scholarly journals On Maintenance and Metabolisms in Soil Microbial Communities

2022 ◽  
Author(s):  
Paul Dijkstra ◽  
Weichao Wu ◽  
Michaela Dippold ◽  
Egbert Schwartz ◽  
Bruce Hungate ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Metabolic Flux ◽  
Soil Microbial Communities ◽  
Soil Ecology ◽  
Future Research ◽  
Flux Analysis ◽  
Maintenance Energy ◽  
Substrate Use ◽  
Soil Microbial ◽  
Use Efficiency

Abstract Biochemistry is an essential yet often undervalued aspect of soil ecology, especially in soil C cycling. We assume based on tradition, intuition or hope that the complexity of biochemistry is confined to the microscopic world, and can be ignored when dealing with whole soil systems. This opinion paper draws attention to patterns caused by basic biochemical processes that permeate the world of ecosystem processes. From these patterns, we can estimate activities of the biochemical reactions of the central C metabolic network and gain insights into the ecophysiology of microbial biosynthesis and growth and maintenance energy requirements; important components of Carbon Use Efficiency (CUE).The biochemical pathways used to metabolize glucose vary from soil to soil, with mostly glycolysis in some soils, and pentose phosphate or Entner-Doudoroff pathways in others. However, notwithstanding this metabolic diversity, glucose use efficiency is high and thus substrate use for maintenance energy and overflow respiration is low in these three soils. These results contradict current dogma based on four decades of research in soil ecology. We identify three main shortcomings in our current understanding of substrate use efficiency: 1) in numeric and conceptual models, we lack appreciation of the strategies that microbes employ to quickly reduce energy needs in response to starvation; 2) production of exudates and microbial turnover affect whole-soil CUE more than variation in maintenance energy demand; and 3) whether tracer experiments can be used to measure the long-term substrate use efficiency of soil microbial communities depends critically on the ability of non-growing cells to take up tracer substrates, how biosynthesis responds to these substrates, as well as on how cellular activities scale to the community level.To move the field of soil ecology forward, future research must consider the details of microbial ecophysiology and develop new tools that enable direct measurement of microbial functioning in intact soils. We submit that 13C metabolic flux analysis is one of those new tools.

scholarly journals Heavy and wet: The consequences of violating assumptions of measuring soil microbial growth efficiency using the 18O water method

Elem Sci Anth ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Grace Pold ◽  
Luiz A. Domeignoz-Horta ◽  
Kristen M. DeAngelis
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Growth ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Growth Efficiency ◽  
Experimental Conditions ◽  
Soil Microbial ◽  
Use Efficiency ◽  
Microbial Growth Efficiency

Soils store more carbon than the biosphere and atmosphere combined, and the efficiency to which soil microorganisms allocate carbon to growth rather than respiration is increasingly considered a proxy for the soil capacity to store carbon. This carbon use efficiency (CUE) is measured via different methods, and more recently, the 18O-H2O method has been embraced as a significant improvement for measuring CUE of soil microbial communities. Based on extrapolating 18O incorporation into DNA to new biomass, this measurement makes various implicit assumptions about the microbial community at hand. Here we conducted a literature review to evaluate how viable these assumptions are and then developed a mathematical model to test how violating them affects estimates of the growth component of CUE in soil. We applied this model to previously collected data from two kinds of soil microbial communities. By changing one parameter at a time, we confirmed our previous observation that CUE was reduced by fungal removal. Our results also show that depending on the microbial community composition, there can be substantial discrepancies between estimated and true microbial growth. Of the numerous implicit assumptions that might be violated, not accounting for the contribution of sources of oxygen other than extracellular water to DNA leads to a consistent underestimation of CUE. We present a framework that allows researchers to evaluate how their experimental conditions may influence their 18O-H2O-based CUE measurements and suggest the parameters that need further constraining to more accurately quantify growth and CUE.

scholarly journals High carbon use efficiency in soil microbial communities is related to balanced growth, not storage compound synthesis

2015 ◽  
Vol 89 ◽  
pp. 35-43 ◽  
Author(s):  
Paul Dijkstra ◽  
Elena Salpas ◽  
Dawson Fairbanks ◽  
Erin B. Miller ◽  
Shannon B. Hagerty ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
High Carbon ◽  
Balanced Growth ◽  
Soil Microbial ◽  
Carbon Use Efficiency ◽  
Compound Synthesis ◽  
Use Efficiency

scholarly journals Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Darine Trabelsi ◽  
Ridha Mhamdi
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Future Research ◽  
Bacterial Strains ◽  
Microbial Inoculants ◽  
Soil Microbial ◽  
Functional Capabilities ◽  
Plant Soil ◽  
Taxonomic Groups ◽  
The Impact

The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research.

scholarly journals Rhizosphere Microbial Communities Are Significantly Affected by Optimized Phosphorus Management in a Slope Farming System

2021 ◽  
Vol 12 ◽  
Author(s):  
Qianxin Deng ◽  
Tong Zhang ◽  
Deti Xie ◽  
Yuheng Yang
Keyword(s):  
Microbial Communities ◽  
Soil Health ◽  
Soil Microbial Communities ◽  
Growth Period ◽  
Farming System ◽  
Environmental Drivers ◽  
Growth Stages ◽  
P Fertilization ◽  
Soil Microbial ◽  
Use Efficiency

Soil rhizosphere microorganisms play crucial roles in promoting plant nutrient absorption and maintaining soil health. However, the effects of different phosphorus (P) managements on soil microbial communities in a slope farming system are poorly understood. Here, rhizosphere microbial communities under two P fertilization levels—conventional (125 kg P2O5 ha–1, P125) and optimal (90 kg P2O5 ha–1, P90)—were compared at four growth stages of maize in a typical sloped farming system. The richness and diversity of rhizosphere bacterial communities showed significant dynamic changes throughout the growth period of maize, while different results were observed in fungal communities. However, both the P fertilization levels and the growth stages influenced the structure and composition of the maize rhizosphere microbiota. Notably, compared to P125, Pseudomonas, Conexibacter, Mycobacterium, Acidothermus, Glomeromycota, and Talaromyces were significantly enriched in the different growth stages of maize under P90, while the relative abundance of Fusarium was significantly decreased during maize harvest. Soil total nitrogen (TN) and pH are the first environmental drivers of change in bacterial and fungal community structures, respectively. The abundance of Gemmatimonadota, Proteobacteria, and Cyanobacteria showed significant correlations with soil TN, while that of Basidiomycota and Mortierellomycota was significantly related to pH. Additionally, P90 strengthened the connection between bacteria, but reduced the links between fungi at the genus level. Our work helps in understanding the role of P fertilization levels in shaping the rhizosphere microbiota and may manipulate beneficial microorganisms for better P use efficiency.

scholarly journals Interactions between plants and soil shaping the root microbiome under abiotic stress

2019 ◽  
Vol 476 (19) ◽  
pp. 2705-2724 ◽  
Author(s):  
Kyle Hartman ◽  
Susannah G. Tringe
Keyword(s):  
Abiotic Stress ◽  
Microbial Communities ◽  
Abiotic Stress Tolerance ◽  
Soil Microbial Communities ◽  
Terrestrial Ecosystems ◽  
Stress Conditions ◽  
Bulk Soil ◽  
Future Research ◽  
Soil Microbial ◽  
Root Microbiome

Abstract Plants growing in soil develop close associations with soil microorganisms, which inhabit the areas around, on, and inside their roots. These microbial communities and their associated genes — collectively termed the root microbiome — are diverse and have been shown to play an important role in conferring abiotic stress tolerance to their plant hosts. In light of growing concerns over the threat of water and nutrient stress facing terrestrial ecosystems, especially those used for agricultural production, increased emphasis has been placed on understanding how abiotic stress conditions influence the composition and functioning of the root microbiome and the ultimate consequences for plant health. However, the composition of the root microbiome under abiotic stress conditions will not only reflect shifts in the greater bulk soil microbial community from which plants recruit their root microbiome but also plant responses to abiotic stress, which include changes in root exudate profiles and morphology. Exploring the relative contributions of these direct and plant-mediated effects on the root microbiome has been the focus of many studies in recent years. Here, we review the impacts of abiotic stress affecting terrestrial ecosystems, specifically flooding, drought, and changes in nitrogen and phosphorus availability, on bulk soil microbial communities and plants that interact to ultimately shape the root microbiome. We conclude with a perspective outlining possible directions for future research needed to advance our understanding of the complex molecular and biochemical interactions between soil, plants, and microbes that ultimately determine the composition of the root microbiome under abiotic stress.

scholarly journals Enhanced carbon acquisition and use efficiency alleviate microbial carbon relative to nitrogen limitation under soil acidification

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Tianpeng Li ◽  
Ruzhen Wang ◽  
Jiangping Cai ◽  
Yani Meng ◽  
Zhirui Wang ◽  
...  
Keyword(s):  
Microbial Biomass ◽  
Microbial Communities ◽  
Soil Ph ◽  
Soil Acidification ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
N Limitation ◽  
Microbial Carbon ◽  
Use Efficiency ◽  
C Limitation

Abstract Background Soil microbial communities cope with an imbalanced supply of resources by adjusting their element acquisition and utilization strategies. Although soil pH has long been considered an essential driver of microbial growth and community composition, little is known about how soil acidification affects microbial acquisition and utilization of carbon (C) and nitrogen (N). To close the knowledge gap, we simulated soil acidification and created a pH gradient by adding eight levels of elemental sulfur (S) to the soil in a meadow steppe. Results We found that S-induced soil acidification strongly enhanced the ratio of fungi to bacteria (F:B) and microbial biomass C to N (MBC:MBN) and subsequently decreased the C:N imbalance between microbial biomass and their resources. The linear decrease in the C:N imbalance with decreasing soil pH implied a conversion from N limitation to C limitation. To cope with enhanced C versus N limitation, soil microbial communities regulated the relative production of enzymes by increasing the ratio of β-glucosidase (BG, C-acquiring enzyme) to leucine aminopeptidase (LAP, N-acquiring enzyme), even though both enzymatic activities decreased with S addition. Structural equation modeling (SEM) suggested that higher C limitation and C:N-acquiring enzyme stimulated microbial carbon-use efficiency (CUE), which counteracted the negative effect of metal stress (i.e., aluminum and manganese) under soil acidification. Conclusions Overall, these results highlight the importance of stoichiometric controls in microbial adaption to soil acidification, which may help predict soil microbial responses to future acid deposition.

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