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Geonczy SE, Hillary LS, Santos-Medellín C, Sorensen JW, Emerson JB. Patchy burn severity explains heterogeneous soil viral and prokaryotic responses to fire in a mixed conifer forest. mSystems 2025:e0174924. [PMID: 40366158 DOI: 10.1128/msystems.01749-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2024] [Accepted: 04/12/2025] [Indexed: 05/15/2025] Open
Abstract
Effects of fire on soil viruses and virus-host dynamics are largely unexplored, despite known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we assessed how viral and prokaryotic communities responded to a prescribed burn in a mixed conifer forest. We sequenced 91 viral-size fraction metagenomes (viromes) and 115 16S rRNA gene amplicon libraries from 120 samples: four samples at five timepoints (two before fire and three after fire) at six sites (four treatment, two control). We hypothesized that compositional differences would be most significant between burned and unburned soils, but instead, plot location best distinguished viral communities, more than treatment (burned or not), depth (0-3 or 3-6 cm), or timepoint. For both viruses and prokaryotes, some burned communities resembled unburned controls, while others were significantly different, revealing heterogeneous responses to fire. These patterns were explained by burn severity, here defined by soil chemistry. Viral but not prokaryotic richness decreased significantly with burn severity, and low viromic DNA yields indicated substantial loss of viral biomass at higher severity. The relative abundances of Firmicutes, Actinobacteriota, and the viruses predicted to infect them increased significantly with burn severity, suggesting survival and viral infection of these fire-responsive and potentially spore-forming taxa. The degree of burn severity experienced by each patch of soil, rather than burn status alone, differed over mere meters in the same fire. Therefore, our analyses highlight the importance of high-resolution, paired biogeochemical data to explain soil community responses to fire. IMPORTANCE The impact of fire on the soil microbiome, particularly on understudied soil viral communities, warrants investigation, given known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we collected 120 soil samples before and after a prescribed burn in a mixed conifer forest to assess the impacts of this disturbance on soil viral and prokaryotic communities. We show that simple categorical comparisons of burned and unburned areas were insufficient to reveal the underlying community response patterns. The patchy nature of the fire (indicated by soil chemistry data) led to significant changes in viral and prokaryotic community composition in areas of high burn severity, while communities that experienced lower burn severity were indistinguishable from those in unburned controls. Our results highlight the importance of considering highly resolved burn severity and biogeochemical measurements, even in nearby soils after the same fire, in order to understand soil microbial responses to prescribed burns.
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Affiliation(s)
- Sara E Geonczy
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | - Luke S Hillary
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | | | - Jess W Sorensen
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
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2
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Kong X, Xu B, Orr JA, Meidl P, Rillig MC, Yang G. Ecosystems have multiple interacting processes that buffer against co-occurring stressors. Trends Ecol Evol 2025; 40:479-488. [PMID: 40155304 DOI: 10.1016/j.tree.2025.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 03/02/2025] [Accepted: 03/04/2025] [Indexed: 04/01/2025]
Abstract
There are multiple processes that buffer the effects of anthropogenic stressors. Much is known about how single buffering processes (e.g., biodiversity, adaptation) mitigate the effects of stressors on ecosystem properties and functions, but how multiple buffering processes combine to mitigate the effects of multiple co-occurring stressors is poorly understood. We outline how single processes (e.g., cross-tolerance) can buffer the effects of multiple stressors, whereas multiple buffering processes can act jointly across ecological and temporal scales to reduce the effects of single or multiple stressors. Synergistic interactions between multiple buffering processes can further enhance ecosystem resistance to multiple stressors. A wider awareness of interacting buffering processes in ecosystems will enhance our understanding of ecosystem stability in the face of multiple stressors.
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Affiliation(s)
- Xiang Kong
- College of Grassland Science and Technology, China Agricultural University, 100193 Beijing, China
| | - Baile Xu
- Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
| | - James A Orr
- Department of Biology, University of Oxford, Oxford, UK; School of the Environment, University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Peter Meidl
- Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
| | - Gaowen Yang
- College of Grassland Science and Technology, China Agricultural University, 100193 Beijing, China.
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3
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Venturini AM, Gontijo JB, Berrios L, Rodrigues JLM, Peay KG, Tsai SM. Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon. Microbiol Spectr 2025; 13:e0156124. [PMID: 40042334 PMCID: PMC11960080 DOI: 10.1128/spectrum.01561-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 01/31/2025] [Indexed: 04/03/2025] Open
Abstract
Amazonian soil microbial communities are known to be altered by land-use change. However, attempts to understand these impacts have focused on broader community alterations or the response of specific microbial groups. Here, we recovered and characterized 69 soil bacterial and archaeal metagenome-assembled genomes (MAGs) from three forests and three pastures of the Eastern Brazilian Amazon and evaluated the impacts of land conversion on their genomic features. Pasture MAGs had significantly higher GC content (64.9% vs 60.2%), genome size (4.0 vs 3.1 Mbp), and number of coding sequences (4,058 vs 3,306) compared to forest genomes. Taxonomically, MAGs belonged to eight phyla; however, most (90%) had low similarity to previously known species, indicating potentially novel taxa at multiple levels. We also observed that the functional profiles associated with biogeochemical cycling and carbohydrate-active enzyme genes were impacted by forest conversion, with pasture MAGs exhibiting a notably higher number of both gene groups. Together, these data constitute the largest single-sourced genomic data set from upland soils of the Brazilian Amazon to date and increase the known MAG richness in these soils by 78%. Our data, therefore, not only add to a neglected yet emerging field but, importantly, highlight that land-use change has drastic impacts on the genomic characteristics and functional traits of dominant soil microbes.IMPORTANCEThe Brazilian Amazon is facing unprecedented threats, including increasing deforestation and degradation, which together impact half of the original forest area. Soil microorganisms are sensitive indicators of land-use change, linked to a rise in microbial methane emissions and antibiotic-resistance genes in the Amazon. However, most Amazonian soil microbes remain unknown, and little attention has been given to their genomes. Using sequencing and bioinformatics, we recovered and characterized 69 soil bacterial and archaeal genomes (metagenome-assembled genomes). These abundant members of the microbial communities diverged across forests and pastures in terms of taxonomic and functional traits. Forest conversion favors organisms with specific genomic features - increased GC content, genome size, and gene number - selecting for microorganisms that can thrive under altered conditions. Our paper helps us understand the intricate relationships between microbes and the environment, which are crucial pieces of information for comprehensive soil health assessments and future policy formulation.
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Affiliation(s)
- Andressa M. Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Environmental Science, American University, Washington, DC, USA
| | - Júlia B. Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
- Department of Land, Air, and Water Resources, University of California-Davis, Davis, California, USA
| | - Louis Berrios
- Department of Biology, Stanford University, Stanford, California, USA
| | - Jorge L. Mazza Rodrigues
- Department of Land, Air, and Water Resources, University of California-Davis, Davis, California, USA
| | - Kabir G. Peay
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Siu M. Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
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Kazarina A, Wiechman H, Sarkar S, Richie T, Lee STM. Recovery of 679 metagenome-assembled genomes from different soil depths along a precipitation gradient. Sci Data 2025; 12:521. [PMID: 40155620 PMCID: PMC11953352 DOI: 10.1038/s41597-025-04884-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 03/24/2025] [Indexed: 04/01/2025] Open
Abstract
Soil contains a diverse community of organisms; these can include archaea, fungi, viruses, and bacteria. In situ identification of soil microorganisms is challenging. The use of genome-centric metagenomics enables the assembly and identification of microbial populations, allowing the categorization and exploration of potential functions living in the complex soil environment. However, the heterogeneity of the soil-inhabiting microbes poses a tremendous challenge, with their functions left unknown, and difficult to culture in lab settings. In this study, using genome assembling strategies from both field core samples and enriched monolith samples, we assembled 679 highly complete metagenome-assembled genomes (MAGs). The ability to identify these MAGs from samples across a precipitation gradient in the state of Kansas (USA) provided insights into the impact of precipitation levels on soil microbial populations. Metabolite modeling of the MAGs revealed that more than 80% of the microbial populations possessed carbohydrate-active enzymes, capable of breaking down chitin and starch.
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Affiliation(s)
- Anna Kazarina
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Hallie Wiechman
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Soumyadev Sarkar
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Tanner Richie
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Sonny T M Lee
- Division of Biology, Kansas State University, Manhattan, Kansas, USA.
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Shen H, Zhou Y, Lin J, Huang Y, Dai Z, Zeng S, Li Y, Dahlgren RA, Xu J. Thermal Compensatory Response of Soil Heterotrophic Respiration Following Wildfire. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2025; 59:5034-5044. [PMID: 40045528 DOI: 10.1021/acs.est.4c11833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
Abstract
Frequent wildfires pose a serious threat to carbon (C) dynamics of forest ecosystems under a warming climate. Yet, how wildfires alter the temperature sensitivity (Q10) of soil heterotrophic respiration (Rh) as a critical parameter determining the C efflux from burned landscapes remains unknown. We conducted a field survey and two confirmatory experiments in two fire-prone regions of China at <1, 3, 6, and 12 months after wildfires (n = 160 soil samples). We found that wildfire generally reduced the Q10 for soil organic and mineral horizons within the first year after wildfire mainly due to substrate depletion, which was confirmed by a uniform inoculation experiment. Mineral protection of organic matter in the mineral horizon rich in iron/aluminum (hydr)oxides and a near-neutral pH in organic horizons of postfire soils further suppressed the Q10. Decreased Q10 persisted in organic horizons even after removing substrate limitation, reflecting the dominance of a thermally adapted, r-strategist microbial community in postfire soils. Moreover, fire-induced low C quality increased Q10, which supported the C quality-temperature hypothesis, but a C-limited condition restricted this stimulatory effect. This study illustrates that a thermal compensatory response of Rh will help maintain C stocks in forest ecosystems after wildfires in a warming world.
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Affiliation(s)
- Haojie Shen
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Yuqi Zhou
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Jiahui Lin
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Yu Huang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Zhongmin Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- The Rural Development Academy, Zhejiang University, Hangzhou 310058, China
| | - Saiqi Zeng
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Yong Li
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Randy A Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, California 95616, United States
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
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Shen H, Huang Y, Lin X, Dai Z, Zhao H, Su WQ, Dahlgren RA, Xu J. Recoupling of Soil Carbon, Nitrogen, and Phosphorus Cycles along a 30 Year Fire Chronosequence in Boreal Forests of China. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2025; 59:4432-4443. [PMID: 39973244 DOI: 10.1021/acs.est.4c08790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
The biogeochemical coupling of soil carbon, nitrogen, and phosphorus (C-N-P) cycles is crucial for maintaining the ecological balance of boreal forests. Yet, the current understanding of wildfire disturbance is only based on changes in elemental contents, thereby lacking any within-ecosystem corroboration of biogeochemical coupling. Here, we conducted a field survey of microbial functional associations for 53 genes related to soil C-N-P cycling from 17 locations spanning a 30 year succession period after high-severity forest fires in the Greater Khingan Mountains (Inner Mongolia-China). We found that bacteria proliferated and dominated the competition with fungi by encoding genes for recalcitrant C decomposition, N fixation, and inorganic N cycling during the postfire early succession. Wildfire prominently decoupled the microbial functional associations of soil C-N-P cycling, particularly in organic-inorganic N turnover. However, over the 30 year succession period, these functional associations recoupled in both soil organic and mineral horizons. Notably, the decoupling of microbial functional associations recovered from a wildfire disturbance faster than the soil C-N-P imbalance. This strong resilience of the microbiome will aid in the recovery of the soil elemental balance and ecosystem stability from the increased intensity of wildfires projected for the boreal forests of China.
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Affiliation(s)
- Haojie Shen
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Yu Huang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Xin Lin
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Zhongmin Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- The Rural Development Academy, Zhejiang University, Hangzhou 310058, China
| | - Haochun Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Wei-Qin Su
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Randy A Dahlgren
- Department of Land, Air and Water Resources, University of California, Davis, California 95616, United States
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
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7
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Cao X, Ma H, Li SA, Huang H, Cui F, Tanentzap AJ. Enhanced Release and Reactivity of Soil Water-Extractable Organic Matter Following Wildfire in a Subtropical Forest. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2025; 59:3992-4002. [PMID: 39982015 DOI: 10.1021/acs.est.4c13557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2025]
Abstract
Climate-driven increases in wildfire frequency may disrupt soil carbon dynamics, potentially creating positive feedback within global carbon cycle. However, the release and lability of soil carbon following wildfire remain unclear, limiting our ability to predict fire impacts on carbon cycling. Here, we investigated chemical alterations in soil water-extractable organic matter (WEOM) following a subtropical forest wildfire by comparing burned soils to an adjacent unburned site. The consensus is that fire-altered DOM is aromatic and less reactive. However, we found that 10 months postfire, burned soils contained nearly three times more water-extractable organic carbon (WEOC) than the control site. Reactomics analysis further revealed an overall 8-fold increase in potential reactivity of this carbon, identified by higher abundances of molecular formulas involved in identified microbial reaction pathways. Specifically, burned soils exhibited elevated potential oxidative enzyme reactions, linked to a higher nominal oxidation state of carbon (NOSC) in WEOM. Metagenomic analysis revealed an enrichment of microbial taxa specialized in degrading aromatic compounds in burned areas, supporting the occurrence of potential microbial reaction pathways acting on WEOM in postfire soils. These findings highlight that wildfires may accelerate soil carbon loss through reactive WEOM mobilization and microbial response, with implications for long-term carbon-climate projections.
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Affiliation(s)
- Xinghong Cao
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Hua Ma
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Sheng-Ao Li
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Hai Huang
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Fuyi Cui
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, School of the Environment, Trent University, Peterborough, Ontario K9L 0G2, Canada
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg 26129, Germany
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8
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Zhang Q, Wang Y, Zhang Y, Zhang J, Hou F, He C, Shi Q, Zhang G, Wang J. Heating-Induced Changes in Content and Molecular Characteristics of Pyrogenic Dissolved Organic Matter across Soil Types. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2025; 59:3937-3948. [PMID: 39968708 DOI: 10.1021/acs.est.4c08306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2025]
Abstract
Wildfires remarkably alter the quantity and quality of dissolved organic matter (DOM) that regulates postfire biogeochemical processes and environmental quality. However, it remains unclear how the heating-induced percent changes (%HIC) in DOM quantity and quality differ among soil types on a wide geographic scale. Here, we used dissolved organic carbon (DOC) quantification, absorption, and fluorescence spectroscopies, and Fourier transform ion cyclotron resonance mass spectrometry to investigate the variations in %HIC in DOM quantity and quality of Chinese soil reference materials after heating at 250 and 400 °C. Our results reveal that as soil pH increased, %HIC in DOC content increased, while %HIC in aromaticity-related indices of DOM decreased for both heating temperatures. Moreover, the %HIC in DOM biolability and contents of aliphatics increased with soil pH for 250 °C heating but remained relatively stable for 400 °C heating. Results suggest that compared to those in acidic soil-dominated forests, wildfires in alkaline soil-dominated forests may cause greater DOM content and biolability in soils, which may facilitate postfire microbial recovery. These findings deepen our understanding of the site-specific impacts of wildfires on DOM and the subsequent implications for biogeochemical cycling and environmental quality across different geographic regions.
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Affiliation(s)
- Qiang Zhang
- Guangdong Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- College of Environmental Science and Engineering, China West Normal University, Nanchong, Sichuan 637009, China
| | - Yinghui Wang
- Guangdong Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yuhang Zhang
- Guangdong Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Junwen Zhang
- Guangdong Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Fuyou Hou
- Guangdong Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry, Guangdong Province Key Laboratory of Environmental Protection and Resources Utilization, and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Junjian Wang
- Guangdong Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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9
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Flores-Piña A, Valencia-Cantero E, Santoyo G. Underground fires shape the structure of microbial communities and select for thermophilic bacteria through a temperature gradient. Microbiol Res 2025; 292:127996. [PMID: 39671811 DOI: 10.1016/j.micres.2024.127996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Revised: 11/14/2024] [Accepted: 12/02/2024] [Indexed: 12/15/2024]
Abstract
A detailed diversity analysis of the prokaryotic and fungal communities in soil impacted by an underground fire located in the Trans-Mexican volcanic belt, Mexico, is described. Microbial diversity data obtained from soils at different depths and temperatures (27 °C, 42 °C, 50 ºC and 54 ºC) were analyzed, and Firmicutes increased in abundance as the temperature augmented, and Proteobacteria mainly decreased in abundance at high temperatures compared to unaffected soils. The fungal phylum Ascomycota was the most abundant, with no significant changes. A clear reduction in the richness of both prokaryotic and eukaryotic operational taxonomic units (OTUs) was observed in the affected soils. At the genus level, Bacillus species were the most abundant among bacteria, while Aspergillus, Penicillium, and Mortierella were dominant fungal genera at higher temperatures. Interestingly, the physicochemical parameters of the affected soils modified organic matter, which was indirectly correlated with the presence of some microbial taxa. Likewise, we obtained 308 soil bacterial isolates from both control and affected soils. Among these, the taxa from the phyla Actinobacteria and Firmicutes demonstrated the highest thermotolerance in the affected soils. Our findings shed light on the impact of underground fires on the structure of microbial communities, favoring an abundance of thermotolerant microbes.
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Affiliation(s)
- Aurora Flores-Piña
- Institute of Biological and Chemical Research, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico
| | - Eduardo Valencia-Cantero
- Institute of Biological and Chemical Research, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico
| | - Gustavo Santoyo
- Institute of Biological and Chemical Research, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, Michoacán 58030, Mexico.
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10
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Van Goethem MW, Bezuidt OKI, Pierneef R, Vikram S, Hopkins DW, Aspray T, Hall G, Woodborne S, Hogg ID, Northen TR, Kong W, Daffonchio D, Cowan DA, Van de Peer Y, Delgado-Baquerizo M, Makhalanyane TP. Novel adaptive immune systems in pristine Antarctic soils. Sci Rep 2025; 15:2368. [PMID: 39827180 PMCID: PMC11742911 DOI: 10.1038/s41598-024-83942-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: 08/29/2024] [Accepted: 12/18/2024] [Indexed: 01/22/2025] Open
Abstract
Antarctic environments are dominated by microorganisms, which are vulnerable to viral infection. Although several studies have investigated the phylogenetic repertoire of bacteria and viruses in these poly-extreme environments with freezing temperatures, high ultra violet irradiation levels, low moisture availability and hyper-oligotrophy, the evolutionary mechanisms governing microbial immunity remain poorly understood. Using genome-resolved metagenomics, we test the hypothesis that Antarctic poly-extreme high-latitude microbiomes harbour diverse adaptive immune systems. Our analysis reveals the prevalence of prophages in bacterial genomes (Bacteroidota and Verrucomicrobiota), suggesting the significance of lysogenic infection strategies in Antarctic soils. Furthermore, we demonstrate the presence of diverse CRISPR-Cas arrays, including Class 1 arrays (Types I-B, I-C, and I-E), alongside systems exhibiting novel gene architecture among their effector cas genes. Notably, a Class 2 system featuring type V variants lacks CRISPR arrays, encodes Cas1 and Cas2 adaptation module genes. Phylogenetic analysis of Cas12 effector proteins hints at divergent evolutionary histories compared to classified type V effectors and indicates that TnpB is likely the ancestor of Cas12 nucleases. Our findings suggest substantial novelty in Antarctic cas sequences, likely driven by strong selective pressures. These results underscore the role of viral infection as a key evolutionary driver shaping polar microbiomes.
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Affiliation(s)
- Marc W Van Goethem
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia
| | - Oliver K I Bezuidt
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Hatfield, Pretoria, 0028, South Africa
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, DSI/NRF SARChI in Marine Microbiomics, University of Pretoria, Hatfield, Pretoria, 0028, South Africa
| | - Rian Pierneef
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Hatfield, Pretoria, 0028, South Africa
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, DSI/NRF SARChI in Marine Microbiomics, University of Pretoria, Hatfield, Pretoria, 0028, South Africa
| | - Surendra Vikram
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
| | - David W Hopkins
- Scotland's Rural College, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Thomas Aspray
- School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Grant Hall
- Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | | | - Ian D Hogg
- Canadian High Arctic Research Station, Polar Knowledge Canada; and School of Science, University of Waikato, Waitkato, New Zealand
| | - Trent R Northen
- Molecular EcoSystems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System and Resources Environment, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia
| | - Don A Cowan
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
| | - Yves Van de Peer
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052, Ghent, Belgium
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Seville, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Seville, Spain
| | - Thulani P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Hatfield, Pretoria, 0028, South Africa.
- Department of Microbiology, Faculty of Science, Stellenbosch University, Stellenbosch, 7600, South Africa.
- The School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, 7600, South Africa.
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11
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Rawstern AH, Hernandez DJ, Afkhami ME. Central Taxa Are Keystone Microbes During Early Succession. Ecol Lett 2025; 28:e70031. [PMID: 39737770 DOI: 10.1111/ele.70031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 11/12/2024] [Accepted: 11/18/2024] [Indexed: 01/01/2025]
Abstract
Microorganisms underpin numerous ecosystem processes and support biodiversity globally. Yet, we understand surprisingly little about what structures environmental microbiomes, including how to efficiently identify key players. Microbiome network theory predicts that highly connected hubs act as keystones, but this has never been empirically tested in nature. Combining culturing, sequencing, networks and field experiments, we isolated 'central' (highly connected, hub taxa), 'intermediate' (moderately connected), and 'peripheral' (weakly/unconnected) microbes and experimentally evaluated their effects on soil microbiome assembly during early succession in nature. Central early colonisers significantly (1) enhanced biodiversity (35%-40% richer communities), (2) reshaped trajectories of microbiome assembly and (3) increased recruitment of additional influential microbes by > 60%. In contrast, peripheral microbes did not increase diversity and were transient taxa, minimally affected by the presence of other microbes. This work elucidates fundamental principles of network theory in microbial ecology and demonstrates for the first time in nature that central microbes act as keystone taxa.
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Affiliation(s)
- Amanda H Rawstern
- Department of Biology, University of Miami, Coral Gables, Florida, USA
| | - Damian J Hernandez
- Department of Biology, University of Miami, Coral Gables, Florida, USA
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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12
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Li X, Han Y, Zhang Y, Shao Q, Dong C, Li J, Ding B, Zhang Y. Effects of wildfire on soil microbial communities in karst forest ecosystems of southern Guizhou Province, China. Appl Environ Microbiol 2024; 90:e0124524. [PMID: 39475286 DOI: 10.1128/aem.01245-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 09/27/2024] [Indexed: 11/21/2024] Open
Abstract
Wildfires are unpredictable disturbances with profound effects on soil properties and microbial communities within forest ecosystems. However, knowledge of post-fire microbial communities in karst forests remains limited. In this study, microbial amplicon sequencing techniques were employed to investigate the impact of wildfires on the composition, diversity, function, and co-occurrence network of soil microbial communities in karst forest landscapes and to identify the key soil physicochemical factors affecting the post-fire microbial communities. The wildfire affected the fungal community to a greater extent than the bacterial community, with the former shifting from a dominance of Basidiomycota to Ascomycota at the phylum level, while the relative abundance of Actinobacteria increased significantly in the bacterial community. Moreover, the wildfire increased the α-diversity of the microbial community and changed the β-diversity. Network analysis indicated significant reductions in the complexity of microbial community networks and the hub microbiome in burned soils compared to those of unburned soils. Functional predictions indicated an increase in the highly abundant functional taxa of chemoheterotrophic and aerobic chemoheterotrophic bacteria, along with a significant rise in saprotrophic functional fungal taxa following the fire. In addition, soil organic matter, total nitrogen, total phosphorus, and soil water content emerged as key soil physicochemical factors affecting post-fire soil microbial communities in the karst forest. Overall, this study revealed the structural and functional characteristics of soil microbial communities and their key influencing factors after a fire in a karst forest, which will provide a valuable theoretical basis for ecosystem restoration after a wildfire.IMPORTANCEDespite the significant impacts of wildfires on forest ecosystems, most existing studies have largely focused on boreal and Mediterranean coniferous forest types, with limited research on the impacts of coniferous and broadleaf forest types in subtropical karst regions. This study reveals the effects of wildfires on soil microbial communities of coniferous and broadleaf forest types in a karst forest. The results of this study not only improve the understanding of the effects of wildfires on the composition, diversity, function, and network of soil microbial communities but also provide a meaningful theoretical basis for post-fire ecosystem restoration in the karst forest.
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Affiliation(s)
- Xu Li
- Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Yanfeng Han
- Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Yunlin Zhang
- Key Laboratory of Ecology and Management on Forest Fire in Higher Education institutions of Guizhou Province/Key Laboratory of Development and Utilization of Biological Resources in Colleges and Universities of Guizhou Province, Guizhou Education University, Guiyang, Guizhou, China
| | - Qiuyu Shao
- Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Chunbo Dong
- Department of Ecology/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Jianfeng Li
- Key Laboratory of Ecology and Management on Forest Fire in Higher Education institutions of Guizhou Province/Key Laboratory of Development and Utilization of Biological Resources in Colleges and Universities of Guizhou Province, Guizhou Education University, Guiyang, Guizhou, China
| | - Bo Ding
- Key Laboratory of Ecology and Management on Forest Fire in Higher Education institutions of Guizhou Province/Key Laboratory of Development and Utilization of Biological Resources in Colleges and Universities of Guizhou Province, Guizhou Education University, Guiyang, Guizhou, China
| | - Yanwei Zhang
- Key Laboratory of Ecology and Management on Forest Fire in Higher Education institutions of Guizhou Province/Key Laboratory of Development and Utilization of Biological Resources in Colleges and Universities of Guizhou Province, Guizhou Education University, Guiyang, Guizhou, China
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13
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Zhu S, Yang P, Yin Y, Zhang S, Lv J, Tian S, Jiang T, Wang D. Influences of wildfire on the soil dissolved organic matter characteristics and its electron-donating capacity. WATER RESEARCH 2024; 266:122382. [PMID: 39298894 DOI: 10.1016/j.watres.2024.122382] [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: 07/01/2024] [Revised: 08/24/2024] [Accepted: 09/02/2024] [Indexed: 09/22/2024]
Abstract
Global increases in the intensity and frequency of wildfires are driving major changes in soil organic matter (SOM) characteristics, including soil dissolved organic matter (DOM). As the most crucial component of SOM, soil DOM plays a pivotal role in the carbon cycle and regulates the environmental fate of contaminants through its versatile reactivities, including electron-donating capacity (EDC). However, it is still being determined how wildfire influences key characteristics of soil DOM and subsequent effects on EDC in forest soils. Thus, we conducted our study to fill this gap with the forest soils of Jinyun Mountain Nature Reserve of China, which experienced an unprecedented wildfire event in 2022. The results from optical characterization, high-performance size-exclusion chromatography (HPSEC), and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) showed decreasing molecular weight but elevating nitrogen-containing molecular formulas of soil DOM in the burned soils. This could be attributed to the Maillard reaction and microbial re-colonies. Additionally, wildfires increased the condensed aromatics and lignin components in soil DOM. In the burned soils, we observed increasing EDC of soil DOM, which accounts for an increase in lignin-derived phenolic components. Overall, the findings of this study demonstrate that eco-disturbances, such as wildfires, induce alterations in the properties of DOM, leading to variations in its reactivity and potentially influencing the fate of environmental pollutants beyond carbon dynamics alone. Thus, incorporating the dynamic properties of soil DOM, particularly in the context of climate change, can enhance the assessment of risks associated with contaminants in soil and water, providing valuable insights.
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Affiliation(s)
- Sihua Zhu
- Interdisciplinary Research Centre for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Peijie Yang
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yongguang Yin
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Siqi Zhang
- Interdisciplinary Research Centre for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Jitao Lv
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shanyi Tian
- Interdisciplinary Research Centre for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Tao Jiang
- Interdisciplinary Research Centre for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing 400716, China; Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, School of Environment and Health, Jianghan University, Wuhan 430056, China.
| | - Dingyong Wang
- Interdisciplinary Research Centre for Agriculture Green Development in Yangtze River Basin, College of Resources and Environment, Southwest University, Chongqing 400716, China
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14
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de Menezes AB, Gashchak S, Wood MD, Beresford NA. Relationships between radiation, wildfire and the soil microbial communities in the Chornobyl Exclusion Zone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175381. [PMID: 39122033 DOI: 10.1016/j.scitotenv.2024.175381] [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: 03/05/2024] [Revised: 08/01/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
There is considerable uncertainty regarding radiation's effects on biodiversity in natural complex ecosystems typically subjected to multiple environmental disturbances and stresses. In this study we characterised the relationships between soil microbial communities and estimated total absorbed dose rates to bacteria, grassy vegetation and trees in the Red Forest region of the Chornobyl Exclusion Zone. Samples were taken from sites of contrasting ecological histories and along burn and no burn areas following a wildfire. Estimated total absorbed dose rates to bacteria reached levels one order of magnitude higher than those known to affect bacteria in laboratory studies. Sites with harsher ecological conditions, notably acidic pH and low soil moisture, tended to have higher radiation contamination levels. No relationship between the effects of fire and radiation were observed. Microbial groups that correlated with high radiation sites were mostly classified to taxa associated with high environmental stress habitats or stress resistance traits. Distance-based linear models and co-occurrence analysis revealed that the effects of radiation on the soil microbiome were minimal. Hence, the association between high radiation sites and specific microbial groups is more likely a result of the harsher ecological conditions in these sites, rather than due to radiation itself. In this study, we provide a starting point for understanding the relationship between soil microbial communities and estimated total absorbed radiation dose rates to different components of an ecosystem highly contaminated with radiation. Our results suggest that soil microbiomes adapted to natural soil conditions are more likely to be resistant to ionising radiation than expected from laboratory studies, which demonstrates the importance of assessing the impact of ionising radiation on soil microbial communities under field conditions.
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Affiliation(s)
- Alexandre Barretto de Menezes
- University of Galway, School of Biological and Chemical Sciences, Ryan Institute, University Road, H91 TK33, Galway, Ireland.
| | - Sergii Gashchak
- Chornobyl Center for Nuclear Safety, Radioactive Waste & Radioecology, International Radioecology Laboratory, Slavutych, Kyiv Region, Ukraine.
| | - Michael D Wood
- School of Science, Engineering & Environment, University of Salford, Manchester M5 4WT, United Kingdom.
| | - Nicholas A Beresford
- School of Science, Engineering & Environment, University of Salford, Manchester M5 4WT, United Kingdom; Centre for Ecology & Hydrology, CEH Lancaster, Lancaster Environment Centre, Library Av., Bailrigg, Lancaster LA1 4AP, United Kingdom
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15
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Han Q, Wang S, Han B, Su W, Yang J, Yu Q, Li H. Temporal dynamics of the diazotrophic community during corpse decomposition. Appl Microbiol Biotechnol 2024; 108:506. [PMID: 39520567 PMCID: PMC11550258 DOI: 10.1007/s00253-024-13329-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 09/20/2024] [Accepted: 10/07/2024] [Indexed: 11/16/2024]
Abstract
Corpse decomposition affects soil organisms through the formation of "cadaver decomposition islands." Soil diazotrophic microbes possess essential ecological functions on nitrogen input and nutrient cycling in the terrestrial ecosystem. However, our knowledge about how soil diazotrophic communities respond to corpse decomposition is lacking. In this study, we focused on the succession patterns and biological interaction of nitrogen-fixing microorganisms during animal (Ochotona curzoniae) corpse decomposition in terrestrial ecosystems by targeting nifH gene with high-throughput sequencing. Our results revealed that corpse decomposition of pikas reduced the α diversity and significantly impacted the β diversity of diazotrophic community across different decomposition stages. The divergent succession of diazotrophic community occurred under corpse pressure. Furthermore, the relative importance of stochasticity to the community assembly was improved by corpse decomposition, while the importance decreased over decomposition time. Cadaver decay also simplified the diazotrophic networks and weakened the biological interactions among diazotrophic populations. Notably, NH4-N was the most important factor affecting diazotrophic community, followed by time and total carbon. This work emphasized that corpse decomposition perhaps influences the process of biological nitrogen fixation by altering soil diazotrophic communities, which is of great significance for understanding the terrestrial ecosystems' nitrogen cycle functions. KEY POINTS: • Corpse decomposition reduced the α diversity of diazotrophic community. • Corpse decomposition improved the stochasticity of diazotrophic community assembly. • Corpse decomposition weakened the interactions among diazotrophic populations.
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Affiliation(s)
- Qian Han
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Binghua Han
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou, 730000, China.
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, China.
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16
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Foley MM, Stone BWG, Caro TA, Sokol NW, Koch BJ, Blazewicz SJ, Dijkstra P, Hayer M, Hofmockel K, Finley BK, Mack M, Marks J, Mau RL, Monsaint-Queeney V, Morrissey E, Propster J, Purcell A, Schwartz E, Pett-Ridge J, Fierer N, Hungate BA. Growth rate as a link between microbial diversity and soil biogeochemistry. Nat Ecol Evol 2024; 8:2018-2026. [PMID: 39294403 DOI: 10.1038/s41559-024-02520-7] [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: 10/25/2023] [Accepted: 07/25/2024] [Indexed: 09/20/2024]
Abstract
Measuring the growth rate of a microorganism is a simple yet profound way to quantify its effect on the world. The absolute growth rate of a microbial population reflects rates of resource assimilation, biomass production and element transformation-some of the many ways in which organisms affect Earth's ecosystems and climate. Microbial fitness in the environment depends on the ability to reproduce quickly when conditions are favourable and adopt a survival physiology when conditions worsen, which cells coordinate by adjusting their relative growth rate. At the population level, relative growth rate is a sensitive metric of fitness, linking survival and reproduction to the ecology and evolution of populations. Techniques combining omics and stable isotope probing enable sensitive measurements of the growth rates of microbial assemblages and individual taxa in soil. Microbial ecologists can explore how the growth rates of taxa with known traits and evolutionary histories respond to changes in resource availability, environmental conditions and interactions with other organisms. We anticipate that quantitative and scalable data on the growth rates of soil microorganisms, coupled with measurements of biogeochemical fluxes, will allow scientists to test and refine ecological theory and advance process-based models of carbon flux, nutrient uptake and ecosystem productivity. Measurements of in situ microbial growth rates provide insights into the ecology of populations and can be used to quantitatively link microbial diversity to soil biogeochemistry.
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Affiliation(s)
- Megan M Foley
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
| | - Bram W G Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tristan A Caro
- Department of Geological Sciences, University of Colorado Boulder, Boulder, CO, USA
| | - Noah W Sokol
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Kirsten Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Brianna K Finley
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michelle Mack
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Jane Marks
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Victoria Monsaint-Queeney
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Ember Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Jeffrey Propster
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biology, New Mexico Highlands University, Las Vegas, NM, USA
| | - Alicia Purcell
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California, Merced, Merced, CA, USA
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, USA
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
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17
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Fajardo-Cantos Á, Peña E, Plaza-Álvarez P, González-Romero J, Moya D, González-Camuñas H, Díaz A, Botella R, Lucas-Borja M, De Las Heras J. Soil response in a Mediterranean forest ecosystem of Southeast Spain following early prescribed burning. Heliyon 2024; 10:e37948. [PMID: 39391506 PMCID: PMC11466612 DOI: 10.1016/j.heliyon.2024.e37948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/05/2024] [Accepted: 09/13/2024] [Indexed: 10/12/2024] Open
Abstract
The escalation of global warming, high temperatures, and wildfire frequency in dry ecosystems, including semi-arid landscapes, has resulted in increased wildfire regimes, compromising ecosystem resistance and resilience. To mitigate these risks, prescribed burning (PB) is being employed as a preventive measure to modify fuel loads in forest ecosystems. However, fire can also impact soil structure and microbiota, which play critical roles in nutrient cycling, biodiversity conservation, and overall ecosystem functioning. Therefore, understanding post-fire processes is essential for sustainable forest management. However, while previous studies have explored the effects of prescribed fire management on semi-arid soil properties in Mediterranean forest ecosystems, gaps remain in our understanding of its specific impact on the physical structure, chemical composition, and biological activities of soils. In this study, we conducted early spring PB in SE Spain in 2021 and assessed the ecological and temporal effects of PB on semi-arid soils. Soil respiration (SR) measurements using automatic CO2 flow chambers were employed to evaluate microbiota recovery. To examine impacts on soil structure we evaluated physicochemical characteristics, soil hydraulic conductivity (SHC), and soil water repellency (SWR). No significant differences were observed in any of the variables studied after one year. However, immediate effects were detected shortly after the PB. Our research specifically targeted soil structure and microbiota in a semi-arid landscape with poor soils, characterized by slower recovery and potentially fragile ecosystems. These results provide valuable insights for forest management practices, indicating that prescribed fire management strategies in similar ecosystems are unlikely to cause adverse effects on soil health. However, further research is warranted to explore the potential effects of prescribed fire intensity and seasonality. Future studies can focus on investigating these factors to provide more targeted recommendations for effective forest management strategies and wildfire prevention efforts.
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Affiliation(s)
- Á. Fajardo-Cantos
- (ECOFOR) Research Group of Forest Ecology, Agricultural and Forest Engineers Higher Technical School, to University of Castilla-La Mancha, in Albacete, Spain
| | - E. Peña
- (ECOFOR) Research Group of Forest Ecology, Agricultural and Forest Engineers Higher Technical School, to University of Castilla-La Mancha, in Albacete, Spain
| | - P. Plaza-Álvarez
- (ECOFOR) Research Group of Forest Ecology, Agricultural and Forest Engineers Higher Technical School, to University of Castilla-La Mancha, in Albacete, Spain
| | - J. González-Romero
- Department of Forestry and Environmental Engineering and Management, Technical University of Madrid, Spain
| | - D. Moya
- (ECOFOR) Research Group of Forest Ecology, Agricultural and Forest Engineers Higher Technical School, to University of Castilla-La Mancha, in Albacete, Spain
| | - H. González-Camuñas
- (ECOFOR) Research Group of Forest Ecology, Agricultural and Forest Engineers Higher Technical School, to University of Castilla-La Mancha, in Albacete, Spain
| | - A. Díaz
- (ECOFOR) Research Group of Forest Ecology, Agricultural and Forest Engineers Higher Technical School, to University of Castilla-La Mancha, in Albacete, Spain
| | - R. Botella
- (ECOFOR) Research Group of Forest Ecology, Agricultural and Forest Engineers Higher Technical School, to University of Castilla-La Mancha, in Albacete, Spain
| | - M.E. Lucas-Borja
- (ECOFOR) Research Group of Forest Ecology, Agricultural and Forest Engineers Higher Technical School, to University of Castilla-La Mancha, in Albacete, Spain
| | - J. De Las Heras
- (ECOFOR) Research Group of Forest Ecology, Agricultural and Forest Engineers Higher Technical School, to University of Castilla-La Mancha, in Albacete, Spain
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18
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Mpakosi A, Cholevas V, Tzouvelekis I, Passos I, Kaliouli-Antonopoulou C, Mironidou-Tzouveleki M. Autoimmune Diseases Following Environmental Disasters: A Narrative Review of the Literature. Healthcare (Basel) 2024; 12:1767. [PMID: 39273791 PMCID: PMC11395540 DOI: 10.3390/healthcare12171767] [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: 07/23/2024] [Revised: 09/02/2024] [Accepted: 09/03/2024] [Indexed: 09/15/2024] Open
Abstract
Environmental disasters are extreme environmental processes such as earthquakes, volcanic eruptions, landslides, tsunamis, floods, cyclones, storms, wildfires and droughts that are the consequences of the climate crisis due to human intervention in the environment. Their effects on human health have alarmed the global scientific community. Among them, autoimmune diseases, a heterogeneous group of disorders, have increased dramatically in many parts of the world, likely as a result of changes in our exposure to environmental factors. However, only a limited number of studies have attempted to discover and analyze the complex association between environmental disasters and autoimmune diseases. This narrative review has therefore tried to fill this gap. First of all, the activation pathways of autoimmunity after environmental disasters have been analyzed. It has also been shown that wildfires, earthquakes, desert dust storms and volcanic eruptions may damage human health and induce autoimmune responses to inhaled PM2.5, mainly through oxidative stress pathways, increased pro-inflammatory cytokines and epithelial barrier damage. In addition, it has been shown that heat stress, in addition to increasing pro-inflammatory cytokines, may also disrupt the intestinal barrier, thereby increasing its permeability to toxins and pathogens or inducing epigenetic changes. In addition, toxic volcanic elements may accelerate the progressive destruction of myelin, which may potentially trigger multiple sclerosis. The complex and diverse mechanisms by which vector-borne, water-, food-, and rodent-borne diseases that often follow environmental diseases may also trigger autoimmune responses have also been described. In addition, the association between post-disaster stress and the onset or worsening of autoimmune disease has been demonstrated. Given all of the above, the rapid restoration of post-disaster health services to mitigate the flare-up of autoimmune conditions is critical.
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Affiliation(s)
- Alexandra Mpakosi
- Department of Microbiology, General Hospital of Nikaia "Agios Panteleimon", 18454 Piraeus, Greece
| | | | - Ioannis Tzouvelekis
- School of Agricultural Technology, Food Technology and Nutrition, Alexander Technological Educational Institute of Thessaloniki, 57400 Thessaloniki, Greece
| | - Ioannis Passos
- Surgical Department, 219, Mobile Army, Surgical Hospital, 68300 Didymoteicho, Greece
| | | | - Maria Mironidou-Tzouveleki
- Department of Pharmacology, School of Medical, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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19
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Sbardellati DL, Vannette RL. Targeted viromes and total metagenomes capture distinct components of bee gut phage communities. MICROBIOME 2024; 12:155. [PMID: 39175056 PMCID: PMC11342477 DOI: 10.1186/s40168-024-01875-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/16/2024] [Indexed: 08/24/2024]
Abstract
BACKGROUND Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens. RESULTS We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments. CONCLUSIONS Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.
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Affiliation(s)
| | - Rachel Lee Vannette
- Department of Entomology and Nematology, University of California Davis, Davis, CA, USA
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20
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Yin G, Guan P, Wang YH, Zhang P, Qu B, Xu S, Zhang G, He C, Shi Q, Wang J. Temporal Variations in Fire Impacts on Characteristics and Composition of Soil-Derived Dissolved Organic Matter at Qipan Mountain, China. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:13772-13782. [PMID: 39058895 DOI: 10.1021/acs.est.4c00446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Dissolved organic matter (DOM), the most reactive fraction of forest soil organic matter, is increasingly impacted by wildfires worldwide. However, few studies have quantified the temporal changes in soil DOM quantity and quality after fire. Here, soil samples were collected after the Qipan Mountain Fire (3-36 months) from pairs of burned and unburned sites. DOM contents and characteristics were analyzed using carbon quantification and various spectroscopic and spectrometric techniques. Compared with the unburned sites, burned sites showed higher contents of bulk DOM and most DOM components 3 months after the fire but lower contents of them 6-36 months after the fire. During the sharp drop of DOM from 3 to 6 months after the fire, carboxyl-rich alicyclic molecule-like and highly unsaturated compounds had greater losses than condensed aromatics. Notably, the burned sites had consistently higher abundances of oxygen-poor dissolved black nitrogen and fluorescent DOM 3-36 months after the fire, particularly the abundance of pyrogenic C2 (excitation/emission maxima of <250/∼400 nm) that increased by 150% before gradually declining. This study advances the understanding of temporal variations in the effects of fire on different soil DOM components, which is crucial for future postfire environmental management.
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Affiliation(s)
- Gege Yin
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Ping Guan
- Liaoning Key Laboratory for Biological Invasions and Global Changes, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Ying-Hui Wang
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Peng Zhang
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Bo Qu
- Liaoning Key Laboratory for Biological Invasions and Global Changes, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Shujun Xu
- Liaoning Key Laboratory for Biological Invasions and Global Changes, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry, Guangdong Province Key Laboratory of Environmental Protection and Resources Utilization, and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, Guangdong 510640, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China
| | - Junjian Wang
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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21
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Charaslertrangsi T, Arunrat N, Sereenonchai S, Wongkamhang PR. Comparison of microbial diversity and metabolic activities in organic and conventional rice farms in Thailand. Microbiol Spectr 2024; 12:e0307123. [PMID: 38912818 PMCID: PMC11302134 DOI: 10.1128/spectrum.03071-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/10/2024] [Indexed: 06/25/2024] Open
Abstract
Studies of the soil microbial community have revealed that several factors, both biotic and abiotic, can influence the community structure, diversity, and function. Human agricultural practice has been one of the key factors that affect microbial structure in soil. In this study, we examined the effect of two rice farming practices (i.e., conventional and organic) on soil microbial diversity and their metabolic activities. We proposed that the use of herbicides and chemical fertilizers in the conventional rice farming may decrease the soil microbial diversity and that it may lead to a decline in soil quality. However, our results show that there is no significant difference in the soil chemical properties, microbial diversity, and microbial metabolic activities between the two agricultural management systems. The wetland water cycling regime of rice agriculture in Thailand perhaps prevents the accumulation of chemicals in the soil, thus subdue the effect of these chemicals on soil microbes. Furthermore, our results showed that the key determinant of soil chemical properties as well as microbial community structure and diversity is the soil physical property, while the farming activity influences the microbial metabolic functions. These findings indicate the complex nature of the soil, microbes, and human farming interactions.IMPORTANCERice is a major export commodity in Thailand. As such, an understanding of the effect of conventional or organic farming approaches on soil microbial community could enable a suitable farming management. In this study, microbial communities were surveyed and compared between the two rice farming practices for their diversity and metabolic activities. Results showed no significant differences in microbial community structure and diversity between the two rice farming practices, but significant differences were observed due to the soil type, namely, clay, silty clay, silty clay loam, loam, and silty loam. Interestingly, significant differences in metabolic functions were also observed in different soil farming activities, such as land rest, period of growth, and post-burning, but not due to conventional or organic practices. These findings showed that the soil physical type and the farming activity impact the microbial community more than whether it is conventional or organically farmed.
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Affiliation(s)
| | - Noppol Arunrat
- Faculty of Environment and Resource Studies, Mahidol University, Nakhon Pathom, Thailand
| | - Sukanya Sereenonchai
- Faculty of Environment and Resource Studies, Mahidol University, Nakhon Pathom, Thailand
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22
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Guo J, Feng H, Peng C, Du J, Wang W, Kneeshaw D, Pan C, Roberge G, Feng L, Chen A. Fire effects on soil CH 4 and N 2O fluxes across terrestrial ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174708. [PMID: 39032756 DOI: 10.1016/j.scitotenv.2024.174708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024]
Abstract
Fire, as a natural disturbance, significantly shapes and influences the functions and services of terrestrial ecosystems via biotic and abiotic processes. Comprehending the influence of fire on soil greenhouse gas dynamics is crucial for understanding the feedback mechanisms between fire disturbances and climate change. Despite work on CO2 fluxes, there is a large uncertainty as to whether and how soil CH4 and N2O fluxes change in response to fire disturbance in terrestrial ecosystems. To narrow this knowledge gap, we performed a meta-analysis synthesizing 3615 paired observations from 116 global studies. Our findings revealed that fire increased global soil CH4 uptake in uplands by 23.2 %, soil CH4 emissions from peatlands by 74.7 %, and soil N2O emissions in terrestrial ecosystems (including upland and peatland) by 18.8 %. Fire increased soil CH4 uptake in boreal, temperate, and subtropical forests by 20.1 %, 38.8 %, and 30.2 %, respectively, and soil CH4 emissions in tropical forests by 193.3 %. Additionally, fire negatively affected soil total carbon (TC; -10.3 %), soil organic carbon (SOC; -15.6 %), microbial biomass carbon (MBC; -44.8 %), dissolved organic carbon (DOC; -27 %), microbial biomass nitrogen (MBN; -24.7 %), soil water content (SWC; -9.2 %), and water table depth (WTD; -68.2 %). Conversely, the fire increased soil bulk density (BD; +10.8 %), ammonium nitrogen (NH4+-N; +46 %), nitrate nitrogen (NO3--N; +54 %), pH (+4.4 %), and soil temperature (+15.4 %). Our meta-regression analysis showed that the positive effects of fire on soil CH4 and N2O emissions were significantly positively correlated with mean annual temperature (MAT) and mean annual precipitation (MAP), indicating that climate warming will amplify the positive effects of fire disturbance on soil CH4 and N2O emissions. Taken together, since higher future temperatures are likely to prolong the fire season and increase the potential of fires, this could lead to positive feedback between warming, fire events, CH4 and N2O emissions, and future climate change.
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Affiliation(s)
- Jiahuan Guo
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, School of Tropical Agriculture and Forestry (School of Agricultural and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou, Hainan 570228, China
| | - Huili Feng
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, School of Tropical Agriculture and Forestry (School of Agricultural and Rural Affairs, School of Rural Revitalization), Hainan University, Haikou, Hainan 570228, China.
| | - Changhui Peng
- Department of Biological Sciences, University of Quebec at Montreal, Montreal, Quebec H3C 3P8, Canada; College of Geographic Science, Hunan Normal University, Changsha, Hunan 410081, China
| | - Juan Du
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Science, Wuhan, Hubei 430223, China
| | - Weifeng Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Daniel Kneeshaw
- Department of Biological Sciences, University of Quebec at Montreal, Montreal, Quebec H3C 3P8, Canada
| | - Chang Pan
- College of Life Sciences, Anqing Normal University, Anqing, Anhui 246011, China
| | - Gabrielle Roberge
- Department of Biological Sciences, University of Quebec at Montreal, Montreal, Quebec H3C 3P8, Canada
| | - Lei Feng
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Anping Chen
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
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23
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Palta Ş, Özel HB, Kanbur S, de Souza TAF. Impact of wildfire on soil characteristics and arbuscular mycorrhizal fungi. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:681. [PMID: 38954029 DOI: 10.1007/s10661-024-12779-9] [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: 11/08/2023] [Accepted: 06/06/2024] [Indexed: 07/04/2024]
Abstract
This study explored whether wildfire alters the soil properties and arbuscular mycorrhizal fungi (AMF) community composition when compared with burnt rangeland, non-burnt rangeland and adjacent tilled in mesothermal ecosystems. The study was carried out in August 2020, 1 year later after wildfire. The results of this study showed that the wildfire played a key role in altering soil characteristics and AMF community composition in Bartin Province located in the Western Black Sea Region. Soil samples were made according to standard methods. AMF spores were isolated according to the wet sieving method, and the spores of AMF were identified according to their morphological characteristics. Analysis of variance was performed to determine the differences between the parameters, and correlation analysis was performed to determine the relationships between the parameters. The highest values of soil organic carbon (2.20%), total nitrogen (0.18%), K2O (74.68 kg/da), root colonization (87.5%) and the frequency of occurrence of Funneliformis geosporum (20%), Claroideoglomus claroideum (16%) and Claroideoglomus etunicatum (11%) were found in burnt rangeland. Sporulation of Acaulospora dilatata, Acaulospora morrowiae, Acaulospora tuberculata, Scutellospora castanea, Scutellospora coralloidea, Scutellospora scutata, Glomus coremioides and Glomus multicaule was either decreased or completely inhibited in the burnt rangeland. While species diversity of AMF (12) decreased, the number of AMF spores (325.6 (number/50 gr soil)) increased in burnt areas. In conclusion, the number of spores and root colonization of AMF increased but species diversity of AMF reduced after the wildfire. In ecosystems with high fire risk where AMF transfer is planned, it is suggested that it would be more appropriate to select species with an increase in spore number after fire.
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Affiliation(s)
- Şahin Palta
- Division of Watershed Management, Subdivision of Range Management, Department of Forest Engineering, Faculty of Forestry, Bartın University, 74100, Bartın, Turkey.
| | - Halil Barış Özel
- Division of Watershed Management, Subdivision of Range Management, Department of Forest Engineering, Faculty of Forestry, Bartın University, 74100, Bartın, Turkey
| | - Sinem Kanbur
- Department of Forestry Engineering, Graduate School, Bartın University, 74100, Bartın, Turkey
| | - Tancredo Augusto Feitosa de Souza
- Agrarian Science Centre, Department of Soils and Rural Engineering, Federal University of Paraíba, João Pessoa, 58397-000, Areia, Paraíba, Brazil
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24
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Cao X, Li SA, Huang H, Ma H. Wildfire Impacts on Molecular Changes of Dissolved Organic Matter during Its Passage through Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 38904350 DOI: 10.1021/acs.est.3c11056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
The frequency and intensity of global wildfires are escalating, leading to an increase in derived pyrogenic dissolved organic matter (pyDOM), which potentially influences the riverine carbon reservoir and poses risks to drinking water safety. However, changes in pyDOM properties as it traverses through soil to water bodies are highly understudied due to the challenges of simulating such processes under laboratory conditions. In this study, we extracted soil DOM along hillslope gradients and soil depths in both burned and unburned catchments post wildfire. Using high-resolution mass spectrometry and a substrate-explicit model, we observed significant increases in the relative abundance of condensed aromatics (ConAC) and tannins in wildfire-affected soil DOM. Wildfire-affected soil DOM also displayed a broader spectrum of molecular and thermodynamic properties, indicative of its diverse composition and reactivity. Furthermore, as the fire-induced weakening of topsoil microbial reprocessing abilities hindered the transformation of plant-derived DOM, the relative abundance of lignin-like compounds increased with soil depth in the fire regions. Meanwhile, the distribution of shared molecular formulas along the hillslope gradient (from shoulder to toeslope) exhibited analogous patterns in both burned and unburned catchments. Although there was an increased prevalence of ConAC and tannin in the burned catchments, the relative abundance of these fractions diminished along the hillslope in all three catchments. Based on the substrate-explicit model, the biodegradability exhibited by wildfire-affected DOM fractions offers the possibility of its conversion along hillslopes. Our findings reveal the spatial distribution of DOM properties after a wildfire, facilitating accurate evaluation of dissolved organic carbon composition involved in the watershed-scale carbon cycle.
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Affiliation(s)
- Xinghong Cao
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Sheng-Ao Li
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Hai Huang
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Hua Ma
- College of Environment and Ecology, Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
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25
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Seidel D, Wurster S, Jenks JD, Sati H, Gangneux JP, Egger M, Alastruey-Izquierdo A, Ford NP, Chowdhary A, Sprute R, Cornely O, Thompson GR, Hoenigl M, Kontoyiannis DP. Impact of climate change and natural disasters on fungal infections. THE LANCET. MICROBE 2024; 5:e594-e605. [PMID: 38518791 DOI: 10.1016/s2666-5247(24)00039-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 03/24/2024]
Abstract
The effects of climate change and natural disasters on fungal pathogens and the risks for fungal diseases remain incompletely understood. In this literature review, we examined how fungi are adapting to an increase in the Earth's temperature and are becoming more thermotolerant, which is enhancing fungal fitness and virulence. Climate change is creating conditions conducive to the emergence of new fungal pathogens and is priming fungi to adapt to previously inhospitable environments, such as polluted habitats and urban areas, leading to the geographical spread of some fungi to traditionally non-endemic areas. Climate change is also contributing to increases in the frequency and severity of natural disasters, which can trigger outbreaks of fungal diseases and increase the spread of fungal pathogens. The populations mostly affected are the socially vulnerable. More awareness, research, funding, and policies on the part of key stakeholders are needed to mitigate the effects of climate change and disaster-related fungal diseases.
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Affiliation(s)
- Danila Seidel
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, University of Cologne, Center of Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center of Medical Mycology (ECMM), Cologne, Germany; German Centre of Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Sebastian Wurster
- ECMM Excellence Center for Medical Mycology, Division of Internal Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Jeffrey D Jenks
- Durham County Department of Public Health, Durham, NC, USA; Division of Infectious Diseases, Department of Medicine, Duke University, Durham, NC, USA
| | - Hatim Sati
- Department of Global Coordination and Partnership on Antimicrobial Resistance, WHO, Geneva, Switzerland
| | - Jean-Pierre Gangneux
- Centre National de Référence des Mycoses et Antifongiques LA-AspC Aspergilloses Chroniques, ECMM Excellence Center for Medical Mycology, Centre Hospitalier Universitaire de Rennes, Rennes, France; University of Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé Environnement Travail) - UMR_S 1085, Rennes, France
| | - Matthias Egger
- Division of Infectious Diseases, ECMM Excellence Center for Medical Mycology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Ana Alastruey-Izquierdo
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Nathan P Ford
- Department of HIV/AIDS and Global Hepatitis Programme, WHO, Geneva, Switzerland
| | - Anuradha Chowdhary
- Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi, India; National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi, India
| | - Rosanne Sprute
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, University of Cologne, Center of Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center of Medical Mycology (ECMM), Cologne, Germany; German Centre of Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Oliver Cornely
- Faculty of Medicine and University Hospital Cologne, University of Cologne, Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany; Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, University of Cologne, Center of Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD) and Excellence Center of Medical Mycology (ECMM), Cologne, Germany; German Centre of Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany; Faculty of Medicine and University Hospital Cologne, Clinical Trials Centre Cologne (ZKS Koln), University of Cologne, Cologne, Germany
| | - George R Thompson
- University of California Davis Center for Valley Fever, University of California Davis, Sacramento, CA, USA; Department of Internal Medicine, Division of Infectious Diseases, University of California Davis Medical Center, Sacramento, CA, USA; Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA
| | - Martin Hoenigl
- Division of Infectious Diseases, ECMM Excellence Center for Medical Mycology, Department of Internal Medicine, Medical University of Graz, Graz, Austria; BioTechMed, Graz, Austria.
| | - Dimitrios P Kontoyiannis
- ECMM Excellence Center for Medical Mycology, Division of Internal Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
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26
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Arunrat N, Sansupa C, Sereenonchai S, Hatano R, Lal R. Fire-Induced Changes in Soil Properties and Bacterial Communities in Rotational Shifting Cultivation Fields in Northern Thailand. BIOLOGY 2024; 13:383. [PMID: 38927263 PMCID: PMC11200764 DOI: 10.3390/biology13060383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024]
Abstract
Fire is a common practice in rotational shifting cultivation (RSC), but little is known about the dynamics of bacterial populations and the impact of fire disturbance in northern Thailand. To fill the research gap, this study aims to investigate the dynamics of soil bacterial communities and examine how the soil's physicochemical properties influence the bacterial communities in RSC fields over a period of one year following a fire. Surface soil samples (0-2 cm depth) were collected from sites with 6 (RSC-6Y) and 12 (RSC-12Y) years of fallow in Chiang Mai Province, northern Thailand at six different time points: before burning, 5 min after burning (summer), 3 months after burning (rainy season), 6 months after burning (rainy season), 9 months after burning (winter), and 12 months after burning (summer). The results revealed a reduction in the soil bacterial communities' diversity and an increase in soil nutrient levels immediately after the fire. The fire significantly influenced the abundance of Firmicutes, Proteobacteria, Acidobacteria, and Planctomycetes, but not that of Actinobacteria. At the genus level, Bacillus, Conexibacter, and Chthoniobacter showed increased abundance following the fire. During the rainy season, a recovery in the abundance of the soil bacterial communities was observed, although soil nutrient availability declined. Soil physicochemical properties such as pH, organic matter, organic carbon, electrical conductivity, cation exchange capacity, nitrate-nitrogen, available phosphorus, exchangeable potassium, total nitrogen, bulk density, sand, and silt contents significantly influenced the composition of bacterial communities. Alpha diversity indices indicated a decrease in diversity immediately after burning, followed by an increase from the early rainy season until the summer season, indicating that seasonal variation affected the composition of the soil bacterial communities. After one year of burning, an increase in bacterial richness was observed, while the diversity of the bacterial communities reverted to pre-burning levels.
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Affiliation(s)
- Noppol Arunrat
- Faculty of Environment and Resource Studies, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Chakriya Sansupa
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Sukanya Sereenonchai
- Faculty of Environment and Resource Studies, Mahidol University, Nakhon Pathom 73170, Thailand;
| | - Ryusuke Hatano
- Laboratory of Soil Science, Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan;
| | - Rattan Lal
- CFAES Rattan Lal Center for Carbon Management and Sequestration, The Ohio State University, 2021 Coffey Rd, Columbus, OH 43210, USA;
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VanderRoest JP, Fowler JA, Rhoades CC, Roth HK, Broeckling CD, Fegel TS, McKenna AM, Bechtold EK, Boot CM, Wilkins MJ, Borch T. Fire Impacts on the Soil Metabolome and Organic Matter Biodegradability. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4167-4180. [PMID: 38385432 DOI: 10.1021/acs.est.3c09797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Global wildfire activity has increased since the 1970s and is projected to intensify throughout the 21st century. Wildfires change the composition and biodegradability of soil organic matter (SOM) which contains nutrients that fuel microbial metabolism. Though persistent forms of SOM often increase postfire, the response of more biodegradable SOM remains unclear. Here we simulated severe wildfires through a controlled "pyrocosm" approach to identify biodegradable sources of SOM and characterize the soil metabolome immediately postfire. Using microbial amplicon (16S/ITS) sequencing and gas chromatography-mass spectrometry, heterotrophic microbes (Actinobacteria, Firmicutes, and Protobacteria) and specific metabolites (glycine, protocatechuate, citric cycle intermediates) were enriched in burned soils, indicating that burned soils contain a variety of substrates that support microbial metabolism. Molecular formulas assigned by 21 T Fourier transform ion cyclotron resonance mass spectrometry showed that SOM in burned soil was lower in molecular weight and featured 20 to 43% more nitrogen-containing molecular formulas than unburned soil. We also measured higher water extractable organic carbon concentrations and higher CO2 efflux in burned soils. The observed enrichment of biodegradable SOM and microbial heterotrophs demonstrates the resilience of these soils to severe burning, providing important implications for postfire soil microbial and plant recolonization and ecosystem recovery.
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Affiliation(s)
- Jacob P VanderRoest
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Julie A Fowler
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Charles C Rhoades
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, Colorado 80526, United States
| | - Holly K Roth
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Corey D Broeckling
- Bioanalysis and Omics Center, Analytical Resources Core, Colorado State University, Fort Collins, 80521, United States
| | - Timothy S Fegel
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, Colorado 80526, United States
| | - Amy M McKenna
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Emily K Bechtold
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Claudia M Boot
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Thomas Borch
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
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28
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Pearman WS, Morales SE, Vaux F, Gemmell NJ, Fraser CI. Host population crashes disrupt the diversity of associated marine microbiomes. Environ Microbiol 2024; 26:e16611. [PMID: 38519875 DOI: 10.1111/1462-2920.16611] [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: 11/05/2023] [Accepted: 03/01/2024] [Indexed: 03/25/2024]
Abstract
Host-associated microbial communities are shaped by myriad factors ranging from host conditions, environmental conditions and other microbes. Disentangling the ecological impact of each of these factors can be particularly difficult as many variables are correlated. Here, we leveraged earthquake-induced changes in host population structure to assess the influence of population crashes on marine microbial ecosystems. A large (7.8 magnitude) earthquake in New Zealand in 2016 led to widespread coastal uplift of up to ~6 m, sufficient to locally extirpate some intertidal southern bull kelp populations. These uplifted populations are slowly recovering, but remain at much lower densities than at nearby, less-uplifted sites. By comparing the microbial communities of the hosts from disturbed and relatively undisturbed populations using 16S rRNA gene amplicon sequencing, we observed that disturbed host populations supported higher functional, taxonomic and phylogenetic microbial beta diversity than non-disturbed host populations. Our findings shed light on microbiome ecological assembly processes, particularly highlighting that large-scale disturbances that affect host populations can dramatically influence microbiome structure. We suggest that disturbance-induced changes in host density limit the dispersal opportunities of microbes, with host community connectivity declining with the density of host populations.
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Affiliation(s)
- William S Pearman
- Department of Marine Science, University of Otago, Dunedin, New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- National Institute of Water and Atmospheric Research Ltd, Auckland, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Felix Vaux
- National Institute of Water and Atmospheric Research Ltd, Auckland, New Zealand
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Ceridwen I Fraser
- Department of Marine Science, University of Otago, Dunedin, New Zealand
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29
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Bandla A, Akhtar H, Lupascu M, Sukri RS, Swarup S. Elevated methane flux in a tropical peatland post-fire is linked to depth-dependent changes in peat microbiome assembly. NPJ Biofilms Microbiomes 2024; 10:8. [PMID: 38253600 PMCID: PMC10803758 DOI: 10.1038/s41522-024-00478-9] [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: 04/27/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Fires in tropical peatlands extend to depth, transforming them from carbon sinks into methane sources and severely limit forest recovery. Peat microbiomes influence carbon transformations and forest recovery, yet our understanding of microbiome shifts post-fire is currently limited. Our previous study highlighted altered relationships between the peat surface, water table, aboveground vegetation, and methane flux after fire in a tropical peatland. Here, we link these changes to post-fire shifts in peat microbiome composition and assembly processes across depth. We report kingdom-specific and depth-dependent shifts in alpha diversity post-fire, with large differences at deeper depths. Conversely, we found shifts in microbiome composition across all depths. Compositional shifts extended to functional groups involved in methane turnover, with methanogens enriched and methanotrophs depleted at mid and deeper depths. Finally, we show that community shifts at deeper depths result from homogeneous selection associated with post-fire changes in hydrology and aboveground vegetation. Collectively, our findings provide a biological basis for previously reported methane fluxes after fire and offer new insights into depth-dependent shifts in microbiome assembly processes, which ultimately underlie ecosystem function predictability and ecosystem recovery.
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Affiliation(s)
- Aditya Bandla
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Hasan Akhtar
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Department of Geography, National University of Singapore, Singapore, Singapore
- School of Liberal Arts and Sciences, RV University, Bengaluru, Karnataka, India
| | - Massimo Lupascu
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
- Department of Geography, National University of Singapore, Singapore, Singapore
| | - Rahayu Sukmaria Sukri
- Institute for Biodiversity and Environmental Research, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Sanjay Swarup
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore.
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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30
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Schuck LK, Neely WJ, Buttimer SM, Moser CF, Barth PC, Liskoski PE, Caberlon CDA, Valiati VH, Tozetti AM, Becker CG. Effects of grassland controlled burning on symbiotic skin microbes in Neotropical amphibians. Sci Rep 2024; 14:959. [PMID: 38200064 PMCID: PMC10781984 DOI: 10.1038/s41598-023-50394-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Climate change has led to an alarming increase in the frequency and severity of wildfires worldwide. While it is known that amphibians have physiological characteristics that make them highly susceptible to fire, the specific impacts of wildfires on their symbiotic skin bacterial communities (i.e., bacteriomes) and infection by the deadly chytrid fungus, Batrachochytrium dendrobatidis, remain poorly understood. Here, we address this research gap by evaluating the effects of fire on the amphibian skin bacteriome and the subsequent risk of chytridiomycosis. We sampled the skin bacteriome of the Neotropical species Scinax squalirostris and Boana leptolineata in fire and control plots before and after experimental burnings. Fire was linked with a marked increase in bacteriome beta dispersion, a proxy for skin microbial dysbiosis, alongside a trend of increased pathogen loads. By shedding light on the effects of fire on amphibian skin bacteriomes, this study contributes to our broader understanding of the impacts of wildfires on vulnerable vertebrate species.
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Affiliation(s)
- Laura K Schuck
- Programa de Pós-Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022-750, Brazil.
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Wesley J Neely
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, 35487, USA
- Department of Biology, Texas State University, San Marcos, TX, 78666, USA
| | - Shannon M Buttimer
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
- Center for Infectious Disease Dynamics and One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Camila F Moser
- Programa de Pos-Graduacão em Zoologia, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Priscila C Barth
- Programa de Pós-Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022-750, Brazil
| | - Paulo E Liskoski
- Programa de Pós-Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022-750, Brazil
| | - Carolina de A Caberlon
- Programa de Pós-Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022-750, Brazil
| | - Victor Hugo Valiati
- Programa de Pós-Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022-750, Brazil
| | - Alexandro M Tozetti
- Programa de Pós-Graduacão em Biologia, Universidade do Vale do Rio dos Sinos, São Leopoldo, RS, 93022-750, Brazil.
| | - C Guilherme Becker
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Center for Infectious Disease Dynamics and One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
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31
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Ellington AJ, Walters K, Christner BC, Fox S, Bonfantine K, Walker C, Lampman P, Vuono DC, Strickland M, Lambert K, Kobziar LN. Dispersal of microbes from grassland fire smoke to soils. THE ISME JOURNAL 2024; 18:wrae203. [PMID: 39404077 PMCID: PMC11525542 DOI: 10.1093/ismejo/wrae203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 09/23/2024] [Accepted: 10/14/2024] [Indexed: 11/02/2024]
Abstract
Wildland fire is increasingly recognized as a driver of bioaerosol emissions, but the effects that smoke-emitted microbes have on the diversity and community assembly patterns of the habitats where they are deposited remain unknown. In this study, we examined whether microbes aerosolized by biomass burning smoke detectably impact the composition and function of soil sinks using lab-based mesocosm experiments. Soils either containing the native microbial community or presterilized by γ-irradiation were inundated with various doses of smoke from native tallgrass prairie grasses. Smoke-inundated, γ-irradiated soils exhibited significantly higher respiration rates than both smoke-inundated, native soils and γ-irradiated soils exposed to ambient air only. Microbial communities in γ-irradiated soils were significantly different between smoke-treated and control soils, which supports the hypothesis that wildland fire smoke can act as a dispersal agent. Community compositions differed based on smoke dose, incubation time, and soil type. Concentrations of phosphate and microbial biomass carbon and nitrogen together with pH were significant predictors of community composition. Source tracking analysis attributed smoke as contributing nearly 30% of the taxa found in smoke-inundated, γ-irradiated soils, suggesting smoke may play a role in the recovery of microbial communities in similar damaged soils. Our findings demonstrate that short-distance microbial dispersal by biomass burning smoke can influence the assembly processes of microbial communities in soils and has implications for a broad range of subjects including agriculture, restoration, plant disease, and biodiversity.
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Affiliation(s)
- Adam J Ellington
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, P.O. Box 110700 Gainesville, FL 32611, United States
| | - Kendra Walters
- Department of Forest, Rangeland, and Fire Sciences, University of Idaho, 1031 N. Academic Way, Coeur d’Alene, ID 83814, United States
| | - Brent C Christner
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, P.O. Box 110700 Gainesville, FL 32611, United States
| | - Sam Fox
- Department of Forest, Rangeland, and Fire Sciences, University of Idaho, 1031 N. Academic Way, Coeur d’Alene, ID 83814, United States
| | - Krista Bonfantine
- Department of Forest, Rangeland, and Fire Sciences, University of Idaho, 1031 N. Academic Way, Coeur d’Alene, ID 83814, United States
| | - Cassie Walker
- Department of Biology, Brigham Young University – Idaho, 525 S Center St., Rexburg, ID 83460, United States
| | - Phinehas Lampman
- Department of Forest, Rangeland, and Fire Sciences, University of Idaho, 1031 N. Academic Way, Coeur d’Alene, ID 83814, United States
| | - David C Vuono
- Department of Civil and Environmental Engineering, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401, United States
| | - Michael Strickland
- Department of Soil and Water Systems, University of Idaho, 875 Perimeter Drive, Moscow, ID 83844, United States
| | - Katie Lambert
- Department of Soil and Water Systems, University of Idaho, 875 Perimeter Drive, Moscow, ID 83844, United States
| | - Leda N Kobziar
- Department of Forest, Rangeland, and Fire Sciences, University of Idaho, 1031 N. Academic Way, Coeur d’Alene, ID 83814, United States
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32
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Nelson AR, Fegel TS, Danczak RE, Caiafa MV, Roth HK, Dunn OI, Turvold CA, Borch T, Glassman SI, Barnes RT, Rhoades CC, Wilkins MJ. Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion. THE ISME JOURNAL 2024; 18:wrae047. [PMID: 38502869 PMCID: PMC11650388 DOI: 10.1093/ismejo/wrae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/12/2024] [Accepted: 03/17/2024] [Indexed: 03/21/2024]
Abstract
Disturbances cause rapid changes to forests, with different disturbance types and severities creating unique ecosystem trajectories that can impact the underlying soil microbiome. Pile burning-the combustion of logging residue on the forest floor-is a common fuel reduction practice that can have impacts on forest soils analogous to those following high-severity wildfire. Further, pile burning following clear-cut harvesting can create persistent openings dominated by nonwoody plants surrounded by dense regenerating conifer forest. A paired 60-year chronosequence of burn scar openings and surrounding regenerating forest after clear-cut harvesting provides a unique opportunity to assess whether belowground microbial processes mirror aboveground vegetation during disturbance-induced ecosystem shifts. Soil ectomycorrhizal fungal diversity was reduced the first decade after pile burning, which could explain poor tree seedling establishment and subsequent persistence of herbaceous species within the openings. Fine-scale changes in the soil microbiome mirrored aboveground shifts in vegetation, with short-term changes to microbial carbon cycling functions resembling a postfire microbiome (e.g. enrichment of aromatic degradation genes) and respiration in burn scars decoupled from substrate quantity and quality. Broadly, however, soil microbiome composition and function within burn scar soils converged with that of the surrounding regenerating forest six decades after the disturbances, indicating potential microbial resilience that was disconnected from aboveground vegetation shifts. This work begins to unravel the belowground microbial processes that underlie disturbance-induced ecosystem changes, which are increasing in frequency tied to climate change.
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Affiliation(s)
- Amelia R Nelson
- Department of Soil and Crop Sciences, Colorado State
University, Fort Collins, CO 80523, United States
| | - Timothy S Fegel
- Rocky Mountain Research Station, US Forest Service,
Fort Collins, CO 80526, United
States
| | - Robert E Danczak
- Division of Biological Sciences, Pacific Northwest National
Laboratory, Richland, WA 99354, United States
| | - Marcos V Caiafa
- Department of Microbiology and Plant Pathology, University of California
Riverside, Riverside, CA 92521, United States
| | - Holly K Roth
- Department of Chemistry, Colorado State University,
Fort Collins, CO 80523, United
States
| | - Oliver I Dunn
- The Environmental Studies Program, Colorado College,
Colorado Springs, CO 80946, United
States
| | - Cosette A Turvold
- The Environmental Studies Program, Colorado College,
Colorado Springs, CO 80946, United
States
| | - Thomas Borch
- Department of Soil and Crop Sciences, Colorado State
University, Fort Collins, CO 80523, United States
- Department of Chemistry, Colorado State University,
Fort Collins, CO 80523, United
States
- Department of Civil and Environmental Engineering, Colorado State
University, Fort Collins, CO 80523, United States
| | - Sydney I Glassman
- Department of Microbiology and Plant Pathology, University of California
Riverside, Riverside, CA 92521, United States
| | - Rebecca T Barnes
- The Environmental Studies Program, Colorado College,
Colorado Springs, CO 80946, United
States
| | - Charles C Rhoades
- Rocky Mountain Research Station, US Forest Service,
Fort Collins, CO 80526, United
States
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State
University, Fort Collins, CO 80523, United States
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33
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Zhou Y, Meng F, Ochieng B, Xu J, Zhang L, Kimirei IA, Feng M, Zhu L, Wang J. Climate and Environmental Variables Drive Stream Biofilm Bacterial and Fungal Diversity on Tropical Mountainsides. MICROBIAL ECOLOGY 2024; 87:28. [PMID: 38182675 DOI: 10.1007/s00248-023-02335-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 12/22/2023] [Indexed: 01/07/2024]
Abstract
High mountain freshwater systems are particularly sensitive to the impacts of global warming and relevant environmental changes. Microorganisms contribute substantially to biogeochemical processes, yet their distribution patterns and driving mechanism in alpine streams remain understudied. Here, we examined the bacterial and fungal community compositions in stream biofilm along the elevational gradient of 745-1874 m on Mt. Kilimanjaro and explored their alpha and beta diversity patterns and the underlying environmental drivers. We found that the species richness and evenness monotonically increased towards higher elevations for bacteria, while were non-significant for fungi. However, both bacterial and fungal communities showed consistent elevational distance-decay relationships, i.e., the dissimilarity of assemblage composition increased with greater elevational differences. Bacterial alpha diversity patterns were mainly affected by chemical variables such as total nitrogen and phosphorus, while fungi were affected by physical variables such as riparian shading and stream width. Notably, climatic variables such as mean annual temperature strongly affected the elevational succession of bacterial and fungal community compositions. Our study is the first exploration of microbial biodiversity and their underlying driving mechanisms for stream ecosystems in tropical alpine regions. Our findings provide insights on the response patterns of tropical aquatic microbial community composition and diversity under climate change.
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Affiliation(s)
- Yanan Zhou
- College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Fanfan Meng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Beryl Ochieng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianing Xu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
- School of Civil Engineering, Southeast University, Nanjing, 210096, China
| | - Lu Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | | | - Muhua Feng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China.
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
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34
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Nelson AR, Rhoades CC, Fegel TS, Roth HK, Caiafa MV, Glassman SI, Borch T, Wilkins MJ. Wildfire impact on soil microbiome life history traits and roles in ecosystem carbon cycling. ISME COMMUNICATIONS 2024; 4:ycae108. [PMID: 39963501 PMCID: PMC11831523 DOI: 10.1093/ismeco/ycae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/01/2024] [Accepted: 08/26/2024] [Indexed: 02/20/2025]
Abstract
Wildfires, which are increasing in frequency and severity with climate change, reduce soil microbial biomass and alter microbial community composition and function. The soil microbiome plays a vital role in carbon (C) and nitrogen (N) cycling, but its complexity makes it challenging to predict post-wildfire soil microbial dynamics and resulting impacts on ecosystem biogeochemistry. The application of biogeochemically relevant conceptual trait-based frameworks to the soil microbiome can distill this complexity, enabling enhanced predictability of soil microbiome recovery following wildfire and subsequent impacts to biogeochemical cycles. Conceptual frameworks that have direct links to soil C and N cycling have been developed for the soil microbiome; the Y-A-S framework overviews soil microbiome life history strategies that have tradeoffs with one another and others have proposed frameworks specific to wildfire. Here, we aimed to delineate post-wildfire changes of bacterial traits in western US coniferous forests to inform how severe wildfire influences soil microbiome recovery and resultant biogeochemical cycling. We utilized a comprehensive metagenome-assembled genome catalog from post-wildfire soils representing 1 to 11 years following low- and high-severity burning to identify traits that enable the persistence of microbial taxa in burned soils and influence ecosystem C and N cycling. We found that high-severity wildfire initially selects for fast growers and, up to a decade post-fire, taxa that invest in genes for acquiring diverse resources from the external environment, which in combination could increase soil C losses. This work begins to disentangle how climate change-induced shifts in wildfire behavior might alter microbially mediated soil biogeochemical cycling.
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Affiliation(s)
- Amelia R Nelson
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, United States
| | - Charles C Rhoades
- Rocky Mountain Research Station, United States Forest Service, Fort Collins, CO 80526, United States
| | - Timothy S Fegel
- Rocky Mountain Research Station, United States Forest Service, Fort Collins, CO 80526, United States
| | - Holly K Roth
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, United States
| | - Marcos V Caiafa
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, United States
| | - Sydney I Glassman
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA 92521, United States
| | - Thomas Borch
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, United States
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, United States
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, United States
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35
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Arnolds KL, Higgins RC, Crandall J, Li G, Linger JG, Guarnieri MT. Risk Assessment of Industrial Microbes Using a Terrestrial Mesocosm Platform. MICROBIAL ECOLOGY 2023; 87:12. [PMID: 38072911 PMCID: PMC10710964 DOI: 10.1007/s00248-023-02321-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
Industrial microbes and bio-derived products have emerged as an integral component of the bioeconomy, with an array of agricultural, bioenergy, and biomedical applications. However, the rapid development of microbial biotechnology raises concerns related to environmental escape of laboratory microbes, detection and tracking thereof, and resultant impact upon native ecosystems. Indeed, though wild-type and genetically modified microbes are actively deployed in industrial bioprocesses, an understanding of microbial interactivity and impact upon the environment is severely lacking. In particular, the persistence and sustained ecosystem impact of industrial microbes following laboratory release or unintentional laboratory escape remains largely unexplored. Herein, we investigate the applicability of soil-sorghum mesocosms for the ecological risk assessment of the industrial microbe, Saccharomyces cerevisiae. We developed and applied a suite of diagnostic and bioinformatic analyses, including digital droplet PCR, microscopy, and phylogenomic analyses to assess the impacts of a terrestrial ecosystem perturbation event over a 30-day time course. The platform enables reproducible, high-sensitivity tracking of S. cerevisiae in a complex soil microbiome and analysis of the impact upon abiotic soil characteristics and soil microbiome population dynamics and diversity. The resultant data indicate that even though S. cerevisiae is relatively short-lived in the soil, a single perturbation event can have sustained impact upon mesocosm soil composition and underlying microbial populations in our system, underscoring the necessity for more comprehensive risk assessment and development of mitigation and biocontainment strategies in industrial bioprocesses.
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Affiliation(s)
- Kathleen L Arnolds
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
| | - Riley C Higgins
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
| | - Jennifer Crandall
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
| | - Gabriella Li
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
| | - Jeffrey G Linger
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Michael T Guarnieri
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Pkwy, Golden, CO, 80401, USA.
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, 80401, USA.
- Renewable & Sustainable Energy Institute, University of Colorado, Boulder, CO, 80303, USA.
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36
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Robinson JM, Hodgson R, Krauss SL, Liddicoat C, Malik AA, Martin BC, Mohr JJ, Moreno-Mateos D, Muñoz-Rojas M, Peddle SD, Breed MF. Opportunities and challenges for microbiomics in ecosystem restoration. Trends Ecol Evol 2023; 38:1189-1202. [PMID: 37648570 DOI: 10.1016/j.tree.2023.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 07/21/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
Microbiomics is the science of characterizing microbial community structure, function, and dynamics. It has great potential to advance our understanding of plant-soil-microbe processes and interaction networks which can be applied to improve ecosystem restoration. However, microbiomics may be perceived as complex and the technology is not accessible to all. The opportunities of microbiomics in restoration ecology are considerable, but so are the practical challenges. Applying microbiomics in restoration must move beyond compositional assessments to incorporate tools to study the complexity of ecosystem recovery. Advances in metaomic tools provide unprecedented possibilities to aid restoration interventions. Moreover, complementary non-omic applications, such as microbial inoculants and biopriming, have the potential to improve restoration objectives by enhancing the establishment and health of vegetation communities.
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Affiliation(s)
- Jake M Robinson
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia; The Aerobiome Innovation & Research Hub, Flinders University, Bedford Park, SA 5042, Australia.
| | - Riley Hodgson
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Siegfried L Krauss
- Kings Park Science, Department of Biodiversity, Conservation, and Attractions, Fraser Avenue, Kings Park, WA 6005, Australia; Environmental and Conservation Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Craig Liddicoat
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia; School of Public Health, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Ashish A Malik
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Belinda C Martin
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia; Ooid Scientific, North Lake, WA 6162, Australia
| | - Jakki J Mohr
- College of Business, University of Montana, Missoula, MT, USA
| | - David Moreno-Mateos
- School of Geography and the Environment, University of Oxford, South Parks Road. Oxford OX1 3QY, UK; Department of Landscape Architecture, Graduate School of Design, Harvard University, Quincy Street. Cambridge, MA 02138, USA; Basque Center for Climate Change - BC3, Ikerbasque Foundation for Science. Edificio Sede 1, Parque Cientifico UPV, 04940 Leioa, Spain
| | - Miriam Muñoz-Rojas
- Departamento de Biologia Vegetal y Ecologia. Universidad de Sevilla, 41004 Sevilla, Spain; Centre for Ecosystem Science, School of Biological, Earth, and Environmental Sciences, University of New South Wales (UNSW) Sydney, Sydney, NSW 2052, Australia
| | - Shawn D Peddle
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
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Porter R, Černoša A, Fernández-Sanmartín P, Cortizas AM, Aranda E, Luo Y, Zalar P, Podlogar M, Gunde-Cimerman N, Gostinčar C. Degradation of polypropylene by fungi Coniochaeta hoffmannii and Pleurostoma richardsiae. Microbiol Res 2023; 277:127507. [PMID: 37793281 DOI: 10.1016/j.micres.2023.127507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023]
Abstract
The urgent need for better disposal and recycling of plastics has motivated a search for microbes with the ability to degrade synthetic polymers. While microbes capable of metabolizing polyurethane and polyethylene terephthalate have been discovered and even leveraged in enzymatic recycling approaches, microbial degradation of additive-free polypropylene (PP) remains elusive. Here we report the isolation and characterization of two fungal strains with the potential to degrade pure PP. Twenty-seven fungal strains, many isolated from hydrocarbon contaminated sites, were screened for degradation of commercially used textile plastic. Of the candidate strains, two identified as Coniochaeta hoffmannii and Pleurostoma richardsiae were found to colonize the plastic fibers using scanning electron microscopy (SEM). Further experiments probing degradation of pure PP films were performed using C. hoffmannii and P. richardsiae and analyzed using SEM, Raman spectroscopy and Fourier transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR). The results showed that the selected fungi were active against pure PP, with distinct differences in the bonds targeted and the degree to which each was altered. Whole genome and transcriptome sequencing was conducted for both strains and the abundance of carbohydrate active enzymes, GC content, and codon usage bias were analyzed in predicted proteomes for each. Enzymatic assays were conducted to assess each strain's ability to degrade naturally occurring compounds as well as synthetic polymers. These investigations revealed potential adaptations to hydrocarbon-rich environments and provide a foundation for further investigation of PP degrading activity in C. hoffmannii and P. richardsiae.
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Affiliation(s)
- Rachel Porter
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Anja Černoša
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Paola Fernández-Sanmartín
- CRETUS, EcoPast Research Group (GI-1553), Departamento de Edafoloxía e Química Agrícola, Faculty of Biology, Universidade de Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Spain
| | - Antonio Martínez Cortizas
- CRETUS, EcoPast Research Group (GI-1553), Departamento de Edafoloxía e Química Agrícola, Faculty of Biology, Universidade de Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Spain
| | - Elisabet Aranda
- University of Granada, Institute of Water Research, Environmental Microbiology Group, Ramón y Cajal n4, 18071 Granada, Spain
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao 266555, China
| | - Polona Zalar
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Matejka Podlogar
- Department for Nanostructured Materials, Jožef Stefan Institute, Jamova cesta 39, Ljubljana, Slovenia
| | - Nina Gunde-Cimerman
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Cene Gostinčar
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Jamnikarjeva 101, Ljubljana, Slovenia.
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McAtamney A, Heaney C, Lizama-Chamu I, Sanchez LM. Reducing Mass Confusion over the Microbiome. Anal Chem 2023; 95:16775-16785. [PMID: 37934885 PMCID: PMC10841885 DOI: 10.1021/acs.analchem.3c02408] [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] [Indexed: 11/09/2023]
Abstract
As genetic tools continue to emerge and mature, more information is revealed about the identity and diversity of microbial community members. Genetic tools can also be used to make predictions about the chemistry that bacteria and fungi produce to function and communicate with one another and the host. Ongoing efforts to identify these products and link genetic information to microbiome chemistry rely on analytical tools. This tutorial highlights recent advancements in microbiome studies driven by techniques in mass spectrometry.
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Affiliation(s)
- Allyson McAtamney
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Casey Heaney
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Itzel Lizama-Chamu
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
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39
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Pinto R, Ansola G, Calvo L, Sáenz de Miera LE. High resilience of soil bacterial communities to large wildfires with an important stochastic component. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165719. [PMID: 37482359 DOI: 10.1016/j.scitotenv.2023.165719] [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: 04/17/2023] [Revised: 06/30/2023] [Accepted: 07/20/2023] [Indexed: 07/25/2023]
Abstract
Wildfires alter the structure and functioning of ecosystems through changes in their biotic and abiotic components. A deeper understanding recovery process concerning diverse communities and properties within these components can provide valuable insights into the ecological effects of wildfires. Therefore, it is appropriate to enhance our understanding of the resilience of bacterial communities after wildfires within Mediterranean ecosystems. In this research, soil bacterial community resilience was evaluated in three types of ecosystems for two fire severities, two years after a large wildfire in Mediterranean ecosystems. The resilience of the soil bacterial community refers to its ability to return to original state after disturbance. This capacity can be estimated by the study of its recovery over time. In this study we evaluated the resilience using the variables: alpha diversity, beta diversity and the changes in abundance of both OTUs (Operational Taxonomic Units) and principal bacterial taxa (phyla, classes or orders). Our results showed that resilience depends on fire severity and type of ecosystem. We studied three ecosystems with different stage in the secondary succession: low maturity shrublands and heathlands, and high maturity oak forests. In general, high resilience in the soil bacterial community was observed in heathlands under low and high fire severity conditions. The other two ecosystems were resilient only under low fire severity. Stochastic replacement of the abundance of the OTUs was observed in all three ecosystems, with a notable impact on oak forests, under during high-severity conditions.
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Affiliation(s)
- Rayo Pinto
- Departamento de Biodiversidad y Gestión Ambiental, Universidad de León. Campus de Vegazana s/n, CP: 24071 León, Spain.
| | - Gemma Ansola
- Departamento de Biodiversidad y Gestión Ambiental, Universidad de León. Campus de Vegazana s/n, CP: 24071 León, Spain.
| | - Leonor Calvo
- Departamento de Biodiversidad y Gestión Ambiental, Universidad de León. Campus de Vegazana s/n, CP: 24071 León, Spain.
| | - Luis E Sáenz de Miera
- Departamento de Biología Molecular, Universidad de León, Campus de Vegazana s/n, CP: 24071 León, Spain.
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Zhang Q, Wang Y, Guan P, Zhang P, Mo X, Yin G, Qu B, Xu S, He C, Shi Q, Zhang G, Dittmar T, Wang J. Temperature Thresholds of Pyrogenic Dissolved Organic Matter in Heating Experiments Simulating Forest Fires. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:17291-17301. [PMID: 37916767 DOI: 10.1021/acs.est.3c05265] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Heating temperature (HT) during forest fires is a critical factor in regulating the quantity and quality of pyrogenic dissolved organic matter (DOM). However, the temperature thresholds at which maximum amounts of DOM are produced (TTmax) and at which the DOC gain turns into net DOC loss (TT0) remain unidentified on a component-specific basis. Here, based on solid-state 13C nuclear magnetic resonance, absorbance and fluorescence spectroscopies, and Fourier transform ion cyclotron resonance mass spectrometry, we analyzed variations in DOM composition in detritus and soil with HT (150-500 °C) and identified temperature thresholds for components on structural, fluorophoric, and molecular formula levels. TTmax was similar for detritus and soil and ranged between 225 and 250 °C for bulk dissolved organic carbon (DOC) and most DOM components. TT0 was consistently lower in detritus than in soil. Moreover, temperature thresholds differed across the DOM components. As the HT increased, net loss was observed initially in molecular formulas tentatively associated with carbohydrates and aliphatics, then proteins, peptides, and polyphenolics, and ultimately condensed aromatics. Notably, at temperatures lower than TT0, particularly at TTmax, burning increased the DOC quantity and thus might increase labile substrates to fuel soil microbial community. These composition-specific variations of DOM with temperature imply nonlinear and multiple temperature-dependent wildfire impacts on soil organic matter properties.
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Affiliation(s)
- Qiang Zhang
- School of Environment, Harbin Institute of Technology, Harbin 150090, China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg 26129, Germany
| | - Yinghui Wang
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg 26129, Germany
| | - Ping Guan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Peng Zhang
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Xiaohan Mo
- School of Urban Planning and Design, Peking University Shenzhen Graduate School, Peking University, Shenzhen, Guangdong 518055, China
| | - Gege Yin
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Bo Qu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Shujun Xu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Chen He
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China
| | - Quan Shi
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry, Guangdong Province Key Laboratory of Environmental Protection and Resources Utilization, and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Thorsten Dittmar
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg 26129, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), University of Oldenburg, Oldenburg 26129, Germany
| | - Junjian Wang
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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41
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Barbour KM, Weihe C, Walters KE, Martiny JBH. Testing the contribution of dispersal to microbial succession following a wildfire. mSystems 2023; 8:e0057923. [PMID: 37747204 PMCID: PMC10654055 DOI: 10.1128/msystems.00579-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/28/2023] [Indexed: 09/26/2023] Open
Abstract
IMPORTANCE Identifying the mechanisms underlying microbial community succession is necessary for predicting how microbial communities, and their functioning, will respond to future environmental change. Dispersal is one mechanism expected to affect microbial succession, yet the difficult nature of manipulating microorganisms in the environment has limited our understanding of its contribution. Using a dispersal exclusion experiment, this study isolates the specific effect of environmental dispersal on bacterial and fungal community assembly over time following a wildfire. The work demonstrates the potential to quantify dispersal impacts on soil microbial communities over time and test how dispersal might further interact with other assembly processes in response to environmental change.
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Affiliation(s)
- Kristin M. Barbour
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, California, USA
| | - Claudia Weihe
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, California, USA
| | | | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, California, USA
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42
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Johnson DB, Woolet J, Yedinak KM, Whitman T. Experimentally determined traits shape bacterial community composition one and five years following wildfire. Nat Ecol Evol 2023; 7:1419-1431. [PMID: 37524797 PMCID: PMC10482699 DOI: 10.1038/s41559-023-02135-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/26/2023] [Indexed: 08/02/2023]
Abstract
Wildfires represent major ecological disturbances, burning 2-3% of Earth's terrestrial area each year with sometimes drastic effects above- and belowground. Soil bacteria offer an ideal, yet understudied system within which to explore fundamental principles of fire ecology. To understand how wildfires restructure soil bacterial communities and alter their functioning, we sought to translate aboveground fire ecology to belowground systems by determining which microbial traits are important post-fire and whether changes in bacterial communities affect carbon cycling. We employed an uncommon approach to assigning bacterial traits, by first running three laboratory experiments to directly determine which microbes survive fires, grow quickly post-fire and/or thrive in the post-fire environment, while tracking CO2 emissions. We then quantified the abundance of taxa assigned to each trait in a large field dataset of soils one and five years after wildfires in the boreal forest of northern Canada. We found that fast-growing bacteria rapidly dominate post-fire soils but return to pre-burn relative abundances by five years post-fire. Although both fire survival and affinity for the post-fire environment were statistically significant predictors of post-fire community composition, neither are particularly influential. Our results from the incubation trials indicate that soil carbon fluxes post-wildfire are not likely limited by microbial communities, suggesting strong functional resilience. From these findings, we offer a traits-based framework of bacterial responses to wildfire.
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Affiliation(s)
| | - Jamie Woolet
- University of Wisconsin-Madison, Madison, WI, USA
- Colorado State University, Fort Collins, CO, USA
| | - Kara M Yedinak
- Forest Products Laboratory, USDA Forest Service, Madison, WI, USA
| | - Thea Whitman
- University of Wisconsin-Madison, Madison, WI, USA.
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43
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Qi L, Song Y, Zhang P, Sun W, Wang W, Yi S, Li J, Liu H, Bi Z, Du N, Guo W. The combined effect of fire and nitrogen addition on biodiversity and herbaceous aboveground productivity in a coastal shrubland. FRONTIERS IN PLANT SCIENCE 2023; 14:1240591. [PMID: 37705707 PMCID: PMC10497117 DOI: 10.3389/fpls.2023.1240591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 07/25/2023] [Indexed: 09/15/2023]
Abstract
Introduction Fire and nitrogen (N) deposition each impact biodiversity and ecosystem productivity. However, the effect of N deposition on ecosystem recovery after fire is still far from understood, especially in coastal wetlands. Methods We selected a typical coastal shrubland to simulate three N deposition levels (0, 10, and 20 g N m-2 year-1) under two different burned conditions (unburned and burned) in the Yellow River Delta of North China. Soil properties, soil microbial biodiversity, shrub growth parameters, herbaceous biodiversity, and aboveground productivity were determined after experimental treatments for 1 year. Results We found that fire had a stronger influence on the ecosystem than N addition. One year after the fire, shrub growth had significantly decreased, while soil pH, soil electrical conductivity, herbaceous biodiversity, soil microbial biodiversity, and herbaceous aboveground productivity significantly increased. Conversely, a single year of N addition only slightly increased herbaceous aboveground productivity. The combined effect of fire and N addition was only significant for fungus biodiversity and otherwise had minimal influence. Interestingly, we found that herbaceous aboveground productivity was positively associated with fungal community diversity under unburned conditions but not in burned shrublands. Fire showed a great impact on soil parameters and biodiversity in the coastal wetland ecosystem even after a full year of recovery. Discussion Fire may also diminish the influence of several belowground factors on herbaceous aboveground productivity, which ultimately reduces recovery and stability. Appropriate N addition may be an effective way to improve the ecosystem productivity in a wetland dominated by shrub species.
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Affiliation(s)
- Luyu Qi
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, China
| | - Yixin Song
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, China
| | - Puyi Zhang
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, China
| | - Wenlong Sun
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, China
| | - Wei Wang
- Observation and Research Station of Bohai Strait Eco-Corridor, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Shijie Yi
- Observation and Research Station of Bohai Strait Eco-Corridor, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Jing Li
- Shandong Yellow River Delta National Nature Reserve Management Committee, Dongying, China
| | - Haifang Liu
- Shandong Yellow River Delta National Nature Reserve Management Committee, Dongying, China
| | - Zhenggang Bi
- Shandong Yellow River Delta National Nature Reserve Management Committee, Dongying, China
| | - Ning Du
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, China
| | - Weihua Guo
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, China
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44
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Liu QZ, Dong CH. Science and technology breakthroughs to advance artificial cultivation of true morels. Front Microbiol 2023; 14:1259144. [PMID: 37670991 PMCID: PMC10475527 DOI: 10.3389/fmicb.2023.1259144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 08/01/2023] [Indexed: 09/07/2023] Open
Affiliation(s)
| | - Cai Hong Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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45
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Niza Costa M, Gil T, Teixeira R, Rodrígues dos Santos AS, Rebelo Romão I, Sequero López C, Vílchez JI. Combined Use of a Bacterial Consortium and Early-Colonizing Plants as a Treatment for Soil Recovery after Fire: A Model Based on Los Guájares (Granada, Spain) Wildfire. BIOLOGY 2023; 12:1093. [PMID: 37626979 PMCID: PMC10452388 DOI: 10.3390/biology12081093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023]
Abstract
During 2022, intense heat waves, together with particularly extreme dry conditions, created a propitious scenario for wildfires, resulting in the area of vegetation consumed in Europe doubling. Mediterranean countries have been particularly affected, reaching 293,155 hectares in Spain, the worst data in the last 15 years. The effects on the vegetation and the soil are devastating, so knowing the recovery factors is essential for after-fire management. Resilient microorganisms play a fundamental role in rapid nutrient recycling, soil structure, and plant colonization in fire-affected soils. In this present work, we have studied emergent microbial communities in the case of the Los Guájares (Granada, Spain) fire, one of the most extensive of the year, to evaluate their role in the recovery of soil and vegetation cover. We aim to discern which are the main actors in order to formulate a new treatment that helps in the ecosystem recovery. Thus, we have found the relevant loss in phosphorous and potassium solubilizers, as well as siderophores or biofilm producers. Here, we decided to use the strains Pseudomonas koreensis AC, Peribacillus frigoritolerans CB, Pseudomonas fluorescens DC, Paenibacillus lautus C, Bacillus toyonensis CD, and Paenarthrobacter nitroguajacolicus AI as a consortium, as they showed most of the capacities required in a regenerative treatment. On the other hand, the microcosm test showed an enhanced pattern of germination of the emerging model plant, Bituminaria bituminosa, as well as a more aggregated structure for soil. This new approach can create a relevant approach in order to recover fire-affected soils in the future.
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Affiliation(s)
- Marla Niza Costa
- Instituto de Tecnologia Química e Biológica (ITQB)-NOVA, iPlantMicro Lab, 2780-157 Oeiras, Portugal; (M.N.C.); (T.G.); (R.T.); (A.S.R.d.S.); (I.R.R.)
| | - Tatiana Gil
- Instituto de Tecnologia Química e Biológica (ITQB)-NOVA, iPlantMicro Lab, 2780-157 Oeiras, Portugal; (M.N.C.); (T.G.); (R.T.); (A.S.R.d.S.); (I.R.R.)
| | - Raquel Teixeira
- Instituto de Tecnologia Química e Biológica (ITQB)-NOVA, iPlantMicro Lab, 2780-157 Oeiras, Portugal; (M.N.C.); (T.G.); (R.T.); (A.S.R.d.S.); (I.R.R.)
| | - Ana Sofía Rodrígues dos Santos
- Instituto de Tecnologia Química e Biológica (ITQB)-NOVA, iPlantMicro Lab, 2780-157 Oeiras, Portugal; (M.N.C.); (T.G.); (R.T.); (A.S.R.d.S.); (I.R.R.)
| | - Inês Rebelo Romão
- Instituto de Tecnologia Química e Biológica (ITQB)-NOVA, iPlantMicro Lab, 2780-157 Oeiras, Portugal; (M.N.C.); (T.G.); (R.T.); (A.S.R.d.S.); (I.R.R.)
| | - Cristina Sequero López
- GeoBioTec, Department of Earth Sciences, NOVA School of Sciences and Technology, Universidade NOVA de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal;
| | - Juan Ignacio Vílchez
- Instituto de Tecnologia Química e Biológica (ITQB)-NOVA, iPlantMicro Lab, 2780-157 Oeiras, Portugal; (M.N.C.); (T.G.); (R.T.); (A.S.R.d.S.); (I.R.R.)
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46
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Kabeshita L, Sloat LL, Fischer EV, Kampf S, Magzamen S, Schultz C, Wilkins MJ, Kinnebrew E, Mueller ND. Pathways framework identifies wildfire impacts on agriculture. NATURE FOOD 2023; 4:664-672. [PMID: 37550540 DOI: 10.1038/s43016-023-00803-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 06/14/2023] [Indexed: 08/09/2023]
Abstract
Wildfires are a growing concern to society and the environment in many parts of the world. Within the United States, the land area burned by wildfires has steadily increased over the past 40 years. Agricultural land management is widely understood as a force that alters fire regimes, but less is known about how wildfires, in turn, impact the agriculture sector. Based on an extensive literature review, we identify three pathways of impact-direct, downwind and downstream-through which wildfires influence agricultural resources (soil, water, air and photosynthetically active radiation), labour (agricultural workers) and products (crops and livestock). Through our pathways framework, we highlight the complexity of wildfire-agriculture interactions and the need for collaborative, systems-oriented research to better quantify the magnitude of wildfire impacts and inform the adaptation of agricultural systems to an increasingly fire-prone future.
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Affiliation(s)
- Lena Kabeshita
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA.
| | - Lindsey L Sloat
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, CO, USA
- Land and Carbon Lab, World Resources Institute, Washington, DC, USA
| | - Emily V Fischer
- Department of Atmospheric Science, Colorado State University, Fort Collins, CO, USA
| | - Stephanie Kampf
- Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, CO, USA
| | - Sheryl Magzamen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Courtney Schultz
- Department of Forest and Rangeland Stewardship, Colorado State University, Fort Collins, CO, USA
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Eva Kinnebrew
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, CO, USA
| | - Nathaniel D Mueller
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, CO, USA
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Hansen FA, James DK, Anderson JP, Meredith CS, Dominguez AJ, Pombubpa N, Stajich JE, Romero-Olivares AL, Salley SW, Pietrasiak N. Landscape characteristics shape surface soil microbiomes in the Chihuahuan Desert. Front Microbiol 2023; 14:1135800. [PMID: 37350785 PMCID: PMC10282155 DOI: 10.3389/fmicb.2023.1135800] [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: 01/01/2023] [Accepted: 05/02/2023] [Indexed: 06/24/2023] Open
Abstract
Introduction Soil microbial communities, including biological soil crust microbiomes, play key roles in water, carbon and nitrogen cycling, biological weathering, and other nutrient releasing processes of desert ecosystems. However, our knowledge of microbial distribution patterns and ecological drivers is still poor, especially so for the Chihuahuan Desert. Methods This project investigated the effects of trampling disturbance on surface soil microbiomes, explored community composition and structure, and related patterns to abiotic and biotic landscape characteristics within the Chihuahuan Desert biome. Composite soil samples were collected in disturbed and undisturbed areas of 15 long-term ecological research plots in the Jornada Basin, New Mexico. Microbial diversity of cross-domain microbial groups (total Bacteria, Cyanobacteria, Archaea, and Fungi) was obtained via DNA amplicon metabarcode sequencing. Sequence data were related to landscape characteristics including vegetation type, landforms, ecological site and state as well as soil properties including gravel content, soil texture, pH, and electrical conductivity. Results Filamentous Cyanobacteria dominated the photoautotrophic community while Proteobacteria and Actinobacteria dominated among the heterotrophic bacteria. Thaumarchaeota were the most abundant Archaea and drought adapted taxa in Dothideomycetes and Agaricomycetes were most abundant fungi in the soil surface microbiomes. Apart from richness within Archaea (p = 0.0124), disturbed samples did not differ from undisturbed samples with respect to alpha diversity and community composition (p ≥ 0.05), possibly due to a lack of frequent or impactful disturbance. Vegetation type and landform showed differences in richness of Bacteria, Archaea, and Cyanobacteria but not in Fungi. Richness lacked strong relationships with soil variables. Landscape features including parent material, vegetation type, landform type, and ecological sites and states, exhibited stronger influence on relative abundances and microbial community composition than on alpha diversity, especially for Cyanobacteria and Fungi. Soil texture, moisture, pH, electrical conductivity, lichen cover, and perennial plant biomass correlated strongly with microbial community gradients detected in NMDS ordinations. Discussion Our study provides first comprehensive insights into the relationships between landscape characteristics, associated soil properties, and cross-domain soil microbiomes in the Chihuahuan Desert. Our findings will inform land management and restoration efforts and aid in the understanding of processes such as desertification and state transitioning, which represent urgent ecological and economical challenges in drylands around the world.
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Affiliation(s)
- Frederick A. Hansen
- Department of Biology, New Mexico State University, Las Cruces, NM, United States
| | - Darren K. James
- Jornada Experimental Range Department, New Mexico State University, Las Cruces, NM, United States
| | - John P. Anderson
- Jornada Experimental Range Department, New Mexico State University, Las Cruces, NM, United States
| | | | - Andrew J. Dominguez
- Plant and Environmental Sciences Department, New Mexico State University, Las Cruces, NM, United States
| | - Nuttapon Pombubpa
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | | | - Shawn W. Salley
- U.S. Department of Agriculture-Natural Resources Conservation Service, Jornada Experimental Range, Las Cruces, NM, United States
| | - Nicole Pietrasiak
- Plant and Environmental Sciences Department, New Mexico State University, Las Cruces, NM, United States
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
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Qin G, Zhang Q, Zhang Z, Chen Y, Zhu J, Yang Y, Peijnenburg WJGM, Qian H. Understanding the ecological effects of the fungicide difenoconazole on soil and Enchytraeus crypticus gut microbiome. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 326:121518. [PMID: 36990340 DOI: 10.1016/j.envpol.2023.121518] [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: 01/12/2023] [Revised: 03/06/2023] [Accepted: 03/25/2023] [Indexed: 06/19/2023]
Abstract
Increasing knowledge of the impacts of pesticides on soil ecological communities is fundamental to a comprehensive understanding of the functional changes in the global agroecosystem industry. In this study, we examined microbial community shifts in the gut of the soil-dwelling organism Enchytraeus crypticus and functional shifts in the soil microbiome (bacteria and viruses) after 21 d of exposure to difenoconazole, one of the main fungicides in intensified agriculture. Our results demonstrated reduced body weight and increased oxidative stress levels of E. crypticus under difenoconazole treatment. Meanwhile, difenoconazole not only altered the composition and structure of the gut microbial community, but also interfered with the soil-soil fauna microecology stability by impairing the abundance of beneficial bacteria. Using soil metagenomics, we revealed that bacterial genes encoding detoxification and viruses encoding carbon cycle genes exhibited a dependent enrichment in the toxicity of pesticides via metabolism. Taken together, these findings advance the understanding of the ecotoxicological impact of residual difenoconazole on the soil-soil fauna micro-ecology, and the ecological importance of virus-encoded auxiliary metabolic genes under pesticide stress.
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Affiliation(s)
- Guoyan Qin
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Ziyao Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Yiling Chen
- Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, 510006, PR China
| | - Jichao Zhu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Yaohui Yang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, Leiden, RA 2300, Netherlands; National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, P.O. Box 1, Bilthoven, Netherlands
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China.
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Sáenz JS, Rios-Galicia B, Rehkugler B, Seifert J. Dynamic Development of Viral and Bacterial Diversity during Grass Silage Preservation. Viruses 2023; 15:951. [PMID: 37112930 PMCID: PMC10146946 DOI: 10.3390/v15040951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/31/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Ensilaging is one of the most common feed preservation processes using lactic acid bacteria to stabilize feed and save feed quality. The silage bacterial community is well known but the role of the virome and its relationship with the bacterial community is scarce. In the present study, metagenomics and amplicon sequencing were used to describe the composition of the bacterial and viral community during a 40-day grass silage preservation. During the first two days, we observed a rapid decrease in the pH and a shift in the bacterial and viral composition. The diversity of the dominant virus operational taxonomic units (vOTUs) decreased throughout the preservation. The changes in the bacterial community resembled the predicted putative host of the recovered vOTUs during each sampling time. Only 10% of the total recovered vOTUs clustered with a reference genome. Different antiviral defense mechanisms were found across the recovered metagenome-assembled genomes (MAGs); however, only a history of bacteriophage infection with Lentilactobacillus and Levilactobacillus was observed. In addition, vOTUs harbored potential auxiliary metabolic genes related to carbohydrate metabolism, organic nitrogen, stress tolerance, and transport. Our data suggest that vOTUs are enriched during grass silage preservation, and they could have a role in the establishment of the bacterial community.
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Affiliation(s)
- Johan S. Sáenz
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR—Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
| | - Bibiana Rios-Galicia
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR—Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
| | - Bianca Rehkugler
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR—Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
| | - Jana Seifert
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70593 Stuttgart, Germany
- HoLMiR—Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen Weg 3, 70593 Stuttgart, Germany
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Baldrian P, López-Mondéjar R, Kohout P. Forest microbiome and global change. Nat Rev Microbiol 2023:10.1038/s41579-023-00876-4. [PMID: 36941408 DOI: 10.1038/s41579-023-00876-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 03/23/2023]
Abstract
Forests influence climate and mitigate global change through the storage of carbon in soils. In turn, these complex ecosystems face important challenges, including increases in carbon dioxide, warming, drought and fire, pest outbreaks and nitrogen deposition. The response of forests to these changes is largely mediated by microorganisms, especially fungi and bacteria. The effects of global change differ among boreal, temperate and tropical forests. The future of forests depends mostly on the performance and balance of fungal symbiotic guilds, saprotrophic fungi and bacteria, and fungal plant pathogens. Drought severely weakens forest resilience, as it triggers adverse processes such as pathogen outbreaks and fires that impact the microbial and forest performance for carbon storage and nutrient turnover. Nitrogen deposition also substantially affects forest microbial processes, with a pronounced effect in the temperate zone. Considering plant-microorganism interactions would help predict the future of forests and identify management strategies to increase ecosystem stability and alleviate climate change effects. In this Review, we describe the impact of global change on the forest ecosystem and its microbiome across different climatic zones. We propose potential approaches to control the adverse effects of global change on forest stability, and present future research directions to understand the changes ahead.
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Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Soil and Water Conservation and Waste Management, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - Petr Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University, Prague, Czech Republic
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