Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function.

GigaScience
Kate ReddingtonBonnie L Brown

Abstract

Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic purposes (drinking water, recreation, agriculture, and industry), it is essential to understand how these activities affect the composition of river microbial consortia. Recent studies have shown that river metagenomes vary considerably, suggesting that microbial community data should be included in broad-scale river ecosystem models. But such ecogenomic studies have not been applied on a broad "aquascape" scale, and few if any have applied the newest nanopore technology. We investigated the metagenomes of 11 rivers across 3 continents using MinION nanopore sequencing, a portable platform that could be useful for future global river monitoring. Up to 10 Gb of data per run were generated with average read lengths of 3.4 kb. Diversity and diagnosis of river function potential was accomplished with 0.5-1.0 ⋅ 106 long reads. Our observations for 7 of the 11 rivers conformed to other river-omic findings, and we exposed previously unrecognized microbial biodiversity in the other 4 rivers. Deeper understanding that emerged is that river microbial cons...Continue Reading

References

Aug 30, 2006·Ecological Applications : a Publication of the Ecological Society of America·Susan P Davies, Susan K Jackson
Nov 7, 2006·Applied and Environmental Microbiology·Christian WinterAndreas H Farnleitner
Feb 17, 2007·American Journal of Physical Medicine & Rehabilitation·Franziska WickMarius C Wick
Mar 5, 2011·Microbiology and Molecular Biology Reviews : MMBR·Ryan J NewtonStefan Bertilsson
Sep 15, 2011·PloS One·Rohit GhaiFlavio Henrique-Silva
Mar 4, 2014·Genome Biology·Derrick E Wood, Steven L Salzberg
May 7, 2014·The Journal of Antimicrobial Chemotherapy·G C A AmosE M Wellington
May 23, 2015·Science·Shinichi SunagawaPeer Bork
Sep 22, 2015·Standards in Genomic Sciences·Bonnie L BrownTimothy L King
Jan 7, 2016·Frontiers in Microbiology·Thea Van RossumFiona S L Brinkman
Aug 31, 2016·Nature Communications·Kristy DeinerFlorian Altermatt
Mar 23, 2017·GigaScience·Bonnie L BrownRima B Franklin
Jul 20, 2017·Microbial Ecology·Pedro C JungerVinicius F Farjalla
Oct 5, 2017·PloS One·Michele MenegonMassimo Delledonne
Sep 5, 2018·Scientific Data·Steven J BillerSallie W Chisholm
Mar 2, 2019·The British Journal of General Practice : the Journal of the Royal College of General Practitioners·Abi Eccles
Apr 3, 2019·International Journal of Environmental Research and Public Health·Steve HamnerTimothy E Ford
May 16, 2019·GigaScience·Samuel M NichollsNicholas J Loman
Jul 13, 2019·Nature Communications·Alexander T DiltheyAdam M Phillippy
Nov 7, 2019·Nature Communications·Jethro S JohnsonGeorge M Weinstock
Oct 24, 2019·Environmental Microbiome·H Soon GweonUNKNOWN REHAB consortium

❮ Previous
Next ❯

Citations

Jan 20, 2021·ELife·Lara UrbanMaximilian R Stammnitz
Jul 3, 2021·Biosensors·Bo LinHongju Mao
Jun 17, 2021·Applied and Environmental Microbiology·Leho TedersooBenjamin Callahan

❮ Previous
Next ❯

Methods Mentioned

BETA
PCAs
PCA
PCR
electrophoresis

Software Mentioned

RAST
fastx
MinION
length
Kraken2
MG
SEED viewer
Porechop
One Codex
EBI

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.