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Gundale MJ, Axelsson EP, Buness V, Callebaut T, DeLuca TH, Hupperts SF, Ibáñez TS, Metcalfe DB, Nilsson MC, Peichl M, Spitzer CM, Stangl ZR, Strengbom J, Sundqvist MK, Wardle DA, Lindahl BD. The biological controls of soil carbon accumulation following wildfire and harvest in boreal forests: A review. GLOBAL CHANGE BIOLOGY 2024; 30:e17276. [PMID: 38683126 DOI: 10.1111/gcb.17276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/29/2024] [Accepted: 03/30/2024] [Indexed: 05/01/2024]
Abstract
Boreal forests are frequently subjected to disturbances, including wildfire and clear-cutting. While these disturbances can cause soil carbon (C) losses, the long-term accumulation dynamics of soil C stocks during subsequent stand development is controlled by biological processes related to the balance of net primary production (NPP) and outputs via heterotrophic respiration and leaching, many of which remain poorly understood. We review the biological processes suggested to influence soil C accumulation in boreal forests. Our review indicates that median C accumulation rates following wildfire and clear-cutting are similar (0.15 and 0.20 Mg ha-1 year-1, respectively), however, variation between studies is extremely high. Further, while many individual studies show linear increases in soil C stocks through time after disturbance, there are indications that C stock recovery is fastest early to mid-succession (e.g. 15-80 years) and then slows as forests mature (e.g. >100 years). We indicate that the rapid build-up of soil C in younger stands appears not only driven by higher plant production, but also by a high rate of mycorrhizal hyphal production, and mycorrhizal suppression of saprotrophs. As stands mature, the balance between reductions in plant and mycorrhizal production, increasing plant litter recalcitrance, and ectomycorrhizal decomposers and saprotrophs have been highlighted as key controls on soil C accumulation rates. While some of these controls appear well understood (e.g. temporal patterns in NPP, changes in aboveground litter quality), many others remain research frontiers. Notably, very little data exists describing and comparing successional patterns of root production, mycorrhizal functional traits, mycorrhizal-saprotroph interactions, or C outputs via heterotrophic respiration and dissolved organic C following different disturbances. We argue that these less frequently described controls require attention, as they will be key not only for understanding ecosystem C balances, but also for representing these dynamics more accurately in soil organic C and Earth system models.
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Affiliation(s)
- Michael J Gundale
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - E Petter Axelsson
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Vincent Buness
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Timon Callebaut
- Department of Environmental Science and Ecology, Umeå University, Umeå, Sweden
| | - Thomas H DeLuca
- College of Forestry, Oregon State University, Corvallis, Oregon, USA
| | - Stefan F Hupperts
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Theresa S Ibáñez
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Daniel B Metcalfe
- Department of Environmental Science and Ecology, Umeå University, Umeå, Sweden
| | - Marie-Charlotte Nilsson
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Matthias Peichl
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Clydecia M Spitzer
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Zsofia R Stangl
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Joachim Strengbom
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maja K Sundqvist
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - David A Wardle
- Department of Environmental Science and Ecology, Umeå University, Umeå, Sweden
| | - Björn D Lindahl
- Department of Soil Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
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2
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Bosch J, Dobbler PT, Větrovský T, Tláskal V, Baldrian P, Brabcová V. Decomposition of Fomes fomentatius fruiting bodies - transition of healthy living fungus into a decayed bacteria-rich habitat is primarily driven by Arthropoda. FEMS Microbiol Ecol 2024; 100:fiae044. [PMID: 38640440 PMCID: PMC11030162 DOI: 10.1093/femsec/fiae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/06/2024] [Accepted: 03/28/2024] [Indexed: 04/21/2024] Open
Abstract
Fomes fomentarius is a widespread, wood-rotting fungus of temperate, broadleaved forests. Although the fruiting bodies of F. fomentarius persist for multiple years, little is known about its associated microbiome or how these recalcitrant structures are ultimately decomposed. Here we used metagenomics and metatranscriptomics to analyse the microbial community associated with healthy living and decomposing F. fomentarius fruiting bodies to assess the functional potential of the fruiting body-associated microbiome and to determine the main players involved in fruiting body decomposition. F. fomentarius sequences in the metagenomes were replaced by bacterial sequences as the fruiting body decomposed. Most CAZymes expressed in decomposing fruiting bodies targeted components of the fungal cell wall with almost all chitin-targeting sequences, plus a high proportion of beta-glucan-targeting sequences, belonging to Arthropoda. We suggest that decomposing fruiting bodies of F. fomentarius represent a habitat rich in bacteria, while its decomposition is primarily driven by Arthropoda. Decomposing fruiting bodies thus represent a specific habitat supporting both microorganisms and microfauna.
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Affiliation(s)
- Jason Bosch
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Priscila Thiago Dobbler
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
| | - Vendula Brabcová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 142 00 Prague, Czechia
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3
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Baldrian P, López-Mondéjar R, Kohout P. Forest microbiome and global change. Nat Rev Microbiol 2023:10.1038/s41579-023-00876-4. [PMID: 36941408 DOI: 10.1038/s41579-023-00876-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 03/23/2023]
Abstract
Forests influence climate and mitigate global change through the storage of carbon in soils. In turn, these complex ecosystems face important challenges, including increases in carbon dioxide, warming, drought and fire, pest outbreaks and nitrogen deposition. The response of forests to these changes is largely mediated by microorganisms, especially fungi and bacteria. The effects of global change differ among boreal, temperate and tropical forests. The future of forests depends mostly on the performance and balance of fungal symbiotic guilds, saprotrophic fungi and bacteria, and fungal plant pathogens. Drought severely weakens forest resilience, as it triggers adverse processes such as pathogen outbreaks and fires that impact the microbial and forest performance for carbon storage and nutrient turnover. Nitrogen deposition also substantially affects forest microbial processes, with a pronounced effect in the temperate zone. Considering plant-microorganism interactions would help predict the future of forests and identify management strategies to increase ecosystem stability and alleviate climate change effects. In this Review, we describe the impact of global change on the forest ecosystem and its microbiome across different climatic zones. We propose potential approaches to control the adverse effects of global change on forest stability, and present future research directions to understand the changes ahead.
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Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Soil and Water Conservation and Waste Management, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
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4
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Pasquini D, Gori A, Pollastrini M, Alderotti F, Centritto M, Ferrini F, Brunetti C. Effects of drought-induced holm oak dieback on BVOCs emissions in a Mediterranean forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159635. [PMID: 36280081 DOI: 10.1016/j.scitotenv.2022.159635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Climate change is impairing tree physiology and growth, causing an increase in tree dieback in many Mediterranean forests. These desiccation phenomena are leading to changes in land cover and plant community composition. Mediterranean plants are capable to emit large amount of Biogenic Volatile Organic Compounds (BVOCs), whose emission and biosynthesis is strongly affected by environmental conditions. This study evaluates the seasonal changes in understory species composition in two forest stands in Southern Tuscany characterized by different levels of Quercus ilex L. crown defoliation (low and high defoliation, LD and HD) and the relationship with BVOCs emissions over three years. We found significant changes in the understory plant community following Q. ilex crown defoliation and mortality, observing an increment in the number of shrubs both in HD and LD stands. The environmental sampling of BVOCs fully reflected the changes in vegetation cover and composition, with a reduction in the amount of monoterpene emissions due to the increasing rates of defoliation and mortality of Q. ilex trees. Our results suggest that terpene emissions from Mediterranean forests would be modified by an increase of Q. ilex dieback, with important consequences for functioning of this forest ecosystem and its atmospheric chemistry.
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Affiliation(s)
- D Pasquini
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy; National Research Council of Italy, Institute for Sustainable Plant Protection (IPSP), Sesto Fiorentino, Florence 50019, Italy.
| | - A Gori
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy; National Research Council of Italy, Institute for Sustainable Plant Protection (IPSP), Sesto Fiorentino, Florence 50019, Italy.
| | - M Pollastrini
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy; National Research Council of Italy, Institute for Sustainable Plant Protection (IPSP), Sesto Fiorentino, Florence 50019, Italy.
| | - F Alderotti
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy; National Research Council of Italy, Institute for Sustainable Plant Protection (IPSP), Sesto Fiorentino, Florence 50019, Italy.
| | - M Centritto
- National Research Council of Italy, Institute for Sustainable Plant Protection (IPSP), Sesto Fiorentino, Florence 50019, Italy.
| | - F Ferrini
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Florence, Italy; National Research Council of Italy, Institute for Sustainable Plant Protection (IPSP), Sesto Fiorentino, Florence 50019, Italy; VALUE Laboratory on Green, Health & Wellbeing, University of Florence, Italy.
| | - C Brunetti
- National Research Council of Italy, Institute for Sustainable Plant Protection (IPSP), Sesto Fiorentino, Florence 50019, Italy.
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Zhao W, Wang DD, Huang KC, Liu S, Reyila M, Sun YF, Li JN, Cui BK. Seasonal variation in the soil fungal community structure of Larix gmelinii forests in Northeast China. Front Microbiol 2023; 14:1106888. [PMID: 37032849 PMCID: PMC10073431 DOI: 10.3389/fmicb.2023.1106888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
Soil fungi play an indispensable role in forest ecosystems by participating in energy flow, material circulation, and assisting plant growth and development. Larix gmelinii is the dominant tree species in the greater Khingan Mountains, which is the only cold temperate coniferous forest in China. Understanding the variations in underground fungi will help us master the situation of L. gmelinii above ground. We collected soil samples from three seasons and analyzed the differences in soil fungal community structure using high-throughput sequencing technology to study the seasonal changes in soil fungal community structure in L. gmelinii forests. We found that the Shannon and Chao1 diversity in autumn was significantly lower than in spring and summer. The community composition and functional guild varied significantly between seasons. Furthermore, we showed that ectomycorrhizal fungi dominated the functional guilds. The relative abundance of ectomycorrhizal fungi increased dramatically from summer to autumn and was significantly negatively correlated with temperature and precipitation. Temperature and precipitation positively affect the alpha diversity of fungi significantly. In addition, pH was negatively correlated with the Chao1 diversity. Temperature and precipitation significantly affected several dominant genera and functional guilds. Among the soil physicochemical properties, several dominant genera were affected by pH, and the remaining individual genera and functional guilds were significantly correlated with total nitrogen, available phosphorus, soil organic carbon, or cation exchange capacity. For the composition of total fungal community, temperature and precipitation, as well as soil physicochemical properties except AP, significantly drove the variation in community composition.
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6
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Metagenomic nanopore sequencing versus conventional diagnosis for identification of the dieback pathogens of mango trees. Biotechniques 2022; 73:261-272. [DOI: 10.2144/btn-2022-0087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Dieback is one of the most dangerous fungal diseases affecting mango trees. In this study, nanopore metagenome sequencing of the root-soil samples and infected plant tissues was conducted to identify the fungal pathogens present. Soil analysis of the infected mango trees showed the abundance of the Dikarya subkingdom (59%) including Lasiodiplodia theobromae (15%), Alternaria alternata (6%), Ceratocystis huliohia and Colletotrichum gloeosporioides. Analysis of the infected plant tissues revealed the presence of A. alternata (34%). The data were deposited in the National Center of Biotechnology Information (PRJNA767267). In conclusion, nanopore metagenome sequencing analysis was a valuable tool to rapidly identify dieback-associated fungal pathogens.
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7
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Martinović T, Kohout P, López-Mondéjar R, Algora Gallardo C, Starke R, Tomšovský M, Baldrian P. Bacterial community in soil and tree roots of Picea abies shows little response to clearcutting. FEMS Microbiol Ecol 2022; 98:6754320. [PMID: 36208910 DOI: 10.1093/femsec/fiac118] [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: 06/02/2022] [Revised: 09/15/2022] [Accepted: 10/06/2022] [Indexed: 01/21/2023] Open
Abstract
Clearcutting represents a standard management practice in temperate forests with dramatic consequences for the forest ecosystem. The removal of trees responsible for the bulk of primary production can result in a complex response of the soil microbiome. While studies have shown that tree root-symbiotic ectomycorrhizal fungi disappear from soil and decomposing fine roots of trees become a hotspot for fungal decomposition, the fate of the bacterial component of the soil microbiome following clearcutting is unclear. Here, we investigated the response of bacterial community composition for 2 years following clearcutting of a Picea abies stand in soil, rhizosphere and tree roots, by 16S rRNA amplicon sequencing. While in the first few months after clearcutting there was no significant response of bacterial community composition in the rhizosphere and soil, bacterial communities associated with tree roots underwent more profound changes over time. Acidobacteria were abundant in rhizosphere and soil, while Firmicutes were strongly represented in the roots. In addition, bacterial communities on decomposing roots were significantly different from those on pre-clearcut live roots. Compared with fungi, the response of bacterial communities to clearcutting was much less pronounced, indicating independent development of the two microbial domains.
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Affiliation(s)
- Tijana Martinović
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
- Faculty of Science, Charles University in Prague, Albertov 6, 128 00, Praha 2, Czech Republic
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
- Faculty of Science, Charles University in Prague, Albertov 6, 128 00, Praha 2, Czech Republic
| | - Rubén López-Mondéjar
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Camelia Algora Gallardo
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Robert Starke
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Michal Tomšovský
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Praha 4, Czech Republic
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8
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Ward EB, Duguid MC, Kuebbing SE, Lendemer JC, Bradford MA. The functional role of ericoid mycorrhizal plants and fungi on carbon and nitrogen dynamics in forests. THE NEW PHYTOLOGIST 2022; 235:1701-1718. [PMID: 35704030 DOI: 10.1111/nph.18307] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Ericoid mycorrhizal (ErM) shrubs commonly occur in forest understories and could therefore alter arbuscular (AM) and/or ectomycorrhizal (EcM) tree effects on soil carbon and nitrogen dynamics. Specifically, ErM fungi have extensive organic matter decay capabilities, and ErM plant and fungal tissues have high concentrations of secondary compounds that can form persistent complexes in the soil. Together, these traits could contribute to organic matter accumulation and inorganic nutrient limitation. These effects could also differ in AM- vs EcM-dominated stands at multiple scales within and among forest biomes by, for instance, altering fungal guild interactions. Most work on ErM effects in forests has been conducted in boreal forests dominated by EcM trees. However, ErM plants occur in c. 96, 69 and 29% of boreal, temperate and tropical forests, respectively. Within tropical montane forests, the effects of ErM plants could be particularly pronounced because their traits are more distinct from AM than EcM trees. Because ErM fungi can function as free-living saprotrophs, they could also be more resilient to forest disturbances than obligate symbionts. Further consideration of ErM effects within and among forest biomes could improve our understanding of how cooccurring mycorrhizal types interact to collectively affect soil carbon and nitrogen dynamics under changing conditions.
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Affiliation(s)
- Elisabeth B Ward
- The Forest School, Yale School of the Environment, Yale University, New Haven, CT, 06511, USA
- The New York Botanical Garden, The Bronx, NY, 10458, USA
| | - Marlyse C Duguid
- The Forest School, Yale School of the Environment, Yale University, New Haven, CT, 06511, USA
| | - Sara E Kuebbing
- The Forest School, Yale School of the Environment, Yale University, New Haven, CT, 06511, USA
| | | | - Mark A Bradford
- The Forest School, Yale School of the Environment, Yale University, New Haven, CT, 06511, USA
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9
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Baldrian P, Bell-Dereske L, Lepinay C, Větrovský T, Kohout P. Fungal communities in soils under global change. Stud Mycol 2022; 103:1-24. [PMID: 36760734 PMCID: PMC9886077 DOI: 10.3114/sim.2022.103.01] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/16/2022] [Indexed: 11/07/2022] Open
Abstract
Soil fungi play indispensable roles in all ecosystems including the recycling of organic matter and interactions with plants, both as symbionts and pathogens. Past observations and experimental manipulations indicate that projected global change effects, including the increase of CO2 concentration, temperature, change of precipitation and nitrogen (N) deposition, affect fungal species and communities in soils. Although the observed effects depend on the size and duration of change and reflect local conditions, increased N deposition seems to have the most profound effect on fungal communities. The plant-mutualistic fungal guilds - ectomycorrhizal fungi and arbuscular mycorrhizal fungi - appear to be especially responsive to global change factors with N deposition and warming seemingly having the strongest adverse effects. While global change effects on fungal biodiversity seem to be limited, multiple studies demonstrate increases in abundance and dispersal of plant pathogenic fungi. Additionally, ecosystems weakened by global change-induced phenomena, such as drought, are more vulnerable to pathogen outbreaks. The shift from mutualistic fungi to plant pathogens is likely the largest potential threat for the future functioning of natural and managed ecosystems. However, our ability to predict global change effects on fungi is still insufficient and requires further experimental work and long-term observations. Citation: Baldrian P, Bell-Dereske L, Lepinay C, Větrovský T, Kohout P (2022). Fungal communities in soils under global change. Studies in Mycology 103: 1-24. doi: 10.3114/sim.2022.103.01.
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Affiliation(s)
- P. Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeòská 1083, 142 20 Prague, Czech Republic,*Corresponding author: Petr Baldrian,
| | - L. Bell-Dereske
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeòská 1083, 142 20 Prague, Czech Republic
| | - C. Lepinay
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeòská 1083, 142 20 Prague, Czech Republic
| | - T. Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeòská 1083, 142 20 Prague, Czech Republic
| | - P. Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeòská 1083, 142 20 Prague, Czech Republic
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10
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Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity. BIOLOGY 2022; 11:biology11091297. [PMID: 36138776 PMCID: PMC9495823 DOI: 10.3390/biology11091297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/20/2022]
Abstract
Simple Summary The innovative concept of environmental DNA has found its foot in aquatic ecosystems but remains an unexplored area of research concerning terrestrial ecosystems. When making management choices, it is important to understand the rate of eDNA degradation, the persistence of DNA in terrestrial habitats, and the variables affecting eDNA detectability for a target species. Therefore an attempt has been made to provide comprehensive information regarding the exertion of eDNA in terrestrial ecosystems from 2012 to 2022. The information provided will assist ecologists, researchers and decision-makers in developing a holistic understanding of environmental DNA and its applicability as a biodiversity monitoring contrivance. Abstract The dearth of cardinal data on species presence, dispersion, abundance, and habitat prerequisites, besides the threats impeded by escalating human pressure has enormously affected biodiversity conservation. The innovative concept of eDNA, has been introduced as a way of overcoming many of the difficulties of rigorous conventional investigations, and is hence becoming a prominent and novel method for assessing biodiversity. Recently the demand for eDNA in ecology and conservation has expanded exceedingly, despite the lack of coordinated development in appreciation of its strengths and limitations. Therefore it is pertinent and indispensable to evaluate the extent and significance of eDNA-based investigations in terrestrial habitats and to classify and recognize the critical considerations that need to be accounted before using such an approach. Presented here is a brief review to summarize the prospects and constraints of utilizing eDNA in terrestrial ecosystems, which has not been explored and exploited in greater depth and detail in such ecosystems. Given these obstacles, we focused primarily on compiling the most current research findings from journals accessible in eDNA analysis that discuss terrestrial ecosystems (2012–2022). In the current evaluation, we also review advancements and limitations related to the eDNA technique.
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11
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González de Andrés E, Gazol A, Querejeta JI, Igual JM, Colangelo M, Sánchez‐Salguero R, Linares JC, Camarero JJ. The role of nutritional impairment in carbon-water balance of silver fir drought-induced dieback. GLOBAL CHANGE BIOLOGY 2022; 28:4439-4458. [PMID: 35320604 PMCID: PMC9540818 DOI: 10.1111/gcb.16170] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/12/2022] [Indexed: 06/01/2023]
Abstract
Rear-edge populations at the xeric distribution limit of tree species are particularly vulnerable to forest dieback triggered by drought. This is the case of silver fir (Abies alba) forests located in Southwestern Europe. While silver fir drought-induced dieback patterns have been previously explored, information on the role played by nutritional impairment is lacking despite its potential interactions with tree carbon-water balances. We performed a comparative analysis of radial growth, intrinsic water-use efficiency (iWUE), oxygen isotopes (δ18 O) and nutrient concentrations in leaves of declining (DD) and non-declining (ND) trees in silver fir in four forests in the Spanish Pyrenees. We also evaluated the relationships among dieback predisposition, intraspecific trait variation (wood density and leaf traits) and rhizosphere soil physical-chemical properties. The onset of growth decline in DD trees occurred more than two decades ago, and they subsequently showed low growth resilience against droughts. The DD trees presented consistently lower foliar concentrations of nutrients such as P, K, Cu and Ni than ND trees. The strong effects of foliar nutrient status on growth resilience indices support the key role played by mineral nutrition in tree functioning and growth before, during and after drought. In contrast, variability in wood density and leaf morphological traits, as well as soil properties, showed weak relationships with tree nutritional status and drought performance. At the low elevation, warmer sites, DD trees showed stronger climate-growth relationships and lower δ18 O than ND trees. The uncoupling between iWUE and δ18 O, together with the positive correlations between P and K leaf concentrations and δ18 O, point to deeper soil/bedrock water sources and vertical decoupling between nutrient and water uptake in DD trees. This study provides novel insights into the mechanisms driving silver fir dieback and highlights the need to incorporate tree nutrition into forest dieback studies.
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Affiliation(s)
| | - Antonio Gazol
- Instituto Pirenaico de Ecología (IPE‐CSIC)ZaragozaSpain
| | | | - José M. Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA‐CSIC)SalamancaSpain
| | - Michele Colangelo
- Instituto Pirenaico de Ecología (IPE‐CSIC)ZaragozaSpain
- Scuola di Scienze AgrarieForestaliAlimentarie AmbientaliUniversità della BasilicataPotenzaItaly
| | - Raúl Sánchez‐Salguero
- Instituto Pirenaico de Ecología (IPE‐CSIC)ZaragozaSpain
- Dpto. de Sistemas FísicosQuímicos y NaturalesUniversidad Pablo de OlavideSevillaSpain
| | - Juan Carlos Linares
- Dpto. de Sistemas FísicosQuímicos y NaturalesUniversidad Pablo de OlavideSevillaSpain
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Wasyliw J, Fellrath EG, Pec GJ, Cale JA, Franklin J, Thomasson C, Erbilgin N, Karst J. Soil inoculation of lodgepole pine seedlings alters root‐associated fungal communities but does not improve seedling performance in beetle‐killed pine stands. Restor Ecol 2022. [DOI: 10.1111/rec.13663] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joshua Wasyliw
- Department of Renewable Resources University of Alberta Edmonton Alberta Canada T6G 2E3
| | - Evan G. Fellrath
- Department of Renewable Resources University of Alberta Edmonton Alberta Canada T6G 2E3
| | - Gregory J. Pec
- Biology Department University of Nebraska at Kearney Kearney Nebraska United States 68849
| | - Jonathan A. Cale
- Department of Renewable Resources University of Alberta Edmonton Alberta Canada T6G 2E3
| | - James Franklin
- Department of Renewable Resources University of Alberta Edmonton Alberta Canada T6G 2E3
| | - Charlotte Thomasson
- Department of Renewable Resources University of Alberta Edmonton Alberta Canada T6G 2E3
| | - Nadir Erbilgin
- Department of Renewable Resources University of Alberta Edmonton Alberta Canada T6G 2E3
| | - Justine Karst
- Department of Renewable Resources University of Alberta Edmonton Alberta Canada T6G 2E3
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13
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Kaal J, Pérez-Rodríguez M, Biester H. Molecular Probing of DOM Indicates a Key Role of Spruce-Derived Lignin in the DOM and Metal Cycles of a Headwater Catchment: Can Spruce Forest Dieback Exacerbate Future Trends in the Browning of Central European Surface Waters? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2747-2759. [PMID: 35104105 DOI: 10.1021/acs.est.1c04719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peatlands of the Northern Hemisphere and Central European coniferous forests experience significant environmental change. The resultant browning of surface waters, that is, elevated concentrations of dissolved organic matter (DOM) and metals, is of interest in the context of the global C cycle, peatland and forest management, and water treatment. In an attempt to identify the causes of this process in the Harz Mountains (Central Germany), we studied the spatiotemporal variations in DOM molecular composition (thermally assisted hydrolysis and methylation combined with GC-MS) and metal concentrations in headwater stream samples. We found strong relationships between DOM and metals and seasonal variations in the DOM quality and tentatively DOM-metal binding mode: during summer base flow, DOM and metal concentrations are low, and all elements other than the alkali and alkaline earth metals (Ca, Mg, Sr, K, and Na) are positively correlated to DOM, whereas during spring and autumn (high discharge), only metals with strong affinity for DOM (Fe, As, Cu, Cr, Pb, and Ti), but not weakly binding ones (Al, Cd, La, Mn, Ni, Zn, and Zr), are correlated to DOM, indicative of selectivity in DOM-metal interactions. The products of polyphenols are the key ingredients of the DOM-metal complexes. We argue the importance of spruce lignin-derived vanillic acid moieties, which are involved in weak (all seasons) and strong, multidentate and/or colloidal, binding (spring and autumn) of metals. Considering the ongoing spruce forest dieback and climate change acceleration, it is tempting to conclude that spruce necromass and forest soils may release vast amounts of lignin-derived DOM and associated metals to headwater streams. This would have significant implications for forest soil C stocks and the management of connected drinking water reservoirs.
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Affiliation(s)
- Joeri Kaal
- Institut für Geoökologie, Abteilung Umweltgeochemie, Technische Universität Braunschweig, Langer Kamp 19C, Braunschweig 38106, Germany
| | - Marta Pérez-Rodríguez
- Institut für Geoökologie, Abteilung Umweltgeochemie, Technische Universität Braunschweig, Langer Kamp 19C, Braunschweig 38106, Germany
| | - Harald Biester
- Institut für Geoökologie, Abteilung Umweltgeochemie, Technische Universität Braunschweig, Langer Kamp 19C, Braunschweig 38106, Germany
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14
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Meyer N, Xu Y, Karjalainen K, Adamczyk S, Biasi C, van Delden L, Martin A, Mganga K, Myller K, Sietiö OM, Suominen O, Karhu K. Living, dead, and absent trees-How do moth outbreaks shape small-scale patterns of soil organic matter stocks and dynamics at the Subarctic mountain birch treeline? GLOBAL CHANGE BIOLOGY 2022; 28:441-462. [PMID: 34672044 DOI: 10.1111/gcb.15951] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Mountain birch forests (Betula pubescens Ehrh. ssp. czerepanovii) at the subarctic treeline not only benefit from global warming, but are also increasingly affected by caterpillar outbreaks from foliage-feeding geometrid moths. Both of these factors have unknown consequences on soil organic carbon (SOC) stocks and biogeochemical cycles. We measured SOC stocks down to the bedrock under living trees and under two stages of dead trees (12 and 55 years since moth outbreak) and treeless tundra in northern Finland. We also measured in-situ soil respiration, potential SOC decomposability, biological (enzyme activities and microbial biomass), and chemical (N, mineral N, and pH) soil properties. SOC stocks were significantly higher under living trees (4.1 ± 2.1 kg m²) than in the treeless tundra (2.4 ± 0.6 kg m²), and remained at an elevated level even 12 (3.7 ± 1.7 kg m²) and 55 years (4.9 ± 3.0 kg m²) after tree death. Effects of tree status on SOC stocks decreased with increasing distance from the tree and with increasing depth, that is, a significant effect of tree status was found in the organic layer, but not in mineral soil. Soil under living trees was characterized by higher mineral N contents, microbial biomass, microbial activity, and soil respiration compared with the treeless tundra; soils under dead trees were intermediate between these two. The results suggest accelerated organic matter turnover under living trees but a positive net effect on SOC stocks. Slowed organic matter turnover and continuous supply of deadwood may explain why SOC stocks remained elevated under dead trees, despite the heavy decrease in aboveground C stocks. We conclude that the increased occurrence of moth damage with climate change would have minor effects on SOC stocks, but ultimately decrease ecosystem C stocks (49% within 55 years in this area), if the mountain birch forests will not be able to recover from the outbreaks.
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Affiliation(s)
- Nele Meyer
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
- Department of Soil Ecology, University of Bayreuth, Bayreuth, Germany
| | - Yi Xu
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Katri Karjalainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Sylwia Adamczyk
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Christina Biasi
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Lona van Delden
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Angela Martin
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Kevin Mganga
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
- Department of Agricultural Sciences, South Eastern Kenya University, Kitui, Kenya
| | - Kristiina Myller
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Outi-Maaria Sietiö
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Otso Suominen
- Biodiversity Unit, Kevo Subarctic Research Institute, University of Turku, Turku, Finland
| | - Kristiina Karhu
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Life Science (Hilife), University of Helsinki, Helsinki, Finland
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15
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Ambrosio E, Feest A. Can Macrofungal Biodiversity Predict Forest Status and Dynamics? A View From South European Mediterranean Forests (Italy). ACTA MYCOLOGICA 2021. [DOI: 10.5586/am.567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Abstract
Fungi are among the most important organisms on earth, and they are essential components of terrestrial ecosystems. Their reproductive structures are strictly dependent and affected by environmental conditions, and community dynamics over time and space may be indirect indicators of the health status of forests. We combined macrofungal biodiversity indices in eight Mediterranean forests in Italy and surveyed 160 plots by standardized surveys, to evaluate the role of macrofungi as early predictors of change in the forest structure. The results show that indices of fungal diversity are influenced by geographic and floristic conditions, and inter- and intra-annual temperature and rainfall fluctuations affect the formation of fungal fruiting bodies. These findings suggest that environmental changes could be reflected by macrofungi, and conservation initiatives should consider the pivotal role that fungi play in biodiversity monitoring.
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16
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Lindahl BD, Kyaschenko J, Varenius K, Clemmensen KE, Dahlberg A, Karltun E, Stendahl J. A group of ectomycorrhizal fungi restricts organic matter accumulation in boreal forest. Ecol Lett 2021; 24:1341-1351. [PMID: 33934481 DOI: 10.1111/ele.13746] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/15/2021] [Accepted: 02/19/2021] [Indexed: 02/06/2023]
Abstract
Boreal forest soils are important global carbon sinks, with significant storage in the organic topsoil. Decomposition of these stocks requires oxidative enzymes, uniquely produced by fungi. Across Swedish boreal forests, we found that local carbon storage in the organic topsoil was 33% lower in the presence of a group of closely related species of ectomycorrhizal fungi - Cortinarius acutus s.l.. This observation challenges the prevailing view that ectomycorrhizal fungi generally act to increase carbon storage in soils but supports the idea that certain ectomycorrhizal fungi can complement free-living decomposers, maintaining organic matter turnover, nutrient cycling and tree productivity under nutrient-poor conditions. The indication that a narrow group of fungi may exert a major influence on carbon cycling questions the prevailing dogma of functional redundancy among microbial decomposers. Cortinarius acutus s.l. responds negatively to stand-replacing disturbance, and associated population declines are likely to increase soil carbon sequestration while impeding long-term nutrient cycling.
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Affiliation(s)
- Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Julia Kyaschenko
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kerstin Varenius
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Karina E Clemmensen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders Dahlberg
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erik Karltun
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Johan Stendahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden
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17
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Viotti C, Bach C, Maillard F, Ziegler-Devin I, Mieszkin S, Buée M. Sapwood and heartwood affect differentially bacterial and fungal community structure and successional dynamics during Quercus petraea decomposition. Environ Microbiol 2021; 23:6177-6193. [PMID: 33848050 DOI: 10.1111/1462-2920.15522] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 11/28/2022]
Abstract
In forests, bacteria and fungi are key players in wood degradation. Still, studies focusing on bacterial and fungal successions during the decomposition process depending on the wood types (i.e. sapwood and heartwood) remain scarce. This study aimed to understand the effect of wood type on the dynamics of microbial ecological guilds in wood decomposition. Using Illumina metabarcoding, bacterial and fungal communities were monitored every 3 months for 3 years from Quercus petraea wood discs placed on forest soil. Wood density and microbial enzymes involved in biopolymer degradation were measured. We observed rapid changes in the bacterial and fungal communities and microbial ecological guilds associated with wood decomposition throughout the experiment. Bacterial and fungal succession dynamics were very contrasted between sapwood and heartwood. The initial microbial communities were quickly replaced by new bacterial and fungal assemblages in the sapwood. Conversely, some initial functional guilds (i.e. endophytes and yeasts) persisted all along the experiment in heartwood and finally became dominant, possibly limiting the development of saprotrophic fungi. Our data also suggested a significant role of bacteria in nitrogen cycle during wood decomposition.
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Affiliation(s)
- Chloé Viotti
- Université de Lorraine, INRAE, UMR IAM, Centre INRAE-Grand Est-Nancy, 54280 Champenoux, Nancy, F-54000, France
| | - Cyrille Bach
- Université de Lorraine, INRAE, UMR IAM, Centre INRAE-Grand Est-Nancy, 54280 Champenoux, Nancy, F-54000, France
| | - François Maillard
- Department of Plant and Microbial Biology University of Minnesota St. Paul, Saint Paul, Minnesota, 55108, USA
| | | | - Sophie Mieszkin
- Université de Lorraine, INRAE, UMR IAM, Centre INRAE-Grand Est-Nancy, 54280 Champenoux, Nancy, F-54000, France
| | - Marc Buée
- Université de Lorraine, INRAE, UMR IAM, Centre INRAE-Grand Est-Nancy, 54280 Champenoux, Nancy, F-54000, France
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18
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Soil Microbiome Composition along the Natural Norway Spruce Forest Life Cycle. FORESTS 2021. [DOI: 10.3390/f12040410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Stand-replacing disturbances are a key element of the Norway spruce (Picea abies) forest life cycle. While the effect of a natural disturbance regime on forest physiognomy, spatial structure and pedocomplexity was well described in the literature, its impact on the microbiome, a crucial soil component that mediates nutrient cycling and stand productivity, remains largely unknown. For this purpose, we conducted research on a chronosequence of sites representing the post-disturbance development of a primeval Norway spruce forest in the Calimani Mts., Romania. The sites were selected along a gradient of duration from 16 to 160 years that ranges from ecosystem regeneration phases of recently disturbed open gaps to old-growth forest stands. Based on DNA amplicon sequencing, we followed bacterial and fungal community composition separately in organic, upper mineral and spodic horizons of present Podzol soils. We observed that the canopy opening and subsequent expansion of the grass-dominated understorey increased soil N availability and soil pH, which was reflected in enlarged bacterial abundance and diversity, namely due to the contribution of copiotrophic bacteria that prefer nutrient-richer conditions. The fungal community composition was affected by the disturbance as well but, contrary to our expectations, with no obvious effect on the relative abundance of ectomycorrhizal fungi. Once the mature stand was re-established, the N availability was reduced, the pH gradually decreased and the original old-growth forest microbial community dominated by acidotolerant oligotrophs recovered. The effect of the disturbance and forest regeneration was most evident in organic horizons, while the manifestation of these events was weaker and delayed in deeper soil horizons.
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19
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Kohout P, Sudová R, Brabcová V, Vosolsobě S, Baldrian P, Albrechtová J. Forest Microhabitat Affects Succession of Fungal Communities on Decomposing Fine Tree Roots. Front Microbiol 2021; 12:541583. [PMID: 33584602 PMCID: PMC7876299 DOI: 10.3389/fmicb.2021.541583] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 01/06/2021] [Indexed: 01/16/2023] Open
Abstract
Belowground litter derived from tree roots has been shown as a principal source of soil organic matter in coniferous forests. Fate of tree root necromass depends on fungal communities developing on the decaying roots. Local environmental conditions which affect composition of tree root mycobiome may also influence fungal communities developing on decaying tree roots. Here, we assessed fungal communities associated with decaying roots of Picea abies decomposing in three microhabitats: soil with no vegetation, soil with ericoid shrubs cover, and P. abies deadwood, for a 2-year period. Forest microhabitat showed stronger effect on structuring fungal communities associated with decaying roots compared to living roots. Some ericoid mycorrhizal fungi showed higher relative abundance on decaying roots in soils under ericoid shrub cover, while saprotrophic fungi had higher relative abundance in roots decomposing inside deadwood. Regardless of the studied microhabitat, we observed decline of ectomycorrhizal fungi and increase of endophytic fungi during root decomposition. Interestingly, we found substantially more fungal taxa with unknown ecology in late stages of root decomposition, indicating that highly decomposed roots may represent so far overlooked niche for soil fungi. Our study shows the importance of microhabitats on the fate of the decomposing spruce roots.
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Affiliation(s)
- Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
- Institute of Botany of the Czech Academy of Sciences, Pruhonice, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Radka Sudová
- Institute of Botany of the Czech Academy of Sciences, Pruhonice, Czechia
| | - Vendula Brabcová
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Stanislav Vosolsobě
- Institute of Botany of the Czech Academy of Sciences, Pruhonice, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Jana Albrechtová
- Institute of Botany of the Czech Academy of Sciences, Pruhonice, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
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20
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Rodriguez-Ramos JC, Cale JA, Cahill JF, Simard SW, Karst J, Erbilgin N. Changes in soil fungal community composition depend on functional group and forest disturbance type. THE NEW PHYTOLOGIST 2021; 229:1105-1117. [PMID: 32557647 DOI: 10.1111/nph.16749] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Disturbances have altered community dynamics in boreal forests with unknown consequences for belowground ecological processes. Soil fungi are particularly sensitive to such disturbances; however, the individual response of fungal guilds to different disturbance types is poorly understood. Here, we profiled soil fungal communities in lodgepole pine forests following a bark beetle outbreak, wildfire, clear-cut logging, and salvage-logging. Using Illumina MiSeq to sequence ITS1 and SSU rDNA, we characterized communities of ectomycorrhizal, arbuscular mycorrhizal, saprotrophic, and pathogenic fungi in sites representing each disturbance type paired with intact forests. We also quantified soil fungal biomass by measuring ergosterol. Abiotic disturbances changed the community composition of ectomycorrhizal fungi and shifted the dominance from ectomycorrhizal to saprotrophic fungi compared to intact forests. The disruption of the soil organic layer with disturbances correlated with the decline of ectomycorrhizal and the increase of arbuscular mycorrhizal fungi. Wildfire changed the community composition of pathogenic fungi but did not affect their proportion and diversity. Fungal biomass declined with disturbances that disrupted the forest floor. Our results suggest that the disruption of the forest floor with disturbances, and the changes in C and nutrient dynamics it may promote, structure the fungal community with implications for fungal biomass-C.
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Affiliation(s)
| | - Jonathan A Cale
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2E3, Canada
| | - James F Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Suzanne W Simard
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Justine Karst
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2E3, Canada
| | - Nadir Erbilgin
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2E3, Canada
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21
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Marín C, Kohout P. Response of soil fungal ecological guilds to global changes. THE NEW PHYTOLOGIST 2021; 229:656-658. [PMID: 33270913 DOI: 10.1111/nph.17054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- César Marín
- Institute of Agri-food, Animal and Environmental Sciences (ICA3), Universidad de O'Higgins, San Fernando, 3070000, Chile
- Center of Applied Ecology and Sustainability, Pontificia Universidad Católica de Chile, Santiago, 8320000, Chile
| | - Petr Kohout
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, Prague, CZ-142 20, Czechia
- Faculty of Science, Charles University, Viničná 7, Prague, CZ-128 44, Czechia
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22
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Castaño C, Camarero JJ, Zas R, Sampedro L, Bonet JA, Alday JG, Oliva J. Insect defoliation is linked to a decrease in soil ectomycorrhizal biomass and shifts in needle endophytic communities. TREE PHYSIOLOGY 2020; 40:1712-1725. [PMID: 32785638 DOI: 10.1093/treephys/tpaa104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Insect outbreaks of increasing frequency and severity in forests are predicted due to climate change. Insect herbivory is known to promote physiological changes in forest trees. However, little is known about whether these plant phenotypic adjustments have cascading effects on tree microbial symbionts such as fungi in roots and foliage. We studied the impact of defoliation by the pine processionary moth in two infested Pinus nigra forests through a multilevel sampling of defoliated and non-defoliated trees. We measured tree growth, nutritional status and carbon allocation to chemical defenses. Simultaneously, we analysed the putative impact of defoliation on the needle endophytes and on the soil fungal communities. Higher concentrations of chemical defenses were found in defoliated trees, likely as a response to defoliation; however, no differences in non-structural carbohydrate reserves were found. In parallel to the reductions in tree growth and changes in chemical defenses, we observed shifts in the composition of needle endophytic and soil fungal communities in defoliated trees. Defoliated trees consistently corresponded with a lower biomass of ectomycorrhizal fungi in both sites, and a higher alpha diversity and greater relative abundance of belowground saprotrophs and pathogens. However, ectomycorrhizal alpha diversity was similar between non-defoliated and defoliated trees. Specific needle endophytes in old needles were strongly associated with non-defoliated trees. The potential role of these endophytic fungi in pine resistance should be further investigated. Our study suggests that lower biomass of ectomycorrhizal fungi in defoliated trees might slow down tree recovery since fungal shifts might affect tree-mycorrhizal feedbacks and can potentially influence carbon and nitrogen cycling in forest soils.
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Affiliation(s)
- Carles Castaño
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - J Julio Camarero
- Instituto Pirenaico de Ecología (IPE-CSIC), 50192 Zaragoza, Spain
| | - Rafael Zas
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas (MBG-CSIC), Apdo 28, 36080 Pontevedra, Spain
| | - Luis Sampedro
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas (MBG-CSIC), Apdo 28, 36080 Pontevedra, Spain
| | - José Antonio Bonet
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida, Av. Rovira Roure, 191, E-25198 Lleida, Spain
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain
| | - Josu G Alday
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida, Av. Rovira Roure, 191, E-25198 Lleida, Spain
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain
| | - Jonàs Oliva
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida, Av. Rovira Roure, 191, E-25198 Lleida, Spain
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain
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23
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Linking Tree Health, Rhizosphere Physicochemical Properties, and Microbiome in Acute Oak Decline. FORESTS 2020. [DOI: 10.3390/f11111153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Forest decline diseases are complex processes driven by biotic and abiotic factors. Although information about host–microbiome–environment interactions in agricultural systems is emerging rapidly, similar studies on tree health are still in their infancy. We used acute oak decline (AOD) as a model system to understand whether the rhizosphere physicochemical properties and microbiome are linked to tree health by studying these two factors in healthy and diseased trees located in three sites in different AOD stages—low, mid and severe. We found significant changes in the rhizosphere properties and microbiome composition across the different AOD sites and between the tree health conditions. Rhizosphere pH correlated with microbiome composition, with the microbial assemblages changing in more acidic soils. At the severe AOD site, the oak trees exhibited the lowest rhizosphere pH and distinct microbiome, regardless of their health condition, whereas, at the low and mid-stage AOD sites, only diseased trees showed lower pH and the microbial composition differed significantly from healthy trees. On these two sites, less extreme soil conditions and a high presence of host-beneficial microbiota were observed in the healthy oak trees. For the first time, this study gathers evidence of associations among tree health conditions, rhizosphere properties and microbiome as well as links aboveground tree decline symptoms to the belowground environment. This provides a baseline of rhizosphere community profiling of UK oak trees and paves the way for these associations to be investigated in other tree species suffering decline disease events.
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24
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Leonard LT, Mikkelson K, Hao Z, Brodie EL, Williams KH, Sharp JO. A comparison of lodgepole and spruce needle chemistry impacts on terrestrial biogeochemical processes during isolated decomposition. PeerJ 2020; 8:e9538. [PMID: 32742804 PMCID: PMC7369028 DOI: 10.7717/peerj.9538] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/23/2020] [Indexed: 12/01/2022] Open
Abstract
This study investigates the isolated decomposition of spruce and lodgepole conifer needles to enhance our understanding of how needle litter impacts near-surface terrestrial biogeochemical processes. Harvested needles were exported to a subalpine meadow to enable a discrete analysis of the decomposition processes over 2 years. Initial chemistry revealed the lodgepole needles to be less recalcitrant with a lower carbon to nitrogen (C:N) ratio. Total C and N fundamentally shifted within needle species over time with decreased C:N ratios for spruce and increased ratios for lodgepole. Differences in chemistry correlated with CO2 production and soil microbial communities. The most pronounced trends were associated with lodgepole needles in comparison to the spruce and needle-free controls. Increased organic carbon and nitrogen concentrations associated with needle presence in soil extractions further corroborate the results with clear biogeochemical signatures in association with needle chemistry. Interestingly, no clear differentiation was observed as a function of bark beetle impacted spruce needles vs those derived from healthy spruce trees despite initial differences in needle chemistry. These results reveal that the inherent chemistry associated with tree species has a greater impact on soil biogeochemical signatures during isolated needle decomposition. By extension, biogeochemical shifts associated with bark beetle infestation are likely driven more by changes such as the cessation of rhizospheric processes than by needle litter decomposition.
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Affiliation(s)
| | | | - Zhao Hao
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eoin L Brodie
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kenneth H Williams
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Rocky Mountain Biological Laboratory, Crested Butte, CO, USA
| | - Jonathan O Sharp
- Colorado School of Mines, Golden, CO, USA.,Rocky Mountain Biological Laboratory, Crested Butte, CO, USA
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25
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Long-term decomposition of litter in the montane forest and the definition of fungal traits in the successional space. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2020.100913] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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26
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Yang T, Tedersoo L, Lin X, Fitzpatrick MC, Jia Y, Liu X, Ni Y, Shi Y, Lu P, Zhu J, Chu H. Distinct fungal successional trajectories following wildfire between soil horizons in a cold-temperate forest. THE NEW PHYTOLOGIST 2020; 227:572-587. [PMID: 32155671 DOI: 10.1111/nph.16531] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/02/2020] [Indexed: 06/10/2023]
Abstract
Soil fungi represent a major component of below-ground biodiversity that determines the succession and recovery of forests after disturbance. However, their successional trajectories and driving mechanisms following wildfire remain unclear. We examined fungal biomass, richness, composition and enzymes across three soil horizons (Oe, A1 and A2) along a near-complete fire chronosequence (1, 2, 8, 14, 30, 49 and c. 260 yr) in cold-temperate forests of the Great Khingan Mountains, China. The importance of soil properties, spatial distance and tree composition were also tested. Ectomycorrhizal fungal richness and β-glucosidase activity were strongly reduced by burning and significantly increased with 'time since fire' in the Oe horizon but not in the mineral horizons. Time since fire and soil C : N ratio were the primary drivers of fungal composition in the Oe and A1/A2 horizons, respectively. Ectomycorrhizal fungal composition was remarkably sensitive to fire history in the Oe horizon, while saprotroph community was strongly affected by time since fire in the deeper soil horizon and this effect emerged 18 years after fire in the A2 horizon. Our study demonstrates pronounced horizon-dependent successional trajectories following wildfire and indicates interactive effects of time since fire, soil stoichiometry and spatial distance in the reassembly of below-ground fungal communities in a cold and fire-prone region.
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Affiliation(s)
- Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Leho Tedersoo
- Natural History Museum, University of Tartu, 14a Ravila, Tartu, 50411, Estonia
| | - Xingwu Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Matthew C Fitzpatrick
- Appalachian Laboratory, University of Maryland Centre for Environmental Science, Frostburg, MD, 21531, USA
| | - Yunsheng Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Pengpeng Lu
- Microbiology Institute of Shaanxi, Shaanxi Academy of Sciences, Xiying Road 76, Xi'an, 710043, China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing, 210008, China
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Pec GJ, Simard SW, Cahill JF, Karst J. The effects of ectomycorrhizal fungal networks on seedling establishment are contingent on species and severity of overstorey mortality. MYCORRHIZA 2020; 30:173-183. [PMID: 32088844 DOI: 10.1007/s00572-020-00940-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
For tree seedlings in boreal forests, ectomycorrhizal (EM) fungal networks may promote, while root competition may impede establishment. Thus, disruption to EM fungal networks may decrease seedling establishment owing to the loss of positive interactions among neighbors. Widespread tree mortality can disrupt EM networks, but it is not clear whether seedling establishment will be limited by the loss of positive interactions or increased by the loss of negative interactions with surrounding roots. Depending upon the relative influence of these mechanisms, widespread tree mortality may have complicated consequences on seedling establishment, and in turn, the composition of future forests. To discern between these possible outcomes and the drivers of seedling establishment, we determined the relative importance of EM fungal networks, root presence, and the bulk soil on the establishment of lodgepole pine and white spruce seedlings along a gradient of beetle-induced tree mortality. We manipulated seedling contact with EM fungal networks and roots through the use of mesh-fabric cylinders installed in soils of lodgepole pine forests experiencing a range of overstorey tree mortality caused by mountain pine beetle. Lodgepole pine seedling survival was higher with access to EM fungal networks in undisturbed pine forests in comparison with that in beetle-killed stands. That is, overstorey tree mortality shifted fungal networks from being a benefit to a cost on seedling survival. In contrast, overstorey tree mortality did not change the relative strength of EM fungal networks, root presence and the bulk soil on survival and biomass of white spruce seedlings. Furthermore, the relative influence of EM fungal networks, root presence, and bulk soils on foliar N and P concentrations was highly contingent on seedling species and overstorey tree mortality. Our results highlight that following large-scale insect outbreak, soil-mediated processes can enable differential population growth of two common conifer species, which may result in species replacement in the future.
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Affiliation(s)
- Gregory J Pec
- Department of Biological Sciences, University of Alberta, B717a, Biological Sciences Building, Edmonton, Alberta, T6G 2E9, Canada.
- Department of Biology, University of Nebraska at Kearney, Kearney, NE, 68849, USA.
| | - Suzanne W Simard
- Department of Forest and Conservation Sciences, University of British Columbia, Forest Sciences Centre #3601-2424 Main Hall, Vancouver, British Columbia, V6T 1Z4, Canada
| | - James F Cahill
- Department of Biological Sciences, University of Alberta, B717a, Biological Sciences Building, Edmonton, Alberta, T6G 2E9, Canada
| | - Justine Karst
- Department of Biological Sciences, University of Alberta, B717a, Biological Sciences Building, Edmonton, Alberta, T6G 2E9, Canada
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
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Hu J, Zhou Y, Lei Z, Liu G, Hua Y, Zhou W, Wan X, Zhu D, Zhao J. Effects of Potamogeton crispus decline in the rhizosphere on the abundance of anammox bacteria and nirS denitrifying bacteria ☆. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 260:114018. [PMID: 31991343 DOI: 10.1016/j.envpol.2020.114018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/17/2020] [Accepted: 01/17/2020] [Indexed: 05/23/2023]
Abstract
Bacteria involved with ecosystem N cycling in the rhizosphere of submerged macrophytes are abundant and diverse. Any declines of submerged macrophytes can have a great influence on the abundance and diversity of denitrifying bacteria and anammox bacteria. Natural decline, tardy decline, and sudden decline methods were applied to cultivated Potamogeton crispus. The abundance of anammox bacteria and nirS denitrifying bacteria in rhizosphere sediment were detected using real-time fluorescent quantitative PCR of 16S rRNA, and phylogenetic trees were constructed to analyze the diversities of these two microbes. The results indicated that the concentration of NH4+ in pore water gradually increased with increasing distances from the roots, whereas, the concentration of NO3- showed a reverse trend. The abundance of anammox bacteria and nirS denitrifying bacteria in sediment of declined P. crispus populations decreased significantly over time. The abundance of these two microbes in the sudden decline group were significantly higher (P > 0.05) than the other decline treatment groups. Furthermore, the abundances of these two microbes were positively correlated, with RDA analyses finding the mole ratio of NH4+/NO3- being the most important positive factor affecting microbe abundance. Phylogenetic analysis indicated that the anammox bacteria Brocadia fuigida and Scalindua wagneri, and nirS denitrifying bacteria Herbaspirillum and Pseudomonas, were the dominant species in declined P. crispus sediment. We suggest the sudden decline of submerged macrophytes would increase the abundance of anammox bacteria and denitrifying bacteria in a relatively short time.
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Affiliation(s)
- Jinlong Hu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuhao Zhou
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ziyan Lei
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guanglong Liu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yumei Hua
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenbing Zhou
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoqiong Wan
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Duanwei Zhu
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianwei Zhao
- Laboratory of Eco-Environmental Engineering Research, College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
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Beck JL, Cale JA, Rodriguez‐Ramos JC, Kanekar SS, Karst J, Cahill JF, Simard SW, Erbilgin N. Changes in soil fungal communities following anthropogenic disturbance are linked to decreased lodgepole pine seedling performance. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jackson L. Beck
- Department of Renewable Resources University of Alberta Edmonton AB Canada
| | - Jonathan A. Cale
- Department of Renewable Resources University of Alberta Edmonton AB Canada
| | | | - Sanat S. Kanekar
- Department of Renewable Resources University of Alberta Edmonton AB Canada
| | - Justine Karst
- Department of Renewable Resources University of Alberta Edmonton AB Canada
| | - James F. Cahill
- Department of Biological Sciences University of Alberta Edmonton AB Canada
| | - Suzanne W. Simard
- Department of Forest & Conservation Sciences University of British Columbia Vancouver BC Canada
| | - Nadir Erbilgin
- Department of Renewable Resources University of Alberta Edmonton AB Canada
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Structural and Functional Dynamics of Soil Microbes following Spruce Beetle Infestation. Appl Environ Microbiol 2020; 86:AEM.01984-19. [PMID: 31732575 DOI: 10.1128/aem.01984-19] [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: 08/28/2019] [Accepted: 11/10/2019] [Indexed: 11/20/2022] Open
Abstract
As the range of bark beetles expands into new forests and woodlands, the need to understand their effects on multiple trophic levels becomes increasingly important. To date, much attention has been paid to the aboveground processes affected by bark beetle infestation, with a focus on photoautotrophs and ecosystem level processes. However, indirect effects of bark beetle on belowground processes, especially the structure and function of soil microbiota remains largely a black box. Our study examined the impacts of bark beetle-induced tree mortality on soil microbial community structure and function using high-throughput sequencing of the soil bacterial and fungal communities and measurements of extracellular enzyme activities. The results suggest bark beetle infestation affected edaphic conditions through increased soil water content, pH, electrical conductivity, and carbon/nitrogen ratio and altered bulk and rhizosphere soil microbial community structure and function. Finally, increased enzymatic activity suggests heightened microbial decomposition following bark beetle infestation. With this increase in enzymatic activity, nutrients trapped in organic substrates may become accessible to seedlings and potentially alter the trajectory of forest regeneration. Our results indicate the need for incorporation of microbial processes into ecosystem level models.IMPORTANCE Belowground impacts of bark beetle infestation have not been explored as thoroughly as their aboveground counterparts. In order to accurately model impacts of bark beetle-induced tree mortality on carbon and nutrient cycling and forest regeneration, the intricacies of soil microbial communities must be examined. In this study, we investigated the structure and function of soil bacterial and fungal communities following bark beetle infestation. Our results show bark beetle infestation to impact soil conditions, as well as soil microbial community structure and function.
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31
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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: 393] [Impact Index Per Article: 98.3] [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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Soil Microbiota of Dystric Cambisol in the High Tatra Mountains (Slovakia) after Windthrow. SUSTAINABILITY 2019. [DOI: 10.3390/su11236851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
There has been much more damage to forests in the Slovak Republic in the second half of the 20th century than to other European countries. Forested mountain massifs have become a filter of industrial and transportation emissions from abroad, as well as from domestic origins. There are not only acidic deposits of sulphur and heavy metals present in forest soils, but other additional environmental problems, such as climate change, storms, fires, floods, droughts, are worsening the situation. Therefore, forest terrestrial ecosystems are becoming more vulnerable due to changes in natural and environmental conditions. In the High Tatra Mountains in Slovakia, which are protected as a national park, four internationally monitored localities were established after the windthrow disaster in 2004 and fire in 2005: REF, with intact forest; EXT, with extracted wood mass; NEX, with non-extracted wood mass; and FIR, the burnt locality. Soils from these localities were microbiologically analysed with special attention to fungi. Bacterial microbiota detected by high-throughput sequencing showed the prevalence of the genera Acidothermus, Mycobacterium, and Nocardia, and a very low presence of the genera Acidibacter, Burkholderia-Paraburkholderia, Optitus and the uncultured genus Desulfurellaceae H16 in the soil sample from the burnt locality when compared with the unburned sites. Additionally, soil mycocoenoses showed a low similarity between the locality with an intact forest ecosystem and the localities with extracted (REF–EXT) and non-extracted (REF–NEX) wood mass. There was no similarity with the burnt locality (FIR), where heat-resistant fungi dominated. It was shown that the windthrow disaster and subsequent extraction or non-extraction of wood mass did not affect the soil microbial communities or their development. On the other hand, the influence of fire was significant.
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Ectomycorrhizal Community on Norway Spruce Seedlings Following Bark Beetle Infestation. FORESTS 2019. [DOI: 10.3390/f10090740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ectomycorrhizal (ECM) fungi importantly influence seedling growth, nutrition, and survival and create an extensive mycelial network interconnecting tree species and enabling resource redistribution. Due to their symbiotic relationship with trees, they are impacted by forest disturbances, which are of increasing relevance due to climate change. The effect of disturbance on seedling colonization and their morphology is still largely unknown. Seedling growth parameters and the ECM fungal assemblage on the roots of Norway spruce (Picea abies (L.) H. Karst.) seedlings were assessed in mature spruce forests attacked and destroyed by bark beetle and in a mature non-attacked forest as a reference. We did not detect significant differences in number of ECM species on seedling roots among forest types, but ECM species composition changed; Tylospora fibrillosa (Burt) Donk, Meliniomyces variabilis Hambl. & Sigler, and Phialocephala fortinii C.J.K. Wang & H.E. Wilcox were characteristic species in the forest destroyed by bark beetle, whereas Lactarius, Cortinarius, and Russula were in the mature forest. Forest type further significantly influenced the height, root length, and root collar thickness of seedlings and the proportion of exploration types of mycorrhizae.
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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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35
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Response of Soil Surface Respiration to Storm and Ips typographus (L.) Disturbance in Boreal Norway Spruce Stands. FORESTS 2019. [DOI: 10.3390/f10040307] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Disturbances such as storm events and bark beetle outbreaks can have a major influence on forest soil carbon (C) cycling. Both autotrophic and heterotrophic soil respiration may be affected by the increase in tree mortality. We studied the effect of a storm in 2010 followed by an outbreak of the European spruce bark beetle (Ips typographus L.) on the soil surface respiration (respiration by soil and ground vegetation) at two Norway spruce (Picea abies L.) dominated sites in southeastern Finland. Soil surface respiration, soil temperature, and soil moisture were measured in three types of plots—living trees (undisturbed), storm-felled trees, and standing dead trees killed by I. typographus—during the summer–autumn period for three years (2015–2017). Measurements at storm-felled tree plots were separated into dead tree detritus-covered (under storm-felled trees) and open-vegetated (on open areas) microsites. The soil surface total respiration for 2017 was separated into its autotrophic and heterotrophic components using trenching. The soil surface total respiration rates at the disturbed plots were 64%–82% of those at the living tree plots at one site and were due to a decrease in autotrophic respiration, but there was no clear difference in soil surface total respiration between the plots at the other site, due to shifts in either autotrophic or heterotrophic respiration. The soil surface respiration rates were related to plot basal area (living and all trees), as well as to soil temperature and soil moisture. As storm and bark beetle disturbances are predicted to become more common in the future, their effects on forest ecosystem C cycling and CO2 fluxes will therefore become increasingly important.
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Abstract
Bark beetle infestation is a widespread phenomenon in temperate forests, which are facing significant weather fluctuations accompanying climate change. Fungi play key roles in forest ecosystems as symbionts of ectomycorrhizal trees, decomposers, or parasites, but the effect of severe disturbances on their communities is largely unknown. The responses of soil fungal communities following bark beetle attack were determined using Illumina sequencing of soil samples from 10 microsites in a mature forest not attacked by bark beetle, a forest attacked by bark beetle, a forest destroyed by bark beetle, and a stand where all trees were removed after a windstorm. The proportion of ITS2 sequences assigned to mycorrhizal fungal species decreased with increased intensity of bark beetle attack (from 70 to 15%), whereas the proportion of saprotrophs increased (from 29 to 77%). Differences in the ectomycorrhizal (ECM) fungal community was further characterized by a decrease in the sequence proportion of Elaphomyces sp. and Russula sp. and an increase in Piloderma sp., Wilcoxina sp., and Thelephora terrestris. Interestingly, the species composition of the ECM fungal community in the forest one year after removing the windstorm-damaged trees was similar to that of the mature forest, despite the sequence proportion attributed to ECM fungi decreased.
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37
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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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38
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Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00547] [Citation(s) in RCA: 303] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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39
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Facile one-pot synthesis of wood based bismuth molybdate nano-eggshells with efficient visible-light photocatalytic activity. Colloids Surf A Physicochem Eng Asp 2018. [DOI: 10.1016/j.colsurfa.2018.08.041] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Schröter K, Wemheuer B, Pena R, Schöning I, Ehbrecht M, Schall P, Ammer C, Daniel R, Polle A. Assembly processes of trophic guilds in the root mycobiome of temperate forests. Mol Ecol 2018; 28:348-364. [PMID: 30276908 DOI: 10.1111/mec.14887] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 09/05/2018] [Accepted: 09/17/2018] [Indexed: 01/09/2023]
Abstract
Root-associated mycobiomes (RAMs) link plant and soil ecological processes, thereby supporting ecosystem functions. Understanding the forces that govern the assembly of RAMs is key to sustainable ecosystem management. Here, we dissected RAMs according to functional guilds and combined phylogenetic and multivariate analyses to distinguish and quantify the forces driving RAM assembly processes. Across large biogeographic scales (>1,000 km) in temperate forests (>100 plots), RAMs were taxonomically highly distinct but composed of a stable trophic structure encompassing symbiotrophic, ectomycorrhizal (55%), saprotrophic (7%), endotrophic (3%) and pathotrophic fungi (<1%). Taxonomic community composition of RAMs is explained by abiotic factors, forest management intensity, dominant tree family (Fagaceae, Pinaceae) and root resource traits. Local RAM assemblies are phylogenetically clustered, indicating stronger habitat filtering on roots in dry, acid soils and in conifer stands than in other forest types. The local assembly of ectomycorrhizal communities is driven by forest management intensity. At larger scales, root resource traits and soil pH shift the assembly process of ectomycorrhizal fungi from deterministic to neutral. Neutral or weak deterministic assembly processes are prevalent in saprotrophic and endophytic guilds. The remarkable consistency of the trophic composition of the RAMs suggests that temperate forests attract fungal assemblages that afford functional resilience under the current range of climatic and edaphic conditions. At local scales, the filtering processes that structure symbiotrophic assemblies can be influenced by forest management and tree selection, but at larger scales, environmental cues and host resource traits are the most prevalent forces.
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Affiliation(s)
- Kristina Schröter
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Bernd Wemheuer
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, Göttingen, Germany.,Centre for Marine Bio-Innovation, School of Biological Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Rodica Pena
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
| | - Ingo Schöning
- Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Martin Ehbrecht
- Silviculture and Forest Ecology of the Temperate Zones, University of Goettingen, Göttingen, Germany
| | - Peter Schall
- Silviculture and Forest Ecology of the Temperate Zones, University of Goettingen, Göttingen, Germany
| | - Christian Ammer
- Silviculture and Forest Ecology of the Temperate Zones, University of Goettingen, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Goettingen, Göttingen, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, University of Goettingen, Göttingen, Germany
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41
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The Abundance of Fungi, Bacteria and Denitrification Genes during Insect Outbreaks in Scots Pine Forests. FORESTS 2018. [DOI: 10.3390/f9080497] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Outbreaks of defoliating insects may affect microbial populations in forests and thereby mass balances and ecosystem functioning. Here, we investigated the microbial dynamics in Scots pine (Pinus sylvestris L.) forests during outbreaks of the nun moth (Lymantria monacha L.) and the pine-tree lappet (Dendrolimus pini L.). We used real-time PCR (polymerase chain reaction) to quantify genes that characterize bacterial and fungal abundance and the denitrification processes (nirK, nirS, nosZ clades I and II) in different forest compartments and we analyzed the C and N content of pine needles, insect feces, larvae, vegetation layers, organic layers, and mineral soil horizons. The infestation of the nun moth increased the bacterial abundance on pine needles, in the vegetation layer, and in the upper organic layer, while fungal populations were increased in the vegetation layer and upper organic layer during both outbreaks. In soil, the abundance of nirK increased after insect defoliation, while the C/N ratios decreased. nosZ clades I and II showed variable responses in different soil layers and to different defoliating insects. Our results illustrate changes in the microbial populations in pine forests that were infested by defoliating insects and changes in the chemical soil properties that foster these populations, indicating a genetic potential for increased soil N2O emissions during the defoliation peak of insect outbreak events.
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Siebers M, Rohr T, Ventura M, Schütz V, Thies S, Kovacic F, Jaeger KE, Berg M, Dörmann P, Schulz M. Disruption of microbial community composition and identification of plant growth promoting microorganisms after exposure of soil to rapeseed-derived glucosinolates. PLoS One 2018; 13:e0200160. [PMID: 29969500 PMCID: PMC6029813 DOI: 10.1371/journal.pone.0200160] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/20/2018] [Indexed: 12/17/2022] Open
Abstract
Land plants are engaged in intricate communities with soil bacteria and fungi indispensable for plant survival and growth. The plant-microbial interactions are largely governed by specific metabolites. We employed a combination of lipid-fingerprinting, enzyme activity assays, high-throughput DNA sequencing and isolation of cultivable microorganisms to uncover the dynamics of the bacterial and fungal community structures in the soil after exposure to isothiocyanates (ITC) obtained from rapeseed glucosinolates. Rapeseed-derived ITCs, including the cyclic, stable goitrin, are secondary metabolites with strong allelopathic affects against other plants, fungi and nematodes, and in addition can represent a health risk for human and animals. However, the effects of ITC application on the different bacterial and fungal organisms in soil are not known in detail. ITCs diminished the diversity of bacteria and fungi. After exposure, only few bacterial taxa of the Gammaproteobacteria, Bacteriodetes and Acidobacteria proliferated while Trichosporon (Zygomycota) dominated the fungal soil community. Many surviving microorganisms in ITC-treated soil where previously shown to harbor plant growth promoting properties. Cultivable fungi and bacteria were isolated from treated soils. A large number of cultivable microbial strains was capable of mobilizing soluble phosphate from insoluble calcium phosphate, and their application to Arabidopsis plants resulted in increased biomass production, thus revealing growth promoting activities. Therefore, inclusion of rapeseed-derived glucosinolates during biofumigation causes losses of microbiota, but also results in enrichment with ITC-tolerant plant microorganisms, a number of which show growth promoting activities, suggesting that Brassicaceae plants can shape soil microbiota community structure favoring bacteria and fungi beneficial for Brassica plants.
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Affiliation(s)
- Meike Siebers
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Thomas Rohr
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Marina Ventura
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Vadim Schütz
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Martin Berg
- Institute for Organic Agriculture, University of Bonn, Bonn, Germany
- Experimental Farm Wiesengut of University of Bonn, Hennef, Germany
| | - Peter Dörmann
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
| | - Margot Schulz
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
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Kopáček J, Evans CD, Hejzlar J, Kaňa J, Porcal P, Šantrůčková H. Factors Affecting the Leaching of Dissolved Organic Carbon after Tree Dieback in an Unmanaged European Mountain Forest. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6291-6299. [PMID: 29738664 DOI: 10.1021/acs.est.8b00478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Forest disturbances affect ecosystem biogeochemistry, water quality, and carbon cycling. We analyzed water chemistry before, during, and after a dieback event at a headwater catchment in the Bohemian Forest (central Europe) together with an un-impacted reference catchment, focusing on drivers and responses of dissolved organic carbon (DOC) leaching. We analyzed data regarding carbon input to the forest floor via litter and throughfall, changes in soil moisture and composition, streamwater chemistry, discharge, and temperature. We observed three key points. (i) In the first 3 years following dieback, DOC production from dead biomass led to increased concentrations in soil, but DOC leaching did not increase due to chemical suppression of its solubility by elevated concentrations of protons and polyvalent cations and elevated microbial demand for DOC associated with high ammonium (NH4+) concentrations. (ii) DOC leaching remained low during the next 2 years because its availability in soils declined, which also left more NH4+ available for nitrifiers, increasing NO3- and proton production that further increased the chemical suppression of DOC mobility. (iii) After 5 years, DOC leaching started to increase as concentrations of NO3-, protons, and polyvalent cations started to decrease in soil water. Our data suggest that disturbance-induced changes in N cycling strongly influence DOC leaching via both chemical and biological mechanisms and that the magnitude of DOC leaching may vary over periods following disturbance. Our study adds insights as to why the impacts of forest disturbances are sometime observed at the local soil scale but not simultaneously on the larger catchment scale.
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Affiliation(s)
- Jiří Kopáček
- Biology Centre CAS, Institute of Hydrobiology , České Budějovice , CZ-37005 Czech Republic
- University of South Bohemia, Faculty of Science , České Budějovice , CZ-37005 Czech Republic
| | - Christopher D Evans
- Centre for Ecology and Hydrology , Deiniol Road , Bangor LL57 2UW , United Kingdom
| | - Josef Hejzlar
- Biology Centre CAS, Institute of Hydrobiology , České Budějovice , CZ-37005 Czech Republic
| | - Jiří Kaňa
- Biology Centre CAS, Institute of Hydrobiology , České Budějovice , CZ-37005 Czech Republic
- Biology Centre CAS, SoWa , České Budějovice , CZ-37005 Czech Republic
| | - Petr Porcal
- Biology Centre CAS, Institute of Hydrobiology , České Budějovice , CZ-37005 Czech Republic
- Biology Centre CAS, SoWa , České Budějovice , CZ-37005 Czech Republic
| | - Hana Šantrůčková
- University of South Bohemia, Faculty of Science , České Budějovice , CZ-37005 Czech Republic
- Biology Centre CAS, SoWa , České Budějovice , CZ-37005 Czech Republic
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Vašutová M, Edwards-Jonášová M, Veselá P, Effenberková L, Fleischer P, Cudlín P. Management regime is the most important factor influencing ectomycorrhizal species community in Norway spruce forests after windthrow. MYCORRHIZA 2018; 28:221-233. [PMID: 29352412 DOI: 10.1007/s00572-018-0820-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/05/2018] [Indexed: 06/07/2023]
Abstract
Ectomycorrhizal (ECM) fungi, as symbionts of many tree species in temperate forests, are thought to play an important role in forest regeneration processes after large disturbances. Their reaction to different disturbance and management regimes was studied in spruce forests (Lariceto-Piceetum) 10 years after a severe windthrow in the Tatra National Park (Slovak Republic). ECM community structure was compared between different "management types″-cleared area (EXT), area affected by wildfire (FIRE), uncleared area left for natural development (NEX), and mature forest as a control (REF). Based on Illumina sequencing of soil samples, we determined that the percentage of sequences assigned to ECM fungi decreased with increasing disturbance and management intensity (REF → NEX → EXT → FIRE). Similarly, the total number of ECM species per each of ten sampling points per plot (100 ha) differed between managed (EXT-11 species, FIRE-9) and unmanaged (NEX-16, REF-14) treatments. On the other hand, the percentage of sequences belonging to ericoid mycorrhizal fungi increased. Management type significantly influenced the composition of the ECM community, while vegetation and soil characteristics explained less data variation. The ECM species assemblage of the unmanaged site (NEX) was the most similar to the mature forest, while that of the burnt site was the most different. Thelephora terrestris dominated in all treatments affected by windthrow, accompanied by Tylospora fibrillosa (NEX) and Tylospora asterophora (EXT and FIRE). Management regime was also the most important factor affecting ECM species composition on the roots of spruce seedlings assessed by Sanger sequencing.
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Affiliation(s)
- Martina Vašutová
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 31, 37005, České Budějovice, Czech Republic.
- Global Change Research Institute, Czech Academy of Sciences, Lipová 1789/9, 37005, České Budějovice, Czech Republic.
| | - Magda Edwards-Jonášová
- Global Change Research Institute, Czech Academy of Sciences, Lipová 1789/9, 37005, České Budějovice, Czech Republic
| | - Petra Veselá
- Global Change Research Institute, Czech Academy of Sciences, Lipová 1789/9, 37005, České Budějovice, Czech Republic
| | - Lenka Effenberková
- Global Change Research Institute, Czech Academy of Sciences, Lipová 1789/9, 37005, České Budějovice, Czech Republic
| | - Peter Fleischer
- Faculty of Forestry, Technical University in Zvolen, T. G. Masaryka 2117/24, 960 53, Zvolen, Slovakia
- Research Station of TANAP, State Forest of TANAP, 059 60, Tatranská Lomnica, Slovakia
| | - Pavel Cudlín
- Global Change Research Institute, Czech Academy of Sciences, Lipová 1789/9, 37005, České Budějovice, Czech Republic
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Kohout P, Charvátová M, Štursová M, Mašínová T, Tomšovský M, Baldrian P. Clearcutting alters decomposition processes and initiates complex restructuring of fungal communities in soil and tree roots. THE ISME JOURNAL 2018; 12:692-703. [PMID: 29335638 PMCID: PMC5864242 DOI: 10.1038/s41396-017-0027-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/01/2017] [Accepted: 10/02/2017] [Indexed: 12/23/2022]
Abstract
Forest management practices often severely affect forest ecosystem functioning. Tree removal by clearcutting is one such practice, producing severe impacts due to the total reduction of primary productivity. Here, we assessed changes to fungal community structure and decomposition activity in the soil, roots and rhizosphere of a Picea abies stand for a 2-year period following clearcutting compared to data from before tree harvest. We found that the termination of photosynthate flow through tree roots into soil is associated with profound changes in soil, both in decomposition processes and fungal community composition. The rhizosphere, representing an active compartment of high enzyme activity and high fungal biomass in the living stand, ceases to exist and starts to resemble bulk soil. Decomposing roots appear to separate from bulk soil and develop into hotspots of decomposition and important fungal biomass pools. We found no support for the involvement of ectomycorrhizal fungi in the decomposition of roots, but we found some evidence that root endophytic fungi may have an important role in the early stages of this process. In soil, activity of extracellular enzymes also decreased in the long term following the end of rhizodeposition by tree roots.
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Affiliation(s)
- Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 142 20, Praha 4, Czech Republic
- Department of Mycorrhizal Symbiosis, Institute of Botany of the CAS, Zámek 1, 252 43, Průhonice, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Praha 2, Czech Republic
| | - Markéta Charvátová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 142 20, Praha 4, Czech Republic
| | - Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 142 20, Praha 4, Czech Republic
| | - Tereza Mašínová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 142 20, Praha 4, Czech Republic
| | - Michal Tomšovský
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 142 20, Praha 4, Czech Republic.
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Disturbance Alters the Relative Importance of Topographic and Biogeochemical Controls on Microbial Activity in Temperate Montane Forests. FORESTS 2018. [DOI: 10.3390/f9020097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Philpott TJ, Barker JS, Prescott CE, Grayston SJ. Limited Effects of Variable-Retention Harvesting on Fungal Communities Decomposing Fine Roots in Coastal Temperate Rainforests. Appl Environ Microbiol 2018; 84:e02061-17. [PMID: 29180362 PMCID: PMC5772223 DOI: 10.1128/aem.02061-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/15/2017] [Indexed: 01/02/2023] Open
Abstract
Fine root litter is the principal source of carbon stored in forest soils and a dominant source of carbon for fungal decomposers. Differences in decomposer capacity between fungal species may be important determinants of fine-root decomposition rates. Variable-retention harvesting (VRH) provides refuge for ectomycorrhizal fungi, but its influence on fine-root decomposers is unknown, as are the effects of functional shifts in these fungal communities on carbon cycling. We compared fungal communities decomposing fine roots (in litter bags) under VRH, clear-cut, and uncut stands at two sites (6 and 13 years postharvest) and two decay stages (43 days and 1 year after burial) in Douglas fir forests in coastal British Columbia, Canada. Fungal species and guilds were identified from decomposed fine roots using high-throughput sequencing. Variable retention had short-term effects on β-diversity; harvest treatment modified the fungal community composition at the 6-year-postharvest site, but not at the 13-year-postharvest site. Ericoid and ectomycorrhizal guilds were not more abundant under VRH, but stand age significantly structured species composition. Guild composition varied by decay stage, with ruderal species later replaced by saprotrophs and ectomycorrhizae. Ectomycorrhizal abundance on decomposing fine roots may partially explain why fine roots typically decompose more slowly than surface litter. Our results indicate that stand age structures fine-root decomposers but that decay stage is more important in structuring the fungal community than shifts caused by harvesting. The rapid postharvest recovery of fungal communities decomposing fine roots suggests resiliency within this community, at least in these young regenerating stands in coastal British Columbia.IMPORTANCE Globally, fine roots are a dominant source of carbon in forest soils, yet the fungi that decompose this material and that drive the sequestration or respiration of this carbon remain largely uncharacterized. Fungi vary in their capacity to decompose plant litter, suggesting that fungal community composition is an important determinant of decomposition rates. Variable-retention harvesting is a forestry practice that modifies fungal communities by providing refuge for ectomycorrhizal fungi. We evaluated the effects of variable retention and clear-cut harvesting on fungal communities decomposing fine roots at two sites (6 and 13 years postharvest), at two decay stages (43 days and 1 year), and in uncut stands in temperate rainforests. Harvesting impacts on fungal community composition were detected only after 6 years after harvest. We suggest that fungal community composition may be an important factor that reduces fine-root decomposition rates relative to those of above-ground plant litter, which has important consequences for forest carbon cycling.
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Affiliation(s)
- Timothy J Philpott
- Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jason S Barker
- Forest Inventory and Analysis, U.S. Forest Service, Portland, Oregon, USA
| | - Cindy E Prescott
- Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sue J Grayston
- Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
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Ecosystem Resilience and Limitations Revealed by Soil Bacterial Community Dynamics in a Bark Beetle-Impacted Forest. mBio 2017; 8:mBio.01305-17. [PMID: 29208740 PMCID: PMC5717385 DOI: 10.1128/mbio.01305-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Forested ecosystems throughout the world are experiencing increases in the incidence and magnitude of insect-induced tree mortality with large ecologic ramifications. Interestingly, correlations between water quality and the extent of tree mortality in Colorado montane ecosystems suggest compensatory effects from adjacent live vegetation that mute responses in less severely impacted forests. To this end, we investigated whether the composition of the soil bacterial community and associated functionality beneath beetle-killed lodgepole pine was influenced by the extent of surrounding tree mortality. The most pronounced changes were observed in the potentially active bacterial community, where alpha diversity increased in concert with surrounding tree mortality until mortality exceeded a tipping point of ~30 to 40%, after which diversity stabilized and decreased. Community structure also clustered in association with the extent of surrounding tree mortality with compositional trends best explained by differences in NH4+ concentrations and C/N ratios. C/N ratios, which were lower in soils under beetle-killed trees, further correlated with the relative abundance of putative nitrifiers and exoenzyme activity. Collectively, the response of soil microorganisms that drive heterotrophic respiration and decay supports observations of broader macroscale threshold effects on water quality in heavily infested forests and could be utilized as a predictive mechanism during analogous ecosystem disruptions. Forests around the world are succumbing to insect infestation with repercussions for local soil biogeochemistry and downstream water quality and quantity. This study utilized microbial community dynamics to address why we are observing watershed scale biogeochemical impacts from forest mortality in some impacted areas but not others. Through a unique “tree-centric” approach, we were able to delineate plots with various tree mortality levels within the same watershed to see if surviving surrounding vegetation altered microbial and biogeochemical responses. Our results suggest that forests with lower overall tree mortality levels are able to maintain “normal” ecosystem function, as the bacterial community appears resistant to tree death. However, surrounding tree mortality influences this mitigating effect with various linear and threshold responses whereupon the bacterial community and its function are altered. Our study lends insight into how microscale responses propagate upward into larger-scale observations, which may be useful for future predictions during analogous disruptions.
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Cline LC, Schilling JS, Menke J, Groenhof E, Kennedy PG. Ecological and functional effects of fungal endophytes on wood decomposition. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12949] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Lauren C. Cline
- Department of Plant and Microbial BiologyUniversity of Minnesota St. Paul MN USA
| | - Jonathan S. Schilling
- Department of Bioproducts and Biosystems EngineeringUniversity of Minnesota St. Paul MN USA
| | - Jon Menke
- Department of Bioproducts and Biosystems EngineeringUniversity of Minnesota St. Paul MN USA
- Cargill Hopkins MN USA
| | - Emily Groenhof
- Department of Bioproducts and Biosystems EngineeringUniversity of Minnesota St. Paul MN USA
| | - Peter G. Kennedy
- Department of Plant and Microbial BiologyUniversity of Minnesota St. Paul MN USA
- Department of Ecology, Evolution and BehaviorUniversity of Minnesota St. Paul MN USA
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50
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Changes of Scots Pine Phyllosphere and Soil Fungal Communities during Outbreaks of Defoliating Insects. FORESTS 2017. [DOI: 10.3390/f8090316] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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