Parque Nacional La Campana soil microbiome Part 2
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB73862 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR12772700_1.fastq.gz | Fastqsanger.gz | |||
| ERR12772700_2.fastq.gz | Fastqsanger.gz | |||
| ERR12772701_1.fastq.gz | Fastqsanger.gz | |||
| ERR12772701_2.fastq.gz | Fastqsanger.gz | |||
| ERR12772702_1.fastq.gz | Fastqsanger.gz |
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Project description:Microbial communities in the landscapes of the Parque Nacional La Campana
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Project description:Parque Nacional La Campana (PNLC) is recognized worldwide for its flora and fauna, rather than for its microbial richness. Our goal was to characterize the structure and composition of microbial communities (bacteria, archaea and fungi) and their relationship with the plant communities typical of PNLC, such as sclerophyllous forest, xerophytic shrubland, hygrophilous forest and dry sclerophyllous forest, distributed along topoclimatic variables, namely, exposure, elevation and slope. The plant ecosystems, the physical and chemical properties of organic matter and the soil microbial composition were characterized by massive sequencing (iTag-16S rRNA, V4 and ITS1-5F) from the DNA extracted from the soil surface (5 cm, n = 16). A contribution of environmental variables, particularly related to each location, is observed. Proteobacteria (35.43%), Actinobacteria (32.86%), Acidobacteria (10.07%), Ascomycota (76.11%) and Basidiomycota (15.62%) were the dominant phyla. The beta diversity (~80% in its axes) indicates that bacteria and archaea are linked to their plant categories, where the xerophytic shrub stands out with the most particular microbial community. More specifically, Crenarchaeote, Humicola and Mortierella were dominant in the sclerophyllous forest; Chloroflexi, Cyanobacteria and Alternaria in the xerophytic shrubland; Solicoccozyma in the dry sclerophyllous forest; and Cladophialophora in the hygrophilous forest. In conclusion, the structure and composition of the microbial consortia is characteristic of PNLC's vegetation, related to its topoclimatic variables, which suggests a strong association within the soil microbiome.
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Project description:Data on marine and brackish-water fishes recorded in the area of the Parque Nacional Sistema Arrecifal Veracruzano in the southwest Gulf of Mexico were extracted from online aggregators of georeferenced location records, the recent ichthyological literature reviewed, and collections and observations made to provide a more complete faunal inventory for that park. Those actions added 95 species to a comprehensive inventory published in 2013, and brought the total to 472 species, an increase of 22%. Seventy-four percent of the additions came from online aggregators of georeferenced species records, which clearly demonstrates the value of reviewing and incorporating such data into species inventories. However, different aggregators recorded different sets of species, and some of their data were linked to outdated taxonomy or included identification errors. Hence individual records from multiple aggregators need to be obtained and reviewed for such issues when using such data to compile and revise faunal inventories. Existing lists also need to be carefully reviewed to ensure that errors are not perpetuated during updates.
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Project description:<p>Coral reef ecosystems are incredibly diverse marine biomes that rely on nutrient cycling by microorganisms to sustain high productivity in generally oligotrophic regions of the ocean. Understanding the composition of extracellular reef metabolites in seawater, the small organic molecules that serve as the currency for microorganisms, may provide insight into benthic-pelagic coupling as well as the complexity of nutrient cycling in coral reef ecosystems. Jardines de la Reina, Cuba is an ideal environment to examine extracellular metabolites across protected and high-quality reefs. Here, we used metabolic methods to quantify specific known metabolites of interest (targeted approach) and to survey trends in metabolite feature composition (untargeted approach) from surface and reef depth (6 – 14 m) seawater overlying forereefs in Jardines de la Reina. We found that untargeted metabolite feature composition was fairly similar between reef depth and surface seawater across the archipelago, corresponding with other biogeochemical and physicochemical measurements and suggesting that environmental conditions were largely homogenous across forereefs within Jardines de la Reina. Additionally, we quantified 32 of 53 detected metabolites, including amino acids, nucleosides, vitamins, and other metabolic intermediates. Two of the quantified metabolites, riboflavin and 5ʹ-methylthioadenosine (MTA), displayed interesting trends by depth and geographic location, respectively. Riboflavin concentrations were higher in reef depth compared to surface seawater, suggesting that riboflavin may be produced by reef organisms at depth and degraded in the surface through photochemical oxidation. 5ʹ-MTA concentrations increased significantly within the central region of the archipelago, displaying biogeographic patterns that warrant further investigation. Here we lay the groundwork for future investigations of variations in metabolite composition across reefs, sources and sinks of reef metabolites, and changes in metabolites over environmental, temporal, and reef health gradients.</p>
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Project description:We recently identified lysine L-lactylation (KL-la) on histones that can be labelled by L-lactate, the end-product of glycolysis. KL-la has two structural isomers, namely N--(carboxyethyl) lysine (Kce) and lysine D-lactylation (KD-la), which can also be caused by metabolites associated with glycolysis. It is unknown if perturbations of glycolysis can lead to dysregulation of KD-la and Kce, in addition to KL-la. Further, current methods have a difficulty to distinguish among these isomers in cellular contexts. To investigate these questions, we first generated specific antibodies against each one of these three modifications. These reagents enable us to distinguish these three isomers. We demonstrated that KL-la, but not KD-la and Kce, is dynamically regulated by glycolysis. KD-la and Kce occur mainly when the major glycolytic pathway is blocked downstream or when the glyoxalase system is incomplete. This result was also independently confirmed by orthogonal HPLC-mass spectrometry, showing that KL-la is the predominant isomer of lactylation on cellular histones. Finally, we demonstrated that lactyl-CoA, an intermediate between L-lactate and lactylation, is dynamically regulated by glycolysis and is positively correlated with KL-la. Thus, our study clearly shows that KL-la, but not KD-la and Kce, is the major glycolytic- and the Warburg-effect associated responsive modification in cells.
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