# Soil nifH-harboring community assemblage varies across pecan cultivars

## TL;DR

This study shows how different pecan tree varieties affect soil microbes involved in nitrogen fixation, with implications for managing soil health in pecan farming.

## Contribution

The study reveals cultivar-specific and soil compartment-specific effects on nifH-harboring microbial communities and nitrogenase activity in pecan soils.

## Key findings

- ‘Mahan’ pecan cultivar showed highest nitrogenase activity in both rhizosphere and bulk soils.
- ‘Jinhua’ bulk soil had distinct microbial signatures with enriched Cyanobacteria and complex microbial networks.
- Rhizobiales and Burkholderiales were identified as key microbial biomarkers in ‘Jinhua’ soils.

## Abstract

This study focused on three pecan (Carya illinoinensis) cultivars (‘Pawnee’, ‘Mahan’, and ‘Jinhua’), systematically assessing variations in soil nitrogenase activity, characteristics traits of nifH-harboring microbial communities across these cultivars.

Using high-throughput sequencing technology, differences in the diversity, community composition, and network structure of nifH-harboring communities in the rhizosphere and bulk soils of pecan were examined across cultivars.

Both cultivar type and soil compartment had significant effects on nitrogenase activity (p < 0.01). Among the three cultivars, ‘Mahan’ exhibited the highest soil nitrogenase activity in both its rhizosphere and bulk soils relative to the other two cultivars. Notably, rhizosphere soils across all cultivars displayed significantly stronger soil nitrogenase activity than their bulk soil counterparts. ‘Mahan’ harbored significantly higher microbial α-diversity (Sobs, Shannon, and Chao indices) than other cultivars (p < 0.05). β-diversity analysis revealed marked community divergence among cultivars, with the most pronounced differences observed in bulk soils. Specifically, the bulk soil of ‘Jinhua’ harbored a distinct microbial signature, marked by significant enrichment of Cyanobacteria and depletion of Alphaproteobacteria. Linear discriminant analysis effect size (LEfSe) further identified Rhizobiales and Burkholderiales as distinct biomarkers for the rhizosphere and bulk soils of ‘Jinhua’, respectively (LDA score > 4.0, p < 0.05). Microbial co-occurrence network analysis showed that the bulk soil of ‘Jinhua’ harbored the most complex microbial interaction network, characterized by the highest number of edges, and average connectivity. In co-occurrence networks, Azohydromonas, Bradyrhizobium, Azoarcus, Rhodomicrobium were found as the keystone taxa in maintaining network stability.

This research elucidates the regulatory roles of pecan cultivars in shaping soil nitrogen fixation functions and microbial community assembly, providing valuable practical implications for precision microbiome management in pecan production.