Inter-trophic networks reveal the central role of methanogens in deposited estuarine soils

As one of the most rapidly accumulating sedimentary regions globally, the Yellow River Delta is characterized by the rapid deposition of sediment near the river’s estuary, this unique character has created an environmental gradient extending from land to sea and a corresponding historical gradient in sediment deposition and nutrient availability, influencing the intricate trophic interactions among different trophic levels within the food web. However, studies of methane-metabolizing microorganisms with other microbial hierarchical levels in estuary soils remains inadequate. This study focused on exploring the distribution patterns, driving factors and microbial interaction patterns of methane-metabolizing microorganisms along the sedimentation gradient in the Yellow River estuary. The researchers’ finding appeared March, 2025 in Soil Ecology Letters.

Ye Deng’s team at the CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences conducted a series of studies on the microorganisms in the Yellow River Delta and made many interesting discoveries. For example, in the Yellow River Delta Coastal Wetland Ecological Experiment Station, they conducted a warming experiment, they found that warming not only altered the diversity of microbial communities, but also affected the interactions among microorganisms, in addition, the negative correlation between the cross-domain network modules and soil organic matter was strengthened under the warming condition, which may pose a threat to the soil carbon storage function. Furthermore, in an inundation experiment, they found that inundation induced the negative interactions between the microorganisms, meanwhile, fungal and cercozoan communities played a dominant role in regulating methane emissions. These interesting studies provided new perspectives on microbial ecology studies in the Yellow River Delta. However, the distribution patterns and drivers of microbes on the landscape scale in the Yellow River Delta are not well understood.

Professor Deng said "The formation of the modern Yellow River Delta began in 1855, it is a complete, typical and young wetland ecosystem. The riverway changing of the Yellow River Delta records the complex process of interaction between the Yellow River and the sea, and also reflects a historical picture of the interweaving of various factors such as geology, climate and human activities. Meanwhile, it provides a suitable and high-quality platform for landscape-scale microbial distribution studies. Studies of microorganisms in the Yellow River Delta help us to reveal the conservation and restoration mechanisms of wetland ecosystems".

In this study, they found that the prokaryotes, fungi, and protists had more significant changes between two regions with distinct deposition ages than across soil depths, while the accumulation of soil organic matter was the most critical external driving force for the succession of microbial communities. The deposition ages of sedimentary soils also altered the methanogenic and methanotrophic communities, with methanogens showing a greater response to environmental gradient changes than methanotrophs. The distribution of methanogens was mainly influenced by the direct regulation of biological factors represented by fungi along the sedimentation gradient. "Our self-developed inter-domain ecological network platform (INAP2, https://inap.denglab.org.cn/) has further investigated the inter-trophic relationships between methane-metabolizing microorganisms and other microbes, and many interesting findings have been obtained." said Professor Deng. Through the molecular ecological networks, they found methanogens play a central role in species interactions as modular hubs, which enhances understanding of the microbial hierarchical web in coastal wetland ecosystems.

The study of wetland soils and wetland soil microorganisms is not only related to biodiversity conservation, water resource regulation and water purification, but also has a profound impact on the global carbon cycle and climate change. Deep research of wetland soils and their microbial communities can help us better understand the function and stability of wetland ecosystems and provide scientific basis for ecological conservation and sustainable development.

DOI: 10.1007/s42832-025-0295-1