scholarly journals Resistance and Resilience of Soil Nitrogen Cycling to Drought and Heat Stress in Rehabilitated Urban Soils

2021 ◽  
Vol 12 ◽  
Author(s):  
Mehdi Fikri ◽  
Catherine Joulian ◽  
Mikael Motelica-Heino ◽  
Marie-Paule Norini ◽  
Jennifer Hellal
Keyword(s):  
Organic Matter ◽  
Drought Stress ◽  
Microbial Communities ◽  
Nitrogen Cycling ◽  
Carbon Cycling ◽  
Urban Soils ◽  
Terrestrial Ecosystems ◽  
Soil Functions ◽  
Microbial Activities ◽  
Stress Changes

In the context of climate change and biodiversity loss, rehabilitation of degraded urban soils is a means of limiting artificialization of terrestrial ecosystems and preventing further degradation of soils. Ecological rehabilitation approaches are available to reinitiate soil functions and enhance plant development. However, little is known about the long-term stability of rehabilitated soils in terms of soil functions when further natural or anthropogenic perturbations occur. Based on rehabilitated urban soils, the present study sought to evaluate the resistance and resilience of soil functions linked to carbon cycling and phosphate dynamics in addition to nitrogen cycling and related microbial communities after a heat and drought stress. A laboratory experiment was conducted in microcosms under controlled temperature conditions, with four contrasted soils collected from a rehabilitated urban brownfield; an initial, non-rehabilitated soil (IS), a technosol with a high organic matter level (HO), and two technosols with less organic matter (LO1 and LO2), together with their respective controls (no stress). Changes in potential denitrification (PDR), nitrification (PNR) rates, and their interactive relationships with soil microbial activities and soil physicochemical properties were determined following a combined heat (40°C) and drought stress period of 21 days. Measurements were carried out immediately after the stress (resistance), and then also 5, 30, and 92 days after soil rewetting at 60% water holding capacity (resilience). Microbial activities involved in soil functions such as carbon cycling and phosphate dynamics proved to be of low resistance in all soils except for IS; however, they were resilient and recovered rapidly after rewetting. On the other hand, the microbial activities and gene abundances that were measured in relation to nitrogen cycling processes showed that for denitrification, activities were more rapidly resilient than gene abundances whereas for nitrification the activities and gene abundances were resilient in the same way. Results suggest that, unless the soils contain high amounts of organic matter, microbial communities in imported soils can be more vulnerable to environmental pressures such as drought and heat than communities already present. This should be considered when rehabilitating degraded soils.

Invasive plant-derived dissolved organic matter alters microbial communities and carbon cycling in soils

2021 ◽  
pp. 108191
Author(s):  
Morgan Luce McLeod ◽  
Lorinda Bullington ◽  
Cory C. Cleveland ◽  
Johannes Rousk ◽  
Ylva Lekberg
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Microbial Communities ◽  
Carbon Cycling ◽  
Invasive Plant

scholarly journals Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260933
Author(s):  
Rachel L. Rubin ◽  
Kate A. Ballantine ◽  
Arden Hegberg ◽  
Jason P. Andras
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Soil Organic Matter ◽  
Microbial Communities ◽  
Ecological Restoration ◽  
Cation Exchange Capacity ◽  
Exchange Capacity ◽  
Soil Functions ◽  
Wetland Development ◽  
Denitrification Potential

Microbial communities are early responders to wetland degradation, and instrumental players in the reversal of this degradation. However, our understanding of soil microbial community structure and function throughout wetland development remains incomplete. We conducted a survey across cranberry farms, young retired farms, old retired farms, flooded former farms, ecologically restored former farms, and natural reference wetlands with no history of cranberry farming. We investigated the relationship between the microbial community and soil characteristics that restoration intends to maximize, such as soil organic matter, cation exchange capacity and denitrification potential. Among the five treatments considered, flooded and restored sites had the highest prokaryote and microeukaryote community similarity to natural wetlands. In contrast, young retired sites had similar communities to farms, and old retired sites failed to develop wetland microbial communities or functions. Canonical analysis of principal coordinates revealed that soil variables, in particular potassium base saturation, sodium, and denitrification potential, explained 45% of the variation in prokaryote communities and 44% of the variation in microeukaryote communities, segregating soil samples into two clouds in ordination space: farm, old retired and young retired sites on one side and restored, flooded, and natural sites on the other. Heat trees revealed possible prokaryotic (Gemmatimonadetes) and microeukaryotic (Rhizaria) indicators of wetland development, along with a drop in the dominance of Nucletmycea in restored sites, a class that includes suspected mycorrhizal symbionts of the cranberry crop. Flooded sites showed the strongest evidence of wetland development, with triple the soil organic matter accumulation, double the cation exchange capacity, and seventy times the denitrification potential compared to farms. However, given that flooding does not promote any of the watershed or habitat benefits as ecological restoration, we suggest that flooding can be used to stimulate beneficial microbial communities and soil functions during the restoration waiting period, or when restoration is not an option.

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 Microbial Organic Matter Degradation Potential in Baltic Sea Sediments Is Influenced by Depositional Conditions andIn SituGeochemistry

2018 ◽  
Vol 85 (4) ◽  
Author(s):  
Laura A. Zinke ◽  
Clemens Glombitza ◽  
Jordan T. Bird ◽  
Hans Røy ◽  
Bo Barker Jørgensen ◽  
...  
Keyword(s):  
Organic Matter ◽  
Baltic Sea ◽  
Microbial Communities ◽  
Carbon Cycling ◽  
Marine Sediments ◽  
Abiotic Factors ◽  
Organic Matter Degradation ◽  
Sediment Types ◽  
Polymer Hydrolysis ◽  
Sediment Carbon

ABSTRACTGlobally, marine sediments are a vast repository of organic matter, which is degraded through various microbial pathways, including polymer hydrolysis and monomer fermentation. The sources, abundances, and quality (i.e., labile or recalcitrant) of the organic matter and the composition of the microbial assemblages vary between sediments. Here, we examine new and previously published sediment metagenomes from the Baltic Sea and the nearby Kattegat region to determine connections between geochemistry and the community potential to degrade organic carbon. Diverse organic matter hydrolysis encoding genes were present in sediments between 0.25 and 67 meters below seafloor and were in higher relative abundances in those sediments that contained more organic matter. New analysis of previously published metatranscriptomes demonstrated that many of these genes were transcribed in two organic-rich Holocene sediments. Some of the variation in deduced pathways in the metagenomes correlated with carbon content and depositional conditions. Fermentation-related genes were found in all samples and encoded multiple fermentation pathways. Notably, genes involved in alcohol metabolism were amongst the most abundant of these genes, indicating that this is an important but underappreciated aspect of sediment carbon cycling. This study is a step towards a more complete understanding of microbial food webs and the impacts of depositional facies on present sedimentary microbial communities.IMPORTANCESediments sequester organic matter over geologic time scales and impact global climate regulation. Microbial communities in marine sediments drive organic matter degradation, but the factors controlling their assemblages and activities, which in turn impact their role in organic matter degradation, are not well understood. Hence, determining the role of microbial communities in carbon cycling in various sediment types is necessary for predicting future sediment carbon cycling. We examined microbial communities in Baltic Sea sediments, which were deposited across various climatic and geographical regimes to determine the relationship between microbial potential for breakdown of organic matter and abiotic factors, including geochemistry and sediment lithology. The findings from this study will contribute to our understanding of carbon cycling in the deep biosphere and how microbial communities live in deeply buried environments.

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.

LDPE microplastics affect soil microbial communities and nitrogen cycling

2021 ◽  
Vol 773 ◽  
pp. 145640
Author(s):  
Lili Rong ◽  
Longfei Zhao ◽  
Leicheng Zhao ◽  
Zhipeng Cheng ◽  
Yiming Yao ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Nitrogen Cycling ◽  
Soil Microbial Communities ◽  
Soil Microbial

scholarly journals Environmental parameters and microbial community profiles as indication towards microbial activities and diversity in aquaponic system compartments

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zala Schmautz ◽  
Carlos A. Espinal ◽  
Andrea M. Bohny ◽  
Fabio Rezzonico ◽  
Ranka Junge ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Profile Analysis ◽  
Operation Mode ◽  
Environmental Parameters ◽  
Plant Production ◽  
Microbial Activities ◽  
Anaerobic Processes ◽  
Abiotic Parameters ◽  
Aerobic And Anaerobic

Abstract Background An aquaponic system couples cultivation of plants and fish in the same aqueous medium. The system consists of interconnected compartments for fish rearing and plant production, as well as for water filtration, with all compartments hosting diverse microbial communities, which interact within the system. Due to the design, function and operation mode of the individual compartments, each of them exhibits unique biotic and abiotic conditions. Elucidating how these conditions shape microbial communities is useful in understanding how these compartments may affect the quality of the water, in which plants and fish are cultured. Results We investigated the possible relationships between microbial communities from biofilms and water quality parameters in different compartments of the aquaponic system. Biofilm samples were analyzed by total community profiling for bacterial and archaeal communities. The results implied that the oxygen levels could largely explain the main differences in abiotic parameters and microbial communities in each compartment of the system. Aerobic system compartments are highly biodiverse and work mostly as a nitrifying biofilter, whereas biofilms in the anaerobic compartments contain a less diverse community. Finally, the part of the system connecting the aerobic and anaerobic processes showed common conditions where both aerobic and anaerobic processes were observed. Conclusion Different predicted microbial activities for each compartment were found to be supported by the abiotic parameters, of which the oxygen saturation, total organic carbon and total nitrogen differentiated clearly between samples from the main aerobic loop and the anaerobic compartments. The latter was also confirmed using microbial community profile analysis.

scholarly journals Trace and major element contents, microbial communities, and enzymatic activities of urban soils of Marrakech city along an anthropization gradient

2019 ◽  
Vol 19 (5) ◽  
pp. 2153-2165 ◽  
Author(s):  
Ahmed Naylo ◽  
Sofia I. Almeida Pereira ◽  
Leila Benidire ◽  
Hicham El Khalil ◽  
Paula M. L. Castro ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Urban Soils ◽  
Major Element ◽  
Enzymatic Activities ◽  
Element Contents

scholarly journals Effects of glyphosate-based herbicides and their active ingredients on earthworms, water infiltration and glyphosate leaching are influenced by soil properties

2021 ◽  
Vol 33 (1) ◽  
Author(s):  
Johann G. Zaller ◽  
Maureen Weber ◽  
Michael Maderthaner ◽  
Edith Gruber ◽  
Eszter Takács ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Properties ◽  
Weed Control ◽  
Amaranthus Retroflexus ◽  
Water Infiltration ◽  
Soil Conditions ◽  
Soil Functions ◽  
Active Ingredients ◽  
Hand Weeding ◽  
Earthworm Activity

Abstract Background Glyphosate-based herbicides (GBHs) are among the most often used pesticides. The hundreds of GBHs used worldwide consist of the active ingredient (AI) glyphosate in form of different salts, possibly other AIs, and various mostly undisclosed co-formulants. Pesticide risk assessments are commonly performed using single AIs or GBHs at standard soil conditions without vegetation. In a greenhouse experiment, we established a weed population with common amaranth (Amaranthus retroflexus) to examine the effects of three GBHs (Roundup LB Plus, Roundup PowerFlex, Touchdown Quattro) and their corresponding AIs (salts of glyphosate isopropylammonium, potassium, diammonium) on the activity and physiological biomarkers (glutathione S-transferase, GST; acetylcholine esterase, AChE) of an ecologically relevant earthworm species (Lumbricus terrestris). GBHs and AIs were applied at recommended doses; hand weeding served as control. Experiments were established with two soil types differing in organic matter content (SOM; 3.0% vs. 4.1%) and other properties. Results Earthworm activity (casting and movement activity) decreased after application of glyphosate formulations or active ingredients compared to hand weeding. We found no consistent pattern that formulations had either higher or lower effects on earthworm activity than their active ingredients; rather, differences were substance-specific. Earthworm activity was little affected by soil organic matter levels. Biomarkers remained unaffected by weed control types; GST but not AChE was decreased under high SOM. Water infiltration after a simulated heavy rainfall was interactively affected by weed control types and SOM. Leachate amount was higher after application of formulations than active ingredients and was higher under low SOM. Glyphosate concentrations in soil and leachate were strongly affected by application of formulations or active ingredients and varied with SOM (significant weed control type x SOM interaction). Conclusions We found that both commercial formulations and pure active ingredients can influence earthworms with consequences on important soil functions. Glyphosate products showed increased, reduced or similar effects than pure glyphosate on particular soil functions; soil properties can substantially alter this. Especially at lower SOM, heavy rainfalls could lead to more glyphosate leaching into water bodies. A full disclosure of co-formulants would be necessary to further decipher their specific contributions to these inconsistent effects.

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