C into single cells by nanoSIMS combined with fluorescence in situ hybridization (FISH). In 55°C fluids from the Menez Gwen system, Mid-Atlantic Ridge, a novel epsilonproteobacterial group related to Nautiliales accounted for nearly all acetate-assimilating cells. In contrast, in 4°C and 37°C fluids from the Manus Basin (Papua New Guinea) Gammaproteobacteria dominated the 13C-acetate-assimilating community, which was supported by 16S rRNA sequences related to Marinobacter and Alteromonas. We also detected yet unidentified, weakly acetate assimilating cells in 72°C fluids (Manus Basin) that were presumably related to Acinetobacter. In particular in the 37°C and 55°C incubations the microbial communities differed from those in native fluids indicating rapid growth of heterotrophic organisms. The instant response suggests that acetate-consumers in diffuse fluids are r-strategists, which quickly exploit their food sources whenever available under the spatially and temporally highly fluctuating conditions at hydrothermal vents. Our data provide first insights into a largely under-investigated part of microbial carbon cycling at hydrothermal vents and reveals potential roles of known and yet unknown heterotrophic microorganisms in these systems.

Biome: root:Environmental:Aquatic:Marine:Hydrothermal vents
Variable Loading Conditions Influence Charge and Current Generation in Multi-Anode Environmental Microbial Fuel Cells

The role of operating conditions, specifically duty cycling, on microbial fuel cell (MFC) performance has only recently been studied. This study uses an environmental MFC containing multiple anodes, positioned in chambered anoxic seawater overlying marine sediments, to explore how varying the time an anode is connected and disconnected from a cathode influences cumulative charge, and finds that a switching interval of 15 seconds when duty cycling among the anodes results in the greatest normalized current density (amps per unit time connected). Further studies demonstrate the overall electrode reaction resistance increases with shorter disconnection times, and there is a minimum time below which current decreases significantly. Microbial diversity analyses reveal a substantial enrichment in sulfur-cycling microbes on the anodes compared to the sediment, though no measurable change in community composition among operational anodes. Based on these data, we posit that, in environmental MFCs, replenishment of depleted chemical species within the biofilm and surrounding diffusion layer is necessary for maximum charge transfer, and that proton flux is not limiting in highly buffered systems. These data underscore the importance of considering all factors, including diffusion and migration flux, microbial community composition, and resting time, when optimizing MFC performance.

Biome: root:Environmental:Aquatic:Marine:Sediment
Microbial Community Diversity Response to a Changing Arctic Ocean

Increasing global temperatures are having a profound impact in the Arctic, including the dramatic loss of multiyear sea ice in 2007 that has continued to the present. The majority of life in the Arctic is microbial and the consequences of climate-mediated changes on microbial marine food webs, which are responsible for biogeochemical cycling and support higher trophic levels, are unknown. We examined microbial communities over time by using high-throughput sequencing of microbial DNA collected between 2003 and 2010 from the subsurface chlorophyll maximum (SCM) layer of the Beaufort Sea (Canadian Arctic). We found that overall this layer has freshened and concentrations of nitrate, the limiting nutrient for photosynthetic production in Arctic seas, have decreased. We compared microbial communities from before and after the record September 2007 sea ice minimum and detected significant differences in communities from all three domains of life. In particular, there were significant changes in species composition of Eukarya, with ciliates becoming more common and heterotrophic marine stramenopiles (MASTs) accounting for a smaller proportion of sequences retrieved after 2007. Within the Archaea, Marine Group I Thaumarchaeota, which earlier represented up to 60% of the Archaea sequences in this layer, have declined to <10%. Bacterial communities overall were less diverse after 2007, with a significant decrease of the Bacteroidetes. These significant shifts suggest that the microbial food webs are sensitive to physical oceanographic changes such as those occurring in the Canadian Arctic over the past decade.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Marine sediment metagenome ICM_DSE

Using 454 sequencing technology to explore eukaryotes diversity in the polar deep-sea sediments.

Biome: root:Environmental:Aquatic:Marine:Sediment
Minor impact of ocean acidification to the structure of an Arctic sediment microbial community

Effects of ocean acidification on the diversity and structure of Arctic surface sediment bacterial and archaeal community was analysed in detail using 16S rRNA 454 pyrosequencing. Intact sediment cores were collected and exposed to one of five different pCO2 concentrations (380 (present day), 540, 750, 1120 and 3000 µatm) and RNA extracted after a period of 14 days exposure. Measurements of diversity and multivariate similarity indicated very little difference between pCO2 treatments. Only when the highest and lowest pCO2 treatments were compared were significant differences evident, namely increases in the abundance of the Halobacteria and differences to the presence/absence structure of the Planctomycetes. Members of the Planctomycetia also increased with increasing pCO2 concentration, particularly the Planctomyces, Schlesneria, Pirellula, Blastopirellula, Rhodopirellula and the Pir4 lineage, indicating that these groups may be able to take advantage of changing pH or pCO2 conditions. The modest response of the microbial communities associated with these sediments may be due to the low pore-water pH already experienced by sediment microbes or be a result of the high buffering capacity of marine sediments.

Biome: root:Environmental:Aquatic:Marine:Sediment
Specialists instead of generalists oxidize alkanes in anoxic marine
                hydrocarbon seep sediments

The anaerobic oxidation of non-methane hydrocarbons mediated by
                sulfate-reducing bacteria (SRB) is a major process of organic matter degradation at
                marine hydrocarbon seeps. Several SRB have been successfully cultured, however,
                knowledge about in situ active organisms is still very limited. Here, we identified
                alkane-degrading key players from two contrasting seeps at the Mediterranean Amon
                Mud Volcano (Amon MV) and Guaymas Basin in the Gulf of California using
                complementary stable-isotope probing (SIP) techniques. Anoxic sediments were
                incubated with 13C-labeled butane or dodecane under close to in situ conditions.
                DNA- and RNA-based SIP in combination with 454-pyrosequencing (PYRO-SIP) allowed the
                identification of four phylogenetically distinct deltaproteobacterial groups of
                alkane-oxidizing SRB within the family Desulfobacteraceae. We named the groups
                degrading short-chain alkanes ‘SCA-SRB1' and ‘SCA-SRB2' and those degrading
                long-chain alkanes ‘LCA-SRB1' and ‘LCA-SRB2'. CARD-FISH with newly developed
                specific probes revealed a high relative in situ abundance of SCA-SRB1 and SCA-SRB2
                with 2% of the total community, while groups LCA-SRB1 and LCA-SRB2 were below 1% of
                total cells. Protein-based SIP (Protein-SIP), which enables to trace stable isotopes
                from substrate to protein, confirmed alkane-degrading key players of the family
                Desulfobacteraceae. In addition, Protein-SIP indicated additional carbon sources for
                13C biosynthesis besides alkanes, and gave insights into possible metabolic
                pathways: (1-methylalkyl)succinylation as initial step of butane degradation and the
                oxidative Wood–Ljungdahl pathway as terminal point of alkane
                degradation.

Biome: root:Environmental:Aquatic:Marine:Sediment
Development and validation of a marine experimental life support system for accessing synergistic effects of climate change and oil pollution on microbial communities

A state of the art marine experimental life support system framework was developed to perform microcosms experiments of climate change and anthropogenic pollutants effects on marine microbial communities. The system can be build with commercially available materials, enabling the reproduction of the same experiment in several locations worldwide. Here the system was validated for microbial ecology studies by comparing the bacterial composition of environmental and microcosm samples with a RNA-based barcode pyrosequencing approach. The OTU composition shift towards anaerobic bacterial groups in manipulates samples, witch can be explained with the operational programme executed. Replicate microcosm maintained a high OTU composition stability, with similar variability to the environmental samples.  This system can be use to establish cause-effect relationships into the effects of climate change and other anthropogenic stressors on specific marine microbial communities. Moreover, the marine experimental life support system versatile design enables its use on ecotoxicology tests.

Biome: root:Environmental:Aquatic:Marine
Marine metagenome ICM_SSD

Spatial Scaling of Microbial Diversity

Biome: root:Environmental:Aquatic:Marine:Sediment
Structuring effect of environmental variables on protistan diversity patterns in two anoxic marine basins

The tenet that 'everything is everywhere, but the environment selects' has influenced microbiology for several decades, and is still debated controversially. However, the proof or disproof of the hypothesis still remains difficult. Scant data from prokaryotic studies suggest that at least over large distances historical separation may overwhelm environmental effects, challenging the above mentioned hypothesis. Though, at smaller spatial scales, environmental effects seem to dominate diversity patterns, while distance effects are of secondary importance. We tried to contribute to the ongoing discussion by investigating patterns of protistan diversity from two geographically separated marine anoxic basins (Cariaco Basin, Venezuela, Framvaren Fjord, Norway). To take distance and environmental effects into account, each basin was sampled at two different locations along an environmental gradient. Biodiversity patterns were analyzed by applying the 454 sequencing technique. Resulting data sets were used to examine overall diversity of samples under study and to compare recorded community patterns based on taxonomic composition and similarity indices. By combining our results with contextual data from both sampling sites we tested for distance effects in relation to contemporary environmental effects.

Biome: root:Environmental:Aquatic:Marine
Metagenomic approach for studying picoeukaryotes in a extreme oligotrophic marginal sea (South Adriatic Sea) during winter mixed conditions

This study investigates this smallest plankton fraction (cells ≤ 3µm) in both prokaryotic and eukaryotic perspective considering changes of the community in the photic zone from coastal to open sea during mixed winter conditions. Using high-throughput sequencing of 16S and 18S rRNA genes along with flow-cytometry counts of bacteria, cyanobacteria and photosynthetic picoeukaryotes (PPEs) we described picoplanktonic community in the oligotrophic ecosystem. With pigment and lipid analyses of picoplankton community, we characterized PPEs and detected specific events in microbial loop. Prokaryotic community was dominated by Alphaproteobacteria, mainly SAR11 clade (44.91%), followed by Gammaproteobacteria (Oceanospirillales and Pseudomonadales, 14.96%), Bacteroidetes, mainly Flavobacteriales (13%), Cyanobacteria (Prochlorococcus and Synechococcus, 9.52%), Marinimicrobia, SAR406 clade (7.97%), Deltaproteobacteria (3.83%), Actinobacteria (2.24%) and Chloroflexi (1.90%). Picoeukaryotes, although the drivers of photosynthetic activity in oligotrophic systems, in this study were dominated by heterotrophic counterparts: Syndiniales, parasitic dinoflagellates (79.67%), other Dinophyta (8.7%) and on two depths Collodaria, family Sphaerozoidae (22.1%) and Polycistinea, Spumellarida (5.0%), while total photoautotrophic fraction of picoeukaryotes were represented with Mamiellophyceae, Stramenopiles, photoautotrophic Cryptophyta and some Haptophyta, together not exceeding 5% of total sequences. Heterotrophic bacteria and cyanobacteria, separated into populations of Prochlorococcus and Synechococcus, had abundances up to 7×105; 2.3×104 and 2.5×104 cells mL-1, respectively. Photoautotrophic picoeukaryotes were most abundant at P600-25m with 3×103 cells mL-1. According to pigment composition, the most prevalent phototrophs in picoplankton were Cyanobacteria and green algae.

Biome: root:Environmental:Aquatic:Marine:Oceanic
Ecological succession leads to chemosynthesis in mats colonizing wood in sea water

We used amplicon and metagenomic sequencing combined with fluorescence in situ hybridization (FISH) to test whether a microbial succession occurs during mat formation and whether the wood fall mats present chemosynthetic features

Biome: root:Environmental:Aquatic:Marine:Oceanic:Benthic
Spatially differing bacterial communities in water columns of the northern Baltic Sea

The Baltic Sea is a large, shallow and strongly stratified brackish water basin. It suffers from eutrophication, toxic cyanobacterial blooms and oxygen depletion, all of which pose a threat to local marine microbial communities. In this study, the diversity and community structure of the northern Baltic Sea bacterial communities in the water column were Ã¢ÂÂ for the first time Ã¢ÂÂ thoroughly studied by 454-sequencing. The spring and autumn bacterial communities were one order of magnitude less diverse than those in recently studied oceanic habitats. Patchiness and strong stratification were clearly detectable, since only less than 1% of OTUs were shared among eleven samples. The community composition was more uniform horizontally (at a fixed depth) at different sites than vertically within one sampling site. Taxonomic affiliations revealed a total of 23 bacterial classes and 169 genera, and five percent of the sequences were assigned unclassified. The cyanobacteria constituted less than two percent of the sequences and potentially toxic cyanobacterial genera were practically absent during the sampling seasons.

Biome: root:Environmental:Aquatic:Marine
Diversity and population structure of Marine Group A in the oxygen minimum zone of the Northeast subarctic Pacific Ocean

NONE

Biome: root:Environmental:Aquatic:Marine
Marine sediment metagenome ICM_CFU

Investigation of prokaryote diversity in the sub-seafloor biosphere by 16S rRNA gene tag (V6) sequencing.

Biome: root:Environmental:Aquatic:Marine:Sediment
MiSeq 16S rRNA gene (Thaumarchaeota 16S rRNA gene) sequences of 12 SCS sediments

DNA from 12 SCS sediments have been extracted and amplified by THAUM494/958R primer pairs (for Thaumarchaeota 16S rRNA gene). The Thaumarchaeota communities of these 12 samples were obtained.

Biome: root:Environmental:Aquatic:Marine:Sediment
MiSeq 16S rRNA gene (archaeal 16S rRNA gene) sequences of 12 SCS sediments

DNA from 12 SCS sediments have been extracted and amplified by 21f/958r & Arch347F/Arch806R primer pairs (for archaeal 16S rRNA gene). The archaeal communities of these 12 samples were obtained.

Biome: root:Environmental:Aquatic:Marine:Sediment
Microbial Community Assembly in Soybean

Soybean has great economic and social importance for Brazil, and nitrogen, the most required nutrient by plants, is fully supplied by bacteria symbiosis. In order to guarantee the biological process maximization, it is necessary to inoculate strains of efficient and competitive bacteria, that accompany the technological development of new cultivars

Biome: root:Environmental:Terrestrial:Soil:Agricultural
EMG produced TPA metagenomics fasta_path of the Shotgun metagenomic analysis of Lake Paajarvi sediment microbes. (PRJEB29513) data set.

The PRJEB29513 Third Party Annotation (TPA) fasta_path was derived from the primary whole genome shotgun (WGS) data set: PRJEB29513.  This project includes samples from the following biomes: root:Environmental:Aquatic:Freshwater:Lentic:Sediment.

Biome: root:Environmental:Aquatic:Freshwater:Sediment
The gut microbiota distinguishes GI-healthy and -unhealthy captive colobineprimates - Hale folivorous primates (HiSeq)

This study focuses on the gut microbe populations of the Guizhou snub-nosed monkey, Rhinopithecus brelichi.

Biome: root:Host-associated:Mammals:Digestive system:Fecal
Latitudinal surveys of algal-associated microorganisms

Over the last decade, disease has emerged from being a long overlooked factor in natural communities to become an increasing focus for ecological research in terrestrial and marine ecosystems. There is also major concern that global warming and other anthropogenic stressors may be responsible for the spread of pathogens, enhanced virulence and decreased resilience of hosts. This project focuses on macroalgae or seaweeds, the dominant habitat-forming organisms in temperate rocky reef communities worldwide. They are the trees of temperate coastal ecosystems. Anthropogenic stressors can have dramatic effects on the health and persistence of large macroalgae and are responsible for extensive losses of habitat-forming algae. Importantly, declines in habitat-forming macroalgae not only impact the algae themselves, but have major effects on the diversity and abundance of associated organisms. During this project, we aim to characterise microbial communities associated with the surfaces of dominant seaweed species on temperate Australian coasts, from northern New South Wales, south to Tasmania and also along the western Australian coastline. Furthermore, we aim to identify potential pathogens associated with stressed specimens and quantify their abundance at different sites and different times and correlate microbial data with various physico-chemical information from each site and specimen. This work will provide baseline data on algal-bacterial associations on a latitudinal scale and may also provide information on the distribution and abundance of potential algal pathogens. We hope also to understand how different environmental conditions influence algal-associated microorganisms and predict how environmental change may affect interactions between these microbes and their hosts.

Biome: root:Host-associated:Algae
Functional description of microbial communities  from biochemical passive reactors treating synthetic Acide Mine Drainage

This study aims to stablish the link between the dynamics of microbial communities with the stability of process and functions of biochemical passive bioreactors for AMD-bioremediation. Dynamics of microbial communities can be simulated at different resolutions, depending on the approximation used to define the interacting units, here we are going to describe the bioreactors microbiome through two of the most common approaches: (1) using 16S rRNA gene data to simulate the dynamics of microbial communities in terms of interactions between taxa; and (2) using the whole metagenome sequencing  to characterize the whole community as a supra-organism performing various functions.

Biome: root:Engineered:Bioreactor
Influence of tillage practices on soil microbial diversity and activity in a long-term corn experimental field under continuous maize production

It is well known that an intensive conventional farming and continuous use of land resources can lead to a decrease of soil sustainability. The aim of this study was to compare the impact of four different tillage practices (minimum tillage MT, shallow ploughing SP, ripper subsoiling RS and conventional tillage DP) on soil profile under both continuous and rotating (wheat, bean, maize) maize production since 1970. The field study was conducted on 24 experimental plots on a loam soil of Fagna, Tuscany (Italy), where soil samples were collected at four different layers of 10 cm each, up to a total depth of 40 cm (0-10, 10-20, 20-30 and 30-40 cm in triplicate) and of 20 cm (0-10 and 10-20 cm) from continuous and rotating maize fields respectively, in order to measure the effect of the different tillage practices on soil organic matter, microbial diversity and microbial activity.

Biome: root:Environmental:Terrestrial:Soil:Loam:Agricultural