# High‐Resolution Community Profiling of Active Bacteria and Eukaryotes in Replant‐Diseased Blueberry Farm Soils From New Jersey, USA

## TL;DR

This study identifies differences in soil microbes between low- and high-yield blueberry farms, which could help diagnose and improve replant disease.

## Contribution

The study introduces a method combining long-read sequencing and SIP to profile active microbes in blueberry farm soils.

## Key findings

- Low-productivity soils showed active Bacillus species, while high-productivity soils had active Burkholderia and Paraburkholderia.
- Eukaryotic species like Candida blankii were enriched in low-yield soils.
- The method can differentiate soil microbiomes and may help detect harmful microbes.

## Abstract

Highbush blueberry (
Vaccinium corymbosum
L.) fields can remain productive for decades. However, some older fields decline in plant health and exhibit lower yields. After re‐planting with new stock, the yields continue to suffer. This condition is termed ‘Replant Disease’. The causative agent(s) in replant disease in New Jersey blueberry fields are unknown. To assess if low‐ and high‐yield blueberry farm soils from two separate farms contained different microbiomes, we coupled long‐read bacterial and eukaryotic ribosomal rRNA operon sequencing using the Oxford Nanopore MinION with stable isotope probing (SIP) to detect 13C/15N‐utilising soil microbial communities. The results indicate multiple Bacillus species were active on 13C/15N‐growth media (predominantly amino acids and glucose) in low‐productivity soils from both farms, while high‐productivity and adjacent forest soils contained active Burkholderia and Paraburkholderia species. Eukaryotic community profiling indicated Candida blankii, Nadsonia starkeyi and Sugiyamaella chiloensis were slightly enriched and active in low‐productivity soils compared with high‐productivity soils. This approach differentiates low‐ and high‐productivity blueberry farm soils by ribosomal RNA operon profiling and SIP. The findings also suggest a diagnostic test of blueberry replant affected soils is feasible and may ultimately be used to improve productivity and potentially detect the responsible pathogenic agent(s) or other deleterious microbes.

Long read bacterial and eukaryotic ribosomal operon sequencing combined with stable isotope probing (SIP) allowed the differentiation of microbiomes in low‐ and high‐yield blueberry farm soils. This report may ultimately be used to improve productivity and potentially detect the responsible pathogenic agent(s) or other deleterious microbes.