Isolation, Description and Genome Analysis of a Putative Novel Methylobacter Species (‘Ca. Methylobacter coli’) Isolated from the Faeces of a Blackbuck (Indian Antelope)

Kumal Khatri,Pranitha Pandit,Monali C Rahalkar,Jyoti Mohite,Rahul A Bahulikar

doi:10.3390/microbiolres12020035

Kumal Khatri, Pranitha Pandit + Show 3 more

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https://doi.org/10.3390/microbiolres12020035

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Abstract

Enteric fermentation of methane by ruminant animals represents a major source of anthropogenic methane. Significantly less information is available on the existence of methanotrophs in the gut of ruminants. Therefore, detailed strain descriptions of methanotrophs isolated from ruminant faeces or gut are rare. We present a first report on the enrichment and isolation of a methanotroph, strain BlB1, from the faeces of an Indian antelope (blackbuck). The 16S rRNA gene sequence of strain BlB1 showed the highest identity (98.40% identity) to Methylobacter marinus A45T and Methylobacter luteus NCIMB 11914T. Strain BlB1 showed coccoidal cells (1.5–2 µm in diameter), which formed chains or aggregates of 3–4 cells of light yellow-coloured colonies on agarose when incubated with methane in the gas phase. The draft genome of BlB1 (JADMKV01) is 4.87 Mbp in size, with a G + C content of 51.3%. The draft genome showed 27.4% digital DNA-DNA hybridization (DDH) and 83.07% average nucleotide identity (ANIb) values with that of its closest phylogenetic neighbour, Methylobacter marinus A45T. Due to the lower values of DDH and ANIb with the nearest species, and <98.7% 16S rRNA gene sequence identity, we propose that strain BlB1 belongs to a novel species of Methylobacter. However, as the culture has to be maintained live and resisted cryopreservation, deposition in culture collections was not possible and hence we propose a Candidatus species name, ‘Ca. Methylobacter coli’ BlB1. ‘Ca. Methylobacter coli’ BlB1 would be the first described methanotroph from ruminants worldwide, with a sequenced draft genome. This strain could be used as a model for studies concerning methane mitigation from ruminants.

Highlights

Ruminants are significant sources of anthropogenic methane emissions and contribute to around 12–37% of global methane emissions [1]
Methanotrophs require oxygen; they exist in places where significantly reduced oxygen quantities are present [7]
The ANIb, AAI, and DNA-DNA hybridization (DDH) values between BlB1 genome and Methylobacter marinus A45, Methylobacter oryzae KRF1, and Methylobacter tundripaludum strains were 73–83%, 70–83%, and 20–27%, respectively (Table 1), which were lower than the threshold values (95% for ANI or AAI and 70% for DDH)

Summary

Introduction

Ruminants are significant sources of anthropogenic methane emissions and contribute to around 12–37% of global methane emissions [1]. Methane is the second most important greenhouse gas and is not assimilated by the ruminant animals and released into the atmosphere contributing to global warming [2]. As the only producers of enteric methane, methanogens are responsible for the contribution of livestock industries to climate change [3]. They have become the focus of research towards developing mitigation strategies. Like wetlands, rice fields, and landfills, methanotrophs or methaneoxidizing bacteria have been the only and the most efficient contributors to methane mitigation [4]. The classical methanotrophs or methane-oxidizing bacteria belong to Gammaproteobacteria (Type I) and Alphaproteobacteria (Type II).

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