Nanopore sequencing is a promising technology used for 16S rRNA gene amplicon sequencing as it can provide full-length 16S reads and has a low up-front cost that allows research groups to set up their own sequencing workflows. To assess whether Nanopore with the improved error rate of the Kit 12 chemistry should be adopted as the preferred sequencing technology instead of Illumina for 16S amplicon sequencing of the gut microbiota, we used a mock community and human faecal samples to compare diversity, richness, and species-level community structure, as well as the replicability of the results. Nanopore had less noise, better accuracy with the mock community, a higher proportion of reads from the faecal samples classified to species, and better replicability. The difference between the Nanopore and Illumina results of the faecal bacterial community structure was significant but small compared to the variation between samples. The results show that Nanopore is a better choice for 16S rRNA gene amplicon sequencing when the focus is on species-level taxonomic resolution, the investigation of rare taxa, or an accurate estimation of richness. Illumina 16S sequencing should be reserved for communities with many unknown species, and for studies that require the resolution of amplicon sequence variants.

/pdf/nanopore-is-preferable-over-illumina-for-16s-amplicon-2zthf123.pdf

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

Differential tolerance of English boxwood to boxwood blight has been linked to the ratio of culturable bacterial and fungal dominance in the leaf tissue of representative samples. To further understand how the whole endophyte communities may involve the tolerance of large samples, we extracted DNA from healthy leaf tissue of previously identified 28 tolerant (T), 41 moderately tolerant (M) and 21 susceptible (S) English boxwood plants, then sequenced associated bacterial and fungal amplicons using the Nanopore MinION platform. The endophyte community did not differ in diversity among the T, M, and S plants, but differed in the abundance of bacteria and fungi, particularly between T and S samples. The bacterial genera Brevundimonas and Ammonifex had higher relative abundance in the T and M communities than in the S community which was more dominant by the fungal genera Botrytis, Thermothelomyces and Chaetomiaceae. The same results were obtained when mother and daughter samples in the T community were compared with controls in the S community, suggesting bacteria as a work force in the T community. Co-occurrence network analyses revealed that the T network had more fungal hubs but less complex with more positive connections than the S network, suggesting that the T community was supported by a healthier network. The resistance of English boxwood to blight is likely attributed to bacteria dominance and a synergic community network. This study is foundational to constructing synthetic communities and using whole communities of tolerant plants through vegetative propagation for microbe-modulated immunity.

Leaf endophyte community composition and network structures differ between tolerant and susceptible English boxwood

Ever-growing cities constantly increase the distance between suburban regions and semi-urban areas on the perimeter of the cities, where traditional crop production can take place with relatively fewer restrictions. The implementation of ultra-short supply chains implies moving the means of crop production as close to inhabitants as possible. Two main directions can be identified as effective for increasing the food resilience of densely populated suburban areas; these are soil-based traditional urban agriculture and high-tech plant factories. Both approaches to crop production offer a certain level of integration with the built environment; however, these alternatives differ in terms of their contributions to environment modulation, agrobiodiversity, social well-being, and food resilience. Vertical farms can produce a high amount of nutritionally rich crops for direct use, although the involvement of inhabitants is minimal; therefore, they can be considered a service function without social advantages. Open-field plant production can contribute to the well-being of locals, but the yields are considered rather supplementary. The combination of both production approaches to strengthen common advantages is less likely; automated production technologies require a low number of highly qualified personnel; therefore, community plant factories cannot be considered possible contributors to urban social well-being in the future. 

Beyond Efficiency: The Social and Ecological Costs of Plant Factories in Urban Farming—A Review

Soil bacteriome diversity and composition of rooftop and surface gardens in urban and peri-urban areas of Bangladesh

Numerous works have reported the impact on soil properties and microbial communities of intensive soil management, but very little is known about the impact caused by traditional agroforestry systems carried out by smallholders. To investigate whether the different smallholder's management between a monoculture plantation of Cordia dodecandra trees and a Silvopastoral system has led to a divergence in these ecosystems, soil properties, as well as soil and Cordia dodecandra rhizosphere microbial communities were analysed by MiSeq amplicon sequencing. The main findings were (i) Large variation in the soil properties of the Silvopastoral system suggests that it has a greater heterogeneity; (ii) Organic carbon, organic matter, carbonates, nitrogen, inorganic phosphorous and calcium, was significantly higher in the soil of the Silvopastoral system. (iii) The relative abundance of the major prokaryotic orders in soil and rhizospheres displayed small differences between the two agroforestry systems, and diversity indexes were slightly higher in the Silvopastoral system. (iv) The fungal orders Hypocreales and Pleosporales were more abundant in the Silvopastoral system than in the monoculture. Other evaluated parameters showed only minor or no difference. Thus, the main conclusion is that these soils have diverged in some properties and fungal orders, but not in their prokaryotic communities. To our knowledge, this is the first report on the divergence in soil properties and microbiota of these two extended smallholder agroforestry systems and therefore can serve as reference for future works.

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

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.

/pdf/characterization-of-the-soil-bacterial-community-from-3mya79bk.pdf

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

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