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Research Article | Ecological and Evolutionary Science

Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium

Roshan Kumar, Helianthous Verma, Shazia Haider, Abhay Bajaj, Utkarsh Sood, Kalaiarasan Ponnusamy, Shekhar Nagar, Mallikarjun N. Shakarad, Ram Krishan Negi, Yogendra Singh, J. P. Khurana, Jack A. Gilbert, Rup Lal
Morgan Langille, Editor
Roshan Kumar
aDepartment of Zoology, University of Delhi, Delhi, India
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Helianthous Verma
aDepartment of Zoology, University of Delhi, Delhi, India
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Shazia Haider
bSchool of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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Abhay Bajaj
aDepartment of Zoology, University of Delhi, Delhi, India
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Utkarsh Sood
aDepartment of Zoology, University of Delhi, Delhi, India
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Kalaiarasan Ponnusamy
cSynthetic Biology Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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Shekhar Nagar
aDepartment of Zoology, University of Delhi, Delhi, India
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Mallikarjun N. Shakarad
aDepartment of Zoology, University of Delhi, Delhi, India
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Ram Krishan Negi
aDepartment of Zoology, University of Delhi, Delhi, India
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Yogendra Singh
aDepartment of Zoology, University of Delhi, Delhi, India
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J. P. Khurana
dInterdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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Jack A. Gilbert
eThe Microbiome Center, Argonne National Laboratory, Argonne, Illinois, USA
fDepartment of Surgery, The Microbiome Center, University of Chicago, Chicago, Illinois, USA
gThe Microbiome Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
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Rup Lal
aDepartment of Zoology, University of Delhi, Delhi, India
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Morgan Langille
Dalhousie University
Roles: Editor
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DOI: 10.1128/mSystems.00020-17
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ABSTRACT

Species belonging to the genus Novosphingobium are found in many different habitats and have been identified as metabolically versatile. Through comparative genomic analysis, we identified habitat-specific genes and regulatory hubs that could determine habitat selection for Novosphingobium spp. Genomes from 27 Novosphingobium strains isolated from diverse habitats such as rhizosphere soil, plant surfaces, heavily contaminated soils, and marine and freshwater environments were analyzed. Genome size and coding potential were widely variable, differing significantly between habitats. Phylogenetic relationships between strains were less likely to describe functional genotype similarity than the habitat from which they were isolated. In this study, strains (19 out of 27) with a recorded habitat of isolation, and at least 3 representative strains per habitat, comprised four ecological groups—rhizosphere, contaminated soil, marine, and freshwater. Sulfur acquisition and metabolism were the only core genomic traits to differ significantly in proportion between these ecological groups; for example, alkane sulfonate (ssuABCD) assimilation was found exclusively in all of the rhizospheric isolates. When we examined osmolytic regulation in Novosphingobium spp. through ectoine biosynthesis, which was assumed to be marine habitat specific, we found that it was also present in isolates from contaminated soil, suggesting its relevance beyond the marine system. Novosphingobium strains were also found to harbor a wide variety of mono- and dioxygenases, responsible for the metabolism of several aromatic compounds, suggesting their potential to act as degraders of a variety of xenobiotic compounds. Protein-protein interaction analysis revealed β-barrel outer membrane proteins as habitat-specific hubs in each of the four habitats—freshwater (Saro_1868), marine water (PP1Y_AT17644), rhizosphere (PMI02_00367), and soil (V474_17210). These outer membrane proteins could play a key role in habitat demarcation and extend our understanding of the metabolic versatility of the Novosphingobium species.

IMPORTANCE This study highlights the significant role of a microorganism’s genetic repertoire in structuring the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe’s respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits in Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium.

  • Copyright © 2017 Kumar et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license .

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Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium
Roshan Kumar, Helianthous Verma, Shazia Haider, Abhay Bajaj, Utkarsh Sood, Kalaiarasan Ponnusamy, Shekhar Nagar, Mallikarjun N. Shakarad, Ram Krishan Negi, Yogendra Singh, J. P. Khurana, Jack A. Gilbert, Rup Lal
mSystems May 2017, 2 (3) e00020-17; DOI: 10.1128/mSystems.00020-17

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Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium
Roshan Kumar, Helianthous Verma, Shazia Haider, Abhay Bajaj, Utkarsh Sood, Kalaiarasan Ponnusamy, Shekhar Nagar, Mallikarjun N. Shakarad, Ram Krishan Negi, Yogendra Singh, J. P. Khurana, Jack A. Gilbert, Rup Lal
mSystems May 2017, 2 (3) e00020-17; DOI: 10.1128/mSystems.00020-17
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KEYWORDS

Novosphingobium
core genome
habitat-specific genes
pangenome
regulatory hubs

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