Trophic Specialization Results in Genomic Reduction in Free-Living Marine <italic toggle="yes">Idiomarina</italic> Bacteria

ABSTRACT The streamlining hypothesis is generally used to explain the genomic reduction events related to the small genome size of free-living bacteria like marine bacteria SAR11. However, our current understanding of the correlation between bacterial genome size and environmental adaptation relies...

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Autores principales:	Qi-Long Qin, Yi Li, Lin-Lin Sun, Zhi-Bin Wang, Shi Wang, Xiu-Lan Chen, Aharon Oren, Yu-Zhong Zhang
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	genome Idiomarina marine bacteria trophic specialization Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/0b586bc4f0b34a669f271cdaea0611b5
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spelling	oai:doaj.org-article:0b586bc4f0b34a669f271cdaea0611b52021-11-15T15:55:14ZTrophic Specialization Results in Genomic Reduction in Free-Living Marine <italic toggle="yes">Idiomarina</italic> Bacteria10.1128/mBio.02545-182150-7511https://doaj.org/article/0b586bc4f0b34a669f271cdaea0611b52019-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02545-18https://doaj.org/toc/2150-7511ABSTRACT The streamlining hypothesis is generally used to explain the genomic reduction events related to the small genome size of free-living bacteria like marine bacteria SAR11. However, our current understanding of the correlation between bacterial genome size and environmental adaptation relies on too few species. It is still unclear whether there are other paths leading to genomic reduction in free-living bacteria. The genome size of marine free-living bacteria of the genus Idiomarina belonging to the order Alteromonadales (Gammaproteobacteria) is much smaller than the size of related genomes from bacteria in the same order. Comparative genomic and physiological analyses showed that the genomic reduction pattern in this genus is different from that of the classical SAR11 lineage. Genomic reduction reconstruction and substrate utilization profile showed that Idiomarina spp. lost a large number of genes related to carbohydrate utilization, and instead they specialized on using proteinaceous resources. Here we propose a new hypothesis to explain genomic reduction in this genus; we propose that trophic specialization increasing the metabolic efficiency for using one kind of substrate but reducing the substrate utilization spectrum could result in bacterial genomic reduction, which would be not uncommon in nature. This hypothesis was further tested in another free-living genus, Kangiella, which also shows dramatic genomic reduction. These findings highlight that trophic specialization is potentially an important path leading to genomic reduction in some marine free-living bacteria, which is distinct from the classical lineages like SAR11. IMPORTANCE The streamlining hypothesis is usually used to explain the genomic reduction events in free-living bacteria like SAR11. However, we find that the genomic reduction phenomenon in the bacterial genus Idiomarina is different from that in SAR11. Therefore, we propose a new hypothesis to explain genomic reduction in this genus based on trophic specialization that could result in genomic reduction, which would be not uncommon in nature. Not only can the trophic specialization hypothesis explain the genomic reduction in the genus Idiomarina, but it also sheds new light on our understanding of the genomic reduction processes in other free-living bacterial lineages.Qi-Long QinYi LiLin-Lin SunZhi-Bin WangShi WangXiu-Lan ChenAharon OrenYu-Zhong ZhangAmerican Society for MicrobiologyarticlegenomeIdiomarinamarine bacteriatrophic specializationMicrobiologyQR1-502ENmBio, Vol 10, Iss 1 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	genome Idiomarina marine bacteria trophic specialization Microbiology QR1-502
spellingShingle	genome Idiomarina marine bacteria trophic specialization Microbiology QR1-502 Qi-Long Qin Yi Li Lin-Lin Sun Zhi-Bin Wang Shi Wang Xiu-Lan Chen Aharon Oren Yu-Zhong Zhang Trophic Specialization Results in Genomic Reduction in Free-Living Marine <italic toggle="yes">Idiomarina</italic> Bacteria
description	ABSTRACT The streamlining hypothesis is generally used to explain the genomic reduction events related to the small genome size of free-living bacteria like marine bacteria SAR11. However, our current understanding of the correlation between bacterial genome size and environmental adaptation relies on too few species. It is still unclear whether there are other paths leading to genomic reduction in free-living bacteria. The genome size of marine free-living bacteria of the genus Idiomarina belonging to the order Alteromonadales (Gammaproteobacteria) is much smaller than the size of related genomes from bacteria in the same order. Comparative genomic and physiological analyses showed that the genomic reduction pattern in this genus is different from that of the classical SAR11 lineage. Genomic reduction reconstruction and substrate utilization profile showed that Idiomarina spp. lost a large number of genes related to carbohydrate utilization, and instead they specialized on using proteinaceous resources. Here we propose a new hypothesis to explain genomic reduction in this genus; we propose that trophic specialization increasing the metabolic efficiency for using one kind of substrate but reducing the substrate utilization spectrum could result in bacterial genomic reduction, which would be not uncommon in nature. This hypothesis was further tested in another free-living genus, Kangiella, which also shows dramatic genomic reduction. These findings highlight that trophic specialization is potentially an important path leading to genomic reduction in some marine free-living bacteria, which is distinct from the classical lineages like SAR11. IMPORTANCE The streamlining hypothesis is usually used to explain the genomic reduction events in free-living bacteria like SAR11. However, we find that the genomic reduction phenomenon in the bacterial genus Idiomarina is different from that in SAR11. Therefore, we propose a new hypothesis to explain genomic reduction in this genus based on trophic specialization that could result in genomic reduction, which would be not uncommon in nature. Not only can the trophic specialization hypothesis explain the genomic reduction in the genus Idiomarina, but it also sheds new light on our understanding of the genomic reduction processes in other free-living bacterial lineages.
format	article
author	Qi-Long Qin Yi Li Lin-Lin Sun Zhi-Bin Wang Shi Wang Xiu-Lan Chen Aharon Oren Yu-Zhong Zhang
author_facet	Qi-Long Qin Yi Li Lin-Lin Sun Zhi-Bin Wang Shi Wang Xiu-Lan Chen Aharon Oren Yu-Zhong Zhang
author_sort	Qi-Long Qin
title	Trophic Specialization Results in Genomic Reduction in Free-Living Marine <italic toggle="yes">Idiomarina</italic> Bacteria
title_short	Trophic Specialization Results in Genomic Reduction in Free-Living Marine <italic toggle="yes">Idiomarina</italic> Bacteria
title_full	Trophic Specialization Results in Genomic Reduction in Free-Living Marine <italic toggle="yes">Idiomarina</italic> Bacteria
title_fullStr	Trophic Specialization Results in Genomic Reduction in Free-Living Marine <italic toggle="yes">Idiomarina</italic> Bacteria
title_full_unstemmed	Trophic Specialization Results in Genomic Reduction in Free-Living Marine <italic toggle="yes">Idiomarina</italic> Bacteria
title_sort	trophic specialization results in genomic reduction in free-living marine <italic toggle="yes">idiomarina</italic> bacteria
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/0b586bc4f0b34a669f271cdaea0611b5
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Trophic Specialization Results in Genomic Reduction in Free-Living Marine <italic toggle="yes">Idiomarina</italic> Bacteria

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