scholarly journals Microbial Necromass in Soils—Linking Microbes to Soil Processes and Carbon Turnover

2021 ◽  
Vol 9 ◽  
Author(s):  
M. Kästner ◽  
A. Miltner ◽  
S. Thiele-Bruhn ◽  
C. Liang
Keyword(s):  
Organic Matter ◽  
Microbial Biomass ◽  
Plant Material ◽  
Microbial Growth ◽  
Tricarboxylic Acid Cycle ◽  
Building Blocks ◽  
Life Strategy ◽  
Soil Processes ◽  
Carbon Turnover ◽  
Molecular Imprint

The organic matter of living plants is the precursor material of the organic matter stored in terrestrial soil ecosystems. Although a great deal of knowledge exists on the carbon turnover processes of plant material, some of the processes of soil organic matter (SOM) formation, in particular from microbial necromass, are still not fully understood. Recent research showed that a larger part of the original plant matter is converted into microbial biomass, while the remaining part in the soil is modified by extracellular enzymes of microbes. At the end of its life, microbial biomass contributes to the microbial molecular imprint of SOM as necromass with specific properties. Next to appropriate environmental conditions, heterotrophic microorganisms require energy-containing substrates with C, H, O, N, S, P, and many other elements for growth, which are provided by the plant material and the nutrients contained in SOM. As easily degradable substrates are often scarce resources in soil, we can hypothesize that microbes optimize their carbon and energy use. Presumably, microorganisms are able to mobilize biomass building blocks (mono and oligomers of fatty acids, amino acids, amino sugars, nucleotides) with the appropriate stoichiometry from microbial necromass in SOM. This is in contrast to mobilizing only nutrients and consuming energy for new synthesis from primary metabolites of the tricarboxylic acid cycle after complete degradation of the substrates. Microbial necromass is thus an important resource in SOM, and microbial mining of building blocks could be a life strategy contributing to priming effects and providing the resources for new microbial growth cycles. Due to the energy needs of microorganisms, we can conclude that the formation of SOM through microbial biomass depends on energy flux. However, specific details and the variability of microbial growth, carbon use and decay cycles in the soil are not yet fully understood and linked to other fields of soil science. Here, we summarize the current knowledge on microbial energy gain, carbon use, growth, decay, and necromass formation for relevant soil processes, e. g. the microbial carbon pump, C storage, and stabilization. We highlight the factors controlling microbial necromass contribution to SOM and the implications for soil carbon use efficiency (CUE) and we identify research needs for process-based SOM turnover modelling and for understanding the variability of these processes in various soil types under different climates.

scholarly journals SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems

2015 ◽  
Vol 8 (10) ◽  
pp. 3441-3470 ◽  
Author(s):  
J. A. Bradley ◽  
A. M. Anesio ◽  
J. S. Singarayer ◽  
M. R. Heath ◽  
S. Arndt
Keyword(s):  
Organic Matter ◽  
Microbial Biomass ◽  
Microbial Growth ◽  
Model Development ◽  
Biogeochemical Cycling ◽  
Biogeochemical Model ◽  
Model Parameters ◽  
Glacier Forefield ◽  
Unconstrained Model

Abstract. SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework designed to simulate microbial dynamics and biogeochemical cycling during initial ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The rationale for model development arises from decades of empirical observations in glacier forefields, and enables a quantitative and process focussed approach. Here, we provide a detailed description of SHIMMER, test its performance in two case study forefields: the Damma Glacier (Switzerland) and the Athabasca Glacier (Canada) and analyse sensitivity to identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Primary production is responsible for the initial build-up of labile substrate that subsequently supports heterotrophic growth. However, allochthonous contributions of organic matter, and nitrogen fixation, are important in sustaining this productivity. The development and application of SHIMMER also highlights aspects of these systems that require further empirical research: quantifying nutrient budgets and biogeochemical rates, exploring seasonality and microbial growth and cell death. This will lead to increased understanding of how glacier forefields contribute to global biogeochemical cycling and climate under future ice retreat.

Investigating nutrient controls over microbial activity in tropical soils

2021 ◽  
Author(s):  
Lucia Fuchslueger
Keyword(s):  
Organic Matter ◽  
Microbial Biomass ◽  
Microbial Communities ◽  
Microbial Activity ◽  
Microbial Growth ◽  
Tropical Soils ◽  
Phosphorus Availability ◽  
Soil P ◽  
Soil Microbial ◽  
Low Phosphorus

<p>The Amazon rainforest is an important sink for atmospheric CO<sub>2</sub> counteracting increased emissions from anthropogenic fossil fuel combustion and land use change storing large amounts of carbon in plant biomass and soils. However, large parts of the Amazon Basin are characterized by highly weathered soils (ultisols and oxisols) with low availability of rock-derived phosphorus (and cations), which are mostly occluded in soil or bound in organic matter. Such low phosphorus availability is thought to be (co-)limiting plant productivity. However, much less is known whether low phosphorus availability influences the activity of heterotrophic microbial communities controlling litter and soil organic matter decomposition and thereby long-term carbon sequestration in tropical soils.</p><p>In tropical soils high temperature and humid conditions allow overall high microbial activity. Over a larger soil phosphorus fertility gradient across several Amazonian rainforest sites, at low P sites almost 40 % of total P was stored in microbial biomass, highlighting the competitive strength of microorganisms and their importance as P reservoir. Across all sites soil microbial biomass was a significant predictor for soil microbial respiration, but mass-specific respiration rates (normalized by microbial biomass C) rather decreased at higher soil P. Using the incorporation of <sup>18</sup>O from labelled water into DNA (i.e., a substrate-independent method) to determine microbial growth, we found significantly lower microbial growth rates per unit of microbial biomass at higher soil P. This resulted in a lower microbial carbon use efficiency, at a narrower C:P stoichiometry in soils with higher P levels, and pointed towards a microbial co-limitation of phosphorus and carbon at low soil P levels. Furthermore, data from a multi-year nutrient manipulation experiment in French Guiana and from short-term lab incubations suggest that microbial communities thriving at low P levels are highly efficient in taking up and storing added P, but do not necessarily respond with increased growth.</p><p>Soil microbial communities play a crucial role in soil carbon and phosphorus cycling in tropical soils as potent competitors for available P. They also play an important role in storing and buffering P losses from highly weathered tropical soils. The potential non-homoeostatic stoichiometric behavior of microbial communities in P cycling is important to consider in soil and ecosystem models based on stoichiometric relationships.</p>

scholarly journals SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems

2015 ◽  
Vol 8 (8) ◽  
pp. 6143-6216 ◽  
Author(s):  
J. A. Bradley ◽  
A. M. Anesio ◽  
J. S. Singarayer ◽  
M. R. Heath ◽  
S. Arndt
Keyword(s):  
Organic Matter ◽  
Microbial Biomass ◽  
Microbial Growth ◽  
Biogeochemical Cycling ◽  
Laboratory Research ◽  
Biogeochemical Model ◽  
Published Data ◽  
Model Parameters ◽  
Empirical Observation ◽  
Glacier Forefield

Abstract. SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework which is developed as part of an interdisciplinary, iterative, model-data based approach fully integrating fieldwork and laboratory experiments with model development, testing, and application. SHIMMER is designed to simulate the establishment of microbial biomass and associated biogeochemical cycling during the initial stages of ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The model mechanistically describes and predicts transformations in carbon, nitrogen and phosphorus through aggregated components of the microbial community as a set of coupled ordinary differential equations. The rationale for development of the model arises from decades of empirical observation on the initial stages of soil development in glacier forefields. SHIMMER enables a quantitative and process focussed approach to synthesising the existing empirical data and advancing understanding of microbial and biogeochemical dynamics. Here, we provide a detailed description of SHIMMER. The performance of SHIMMER is then tested in two case studies using published data from the Damma Glacier forefield in Switzerland and the Athabasca Glacier in Canada. In addition, a sensitivity analysis helps identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass, and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Simulation results indicate that primary production is responsible for the initial build-up of substrate that subsequently supports heterotrophic growth. However, allochthonous contributions of organic matter are identified as important in sustaining this productivity. Microbial production in young soils is supported by labile organic matter, whereas carbon stocks in older soils are more refractory. Nitrogen fixing bacteria are responsible for the initial accumulation of available nitrates in the soil. Biogeochemical rates are highly seasonal, as observed in experimental data. The development and application of SHIMMER not only provides important new insights into forefield dynamics, but also highlights aspects of these systems that require further field and laboratory research. The most pressing advances need to come in quantifying nutrient budgets and biogeochemical rates, in exploring seasonality, the fate of allochthonous deposition in relation to autochthonous production, and empirical studies of microbial growth and cell death, to increase understanding of how glacier forefield development contributes to the global biogeochemical cycling and climate in the future.

scholarly journals Nitrogen Immobilisation and Microbial Biomass Build-Up Induced by Miscanthus x giganteus L. Based Fertilisers

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1386
Author(s):  
Michael Stotter ◽  
Florian Wichern ◽  
Ralf Pude ◽  
Martin Hamer
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Microbial Biomass ◽  
Triticum Aestivum L ◽  
Microbial Biomass C ◽  
Microbial Biomass N ◽  
Miscanthus X Giganteus ◽  
Organic Fertilisers ◽  
Biomass N ◽  
Set Up

Cultivation of Miscanthus x giganteus L. (Mis) with annual harvest of biomass could provide an additional C source for farmers. To test the potential of Mis-C for immobilizing inorganic N from slurry or manure and as a C source for soil organic matter build-up in comparison to wheat (Triticum aestivum L.) straw (WS), a greenhouse experiment was performed. Pot experiments with ryegrass (Lolium perenne L.) were set up to investigate the N dynamics of two organic fertilisers based on Mis at Campus Klein-Altendorf, Germany. The two fertilisers, a mixture of cattle slurry and Mis as well as cattle manure from Mis-bedding material resulted in a slightly higher N immobilisation. Especially at the 1st and 2nd harvest, they were partly significantly different compared with the WS treatments. The fertilisers based on Mis resulted in a slightly higher microbial biomass C and microbial biomass N and thus can be identified as an additional C source to prevent nitrogen losses and for the build-up of soil organic matter (SOM) in the long-term.

Microbial and biochemical changes induced by rotation and tillage in a soil under barley production

1993 ◽  
Vol 73 (1) ◽  
pp. 39-50 ◽  
Author(s):  
D. A. Angers ◽  
N. Bissonnette ◽  
A. Légère ◽  
N. Samson
Keyword(s):  
Alkaline Phosphatase ◽  
Organic Matter ◽  
Microbial Biomass ◽  
Phosphatase Activity ◽  
Alkaline Phosphatase Activity ◽  
Soil Layer ◽  
Red Clover ◽  
Organic C ◽  
Top Soil ◽  
Total Organic C

Crop rotations and tillage practices can modify not only the total amount of organic matter (OM) in soils but also its composition. The objective of this study was to determine the changes in total organic C, microbial biomass C (MBC), carbohydrates and alkaline phosphatase activity induced by 4 yr of different rotation and tillage combinations on a Kamouraska clay in La Pocatière, Quebec. Two rotations (continuous barley (Hordeum vulgare L.) versus a 2-yr barley–red clover (Trifolium pratense L.) rotation) and three tillage treatments (moldboard plowing (MP), chisel plowing (CP) and no-tillage (NT)) were compared in a split-plot design. Total organic C was affected by the tillage treatments but not by the rotations. In the top soil layer (0–7.5 cm), NT and CP treatments had C contents 20% higher than the MP treatment. In the same soil layer, MBC averaged 300 mg C kg−1 in the MP treatment and up to 600 mg C kg−1 in the NT soil. Hot-water-extractable and acid-hydrolyzable carbohydrates were on average 40% greater under reduced tillage than under MP. Both carbohydrate fractions were also slightly larger in the rotation than in the soil under continuous barley. The ratios of MBC and carbohydrate C to total organic C suggested that there was a significant enrichment of the OM in labile forms as tillage intensity was reduced. Alkaline phosphatase activity was 50% higher under NT and 20% higher under CP treatments than under MP treatment and, on average, 15% larger in the rotation than in the continuous barley treatment. Overall, the management-induced differences were slightly greater in the top layer (0–7.5 cm) than in the lower layer of the Ap horizon (7.5–15 cm). All the properties measured were highly correlated with one another. They also showed significant temporal variations that were, in most cases, independent of the treatments. Four years of conservation tillage and, to a lesser extent, rotation with red clover resulted in greater OM in the top soil layer compared with the more intensive systems. This organic matter was enriched in labile forms. Key words: Soil management, soil quality, organic matter, carbohydrates, microbial biomass, phosphatase

scholarly journals ORCHIMIC (v1.0), a microbe-driven model for soil organic matter decomposition designed for large-scale applications

2018 ◽  
Author(s):  
Ye Huang ◽  
Bertrand Guenet ◽  
Philippe Ciais ◽  
Ivan A. Janssens ◽  
Jennifer L. Soong ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Biomass ◽  
Input Data ◽  
Priming Effect ◽  
Temporal Dynamics ◽  
Litter Input ◽  
Decomposition Models ◽  
Soc Stock ◽  
Global Vegetation ◽  
Soc Decomposition

Abstract. The role of soil microorganisms in regulating soil organic matter (SOM) decomposition is of primary importance in the carbon cycle, and in particular in the context of global change. Modelling soil microbial community dynamics to simulate its impact on soil gaseous carbon (C) emissions and nitrogen (N) mineralization at large spatial scales is a recent research field with the potential to improve predictions of SOM responses to global climate change. We here present a SOM model called ORCHIMIC whose input data that are consistent with those of global vegetation models. The model simulates decomposition of SOM by explicitly accounting for enzyme production and distinguishing three different microbial functional groups: fresh organic matter (FOM) specialists, SOM specialists, and generalists, while implicitly also accounting for microbes that do not produce extracellular enzymes, i.e. cheaters. This ORCHIMIC model and two other organic matter decomposition models, CENTURY (based on first order kinetics and representative for the structure of most current global soil carbon models) and PRIM (with FOM accelerating the decomposition rate of SOM) were calibrated to reproduce the observed respiration fluxes from FOM and SOM and their possible interactions from incubation experiments of Blagodatskaya et al. (2014). Among the three models, ORCHIMIC was the only one that captured well both the temporal dynamics of the respiratory fluxes and the magnitude of the priming effect observed during the incubation experiment. ORCHIMIC also reproduced well the temporal dynamics of microbial biomass. We then applied different idealized changes to the model input data, i.e. a 5 K stepwise increase of temperature and/or a doubling of plant litter inputs. Under 5 K warming, ORCHIMIC predicted a 0.002 K−1 decrease in the C use efficiency (defined as the ratio of C allocated to microbial growth to the sum of C allocated to growth and respiration) and a 3 % loss of SOC. Under the double litter input scenario, ORCHIMIC predicted a doubling of microbial biomass, while SOC stock increased by less than 1 % due to the priming effect. This limited increase in SOC stock contrasted with the proportional increase in SOC stock as modelled by the conventional SOC decomposition model (CENTURY), which cannot reproduce the priming effect. If temperature increased by 5 K and litter input is doubled, the model predicted almost the same loss of SOC as when only temperature was increased. These tests suggest that the responses of SOC stock to warming and increasing input may differ a lot from those simulated by conventional SOC decomposition models, when microbial dynamics is included. The next step is to incorporate the ORCHIMIC model into a global vegetation model to perform simulations for representative sites and future scenarios.

Temperature effects on organic matter and microbial biomass dynamics in temperate and tropical soils

1998 ◽  
Vol 30 (10-11) ◽  
pp. 1309-1315 ◽  
Author(s):  
B. Grisi ◽  
C. Grace ◽  
P.C. Brookes ◽  
A. Benedetti ◽  
M.T. Dell'abate
Keyword(s):  
Organic Matter ◽  
Microbial Biomass ◽  
Temperature Effects ◽  
Tropical Soils ◽  
Biomass Dynamics

scholarly journals Identification of Xylem Occlusions Occurring in CutClematis(ClematisL., fam.RanunculaceaeJuss.) Stems during Their Vase Life

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Agata Jedrzejuk ◽  
Julia Rochala ◽  
Jacek Zakrzewski ◽  
Julita Rabiza-Świder
Keyword(s):  
Water Uptake ◽  
Plant Material ◽  
Microbial Growth ◽  
Vascular System ◽  
Vase Life ◽  
Cut Flower ◽  
Cut Flowers ◽  
Bacterial Development ◽  
Growth Formation ◽  
New Treatments

During the vase life of cut stems obstruction of xylem vessels occurs due to microbial growth, formation of tyloses, deposition of materials in the lumen of xylem vessels and the presence of air emboli in the vascular system. Such obstructions may restrict water uptake and its transport towards upwards thus lowering their ornamental value and longevity of cut flowers.Clematisis a very attractive plant material which may be used as cut flower in floral compositions. Nothing is known about the histochemical or cytological nature of xylem blockages occurring in cut stems of this plant. This study shows that inclematis, tyloses are the main source of occlusions, although bacteria and some amorphic substances may also appear inside the vessels. A preservative composed of 200 mg dm−38-HQC (8-hydroxyquinolin citrate) and 2% sucrose arrested bacterial development and the growth of tyloses. This information can be helpful in the development of new treatments to improve keeping qualities of cutclematisstems.

Soil microbial biomass—Interpretation and consideration for soil monitoring

Soil Research ◽  
2011 ◽  
Vol 49 (4) ◽  
pp. 287 ◽  
Author(s):  
V. Gonzalez-Quiñones ◽  
E. A. Stockdale ◽  
N. C. Banning ◽  
F. C. Hoyle ◽  
Y. Sawada ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Biomass ◽  
Soil Microorganisms ◽  
Soil Microbial Biomass ◽  
Biological Function ◽  
Anthropogenic Change ◽  
Soil Monitoring ◽  
Soil Microbial ◽  
Quality Assessments ◽  
The Impact

Since 1970, measurement of the soil microbial biomass (SMB) has been widely adopted as a relatively simple means of assessing the impact of environmental and anthropogenic change on soil microorganisms. The SMB is living and dynamic, and its activity is responsible for the regulation of organic matter transformations and associated energy and nutrient cycling in soil. At a gross level, an increase in SMB is considered beneficial, while a decline in SMB may be considered detrimental if this leads to a decline in biological function. However, absolute SMB values are more difficult to interpret. Target or reference values of SMB are needed for soil quality assessments and to allow ameliorative action to be taken at an appropriate time. However, critical values have not yet been successfully identified for SMB. This paper provides a conceptual framework which outlines how SMB values could be interpreted and measured, with examples provided within an Australian context.

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