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#MicrobialEcology

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Public
NIOO-KNAW

New publication: Harnessing the synergy of Urochloa brizantha and #Amazonian Dark Earth #microbiomes for enhanced #pasture recovery. #ecologicalrestoration #biodiversity #sustainability #microbialecology #soilscience
doi.org/10.1186/s12866-024-037

BioMed CentralHarnessing the synergy of Urochloa brizantha and Amazonian Dark Earth microbiomes for enhanced pasture recovery - BMC MicrobiologyAmazonian Dark Earths (ADEs) are fertile soils from the Amazon rainforest that harbor microorganisms with biotechnological potential. This study aimed to investigate the individual and potential synergistic effects of a 2% portion of ADEs and Urochloa brizantha cv. Marandu roots (Brazil’s most common grass species used for pastures) on soil prokaryotic communities and overall soil attributes in degraded soil. We conducted a comprehensive plant succession experiment in the greenhouse, utilizing vase soil samples for next-generation sequencing of 16 S rDNA, enzymatic activity assays, and soil chemical properties analysis. Univariate and multivariate analyses were performed to understand better the prokaryotic interactions within soil environments influenced by ADEs and U. brizantha roots, including differential abundance, diversity, and network analyses. Our findings reveal a complementary relationship between U. brizantha and ADEs, each contributing to distinct positive aspects of soil bacterial communities and quality. The combined influence of U. brizantha roots and ADEs exhibited synergies that enhanced prokaryotic diversity and enzyme activity. This balance supported plant growth and increased the general availability of beneficial bacteria in the soil, such as Chujaibacter and Curtobacterium while reducing the presence of potentially pathogenic taxa. This research provided valuable insights into the intricate dynamics of plant-soil feedback, emphasizing the potential for complementary interactions between specific plant species and unique soil environments like ADEs. The findings highlight the potential for pasture ecological rehabilitation and underscore the benefits of integrating plant and soil management strategies to optimize soil characteristics.
Public
nf-core

🦠 Interested in #nextflow & anything 'meta-' ?(#metagenomics, #metabarcoding, #metatranscriptomics, #metaproteomics, #microbes #MicrobialEcology & more!)

📆 Join us next Tuesday 13:00 CEST (3rd September) for an nf-core #bytesize for the #metaomics #nfcore special interest group! (Also on YouTube after!)

🤝 We will introduce how we want the community to work together with #users and #bioinformatics developers to make the best pipelines for anything 'meta-'

ℹ️ Zoom: nf-co.re/events/2024/bytesize_

nf-co.reBytesize: Special Interest Group meta-omicsDaniel Lundin (Linnaeus University / Stockholm University), James Fellows Yates (HKI Jena / MPI-EVA Leipzig) and Carson J. Miller (University of Washington)
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Raphael Eisenhofer

1) Want to know how much of your metagenome is eukaryotic? No references? No problem. We developed SingleM microbial fraction (SMF) and ran it on 250k metagenomes biorxiv.org/content/10.1101/20.

If you know what Eukaryotes are there, you can filter reads by mapping to their genomes. However, often you don’t know what’s in your sample, or the euk doesn’t have a genome.

bioRxiv · Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patternsMetagenomes often contain many reads derived from eukaryotes. However, there is usually no reliable method for estimating the prevalence of non-microbial reads in a metagenome, forcing many analysis techniques to make the often-faulty assumption that all reads are microbial. For instance, the success of metagenome-assembled genome (MAG) recovery efforts is assessed by the number of reads mapped to recovered MAGs, a procedure which will underestimate the true fidelity if eukaryotic reads are present. Here we present SingleM microbial_fraction (SMF), a scalable algorithm that robustly estimates the number of bacterial and archaeal reads in a metagenome, and the average microbial genome size. SMF does not use eukaryotic reference genome data and can be applied to any Illumina metagenome. Based on SMF, we propose the Domain-Adjusted Mapping Rate (DAMR) as an improved metric to assess microbial genome recovery from metagenomes. We benchmark SMF on simulated and real data, and demonstrate how DAMRs can guide genome recovery. Applying SMF to 136,284 publicly available metagenomes, we report substantial variation in microbial fractions and biome-specific patterns of microbial abundance, providing insights into how microorganisms and eukaryotes are distributed across Earth. Finally, we show that substantial amounts of human host DNA sequence data have been deposited in public metagenome repositories, possibly counter to ethical directives that mandate screening of these reads prior to release. As the adoption of metagenomic sequencing continues to grow, we foresee SMF being a valuable tool for the appraisal of genome recovery efforts, and the recovery of global patterns of microorganism distribution. ### Competing Interest Statement The authors have declared no competing interest.
#metagenomics#bioinformatics#genomics
Public
Kathe Todd-Brown

Models are the bridge between theory and data. With new omics and other tools being increasing applied to soil carbon cycling, how well are our models making this connection? Schimel 2023 doi.org/10.1016/j.soilbio.2023 concludes that microbial explicit models are still, very much, in the development phase and outlines why this is a hard problem. #SoilCarbonModel #MicrobialEcology #SoilBGC #SoilCarbonCycling #ReviewArticle #SciLit

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Kostas Kormas

The AnimalAssociatedMetagenomeDB reveals a bias towards #livestock and developed countries and blind spots in functional-potential studies of #animal-associated #microbiomes

animalmicrobiome.biomedcentral

#gutmicrobes #hostmicrobiota #hostmicrobe #microbialecology #symbiosis #microbeinteractions @MicrobioJC @PeerJ @IMPACTT @openscience @MicrobioJC @bioRxiv_microbio

BioMed CentralThe AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes - Animal MicrobiomeBackground Metagenomic data can shed light on animal-microbiome relationships and the functional potential of these communities. Over the past years, the generation of metagenomics data has increased exponentially, and so has the availability and reusability of data present in public repositories. However, identifying which datasets and associated metadata are available is not straightforward. We created the Animal-Associated Metagenome Metadata Database (AnimalAssociatedMetagenomeDB - AAMDB) to facilitate the identification and reuse of publicly available non-human, animal-associated metagenomic data, and metadata. Further, we used the AAMDB to (i) annotate common and scientific names of the species; (ii) determine the fraction of vertebrates and invertebrates; (iii) study their biogeography; and (iv) specify whether the animals were wild, pets, livestock or used for medical research. Results We manually selected metagenomes associated with non-human animals from SRA and MG-RAST. Next, we standardized and curated 51 metadata attributes (e.g., host, compartment, geographic coordinates, and country). The AAMDB version 1.0 contains 10,885 metagenomes associated with 165 different species from 65 different countries. From the collected metagenomes, 51.1% were recovered from animals associated with medical research or grown for human consumption (i.e., mice, rats, cattle, pigs, and poultry). Further, we observed an over-representation of animals collected in temperate regions (89.2%) and a lower representation of samples from the polar zones, with only 11 samples in total. The most common genus among invertebrate animals was Trichocerca (rotifers). Conclusion Our work may guide host species selection in novel animal-associated metagenome research, especially in biodiversity and conservation studies. The data available in our database will allow scientists to perform meta-analyses and test new hypotheses (e.g., host-specificity, strain heterogeneity, and biogeography of animal-associated metagenomes), leveraging existing data. The AAMDB WebApp is a user-friendly interface that is publicly available at https://webapp.ufz.de/aamdb/ .
Public
Kathe Todd-Brown

Biodiviersity interactions with multiple anthropogenic global change factors shows a fall off effect as the number of those factors increase. Not entirely convinced they captured function here but overall an interesting study. Yang etal 2022 nature.com/articles/s41467-022 #microbialEcology #GlobalChange #SciLit

NatureMultiple anthropogenic pressures eliminate the effects of soil microbial diversity on ecosystem functions in experimental microcosms - Nature CommunicationsIt is unclear whether the positive effects of biodiversity on ecosystem functioning are maintained under multifaceted anthropogenic disturbance. In this experiment, the authors show that multiple simultaneous stressors can negate the positive effect of microbial diversity on soil functions.
Public
Kostas Kormas

Save the #microbes to save the #planet
tinyurl.com/57xmt8mu

@IMPACTT @MicrobioJC #SciComm @academicchatter @academicsunite @openscience @bykriscampbell
@EUClimateAction @climatecrisis
@academicchatter @academicsunite
#academicchatter @openscience
@phdlife @PhD_Genie @phdstudents
#phdlife #highereducation #postdocjobs #postdocposition #postdoclife #research #studyabroad #OpenScience #microbialecology #symbiosis @MicrobioJC @PeerJ @peerjlife
#CIRCLESEU

BioMed CentralSave the microbes to save the planet. A call to action of the International Union of the Microbiological Societies (IUMS) - One Health OutlookOur planet is populated by at least a trillion species of microorganisms. Every life form is sustained by them and they make the planet habitable. Only a minority of them, about 1400 species, cause infectious diseases that are responsible for human morbidity, mortality, pandemics and the resulting huge economic losses. Modern human activities, environmental changes and the attempt to control infectious agents using broad spectrum antibiotics and disinfectants jeopardize the global microbial diversity. The International Union of the Microbiological Societies (IUMS) is launching a call to action to mobilize all microbiological societies globally to promote the development of sustainable solutions to control infectious agents while preserving the global microbial diversity and the healthy life of our planet.
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