Next-generation sequencing (NGS) in the microbiological world: How to make the most of your money

AT Vincent, N Derome, B Boyle, AI Culley… - Journal of …, 2017 - Elsevier
The Sanger sequencing method produces relatively long DNA sequences of unmatched
quality and has been considered for long time as the gold standard for sequencing DNA …

Adaptive genetic traits in pelagic freshwater microbes

MC Chiriac, M Haber… - Environmental …, 2023 - Wiley Online Library
Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and
oceans and can be broadly categorized in two groups: free‐living, specialized oligotrophs …

Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria

SA Muñoz-Gómez, E Susko, K Williamson… - Nature ecology & …, 2022 - nature.com
Determining the phylogenetic origin of mitochondria is key to understanding the ancestral
mitochondrial symbiosis and its role in eukaryogenesis. However, the precise evolutionary …

Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity

KT Jurdzinski, M Mehrshad, LF Delgado, Z Deng… - Science …, 2023 - science.org
The crossing of environmental barriers poses major adaptive challenges. Rareness of
freshwater-marine transitions separates the bacterial communities, but how these are …

Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes

DK Ngugi, MM Salcher, AS Andrei, R Ghai, F Klotz… - Science …, 2023 - science.org
Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their
genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral …

Genomes of novel microbial lineages assembled from the sub-ice waters of Lake Baikal

PJ Cabello-Yeves, TI Zemskaya… - Applied and …, 2018 - journals.asm.org
We present a metagenomic study of Lake Baikal (East Siberia). Two samples obtained from
the water column under the ice cover (5 and 20 m deep) in March 2016 have been deep …

The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling

M Mehrshad, F Rodriguez-Valera… - The ISME …, 2018 - academic.oup.com
The dark ocean microbiota represents the unknown majority in the global ocean waters. The
SAR202 cluster belonging to the phylum Chloroflexi was the first microbial lineage …

Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat

PJ Cabello‐Yeves, TI Zemskaya… - Limnology and …, 2020 - Wiley Online Library
Lake Baikal is the deepest lake in the world. Its depth provides the only bathypelagic (>
1000 m deep) freshwater habitat on Earth and its oxic, ultra‐oligotrophic features make it a …

Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes

H Mazur-Marzec, AF Andersson… - FEMS Microbiology …, 2024 - academic.oup.com
Until recently, the data on the diversity of the entire microbial community from the Baltic Sea
were relatively rare and very scarce. However, modern molecular methods have provided …

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics

PJ Cabello-Yeves, C Callieri, A Picazo… - Environmental …, 2021 - Springer
Abstract Background The Black Sea is the largest brackish water body in the world, although
it is connected to the Mediterranean Sea and presents an upper water layer similar to some …