Characterizing microbial communities associated with northern root-knot nematode (Meloidogyne hapla) occurrence and soil health

Isaac Lartey; Gian M N Benucci; Terence L Marsh; Gregory M Bonito; Haddish Melakeberhan

doi:10.3389/fmicb.2023.1267008

Characterizing microbial communities associated with northern root-knot nematode (Meloidogyne hapla) occurrence and soil health

Front Microbiol. 2023 Nov 10:14:1267008. doi: 10.3389/fmicb.2023.1267008. eCollection 2023.

Authors

Isaac Lartey¹, Gian M N Benucci², Terence L Marsh³, Gregory M Bonito², Haddish Melakeberhan¹

Affiliations

¹ Agricultural Nematology Laboratory, Department of Horticulture, Michigan State University, East Lansing, MI, United States.
² Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, United States.
³ Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States.

Abstract

The northern root-knot nematode (Meloidogyne hapla) causes extensive damage to agricultural crops globally. In addition, M. hapla populations with no known genetic or morphological differences exhibit parasitic variability (PV) or reproductive potential based on soil type. However, why M. hapla populations from mineral soil with degraded soil health conditions have a higher PV than populations from muck soil is unknown. To improve our understanding of soil bio-physicochemical conditions in the environment where M. hapla populations exhibited PV, this study characterized the soil microbial community and core- and indicator-species structure associated with M. hapla occurrence and soil health conditions in 15 Michigan mineral and muck vegetable production fields. Bacterial and fungal communities in soils from where nematodes were isolated were characterized with high throughput sequencing of 16S and internal transcribed spacer (ITS) rDNA. Our results showed that M. hapla-infested, as well as disturbed and degraded muck fields, had lower bacterial diversity (observed richness and Shannon) compared to corresponding mineral soil fields or non-infested mineral fields. Bacterial and fungal community abundance varied by soil group, soil health conditions, and/or M. hapla occurrence. A core microbial community was found to consist of 39 bacterial and 44 fungal sub-operational taxonomic units (OTUs) across all fields. In addition, 25 bacteria were resolved as indicator OTUs associated with M. hapla presence or absence, and 1,065 bacteria as indicator OTUs associated with soil health conditions. Out of the 1,065 bacterial OTUs, 73.9% indicated stable soil health, 8.4% disturbed, and 0.4% degraded condition; no indicators were common to the three categories. Collectively, these results provide a foundation for an in-depth understanding of the environment where M. hapla exists and conditions associated with parasitic variability.

Keywords: core microbiome; health; indicator species; nematode-microbe interaction; parasitic variability; soil.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The study was funded by MSU College of Agriculture and Natural Resources, MSU Graduate School, MSU AgBioResearch, and USDA/NIFA Hatch Project (MICL #1792) of HM. GB was supported through US National Science Foundation (NSF) DEB 1737898 and Michigan State University AgBioResearch NIFA project MICL02416.