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Haidar R, Compant S, Robert C, Antonielli L, Yacoub A, Grélard A, Loquet A, Brader G, Guyoneaud R, Attard E, Rey P. Two Paenibacillus spp. strains promote grapevine wood degradation by the fungus Fomitiporia mediterranea: from degradation experiments to genome analyses. Sci Rep 2024; 14:15779. [PMID: 38982270 PMCID: PMC11233627 DOI: 10.1038/s41598-024-66620-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024] Open
Abstract
Ascomycetes, basidiomycetes and deuteromycetes can degrade wood, but less attention has been paid to basidiomycetes involved in Esca, a major Grapevine Trunk Disease. Using a wood sawdust microcosm system, we compared the wood degradation of three grapevine cultivars inoculated with Fomitiporia mediterranea M. Fisch, a basidiomycete responsible for white-rot development and involved in Esca disease. The grapevine cultivar Ugni blanc was more susceptible to wood degradation caused by F. mediterranea than the cultivars Cabernet Sauvignon and Merlot. Solid-state Nuclear Magnetic Resonance (NMR) spectroscopy showed that F. mediterranea preferentially degrades lignin and hemicellulose over cellulose (preferential, successive or sequential white-rot). In addition, co-inoculation of sawdust with two cellulolytic and xylanolytic bacterial strains of Paenibacillus (Nakamura) Ash (Paenibacillus sp. (S231-2) and P. amylolyticus (S293)), enhanced F. mediterranea ability to degrade Ugni blanc. The NMR data further showed that the increase in Ugni blanc sawdust degradation products was greater when bacteria and fungi were inoculated together. We also demonstrated that these two bacterial strains could degrade the wood components of Ugni blanc sawdust. Genome analysis of these bacterial strains revealed numerous genes predicted to be involved in cellulose, hemicellulose, and lignin degradation, as well as several other genes related to bacteria-fungi interactions and endophytism inside the plant. The occurrence of this type of bacteria-fungus interaction could explain, at least in part, why necrosis develops extensively in certain grapevine varieties such as Ugni blanc.
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Affiliation(s)
- Rana Haidar
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France.
- INRAE, UMR1065 Santé et Agroécologie du Vignoble (SAVE), ISVV, 33883, Villenave d'Ornon, France.
| | - Stéphane Compant
- Bioresources Unit, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430, Tulln, Austria
| | - Coralie Robert
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, 33607, Pessac, France
| | - Livio Antonielli
- Bioresources Unit, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430, Tulln, Austria
| | - Amira Yacoub
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France
- INRAE, UMR1065 Santé et Agroécologie du Vignoble (SAVE), ISVV, 33883, Villenave d'Ornon, France
| | - Axelle Grélard
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, 33607, Pessac, France
| | - Antoine Loquet
- Institut de Chimie et Biologie des Membranes et des Nanoobjets, IECB, CNRS, Université de Bordeaux, 33607, Pessac, France
| | - Günter Brader
- Bioresources Unit, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad Lorenz Straße 24, 3430, Tulln, Austria
| | - Rémy Guyoneaud
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France
| | - Eléonore Attard
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France
| | - Patrice Rey
- E2S UPPA, CNRS, IPREM UMR5254, Université de Pau et des Pays de l'Adour, Pau, France
- INRAE, UMR1065 Santé et Agroécologie du Vignoble (SAVE), ISVV, 33883, Villenave d'Ornon, France
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Truong NH, Le TTH, Nguyen HD, Nguyen HT, Dao TK, Tran TMN, Tran HL, Nguyen DT, Nguyen TQ, Phan THT, Do TH, Phan NH, Ngo TCN, Vu VV. Sequence and structure analyses of lytic polysaccharide monooxygenases mined from metagenomic DNA of humus samples around white-rot fungi in Cuc Phuong tropical forest, Vietnam. PeerJ 2024; 12:e17553. [PMID: 38938609 PMCID: PMC11210479 DOI: 10.7717/peerj.17553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 05/20/2024] [Indexed: 06/29/2024] Open
Abstract
Background White-rot fungi and bacteria communities are unique ecosystems with different types of symbiotic interactions occurring during wood decomposition, such as cooperation, mutualism, nutritional competition, and antagonism. The role of chitin-active lytic polysaccharide monooxygenases (LPMOs) in these symbiotic interactions is the subject of this study. Method In this study, bioinformatics tools were used to analyze the sequence and structure of putative LPMOs mined by hidden Markov model (HMM) profiles from the bacterial metagenomic DNA database of collected humus samples around white-rot fungi in Cuc Phuong primary forest, Vietnam. Two genes encoding putative LPMOs were expressed in E. coli and purified for enzyme activity assay. Result Thirty-one full-length proteins annotated as putative LPMOs according to HMM profiles were confirmed by amino acid sequence comparison. The comparison results showed that although the amino acid sequences of the proteins were very different, they shared nine conserved amino acids, including two histidine and one phenylalanine that characterize the H1-Hx-Yz motif of the active site of bacterial LPMOs. Structural analysis of these proteins revealed that they are multidomain proteins with different functions. Prediction of the catalytic domain 3-D structure of these putative LPMOs using Alphafold2 showed that their spatial structures were very similar in shape, although their protein sequences were very different. The results of testing the activity of proteins GL0247266 and GL0183513 show that they are chitin-active LPMOs. Prediction of the 3-D structures of these two LPMOs using Alphafold2 showed that GL0247266 had five functional domains, while GL0183513 had four functional domains, two of which that were similar to the GbpA_2 and GbpA_3 domains of protein GbpA of Vibrio cholerae bacteria. The GbpA_2 - GbpA_3 complex was also detected in 11 other proteins. Based on the structural characteristics of functional domains, it is possible to hypothesize the role of chitin-active GbpA-like LPMOs in the relationship between fungal and bacterial communities coexisting on decomposing trees in primary forests.
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Affiliation(s)
- Nam-Hai Truong
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Thi-Thu-Hong Le
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Hong-Duong Nguyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | | | - Trong-Khoa Dao
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Thi-Minh-Nguyet Tran
- The Key Laboratory of Enzyme and Protein Technology (KLEPT), VNU University of Science, Hanoi, Vietnam
| | - Huyen-Linh Tran
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Dinh-Trong Nguyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Thi-Quy Nguyen
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Thi-Hong-Thao Phan
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Thi-Huyen Do
- Institute of Biotechnology (IBT), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - Ngoc-Han Phan
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh, Vietnam
| | - Thi-Cam-Nhung Ngo
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh, Vietnam
| | - Van-Van Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh, Vietnam
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Carmichael MJ, Martinez M, Bräuer SL, Ardón M. Microbial Communities in Standing Dead Trees in Ghost Forests are Largely Aerobic, Saprophytic, and Methanotrophic. Curr Microbiol 2024; 81:229. [PMID: 38896154 PMCID: PMC11186919 DOI: 10.1007/s00284-024-03767-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Standing dead trees (snags) are recognized for their influence on methane (CH4) cycling in coastal wetlands, yet the biogeochemical processes that control the magnitude and direction of fluxes across the snag-atmosphere interface are not fully elucidated. Herein, we analyzed microbial communities and fluxes at one height from ten snags in a ghost forest wetland. Snag-atmosphere CH4 fluxes were highly variable (- 0.11-0.51 mg CH4 m-2 h-1). CH4 production was measured in three out of ten snags; whereas, CH4 consumption was measured in two out of ten snags. Potential CH4 production and oxidation in one core from each snag was assayed in vitro. A single core produced CH4 under anoxic and oxic conditions, at measured rates of 0.7 and 0.6 ng CH4 g-1 h-1, respectively. Four cores oxidized CH4 under oxic conditions, with an average rate of - 1.13 ± 0.31 ng CH4 g-1 h-1. Illumina sequencing of the V3/V4 region of the 16S rRNA gene sequence revealed diverse microbial communities and indicated oxidative decomposition of deadwood. Methanogens were present in 20% of the snags, with a mean relative abundance of < 0.0001%. Methanotrophs were identified in all snags, with a mean relative abundance of 2% and represented the sole CH4-cycling communities in 80% of the snags. These data indicate potential for microbial attenuation of CH4 emissions across the snag-atmosphere interface in ghost forests. A better understanding of the environmental drivers of snag-associated microbial communities is necessary to forecast the response of CH4 cycling in coastal ghost forest wetlands to a shifting coastal landscape.
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Affiliation(s)
- Mary Jane Carmichael
- Departments of Biology and Environmental Studies, Hollins University, Roanoke, VA, 24020, USA.
| | - Melinda Martinez
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, MD, 20708, USA
| | - Suzanna L Bräuer
- Department of Biology, Appalachian State University, Boone, NC, 28608, USA
| | - Marcelo Ardón
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
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Doménech-Pascual A, Carrasco-Barea L, Gich F, Boadella J, Freixinos Campillo Z, Gómez Cerezo R, Butturini A, Romaní AM. Differential response of bacteria and fungi to drought on the decomposition of Sarcocornia fruticosa woody stems in a saline stream. Environ Microbiol 2024; 26:e16661. [PMID: 38849711 DOI: 10.1111/1462-2920.16661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/10/2024] [Indexed: 06/09/2024]
Abstract
Inland saline ecosystems suffer multiple stresses (e.g., high radiation, salinity, water scarcity) that may compromise essential ecosystem functions such as organic matter decomposition. Here, we investigated the effects of drought on microbial colonization and decomposition of Sarcocornia fruticosa woody stems across different habitats in a saline watershed: on the dry floodplain, submerged in the stream channel and at the shoreline (first submerged, then emerged). Unexpectedly, weight loss was not enhanced in the submerged stems, while decomposition process differed between habitats. On the floodplain, it was dominated by fungi and high cellulolytic activity; in submerged conditions, a diverse community of bacteria and high ligninolytic activity dominated; and, on the shoreline, enzyme activities were like submerged conditions, but with a fungal community similar to the dry conditions. Results indicate distinct degradation paths being driven by different stress factors: strong water scarcity and photodegradation in dry conditions, and high salinity and reduced oxygen in wet conditions. This suggests that fungi are more resistant to drought, and bacteria to salinity. Overall, in saline watersheds, variations in multiple stress factors exert distinct environmental filters on bacteria and fungi and their role in the decomposition of plant material, affecting carbon cycling and microbial interactions.
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Affiliation(s)
| | - Lorena Carrasco-Barea
- Plant Physiology Unit, Department of Environmental Sciences, University of Girona, Girona, Spain
| | - Frederic Gich
- Molecular Microbial Ecology Group (gEMM-IEA), Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Judit Boadella
- GRECO, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | | | - Rosa Gómez Cerezo
- Department of Ecology and Hydrology, University of Murcia, Murcia, Spain
| | - Andrea Butturini
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Barcelona, Spain
| | - Anna M Romaní
- GRECO, Institute of Aquatic Ecology, University of Girona, Girona, Spain
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Yang S, Sun J, Wang C, Li S, Li Z, Luo W, Wei G, Chen W. Residue quality drives SOC sequestration by altering microbial taxonomic composition and ecophysiological function in desert ecosystem. ENVIRONMENTAL RESEARCH 2024; 250:118518. [PMID: 38382662 DOI: 10.1016/j.envres.2024.118518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Plant residues are important sources of soil organic carbon in terrestrial ecosystems. The degradation of plant residue by microbes can influence the soil carbon cycle and sequestration. However, little is known about the microbial composition and function, as well as the accumulation of soil organic carbon (SOC) in response to the inputs of different quality plant residues in the desert environment. The present study evaluated the effects of plant residue addition from Pinus sylvestris var. mongolica (Pi), Artemisia desertorum (Ar) and Amorpha fruticosa (Am) on desert soil microbial community composition and function in a field experiment in the Mu Us Desert. The results showed that the addition of the three plant residues with different C/N ratios induced significant variation in soil microbial communities. The Am treatment (low C/N ratio) improved microbial diversity compared with the Ar and Pi treatments (medium and high C/N ratios). The variations in the taxonomic and functional compositions of the dominant phyla Actinobacteria and Proteobacteria were higher than those of the other phyla among the different treatments. Moreover, the network links between Proteobacteria and other phyla and the CAZyme genes abundances from Proteobacteria increased with increasing residue C/N, whereas those decreased for Actinobacteria. The SOC content of the Am, Ar and Pi treatments increased by 45.73%, 66.54% and 107.99%, respectively, as compared to the original soil. The net SOC accumulation was positively correlated with Proteobacteria abundance and negatively correlated with Actinobacteria abundance. These findings showed that changing the initial quality of plant residue from low C/N to high C/N can result in shifts in taxonomic and functional composition from Actinobacteria to Proteobacteria, which favors SOC accumulation. This study elucidates the ecophysiological roles of Actinobacteria and Proteobacteria in the desert carbon cycle, expands our understanding of the potential microbial-mediated mechanisms by which plant residue inputs affect SOC sequestration in desert soils, and provides valuable guidance for species selection in desert vegetation reconstruction.
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Affiliation(s)
- Shanshan Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Jieyu Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Chang Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Shuyue Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Zubing Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Wen Luo
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Shaanxi, China.
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6
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Shi B, Wang X, Yang S, Chen H, Zhao Y, Shen J, Xie M, Huang B. Changes and driving factors of microbial community composition and functional groups during the decomposition of Pinus massoniana deadwood. Ecol Evol 2024; 14:e11210. [PMID: 38571805 PMCID: PMC10985386 DOI: 10.1002/ece3.11210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024] Open
Abstract
Clarifying changes in the microbial community in deadwood at different stages of decomposition is crucial for comprehending the role of deadwood in the biogeochemical processes and the sustainability of forest development. However, there have been no reports on the dynamics of microbial community during the decomposition of Pinus massoniana. We used the "space-for-time" substitution to analyze the characteristics of microbial community changes and the key influencing factors in the P. massoniana deadwood during different decomposition stages by 16S and ITS rRNA gene sequencing. The results suggest that the microbial community structure of the early decomposition (decay class I) was significantly different from the other decay classes, while the diversity and richness of the microbial community were the highest in the late decomposition (decay class V). The Linear Discriminant Analysis Effect Size analysis revealed that most bacterial and fungal taxa were significantly enriched in decay classes I and V deadwood. During the initial stages of decomposition, the relative abundance of the bacterial functional group responsible for carbohydrate metabolism was greater than the later stages. As decomposition progressed, the relative abundance of saprophytic fungi gradually decreased, and there was a shift in the comparative abundance of mixed saprophytic-symbiotic fungi from low to high before eventually decreasing. Total organic carbon, total nitrogen, carbon-to-nitrogen ratio, total potassium, total phenol, condensed tannin, lignin, and cellulose were significantly correlated with microbial community structure, with the carbon-to-nitrogen ratio having the greatest effect. Our results indicate that the physicochemical properties of deadwood, microbial community structural composition and functional group changes were related to the decay class, among which the carbon-to-nitrogen ratio may be an important factor affecting the composition and diversity of microbial communities.
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Affiliation(s)
- Bingyang Shi
- Forestry CollegeGuizhou UniversityGuiyangGuizhouChina
| | - Xiurong Wang
- Forestry CollegeGuizhou UniversityGuiyangGuizhouChina
| | - Shuoyuan Yang
- Forestry CollegeGuizhou UniversityGuiyangGuizhouChina
| | - Hongmei Chen
- Forestry CollegeGuizhou UniversityGuiyangGuizhouChina
| | - Yang Zhao
- Forestry CollegeGuizhou UniversityGuiyangGuizhouChina
| | - Junjie Shen
- Forestry CollegeGuizhou UniversityGuiyangGuizhouChina
| | - Meixuan Xie
- Forestry CollegeGuizhou UniversityGuiyangGuizhouChina
| | - Bufang Huang
- Forestry CollegeGuizhou UniversityGuiyangGuizhouChina
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Schrader L, Trautner J, Tebbe CC. Identifying environmental factors affecting the microbial community composition on outdoor structural timber. Appl Microbiol Biotechnol 2024; 108:254. [PMID: 38446240 PMCID: PMC10917859 DOI: 10.1007/s00253-024-13089-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/19/2024] [Accepted: 02/25/2024] [Indexed: 03/07/2024]
Abstract
Timber wood is a building material with many positive properties. However, its susceptibility to microbial degradation is a major challenge for outdoor usage. Although many wood-degrading fungal species are known, knowledge on their prevalence and diversity causing damage to exterior structural timber is still limited. Here, we sampled 46 decaying pieces of wood from outdoor constructions in the area of Hamburg, Germany; extracted their DNA; and investigated their microbial community composition by PCR amplicon sequencing of the fungal ITS2 region and partial bacterial 16S rRNA genes. In order to establish a link between the microbial community structure and environmental factors, we analysed the influence of wood species, its C and N contents, the effect of wood-soil contact, and the importance of its immediate environment (city, forest, meadow, park, respectively). We found that fungal and bacterial community composition colonising exterior timber was similar to fungi commonly found in forest deadwood. Of all basidiomycetous sequences retrieved, some, indicative for Perenniporia meridionalis, Dacrymyces capitatus, and Dacrymyces stillatus, were more frequently associated with severe wood damage. Whilst the most important environmental factor shaping fungal and bacterial community composition was the wood species, the immediate environment was important for fungal species whilst, for the occurrence of bacterial taxa, soil contact had a high impact. No influence was tangible for variation of the C or N content. In conclusion, our study demonstrates that wood colonising fungal and bacterial communities are equally responsive in their composition to wood species, but respond differently to environmental factors. KEY POINTS: • Perenniporia meridionalis and Dacrymyces are frequently associated with wood damage • Fungal community composition on timber is affected by its surrounding environment • Bacterial community composition on structural timber is affected by soil contact.
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Affiliation(s)
- Lauritz Schrader
- Thünen Institute of Wood Research, Leuschnerstraße 91, 21031, Hamburg, Germany
| | - Jochen Trautner
- Thünen Institute of Wood Research, Leuschnerstraße 91, 21031, Hamburg, Germany
| | - Christoph C Tebbe
- Thünen Institute of Biodiversity, Bundesallee 65, 38116, Brunswick, Germany.
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Liu G, Sun J, Xie P, Guo C, Zhu K, Tian K. Climate warming enhances microbial network complexity by increasing bacterial diversity and fungal interaction strength in litter decomposition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168444. [PMID: 37949122 DOI: 10.1016/j.scitotenv.2023.168444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Abstract
Microbial communities are important drivers of plant litter decomposition; however, the mechanisms of microbial co-occurrence networks and their network interaction dynamics in response to climate warming in wetlands remain unclear. Here, we conducted a 1.5-year warming experiment on the bacterial and fungal communities involved in litter decomposition in a typical wetland. The results showed that warming accelerated the decomposition of litter and had a greater effect on the diversity of bacteria than on that of fungi. Dominant bacterial communities, such as Bacteroidia, Alphaproteobacteria, and Actinobacteria, and dominant fungal communities, such as Leotiomycetes and Sordariomycetes, showed significant positive correlations with lignin and cellulose. Co-occurrence networks revealed that the average path length and betweenness centrality under warming conditions increased in the bacterial community but decreased in the fungal community. Both bacterial and fungal networks in the 2.0 °C warming treatment had the highest ratio of positive links (58.53 % and 98.14 %), indicating that moderate warming can promote the positive correlations and symbiotic relationships observed in the microbial community. This also suggests that small-world characteristics and weak-link advantages accelerate diffusion, and scale-free features facilitate propagation in microbial communities in response to climate warming. Logistic growth and Lotka-Volterra competition models revealed that climate warming enhances microbial network complexity mainly by increasing bacterial diversity and fungal interaction strength in litter decomposition. However, the symbiotic relationship decreased slightly under 4.0 °C warming, indicating that climate warming is a random attack rather than a targeted attack, and the microbial network has strong resistance to random attack, as shown by the highly robust dynamic performance of the microbial network in litter decomposition. Overall, the microbial community in litter decomposition responded to climate warming and shifted its network interactions, leading to further changes in emergent network topology and dynamics, thus accelerating litter decomposition in wetlands.
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Affiliation(s)
- Guodong Liu
- College of Geography and Tourism, Qufu Normal University, Rizhao 276826, China; Key Laboratory of Lake Nansi Wetland Ecological and Environmental Protection, Rizhao 276826, China.
| | - Jinfang Sun
- College of Geography and Tourism, Qufu Normal University, Rizhao 276826, China; Key Laboratory of Lake Nansi Wetland Ecological and Environmental Protection, Rizhao 276826, China.
| | - Peng Xie
- College of Geography and Tourism, Qufu Normal University, Rizhao 276826, China
| | - Chao Guo
- College of Geography and Tourism, Qufu Normal University, Rizhao 276826, China
| | - Kaixiang Zhu
- College of Geography and Tourism, Qufu Normal University, Rizhao 276826, China
| | - Kun Tian
- National Plateau Wetlands Research Center/Southwest Forestry University, Kunming 650224, China
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Wang C, Kuzyakov Y. Mechanisms and implications of bacterial-fungal competition for soil resources. THE ISME JOURNAL 2024; 18:wrae073. [PMID: 38691428 PMCID: PMC11104273 DOI: 10.1093/ismejo/wrae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/24/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Elucidating complex interactions between bacteria and fungi that determine microbial community structure, composition, and functions in soil, as well as regulate carbon (C) and nutrient fluxes, is crucial to understand biogeochemical cycles. Among the various interactions, competition for resources is the main factor determining the adaptation and niche differentiation between these two big microbial groups in soil. This is because C and energy limitations for microbial growth are a rule rather than an exception. Here, we review the C and energy demands of bacteria and fungi-the two major kingdoms in soil-the mechanisms of their competition for these and other resources, leading to niche differentiation, and the global change impacts on this competition. The normalized microbial utilization preference showed that bacteria are 1.4-5 times more efficient in the uptake of simple organic compounds as substrates, whereas fungi are 1.1-4.1 times more effective in utilizing complex compounds. Accordingly, bacteria strongly outcompete fungi for simple substrates, while fungi take advantage of complex compounds. Bacteria also compete with fungi for the products released during the degradation of complex substrates. Based on these specifics, we differentiated spatial, temporal, and chemical niches for these two groups in soil. The competition will increase under the main five global changes including elevated CO2, N deposition, soil acidification, global warming, and drought. Elevated CO2, N deposition, and warming increase bacterial dominance, whereas soil acidification and drought increase fungal competitiveness.
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Affiliation(s)
- Chaoqun Wang
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China
- Biogeochemistry of Agroecosystems, University of Göttingen, Göttingen 37077, Germany
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver V6T1Z4, Canada
| | - Yakov Kuzyakov
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China
- Department of Soil Science of Temperate Ecosystems, University of Göttingen, Göttingen 37077, Germany
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10
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Ren W, Penttilä R, Kasanen R, Asiegbu FO. Interkingdom and intrakingdom interactions in the microbiome of Heterobasidion fruiting body and associated decayed woody tissues. Appl Environ Microbiol 2023; 89:e0140623. [PMID: 38014962 PMCID: PMC10734517 DOI: 10.1128/aem.01406-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 10/06/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE We applied macro- (forest stand and forest management) and micro-scale (bacterial and fungal community) analyses for a better understanding of the Heterobasidion pathosystem and associated wood decay process. The core microbiome, as defined by hierarchy analysis and a consistent model, and environmental factors correlation with the community assembly were found to be novel.
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Affiliation(s)
- Wenzi Ren
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Reijo Penttilä
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Risto Kasanen
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Fred O. Asiegbu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
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11
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Mannaa M, Han G, Jeong T, Kang M, Lee D, Jung H, Seo YS. Taxonomy-guided selection of Paraburkholderia busanensis sp. nov.: a versatile biocontrol agent with mycophagy against Colletotrichum scovillei causing pepper anthracnose. Microbiol Spectr 2023; 11:e0242623. [PMID: 37861313 PMCID: PMC10715207 DOI: 10.1128/spectrum.02426-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/04/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE Traditional control methods for postharvest diseases rely on fungicides, which cause human health and environmental concerns. This study introduces a taxonomy-guided strategy for selecting biocontrol agents. By focusing on Paraburkholderia group, which harbors diverse plant-beneficial strains, the inadvertent selection of harmful strains was circumvented, thereby obviating the need for laborious in vitro screening assays. A highly promising candidate, strain P39, has been identified, exhibiting remarkable biocontrol activity against Colletotrichum scovillei. Through comprehensive genomic, physiological, and biochemical analyses, P39 was characterized as a novel species within the Paraburkholderia genus and designated Paraburkholderia busanensis. Moreover, these findings deepen our understanding of bacterial-fungal interactions, as they elucidate a potential pathway for the utilization of fungal chitin, thereby enhancing our understanding of bacterial mycophagy. P. busanensis is a promising source of antifungal volatiles and putative novel secondary metabolites.
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Affiliation(s)
- Mohamed Mannaa
- Department of Microbiology, Pusan National University, Busan, South Korea
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
- Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Gil Han
- Department of Microbiology, Pusan National University, Busan, South Korea
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Taeho Jeong
- Department of Microbiology, Pusan National University, Busan, South Korea
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Minhee Kang
- Department of Microbiology, Pusan National University, Busan, South Korea
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Duyoung Lee
- Department of Microbiology, Pusan National University, Busan, South Korea
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Hyejung Jung
- Department of Microbiology, Pusan National University, Busan, South Korea
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan, South Korea
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
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12
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Embacher J, Zeilinger S, Kirchmair M, Neuhauser S. Prokaryote communities associated with different types of tissue formed and substrates inhabited by Serpula lacrymans. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:642-655. [PMID: 37789578 PMCID: PMC10667670 DOI: 10.1111/1758-2229.13191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 07/07/2023] [Indexed: 10/05/2023]
Abstract
The basidiomycete Serpula lacrymans is responsible for major timber devastation in houses. Basidiomycetes are known to harbour a diverse but poorly understood microbial community of bacteria, archaea, yeasts and filamentous fungi. In this study, we used amplicon-sequencing to analyse the abundance and composition of prokaryotic communities associated with fruiting bodies of S. lacrymans and compared them to communities of surrounding material to access the 'background' community structure. Our findings indicate that bacterial genera cluster depended on sample type and that the main driver for microbial diversity is specimen, followed by sample origin. The most abundant bacterial phylum identified in the fruiting bodies was Pseudomonadota, followed by Actinomycetota and Bacteroidota. The prokaryote community of the mycelium was dominated by Actinomycetota, Halobacterota and Pseudomonadota. Actinomycetota was the most abundant phylum in both environment samples (infested timber and underground scree), followed by Bacillota in wood and Pseudomonadota in underground samples. Nocardioides, Pseudomonas, Pseudonochardia, Streptomyces and Rubrobacter spp. were among others found to comprise the core microbiome of S. lacrymans basidiocarps. This research contributes to the understanding of the holobiont S. lacrymans and gives hints to potential bacterial phyla important for its development and lifestyle.
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Affiliation(s)
- Julia Embacher
- Institute of Microbiology, Universität InnsbruckInnsbruckAustria
| | | | - Martin Kirchmair
- Institute of Microbiology, Universität InnsbruckInnsbruckAustria
| | - Sigrid Neuhauser
- Institute of Microbiology, Universität InnsbruckInnsbruckAustria
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13
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Roy F, Ibayev O, Arnstadt T, Bässler C, Borken W, Groß C, Hoppe B, Hossen S, Kahl T, Moll J, Noll M, Purahong W, Schreiber J, Weisser WW, Hofrichter M, Kellner H. Nitrogen addition increases mass loss of gymnosperm but not of angiosperm deadwood without changing microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165868. [PMID: 37516186 DOI: 10.1016/j.scitotenv.2023.165868] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
Enhanced nitrogen (N) deposition due to combustion of fossil fuels and agricultural fertilization is a global phenomenon which has severely altered carbon (C) and N cycling in temperate forest ecosystems in the northern hemisphere. Although deadwood holds a substantial amount of C in forest ecosystems and thus plays a crucial role in nutrient cycling, the effect of increased N deposition on microbial processes and communities, wood chemical traits and deadwood mass loss remains unclear. Here, we simulated high N deposition rates by adding reactive N in form of ammonium-nitrate (40 kg N ha-1 yr-1) to deadwood of 13 temperate tree species over nine years in a field experiment in Germany. Non-treated deadwood from the same logs served as control with background N deposition. Our results show that chronically elevated N levels alters deadwood mass loss alongside respiration, enzymatic activities and wood chemistry depending on tree clade and species. In gymnosperm deadwood, elevated N increased mass loss by +38 %, respiration by +37 % and increased laccase activity 12-fold alongside increases of white-rot fungal abundance +89 % (p = 0.03). Furthermore, we observed marginally significant (p = 0.06) shifts of bacterial communities in gymnosperm deadwood. In angiosperm deadwood, we did not detect consistent effects on mass loss, physico-chemical properties, extracellular enzymatic activity or changes in microbial communities except for changes in abundance of 10 fungal OTUs in seven tree species and 28 bacterial OTUs in 10 tree species. We conclude that N deposition alters decomposition processes exclusively in N limited gymnosperm deadwood in the long term by enhancing fungal activity as expressed by increases in respiration rate and extracellular enzyme activity with minor shifts in decomposing microbial communities. By contrast, deadwood of angiosperm tree species had higher N concentrations and mass loss as well as community composition did not respond to N addition.
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Affiliation(s)
- Friederike Roy
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Markt 23, D-02763 Zittau, Germany
| | - Orkhan Ibayev
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Markt 23, D-02763 Zittau, Germany
| | - Tobias Arnstadt
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Markt 23, D-02763 Zittau, Germany
| | - Claus Bässler
- Institute for Ecology, Evolution and Diversity, Department of Conservation Biology, Goethe-Universität Frankfurt, Max-von-Laue-Str. 13, D-60438 Frankfurt am Main, Germany; National Park Bavarian Forest, Freyunger Str. 2, D-94481 Grafenau, Germany
| | - Werner Borken
- Institute for Soil Ecology, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, D-95448 Bayreuth, Germany
| | - Christina Groß
- Institute for Soil Ecology, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, D-95448 Bayreuth, Germany
| | - Björn Hoppe
- Institute for National and International Plant Health, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Messeweg 11/12, D-38104 Braunschweig, Germany
| | - Shakhawat Hossen
- Institute for Bioanalysis, University of Applied Sciences Coburg, Friedrich-Streib-Straße 2, D-96450 Coburg, Germany
| | - Tiemo Kahl
- UNESCO-Biosphärenreservat Thüringer Wald, Schmiedefeld a. Rstg, Brunnenstraße 1, D-98528 Suhl, Germany
| | - Julia Moll
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Th.-Lieser- Str. 4, D-06120 Halle (Saale), Germany
| | - Matthias Noll
- Institute for Bioanalysis, University of Applied Sciences Coburg, Friedrich-Streib-Straße 2, D-96450 Coburg, Germany
| | - Witoon Purahong
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Th.-Lieser- Str. 4, D-06120 Halle (Saale), Germany
| | - Jasper Schreiber
- Institute for Ecology, Evolution and Diversity, Department of Conservation Biology, Goethe-Universität Frankfurt, Max-von-Laue-Str. 13, D-60438 Frankfurt am Main, Germany
| | - Wolfgang W Weisser
- Terrestrial Ecology Research Group, Technical University of Munich, D-85354 Freising, Germany
| | - Martin Hofrichter
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Markt 23, D-02763 Zittau, Germany
| | - Harald Kellner
- Department of Bio- and Environmental Sciences, International Institute Zittau, Technische Universität Dresden, Markt 23, D-02763 Zittau, Germany.
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14
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Pioli S, Clagnan E, Chowdhury AA, Bani A, Borruso L, Ventura M, Tonon G, Brusetti L. Structural and functional microbial diversity in deadwood respond to decomposition dynamics. Environ Microbiol 2023; 25:2351-2367. [PMID: 37403552 DOI: 10.1111/1462-2920.16459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023]
Abstract
We investigated the changes in microbial community diversities and functions in natural downed wood at different decay stages in a natural oak forest in the Italian Alps, through metagenomics analysis and in vitro analysis. Alfa diversity of bacterial communities was affected by the decay stage and log characteristics, while beta diversity was mainly driven by log diameter. Fungal and archaeal beta diversities were affected by the size of the sampled wood (log diameter), although, fungi were prominently driven by wood decay stage. The analysis of genes targeting cell wall degradation revealed higher abundances of cellulose and pectin-degrading enzymes in bacteria, while in fungi the enzymes targeting cellulose and hemicellulose were more abundant. The decay class affected the abundance of single enzymes, revealing a shift in complex hydrocarbons degradation pathways along the decay process. Moreover, we found that the genes related to Coenzyme M biosynthesis to be the most abundant especially at early stages of wood decomposition while the overall methanogenesis did not seem to be influenced by the decay stage. Intra- and inter-kingdom interactions between bacteria and fungi revealed complex pattern of community structure in response to decay stage possibly reflecting both direct and indirect interactions.
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Affiliation(s)
- Silvia Pioli
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
- Institute of Research on Terrestrial Ecosystems (IRET), National Research Council (CNR), Monterotondo Scalo (RM), Italy
| | - Elisa Clagnan
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Atif Aziz Chowdhury
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Alessia Bani
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Maurizio Ventura
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Giustino Tonon
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
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15
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Mori T, Terashima T, Matsumura M, Tsuruta K, Dohra H, Kawagishi H, Hirai H. Construction of white-rot fungal-bacterial consortia with improved ligninolytic properties and stable bacterial community structure. ISME COMMUNICATIONS 2023; 3:61. [PMID: 37349534 PMCID: PMC10287725 DOI: 10.1038/s43705-023-00270-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023]
Abstract
It is believed that wood-rot fungi change their wood decay activities due to influences from co-existing bacterial communities; however, it is difficult to elucidate experimentally the interaction mechanisms in fungal-bacterial consortia because the bacterial community structure is quite unstable and readily changes. Indeed, the wood decay properties of fungal-bacterial consortia consisting of a white-rot fungus Phanerochaete sordida YK-624 and a natural bacterial community changed dramatically during several sub-cultivations on wood. Therefore, development of a sub-cultivation method that imparts stability to the bacterial community structure and fungal phenotype was attempted. The adopted method using agar medium enabled maintenance of fungal phenotypes relating to wood decay and the bacterial community even through dozens of repetitive sub-cultures. Some bacterial metabolic pathways identified based on gene predictions were screened as candidates involved in P. sordida-bacterial interactions. In particular, pathways related to prenyl naphthoquinone biosynthesis appeared to be involved in an interaction that promotes higher lignin degradation selectivity by the consortia, as naphthoquinone derivatives induced phenol-oxidizing activity. Based on these results, it is expected that detailed analyses of the relationship between the wood-degrading properties of white-rot fungal-bacterial consortia and bacterial community structures will be feasible using the sub-cultivation method developed in this study.
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Affiliation(s)
- Toshio Mori
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga‑ku, Shizuoka, 422‑8529, Japan.
| | - Taiki Terashima
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Masaki Matsumura
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Koudai Tsuruta
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Hideo Dohra
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga‑ku, Shizuoka, 422‑8529, Japan
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga‑ku, Shizuoka, 422‑8529, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Hirokazu Kawagishi
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga‑ku, Shizuoka, 422‑8529, Japan
| | - Hirofumi Hirai
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga‑ku, Shizuoka, 422‑8529, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
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16
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Zhang L, Li J, Wang Z, Zhang D, Liu H, Wang J, Wu F, Wang X, Zhou X. Litter mixing promoted decomposition and altered microbial community in common bean root litter. BMC Microbiol 2023; 23:148. [PMID: 37217839 DOI: 10.1186/s12866-023-02871-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Decomposition of plant litter is a key driver of carbon and nutrient cycling in terrestrial ecosystems. Mixing litters of different plant species may alter the decomposition rate, but its effect on the microbial decomposer community in plant litter is not fully understood. Here, we tested the effects of mixing with maize (Zea mays L.) and soybean [Glycine max (Linn.) Merr.] stalk litters on the decomposition and microbial decomposer communities of common bean (Phaseolus vulgaris L.) root litter at the early decomposition stage in a litterbag experiment. RESULTS Mixing with maize stalk litter, soybean stalk litter, and both of these litters increased the decomposition rate of common bean root litter at 56 day but not 14 day after incubation. Litter mixing also increased the decomposition rate of the whole liter mixture at 56 day after incubation. Amplicon sequencing found that litter mixing altered the composition of bacterial (at 56 day after incubation) and fungal communities (at both 14 and 56 day after incubation) in common bean root litter. Litter mixing increased the abundance and alpha diversity of fungal communities in common bean root litter at 56 day after incubation. Particularly, litter mixing stimulated certain microbial taxa, such as Fusarium, Aspergillus and Stachybotrys spp. In addition, a pot experiment with adding litters in the soil showed that litter mixing promoted growth of common bean seedlings and increased soil nitrogen and phosphorus contents. CONCLUSIONS This study showed that litter mixing can promote the decomposition rate and cause shifts in microbial decomposer communities, which may positively affect crop growth.
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Affiliation(s)
- Linlin Zhang
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Jiawei Li
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Zhilin Wang
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Dinghong Zhang
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Hui Liu
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Jia Wang
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Fengzhi Wu
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Xue Wang
- Northeast Agricultural University Library, Northeast Agricultural University, Harbin, China.
| | - Xingang Zhou
- Department of Horticulture, Northeast Agricultural University, Harbin, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China.
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17
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Wang C, Smith GR, Gao C, Peay KG. Dispersal changes soil bacterial interactions with fungal wood decomposition. ISME COMMUNICATIONS 2023; 3:44. [PMID: 37137953 PMCID: PMC10156657 DOI: 10.1038/s43705-023-00253-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 05/05/2023]
Abstract
Although microbes are the major agent of wood decomposition - a key component of the carbon cycle - the degree to which microbial community dynamics affect this process is unclear. One key knowledge gap is the extent to which stochastic variation in community assembly, e.g. due to historical contingency, can substantively affect decomposition rates. To close this knowledge gap, we manipulated the pool of microbes dispersing into laboratory microcosms using rainwater sampled across a transition zone between two vegetation types with distinct microbial communities. Because the laboratory microcosms were initially identical this allowed us to isolate the effect of changing microbial dispersal directly on community structure, biogeochemical cycles and wood decomposition. Dispersal significantly affected soil fungal and bacterial community composition and diversity, resulting in distinct patterns of soil nitrogen reduction and wood mass loss. Correlation analysis showed that the relationship among soil fungal and bacterial community, soil nitrogen reduction and wood mass loss were tightly connected. These results give empirical support to the notion that dispersal can structure the soil microbial community and through it ecosystem functions. Future biogeochemical models including the links between soil microbial community and wood decomposition may improve their precision in predicting wood decomposition.
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Affiliation(s)
- Cong Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Gabriel Reuben Smith
- Global Ecosystem Ecology, Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, Zürich, 8092, Switzerland
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Cheng Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA.
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18
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Probst M, Telagathoti A, Siewert B, Khomenko I, Betta E, Biasioli F, Peintner U. Co-cultivation of Mortierellaceae with Pseudomonas helmanticensis affects both their growth and volatilome. Sci Rep 2023; 13:2213. [PMID: 36750680 PMCID: PMC9905594 DOI: 10.1038/s41598-023-29134-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Volatile organic compounds (VOCs) might mediate microbial interactions, especially in spatially structured environments, such as soil. However, the variety and specificity of VOC production are poorly understood. Here, we studied 25 Mortierellaceae strains belonging to the genera Linnemannia and Entomortierella in both pure and co-culture with Pseudomonas helmanticensis under laboratory conditions. We analysed both the fungal growth depending on co-cultivation and the cultures' volatilomes applying proton-transfer-reaction time-of-flight and gas chromatography-mass spectrometry (PTR-ToF-MS and GC-MS). In a strain-specific manner, we found the fungi's radial growth rate and colony morphology affected by the presence of P. helmanticensis. The fungus seemed to generally reduce the bacterial growth. The volatilomes of the fungal and bacterial pure and co-cultures were diverse. While the fungi frequently consumed VOCs, P. helmanticensis produced a higher diversity and amount of VOCs than any fungal strain. Our results support that both the pure and co-culture volatilomes are taxonomically conserved. Taken together, our data supports the relevance of VOCs in Mortierellaceae-P. helmanticensis interaction. We also discuss individual VOCs that appear relevant in the interaction.
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Affiliation(s)
- Maraike Probst
- Department of Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Anusha Telagathoti
- Department of Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Bianka Siewert
- Institute of Pharmacy, Center for Chemistry and Biomedicine, Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, Innrain 80 - 82/IV, 6020, Innsbruck, Austria
| | - Iuliia Khomenko
- Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38010, San Michele all'Adige, Italy
| | - Emanuela Betta
- Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38010, San Michele all'Adige, Italy
| | - Franco Biasioli
- Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38010, San Michele all'Adige, Italy
| | - Ursula Peintner
- Department of Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
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19
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Valette N, Legout A, Goodell B, Alfredsen G, Auer L, Gelhaye E, Derrien D. Impact of Norway spruce pre-degradation stages induced by Gloeophyllum trabeum on fungal and bacterial communities. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Kalntremtziou M, Papaioannou IA, Vangalis V, Polemis E, Pappas KM, Zervakis GI, Typas MA. Evaluation of the lignocellulose degradation potential of Mediterranean forests soil microbial communities through diversity and targeted functional metagenomics. Front Microbiol 2023; 14:1121993. [PMID: 36922966 PMCID: PMC10008878 DOI: 10.3389/fmicb.2023.1121993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/31/2023] [Indexed: 02/28/2023] Open
Abstract
The enzymatic arsenal of several soil microorganisms renders them particularly suitable for the degradation of lignocellulose, a process of distinct ecological significance with promising biotechnological implications. In this study, we investigated the spatiotemporal diversity and distribution of bacteria and fungi with 16S and Internally Trascribed Spacer (ITS) ribosomal RNA next-generation-sequencing (NGS), focusing on forest mainland Abies cephalonica and insular Quercus ilex habitats of Greece. We analyzed samples during winter and summer periods, from different soil depths, and we applied optimized and combined targeted meta-omics approaches aiming at the peroxidase-catalase family enzymes to gain insights into the lignocellulose degradation process at the soil microbial community level. The microbial communities recorded showed distinct patterns of response to season, soil depth and vegetation type. Overall, in both forests Proteobacteria, Actinobacteria, Acidobacteria were the most abundant bacteria phyla, while the other phyla and the super-kingdom of Archaea were detected in very low numbers. Members of the orders Agaricales, Russulales, Sebacinales, Gomphales, Geastrales, Hysterangiales, Thelephorales, and Trechisporales (Basidiomycota), and Pezizales, Sordariales, Eurotiales, Pleosporales, Helotiales, and Diaporthales (Ascomycota) were the most abundant for Fungi. By using optimized "universal" PCR primers that targeted the peroxidase-catalase enzyme family, we identified several known and novel sequences from various Basidiomycota, even from taxa appearing at low abundance. The majority of the sequences recovered were manganese peroxidases from several genera of Agaricales, Hysterangiales, Gomphales, Geastrales, Russulales, Hymenochaetales, and Trechisporales, while lignin -and versatile-peroxidases were limited to two to eight species, respectively. Comparisons of the obtained sequences with publicly available data allowed a detailed structural analysis of polymorphisms and functionally relevant amino-acid residues at phylogenetic level. The targeted metagenomics applied here revealed an important role in lignocellulose degradation of hitherto understudied orders of Basidiomycota, such as the Hysterangiales and Gomphales, while it also suggested the auxiliary activity of particular members of Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes. The application of NGS-based metagenomics approaches allows a better understanding of the complex process of lignocellulolysis at the microbial community level as well as the identification of candidate taxa and genes for targeted functional investigations and genetic modifications.
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Affiliation(s)
- Maria Kalntremtziou
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis A Papaioannou
- Zentrum für Molekulare Biologie der Universität Heidelberg, ZMBH, University of Heidelberg, Heidelberg, Germany
| | - Vasileios Vangalis
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Elias Polemis
- Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece
| | - Katherine M Pappas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios I Zervakis
- Laboratory of General and Agricultural Microbiology, Agricultural University of Athens, Athens, Greece
| | - Milton A Typas
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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21
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The Necrobiome of Deadwood: The Life after Death. ECOLOGIES 2022. [DOI: 10.3390/ecologies4010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In recent decades, sustainable forest management has been increasingly recognized, promoting the diffusion of silvicultural practices aimed at considering all components of the forest system. Deadwood is an important component of the forest ecosystem. It plays a fundamental role in providing nutrients and habitats for a wide variety of saprotrophic and heterotrophic organisms and significantly contributes to soil formation and carbon storage. Deadwood is inhabited by a plethora of organisms from various kingdoms that have evolved the ability to utilize decaying organic matter. This community, consisting of both eukaryotic and prokaryotic species, can be defined as “necrobiome”. Through the interactions between its various members, the necrobiome influences the decay rates of deadwood and plays a crucial role in the balance between organic matter decomposition, carbon sequestration, and gas exchanges (e.g., CO2) with the atmosphere. The present work aims to provide an overview of the biodiversity and role of the microbial communities that inhabit deadwood and their possible involvement in greenhouse gas (CO2, N2O, and CH4) emissions.
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22
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First Description of Akanthomyces uredinophilus comb. nov. from Hemipteran Insects in America. DIVERSITY 2022. [DOI: 10.3390/d14121118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Filamentous fungi of the genera Lecanicillium and Akanthomyces (Ascomycota: Hypocreales: Cordycipitaceae) have been isolated from a variety of insect orders and are of particular interest as biological control agents for phloem-sucking plant pests. Three aphid- and whitefly-pathogenic fungal strains that had been isolated from naturally infected Trialeurodes vaporariorum and Myzus persicae in Argentina were assigned to the species Lecanicillium uredinophilum by combined analyses of morphology and ITS, LSU, EF1A, RPB1 and RPB2-based molecular taxonomy, giving rise to both the first description of this fungus from hemipteran insects and its first report from outside South-East Asia, especially from the American continent. A combination of phylogenetic reconstruction and analysis of pair-wise sequence similarities demonstrated that—reflecting recent changes in the systematics of Cordycipitaceae—the entire species L. uredinophilum should be transferred to the genus Akanthomyces. Consequently, the introduction of a new taxon, Akanthomaces uredinophilus comb. nov., was proposed. Moreover, extensive data mining for cryptic A. uredinophilus sequences revealed that (i) the fungus is geographically widely distributed, including earlier unrecognized isolations from further American countries such as the USA, Mexico, and Colombia, and (ii) entomopathogenic and mycoparasitic lifestyles are predominant in this species.
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23
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Fungal community succession on decomposing leaf litter across five phylogenetically related tree species in a subtropical forest. FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00508-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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24
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Biodeterioration Assessment of a Unique Old Pharaonic Kingdom Wooden Statue Using Advanced Diagnostic Techniques. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12147020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A recently discovered Egyptian wooden statue of King Djedefre was studied together with some surrounding burial soil samples for assessing the statue biodeterioration. The wooden morphological characterisation identified the hardwood Acacia nilotica as the wood type. X-ray diffraction, micro-FT-IR spectroscopy, and scanning electron microscopy with an X-ray spectrometer were used to evaluate the wood deterioration degree and the soil contribution in wood biodeterioration. Microbiological analyses (fluorescent in situ hybridisation and polymerase chain reaction) were also performed to detect the microbial attack on the statue. The prolonged interaction of the statue with the burial environment caused a strong wood decay due to biotic (fungi and bacteria) and abiotic factors (e.g., humidity fluctuations of the burial environment), which caused the severe cracking and collapsing of the wood structures. The analyses of the burial soil mineral composition were relevant for obtaining an overall picture of the statue deterioration. The results are useful for planning the right conservation procedures for this very particular and important wooden statue. Furthermore, analysis of the woody cell wall will help in the selection of appropriate consolidation and recovery treatments. Because the statue is a unique single piece of wood, and the morphological observations indicated that it is a bald woman in a sitting position, this statue will provide new and interesting knowledge of Egyptian culture.
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25
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Velasco-Rodríguez Ó, Fil M, Heggeset TMB, Degnes KF, Becerro-Recio D, Kolsaková K, Haugen T, Jønsson M, Toral-Martínez M, García-Estrada C, Sola-Landa A, Josefsen KD, Sletta H, Barreiro C. Characterization of Microbial Diversity in Decayed Wood from a Spanish Forest: An Environmental Source of Industrially Relevant Microorganisms. Microorganisms 2022; 10:1249. [PMID: 35744767 PMCID: PMC9227542 DOI: 10.3390/microorganisms10061249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/20/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022] Open
Abstract
Rotting wood is inhabited by a large diversity of bacteria, fungi, and insects with complex environmental relationships. The aim of this work was to study the composition of the microbiota (bacteria and fungi) in decaying wood from a northwest Spanish forest as a source of industrially relevant microorganisms. The analyzed forest is situated in a well-defined biogeographic area combining Mediterranean and temperate macrobioclimates. Bacterial diversity, determined by metagenome analyses, was higher than fungal heterogeneity. However, a total of 194 different cultivable bacterial isolates (mainly Bacillaceae, Streptomycetaceae, Paenibacillaceae, and Microbacteriaceae) were obtained, in contrast to 343 fungal strains (mainly Aspergillaceae, Hypocreaceae, and Coniochaetaceae). Isolates traditionally known as secondary metabolite producers, such as Actinobacteria and members of the Penicillium genus, were screened for their antimicrobial activity by the detection of antibiotic biosynthetic clusters and competitive bioassays against fungi involved in wood decay. In addition, the ability of Penicillium isolates to degrade cellulose and release ferulic acid from wood was also examined. These results present decaying wood as an ecologically rich niche and a promising source of biotechnologically interesting microorganisms.
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Affiliation(s)
- Óscar Velasco-Rodríguez
- INBIOTEC (Instituto de Biotecnología de León), Avda Real 1, 24006 León, Spain; (Ó.V.-R.); (M.F.); (D.B.-R.); (K.K.); (M.T.-M.); (C.G.-E.); (A.S.-L.)
| | - Mariana Fil
- INBIOTEC (Instituto de Biotecnología de León), Avda Real 1, 24006 León, Spain; (Ó.V.-R.); (M.F.); (D.B.-R.); (K.K.); (M.T.-M.); (C.G.-E.); (A.S.-L.)
| | - Tonje M. B. Heggeset
- SINTEF Industry, Department of Biotechnology and Nanomedicine, P.O. Box 4760 Torgarden, N-7465 Trondheim, Norway; (T.M.B.H.); (K.F.D.); (T.H.); (M.J.); (K.D.J.); (H.S.)
| | - Kristin F. Degnes
- SINTEF Industry, Department of Biotechnology and Nanomedicine, P.O. Box 4760 Torgarden, N-7465 Trondheim, Norway; (T.M.B.H.); (K.F.D.); (T.H.); (M.J.); (K.D.J.); (H.S.)
| | - David Becerro-Recio
- INBIOTEC (Instituto de Biotecnología de León), Avda Real 1, 24006 León, Spain; (Ó.V.-R.); (M.F.); (D.B.-R.); (K.K.); (M.T.-M.); (C.G.-E.); (A.S.-L.)
| | - Katarina Kolsaková
- INBIOTEC (Instituto de Biotecnología de León), Avda Real 1, 24006 León, Spain; (Ó.V.-R.); (M.F.); (D.B.-R.); (K.K.); (M.T.-M.); (C.G.-E.); (A.S.-L.)
| | - Tone Haugen
- SINTEF Industry, Department of Biotechnology and Nanomedicine, P.O. Box 4760 Torgarden, N-7465 Trondheim, Norway; (T.M.B.H.); (K.F.D.); (T.H.); (M.J.); (K.D.J.); (H.S.)
| | - Malene Jønsson
- SINTEF Industry, Department of Biotechnology and Nanomedicine, P.O. Box 4760 Torgarden, N-7465 Trondheim, Norway; (T.M.B.H.); (K.F.D.); (T.H.); (M.J.); (K.D.J.); (H.S.)
| | - Macarena Toral-Martínez
- INBIOTEC (Instituto de Biotecnología de León), Avda Real 1, 24006 León, Spain; (Ó.V.-R.); (M.F.); (D.B.-R.); (K.K.); (M.T.-M.); (C.G.-E.); (A.S.-L.)
| | - Carlos García-Estrada
- INBIOTEC (Instituto de Biotecnología de León), Avda Real 1, 24006 León, Spain; (Ó.V.-R.); (M.F.); (D.B.-R.); (K.K.); (M.T.-M.); (C.G.-E.); (A.S.-L.)
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana, s/n, 24007 León, Spain
| | - Alberto Sola-Landa
- INBIOTEC (Instituto de Biotecnología de León), Avda Real 1, 24006 León, Spain; (Ó.V.-R.); (M.F.); (D.B.-R.); (K.K.); (M.T.-M.); (C.G.-E.); (A.S.-L.)
| | - Kjell D. Josefsen
- SINTEF Industry, Department of Biotechnology and Nanomedicine, P.O. Box 4760 Torgarden, N-7465 Trondheim, Norway; (T.M.B.H.); (K.F.D.); (T.H.); (M.J.); (K.D.J.); (H.S.)
| | - Håvard Sletta
- SINTEF Industry, Department of Biotechnology and Nanomedicine, P.O. Box 4760 Torgarden, N-7465 Trondheim, Norway; (T.M.B.H.); (K.F.D.); (T.H.); (M.J.); (K.D.J.); (H.S.)
| | - Carlos Barreiro
- INBIOTEC (Instituto de Biotecnología de León), Avda Real 1, 24006 León, Spain; (Ó.V.-R.); (M.F.); (D.B.-R.); (K.K.); (M.T.-M.); (C.G.-E.); (A.S.-L.)
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Universidad de León, Campus de Vegazana, 24071 León, Spain
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David ME, Ion RM, Grigorescu RM, Iancu L, Constantin M, Stirbescu RM, Gheboianu AI. Wood Surface Modification with Hybrid Materials Based on Multi-Walled Carbon Nanotubes. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:1990. [PMID: 35745330 PMCID: PMC9229745 DOI: 10.3390/nano12121990] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/05/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023]
Abstract
In this work, new treatments based on multi-walled carbon nanotubes (MWCNTs), MWCNTs decorated with zinc oxide (ZnO), MWCNTs decorated with hydroxyapatite (HAp) and MWCNTs decorated with silver (Ag) nanoparticles dispersed in PHBHV solution are proposed for improving sound oak wood properties. We hypothesize that the solutions containing decorated MWCNTs will be more efficient as wood consolidants, not only because of the improved mechanical properties of the treated wood but also because of the hydrophobic layer created on the wood surface. In order to test these hypotheses, the treatments' potential was investigated by a number of complex methods, such as colorimetric parameter measurements, water absorption tests, mechanical tests, artificial aging and antifungal tests. The data confirm that the treated wood materials have moderate stability, and the color differences are not perceived with the naked eye. A significant improvement of the treated samples was observed by water absorption, humidity and mechanical tests compared to untreated wood. The best results were obtained for samples treated by brushing with solutions based on decorated CNTs, which confirms that a uniform and thicker layer is needed on the surface to ensure better protection. The wood behavior with accelerated aging revealed that the control sample degraded faster compared to the other treated samples. Antifungal tests showed that higher growth inhibition was obtained for samples treated with 0.2% MWCNTs_ZnO + PHBHV. Considering all of the obtained results, it can be concluded that the most effective treatment was MWCNTs_ZnO + PHBHV at a nanocomposite concentration of 0.2%, applied by brushing. Thus, wood protection against mold and fungi will be achieved, simultaneously ensuring improved mechanical strength and water barrier properties and therefore maintaining the structural integrity of sound oak wood over time.
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Affiliation(s)
- Madalina Elena David
- National Institute for Research & Development in Chemistry and Petrochemistry—ICECHIM, 060021 Bucharest, Romania; (R.M.G.); (L.I.); (M.C.)
- Doctoral School of Materials Engineering Department, Valahia University of Targoviste, 130004 Targoviste, Romania
| | - Rodica-Mariana Ion
- National Institute for Research & Development in Chemistry and Petrochemistry—ICECHIM, 060021 Bucharest, Romania; (R.M.G.); (L.I.); (M.C.)
- Doctoral School of Materials Engineering Department, Valahia University of Targoviste, 130004 Targoviste, Romania
| | - Ramona Marina Grigorescu
- National Institute for Research & Development in Chemistry and Petrochemistry—ICECHIM, 060021 Bucharest, Romania; (R.M.G.); (L.I.); (M.C.)
| | - Lorena Iancu
- National Institute for Research & Development in Chemistry and Petrochemistry—ICECHIM, 060021 Bucharest, Romania; (R.M.G.); (L.I.); (M.C.)
| | - Mariana Constantin
- National Institute for Research & Development in Chemistry and Petrochemistry—ICECHIM, 060021 Bucharest, Romania; (R.M.G.); (L.I.); (M.C.)
| | - Raluca Maria Stirbescu
- Institute of Multidisciplinary Research for Science and Technology, Valahia University of Targoviste, 130004 Targoviste, Romania; (R.M.S.); (A.I.G.)
| | - Anca Irina Gheboianu
- Institute of Multidisciplinary Research for Science and Technology, Valahia University of Targoviste, 130004 Targoviste, Romania; (R.M.S.); (A.I.G.)
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Meena M, Yadav G, Sonigra P, Nagda A, Mehta T, Swapnil P, Marwal A, Kumar S. Multifarious Responses of Forest Soil Microbial Community Toward Climate Change. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02051-3. [PMID: 35657425 DOI: 10.1007/s00248-022-02051-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO2, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.
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Affiliation(s)
- Mukesh Meena
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India.
| | - Garima Yadav
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Priyankaraj Sonigra
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Adhishree Nagda
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Tushar Mehta
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Prashant Swapnil
- Department of Botany, School of Biological Science, Central University of Punjab, Bhatinda, Punjab, 151401, India
| | - Avinash Marwal
- Department of Biotechnology, Vigyan Bhawan - Block B, New Campus, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Sumit Kumar
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
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28
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Ensiling with rumen fluid promoted Irpex lacteus colonization on the non-sterile naked oat straw for enhanced lignocellulose degradation and enzymatic hydrolysis. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108462] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Litter Mixing Alters Microbial Decomposer Community to Accelerate Tomato Root Litter Decomposition. Microbiol Spectr 2022; 10:e0018622. [PMID: 35604181 PMCID: PMC9241821 DOI: 10.1128/spectrum.00186-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Mixing plant litters of multiple species can alter litter decomposition, a key driver of carbon and nutrient cycling in terrestrial ecosystems. Changes in microbial decomposer communities is proposed as one of the mechanisms explaining this litter-mixture effect, but the underlying mechanism is unclear. In a microcosm litterbag experiment, we found that, at the early stage of decomposition, litter mixing promoted tomato root litter decomposition, thus generating a synergistic nonadditive litter-mixture effect. The transplanting decomposer community experiment showed that changes in microbial decomposer communities contributed to the nonadditive litter-mixture effect on tomato root litter decomposition. Moreover, litter mixing altered the abundance and diversity of bacterial and fungal communities on tomato root litter. Litter mixing also stimulated several putative keystone operational taxonomic units (OTUs) in the microbial correlation network, such as Fusarium sp. fOTU761 and Microbacterium sp. bOTU6632. Then, we isolated and cultured representative isolates of these two taxa, named Fusarium sp. F13 and Microbacterium sp. B26. Subsequent in vitro tests found that F13, but not B26, had strong decomposing ability; moreover, these two isolates developed synergistic interaction, thus promoted litter decomposition in coculture. Addition of F13 or B26 both promoted the decomposing activity of the resident decomposer community on tomato root litter, confirming their importance for litter decomposition. Overall, litter mixing promoted tomato root litter decomposition through altering microbial decomposers, especially through stimulating certain putative keystone taxa. IMPORTANCE Microbial decomposer community plays a key role in litter decomposition, which is an important regulator of soil carbon and nutrient cycling. Though changes in decomposer communities has been proposed as one of the potential underlying mechanisms driving the litter-mixture effects, direct evidence is still lacking. Here, we demonstrated that litter mixing stimulated litter decomposition through altering microbial decomposers at the early stage of decomposition. Moreover, certain putative keystone taxa stimulated by litter mixing contributed to the nonadditive litter-mixture effect. In vitro culturing validated the role of these taxa in litter decomposition. This study also highlights the possibility of regulating litter decomposition through manipulating certain microbial taxa.
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Brabcová V, Tláskal V, Lepinay C, Zrůstová P, Eichlerová I, Štursová M, Müller J, Brandl R, Bässler C, Baldrian P. Fungal Community Development in Decomposing Fine Deadwood Is Largely Affected by Microclimate. Front Microbiol 2022; 13:835274. [PMID: 35495708 PMCID: PMC9045801 DOI: 10.3389/fmicb.2022.835274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/11/2022] [Indexed: 11/16/2022] Open
Abstract
Fine woody debris (FWD) represents the majority of the deadwood stock in managed forests and serves as an important biodiversity hotspot and refuge for many organisms, including deadwood fungi. Wood decomposition in forests, representing an important input of nutrients into forest soils, is mainly driven by fungal communities that undergo continuous changes during deadwood decomposition. However, while the assembly processes of fungal communities in long-lasting coarse woody debris have been repeatedly explored, similar information for the more ephemeral habitat of fine deadwood is missing. Here, we followed the fate of FWD of Fagus sylvatica and Abies alba in a Central European forest to describe the assembly and diversity patterns of fungal communities over 6 years. Importantly, the effect of microclimate on deadwood properties and fungal communities was addressed by comparing FWD decomposition in closed forests and under open canopies because the large surface-to-volume ratio of FWD makes it highly sensitive to temperature and moisture fluctuations. Indeed, fungal biomass increases and pH decreases were significantly higher in FWD under closed canopy in the initial stages of decomposition indicating higher fungal activity and hence decay processes. The assembly patterns of the fungal community were strongly affected by both tree species and microclimatic conditions. The communities in the open/closed canopies and in each tree species were different throughout the whole succession with only limited convergence in time in terms of both species and ecological guild composition. Decomposition under the open canopy was characterized by high sample-to-sample variability, showing the diversification of fungal resources. Tree species-specific fungi were detected among the abundant species mostly during the initial decomposition, whereas fungi associated with certain canopy cover treatments were present evenly during decomposition. The species diversity of forest stands and the variability in microclimatic conditions both promote the diversity of fine woody debris fungi in a forest.
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Affiliation(s)
- Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Clémentine Lepinay
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Petra Zrůstová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Ivana Eichlerová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Jörg Müller
- Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany.,Bavarian Forest National Park, Grafenau, Germany
| | - Roland Brandl
- Animal Ecology, Department of Ecology, Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Claus Bässler
- Bavarian Forest National Park, Grafenau, Germany.,Department of Conservation Biology, Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt, Germany
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
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31
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Ren W, Penttilä R, Kasanen R, Asiegbu FO. Bacteria Community Inhabiting Heterobasidion Fruiting Body and Associated Wood of Different Decay Classes. Front Microbiol 2022; 13:864619. [PMID: 35591994 PMCID: PMC9111749 DOI: 10.3389/fmicb.2022.864619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
The microbiome of Heterobasidion-induced wood decay of living trees has been previously studied; however, less is known about the bacteria biota of its perennial fruiting body and the adhering wood tissue. In this study, we investigated the bacteria biota of the Heterobasidion fruiting body and its adhering deadwood. Out of 7,462 operational taxonomic units (OTUs), about 5,918 OTUs were obtained from the fruiting body and 5,469 OTUs were obtained from the associated dead wood. Interestingly, an average of 52.6% of bacteria biota in the fruiting body was shared with the associated dead wood. The overall and unique OTUs had trends of decreasing from decay classes 1 to 3 but increasing in decay class 4. The fruiting body had the highest overall and unique OTUs number in the fourth decay class, whereas wood had the highest OTU in decay class 1. Sphingomonas spp. was significantly higher in the fruiting body, and phylum Firmicutes was more dominant in wood tissue. The FAPROTAX functional structure analysis revealed nutrition, energy, degradation, and plant-pathogen-related functions of the communities. Our results also showed that bacteria communities in both substrates experienced a process of a new community reconstruction through the various decay stages. The process was not synchronic in the two substrates, but the community structures and functions were well-differentiated in the final decay class. The bacteria community was highly dynamic; the microbiota activeness, community stability, and functions changed with the decay process. The third decay class was an important turning point for community restructuring. Host properties, environmental factors, and microbial interactions jointly influenced the final community structure. Bacteria community in the fruiting body attached to the living standing tree was suppressed compared with those associated with dead wood. Bacteria appear to spread from wood tissue of the standing living tree to the fruiting body, but after the tree is killed, bacteria moved from fruiting body to wood. It is most likely that some of the resident endophytic bacteria within the fruiting body are either parasitic, depending on it for their nutrition, or are mutualistic symbionts.
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Affiliation(s)
- Wenzi Ren
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Reijo Penttilä
- Natural Resources Institute of Finland (Luke), Helsinki, Finland
| | - Risto Kasanen
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Fred O. Asiegbu
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland
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Ferrer A, Heath KD, Mosquera SL, Suaréz Y, Dalling JW. Assembly of wood-inhabiting archaeal, bacterial and fungal communities along a salinity gradient: common taxa are broadly distributed but locally abundant in preferred habitats. FEMS Microbiol Ecol 2022; 98:6566339. [PMID: 35404430 DOI: 10.1093/femsec/fiac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 11/12/2022] Open
Abstract
Wood decomposition in water is a key ecosystem process driven by diverse microbial taxa that likely differ in their affinities for freshwater, estuarine, and marine habitats. How these decomposer communities assemble in situ or potentially colonize from other habitats remains poorly understood. At three watersheds on Coiba Island, Panama, we placed replicate sections of branch wood of a single tree species on land, and in freshwater, estuarine and marine habitats that constitute a downstream salinity gradient. We sequenced archaea, bacteria and fungi from wood samples collected after 3, 9, and 15 months to examine microbial community composition, and to examine habitat specificity and abundance patterns. We found these microbial communities were broadly structured by similar factors, with a strong effect of salinity, but little effect of watershed identity on compositional variation. Moreover, common aquatic taxa were also present in wood incubated on land. Our results suggest that taxa either dispersed to both terrestrial and aquatic habitats, or that microbes with broad habitat ranges were initially present in the wood as endophytes. Nonetheless, these habitat generalists varied greatly in abundance across habitats suggesting an important role for habitat filtering in maintaining distinct aquatic communities in freshwater, estuarine and marine habitats.
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Affiliation(s)
- Astrid Ferrer
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Sergio L Mosquera
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| | - Yaraví Suaréz
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| | - James W Dalling
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
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Lunde LF, Jacobsen R, Kauserud H, Boddy L, Nybakken L, Sverdrup-Thygeson A, Birkemoe T. Legacies of invertebrate exclusion and tree secondary metabolites control fungal communities in dead wood. Mol Ecol 2022; 31:3241-3253. [PMID: 35363919 PMCID: PMC9322270 DOI: 10.1111/mec.16448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/28/2022] [Indexed: 11/29/2022]
Abstract
During decomposition of organic matter, microbial communities may follow different successional trajectories depending on the initial environment and colonizers. The timing and order of the species arrival (assembly history) can lead to divergent communities through priority effects. We explored how assembly history and resource quality affected fungal communities and decay rate of decomposing wood, 1.5 and 4.5 years after tree felling. Additionally, we investigated the effect of invertebrate exclusion during the first two summers. We measured initial resource quality of bark and wood of aspen (Populus tremula) logs and surveyed the fungal communities by DNA metabarcoding at different times during succession. We found that gradients in fungal community composition were related to resource quality and discuss how this may reflect different fungal life history strategies. As with previous studies, the initial amount of bark tannins was negatively correlated with wood decomposition rate over 4.5 years. The initial fungal community explained variation in community composition after 1.5, but not 4.5 years, of succession. Although the assembly history of initial colonizers may cause alternate trajectories in successional communities, our results indicate that the communities may converge with the arrival of secondary colonizers. We also identified a strong legacy of invertebrate exclusion on fungal communities, even after 4.5 years of succession, thereby adding crucial knowledge on the importance of invertebrates in affecting fungal community development. By measuring and manipulating aspects of assembly history and resource quality that have rarely been studied, we expand our understanding of the complexity of fungal community dynamics.
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Affiliation(s)
- Lisa Fagerli Lunde
- Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management, 1432, Ås, Norway
| | - Rannveig Jacobsen
- Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management, 1432, Ås, Norway.,Norwegian Institute for Nature Research (NINA), 0855, Oslo, Norway
| | - Håvard Kauserud
- University of Oslo, Section for Genetics and Evolutionary Biology (EVOGENE), 0316, Oslo, Norway
| | - Lynne Boddy
- Cardiff University, School of Biosciences, Cardiff, UK
| | - Line Nybakken
- Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management, 1432, Ås, Norway
| | - Anne Sverdrup-Thygeson
- Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management, 1432, Ås, Norway
| | - Tone Birkemoe
- Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management, 1432, Ås, Norway
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Haq IU, Hillmann B, Moran M, Willard S, Knights D, Fixen KR, Schilling JS. Bacterial communities associated with wood rot fungi that use distinct decomposition mechanisms. ISME COMMUNICATIONS 2022; 2:26. [PMID: 37938255 PMCID: PMC9723729 DOI: 10.1038/s43705-022-00108-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 05/11/2023]
Abstract
Wood decomposer fungi are grouped by how they extract sugars from lignocellulose. Brown rot fungi selectively degrade cellulose and hemicellulose, leaving lignin intact, and white rot fungi degrade all components. Many trees are susceptible to both rot types, giving carbon in Earth's woody biomass, specifically lignin, a flexible fate that is affected not only by the fungal decomposition mechanism but also the associated microbial community. However, little is understood about how rot type may influence the microbial community in decaying wood. In this study, we quantified bacterial communities associated with Fomes fomentarius (white rot) and Fomitopsis betulina (brown rot) found on a shared tree host species, birch (Betula papyrifera). We collected 25 wood samples beneath sporocarps of F. fomentarius (n = 13) and F. betulina (n = 12) on standing dead trees, and coupled microbial DNA sequencing with chemical signatures of rot type (pH and lignin removal). We found that bacterial communities for both fungi were dominated by Proteobacteria, a commonly reported association. However, rot type exerted significant influence on less abundant taxa in ways that align logically with fungal traits. Amplicon sequence variants (ASVs) were enriched in Firmicutes in white-rotted wood, and were enriched in Alphaproteobacteria, Actinobacteria and Acidobacteria in lower pH brown rot. Our results suggest that wood decomposer strategies may exert significant selection effects on bacteria, or vice versa, among less-abundant taxa that have been overlooked when using abundance as the only measure of influence.
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Affiliation(s)
- Irshad Ul Haq
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Molly Moran
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
| | - Samuel Willard
- Department of Life Sciences, Imperial College London, London, UK
| | - Dan Knights
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Kathryn R Fixen
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Jonathan S Schilling
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA.
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA.
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Establishment of a Laboratory Scale Set-Up with Controlled Temperature and High Humidity to Investigate Dry Matter Losses of Wood Chips from Poplar during Storage. FORESTS 2022. [DOI: 10.3390/f13030459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The aim of this work was to improve the understanding of dry matter losses (DML) that occur in wood chips during the initial phase of storage in outdoor piles. For this purpose, a laboratory scale storage chamber was developed and investigated regarding its ability to recreate the conditions that chips undergo during the initial phase of outdoor storage. Three trials with poplar Max-4 (Populus maximowiczii Henry × Populus nigra L.) chips were performed for 6–10 weeks in the storage chamber under controlled temperature and assisted humidity. Two different set-ups were investigated to maintain a high relative humidity (RH) inside the storage chamber; one using water containers, and one assisted with a humidifier. Moisture content (MC) and DML of the chips were measured at different storage times to evaluate their storage behaviour in the chamber. Additionally, microbiological analyses of the culturable fraction of saproxylic microbiota were performed, with a focus on mesophilic fungi, but discriminating also xerophilic fungi, and mesophilic bacteria, with focus on actinobacteria, in two trials, to gain a view on the poplar wood chip-inhabiting microorganisms as a function of storage conditions (moisture, temperature) and time. Results show that DML up to 8.8–13.7% occurred in the chips within 6–10 storage weeks. The maximum DML were reached in the trial using the humidifier, which seemed a suitable technique to keep a high RH in the testing chamber, and thus, to analyse the wood chips in conditions comparable to those in outdoor piles during the initial storage phase.
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Maillard F, Jusino MA, Andrews E, Moran M, Vaziri GJ, Banik MT, Fanin N, Trettin CC, Lindner DL, Schilling JS. Wood-decay type and fungal guild dominance across a North American log transplant experiment. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2022.101151] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Tanunchai B, Kalkhof S, Guliyev V, Wahdan SFM, Krstic D, Schädler M, Geissler A, Glaser B, Buscot F, Blagodatskaya E, Noll M, Purahong W. Nitrogen fixing bacteria facilitate microbial biodegradation of a bio-based and biodegradable plastic in soils under ambient and future climatic conditions. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:233-241. [PMID: 35048922 DOI: 10.1039/d1em00426c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We discovered a biological mechanism supporting microbial degradation of bio-based poly(butylene succinate-co-adipate) (PBSA) plastic in soils under ambient and future climates. Here, we show that nitrogen-fixing bacteria facilitate the microbial degradation of PBSA by enhancing fungal abundance, accelerating plastic-degrading enzyme activities, and shaping/interacting with plastic-degrading fungal communities.
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Affiliation(s)
- Benjawan Tanunchai
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany.
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Stefan Kalkhof
- Coburg University of Applied Sciences and Arts, Institute for Bioanalysis, Friedrich-Streib-Str. 2, D-96450 Coburg, Germany.
| | - Vusal Guliyev
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany.
- Institute of Soil Science and Agrochemistry of Azerbaijan National Academy of Sciences, M.Rahim, AZ1073, Baku, Azerbaijan
| | - Sara Fareed Mohamed Wahdan
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany.
- Department of Botany, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
| | - Dennis Krstic
- Coburg University of Applied Sciences and Arts, Institute for Bioanalysis, Friedrich-Streib-Str. 2, D-96450 Coburg, Germany.
| | - Martin Schädler
- UFZ-Helmholtz Centre for Environmental Research, Department of Community Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
| | - Andreas Geissler
- Department of Macromolecular Chemistry and Paper Chemistry, Technical University of Darmstadt, Darmstadt D-64287, Germany
| | - Bruno Glaser
- Soil Biogeochemistry, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 3, 06120 Halle, Germany
| | - François Buscot
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
| | - Evgenia Blagodatskaya
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany.
- RUDN University, 6 Miklukho-Maklaya St, Moscow, 117198, Russia
| | - Matthias Noll
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
- Coburg University of Applied Sciences and Arts, Institute for Bioanalysis, Friedrich-Streib-Str. 2, D-96450 Coburg, Germany.
| | - Witoon Purahong
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle (Saale), Germany.
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Wójcik-Fatla A, Mackiewicz B, Sawczyn-Domańska A, Sroka J, Siwiec J, Paściak M, Szponar B, Pawlik K, Dutkiewicz J. Timber-colonizing gram-negative bacteria as potential causative agents of respiratory diseases in woodworkers. Int Arch Occup Environ Health 2022; 95:1179-1193. [PMID: 35015109 PMCID: PMC9273545 DOI: 10.1007/s00420-021-01829-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022]
Abstract
Occurrence Gram-negative bacteria occur commonly in the inner tissues of stored coniferous and deciduous timber, showing a marked variation in numbers. The greatest maximal numbers are found in the sapwood of coniferous timber. The common constituents of the Gram-negative biota are potentially pathogenic species of Enterobacteriaceae family of the genera Rahnella, Pantoea, Enterobacter, and Klebsiella. The air of wood-processing facilities is polluted with the wood-borne Gram-negative bacteria and produced by them endotoxin, as demonstrated worldwide by numerous studies. Effects There are three potential pathways of the pathogenic impact of wood-borne Gram-negative bacteria on exposed woodworkers: allergic, immunotoxic, and infectious. Allergic impact has been underestimated for a long time with relation to Gram-negative bacteria. Hopefully, the recent demonstration of the first documented case of hypersensitivity pneumonitis (HP) in woodworkers caused by Pantoea agglomerans which developed in extremely large quantities in birch sapwood, would speed up finding of new wood-related cases of HP caused by Gram-negative bacteria. The second pathway is associated with endotoxin, exerting strong immunotoxic (excessively immunostimulative) action. It has been demonstrated that endotoxin is released into wood dust in the form of nano-sized microvesicles, by peeling off the outer membrane of bacteria. Endotoxin microvesicles are easily inhaled by humans together with dust because of small dimensions and aerodynamic shape. Afterwards, they cause a nonspecific activation of lung macrophages, which release numerous inflammatory mediators causing an inflammatory lung reaction, chest tightness, fever, gas exchange disorders, and bronchospasm, without radiographic changes. The resulting disease is known as “Organic Dust Toxic Syndrome” or “toxic pneumonitis.” The potential third pathway of pathogenic impact is infection. The suspected species is Klebsiella pneumoniae that may occur commonly in wood dust; however, until now this pathway has not been confirmed. Conclusion Summarizing, Gram-negative bacteria-inhabiting timber should be considered, besides filamentous fungi and actinobacteria, as important risk factors of occupational disease in woodworkers that could be either HP with allergenic background or toxic pneumonitis elicited by endotoxin. Supplementary Information The online version contains supplementary material available at 10.1007/s00420-021-01829-1.
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Affiliation(s)
- Angelina Wójcik-Fatla
- Department of Health Biohazards and Parasitology, Institute of Rural Health, Jaczewskiego 2, 20-090, Lublin, Poland.
| | - Barbara Mackiewicz
- Department of Pneumology, Oncology and Allergology, Medical University of Lublin, Lublin, Poland
| | - Anna Sawczyn-Domańska
- Department of Health Biohazards and Parasitology, Institute of Rural Health, Jaczewskiego 2, 20-090, Lublin, Poland
| | - Jacek Sroka
- Department of Health Biohazards and Parasitology, Institute of Rural Health, Jaczewskiego 2, 20-090, Lublin, Poland.,Department of Parasitology and Invasive Diseases, National Veterinary Research Institute, Puławy, Poland
| | - Jan Siwiec
- Department of Pneumology, Oncology and Allergology, Medical University of Lublin, Lublin, Poland
| | - Mariola Paściak
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Bogumiła Szponar
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Krzysztof Pawlik
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Jacek Dutkiewicz
- Department of Health Biohazards and Parasitology, Institute of Rural Health, Jaczewskiego 2, 20-090, Lublin, Poland
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Zhang J, Sayer EJ, Zhou J, Li Y, Li Y, Li Z, Wang F. Long-term fertilization modifies the mineralization of soil organic matter in response to added substrate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149341. [PMID: 34375236 DOI: 10.1016/j.scitotenv.2021.149341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 07/14/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
The turnover of SOC in soils is strongly influenced by the availability of substrate and nutrients, especially nitrogen (N) and phosphorus (P). Here, we assessed how long-term fertilization modified SOM mineralization in response to added substrate in a tropical forest. We carried out a 90-day incubation study in which we added two structurally similar compounds which differed in microbial metabolic availability: corn cellulose or corn starch to soils collected from a long-term (11 years) factorial N and P fertilization experiment site in a tropical forest in south China. We measured total soil mineralization rate (CO2 efflux) to characterize SOM mineralization and using 13C isotope signatures to determine the source of the CO2 (original soil C or added substrate) and assessed changes in extracellular enzyme activities: acid phosphomonoesterase (AP), β-1,4-glucosidase (BG), β-1,4- N-acetaminophen glucosidase (NAG), phenol oxidase (PHO) and peroxidase (PER), and microbial biomarkers to determine whether nutrient stoichiometry and decomposer communities explain differences in SOM mineralization rates. Total C mineralization increased substantially with substrate addition, particularly cellulose (5.38, 7.13, 5.58 and 5.37 times for N, P, NP fertilization and CK, respectively) compared to no substrate addition, and original soil C mineralization was further enhanced in long-term N (3.40% and 5.18% for cellulose and starch addition, respectively) or NP (35.11% for cellulose addition) fertilized soils compared to control treatment. Enzyme activities were stimulated by the addition of both substrates but suppressed by P-fertilization. Addition of both substrates increased microbial investment in P-acquisition, but only starch addition promoted C investment in N-acquisition. Finally, fungal abundance increased with substrate addition to a greater extent than bacterial abundance, particularly in cellulose-amended soils, and the effect was amplified by long-term fertilization. Our findings indicate that SOM mineralization might be enhanced in N and P enrichment ecosystems, since the litter input can liberate microbes from C limitation and stimulate SOM mineralization if N and P are sufficient. Our study further demonstrates that structurally similar substrates can have distinct effects on SOM mineralization and the extent of SOM mineralization is strongly dependent on elemental stoichiometry, as well as the resource requirements of microbial decomposers.
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Affiliation(s)
- Jingfan Zhang
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied Botany, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; University of Chinese Academy of Sciences, Beijing 100049, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China
| | - Emma J Sayer
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK; Smithsonian Tropical Research Institute, P.O. Box 0843-03092, Balboa, Ancon, Panama, Panama
| | - Jinge Zhou
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied Botany, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; University of Chinese Academy of Sciences, Beijing 100049, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China
| | - Yingwen Li
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied Botany, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Yongxing Li
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied Botany, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Zhian Li
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied Botany, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China
| | - Faming Wang
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Guangdong Provincial Key Laboratory of Applied Botany, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China.
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40
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Microbial Diversity and Ecosystem Functioning in Deadwood of Black Pine of a Temperate Forest. FORESTS 2021. [DOI: 10.3390/f12101418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The present study provides a deeper insight on variations of microbial abundance and community composition concerning specific environmental parameters related to deadwood decay, focusing on a mesocosm experiment conducted with deadwood samples from black pine of different decay classes. The chemical properties and microbial communities of deadwood changed over time. The total carbon percentage remained constant in the first stage of decomposition, showing a significant increase in the last decay class. The percentage of total nitrogen and the abundances of nifH harbouring bacteria significantly increased as decomposition advanced, suggesting N wood-enrichment by microbial N immobilization and/or N2-fixation. The pH slightly decreased during decomposition and significantly correlated with fungal abundance. CO2 production was higher in the last decay class 5 and positively correlated with bacterial abundance. Production of CH4 was registered in one sample of decay class 3, which correlates with the highest abundance of methanogenic archaea that probably belonged to Methanobrevibacter genus. N2O consumption increased along decomposition progress, indicating a complete reduction of nitrate compounds to N2 via denitrification, as proved by the highest nosZ gene copy number in decay class 5. Conversely, our results highlighted a low involvement of nitrifying communities in deadwood decomposition.
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Pellicciaro M, Lione G, Ongaro S, Gonthier P. Comparative Efficacy of State-of-the-Art and New Biological Stump Treatments in Forests Infested by the Native and the Alien Invasive Heterobasidion Species Present in Europe. Pathogens 2021; 10:pathogens10101272. [PMID: 34684221 PMCID: PMC8539811 DOI: 10.3390/pathogens10101272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 11/18/2022] Open
Abstract
The Heterobasidion annosum species complex includes major fungal pathogens of conifers worldwide. State-of-the-art preventative stump treatments with urea or with commercial formulations of the fungal biological control agent Phlebiopsis gigantea (i.e., Rotstop®) may become no longer available or are not approved for use in many areas of Europe infested by the three native Heterobasidion species and by the North American invasive H. irregulare, making the development of new treatments timely. The efficacy of Proradix® (based on Pseudomonas protegens strain DSMZ 13134), the cell-free filtrate (CFF) of the same bacterium, a strain of P. gigantea (MUT 6212) collected in the invasion area of H. irregulare in Italy, Rotstop®, and urea was comparatively investigated on a total of 542 stumps of Abies alba, Picea abies, Pinus pinea, and P. sylvestris in forest stands infested by the host-associated Heterobasidion species. Additionally, 139 logs of P. pinea were also treated. Results support the good performances of Rotstop®, and especially of urea against the native Heterobasidion species on stumps of their preferential hosts and, for the first time, towards the invasive North American H. irregulare on stumps of P. pinea. In some experiments, the effectiveness of Proradix® and of the strain of P. gigantea was weak, whereas the CFF of P. protegens strain DSMZ 13134 performed as a valid alternative to urea and Rotstop®. The mechanism of action of this treatment hinges on antibiosis; therefore, further improvements could be possible by identifying the active molecules and/or by optimizing their production. Generally, the performance of the tested treatments is not correlated with the stump size.
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Ge W, Zhang ZY, Dong CB, Han YF, Deshmukh SK, Liang ZQ. Bacterial Community Analysis and Potential Functions of Core Taxa in Different Parts of the Fungus Cantharellus cibarius. Pol J Microbiol 2021; 70:373-385. [PMID: 34584531 PMCID: PMC8459004 DOI: 10.33073/pjm-2021-035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/25/2021] [Accepted: 07/25/2021] [Indexed: 11/05/2022] Open
Abstract
Cantharellus cibarius is a widely distributed, popular, edible fungus with high nutritional and economic value. However, significant challenges persist in the microbial ecology and artificial cultivation of C. cibarius. Based on the 16S rRNA sequencing data, this study analyzed bacterial community structures and diversity of fruit bodies and rhizomorph parts of C. cibarius and mycosphere samples (collected in the Wudang District, Guiyang, Guizhou Province, China). It explored the composition and function of the core bacterial taxa. The analyzed results showed that the rhizomorph bacterial community structure was similar to mycosphere, but differed from the fruit bodies. Members of the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium complex had the highest abundance in the fruit bodies. However, they were either absent or low in abundance in the rhizomorphs and mycosphere. At the same time, members of the Burkholderia-Caballeronia-Paraburkholderia complex were abundant in the fruit bodies and rhizomorphs parts of C. cibarius, as well as mycosphere. Through functional annotation of core bacterial taxa, we found that there was an apparent trend of potential functional differentiation of related bacterial communities in the fruit body and rhizomorph: potential functional groups of core bacterial taxa in the fruit bodies centered on nitrogen fixation, nitrogen metabolism, and degradation of aromatic compounds, while those in rhizomorphs focused on aerobic chemoheterotrophy, chemoheterotrophy, defense against soil pathogens, decomposition of complex organic compounds, and uptake of insoluble inorganic compounds. The analysis of functional groups of bacteria with different structures is of great significance to understand that bacteria promote the growth and development of C. cibarius.
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Affiliation(s)
- Wei Ge
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China
| | - Zhi-Yuan Zhang
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China
| | - Chun-Bo Dong
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China
| | - Yan-Feng Han
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China
| | - Sunil K Deshmukh
- TERI-Deakin Nano Biotechnology Centre, The Energy and Resources Institute, New Delhi, India
| | - Zong-Qi Liang
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China
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Mieszkin S, Pouder E, Uroz S, Simon-Colin C, Alain K. Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov., Two Acidophilic Bacteria Isolated from Decaying Wood, Hydrolyzing Cellulose and Producing Poly-3-hydroxybutyrate. Microorganisms 2021; 9:microorganisms9102053. [PMID: 34683374 PMCID: PMC8537097 DOI: 10.3390/microorganisms9102053] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/17/2021] [Accepted: 09/25/2021] [Indexed: 12/02/2022] Open
Abstract
Two novel strains, HW T2.11T and HW T5.17T, were isolated from decaying wood (forest of Champenoux, France). Study of the 16S rRNA sequence similarity indicated that the novel strains belong to the genus Acidisoma. The sequence similarity of the 16S rRNA gene of HW T2.11T with the corresponding sequences of A. tundrae and A. sibiricum was 97.30% and 97.25%, while for HW T5.17T it was 96.85% and 97.14%, respectively. The DNA G+C contents of the strains were 62.32–62.50%. Cells were Gram-negative coccobacilli that had intracellular storage granules (poly-3-hydroxybutyrate (P3HB)) that confer resistance to environmental stress conditions. They were mesophilic and acidophilic organisms growing at 8–25 °C, at a pH of 2.0–6.5, and were capable of using a wide range of organic compounds and complex biopolymers such as starch, fucoidan, laminarin, pectin and cellulose, the latter two being involved in wood composition. The major cellular fatty acid was cyclo C19:0ω8c and the major quinone was Q-10. Overall, genome relatedness indices between genomes of strains HW T2.11T and HW T5.17T (Orthologous Average Nucleotide Identity (OrthoANI) value = 83.73% and digital DNA-DNA hybridization score = 27.5%) confirmed that they belonged to two different species. Genetic predictions indicate that the cyclopropane fatty acid (CFA) pathway is present, conferring acid-resistance properties to the cells. The two novel strains might possess a class IV polyhydroxyalcanoate (PHA) synthase operon involved in the P3HB production pathway. Overall, the polyphasic taxonomic analysis shows that these two novel strains are adapted to harsh environments such as decaying wood where the organic matter is difficult to access, and can contribute to the degradation of dead wood. These strains represent novel species of the genus Acidisoma, for which the names Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov. are proposed. The type strains of Acidisoma silvae and Acidisomacellulosilytica are, respectively, HW T2.11T (DSM 111006T; UBOCC-M-3364T) and HW T5.17T (DSM 111007T; UBOCC-M-3365T).
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Affiliation(s)
- Sophie Mieszkin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
- Centre INRAE-Grand Est-Nancy, Université de Lorraine, INRAE, UMR IAM, 54280 Champenoux, F-54000 Nancy, France;
- Correspondence:
| | - Eva Pouder
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
| | - Stéphane Uroz
- Centre INRAE-Grand Est-Nancy, Université de Lorraine, INRAE, UMR IAM, 54280 Champenoux, F-54000 Nancy, France;
| | - Christelle Simon-Colin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
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Bánfi R, Pohner Z, Szabó A, Herczeg G, Kovács GM, Nagy A, Márialigeti K, Vajna B. Succession and potential role of bacterial communities during Pleurotus ostreatus production. FEMS Microbiol Ecol 2021; 97:fiab125. [PMID: 34498665 PMCID: PMC8445668 DOI: 10.1093/femsec/fiab125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 09/07/2021] [Indexed: 11/21/2022] Open
Abstract
There is an increasing interest in studying bacterial-fungal interactions (BFIs), also the interactions of Pleurotus ostreatus, a model white-rot fungus and important cultivated mushroom. In Europe, P. ostreatus is produced on a wheat straw-based substrate with a characteristic bacterial community, where P. ostreatus is exposed to the microbiome during substrate colonisation. This study investigated how the bacterial community structure was affected by the introduction of P. ostreatus into the mature substrate. Based on the results obtained, the effect of the presence and absence of this microbiome on P. ostreatus production in an experimental cultivation setup was determined. 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) and amplicon sequencing revealed a definite succession of the microbiome during substrate colonisation and fruiting body production: a sharp decrease in relative abundance of Thermus spp. and Actinobacteria, and the increasing dominance of Bacillales and Halomonas spp. The introduced experimental cultivation setup proved the protective role of the microbial community against competing fungi without affecting P. ostreatus growth. We could also demonstrate that this effect could be attributed to both living microbes and their secreted metabolites. These findings highlight the importance of bacterial-fungal interactions during mushroom production.
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Affiliation(s)
- Renáta Bánfi
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Zsuzsanna Pohner
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Herman Ottó út 15, H-1022 Budapest, Hungary
| | - Attila Szabó
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Gábor Herczeg
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Gábor M Kovács
- Department of Plant Anatomy, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Adrienn Nagy
- Pilze-Nagy Ltd., Talfája 50., H-6000 Kecskemét, Hungary
| | - Károly Márialigeti
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Balázs Vajna
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
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Genomic and Experimental Investigations of Auriscalpium and Strobilurus Fungi Reveal New Insights into Pinecone Decomposition. J Fungi (Basel) 2021; 7:jof7080679. [PMID: 34436218 PMCID: PMC8401616 DOI: 10.3390/jof7080679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
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.
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Moll J, Roy F, Bässler C, Heilmann-Clausen J, Hofrichter M, Kellner H, Krabel D, Schmidt JH, Buscot F, Hoppe B. First Evidence That Nematode Communities in Deadwood Are Related to Tree Species Identity and to Co-Occurring Fungi and Prokaryotes. Microorganisms 2021; 9:microorganisms9071454. [PMID: 34361890 PMCID: PMC8304250 DOI: 10.3390/microorganisms9071454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 06/30/2021] [Accepted: 07/03/2021] [Indexed: 01/02/2023] Open
Abstract
Nematodes represent a diverse and ubiquitous group of metazoans in terrestrial environments. They feed on bacteria, fungi, plants, other nematodes or parasitize a variety of animals and hence may be considered as active members of many food webs. Deadwood is a structural component of forest ecosystems which harbors many niches for diverse biota. As fungi and bacteria are among the most prominent decomposing colonizers of deadwood, we anticipated frequent and diverse nematode populations to co-occur in such ecosystems. However, knowledge about their ability to colonize this habitat is still limited. We applied DNA-based amplicon sequencing (metabarcoding) of the 18S rRNA gene to analyze nematode communities in sapwood and heartwood of decaying logs from 13 different tree species. We identified 247 nematode ASVs (amplicon sequence variants) from 27 families. Most of these identified families represent bacterial and fungal feeders. Their composition strongly depended on tree species identity in both wood compartments. While pH and water content were the only wood properties that contributed to nematodes' distribution, co-occurring fungal and prokaryotic (bacteria and archaea) α- and β-diversities were significantly related to nematode communities. By exploring thirteen different tree species, which exhibit a broad range of wood characteristics, this study provides first and comprehensive insights into nematode diversity in deadwood of temperate forests and indicates connectivity to other wood-inhabiting organisms.
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Affiliation(s)
- Julia Moll
- Helmholtz Centre for Environmental Research—UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany; (F.R.); (F.B.)
- Correspondence: (J.M.); (B.H.)
| | - Friederike Roy
- Helmholtz Centre for Environmental Research—UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany; (F.R.); (F.B.)
- Institute of Forest Botany, Technische Universität Dresden, 01737 Tharandt, Germany;
| | - Claus Bässler
- Department of Conservation Biology, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany;
- Department of Research, National Park Bavarian Forest, 94481 Grafenau, Germany
| | - Jacob Heilmann-Clausen
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - Martin Hofrichter
- Institute of Environmental Biotechnology, Technische Universität Dresden, IHI Zittau, 02763 Zittau, Germany; (M.H.); (H.K.)
| | - Harald Kellner
- Institute of Environmental Biotechnology, Technische Universität Dresden, IHI Zittau, 02763 Zittau, Germany; (M.H.); (H.K.)
| | - Doris Krabel
- Institute of Forest Botany, Technische Universität Dresden, 01737 Tharandt, Germany;
| | - Jan Henrik Schmidt
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany;
| | - François Buscot
- Helmholtz Centre for Environmental Research—UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany; (F.R.); (F.B.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle—Jena—Leipzig, 04103 Leipzig, Germany
| | - Björn Hoppe
- Institute for National and International Plant Health, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany
- Correspondence: (J.M.); (B.H.)
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Screening of Antibiotic Gene Clusters in Microorganisms Isolated from Wood. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2296:151-165. [PMID: 33977446 DOI: 10.1007/978-1-0716-1358-0_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The biosphere of Earth is made up of a variety of ecosystems governed by complex biological interactions, some of them mediated by microbial bioactive secondary metabolites. These metabolites such as antibiotics (e.g., polyketides and nonribosomal peptides) have been receiving increasing attention, due to their multiple pharmaceutical uses. Besides, antibiotic resistance is on the rise, and it is currently regarded as one of the greatest threats to global human health. The screening of novel antimicrobial polyketides and nonribosomal peptides in poorly studied ecosystems is an interesting alternative to address the problem of antibiotic resistance. This chapter updates a molecular method to identify antibiotics gene clusters and their subsequent production and activity validation. On the one hand, a PCR method based on degenerated primers for nonribosomal peptide synthases (NRPS) and the polyketide synthases (PKS) genes is used as an initial fast screening. On the other hand, a bioassay-based method is the protocol selected for the production confirmation and antibacterial effect estimation. These methods are applied to screen Actinobacteria and Penicillium species as main antibiotic producers isolated from wood.
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Tláskal V, Baldrian P. Deadwood-Inhabiting Bacteria Show Adaptations to Changing Carbon and Nitrogen Availability During Decomposition. Front Microbiol 2021; 12:685303. [PMID: 34220772 PMCID: PMC8247643 DOI: 10.3389/fmicb.2021.685303] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/04/2021] [Indexed: 01/01/2023] Open
Abstract
Deadwood decomposition is responsible for a significant amount of carbon (C) turnover in natural forests. While fresh deadwood contains mainly plant compounds and is extremely low in nitrogen (N), fungal biomass and N content increase during decomposition. Here, we examined 18 genome-sequenced bacterial strains representing the dominant deadwood taxa to assess their adaptations to C and N utilization in deadwood. Diverse gene sets for the efficient decomposition of plant and fungal cell wall biopolymers were found in Acidobacteria, Bacteroidetes, and Actinobacteria. In contrast to these groups, Alphaproteobacteria and Gammaproteobacteria contained fewer carbohydrate-active enzymes and depended either on low-molecular-mass C sources or on mycophagy. This group, however, showed rich gene complements for N2 fixation and nitrate/nitrite reduction—key assimilatory and dissimilatory steps in the deadwood N cycle. We show that N2 fixers can obtain C independently from either plant biopolymers or fungal biomass. The succession of bacteria on decomposing deadwood reflects their ability to cope with the changing quality of C-containing compounds and increasing N content.
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Affiliation(s)
- Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
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Clocchiatti A, Hannula SE, Rizaludin MS, Hundscheid MPJ, klein Gunnewiek PJA, Schilder MT, Postma J, de Boer W. Impact of Cellulose-Rich Organic Soil Amendments on Growth Dynamics and Pathogenicity of Rhizoctonia solani. Microorganisms 2021; 9:microorganisms9061285. [PMID: 34204724 PMCID: PMC8231496 DOI: 10.3390/microorganisms9061285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/25/2021] [Accepted: 06/03/2021] [Indexed: 01/04/2023] Open
Abstract
Cellulose-rich amendments stimulate saprotrophic fungi in arable soils. This may increase competitive and antagonistic interactions with root-infecting pathogenic fungi, resulting in lower disease incidence. However, cellulose-rich amendments may also stimulate pathogenic fungi with saprotrophic abilities, thereby increasing plant disease severity. The current study explores these scenarios, with a focus on the pathogenic fungus Rhizoctonia solani. Saprotrophic growth of R. solani on cellulose-rich materials was tested in vitro. This confirmed paper pulp as a highly suitable substrate for R. solani, whereas its performance on wood sawdusts varied with tree species. In two pot experiments, the effects of amendment of R. solani-infected soil with cellulose-rich materials on performance of beetroot seedlings were tested. All deciduous sawdusts and paper pulp stimulated soil fungal biomass, but only oak, elder and beech sawdusts reduced damping-off of beetroot. Oak sawdust amendment gave a consistent stimulation of saprotrophic Sordariomycetes fungi and of seedling performance, independently of the time between amendment and sowing. In contrast, paper pulp caused a short-term increase in R. solani abundance, coinciding with increased disease severity for beet seedlings sown immediately after amendment. However, damping-off of beetroot was reduced if plants were sown two or four weeks after paper pulp amendment. Cellulolytic bacteria, including Cytophagaceae, responded to paper pulp during the first two weeks and may have counteracted further spread of R. solani. The results showed that fungus-stimulating, cellulose-rich amendments have potential to be used for suppression of R. solani. However, such amendments require a careful consideration of material choice and application strategy.
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Affiliation(s)
- Anna Clocchiatti
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (M.S.R.); (M.P.J.H.); (P.J.A.k.G.)
- Correspondence: (A.C.); (W.d.B.)
| | - Silja Emilia Hannula
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands;
| | - Muhammad Syamsu Rizaludin
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (M.S.R.); (M.P.J.H.); (P.J.A.k.G.)
| | - Maria P. J. Hundscheid
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (M.S.R.); (M.P.J.H.); (P.J.A.k.G.)
| | - Paulien J. A. klein Gunnewiek
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (M.S.R.); (M.P.J.H.); (P.J.A.k.G.)
| | - Mirjam T. Schilder
- Biointeractions and Plant Health, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (M.T.S.); (J.P.)
| | - Joeke Postma
- Biointeractions and Plant Health, Wageningen University & Research, 6708 PB Wageningen, The Netherlands; (M.T.S.); (J.P.)
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (M.S.R.); (M.P.J.H.); (P.J.A.k.G.)
- Soil Biology Group, Wageningen University, 6708 PB Wageningen, The Netherlands
- Correspondence: (A.C.); (W.d.B.)
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50
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Dai Z, Trettin CC, Burton AJ, Jurgensen MF, Page-Dumroese DS, Forschler BT, Schilling JS, Lindner DL. Coarse woody debris decomposition assessment tool: Model development and sensitivity analysis. PLoS One 2021; 16:e0251893. [PMID: 34086700 PMCID: PMC8177548 DOI: 10.1371/journal.pone.0251893] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/04/2021] [Indexed: 11/18/2022] Open
Abstract
Coarse woody debris (CWD) is an important component in forests, hosting a variety of organisms that have critical roles in nutrient cycling and carbon (C) storage. We developed a process-based model using literature, field observations, and expert knowledge to assess woody debris decomposition in forests and the movement of wood C into the soil and atmosphere. The sensitivity analysis was conducted against the primary ecological drivers (wood properties and ambient conditions) used as model inputs. The analysis used eighty-nine climate datasets from North America, from tropical (14.2° N) to boreal (65.0° N) zones, with large ranges in annual mean temperature (26.5°C in tropical to -11.8°C in boreal), annual precipitation (6,143 to 181 mm), annual snowfall (0 to 612 kg m-2), and altitude (3 to 2,824 m above mean see level). The sensitivity analysis showed that CWD decomposition was strongly affected by climate, geographical location and altitude, which together regulate the activity of both microbial and invertebrate wood-decomposers. CWD decomposition rate increased with increments in temperature and precipitation, but decreased with increases in latitude and altitude. CWD decomposition was also sensitive to wood size, density, position (standing vs downed), and tree species. The sensitivity analysis showed that fungi are the most important decomposers of woody debris, accounting for over 50% mass loss in nearly all climatic zones in North America. The model includes invertebrate decomposers, focusing mostly on termites, which can have an important role in CWD decomposition in tropical and some subtropical regions. The role of termites in woody debris decomposition varied widely, between 0 and 40%, from temperate areas to tropical regions. Woody debris decomposition rates simulated for eighty-nine locations in North America were within the published range of woody debris decomposition rates for regions in northern hemisphere from 1.6° N to 68.3° N and in Australia.
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Affiliation(s)
- Zhaohua Dai
- Center for Forested Watershed Research, USDA Forest Service, Cordesville, South Carolina, United States of America
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, United States of America
- * E-mail:
| | - Carl C. Trettin
- Center for Forested Watershed Research, USDA Forest Service, Cordesville, South Carolina, United States of America
| | - Andrew J. Burton
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, United States of America
| | - Martin F. Jurgensen
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, United States of America
| | | | - Brian T. Forschler
- Department of Entomology, University of Georgia, Athens, Georgia, United States of America
| | - Jonathan S. Schilling
- Plant & Microbial Biology, Itasca Biological Station & Laboratories, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Daniel L. Lindner
- Northern Research Station, USDA Forest Service, Madison, Wisconsin, United States of America
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