Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation

Steinbach, Annelie; Schulz, Stefanie; Giebler, Julia; Schulz, Stephan; Pronk, Geertje Johanna; Kögel‐Knabner, Ingrid; Harms, Hauke; Wick, Lukas Y.; Schloter, Michael

doi:10.1038/ismej.2014.243

Cited by 24 publications

(15 citation statements)

References 21 publications

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“…They allow for insight into fundamental questions about soil aggregate development38, organic matter turnover39 and mineralogical influences on microbial communities and decomposition404142. Here we use model soils for real-time monitoring of microbial-SOM formation and demonstrate that microbial processing of simple C substrates produced an abundance of stable, chemically diverse SOM dominated by microbial proteins and lipids, comparable to natural soils.…”

Section: Discussionmentioning

confidence: 95%

“…Variations in SOM chemistry with mineralogy have previously been attributed to differences in dominant binding mechanisms and selective adsorption among mineral types5253. However, such differences can also result from divergent microbial communities4041, and thus the production of chemically different microbial SOM compounds43. Indeed, in kaolinite soil both fungal and lipid abundances were greater relative to montmorillonite soil.…”

Section: Discussionmentioning

confidence: 99%

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Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

2016

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Soil organic matter (SOM) and the carbon and nutrients therein drive fundamental submicron- to global-scale biogeochemical processes and influence carbon-climate feedbacks. Consensus is emerging that microbial materials are an important constituent of stable SOM, and new conceptual and quantitative SOM models are rapidly incorporating this view. However, direct evidence demonstrating that microbial residues account for the chemistry, stability and abundance of SOM is still lacking. Further, emerging models emphasize the stabilization of microbial-derived SOM by abiotic mechanisms, while the effects of microbial physiology on microbial residue production remain unclear. Here we provide the first direct evidence that soil microbes produce chemically diverse, stable SOM. We show that SOM accumulation is driven by distinct microbial communities more so than clay mineralogy, where microbial-derived SOM accumulation is greatest in soils with higher fungal abundances and more efficient microbial biomass production.

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Section: Discussionmentioning

confidence: 95%

Section: Discussionmentioning

confidence: 99%

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

2016

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“…There are several studies reporting a significant effect of mineral composition such as different clay minerals or Fe oxides on bacterial communities in incubation experiments with artificial soils ( Babin et al, 2013 ; Heckman et al, 2013 ; Vogel et al, 2014 ; Steinbach et al, 2015 ). On the contrary, we detected only a slight soil age effect for bacterial T-RFLP profiles analyzed with HhaI ( Table 3 ).…”

Section: Discussionmentioning

confidence: 99%

Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development

et al. 2017

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Along a long-term ecosystem development gradient, soil nutrient contents and mineralogical properties change, therefore probably altering soil microbial communities. However, knowledge about the dynamics of soil microbial communities during long-term ecosystem development including progressive and retrogressive stages is limited, especially in mineral soils. Therefore, microbial abundances (quantitative PCR) and community composition (pyrosequencing) as well as their controlling soil properties were investigated in soil depth profiles along the 120,000 years old Franz Josef chronosequence (New Zealand). Additionally, in a microcosm incubation experiment the effects of particular soil properties, i.e., soil age, soil organic matter fraction (mineral-associated vs. particulate), O2 status, and carbon and phosphorus additions, on microbial abundances (quantitative PCR) and community patterns (T-RFLP) were analyzed. The archaeal to bacterial abundance ratio not only increased with soil depth but also with soil age along the chronosequence, coinciding with mineralogical changes and increasing phosphorus limitation. Results of the incubation experiment indicated that archaeal abundances were less impacted by the tested soil parameters compared to Bacteria suggesting that Archaea may better cope with mineral-induced substrate restrictions in subsoils and older soils. Instead, archaeal communities showed a soil age-related compositional shift with the Bathyarchaeota, that were frequently detected in nutrient-poor, low-energy environments, being dominant at the oldest site. However, bacterial communities remained stable with ongoing soil development. In contrast to the abundances, the archaeal compositional shift was associated with the mineralogical gradient. Our study revealed, that archaeal and bacterial communities in whole soil profiles are differently affected by long-term soil development with archaeal communities probably being better adapted to subsoil conditions, especially in nutrient-depleted old soils.

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“…22,23 For example, Steinbach et al 24 reported that metal oxides have significant impacts on alkane-degrading community structure and the effects increased during soil maturation. Recently, several studies have examined the effects of soil minerals on the viability of bacterial cells.…”

Section: Introductionmentioning

confidence: 99%

Bacillus subtilis biofilm development in the presence of soil clay minerals and iron oxides

Peng

Walker

et al. 2017

npj Biofilms Microbiomes

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Clay minerals and metal oxides, as important parts of the soil matrix, play crucial roles in the development of microbial communities. However, the mechanism underlying such a process, particularly on the formation of soil biofilm, remains poorly understood. Here, we investigated the effects of montmorillonite, kaolinite, and goethite on the biofilm formation of the representative soil bacteria Bacillus subtilis. The bacterial biofilm formation in goethite was found to be impaired in the initial 24 h but burst at 48 h in the liquid–air interface. Confocal laser scanning microscopy showed that the biofilm biomass in goethite was 3–16 times that of the control, montmorillonite, and kaolinite at 48 h. Live/Dead staining showed that cells had the highest death rate of 60% after 4 h of contact with goethite, followed by kaolinite and montmorillonite. Atomic force microscopy showed that the interaction between goethite and bacteria may injure bacterial cells by puncturing cell wall, leading to the swarming of bacteria toward the liquid–air interface. Additionally, the expressions of abrB and sinR, key players in regulating the biofilm formation, were upregulated at 24 h and downregulated at 48 h in goethite, indicating the initial adaptation of the cells to minerals. A model was proposed to describe the effects of goethite on the biofilm formation. Our findings may facilitate a better understanding of the roles of soil clays in biofilm development and the manipulation of bacterial compositions through controlling the biofilm in soils.

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Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation

Cited by 24 publications

References 21 publications

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development

Bacillus subtilis biofilm development in the presence of soil clay minerals and iron oxides

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