Microbial plankton play a central role in marine biogeochemical cycles, but the timing in which abundant lineages diversified into ocean environments remains unclear. Here, we reconstructed the timeline in which major clades of bacteria and archaea colonized the ocean using a high-resolution benchmarked phylogenetic tree that allows for simultaneous and direct comparison of the ages of multiple divergent lineages. Our findings show that the diversification of the most prevalent marine clades spans throughout a period of 2.2 Ga, with most clades colonizing the ocean during the last 800 million years. The oldest clades - SAR202, SAR324, . Marinimicrobia, and Marine Group II - diversified around the time of the Great Oxidation Event, during which oxygen concentration increased but remained at microaerophilic levels throughout the Mid-Proterozoic, consistent with the prevalence of some clades within these groups in oxygen minimum zones today. We found the diversification of the prevalent heterotrophic marine clades SAR11, SAR116, SAR92, SAR86, and Roseobacter as well as the Marine Group I to occur near to the Neoproterozoic Oxygenation Event (0.8-0.4 Ga). The diversification of these clades is concomitant with an overall increase of oxygen and nutrients in the ocean at this time, as well as the diversification of eukaryotic algae, consistent with the previous hypothesis that the diversification of heterotrophic bacteria is linked to the emergence of large eukaryotic phytoplankton. The youngest clades correspond to the widespread phototrophic clades and , whose diversification happened after the Phanerozoic Oxidation Event (0.45-0.4 Ga), in which oxygen concentrations had already reached their modern levels in the atmosphere and the ocean. Our work clarifies the timing at which abundant lineages of bacteria and archaea colonized the ocean, thereby providing key insights into the evolutionary history of lineages that comprise the majority of prokaryotic biomass in the modern ocean.
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http://dx.doi.org/10.7554/eLife.88268 | DOI Listing |
Sci Rep
January 2025
Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
The Mycobacterium avium complex (MAC) is a group of closely related nontuberculous mycobacteria that can cause various diseases in humans. In this study, genome sequencing, comprehensive genomic analysis, and antimicrobial susceptibility testing of 66 MAC clinical isolates from King Chulalongkorn Memorial Hospital, Bangkok, Thailand were carried out. Whole-genome average nucleotide identity (ANI) revealed the MAC species distribution, comprising 54 (81.
View Article and Find Full Text PDFPlant Physiol Biochem
December 2024
National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Sanya Institute, Nanjing Agricultural University, Zhongshan Biological Breeding Laboratory, Nanjing, 210095, PR China; College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009, China. Electronic address:
Radish is an important annual root vegetable crop, whose yield is largely dependent on taproot thickening and development. However, the regulatory network of WOXs-mediated taproot development remains poorly understood in radish. Herein, the RsWOX13 was classified in an ancient clade of the WOX gene family that harbors a conserved homeodomain.
View Article and Find Full Text PDFAm J Bot
January 2025
Department of Biology, University of Idaho, Moscow, 83844, Idaho, USA.
Premise: Considering rapidly changing fire regimes due to anthropogenic disturbances to climate and fuel loads, it is crucial to understand the underpinnings driving fire-adapted trait evolution. Among the oldest lineages affected by fire is Coniferae. This lineage occupies a variety of fire prone and non-fire prone habitats across all hemispheres and has four fire-adapted traits: (1) thick bark; (2) serotiny; (3) seedling grass stage; and (4) resprouting ability.
View Article and Find Full Text PDFSci Rep
January 2025
Analytical Research Center for Experimental Sciences, Saga University, Saga, Japan.
The chloroplast (cp) genome is a widely used tool for exploring plant evolutionary relationships, yet its effectiveness in fully resolving these relationships remains uncertain. Integrating cp genome data with nuclear DNA information offers a more comprehensive view but often requires separate datasets. In response, we employed the same raw read sequencing data to construct cp genome-based trees and nuclear DNA phylogenetic trees using Read2Tree, a cost-efficient method for extracting conserved nuclear gene sequences from raw read data, focusing on the Aurantioideae subfamily, which includes Citrus and its relatives.
View Article and Find Full Text PDFMol Genet Genomics
January 2025
Department of Botany, Biology Institute, UnB, Brasília, DF, 70910-900, Brazil.
Precursors of microRNAs (pre-miRNAs) are less used in silico to mine miRNAs. This study developed PmiR-Select based on covariance models (CMs) to identify new pre-miRNAs, detecting conserved secondary structural features across RNA sequences and eliminating the redundancy. The pipeline preceded PmiR-Select filtered 20% plant pre-miRNAs (from 38589 to 8677) from miRBase.
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