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Humic acid-dependent respiratory growth of Methanosarcina acetivorans involves pyrroloquinoline quinone

The ISME Journal volume 17, pages 2103–2111 (2023)Cite this article

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Abstract

Although microbial humus respiration plays a critical role in organic matter decomposition and biogeochemical cycling of elements in diverse anoxic environments, the role of methane-producing species (methanogens) is not well defined. Here we report that a major fraction of humus, humic acid reduction enhanced the growth of Methanosarcina acetivorans above that attributed to methanogenesis when utilizing the energy sources methanol or acetate, results which showed both respiratory and fermentative modes of energy conservation. Growth characteristics with methanol were the same for an identically cultured mutant deleted for the gene encoding a multi-heme cytochrome c (MmcA), results indicating MmcA is not essential for respiratory electron transport to humic acid. Transcriptomic analyses revealed that growth with humic acid promoted the upregulation of genes annotated as cell surface pyrroloquinoline quinone (PQQ)-binding proteins. Furthermore, PQQ isolated from the membrane fraction was more abundant in humic acid-respiring cells, and the addition of PQQ improved efficiency of the extracellular electron transport. Given that the PQQ-binding proteins are widely distributed in methanogens, the findings extend current understanding of microbial humus respiration in the context of global methane dynamics.

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Fig. 1: Growth parameters of M. acetivorans grown with or without HA.
Fig. 2: A gene cluster ranged from MA4284 to MA4315 was upregulated in HA-respiring cells compared to nonrespiring cells of M. acetivorans.
Fig. 3: Isolation of PQQ from the membrane fraction of M. acetivorans and analysis by LC–MS.
Fig. 4: Potential roles of PQQ and MP in extracellular electron transport.
Fig. 5: Prevalence of PQQ-binding β-propeller repeat proteins and predicted homologues.

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Data availability

Illumina sequence reads have been submitted to the SRA NCBI database under Bioprojects PRJNA859665 and PRJNA862363 including Biosamples SAMN29793682 (SRX16315150 to SRX16315152), SAMN29793683 (SRX16315153 to SRX16315155), SAMN29975242 (SRX16673125 to SRX16673127), and SAMN29975243 (SRX16673128 to SRX16673130).

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Acknowledgements

The authors thank Sen Wang from State Key laboratory of Microbial Technology of Shandong University for help and guidance in SEM. The authors thank Wenshan Qi from Biozeron Co., Ltd. for his technical assistance of RNA-Seq in this study. The authors thank Dr. Lovley’s group for providing ∆hpt and ∆hpt∆mmcA of M. acetivorans. This work was supported by National Natural Science Foundation of China (22008142), Natural Science Foundation of Shandong Province (ZR2022YQ31), Natural Science Foundation of Jiangsu Province (BK20200232), and Qilu Youth Talent Program of Shandong University. Prof. Shuguang Wang acknowledges Taishan Scholars project of Shandong Province (NO. tstp20230604).

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  1. These authors contributed equally: Yuanxu Song, Rui Huang, Ling Li.

Authors and Affiliations

  1. Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, 266237, China

    Yuanxu Song, Rui Huang, Kaifeng Du, Fanping Zhu, Chao Song, Xianzheng Yuan, Shuguang Wang & Zhen Yan

  2. State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, 266237, Shandong, China

    Ling Li & Mingyu Wang

  3. Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA

    James G. Ferry

  4. Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

    Shungui Zhou

  5. Suzhou Research Institute, Shandong University, Suzhou, 215123, Jiangsu, China

    Zhen Yan

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Contributions

ZY and JF conceived and designed the study; YS, KD, LL, RH and FZ performed the experiment and collected the data; ZY, RH, YS, LL and MW wrote the manuscript; ZY, RH, CS, XY, SZ, MW, SW and JF analyzed and interpreted the data; ZY, RH, CS, XY, SZ, MW, SW and JF revised the manuscript.

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Correspondence to Mingyu Wang, Shuguang Wang or Zhen Yan.

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Song, Y., Huang, R., Li, L. et al. Humic acid-dependent respiratory growth of Methanosarcina acetivorans involves pyrroloquinoline quinone. ISME J 17, 2103–2111 (2023). https://doi.org/10.1038/s41396-023-01520-y

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