Dataset Information

Characterization of the soil resistome and mobilome in Namib Desert soils.

ABSTRACT: The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.

SUBMITTER: Naidoo Y

PROVIDER: S-EPMC11300574 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature

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Characterization of the soil resistome and mobilome in Namib Desert soils.

Naidoo Yashini Y Pierneef Rian E RE Cowan Don A DA Valverde Angel A

International microbiology : the official journal of the Spanish Society for Microbiology 20231116 4

The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs ...[more]

PMID: 37968548

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Project description:UnlabelledFairy circles (FCs) are barren circular patches of soil surrounded by grass species. Their origin is poorly understood. FCs feature in both the gravel plains and the dune fields of the Namib Desert. While a substantial number of hypotheses to explain the origin and/or maintenance of fairy circles have been presented, none are completely consistent with either their properties or their distribution. In this study, we investigated the hypothesis that FC formation in dunes and gravel plains is due to microbial phytopathogenesis. Surface soils from five gravel plain and five dune FCs, together with control soil samples, were analyzed using high-throughput sequencing of bacterial/archaeal (16S rRNA gene) and fungal (internal transcribed spacer [ITS] region) phylogenetic markers. Our analyses showed that gravel plain and dune FC microbial communities are phylogenetically distinct and that FC communities differ from those of adjacent vegetated soils. Furthermore, various soil physicochemical properties, particularly the pH, the Ca, P, Na, and SO4 contents, the soil particle size, and the percentage of carbon, significantly influenced the compositions of dune and gravel plain FC microbial communities, but none were found to segregate FC and vegetated soil communities. Nevertheless, 9 bacterial, 1 archaeal, and 57 fungal phylotypes were identified as FC specific, since they were present within the gravel plain and dune FC soils only, not in the vegetated soils. Some of these FC-specific phylotypes were assigned to taxa known to harbor phytopathogenic microorganisms. This suggests that these FC-specific microbial taxa may be involved in the formation and/or maintenance of Namib Desert FCs.ImportanceFairy circles (FCs) are mysterious barren circular patches of soil found within a grass matrix in the dune fields and gravel plains of the Namib Desert. Various hypotheses attempting to explain this phenomenon have been proposed. To date, however, none have been successful in fully explaining the etiology of FCs, particularly since gravel plain FCs have been largely ignored. In this study, we investigated the hypothesis that microorganisms could be involved in the FC phenomenon through phytopathogenesis. We show that the microbial communities in FC and control vegetated soil samples were significantly different. Furthermore, we detected 67 FC-specific microbial phylotypes, i.e., phylotypes present solely in both gravel plain and dune FC soils, some of which were closely related to known phytopathogens. Our results, therefore, demonstrate that microorganisms may play a role in the formation and/or maintenance of Namib Desert FCs, possibly via phytopathogenic activities.

Project description:Biosolids that are applied to agricultural soil as an organic fertilizer are frequently contaminated with pharmaceutical residues that have persisted during wastewater treatment and partitioned into the organic phase. Macrolide antibiotics, which serve as a critically important human medicine, have been detected within biosolids. To determine the impacts of macrolide antibiotics on soil bacteria, every year for a decade, a series of replicated field plots received an application of a mixture of erythromycin, clarithromycin, and azithromycin at a realistic (0.1 mg kg soil-1) or an unrealistically high (10 mg kg soil-1) dose or were left untreated. The effects of repeated antibiotic exposure on the soil bacterial community, resistome, mobilome, and integron gene cassette content were evaluated by 16S rRNA and integron gene cassette amplicon sequencing, as well as whole-metagenome sequencing. At the unrealistically high dose, the overall diversity of the resistome and mobilome was altered, as 21 clinically important antibiotic resistance genes predicted to encode resistance to 10 different antibiotic drug classes were increased and 20 mobile genetic element variants (tnpA, intI1, tnpAN, and IS91) were increased. In contrast, at the realistic dose, no effect was observed on the overall diversity of the soil bacterial community, resistome, mobilome, or integron gene cassette-carrying genes. Overall, these results suggest that macrolide antibiotics entrained into soil at concentrations anticipated with biosolid applications would not result in major changes to these endpoints. IMPORTANCE Biosolids, produced from the treatment of sewage sludge, are rich in plant nutrients and are a valuable alternative to inorganic fertilizer when applied to agricultural soil. However, the use of biosolids in agriculture, which are frequently contaminated with pharmaceuticals, such as macrolide antibiotics, may pose a risk to human health by selecting for antibiotic resistance genes that could be transferred to plant-based food destined for human consumption. The consequences of long-term, repeated macrolide antibiotic exposure on the diversity of the soil bacterial community, resistome, and mobilome were evaluated. At unrealistically high concentrations, macrolide antibiotics alter the overall diversity of the resistome and mobilome, enriching for antibiotic resistance genes and mobile genetic elements of concern to human health. However, at realistic antibiotic concentrations, no effect on these endpoints was observed, suggesting that current biosolids land management practices are unlikely to pose a risk to human health due to macrolide antibiotic contamination alone.

Dataset Information

Characterization of the soil resistome and mobilome in Namib Desert soils.

Publications

Characterization of the soil resistome and mobilome in Namib Desert soils.

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