Karst spring microbiome: Diversity, core taxa, and community response to pathogens and antibiotic resistance gene contamination

Szekeres, Edina; Baricz, Andreea; Cristea, Adorján; Levei, Erika Andrea; Stupar, Zamfira; Brad, Traian; Kenesz, Marius; Moldovan, Oana Teodora; Banciu, Horia Leonard

doi:10.1016/j.scitotenv.2023.165133

Cited by 3 publications

(2 citation statements)

References 78 publications

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“…Core taxa were screened from the OUT level. OUTs occurring in at least 50% of the samples and with a relative abundance of at least 0.1% were defined as core taxa ( Szekeres et al, 2023 ). The niche breadth indexes were calculated using the “spaa” package based on the Levins model ( Zhang and Zhang, 2013 ).…”

Section: Methodsmentioning

confidence: 99%

Comparison of the response of microbial communities to region and rootstock disease differences in tobacco soils of southwestern China

Yi,

Li,

Shang

et al. 2023

Front. Microbiol.

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IntroductionSoil microorganisms are essential for crop growth and production as part of soil health. However, our current knowledge of microbial communities in tobacco soils and their impact factors is limited.MethodsIn this study, we compared the characterization of bacterial and fungal communities in tobacco soils and their response to regional and rootstock disease differences.Results and discussionThe results showed that the diversity and composition of bacterial and fungal communities responded more strongly to regional differences than to rootstock diseases, while bacterial niche breadth was more sensitive than fungi to regional differences. Similarly, the core bacterial and fungal taxa shared by the three regions accounted for 21.73% and 20.62% of all OTUs, respectively, which was much lower than that shared by RD and NRD in each region, ranging from 44.87% to 62.14%. Meanwhile, the differences in topological characteristics, connectivity, and stability of microbial networks in different regions also verified the high responsiveness of microbial communities to regions. However, rootstock diseases had a more direct effect on fungal communities than regional differences.ConclusionThis provided insight into the interactions between microbial communities, regional differences, and rootstock diseases, with important implications for maintaining soil health and improving tobacco yield and quality.

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Section: Methodsmentioning

confidence: 99%

Comparison of the response of microbial communities to region and rootstock disease differences in tobacco soils of southwestern China

Yi,

Li,

Shang

et al. 2023

Front. Microbiol.

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“…And vice versa: in the absence of conditions for maintaining the stable vital activity of certain types of microorganisms, their development slows down, and their composition and quantity degrade. Such communities are gradually replaced by species better adapted to new conditions [26,27].…”

Section: Introductionmentioning

confidence: 99%

Microbiomes of Primary Soils and Mining Heaps of Polymetallic Ore Quarries

Dorogaya,

Abakumov,

Zverev

et al. 2024

Applied Sciences

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This research evaluates the development of microbiomes in primary soils, forming in various mining dumps in the arid terrain in the Republic of Bashkortostan, Russia. A metagenomic analysis of the communities was performed by sequencing extended gene sequences. The evaluation of the agro-chemical properties was in accordance with conventional pedology methods. Inverse voltammetry was used to measure the heavy metals (lead, cadmium, mercury, zinc, copper, and nickel) and arsenic content. In all the samples studied, Actinobacteria and Proteobacteria phylas dominated, and, in smaller numbers, Acidobacteria and Bacteroidetes were present. In the natural samples, the proportion of Actinobacteria was higher, and the proportions of Proteobacteria and Bacteroidetes were lower than in the samples from anthropogenically disrupted soils. Verrucomicrobia bacteria and Thaumarchaeota archaea were not found in the forming soils of the Kulyurtau and Tubinsky quarries, although in all other samples, there was a significant content of representatives of these types. Soil formation was observed at the Kulyurtau and Tubinsky mines, with a self-restoration period of more than 30 years. The microbial communities of the forming soils were similar in species richness to the background soils, and the alpha diversity showed a high level of dispersion, although the beta diversity had a different clustering, but the absence of Verrucomicrobia and Thaumarchaeota phyla in the samples from both sites indicates the underdevelopment of new soils compared with the natural background. Agrochemical indicators showed a dependence on the type of growing vegetation and the degree of anthropogenic load, and the correlation with the microbial composition of soils was traced poorly.

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Tackling the Soil Microbiome – Challenges and Oportunities

Mlesnita

2024

J. Exp. Molec. Biol.

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The health of the terrestrial ecosystems is directly dependent on the microbial composition that fulfills essential functions, such as sustaining plant growth, nutrient cycling and carbon sequestration. The study of the soil microbiome has gained popularity in the last decades due to its significant impact on the health of the environment and its inhabitants. This review explores the diversity and functions of soil microbial communities, with a particular focus on microbial dark matter, a subset of organisms that cannot be cultured through classical microbiological techniques. The evolution of DNA extraction methods and sequencing technologies coupled with the transition from amplicon sequencing to metagenome-assembled genomes (MAGs) and continuously developing bioinformatic pipelines has led to the discovery of novel microbial taxa, community networks, metabolic pathways and potentially useful molecules. Soil microbiome research is gaining momentum in Romania, as a big part of studies try to assess the impact of agricultural practices on the environment. Designing sustainable agricultural practices and implementing them with the goal of preserving the heterogeneity of the microbiome contributes significantly to the resilience of ecosystems, preserving the health of the environment, as well as the well-being of its residents.

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Karst spring microbiome: Diversity, core taxa, and community response to pathogens and antibiotic resistance gene contamination

Cited by 3 publications

References 78 publications

Comparison of the response of microbial communities to region and rootstock disease differences in tobacco soils of southwestern China

Comparison of the response of microbial communities to region and rootstock disease differences in tobacco soils of southwestern China

Microbiomes of Primary Soils and Mining Heaps of Polymetallic Ore Quarries

Tackling the Soil Microbiome – Challenges and Oportunities

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