[HTML][HTML] Microbial mat ecosystems: structure types, functional diversity, and biotechnological application

CM Prieto-Barajas, E Valencia-Cantero… - Electronic Journal of …, 2018 - Elsevier
Microbial mats are horizontally stratified microbial communities, exhibiting a structure
defined by physiochemical gradients, which models microbial diversity, physiological …

High throughput sequencing methods and analysis for microbiome research

JM Di Bella, Y Bao, GB Gloor, JP Burton… - Journal of microbiological …, 2013 - Elsevier
High-throughput sequencing technology is rapidly improving in quality, speed and cost. It is
therefore becoming more widely used to study whole communities of prokaryotes in many …

Binning metagenomic contigs by coverage and composition

J Alneberg, BS Bjarnason, I De Bruijn, M Schirmer… - Nature …, 2014 - nature.com
Shotgun sequencing enables the reconstruction of genomes from complex microbial
communities, but because assembly does not reconstruct entire genomes, it is necessary to …

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

R Caspi, T Altman, R Billington, K Dreher… - Nucleic acids …, 2014 - academic.oup.com
Abstract The MetaCyc database (MetaCyc. org) is a comprehensive and freely accessible
database describing metabolic pathways and enzymes from all domains of life. MetaCyc …

Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States

N Fierer, J Ladau, JC Clemente, JW Leff, SM Owens… - Science, 2013 - science.org
Native tallgrass prairie once dominated much of the midwestern United States, but this
biome and the soil microbial diversity that once sustained this highly productive system have …

[HTML][HTML] Genome reduction in an abundant and ubiquitous soil bacterium 'Candidatus Udaeobacter copiosus'

TE Brewer, KM Handley, P Carini, JA Gilbert… - Nature …, 2016 - nature.com
Although bacteria within the Verrucomicrobia phylum are pervasive in soils around the
world, they are under-represented in both isolate collections and genomic databases. Here …

[HTML][HTML] Metagenome-assembled genomes uncover a global brackish microbiome

LW Hugerth, J Larsson, J Alneberg, MV Lindh… - Genome biology, 2015 - Springer
Background Microbes are main drivers of biogeochemical cycles in oceans and lakes.
Although the genome is a foundation for understanding the metabolism, ecology and …

Verrucomicrobia are candidates for polysaccharide-degrading bacterioplankton in an arctic fjord of Svalbard

Z Cardman, C Arnosti, A Durbin… - Applied and …, 2014 - Am Soc Microbiol
In Arctic marine bacterial communities, members of the phylum Verrucomicrobia are
consistently detected, although not typically abundant, in 16S rRNA gene clone libraries and …

Distinction between Cr and other heavy–metal–resistant bacteria involved in C/N cycling in contaminated soils of copper producing sites

J Zhang, Q Shi, S Fan, Y Zhang, M Zhang… - Journal of hazardous …, 2021 - Elsevier
For typical copper producing provinces of Heilongjiang, Henan, Inner Mongolia, Jiangxi,
Shandong, Tibet, and Yunnan in China, 90% of sampling sites were heavily polluted with …

[HTML][HTML] Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil

C Pepe-Ranney, AN Campbell, CN Koechli… - Frontiers in …, 2016 - frontiersin.org
We explored microbial contributions to decomposition using a sophisticated approach to
DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological …