Evolutionary Timeline and Genomic Plasticity Underlying the Lifestyle Diversity in <italic toggle="yes">Rhizobiales</italic>

ABSTRACT Members of the order Rhizobiales include those capable of nitrogen fixation in nodules as well as pathogens of animals and plants. This lifestyle diversity has important implications for agricultural and medical research. Leveraging large-scale genomic data, we infer that Rhizobiales origin...

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Autores principales:	Sishuo Wang, Andrew Meade, Hon-Ming Lam, Haiwei Luo
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	Rhizobiales rhizobia lifestyle evolution molecular clock bacterial evolution microbial evolution Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/7a25dae7c7a0461eb78b81f6d46aa8bd
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spelling	oai:doaj.org-article:7a25dae7c7a0461eb78b81f6d46aa8bd2021-12-02T18:15:46ZEvolutionary Timeline and Genomic Plasticity Underlying the Lifestyle Diversity in <italic toggle="yes">Rhizobiales</italic>10.1128/mSystems.00438-202379-5077https://doaj.org/article/7a25dae7c7a0461eb78b81f6d46aa8bd2020-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00438-20https://doaj.org/toc/2379-5077ABSTRACT Members of the order Rhizobiales include those capable of nitrogen fixation in nodules as well as pathogens of animals and plants. This lifestyle diversity has important implications for agricultural and medical research. Leveraging large-scale genomic data, we infer that Rhizobiales originated as a free-living ancestor ∼1,500 million years ago (Mya) and that the later emergence of host-associated lifestyles broadly coincided with the rise of their eukaryotic hosts. In particular, the first nodulating lineage arose from either Azorhizobium or Bradyrhizobium 150 to 80 Mya, a time range in general concurrent with the emergence of legumes. The rates of lifestyle transitions are highly variable; nodule association is more likely to be lost than gained, whereas animal association likely represents an evolutionary dead end. We searched for statistical correlations between gene presence and lifestyle and identified genes likely contributing to the transition and adaptation to the same lifestyle in divergent lineages. Among the genes potentially promoting successful transitions to major nodulation lineages, the nod and nif clusters for nodulation and nitrogen fixation, respectively, were repeatedly acquired during each transition; the fix, dct, and phb clusters involved in energy conservation under micro-oxic conditions were present in the nonnodulating ancestors; and the secretion systems were acquired in lineage-specific patterns. Our study data suggest that increased eukaryote diversity drives lifestyle diversification of bacteria and highlight both acquired and preexisting traits facilitating the origin of host association. IMPORTANCE Bacteria form diverse interactions with eukaryotic hosts. This is well represented by the Rhizobiales, a clade of Alphaproteobacteria strategically important for their large diversity of lifestyles with implications for agricultural and medical research. To investigate their lifestyle evolution, we compiled a comprehensive data set of genomes and lifestyle information for over 1,000 Rhizobiales genomes. We show that the origins of major host-associated lineages in Rhizobiales broadly coincided with the emergences of their host plants/animals, suggesting bacterium-host interactions as a driving force in the evolution of Rhizobiales. We further found that, in addition to gene gains, preexisting traits and recurrent losses of specific genomic traits may have played underrecognized roles in the origin of host-associated lineages, providing clues to genetic engineering of microbial agricultural inoculants and prevention of the emergence of potential plant/animal pathogens.Sishuo WangAndrew MeadeHon-Ming LamHaiwei LuoAmerican Society for MicrobiologyarticleRhizobialesrhizobialifestyle evolutionmolecular clockbacterial evolutionmicrobial evolutionMicrobiologyQR1-502ENmSystems, Vol 5, Iss 4 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Rhizobiales rhizobia lifestyle evolution molecular clock bacterial evolution microbial evolution Microbiology QR1-502
spellingShingle	Rhizobiales rhizobia lifestyle evolution molecular clock bacterial evolution microbial evolution Microbiology QR1-502 Sishuo Wang Andrew Meade Hon-Ming Lam Haiwei Luo Evolutionary Timeline and Genomic Plasticity Underlying the Lifestyle Diversity in <italic toggle="yes">Rhizobiales</italic>
description	ABSTRACT Members of the order Rhizobiales include those capable of nitrogen fixation in nodules as well as pathogens of animals and plants. This lifestyle diversity has important implications for agricultural and medical research. Leveraging large-scale genomic data, we infer that Rhizobiales originated as a free-living ancestor ∼1,500 million years ago (Mya) and that the later emergence of host-associated lifestyles broadly coincided with the rise of their eukaryotic hosts. In particular, the first nodulating lineage arose from either Azorhizobium or Bradyrhizobium 150 to 80 Mya, a time range in general concurrent with the emergence of legumes. The rates of lifestyle transitions are highly variable; nodule association is more likely to be lost than gained, whereas animal association likely represents an evolutionary dead end. We searched for statistical correlations between gene presence and lifestyle and identified genes likely contributing to the transition and adaptation to the same lifestyle in divergent lineages. Among the genes potentially promoting successful transitions to major nodulation lineages, the nod and nif clusters for nodulation and nitrogen fixation, respectively, were repeatedly acquired during each transition; the fix, dct, and phb clusters involved in energy conservation under micro-oxic conditions were present in the nonnodulating ancestors; and the secretion systems were acquired in lineage-specific patterns. Our study data suggest that increased eukaryote diversity drives lifestyle diversification of bacteria and highlight both acquired and preexisting traits facilitating the origin of host association. IMPORTANCE Bacteria form diverse interactions with eukaryotic hosts. This is well represented by the Rhizobiales, a clade of Alphaproteobacteria strategically important for their large diversity of lifestyles with implications for agricultural and medical research. To investigate their lifestyle evolution, we compiled a comprehensive data set of genomes and lifestyle information for over 1,000 Rhizobiales genomes. We show that the origins of major host-associated lineages in Rhizobiales broadly coincided with the emergences of their host plants/animals, suggesting bacterium-host interactions as a driving force in the evolution of Rhizobiales. We further found that, in addition to gene gains, preexisting traits and recurrent losses of specific genomic traits may have played underrecognized roles in the origin of host-associated lineages, providing clues to genetic engineering of microbial agricultural inoculants and prevention of the emergence of potential plant/animal pathogens.
format	article
author	Sishuo Wang Andrew Meade Hon-Ming Lam Haiwei Luo
author_facet	Sishuo Wang Andrew Meade Hon-Ming Lam Haiwei Luo
author_sort	Sishuo Wang
title	Evolutionary Timeline and Genomic Plasticity Underlying the Lifestyle Diversity in <italic toggle="yes">Rhizobiales</italic>
title_short	Evolutionary Timeline and Genomic Plasticity Underlying the Lifestyle Diversity in <italic toggle="yes">Rhizobiales</italic>
title_full	Evolutionary Timeline and Genomic Plasticity Underlying the Lifestyle Diversity in <italic toggle="yes">Rhizobiales</italic>
title_fullStr	Evolutionary Timeline and Genomic Plasticity Underlying the Lifestyle Diversity in <italic toggle="yes">Rhizobiales</italic>
title_full_unstemmed	Evolutionary Timeline and Genomic Plasticity Underlying the Lifestyle Diversity in <italic toggle="yes">Rhizobiales</italic>
title_sort	evolutionary timeline and genomic plasticity underlying the lifestyle diversity in <italic toggle="yes">rhizobiales</italic>
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/7a25dae7c7a0461eb78b81f6d46aa8bd
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Evolutionary Timeline and Genomic Plasticity Underlying the Lifestyle Diversity in <italic toggle="yes">Rhizobiales</italic>

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