Characterization of the Soil Bacterial Community from Selected Boxwood Gardens across the United States

Abstract

In a recent study, we observed a rapid decline of the boxwood blight pathogen Calonectria pseudonaviculata (Cps) soil population in all surveyed gardens across the United States, and we speculated that these garden soils might be suppressive to Cps. This study aimed to characterize the soil bacterial community in these boxwood gardens. Soil samples were taken from one garden in California, Illinois, South Carolina, and Virginia and two in New York in early summer and late fall of 2017 and 2018. Soil DNA was extracted and its 16S rRNA amplicons were sequenced using the Nanopore MinION® platform. These garden soils were consistently dominated by Rhizobiales and Burkholderiales, regardless of garden location and sampling time. These two orders contain many species or strains capable of pathogen suppression and plant fitness improvement. Overall, 66 bacterial taxa were identified in this study that are known to have strains with biological control activity (BCA) against plant pathogens. Among the most abundant were Pseudomonas spp. and Bacillus spp., which may have contributed to the Cps decline in these garden soils. This study highlights the importance of soil microorganisms in plant health and provides a new perspective on garden disease management using the soil microbiome.

Divergence in the soil and rhizosphere microbial communities of monoculture and silvopastoral traditional C. dodecandra agroforestry systems in Yucatan, Mexico

“…Most are bacterial orders frequently found in soils (e.g. Li et al, 2022; Mhete et al, 2020; Wang et al, 2018), nevertheless the presence of Nitrososphaerales, which belong to the archaeal phylum Thaumarchaeota, draws attention because its relatively high proportion (4.6%–8.5%). All described isolates of Nitrososphaerales are obligate aerobes, mesophilic or moderately thermophilic, and exhibit chemolithoautotrophic metabolism via ammonia oxidation and CO 2 fixation (Kerou et al, 2016).…”

Nanopore Is Preferable over Illumina for 16S Amplicon Sequencing of the Gut Microbiota When Species-Level Taxonomic Classification, Accurate Estimation of Richness, or Focus on Rare Taxa Is Required

“…In addition, it is a small portable device, allowing the processing of samples on site without the need of elaborate laboratory infrastructure. Consequently, there is growing interest in using Nanopore for 16S rRNA gene amplicon sequencing, and recent publications have demonstrated its success with a variety of samples, for example freshwater [ 5 ], seawater and algal surfaces [ 6 ], soil [ 7 , 8 ], surfaces in the international space station [ 9 ], animal feces [ 10 ], urine [ 11 ], buccal and rectal swabs [ 12 ], ophthalmic samples [ 13 ], bronchoalveolar lavage fluid, blood, pleural and ascitic fluid, cerebrospinal fluid, and wound secretions [ 14 ].…”