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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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2
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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 2024:10.1038/s41559-024-02520-7. [PMID: 39294403 DOI: 10.1038/s41559-024-02520-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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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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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] [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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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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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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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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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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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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10
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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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11
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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: 0] [Impact Index Per Article: 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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12
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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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13
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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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14
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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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15
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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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16
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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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17
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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 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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18
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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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19
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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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20
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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: 0] [Impact Index Per Article: 0] [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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21
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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: 1.0] [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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22
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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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23
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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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24
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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: 5] [Impact Index Per Article: 5.0] [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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25
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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: 2] [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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26
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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: 2.0] [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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27
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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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28
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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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29
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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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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: 26] [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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Palmer B, Pietrasiak N, Cobb P, Lipson D. Using simulated wildland fire to assess microbial survival at multiple depths from biocrust and bare soils. Front Microbiol 2023; 14:1123790. [PMID: 37007522 PMCID: PMC10064808 DOI: 10.3389/fmicb.2023.1123790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
IntroductionSurface soil microbial communities are directly exposed to the heat from wildland fires. Due to this, the microbial community composition may be stratified within the soil profile with more heat tolerant microbes near the surface and less heat tolerant microbes, or mobile species found deeper in the soil. Biological soil crusts, biocrusts, are found on the soil surface and contain a diverse microbial community that is directly exposed to the heat from wildland fires.MethodsHere, we used a simulated fire mesocosm along with a culture-based approach and molecular characterization of microbial isolates to understand the stratification of biocrust and bare soil microbes after low severity (450°C) and high severity (600°C) fires. We cultured and sequenced microbial isolates from 2 to 6 cm depth from both fire types.ResultsThe isolates were stratified along the soil depth. Green algal isolates were less thermotolerant and found in the deeper depths (4–6 cm) and the control soils, while several cyanobacteria in Oscillatoriales, Synechococcales, and Nostocales were found at 2–3 cm depth for both fire temperatures. An Alphaproteobacteria isolate was common across several depths, both fire types, and both fire temperatures. Furthermore, we used RNA sequencing at three depths after the high severity fire and one control to determine what microbial community is active following a fire. The community was dominated by Gammaproteobacteria, however some Cyanobacteria ASVs were also present.DiscussionHere we show evidence of stratification of soil and biocrust microbes after a fire and provide evidence that these microbes are able to survive the heat from the fire by living just below the soil surface. This is a steppingstone for future work on the mechanisms of microbial survival after fire and the role of soil insulation in creating resilient communities.
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Affiliation(s)
- Brianne Palmer
- Department of Biology, San Diego State University, San Diego, CA, United States
- Department of Plant Science, University of California, Davis, Davis, CA, United States
- *Correspondence: Brianne Palmer,
| | - Nicole Pietrasiak
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Polina Cobb
- Department of Biology, San Diego State University, San Diego, CA, United States
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, San Diego, CA, United States
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, United States
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Mirzaei J, Heydari M, Omidipour R, Jafarian N, Carcaillet C. Decrease in Soil Functionalities and Herbs' Diversity, but Not That of Arbuscular Mycorrhizal Fungi, Linked to Short Fire Interval in Semi-Arid Oak Forest Ecosystem, West Iran. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12051112. [PMID: 36903972 PMCID: PMC10005139 DOI: 10.3390/plants12051112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 05/19/2023]
Abstract
The semi-arid forest ecosystems of western Iran dominated by Quercus brantii are often disturbed by wildfires. Here, we assessed the effects of short fire intervals on the soil properties and community diversity of herbaceous plants and arbuscular mycorrhizal fungi (AMF), as well as the interactions between these ecosystem features. Plots burned once or twice within 10 years were compared to unburned plots over a long time period (control sites). Soil physical properties were not affected by the short fire interval, except bulk density, which increased. Soil geochemical and biological properties were affected by the fires. Soil organic matter and nitrogen concentrations were depleted by two fires. Short intervals impaired microbial respiration, microbial biomass carbon, substrate-induced respiration, and urease enzyme activity. The successive fires affected the AMF's Shannon diversity. The diversity of the herb community increased after one fire and dropped after two, indicating that the whole community structure was altered. Two fires had greater direct than indirect effects on plant and fungal diversity, as well as soil properties. Short-interval fires depleted soil functional properties and reduced herb diversity. With short-interval fires probably fostered by anthropogenic climate change, the functionalities of this semi-arid oak forest could collapse, necessitating fire mitigation.
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Affiliation(s)
- Javad Mirzaei
- Department of Forest Science, Faculty of Agriculture, Ilam University, Ilam 69315-516, Iran
- Correspondence:
| | - Mehdi Heydari
- Department of Forest Science, Faculty of Agriculture, Ilam University, Ilam 69315-516, Iran
| | - Reza Omidipour
- Department of Rangeland and Watershed Management, Faculties of Natural Resources and Earth Sciences, Shahrekord University, Shahrekord 8818634141, Iran
| | - Nahid Jafarian
- Department of Forest Science, Faculty of Agriculture, Ilam University, Ilam 69315-516, Iran
| | - Christopher Carcaillet
- Ecole Pratique des Hautes Etudes (EPHE), Paris Sciences & Lettres Université (PSL), F-75014 Paris, France
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE (UMR 5023 LEHNA), F-69622 Villeurbanne, France
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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Antoszewski M, Mierek-Adamska A, Dąbrowska GB. The Importance of Microorganisms for Sustainable Agriculture-A Review. Metabolites 2022; 12:1100. [PMID: 36422239 PMCID: PMC9694901 DOI: 10.3390/metabo12111100] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 08/27/2023] Open
Abstract
In the face of climate change, progressive degradation of the environment, including agricultural land negatively affecting plant growth and development, endangers plant productivity. Seeking efficient and sustainable agricultural techniques to replace agricultural chemicals is one of the most important challenges nowadays. The use of plant growth-promoting microorganisms is among the most promising approaches; however, molecular mechanisms underneath plant-microbe interactions are still poorly understood. In this review, we summarized the knowledge on plant-microbe interactions, highlighting the role of microbial and plant proteins and metabolites in the formation of symbiotic relationships. This review covers rhizosphere and phyllosphere microbiomes, the role of root exudates in plant-microorganism interactions, the functioning of the plant's immune system during the plant-microorganism interactions. We also emphasized the possible role of the stringent response and the evolutionarily conserved mechanism during the established interaction between plants and microorganisms. As a case study, we discussed fungi belonging to the genus Trichoderma. Our review aims to summarize the existing knowledge about plant-microorganism interactions and to highlight molecular pathways that need further investigation.
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Affiliation(s)
| | - Agnieszka Mierek-Adamska
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Toruń, Poland
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Roth HK, Nelson AR, McKenna AM, Fegel TS, Young RB, Rhoades CC, Wilkins MJ, Borch T. Impact of beaver ponds on biogeochemistry of organic carbon and nitrogen along a fire-impacted stream. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:1661-1677. [PMID: 36004537 DOI: 10.1039/d2em00184e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Wildfires, which are increasing in frequency and severity in the western U.S., impact water quality through increases in erosion, and transport of nutrients and metals. Meanwhile, beaver populations have been increasing since the early 1900s, and the ponds they create slow or impound hydrologic and elemental fluxes, increase soil saturation, and have a high potential to transform redox active elements (e.g., oxygen, nitrogen, sulfur, and metals). However, it remains unknown how the presence of beaver ponds in burned watersheds may impact retention and transformation of chemical constituents originating in burned uplands (e.g., pyrogenic dissolved organic matter; pyDOM) and the consequences for downstream water quality. Here, we investigate the impact of beaver ponds on the chemical properties and molecular composition of dissolved forms of C and N, and the microbial functional potential encoded within these environments. The chemistry and microbiology of surface water and sediment changed along a stream sequence starting upstream of fire and flowing through multiple beaver ponds and interconnecting stream reaches within a burned high-elevation forest watershed. The relative abundance of N-containing compounds increased in surface water of the burned beaver ponds, which corresponded to lower C/N and O/C, and higher aromaticity as characterized by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The resident microbial communities lack the capacity to process such aromatic pyDOM, though genomic analyses demonstrate their potential to metabolize various compounds in the anaerobic sediments of the beaver ponds. Collectively, this work highlights the role of beaver ponds as biological "hotspots" with unique biogeochemistry in fire-impacted systems.
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Affiliation(s)
- Holly K Roth
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
| | - Amelia R Nelson
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Amy M McKenna
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
- National High Magnetic Field Laboratory, Ion Cyclotron Resonance Facility, Florida State University, FL, USA
| | - Timothy S Fegel
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, CO, USA
| | - Robert B Young
- Chemical Analysis & Instrumentation Laboratory, New Mexico State University, Las Cruces, NM, USA
| | - Charles C Rhoades
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, CO, USA
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Thomas Borch
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
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Soil microbiota takes the heat. Nat Rev Microbiol 2022; 20:638. [PMID: 36138155 DOI: 10.1038/s41579-022-00806-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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