scholarly journals Linking Genes to Traits in Fungi

2021 ◽  
Author(s):  
A. L. Romero-Olivares ◽  
E. W. Morrison ◽  
A. Pringle ◽  
S. D. Frey
Keyword(s):  
Organic Matter ◽  
Nitrogen Uptake ◽  
Brown Rot ◽  
Terrestrial Ecosystems ◽  
Organic Matter Decomposition ◽  
Gene Frequencies ◽  
Ecological Processes ◽  
Linked Gene ◽  
Carbon Cycles ◽  
Brown Rot Fungi

AbstractFungi are mediators of the nitrogen and carbon cycles in terrestrial ecosystems. Examining how nitrogen uptake and organic matter decomposition potential differs in fungi can provide insight into the underlying mechanisms driving fungal ecological processes and ecosystem functioning. In this study, we assessed the frequency of genes encoding for specific enzymes that facilitate nitrogen uptake and organic matter decomposition in 879 fungal genomes with fungal taxa grouped into trait-based categories. Our linked gene-trait data approach revealed that gene frequencies vary across and within trait-based groups and that trait-based categories differ in trait space. We present two examples of how this linked gene-trait approach can be used to address ecological questions. First, we show that this type of approach can help us better understand, and potentially predict, how fungi will respond to environmental stress. Specifically, we found that trait-based categories with high nitrogen uptake gene frequency increased in relative abundance when exposed to high soil nitrogen enrichment. Second, by comparing frequencies of nitrogen uptake and organic matter decomposition genes, we found that most ectomycorrhizal fungi in our dataset have similar gene frequencies to brown rot fungi. This demonstrates that gene-trait data approaches can shed light on potential evolutionary trajectories of life history traits in fungi. We present a framework for exploring nitrogen uptake and organic matter decomposition gene frequencies in fungal trait-based groups and provide two concise examples on how to use our framework to address ecological questions from a mechanistic perspective.

Influence of carbon and nitrogen on cellulose and lignin degradation in forest soils

1995 ◽  
Vol 25 (8) ◽  
pp. 1231-1236 ◽  
Author(s):  
James A. Entry ◽  
Carole B. Backman
Keyword(s):  
Organic Matter ◽  
Soil Type ◽  
Fungal Biomass ◽  
Lignin Degradation ◽  
Cellulose Degradation ◽  
Bacterial Biomass ◽  
Terrestrial Ecosystems ◽  
Organic Matter Decomposition ◽  
Decomposition Rates ◽  
C And N

The concentration of lignin in plant tissue is a major factor controlling organic matter decomposition rates in terrestrial ecosystems. Microcosms were used to determine the influence of C and N additions on active bacterial and active fungal biomass, cellulose degradation, and lignin degradation at 4, 8, and 12 weeks in soils from the Tuskeege National Forest in southern Alabama. Active bacterial and active fungal biomass was determined by direct microscopy; cellulose and lignin degradation were measured radiometrically. The experimental design was a 33 latin square. Treatments were as follows: soil type, soil C (soils amended with the equivalent of 0, 400, or 800 kg C•ha−1 as cellulose), and soil N (soils amended with the equivalent of 0, 250, or 500 kg N•ha−1 as NH4NO3). Active bacterial biomass, active fungal biomass, and cellulose and lignin degradation did not differ with soil type. Active bacterial biomass was not affected by N or C additions. As C and N concentrations increased, active fungal biomass as well as cellulose and lignin degradation increased. The concentration of C and N (together) in the soil correlated with both cellulose and lignin degradation (r2 = 0.76, p < 0.001; r2 = 0.44, p < 0.001, respectively). Active fungal biomass correlated curvilinearly with both cellulose and lignin degradation (r2 = 0.38, p < 0.001; r2 = 0.33, p < 0.001, respectively). The lignin:N ratio is often used to predict organic matter decomposition rates in terrestrial ecosystems. These results lead us to conclude that a cellulose:lignin:N ratio may be a more accurate predictor of organic matter decomposition rates than C:N ratio or lignin:N ratios.

scholarly journals The biophysics, ecology, and biogeochemistry of functionally diverse, vertically and horizontally heterogeneous ecosystems: the Ecosystem Demography model, version 2.2 – Part 2: Model evaluation for tropical South America

2019 ◽  
Vol 12 (10) ◽  
pp. 4347-4374 ◽  
Author(s):  
Marcos Longo ◽  
Ryan G. Knox ◽  
Naomi M. Levine ◽  
Abigail L. S. Swann ◽  
David M. Medvigy ◽  
...  
Keyword(s):  
South America ◽  
Regional Distribution ◽  
Terrestrial Ecosystems ◽  
Environmental Drivers ◽  
Emergent Properties ◽  
Ecological Processes ◽  
Carbon Cycles ◽  
Model Version ◽  
Tropical South America

Abstract. The Ecosystem Demography model version 2.2 (ED-2.2) is a terrestrial biosphere model that simulates the biophysical, ecological, and biogeochemical dynamics of vertically and horizontally heterogeneous terrestrial ecosystems. In a companion paper (Longo et al., 2019a), we described how the model solves the energy, water, and carbon cycles, and verified the high degree of conservation of these properties in long-term simulations that include long-term (multi-decadal) vegetation dynamics. Here, we present a detailed assessment of the model's ability to represent multiple processes associated with the biophysical and biogeochemical cycles in Amazon forests. We use multiple measurements from eddy covariance towers, forest inventory plots, and regional remote-sensing products to assess the model's ability to represent biophysical, physiological, and ecological processes at multiple timescales, ranging from subdaily to century long. The ED-2.2 model accurately describes the vertical distribution of light, water fluxes, and the storage of water, energy, and carbon in the canopy air space, the regional distribution of biomass in tropical South America, and the variability of biomass as a function of environmental drivers. In addition, ED-2.2 qualitatively captures several emergent properties of the ecosystem found in observations, specifically observed relationships between aboveground biomass, mortality rates, and wood density; however, the slopes of these relationships were not accurately captured. We also identified several limitations, including the model's tendency to overestimate the magnitude and seasonality of heterotrophic respiration and to overestimate growth rates in a nutrient-poor tropical site. The evaluation presented here highlights the potential of incorporating structural and functional heterogeneity within biomes in Earth system models (ESMs) and to realistically represent their impacts on energy, water, and carbon cycles. We also identify several priorities for further model development.

scholarly journals Involutin Is an Fe3+Reductant Secreted by the Ectomycorrhizal Fungus Paxillus involutus during Fenton-Based Decomposition of Organic Matter

2015 ◽  
Vol 81 (24) ◽  
pp. 8427-8433 ◽  
Author(s):  
Firoz Shah ◽  
Daniel Schwenk ◽  
César Nicolás ◽  
Per Persson ◽  
Dirk Hoffmeister ◽  
...  
Keyword(s):  
Organic Matter ◽  
Ectomycorrhizal Fungi ◽  
Brown Rot ◽  
Ectomycorrhizal Fungus ◽  
Organic Matter Decomposition ◽  
Mineral Nutrient ◽  
Paxillus Involutus ◽  
Fenton Chemistry ◽  
Content Type

ABSTRACTEctomycorrhizal fungi play a key role in mobilizing nutrients embedded in recalcitrant organic matter complexes, thereby increasing nutrient accessibility to the host plant. Recent studies have shown that during the assimilation of nutrients, the ectomycorrhizal fungusPaxillus involutusdecomposes organic matter using an oxidative mechanism involving Fenton chemistry (Fe2++ H2O2+ H+→ Fe3++ ˙OH + H2O), similar to that of brown rot wood-decaying fungi. In such fungi, secreted metabolites are one of the components that drive one-electron reductions of Fe3+and O2, generating Fenton chemistry reagents. Here we investigated whether such a mechanism is also implemented byP. involutusduring organic matter decomposition. Activity-guided purification was performed to isolate the Fe3+-reducing principle secreted byP. involutusduring growth on a maize compost extract. The Fe3+-reducing activity correlated with the presence of one compound. Mass spectrometry and nuclear magnetic resonance (NMR) identified this compound as the diarylcyclopentenone involutin. A major part of the involutin produced byP. involutusduring organic matter decomposition was secreted into the medium, and the metabolite was not detected when the fungus was grown on a mineral nutrient medium. We also demonstrated that in the presence of H2O2, involutin has the capacity to drive anin vitroFenton reaction via Fe3+reduction. Our results show that the mechanism for the reduction of Fe3+and the generation of hydroxyl radicals via Fenton chemistry by ectomycorrhizal fungi during organic matter decomposition is similar to that employed by the evolutionarily related brown rot saprotrophs during wood decay.

Design and test of a generic cohort model of soil organic matter decomposition: the SOMKO model

2001 ◽  
Vol 10 (6) ◽  
pp. 639-660 ◽  
Author(s):  
Jacques Gignoux ◽  
Joanna House ◽  
David Hall ◽  
Dominique Masse ◽  
Hassan B. Nacro ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Organic Matter Decomposition ◽  
Cohort Model ◽  
Soil Organic Matter Decomposition

scholarly journals Lignocellulosic Waste Pretreatment Solely via Biocatalysis as a Partial Simultaneous Lignino-Holocellulolysis Process

Catalysts ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 668
Author(s):  
Justine Oma Angadam ◽  
Seteno Karabo Obed Ntwampe ◽  
Boredi Silas Chidi ◽  
Jun Wei Lim ◽  
Vincent Ifeanyi Okudoh
Keyword(s):  
Literature Review ◽  
Digestive Enzyme ◽  
Interdisciplinary Approach ◽  
Brown Rot ◽  
Lignocellulosic Waste ◽  
Brown Rot Fungi ◽  
Hydrolysis Products ◽  
Plant Exudates ◽  
Rapid Industrialization ◽  
Environmentally Friendly Approach

Human endeavors generate a significant quantity of bio-waste, even lignocellulosic waste, due to rapid industrialization and urbanization, and can cause pollution to aquatic ecosystems, and contribute to detrimental animal and human health because of the toxicity of consequent hydrolysis products. This paper contributes to a new understanding of the lignocellulosic waste bio-pretreatment process from a literature review, which can provide better biorefinery operational outcomes. The simultaneous partial biological lignin, cellulose and hemicellulose lysis, i.e., simultaneous semi-lignino-holocellulolysis, is aimed at suggesting that when ligninolysis ensues, holocellulolysis is simultaneously performed for milled lignocellulosic waste instead of having a sequential process of initial ligninolysis and subsequent holocellulolysis as is currently the norm. It is presumed that such a process can be solely performed by digestive enzyme cocktails from the monkey cups of species such as Nepenthes, white and brown rot fungi, and some plant exudates. From the literature review, it was evident that the pretreatment of milled lignocellulosic waste is largely incomplete, and ligninolysis including holocellulolysis ensues simultaneously when the waste is milled. It is further proposed that lignocellulosic waste pretreatment can be facilitated using an environmentally friendly approach solely using biological means. For such a process to be understood and applied on an industrial scale, an interdisciplinary approach using process engineering and microbiology techniques is required.

Unraveling the natural durability of wood: revealing the impact of decay-influencing characteristics other than fungicidal components

Holzforschung ◽  
2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Liselotte De Ligne ◽  
Jan Van den Bulcke ◽  
Jan M. Baetens ◽  
Bernard De Baets ◽  
Gang Wang ◽  
...  
Keyword(s):  
Wood Species ◽  
Prunus Avium ◽  
Brown Rot ◽  
Natural Durability ◽  
Anatomical Features ◽  
Brown Rot Fungi ◽  
Material Characteristics ◽  
The One ◽  
Block Test ◽  
The Impact

AbstractThe effect of fungicidal components in wood has been known for ages, yet there is no method to assess the impact of such components on the durability of a wood species, as compared to other material characteristics that influence decay. In this paper, the importance of fungicidal effects on the natural durability of 10 wood species is assessed in relation to other decay-influencing factors with a new test, the so-called ‘paste test’. By comparing results from this test with the ‘mini-block test’, on both heartwood and leached sapwood, insight is gained into the significance of fungicidal components on the one hand and other material characteristics on the other hand. The durability of species such as Prunus avium was attributed mainly to fungicidal components. For species such as Pterocarpus soyauxii, durability seemed to be an effect of both fungicidal components and moisture-regulating components, while the latter seemed to be of main importance in regulating the decay of Aucoumea klaineana and Entandrophragma cylindricum. Wood-anatomical features, such as the parenchyma content (in case of brown rot fungi) and the vessel-fiber ratio, possibly affect degradation as well. This work shows that fungicidal components are not always of major importance for the durability of a wood species. The authors hereby emphasize the importance of moisture-regulating components and wood anatomy on the durability of wood.

Soil drying and organic matter decomposition

1967 ◽  
Vol 26 (2) ◽  
pp. 269-276 ◽  
Author(s):  
W. O. Enwezor
Keyword(s):  
Organic Matter ◽  
Organic Matter Decomposition ◽  
Soil Drying
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