scholarly journals Evaluation of Microbe-Driven Soil Organic Matter Quantity and Quality by Thermodynamic Theory

mBio ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jianwei Zhang ◽  
Youzhi Feng ◽  
Meng Wu ◽  
Ruirui Chen ◽  
Zhongpei Li ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Terrestrial Ecosystems ◽  
Thermodynamic Theory ◽  
Ion Cyclotron Resonance ◽  
Soil Microbial ◽  
Region Scale ◽  
Thermodynamic Quality

ABSTRACT Microbial communities, coupled with substrate quality and availability, regulate the stock (formation versus mineralization) of soil organic matter (SOM) in terrestrial ecosystems. However, our understanding of how soil microbes interact with contrasting substrates influencing SOM quantity and quality is still very superficial. Here, we used thermodynamic theory principles and Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) to evaluate the linkages between dissolved organic matter (DOM [organic substrates in soil that are readily available]), thermodynamic quality, and microbial communities. We investigated soils from subtropical paddy ecosystems across a 1,000-km gradient and comprising contrasting levels of SOM content and nutrient availability. Our region-scale study suggested that soils with a larger abundance of readily accessible resources (i.e., lower Gibbs free energy) supported higher levels of microbial diversity and higher SOM content. We further advocated a novel phylotype-level microbial classification based on their associations with OM quantities and qualities and identified two contrasting clusters of bacterial taxa: phylotypes that are highly positively correlated with thermodynamically favorable DOM and larger SOM content versus those which are associated with less-favorable DOM and lower SOM content. Both groups are expected to play critical roles in regulating SOM contents in the soil. By identifying the associations between microbial phylotypes of different life strategies and OM qualities and quantities, our study indicates that thermodynamic theory can act as a proxy for the relationship between OM and soil microbial communities and should be considered in models of soil organic matter preservation. IMPORTANCE Microbial communities are known to be important drivers of organic matter (OM) accumulation in terrestrial ecosystems. However, despite the importance of these soil microbes and processes, the mechanisms behind these microbial-SOM associations remain poorly understood. Here, we used the principles of thermodynamic theory and novel Fourier transform ion cyclotron resonance mass spectrometry techniques to investigate the links between microbial communities and dissolved OM (DOM) thermodynamic quality in soils across a 1,000-km gradient and comprising contrasting nutrient and C contents. Our region-scale study provided evidence that soils with a larger amount of readily accessible resources (i.e., lower Gibbs free energy) supported higher levels of microbial diversity and larger SOM content. Moreover, we created a novel phylotype-level microbial classification based on the associations between microbial taxa and DOM quantities and qualities. We found two contrasting clusters of bacterial taxa based on their level of association with thermodynamically favorable DOM and SOM content. Our study advances our knowledge on the important links between microbial communities and SOM. Moreover, by identifying the associations between microbial phylotypes of different life strategies and OM qualities and quantities, our study indicates that thermodynamic theory can act as a proxy for the relationship between OM and soil microbial communities. Together, our findings support that the association between microbial species taxa and substrate thermodynamic quality constituted an important complement explanation for soil organic matter preservation.

scholarly journals Biogeographic Changes in Forest Soil Microbial Communities of Offshore Islands—A Case Study of Remote Islands in Taiwan

Forests ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 4
Author(s):  
Ed-Haun Chang ◽  
Isheng Jason Tsai ◽  
Shih-Hao Jien ◽  
Guanglong Tian ◽  
Chih-Yu Chiu
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Microbial Communities ◽  
Phospholipid Fatty Acid ◽  
Soil Microbial Communities ◽  
Chemical Properties ◽  
Principal Component ◽  
Factors Affecting ◽  
Soil Microbial

Biogeographic separation has been an important cause of faunal and floral distribution; however, little is known about the differences in soil microbial communities across islands. In this study, we determined the structure of soil microbial communities by analyzing phospholipid fatty acid (PLFA) profiles and comparing enzymatic activities as well as soil physio-chemical properties across five subtropical granite-derived and two tropical volcanic (andesite-derived) islands in Taiwan. Among these islands, soil organic matter, pH, urease, and PLFA biomass were higher in the tropical andesite-derived than subtropical granite-derived islands. Principal component analysis of PLFAs separated these islands into three groups. The activities of soil enzymes such as phosphatase, β-glucosidase, and β-glucosaminidase were positively correlated with soil organic matter and total nitrogen. Redundancy analysis of microbial communities and environmental factors showed that soil parent materials and the climatic difference are critical factors affecting soil organic matter and pH, and consequently the microbial community structure.

A novel fluxomics approach to decipher the flux partitioning between anabolic and catabolic processes in soil microbial communities

2020 ◽  
Author(s):  
Theresa Böckle ◽  
Yuntao Hu ◽  
Jörg Schnecker ◽  
Wolfgang Wanek
Keyword(s):  
Amino Acids ◽  
Organic Matter ◽  
Soil Organic Matter ◽  
Microbial Communities ◽  
Metabolic Pathways ◽  
Isotope Labeling ◽  
Soil Microbial Communities ◽  
Microbial Activities ◽  
Soil Microbial ◽  
Wide Range

<p>The activities of soil microorganisms drive soil carbon (C) and nutrient cycling and therefore play an important role in local and global terrestrial C dynamics and nutrient cycles. Unfortunately, soil microbial activities have been defined mostly by measurements of heterotrophic respiration, potential enzyme activities, or net N processes. However, soil microbial activities comprise more than just catabolic processes such as respiration and N mineralization. Recently anabolic processes (biosynthesis and growth) and the partitioning between anabolic and catabolic processes in soil microbial metabolism have gained more attention as they control microbial soil organic matter formation. Understanding the controls on these processes allows an improved understanding of the key roles that soil microbes play in organic matter decomposition (catabolic processes) and soil organic matter sequestration (anabolic processes leading to growth, biomass and necromass formation), and their potential feedback to global change.</p><p>Generally, there are two approaches to study the metabolism of soil microbial communities: First, position-specific isotope labeling is a tool that allows the tracing of <sup>13</sup>C-atoms in organic molecules on their way through the network of metabolic pathways and second, metabolomics and fluxomics approaches can enable disentangling the highly complex metabolic networks of microbial communities, which however have rarely (metabolomics) or never (fluxomics) been applied to soils.</p><p>In this study we developed a targeted soil metabolomics approach coupled to <sup>13</sup>C isotope tracing (fluxomics), in which we extract, purify and measure a preselected set of key metabolites. Our aim was to cover the wide spectrum of soil microbial metabolic pathways based on the analysis of biomarker metabolites being unique to specific metabolic pathways such as  glycolysis/gluconeogenesis (e.g. fructose 1,6-bisphosphate), the pentose phosphate pathway (ribose-5-phosphate), the citric acid cycle (α-ketoglutaric acid), purine and pyrimidine metabolism (UMP, AMP, allantoin), amino acid biosynthesis and degradation (10proteinogenic amino acids and their intermediates), the urea cycle (ornithine), amino sugar metabolism (N-Acetyl-D-Glucosamine and –muramic acid) and the shikimate pathway (shikimate). The minute concentrations of these primary metabolites are extracted from soils by 1 M KCl including 5 % chloroform, salts are removed by freeze-drying, methanol dissolution and cation-/anion-exchange chromatography and the metabolites and their isotopomers quantified by UPLC-Orbitrap mass spectrometry. To cover the wide range of metabolites, compound separations are performed by  hydrophilic interaction chromatography (HILIC) for metabolites such as amino acids, (poly-)amines, nucleosides and nucleobases and by Ion chromatography (IC), to separate charged molecules like amino sugars, sugar phosphates and organic acids.  Here we will show fluxomics results from a laboratory soil warming experiment where we added <sup>13</sup>C-glucose to a temperate forest soil as a proof of concept.</p>

scholarly journals Rapid increases in soil pH solubilise organic matter, dramatically increase denitrification potential and strongly stimulate microorganisms from theFirmicutesphylum

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6090 ◽  
Author(s):  
Craig R. Anderson ◽  
Michelle E. Peterson ◽  
Rebekah A. Frampton ◽  
Simon R. Bulman ◽  
Sandi Keenan ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Soil Ph ◽  
Soil Microbial Communities ◽  
Fertilizer Application ◽  
Detailed Knowledge ◽  
Ph Change ◽  
Ph Changes ◽  
Soil Microbial ◽  
Chemical Attributes

Rapid and transient changes in pH frequently occur in soil, impacting dissolved organic matter (DOM) and other chemical attributes such as redox and oxygen conditions. Although we have detailed knowledge on microbial adaptation to long-term pH changes, little is known about the response of soil microbial communities to rapid pH change, nor how excess DOM might affect key aspects of microbial N processing. We used potassium hydroxide (KOH) to induce a range of soil pH changes likely to be observed after livestock urine or urea fertilizer application to soil. We also focus on nitrate reductive processes by incubating microcosms under anaerobic conditions for up to 48 h. Soil pH was elevated from 4.7 to 6.7, 8.3 or 8.8, and up to 240-fold higher DOM was mobilized by KOH compared to the controls. This increased microbial metabolism but there was no correlation between DOM concentrations and CO2respiration nor N-metabolism rates. Microbial communities became dominated byFirmicutesbacteria within 16 h, while few changes were observed in the fungal communities. Changes in N-biogeochemistry were rapid and denitrification enzyme activity (DEA) increased up to 25-fold with the highest rates occurring in microcosms at pH 8.3 that had been incubated for 24-hour prior to measuring DEA. Nitrous oxide reductase was inactive in the pH 4.7 controls but at pH 8.3 the reduction rates exceeded 3,000 ng N2–N g−1h−1in the presence of native DOM. Evidence for dissimilatory nitrate reduction to ammonium and/or organic matter mineralisation was observed with ammonium increasing to concentrations up to 10 times the original native soil concentrations while significant concentrations of nitrate were utilised. Pure isolates from the microcosms were dominated byBacillusspp. and exhibited varying nitrate reductive potential.

scholarly journals The response of soil microbial communities to variation in annual precipitation depends on soil nutritional status in an oligotrophic desert

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4007 ◽  
Author(s):  
Cristina Montiel-González ◽  
Yunuen Tapia-Torres ◽  
Valeria Souza ◽  
Felipe García-Oliva
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Soil Water Potential ◽  
Soil Microbial Communities ◽  
Desert Ecosystem ◽  
Annual Precipitation ◽  
Climate Change Scenarios ◽  
Desert Ecosystems ◽  
Soil Microbial ◽  
Physiological Adjustments

Background Soil microbial communities (SMC) play a central role in the structure and function of desert ecosystems. However, the high variability of annual precipitation could results in the alteration of SMC and related biological processes depending on soil water potential. The nature of the physiological adjustments made by SMC in order to obtain energy and nutrients remains unclear under different soil resource availabilities in desert ecosystems. In order to examine this dynamic, the present study examined the effects of variation in annual precipitation on physiological adjustments by the SMC across two vegetation-soil systems of different soil organic matter input in an oligotrophic desert ecosystem. Methods We collected soil samples in the Cuatro Ciénegas Basin (Mexico) under two vegetation covers: rosetophylous scrub (RS) and grassland (G), that differ in terms of quantity and quality of organic matter. Collections were conducted during the years 2011, 2012, 2013 and 2014, over which a noticeable variation in the annual precipitation occurred. The ecoenzymatic activity involved in the decomposition of organic matter, and the concentration of dissolved, available and microbial biomass nutrients, were determined and compared between sites and years. Results In 2011, we observed differences in bacterial taxonomic composition between the two vegetation covers. The lowest values of dissolved, available and microbial nutrients in both cover types were found in 2012. The G soil showed higher values of dissolved and available nutrients in the wet years. Significant positive correlations were detected between precipitation and the ratios Cmic:Nmic and Cmic:Pmic in the RS soil and Cmic:Pmic and Nmic:Pmic in the G soil. The slopes of the regression with Cmic and Nmic were higher in the G soil and lower in the RS soil. Moreover, the SMC under each vegetation cover were co-limited by different nutrients and responded to the sum of water stress and nutrient limitation. Discussion Soil community within both sites (RS and G) may be vulnerable to drought. However, the community of the site with lower resources (RS) is well adapted to acquire P resources by ecoenzyme upregulation during years with adequate precipitation, suggesting that this community is resilient after drought occurs. Under the Global Climate Change scenarios for desert ecosystems that predict reduced annual precipitation and an increased intensity and frequency of torrential rains and drought events, the soil microbial communities of both sites could be vulnerable to drought through C and P co-limitation and reallocation of resources to physiological acclimatization strategies in order to survive.

scholarly journals THE SOIL MICROBIAL COENOSIS STATE UNDER VARIOUS CROPS IN CASE OF INTRODUCING THE MIXTURE OF SILICON-CONTAINING MINERALS

2015 ◽  
Vol 22 ◽  
pp. 30-36
Author(s):  
N. E. Ellanska ◽  
N. V. Zaimenko ◽  
O. P. Yunosheva
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Sugar Beet ◽  
Soil Microbial Communities ◽  
Trophic Groups ◽  
Rhizospheric Soil ◽  
Soil Microbiota ◽  
Soil Microbial ◽  
Corn Plants ◽  
Positive Effect

In the conditions of stationary experiment the features of the formation of microbial coenosis in the rhizosphere of sugar beet, soybean and corn plants were studied in case of introducing silicon-containing mixtures into the soil. It was shown that the number of representatives of separate eco-trophic groups of microorganisms varies depending on the culture and introduced mixture. Soil microbial communities from under soybean and corn were characterized by the biggest changes, especially in case of mineralized sapropel introduction. Positive effect on sugar beet rhizospheric soil microbiota was made by mixtures: high-bog peat + siliconcontaining minerals and potassium silicate + silicon-containing minerals + sapropel. The processes of soil organic matter mineralization were quite balanced.

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