Alive and kicking: Why dormant soil microorganisms matter

Joergensen, Rainer Georg; Wichern, Florian

doi:10.1016/j.soilbio.2017.10.022

Cited by 217 publications

(115 citation statements)

References 270 publications

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“…The simulated behavior of microbial functional groups supports experimental evidence of the importance of metabolic activation/deactivation strategies by microbial functional groups for regulating C turnover in soil (Placella et al, 2012;Joergensen and Wichern, 2018;Salazar et al, 2019). Our finding that interactions between microbial functional groups are controlled by the spatial localization of microorganisms is in agreement with previous results from individual-based modeling (Allison, 2005;Kaiser et al, 2015;Portell et al, 2018).…”

Section: Discussionsupporting

confidence: 90%

“…SpatC accounts for three functional microbial types: oligotrophs (B O ), copiotrophs (B C ) and copiotrophic cheaters (B CC ) (Equations 7-11). All microbial groups are considered to be able to switch from an active to a dormant physiological state (Lennon and Jones, 2011;Blagodatskaya and Kuzyakov, 2013;Joergensen and Wichern, 2018) with different parameterizations for different functional types (Table 1, Figure 2). Active microorganisms use dissolved small biopolymers and monomers for growth, while dormant microorganisms do not grow.…”

Section: Functional Microbial Groupsmentioning

confidence: 99%

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Spatial Control of Carbon Dynamics in Soil by Microbial Decomposer Communities

Pagel

Kriesche

Uksa

et al. 2020

Front. Environ. Sci.

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Trait-based models have improved the understanding and prediction of soil organic matter dynamics in terrestrial ecosystems. Microscopic observations and pore scale models are now increasingly used to quantify and elucidate the effects of soil heterogeneity on microbial processes. Combining both approaches provides a promising way to accurately capture spatial microbial-physicochemical interactions and to predict overall system behavior. The present study aims to quantify controls on carbon (C) turnover in soil due to the mm-scale spatial distribution of microbial decomposer communities in soil. A new spatially explicit trait-based model (SpatC) has been developed that captures the combined dynamics of microbes and soil organic matter (SOM) by taking into account microbial life-history traits and SOM accessibility. Samples of spatial distributions of microbes at µm-scale resolution were generated using a spatial statistical model based on Log Gaussian Cox Processes which was originally used to analyze distributions of bacterial cells in soil thin sections. These µm-scale distribution patterns were then aggregated to derive distributions of microorganisms at mm-scale. We performed Monte-Carlo simulations with microbial distributions that differ in mm-scale spatial heterogeneity and functional community composition (oligotrophs, copiotrophs, and copiotrophic cheaters). Our modeling approach revealed that the spatial distribution of soil microorganisms triggers spatiotemporal patterns of C utilization and microbial succession. Only strong spatial clustering of decomposer communities induces a diffusion limitation of the substrate supply on the microhabitat scale, which significantly reduces the total decomposition of C compounds and the overall microbial growth. However, decomposer communities act as functionally redundant microbial guilds with only slight changes in C utilization. The combined statistical and process-based modeling approach derives distribution patterns of microorganisms at the mm-scale from microbial biogeography at microhabitat scale (µm) and quantifies the emergent macroscopic (cm) microbial and C dynamics. Thus, it effectively links observable process dynamics to the spatial control by microbial communities. Our study highlights a powerful approach that can provide further insights into the biological control of soil organic matter turnover.

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Section: Discussionsupporting

confidence: 90%

Section: Functional Microbial Groupsmentioning

confidence: 99%

Spatial Control of Carbon Dynamics in Soil by Microbial Decomposer Communities

Pagel

Kriesche

Uksa

et al. 2020

Front. Environ. Sci.

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“…However, this was not represented by lower SOM accumulation in soil B as SOC content in both soils was the same, probably because the qCO 2 was on an overall low level as compared to other studies (Wichern et al, 2003(Wichern et al, , 2006Hartman and Richardson, 2013;Iqbal et al, 2016). Further, next to C lost as CO 2 for a full microbial CUE assessment also microbial necromass and other microbial metabolites need to be considered (Joergensen and Wichern, 2018), which we were not able to do in the present study. However, it can be concluded that short term abiotic stress, such as salinity or anoxic conditions, does not directly trigger metabolic adaptation of the whole microbial community, but rather results in survival of the microbes better adapted to stress and likely having adapted energy intensive metabolic mechanisms as explained above.…”

Section: Distinct Microbial Response Of Different Soils Indicate Soilcontrasting

confidence: 63%

“…The relative increase of saprotrophic fungi as indicated by the ergosterol-to-microbial biomass C ratio was positively related to an increase of the metabolic quotient qCO 2, a simple indicator of the demand of microorganisms to maintain their biomass or a simplified carbon use efficiency (CUE) (Joergensen and Wichern, 2018) Consequently, increased fungal dominance will result in lower C use efficiency as shown earlier (Nannipieri et al, 2003;Iqbal et al, 2016) and may result in organic matter loss in the long run. A higher specific metabolic activity may reflect stronger catabolic activity and production of osmolytes, cell repair or detoxification (Jones et al, 2019) and thus reflects an adaptation of the soil microbial community to abiotic stress, such as salinity (Wichern et al, 2006).…”

Section: Distinct Microbial Response Of Different Soils Indicate Soilmentioning

confidence: 90%

Organic Amendments Alleviate Salinity Effects on Soil Microorganisms and Mineralisation Processes in Aerobic and Anaerobic Paddy Rice Soils

Wichern

Islam

Hemkemeyer

et al. 2020

Front. Sustain. Food Syst.

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Sea-water level rise leads to increased saltwater intrusion causing soil salinity on arable land with negative effects on soil microbial processes. Organic amendments are known to reduce the effects of salinity on soil microorganisms, therefore positively influencing microbial activity and nutrient cycling. However, the extent of this effect in paddy rice soils under aerobic compared to anaerobic conditions is unknown. Consequently, benefits of organic matter addition on carbon (C) and nitrogen (N) mineralisation under saline conditions were evaluated in a short-term laboratory incubation experiment. Two soils from Bangladesh were incubated with rice straw, manure or a manure-rice straw mixture at 50 and 100% water holding capacity (25 • C, 27 days). In addition, NaCl was added to half of the samples, which resulted in a set of non-saline (EC e = 1.1-1.3 dS m −1 ) and saline (EC e = 24.0-32.4 dS m −1 ) soils. Soil respiration (CO 2 -release) was measured throughout the experiment. At the end of the experiment, dissolved organic C, inorganic N, microbial biomass as well as bacterial, archaeal, and fungal domains were determined. Overall, effects of substrate addition overruled effects caused by salinity and water content. Microbial activity and biomass in particular fungi increased most strongly after rice straw addition and resulted in N immobilisation independent of moisture level. Rice straw and manure alleviated the effects of salinity on microorganisms; these were therefore mainly detectable in the non-amended soils. The reason for this is likely a higher C availability for soil microorganisms after amendment of organic materials, which allows them to produce osmolytes, counteracting the osmotic effects of increased salinity. However, the microbial communities of the two soils under investigation showed different response patterns to salinity reflected by a substantially higher fungi-bacteria ratio in soil B prone to salinity at 50% WHC as compared to soil A. Likewise, the metabolic quotient Wichern et al. Salinity Alleviation and Soil Microorganismswas higher in soil B and not affected by any of the short term treatments, revealing a soil legacy. Our results highlight the importance of organic amendments, such as rice straw to paddy soils under saline conditions to reduce negative effects on soil microbial processes, allowing them to maintain their major functions.

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“…). However, dormant microbial communities within soil have also been hypothesized to be powerful pools of potential diversity and can respond rapidly to changes in environmental inputs (Joergensen and Wichern , Kearns and Shade , Nelson et al. ).…”

Section: Discussionmentioning

confidence: 99%