Long-term organic fertilization reshapes soil bacterial communities in Chattogram fields

Soils that have been fertilized in different ways for roughly two decades harbor measurably different bacterial communities, according to a new study of agricultural fields in Chattogram, Bangladesh. Researchers sampled six plots managed with chemical fertilizers and six plots managed with cattle manure, all maintained under consistent field management by the Department of Soil Science at the University of Chittagong, and profiled their bacterial communities using Oxford Nanopore long-read sequencing of the full V1–V9 region of the 16S rRNA gene. The work, published in Genomics & Informatics, is described by its authors as the first application of this full-length sequencing strategy to fertilization-driven changes in bacterial communities in agricultural soils of the Chattogram region.

The study was observational and comparative in design. Soil samples were collected in December 2025 from the top 20 centimeters of crop fields, with multiple subsamples pooled into one composite sample per plot. Twelve samples were sequenced in total. In the chemically fertilized regime, urea, triple superphosphate, and muriate of potash supplied nitrogen, phosphorus, and potassium, while the organic regime relied on cattle manure. The researchers emphasize that the two regimes were established in separate plots, so the comparison reflects long-standing differences in field management rather than a controlled experiment in which fertilizer type was randomly assigned.

Sequencing identified 431 taxonomic features across the samples, assigned to 19 bacterial phyla. Of these features, 269 were shared between the two fertilizer groups, 92 were unique to the organically fertilized soils, and 70 were unique to the chemically fertilized soils. Beta diversity analysis based on Bray–Curtis dissimilarity, visualized with principal coordinate analysis and non-metric multidimensional scaling, showed a significant difference in community composition between the groups, with a PERMANOVA test yielding p = 0.003 and an R² of 0.84016. The authors interpret this R² value as indicating that the fertilization regime was associated with a substantial proportion of the observed variation in bacterial community composition.

Alpha diversity results were more nuanced. The observed species, Chao1, and ACE indices, which are richness-based measures, showed no significant differences between the treatments. However, the Shannon, Simpson, and InvSimpson indices, which account for both richness and evenness, differed significantly between the groups, with the Wilcoxon rank-sum test giving p < 0.05. In the discussion, the authors report that these evenness-sensitive indices indicated a significant increase in bacterial diversity under chemical fertilization, suggesting a more balanced and evenly distributed community under that regime even though richness-based metrics remained unchanged. The authors caution that the observed alpha diversity patterns do not show increased diversity under organic fertilization.

At the phylum level, organically fertilized soils were dominated by Firmicutes (24.57%), Proteobacteria (22.76%), and Planctomycetota (20.29%), while chemically fertilized soils were led by Proteobacteria (28.58%), Planctomycetota (20.29%), and Firmicutes (15.63%). At the genus level, Bacillus was the most abundant taxon in both groups, but its relative abundance was substantially higher under organic amendment, at 14.77 ± 0.790% compared with 8.84 ± 1.255% under chemical fertilization (FDR < 0.001). Gemmataceae_uncultured followed a similar pattern, at 11.60 ± 0.441% versus 7.65 ± 0.689% (FDR < 0.001), as did Xanthobacteraceae_uncultured at 4.15 ± 0.204% versus 2.88 ± 0.197% (FDR < 0.001). Tumebacillus (2.73 ± 0.183% versus 1.35 ± 0.171%) and Paenibacillus (2.50 ± 0.155% versus 2.02 ± 0.173%) were also significantly more abundant under organic fertilization, with FDR < 0.001 in both cases.

Several taxa showed the opposite pattern. Isosphaeraceae_uncultured was more abundant in chemically fertilized soils (4.30 ± 0.365%) than in organically fertilized soils (2.14 ± 0.224%; FDR < 0.001), and Gemmatimonadaceae_uncultured was also enriched under chemical fertilization (2.12 ± 0.311% versus 1.56 ± 0.160%; FDR = 0.004). Bradyrhizobium showed a modestly higher abundance under chemical fertilization (3.33 ± 0.240% versus 2.90 ± 0.216%), although the authors report this difference with an FDR of 0.055, which falls just above their significance threshold of 0.05. The difference in Pirellula abundance (1.54 ± 0.150% versus 1.28 ± 0.125%) was likewise not statistically significant (FDR = 0.076), and Roseiflexaceae_uncultured did not differ significantly between treatments (FDR = 0.368).

The authors highlight that several of the taxa enriched under organic fertilization, including Bacillus, Paenibacillus, Bradyrhizobium, and Tumebacillus, are well-documented plant growth-promoting bacteria known for roles such as phosphate solubilization, nitrogen fixation, phytohormone production, siderophore-mediated nutrient acquisition, and pathogen suppression. They note that the higher abundance of these genera in organically fertilized soils suggests that prolonged organic amendment may foster beneficial rhizosphere microorganisms. Members of Xanthobacteraceae perform nitrogen fixation and degrade aromatic compounds, while Gemmataceae, part of the Planctomycetes group, is associated with the degradation of complex polysaccharides and other recalcitrant organic compounds. In chemically fertilized soils, the enriched Gemmatimonadaceae is known for polyphosphate accumulation and drought tolerance, suggesting adaptation to nutrient-enriched or resource-limited environments.

Functional profiling using METAGENassist predictions separated the two treatments in a principal component analysis and suggested differing functional orientations. Under chemical fertilization, the community showed relatively higher representation of nitrogen-fixing bacteria (5.25% versus 4.47% under organic) and redox-associated functions such as sulfate reduction (14.77% versus 14.33%), ammonia oxidation (14.51% versus 14.02%), and nitrite reduction (14.33% versus 13.67%). Under organic fertilization, functions associated with organic matter degradation were comparatively better represented, including xylan degradation (8.86% versus 7.62%) and chitin degradation (8.58% versus 7.78%), along with streptomycin-producing functions (6.09% versus 4.51%). The authors stress that these functional profiles are predictions derived from 16S rRNA data and were not experimentally validated, so they indicate possible differences in microbial capacity rather than measured functional outcomes.

Soil chemistry differed between the regimes in ways that paralleled the microbial patterns. Chemically fertilized soils contained higher phosphorus (35.33 ± 2.16 versus 7.5 ± 1.05) and boron (0.48 ± 0.04 versus 0.35 ± 0.04), while organically fertilized soils had higher sulfur, potassium, and nitrogen, along with higher organic matter (1.98 ± 0.14 versus 1.49 ± 0.07), organic carbon (1.13 ± 0.08 versus 0.86 ± 0.05), and pH (5.90 ± 0.09 versus 5.57 ± 0.08), all with p < 0.001. Heavy metal concentrations also differed, with lead and iron higher under chemical fertilization and cadmium, nickel, chromium, manganese, and zinc higher under organic fertilization. Spearman’s rank correlation analysis revealed strong positive associations between several nutrients and specific taxa; for example, nitrogen correlated strongly with Bacillus (rs = 0.78), Gemmataceae_uncultured (rs = 0.91), Tumebacillus (rs = 0.84), Paenibacillus (rs = 0.80), and Xanthobacteraceae_uncultured (rs = 0.86), and organic matter correlated with Bacillus (rs = 0.84) and Tumebacillus (rs = 0.89). The authors explicitly caution that these correlations do not necessarily indicate direct causal effects of nutrients on the abundance or activity of these taxa.

The authors frame their findings as evidence that the effects of fertilization on soil bacterial communities may extend beyond overall richness to involve changes in community structure and relative abundance. They also acknowledge important limitations: the study provides limited information on fertilizer composition, cropping history, and climatic variability; the functional predictions were not experimentally validated; and the effects of fertilization on soil fertility and long-term agricultural sustainability should be assessed in the context of broader soil attributes and microbial community features. All sequencing data have been deposited in the NCBI Sequence Read Archive under BioProject accession PRJNA1415714, allowing independent verification of the taxonomic and diversity analyses reported for these twelve Chattogram soil samples.

Subject of Research: Effects of long-term chemical versus organic fertilization on soil bacterial communities in Chattogram, Bangladesh

Article Title: Impact of extended fertilization on soil microbial diversity: a comparative full-length 16S rRNA amplicon analysis

Article References: Chamonara, K., Masum, M. H. U., Faria, F. F., Chowdhury, S., Khan, M. S. R., & Kashem, M. A. (2026). Impact of extended fertilization on soil microbial diversity: a comparative full-length 16S rRNA amplicon analysis. Genomics & Informatics, 24(1), Article 20. https://doi.org/10.1186/s44342-026-00078-3

Image Credits: AI Generated

DOI: 10.1186/s44342-026-00078-3

Keywords: soil microbiome, 16S rRNA sequencing, Oxford Nanopore, organic fertilizer, chemical fertilizer, Bangladesh, plant growth-promoting bacteria, Bacillus, beta diversity, PERMANOVA, soil fertility, agricultural sustainability