  Citation: Ryadin, A.R.; Janz, D.; Schneider, D.; Tjoa, A.; Irawan, B.; Daniel, R.; Polle, A. Early Effects of Fertilizer and Herbicide Reduction on Root-Associated Biota in Oil Palm Plantations. Agronomy 2022, 12, 199. https://doi.org/10.3390/ agronomy12010199 Academic Editors: Helena Freitas and Rui S. Oliveira Received: 22 December 2021 Accepted: 11 January 2022 Published: 14 January 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). agronomy Article Early Effects of Fertilizer and Herbicide Reduction on Root-Associated Biota in Oil Palm Plantations Aisjah R. Ryadin 1,2 , Dennis Janz 1 , Dominik Schneider 3 , Aiyen Tjoa 4 , Bambang Irawan 5 , Rolf Daniel 3 and Andrea Polle 1, * 1 Forest Botany and Tree Physiology, University of Goettingen, 37077 Göttingen, Germany; aisjahr@yahoo.com (A.R.R.); djanz@gwdg.de (D.J.) 2 Agriculture Faculty, Khairun University, Ternate 97719, Indonesia 3 Genomic and Applied Microbiology and Göttingen Genomics Laboratory, University of Goettingen, 37077 Göttingen, Germany; dschnei1@gwdg.de (D.S.); rdaniel@gwdg.de (R.D.) 4 Faculty of Agriculture, Tadulako University, Palu 94118, Indonesia; aiyenb@yahoo.com 5 Forestry Department, Agriculture Faculty, University of Jambi, Jambi 36361, Indonesia; irawanbam@yahoo.com * Correspondence: apolle@gwdg.de Abstract: To secure high yield, tropical oil palm plantations are fertilized, and understory vegetation is controlled by chemical clearing with herbicides. These treatments cause a drastic turnover of soil microbes and cause loss of beneficial mycorrhizal fungi. Here, we tested if reduced fertilization and weeding instead of conventional treatments restored beneficial ecological groups associated with roots. We conducted our study one year after the start of the reduced management in large-scale oil palm plantations. We hypothesized that reduced fertilizer application and weeding result in shifts of the root-associated species composition because changes in the management regimes affect belowground biomass and nutrients in soil and roots. Alternatively, we hypothesized that the legacy of massive soil fertilization and herbicide application preclude compositional shifts of root-associated biota within short time periods. We did not find any significant treatment effects on root nutrient contents, root biomass, and nutrients in soil. At the level of species (based on operational taxonomic units obtained by Illumina sequencing) or phyla, no significant effects of reduced management were observed. However, distinct functional groups showed early responses to the treatments: nematodes decreased in response to weeding; yeasts and ectomycorrhizal-multitrophic fungi increased under fertilizer treatments; arbuscular mycorrhizal fungi increased under fertilizer reduction. Since the responsive ecological groups were represented by low sequence abundances, their responses were masked by very high sequence abundances of saprotrophic and pathotrophic fungi. Thus, the composition of the whole root-associated community was unaffected by reduced management. In conclusion, our results show that changes in management regimes start to re-wire critical constituents of soil–plant food webs. Keywords: microbiome; mycorrhiza; plantation management; root biomass; sustainability; tropics 1. Introduction The main driver of tropical rain forest transformation in south-east Asia is the ex- pansion of oil palm plantations [1,2]. Palm oil is the most lucrative oil crop in the world and Indonesia is one of the main producers and exporters of this commodity [3,4]. The expansion of areas for palm oil production has benefited the economic situation of small- holder farmers and decreased the country’s dependence on the import of fossil fuels [5,6]. However, the high deforestation rate to enlarge plantation areas [7,8] comes with ecological trade-offs in biodiversity and ecosystem functions [9,10]. Multiple studies on Sumatera, a hotspot of expanding oil palm (Elaeis guineensis Jacq.) cultivation, show that aboveground species richness is drastically declining after Agronomy 2022, 12, 199. https://doi.org/10.3390/agronomy12010199 https://www.mdpi.com/journal/agronomy