A PHP Error was encountered

Severity: Warning

Message: file_get_contents(https://...@gmail.com&api_key=61f08fa0b96a73de8c900d749fcb997acc09): Failed to open stream: HTTP request failed! HTTP/1.1 429 Too Many Requests

Filename: helpers/my_audit_helper.php

Line Number: 143

Backtrace:

File: /var/www/html/application/helpers/my_audit_helper.php
Line: 143
Function: file_get_contents

File: /var/www/html/application/helpers/my_audit_helper.php
Line: 209
Function: simplexml_load_file_from_url

File: /var/www/html/application/helpers/my_audit_helper.php
Line: 994
Function: getPubMedXML

File: /var/www/html/application/helpers/my_audit_helper.php
Line: 3134
Function: GetPubMedArticleOutput_2016

File: /var/www/html/application/controllers/Detail.php
Line: 574
Function: pubMedSearch_Global

File: /var/www/html/application/controllers/Detail.php
Line: 488
Function: pubMedGetRelatedKeyword

File: /var/www/html/index.php
Line: 316
Function: require_once

Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota. | LitMetric

AI Article Synopsis

  • - The NTL-LTER program studies how freshwater lakes, like Lake Mendota, respond to environmental changes over nearly two decades, focusing on metagenomic data collected from 2000 to 2019.
  • - Researchers used a specialized tool called MetaHipMer to compile over 10 terabases of sequencing data into 1,894 unique, high-quality metagenome-assembled genomes (MAGs), primarily from bacteria and some eukaryotes.
  • - This extensive dataset offers valuable insights into microbial diversity and dynamics in freshwater ecosystems, including the identification of thousands of viral sequences, aiding in future ecological research.

Article Abstract

The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11374980PMC
http://dx.doi.org/10.1038/s41597-024-03826-8DOI Listing

Publication Analysis

Top Keywords

lake mendota
8
coassembly binning
4
binning twenty-year
4
twenty-year metagenomic
4
metagenomic time-series
4
time-series lake
4
mendota north
4
north temperate
4
temperate lakes
4
lakes long-term
4

Similar Publications

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!