Abstract：
Soil microbiome science, rapidly evolving, predominantly focuses on field crop soils. However, understanding garden soil microbiomes is essential for enhancing food production sustainability in garden environments. This study aimed to unveil the bacteriome diversity and composition in rooftop garden soils (RGS) and surface garden soils (SGS) across urban (Dhaka North and Dhaka South City Corporations) and peri-urban (Gazipur City Corporation) areas of Dhaka Division, Bangladesh. We analyzed 11 samples, including six RGS and five SGS samples from 11 individual gardens using 16S rRNA (V3-V4 region) gene-based amplicon sequencing. A total of 977 operational taxonomic units (OTUs), including 270 and 707 in RGS and SGS samples, respectively, were identified. The observed OTUs were represented by 21 phyla, 45 classes, 84 orders, 173 families, and 293 genera of bacteria. Alpha diversity indices revealed significantly higher bacterial diversity in SGS samples (p = 0.01), while beta diversity analyses indicated distinct bacteriome compositions between RGS and SGS samples (p = 0.028, PERMANOVA). Despite substantial taxonomic variability between sample categories, there was also a considerable presence of shared bacterial taxa. At the phylum level, Bacilliota (61.14%), Pseudomonadota (23.42%), Actinobacteria (6.33%), and Bacteroidota (3.32%) were the predominant bacterial phyla (comprising > 94.0% of the total abundances) in both types of garden soil samples. Of the identified genera, Bacillus (69.73%) and Brevibacillus (18.81%) in RGS and Bacillus (19.22%), Methylophaga (19.21%), Acinetobacter (6.27%), Corynebacterium (5.06%), Burkholderia (4.78%), Paracoccus (3.98%) and Lysobacter (2.07%) in SGS were the major bacterial genera. Importantly, we detected that 52.90% of genera were shared between RGS and SGS soil samples. Our data reveal unique and shared bacteriomes with probiotic potential in soil samples from both rooftop and surface gardens. Further studies should explore the functional roles of shared bacterial taxa in garden soils and how urban environmental factors affect microbiome composition to optimize soil health and sustainable food production.
摘要：
土壤微生物组科学，快速发展，主要集中在田间作物土壤上。然而,了解花园土壤微生物对于提高花园环境中粮食生产的可持续性至关重要。这项研究旨在揭示达卡地区城市（达卡北部和达卡南部城市公司）和城市周边地区（加济布尔市公司）的屋顶花园土壤（RGS）和地表花园土壤（SGS）的细菌多样性和组成。孟加拉国。我们分析了11个样本,包括来自11个单独花园的6个RGS和5个SGS样本，使用基于16SrRNA（V3-V4区域）基因的扩增子测序。共有977个操作分类单位(OTU)，包括RGS和SGS样品中的270和707，分别,已确定。观察到的OTU由21门代表，45班,84个订单，173个家庭,和293属细菌。Alpha多样性指数显示SGS样本中细菌多样性显著较高（p=0.01），而β多样性分析表明RGS和SGS样品之间有不同的细菌组组成(p=0.028，PERMANOVA)。尽管样本类别之间的分类差异很大，也有相当多的共享细菌类群的存在。在门一级，芽孢杆菌（61.14%），Pseudomonadota(23.42%),放线菌(6.33%),和拟杆菌（3.32％）是两种类型的花园土壤样品中的主要细菌门（占总丰度的94.0％）。在确定的属中，RGS中的芽孢杆菌(69.73%)和短芽孢杆菌(18.81%)和芽孢杆菌(19.22%),甲基phaga（19.21%），不动杆菌（6.27%），棒状杆菌(5.06%),伯克霍尔德菌（4.78%），SGS中副球菌（3.98％）和溶杆菌（2.07％）是主要的细菌属。重要的是,我们检测到52.90%的属在RGS和SGS土壤样品之间共享。我们的数据揭示了来自屋顶和地面花园的土壤样品中具有益生菌潜力的独特和共享的细菌。进一步的研究应探索共享细菌类群在花园土壤中的功能作用，以及城市环境因素如何影响微生物组组成，以优化土壤健康和可持续粮食生产。
