Microbiomes of soils

Margerison, Reuben; Nicolitch, Océane; Zhang, Yaqian

doi:10.1017/9781108654418.003

Cited by 2 publications

(3 citation statements)

References 190 publications

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“…Soil microorganisms are extremely diverse and play key roles in soil nutrient cycling and plant growth (Bardgett and Van Der Putten, 2014). Among these, protists (nonfungal microbial eukaryotes) are important contributors to nutrient cycling and soil respiration (Adl and Gupta, 2006;Margerison et al, 2020). Phototrophic protists fix atmospheric carbon and thus participate in the carbon cycle (Geisen et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Soil protist function varies with elevation in the Swiss Alps

Mazel

Malard

Niculita‐Hirzel

et al. 2021

Environmental Microbiology

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Summary Protists are abundant and play key trophic functions in soil. Documenting how their trophic contributions vary across large environmental gradients is essential to understand and predict how biogeochemical cycles will be impacted by global changes. Here, using amplicon sequencing of environmental DNA in open habitat soil from 161 locations spanning 2600 m of elevation in the Swiss Alps (from 400 to 3000 m), we found that, over the whole study area, soils are dominated by consumers, followed by parasites and phototrophs. In contrast, the proportion of these groups in local communities shows large variations in relation to elevation. While there is, on average, three times more consumers than parasites at low elevation (400–1000 m), this ratio increases to 12 at high elevation (2000–3000 m). This suggests that the decrease in protist host biomass and diversity toward mountains tops impact protist functional composition. Furthermore, the taxonomic composition of protists that infect animals was related to elevation while that of protists that infect plants or of protist consumers was related to soil pH. This study provides a first step to document and understand how soil protist functions vary along the elevational gradient.

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Section: Introductionmentioning

confidence: 99%

Soil protist function varies with elevation in the Swiss Alps

Mazel

Malard

Niculita‐Hirzel

et al. 2021

Environmental Microbiology

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“…In soils, microbes preserve homeostasis by mainly contributing to the biogeochemical cycles of the major elements (e.g. carbon, nitrogen, phosphorous and sulfur), nutrients, water and organic waste cycling, matter decomposition and soil fertility (Dominati et al ., 2010; Starke et al ., 2019; Margerison et al ., 2020; Pylro et al ., 2020). Microbial soil communities are also responsive to anthropogenic pressures (e.g.…”

Section: Introductionmentioning

confidence: 99%

“…However, despite its importance, the soil environment is one of the least studied habitats. Since biological and functional diversity is crucial to maintaining ecosystems and thus for the sustainability of the planet, the study of microbial communities and their relationship with environmental changes is essential to understand soil dynamics (Bastida et al ., 2014; Zhou et al ., 2015; Bouchez et al ., 2016; Wang et al ., 2016; Starke et al ., 2019; Margerison et al ., 2020; Pylro et al ., 2020). Recent advances in DNA sequencing technologies are increasingly showing that microbial soil communities are enormously diverse ranking among the most abundant, complex and diverse groups of organisms on Earth (Torsvik and Ovreas, 2002; Myrold et al ., 2013; Delgado‐Baquerizo et al ., 2018; Harrison and Cameron, 2020).…”

Section: Introductionmentioning

confidence: 99%

Meta‐omic evaluation of bacterial microbial community structure and activity for the environmental assessment of soils: overcoming protein extraction pitfalls

Herruzo-Ruiz

Fuentes-Almagro

Jiménez-Pastor

et al. 2021

Environmental Microbiology

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Microorganisms play unique, essential and integral roles in the biosphere. This work aims to assess the utility of soil's metaomics for environmental diagnosis. Doñana National Park (DNP) was selected as a natural lab since it contains a strictly protected core that is surrounded by numerous threats of pollution. Culture-independent high-throughput molecular tools were used to evaluate the alterations of the global structure and metabolic activities of the microbiome. 16S rRNA sequencing shows lower bacterial abundance and diversity in areas historically exposed to contamination that surround DNP. For metaproteo mics, an innovative post-alkaline protein extraction protocol was developed. After NaOH treatment, successive washing with Tris-HCl buffer supplemented with glycerol was essential to eliminate interferences. Starting from soils with different physicochemical characteristics, the method renders proteins with a remarkable resolution on SDS-PAGE gels. The proteins extracted were analysed by using an in-house database constructed from the rRNA data. LC-MS/ MS analysis identified 2182 non-redundant proteins with 135 showing significant differences in relative abundance in the soils around DNP. Relevant global biological processes were altered in response to the environmental changes, such as protective and antioxidant mechanisms, translation, folding and homeostasis of proteins, membrane transport and aerobic respiratory metabolism.

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Microbiomes of soils

Cited by 2 publications

References 190 publications

Soil protist function varies with elevation in the Swiss Alps

Soil protist function varies with elevation in the Swiss Alps

Meta‐omic evaluation of bacterial microbial community structure and activity for the environmental assessment of soils: overcoming protein extraction pitfalls

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