Adjustable microbial cross-feedings adapt to landforms in the Yangtze River

A team led by Sitong Liu from Peking University conducted a study along a 4300-kilometer gradient of the Yangtze River (covering 12 mountain-foothill sites and 15 plain sites). Through metagenomic assembly, they obtained 224 metagenome-assembled genomes (MAGs), including 8 high-completeness comammox Nitrospira genomes, aiming to explore the adaptation mechanisms of microorganisms to the complex terrain of the Yangtze River.

The study found that the total relative abundance of comammox Nitrospira showed no significant difference across different landforms. However, the microbial community network in mountain-foothill regions had stronger cohesion, and comammox Nitrospira had closer connections with other microorganisms, which allowed them to maintain a stable abundance in oligotrophic environments, while the abundance of other ammonia-oxidizing bacteria was lower in this region.

The 8 comammox Nitrospira could be divided into two groups with different niche strategies: Group I had low betweenness centrality, participated in direct interactions within the community, and had a broader niche breadth; Group II had high betweenness centrality and served as a “bridge” between microbial groups.

Functionally, comammox Nitrospira cannot synthesize vitamin B6 but can produce molybdenum cofactor (MOCO). In contrast, most symbiotic bacteria are capable of synthesizing vitamin B6 yet lack the ability to produce MOCO. Therefore, comammox Nitrospira and symbiotic bacteria form a metabolic mutualistic relationship: comammox Nitrospira provides MOCO, and symbiotic bacteria supply vitamin B6 in return. Experiments showed that the addition of vitamin B6 could increase the growth rate, transcriptional activity of nitrification functional genes, and energy metabolism flux of comammox Nitrospira.

The study also pioneered the metabolomic analysis of metagenomes using fBa and optimization (MAMBO) algorithm and found that the actual number of metabolites exchanged between them reached 71, far exceeding the 2 traditionally recognized. Moreover, there were topographic differences in cross-feeding modes: comammox Nitrospira in mountain-foothill regions were “net absorbers”, absorbing more amino acids and vitamin B6; while in plain regions, they were “net secretors”. This adjustment enhanced the adaptability of comammox Nitrospira in oligotrophic environments and nitrogen conversion efficiency.

The conclusion points out that river landforms affect microbial adaptation strategies by regulating microbial cross-feeding modes. This mechanism expands the understanding in niche construction, material cycling, and survival strategies, and provides a theoretical basis for water ecological restoration.

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Contact the author: Sitong Liu, liusitong@pku.edu.cn

-College of Environmental Sciences and Engineering, State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems, Peking University, Beijing 100871, China

-Eco-environment and Resource Efficiency Research Laboratory, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China

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