Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

TO Delmont, M Gaia, DD Hinsinger, P Fremont… - Cell Genomics, 2022 - cell.com
Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate.
However, their poor representation in culture collections limits our understanding of the …

Diatoms and their microbiomes in complex and changing polar oceans

R Gilbertson, E Langan, T Mock - Frontiers in Microbiology, 2022 - frontiersin.org
Diatoms, a key group of polar marine microbes, support highly productive ocean
ecosystems. Like all life on earth, diatoms do not live in isolation, and they are therefore …

Multi-omics for studying and understanding polar life

MS Clark, JI Hoffman, LS Peck, L Bargelloni… - Nature …, 2023 - nature.com
Polar ecosystems are experiencing amongst the most rapid rates of regional warming on
Earth. Here, we discuss 'omics' approaches to investigate polar biodiversity, including the …

Tiara: deep learning-based classification system for eukaryotic sequences

M Karlicki, S Antonowicz, A Karnkowska - Bioinformatics, 2022 - academic.oup.com
Motivation With a large number of metagenomic datasets becoming available, eukaryotic
metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear …

Updated virophage taxonomy and distinction from polinton-like viruses

S Roux, MG Fischer, T Hackl, LA Katz, F Schulz… - Biomolecules, 2023 - mdpi.com
Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-
infection of a protist (ie, microeukaryotic) host and represent an exceptional case of …

Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton

H Alexander, SK Hu, AI Krinos, M Pachiadaki, BJ Tully… - mBio, 2023 - Am Soc Microbiol
Metagenomics is a powerful method for interpreting the ecological roles and physiological
capabilities of mixed microbial communities. Yet, many tools for processing metagenomic …

Bio-organic fertilizer promotes pear yield by shaping the rhizosphere microbiome composition and functions

Z Wang, T Yang, X Mei, N Wang, X Li… - Microbiology …, 2022 - Am Soc Microbiol
Bio-organic fertilizers (BOF) containing both organic amendments and beneficial
microorganisms have been consistently shown to improve soils fertility and yield. However …

Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

H Doré, U Guyet, J Leconte, GK Farrant, B Alric… - The ISME …, 2023 - academic.oup.com
The ever-increasing number of available microbial genomes and metagenomes provides
new opportunities to investigate the links between niche partitioning and genome evolution …

Multiomics in the central Arctic Ocean for benchmarking biodiversity change

T Mock, W Boulton, JP Balmonte, K Barry… - PLoS …, 2022 - journals.plos.org
Multiomics approaches need to be applied in the central Arctic Ocean to benchmark
biodiversity change and to identify novel species and their genes. As part of MOSAiC …

VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

JL Espinoza, CL Dupont - BMC bioinformatics, 2022 - Springer
Background With the advent of metagenomics, the importance of microorganisms and how
their interactions are relevant to ecosystem resilience, sustainability, and human health has …