Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize–palisade grass intercropping

Ahmad Nuruddin Khoiri; Nídia Raquel Costa; Carlos Alexandre Costa Crusciol; Cristiano Magalhães Pariz; Ciniro Costa; Juliano Carlos Calonego; André Michel de Castilhos; Daniel Martins de Souza; Paulo Roberto de Lima Meirelles; Igor Vilela Cru; Luiz Gustavo Moretti; João William Bossolani; Eiko Eurya Kuramae

doi:10.1186/s40793-025-00727-0

Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize–palisade grass intercropping

Ahmad Nuruddin Khoiri
, Nídia Raquel Costa
, Carlos Alexandre Costa Crusciol
, Cristiano Magalhães Pariz
, Ciniro Costa
, Juliano Carlos Calonego
, André Michel de Castilhos
, Daniel Martins de Souza
, Paulo Roberto de Lima Meirelles
, Igor Vilela Cru
, Luiz Gustavo Moretti
, João William Bossolani
, Eiko Eurya Kuramae^* (Co-auteur)

^*Corresponding author voor dit werk

NIOO - Microbial Ecology (ME)

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

7 Citaten (Scopus)

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Background: Intercropping systems enhance agricultural sustainability by promoting ecosystem multifunctionality (EMF). This study examined the impact of adding pigeon pea (M + PG + PP) into a maize–palisade grass (M + PG) intercropping system under a no-till system (NTS) on soil microbial communities and ecosystem services. After five consecutive growing seasons, bulk soil samples from a soybean-based crop-livestock system were analyzed using metagenomics. Results: The inclusion of pigeon pea significantly improved the EMF index, with higher plant productivity and slightly enhanced outcomes in soil health, lamb meat productivity, and climate protection. The M + PG + PP treatment enriched Bradyrhizobium spp., which were positively correlated with soil health, plant productivity, and EMF index. Functional analysis indicated that M + PG + PP treatment enhanced nitrogen metabolism, biofilm formation, and exopolysaccharide (EPS) biosynthesis, improving soil fertility and microbial activity. Similarly, functional analysis of microbial plant growth-promoting traits revealed that the M + PG + PP treatment promoted microbial functions related to nitrogen and iron acquisition, sulfur assimilation, and plant colonization, all essential for plant growth and nutrient cycling. In contrast, the M + PG treatment primarily enhanced pathways related to competitive exclusion and phytohormone production. Conclusions: These findings highlight the importance of incorporating legumes such as pigeon pea into intercropping systems to optimize ecosystem services, enhance soil health, and promote long-term agricultural productivity and sustainability.

Originele taal-2	Engels
Artikelnummer	60
Tijdschrift	Environmental Microbiome
Volume	20
DOI's	https://doi.org/10.1186/s40793-025-00727-0
Status	Gepubliceerd - 04 jun. 2025

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10.1186/s40793-025-00727-0Licentie: CC BY-NC-ND

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Khoiri, A. N., Costa, N. R., Crusciol, C. A. C., Pariz, C. M., Costa, C., Calonego, J. C., de Castilhos, A. M., de Souza, D. M., de Lima Meirelles, P. R., Cru, I. V., Moretti, L. G., Bossolani, J. W., & Kuramae, E. E. (2025). Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize–palisade grass intercropping. Environmental Microbiome, 20, Artikel 60. https://doi.org/10.1186/s40793-025-00727-0

@article{4345ff6ecf25495b9b935ef134a0ae30,

title = "Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize–palisade grass intercropping",

abstract = "Background: Intercropping systems enhance agricultural sustainability by promoting ecosystem multifunctionality (EMF). This study examined the impact of adding pigeon pea (M + PG + PP) into a maize–palisade grass (M + PG) intercropping system under a no-till system (NTS) on soil microbial communities and ecosystem services. After five consecutive growing seasons, bulk soil samples from a soybean-based crop-livestock system were analyzed using metagenomics. Results: The inclusion of pigeon pea significantly improved the EMF index, with higher plant productivity and slightly enhanced outcomes in soil health, lamb meat productivity, and climate protection. The M + PG + PP treatment enriched Bradyrhizobium spp., which were positively correlated with soil health, plant productivity, and EMF index. Functional analysis indicated that M + PG + PP treatment enhanced nitrogen metabolism, biofilm formation, and exopolysaccharide (EPS) biosynthesis, improving soil fertility and microbial activity. Similarly, functional analysis of microbial plant growth-promoting traits revealed that the M + PG + PP treatment promoted microbial functions related to nitrogen and iron acquisition, sulfur assimilation, and plant colonization, all essential for plant growth and nutrient cycling. In contrast, the M + PG treatment primarily enhanced pathways related to competitive exclusion and phytohormone production. Conclusions: These findings highlight the importance of incorporating legumes such as pigeon pea into intercropping systems to optimize ecosystem services, enhance soil health, and promote long-term agricultural productivity and sustainability.",

keywords = "Cajanus cajan, Crop-livestock integration, legume-Bradyrhizobium interaction, Shotgun metagenomics, Soil fertility, Sustainable agriculture",

author = "Khoiri, \{Ahmad Nuruddin\} and Costa, \{N{\'i}dia Raquel\} and Crusciol, \{Carlos Alexandre Costa\} and Pariz, \{Cristiano Magalh{\~a}es\} and Ciniro Costa and Calonego, \{Juliano Carlos\} and \{de Castilhos\}, \{Andr{\'e} Michel\} and \{de Souza\}, \{Daniel Martins\} and \{de Lima Meirelles\}, \{Paulo Roberto\} and Cru, \{Igor Vilela\} and Moretti, \{Luiz Gustavo\} and Bossolani, \{Jo{\~a}o William\} and Kuramae, \{Eiko Eurya\}",

note = "Data archiving: no NIOO data",

year = "2025",

month = jun,

day = "4",

doi = "10.1186/s40793-025-00727-0",

language = "English",

volume = "20",

journal = "Environmental Microbiome",

issn = "2524-6372",

publisher = "BioMed Central",

}

Khoiri, AN, Costa, NR, Crusciol, CAC, Pariz, CM, Costa, C, Calonego, JC, de Castilhos, AM, de Souza, DM, de Lima Meirelles, PR, Cru, IV, Moretti, LG, Bossolani, JW & Kuramae, EE 2025, 'Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize–palisade grass intercropping', Environmental Microbiome, vol. 20, 60. https://doi.org/10.1186/s40793-025-00727-0

Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize–palisade grass intercropping. / Khoiri, Ahmad Nuruddin; Costa, Nídia Raquel; Crusciol, Carlos Alexandre Costa et al.
In: Environmental Microbiome, Vol. 20, 60, 04.06.2025.

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

TY - JOUR

T1 - Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize–palisade grass intercropping

AU - Khoiri, Ahmad Nuruddin

AU - Costa, Nídia Raquel

AU - Crusciol, Carlos Alexandre Costa

AU - Pariz, Cristiano Magalhães

AU - Costa, Ciniro

AU - Calonego, Juliano Carlos

AU - de Castilhos, André Michel

AU - de Souza, Daniel Martins

AU - de Lima Meirelles, Paulo Roberto

AU - Cru, Igor Vilela

AU - Moretti, Luiz Gustavo

AU - Bossolani, João William

AU - Kuramae, Eiko Eurya

N1 - Data archiving: no NIOO data

PY - 2025/6/4

Y1 - 2025/6/4

N2 - Background: Intercropping systems enhance agricultural sustainability by promoting ecosystem multifunctionality (EMF). This study examined the impact of adding pigeon pea (M + PG + PP) into a maize–palisade grass (M + PG) intercropping system under a no-till system (NTS) on soil microbial communities and ecosystem services. After five consecutive growing seasons, bulk soil samples from a soybean-based crop-livestock system were analyzed using metagenomics. Results: The inclusion of pigeon pea significantly improved the EMF index, with higher plant productivity and slightly enhanced outcomes in soil health, lamb meat productivity, and climate protection. The M + PG + PP treatment enriched Bradyrhizobium spp., which were positively correlated with soil health, plant productivity, and EMF index. Functional analysis indicated that M + PG + PP treatment enhanced nitrogen metabolism, biofilm formation, and exopolysaccharide (EPS) biosynthesis, improving soil fertility and microbial activity. Similarly, functional analysis of microbial plant growth-promoting traits revealed that the M + PG + PP treatment promoted microbial functions related to nitrogen and iron acquisition, sulfur assimilation, and plant colonization, all essential for plant growth and nutrient cycling. In contrast, the M + PG treatment primarily enhanced pathways related to competitive exclusion and phytohormone production. Conclusions: These findings highlight the importance of incorporating legumes such as pigeon pea into intercropping systems to optimize ecosystem services, enhance soil health, and promote long-term agricultural productivity and sustainability.

AB - Background: Intercropping systems enhance agricultural sustainability by promoting ecosystem multifunctionality (EMF). This study examined the impact of adding pigeon pea (M + PG + PP) into a maize–palisade grass (M + PG) intercropping system under a no-till system (NTS) on soil microbial communities and ecosystem services. After five consecutive growing seasons, bulk soil samples from a soybean-based crop-livestock system were analyzed using metagenomics. Results: The inclusion of pigeon pea significantly improved the EMF index, with higher plant productivity and slightly enhanced outcomes in soil health, lamb meat productivity, and climate protection. The M + PG + PP treatment enriched Bradyrhizobium spp., which were positively correlated with soil health, plant productivity, and EMF index. Functional analysis indicated that M + PG + PP treatment enhanced nitrogen metabolism, biofilm formation, and exopolysaccharide (EPS) biosynthesis, improving soil fertility and microbial activity. Similarly, functional analysis of microbial plant growth-promoting traits revealed that the M + PG + PP treatment promoted microbial functions related to nitrogen and iron acquisition, sulfur assimilation, and plant colonization, all essential for plant growth and nutrient cycling. In contrast, the M + PG treatment primarily enhanced pathways related to competitive exclusion and phytohormone production. Conclusions: These findings highlight the importance of incorporating legumes such as pigeon pea into intercropping systems to optimize ecosystem services, enhance soil health, and promote long-term agricultural productivity and sustainability.

KW - Cajanus cajan

KW - Crop-livestock integration

KW - legume-Bradyrhizobium interaction

KW - Shotgun metagenomics

KW - Soil fertility

KW - Sustainable agriculture

U2 - 10.1186/s40793-025-00727-0

DO - 10.1186/s40793-025-00727-0

M3 - Article

AN - SCOPUS:105007233896

SN - 2524-6372

VL - 20

JO - Environmental Microbiome

JF - Environmental Microbiome

M1 - 60

ER -

Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize–palisade grass intercropping

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