4.5 Article

Comprehensive Phylogenomics of Methylobacterium Reveals Four Evolutionary Distinct Groups and Underappreciated Phyllosphere Diversity

Related references

Note: Only part of the references are listed.
Article Microbiology

Fine-Scale Adaptations to Environmental Variation and Growth Strategies Drive Phyllosphere Methylobacterium Diversity

Jean-Baptiste Leducq et al.

Summary: This study discovered a significant diversity of Methylobacterium on plant leaves and demonstrated the biogeographic, seasonal, and growth strategy characteristics of this diversity. The results revealed the temperature adaptation, geographical and seasonal structuring of Methylobacterium diversity. The study also revealed a progressive replacement of lineages with different growth strategies at the end of the growing season.
Article Microbiology

Aerobic Methoxydotrophy: Growth on Methoxylated Aromatic Compounds by Methylobacteriaceae

Jessica A. Lee et al.

Summary: This article describes a group of Methylobacterium strains that can metabolize methoxy groups from aromatic compounds and suggests that this ability may be ancestral to two clades of Methylobacterium. The study also found that these aromatic-degrading Methylobacterium are particularly abundant in soil and root environments based on published metagenome data. Furthermore, the research revealed that Methylobacterium do not excrete formaldehyde as a byproduct during lignin degradation.

FRONTIERS IN MICROBIOLOGY (2022)

Article Biology

Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species

Thomas Sakoparnig et al.

Summary: Recombination is common in bacteria, and phylogenies based on whole genome alignments may not accurately reflect clonal relationships but rather the distribution of recombination rates among lineages. Bacterial populations are structured in a way that recombination rates vary drastically between lineages, leading to a complex pattern of genetic diversity.

ELIFE (2021)

Review Biochemistry & Molecular Biology

Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century

Eugene Koonin et al.

Summary: Prokaryote genomics has seen significant progress in the past 25 years, with exponential growth of the database. Advances in technology have led to an increasingly unbiased understanding of the characteristics of global prokaryotic diversity.

TRENDS IN MICROBIOLOGY (2021)

Article Microbiology

Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species

Ola Alessa et al.

Summary: This study used a comprehensive comparative genomics approach to reveal the phylogenetic relationships among PPFMs and explain the genotypic differences that confer their different phenotypes. The research found that methylotrophy, nitrate utilization, and anoxygenic photosynthesis are distinguishing features of PPFMs from other members of Methylobacteriaceae. Additionally, some strains lack MxaF-type methanol dehydrogenase but possess XoxF-type MDH enabling growth on methanol in the presence of lanthanum.

FRONTIERS IN MICROBIOLOGY (2021)

Article Microbiology

Methylobacterium ajmalii sp. nov., Isolated From the International Space Station

Swati Bijlani et al.

Summary: Three novel bacterial strains, IF7SW-B2(T), IIF1SW-B5, and IIF4SW-B5, belonging to the genus Methylobacterium, were isolated from the International Space Station (ISS). These strains are proposed to be a new species named Methylobacterium ajmalii based on genomic, phylogenetic, biochemical, and fatty acid analyses.

FRONTIERS IN MICROBIOLOGY (2021)

Article Microbiology

Methylobacterium durans sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil

Jiyoun Kim et al.

ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY (2020)

Article Microbiology

Methylobacterium crusticola sp. nov., isolated from biological soil crusts

Li Juan Jia et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2020)

Article Microbiology

Methylobacterium terricola sp. nov., a gamma radiation-resistan bacterium isolated from gamma ray-irradiated soil

Jiyoun Kim et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2020)

Article Biochemistry & Molecular Biology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Microbiology

Methylobacterium planium sp. nov., isolated from a lichen sample

Longqian Jiang et al.

ARCHIVES OF MICROBIOLOGY (2020)

Article Microbiology

Methylobacterium nonmethylotrophicum sp. nov., isolated from tungsten mine tailing

Guang-Da Feng et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2020)

Article Biochemical Research Methods

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

Emmanuel Paradis et al.

BIOINFORMATICS (2019)

Article Microbiology

Methylobacterium oryzihabitans sp. nov., isolated from water sampled from a rice paddy field

Wen-Ming Chen et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2019)

Article Genetics & Heredity

Genomic features of bacterial adaptation to plants

Asaf Levy et al.

NATURE GENETICS (2018)

Article Biochemical Research Methods

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

Chao Zhang et al.

BMC BIOINFORMATICS (2018)

Article Ecology

Bacterial diversification through geological time

Stilianos Louca et al.

NATURE ECOLOGY & EVOLUTION (2018)

Article Microbiology

Using Core Genome Alignments To Assign Bacterial Species

Matthew Chung et al.

MSYSTEMS (2018)

Article Microbiology

Enterovirga rhinocerotis gen. nov., sp nov., isolated from Rhinoceros unicornis faeces

Xiu Chen et al.

ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY (2017)

Article Biochemistry & Molecular Biology

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

Erfan Sayyari et al.

MOLECULAR BIOLOGY AND EVOLUTION (2016)

Review Genetics & Heredity

What Is Speciation?

B. Jesse Shapiro et al.

PLOS GENETICS (2016)

Article Biotechnology & Applied Microbiology

Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

Ruth Davidson et al.

BMC GENOMICS (2015)

Review Biotechnology & Applied Microbiology

Biotechnological and Agronomic Potential of Endophytic Pink-Pigmented Methylotrophic Methylobacterium spp.

Manuella Nobrega Dourado et al.

BIOMED RESEARCH INTERNATIONAL (2015)

Article Biochemical Research Methods

Quartet Inference from SNP Data Under the Coalescent Model

Julia Chifman et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

ASTRAL: genome-scale coalescent-based species tree estimation

S. Mirarab et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Evolutionary Biology

Selecting optimal partitioning schemes for phylogenomic datasets

Robert Lanfear et al.

BMC EVOLUTIONARY BIOLOGY (2014)

Article Microbiology

Psychroglaciecola arctica gen. nov., sp nov., isolated from Arctic glacial foreland soil

Zhihao Qu et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2014)

Review Microbiology

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

Jongsik Chun et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2014)

Review Environmental Sciences

Microbiology of the Anthropocene

Michael R. Gillings et al.

ANTHROPOCENE (2014)

Article Biochemical Research Methods

Accurate and universal delineation of prokaryotic species

Daniel R. Mende et al.

NATURE METHODS (2013)

Article Microbiology

Complete Genome Sequences of Six Strains of the Genus Methylobacterium

Christopher J. Marx et al.

JOURNAL OF BACTERIOLOGY (2012)

Article Biochemistry & Molecular Biology

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

Robert Lanfear et al.

MOLECULAR BIOLOGY AND EVOLUTION (2012)

Editorial Material Microbiology

Evolution of genome base composition and genome size in bacteria

Hiromi Nishida

FRONTIERS IN MICROBIOLOGY (2012)

Article Multidisciplinary Sciences

Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

Christopher J. Creevey et al.

PLOS ONE (2011)

Article Evolutionary Biology

Factors affecting the concordance between orthologous gene trees and species tree in bacteria

Santiago Castillo-Ramirez et al.

BMC EVOLUTIONARY BIOLOGY (2008)

Article Biotechnology & Applied Microbiology

The RAST server: Rapid annotations using subsystems technology

Ramy K. Aziz et al.

BMC GENOMICS (2008)

Article Multidisciplinary Sciences

Methane emissions from terrestrial plants under aerobic conditions

F Keppler et al.

NATURE (2006)

Review Microbiology

Towards a prokaryotic genomic taxonomy

T Coenye et al.

FEMS MICROBIOLOGY REVIEWS (2005)

Article Microbiology

Methylobacterium nodulans sp nov., for a group of aerobic, facultatively methylotrophic, legume root-nodule-forming and nitrogen-fixing bacteria

P Jourand et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2004)

Article Microbiology

Microvirga subterranea gen. nov., sp nov., a moderate thermophile from a deep subsurface Australian thermal aquifer

S Kanso et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2003)

Article Biochemistry & Molecular Biology

Cytoscape: A software environment for integrated models of biomolecular interaction networks

P Shannon et al.

GENOME RESEARCH (2003)

Article Microbiology

Aerobic methylobacteria are capable of synthesizing auxins

EG Ivanova et al.

MICROBIOLOGY (2001)