scholarly journals Genomic and Experimental Investigations of Auriscalpium and Strobilurus Fungi Reveal New Insights into Pinecone Decomposition

2021 ◽  
Vol 7 (8) ◽  
pp. 679
Author(s):  
Panmeng Wang ◽  
Jianping Xu ◽  
Gang Wu ◽  
Tiezhi Liu ◽  
Zhu L. Yang
Keyword(s):  
Organic Matter ◽  
Fungal Species ◽  
Ecosystem Dynamics ◽  
Living Systems ◽  
Experimental Investigations ◽  
Genome Sequences ◽  
Carbohydrate Active Enzymes ◽  
Efficient Utilization ◽  
Competition And Cooperation ◽  
Pinus Yunnanensis

Saprophytic fungi (SPF) play vital roles in ecosystem dynamics and decomposition. However, because of the complexity of living systems, our understanding of how SPF interact with each other to decompose organic matter is very limited. Here we studied their roles and interactions in the decomposition of highly specialized substrates between the two genera Auriscalpium and Strobilurus fungi-colonized fallen pinecones of the same plant sequentially. We obtained the genome sequences from seven fungal species with three pairs: A. orientale-S. luchuensis, A. vulgare-S. stephanocystis and A. microsporum-S. pachcystidiatus/S. orientalis on cones of Pinus yunnanensis, P. sylvestris and P. armandii, respectively, and the organic profiles of substrate during decomposition. Our analyses revealed evidence for both competition and cooperation between the two groups of fungi during decomposition, enabling efficient utilization of substrates with complementary profiles of carbohydrate active enzymes (CAZymes). The Auriscalpium fungi are highly effective at utilizing the primary organic carbon, such as lignin, and hemicellulose in freshly fallen cones, facilitated the invasion and colonization by Strobilurus fungi. The Strobilurus fungi have genes coding for abundant CAZymes to utilize the remaining organic compounds and for producing an arsenal of secondary metabolites such as strobilurins that can inhibit other fungi from colonizing the pinecones.

scholarly journals Genomic and Experimental Investigations of Auriscalpium and Strobilurus Fungi Reveal New Insights into Pinecone Decomposition

2021 ◽  
Author(s):  
Panmeng Wang ◽  
Jianping Xu ◽  
Gang Wu ◽  
Tiezhi Liu ◽  
Zhu L. Yang
Keyword(s):  
Ecosystem Dynamics ◽  
Experimental Investigations ◽  
Chemical Compositions ◽  
Carbohydrate Active Enzymes ◽  
Saprophytic Fungi ◽  
Effective Utilization ◽  
Field Surveys ◽  
Substrate Specificities ◽  
Competition And Cooperation ◽  
Pinus Yunnanensis

Saprophytic fungi play vital roles in nutrient cycling and ecosystem dynamics. However, our understanding of how saprophytic fungi interact with each other to decompose organic matter is very limited. Here, we conducted field surveys of pinecone-colonizing/decomposing mushrooms, investigated the chemical compositions of decomposing pinecones, and analyzed seven new genomes of three pairs of mushrooms in the genera Auriscalpium and Strobilurus with substrate specificities. Each pair of mushrooms successively colonizes the pinecones of a different pine species: A. orientale-S. luchuensis on Pinus yunnanensis, A. vulgare-S. stephanocystis on Pinus sylvestris, and A. microsporum-S. pachcystidiatus/S. orientalis on Pinus armandii. Our analyses revealed evidence for both competition and cooperation between Auriscalpium and Strobilurus fungi during pinecone decomposition. Their successive colonization of the two fungi groups with complementary profiles of carbohydrate-active enzymes enabled efficient decomposition and utilization of pinecones. The Auriscalpium fungi are highly effective at utilizing the recalcitrant primary organic carbons such as lignin and hemicellulose in freshly fallen pinecones. The decomposition by Auriscalpium fungi enabled the successive colonization by Strobilurus fungi which can produce an arsenal of secondary metabolites such as strobilurins to inhibit other fungi and have abundant carbohydrate-active enzymes for effective utilization of the remaining organic compounds in pinecones.

scholarly journals New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences

2021 ◽  
Vol 7 (3) ◽  
pp. 207
Author(s):  
Lene Lange ◽  
Kristian Barrett ◽  
Anne S. Meyer
Keyword(s):  
Fungal Species ◽  
Fungal Genome ◽  
Sequencing Data ◽  
Carbohydrate Active Enzymes ◽  
New Approach ◽  
Fungal Enzyme ◽  
Biomass Processing ◽  
Fungal Genomes ◽  
Robust Prediction ◽  
Fungal Kingdom

Fungal genome sequencing data represent an enormous pool of information for enzyme discovery. Here, we report a new approach to identify and quantitatively compare biomass-degrading capacity and diversity of fungal genomes via integrated function-family annotation of carbohydrate-active enzymes (CAZymes) encoded by the genomes. Based on analyses of 1932 fungal genomes the most potent hotspots of fungal biomass processing CAZymes are identified and ranked according to substrate degradation capacity. The analysis is achieved by a new bioinformatics approach, Conserved Unique Peptide Patterns (CUPP), providing for CAZyme-family annotation and robust prediction of molecular function followed by conversion of the CUPP output to lists of integrated “Function;Family” (e.g., EC 3.2.1.4;GH5) enzyme observations. An EC-function found in several protein families counts as different observations. Summing up such observations allows for ranking of all analyzed genome sequenced fungal species according to richness in CAZyme function diversity and degrading capacity. Identifying fungal CAZyme hotspots provides for identification of fungal species richest in cellulolytic, xylanolytic, pectinolytic, and lignin modifying enzymes. The fungal enzyme hotspots are found in fungi having very different lifestyle, ecology, physiology and substrate/host affinity. Surprisingly, most CAZyme hotspots are found in enzymatically understudied and unexploited species. In contrast, the most well-known fungal enzyme producers, from where many industrially exploited enzymes are derived, are ranking unexpectedly low. The results contribute to elucidating the evolution of fungal substrate-digestive CAZyme profiles, ecophysiology, and habitat adaptations, and expand the knowledge base for novel and improved biomass resource utilization.

scholarly journals Coastal hypoxia and sediment biogeochemistry

2009 ◽  
Vol 6 (7) ◽  
pp. 1273-1293 ◽  
Author(s):  
J. J. Middelburg ◽  
L. A. Levin
Keyword(s):  
Organic Matter ◽  
Bottom Water ◽  
Water Exchange ◽  
Transport Processes ◽  
Ecosystem Dynamics ◽  
Ecosystem Functions ◽  
Oxygen Levels ◽  
Concise Review ◽  
Water Oxygen ◽  
Sediment Biogeochemistry

Abstract. The intensity, duration and frequency of coastal hypoxia (oxygen concentration <63 μM) are increasing due to human alteration of coastal ecosystems and changes in oceanographic conditions due to global warming. Here we provide a concise review of the consequences of coastal hypoxia for sediment biogeochemistry. Changes in bottom-water oxygen levels have consequences for early diagenetic pathways (more anaerobic at expense of aerobic pathways), the efficiency of re-oxidation of reduced metabolites and the nature, direction and magnitude of sediment-water exchange fluxes. Hypoxia may also lead to more organic matter accumulation and burial and the organic matter eventually buried is also of higher quality, i.e. less degraded. Bottom-water oxygen levels also affect the organisms involved in organic matter processing with the contribution of metazoans decreasing as oxygen levels drop. Hypoxia has a significant effect on benthic animals with the consequences that ecosystem functions related to macrofauna such as bio-irrigation and bioturbation are significantly affected by hypoxia as well. Since many microbes and microbial-mediated biogeochemical processes depend on animal-induced transport processes (e.g. re-oxidation of particulate reduced sulphur and denitrification), there are indirect hypoxia effects on biogeochemistry via the benthos. Severe long-lasting hypoxia and anoxia may result in the accumulation of reduced compounds in sediments and elimination of macrobenthic communities with the consequences that biogeochemical properties during trajectories of decreasing and increasing oxygen may be different (hysteresis) with consequences for coastal ecosystem dynamics.

scholarly journals Genome Sequences and Metagenome-Assembled Genome Sequences of Microbial Communities Enriched on Phytoplankton Exometabolites

2020 ◽  
Vol 9 (30) ◽  
Author(s):  
He Fu ◽  
Christa B. Smith ◽  
Shalabh Sharma ◽  
Mary Ann Moran
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Marine Bacteria ◽  
Bacterial Communities ◽  
Draft Genome ◽  
Marine Phytoplankton ◽  
Genome Sequences ◽  
Phytoplankton Cells

ABSTRACT We report 11 bacterial draft genome sequences and 38 metagenome-assembled genomes (MAGs) from marine phytoplankton exometabolite enrichments. The genomes and MAGs represent marine bacteria adapted to the metabolite environment of phycospheres, organic matter-rich regions surrounding phytoplankton cells, and are useful for exploring functional and taxonomic attributes of phytoplankton-associated bacterial communities.

Numerical modelling of the benthic-pelagic coupling in coastal marine ecosystems at contrasting sites

2020 ◽  
Author(s):  
Carolina Amadio ◽  
Marco Zavatarelli ◽  
Tomas Lovato ◽  
Momme Butenschoen
Keyword(s):  
Organic Matter ◽  
Inorganic Compounds ◽  
Marine Ecosystem ◽  
Ecosystem Dynamics ◽  
Shortwave Radiation ◽  
Global Ocean ◽  
In Situ Data ◽  
Benthic Pelagic Coupling ◽  
Diffusive Fluxes ◽  
St Helena

&lt;p&gt;Continental shelves cover less than 5% of the global ocean surface, but play a crucial role in the marine global biogeochemical cycling. Coastal ecosystem dynamics are governed and constrained to a wide extent by the biogeochemical processes occurring in the benthic domain. Such processes define the so called benthic-pelagic coupling (hereafter BPC), i.e. two-way exchange of organic matter (particulate and dissolved) and inorganic compounds. The physically mediated exchanges structuring the BPC are constituted by the sinking and resuspension fluxes of particulate organic matter and by the diffusion of inorganic nutrients. Despite its importance and the continuous enhancement of model resolution, the BPC in global marine ecosystem models is generally roughly approximated. Moreover, observational data focusing on the BPC dynamics are fairly scanty in time and space, thereby hampering model parameterization and validation. The main objectives of this study are to develop and test a numerical model addressing BPC processes and to evaluate ecosystem dynamics in marine areas with different climatic and ecological characteristics. In particular, we here focused on two key interaction processes: the sinking velocity of particulate matter and the diffusive fluxes of inorganic dissolved nutrients at the benthic-pelagic interface. The benthic sub-model has been calibrated accounting for the complex pelagic food web and for the main ecological and physical characteristics of continental shelf areas in different sites: Gulf of Trieste (Italy), St. Helena Bay (South Africa), Svinoy Fyr (Norway). At each study area, the one-dimensional coupled BFM-NEMO modelling system was setup by prescribing temperature and salinity vertical profiles in NEMO, while the shortwave radiation acts as a primary forcing of BFM. Model results have been validated with available in situ data.&lt;/p&gt;&lt;p&gt;Sensitivity tests has been performed to investigate the role of the BPC exchanges in determining the pelagic biogeochemical cycles and to carry out a comparative analysis accounting for each site characteristics.&lt;/p&gt;

Soil Improvement of Pinus yunnanensis Forest at Different Age in Central Yunnan Plateau

2013 ◽  
Vol 864-867 ◽  
pp. 2565-2568
Author(s):  
Jin Xia Wu ◽  
Yan Xia Wang ◽  
Qi Bo Chen ◽  
Zhi Long Tong
Keyword(s):  
Organic Matter ◽  
Nitrogen Content ◽  
Total Nitrogen ◽  
Ph Value ◽  
Secondary Forest ◽  
Soil Bulk Density ◽  
Total Nitrogen Content ◽  
Planted Forest ◽  
Pinus Yunnanensis ◽  
Natural Water Content

Took the Pinus yunnanensis forest as the research object, and took planted forest for control, carried on a research in soil physicochemical properties of different forest ages of Pinus yunnanensis. The results show that: For secondary forests at different ages, (1) middle-aged forest has the smallest soil bulk density and largest soil natural water content. Compared with the same age planted forest, secondary forest has smaller soil bulk density and larger soil natural water content.(2) Middle-aged forest has the smallest soil pH value, and the tallest total nitrogen content and soil organic matter in the 0-20cm soil layer. Compared with the same age planted forest, secondary forest has smaller pH value. While its soil organic matter and total nitrogen content are more than planted forest significantly.(3)There is an extremely significant negative correlation among pH value, soil organic carbon and total nitrogen content; while an extremely significant positive correlation between soil organic carbon and total nitrogen content.

scholarly journals Coastal hypoxia and sediment biogeochemistry

2009 ◽  
Vol 6 (2) ◽  
pp. 3655-3706 ◽  
Author(s):  
J. J. Middelburg ◽  
L. A. Levin
Keyword(s):  
Organic Matter ◽  
Bottom Water ◽  
Water Exchange ◽  
Transport Processes ◽  
Ecosystem Dynamics ◽  
Ecosystem Functions ◽  
Oxygen Levels ◽  
Concise Review ◽  
Water Oxygen ◽  
Sediment Biogeochemistry

Abstract. The intensity, duration and frequency of coastal hypoxia (oxygen concentration <63 μM) are increasing due to human alteration of coastal ecosystems and changes in oceanographic conditions due to global warming. Here we provide a concise review of the consequences of coastal hypoxia for sediment biogeochemistry. Changes in bottom-water oxygen levels have consequences for early diagenetic pathways (more anaerobic at expense of aerobic pathways), the efficiency of re-oxidation of reduced metabolites and the nature, direction and magnitude of sediment-water exchange fluxes. Hypoxia may also lead to more organic matter accumulation and burial and the organic matter eventually buried is also of higher quality, i.e. less degraded. Bottom-water oxygen levels also affect the organisms involved in organic matter processing with the contribution of metazoans decreasing as oxygen levels drop. Hypoxia has a significant effect on benthic animals with the consequences that ecosystem functions related to macrofauna such as bio-irrigation and bioturbation are significantly affected by hypoxia as well. Since many microbes and microbial-mediated biogeochemical processes depend on animal induced transport processes (e.g. re-oxidation of particulate reduced sulphur and denitrification), there are indirect hypoxia effects on biogeochemistry via the benthos. Severe long-lasting hypoxia and anoxia may result in the accumulation of reduced compounds in sediments and elimination of macrobenthic communities with the consequences that biogeochemical properties during trajectories of decreasing and increasing oxygen may be different (hysteresis) with consequences for coastal ecosystem dynamics.

scholarly journals BFM17 v1.0: Reduced-Order Biogeochemical Flux Model for Upper Ocean Biophysical Simulations

2020 ◽  
Author(s):  
Katherine M. Smith ◽  
Skyler Kern ◽  
Peter E. Hamlington ◽  
Marco Zavatarelli ◽  
Nadia Pinardi ◽  
...  
Keyword(s):  
Organic Matter ◽  
Observational Data ◽  
Functional Group ◽  
Computational Cost ◽  
Open Ocean ◽  
Ecosystem Dynamics ◽  
Nutrient Ratios ◽  
Group Approach ◽  
Reduced Order ◽  
Flux Model

Abstract. We present a newly developed reduced-order biogeochemical flux model that is complex and flexible enough to capture open-ocean ecosystem dynamics, but reduced enough to incorporate into highly resolved numerical simulations with limited additional computational cost. The reduced-order model, which is derived from the full 56 state variable Biogeochemical Flux Model (BFM56; Vichi et al. (2007)), follows a biological and chemical functional group approach and allows for the development of critical non-Redfield nutrient ratios. Matter is expressed in units of carbon, nitrogen, and phosphate, following techniques used in more complex models. To reduce the overall computational cost and to focus on open-ocean conditions, the reduced model eliminates certain processes, such as benthic, silicate, and iron influences, and parameterizes others, such as the bacterial loop. The model explicitly tracks 17 state variables, divided into phytoplankton, zooplankton, dissolved organic matter, particulate organic matter, and nutrient groups. It is correspondingly called the Biogeochemical Flux Model 17 (BFM17). After providing a detailed description of BFM17, we couple it with the one-dimensional Princeton Ocean Model (POM) for validation using observational data from the Sargasso Sea. Results show good agreement with the observational data and with corresponding results from BFM56, including the ability to capture the subsurface chlorophyll maximum and bloom intensity. In comparison to previous reduced-order models of similar size, BFM17 provides improved correlations between model output and field data, indicating that significant improvements in the reproduction of in situ data can be achieved with a low number of variables, while maintaining the functional group approach.

scholarly journals The influence of detergents on the bioproduction of organic matter and the enzymatic activity of two fungal species

2002 ◽  
Vol 52 (4) ◽  
pp. 267-272 ◽  
Author(s):  
Stojanovic Jelica ◽  
Velickovic D. ◽  
Vucetic J.
Keyword(s):  
Organic Matter ◽  
Enzymatic Activity ◽  
Fungal Species

scholarly journals Complete Mitochondrial Genome Sequences of Nine Aspergillus flavus Strains

2021 ◽  
Vol 10 (45) ◽  
Author(s):  
Miya Hugaboom ◽  
Max L. Beck ◽  
Katherine H. Carrubba ◽  
D. Vignesh Chennupati ◽  
Aryan Gupta ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Genome ◽  
Aspergillus Flavus ◽  
Complete Mitochondrial Genome ◽  
Nuclear Genome ◽  
Fungal Species ◽  
Genome Sequences ◽  
Content Type

Nuclear genome sequences incompletely characterize the genomic content and thus the genetic diversity of fungal species. Here, we present the complete mitochondrial genome sequences of nine Aspergillus flavus strains, providing useful information for inter- and intraspecific analyses.

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