1
|
Vassilev I, Rinta-Kanto JM, Kokko M. Comparing the performance of fluidized and fixed granular activated carbon beds as cathodes for microbial electrosynthesis of carboxylates from CO 2. BIORESOURCE TECHNOLOGY 2024; 403:130896. [PMID: 38795921 DOI: 10.1016/j.biortech.2024.130896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 05/28/2024]
Abstract
Microbial electrosynthesis (MES) can use renewable electricity to power microbial conversion of carbon dioxide (CO2) into carboxylates. To ensure high productivities in MES, good mass transfer must be ensured, which could be accomplished with fluidization of granular activated carbon (GAC). In this study, fluidized and fixed GAC bed cathodes were compared. Acetate production rate and current density were 42 % and 47 % lower, respectively, in fluidized than fixed bed reactors. Although similar microbial consortium dominated by Eubacterium and Proteiniphilum was observed, lowest biomass quantity was measured with fixed GAC bed indicating higher specific acetate production rates compared to fluidized GAC bed. Furthermore, charge efficiency was the highest and charge recovery in carboxylates the lowest in fixed GAC beds indicating enhanced hydrogen evolution and need for enhancing CO2 feeding to enable higher production rates of acetate. Overall, fixed GAC beds have higher efficiency for acetate production in MES than fluidized GAC beds.
Collapse
Affiliation(s)
- Igor Vassilev
- Faculty of Engineering and Natural Sciences, Tampere University, Finland
| | | | - Marika Kokko
- Faculty of Engineering and Natural Sciences, Tampere University, Finland.
| |
Collapse
|
2
|
Carmichael MJ, Martinez M, Bräuer SL, Ardón M. Microbial Communities in Standing Dead Trees in Ghost Forests are Largely Aerobic, Saprophytic, and Methanotrophic. Curr Microbiol 2024; 81:229. [PMID: 38896154 PMCID: PMC11186919 DOI: 10.1007/s00284-024-03767-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Standing dead trees (snags) are recognized for their influence on methane (CH4) cycling in coastal wetlands, yet the biogeochemical processes that control the magnitude and direction of fluxes across the snag-atmosphere interface are not fully elucidated. Herein, we analyzed microbial communities and fluxes at one height from ten snags in a ghost forest wetland. Snag-atmosphere CH4 fluxes were highly variable (- 0.11-0.51 mg CH4 m-2 h-1). CH4 production was measured in three out of ten snags; whereas, CH4 consumption was measured in two out of ten snags. Potential CH4 production and oxidation in one core from each snag was assayed in vitro. A single core produced CH4 under anoxic and oxic conditions, at measured rates of 0.7 and 0.6 ng CH4 g-1 h-1, respectively. Four cores oxidized CH4 under oxic conditions, with an average rate of - 1.13 ± 0.31 ng CH4 g-1 h-1. Illumina sequencing of the V3/V4 region of the 16S rRNA gene sequence revealed diverse microbial communities and indicated oxidative decomposition of deadwood. Methanogens were present in 20% of the snags, with a mean relative abundance of < 0.0001%. Methanotrophs were identified in all snags, with a mean relative abundance of 2% and represented the sole CH4-cycling communities in 80% of the snags. These data indicate potential for microbial attenuation of CH4 emissions across the snag-atmosphere interface in ghost forests. A better understanding of the environmental drivers of snag-associated microbial communities is necessary to forecast the response of CH4 cycling in coastal ghost forest wetlands to a shifting coastal landscape.
Collapse
Affiliation(s)
- Mary Jane Carmichael
- Departments of Biology and Environmental Studies, Hollins University, Roanoke, VA, 24020, USA.
| | - Melinda Martinez
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, MD, 20708, USA
| | - Suzanna L Bräuer
- Department of Biology, Appalachian State University, Boone, NC, 28608, USA
| | - Marcelo Ardón
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| |
Collapse
|
3
|
Yao H, Rinta-Kanto JM, Vassilev I, Kokko M. Methanol as a co-substrate with CO 2 enhances butyrate production in microbial electrosynthesis. Appl Microbiol Biotechnol 2024; 108:372. [PMID: 38874789 PMCID: PMC11178620 DOI: 10.1007/s00253-024-13218-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 05/28/2024] [Accepted: 06/02/2024] [Indexed: 06/15/2024]
Abstract
Methanol is a promising feedstock for the bio-based economy as it can be derived from organic waste streams or produced electrochemically from CO2. Acetate production from CO2 in microbial electrosynthesis (MES) has been widely studied, while more valuable compounds such as butyrate are currently attracting attention. In this study, methanol was used as a co-substrate with CO2 to enhance butyrate production in MES. Feeding with CO2 and methanol resulted in the highest butyrate production rates and titres of 0.36 ± 0.01 g L-1 d-1 and 8.6 ± 0.2 g L-1, respectively, outperforming reactors with only CO2 feeding (0.20 ± 0.03 g L-1 d-1 and 5.2 ± 0.1 g L-1, respectively). Methanol acted as electron donor and as carbon source, both of which contributed ca. 50% of the carbon in the products. Eubacterium was the dominant genus with 52.6 ± 2.5% relative abundance. Thus, we demonstrate attractive route for the use of the C1 substrates, CO2 and methanol, to produce mainly butyrate. KEY POINTS: • Butyrate was the main product from methanol and CO2 in MES • Methanol acted as both carbon and electron source in MES • Eubacterium dominating microbial culture was enriched in MES.
Collapse
Affiliation(s)
- Hui Yao
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, 33720, Tampere, Finland
| | - Johanna M Rinta-Kanto
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, 33720, Tampere, Finland
| | - Igor Vassilev
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, 33720, Tampere, Finland
| | - Marika Kokko
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, 33720, Tampere, Finland.
| |
Collapse
|
4
|
Shi B, Wang X, Yang S, Chen H, Zhao Y, Shen J, Xie M, Huang B. Changes and driving factors of microbial community composition and functional groups during the decomposition of Pinus massoniana deadwood. Ecol Evol 2024; 14:e11210. [PMID: 38571805 PMCID: PMC10985386 DOI: 10.1002/ece3.11210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024] Open
Abstract
Clarifying changes in the microbial community in deadwood at different stages of decomposition is crucial for comprehending the role of deadwood in the biogeochemical processes and the sustainability of forest development. However, there have been no reports on the dynamics of microbial community during the decomposition of Pinus massoniana. We used the "space-for-time" substitution to analyze the characteristics of microbial community changes and the key influencing factors in the P. massoniana deadwood during different decomposition stages by 16S and ITS rRNA gene sequencing. The results suggest that the microbial community structure of the early decomposition (decay class I) was significantly different from the other decay classes, while the diversity and richness of the microbial community were the highest in the late decomposition (decay class V). The Linear Discriminant Analysis Effect Size analysis revealed that most bacterial and fungal taxa were significantly enriched in decay classes I and V deadwood. During the initial stages of decomposition, the relative abundance of the bacterial functional group responsible for carbohydrate metabolism was greater than the later stages. As decomposition progressed, the relative abundance of saprophytic fungi gradually decreased, and there was a shift in the comparative abundance of mixed saprophytic-symbiotic fungi from low to high before eventually decreasing. Total organic carbon, total nitrogen, carbon-to-nitrogen ratio, total potassium, total phenol, condensed tannin, lignin, and cellulose were significantly correlated with microbial community structure, with the carbon-to-nitrogen ratio having the greatest effect. Our results indicate that the physicochemical properties of deadwood, microbial community structural composition and functional group changes were related to the decay class, among which the carbon-to-nitrogen ratio may be an important factor affecting the composition and diversity of microbial communities.
Collapse
Affiliation(s)
- Bingyang Shi
- Forestry CollegeGuizhou UniversityGuiyangGuizhouChina
| | - Xiurong Wang
- Forestry CollegeGuizhou UniversityGuiyangGuizhouChina
| | - Shuoyuan Yang
- Forestry CollegeGuizhou UniversityGuiyangGuizhouChina
| | - Hongmei Chen
- Forestry CollegeGuizhou UniversityGuiyangGuizhouChina
| | - Yang Zhao
- Forestry CollegeGuizhou UniversityGuiyangGuizhouChina
| | - Junjie Shen
- Forestry CollegeGuizhou UniversityGuiyangGuizhouChina
| | - Meixuan Xie
- Forestry CollegeGuizhou UniversityGuiyangGuizhouChina
| | - Bufang Huang
- Forestry CollegeGuizhou UniversityGuiyangGuizhouChina
| |
Collapse
|
5
|
Pioli S, Clagnan E, Chowdhury AA, Bani A, Borruso L, Ventura M, Tonon G, Brusetti L. Structural and functional microbial diversity in deadwood respond to decomposition dynamics. Environ Microbiol 2023; 25:2351-2367. [PMID: 37403552 DOI: 10.1111/1462-2920.16459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023]
Abstract
We investigated the changes in microbial community diversities and functions in natural downed wood at different decay stages in a natural oak forest in the Italian Alps, through metagenomics analysis and in vitro analysis. Alfa diversity of bacterial communities was affected by the decay stage and log characteristics, while beta diversity was mainly driven by log diameter. Fungal and archaeal beta diversities were affected by the size of the sampled wood (log diameter), although, fungi were prominently driven by wood decay stage. The analysis of genes targeting cell wall degradation revealed higher abundances of cellulose and pectin-degrading enzymes in bacteria, while in fungi the enzymes targeting cellulose and hemicellulose were more abundant. The decay class affected the abundance of single enzymes, revealing a shift in complex hydrocarbons degradation pathways along the decay process. Moreover, we found that the genes related to Coenzyme M biosynthesis to be the most abundant especially at early stages of wood decomposition while the overall methanogenesis did not seem to be influenced by the decay stage. Intra- and inter-kingdom interactions between bacteria and fungi revealed complex pattern of community structure in response to decay stage possibly reflecting both direct and indirect interactions.
Collapse
Affiliation(s)
- Silvia Pioli
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
- Institute of Research on Terrestrial Ecosystems (IRET), National Research Council (CNR), Monterotondo Scalo (RM), Italy
| | - Elisa Clagnan
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Atif Aziz Chowdhury
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Alessia Bani
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Maurizio Ventura
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Giustino Tonon
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bolzano/Bozen, Bolzano/Bozen, Italy
| |
Collapse
|
6
|
Wang Z, Xu M, Li F, Bai Y, Hou J, Li X, Cao R, Deng Y, Jiang Y, Wang H, Yang W. Changes in soil bacterial communities and functional groups beneath coarse woody debris across a subalpine forest successional series. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
|
7
|
Hajdu-Rahkama R, Özkaya B, Lakaniemi AM, Puhakka JA. Potential of biological sulphur recovery from thiosulphate by haloalkaliphilic Thioalkalivibrio denitrificans. ENVIRONMENTAL TECHNOLOGY 2023; 44:804-816. [PMID: 34615437 DOI: 10.1080/09593330.2021.1985620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
The aim of this study was to investigate the potential for elemental sulphur recovery from sulphurous solutions under aerobic and anoxic conditions by haloalkalophilic Thioalkalivibrio denitrificans at 0.8-19.6 g S2O32--S L-1 and 0.2-0.58 g NO2 L-1, respectively. The experiments were conducted as batch assays with haloalkaline (pH 10 and ≥ 14 g Na+ L-1) thiosulphate solution. Aerobically, the highest biotransformation rate of thiosulphate obtained was 0.03 h-1 at 8.5 g L S2O32--S. Based on Monod model, the maximum substrate utilisation rate (qm) was 0.024 h-1 with half saturation constant (Ks) 0.42 g S2O32--S L-1 at initial [S2O32--S] of 14 g L-1. S0 accumulated at [S2O32--S] ≥ 1.5 g L-1 (10% yield at initial 9.5 g S2O32--S L-1) and the highest S0 yield estimated with the model was 61% with initial [S2O32--S] of 16.5 g L-1. Anoxically, the maximum nitrite removal rate based on Monod modelling was 0.011 h-1 with Ks = 0.84 g NO2- L-1. Aerobically and anoxically the maximum specific growth rates (µm) were 0.046 and 0.022 h-1, respectively. In summary, high-rate aerobic biotransformation kinetics of thiosulphate were demonstrated, whereas the rates were slower and no S0 accumulated under anoxic conditions. Thus, future developments of biotechnical applications for the recovery of S0 from haloalkaline streams from the process industry should focus on aerobic treatment.HighlightsHaloalkaline S2O32- biotransformations kinetics by Thioalkalivibrio denitrificansAerobic thiosulphate-S bioconversion up to 0.024 h-1 with Ks = 0.42 g S2O32--S L-110% S0 yield with initial 9.5 g S2O32--S L-1 in aerobic conditionAnoxic NO2 removal up to 0.01 h-1 with Ks = 0.84 g NO2- L-1.
Collapse
Affiliation(s)
- Réka Hajdu-Rahkama
- Faculty of Engineering and Natural Sciences, Bio- and Circular Economy Research Group, Tampere University, Tampere, Finland
| | - Bestamin Özkaya
- Faculty of Engineering and Natural Sciences, Bio- and Circular Economy Research Group, Tampere University, Tampere, Finland
- Department of Environmental Engineering, Yildiz Technical University, Istanbul, Turkey
| | - Aino-Maija Lakaniemi
- Faculty of Engineering and Natural Sciences, Bio- and Circular Economy Research Group, Tampere University, Tampere, Finland
| | - Jaakko A Puhakka
- Faculty of Engineering and Natural Sciences, Bio- and Circular Economy Research Group, Tampere University, Tampere, Finland
| |
Collapse
|
8
|
Moll J, Hoppe B. Evaluation of primers for the detection of deadwood-inhabiting archaea via amplicon sequencing. PeerJ 2022; 10:e14567. [PMID: 36573238 PMCID: PMC9789694 DOI: 10.7717/peerj.14567] [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: 08/10/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Archaea have been reported from deadwood of a few different tree species in temperate and boreal forest ecosystems in the past. However, while one of their functions is well linked to methane production any additional contribution to wood decomposition is not understood and underexplored which may be also attributed to lacking investigations on their diversity in this substrate. With this current work, we aim at encouraging further investigations by providing aid in primer choice for DNA metabarcoding using Illumina amplicon sequencing. We tested 16S primer pairs on genomic DNA extracted from woody tissue of four temperate deciduous tree species. Three primer pairs were specific to archaea and one prokaryotic primer pair theoretically amplifies both, bacterial and archaeal DNA. Methanobacteriales and Methanomassiliicoccales have been consistently identified as dominant orders across all datasets but significant variability in ASV richness was observed using different primer combinations. Nitrososphaerales have only been identified when using archaea-specific primer sets. In addition, the most commonly applied primer combination targeting prokaryotes in general yielded the lowest relative proportion of archaeal sequences per sample, which underlines the fact, that using target specific primers unraveled a yet unknown diversity of archaea in deadwood. Hence, archaea seem to be an important group of the deadwood-inhabiting community and further research is needed to explore their role during the decomposition process.
Collapse
Affiliation(s)
- Julia Moll
- Department of Soil Ecology, Helmholtz Centre for Environmental Research—UFZ, Halle (Saale), Germany
| | - Björn Hoppe
- Institute for National and International Plant Health, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| |
Collapse
|
9
|
Meena M, Yadav G, Sonigra P, Nagda A, Mehta T, Swapnil P, Marwal A, Kumar S. Multifarious Responses of Forest Soil Microbial Community Toward Climate Change. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02051-3. [PMID: 35657425 DOI: 10.1007/s00248-022-02051-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO2, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.
Collapse
Affiliation(s)
- Mukesh Meena
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India.
| | - Garima Yadav
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Priyankaraj Sonigra
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Adhishree Nagda
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Tushar Mehta
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Prashant Swapnil
- Department of Botany, School of Biological Science, Central University of Punjab, Bhatinda, Punjab, 151401, India
| | - Avinash Marwal
- Department of Biotechnology, Vigyan Bhawan - Block B, New Campus, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Sumit Kumar
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
| |
Collapse
|
10
|
Ferrer A, Heath KD, Mosquera SL, Suaréz Y, Dalling JW. Assembly of wood-inhabiting archaeal, bacterial and fungal communities along a salinity gradient: common taxa are broadly distributed but locally abundant in preferred habitats. FEMS Microbiol Ecol 2022; 98:6566339. [PMID: 35404430 DOI: 10.1093/femsec/fiac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 11/12/2022] Open
Abstract
Wood decomposition in water is a key ecosystem process driven by diverse microbial taxa that likely differ in their affinities for freshwater, estuarine, and marine habitats. How these decomposer communities assemble in situ or potentially colonize from other habitats remains poorly understood. At three watersheds on Coiba Island, Panama, we placed replicate sections of branch wood of a single tree species on land, and in freshwater, estuarine and marine habitats that constitute a downstream salinity gradient. We sequenced archaea, bacteria and fungi from wood samples collected after 3, 9, and 15 months to examine microbial community composition, and to examine habitat specificity and abundance patterns. We found these microbial communities were broadly structured by similar factors, with a strong effect of salinity, but little effect of watershed identity on compositional variation. Moreover, common aquatic taxa were also present in wood incubated on land. Our results suggest that taxa either dispersed to both terrestrial and aquatic habitats, or that microbes with broad habitat ranges were initially present in the wood as endophytes. Nonetheless, these habitat generalists varied greatly in abundance across habitats suggesting an important role for habitat filtering in maintaining distinct aquatic communities in freshwater, estuarine and marine habitats.
Collapse
Affiliation(s)
- Astrid Ferrer
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Sergio L Mosquera
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| | - Yaraví Suaréz
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| | - James W Dalling
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| |
Collapse
|
11
|
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.
Collapse
|
12
|
Mieszkin S, Pouder E, Uroz S, Simon-Colin C, Alain K. Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov., Two Acidophilic Bacteria Isolated from Decaying Wood, Hydrolyzing Cellulose and Producing Poly-3-hydroxybutyrate. Microorganisms 2021; 9:microorganisms9102053. [PMID: 34683374 PMCID: PMC8537097 DOI: 10.3390/microorganisms9102053] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/17/2021] [Accepted: 09/25/2021] [Indexed: 12/02/2022] Open
Abstract
Two novel strains, HW T2.11T and HW T5.17T, were isolated from decaying wood (forest of Champenoux, France). Study of the 16S rRNA sequence similarity indicated that the novel strains belong to the genus Acidisoma. The sequence similarity of the 16S rRNA gene of HW T2.11T with the corresponding sequences of A. tundrae and A. sibiricum was 97.30% and 97.25%, while for HW T5.17T it was 96.85% and 97.14%, respectively. The DNA G+C contents of the strains were 62.32–62.50%. Cells were Gram-negative coccobacilli that had intracellular storage granules (poly-3-hydroxybutyrate (P3HB)) that confer resistance to environmental stress conditions. They were mesophilic and acidophilic organisms growing at 8–25 °C, at a pH of 2.0–6.5, and were capable of using a wide range of organic compounds and complex biopolymers such as starch, fucoidan, laminarin, pectin and cellulose, the latter two being involved in wood composition. The major cellular fatty acid was cyclo C19:0ω8c and the major quinone was Q-10. Overall, genome relatedness indices between genomes of strains HW T2.11T and HW T5.17T (Orthologous Average Nucleotide Identity (OrthoANI) value = 83.73% and digital DNA-DNA hybridization score = 27.5%) confirmed that they belonged to two different species. Genetic predictions indicate that the cyclopropane fatty acid (CFA) pathway is present, conferring acid-resistance properties to the cells. The two novel strains might possess a class IV polyhydroxyalcanoate (PHA) synthase operon involved in the P3HB production pathway. Overall, the polyphasic taxonomic analysis shows that these two novel strains are adapted to harsh environments such as decaying wood where the organic matter is difficult to access, and can contribute to the degradation of dead wood. These strains represent novel species of the genus Acidisoma, for which the names Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov. are proposed. The type strains of Acidisoma silvae and Acidisomacellulosilytica are, respectively, HW T2.11T (DSM 111006T; UBOCC-M-3364T) and HW T5.17T (DSM 111007T; UBOCC-M-3365T).
Collapse
Affiliation(s)
- Sophie Mieszkin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
- Centre INRAE-Grand Est-Nancy, Université de Lorraine, INRAE, UMR IAM, 54280 Champenoux, F-54000 Nancy, France;
- Correspondence:
| | - Eva Pouder
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
| | - Stéphane Uroz
- Centre INRAE-Grand Est-Nancy, Université de Lorraine, INRAE, UMR IAM, 54280 Champenoux, F-54000 Nancy, France;
| | - Christelle Simon-Colin
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E, Université de Brest, CNRS, Ifremer, IUEM, Rue Dumont d’Urville, F-29280 Plouzané, France; (E.P.); (C.S.-C.); (K.A.)
| |
Collapse
|
13
|
Moll J, Roy F, Bässler C, Heilmann-Clausen J, Hofrichter M, Kellner H, Krabel D, Schmidt JH, Buscot F, Hoppe B. First Evidence That Nematode Communities in Deadwood Are Related to Tree Species Identity and to Co-Occurring Fungi and Prokaryotes. Microorganisms 2021; 9:microorganisms9071454. [PMID: 34361890 PMCID: PMC8304250 DOI: 10.3390/microorganisms9071454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 06/30/2021] [Accepted: 07/03/2021] [Indexed: 01/02/2023] Open
Abstract
Nematodes represent a diverse and ubiquitous group of metazoans in terrestrial environments. They feed on bacteria, fungi, plants, other nematodes or parasitize a variety of animals and hence may be considered as active members of many food webs. Deadwood is a structural component of forest ecosystems which harbors many niches for diverse biota. As fungi and bacteria are among the most prominent decomposing colonizers of deadwood, we anticipated frequent and diverse nematode populations to co-occur in such ecosystems. However, knowledge about their ability to colonize this habitat is still limited. We applied DNA-based amplicon sequencing (metabarcoding) of the 18S rRNA gene to analyze nematode communities in sapwood and heartwood of decaying logs from 13 different tree species. We identified 247 nematode ASVs (amplicon sequence variants) from 27 families. Most of these identified families represent bacterial and fungal feeders. Their composition strongly depended on tree species identity in both wood compartments. While pH and water content were the only wood properties that contributed to nematodes' distribution, co-occurring fungal and prokaryotic (bacteria and archaea) α- and β-diversities were significantly related to nematode communities. By exploring thirteen different tree species, which exhibit a broad range of wood characteristics, this study provides first and comprehensive insights into nematode diversity in deadwood of temperate forests and indicates connectivity to other wood-inhabiting organisms.
Collapse
Affiliation(s)
- Julia Moll
- Helmholtz Centre for Environmental Research—UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany; (F.R.); (F.B.)
- Correspondence: (J.M.); (B.H.)
| | - Friederike Roy
- Helmholtz Centre for Environmental Research—UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany; (F.R.); (F.B.)
- Institute of Forest Botany, Technische Universität Dresden, 01737 Tharandt, Germany;
| | - Claus Bässler
- Department of Conservation Biology, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany;
- Department of Research, National Park Bavarian Forest, 94481 Grafenau, Germany
| | - Jacob Heilmann-Clausen
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - Martin Hofrichter
- Institute of Environmental Biotechnology, Technische Universität Dresden, IHI Zittau, 02763 Zittau, Germany; (M.H.); (H.K.)
| | - Harald Kellner
- Institute of Environmental Biotechnology, Technische Universität Dresden, IHI Zittau, 02763 Zittau, Germany; (M.H.); (H.K.)
| | - Doris Krabel
- Institute of Forest Botany, Technische Universität Dresden, 01737 Tharandt, Germany;
| | - Jan Henrik Schmidt
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany;
| | - François Buscot
- Helmholtz Centre for Environmental Research—UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany; (F.R.); (F.B.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle—Jena—Leipzig, 04103 Leipzig, Germany
| | - Björn Hoppe
- Institute for National and International Plant Health, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany
- Correspondence: (J.M.); (B.H.)
| |
Collapse
|
14
|
Tláskal V, Baldrian P. Deadwood-Inhabiting Bacteria Show Adaptations to Changing Carbon and Nitrogen Availability During Decomposition. Front Microbiol 2021; 12:685303. [PMID: 34220772 PMCID: PMC8247643 DOI: 10.3389/fmicb.2021.685303] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/04/2021] [Indexed: 01/01/2023] Open
Abstract
Deadwood decomposition is responsible for a significant amount of carbon (C) turnover in natural forests. While fresh deadwood contains mainly plant compounds and is extremely low in nitrogen (N), fungal biomass and N content increase during decomposition. Here, we examined 18 genome-sequenced bacterial strains representing the dominant deadwood taxa to assess their adaptations to C and N utilization in deadwood. Diverse gene sets for the efficient decomposition of plant and fungal cell wall biopolymers were found in Acidobacteria, Bacteroidetes, and Actinobacteria. In contrast to these groups, Alphaproteobacteria and Gammaproteobacteria contained fewer carbohydrate-active enzymes and depended either on low-molecular-mass C sources or on mycophagy. This group, however, showed rich gene complements for N2 fixation and nitrate/nitrite reduction—key assimilatory and dissimilatory steps in the deadwood N cycle. We show that N2 fixers can obtain C independently from either plant biopolymers or fungal biomass. The succession of bacteria on decomposing deadwood reflects their ability to cope with the changing quality of C-containing compounds and increasing N content.
Collapse
Affiliation(s)
- Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
| |
Collapse
|
15
|
Embacher J, Neuhauser S, Zeilinger S, Kirchmair M. Microbiota Associated with Different Developmental Stages of the Dry Rot Fungus Serpula lacrymans. J Fungi (Basel) 2021; 7:354. [PMID: 33946450 PMCID: PMC8147175 DOI: 10.3390/jof7050354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/19/2022] Open
Abstract
The dry rot fungus Serpula lacrymans causes significant structural damage by decaying construction timber, resulting in costly restoration procedures. Dry rot fungi decompose cellulose and hemicellulose and are often accompanied by a succession of bacteria and other fungi. Bacterial-fungal interactions (BFI) have a considerable impact on all the partners, ranging from antagonistic to beneficial relationships. Using a cultivation-based approach, we show that S. lacrymans has many co-existing, mainly Gram-positive, bacteria and demonstrate differences in the communities associated with distinct fungal parts. Bacteria isolated from the fruiting bodies and mycelia were dominated by Firmicutes, while bacteria isolated from rhizomorphs were dominated by Proteobacteria. Actinobacteria and Bacteroidetes were less abundant. Fluorescence in situ hybridization (FISH) analysis revealed that bacteria were not present biofilm-like, but occurred as independent cells scattered across and within tissues, sometimes also attached to fungal spores. In co-culture, some bacterial isolates caused growth inhibition of S. lacrymans, and vice versa, and some induced fungal pigment production. It was found that 25% of the isolates could degrade pectin, 43% xylan, 17% carboxymethylcellulose, and 66% were able to depolymerize starch. Our results provide first insights for a better understanding of the holobiont S. lacrymans and give hints that bacteria influence the behavior of S. lacrymans in culture.
Collapse
Affiliation(s)
| | | | | | - Martin Kirchmair
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria; (J.E.); (S.N.); (S.Z.)
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Abstract
Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Fungal-bacterial interactions play a key role in the functioning of many ecosystems. Thus, understanding their interactive dynamics is of central importance for gaining predictive knowledge on ecosystem functioning. However, it is challenging to disentangle the mechanisms behind species associations from observed co-occurrence patterns, and little is known about the directionality of such interactions. Here, we applied joint species distribution modeling to high-throughput sequencing data on co-occurring fungal and bacterial communities in deadwood to ask whether fungal and bacterial co-occurrences result from shared habitat use (i.e., deadwood’s properties) or whether there are fungal-bacterial interactive associations after habitat characteristics are taken into account. Moreover, we tested the hypothesis that the interactions are mainly modulated through fungal communities influencing bacterial communities. For that, we quantified how much the predictive power of the joint species distribution models for bacterial and fungal community improved when accounting for the other community. Our results show that fungi and bacteria form tight association networks (i.e., some species pairs co-occur more frequently and other species pairs co-occur less frequently than expected by chance) in deadwood that include common (or opposite) responses to the environment as well as (potentially) biotic interactions. Additionally, we show that information about the fungal occurrences and abundances increased the power to predict the bacterial abundances substantially, whereas information about the bacterial occurrences and abundances increased the power to predict the fungal abundances much less. Our results suggest that fungal communities may mainly affect bacteria in deadwood. IMPORTANCE Understanding the interactive dynamics between fungal and bacterial communities is important to gain predictive knowledge on ecosystem functioning. However, little is known about the mechanisms behind fungal-bacterial associations and the directionality of species interactions. Applying joint species distribution modeling to high-throughput sequencing data on co-occurring fungal-bacterial communities in deadwood, we found evidence that nonrandom fungal-bacterial associations derive from shared habitat use as well as (potentially) biotic interactions. Importantly, the combination of cross-validations and conditional cross-validations helped us to answer the question about the directionality of the biotic interactions, providing evidence that suggests that fungal communities may mainly affect bacteria in deadwood. Our modeling approach may help gain insight into the directionality of interactions between different components of the microbiome in other environments.
Collapse
|
18
|
Fan S, Sun Y, Ter Heijne A, Chen WS, Buisman CJN. Effect of nitrogen, phosphorus and pH on biological wood oxidation at 42 °C. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 726:138569. [PMID: 32344251 DOI: 10.1016/j.scitotenv.2020.138569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/01/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Biological wood oxidation (BWO) is proposed as a cleaner alternative to wood combustion for heat production and wood waste management. Currently, BWO is not extensively studied and little is known about it. Nevertheless, given the composition of wood residues, which is dominated by carbon, nutrient availability may become a limiting factor during BWO. Our objective was to study the nutrition requirements for sustaining the BWO. For this purpose, three different factors including nitrogen addition, phosphorus addition and pH, were studied. Oxygen consumption and mass loss were monitored and used to evaluate the impact of nutrition on BWO and to calculate the theoretical heat production. The result showed that nitrogen addition at a relatively low level (2.5-10 mg/g) enhanced the cumulative oxygen consumption by 60-124% and mass loss by 28-95%, when compared with the BWO without nitrogen addition. The highest nitrogen addition examined in this research (20 mg/g), on the other hand, did not enhance BWO. Different phosphorus addition (0.5-5 mg/g) and pH (4-6) had little impacts on BWO. The highest theoretical heat production rate (0.63 W/kg dry wood biomass) was achieved using 2.5 mg/g nitrogen addition with a 95-day incubation. This suggests that nitrogen addition is required and able to sustain BWO. Besides, the cumulative oxygen consumption showed a good linear relationship with mass loss. This study provides the first indication on the effective quantify of nitrogen addition for enhancing BWO, which contributes to the selection of nutrient source for BWO in future studies.
Collapse
Affiliation(s)
- Shiyang Fan
- Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Yue Sun
- Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Annemiek Ter Heijne
- Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Wei-Shan Chen
- Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands.
| | - Cees J N Buisman
- Environmental Technology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, Leeuwarden, the Netherlands
| |
Collapse
|
19
|
Cragg SM, Friess DA, Gillis LG, Trevathan-Tackett SM, Terrett OM, Watts JEM, Distel DL, Dupree P. Vascular Plants Are Globally Significant Contributors to Marine Carbon Fluxes and Sinks. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:469-497. [PMID: 31505131 DOI: 10.1146/annurev-marine-010318-095333] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
More than two-thirds of global biomass consists of vascular plants. A portion of the detritus they generate is carried into the oceans from land and highly productive blue carbon ecosystems-salt marshes, mangrove forests, and seagrass meadows. This large detrital input receives scant attention in current models of the global carbon cycle, though for blue carbon ecosystems, increasingly well-constrained estimates of biomass, productivity, and carbon fluxes, reviewed in this article, are now available. We show that the fate of this detritus differs markedly from that of strictly marine origin, because the former contains lignocellulose-an energy-rich polymer complex of cellulose, hemicelluloses, and lignin that is resistant to enzymatic breakdown. This complex can be depolymerized for nutritional purposes by specialized marine prokaryotes, fungi, protists, and invertebrates using enzymes such as glycoside hydrolases and lytic polysaccharide monooxygenases to release sugar monomers. The lignin component, however, is less readily depolymerized, and detritus therefore becomes lignin enriched, particularly in anoxic sediments, and forms a major carbon sink in blue carbon ecosystems. Eventual lignin breakdown releases a wide variety of small molecules that may contribute significantly to the oceanic pool of recalcitrant dissolved organic carbon. Marine carbon fluxes and sinks dependent on lignocellulosic detritus are important ecosystem services that are vulnerable to human interventions. These services must be considered when protecting blue carbon ecosystems and planning initiatives aimed at mitigating anthropogenic carbon emissions.
Collapse
Affiliation(s)
- Simon M Cragg
- Institute of Marine Sciences, University of Portsmouth, Portsmouth PO4 9LY, United Kingdom;
| | - Daniel A Friess
- Department of Geography, National University of Singapore, Singapore 117570;
| | - Lucy G Gillis
- Leibniz-Zentrum für Marine Tropenforschung (ZMT), 28359 Bremen, Germany;
| | - Stacey M Trevathan-Tackett
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Burwood, Victoria 3125, Australia;
| | - Oliver M Terrett
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom; ,
| | - Joy E M Watts
- School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom;
| | - Daniel L Distel
- Ocean Genome Legacy Center of New England Biolabs, Marine Science Center, Northeastern University, Nahant, Massachusetts 01908, USA;
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom; ,
| |
Collapse
|
20
|
Johnston SR, Hiscox J, Savoury M, Boddy L, Weightman AJ. Highly competitive fungi manipulate bacterial communities in decomposing beech wood (Fagus sylvatica). FEMS Microbiol Ecol 2019; 95:5218414. [PMID: 30496397 PMCID: PMC6301287 DOI: 10.1093/femsec/fiy225] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/08/2018] [Indexed: 12/22/2022] Open
Abstract
The bacterial communities in decomposing wood are receiving increased attention, but their interactions with wood-decay fungi are poorly understood. This is the first field study to test the hypothesis that fungi are responsible for driving bacterial communities in beech wood (Fagus sylvatica). A meta-genetic approach was used to characterise bacterial and fungal communities in wood that had been laboratory-colonised with known wood-decay fungi, and left for a year at six woodland sites. Alpha-, Beta- and Gammaproteobacteria and Acidobacteria were the proportionally dominant bacterial taxa, as in previous studies. Pre-colonising wood with decay fungi had a clear effect on the bacterial community, apparently via direct fungal influence; the bacterial and fungal communities present at the time of collection explained nearly 60% of their mutual covariance. Site was less important than fungal influence in determining bacterial communities, but the effects of pre-colonisation were more pronounced at some sites than at others. Wood pH was also a strong bacterial predictor, but was itself under considerable fungal influence. Burkholderiaceae and Acidobacteriaceae showed directional responses against the trend of the bacterial community as a whole.
Collapse
Affiliation(s)
- Sarah R Johnston
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff. CF10 3AX. Wales, UK
| | - Jennifer Hiscox
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff. CF10 3AX. Wales, UK
| | - Melanie Savoury
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff. CF10 3AX. Wales, UK
| | - Lynne Boddy
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff. CF10 3AX. Wales, UK
| | - Andrew J Weightman
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff. CF10 3AX. Wales, UK
| |
Collapse
|
21
|
Increasing oxygen deficiency changes rare and moderately abundant bacterial communities in coastal soft sediments. Sci Rep 2019; 9:16341. [PMID: 31704947 PMCID: PMC6841974 DOI: 10.1038/s41598-019-51432-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/25/2019] [Indexed: 11/20/2022] Open
Abstract
Coastal hypoxia is a major environmental problem worldwide. Hypoxia-induced changes in sediment bacterial communities harm marine ecosystems and alter biogeochemical cycles. Nevertheless, the resistance of sediment bacterial communities to hypoxic stress is unknown. We investigated changes in bacterial communities during hypoxic-anoxic disturbance by artificially inducing oxygen deficiency to the seafloor for 0, 3, 7, and 48 days, with subsequent molecular biological analyses. We further investigated relationships between bacterial communities, benthic macrofauna and nutrient effluxes across the sediment-water-interface during hypoxic-anoxic stress, considering differentially abundant operational taxonomic units (OTUs). The composition of the moderately abundant OTUs changed significantly after seven days of oxygen deficiency, while the abundant and rare OTUs first changed after 48 days. High bacterial diversity maintained the resistance of the communities during oxygen deficiency until it dropped after 48 days, likely due to anoxia-induced loss of macrofaunal diversity and bioturbation. Nutrient fluxes, especially ammonium, correlated positively with the moderate and rare OTUs, including potential sulfate reducers. Correlations may reflect bacteria-mediated nutrient effluxes that accelerate eutrophication. The study suggests that even slightly higher bottom-water oxygen concentrations, which could sustain macrofaunal bioturbation, enable bacterial communities to resist large compositional changes and decrease the harmful consequences of hypoxia in marine ecosystems.
Collapse
|
22
|
Jones JM, Heath KD, Ferrer A, Brown SP, Canam T, Dalling JW. Wood decomposition in aquatic and terrestrial ecosystems in the tropics: contrasting biotic and abiotic processes. FEMS Microbiol Ecol 2019; 95:5184448. [PMID: 30445583 DOI: 10.1093/femsec/fiy223] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 11/13/2018] [Indexed: 01/01/2023] Open
Abstract
Wood decomposition, a critical process in carbon and nutrient cycles, is influenced by environmental conditions, decomposer communities and substrate composition. While these factors differ between land and stream habitats, across-habitat comparisons of wood decay processes are rare, limiting our ability to evaluate the context- dependency of the drivers of decay. Here we tracked wood decomposition of three tree species placed in stream and terrestrial habitats in a lowland tropical forest in Panama. At 3 and 11 months we measured mass loss, wood nitrogen and wood polymer concentrations, and sampled wood-associated fungal and bacterial communities. After 11 months of decay we found that mass loss occurred 9% faster in streams than on land, but loss of cellulose, hemicellulose and lignin did not differ between habitats. We also observed large differences in microbial decomposer communities between habitats. Overall, we found faster mass loss of wood in water, but no differences in biotic decay processes between habitats despite distinct microbial communities in streams and on land. Our research challenges the assumption that wood decays relatively slowly in water reflecting unfavorable environmental conditions and a limited capacity of aquatic microbial communities to effectively degrade wood polymers.
Collapse
Affiliation(s)
- Jennifer M Jones
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Astrid Ferrer
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shawn P Brown
- Department of Biological Sciences, The University of Memphis, Memphis, TN 38152, USA
| | - Thomas Canam
- Department of Biology, Eastern Illinois University, Charleston, IL 61920, USA
| | - James W Dalling
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| |
Collapse
|
23
|
Gonzalez-Escobedo R, Briones-Roblero CI, López MF, Rivera-Orduña FN, Zúñiga G. Changes in the Microbial Community of Pinus arizonica Saplings After Being Colonized by the Bark Beetle Dendroctonus rhizophagus (Curculionidae: Scolytinae). MICROBIAL ECOLOGY 2019; 78:102-112. [PMID: 30349964 DOI: 10.1007/s00248-018-1274-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/09/2018] [Indexed: 06/08/2023]
Abstract
The death of trees is an ecological process that promotes regeneration, organic matter recycling, and the structure of communities. However, diverse biotic and abiotic factors can disturb this process. Dendroctonus bark beetles (Curculionidae: Scolytinae) are natural inhabitants of pine forests, some of which produce periodic outbreaks, killing thousands of trees in the process. These insects spend almost their entire life cycle under tree bark, where they reproduce and feed on phloem. Tunneling and feeding of the beetles result in the death of the tree and an alteration of the resident microbiota as well as the introduction of microbes that the beetles vector. To understand how microbial communities in subcortical tissues of pines change after they are colonized by the bark beetle Dendroctonus rhizophagus, we compare both the bacterial and fungal community structures in two colonization stages of Pinus arizonica (Arizona pine) employing Illumina MiSeq. Our findings showed significant differences in diversity and the dominance of bacterial community in the two colonization stages with Shannon (P = 0.004) and Simpson (P = 0.0006) indices, respectively, but not in species richness with Chao1 (P = 0.19). In contrast, fungal communities in both stages showed significant differences in species richness with Chao1 (P = 0.0003) and a diversity with Shannon index (P = 0.038), but not in the dominance with the Simpson index (P = 0.12). The β-diversity also showed significant changes in the structure of bacterial and fungal communities along the colonization stages, maintaining the dominant members in both cases. Our results suggest that microbial communities present in the Arizona pine at the tree early colonization stage by bark beetle change predictably over time.
Collapse
Affiliation(s)
- Roman Gonzalez-Escobedo
- Posgrado en Ciencias Quimicobiológicas, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n. Delegación Miguel Hidalgo, CP 11340, Mexico City, Mexico
| | - Carlos I Briones-Roblero
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n. Delegación Miguel Hidalgo, CP 11340, Mexico City, Mexico
| | - María Fernanda López
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n. Delegación Miguel Hidalgo, CP 11340, Mexico City, Mexico
| | - Flor N Rivera-Orduña
- Laboratorio de Ecología Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n. Delegación Miguel Hidalgo, CP 11340, Mexico City, Mexico
| | - Gerardo Zúñiga
- Laboratorio de Variación Biológica y Evolución, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n. Delegación Miguel Hidalgo, CP 11340, Mexico City, Mexico.
| |
Collapse
|
24
|
Kuramae EE, Leite MFA, Suleiman AKA, Gough CM, Castillo BT, Faller L, Franklin RB, Syring J. Wood Decay Characteristics and Interspecific Interactions Control Bacterial Community Succession in Populus grandidentata (Bigtooth Aspen). Front Microbiol 2019; 10:979. [PMID: 31143163 PMCID: PMC6520631 DOI: 10.3389/fmicb.2019.00979] [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: 01/23/2019] [Accepted: 04/18/2019] [Indexed: 02/01/2023] Open
Abstract
Few studies have investigated bacterial community succession and the role of bacterial decomposition over a continuum of wood decay. Here, we identified how (i) the diversity and abundance of bacteria changed along a chronosequence of decay in Populus grandidentata (bigtooth aspen); (ii) bacterial community succession was dependent on the physical and chemical characteristics of the wood; (iii) interspecific bacterial interactions may mediate community structure. Four hundred and fifty-nine taxa were identified through Illumina sequencing of 16S rRNA amplicons from samples taken along a continuum of decay, representing standing dead trees, downed wood, and soil. Community diversity increased as decomposition progressed, peaking in the most decomposed trees. While a small proportion of taxa displayed a significant pattern in regards to decay status of the host log, many bacterial taxa followed a stochastic distribution. Changes in the water availability and chemical composition of standing dead and downed trees and soil were strongly coupled with shifts in bacterial communities. Nitrogen was a major driver of succession and nitrogen-fixing taxa of the order Rhizobiales were abundant early in decomposition. Recently downed logs shared 65% of their bacterial abundance with the microbiomes of standing dead trees while only sharing 16% with soil. As decay proceeds, bacterial communities appear to respond less to shifting resource availability and more to interspecific bacterial interactions – we report an increase in both the proportion (+9.3%) and the intensity (+62.3%) of interspecific interactions in later stages of decomposition, suggesting the emergence of a more complex community structure as wood decay progresses.
Collapse
Affiliation(s)
- Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Afnan K A Suleiman
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Christopher M Gough
- Department of Biology, Virginia Commonwealth University, Richmond, VA, United States
| | - Buck T Castillo
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
| | - Lewis Faller
- Department of Biology, Linfield College, McMinnville, OR, United States
| | - Rima B Franklin
- Department of Biology, Virginia Commonwealth University, Richmond, VA, United States
| | - John Syring
- Department of Biology, Linfield College, McMinnville, OR, United States
| |
Collapse
|
25
|
Novel insights into plant-associated archaea and their functioning in arugula ( Eruca sativa Mill.). J Adv Res 2019; 19:39-48. [PMID: 31341668 PMCID: PMC6629838 DOI: 10.1016/j.jare.2019.04.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 04/24/2019] [Accepted: 04/24/2019] [Indexed: 01/21/2023] Open
Abstract
A plant's microbiota has various implications for the plant's health and performance; however, the roles of many microbial lineages, particularly Archaea, have not been explored in detail. In the present study, analysis of archaea-specific 16S rRNA gene fragments and shotgun-sequenced metagenomes was combined with visualization techniques to obtain the first insights into the archaeome of a common salad plant, arugula (Eruca sativa Mill.). The archaeal communities associated with the soil, rhizosphere and phyllosphere were distinct, but a high proportion of community members were shared among all analysed habitats. Soil habitats exhibited the highest diversity of Archaea, followed by the rhizosphere and the phyllosphere. The archaeal community was dominated by Thaumarchaeota and Euryarchaeota, with the most abundant taxa assigned to Candidatus Nitrosocosmicus, species of the 'Soil Crenarchaeotic Group' and, interestingly, Methanosarcina. Moreover, a large number of archaea-assigned sequences remained unassigned at lower taxonomic levels. Overall, analysis of shotgun-sequenced total-community DNA revealed a more diverse archaeome. Differences were evident at the class level and at higher taxonomic resolutions when compared to results from the 16S rRNA gene fragment amplicon library. Functional assessments primarily revealed archaeal genes related to response to stress (especially oxidative stress), CO2 fixation, and glycogen degradation. Microscopic visualizations of fluorescently labelled archaea in the phyllosphere revealed small scattered colonies, while archaea in the rhizosphere were found to be embedded within large bacterial biofilms. Altogether, Archaea were identified as a rather small but niche-specific component of the microbiomes of the widespread leafy green plant arugula.
Collapse
|
26
|
Lohberger A, Spangenberg JE, Ventura Y, Bindschedler S, Verrecchia EP, Bshary R, Junier P. Effect of Organic Carbon and Nitrogen on the Interactions of Morchella spp. and Bacteria Dispersing on Their Mycelium. Front Microbiol 2019; 10:124. [PMID: 30881350 PMCID: PMC6405442 DOI: 10.3389/fmicb.2019.00124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 01/21/2019] [Indexed: 01/14/2023] Open
Abstract
In this study we investigated how the source of organic carbon (Corg) and nitrogen (Norg) affects the interactions between fungi of the genus Morchella and bacteria dispersing along their hyphae (fungal highways; FH). We demonstrated that bacteria using FH increase the hydrolysis of an organic nitrogen source that only the fungus can degrade. Using purified fungal exudates, we found that this increased hydrolysis was due to bacteria enhancing the activity of proteolytic enzymes produced by the fungus. The same effect was shown for various fungal and bacterial strains. The effect of this enhanced proteolytic activity on bacterial and fungal biomass production varied accordingly to the source of Corg and Norg provided. An increase in biomass for both partners 5 days post-inoculation was only attained with a Norg source that the bacterium could not degrade and when additional Corg was present in the medium. In contrast, all other combinations yielded a decrease on biomass production in the co-cultures compared to individual growth. The coupled cycling of Corg and Norg is rarely considered when investigating the role of microbial activity on soil functioning. Our results show that cycling of these two elements can be related through cross-chemical reactions in independent, albeit interacting microbes. In this way, the composition of organic material could greatly alter nutrient turnover due to its effect on the outcome of interactions between fungi and bacteria that disperse on their mycelia.
Collapse
Affiliation(s)
- Andrea Lohberger
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Laboratory of Biogeosciences, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Jorge E. Spangenberg
- Stable Isotope and Organic Geochemistry Laboratories, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Yolanda Ventura
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Eric P. Verrecchia
- Laboratory of Biogeosciences, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Redouan Bshary
- Laboratory of Eco-ethology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| |
Collapse
|
27
|
Moll J, Kellner H, Leonhardt S, Stengel E, Dahl A, Bässler C, Buscot F, Hofrichter M, Hoppe B. Bacteria inhabiting deadwood of 13 tree species are heterogeneously distributed between sapwood and heartwood. Environ Microbiol 2018; 20:3744-3756. [PMID: 30109768 DOI: 10.1111/1462-2920.14376] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/12/2018] [Accepted: 08/07/2018] [Indexed: 01/02/2023]
Abstract
Deadwood represents an important structural component of forest ecosystems, where it provides diverse niches for saproxylic biota. Although wood-inhabiting prokaryotes are involved in its degradation, knowledge about their diversity and the drivers of community structure is scarce. To explore the effect of deadwood substrate on microbial distribution, the present study focuses on the microbial communities of deadwood logs from 13 different tree species investigated using an amplicon based deep-sequencing analysis. Sapwood and heartwood communities were analysed separately and linked to various relevant wood physico-chemical parameters. Overall, Proteobacteria, Acidobacteria and Actinobacteria represented the most dominant phyla. Microbial OTU richness and community structure differed significantly between tree species and between sapwood and heartwood. These differences were more pronounced for heartwood than for sapwood. The pH value and water content were the most important drivers in both wood compartments. Overall, investigating numerous tree species and two compartments provided a remarkably comprehensive view of microbial diversity in deadwood.
Collapse
Affiliation(s)
- Julia Moll
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
| | - Harald Kellner
- Department of Bio- and Environmental Sciences, Technical University Dresden - International Institute (IHI) Zittau, Zittau, Germany
| | - Sabrina Leonhardt
- Department of Bio- and Environmental Sciences, Technical University Dresden - International Institute (IHI) Zittau, Zittau, Germany
| | - Elisa Stengel
- Department of Bio- and Environmental Sciences, Technical University Dresden - International Institute (IHI) Zittau, Zittau, Germany.,Department of Animal Ecology and Tropical Biology (Zoology III), University of Würzburg, Field Station Fabrikschleichach, Würzburg, Germany
| | - Andreas Dahl
- Biotechnology Center - Deep Sequencing Group - SFB655, Technical University Dresden, Dresden, Germany
| | - Claus Bässler
- Department of Conservation and Research, Bavarian Forest National Park, Grafenau, Germany.,Department of Ecology and Ecosystem management, Technical University of Munich, Chair for Terrestrial Ecology, Freising, Germany
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Martin Hofrichter
- Department of Bio- and Environmental Sciences, Technical University Dresden - International Institute (IHI) Zittau, Zittau, Germany
| | - Björn Hoppe
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany.,Julius Kühn-Institute, Institute for National and International Plant Health, Braunschweig, Germany
| |
Collapse
|
28
|
Probst M, Gómez-Brandón M, Bardelli T, Egli M, Insam H, Ascher-Jenull J. Bacterial communities of decaying Norway spruce follow distinct slope exposure and time-dependent trajectories. Environ Microbiol 2018; 20:3657-3670. [DOI: 10.1111/1462-2920.14359] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 06/26/2018] [Accepted: 07/08/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Maraike Probst
- Institute of Microbiology, University of Innsbruck; Innsbruck Austria
| | - María Gómez-Brandón
- Institute of Microbiology, University of Innsbruck; Innsbruck Austria
- Departamento de Ecología y Biología Animal; Universidad de Vigo; Vigo Spain
| | - Tommaso Bardelli
- Institute of Microbiology, University of Innsbruck; Innsbruck Austria
- Department of Agrifood and Environmental Science; University of Florence; Florence Italy
| | - Markus Egli
- Department of Geography; University of Zürich; Zürich Switzerland
| | - Heribert Insam
- Institute of Microbiology, University of Innsbruck; Innsbruck Austria
| | - Judith Ascher-Jenull
- Institute of Microbiology, University of Innsbruck; Innsbruck Austria
- Department of Agrifood and Environmental Science; University of Florence; Florence Italy
| |
Collapse
|
29
|
Tláskal V, Zrustová P, Vrška T, Baldrian P. Bacteria associated with decomposing dead wood in a natural temperate forest. FEMS Microbiol Ecol 2018; 93:4604780. [PMID: 29126113 DOI: 10.1093/femsec/fix157] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/07/2017] [Indexed: 01/05/2023] Open
Abstract
Dead wood represents an important pool of organic matter in forests and is one of the sources of soil formation. It has been shown to harbour diverse communities of bacteria, but their roles in this habitat are still poorly understood. Here, we describe the bacterial communities in the dead wood of Abies alba, Picea abies and Fagus sylvatica in a temperate natural forest in Central Europe. An analysis of environmental factors showed that decomposing time along with pH and water content was the strongest drivers of community composition. Bacterial biomass positively correlated with N content and increased with decomposition along with the concurrent decrease in the fungal/bacterial biomass ratio. Rhizobiales and Acidobacteriales were abundant bacterial orders throughout the whole decay process, but many bacterial taxa were specific either for young (<15 years) or old dead wood. During early decomposition, bacterial genera able to fix N2 and to use simple C1 compounds (e.g. Yersinia and Methylomonas) were frequent, while wood in advanced decay was rich in taxa typical of forest soils (e.g. Bradyrhizobium and Rhodoplanes). Although the bacterial contribution to dead wood turnover remains unclear, the community composition appears to reflect the changing conditions of the substrate and suggests broad metabolic capacities of its members.
Collapse
Affiliation(s)
- Vojtech Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídenská 1083, 14220 Praha 4, Czech Republic
| | - Petra Zrustová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídenská 1083, 14220 Praha 4, Czech Republic
| | - Tomáš Vrška
- Silva Tarouca Research Institute for Landscape and Ornamental Gardening, Lidická 25/27, Brno 60200, Czech Republic
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídenská 1083, 14220 Praha 4, Czech Republic
| |
Collapse
|
30
|
Baldrian P. Microbial activity and the dynamics of ecosystem processes in forest soils. Curr Opin Microbiol 2017; 37:128-134. [DOI: 10.1016/j.mib.2017.06.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 06/21/2017] [Indexed: 01/16/2023]
|
31
|
Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change. Microbiol Mol Biol Rev 2017; 81:81/2/e00063-16. [PMID: 28404790 DOI: 10.1128/mmbr.00063-16] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously.
Collapse
|
32
|
Baldrian P. Forest microbiome: diversity, complexity and dynamics. FEMS Microbiol Rev 2016; 41:109-130. [DOI: 10.1093/femsre/fuw040] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2016] [Indexed: 12/13/2022] Open
|
33
|
Johnston SR, Boddy L, Weightman AJ. Bacteria in decomposing wood and their interactions with wood-decay fungi. FEMS Microbiol Ecol 2016; 92:fiw179. [PMID: 27559028 DOI: 10.1093/femsec/fiw179] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2016] [Indexed: 01/02/2023] Open
Abstract
The fungal community within dead wood has received considerable study, but far less attention has been paid to bacteria in the same habitat. Bacteria have long been known to inhabit decomposing wood, but much remains underexplored about their identity and ecology. Bacteria within the dead wood environment must interact with wood-decay fungi, but again, very little is known about the form this takes; there are indications of both antagonistic and beneficial interactions within this fungal microbiome. Fungi are hypothesised to play an important role in shaping bacterial communities in wood, and conversely, bacteria may affect wood-decay fungi in a variety of ways. This minireview considers what is currently known about bacteria in wood and their interactions with fungi, and proposes possible associations based on examples from other habitats. It aims to identify key knowledge gaps and pressing questions for future research.
Collapse
Affiliation(s)
- Sarah R Johnston
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Lynne Boddy
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Andrew J Weightman
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, UK
| |
Collapse
|