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Anaerobic methanotroph ‘Candidatus Methanoperedens nitroreducens’ has a pleomorphic life cycle

Nature Microbiology volume 8, pages 321–331 (2023)Cite this article

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Abstract

‘Candidatus Methanoperedens’ are anaerobic methanotrophic (ANME) archaea with global importance to methane cycling. Here meta-omics and fluorescence in situ hybridization (FISH) were applied to characterize a bioreactor dominated by ‘Candidatus Methanoperedens nitroreducens’ performing anaerobic methane oxidation coupled to nitrate reduction. Unexpectedly, FISH revealed the stable co-existence of two ‘Ca. M. nitroreducens’ morphotypes: the archetypal coccobacilli microcolonies and previously unreported planktonic rods. Metagenomic analysis showed that the ‘Ca. M. nitroreducens’ morphotypes were genomically identical but had distinct gene expression profiles for proteins associated with carbon metabolism, motility and cell division. In addition, a third distinct phenotype was observed, with some coccobacilli ‘Ca. M. nitroreducens’ storing carbon as polyhydroxyalkanoates. The phenotypic variation of ‘Ca. M. nitroreducens’ probably aids their survival and dispersal in the face of sub-optimal environmental conditions. These findings further demonstrate the remarkable ability of members of the ‘Ca. Methanoperedens’ to adapt to their environment.

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Fig. 1: Composite FISH micrographs of abundant populations in the bioreactor biomass.
Fig. 2: Community profiles for the bioreactor community and filtration fractions.
Fig. 3: Differential expression of key pathways for ‘Ca. M. nitroreducens’.
Fig. 4: Schematic of the carbon and electron flow for the bioreactor community.
Fig. 5: Proposed model for the pleomorphic lifestyle of ‘Ca. M. nitroreducens’.

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Data availability

All sequencing data generated in this study are deposited in NCBI bioproject PRJNA836951. Accession numbers SAMN28229058–SAMN28229071 represent the metagenomic and metatranscriptomic reads and SAMN28180289–SAMN28180328 and SAMN28196132 represent the assembled MAGs and prophage.

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Acknowledgements

This work was supported by the Australian Research Council (ARC; FT170100070, G.W.T.; FT190100211, S.J.M.), the US Department of Energy’s Office of Biological Environmental Research (DE-SC0016469, G.W.T.) and Queensland University of Technology (QUT). Z.Y. was supported by an Australian Research Council Laureate Fellowship (FL170100086).

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  1. These authors contributed equally: Simon J. McIlroy, Andy O. Leu.

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  1. Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia

    Simon J. McIlroy, Andy O. Leu, Rhys Newell, Ben J. Woodcroft & Gene W. Tyson

  2. Australian Centre for Water and Environmental Biotechnology (ACWEB), Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia

    Xueqin Zhang, Zhiguo Yuan & Shihu Hu

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Contributions

S.J.M., A.O.L. and G.W.T designed the experiments and wrote the manuscript. S.J.M. performed the single-cell visualization. A.O.L. and R.N. performed the bioinformatic analyses, and X.Z. operated the bioreactors. All authors contributed to the drafting of the manuscript.

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Correspondence to Simon J. McIlroy.

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Extended data

Extended Data Fig. 1 Bioreactor performance values.

a. Performance profile around the metatranscriptomic sampling point on Day 1682 b. Long-term transformation rates for NO3−, NH4+ and CH4 (consumption) and N2 (production). c. Community profile of the bioreactor based on 16S rRNA amplicon sequencing. All taxa that are present in >1% in at least one sample are included and ordered by their abundance on Day 1682.

Extended Data Fig. 2 Summary of size fractionation of the bioreactor biomass.

a. Schematic of the workflow used for the filtration experiment. b.–d. Micrographs showing the success of the biomass filtration. b. Unfiltered biomass; c. Retentate fraction >5 µm; d. Filtrate fraction <5 µm. b.-d. Differential interference contrast (DIC) image of the biomass (top panels) and corresponding field of view with FISH (bottom panels). ‘Ca. M. nitroreducens’ cells appear green (AAA-FW-641 probe). Displayed representative FISH images are supported by the observation of 3 individual hybridisations for each of the size fractions. Scale bars represent 20 µm.

Extended Data Fig. 3 Analyses of the prophage in ‘Ca. M. nitroreducens’.

a. Genome map of the integrated prophage. b. Coverage depth profiles for i. filtrate (F) and ii. retentate (R) derived long Nanopore sequence reads mapped to the Methanoperedens-1 MAG. Only long reads mapping at Q20 were included in the analyses. c. Coverage depth profiles for i. F and ii. R derived Illumina short sequence reads mapped to the Methanoperedens-1 MAG. The average coverage ratio of phage to host (shaded in grey) is displayed for each fraction. Note that the supernatant for the filtrate fraction, likely containing phage, was discarded.

Extended Data Fig. 4 Expression of key pathways for abundant populations in the bioreactor.

a. Genes related to nitrogen metabolism; b. Genes involved in the reversible conversion of acetate to acetyl-CoA. TPM values for the catalytic subunit are given for abundant phylotypes. Values for F = Filtrate fraction; R = Retentate fraction. nar/nas = nitrate reductase; nir = nitrite reductase (nitric oxide forming); nrf = nitrite reductase (ammonia-forming); nor = nitric oxide reductase; nos = nitrous oxide reductase; hzs = hydrazine synthase; hzo = hydrazine oxidoreductase; pta = phosphate acetyltransferase; ack = acetate kinase; acs/acd = acetate-CoA ligase.

Extended Data Fig. 5 Micrographs showing polyhydroxyalkanoate (PHA) storage by coccobacilli ‘Ca. M. nitroreducens’ cells.

a. and b. ‘Ca. M. nitroreducens nitroreducens’ (FISH, AAA-FW-641); c. Negative FISH control (non-EUB); d. All bacteria (FISH, EUBmix). Images within each set are the same field of view. For all image sets: i. DIC images; ii. FISH (green); iii. pre-Nile Blue A stain control; iv. Nile Blue A positive lipid inclusions (appear red). a.ii., b.ii. and c.ii. are taken with the same image settings. All iii. and iv. images are taken with the same image settings. Scale bars represent 20 µm in all images. Representative image sets were selected for each probe set from >4 fields of view across 2 independent FISH hybridisations. In support of these observations, visual assessment of (>10 wells; 8 µl biomass per well) Nile Blue A stained biomass did not identify any PHA positive cells that did not exhibit the distinctive ‘Ca. M. nitroreducens’ coccobacilli morphotype. ‘Ca. M. nitroreducens’ was also the only population with high expression of the PHA synthase gene (phaC; Fig. 2b).

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McIlroy, S.J., Leu, A.O., Zhang, X. et al. Anaerobic methanotroph ‘Candidatus Methanoperedens nitroreducens’ has a pleomorphic life cycle. Nat Microbiol 8, 321–331 (2023). https://doi.org/10.1038/s41564-022-01292-9

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