Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert

Sáenz, Johan S.; Airo, Alessandro; Schulze‐Makuch, Dirk; Schloter, Michael; Vestergaard, Gisle

doi:10.3390/d11110205

Cited by 5 publications

(2 citation statements)

References 70 publications

(87 reference statements)

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“…Overall, the functional profile of these soils is consistent with reports from other studies carried out in hot deserts [74,75]. Expectedly, the core functional profile included a relatively high abundance of protein families linked to general housekeeping functions (i.e.…”

Section: Soil Functional Profilesupporting

confidence: 87%

Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils

et al. 2021

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Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and 'resistance to antibiotics and toxic compounds' related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils.

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Section: Soil Functional Profilesupporting

confidence: 87%

Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils

et al. 2021

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“…Furthermore, MGEs are enriched in extreme environments, such as antibiotic-exposed niches, where they contribute to niche adaptation. 48 In E. faecium MGEs, including plasmids, phages, genomic islands and especially ISs (IS 3 , IS 110 , IS 256 and IS 16 ), are more prevalent in clinical than in commensal strains. 49–51 MGEs, like plasmids, prophages, ISs (IS 256 ) and other transposons, are numerous in clinical Staphylococcus haemolyticus strains, 52 and specific MGEs are associated with epidemic S. aureus , 53 , 54 Escherichia coli 55 , 56 and Klebsiella pneumoniae clones.…”

Section: Intrinsic Characteristics Of Mges Related To the Occurrence ...mentioning

confidence: 99%

Transiently silent acquired antimicrobial resistance: an emerging challenge in susceptibility testing

Wagner

Howden

Sundsfjord

et al. 2023

Journal of Antimicrobial Chemotherapy

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Acquisition and expression of antimicrobial resistance (AMR) mechanisms in bacteria are often associated with a fitness cost. Thus, evolutionary adaptation and fitness cost compensation may support the advance of subpopulations with a silent resistance phenotype when the antibiotic selection pressure is absent. However, reports are emerging on the transient nature of silent acquired AMR, describing genetic alterations that can change the expression of these determinants to a clinically relevant level of resistance, and the association with breakthrough infections causing treatment failures. This phenomenon of transiently silent acquired AMR (tsaAMR) is likely to increase, considering the overall expansion of acquired AMR in bacterial pathogens. Moreover, the augmented use of genotypic methods in combination with conventional phenotypic antimicrobial susceptibility testing (AST) will increasingly enable the detection of genotype and phenotype discrepancy. This review defines tsaAMR as acquired antimicrobial resistance genes with a corresponding phenotype within the wild-type distribution or below the clinical breakpoint for susceptibility for which genetic alterations can mediate expression to a clinically relevant level of resistance. References to in vivo resistance development and therapeutic failures caused by selected resistant subpopulations of tsaAMR in Gram-positive and Gram-negative pathogens are given. We also describe the underlying molecular mechanisms, including alterations in the expression, reading frame or copy number of AMR determinants, and discuss the clinical relevance concerning challenges for conventional AST.

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Characterization of the soil resistome and mobilome in Namib Desert soils

Naidoo,

Pierneef,

Cowan

et al. 2023

Int Microbiol

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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.

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Functional Traits Co-Occurring with Mobile Genetic Elements in the Microbiome of the Atacama Desert

Cited by 5 publications

References 70 publications

Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils

Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils

Transiently silent acquired antimicrobial resistance: an emerging challenge in susceptibility testing

Characterization of the soil resistome and mobilome in Namib Desert soils

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