Cryptogam-associated microbial processes shaping N2O and CH4 cycling in Amazonian peat swamp forests

Tropical wetlands are among the most important regulators of the global carbon (C) and nitrogen (N) cycles, largely through microbially mediated processes that control greenhouse gas (GHG) production and consumption. Tropical peat forests play a key role in these biogeochemical cycles by storing large amounts of organic matter and regulating gas exchanges between soils and the atmosphere, with their functioning strongly influenced by vegetation composition and seasonal shifts between dry and rainy periods. Amazonian peatlands are emerging as potentially significant sources and sinks of nitrous oxide (N₂O) and methane (CH₄), depending on climatic conditions and climate change, including more frequent droughts and increasing irregularity between rainy and dry seasons. Despite their importance for climate regulation, the links between peat forest structure, microbial C and N cycling, and ecosystem-scale GHG fluxes remain poorly quantified. In addition to vascular plants, cryptogams such as mosses and lichens may exert important yet understudied controls on microbial activity, thereby potentially affecting N₂O and CH₄ emissions in aboveground compartments.

This study aims to assess how cryptogam-associated microbial processes affect N₂O and CH₄ fluxes in the Quistococha peat swamp forest and Zungarococha secondary peat swamp forest of Peruvian Amazon, and to evaluate how these processes  differ between forest types.

A total of 25 cryptogam samples were collected from two sites in the Loreto Region of northern Peru. Quistococha is an intact peat swamp forest dominated by Mauritia, Tabebuya, and Caspi, whereas Zungarococha is a secondary peat swamp forest dominated by Cashapona, Mauritia, Hebea, Caspi, M_Beuna, Symphonia, and Cumala. Samples were collected from the stems of trees and palms during two campaigns, in rainy and dry seasons. Metagenomic sequencing of cryptogams was performed to investigate microbial functional potential related to C and N cycling and its relationship with forest type.

Our results show that: (1) Cashapona, Caspi, Cumala, and Hebea exhibited similar functional gene abundance patterns across different seasons and sites, suggesting relatively stable microbial functional characteristics; (2) genes associated with N fixation, dissimilatory nitrate reduction to ammonium (DNRA), and nitrification–processes regulating N availability and potential N₂O production–were more abundant in Zungarococha, especially during the rainy season; (3) genes related to methanogenesis (CH₄ production) and methanotrophy (CH₄ oxidation) were present at relatively low abundances at both sites, with no significant seasonal differences; (4) most functional genes related to C and N cycling were more abundant in Zungarococha than in Quistococha, with peak abundances during the rainy season , whereas in Quistococha, genes related to methanotrophy, N fixation, nitrification, and denitrification (also influencing N₂O consumption) were more abundant during the dry season; (5) Burkholderiaceae and Methanobacteria were more abundant in Zungarococha, Methylococcales and Opitutae were more abundant during the dry season, and Oscillatoriales were more abundant in the rainy season, which are affecting C and N cycling.