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Wang X, Zhu J, Liu Q, Fu Q, Hu H, Huang Q. Role of genes encoding microbial carbohydrate-active enzymes in the accumulation and dynamics of organic carbon in subtropical forest soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170295. [PMID: 38278240 DOI: 10.1016/j.scitotenv.2024.170295] [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: 08/08/2023] [Revised: 12/27/2023] [Accepted: 01/18/2024] [Indexed: 01/28/2024]
Abstract
Microbial anabolism and catabolism regulate the accumulation and dynamics of soil organic carbon (SOC). However, very little attention has been paid to the role of microbial functional traits in the accumulation and dynamics of SOC in forest soils. In this study, nine forest soils were selected at three altitudes (600 m, 1200 m, and 1500 m) and three soil depths (0-15 cm, 15-30 cm, and 30-45 cm) located in Jiugong Mountain. Vertical traits of functional genes encoding microbial carbohydrate-active enzymes (CAZymes) were observed using metagenomic sequencing. Soil amino sugars were used as biomarkers to indicate microbial residue carbon (MRC). The results showed that GH1 (β-glucosidase: 147.49 TPM) and GH3 (β-glucosidase: 109.09 TPM) were the dominant genes for plant residue decomposition, and their abundance increased with soil depth and peaked in the deep soil at 600 m (GH1: 147.89 TPM; GH3: 109.59 TPM). The highest abundance of CAZymes for fungal and bacterial residue decomposition were GH18 (chitinase: 30.81 TPM) and GH23 (lysozyme: 58.02 TPM), respectively. The abundance of GH18 increased with soil depth, while GH23 showed the opposite trend. Moreover, MRC accumulation was significantly positively correlated with CAZymes involved in the degradation of hemicellulose (r = 0.577, p = 0.002). Compared with the soil before incubation, MRC in the topsoil at the low and middle altitudes after incubation increased by 4 % and 8 %, respectively, while MRC in the soils at 1500 m tended to decrease (p > 0.05). The mineralization capacity of SOC at 1500 m was significantly higher than that at 1200 m and 600 m (p < 0.05). Our results suggested that microbial function for degrading plant residue components, especially hemicellulose and lignin, contributed greatly to SOC accumulation and dynamics. These results were vital for understanding the roles of microbial functional traits in C cycling in forest.
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Affiliation(s)
- Xinran Wang
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Zhu
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qianru Liu
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingling Fu
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongqing Hu
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtse River), Ministry of Agriculture and Rural Affairs, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
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Zou JY, Cadotte MW, Bässler C, Brandl R, Baldrian P, Borken W, Stengel E, Luo YH, Müller J, Seibold S. Wood decomposition is increased by insect diversity, selection effects, and interactions between insects and microbes. Ecology 2023; 104:e4184. [PMID: 37787980 DOI: 10.1002/ecy.4184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 08/03/2023] [Accepted: 09/07/2023] [Indexed: 10/04/2023]
Abstract
Biodiversity drives ecosystem processes, but its influence on deadwood decomposition is poorly understood. To test the effects of insect diversity on wood decomposition, we conducted a mesocosm experiment manipulating the species richness and functional diversity of beetles. We applied a novel approach using computed tomography scanning to quantify decomposition by insects and recorded fungal and bacterial communities. Decomposition rates increased with both species richness and functional diversity of beetles, but the effects of functional diversity were linked to beetle biomass, and to the presence of one large-bodied species in particular. This suggests that mechanisms behind observed biodiversity effects are the selection effect, which is linked to the occurrence probability of large species, and the complementarity effect, which is driven by functional differentiation among species. Additionally, beetles had significant indirect effects on wood decomposition via bacterial diversity, fungal community composition, and fungal biomass. Our experiment shows that wood decomposition is driven by beetle diversity and its interactions with bacteria and fungi. This highlights that both insect and microbial biodiversity are critical to maintaining ecosystem functioning.
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Affiliation(s)
- Jia-Yun Zou
- School of Life Sciences, Ecosystem Dynamics and Forest Management Research Group, Technical University of Munich, Freising, Germany
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Marc W Cadotte
- Biological Sciences, University of Toronto-Scarborough, Toronto, Ontario, Canada
| | - Claus Bässler
- Bavarian Forest National Park, Grafenau, Germany
- Institute for Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany
- Ecology of Fungi, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Roland Brandl
- Faculty of Biology, Department of Ecology, Animal Ecology, Philipps-Universität Marburg, Marburg, Germany
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Werner Borken
- Department of Soil Ecology, University of Bayreuth, Bayreuth, Germany
| | - Elisa Stengel
- Field Station Fabrikschleichach, Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jörg Müller
- Bavarian Forest National Park, Grafenau, Germany
- Field Station Fabrikschleichach, Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sebastian Seibold
- School of Life Sciences, Ecosystem Dynamics and Forest Management Research Group, Technical University of Munich, Freising, Germany
- Technische Universität Dresden, Forest Zoology, Tharandt, Germany
- Berchtesgaden National Park, Berchtesgaden, Germany
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Khatri S, Chaudhary P, Shivay YS, Sharma S. Role of Fungi in Imparting General Disease Suppressiveness in Soil from Organic Field. MICROBIAL ECOLOGY 2023; 86:2047-2059. [PMID: 37010558 DOI: 10.1007/s00248-023-02211-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Soil microbial communities are key players responsible for imparting suppressive potential to the soil against soil-borne phytopathogens. Fungi have an immense potential to inhibit soil-borne phytopathogens, but the fungal counterpart has been less explored in this context. We assessed the composition of fungal communities in soil under long-term organic and conventional farming practice, and control soil. The disease-suppressive potential of organic field was already established. A comparative analysis of the disease suppressiveness contributed by the fungal component of soil from conventional and organic farms was assessed using dual culture assays. The quantification of biocontrol markers and total fungi was done; the characterization of fungal community was carried out using ITS-based amplicon sequencing. Soil from organic field exhibited higher disease-suppressive potential than that from conventional farming, against the pathogens selected for the study. Higher levels of hydrolytic enzymes such as chitinase and cellulase, and siderophore production were observed in soil from the organic field compared to the conventional field. Differences in community composition were observed under conventional and organic farming, with soil from organic field exhibiting specific enrichment of key biocontrol fungal genera. The fungal alpha diversity was lower in soil from the organic field compared to the conventional field. Our results highlight the role of fungi in contributing to general disease-suppressive ability of the soil against phytopathogens. The identification of fungal taxa specifically associated with organic farming can aid in understanding the mechanism of disease suppression under such a practice, and can be exploited to induce general disease suppressiveness in otherwise conducive soil.
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Affiliation(s)
- Shivani Khatri
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Priya Chaudhary
- UQ-IITD Academy of Research, IIT Delhi, New Delhi, 110016, India
| | - Yashbir S Shivay
- Division of Agronomy, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India.
- UQ-IITD Academy of Research, IIT Delhi, New Delhi, 110016, India.
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Borovička J, Sácký J, Kaňa A, Walenta M, Ackerman L, Braeuer S, Leonhardt T, Hršelová H, Goessler W, Kotrba P. Cadmium in the hyperaccumulating mushroom Thelephora penicillata: Intracellular speciation and isotopic composition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 855:159002. [PMID: 36155032 DOI: 10.1016/j.scitotenv.2022.159002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/05/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Thelephora penicillata is an ectomycorrhizal mushroom that can accumulate extraordinarily high concentrations of Cd, As, Cu, and Zn in its fruit-bodies. To better understand its element accumulation ability, we compared the element concentrations in T. penicillata with 10 distinct ectomycorrhizal mushroom species growing at the same site (Karlina Pila, Czech Republic). On average, T. penicillata accumulated 330, 2130, 26, and 4 times more Cd, As, Cu, and Zn, respectively, than other mushrooms. Size-exclusion chromatography and an electrophoretic analysis of T. penicillata cell extracts indicate that intracellular Cd may be present mainly in >1 kDa, presumably compartmentalized, Cd species, and partially binding with 6-kDa cysteinyl-containing peptide(s) resembling metallothioneins. The cadmium isotopic composition of mushroom fruit-bodies, soil digests, and soil extracts was investigated by thermal ionization mass spectrometry (TIMS) with double spike correction. The isotopic composition (δ114/110Cd) of ectomycorrhizal mushrooms from Karlina Pila varied in a wide range of -0.37 to +0.14 ‰. However, remarkably low δ114/110Cd values were observed in the majority of the investigated mushrooms when compared to the relatively homogeneous Cd isotopic composition of bulk soil (δ114/110Cd = +0.09 ‰) and the comparatively heavy isotopic composition of soil extracts (mean δ114/110Cd values of +0.11 ± 0.01 ‰ and +0.22 ± 0.01 ‰, depending on the extraction method). The isotopic composition of Cd hyperaccumulated in T. penicillata essentially matched the mycoavailable soil Cd fraction. However, most isotopic data indicates isotopic fractionation at the soil/fruit-body interface, which could be of environmental significance.
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Affiliation(s)
- Jan Borovička
- Institute of Geology of the Czech Academy of Sciences, Rozvojová 269, 16500 Prague 6, Czech Republic; Nuclear Physics Institute of the Czech Academy of Sciences, Hlavní 130, 25068 Husinec-Řež, Czech Republic.
| | - Jan Sácký
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 3, 166 28 Prague, Czech Republic
| | - Antonín Kaňa
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Martin Walenta
- University of Graz, Institute of Chemistry, Universitaetsplatz 1, 8010 Graz, Austria
| | - Lukáš Ackerman
- Institute of Geology of the Czech Academy of Sciences, Rozvojová 269, 16500 Prague 6, Czech Republic
| | - Simone Braeuer
- University of Graz, Institute of Chemistry, Universitaetsplatz 1, 8010 Graz, Austria
| | - Tereza Leonhardt
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 3, 166 28 Prague, Czech Republic
| | - Hana Hršelová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Walter Goessler
- University of Graz, Institute of Chemistry, Universitaetsplatz 1, 8010 Graz, Austria
| | - Pavel Kotrba
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 3, 166 28 Prague, Czech Republic
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Jörgensen K, Clemmensen KE, Wallander H, Lindahl BD. Do ectomycorrhizal exploration types reflect mycelial foraging strategies? THE NEW PHYTOLOGIST 2023; 237:576-584. [PMID: 36271619 PMCID: PMC10098516 DOI: 10.1111/nph.18566] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/01/2022] [Indexed: 05/19/2023]
Abstract
Ectomycorrhizal exploration types are commonly assumed to denote spatial foraging patterns and resource-related niches of extraradical mycelia. However, empirical evidence of the consistency of foraging strategies within exploration types is lacking. Here, we analysed ectomycorrhizal foraging patterns by incubating root-excluding ingrowth mesh bags filled with six different substrates in mature Picea abies forests. High-throughput sequencing was used to characterise ectomycorrhizal fungal communities in the mesh bags and on adjacent fine roots after one growing season. Contrary to expectations, many ectomycorrhizal genera of exploration types that are thought to produce little extraradical mycelium colonised ingrowth bags extensively, whereas genera commonly associated with ample mycelial production occurred sparsely in ingrowth bags relative to their abundance on roots. Previous assumptions about soil foraging patterns of exploration types do not seem to hold. Instead, we propose that variation in the proliferation of extraradical mycelium is related to intergeneric differences in mycelial longevity and the mobility of targeted resources.
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Affiliation(s)
- Karolina Jörgensen
- Department of Soil and EnvironmentSwedish University of Agricultural SciencesBox 7014SE‐750 07UppsalaSweden
- Department of Biological SciencesUniversity of BergenBox 7803NO‐5020BergenNorway
| | - Karina E. Clemmensen
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesBox 7026SE‐750 07UppsalaSweden
| | - Håkan Wallander
- Department of BiologyLund UniversitySölvegatan 37223 26LundSweden
| | - Björn D. Lindahl
- Department of Soil and EnvironmentSwedish University of Agricultural SciencesBox 7014SE‐750 07UppsalaSweden
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Fungi Present in the Organic and Mineral Layers of Six Broad-Leaved Tree Plantations as Assessed by the Plate Dilution Method. DIVERSITY 2022. [DOI: 10.3390/d15010008] [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
This study examined the distribution of culturable fungi and predominant genera in the organic layer and in the upper layers of the mineral soil of six broad-leaved tree plantations in autumn, after the full fall of leaves. In total, 1335 fungal isolates were recovered from an organic layer and two mineral layers (0–4 cm and 5–8 cm) of soil. The structure of fungal genera differed in the tree plantations and in the three studied soil layers. The organic layer was the layer most populated by fungi compared to the mineral layers. In the organic layer, Penicillium and phyllosphere fungi such as Cladosporium and Phoma dominated. Deeper in the soil, the dominance of certain genera decreased with the increase in Trichoderma, Mucor, Mortierella, and entomopathogenic fungi such as Paecilomyces and Beauveria. Penicillium was one of the most abundant fungi in all soil layers studied.
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7
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Seibold S, Müller J, Allner S, Willner M, Baldrian P, Ulyshen MD, Brandl R, Bässler C, Hagge J, Mitesser O. Quantifying wood decomposition by insects and fungi using computed tomography scanning and machine learning. Sci Rep 2022; 12:16150. [PMID: 36168033 PMCID: PMC9515192 DOI: 10.1038/s41598-022-20377-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 09/13/2022] [Indexed: 11/18/2022] Open
Abstract
Wood decomposition is a central process contributing to global carbon and nutrient cycling. Quantifying the role of the major biotic agents of wood decomposition, i.e. insects and fungi, is thus important for a better understanding of this process. Methods to quantify wood decomposition, such as dry mass loss, suffer from several shortcomings, such as destructive sampling or subsampling. We developed and tested a new approach based on computed tomography (CT) scanning and semi-automatic image analysis of logs from a field experiment with manipulated beetle communities. We quantified the volume of beetle tunnels in wood and bark and the relative wood volume showing signs of fungal decay and compared both measures to classic approaches. The volume of beetle tunnels was correlated with dry mass loss and clearly reflected the differences between beetle functional groups. Fungal decay was identified with high accuracy and strongly correlated with ergosterol content. Our data show that this is a powerful approach to quantify wood decomposition by insects and fungi. In contrast to other methods, it is non-destructive, covers entire deadwood objects and provides spatially explicit information opening a wide range of research options. For the development of general models, we urge researchers to publish training data.
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Affiliation(s)
- Sebastian Seibold
- Ecosystem Dynamics and Forest Management Group, Technical University of Munich, 85354, Freising, Germany. .,Berchtesgaden National Park, Doktorberg 6, 83471, Berchtesgaden, Germany. .,Terrestrial Ecology Research Group, Technical University of Munich, 85354, Freising, Germany.
| | - Jörg Müller
- Field Station Fabrikschleichach, Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Glashüttenstrasse 5, 96181, Rauhenebrach, Germany.,Bavarian Forest National Park, Freyungerstrasse 2, 94481, Grafenau, Germany
| | | | - Marian Willner
- MITOS GmbH, Lichtenbergstrasse 8, 85748, Garching, Germany
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220, Praha 4, Czech Republic
| | | | - Roland Brandl
- Faculty of Biology, Department of Ecology, Animal Ecology, Philipps-Universität Marburg, Karl-Von-Frisch Strasse 8, 35032, Marburg, Germany
| | - Claus Bässler
- Bavarian Forest National Park, Freyungerstrasse 2, 94481, Grafenau, Germany.,Faculty of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Jonas Hagge
- Forest Nature Conservation, Northwest German Forest Research Institute NW-FVA, 34346, Hann. Münden, Germany.,Forest Nature Conservation, Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Mitesser
- Field Station Fabrikschleichach, Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Glashüttenstrasse 5, 96181, Rauhenebrach, Germany
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Arshad M, Naqqash T, Tahir M, Leveau JH, Zaheer A, Tahira SA, Saeed NA, Asad S, Sajjad M. Comparison of bacterial diversity, root exudates and soil enzymatic activities in the rhizosphere of AVP1-transgenic and non-transgenic wheat (Triticum aestivum L.). J Appl Microbiol 2022; 133:3094-3112. [PMID: 35908279 DOI: 10.1111/jam.15751] [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: 05/08/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 11/26/2022]
Abstract
AIMS Soil microbial communities are among the most diverse communities that might be affected due to transgenic crops. Therefore, risk assessment studies on transgenes are essentially required as any adverse effects may depend not only on the specific gene and crop involved but also on soil conditions. METHODS AND RESULTS The present study deals with the comparison of bacterial populations, root exudates, and activities of soil enzymes in non-transgenic and AVP1-transgenic wheat rhizosphere, overexpressing vacuolar H+pyrophosphatase for salinity and drought stress tolerance. Amounts of organic acids and sugars produced as root exudates and activities of dehydrogenase, phosphatase, and protease enzymes in soil solution showed no significant differences in AVP1-transgenic and non-transgenic wheat rhizosphere, except for urease and phenol oxidase activities. The higher copy number of nifH gene showed the abundance of nitrogen-fixing bacteria in the rhizosphere of AVP1-transgenic wheat compared with non-transgenic wheat. nifH gene sequence analysis indicated the common diazotrophic genera Azospirillum, Bradyrhizobium, Rhizobium, and Pseudomonas in AVP1-transgenic and non-transgenic wheat except for Zoogloea detected only in non-transgenic wheat. Using 454-pyrosequencing of 16S rRNA gene from soil DNA, a total of 156, 282 sequences of 18 phyla were obtained, which represented bacterial (128,006), Archeal (7,928), and unclassified (21,568) sequences. Proteobacteria, Crenarchaeota, and Firmicutes were the most abundant phyla in transgenic and non-transgenic wheat rhizosphere. Further comparison of different taxonomic units at the genus level showed similar distribution in transgenic and non-transgenic wheat rhizosphere. CONCLUSION We conclude that AVP1 gene in transgenic wheat has no apparent adverse effects on the soil environment and different bacterial communities. However, bacterial community depends on several other factors not only genetic composition of the host plants. SIGNIFICANCE OF THE STUDY The present research supports introduction and cultivation of transgenic plants in agricultural systems without any adverse effects on indigenous bacterial communities and soil ecosystem.
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Affiliation(s)
- Muhammad Arshad
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad and Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Tahir Naqqash
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Tahir
- Department of Environmental Science, COMSATS University Islamabad, Vehari
| | - Johan H Leveau
- Department of Plant Pathology, One Shield's Avenue, University of California Davis, CA, USA
| | - Ahmad Zaheer
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | | | - Nasir Ahmad Saeed
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad and Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Shaheen Asad
- National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad and Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
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Cambisol Mycobiome in a Long-Term Field Experiment with Korean Pine as a Sole Edificator: A Case Study. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2030036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A culture-independent mycobiome survey in Haplic Cambisol under Korean pine in a long-term field experiment in the Russian Far East was conducted using sequence analysis of the ITS region amplified with ITS3/ITS4 primers using the metagenomic DNA as a matrix. Overall 758 fungal OTUs were identified, representing 15 phyla, 47 classes, 104 orders, 183 families, and 258 genera. More OTUs represented the Ascomycota phylum (513) than Basidiomycota (113), with both phyla together comprising 95% of the relative abundance. The Leotiomycetes class was ultimately prevailing; apparently contributing significantly to the organic matter decomposition and microbial biomass in soil, as shown by a PCA. Only two dominant OTUs (Pseudogymnoascus sp. and Hyaloscyphaceae, both Ascomycota) were common in the studied samples. The presented high mycobiome diversity in soil under the monospecies artificial forest, where Korean pine had been the sole edificator for forty years, allows concluding that plant chemistry diversity is the main factor shaping the soil mycobiome in such an environment. The obtained data provide a reference for further studies of soil mycobiota, especially under Korean pine with its aesthetic, as well as nut-producing, potential. The results can be helpful in the targeted creating of a soil mycobiome beneficial for pines in afforestation and remediation contexts.
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Abstract
Anoxic microsites arising in fungal biofilms may foster the presence of obligate anaerobes. Here, we analyzed whether and to which degree hyphae of Coprinopsis cinerea thriving in oxic habitats enable the germination, growth, and dispersal of the obligate anaerobic soil bacterium Clostridium acetobutylicum. Time-resolved optical oxygen mapping, microscopy, and metabolite analysis revealed the formation and persistence of anoxic circum hyphal niches, allowing for spore germination, growth, and fermentative activity of the obligate anaerobe in an otherwise inhabitable environment. Hypoxic liquid films containing 80% ± 10% of atmospheric oxygen saturation around single air-exposed hyphae thereby allowed for efficient clostridial dispersal amid spatially separated (>0.5 cm) anoxic sites. Hyphae hence may serve as good networks for the activity and spatial organization of obligate anaerobic bacteria in oxygenated heterogeneous environments such as soil.
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11
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Mundra S, Kauserud H, Økland T, Nordbakken J, Ransedokken Y, Kjønaas OJ. Shift in tree species changes the belowground biota of boreal forests. THE NEW PHYTOLOGIST 2022; 234:2073-2087. [PMID: 35307841 PMCID: PMC9325058 DOI: 10.1111/nph.18109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
The replacement of native birch with Norway spruce has been initiated in Norway to increase long-term carbon storage in forests. However, there is limited knowledge on the impacts that aboveground changes will have on the belowground microbiota. We examined which effects a tree species shift from birch to spruce stands has on belowground microbial communities, soil fungal biomass and relationships with vegetation biomass and soil organic carbon (SOC). Replacement of birch with spruce negatively influenced soil bacterial and fungal richness and strongly altered microbial community composition in the forest floor layer, most strikingly for fungi. Tree species-mediated variation in soil properties was a major factor explaining variation in bacterial communities. For fungi, both soil chemistry and understorey vegetation were important community structuring factors, particularly for ectomycorrhizal fungi. The relative abundance of ectomycorrhizal fungi and the ectomycorrhizal : saprotrophic fungal ratio were higher in spruce compared to birch stands, particularly in the deeper mineral soil layers, and vice versa for saprotrophs. The positive relationship between ergosterol (fungal biomass) and SOC stock in the forest floor layer suggests higher carbon sequestration potential in spruce forest soil, alternatively, that the larger carbon stock leads to an increase in soil fungal biomass.
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Affiliation(s)
- Sunil Mundra
- Section for Genetics and Evolutionary Biology (EvoGene)Department of BiosciencesUniversity of OsloPO Box 1066 BlindernOsloNO‐0316Norway
- Department of BiologyCollege of ScienceUnited Arab Emirates UniversityPO Box 15551Al‐Ain, Abu‐DhabiUnited Arab Emirates
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EvoGene)Department of BiosciencesUniversity of OsloPO Box 1066 BlindernOsloNO‐0316Norway
| | - Tonje Økland
- Norwegian Institute of Bioeconomy ResearchPO Box 115ÅsNO‐1431Norway
| | | | - Yngvild Ransedokken
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesPO Box 5003ÅsNO‐1432Norway
| | - O. Janne Kjønaas
- Norwegian Institute of Bioeconomy ResearchPO Box 115ÅsNO‐1431Norway
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12
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Effects of broad-spectrum antibiotics on the colonisation of probiotic yeast Saccharomyces boulardii in the murine gastrointestinal tract. Sci Rep 2022; 12:8862. [PMID: 35614092 PMCID: PMC9133042 DOI: 10.1038/s41598-022-12806-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/19/2022] [Indexed: 11/24/2022] Open
Abstract
Mouse models are commonly used to study the colonisation profiles of microorganisms introduced to the gastrointestinal tract. Three commonly used mouse models include conventional, germ-free, and antibiotic-treated mice. However, colonisation resistance in conventional mice and specialised equipment for germ-free mice are usually limiting factors in their applications. In this study, we sought to establish a robust colonisation model for Saccharomyces boulardii, a probiotic yeast that has caught attention in the field of probiotics and advanced microbiome therapeutics. We characterised the colonisation of S. boulardii in conventional mice and mice treated with a cocktail of broad-spectrum antibiotics, including ampicillin, kanamycin, metronidazole and vancomycin. We found colonisation levels increased up to 10,000-fold in the antibiotic-treated mice compared to nonantibiotic-treated mice. Furthermore, S. boulardii was detected continuously in more than 75% of mice for 10 days after the last administration in antibiotic-treated mice, in contrast to in nonantibiotic-treated mice where S. boulardii was undetectable in less than 2 days. Finally, we demonstrated that this antibiotic cocktail can be used in two commonly used mouse strains, C57BL/6 and ob/ob mice, both achieving ~ 108 CFU/g of S. boulardii in faeces. These findings highlight that the antibiotic cocktail used in this study is an advantageous tool to study S. boulardii based probiotic and advanced microbiome therapeutics.
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Németh JB, Knapp DG, Kósa A, Hegedűs PÁ, Herczeg G, Vági P, Kovács GM. Micro-scale Experimental System Coupled with Fluorescence-based Estimation of Fungal Biomass to Study Utilisation of Plant Substrates. MICROBIAL ECOLOGY 2022; 83:714-723. [PMID: 34218293 PMCID: PMC8979871 DOI: 10.1007/s00248-021-01794-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
The degradation capacity and utilisation of complex plant substrates are crucial for the functioning of saprobic fungi and different plant symbionts with fundamental functions in ecosystems. Measuring the growth capacity and biomass of fungi on such systems is a challenging task. We established a new micro-scale experimental setup using substrates made of different plant species and organs as media for fungal growth. We adopted and tested a reliable and simple titration-based method for the estimation of total fungal biomass within the substrates using fluorescence-labelled lectin. We found that the relationship between fluorescence intensity and fungal dry weight was strong and linear but differed among fungi. The effect of the plant organ (i.e. root vs. shoot) used as substrate on fungal growth differed among plant species and between root endophytic fungal species. The novel microscale experimental system is useful for screening the utilisation of different substrates, which can provide insight into the ecological roles and functions of fungi. Furthermore, our fungal biomass estimation method has applications in various fields. As the estimation is based on the fungal cell wall, it measures the total cumulative biomass produced in a certain environment.
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Affiliation(s)
- Julianna B Németh
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
| | - Dániel G Knapp
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
| | - Annamária Kósa
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
| | - Panna Á Hegedűs
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
| | - Gábor Herczeg
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
| | - Pál Vági
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
| | - Gábor M Kovács
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary.
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Carl S, Mohr S, Sahm R, Baschien C. Laboratory conditions can change the complexity and composition of the natural aquatic mycobiome on Alnus glutinosa leaf litter. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2022.101142] [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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15
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Hutchinson MI, Bell TAS, Gallegos-Graves LV, Dunbar J, Albright M. Merging Fungal and Bacterial Community Profiles via an Internal Control. MICROBIAL ECOLOGY 2021; 82:484-497. [PMID: 33410932 DOI: 10.1007/s00248-020-01638-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
Integrated measurements of fungi and bacteria are critical to understand how interactions between these taxa drive key processes in ecosystems ranging from soils to animal guts. High-throughput amplicon sequencing is commonly used to census microbiomes, but the genetic markers targeted for fungi and bacteria (typically ribosomal regions) are domain-specific so profiling must be performed separately, obscuring relationships between these groups. To solve this problem, we developed a spike-in method with an internal control (IC) construct containing primer sites commonly used for bacterial and fungal taxonomic profiling. The internal control offers several advantages: estimation of absolute abundances, estimation of fungal to bacterial ratios (F:B), integration of bacterial and fungal profiles for holistic community analysis, and lower costs compared to other quantitation methods. To validate the IC as a scaling method, we compared IC-derived measures of F:B to measures from quantitative PCR (qPCR) using a commercial mock community (the ZymoBiomic Microbial Community DNA Standard II, containing two fungi and eight bacteria) and complex environmental samples. For both the mock community and the environmental samples, the IC produced F:B values that were statistically consistent with qPCR. Merging the environmental fungal and bacterial profiles based on the IC-derived F:B values revealed new relationships among samples in terms of community similarity. This IC method is the first spike-in method to employ a single construct for cross-domain amplicon sequencing, offering more reliable measurements.
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Affiliation(s)
- Miriam I Hutchinson
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA
| | - Tisza A S Bell
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | | | - John Dunbar
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA
| | - Michaeline Albright
- Biosciences Division, Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM, 87545, USA.
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16
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Adamczyk B. How do boreal forest soils store carbon? Bioessays 2021; 43:e2100010. [PMID: 33956367 DOI: 10.1002/bies.202100010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 01/02/2023]
Abstract
Boreal forests store a globally significant pool of carbon (C), mainly in tree biomass and soil organic matter (SOM). Although crucial for future climate change predictions, the mechanisms underlying C stabilization are not well understood. Here, recently discovered mechanisms behind SOM stabilization, their level of understanding, interrelations, and future directions in the field are provided. A recently unraveled mechanism behind C stabilization via interaction of root-derived tannins with fungal necromass emphasizing fungal necromass chemistry is brought forth. The long-lasting dogma of the stability of SOM on minerals is challenged and the newest insights from the field of soil fauna and their influence on SOM stabilization are provided. In conclusion, mechanisms unraveled during the last decade are crucial steps forward to draw a holistic view of the main drivers of SOM stabilization.
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Piñuela Y, Alday JG, Oliach D, Castaño C, Bolaño F, Colinas C, Bonet JA. White mulch and irrigation increase black truffle soil mycelium when competing with summer truffle in young truffle orchards. MYCORRHIZA 2021; 31:371-382. [PMID: 33515357 DOI: 10.1007/s00572-020-01018-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
The black truffle (Tuber melanosporum Vittad.) and the summer truffle (Tuber aestivum Vittad.) are two of the most appreciated edible fungi worldwide. The natural distributions of both species partially overlap. However, the interspecific interactions between these truffles and how irrigation and mulching techniques impact the dynamics between them are still unknown. Here, an experimental truffle plantation with Quercus ilex was established in Maials (Catalonia, Spain), combining three soil mulch treatments (white mulch, black mulch and bare soil as a control) and two irrigation regimes (irrigated and non-irrigated as a control) to investigate truffle mycelial dynamics in soil when both truffle species co-occur. The development of truffle mycelium in two different seasons (spring and autumn) in two consecutive years (2017 and 2018) was quantified using qPCR. Truffle mycelia of both species showed greatest development under white mulch. When mycelia of both truffle species co-occurred in soil, irrigation combined with white mulch resulted in greater quantities of T. melanosporum mycelial biomass, whereas the control irrigation treatment favoured the development of T. aestivum. Mulch treatments were also advantageous for seedling growth, which was expressed as root collar diameter and its increment during the study period. Significant relationships between root collar diameter and root growth and the amount of mycelial biomass in the soil were observed for both truffle species. Our results indicate the potential advantages of using white mulch to support irrigation in truffle plantations located in areas with dry Mediterranean climatic conditions to promote the development of Tuber mycelium.
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Affiliation(s)
- Yasmine Piñuela
- Department of Crop and Forest Sciences, University of Lleida, 25198, Lleida, Spain.
- Forest Science and Technology Centre of Catalonia (CTFC), Crta. Sant Llorenç de Morunys km 2, 25280, Solsona, Spain.
| | - Josu G Alday
- Department of Crop and Forest Sciences, University of Lleida, 25198, Lleida, Spain
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | - Daniel Oliach
- Department of Crop and Forest Sciences, University of Lleida, 25198, Lleida, Spain
- Forest Science and Technology Centre of Catalonia (CTFC), Crta. Sant Llorenç de Morunys km 2, 25280, Solsona, Spain
| | - Carles Castaño
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden
| | - Francesc Bolaño
- Department of Crop and Forest Sciences, University of Lleida, 25198, Lleida, Spain
- Forest Science and Technology Centre of Catalonia (CTFC), Crta. Sant Llorenç de Morunys km 2, 25280, Solsona, Spain
| | - Carlos Colinas
- Department of Crop and Forest Sciences, University of Lleida, 25198, Lleida, Spain
- Forest Science and Technology Centre of Catalonia (CTFC), Crta. Sant Llorenç de Morunys km 2, 25280, Solsona, Spain
| | - José Antonio Bonet
- Department of Crop and Forest Sciences, University of Lleida, 25198, Lleida, Spain
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, 25198, Lleida, Spain
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Liu Y, Qu ZL, Liu B, Ma Y, Xu J, Shen WX, Sun H. The Impact of Pine Wood Nematode Infection on the Host Fungal Community. Microorganisms 2021; 9:microorganisms9050896. [PMID: 33922224 PMCID: PMC8146488 DOI: 10.3390/microorganisms9050896] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 01/29/2023] Open
Abstract
Pine wilt disease (PWD), caused by pinewood nematode (PWN) Bursaphelenchus xylophilus, is globally one of the most destructive diseases of pine forests, especially in China. However, little is known about the effect of PWD on the host microbiome. In this study, the fungal community and functional structures in the needles, roots, and soil of and around Pinus thunbergii naturally infected by PWN were investigated by using high-throughput sequencing coupled with the functional prediction (FUNGuild). The results showed that fungal richness, diversity, and evenness in the needles of diseased trees were significantly lower than those of healthy ones (p < 0.05), whereas no differences were found in the roots and soil. Principal coordinate analysis (PCoA) showed that the fungal community and functional structures significantly differed only in the needles of diseased and healthy trees, but not in the soil and roots. Functionally, the saprotrophs had a higher abundance in the needles of diseased trees, whereas symbiotrophs abundance was higher in the needles of healthy trees (linear discriminant analysis (LDA) > 2.0, p < 0.05). These results indicated that PWN infection primarily affected the fungal community and functional structures in the needles of P. thunbergii, but not the roots and soil.
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Affiliation(s)
- Yi Liu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (Z.-L.Q.); (B.L.); (Y.M.); (J.X.)
| | - Zhao-Lei Qu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (Z.-L.Q.); (B.L.); (Y.M.); (J.X.)
| | - Bing Liu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (Z.-L.Q.); (B.L.); (Y.M.); (J.X.)
| | - Yang Ma
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (Z.-L.Q.); (B.L.); (Y.M.); (J.X.)
| | - Jie Xu
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (Z.-L.Q.); (B.L.); (Y.M.); (J.X.)
| | - Wen-Xiao Shen
- School of Foreign Language, Nanjing University of Finance and Economics, Nanjing 210046, China;
| | - Hui Sun
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; (Y.L.); (Z.-L.Q.); (B.L.); (Y.M.); (J.X.)
- Correspondence: ; Tel.: +86-13-851-724-350
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19
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Mundra S, Kjønaas OJ, Morgado LN, Krabberød AK, Ransedokken Y, Kauserud H. Soil depth matters: shift in composition and inter-kingdom co-occurrence patterns of microorganisms in forest soils. FEMS Microbiol Ecol 2021; 97:fiab022. [PMID: 33547899 PMCID: PMC7948073 DOI: 10.1093/femsec/fiab022] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/04/2021] [Indexed: 02/01/2023] Open
Abstract
Soil depth represents a strong physiochemical gradient that greatly affects soil-dwelling microorganisms. Fungal communities are typically structured by soil depth, but how other microorganisms are structured is less known. Here, we tested whether depth-dependent variation in soil chemistry affects the distribution and co-occurrence patterns of soil microbial communities. This was investigated by DNA metabarcoding in conjunction with network analyses of bacteria, fungi, as well as other micro-eukaryotes, sampled in four different soil depths in Norwegian birch forests. Strong compositional turnover in microbial assemblages with soil depth was detected for all organismal groups. Significantly greater microbial diversity and fungal biomass appeared in the nutrient-rich organic layer, with sharp decrease towards the less nutrient-rich mineral zones. The proportions of copiotrophic bacteria, Arthropoda and Apicomplexa were markedly higher in the organic layer, while patterns were opposite for oligotrophic bacteria, Cercozoa, Ascomycota and ectomycorrhizal fungi. Network analyses indicated more intensive inter-kingdom co-occurrence patterns in the upper mineral layer (0-5 cm) compared to the above organic and the lower mineral soil, signifying substantial influence of soil depth on biotic interactions. This study supports the view that different microbial groups are adapted to different forest soil strata, with varying level of interactions along the depth gradient.
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Affiliation(s)
- Sunil Mundra
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, Abu-Dhabi, UAE
| | - O Janne Kjønaas
- NIBIO, Department of Terrestrial Ecology, NO-1431 Ås, Norway
| | - Luis N Morgado
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
- Naturalis Biodiversity Center, 2300 RA Leiden, the Netherlands
| | - Anders Kristian Krabberød
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Yngvild Ransedokken
- Faculty of Environmental and Natural Resource Management, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
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20
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Peltoniemi K, Adamczyk S, Fritze H, Minkkinen K, Pennanen T, Penttilä T, Sarjala T, Laiho R. Site fertility and soil water-table level affect fungal biomass production and community composition in boreal peatland forests. Environ Microbiol 2020; 23:5733-5749. [PMID: 33350006 DOI: 10.1111/1462-2920.15368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 11/28/2022]
Abstract
A substantial amount of below-ground carbon (C) is suggested to be associated with fungi, which may significantly affect the soil C balance in forested ecosystems. Ergosterol from in-growth mesh bags and litterbags was used to estimate fungal biomass production and community composition in drained peatland forests with differing fertility. Extramatrical mycelia (EMM) biomass production was generally higher in the nutrient-poor site, increased with deeper water table level and decreased along the length of the recovery time. EMM biomass production was of the same magnitude as in mineral-soil forests. Saprotrophic fungal biomass production was higher in the nutrient-rich site. Both ectomycorrhizal (ECM) and saprotrophic fungal community composition changed according to site fertility and water table level. ECM fungal community composition with different exploration types may explain the differences in fungal biomass production between peatland forests. Melanin-rich Hyaloscypha may indicate decreased turnover of biomass in nutrient-rich young peatland forest. Genera Lactarius and Laccaria may be important in nutrient rich and Piloderma in the nutrient-poor conditions, respectively. Furthermore, Paxillus involutus and Cortinarius sp. may be important generalists in all sites and responsible for EMM biomass production during the first summer months. Saprotrophs showed a functionally more diverse fungal community in the nutrient-rich site.
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Affiliation(s)
- Krista Peltoniemi
- Natural Resources Institute Finland (LUKE), Natural Resources, Latokartanonkaari 9, Helsinki, FI-00790, Finland
| | - Sylwia Adamczyk
- Natural Resources Institute Finland (LUKE), Natural Resources, Latokartanonkaari 9, Helsinki, FI-00790, Finland
| | - Hannu Fritze
- Natural Resources Institute Finland (LUKE), Natural Resources, Latokartanonkaari 9, Helsinki, FI-00790, Finland
| | - Kari Minkkinen
- Department of Forest Sciences, University of Helsinki, Latokartanonkaari 7, Helsinki, FI-00790, Finland
| | - Taina Pennanen
- Natural Resources Institute Finland (LUKE), Natural Resources, Latokartanonkaari 9, Helsinki, FI-00790, Finland
| | - Timo Penttilä
- Natural Resources Institute Finland (LUKE), Natural Resources, Latokartanonkaari 9, Helsinki, FI-00790, Finland
| | - Tytti Sarjala
- Natural Resources Institute Finland (LUKE), Production Systems, Kaironiementie 15, Parkano, FI-39700, Finland
| | - Raija Laiho
- Natural Resources Institute Finland (LUKE), Natural Resources, Latokartanonkaari 9, Helsinki, FI-00790, Finland
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21
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22
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Castaño C, Berlin A, Brandström Durling M, Ihrmark K, Lindahl BD, Stenlid J, Clemmensen KE, Olson Å. Optimized metabarcoding with Pacific biosciences enables semi-quantitative analysis of fungal communities. THE NEW PHYTOLOGIST 2020; 228:1149-1158. [PMID: 32531109 DOI: 10.1111/nph.16731] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Recent studies have questioned the use of high-throughput sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region to derive a semi-quantitative representation of fungal community composition. However, comprehensive studies that quantify biases occurring during PCR and sequencing of ITS amplicons are still lacking. We used artificially assembled communities consisting of 10 ITS-like fragments of varying lengths and guanine-cytosine (GC) contents to evaluate and quantify biases during PCR and sequencing with Illumina MiSeq, PacBio RS II and PacBio Sequel I technologies. Fragment length variation was the main source of bias in observed community composition relative to the template, with longer fragments generally being under-represented for all sequencing platforms. This bias was three times higher for Illumina MiSeq than for PacBio RS II and Sequel I. All 10 fragments in the artificial community were recovered when sequenced with PacBio technologies, whereas the three longest fragments (> 447 bases) were lost when sequenced with Illumina MiSeq. Fragment length bias also increased linearly with increasing number of PCR cycles but could be mitigated by optimization of the PCR setup. No significant biases related to GC content were observed. Despite lower sequencing output, PacBio sequencing was better able to reflect the community composition of the template than Illumina MiSeq sequencing.
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Affiliation(s)
- Carles Castaño
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Anna Berlin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Katharina Ihrmark
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Karina E Clemmensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
| | - Åke Olson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, SE-75007, Sweden
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23
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Mešić A, Šamec D, Jadan M, Bahun V, Tkalčec Z. Integrated morphological with molecular identification and bioactive compounds of 23 Croatian wild mushrooms samples. FOOD BIOSCI 2020. [DOI: 10.1016/j.fbio.2020.100720] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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24
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Štursová M, Kohout P, Human ZR, Baldrian P. Production of Fungal Mycelia in a Temperate Coniferous Forest Shows Distinct Seasonal Patterns. J Fungi (Basel) 2020; 6:E190. [PMID: 32993121 PMCID: PMC7712845 DOI: 10.3390/jof6040190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
In temperate forests, climate seasonality restricts the photosynthetic activity of primary producers to the warm season from spring to autumn, while the cold season with temperatures below the freezing point represents a period of strongly reduced plant activity. Although soil microorganisms are active all-year-round, their expressions show seasonal patterns. This is especially visible on the ectomycorrhizal fungi, the most abundant guild of fungi in coniferous forests. We quantified the production of fungal mycelia using ingrowth sandbags in the organic layer of soil in temperate coniferous forest and analysed the composition of fungal communities in four consecutive seasons. We show that fungal biomass production is as low as 0.029 µg g-1 of sand in December-March, while it reaches 0.122 µg g-1 in June-September. The majority of fungi show distinct patterns of seasonal mycelial production, with most ectomycorrhizal fungi colonising ingrowth bags in the spring or summer, while the autumn and winter colonisation was mostly due to moulds. Our results indicate that fungal taxa differ in their seasonal patterns of mycelial production. Although fungal biomass turnover appears all-year-round, its rates are much faster in the period of plant activity than in the cold season.
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Affiliation(s)
- Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic; (P.K.); (Z.R.H.)
| | | | | | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic; (P.K.); (Z.R.H.)
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Changes in Chemical and Microbial Soil Parameters Following 8 Years of Deadwood Decay: An Experiment with Logs of 13 Tree Species in 30 Forests. Ecosystems 2020. [DOI: 10.1007/s10021-020-00562-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Starke R, Morais D, Větrovský T, López Mondéjar R, Baldrian P, Brabcová V. Feeding on fungi: genomic and proteomic analysis of the enzymatic machinery of bacteria decomposing fungal biomass. Environ Microbiol 2020; 22:4604-4619. [PMID: 32743948 DOI: 10.1111/1462-2920.15183] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 07/21/2020] [Accepted: 07/31/2020] [Indexed: 11/29/2022]
Abstract
Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a broad suite of carbohydrate-active enzymes, peptidases and transporters. In the extracellular proteome, only Ewingella americana expressed chitinases while the two Pseudomonas isolates attacked chitin by lytic chitin monooxygenase, deacetylation and deamination. Variovorax sp. expressed enzymes acting on the side-chains of various glucans and the chitin backbone. Surprisingly, despite its genomic potential, Pedobacter sp. did not produce extracellular proteins to decompose fungal mycelia but presumably feeds on simple substrates. The ecological roles of the five individual strains exhibited complementary features for a fast and efficient decomposition of dead fungal biomass by the entire bacterial community.
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Affiliation(s)
- Robert Starke
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Ruben López Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
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Guhr A, Kircher S. Drought-Induced Stress Priming in Two Distinct Filamentous Saprotrophic Fungi. MICROBIAL ECOLOGY 2020; 80:27-33. [PMID: 31950228 PMCID: PMC7338827 DOI: 10.1007/s00248-019-01481-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/22/2019] [Indexed: 05/04/2023]
Abstract
Sessile organisms constantly face environmental fluctuations and especially drought is a common stressor. One adaptive mechanism is "stress priming," the ability to cope with a severe stress ("triggering") by retaining information from a previous mild stress event ("priming"). While plants have been extensively investigated for drought-induced stress priming, no information is available for saprotrophic filamentous fungi, which are highly important for nutrient cycles. Here, we investigated the potential for drought-induced stress priming of one strain each of two ubiquitous species, Neurospora crassa and Penicillium chrysogenum. A batch experiment with 4 treatments was conducted on a sandy soil: exposure to priming and/or triggering as well as non-stressed controls. A priming stress was caused by desiccation to pF 4. The samples were then rewetted and after 1-, 7-, or 14-days of recovery triggered (pF 6). After triggering, fungal biomass, respiration, and β-glucosidase activity were quantified. P. chrysogenum showed positive stress priming effects. After 1 day of recovery, biomass as well as β-glucosidase activity and respiration were 0.5 to 5 times higher during triggering. Effects on biomass and activity decreased with prolonged recovery but lasted for 7 days and minor effects were still detectable after 14 days. Without triggering, stress priming had a temporary negative impact on biomass but this reversed after 14 days. For N. crassa, no stress priming effect was observed on the tested variables. The potential for drought-induced stress priming seems to be species specific with potentially high impact on composition and activity of fungal communities considering the expected increase of drought events.
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Affiliation(s)
- Alexander Guhr
- Department of Soil Ecology, BayCEER, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95448, Bayreuth, Germany.
| | - Sophia Kircher
- Department of Soil Ecology, BayCEER, University of Bayreuth, Dr.-Hans-Frisch-Straße 1-3, 95448, Bayreuth, Germany
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28
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New method for rapid identification and quantification of fungal biomass using ergosterol autofluorescence. Talanta 2020; 219:121238. [PMID: 32887129 DOI: 10.1016/j.talanta.2020.121238] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 01/06/2023]
Abstract
This research reports on the development of a method to identify and quantify fungal biomass based on ergosterol autofluorescence using excitation-emission matrix (EEM) measurements. In the first stage of this work, several ergosterol extraction methods were evaluated by APCI-MS, where the ultrasound-assisted procedure showed the best results. Following an experimental design, various quantities of the dried mycelium of the fungus Schizophyllum commune were mixed with the starchy solid residue (BBR) from the babassu (Orbignya sp.) oil industry, and these samples were subjected to several ergosterol extraction methods. The EEM spectral data of the samples were subjected to Principal Component Analysis (PCA), which showed the possibility to qualitatively evaluate the presence of ergosterol in the samples by ergosterol autofluorescence without the addition of any reagent. In order to assess the feasibility of quantifying fungal biomass using ergosterol autofluorescence, the EEM spectral data and known amounts of fungal biomass were modeled using partial least squares (PLS) regression and a procedure of backward selection of predictors (AutoPLS) was applied to select the Excitation-Emission wavelength pairs that provide the lowest prediction error. The results revealed that the amount of fungal biomass in samples containing interfering substances (BBR) can be accurately predicted with R2CV = 0.939, R2P = 0.936, RPDcv = 4.07, RPDp = 4.06, RMSECV = 0.0731 and RMSEP = 0.0797. In order to obtain an easy-to-understand equation that expresses the relationship between fungal biomass and fluorescence intensity, multiple linear regression (MLR) was applied to the VIP variables selected by the AutoPLS method. The MLR model selected only 2 variables and showed a very good performance, with R2CV = 0.862, R2P = 0.809, RPDcv = 2.18, RPDp = 2.35, RMSECV = 0.137 and RMSEP = 0.138. This study demonstrated that ergosterol autofluorescence can be successfully used to quantify fungal biomass even when mixed with agroindustrial residues, in this case BBR.
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Jomura M, Kuwayama T, Soma Y, Yamaguchi M, Komatsu M, Maruyama Y. Mycelial biomass estimation and metabolic quotient of Lentinula edodes using species-specific qPCR. PLoS One 2020; 15:e0232049. [PMID: 32421692 PMCID: PMC7233531 DOI: 10.1371/journal.pone.0232049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 04/06/2020] [Indexed: 11/19/2022] Open
Abstract
Lentinula edodes, commonly known as shiitake, is an edible mushroom that is cultivated and consumed around the globe, especially in Asia. Monitoring mycelial growth inside a woody substrate is difficult, but it is essential for effective management of mushroom cultivation. Mycelial biomass also affects the rate of wood decomposition under natural conditions and must be known to determine the metabolic quotient, an important ecophysiological parameter of fungal growth. Therefore, developing a method to measure it inside a substrate would be very useful. In this study, as the first step in understanding species-specific rates of fungal decomposition of wood, we developed species-specific primers and qPCR procedures for L. edodes. We tested primer specificity using strains of L. edodes from Japan and Southeast Asia, as well as related species of fungi and plant species for cultivation of L. edodes, and generated a calibration curve for quantification of mycelial biomass in wood dust inoculated with L. edodes. The qPCR procedure we developed can specifically detect L. edodes and allowed us to quantify the increase in L. edodes biomass in wood dust substrate and calculate the metabolic quotient based on the mycelial biomass and respiration rate. Development of a species-specific method for biomass quantification will be useful for both estimation of mycelial biomass and determining the kinetics of fungal growth in decomposition processes.
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Affiliation(s)
- Mayuko Jomura
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
- * E-mail:
| | - Tomoko Kuwayama
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Yuto Soma
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | | | - Masabumi Komatsu
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Yutaka Maruyama
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
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Dong SJ, Jiang YL, Peng J, Zhang CX, Zhu Q, Wang QQ, Liao YN, Pi WL, Dong XY, Yuan JP, Wang JH. Evaluation of ergosterol composition and esterification rate in fungi isolated from mangrove soil, long-term storage of broken spores, and two soils. Appl Microbiol Biotechnol 2020; 104:5461-5475. [PMID: 32333053 DOI: 10.1007/s00253-020-10601-3] [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: 01/28/2020] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 11/26/2022]
Abstract
Ergosterol is an important fungal-specific biomarker, but its use for fungal biomass estimation is still varied. It is important to distinguish between free and esterified ergosterols, which are mainly located on the plasma membrane and the cytosolic lipid particles, respectively. The present study analyzes free and esterified ergosterol contents in: (1) the fifty-nine strains of culturable fungi isolated from mangrove soil, (2) the broken spores of the fungus Ganoderma lucidum stored in capsule for more than 12 years, and (3) the mangrove soil and nearby campus wood soil samples by high performance liquid chromatography (HPLC). The results show that the contents of free and esterified ergosterols varied greatly in fifty-nine strains of fungi after 5 days of growth, indicating the diversity of ergosterol composition in fungi. The average contents of free and total ergosterols from the fifty-nine strains of fungi are 4.4 ± 1.5 mg/g and 6.1 ± 1.9 mg/g dry mycelia, respectively, with an average ergosterol esterification rate of 27.4%. The present study suggests that the fungi might be divided into two classes, one is fungi with high esterification rates (e.g., more than 27%) such as Nectria spp. and Fusarium spp., and the other is fungi with low esterification rates (e.g., less than 27%) such as Penicillium spp. and Trichoderma spp. Moreover, the ergosterol esterification rate in the spores of G. lucidum is 91.4% with a very small amount of free ergosterol (0.015 mg/g), compared with 41.9% with a higher level of free ergosterol (0.499 mg/g) reported in our previous study in 2007, indicating that free ergosterol degrades more rapidly than esterified ergosterol. In addition, the ergosterol esterification rates in mangrove soil and nearby campus wood soil samples range from 0 to 39.0%, compared with 80% in an old soil organic matter reported in a previous study, indicating the potential relationship between aging degree of fungi or soil and esterification rate. The present study proposes that both free and esterified ergosterols should be analyzed for fungal biomass estimation. When the ergosterol esterification rates in soils are higher, free ergosterol might be a better marker for fungal biomass. It is speculated that the ergosterol esterification rate in soils might contain some important information, such as the age of old-growth forests over time scales of centuries to millennia, besides the senescence degree of fungal mycelia in soils. KEY POINTS: • Fungi might be divided into two classes depending on ergosterol esterification rates. • Ergosterol esterification rate of broken spores stored for long time raised evidently. • Both free and esterified ergosterols should be analyzed for fungal biomass estimate. • Free ergosterol is a better marker for fungal biomass with a high esterification rate.
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Affiliation(s)
- Shu-Jun Dong
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, People's Republic of China
| | - Yun-Lin Jiang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, People's Republic of China
| | - Juan Peng
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China.
| | - Chen-Xi Zhang
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Qing Zhu
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Qin-Qing Wang
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Yi-Nan Liao
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, People's Republic of China
| | - Wei-Ling Pi
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, People's Republic of China
| | - Xi-Yang Dong
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, People's Republic of China
| | - Jian-Ping Yuan
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, People's Republic of China.
| | - Jiang-Hai Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, People's Republic of China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
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Albright MBN, Runde A, Lopez D, Gans J, Sevanto S, Woolf D, Dunbar J. Effects of initial microbial biomass abundance on respiration during pine litter decomposition. PLoS One 2020; 15:e0224641. [PMID: 32059014 PMCID: PMC7021309 DOI: 10.1371/journal.pone.0224641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/23/2020] [Indexed: 11/18/2022] Open
Abstract
Microbial biomass is increasingly used to predict respiration in soil organic carbon (SOC) models. Its increased use combined with the difficulty of accurately measuring this variable points a need to directly assess the importance of microbial biomass abundance for carbon (C) cycling. To test the hypothesis that the initial microbial biomass abundance (i.e. biomass abundance on new plant litter) is a strong driver of plant litter C cycling, we manipulated biomass abundance by 10 and 100-fold dilution and composition using 12 source communities on sterile pine litter and measured respiration in microcosms for 30 days. In the first two days of microbial growth on fresh litter, a 100-fold difference in initial biomass abundance caused an average difference in respiration of nearly 300%, but the effect rapidly declined to less than 30% in 10 days and to 14% in 30 days. Parallel simulations with a soil carbon model, SOMIC 1.0, also predicted a 14% difference over 30 days, consistent with the experimental results. Model simulations predicted convergence of cumulative CO2 to within 10% in three months and within 4% in three years. Rapid microbial growth, evidenced by appearance of visible microbial mats on the litter during the first week of incubation, likely attenuates the effects of large initial differences in biomass abundance. In contrast, the persistence of source community as an explanatory factor in driving differences in respiration across microcosms supports the importance of microbial composition in C cycling. Overall, the results suggest that the initial abundance of microbial biomass on litter is a weak driver of C flux from litter decomposition over long timescales (months to years) when litter communities have equal nutrient availability. By extension, slight variation in the timing of microbial dispersal to fresh litter is likely to be a minor factor in long-term C flux.
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Affiliation(s)
- Michaeline B. N. Albright
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
- * E-mail:
| | - Andreas Runde
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Deanna Lopez
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Jason Gans
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Sanna Sevanto
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Dominic Woolf
- College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States of America
| | - John Dunbar
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
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Coleine C, Pombubpa N, Zucconi L, Onofri S, Stajich JE, Selbmann L. Endolithic Fungal Species Markers for Harshest Conditions in the McMurdo Dry Valleys, Antarctica. Life (Basel) 2020; 10:E13. [PMID: 32041249 PMCID: PMC7175349 DOI: 10.3390/life10020013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/24/2020] [Accepted: 02/04/2020] [Indexed: 02/03/2023] Open
Abstract
The microbial communities that inhabit lithic niches inside sandstone in the Antarctic McMurdo Dry Valleys of life's limits on Earth. The cryptoendolithic communities survive in these ice-free areas that have the lowest temperatures on Earth coupled with strong thermal fluctuations, extreme aridity, oligotrophy and high levels of solar and UV radiation. In this study, based on DNA metabarcoding, targeting the fungal Internal Transcribed Spacer region 1 (ITS1) and multivariate statistical analyses, we supply the first comprehensive overview onto the fungal diversity and composition of these communities sampled over a broad geographic area of the Antarctic hyper-arid cold desert. Six locations with surfaces that experience variable sun exposure were sampled to compare communities from a common area across a gradient of environmental pressure. The Operational Taxonomic Units (OTUs) identified were primarily members of the Ascomycota phylum, comprised mostly of the Lecanoromycetes and Dothideomycetes classes. The fungal species Friedmanniomyces endolithicus, endemic to Antarctica, was found to be a marker species to the harshest conditions occurring in the shady, south exposed rock surfaces. Analysis of community composition showed that sun exposure was an environmental property that explained community diversity and structured endolithic colonization.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (C.C.); (L.Z.); (S.O.)
| | - Nuttapon Pombubpa
- Department of Microbiology and Plant Pathology and Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA;
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (C.C.); (L.Z.); (S.O.)
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (C.C.); (L.Z.); (S.O.)
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology and Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA;
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (C.C.); (L.Z.); (S.O.)
- Italian National Antarctic Museum (MNA), Mycological Section, 16166 Genoa, Italy
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33
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Nilsson RH, Anslan S, Bahram M, Wurzbacher C, Baldrian P, Tedersoo L. Mycobiome diversity: high-throughput sequencing and identification of fungi. Nat Rev Microbiol 2020; 17:95-109. [PMID: 30442909 DOI: 10.1038/s41579-018-0116-y] [Citation(s) in RCA: 397] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
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Affiliation(s)
- R Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Sten Anslan
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Garching, Germany
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Leho Tedersoo
- Natural History Museum of Tartu University, Tartu, Estonia
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34
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Larsbrink J, McKee LS. Bacteroidetes bacteria in the soil: Glycan acquisition, enzyme secretion, and gliding motility. ADVANCES IN APPLIED MICROBIOLOGY 2020; 110:63-98. [PMID: 32386606 DOI: 10.1016/bs.aambs.2019.11.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The secretion of extracellular enzymes by soil microbes is rate-limiting in the recycling of biomass. Fungi and bacteria compete and collaborate for nutrients in the soil, with wide ranging ecological impacts. Within soil microbiota, the Bacteroidetes tend to be a dominant phylum, just like in human and animal intestines. The Bacteroidetes thrive because of their ability to secrete diverse arrays of carbohydrate-active enzymes (CAZymes) that target the highly varied glycans in the soil. Bacteroidetes use an energy-saving system of genomic organization, whereby most of their CAZymes are grouped into Polysaccharide Utilization Loci (PULs). These loci enable high level production of specific CAZymes only when their substrate glycans are abundant in the local environment. This gives the Bacteroidetes a clear advantage over other species in the competitive soil environment, further enhanced by the phylum-specific Type IX Secretion System (T9SS). The T9SS is highly effective at secreting CAZymes and/or tethering them to the cell surface, and is tightly coupled to the ability to rapidly glide over solid surfaces, a connection that promotes an active hunt for nutrition. Although the soil Bacteroidetes are less well studied than human gut symbionts, research is uncovering important biochemical and physiological phenomena. In this review, we summarize the state of the art on research into the CAZymes secreted by soil Bacteroidetes in the contexts of microbial soil ecology and the discovery of novel CAZymes for use in industrial biotechnology. We hope that this review will stimulate further investigations into the somewhat neglected enzymology of non-gut Bacteroidetes.
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Affiliation(s)
- Johan Larsbrink
- Wallenberg Wood Science Center, Gothenburg and Stockholm, Sweden; Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lauren Sara McKee
- Wallenberg Wood Science Center, Gothenburg and Stockholm, Sweden; Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.
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35
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A glance into the black box: Novel species-specific quantitative real-time PCR assays to disentangle aquatic hyphomycete community composition. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.08.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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36
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Liu X, Ge W, Zhang X, Chai C, Wu J, Xiang D, Chen X. Biodegradation of aged polycyclic aromatic hydrocarbons in agricultural soil by Paracoccus sp. LXC combined with humic acid and spent mushroom substrate. JOURNAL OF HAZARDOUS MATERIALS 2019; 379:120820. [PMID: 31271936 DOI: 10.1016/j.jhazmat.2019.120820] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/30/2019] [Accepted: 06/24/2019] [Indexed: 06/09/2023]
Abstract
Paracoccus sp. LXC combined with humic acid (HA) and spent mushroom substrate (SMS) obtained from Auricularia auricular and Sarcomyxa edulis was tested for the remediation of agricultural soil contaminated with aged polycyclic aromatic hydrocarbons (PAHs). The biomass and diversity of bacteria and fungi and the soil enzyme activity were analyzed. PAH removal and dissipation kinetics were examined. The highest degradation rate of PAHs was 56.5% when soil was amended with Paracoccus sp. LXC combined with HA and unsterilized SMS from A. auricular. The half-life of PAHs decreased from 2323.3 days in natural attenuation to 66.6-277.2 days in amended treatments. Soil treated with Paracoccus sp. LXC combined with HA and SMS from A. auricular acquired high contents of organic matter and nutrients. HA and SMS aided the growth of PAH-degrading bacteria and promoted the diversity of bacteria but not of fungi. The degradation rate of PAHs was mainly correlated positively with soil laccase activity. Low- and middle-molecular-weight PAHs were significantly removed by Paracoccus sp. LXC, HA and SMS. High-molecular-weight PAHs were removed by SMS but not by Paracoccus sp. LXC. Biodegradation by Paracoccus sp. LXC combined with HA and SMS is a promising choice for remediating aged PAH-contaminated agricultural soils.
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Affiliation(s)
- Xiuchu Liu
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wei Ge
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiaomei Zhang
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Chai
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Juan Wu
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Dan Xiang
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiaoyu Chen
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China
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37
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Wang Y, Sen K, He Y, Xie Y, Wang G. Impact of environmental gradients on the abundance and diversity of planktonic fungi across coastal habitats of contrasting trophic status. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 683:822-833. [PMID: 31154160 DOI: 10.1016/j.scitotenv.2019.05.204] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
Fungal communities in the coastal waters have long been known to be dynamic with a significant role in organic matter cycling. However, the effects of environmental gradients on their community structures are poorly described. Here we studied three coastal sites off the South China Sea, namely Pearl River Estuary (PE), Shenzhen Bay (SB), and Daya Bay (DB) with contrasting trophic status and heterogenous local influences. Environmental analysis of these sites suggested higher nutrient and low salinity levels at PE and SB with wide variability compared to DB. Average molecular abundances (18S rRNA gene copy numbers) at sites PE (1.05 ± 0.27 × 107 copies L-1) and SB (1.2 ± 0.69 × 107 copies L-1) were similar and significantly higher (P < 0.05) than that at site DB (5.5 ± 9.5 × 105 copies L-1). Although planktonic fungi were molecularly abundant at the three sites, live fungal biomass based on ergosterol assay was detected only at some stations of PE and SB. Both molecular abundance and live biomass were significantly correlated with chemical oxygen demand, nutrients, and phytoplankton biomass, supporting their role in detritus turnover. The fungal communities were unprecedently diverse with the ubiquitous dominance of Dikarya and the occasional predominance of Glomeromycota, Mucoromycota, Mortierellomycota, and Chytridiomycota. A total of 24 classes, 46 orders, 71 families, 59 genera, and eight species were classified within the eight detected phyla, including the new finding of ascomycetous class Geoglossomycetes in coastal waters. Salinity and nitrate were the significant (r2 = 0.70, P < 0.05) factors that determined the β-diversity of fungal communities. Overall, this study suggests that although planktonic fungi are ubiquitous in coastal habitats, their molecular abundances and diversities (both α and β) are significantly determined by environmental gradients, particularly the salinity, COD and nitrate levels of coastal waters.
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Affiliation(s)
- Yaqiong Wang
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China; School of Ecology, Environment and Resources, Qinghai University for Nationalities, Xining, Qinghai 810007, China
| | - Kalyani Sen
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Yaodong He
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Yunxuan Xie
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Guangyi Wang
- Center for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.
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Qin M, Shi G, Miranda JP, Liu Y, Meng Y, Pan J, Chai Y, Jiang S, Zhou G, Feng H, Zhang Q. Revegetation differentially influences microbial trophic groups in a Qinghai-Tibetan alpine steppe ecosystem. J Basic Microbiol 2019; 59:992-1003. [PMID: 31410872 DOI: 10.1002/jobm.201900149] [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: 03/18/2019] [Accepted: 07/25/2019] [Indexed: 11/08/2022]
Abstract
Revegetation accelerates the recovery of degraded lands. Different microbial trophic groups underpin this acceleration from the aspects of soil structure stabilization, nutrient accumulation, and ecosystem functions. However, little is known about how revegetation influences the community and biodiversity of different soil microbial trophic groups. Here, six revegetation treatments with different plantings of plant species were established at an excavation pit in the Qinghai-Tibetan Plateau. Communities of plant, bacteria, and several key soil fungal groups were investigated after 12 years of revegetation. Plant and all microbial trophic group compositions were markedly influenced by revegetation treatments. Total fungal and pathogenic fungal compositions were not significantly predicted by any factor of plant and soil, but arbuscular mycorrhizal fungal composition could be mainly predicted by plant composition and plant P content. Bacterial composition was mainly determined by soil total N, organic carbon concentration, and moisture content; and saprotrophic fungal composition was mainly determined by soil organic carbon. Soil pH was the strongest factor to predict bacterial metabolic functions. Our findings highlight that even the differences of microbial compositions were because of different revegetation treatments, but each trophic microbial composition had different relations with plant and/or soil; especially, the bacterial community and metabolic functions and saprotrophic fungal community were more correlated with soil properties rather than plant community or characteristics per se.
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Affiliation(s)
- Mingsen Qin
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China.,Key Laboratory of Southwest China Wildlife Resources Conservation, China West Normal University, Nanchong, China
| | - Guoxi Shi
- Key Laboratory of Utilization of Agricultural Solid Waste Resource, Tianshui Normal University, Tianshui, China
| | | | - Yongjun Liu
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
| | - Yiming Meng
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
| | - Jianbin Pan
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
| | - Yuxing Chai
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
| | - Shengjing Jiang
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
| | - Guoying Zhou
- The Key Laboratory of Restoration Ecology in Cold Region of Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Huyuan Feng
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China.,State Key Laboratory of Frozen Soil Engineering, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Qi Zhang
- School of Life Sciences, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
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Pieristè M, Chauvat M, Kotilainen TK, Jones AG, Aubert M, Robson TM, Forey E. Solar UV-A radiation and blue light enhance tree leaf litter decomposition in a temperate forest. Oecologia 2019; 191:191-203. [PMID: 31363838 PMCID: PMC6732127 DOI: 10.1007/s00442-019-04478-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 07/23/2019] [Indexed: 11/30/2022]
Abstract
Sunlight can accelerate the decomposition process through an ensemble of direct and indirect processes known as photodegradation. Although photodegradation is widely studied in arid environments, there have been few studies in temperate regions. This experiment investigated how exposure to solar radiation, and specifically UV-B, UV-A, and blue light, affects leaf litter decomposition under a temperate forest canopy in France. For this purpose, we employed custom-made litterbags built using filters that attenuated different regions of the solar spectrum. Litter mass loss and carbon to nitrogen (C:N) ratio of three species: European ash (Fraxinus excelsior), European beech (Fagus sylvatica) and pedunculate oak (Quercus robur), differing in their leaf traits and decomposition rate, were analysed over a period of 7–10 months. Over the entire period, the effect of treatments attenuating blue light and solar UV radiation on leaf litter decomposition was similar to that of our dark treatment, where litter lost 20–30% less mass and had a lower C:N ratio than under the full-spectrum treatment. Moreover, decomposition was affected more by the filter treatment than mesh size, which controlled access by mesofauna. The effect of filter treatment differed among the three species and appeared to depend on litter quality (and especially C:N), producing the greatest effect in recalcitrant litter (F. sylvatica). Even under the reduced irradiance found in the understorey of a temperate forest, UV radiation and blue light remain important in accelerating surface litter decomposition.
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Affiliation(s)
- Marta Pieristè
- Organismal and Evolutionary Biology (OEB), Viikki Plant Science Centre (ViPS), University of Helsinki, P.O. Box 65, Viikinkaari1, 00014, Helsinki, Finland. .,Normandie Université, UNIROUEN, IRSTEA, ECODIV, FR Scale CNRS 3730, Rouen, France.
| | - Matthieu Chauvat
- Normandie Université, UNIROUEN, IRSTEA, ECODIV, FR Scale CNRS 3730, Rouen, France
| | - Titta K Kotilainen
- Organismal and Evolutionary Biology (OEB), Viikki Plant Science Centre (ViPS), University of Helsinki, P.O. Box 65, Viikinkaari1, 00014, Helsinki, Finland.,Natural Resources Institute Finland, Itäinen Pitkäkatu 4a, 20520, Turku, FI, Finland
| | - Alan G Jones
- Earthwatch Institute, Mayfield House, 256 Banbury Road, Oxford, OX2 7DE, UK.,Forest Systems, Scion. 49 Sala Street, Private Bag 3020, Rotorua, 3046, New Zealand
| | - Michaël Aubert
- Normandie Université, UNIROUEN, IRSTEA, ECODIV, FR Scale CNRS 3730, Rouen, France
| | - T Matthew Robson
- Organismal and Evolutionary Biology (OEB), Viikki Plant Science Centre (ViPS), University of Helsinki, P.O. Box 65, Viikinkaari1, 00014, Helsinki, Finland
| | - Estelle Forey
- Normandie Université, UNIROUEN, IRSTEA, ECODIV, FR Scale CNRS 3730, Rouen, France
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40
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Tedersoo L, Bahram M. Mycorrhizal types differ in ecophysiology and alter plant nutrition and soil processes. Biol Rev Camb Philos Soc 2019; 94:1857-1880. [PMID: 31270944 DOI: 10.1111/brv.12538] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 05/27/2019] [Accepted: 05/30/2019] [Indexed: 12/13/2022]
Abstract
Mycorrhizal fungi benefit plants by improved mineral nutrition and protection against stress, yet information about fundamental differences among mycorrhizal types in fungi and trees and their relative importance in biogeochemical processes is only beginning to accumulate. We critically review and synthesize the ecophysiological differences in ectomycorrhizal, ericoid mycorrhizal and arbuscular mycorrhizal symbioses and the effect of these mycorrhizal types on soil processes from local to global scales. We demonstrate that guilds of mycorrhizal fungi display substantial differences in genome-encoded capacity for mineral nutrition, particularly acquisition of nitrogen and phosphorus from organic material. Mycorrhizal associations alter the trade-off between allocation to roots or mycelium, ecophysiological traits such as root exudation, weathering, enzyme production, plant protection, and community assembly as well as response to climate change. Mycorrhizal types exhibit differential effects on ecosystem carbon and nutrient cycling that affect global elemental fluxes and may mediate biome shifts in response to global change. We also note that most studies performed to date have not been properly replicated and collectively suffer from strong geographical sampling bias towards temperate biomes. We advocate that combining carefully replicated field experiments and controlled laboratory experiments with isotope labelling and -omics techniques offers great promise towards understanding differences in ecophysiology and ecosystem services among mycorrhizal types.
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Affiliation(s)
- Leho Tedersoo
- Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia.,Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, 50411 Tartu, Estonia.,Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden
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41
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Adamczyk B, Sietiö OM, Biasi C, Heinonsalo J. Interaction between tannins and fungal necromass stabilizes fungal residues in boreal forest soils. THE NEW PHYTOLOGIST 2019; 223:16-21. [PMID: 30721536 DOI: 10.1111/nph.15729] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Bartosz Adamczyk
- Department of Agricultural Sciences, University of Helsinki, PO Box 66, Helsinki, Finland
- Institute for Atmospheric and Earth System Research (INAR), University of Helsinki, PO Box 64, Helsinki, Finland
- Natural Resources Institute Finland (Luke), PO Box 2, Helsinki, Finland
| | - Outi-Maaria Sietiö
- Institute for Atmospheric and Earth System Research (INAR), University of Helsinki, PO Box 64, Helsinki, Finland
- Department of Microbiology, University of Helsinki, PO Box 33, Helsinki, Finland
| | - Christina Biasi
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 1627, Helsinki, Finland
| | - Jussi Heinonsalo
- Institute for Atmospheric and Earth System Research (INAR), University of Helsinki, PO Box 64, Helsinki, Finland
- Department of Forest Sciences, University of Helsinki, PO Box 33, Helsinki, Finland
- Finnish Meteorological Institute, Climate System Research, PO Box 503, Helsinki, Finland
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42
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Angst Š, Baldrian P, Harantová L, Cajthaml T, Frouz J. Different twig litter (Salix caprea) diameter does affect microbial community activity and composition but not decay rate. FEMS Microbiol Ecol 2019; 94:5046416. [PMID: 29961854 DOI: 10.1093/femsec/fiy126] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/23/2018] [Indexed: 12/21/2022] Open
Abstract
Small twigs represent a substantial input of organic carbon into forest soils, but potential influencing factors on their decomposition have rarely been investigated. Here, we studied potential effects of twig size on decomposition and associated composition and activity of microbial communities during decomposition. Because the surface area for microbial colonization and the volume of accessible substrate increases with decreasing twig size, we hypothesized that twig size affects both microbial community and decomposition rate. Litterbags with twigs (Salix caprea) of two different diameters were placed within the litter layer and consecutively collected over a seven-year period. We determined the mass loss and microbial measures after each sampling event. The observed microbial parameters suggested a faster microbial colonization of thin twigs, where the proportion of bacteria was higher than in thick twigs. The development of the microbial community in thick twigs was more gradual and the proportion of fungi was higher. Despite this differential and successional development of microbial communities (and against our hypothesis), the mass loss among different twig diameters did not differ after our seven-year experiment, indicating that surface-to-volume ratios, though a primary control on microbial succession, may have limited predictive power for twig decomposition rates.
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Affiliation(s)
- Šárka Angst
- Biology Centre of the Czech Academy of Sciences, v. v. i., SoWa Research Infrastructure & Institute of Soil Biology, Na Sádkách 7, CZ 37005 Ceské Budejovice, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, v. v. i., Vídenská 1083, CZ 14220 Praha, Czech Republic
| | - Lenka Harantová
- Institute of Microbiology of the Czech Academy of Sciences, v. v. i., Vídenská 1083, CZ 14220 Praha, Czech Republic
| | - Tomáš Cajthaml
- Institute of Microbiology of the Czech Academy of Sciences, v. v. i., Vídeňská 1083, CZ 14220 Praha, Czech Republic.,Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Benátská 2, CZ 12800, Praha 2, Czech Republic
| | - Jan Frouz
- Biology Centre of the Czech Academy of Sciences, v. v. i., SoWa Research Infrastructure & Institute of Soil Biology, Na Sádkách 7, CZ 37005 České Budějovice, Czech Republic.,Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Benátská 2, CZ 12800, Praha 2, Czech Republic
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43
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Pec GJ, Cahill, Jr. JF. Large-scale insect outbreak homogenizes the spatial structure of ectomycorrhizal fungal communities. PeerJ 2019; 7:e6895. [PMID: 31123638 PMCID: PMC6512761 DOI: 10.7717/peerj.6895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 04/02/2019] [Indexed: 11/20/2022] Open
Abstract
Ectomycorrhizal fungi (plant symbionts) are diverse and exist within spatially variable communities that play fundamental roles in the functioning of terrestrial ecosystems. However, the underlying ecological mechanisms that maintain and regulate the spatial structuring of ectomycorrhizal fungal communities are both complex and remain poorly understood. Here, we use a gradient of mountain pine beetle (Dendroctonus ponderosae) induced tree mortality across eleven stands in lodgepole pine (Pinus contorta) forests of western Canada to investigate: (i) the degree to which spatial structure varies within this fungal group, and (ii) how these patterns may be driven by the relative importance of tree mortality from changes in understory plant diversity, productivity and fine root biomass following tree death. We found that the homogeneity of the ectomycorrhizal fungal community increased with increasing tree death, aboveground understory productivity and diversity. Whereas, the independent effect of fine root biomass, which declined along the same gradient of tree mortality, increased the heterogeneity of the ectomycorrhizal fungal community. Together, our results demonstrate that large-scale biotic disturbance homogenizes the spatial patterns of ectomycorrhizal fungal communities.
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Affiliation(s)
- Gregory J. Pec
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, United States of America
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
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44
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Lofgren LA, Uehling JK, Branco S, Bruns TD, Martin F, Kennedy PG. Genome‐based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles. Mol Ecol 2019; 28:721-730. [DOI: 10.1111/mec.14995] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/22/2018] [Accepted: 11/27/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Lotus A. Lofgren
- Department of Plant and Microbial Biology University of Minnesota St. Paul Minnesota
| | - Jessie K. Uehling
- Department of Plant and Microbial Biology University of California Berkeley Berkeley California
| | - Sara Branco
- Department of Microbiology and Immunology Montana State University Bozeman Montana
| | - Thomas D. Bruns
- Department of Plant and Microbial Biology University of California Berkeley Berkeley California
| | - Francis Martin
- Laboratoire d'Excellence ARBRE, Interactions Arbres/Micro‐organismes, INRA UMR1136 INRA‐Université de Lorraine Champenoux France
| | - Peter G. Kennedy
- Department of Plant and Microbial Biology University of Minnesota St. Paul Minnesota
- Department of Ecology, Evolution and Behavior University of Minnesota St. Paul Minnesota
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45
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Baldrian P. The known and the unknown in soil microbial ecology. FEMS Microbiol Ecol 2019; 95:5281230. [DOI: 10.1093/femsec/fiz005] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/08/2019] [Indexed: 12/22/2022] Open
Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220 Praha 4, Czech Republic
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46
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Halbwachs H, Easton GL, Bol R, Hobbie EA, Garnett MH, Peršoh D, Dixon L, Ostle N, Karasch P, Griffith GW. Isotopic evidence of biotrophy and unusual nitrogen nutrition in soil-dwelling Hygrophoraceae. Environ Microbiol 2018; 20:3573-3588. [PMID: 30105856 PMCID: PMC6849620 DOI: 10.1111/1462-2920.14327] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 06/14/2018] [Accepted: 06/14/2018] [Indexed: 02/04/2023]
Abstract
Several lines of evidence suggest that the agaricoid, non-ectomycorrhizal members of the family Hygrophoraceae (waxcaps) are biotrophic with unusual nitrogen nutrition. However, methods for the axenic culture and lab-based study of these organisms remain to be developed, so our current knowledge is limited to field-based investigations. Addition of nitrogen, lime or organophosphate pesticide at an experimental field site (Sourhope) suppressed fruiting of waxcap basidiocarps. Furthermore, stable isotope natural abundance in basidiocarps were unusually high in 15 N and low in 13 C, the latter consistent with mycorrhizal nutritional status. Similar patterns were found in waxcap basidiocarps from diverse habitats across four continents. Additional data from 14 C analysis of basidiocarps and 13 C pulse label experiments suggest that these fungi are not saprotrophs but rather biotrophic endophytes and possibly mycorrhizal. The consistently high but variable δ15 N values (10-20‰) of basidiocarps further indicate that N acquisition or processing differ from other fungi; we suggest that N may be derived from acquisition of N via soil fauna high in the food chain.
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Affiliation(s)
- Hans Halbwachs
- Bavarian Forest National ParkFreyunger Str. 2, 94481, GrafenauGermany
| | - Gary L. Easton
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAdeilad Cledwyn, Penglais, Aberystwyth, Ceredigion, SY23 3DD, WalesUK
| | - Roland Bol
- Institute of Bio‐ and Geosciences, Agrosphere (IBG‐3). Forschungszentrum Jülich GmbHWilhelm‐Johnen‐Straße, 52428, JülichGermany
| | - Erik A. Hobbie
- Earth Systems Research Center, Morse HallUniversity of New Hampshire8 College Road, DurhamNH, 03824‐3525USA
| | - Mark H Garnett
- NERC Radiocarbon FacilityScottish Enterprise Technology ParkRankine Avenue, East Kilbride, G75 0QFScotland, UK
| | - Derek Peršoh
- Department of GeobotanyRuhr‐Universität BochumGebäude ND 03/170, Universitätsstraße 150, 44780, BochumGermany
| | - Liz Dixon
- Sustainable Soils and Grassland Systems, Rothamsted ResearchNorth Wyke, Okehampton, Devon, EX20 2SBEngland, UK
| | - Nick Ostle
- Lancaster Environment CentreLancaster UniversityLancaster, LA1 4YQEngland, UK
| | - Peter Karasch
- German Mycological SocietyKirchl 78. D‐94545, HohenauGermany
| | - Gareth W. Griffith
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAdeilad Cledwyn, Penglais, Aberystwyth, Ceredigion, SY23 3DD, WalesUK
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Coleine C, Zucconi L, Onofri S, Pombubpa N, Stajich JE, Selbmann L. Sun Exposure Shapes Functional Grouping of Fungi in Cryptoendolithic Antarctic Communities. Life (Basel) 2018; 8:E19. [PMID: 29865244 PMCID: PMC6027399 DOI: 10.3390/life8020019] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 05/30/2018] [Accepted: 05/31/2018] [Indexed: 11/16/2022] Open
Abstract
Antarctic cryptoendolithic microbial communities dominate ice-free areas of continental Antarctica, among the harshest environments on Earth. The endolithic lifestyle is a remarkable adaptation to the exceptional environmental extremes of this area, which is considered the closest terrestrial example to conditions on Mars. Recent efforts have attempted to elucidate composition of these extremely adapted communities, but the functionality of these microbes have remained unexplored. We have tested for interactions between measured environmental characteristics, fungal community membership, and inferred functional classification of the fungi present and found altitude and sun exposure were primary factors. Sandstone rocks were collected in Victoria Land, Antarctica along an altitudinal gradient from 834 to 3100 m a.s.l.; differently sun-exposed rocks were selected to test the influence of this parameter on endolithic settlement. Metabarcoding targeting the fungal internal transcribed spacer region 1 (ITS1) was used to catalogue the species found in these communities. Functional profile of guilds found in the samples was associated to species using FUNGuild and variation in functional groups compared across sunlight exposure and altitude. Results revealed clear dominance of lichenized and stress-tolerant fungi in endolithic communities. The main variations in composition and abundance of functional groups among sites correlated to sun exposure, but not to altitude.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy.
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy.
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy.
| | - Nuttapon Pombubpa
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA.
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA.
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy.
- Italian National Antarctic Museum (MNA), Mycological Section, Genoa 16166, Italy.
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48
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Reczuga MK, Lamentowicz M, Mulot M, Mitchell EAD, Buttler A, Chojnicki B, Słowiński M, Binet P, Chiapusio G, Gilbert D, Słowińska S, Jassey VEJ. Predator-prey mass ratio drives microbial activity under dry conditions in Sphagnum peatlands. Ecol Evol 2018; 8:5752-5764. [PMID: 29938090 PMCID: PMC6010735 DOI: 10.1002/ece3.4114] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/13/2018] [Accepted: 03/29/2018] [Indexed: 01/17/2023] Open
Abstract
Mid- to high-latitude peatlands are a major terrestrial carbon stock but become carbon sources during droughts, which are increasingly frequent as a result of climate warming. A critical question within this context is the sensitivity to drought of peatland microbial food webs. Microbiota drive key ecological and biogeochemical processes, but their response to drought is likely to impact these processes. Peatland food webs have, however, been little studied, especially the response of microbial predators. We studied the response of microbial predators (testate amoebae, ciliates, rotifers, and nematodes) living in Sphagnum moss carpet to droughts, and their influence on lower trophic levels and on related microbial enzyme activity. We assessed the impact of reduced water availability on microbial predators in two peatlands using experimental (Linje mire, Poland) and natural (Forbonnet mire, France) water level gradients, reflecting a sudden change in moisture regime (Linje), and a typically drier environment (Forbonnet). The sensitivity of different microbial groups to drought was size dependent; large sized microbiota such as testate amoebae declined most under dry conditions (-41% in Forbonnet and -80% in Linje). These shifts caused a decrease in the predator-prey mass ratio (PPMR). We related microbial enzymatic activity to PPMR; we found that a decrease in PPMR can have divergent effects on microbial enzymatic activity. In a community adapted to drier conditions, decreasing PPMR stimulated microbial enzyme activity, while in extreme drought experiment, it reduced microbial activity. These results suggest that microbial enzymatic activity resulting from food web structure is optimal only within a certain range of PPMR, and that different trophic mechanisms are involved in the response of peatlands to droughts. Our findings confirm the importance of large microbial consumers living at the surface of peatlands on the functioning of peatlands, and illustrate their value as early warning indicators of change.
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Affiliation(s)
- Monika K. Reczuga
- Laboratory of Wetland Ecology and MonitoringFaculty of Geographical and Geological SciencesAdam Mickiewicz UniversityPoznańPoland
- Department of Biogeography and PalaeoecologyFaculty of Geographical and Geological SciencesAdam Mickiewicz UniversityPoznańPoland
- Faculty of BiologyAdam Mickiewicz UniversityPoznańPoland
| | - Mariusz Lamentowicz
- Laboratory of Wetland Ecology and MonitoringFaculty of Geographical and Geological SciencesAdam Mickiewicz UniversityPoznańPoland
- Department of Biogeography and PalaeoecologyFaculty of Geographical and Geological SciencesAdam Mickiewicz UniversityPoznańPoland
| | - Matthieu Mulot
- Laboratory of Soil BiodiversityUniversity of NeuchatelNeuchatelSwitzerland
| | - Edward A. D. Mitchell
- Laboratory of Soil BiodiversityUniversity of NeuchatelNeuchatelSwitzerland
- Jardin Botanique de NeuchâtelNeuchatelSwitzerland
| | - Alexandre Buttler
- Laboratory of Wetland Ecology and MonitoringFaculty of Geographical and Geological SciencesAdam Mickiewicz UniversityPoznańPoland
- Swiss Federal Research InstituteWSL Site LausanneLausanneSwitzerland
- Laboratoire des Systèmes ÉcologiquesSchool of Architecture, Civil and Environmental EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- Laboratoire de Chrono‐EnvironnementUMR CNRS 6249UFR des Sciences et TechniquesUniversité de Franche‐ComtéBesançonFrance
| | - Bogdan Chojnicki
- Department of MeteorologyFaculty of Environmental Engineering and Spatial ManagementPoznan University of Life Sciences60‐649 PoznańPoland
| | - Michał Słowiński
- Department of Environmental Resources and GeohazardPolish Academy of SciencesInstitute of Geography and Spatial OrganizationWarszawaPoland
| | - Philippe Binet
- Laboratoire de Chrono‐EnvironnementUMR CNRS 6249UFR des Sciences et TechniquesUniversité de Franche‐ComtéBesançonFrance
| | - Geneviève Chiapusio
- Laboratoire de Chrono‐EnvironnementUMR CNRS 6249UFR des Sciences et TechniquesUniversité de Franche‐ComtéBesançonFrance
- UMR CARRTEL INRA 042 University of Savoie Mont‐BlancFR‐ 73376 Le Bourget du lacFrance
| | - Daniel Gilbert
- Laboratoire de Chrono‐EnvironnementUMR CNRS 6249UFR des Sciences et TechniquesUniversité de Franche‐ComtéBesançonFrance
| | - Sandra Słowińska
- Department of Geoecology and ClimatologyPolish Academy of SciencesInstitute of Geography and Spatial OrganizationWarsawPoland
| | - Vincent E. J. Jassey
- Swiss Federal Research InstituteWSL Site LausanneLausanneSwitzerland
- Laboratoire des Systèmes ÉcologiquesSchool of Architecture, Civil and Environmental EngineeringÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- Laboratoire d'Ecologie Fonctionnelle et Environnement (Ecolab)INPT, UPS, CNRSUniversité de ToulouseToulouse CedexFrance
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Stringlis IA, Yu K, Feussner K, de Jonge R, Van Bentum S, Van Verk MC, Berendsen RL, Bakker PAHM, Feussner I, Pieterse CMJ. MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health. Proc Natl Acad Sci U S A 2018; 115:E5213-E5222. [PMID: 29686086 DOI: 10.1094/pbiomes-11-18-0050-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Abstract
Plant roots nurture a tremendous diversity of microbes via exudation of photosynthetically fixed carbon sources. In turn, probiotic members of the root microbiome promote plant growth and protect the host plant against pathogens and pests. In the Arabidopsis thaliana-Pseudomonas simiae WCS417 model system the root-specific transcription factor MYB72 and the MYB72-controlled β-glucosidase BGLU42 emerged as important regulators of beneficial rhizobacteria-induced systemic resistance (ISR) and iron-uptake responses. MYB72 regulates the biosynthesis of iron-mobilizing fluorescent phenolic compounds, after which BGLU42 activity is required for their excretion into the rhizosphere. Metabolite fingerprinting revealed the antimicrobial coumarin scopoletin as a dominant metabolite that is produced in the roots and excreted into the rhizosphere in a MYB72- and BGLU42-dependent manner. Shotgun-metagenome sequencing of root-associated microbiota of Col-0, myb72, and the scopoletin biosynthesis mutant f6'h1 showed that scopoletin selectively impacts the assembly of the microbial community in the rhizosphere. We show that scopoletin selectively inhibits the soil-borne fungal pathogens Fusarium oxysporum and Verticillium dahliae, while the growth-promoting and ISR-inducing rhizobacteria P. simiae WCS417 and Pseudomonas capeferrum WCS358 are highly tolerant of the antimicrobial effect of scopoletin. Collectively, our results demonstrate a role for coumarins in microbiome assembly and point to a scenario in which plants and probiotic rhizobacteria join forces to trigger MYB72/BGLU42-dependent scopolin production and scopoletin excretion, resulting in improved niche establishment for the microbial partner and growth and immunity benefits for the host plant.
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Affiliation(s)
- Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Ke Yu
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Kirstin Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, 37077 Göttingen, Germany
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Sietske Van Bentum
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Marcel C Van Verk
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Peter A H M Bakker
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, 37077 Göttingen, Germany
- Department of Plant Biochemistry, Göttingen Center for Molecular Biosciences, University of Göttingen, 37077 Göttingen, Germany
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, 3508 TB Utrecht, The Netherlands;
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Nurika I, Eastwood DC, Barker GC. A comparison of ergosterol and PLFA methods for monitoring the growth of ligninolytic fungi during wheat straw solid state cultivation. J Microbiol Methods 2018; 148:49-54. [DOI: 10.1016/j.mimet.2018.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/05/2018] [Accepted: 03/14/2018] [Indexed: 11/25/2022]
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