Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data

Abstract

Over the last 60 years, the use of hexachlorocyclohexane (HCH) as a pesticide has resulted in the production of >4 million tons of HCH waste, which has been dumped in open sinks across the globe. Here, the combination of the genomes of two genetic subspecies (Sphingobium japonicum UT26 and Sphingobium indicum B90A; isolated from two discrete geographical locations, Japan and India, respectively) capable of degrading HCH, with metagenomic data from an HCH dumpsite (∼450 mg HCH per g soil), enabled the reconstruction and validation of the last-common ancestor (LCA) genotype. Mapping the LCA genotype (3128 genes) to the subspecies genomes demonstrated that >20% of the genes in each subspecies were absent in the LCA. This includes two enzymes from the ‘upper' HCH degradation pathway, suggesting that the ancestor was unable to degrade HCH isomers, but descendants acquired lin genes by transposon-mediated lateral gene transfer. In addition, anthranilate and homogentisate degradation traits were found to be strain (selectively retained only by UT26) and environment (absent in the LCA and subspecies, but prevalent in the metagenome) specific, respectively. One draft secondary chromosome, two near complete plasmids and eight complete lin transposons were assembled from the metagenomic DNA. Collectively, these results reinforce the elastic nature of the genus Sphingobium, and describe the evolutionary acquisition mechanism of a xenobiotic degradation phenotype in response to environmental pollution. This also demonstrates for the first time the use of metagenomic data in ancestral genotype reconstruction, highlighting its potential to provide significant insight into the development of such phenotypes.

Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics

“…1). For instance, chemical contaminated environment such as hexachlorocyclohexane (HCH) dumpsite has been found to be dominated by Sphingomonads and Pseudomonads [11,12]. Similarly, soil microcosms are dominantly characterized by Rhodanobacter, Burkholderia, Acidobacteria [13].…”

“…(Table 1). A study using metagenome recruitment data across hexachlorocyclohexane (HCH) dumpsite led to reconstruction of last common ancestor of HCH degrading Sphingobium species after discounting MGIs and genomic islands (GIs) which provided an evidence for horizontal gene transfers (HGT) driven acquisition of HCH degrading enzyme arsenal mobilized by environmental pollution [12] ( Table 1). In addition, metagenome reads based recruitment analysis also revealed the pivotal role of integron and its associated transposase gene (TnpA6100) in enabling HGTs as a stress response across Pseudomonas community inhabiting HCH contaminated environment [17].…”

“…The problem can be resolved to some extent by using genomics and metagenomics data together delineating the pan-genome dynamics of a community distinctly elucidating environment specific lifestyles adopted by bacteria ( Fig. 1) [12,13].…”

“…Ever since its discovery 'metagenomics' has been largely used to decipher the overall taxonomic composition at an environment focusing more on 'meta' and less on 'genomics' part except for the organismal reconstruction at the species/strain or pan-genome level (multiple species of a specific genus) [12,14]. While there are numerous studies based on using genomics and metagenomics independently, it has not been until recently that the potential of mining genome and metagenome datasets together was exploited to unveil complex environmenthost interactions.…”

Luteimonas tolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil

“…We have been analysing bacterial diversity from the hexachlorocyclohexane (HCH)-dumpsite situated at Ummari village, Lucknow, India by using culture-dependent (Kumar et al, 2008;Singh & Lal, 2009;Kumari et al, 2009;Dadhwal et al, 2009;Bala et al, 2010;Sharma et al, 2010;Garg et al, 2012;Singh et al, 2013Singh et al, , 2014Singh et al, , 2015Dwivedi et al, 2013;Kumar et al, 2015;Verma et al, 2015;Mahato et al, 2016) and culture independent (Sangwan et al, 2012(Sangwan et al, , 2014 approaches. In order to continue our efforts to characterize bacteria, soil samples were collected from the HCH-contaminated field located at Ummari, Lucknow, India.…”