The methane-oxidizing microbial communities of three maar lakes in tropical monsoon Asia

Iona Eunice C Bicaldo; Karol Sophia Agape R Padilla; Tzu-Hsuan Tu; Wan Ting Chen; Milette U Mendoza-Pascual; Carmela Vannette B Vicera; Justine R de Leon; Kamille N Poblete; Eleanor S Austria; Mark Louie D Lopez; Yuki Kobayashi; Fuh-Kwo Shiah; Rey Donne S Papa; Noboru Okuda; Pei-Ling Wang; Li-Hung Lin

doi:10.3389/fmicb.2024.1410666

The methane-oxidizing microbial communities of three maar lakes in tropical monsoon Asia

Front Microbiol. 2024 Jul 9:15:1410666. doi: 10.3389/fmicb.2024.1410666. eCollection 2024.

Authors

Iona Eunice C Bicaldo^#^{1

2}, Karol Sophia Agape R Padilla^#^{1

3

4}, Tzu-Hsuan Tu^{5

6}, Wan Ting Chen⁵, Milette U Mendoza-Pascual⁷, Carmela Vannette B Vicera⁸, Justine R de Leon^{2

8}, Kamille N Poblete¹, Eleanor S Austria⁹, Mark Louie D Lopez¹⁰, Yuki Kobayashi¹¹, Fuh-Kwo Shiah¹², Rey Donne S Papa^{1

2

8}, Noboru Okuda^{11

13

14}, Pei-Ling Wang^{15

16}, Li-Hung Lin^{5

16}

Affiliations

¹ The Graduate School, University of Santo Tomas, Manila, Philippines.
² Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines.
³ Philippine Genome Center, University of the Philippines, Quezon City, Philippines.
⁴ Department of Science and Technology, Science Education Institute, Taguig, Philippines.
⁵ Department of Geosciences, National Taiwan University, Taipei, Taiwan.
⁶ Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan.
⁷ Department of Environmental Science, School of Science and Engineering, Ateneo Research Institute for Science and Engineering, Ateneo de Manila University, Quezon City, Philippines.
⁸ Department of Biological Sciences, University of Santo Tomas, Manila, Philippines.
⁹ Biology Department, Adamson University, Manila, Philippines.
¹⁰ Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
¹¹ Center for Ecological Research, Kyoto University, Shiga, Japan.
¹² Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.
¹³ Research Center for Inland Seas, Kobe University, Kobe, Japan.
¹⁴ Research Institute for Humanity and Nature, Kamigamo Motoyama, Kita Ward, Kyoto, Japan.
¹⁵ Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
¹⁶ Research Center for Future Earth, National Taiwan University, Taipei, Taiwan.

^# Contributed equally.

Abstract

Methane-oxidizing bacteria (MOB) is a group of planktonic microorganisms that use methane as their primary source of cellular energy. For tropical lakes in monsoon Asia, there is currently a knowledge gap on MOB community diversity and the factors influencing their abundance. Herewith, we present a preliminary assessment of the MOB communities in three maar lakes in tropical monsoon Asia using Catalyzed Reporter Deposition, Fluorescence In-Situ Hybridization (CARD-FISH), 16S rRNA amplicon sequencing, and pmoA gene sequencing. Correlation analysis between MOB abundances and lakes' physicochemical parameters following seasonal monsoon events were performed to explain observed spatial and temporal patterns in MOB diversity. The CARD-FISH analyses detected the three MOB types (I, II, and NC10) which aligned with the results from 16S rRNA amplicons and pmoA gene sequencing. Among community members based on 16S rRNA genes, Proteobacterial Type I MOB (e.g., Methylococcaceae and Methylomonadaceae), Proteobacterial Type II (Methylocystaceae), Verrucomicrobial (Methylacidiphilaceae), Methylomirabilota/NC10 (Methylomirabilaceae), and archaeal ANME-1a were found to be the dominant methane-oxidizers in three maar lakes. Analysis of microbial diversity and distribution revealed that the community compositions in Lake Yambo vary with the seasons and are more distinct during the stratified period. Temperature, DO, and pH were significantly and inversely linked with type I MOB and Methylomirabilota during stratification. Only MOB type I was influenced by monsoon changes. This research sought to establish a baseline for the diversity and ecology of planktonic MOB in tropical monsoon Asia to better comprehend their contribution to the CH₄ cycle in tropical freshwater ecosystems.

Keywords: 16S rRNA gene; CARD-FISH; NC10; Proteobacteria; Verrucomicrobia; pmoA.

Grants and funding

The field research was funded by the Japan Society for the Promotion of Science (JSPS) Grant- in-aid no. 24405007 and 16H05774 of NO as well as the DOST JSPS Joint Research Program (JRP) funding of RP (January 2021 – December 2022), Research Institute for Humanity and Nature Project (D06- 14200119), and Bilateral Joint Research Projects (JPJSBP120208602) of NO, while molecular processing and sequencing analysis were funded by the National Taiwan University, Department of Geosciences through L-HL and P-LW. Likewise, some requisite research expenditures are supported by the Taiwanese Ministry of Education (NTU-113L901005) to P-LW and the National Science and Technology Council (112-2116-M-002-010) to L-HL. Other additional research funding was shouldered by the Department of Science and Technology - Accelerated Science and Technology Human Resource Development Program (DOST-ASTHRDP), through the scholarships of the Philippine authors KSAR Padilla and MM-P. This research was also monitored by the Department of Science and Technology – National Research Council of the Philippines (DOST-NRCP).