Genomic Variations Underlying Speciation and Niche Specialization of <italic toggle="yes">Shewanella baltica</italic>

ABSTRACT Shewanella baltica was the dominant culturable nitrate-reducing bacterium in the eutrophic and strongly stratified Baltic Sea in the 1980s, where it primarily inhabited the oxic-anoxic transition zone. The genomic structures of 46 of these isolates were investigated through comparative geno...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Jie Deng, Jennifer M. Auchtung, Konstantinos T. Konstantinidis, Ingrid Brettar, Manfred G. Höfle, James M. Tiedje
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	Shewanella baltica comparative genomics speciation adaptation Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/381f40c2320441f19f78a9056ebe2802
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:381f40c2320441f19f78a9056ebe2802
record_format	dspace
spelling	oai:doaj.org-article:381f40c2320441f19f78a9056ebe28022021-12-02T19:46:17ZGenomic Variations Underlying Speciation and Niche Specialization of <italic toggle="yes">Shewanella baltica</italic>10.1128/mSystems.00560-192379-5077https://doaj.org/article/381f40c2320441f19f78a9056ebe28022019-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00560-19https://doaj.org/toc/2379-5077ABSTRACT Shewanella baltica was the dominant culturable nitrate-reducing bacterium in the eutrophic and strongly stratified Baltic Sea in the 1980s, where it primarily inhabited the oxic-anoxic transition zone. The genomic structures of 46 of these isolates were investigated through comparative genomic hybridization (CGH), which revealed a gradient of genomic similarity, ranging from 65% to as high as 99%. The core genome of the S. baltica species was enriched in anaerobic respiration-associated genes. Auxiliary genes, most of which locate within a few genomic islands (GIs), were nonuniformly distributed among the isolates. Specifically, hypothetical and mobile genetic element (MGE)-associated genes dominated intraclade gene content differences, whereas gain/loss of functional genes drove gene content differences among less related strains. Among the major S. baltica clades, gene signatures related to specific redox-driven and spatial niches within the water column were identified. For instance, genes involved in anaerobic respiration of sulfur compounds may provide key adaptive advantages for clade A strains in anoxic waters where sulfur-containing electron acceptors are present. Genes involved in cell motility, in particular, a secondary flagellar biosynthesis system, may be associated with the free-living lifestyle by clade E strains. Collectively, this study revealed characteristics of genome variations present in the water column and active speciation of S. baltica strains, driven by niche partitioning and horizontal gene transfer (HGT). IMPORTANCE Speciation in nature is a fundamental process driving the formation of the vast microbial diversity on Earth. In the central Baltic Sea, the long-term stratification of water led to formation of a large-scale vertical redoxcline that provided a gradient of environmental niches with respect to the availability of electron acceptors and donors. The region was home to Shewanella baltica populations, which composed the dominant culturable nitrate-reducing bacteria, particularly in the oxic-anoxic transition zone. Using the collection of S. baltica isolates as a model system, genomic variations showed contrasting gene-sharing patterns within versus among S. baltica clades and revealed genomic signatures of S. baltica clades related to redox niche specialization as well as particle association. This study provides important insights into genomic mechanisms underlying bacterial speciation within this unique natural redoxcline.Jie DengJennifer M. AuchtungKonstantinos T. KonstantinidisIngrid BrettarManfred G. HöfleJames M. TiedjeAmerican Society for MicrobiologyarticleShewanella balticacomparative genomicsspeciationadaptationMicrobiologyQR1-502ENmSystems, Vol 4, Iss 5 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Shewanella baltica comparative genomics speciation adaptation Microbiology QR1-502
spellingShingle	Shewanella baltica comparative genomics speciation adaptation Microbiology QR1-502 Jie Deng Jennifer M. Auchtung Konstantinos T. Konstantinidis Ingrid Brettar Manfred G. Höfle James M. Tiedje Genomic Variations Underlying Speciation and Niche Specialization of <italic toggle="yes">Shewanella baltica</italic>
description	ABSTRACT Shewanella baltica was the dominant culturable nitrate-reducing bacterium in the eutrophic and strongly stratified Baltic Sea in the 1980s, where it primarily inhabited the oxic-anoxic transition zone. The genomic structures of 46 of these isolates were investigated through comparative genomic hybridization (CGH), which revealed a gradient of genomic similarity, ranging from 65% to as high as 99%. The core genome of the S. baltica species was enriched in anaerobic respiration-associated genes. Auxiliary genes, most of which locate within a few genomic islands (GIs), were nonuniformly distributed among the isolates. Specifically, hypothetical and mobile genetic element (MGE)-associated genes dominated intraclade gene content differences, whereas gain/loss of functional genes drove gene content differences among less related strains. Among the major S. baltica clades, gene signatures related to specific redox-driven and spatial niches within the water column were identified. For instance, genes involved in anaerobic respiration of sulfur compounds may provide key adaptive advantages for clade A strains in anoxic waters where sulfur-containing electron acceptors are present. Genes involved in cell motility, in particular, a secondary flagellar biosynthesis system, may be associated with the free-living lifestyle by clade E strains. Collectively, this study revealed characteristics of genome variations present in the water column and active speciation of S. baltica strains, driven by niche partitioning and horizontal gene transfer (HGT). IMPORTANCE Speciation in nature is a fundamental process driving the formation of the vast microbial diversity on Earth. In the central Baltic Sea, the long-term stratification of water led to formation of a large-scale vertical redoxcline that provided a gradient of environmental niches with respect to the availability of electron acceptors and donors. The region was home to Shewanella baltica populations, which composed the dominant culturable nitrate-reducing bacteria, particularly in the oxic-anoxic transition zone. Using the collection of S. baltica isolates as a model system, genomic variations showed contrasting gene-sharing patterns within versus among S. baltica clades and revealed genomic signatures of S. baltica clades related to redox niche specialization as well as particle association. This study provides important insights into genomic mechanisms underlying bacterial speciation within this unique natural redoxcline.
format	article
author	Jie Deng Jennifer M. Auchtung Konstantinos T. Konstantinidis Ingrid Brettar Manfred G. Höfle James M. Tiedje
author_facet	Jie Deng Jennifer M. Auchtung Konstantinos T. Konstantinidis Ingrid Brettar Manfred G. Höfle James M. Tiedje
author_sort	Jie Deng
title	Genomic Variations Underlying Speciation and Niche Specialization of <italic toggle="yes">Shewanella baltica</italic>
title_short	Genomic Variations Underlying Speciation and Niche Specialization of <italic toggle="yes">Shewanella baltica</italic>
title_full	Genomic Variations Underlying Speciation and Niche Specialization of <italic toggle="yes">Shewanella baltica</italic>
title_fullStr	Genomic Variations Underlying Speciation and Niche Specialization of <italic toggle="yes">Shewanella baltica</italic>
title_full_unstemmed	Genomic Variations Underlying Speciation and Niche Specialization of <italic toggle="yes">Shewanella baltica</italic>
title_sort	genomic variations underlying speciation and niche specialization of <italic toggle="yes">shewanella baltica</italic>
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/381f40c2320441f19f78a9056ebe2802
work_keys_str_mv	AT jiedeng genomicvariationsunderlyingspeciationandnichespecializationofitalictoggleyesshewanellabalticaitalic AT jennifermauchtung genomicvariationsunderlyingspeciationandnichespecializationofitalictoggleyesshewanellabalticaitalic AT konstantinostkonstantinidis genomicvariationsunderlyingspeciationandnichespecializationofitalictoggleyesshewanellabalticaitalic AT ingridbrettar genomicvariationsunderlyingspeciationandnichespecializationofitalictoggleyesshewanellabalticaitalic AT manfredghofle genomicvariationsunderlyingspeciationandnichespecializationofitalictoggleyesshewanellabalticaitalic AT jamesmtiedje genomicvariationsunderlyingspeciationandnichespecializationofitalictoggleyesshewanellabalticaitalic
_version_	1718376018579816448

Genomic Variations Underlying Speciation and Niche Specialization of <italic toggle="yes">Shewanella baltica</italic>

Ejemplares similares