SantiagoSanchezF/mgnify_study_descriptions huggingface dataset:
Drivers of Diversity for Microbial Communities Inhabiting Halites from the Hyper-arid Zone of the Atacama Desert

The Atacama Desert is one of the oldest and driest deserts in the world and its hyper-arid core is described as ?the most barren region imaginable?. Under these extreme moisture, thermal, and solar radiation stress, habitats inside halite pinnacles harbour flourishing microbial communities. We use a combination of high-throughput sequencing and microscopy methods to characterize the microbial assemblages of halites collected in several areas of the desert. We found communities dominated by Archaea and relying on a single phylotype of Halothece cyanobacteria for primary production. A few other phylotypes of salt-adapted bacteria and archaea, including Salinibacter, Halorhabdus, and Halococcus were major components of the halite communities indicating specific adaptations to the unique halite environments. Multivariate statistical analyses of diversity metrics clearly separated the halite communities from that of the surrounding soil and revealed a distribution patterns of halite communities strongly correlated to atmospheric moisture. Communities from halites exposed to costal fogs were more diverse than halites from the Yungay area, in both their archaeal and bacterial assemblages, and were colonized by a novel algae related to oceanic picoplankton of the Mamiellales. In contrast, we did not find any algae in the Yungay pinnacles suggesting that the environmental conditions in this habitat might be at the limit for eukaryotic life.

Biome: root:Environmental:Terrestrial:Soil:Desert
Methane inhibition alters the microbial community, hydrogen flow and fermentation response in the rumen of cattle.

The effects of the anti-methanogenic compound, chloroform, on rumen fermentation, microbial ecology and H2 /CH4 production were investigated in vivo. Eight rumen fistulated Brahman steers were fed a roughage hay diet (Rhode grass hay) or roughage hay:concentrate diet (60:40) with increasing levels (low, mid and high) of chloroform in a cylcodextrin matrix. The increasing levels of chloroform resulted in an increase in H2 expelled as CH4 production decreased with no effect on dry matter intakes. The amount of expelled H2 per mole of decreased methane, was lower for the roughage hay diet suggesting a more efficient redirection of hydrogen into other microbial products compared with concentrate diet. A shift in rumen fermentation towards propionate and branched-chain fatty acids was observed for both diets. Animals fed with the hay:concentrate diet had both higher formate concentration and H2 expelled than those  fed only roughage hay.  Metabolomic analyses revealed an increase in amino acids, organic and nucleic acids for both diets when methanogenesis was inhibited. These changes in the rumen metabolism were accompanied by a shift in the microbiota with an increase in Bacteroidetes:Firmicutes ratio and a decrease in archaea and Synergistetes for both diets. Within the Bacteroidetes family, some OTUs assigned to Prevotella were promoted under choloroform treatment. These bacteria may be partly responsible for the increase in amino acids and propionic acid in the rumen. No significant changes were observed for abundance of fibrolytic bacteria, protozoa and fungi, which suggests that fibre degradation was not impaired. The observed 30% decrease in methanogenesis did not adversely affect rumen metabolism and the rumen microbiota was able to adapt and redirect metabolic H2 into microbial end-products for both diets. However, dietary supplements or microbial treatments may also be required to capture any additional H2 expelled by the animal to further improve rumen efficiency.

Biome: root:Host-associated:Mammals:Digestive system:Foregut:Rumen
Experimental trial using phytase in the diet for broiler

The aim is to verify the impact of the phytase added in the broiler diet on microbial profile of caecum and broiler meat

Biome: root:Host-associated:Birds
An integrated multi-omics approach reveals the effects of supplementing grass or grass hay with vitamin E on the rumen microbiome and its function

Rumen function is generally sub-optimal leading to losses in the form of methane and nitrogen. Analysis of the rumen microbiome is thus important to understand underlying microbial activity under different feeding strategies. This study investigated the effect of forage conservation method and vitamin E supplementation on rumen function using the rumen simulation technique (Rusitec). Dietary treatments consisted of ryegrass (GRA) or ryegrass hay (HAY) supplemented with 20% concentrate containing zero or 50 IU/d vitamin E, as ?-tocopheryl acetate, according to a 2?2 factorial design. Forage conservation method did not substantially change the nutrient composition but had a profound impact on the structure and diversity of the main rumen microbial communities. HAY diets promoted a more complex bacterial community (+38 OTUs) dominated by Firmicutes. This adaptation, together with increased rumen protozoa levels and greater diversity in the bacterial and methanogen communities, led to greater fibre degradation (+12%) in HAY diets, but also to greater proteolysis (+15%) than observed with GRA diets. Inter-species H transfer between fibrolytic bacteria, protozoa and methanogens was greater in HAY diets, which resulted in higher metabolic H recovery and ultimately higher methane emissions (+35%). On the contrary, GRA diets promoted more simplified methanogen and bacterial communities. This bacterial community was dominated by Bacteroidetes and Lactobacillus, thus lactate formation may have acted as an alternative H sink in GRA diets. Moreover the structure of the bacterial community with GRA diets was highly correlated with N utilization, and GRA diets promoted greater bacterial growth and microbial protein synthesis (+16%), as well as a more efficient microbial protein synthesis (+22%). A dose-response experiment using batch cultures revealed that ?-tocopheryl acetate was more effective than ?-tocopherol in improving rumen fermentation, moreover a high vitamin E dose (500 IU/L) had a negative impact on rumen function. This improvement consisted of a small increase in feed degradability (+8%), possibly as a result of the antioxidant properties of vitamin E which led to higher bacterial and protozoal levels. Moreover, vitamin E supplementation promoted substantial changes in the methanogen community suggesting that some methanogen species are particularly sensitive to oxidative stresses. Our findings suggested that when possible  grass should be fed instead of grass hay, in order to improve rumen function and to decrease the environmental impact of livestock agriculture.

Biome: root:Host-associated:Mammals:Digestive system:Stomach:Rumen
Testing 602

First attempt to figure this out

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
FVB F Partial Co2

Diet effects on FVB microbiome

Biome: root:Host-associated:Mammals:Digestive system:Large intestine:Fecal
FVB Partial Co1

Examining effect of diet on microbiome in cohort1

Biome: root:Host-associated:Mammals:Digestive system:Midgut
Bacterial Communities Associated with Atherosclerotic Plaques from Patients with Atherosclerosis

16S rRNA amplicon sequencing

Biome: root:Host-associated:Human:Circulatory system
Studying the presence and selection of antibiotic resistance genes

Antibiotic resistance genes can directly enter WWTPs, pass through the WWTPs, and enter receiving waters, thus potentially spreading resistance and posing a growing concern to the public. My goals here are two-fold. First, I want to test if specific operating metrics, such as temperature, pH, BOD concentration, and N concentration, have an influence on the presence and persistence of antibiotic resistance genes in sludge communities. Second, I want to determine whether antibiotic resistance genes are under active selection within WWTPs. To accomplish this second goal, I will evaluate whether antibiotic resistance genes are actively transcribed, which would suggest potential direct selection. I will also test whether antibiotic resistance genes correlate with biodiversity, where I expect that a negative relationship between biodiversity and antibiotic resistance genes is indicative of active selection. I will use a metagenomics and metatranscriptomics approach to test for the presence and expression of target genes. This will help identify potential selection pressures that enable antibiotic resistance genes to pass through WWTPs and be released into receiving waters.

Biome: root:Engineered:Wastewater:Activated Sludge
Diversity and rehabilitation of prokaryotic communities of European biological soil crusts

Biological soil crusts (biocrusts) play vital roles in dryland regions that cover over 35% of the Earth?s land mass, including 24% of Europe. They provide important ecosystem services such as limitation of soil erosion, retention of water, improving soil fertility, and nitrogen and carbon fixation. Here, we present a characterization of the prokaryotic components of European biocrusts, particularly in light of the fact that biocrusts are very susceptible to land use change, long-term farming and chronic physical disturbance. Knowledge of soil microorganisms is rarely considered within the context of biodiversity management, although the diversity and services provided by soil biota are of decisive importance for intact ecosystem function. Secondly, a rehabilitation study was carried out in order to investigate the recovery processes of biocrusts in response to anthropogenic perturbation. The successional pattern of recovery was assessed in the form of returning organisms including bacteria, fungi, algae, lichens, bryophytes and higher plants.

Biome: root:Environmental:Terrestrial:Soil:Desert
Glacial snow and soil Targeted Locus (Loci)

This study was to investigate the dominant bacterial community from glacial snow and how they changed when they were exposed to glacial soil.

Biome: root:Environmental
Virus diversity in Namib Desert soils

The taxonomic composition of soil viruses along the Namib Desert aridity gradient was assessed using deep sequencing of metavirome libraries extracted from surface soils. Soil physicochemical data were used to determine influences, if any, on the observed soil-specific taxonomic compositions of virus communities.

Biome: root:Environmental:Terrestrial:Soil:Sand:Desert
Influence of biodiversity on the functionality of activated sludge communities

We are addressing a critical and unresolved ecological question: When are community composition and biodiversity important for the provision of a particular ecosystem function and when are they not? We hypothesize that community composition and biodiversity are more important for rare ecosystem functions than for common ecosystem functions. If an ecosystem function is rare, then differences or changes in community composition could have profound effects on the biotransformation rate of that function. In contrast, if an ecosystem function is common, then differences or changes in community composition are unlikely to have an effect on that function.

Biome: root:Engineered:Wastewater:Industrial wastewater
Mock Community Sample

Mock Community Sample

Biome: root:Engineered:Modeled
Comparison of two soil microbiomes with different organic matter content

Comparison of two microbiomes of two adjacents environments in Florianopolis (Brasil): a rich organic matter/high plant diversity env. ("Forest") and a poor sand-like dune env. with sea influence ("Dune").

Biome: root:Environmental:Terrestrial:Soil
Wisconsin, Switchgrass soil metagenome reference core Project

none provided

Biome: root:Environmental:Terrestrial:Soil:Grasslands
Microbial biodiversity and structure in soil affects the composition of pyrrolizidine alkaloids in Jacobaea vulgaris

Secondary metabolites like pyrrolizidine alkaloids (PAs) act as defense compounds against aboveground and belowground attackers. We studied to get a better understanding of relevance of microbial diversity in the rhizosphere for plant growth and behavior, specifically related to secondary metabolites production. We made soil dilution to compare the composition of soil microbial communities of soil suspension, incubation and rhizosphere soil by 16s rRNA high throughput pyrosequencing, as a consequence, to determine the effects on plant behaviors. The dilution procedure leads to reduction of the diversity of bacteria at the phylum level. After regrown, the structure of microbial community in the rhizosphere changed significantly as compared to the composition in the incubated soil. Jacobeae vulgaris as model plants growing in the soil where microbial diversity were decreased, had a higher biomass and higher amount of free base form of PAs? production, which indicates the reduction of soil microbial community in the rhizosphere shows significant feedback. Our study adds evidence that soil microbes may play a role in the evolution of plant secondary metabolites in plants.

Biome: root:Environmental:Terrestrial:Soil
Agricultural soils from the East China

To understand AOA and AOB distribution in different kind of soils in the East China.

Biome: root:Environmental:Terrestrial:Soil
Compartmentalization of the microbial community structure in submerged aerobic membrane bioreactors treating wastewater

This study examines the distribution of biomass within submerged membrane bioreactor (MBR) systems, and how, from an engineering and ecological perspective, this may be important to the function, design and operation of submerged MBRs for wastewater treatment.  The microbial-membrane interface, particularly with respect to biofouling, can be a defining feature of the MBR process in biological wastewater treatment. Submerged aerobic MBRs are revealed to be a series of compartments: mixed liquor suspended biomass (MLSB); extra-membrane loosely bound biofilm (EMLB); extra-membrane tightly bound biofilm (EMTB);  and intra-membrane core biofilm (IMCB; formed in voids 20 - 100 ?m in diameter) with both flat sheet and hollow-fibre membranes. Microscopy and 16S rRNA gene sequencing were used to characterize the biomass from these compartments within a laboratory scale aerobic MBR feed with synthetic wastewater. Although there were similarities distinct differences in the predominant populations between compartments were observed,  Dysgonomonas, a facultative anaerobe, Acetobacterium, a gram-positive anaerobe, and Blastobacter, capable of nitrogen-fixation, were predominant in the IMCB. Xanthobacter, a denitrifier , and Subtercola, a floc-forming bacteria were present in the MLSB. Rhodocista, known to be a phototroph or aerobic chemoheterotroph was found in the MLSB as well as the EMTB and EMLB. Mycoplana and Caldimonas, aerobic chemoorganoheterotrophs, were unique to EMLB and EMTB, respectively. Changes in substrate availability, including dissolved oxygen concentration, and microenviornmental conditions across the compartments, are likely important factors shaping these communities within these compartments.

Biome: root:Engineered:Bioremediation:Terephthalate:Wastewater:Bioreactor
Diversity and Abundance of Ammonia Oxidizing Archaea in the Coastal Sea Surface Microlayer

This is a part of a project targeting the distribution and diversity of ammonia oxidizing archaea in the sea surface microlayer (SML). Previous reports have reported the high abundance of Thaumarcheota in the SML in lake environments but the distribution of archaea in the SML of marine environments have yet to be investigated. Using 16S rRNA gene pyrosequencing and qualitative PCR techniques, we found that the relative abundance of phylum Thaumarchaeota can also be high in the SML and their abundances were weakly co-related to the chlorophyll-a and transparent exopolymer particles concentrations in the SML. Additionally, archaeal groups originating from soil or terrestrial were also found in higher proportions in the SML compared to the underlying water (20cm).

Biome: root:Environmental:Aquatic:Marine:Coastal
454Titanium barcoded pyrosequencing of the 16S rRNA and proteorhodopsin-containing photoheterotrophs genes was used to characterize the structure and microbial diversity across a seasonal change (August to March), in waters off Maria Island.

Observational and modelling studies have shown that currents along the east coast boundary of Tasmania are influenced by the strength of a residual East Australian current (EAC), experiencing distinctive seasonal and interannual variation in water properties. In this study we investigated whether the influence of the EAC changes the microbial community structure, including photoheterotrophic proteorhodopsin-containing bacteria (PRB), a key component of the microbial community. Seawater samples were collected from August 2011 to March 2012 from surface waters at the National Reference Station Maria Island Mooring. The microbial communities were characterized by 454 pyrosequencing of the 16S rRNA and proteorhodopsin genes. Our data show marked changes in microbial assemblages over the season, in particular in February and March. The maximal effect of the EAC was observed by the increased abundance of Prochlorococcus spp., associated with warm and highly oligotrophic open ocean waters. PRB sequence diversity indicated that Alphaproteobacteria related clades SAR116 and SAR11 predominated at most times while Archaea marine group II predominated mostly in winter. Quantitative PCR demonstrated that SAR 11 PRB populations were more abundant during the last months of summer and were positively correlated with pigments (i.e. divinyl chlorophyll a and zeaxanthin), and inversely correlated to nutrient (NO2-/NO3- and PO43-) concentrations. Overall, these findings indicate that further increases in the influence of the EAC could alter the bacterioplankton community structure towards that of typical of open ocean systems.

Biome: root:Environmental:Aquatic:Marine
Metagenomic Characterisation of Opaque Beer Industry Wastewater, Zvishavane

The availability of clean portable water has been a challenge for many Zimbabwean municipalities over the years. Currently, several towns and cities are facing water quality problems generally caused by pollution due to inadequate maintenance of waste water treatment plants, expensive waste water treatment technologies and poor institutional framework. In this study the waste water treatment efficiencies of 15 opaque beer brewery waste water treatment plants were determining by measuring how each plant altered known physico-chemical indicators of waste water quality. It was assumed that the observed degree of alteration in waste water physico-chemical properties was due a number of factors, with the plant?s microbial diversity and load being a key factor. The thinking behind this assumption is that where you have more microorganisms of many different types, you are likely to find more efficient degradation of wastewater than in the opposite scenario. As a consequence, the study also sought to determine the microbial diversity in the two extremes, i.e. in the plant with the highest and lowest degree of alteration of wastewater physico-chemical parameters.

Biome: root:Engineered:Wastewater:Water and sludge
Metagenomic Characterisation of Opaque Beer Industry Wastewater, Fairbridge

The availability of clean portable water has been a challenge for many Zimbabwean municipalities over the years. Currently, several towns and cities are facing water quality problems generally caused by pollution due to inadequate maintenance of waste water treatment plants, expensive waste water treatment technologies and poor institutional framework. In this study the waste water treatment efficiencies of 15 opaque beer brewery waste water treatment plants were determining by measuring how each plant altered known physico-chemical indicators of waste water quality. It was assumed that the observed degree of alteration in waste water physico-chemical properties was due a number of factors, with the plant?s microbial diversity and load being a key factor. The thinking behind this assumption is that where you have more microorganisms of many different types, you are likely to find more efficient degradation of wastewater than in the opposite scenario. As a consequence, the study also sought to determine the microbial diversity in the two extremes, i.e. in the plant with the highest and lowest degree of alteration of wastewater physico-chemical parameters.

Biome: root:Engineered:Wastewater:Water and sludge
Structure and functions of the bacterial root microbiota in wild and domesticated barley and signatures of positive selection in the rhizosphere metagenome

We have profiled the rhizosphere and the root bacterial communities retrieved from soil-grown, wild, landrace and modern accessions of barley using a 16S rRNA gene amplicon pyrosequencing approach. Phylogenetic assignment of the generated sequencing reads revealed that the microbial communities thriving at the barley root-soil interface appears to be gated, as indicated by a narrow phylogenetic composition, largely dominated by members of the families Flavobacteriaceae, Rhizobiaceae and Comamonadaceae Interestingly, constrained ordinations and linear model analysis revealed that host microhabitats (i.e. root and rhizosphere) are the major determinants of the barley microbiota, while the host genotype determines its ribotype profiles to a limited extent, suggesting that the structure of the barley microbiota is a conserved trait in the tested accessions.  To gain insights on the molecular cues underlying microbial recruitment at the root-soil interface, we reconstructed 20Gbp of the barley rhizosphere metagenome. Interestingly, we observed that ~10% of the protein families encoded by the barley microbiome display a ratio between non-synonymous and synonymous substitutions (w) significantly higher than the mean of the sequenced metagenome. Intriguingly, these data might indicate an evolutionary pressure on proteins required for the microbial colonisation of the rhizosphere. Remarkably, proteins previously reported in host-microbe interactions studies (e.g. putative bacterial effectors) showed a w significantly different across genotypes, suggesting that host genetic traits contribute, at least in part, to bacterial functional diversification in the rhizosphere.  Our work provides a foundation for future studies aiming at the characterisation of the genetic bases of plant-microbiota interactions and, in the long term, the introgression of the microbiota metabolic potential into plant breeding

Biome: root:Host-associated:Plants:Rhizosphere