From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems

DR Garza, BE Dutilh - Cellular and Molecular Life Sciences, 2015 - Springer
Microorganisms and the viruses that infect them are the most numerous biological entities
on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their …

Big answers from small worlds: a user's guide for protist microcosms as a model system in ecology and evolution

F Altermatt, EA Fronhofer, A Garnier… - Methods in Ecology …, 2015 - Wiley Online Library
Laboratory microcosm experiments using protists as model organisms have a long tradition
and are widely used to investigate general concepts in population biology, community …

metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

J Bengtsson‐Palme, M Hartmann… - Molecular ecology …, 2015 - Wiley Online Library
The ribosomal rRNA genes are widely used as genetic markers for taxonomic identification
of microbes. Particularly the small subunit (SSU; 16S/18S) rRNA gene is frequently used for …

Metagenomic 16S rDNA I llumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

R Logares, S Sunagawa, G Salazar… - Environmental …, 2014 - Wiley Online Library
Sequencing of 16S rDNA polymerase chain reaction (PCR) amplicons is the most common
approach for investigating environmental prokaryotic diversity, despite the known biases …

The Majority of Active Rhodobacteraceae in Marine Sediments Belong to Uncultured Genera: A Molecular Approach to Link Their Distribution to Environmental …

M Pohlner, L Dlugosch, B Wemheuer, H Mills… - Frontiers in …, 2019 - frontiersin.org
General studies on benthic microbial communities focus on fundamental biogeochemical
processes or the most abundant constituents. Thereby, minor fractions such as the …

Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria

R Ghai, CM Mizuno, A Picazo, A Camacho… - Scientific reports, 2013 - nature.com
We describe a deep-branching lineage of marine Actinobacteria with very low GC content
(33%) and the smallest free living cells described yet (cell volume ca. 0.013 μm3), even …

Key roles for freshwater A ctinobacteria revealed by deep metagenomic sequencing

R Ghai, CM Mizuno, A Picazo, A Camacho… - Molecular …, 2014 - Wiley Online Library
Freshwater ecosystems are critical but fragile environments directly affecting society and its
welfare. However, our understanding of genuinely freshwater microbial communities …

Taxonomic profiling and functional gene annotation of microbial communities in sediment of river Ganga at Kanpur, India: insights from whole-genome metagenomics …

AK Rout, B Dehury, PK Parida, DJ Sarkar… - … Science and Pollution …, 2022 - Springer
The perennial river Ganga is recognized as one of India's largest rivers of India, but due to
continuous anthropogenic activities, the river's ecosystem is under threat. Next-generation …

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate

MW Henson, VC Lanclos, BC Faircloth… - The ISME …, 2018 - academic.oup.com
Evolutionary transitions between fresh and salt water happen infrequently among
bacterioplankton. Within the ubiquitous and highly abundant heterotrophic …

Occurrence and biodegradation of hydrocarbons at high salinities

C Abou Khalil, VL Prince, RC Prince, CW Greer… - Science of the Total …, 2021 - Elsevier
Hypersaline environments are found around the world, above and below ground, and many
are exposed to hydrocarbons on a continuous or a frequent basis. Some surface …