Fifteen-year cattle manure application reshapes phoD- and gcd-harboring microbiomes, enhancing vegetable yields
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Fifteen-year cattle manure application reshapes phoD- and gcd-harboring microbiomes, enhancing vegetable yields

17/12/2025 Frontiers Journals
Long-term cattle manure application significantly influences soil phosphorus (P) cycling and associated microbial communities in agricultural systems. However, the mechanisms by which P-transforming microbial communities and their ecological networks mediate P cycling and crop productivity under sustained organic amendment remain poorly understood. This study demonstrates that combined manure and chemical fertilizer (M+CF) in the open-field lettuce cropping system at Dali enhanced both diversity (+45.3%) and abundance (+290%) of gcd-harboring bacteria, and also increased positive microbial correlations by 74.6% through network analysis.The researchers’ finding appeared 06 October, 2025 in Soil Ecology Letters.

A series of studies on sustainable nutrient management in intensive cropping systems have been conducted by Baokun Leiʼs team at the Institute of Agricultural Environment and Resources, Yunnan Academy of Agricultural Sciences (YAAS), and many interesting findings have been obtained. For example, they identified previously unreported keystone taxa that play crucial roles in phosphorus transformation processes, providing new insights into the ecological mechanisms underpinning sustainable phosphorus management. They also established clear relationships between microbial community structure, enzyme activities, and vegetable productivity, offering a holistic understanding of how microbial-mediated processes influence agricultural outcomes over extended time periods.

Senior researcher Lei said, “Based on preliminary research and regional environmental regulations prohibiting exclusive chemical fertilizer usage in the Lake Erhai watershed, we focus on cattle manure-only application and combined application of cattle manure and chemical fertilizer, and we want to find out which long-term vegetable fertilizer application method is more efficient in phosphorus utilization of vegetables and which one is more friendly to the environmental protection of the Lake Erhai watershed.”

In this study, 15 years of cattle manure application significantly alters the abundance, diversity, and composition of phosphorus-cycling microorganisms harboring key functional genes (phoD and gcd), with distinct community assemblages developing in response to different fertilization regimes.

“We also used the method of ecological network analysis to infer functional microbial communities governing P transformation of soil microbes at long-term organic amendments and to understand the P transformation of soil microbes from the perspective of soil enzyme activities,” said Senior researcher Lei. Abundance and compositional structure of functional microbial communities harboring key P-cycling genes differ markedly among different fertilization regimes, suggesting distinctive community assemblages. Key species in the co-occurring networks were identified, which provides the further information for managing soil P-cycling through the regulation of key species.

“The study is from a 15-year field experiment investigating how sustained cattle manure application, alone or in combination with chemical fertilizers, influences phosphorus-cycling microbial communities and their ecological networks in intensively managed vegetable production systems. The study addresses critical knowledge gaps regarding the mechanistic understanding of how long-term organic amendments shape functional microbial communities governing phosphorus transformation processes.”

Long-term fertilization strategies can optimize soil P use efficiency, enhance microbial-mediated P transformations, and improve vegetable yields. Particularly for regions grappling with the pressures of intensive cultivation and the challenges of environmental phosphorus management, sustainable agricultural practices are of great significance.
DOI：10.1007/s42832-025-0351-x
https://doi.org/10.1007/s42832-025-0351-x
Fichiers joints
  • Fig.1Activities of four soil phosphorus transformation enzymes in the vegetable field under different fertilization treatments were shown in (Fig.1a). Correlation analyses and Mantel analyses between the gcd and phoD gene abundances and alpha diversity (gcd a, phoD a) were presented in (Fig.1b). Outcomes of the piecewise structural equation model analysis evaluating the effects of soil pH, soil organic matter content, Olsen P content, gene abundances ,alpha diversity of gcd, gcd a (Fig.2a), and phoD, phoD a (Fig.2b), respectively, and enzyme activities (ALP, PDE, ACP, DHA) on lettuce yield under long-term manure application were shown. Network structure and keystone taxa of phosphorus-solubilizing microbial communities under long-term cow manure application were shown: Fig.3 (a‒c) represented gcd-harboring and (d‒f) represented phoD-harboring communities. Panels represent treatments: (a, d) CK, (b, e) M, and (c, f) M+CF. Green lines indicate positive connections, and red lines indicate negative connections.
  • Fig.2
  • Fig.3
17/12/2025 Frontiers Journals
Regions: Asia, China, North America, United States
Keywords: Science, Agriculture & fishing

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