Rojas-Chacón José Andrés, Echeverría-Beirute Fabián, Jiménez-Madrigal José Pablo, Varela-Benavides Ingrid, Faggioli Valeria, Berkelmann Dirk, Gatica-Arias Andrés
Maestría en Ciencia y Tecnología Para La Sostenibilidad, Instituto Tecnológico de Costa Rica, San Carlos Campus, 159-7050, Alajuela, Costa Rica.
CABANAnet (Capacity Building for Bioinformatics in Latin America), San José, 2060-11501, Costa Rica.
World J Microbiol Biotechnol. 2025 Jun 25;41(7):220. doi: 10.1007/s11274-025-04407-6.
Understanding the interactions between soil bacteria, fungi, and nematodes in coffee agroecosystems is crucial for optimizing sustainable agriculture. This study investigated the composition and functional dynamics of these communities under conventional and sustainable management systems. Soil samples were collected from three major coffee-growing regions in Costa Rica, representing different agricultural regimes. Nematode community was analyzed using optical microscopy, while microbial communities were analyzed using high-throughput sequencing. In both cases, bioinformatic tools were used for functional prediction based on taxonomy.. Herbivorous nematodes dominated both systems, while bacterivores (Rhabditidae, Cephalobidae) and fungivores (Aphelenchoidae) were significantly more abundant in soils subject to sustainable practice (p < 0.05). Nematode maturity indices and food web diagnostics showed no significant differences between systems, even though metabolic footprints related to organic matter decomposition varied (p < 0.05). Bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria, and Chloroflexi, while the fungal community was largely composed of Ascomycota (53.21% in both systems). The fungal genus Mortierella was particularly prevalent. Soil pH, along with Ca, Mg, K, and extractable acidity, influenced community composition. Functional profiles revealed higher gene abundances linked to nutrient and energy cycling in sustainable systems, particularly phosphorus and sulfur metabolism. Saprotroph-symbiotroph fungi were more common in sustainable soils, while pathotrophic fungi dominated conventional systems. This is the first comprehensive analysis of bacteria, fungi, and nematodes across different agricultural practices in coffee agroecosystems in Costa Rica.
了解咖啡农业生态系统中土壤细菌、真菌和线虫之间的相互作用对于优化可持续农业至关重要。本研究调查了传统和可持续管理系统下这些群落的组成和功能动态。从哥斯达黎加三个主要咖啡种植区采集土壤样本，代表不同的农业制度。使用光学显微镜分析线虫群落，同时使用高通量测序分析微生物群落。在这两种情况下，都使用生物信息学工具基于分类学进行功能预测。植食性线虫在两个系统中均占主导地位，而在采用可持续做法的土壤中，食细菌线虫（杆线虫科、头叶线虫科）和食真菌线虫（滑刃线虫科）的数量明显更多（p < 0.05）。尽管与有机质分解相关的代谢足迹有所不同（p < 0.05），但线虫成熟度指数和食物网诊断显示两个系统之间没有显著差异。细菌群落以变形菌门、酸杆菌门和绿弯菌门为主，而真菌群落主要由子囊菌门组成（两个系统中均为53.21%）。被孢霉属真菌尤为普遍。土壤pH值以及钙、镁、钾和可提取酸度影响群落组成。功能概况显示，可持续系统中与养分和能量循环相关的基因丰度更高，尤其是磷和硫代谢。腐生共生真菌在可持续土壤中更为常见，而致病真菌在传统系统中占主导地位。这是对哥斯达黎加咖啡农业生态系统中不同农业实践下细菌、真菌和线虫的首次综合分析。
