Paper · 2026 · Journal of Sustainable Agriculture and Environment

Fully Organic Agroforestry Practices in Rice Cultivation: Effects on Soil Bacterial Microbiota, Soil Health and Grain Quality

Martina Nasuelli; Irene Pellegrino; Maria Cavaletto; et al.

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Open access · cc-by

Abstract

ABSTRACT Introduction Sustainable practices are increasingly recognised for benefiting soil biodiversity, health, and overall grain quality. This study examined a unique rice agroecosystem adopting fully organic practices and agroforestry through a seasonal characterisation of soil bacterial microbiota and physicochemical parameters. Furthermore, the first nutritional characterisation of an heirloom rice variety was provided, explicitly detailing how the soil biodiversity and parameters influence the grain quality. Materials and Methods Following the rice growth cycle, soil bacterial microbiota were studied through a metabarcoding approach on environmental DNA. Soil physicochemical properties were determined with standardised protocols and an FT‐IR analysis on the labile and recalcitrant carbon. Besides, the grain nutritional profile was obtained using standardised kits and protocols, while grain protein quantification was performed by combining SDS‐PAGE assay and MALDI‐TOF mass spectrometry. Results Microbiota profiling highlighted the cover crops field's role in hosting functionally important bacteria, in support of the subsequent rice cultivation. Taxonomical and functional diversity significantly increased across the rice growing season, peaking at flowering, a delicate physiological phase directly impacting crop yields. Soil ROC, OM and flooding conditions primarily drove the bacteria community dissimilarity inter‐stages ( R 2 = 0.637). The sustainable practices employed for rice cultivation (i.e., green mulching, zero external inputs) led to a stabilisation of TOC and OM, increased available labile C, and to a carbon sequestration at the end of the growing season (7%), besides soil N and P conservation. Correlation analysis showed that CEC, C/N and bacterial diversity mainly influenced the carbohydrate fraction of the rice grain, with an indirect effect on the protein content. Conclusion Through a multidisciplinary approach, this study highlights that sustainable rice cultivation provides vital ecosystem services by positively affecting bacterial biodiversity, nutrient cycling, and grain quality. These sustainable practices represent an evidence‐based strategy to achieve global Sustainable Development Goals and to redesign rice agriculture.

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Claims 9

Observationobservedoriginal resultmeasured

Claim · model-written summary

Cover crop fields hosted functionally important bacteria for subsequent rice cultivation.

Outcome
functionally important bacteriae0
Setting
cover crops fielde0

Organisms pictured · Representative pictures of the matched species, not figures from the paper.

Oryza sativa
Oryza sativa · Taxon · picture from its Wikimedia Commons categoryDesmanthus4food · CC BY-SA 3.0 us · Wikimedia Commons ↗

Verbatim

e0

“Microbiota profiling highlighted the cover crops field's role in hosting functionally important bacteria, in support of the subsequent rice cultivation”

✓ located verbatim in the source · abstract, characters 1016–1167 · show in text ↑
Observationobservedoriginal resultsignificant (as stated)measured

Claim · model-written summary

Soil bacterial taxonomic and functional diversity increased during the rice season and peaked at flowering.

Organ / stage
floweringe0
Interactor
bacteriale1other
Outcome
Taxonomical and functional diversitye0
Direction
increasede0

Organisms pictured · Representative pictures of the matched species, not figures from the paper.

Oryza sativa
Oryza sativa · Taxon · picture from its Wikimedia Commons categoryDesmanthus4food · CC BY-SA 3.0 us · Wikimedia Commons ↗

Verbatim

e0

“Taxonomical and functional diversity significantly increased across the rice growing season, peaking at flowering”

✓ located verbatim in the source · abstract, characters 1169–1282 · show in text ↑
e1

“soil bacterial microbiota were studied through a metabarcoding approach”

✓ located verbatim in the source · abstract, characters 576–647 · show in text ↑
e2

“rice growing season”

✓ located verbatim in the source · abstract, characters 1241–1260 · show in text ↑
Associationobservedoriginal resultmeasured

Claim · model-written summary

ROC, OM and flooding explained between-stage soil bacterial community dissimilarity.

Interactor
bacteriaBacteriae0other
Outcome
bacteria community dissimilaritye0
Value
R 2 = 0.637e0
Setting
flooding conditionse0

Not reportedDirection

Organisms pictured · Representative pictures of the matched species, not figures from the paper.

Oryza sativa
Oryza sativa · Taxon · picture from its Wikimedia Commons categoryDesmanthus4food · CC BY-SA 3.0 us · Wikimedia Commons ↗

Verbatim

e0

“Soil ROC, OM and flooding conditions primarily drove the bacteria community dissimilarity inter‐stages ( R 2 = 0.637)”

✓ located verbatim in the source · abstract, characters 1347–1464 · show in text ↑
e1

“soil bacterial microbiota were studied”

✓ located verbatim in the source · abstract, characters 576–614 · show in text ↑
e2

“rice growth cycle”

✓ located verbatim in the source · abstract, characters 557–574 · show in text ↑
Intervention effectobservedoriginal resultpositivemeasured

Claim · model-written summary

Organic rice practices stabilised TOC and OM.

Treatment
green mulching, zero external inputse0
Outcome
TOC and OMe0
Direction
stabilisatione0

Not reportedComparator

Organisms pictured · Representative pictures of the matched species, not figures from the paper.

Oryza sativa
Oryza sativa · Taxon · picture from its Wikimedia Commons categoryDesmanthus4food · CC BY-SA 3.0 us · Wikimedia Commons ↗

Verbatim

e0

“The sustainable practices employed for rice cultivation (i.e., green mulching, zero external inputs) led to a stabilisation of TOC and OM”

✓ located verbatim in the source · abstract, characters 1466–1603 · show in text ↑
Intervention effectobservedoriginal resultpositivemeasured

Claim · model-written summary

Organic rice practices increased available labile carbon.

Treatment
green mulching, zero external inputse1
Outcome
available labile Ce0
Direction
increasede0

Not reportedComparator

Organisms pictured · Representative pictures of the matched species, not figures from the paper.

Oryza sativa
Oryza sativa · Taxon · picture from its Wikimedia Commons categoryDesmanthus4food · CC BY-SA 3.0 us · Wikimedia Commons ↗

Verbatim

e0

“increased available labile C”

✓ located verbatim in the source · abstract, characters 1605–1633 · show in text ↑
e1

“sustainable practices employed for rice cultivation (i.e., green mulching, zero external inputs)”

✓ located verbatim in the source · abstract, characters 1470–1566 · show in text ↑
Intervention effectobservedoriginal resultpositivemeasured

Claim · model-written summary

Organic rice practices produced 7% carbon sequestration at season end.

Treatment
green mulching, zero external inputse1
Outcome
carbon sequestratione0
Direction
increaseinferrede0
Value
7%e0

Not reportedComparator

Organisms pictured · Representative pictures of the matched species, not figures from the paper.

Oryza sativa
Oryza sativa · Taxon · picture from its Wikimedia Commons categoryDesmanthus4food · CC BY-SA 3.0 us · Wikimedia Commons ↗

Verbatim

e0

“carbon sequestration at the end of the growing season (7%)”

✓ located verbatim in the source · abstract, characters 1644–1702 · show in text ↑
e1

“sustainable practices employed for rice cultivation (i.e., green mulching, zero external inputs)”

✓ located verbatim in the source · abstract, characters 1470–1566 · show in text ↑
Intervention effectobservedoriginal resultpositivemeasured

Claim · model-written summary

Organic rice practices conserved soil nitrogen and phosphorus.

Treatment
green mulching, zero external inputse1
Outcome
soil N and P conservatione0

Not reportedComparatorDirection

Organisms pictured · Representative pictures of the matched species, not figures from the paper.

Oryza sativa
Oryza sativa · Taxon · picture from its Wikimedia Commons categoryDesmanthus4food · CC BY-SA 3.0 us · Wikimedia Commons ↗

Verbatim

e0

“soil N and P conservation”

✓ located verbatim in the source · abstract, characters 1712–1737 · show in text ↑
e1

“sustainable practices employed for rice cultivation (i.e., green mulching, zero external inputs)”

✓ located verbatim in the source · abstract, characters 1470–1566 · show in text ↑
Associationobservedoriginal resultmeasured

Claim · model-written summary

CEC, C/N and bacterial diversity mainly influenced rice grain carbohydrate fraction.

Interactor
bacteriale0other
Outcome
carbohydrate fraction of the rice graine0
Setting
CEC, C/N and bacterial diversitye0

Not reportedDirection

Organisms pictured · Representative pictures of the matched species, not figures from the paper.

Oryza sativa
Oryza sativa · Taxon · picture from its Wikimedia Commons categoryDesmanthus4food · CC BY-SA 3.0 us · Wikimedia Commons ↗

Verbatim

e0

“CEC, C/N and bacterial diversity mainly influenced the carbohydrate fraction of the rice grain”

✓ located verbatim in the source · abstract, characters 1772–1866 · show in text ↑
Associationobservedoriginal resultmeasured

Claim · model-written summary

CEC, C/N and bacterial diversity indirectly affected rice grain protein content.

Interactor
bacteriale0other
Outcome
protein contente0
Setting
CEC, C/N and bacterial diversitye0

Not reportedDirection

Organisms pictured · Representative pictures of the matched species, not figures from the paper.

Oryza sativa
Oryza sativa · Taxon · picture from its Wikimedia Commons categoryDesmanthus4food · CC BY-SA 3.0 us · Wikimedia Commons ↗

Verbatim

e0

“CEC, C/N and bacterial diversity mainly influenced the carbohydrate fraction of the rice grain, with an indirect effect on the protein content”

✓ located verbatim in the source · abstract, characters 1772–1914 · show in text ↑

mulching · soil: chemistry · Oryza sativa (rice)Positive and negative results

7 papers: 6 positive, 1 negative or no effect

5 papers in the same direction as this paper · 1 in the opposite direction

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