Metagenomics: genomic analysis of microbial communities

CS Riesenfeld, PD Schloss, J Handelsman - Annu. Rev. Genet., 2004 - annualreviews.org
▪ Abstract Uncultured microorganisms comprise the majority of the planet's biological
diversity. Microorganisms represent two of the three domains of life and contain vast …

The diversity of small eukaryotic phytoplankton (≤ 3 μm) in marine ecosystems

D Vaulot, W Eikrem, M Viprey… - FEMS microbiology …, 2008 - academic.oup.com
Small cells dominate photosynthetic biomass and primary production in many marine
ecosystems. Traditionally, picoplankton refers to cells≤ 2 μm. Here we extend the size …

Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus

P Flombaum, JL Gallegos… - Proceedings of the …, 2013 - National Acad Sciences
The Cyanobacteria Prochlorococcus and Synechococcus account for a substantial fraction
of marine primary production. Here, we present quantitative niche models for these lineages …

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

FA Matsen, RB Kodner, EV Armbrust - BMC bioinformatics, 2010 - Springer
Background Likelihood-based phylogenetic inference is generally considered to be the most
reliable classification method for unknown sequences. However, traditional likelihood-based …

Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene

F Zhu, R Massana, F Not, D Marie… - FEMS microbiology …, 2005 - academic.oup.com
Abstract A quantitative PCR (QPCR) assay based on the use of SYBR Green I was
developed to assess the abundance of specific groups of picoeukaryotes in marine waters …

Transfer of photosynthesis genes to and from Prochlorococcus viruses

D Lindell, MB Sullivan, ZI Johnson… - Proceedings of the …, 2004 - National Acad Sciences
Comparative genomics gives us a new window into phage–host interactions and their
evolutionary implications. Here we report the presence of genes central to oxygenic …

Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts

MB Sullivan, D Lindell, JA Lee, LR Thompson… - PLoS …, 2006 - journals.plos.org
Cyanophages (cyanobacterial viruses) are important agents of horizontal gene transfer
among marine cyanobacteria, the numerically dominant photosynthetic organisms in the …

Phyto REF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy

J Decelle, S Romac, RF Stern… - Molecular ecology …, 2015 - Wiley Online Library
Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of
the biosphere. The ongoing environmental metabarcoding revolution opens the perspective …

Phylogeny and taxonomy of Synechococcus–like cyanobacteria

J Komarek, JR Johansen, J Smarda, O Strunecký - Fottea, 2020 - collected.jcu.edu
Unicellular cyanobacteria constitute a substantial, ecologically important part of freshwater
and marine microflora. Solitary, elongated cyanobacterial cells without apparent slime …

Ecology of viruses in soils: past, present and future perspectives

M Kimura, ZJ Jia, N Nakayama… - Soil Science and Plant …, 2008 - Taylor & Francis
Viruses play important roles in biogeochemical nutrient cycles and act as genomic
reservoirs in marine and freshwater environments, the understanding of which brought …