High-resolution community profiling of active bacteria and eukaryotes in replant-diseased blueberry farm soils from New Jersey, USA

Authors: MIRZOYAN, SEDA - Rutgers University; Polashock, James; KERKHOF, LEE - Rutgers University

Submitted to: Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/5/2026
Publication Date: 3/17/2026
Citation: Mirzoyan, S., Polashock, J.J., Kerkhof, L.J. 2026. High-resolution community profiling of active bacteria and eukaryotes in replant-diseased blueberry farm soils from New Jersey, USA. Environmental Microbiology. 28(3). Article e70280. https://doi.org/10.1111/1462-2920.70280.
DOI: https://doi.org/10.1111/1462-2920.70280

Interpretive Summary: Cultivated blueberry grows in acidic soils with high organic content. Although blueberry fields can remain productive for decades, some older fields can decline in plant health and productivity. Replanting often does not solve the problem, suggesting a soil-related problem. To begin addressing this issue, we characterized the active microorganisms from the root zone of blueberries from two farms (high and low productivity soils from each farm) and compared them with adjacent forest soils. We used a method that 'labeled' the DNA from microbes present in the soil. Using this technique, over 13,000 bacterial and fungal microbes inhabiting these soils were detected. The results demonstrated distinct differences between high and low productivity soils for both bacteria and fungi. These results provide diagnostic tools to detect microbes present in these soils that may promote plant health or contribute to plant decline. The results will be of value to scientists conducting research to improve crop productivity and disease management strategies.

Technical Abstract: Highbush blueberry (Vaccinium corymbosum L.) fields can remain productive for decades. However, some older fields declinein 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- andhigh-yield blueberry farm soils from two separate farms contained different microbiomes, we coupled long-read bacterial andeukaryotic ribosomal rRNA operon sequencing using the Oxford Nanopore MinION with stable isotope probing (SIP) to detect13C/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 forestsoils 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 profil-ing and SIP. The findings also suggest a diagnostic test of blueberry replant affected soils is feasible and may ultimately be usedto improve productivity and potentially detect the responsible pathogenic agent(s) or other deleterious microbes.