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The Necrobiome of Deadwood: The Life after Death. ECOLOGIES 2022. [DOI: 10.3390/ecologies4010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In recent decades, sustainable forest management has been increasingly recognized, promoting the diffusion of silvicultural practices aimed at considering all components of the forest system. Deadwood is an important component of the forest ecosystem. It plays a fundamental role in providing nutrients and habitats for a wide variety of saprotrophic and heterotrophic organisms and significantly contributes to soil formation and carbon storage. Deadwood is inhabited by a plethora of organisms from various kingdoms that have evolved the ability to utilize decaying organic matter. This community, consisting of both eukaryotic and prokaryotic species, can be defined as “necrobiome”. Through the interactions between its various members, the necrobiome influences the decay rates of deadwood and plays a crucial role in the balance between organic matter decomposition, carbon sequestration, and gas exchanges (e.g., CO2) with the atmosphere. The present work aims to provide an overview of the biodiversity and role of the microbial communities that inhabit deadwood and their possible involvement in greenhouse gas (CO2, N2O, and CH4) emissions.
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Yang S, Poorter L, Kuramae EE, Sass-Klaassen U, Leite MFA, Costa OYA, Kowalchuk GA, Cornelissen JHC, van Hal J, Goudzwaard L, Hefting MM, van Logtestijn RSP, Sterck FJ. Stem traits, compartments, and tree species affect fungal communities on decaying wood. Environ Microbiol 2022; 24:3625-3639. [PMID: 35229433 PMCID: PMC9544286 DOI: 10.1111/1462-2920.15953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/12/2022] [Accepted: 02/23/2022] [Indexed: 12/01/2022]
Abstract
Dead wood quantity and quality is important for forest biodiversity, by determining wood‐inhabiting fungal assemblages. We therefore evaluated how fungal communities were regulated by stem traits and compartments (i.e. bark, outer‐ and inner wood) of 14 common temperate tree species. Fresh logs were incubated in a common garden experiment in a forest site in the Netherlands. After 1 and 4 years of decay, the fungal composition of different compartments was assessed using Internal Transcribed Spacer amplicon sequencing. We found that fungal alpha diversity differed significantly across tree species and stem compartments, with bark showing significantly higher fungal diversity than wood. Gymnosperms and Angiosperms hold different fungal communities, and distinct fungi were found between inner wood and other compartments. Stem traits showed significant afterlife effects on fungal communities; traits associated with accessibility (e.g. conduit diameter), stem chemistry (e.g. C, N, lignin) and physical defence (e.g. density) were important factors shaping fungal community structure in decaying stems. Overall, stem traits vary substantially across stem compartments and tree species, thus regulating fungal communities and the long‐term carbon dynamics of dead trees.
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Affiliation(s)
- Shanshan Yang
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Lourens Poorter
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708, PB, Wageningen, the Netherlands.,Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Ute Sass-Klaassen
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708, PB, Wageningen, the Netherlands.,Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Ohana Y A Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708, PB, Wageningen, the Netherlands
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Johannes H C Cornelissen
- Systems Ecology, Department of Ecological Science, VU University (Vrije Universiteit) Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Jurgen van Hal
- Systems Ecology, Department of Ecological Science, VU University (Vrije Universiteit) Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Leo Goudzwaard
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Mariet M Hefting
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Richard S P van Logtestijn
- Systems Ecology, Department of Ecological Science, VU University (Vrije Universiteit) Amsterdam, De Boelelaan 1085, 1081, HV, Amsterdam, The Netherlands
| | - Frank J Sterck
- Forest Ecology and Forest Management Group, Wageningen University and Research, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
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Lee M, Powell JR, Oberle B, Unda F, Mansfield SD, Dalrymple R, Rigg J, Cornwell WK, Zanne AE. Initial wood trait variation overwhelms endophyte community effects for explaining decay trajectories. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marissa Lee
- Department of Biological Sciences The George Washington University Washington DC United States
| | - Jeff R. Powell
- Hawkesbury Institute for the Environment University of Western Sydney Hawkesbury Australia
| | - Brad Oberle
- Division of Natural Sciences New College of Florida Sarasota FL United States
| | - Faride Unda
- Department of Wood Science University of British Columbia Vancouver Canada
| | - Shawn D. Mansfield
- Department of Wood Science University of British Columbia Vancouver Canada
| | - Rhiannon Dalrymple
- Evolution & Ecology Research Centre School of Biological Earth and Environmental Sciences University of New South Wales Sydney Australia
| | - Jessica Rigg
- Elizabeth Macarthur Agricultural Institute Department of Primary Industries NSW Meanagle Australia
| | - William K. Cornwell
- Evolution & Ecology Research Centre School of Biological Earth and Environmental Sciences University of New South Wales Sydney Australia
| | - Amy E. Zanne
- Department of Biological Sciences The George Washington University Washington DC United States
- Department of Biology University of Miami Miami FL United States
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Yang S, Limpens J, Sterck FJ, Sass‐Klaassen U, Cornelissen JHC, Hefting M, van Logtestijn RSP, Goudzwaard L, Dam N, Dam M, Veerkamp MT, van den Berg B, Brouwer E, Chang C, Poorter L. Dead wood diversity promotes fungal diversity. OIKOS 2021. [DOI: 10.1111/oik.08388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Shanshan Yang
- Forest Ecology and Forest Management Group, Wageningen Univ. and Research Wageningen the Netherlands
| | - Juul Limpens
- Plant Ecology and Nature Conservation Group, Wageningen Univ. and Research Wageningen the Netherlands
| | - Frank J. Sterck
- Forest Ecology and Forest Management Group, Wageningen Univ. and Research Wageningen the Netherlands
| | - Ute Sass‐Klaassen
- Forest Ecology and Forest Management Group, Wageningen Univ. and Research Wageningen the Netherlands
| | | | - Mariet Hefting
- Landscape Ecology, Inst. of Environmental Biology, Utrecht Univ. Utrecht the Netherlands
| | | | - Leo Goudzwaard
- Forest Ecology and Forest Management Group, Wageningen Univ. and Research Wageningen the Netherlands
| | | | | | | | | | - Emiel Brouwer
- B‐WARE Research Centre, Radboud Univ. Nijmegen the Netherlands
| | - Chenghui Chang
- Systems Ecology, Dept of Ecological Science, VU Univ. (Vrije Univ.) Amsterdam Amsterdam the Netherlands
| | - Lourens Poorter
- Forest Ecology and Forest Management Group, Wageningen Univ. and Research Wageningen the Netherlands
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Microbial Diversity and Ecosystem Functioning in Deadwood of Black Pine of a Temperate Forest. FORESTS 2021. [DOI: 10.3390/f12101418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The present study provides a deeper insight on variations of microbial abundance and community composition concerning specific environmental parameters related to deadwood decay, focusing on a mesocosm experiment conducted with deadwood samples from black pine of different decay classes. The chemical properties and microbial communities of deadwood changed over time. The total carbon percentage remained constant in the first stage of decomposition, showing a significant increase in the last decay class. The percentage of total nitrogen and the abundances of nifH harbouring bacteria significantly increased as decomposition advanced, suggesting N wood-enrichment by microbial N immobilization and/or N2-fixation. The pH slightly decreased during decomposition and significantly correlated with fungal abundance. CO2 production was higher in the last decay class 5 and positively correlated with bacterial abundance. Production of CH4 was registered in one sample of decay class 3, which correlates with the highest abundance of methanogenic archaea that probably belonged to Methanobrevibacter genus. N2O consumption increased along decomposition progress, indicating a complete reduction of nitrate compounds to N2 via denitrification, as proved by the highest nosZ gene copy number in decay class 5. Conversely, our results highlighted a low involvement of nitrifying communities in deadwood decomposition.
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Probst M, Ascher-Jenull J, Insam H, Gómez-Brandón M. The Molecular Information About Deadwood Bacteriomes Partly Depends on the Targeted Environmental DNA. Front Microbiol 2021; 12:640386. [PMID: 33986733 PMCID: PMC8110828 DOI: 10.3389/fmicb.2021.640386] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/22/2021] [Indexed: 01/04/2023] Open
Abstract
Microbiome studies mostly rely on total DNA extracts obtained directly from environmental samples. The total DNA consists of both intra- and extracellular DNA, which differ in terms of their ecological interpretation. In the present study, we have investigated for the first time the differences among the three DNA types using microbiome sequencing of Picea abies deadwood logs (Hunter decay classes I, III, and V). While the bacterial compositions of all DNA types were comparable in terms of more abundant organisms and mainly depended on the decay class, we found substantial differences between DNA types with regard to less abundant amplicon sequence variants (ASVs). The analysis of the sequentially extracted intra- and extracellular DNA fraction, respectively, increased the ecological depth of analysis compared to the directly extracted total DNA pool. Both DNA fractions were comparable in proportions and the extracellular DNA appeared to persist in the P. abies deadwood logs, thereby causing its masking effect. Indeed, the extracellular DNA masked the compositional dynamics of intact cells in the total DNA pool. Our results provide evidence that the choice of DNA type for analysis might benefit a study’s answer to its respective ecological question. In the deadwood environment researched here, the differential analysis of the DNA types underlined the relevance of Burkholderiales, Rhizobiales and other taxa for P. abies deadwood decomposition and revealed that the role of Acidobacteriota under this scenario might be underestimated, especially compared to Actinobacteriota.
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Affiliation(s)
- Maraike Probst
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | | | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - María Gómez-Brandón
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria.,Grupo de Ecoloxía Animal (GEA), Universidade de Vigo, Vigo, Spain
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