Consistent functional genes in methanogens along soil profiles in a temperate marshland

Abstract

Wetlands are the primary natural source of atmospheric methane (CH₄), the second most potent greenhouse gas. CH₄ production mainly occurs along the soil profile, while how functional genes associated with CH₄ production change along soil profile remains elusive. Our study integrateddepth-stratified (0–100 cm) measurements of CH₄ production potential, soil characteristics, methanogenic gene abundance, and methanogen community composition involved in different methanogenesis pathways in a temperate marshland, northeast China, to explore how microbial and soil environmental factors regulate CH₄ production potential. Our results showed that CH₄ production potential decreased significantly with increasing soil depth, consistent with the decline in total microbial biomass, gene abundance, and community diversity. Moreover, methanogenic functional groups with distinct ecological strategies exhibited more pronounced shifts than functional genes in four pathways, particularly the H₂/CO₂ and methylotrophic facultative group declined significantly with depth. Furthermore, methanogenic functional groups showed stronger correlations with soil properties (e.g., NO₃^‒-N, NH₄⁺-N, TN, SWC, MBC, and MBN) than functional genes. Structural equation modeling revealed that soil physicochemical properties and methanogenic functional group composition (not gene relative abundance) significantly impacted CH₄ production potential, with coefficients of 0.67 and 0.41, respectively. Our findings establish that functional group identity, reflecting ecological strategy, supersedes genetic potential in regulating CH₄ production along soil profiles. This study offers critical insights into vertical variations in microbial control over wetland CH₄ cycling and advocates microbial models that use microbial biomass to represent microbial functions.

Graphical abstract

Keywords

CH₄ production / methanogenic pathways / functional genes / methanogen communities / wetland

Highlight

	● CH4 production potential declines along soil profile in a temperate marshland.
	● Key methanogenic groups decline more sharply with depth than gene abundance.
	● Methanogenic groups correlate more strongly with soil properties than genes.
	● Methanogen functional group strategy outweigh genetic potential in CH4 regulation.

References

[1] Altor, A.E., Mitsch, W.J., 2008. Methane and carbon dioxide dynamics in wetland mesocosms: effects of hydrology and soils. Ecological Applications18, 1307–1320.

[2] Angel, R., Claus, P., Conrad, R., 2012. Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. The ISME Journal6, 847–862.

[3] Angel, R., Matthies, D., Conrad, R., 2011. Activation of methanogenesis in arid biological soil crusts despite the presence of oxygen. PLoS One6, e20453.

[4] Bååth, E., Anderson, T.H., 2003. Comparison of soil fungal/bacterial ratios in a pH gradient using physiological and PLFA-based techniques. Soil Biology and Biochemistry35, 955–963.

[5] Bergman, I., Klarqvist, M., Nilsson, M., 2000. Seasonal variation in rates of methane production from peat of various botanical origins: effects of temperature and substrate quality. FEMS Microbiology Ecology33, 181–189.

[6] Bhatia, A., Pathak, H., Jain, N., Singh, P.K., Singh, A.K., 2005. Global warming potential of manure amended soils under rice-wheat system in the Indo-Gangetic plains. Atmospheric Environment39, 6976–6984.

[7] Bodelier, P.L.E., Laanbroek, H.J., 2004. Nitrogen as a regulatory factor of methane oxidation in soils and sediments. FEMS Microbiology Ecology47, 265–277.

[8] Bridgham, S.D., Cadillo-Quiroz, H., Keller, J.K., Zhuang, Q.L., 2013. Methane emissions from wetlands: biogeochemical, microbial, and modeling perspectives from local to global scales. Global Change Biology19, 1325–1346.

[9] Bridgham, S.D., Megonigal, J.P., Keller, J.K., Bliss, N.B., Trettin, C., 2006. The carbon balance of North American wetlands. Wetlands26, 889–916.

[10] Buchfink, B., Xie, C., Huson, D.H., 2015. Fast and sensitive protein alignment using DIAMOND. Nature Methods12, 59–60.

[11] Cadillo-Quiroz, H., Bräuer, S., Yashiro, E., Sun, C., Yavitt, J., Zinder, S., 2006. Vertical profiles of methanogenesis and methanogens in two contrasting acidic peatlands in central New York State, USA. Environmental Microbiology8, 1428–1440.

[12] Change, O.C., 2007. Intergovernmental panel on climate change. World Meteorological Organization52, 1–43.

[13] Chen, Z.N., Shao, X.X., Xu, X.Y., He, X.Y., 2018. Optimized digital speckle patterns for digital image correlation by consideration of both accuracy and efficiency. Applied Optics57, 884–893.

[14] Ciais, P., Sabine, C., Bala, G., Bopp, L., Brovkin, V., Canadell, J., Chhabra, A., Defries, R., Galloway, J., Heimann, M., 2013. Carbon and other biogeochemical cycles. In: IPCC, ed. Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge: Cambridge University Press, 465–570.

[15] Conrad, R., 1989. Control of methane production in terrestrial ecosystems. In: Andreae, M.O., Schimel, D.S., eds. Exchange of Trace Gases Between Terrestrial Ecosystems and the Atmosphere. New York: John Wiley, 39–58.

[16] Conrad, R., 1996. Soil microorganisms as controllers of atmospheric trace gases (H₂, CO, CH₄, OCS, N₂O, and NO). Microbiological Reviews60, 609–640.

[17] Conrad, R., 1999. Contribution of hydrogen to methane production and control of hydrogen concentrations in methanogenic soils and sediments. FEMS Microbiology Ecology28, 193–202.

[18] Conrad, R., 2005. Quantification of methanogenic pathways using stable carbon isotopic signatures: a review and a proposal. Organic Geochemistry36, 739–752.

[19] Conrad, R., 2007. Microbial ecology of methanogens and methanotrophs. Advances in Agronomy96, 1–63.

[20] Deng, Y.C., Liu, P.F., Conrad, R., 2019. Effect of temperature on the microbial community responsible for methane production in alkaline NamCo wetland soil. Soil Biology and Biochemistry132, 69–79.

[21] Evans, P.N., Boyd, J.A., Leu, A.O., Woodcroft, B.J., Parks, D.H., Hugenholtz, P., Tyson, G.W., 2019. An evolving view of methane metabolism in the Archaea. Nature Reviews Microbiology17, 219–232.

[22] Ferry, J.G., 1992. Methane from acetate. Journal of Bacteriology174, 5489–5495.

[23] Fierer, N., Schimel, J.P., Holden, P.A., 2003. Variations in microbial community composition through two soil depth profiles. Soil Biology and Biochemistry35, 167–176.

[24] Freitag, T.E., Prosser, J.I., 2009. Correlation of methane production and functional gene transcriptional activity in a peat soil. Applied and Environmental Microbiology75, 6679–6687.

[25] Frostegård, Å., Tunlid, A., Bååth, E., 1993. Phospholipid fatty acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals. Applied and Environmental Microbiology59, 3605–3617.

[26] Fu, J., Liu, J., Wang, X.W., Zhang, M.D., Chen, W.W., Chen, B., 2020. Ecological risk assessment of wetland vegetation under projected climate scenarios in the Sanjiang Plain, China. Journal of Environmental Management273, 111108.

[27] Galand, P.E., Fritze, H., Yrjälä, K., 2003. Microsite-dependent changes in methanogenic populations in a boreal oligotrophic fen. Environmental Microbiology5, 1133–1143.

[28] Galand, P.E., Saarnio, S., Fritze, H., Yrjälä, K., 2002. Depth related diversity of methanogen Archaea in Finnish oligotrophic fen. FEMS Microbiology Ecology42, 441–449.

[29] Grace, J.B., Bollen, K.A., 2008. Representing general theoretical concepts in structural equation models: the role of composite variables. Environmental and Ecological Statistics15, 191–213.

[30] He, L.Y., Rodrigues, J.L.M., Soudzilovskaia, N.A., Barceló, M., Olsson, P.A., Song, C.C., Tedersoo, L., Yuan, F.H., Yuan, F.M., Lipson, D.A., Xu, X.F., 2020. Global biogeography of fungal and bacterial biomass carbon in topsoil. Soil Biology and Biochemistry151, 108024.

[31] Holmes, M.E., Chanton, J.P., Bae, H.S., Ogram, A., 2014. Effect of nutrient enrichment on δ¹³CH₄ and the methane production pathway in the Florida Everglades. Journal of Geophysical Research: Biogeosciences119, 1267–1280.

[32] Intergovernmental Panel on Climate Change, 2021. Climate Change 2021: The Physical Science Basis. New York: Cambridge University Press.

[33] Jerman, V., Danevčič, T., Mandic-Mulec, I., 2017. Methane cycling in a drained wetland soil profile. Journal of Soils and Sediments17, 1874–1882.

[34] Jerman, V., Metje, M., Mandić-Mulec, I., Frenzel, P., 2009. Wetland restoration and methanogenesis: the activity of microbial populations and competition for substrates at different temperatures. Biogeosciences6, 1127–1138.

[35] Kelley, C.A., Chanton, J.P., Bebout, B.M., 2015. Rates and pathways of methanogenesis in hypersaline environments as determined by ¹³C-labeling. Biogeochemistry126, 329–341.

[36] Kluge, B., Wessolek, G., Facklam, M., Lorenz, M., Schwärzel, K., 2008. Long-term carbon loss and CO₂-C release of drained peatland soils in northeast Germany. European Journal of Soil Science59, 1076–1086.

[37] Kong, D.L., Li, S.Q., Jin, Y.G., Wu, S., Chen, J., Hu, T., Wang, H., Liu, S.W., Zou, J.W., 2019. Linking methane emissions to methanogenic and methanotrophic communities under different fertilization strategies in rice paddies. Geoderma347, 233–243.

[38] Kyebogola, S., Burras, L.C., Miller, B.A., Semalulu, O., Yost, R.S., Tenywa, M.M., Lenssen, A.W., Kyomuhendo, P., Smith, C., Luswata, C.K., Majaliwa, M.J.G., Goettsch, L., Colfer, C.J.P., Mazur, R.E., 2020. Comparing Uganda’s indigenous soil classification system with World Reference Base and USDA Soil Taxonomy to predict soil productivity. Geoderma Regional22, e00296.

[39] Landman, W., 2010. Climate change 2007: the physical science basis. South African Geographical Journal92, 86–87.

[40] Le Mer, J., Roger, P., 2001. Production, oxidation, emission and consumption of methane by soils: a review. European Journal of Soil Biology37, 25–50.

[41] Lefcheck, J.S., 2016. PIECEWISESEM: piecewise structural equation modelling in R for ecology, evolution, and systematics. Methods in Ecology and Evolution7, 573–579.

[42] Levins, R., 1968. Evolution in Changing Environments: Some Theoretical Explorations. Princeton: Princeton University Press.

[43] Li, D., Ni, H.W., Jiao, S., Lu, Y.H., Zhou, J.Z., Sun, B., Liang, Y.T., 2021. Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies. Microbiome9, 20.

[44] Li, D.H., Liu, C.M., Luo, R.B., Sadakane, K., Lam, T.W., 2015. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics31, 1674–1676.

[45] Li, R.Q., Li, Y.R., Kristiansen, K., Wang, J., 2008. SOAP: short oligonucleotide alignment program. Bioinformatics24, 713–714.

[46] Liu, D.Y., Ding, W.X., Jia, Z.J., Cai, Z.C., 2011. Relation between methanogenic archaea and methane production potential in selected natural wetland ecosystems across China. Biogeosciences8, 329–338.

[47] Liu, Y.C., Whitman, W.B., 2008. Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Annals of the New York Academy of Sciences1125, 171–189.

[48] Louca, S., Polz, M.F., Mazel, F., Albright, M.B.N., Huber, J.A., O'Connor, M.I., Ackermann, M., Hahn, A.S., Srivastava, D.S., Crowe, S.A., Doebeli, M., Parfrey, L.W., 2018. Function and functional redundancy in microbial systems. Nature Ecology & Evolution2, 936–943.

[49] Moore-Kucera, J., Dick, R.P., 2008. PLFA profiling of microbial community structure and seasonal shifts in soils of a Douglas-fir chronosequence. Microbial Ecology55, 500–511.

[50] Nazaries, L., Murrell, J.C., Millard, P., Baggs, L., Singh, B.K., 2013. Methane, microbes and models: fundamental understanding of the soil methane cycle for future predictions. Environmental Microbiology15, 2395–2417.

[51] Noguchi, H., Park, J., Takagi, T., 2006. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Research34, 5623–5630.

[52] Noll, M., Matthies, D., Frenzel, P., Derakshani, M., Liesack, W., 2005. Succession of bacterial community structure and diversity in a paddy soil oxygen gradient. Environmental Microbiology7, 382–395.

[53] Oremland, R.S., 1988. The Biogeochemistry of Methanogenic Bacteria. New York: Wiley.

[54] Penning, H., Conrad, R., 2007. Quantification of carbon flow from stable isotope fractionation in rice field soils with different organic matter content. Organic Geochemistry38, 2058–2069.

[55] Richter, D.D., Markewitz, D., 1995. How deep is soil? Soil, the zone of the earth’s crust that is biologically active, is much deeper than has been thought by many ecologists. BioScience45, 600–609.

[56] Rodhe, H., 1990. A comparison of the contribution of various gases to the greenhouse effect. Science248, 1217–1219.

[57] Rooney-Varga, J.N., Giewat, M.W., Duddleston, K.N., Chanton, J.P., Hines, M.E., 2007. Links between archaeal community structure, vegetation type and methanogenic pathway in Alaskan peatlands. FEMS Microbiology Ecology60, 240–251.

[58] Shrestha, P.M., Kube, M., Reinhardt, R., Liesack, W., 2009. Transcriptional activity of paddy soil bacterial communities. Environmental Microbiology11, 960–970.

[59] Smith, L.C., Orgiazzi, A., Eisenhauer, N., Cesarz, S., Lochner, A., Jones, A., Bastida, F., Patoine, G., Reitz, T., Buscot, F., Rillig, M.C., Heintz-Buschart, A., Lehmann, A., Guerra, C.A., 2021. Large-scale drivers of relationships between soil microbial properties and organic carbon across Europe. Global Ecology and Biogeography30, 2070–2083.

[60] Song, C.C., Xu, X.F., Tian, H.Q., Wang, Y.Y., 2009. Ecosystem-atmosphere exchange of CH₄ and N₂O and ecosystem respiration in wetlands in the Sanjiang Plain, Northeastern China. Global Change Biology15, 692–705.

[61] Song, Y.Y., Song, C.C., Yang, G.S., Miao, Y.Q., Wang, J.Y., Guo, Y.D., 2012. Changes in labile organic carbon fractions and soil enzyme activities after marshland reclamation and restoration in the Sanjiang Plain in Northeast China. Environmental Management50, 418–426.

[62] Song, Y.Y., Sun, L., Song, C.C., Li, M.T., Liu, Z.D., Zhu, M.Y., Chen, S., Yuan, J.B., Gao, J.L., Wang, X.W., Wang, W.J., 2023. Responses of soil microbes and enzymes to long-term warming incubation in different depths of permafrost peatland soil. Science of the Total Environment900, 165733.

[63] Starnawski, P., Bataillon, T., Ettema, T.J.G., Jochum, L.M., Schreiber, L., Chen, X.H., Lever, M.A., Polz, M.F., Jørgensen, B.B., Schramm, A., Kjeldsen, K.U., 2017. Microbial community assembly and evolution in subseafloor sediment. Proceedings of the National Academy of Sciences of the United States of America114, 2940–2945.

[64] Thauer, R.K., Kaster, A.K., Seedorf, H., Buckel, W., Hedderich, R., 2008. Methanogenic archaea: ecologically relevant differences in energy conservation. Nature Reviews Microbiology6, 579–591.

[65] Tivey, M.K., 2007. Generation of seafloor hydrothermal vent fluids and associated mineral deposits. Oceanography20, 50–65.

[66] Trumbore, S., 2000. Age of soil organic matter and soil respiration: Radiocarbon constraints on belowground C dynamics. Ecological Applications10, 399–411.

[67] Updegraff, K., Pastor, J., Bridgham, S.D., Johnston, C.A., 1995. Environmental and substrate controls over carbon and nitrogen mineralization in northern wetlands. Ecological Applications5, 151–163.

[68] Valentine, D.W., Holland, E.A., Schimel, D.S., 1994. Ecosystem and physiological controls over methane production in northern wetlands. Journal of Geophysical Research: Atmospheres99, 1563–1571.

[69] Vance, E.D., Brookes, P.C., Jenkinson, D.S., 1987. An extraction method for measuring soil microbial biomass C. Soil Biology and Biochemistry19, 703–707.

[70] Vanwonterghem, I., Evans, P.N., Parks, D.H., Jensen, P.D., Woodcroft, B.J., Hugenholtz, P., Tyson, G.W., 2016. Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nature Microbiology1, 16170.

[71] Wang, L.L., Song, C.C., Song, Y.Y., Guo, Y.D., Wang, X.W., Sun, X.X., 2010. Effects of reclamation of natural wetlands to a rice paddy on dissolved carbon dynamics in the Sanjiang Plain, Northeastern China. Ecological Engineering36, 1417–1423.

[72] Wang, N.N., Zhu, X.H., Zuo, Y.J., Liu, J.Z., Yuan, F.H., Guo, Z.Y., Zhang, L.H., Sun, Y., Gong, C., Guo, D.F., Song, C.C., Xu, X.F., 2023. Microbial mechanisms for methane source-to-sink transition after wetland conversion to cropland. Geoderma429, 116229.

[73] Wang, N.N., Zhu, X.H., Zuo, Y.J., Liu, J.Z., Yuan, F.H., Guo, Z.Y., Zhang, L.H., Sun, Y., Gong, C., Song, C.C., 2022. Metagenomic evidence of suppressed methanogenic pathways along soil profile after wetland conversion to cropland. Frontiers in Microbiology13, 930694.

[74] Wardle, D.A., Ghani, A., 1995. Why is the strength of relationships between pairs of methods for estimating soil microbial biomass often so variable?. Soil Biology and Biochemistry27, 821–828.

[75] Weedon, J.T., Aerts, R., Kowalchuk, G.A., Van Logtestijn, R., Andringa, D., Van Bodegom, P.M., 2013. Temperature sensitivity of peatland C and N cycling: Does substrate supply play a role. Soil Biology and Biochemistry61, 109–120.

[76] Wu, J., Joergensen, R.G., Pommerening, B., Chaussod, R., Brookes, P.C., 1990. Measurement of soil microbial biomass C by fumigation-extraction–an automated procedure. Soil Biology and Biochemistry22, 1167–1169.

[77] Wu, X.H., Wang, W., Xie, K.J., Yin, C.M., Hou, H.J., Xie, X.L., 2019. Combined effects of straw and water management on CH₄ emissions from rice fields. Journal of Environmental Management231, 1257–1262.

[78] Xu, X.F., Schimel, J.P., Janssens, I.A., Song, X., Song, C.C., Yu, G.R., Sinsabaugh, R.L., Tang, D.D., Zhang, X.C., Thornton, P.E., 2017. Global pattern and controls of soil microbial metabolic quotient. Ecological Monographs87, 429–441.

[79] Yao, H., Conrad, R., Wassmann, R., Neue, H.U., 1999. Effect of soil characteristics on sequential reduction and methane production in sixteen rice paddy soils from China, the Philippines, and Italy. Biogeochemistry47, 269–295.

[80] Zhang, Q.W., Yang, G.B., Song, Y.T., Kou, D., Wang, G.Q., Zhang, D.Y., Qin, S.Q., Mao, C., Feng, X.H., Yang, Y.H., 2019. Magnitude and drivers of potential methane oxidation and production across the Tibetan Alpine Permafrost Region. Environmental Science & Technology53, 14243–14252.

[81] Zhou, Z., Zhang, C.J., Liu, P.F., Fu, L., Laso-Pérez, R., Yang, L., Bai, L.P., Li, J., Yang, M., Lin, J.Z., Wang, W.D., Wegener, G., Li, M., Cheng, L., 2022. Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species. Nature601, 257–262.

RIGHTS & PERMISSIONS

Higher Education Press