The Diversity and Abundance of Bacterial Community in Pepper, the "King of Spices" (Piper nigrum)
DOI:
https://doi.org/10.11113/mjfas.v22n4.5381Keywords:
Plant-microbe interaction, 16S amplicon sequencing, rhizosphere microbiome, Piper nigrumAbstract
Pepper (Piper nigrum L.) is one of the most widely consumed spices. Indonesia has become a significant producer and exporter of high-quality pepper, known for its unique flavour. The interactions between plants and microbes have been widely studied. However, comprehensive information on Indonesian pepper biotic (microbiome) and abiotic (soil and climate) factors has not been reported in detail. This study investigated bacterial diversity, abundance, and community structure in pepper plantations from three major production regions—Lampung, Bangka, and Belitung—across root endosphere, rhizosphere, and bulk soil compartments using 16S rRNA gene amplicon sequencing of the V3–V4 region. Sequencing generated sufficient high-quality data, with final nonchimeric read counts ranging from 43,972 ± 2,564 to 66,171 ± 819 across sample groups. Soil properties differed among regions, with Lampung showing higher rhizosphere pH (6.00), NH₄ (11.91 ppm), K (106.24 ppm), Ca (2918.73 ppm), Mn (129.12 ppm), Cu (0.57 ppm), and Zn (1.32 ppm), whereas Bangka showed higher organic C (3.27%), total N (0.25%), EC (246.33 µS/cm), Fe (8.98 ppm), and Sn (5.656 ppm). A total of 25 bacterial phyla were detected, with Proteobacteria dominating root endosphere (60–78%) and rhizosphere samples (44–56%), while Acidobacteriota was more abundant in bulk soil (36–41%). At the genus level, Acinetobacter was enriched in plant-associated compartments, reaching approximately 68% in Rhizosphere_Lampung, 50% in Rhizosphere_Belitung, and 38% in Root EC_Bangka. Other dominant genera showed compartment- and location-specific patterns, including Enterobacter and Klebsiella in Root EC_Belitung, Burkholderia–Caballeronia–Paraburkholderia, Bacillus, and Chryseobacterium in Rhizosphere_Bangka, and Sinomonas and Acidothermus in bulk soil. Alpha diversity showed that the rhizosphere was the main hotspot of diversity, with median Observed ASVs of 810–860 and the highest shared richness among regions (258 ASVs). Weighted UniFrac PCoA revealed clear community separation, with PCoA1 and PCoA2 explaining 31.86% and 15.32% of variation, respectively. PCA and RDA further indicated that Proteobacteria, Acidobacteriota, Actinobacteriota, Chloroflexi, Acinetobacter, Chryseobacterium, Enterobacter, and Sinomonas contributed to bacterial community differentiation. These findings indicate that Indonesian pepper bacterial communities are structured by plant compartment and regional edaphic heterogeneity.
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Copyright (c) 2026 Nia Asiani, Ana Feronika Irawati, Yuda Purwana Roswanjaya, Ahmed IbrahimAlrashid Yousif, Sulastri, Bambang Sukmadi, Ahmad Arivin Rivaie, Rita Harni, Tri Lestari, Nurmalinda, Nur Alfi Saryanah, Iskandar Zulkarnaen, Muhammad Zulhiyadi Nanda
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