Recent progress in understanding the ecology and molecular genetics of soil mineral weathering bacteria

Uroz, Stéphane; Picard, Laura; Turpault, Marie–Pierre

doi:10.1016/j.tim.2022.01.019

Cited by 26 publications

(8 citation statements)

References 102 publications

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“…In contrast to spheres characterized by high C availability, the mineralosphere provides a low-C and mineral-rich environment (Uroz et al, 2022), where the surface attachment of microbes to soil particles modifies a range of biogeochemical processes, such as SOM decomposition and soil-borne pathogenicity (Ahmed & Holmström, 2015;Chenu & Stotzky, 2002;Kandeler et al, 2019;Wu et al, 2014). Also, microorganisms that are specifically adapted and preferentially colonize this habitat contribute to mineral weathering (Ahmed et al, 2017;Colin et al, 2017;Uroz et al, 2012Uroz et al, , 2015Vieira et al, 2020), thus releasing nutritional elements into the soil solution that are then potentially available for transport to and microbial transformation in other microhabitats.…”

Section: Microbial Habitats At the Micro-scalementioning

confidence: 99%

Soil water status shapes nutrient cycling in agroecosystems from micrometer to landscape scales

Bauke

Amelung

Bol

et al. 2022

J. Plant Nutr. Soil Sci.

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Soil water status, which refers to the wetness or dryness of soils, is crucial for the productivity of agroecosystems, as it determines nutrient cycling and uptake physically via transport, biologically via the moisture‐dependent activity of soil flora, fauna, and plants, and chemically via specific hydrolyses and redox reactions. Here, we focus on the dynamics of nitrogen (N), phosphorus (P), and sulfur (S) and review how soil water is coupled to the cycling of these elements and related stoichiometric controls across different scales within agroecosystems. These scales span processes at the molecular level, where nutrients and water are consumed, to processes in the soil pore system, within a soil profile and across the landscape. We highlight that with increasing mobility of the nutrients in water, water‐based nutrient flux may alleviate or even exacerbate imbalances in nutrient supply within soils, for example, by transport of mobile nutrients towards previously depleted microsites (alleviating imbalances), or by selective loss of mobile nutrients from microsites (increasing imbalances). These imbalances can be modulated by biological activity, especially by fungal hyphae and roots, which contribute to nutrient redistribution within soils, and which are themselves dependent on specific, optimal water availability. At larger scales, such small‐scale effects converge with nutrient inputs from atmospheric (wet deposition) or nonlocal sources and with nutrient losses from the soil system towards aquifers. Hence, water acts as a major control in nutrient cycling across scales in agroecosystems and may either exacerbate or remove spatial disparities in the availability of the individual nutrients (N, P, S) required for biological activity.

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Section: Microbial Habitats At the Micro-scalementioning

confidence: 99%

Soil water status shapes nutrient cycling in agroecosystems from micrometer to landscape scales

Bauke

Amelung

Bol

et al. 2022

J. Plant Nutr. Soil Sci.

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“…In addition, minerals impact the differential gene expression and functional groups of microbial community [ 34 – 36 ]. Many mineral elements (i.e., Cu, Mo, Fe, Ni, V, and P) contained in minerals act as critical factors [ 37 , 38 ] and promote many aspects of microbial metabolisms and growth.…”

Section: Introductionmentioning

confidence: 99%

Effects of Mineral on Taxonomic and Functional Structures of Microbial Community in Tengchong Hot Springs via in-situ cultivation

Hou

Wang

et al. 2023

Environmental Microbiome

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Diverse mineralogical compositions occur in hot spring sediments, but the impact of minerals on the diversity and structure of microbial communities remains poorly elucidated. In this study, different mineral particles with various chemistries (i.e., hematite, biotite, K-feldspar, quartz, muscovite, aragonite, serpentine, olivine, barite, apatite, and pyrite) were incubated for ten days in two Tengchong hot springs, one alkaline (pH ~ 8.34) with a high temperature (~ 82.8 °C) (Gumingquan, short as GMQ) and one acidic (pH ~ 3.63) with a relatively low temperature (~ 43.3 °C) (Wenguangting, short as WGT), to determine the impacts of minerals on the microbial communities taxonomic and functional diversities. Results showed that the mineral-associated bacterial taxa differed from those of the bulk sediment samples in the two hot springs. The relative abundance of Proteobacteria, Euryarchaeota, and Acidobacteria increased in all minerals, indicating that these microorganisms are apt to colonize on solid surfaces. The α-diversity indices of the microbial communities on the mineral surfaces in the WGT were higher than those from the bulk sediment samples (p < 0.05), which may be caused by the stochastically adhering process on the mineral surface during 10-day incubation, different from the microbial community in sediment which has experienced long-term environmental and ecological screening. Chemoheterotrophy increased with minerals incubation, which was high in most cultured minerals (the relative contents were 5.8 − 21.4%). Most notably, the sulfate respiration bacteria (mainly related to Desulfobulbaceae and Syntrophaceae) associated with aragonite in the acidic hot spring significantly differed from other minerals, possibly due to the pH buffering effect of aragonite providing more favorable conditions for their survival and proliferation. By comparison, aragonite cultured in the alkaline hot spring highly enriched denitrifying bacteria and may have promoted the nitrogen cycle within the system. Collectively, we speculated that diverse microbes stochastically adhered on the surface of minerals in the water flows, and the physicochemical properties of minerals drove the enrichment of certain microbial communities and functional groups during the short-term incubation. Taken together, these findings thereby provide novel insights into mechanisms of community assembly and element cycling in the terrestrial hydrothermal system associated with hot springs.

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“…Identification of novel enzymes provides an opportunity for industrial applications of enzyme immobilization. Similarly, a molecular understanding of microbial activity will be helpful in understanding the entire biogeochemical cycle [ 16 ]. Very little is known in the case of microbial activity involved in silicate solubilization.…”

Section: Introductionmentioning

confidence: 99%

Genomic Landscape Highlights Molecular Mechanisms Involved in Silicate Solubilization, Stress Tolerance, and Potential Growth-Promoting Activity of Bacterium Enterobacter sp. LR6

Raturi

Sharma

Mandlik

et al. 2022

Cells

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Silicon (Si) is gaining widespread attention due to its prophylactic activity to protect plants under stress conditions. Despite Si’s abundance in the earth’s crust, most soils do not have enough soluble Si for plants to absorb. In the present study, a silicate-solubilizing bacterium, Enterobacter sp. LR6, was isolated from the rhizospheric soil of rice and subsequently characterized through whole-genome sequencing. The size of the LR6 genome is 5.2 Mb with a GC content of 54.9% and 5182 protein-coding genes. In taxogenomic terms, it is similar to E. hormaechei subsp. xiangfangensis based on average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH). LR6 genomic data provided insight into potential genes involved in stress response, secondary metabolite production, and growth promotion. The LR6 genome contains two aquaporins, of which the aquaglyceroporin (GlpF) is responsible for the uptake of metalloids including arsenic (As) and antimony (Sb). The yeast survivability assay confirmed the metalloid transport activity of GlpF. As a biofertilizer, LR6 isolate has a great deal of tolerance to high temperatures (45 °C), salinity (7%), and acidic environments (pH 9). Most importantly, the present study provides an understanding of plant-growth-promoting activity of the silicate-solubilizing bacterium, its adaptation to various stresses, and its uptake of different metalloids including As, Ge, and Si.

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Recent progress in understanding the ecology and molecular genetics of soil mineral weathering bacteria

Cited by 26 publications

References 102 publications

Soil water status shapes nutrient cycling in agroecosystems from micrometer to landscape scales

Soil water status shapes nutrient cycling in agroecosystems from micrometer to landscape scales

Effects of Mineral on Taxonomic and Functional Structures of Microbial Community in Tengchong Hot Springs via in-situ cultivation

Genomic Landscape Highlights Molecular Mechanisms Involved in Silicate Solubilization, Stress Tolerance, and Potential Growth-Promoting Activity of Bacterium Enterobacter sp. LR6

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