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Nair GR, Kooverjee BB, de Scally S, Cowan DA, Makhalanyane TP. Changes in nutrient availability substantially alter bacteria and extracellular enzymatic activities in Antarctic soils. FEMS Microbiol Ecol 2024; 100:fiae071. [PMID: 38697936 PMCID: PMC11107947 DOI: 10.1093/femsec/fiae071] [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: 09/06/2023] [Revised: 03/07/2024] [Accepted: 05/01/2024] [Indexed: 05/05/2024] Open
Abstract
In polar regions, global warming has accelerated the melting of glacial and buried ice, resulting in meltwater run-off and the mobilization of surface nutrients. Yet, the short-term effects of altered nutrient regimes on the diversity and function of soil microbiota in polyextreme environments such as Antarctica, remains poorly understood. We studied these effects by constructing soil microcosms simulating augmented carbon, nitrogen, and moisture. Addition of nitrogen significantly decreased the diversity of Antarctic soil microbial assemblages, compared with other treatments. Other treatments led to a shift in the relative abundances of these microbial assemblages although the distributional patterns were random. Only nitrogen treatment appeared to lead to distinct community structural patterns, with increases in abundance of Proteobacteria (Gammaproteobateria) and a decrease in Verrucomicrobiota (Chlamydiae and Verrucomicrobiae).The effects of extracellular enzyme activities and soil parameters on changes in microbial taxa were also significant following nitrogen addition. Structural equation modeling revealed that nutrient source and extracellular enzyme activities were positive predictors of microbial diversity. Our study highlights the effect of nitrogen addition on Antarctic soil microorganisms, supporting evidence of microbial resilience to nutrient increases. In contrast with studies suggesting that these communities may be resistant to change, Antarctic soil microbiota responded rapidly to augmented nutrient regimes.
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Affiliation(s)
- Girish R Nair
- Department of Microbiology, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa
- Centre for Epidemic Response and Innovation, School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Bhaveni B Kooverjee
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Storme de Scally
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Thulani P Makhalanyane
- Department of Microbiology, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa
- Centre for Epidemic Response and Innovation, School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
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Thamizharasan A, Rajaguru VRR, Gajalakshmi S, Lim JW, Greff B, Rajagopal R, Chang SW, Ravindran B, Awasthi MK. Investigation on the physico-chemical properties of soil and mineralization of three selected tropical tree leaf litter. ENVIRONMENTAL RESEARCH 2024; 243:117752. [PMID: 38008202 DOI: 10.1016/j.envres.2023.117752] [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: 10/04/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 11/28/2023]
Abstract
Plant leaf litter has a major role in the structure and function of soil ecosystems as it is associated with nutrient release and cycling. The present study is aimed to understand how well the decomposing leaf litter kept soil organic carbon and nitrogen levels stable during an incubation experiment that was carried out in a lab setting under controlled conditions and the results were compared to those from a natural plantation. In natural site soil samples, Anacardium. occidentale showed a higher value of organic carbon at surface (1.14%) and subsurface (0.93%) and Azadirachta. indica exhibited a higher value of total nitrogen at surface (0.28%) and subsurface sample (0.14%). In the incubation experiment, Acacia auriculiformis had the highest organic carbon content initially (5.26%), whereas A. occidentale had the highest nitrogen level on 30th day (0.67%). The overall carbon-nitrogen ratio showed a varied tendency, which may be due to dynamic changes in the complex decomposition cycle. The higher rate of mass loss and decay was observed in A. indica leaf litter, the range of the decay constant is 1.26-2.22. The morphological and chemical changes of soil sample and the vermicast were substantained using scanning electron microscopy (SEM) and Fourier transmission infrared spectroscopy (FT-IR).
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Affiliation(s)
- A Thamizharasan
- Centre for Pollution Control and Environmental Engineering, Pondicherry University, Kalapet, Puducherry, India
| | - V R R Rajaguru
- Centre for Pollution Control and Environmental Engineering, Pondicherry University, Kalapet, Puducherry, India
| | - S Gajalakshmi
- Centre for Pollution Control and Environmental Engineering, Pondicherry University, Kalapet, Puducherry, India.
| | - Jun Wei Lim
- HICoE-Centre for Biofuel and Biochemical Research, Institute of Self-Sustainable Building, Department of Fundamental and Applied Sciences, Universiti Teknologi PETRONAS, 32610, Seri Iskandar, Perak, Darul Ridzuan, Malaysia
| | - Babett Greff
- Department of Food Science, Albert Kázmér Faculty of Mosomagyaróvár, Széchenyi István University, Lucsony street 15-17, 9200 Mosonmagyaróvár, Hungary
| | - Rajinikanth Rajagopal
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, 2000 College Street, Sherbrooke, QC, J1M 1Z3, Canada
| | - Soon Woong Chang
- Department of Environmental Energy and Engineering, Kyonggi University Yeongtong-Gu, Suwon, Gyeonggi-Do, 16227, Republic of Korea
| | - Balasubramani Ravindran
- Department of Medical Biotechnology and Integrative Physiology, Institute of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Thandalam, Chennai, 602105, Tamil Nadu, India; Department of Environmental Energy and Engineering, Kyonggi University Yeongtong-Gu, Suwon, Gyeonggi-Do, 16227, Republic of Korea.
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
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Scheel M, Zervas A, Rijkers R, Tveit AT, Ekelund F, Campuzano Jiménez F, Christensen TR, Jacobsen CS. Abrupt permafrost thaw triggers activity of copiotrophs and microbiome predators. FEMS Microbiol Ecol 2023; 99:fiad123. [PMID: 37796894 PMCID: PMC10599396 DOI: 10.1093/femsec/fiad123] [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: 03/01/2023] [Revised: 08/31/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023] Open
Abstract
Permafrost soils store a substantial part of the global soil carbon and nitrogen. However, global warming causes abrupt erosion and gradual thaw, which make these stocks vulnerable to microbial decomposition into greenhouse gases. Here, we investigated the microbial response to abrupt in situ permafrost thaw. We sequenced the total RNA of a 1 m deep soil core consisting of up to 26 500-year-old permafrost material from an active abrupt erosion site. We analysed the microbial community in the active layer soil, the recently thawed, and the intact permafrost, and found maximum RNA:DNA ratios in recently thawed permafrost indicating a high microbial activity. In thawed permafrost, potentially copiotrophic Burkholderiales and Sphingobacteriales, but also microbiome predators dominated the community. Overall, both thaw-dependent and long-term soil properties significantly correlated with changes in community composition, as did microbiome predator abundance. Bacterial predators were dominated in shallower depths by Myxococcota, while protozoa, especially Cercozoa and Ciliophora, almost tripled in relative abundance in thawed layers. Our findings highlight the ecological importance of a diverse interkingdom and active microbial community highly abundant in abruptly thawing permafrost, as well as predation as potential biological control mechanism.
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Affiliation(s)
- Maria Scheel
- Department of Environmental Science, Aarhus University, Roskilde 4000, Denmark
- Department of Ecoscience, Aarhus University, Roskilde 4000, Denmark
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Roskilde 4000, Denmark
| | - Ruud Rijkers
- Department of Ecological Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Department of Environmental Science, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, University of Tromsø, Tromsø 9019, Norway
| | - Flemming Ekelund
- Department of Environmental Science, Aarhus University, Roskilde 4000, Denmark
- Department of Biology, Copenhagen University, DK-2200 Copenhagen, Denmark
| | | | - Torben R Christensen
- Department of Ecoscience, Aarhus University, Roskilde 4000, Denmark
- Water, Energy and Environmental Engineering Research Unit, University of Oulu, FI-90014 Oulu, Finland
| | - Carsten S Jacobsen
- Department of Environmental Science, Aarhus University, Roskilde 4000, Denmark
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Win TT, Song KG. Metagenomics and proteomics profiling of extracellular polymeric substances from municipal waste sludge and their application for soil and water bioremediation. CHEMOSPHERE 2023; 339:139767. [PMID: 37562501 DOI: 10.1016/j.chemosphere.2023.139767] [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: 06/01/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
This study assessed the components of anaerobically digested sludge, activated sludge, and microbial and extracellular polymeric substance (EPS) enzymes to identify the mechanisms underlying nitrogen removal and soil regeneration. 16S rRNA gene amplicon-based sequencing was used to determine the microbial community composition and the related National Center for Biotechnology Information (NCBI) protein database was used to construct a conventional library from the observed community. EPS components were identified using gel-free proteomic (Liquid Chromatography with tandem mass spectrometry-LC/MS/MS) methods. Alginate-like EPS from aerobically activated sludge have strong potential for soil aggregation and water-holding capacity, whereas total EPS from anaerobic sludge have significant potential for ammonia removal under salt stress. Fourier transform infrared spectroscopy (FTIR) revealed that both EPS may contain proteins, carbohydrates, humic compounds, uronic acid, and DNA and determined the presence of O-H, N-H, C-N, CO, and C-H functional groups. These results demonstrate that the overall enzyme activity may be inactivated at 30 g L-1 of salinity. An annotation found in Kyoto Encyclopedia of Genes and Genomes (KEGG)- KEGG Automatic Annotation Server (KAAS) revealed that the top two metabolic activities in the EPS generated from the anaerobic sludge were methane and nitrogen metabolism. Therefore, we focused on the nitrogen metabolism reference map 00910. EPS from the anaerobically digested sludge exhibited nitrate reductase, nitrite reductase, and dehydrogenase activities. Assimilatory nitrate reduction, denitrification, nitrification, and anammox removed ammonia biochemically. The influence of microbial extracellular metabolites on water-holding capacity and soil aggregation was also investigated. The KAAS-KEGG annotation server was used to identify the main enzymes in the activated sludge-derived alginate-like extracellular EPS (ALE-EPS) samples. These include hydrolases, oxidoreductases, lyases, ligases, and transporters, which contribute to soil fertility and stability. This study improves our understanding of the overall microbial community structure and the associated biochemical processes, which are related to distinct functional genes or enzymes involved in nitrogen removal and soil aggregation. In contrast to conventional methods, microbial association with proteomics can be used to investigate ecological relationships, establishments, key player species, and microbial responses to environmental changes. Linking the metagenome to off-gel proteomics and bioinformatics solves the problem of analyzing metabolic pathways in complex environmental samples in a cost-effective manner.
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Affiliation(s)
- Theint Theint Win
- Center for Water Cycle Research, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea; Cental Biotechnology Research Department, Yangon Technological University, Insein, 11101, Yangon, Myanmar
| | - Kyung Guen Song
- Center for Water Cycle Research, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea; Division of Energy and Environment Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Republic of Korea.
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5
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Zhang SH, Wang Y, Hu JJ, Chen WJ, Wu JL, Seah RWX, Zhu YC, Guo ZP, Chen J. Bamboo charcoal affects soil properties and bacterial community in tea plantations. Open Life Sci 2023; 18:20220681. [PMID: 37589012 PMCID: PMC10426720 DOI: 10.1515/biol-2022-0681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/16/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023] Open
Abstract
Bamboo charcoal, a type of manufactured biochar, is produced by pyrolyzing bamboo residue under anoxic conditions. Its beneficial properties in absorption, catalyst support, and agricultural function have attracted significant attention; however, relatively few studies have examined its effects on the soil microbiota. In this study, we analyzed the effects of bamboo charcoal on soil physicochemical properties, enzymes, and microbial community structure in tea plantations and investigated the optimal amount of bamboo charcoal to be added to organic fertilizer. The results show that bamboo charcoal can further increase soil available nitrogen, total and available phosphorus and potassium, organic carbon content, pH, and urease activity. However, only the combined use of bamboo charcoal and organic fertilizer significantly increased total nitrogen, sucrase, and β-glucosidase activities in the soil. Bamboo charcoal also significantly increased the Chao1 and Shannon indices of microbiota diversity in a concentration-dependent manner. The structure of the bacterial community changed significantly after the bamboo charcoal addition, with Proteobacteria, Actinobacteria, and Firmicutes increasing and Acidobacteria decreasing. This study provides fundamental insights into the suitability of bamboo charcoal application for the ecological remediation of diseased soils.
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Affiliation(s)
- Si-Hai Zhang
- College of Liangshan, Lishui University, Lishui323000, China
| | - Yue Wang
- College of Horticulture Science, Zhejiang A&F University, Hangzhou311300, China
| | - Jin-Jie Hu
- College of Ecology, Lishui University, No. 1 Xueyuan Road, Lishui323000, China
| | - Wei-Jia Chen
- College of Ecology, Lishui University, No. 1 Xueyuan Road, Lishui323000, China
| | - Jia-Le Wu
- College of Ecology, Lishui University, No. 1 Xueyuan Road, Lishui323000, China
| | - Rachel Wan Xin Seah
- Department of Biological Science, National University of Singapore, Singapore117558, Singapore
| | - Yang-Chun Zhu
- College of Ecology, Lishui University, No. 1 Xueyuan Road, Lishui323000, China
| | - Zhi-Ping Guo
- College of Ecology, Lishui University, No. 1 Xueyuan Road, Lishui323000, China
| | - Jie Chen
- College of Ecology, Lishui University, No. 1 Xueyuan Road, Lishui323000, China
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6
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Dias Samarajeewa A, Velicogna JR, Schwertfeger DM, Meier MJ, Subasinghe RM, Princz JI, Scroggins RP, Beaudette LA. Cerium oxide nanoparticles (nCeO 2) exert minimal adverse effects on microbial communities in soils with and without biosolids amendment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-27313-6. [PMID: 37166732 DOI: 10.1007/s11356-023-27313-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/25/2023] [Indexed: 05/12/2023]
Abstract
Increased use of nano-cerium oxide (nCeO2) in an array of industrial applications has raised environmental concerns due to potential increased loadings to the soil environment. This research investigated the potential adverse effects of nCeO2 (10-30 nm) on the soil microbial community in two exposure scenarios: direct application to soil, and indirect application to soil through chemical spiking of biosolids, followed by mixing into soil. Total Ce in test soils without, and with biosolids amendment, ranged from 44 to 770, and 73 to 664 mg Ce kg-1 soil, respectively. In order to help distinguish whether observed effects were elicited by the solid-phase colloids or the activity of dissolved Ce, a soluble Ce salt (Ce (NO3)3) treatment was included in select assays. A suite of tests was used to investigate effects on critical processes: microbial growth (heterotrophic plate count), microbial activity (organic matter (OM) decomposition, enzyme activity and, nitrification) and diversity (structural and functional). Although results showed significant inhibition on microbial growth in soil without biosolids amendment at ≥ 156 mg Ce kg-1 soil by week 5, these results were inconsistent and non-significant thereafter. In general, nCeO2 showed no evidence of consistent adverse effects on OM decomposition, nitrification, soil enzyme activities and functional diversity. Leucine aminopeptidase showed significant (p< 0.05) stimulatory effects over time at ≥ 44 mg Ce kg-1 in soils without biosolids, which was not observed in soils with biosolids amendment. The lack of inhibitory effects of nCeO2 may be attributed to its low solubility; Ce in soil extracts (0.01 M CaCl2) were all below detection (< 0.003 mg kg-1) in the nCeO2-spiked soils, but detectable in the Ce (NO3)3 samples. In contrast, soluble Ce at 359 mg Ce kg-1 showed a significant reduction in OM decomposition and effects on microbial genomic diversity based on the 16S rDNA data in soils with and without biosolids amendment (359 and 690 mg Ce kg-1). The nCeO2 behaviour and effects information described herein are expected to help fulfill data gaps for the characterization of this priority nanomaterial.
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Affiliation(s)
- Ajith Dias Samarajeewa
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada.
| | - Jessica R Velicogna
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada
| | - Dina M Schwertfeger
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada
| | - Matthew J Meier
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada
| | - Renuka M Subasinghe
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada
| | - Juliska I Princz
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada
| | - Rick P Scroggins
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada
| | - Lee A Beaudette
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada
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Chen X, Dai Y, Zhao M, Löffler FE, Zhuang J. Hydrobiological Mechanism Controlling the Synergistic Effects of Unsaturated Flow and Soil Organic Matter on the Degradation of Emerging Organic Contaminants in Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11409-11417. [PMID: 35905382 DOI: 10.1021/acs.est.2c03013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Hydrology is a key factor influencing microbial degradation of emerging organic contaminants (EOCs) in soils, but the underlying mechanisms are not clear. In this study, biotic and abiotic column experiments were performed to investigate the removal and degradation of five EOCs in soils with different soil organic matter (SOM) contents under saturated and unsaturated flow conditions. In biotic experiments, 54-90% of bisphenol A (BPA) and 9-22% of ibuprofen (IBU) were removed from the aqueous phase of saturated columns due to adsorption and biodegradation. The biodegradation removed 26-65% of BPA and 1-22% of IBU. Decreasing soil pore water saturation from 100 to 80% increased BPA removal to 97-100% and IBU removal to 42-43% due to increased biodegradation (67-81% for BPA and 36-39% for IBU). No significant removal of BPA and IBU was observed in SOM-removed soils under saturated and unsaturated flow conditions. The desaturation did not influence sorptive losses of BPA (<27%) and IBU (<7%), suggesting their negligible adsorption at air-water interfaces but increased biodegradation of BPA and IBU sorbed at SOM-water interfaces. The study shows that soil drying and SOM can synergistically degrade BPA and IBU but have no effect on recalcitrant carbamazepine, tetracycline, and ciprofloxacin.
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Affiliation(s)
- Xijuan Chen
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Yuanyuan Dai
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
| | - Mingyang Zhao
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, Liaoning 110016, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Frank E Löffler
- Department of Microbiology, Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biosystems Engineering and Soil Science, Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jie Zhuang
- Department of Biosystems Engineering and Soil Science, Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Tennessee 37996, United States
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Yun J, Jung JY, Kwon MJ, Seo J, Nam S, Lee YK, Kang H. Temporal Variations Rather than Long-Term Warming Control Extracellular Enzyme Activities and Microbial Community Structures in the High Arctic Soil. MICROBIAL ECOLOGY 2022; 84:168-181. [PMID: 34498119 DOI: 10.1007/s00248-021-01859-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
In Arctic soils, warming accelerates decomposition of organic matter and increases emission of greenhouse gases (GHGs), contributing to a positive feedback to climate change. Although microorganisms play a key role in the processes between decomposition of organic matter and GHGs emission, the effects of warming on temporal responses of microbial activity are still elusive. In this study, treatments of warming and precipitation were conducted from 2012 to 2018 in Cambridge Bay, Canada. Soils of organic and mineral layers were collected monthly from June to September in 2018 and analyzed for extracellular enzyme activities and bacterial community structures. The activity of hydrolases was the highest in June and decreased thereafter over summer in both organic and mineral layers. Bacterial community structures changed gradually over summer, and the responses were distinct depending on soil layers and environmental factors; water content and soil temperature affected the shift of bacterial community structures in both layers, whereas bacterial abundance, dissolved organic carbon, and inorganic nitrogen did so in the organic layer only. The activity of hydrolases and bacterial community structures did not differ significantly among treatments but among months. Our results demonstrate that temporal variations may control extracellular enzyme activities and microbial community structure rather than the small effect of warming over a long period in high Arctic soil. Although the effects of the treatments on microbial activity were minor, our study provides insight that microbial activity may increase due to an increase in carbon availability, if the growing season is prolonged in the Arctic.
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Affiliation(s)
- Jeongeun Yun
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, Korea
| | - Ji Young Jung
- Korea Polar Research Institute, Incheon, 21990, Korea
| | - Min Jung Kwon
- Laboratoire Des Sciences du Climat Et de I'Environnement, LSCE, 91191, Gif sur Yvette, France
| | - Juyoung Seo
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, Korea
| | - Sungjin Nam
- Korea Polar Research Institute, Incheon, 21990, Korea
| | - Yoo Kyung Lee
- Korea Polar Research Institute, Incheon, 21990, Korea
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, Korea.
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Hu J, Zhou Q, Cao Q, Hu J. Effects of ecological restoration measures on vegetation and soil properties in semi-humid sandy land on the southeast Qinghai-Tibetan Plateau, China. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02000] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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10
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Yang J, Duan Y, Guo Y, Li Z, Ni X, Zhang J, Awasthi MK, Li H. Grass waste utilization to alter aggregate-related carbon chemical composition and fungal community structure in apple orchard. CHEMOSPHERE 2022; 287:132404. [PMID: 34597634 DOI: 10.1016/j.chemosphere.2021.132404] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/30/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
The grass-waste management model affects soil organic carbon (SOC) and the microorganism community structure; however, studies on the relationship between the fungal community structure and the SOC chemical component at the aggregate level are poor. Solid-state 13C NMR and 18 S rDNA methods were used to evaluate the relationship between the SOC chemical composition and fungal community abundance at the aggregate level. Grass mulching significantly increased the percentage of labile carbon O-alkyl C (5.19%-11.79%) and decreased the instability of SOC (1.38-0.69). Microaggregates contained higher alkyl C (33.77%) and lower aromatic C (18.31%), and the A/O-A ratio (1.03) was higher than that of macroaggregates (0.89-0.96). Ascomycota, Basidiomycota and Mortierellomycota dominated the fungal community at the phylum level, and their abundance increased after grass mulching. Microaggregates supported more microbial diversity and richness and were rich in the Ascomycota (36.69%-67.49%) phylum, while LM aggregates were rich in Basidiomycota (5.62%-39.84%). We proved that changes in the O-alkyl C, carbonyl C, aromatic C and alkyl C of SOC chemical components were closely connected to fungal community composition, which together explained the change in fungal composition by 63.81%-71.99% among aggregates. We concluded that alterations in the chemical form of organic carbon were closely related to a change in the soil fungal community. This connection has a positive impact on soil nutrient utilization and SOC conversion in fruit-grass composite ecosystems and promotes the understanding of the relationship between the soil microbial community and nutrient cycling during long-term grass waste utilization.
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Affiliation(s)
- Jianfeng Yang
- College of Natural Resources and Environment, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi, 712100, China; Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, China
| | - Yumin Duan
- College of Natural Resources and Environment, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi, 712100, China; Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, China
| | - Yaru Guo
- College of Natural Resources and Environment, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi, 712100, China; Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, China
| | - Zelin Li
- College of Natural Resources and Environment, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi, 712100, China; Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, China
| | - Xinhua Ni
- College of Natural Resources and Environment, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi, 712100, China; Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, China
| | - Jiatao Zhang
- College of Natural Resources and Environment, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi, 712100, China; Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi, 712100, China; Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, China.
| | - Huike Li
- College of Natural Resources and Environment, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi, 712100, China; Key Laboratory of Plant Nutrition and the Agro-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, China.
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Alves RJE, Callejas IA, Marschmann GL, Mooshammer M, Singh HW, Whitney B, Torn MS, Brodie EL. Kinetic Properties of Microbial Exoenzymes Vary With Soil Depth but Have Similar Temperature Sensitivities Through the Soil Profile. Front Microbiol 2021; 12:735282. [PMID: 34917043 PMCID: PMC8669745 DOI: 10.3389/fmicb.2021.735282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
Current knowledge of the mechanisms driving soil organic matter (SOM) turnover and responses to warming is mainly limited to surface soils, although over 50% of global soil carbon is contained in subsoils. Deep soils have different physicochemical properties, nutrient inputs, and microbiomes, which may harbor distinct functional traits and lead to different SOM dynamics and temperature responses. We hypothesized that kinetic and thermal properties of soil exoenzymes, which mediate SOM depolymerization, vary with soil depth, reflecting microbial adaptation to distinct substrate and temperature regimes. We determined the Michaelis-Menten (MM) kinetics of three ubiquitous enzymes involved in carbon (C), nitrogen (N) and phosphorus (P) acquisition at six soil depths down to 90 cm at a temperate forest, and their temperature sensitivity based on Arrhenius/Q10 and Macromolecular Rate Theory (MMRT) models over six temperatures between 4–50°C. Maximal enzyme velocity (Vmax) decreased strongly with depth for all enzymes, both on a dry soil mass and a microbial biomass C basis, whereas their affinities increased, indicating adaptation to lower substrate availability. Surprisingly, microbial biomass-specific catalytic efficiencies also decreased with depth, except for the P-acquiring enzyme, indicating distinct nutrient demands at depth relative to microbial abundance. These results suggested that deep soil microbiomes encode enzymes with intrinsically lower turnover and/or produce less enzymes per cell, reflecting distinct life strategies. The relative kinetics between different enzymes also varied with depth, suggesting an increase in relative P demand with depth, or that phosphatases may be involved in C acquisition. Vmax and catalytic efficiency increased consistently with temperature for all enzymes, leading to overall higher SOM-decomposition potential, but enzyme temperature sensitivity was similar at all depths and between enzymes, based on both Arrhenius/Q10 and MMRT models. In a few cases, however, temperature affected differently the kinetic properties of distinct enzymes at discrete depths, suggesting that it may alter the relative depolymerization of different compounds. We show that soil exoenzyme kinetics may reflect intrinsic traits of microbiomes adapted to distinct soil depths, although their temperature sensitivity is remarkably uniform. These results improve our understanding of critical mechanisms underlying SOM dynamics and responses to changing temperatures through the soil profile.
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Affiliation(s)
- Ricardo J Eloy Alves
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ileana A Callejas
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Civil and Environmental Engineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - Gianna L Marschmann
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Maria Mooshammer
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
| | - Hans W Singh
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Bizuayehu Whitney
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Margaret S Torn
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Energy and Resources Group, University of California, Berkeley, Berkeley, CA, United States
| | - Eoin L Brodie
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
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12
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Esiana BOI, Coates CJ, Adderley WP, Berns AE, Bol R. Phenoloxidase activity and organic carbon dynamics in historic Anthrosols in Scotland, UK. PLoS One 2021; 16:e0259205. [PMID: 34705877 PMCID: PMC8550383 DOI: 10.1371/journal.pone.0259205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/14/2021] [Indexed: 11/19/2022] Open
Abstract
Phenolic compounds are chemical precursor building blocks of soil organic matter. Their occurrence can be inhibitory to certain enzymes present in soil, thereby influencing the rate of decomposition of soil organic matter. Microbe-derived phenoloxidases (laccases) are extracellular enzymes capable of degrading recalcitrant polyphenolic compounds. In this study, our aim was to investigate the relationships between phenoloxidase enzyme activity, organic carbon content and microbial abundance in the context of long-term anthropogenically amended soils. To achieve this, we used a series of complementary biochemical analytical methods including gas chromatography, enzyme assays and solid-state Carbon-13 Cross Polarisation Magic-Angle Spinning Nuclear Magnetic Resonance Spectroscopy (13C CPMAS NMR). Using several anthrosols found in St Andrews (Scotland, UK) that had been subjected to intense anthropogenic modification since the medieval period (11th century AD) to present-day, we were able to scope the impact of past waste disposal on soils. The long-term anthropogenic impact led to organic matter-rich soils. Overall, phenoloxidase activity increased by up to 2-fold with soil depth (up to 100 cm) and was inversely correlated with microbial biomass. Solid-state 13C NMR characterisation of carbon species revealed that the observed decline in soil organic matter with depth corresponded to decreases in the labile organic carbon fractions as evidenced by changes in the O/N-alkyl C region of the spectra. The increase in phenoloxidase activity with depth would appear to be a compensatory mechanism for the reduced quantities of organic carbon and lower overall nutrient environment in subsoils. By enzymatically targeting phenolic compounds, microbes can better utilise recalcitrant carbon when other labile soil carbon sources become limited, thereby maintaining metabolic processes.
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Affiliation(s)
- Benneth O. I. Esiana
- Faculty of Natural Sciences, Biological and Environmental Sciences, University of Stirling, Stirling, Scotland, United Kingdom
- Graduate School – Research, Aomori Public University, Aomori, Japan
- * E-mail: (BOIE); (CJC)
| | - Christopher J. Coates
- Faculty of Natural Sciences, Biological and Environmental Sciences, University of Stirling, Stirling, Scotland, United Kingdom
- Faculty of Science and Engineering, Department of Biosciences, Swansea University, Swansea, Wales, United Kingdom
- * E-mail: (BOIE); (CJC)
| | - W. Paul Adderley
- Faculty of Natural Sciences, Biological and Environmental Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Anne E. Berns
- Institute of Bio- and Geosciences (IBG-3 Agrosphere), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Roland Bol
- Institute of Bio- and Geosciences (IBG-3 Agrosphere), Forschungszentrum Jülich GmbH, Jülich, Germany
- School of Natural Sciences, Environment Centre Wales, Bangor University, Bangor, Wales, United Kingdom
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13
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Fungi in Permafrost-Affected Soils of the Canadian Arctic: Horizon- and Site-Specific Keystone Taxa Revealed by Co-Occurrence Network. Microorganisms 2021; 9:microorganisms9091943. [PMID: 34576837 PMCID: PMC8466989 DOI: 10.3390/microorganisms9091943] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 01/16/2023] Open
Abstract
Permafrost-affected soil stores a significant amount of organic carbon. Identifying the biological constraints of soil organic matter transformation, e.g., the interaction of major soil microbial soil organic matter decomposers, is crucial for predicting carbon vulnerability in permafrost-affected soil. Fungi are important players in the decomposition of soil organic matter and often interact in various mutualistic relationships during this process. We investigated four different soil horizon types (including specific horizons of cryoturbated soil organic matter (cryoOM)) across different types of permafrost-affected soil in the Western Canadian Arctic, determined the composition of fungal communities by sequencing (Illumina MPS) the fungal internal transcribed spacer region, assigned fungal lifestyles, and by determining the co-occurrence of fungal network properties, identified the topological role of keystone fungal taxa. Compositional analysis revealed a significantly higher relative proportion of the litter saprotroph Lachnum and root-associated saprotroph Phialocephala in the topsoil and the ectomycorrhizal close-contact exploring Russula in cryoOM, whereas Sites 1 and 2 had a significantly higher mean proportion of plant pathogens and lichenized trophic modes. Co-occurrence network analysis revealed the lowest modularity and average path length, and highest clustering coefficient in cryoOM, which suggested a lower network resistance to environmental perturbation. Zi-Pi plot analysis suggested that some keystone taxa changed their role from generalist to specialist, depending on the specific horizon concerned, Cladophialophora in topsoil, saprotrophic Mortierella in cryoOM, and Penicillium in subsoil were classified as generalists for the respective horizons but specialists elsewhere. The litter saprotrophic taxon Cadophora finlandica played a role as a generalist in Site 1 and specialist in the rest of the sites. Overall, these results suggested that fungal communities within cryoOM were more susceptible to environmental change and some taxa may shift their role, which may lead to changes in carbon storage in permafrost-affected soil.
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14
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Bacterial Number and Genetic Diversity in a Permafrost Peatland (Western Siberia): Testing a Link with Organic Matter Quality and Elementary Composition of a Peat Soil Profile. DIVERSITY 2021. [DOI: 10.3390/d13070328] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Permafrost peatlands, containing a sizable amount of soil organic carbon (OC), play a pivotal role in soil (peat) OC transformation into soluble and volatile forms and greatly contribute to overall natural CO2 and CH4 emissions to the atmosphere under ongoing permafrost thaw and soil OC degradation. Peat microorganisms are largely responsible for the processing of this OC, yet coupled studies of chemical and bacterial parameters in permafrost peatlands are rather limited and geographically biased. Towards testing the possible impact of peat and peat pore water chemical composition on microbial population and diversity, here we present results of a preliminary study of the western Siberia permafrost peatland discontinuous permafrost zone. The quantitative evaluation of microorganisms and determination of microbial diversity along a 100 cm thick peat soil column, which included thawed and frozen peat and bottom mineral horizon, was performed by RT-PCR and 16S rRNA gene-based metagenomic analysis, respectively. Bacteria (mainly Proteobacteria, Acidobacteria, Actinobacteria) strongly dominated the microbial diversity (99% sequences), with a negligible proportion of archaea (0.3–0.5%). There was a systematic evolution of main taxa according to depth, with a maximum of 65% (Acidobacteria) encountered in the active layer, or permafrost boundary (50–60 cm). We also measured C, N, nutrients and ~50 major and trace elements in peat (19 samples) as well as its pore water and dispersed ice (10 samples), sampled over the same core, and we analyzed organic matter quality in six organic and one mineral horizon of this core. Using multiparametric statistics (PCA), we tested the links between the total microbial number and 16S rRNA diversity and chemical composition of both the solid and fluid phase harboring the microorganisms. Under climate warming and permafrost thaw, one can expect a downward movement of the layer of maximal genetic diversity following the active layer thickening. Given a one to two orders of magnitude higher microbial number in the upper (thawed) layers compared to bottom (frozen) layers, an additional 50 cm of peat thawing in western Siberia may sizably increase the total microbial population and biodiversity of active cells.
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15
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Varsadiya M, Urich T, Hugelius G, Bárta J. Microbiome structure and functional potential in permafrost soils of the Western Canadian Arctic. FEMS Microbiol Ecol 2021; 97:6102547. [PMID: 33452882 DOI: 10.1093/femsec/fiab008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/13/2021] [Indexed: 01/12/2023] Open
Abstract
Substantial amounts of topsoil organic matter (OM) in Arctic Cryosols have been translocated by the process of cryoturbation into deeper soil horizons (cryoOM), reducing its decomposition. Recent Arctic warming deepens the Cryosols´ active layer, making more topsoil and cryoOM carbon accessible for microbial transformation. To quantify bacteria, archaea and selected microbial groups (methanogens - mcrA gene and diazotrophs - nifH gene) and to investigate bacterial and archaeal diversity, we collected 83 soil samples from four different soil horizons of three distinct tundra types located in Qikiqtaruk (Hershel Island, Western Canada). In general, the abundance of bacteria and diazotrophs decreased from topsoil to permafrost, but not for cryoOM. No such difference was observed for archaea and methanogens. CryoOM was enriched with oligotrophic (slow-growing microorganism) taxa capable of recalcitrant OM degradation. We found distinct microbial patterns in each tundra type: topsoil from wet-polygonal tundra had the lowest abundance of bacteria and diazotrophs, but the highest abundance of methanogens. Wet-polygonal tundra, therefore, represented a hotspot for methanogenesis. Oligotrophic and copiotrophic (fast-growing microorganism) genera of methanogens and diazotrophs were distinctly distributed in topsoil and cryoOM, resulting in different rates of nitrogen flux into these horizons affecting OM vulnerability and potential CO2 and CH4 release.
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Affiliation(s)
- Milan Varsadiya
- Department of Ecosystems Biology, University of South Bohemia in České Budějovice, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8 17487 Greifswald, Germany
| | - Gustaf Hugelius
- Department of Physical Geography, Stockholm University, 106 91, Stockholm, Sweden
| | - Jiří Bárta
- Department of Ecosystems Biology, University of South Bohemia in České Budějovice, Branišovská 31, 370 05 České Budějovice, Czech Republic
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16
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Wei JM, Cui LJ, Li W, Ping YM, Li W. Denitrifying bacterial communities in surface-flow constructed wetlands during different seasons: characteristics and relationships with environment factors. Sci Rep 2021; 11:4918. [PMID: 33649362 PMCID: PMC7921683 DOI: 10.1038/s41598-021-82438-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/11/2021] [Indexed: 11/20/2022] Open
Abstract
Denitrification is an important part of the nitrogen cycle and the key step to removal of nitrogen in surface-flow wetlands. In this study, we explored space–time analysis with high-throughput sequencing to elucidate the relationships between denitrifying bacteria community structures and environmental factors during different seasons. Our results showed that along the flow direction of different processing units, there were dynamic changes in physical and chemical indicators. The bacterial abundance indexes (ACEs) in May, August, and October were 686.8, 686.8, and 996.2, respectively, whereas the Shannon-Weiner indexes were 3.718, 4.303, and 4.432, respectively. Along the flow direction, the denitrifying bacterial abundance initially increased and then decreased subsequently during the same months, although diversity tended to increase. The abundance showed similar changes during the different months. Surface flow wetlands mainly contained the following denitrifying bacteria genus: unclassified Bacteria (37.12%), unclassified Proteobacteria (18.16%), Dechloromonas (16.21%), unranked environmental samples (12.51%), unclassified Betaproteobacteria (9.73%), unclassified Rhodocyclaceae (2.14%), and Rhodanobacter (1.51%). During different seasons, the same unit showed alternating changes, and during the same season, bacterial community structures were influenced by the second genus proportion in different processing units. ACEs were strongly correlated with temperature, dissolved oxygen, and pH. Bacterial diversity was strongly correlated with temperature, electrical conductivity, pH, and oxidation reduction potential. Denitrifying bacteria are greatly affected by environmental factors such as temperature and pH.
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Affiliation(s)
- Jia-Ming Wei
- Beijing Construction Engineering Group Environmental Remediation Co. Ltd, Beijing, 100051, China.,National Engineering Laboratory for Site Remediation Technologies, Beijing, 100872, China
| | - Li-Juan Cui
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China. .,The Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing, 100091, China. .,Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing, 101399, China.
| | - Wei Li
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China.,The Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing, 100091, China.,Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing, 101399, China
| | - Yun-Mei Ping
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China.,The Beijing Key Laboratory of Wetland Ecological Function and Restoration, Beijing, 100091, China.,Beijing Hanshiqiao National Wetland Ecosystem Research Station, Beijing, 101399, China
| | - Wan Li
- Beijing Construction Engineering Group Environmental Remediation Co. Ltd, Beijing, 100051, China.,National Engineering Laboratory for Site Remediation Technologies, Beijing, 100872, China
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17
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Gupta P, Vakhlu J, Sharma YP, Imchen M, Kumavath R. Metagenomic insights into the fungal assemblages of the northwest Himalayan cold desert. Extremophiles 2020; 24:749-758. [PMID: 32705341 DOI: 10.1007/s00792-020-01191-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 07/13/2020] [Indexed: 11/26/2022]
Abstract
Psychrophilic fungi are a critical biotic component in cold deserts that serves a central role in nutrient recycling and biogeochemical cycles. Despite their ecological significance, culture-independent studies on psychrophilic mycobiome are limited. In the present study, the fungal diversity patterns across the Drass, an Indian cold desert in the Himalaya, were indexed by targeted amplicon pyrosequencing (ITS). In the Drass dataset, Ascomycota was represented by 92 genera, while 22 genera represented Basidiomycota. The most abundant genus was Conocybe (20.46%). Most of the identified genera were reported in the literature to be prolific extracellular hydrolytic enzyme producers. To identify whether the Drass fungal assemblages share similarities to other cold deserts, these were further compared to Antarctic and Arctic cold deserts. Comparative analysis across the three cold deserts indicated the dominance of Dikarya (Ascomycota and Basidiomycota). The observed alpha diversity, Shannon index as well as Pielou's evenness was highest in the Antarctic followed by Drass and Arctic datasets. The genera Malassezia, Preussia, Pseudogymnoascus, Cadophora, Geopora, Monodictys, Tetracladium, Titaea, Mortierella, and Cladosporium were common to all the cold deserts. Furthermore, Conocybe was represented predominantly in Drass. Interestingly, the genus Conocybe has not been previously reported from any other studies on Antarctic or Arctic biomes. To the best of our knowledge, this is the first fungal metagenome study in Drass soil. Our analysis shows that despite the similarities of low temperature among the cold deserts, a significant differential abundance of fungal communities prevails in the global cold deserts.
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Affiliation(s)
- Puja Gupta
- School of Biotechnology, University of Jammu, Jammu, 180006, Jammu and Kashmir, India.
| | - Jyoti Vakhlu
- School of Biotechnology, University of Jammu, Jammu, 180006, Jammu and Kashmir, India.
| | - Yash Pal Sharma
- Department of Botany, University of Jammu, Jammu, 180006, Jammu and Kashmir, India
| | - Madangchanok Imchen
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Kasaragod, Periya, 671320, India
| | - Ranjith Kumavath
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Kasaragod, Periya, 671320, India.
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18
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Robertson LM, Wu S, You F, Huang L, Southam G, Chan TS, Lu YR, Bond PL. Geochemical and mineralogical changes in magnetite Fe-ore tailings induced by biomass organic matter amendment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 724:138196. [PMID: 32272405 DOI: 10.1016/j.scitotenv.2020.138196] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
Direct phytostabilization of alkaline and finely textured Fe-ore tailings is a key challenge for sustainable rehabilitation of tailings landscapes, due to limited topsoil resources available for constructing functional root-zones. The eco-engineering of soils (i.e. technosol) from tailings through the deliberate combination of technic materials with ecological inputs (e.g. biomass, water, topsoil and organisms) may provide a cost-effecctive and sustainable alternative to topsoil-based option for tailings rehabilitation. This approach purposefully accelerates in situ mineral weathering and the development of soil-like physicochemical and biological properties and functions in the tailings. The present study aimed to characterize mineralogical and geochemical changes associated with soil formation in Fe-ore tailings, by admixing biomass organic matter (BOM) and soil inoculum under well-watered conditions. Magnetite Fe-ore tailings (pH ~9.5) were amended with 3% (w/w) BOM (Lucerne hay) and natural soil microbial communities and incubated for 68 days in a microcosm study. BOM amendment with soil inoculum resulted in a rapid neutralization of alkaline pH conditions in the tailings. The weathering of magnetite and biotite-like phyllosilicates were accelerated, resulting in increased concentrations of soluble Mg, K, Fe, Ca, and Si in porewater. Evidence of the accelerated weathering was verified by synchrotron-based Fe K-edge X-ray absorption fine structure (XAFS) spectroscopy analysis, showing the presence of possibly Fe (III)-oxalates. The weathering resulted in eroded morphological surfaces of Fe-bearing minerals in the BOM treated tailings. This study confirmed the expected geochemical and mineralogical changes in the magnetite Fe-ore tailings induced by BOM amendment, providing a fundamental basis for eco-engineering tailings into soil-like technosol.
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Affiliation(s)
- Lachlan M Robertson
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Songlin Wu
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Fang You
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Longbin Huang
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Gordon Southam
- School of Earth & Environmental Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ting-Shan Chan
- National Synchrotron Radiation Research Centre, Hsinchu Science Park, Hsinchu 300, Taiwan
| | - Ying-Rui Lu
- National Synchrotron Radiation Research Centre, Hsinchu Science Park, Hsinchu 300, Taiwan
| | - Phillip L Bond
- Formerly Advanced Water Management Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
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19
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Chen H, Wang Y, Sun X, Peng Y, Xiao L. Mixing effect of polylactic acid microplastic and straw residue on soil property and ecological function. CHEMOSPHERE 2020; 243:125271. [PMID: 31760289 DOI: 10.1016/j.chemosphere.2019.125271] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 10/28/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
Microplastics have become a contaminant of increasing concern in soils. Although biodegradable plastics were considered as alternatives of traditional plastics, some evidence showed that biodegradable plastics might produce more microplastics. Until now, the effect of biodegradable microplastics on soil functions and processes, as well as microbial communities is uncertain. Based on high throughput sequencing, enzymatic activity assay and dynamic analysis of soil carbon and nitrogen, we investigated the effects of biodegradable polylactic acid microplastics (PLA MPs) on soil microbiota and related ecological processes under conditions of high or low carbon content. The results showed that PLA MPs had no significant effect on the overall diversity and composition of bacterial communities or related ecosystem functions and processes. However, co-occurrence network analysis revealed that PLA MPs impacted the interactions between constituent species, which might have legacy effect on soil bacterial communities and functions. Our data also revealed that PLA MPs could trade off the priming effect of carbon source. Our results provided an integrated picture in understanding the effects of PLA MPs on soil microbes, properties and ecological functions, which will help to further understand the effects of MPs on terrestrial ecosystems.
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Affiliation(s)
- Huiping Chen
- State Key Laboratory of Pollution Control & Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Yuhuang Wang
- State Key Laboratory of Pollution Control & Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Xi Sun
- State Key Laboratory of Pollution Control & Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Yuke Peng
- State Key Laboratory of Pollution Control & Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Lin Xiao
- State Key Laboratory of Pollution Control & Resources Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China.
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20
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Karthick A, Roy B, Chattopadhyay P. A review on the application of chemical surfactant and surfactant foam for remediation of petroleum oil contaminated soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 243:187-205. [PMID: 31096172 DOI: 10.1016/j.jenvman.2019.04.092] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 05/25/2023]
Abstract
Soil, exposed to petroleum oil contaminants (in the form of petrol, diesel, gasoline, crude oil, used motor oil), may cause potential damage to the environment, animal and human health. In this review article, mechanisms of the petroleum oil contaminant removal from soil by chemical surfactant systems such as surfactant solution, surfactant foam and nanoparticle stabilized surfactant foams are explained. Laboratory based research works, reported within the last decade on the application of similar systems towards the removal of petroleum oil contaminant from the soil, have been discussed. It is an important fact that the commercial implementation of the chemical surfactant based technology depends on the environmental properties (biodegradability and toxicity) of the surfactants. In recent times, surfactant foam and nanoparticle stabilized surfactant foam are becoming more popular and considered advantageous over the use of surfactant solution alone. However, more research works have to be conducted on nanoparticle stabilized foam. The impact of physicochemical properties of the nanoparticles on soil remediation has to be explored in depth.
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Affiliation(s)
- Arun Karthick
- Department of Chemical Engineering, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, VidyaVihar, 333031, Rajasthan, India.
| | - Banasri Roy
- Department of Chemical Engineering, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, VidyaVihar, 333031, Rajasthan, India.
| | - Pradipta Chattopadhyay
- Department of Chemical Engineering, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, VidyaVihar, 333031, Rajasthan, India.
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21
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Altshuler I, Hamel J, Turney S, Magnuson E, Lévesque R, Greer CW, Whyte LG. Species interactions and distinct microbial communities in high Arctic permafrost affected cryosols are associated with the CH 4 and CO 2 gas fluxes. Environ Microbiol 2019; 21:3711-3727. [PMID: 31206918 DOI: 10.1111/1462-2920.14715] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 05/27/2019] [Accepted: 06/10/2019] [Indexed: 11/29/2022]
Abstract
Microbial metabolism of the thawing organic carbon stores in permafrost results in a positive feedback loop of greenhouse gas emissions. CO2 and CH4 fluxes and the associated microbial communities in Arctic cryosols are important in predicting future warming potential of the Arctic. We demonstrate that topography had an impact on CH4 and CO2 flux at a high Arctic ice-wedge polygon terrain site, with higher CO2 emissions and lower CH4 uptake at troughs compared to polygon interior soils. The pmoA sequencing suggested that USCα cluster of uncultured methanotrophs is likely responsible for observed methane sink. Community profiling revealed distinct assemblages across the terrain at different depths. Deeper soils contained higher abundances of Verrucomicrobia and Gemmatimonadetes, whereas the polygon interior had higher Acidobacteria and lower Betaproteobacteria and Deltaproteobacteria abundances. Genome sequencing of isolates from the terrain revealed presence of carbon cycling genes including ones involved in serine and ribulose monophosphate pathways. A novel hybrid network analysis identified key members that had positive and negative impacts on other species. Operational Taxonomic Units (OTUs) with numerous positive interactions corresponded to Proteobacteria, Candidatus Rokubacteria and Actinobacteria phyla, while Verrucomicrobia and Acidobacteria members had negative impacts on other species. Results indicate that topography and microbial interactions impact community composition.
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Affiliation(s)
- Ianina Altshuler
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Jérémie Hamel
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, QC, Québec, Canada
| | - Shaun Turney
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Elisse Magnuson
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Roger Lévesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, QC, Québec, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada.,National Research Council of Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
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22
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Truong C, Gabbarini LA, Corrales A, Mujic AB, Escobar JM, Moretto A, Smith ME. Ectomycorrhizal fungi and soil enzymes exhibit contrasting patterns along elevation gradients in southern Patagonia. THE NEW PHYTOLOGIST 2019; 222:1936-1950. [PMID: 30689219 DOI: 10.1111/nph.15714] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
The biological and functional diversity of ectomycorrhizal (ECM) associations remain largely unknown in South America. In Patagonia, the ECM tree Nothofagus pumilio forms monospecific forests along mountain slopes without confounding effects of vegetation on plant-fungi interactions. To determine how fungal diversity and function are linked to elevation, we characterized fungal communities, edaphic variables, and eight extracellular enzyme activities along six elevation transects in Tierra del Fuego (Argentina and Chile). We also tested whether pairing ITS1 rDNA Illumina sequences generated taxonomic biases related to sequence length. Fungal community shifts across elevations were mediated primarily by soil pH with the most species-rich fungal families occurring mostly within a narrow pH range. By contrast, enzyme activities were minimally influenced by elevation but correlated with soil factors, especially total soil carbon. The activity of leucine aminopeptidase was positively correlated with ECM fungal richness and abundance, and acid phosphatase was correlated with nonECM fungal abundance. Several fungal lineages were undetected when using exclusively paired or unpaired forward ITS1 sequences, and these taxonomic biases need reconsideration for future studies. Our results suggest that soil fungi in N. pumilio forests are functionally similar across elevations and that these diverse communities help to maintain nutrient mobilization across the elevation gradient.
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Affiliation(s)
- Camille Truong
- Instituto de Biología, Universidad Nacional Autónoma de México, CP, 04510, Ciudad de México, México
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Luciano A Gabbarini
- Programa Interacciones Biológicas, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, B1876BX, Argentina
| | - Adriana Corrales
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
- Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, DC, 111221, Colombia
| | - Alija B Mujic
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, California State University at Fresno, Fresno, CA, 93740, USA
| | - Julio M Escobar
- Centro Austral de Investigaciones Científicas (CONICET), Ushuaia, V9410BFD, Tierra del Fuego, Argentina
| | - Alicia Moretto
- Centro Austral de Investigaciones Científicas (CONICET), Ushuaia, V9410BFD, Tierra del Fuego, Argentina
- Universidad Nacional de Tierra del Fuego, Ushuaia, V9410BFD, Tierra del Fuego, Argentina
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
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23
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Chen Y, Liu Y, Zhang J, Yang W, He R, Deng C. Microclimate exerts greater control over litter decomposition and enzyme activity than litter quality in an alpine forest-tundra ecotone. Sci Rep 2018; 8:14998. [PMID: 30301949 PMCID: PMC6177423 DOI: 10.1038/s41598-018-33186-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/19/2018] [Indexed: 11/09/2022] Open
Abstract
Plant litter decomposition is an important biogeochemical process in terrestrial ecosystems. Although climate and substrate quality controls over litter decomposition are reasonably well understood, their impacts on lignocellulose degradation and lignocellulolytic enzymes remain elusive. Here, the decomposition of three leaf litters derived from Salix paraplesia (SP), Deyeuxia scabrescens (DS), and Ajuga ovalifolia (AO), was studied across an alpine forest-tundra ecotone during one snow-covered season with the objective of distinguishing between the effects of microclimate and litter quality on litter decomposition rates and lignocellulolytic enzymes. The results showed that both microclimate and litter quality affected lignocellulose degradation rates and lignocellulolytic enzyme activities; however, microclimate factors had the greater effects. Interestingly, freeze-thaw cycles and moisture were the predominant factors explaining the variations in decomposition rate and enzyme activities. Higher cellulose degradation rates were associated with higher cellulose concentrations. Cellulolytic enzymes had a greater effect on litter decomposition than did ligninolytic enzymes at the early decomposition stage. Litter decomposition and enzyme activities should be given more attention under global climate change, as the direction and magnitude of changes in microclimate factors and litter quality could strongly influence the nutrient cycling and energy fluxes of alpine ecosystems.
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Affiliation(s)
- Yamei Chen
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Liu
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, 611130, China.
- Collaborative Innovation Centre of Ecological Security in the Upper Reaches of the Yangtze River, Chengdu, 611130, China.
| | - Jian Zhang
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, 611130, China
- Collaborative Innovation Centre of Ecological Security in the Upper Reaches of the Yangtze River, Chengdu, 611130, China
| | - Wanqin Yang
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, 611130, China
- Collaborative Innovation Centre of Ecological Security in the Upper Reaches of the Yangtze River, Chengdu, 611130, China
| | - Runlian He
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Changchun Deng
- Long-term Research Station of Alpine Forest Ecosystems, Institute of Ecology & Forestry, Sichuan Agricultural University, Chengdu, 611130, China
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24
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Trivedi P, Delgado‐Baquerizo M, Jeffries TC, Trivedi C, Anderson IC, Lai K, McNee M, Flower K, Pal Singh B, Minkey D, Singh BK. Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content. Environ Microbiol 2017; 19:3070-3086. [DOI: 10.1111/1462-2920.13779] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 04/20/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Pankaj Trivedi
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityLocked Bag 1797Penrith South NSW2751, Australia
- Department of Bioagricultural Sciences and Pest ManagementColorado State UniversityFort Collins CO80523, USA
| | - Manuel Delgado‐Baquerizo
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityLocked Bag 1797Penrith South NSW2751, Australia
- Cooperative Institute for Research in Environmental SciencesUniversity of ColoradoBoulder CO80309, USA
| | - Thomas C. Jeffries
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityLocked Bag 1797Penrith South NSW2751, Australia
| | - Chanda Trivedi
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityLocked Bag 1797Penrith South NSW2751, Australia
| | - Ian C. Anderson
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityLocked Bag 1797Penrith South NSW2751, Australia
| | - Kaitao Lai
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityLocked Bag 1797Penrith South NSW2751, Australia
| | - Matthew McNee
- Western Australian No‐Tillage Farmers AssociationLeeuwin Centre, CSIRO65, Brockway RoadFloreat WA6014, Australia
| | - Kenneth Flower
- School of Plant Biology and Institute of AgricultureThe University of Western Australia35 Stirling HighwayCrawley WA6009, Australia
| | - Bhupinder Pal Singh
- NSW Department of Primary IndustriesElizabeth Macarthur Agricultural InstituteMenangle NSW2568, Australia
| | - David Minkey
- Western Australian No‐Tillage Farmers AssociationLeeuwin Centre, CSIRO65, Brockway RoadFloreat WA6014, Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityLocked Bag 1797Penrith South NSW2751, Australia
- Global Centre for Land Based InnovationWestern Sydney UniversityBuilding L9, Locked Bag 1797Penrith South NSW2751, Australia
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25
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Morgalev YN, Lushchaeva IV, Morgaleva TG, Kolesnichenko LG, Loiko SV, Krickov IV, Lim A, Raudina TV, Volkova II, Shirokova LS, Morgalev SY, Vorobyev SN, Kirpotin SN, Pokrovsky OS. Bacteria primarily metabolize at the active layer/permafrost border in the peat core from a permafrost region in western Siberia. Polar Biol 2017. [DOI: 10.1007/s00300-017-2088-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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26
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De la Cruz-Barrón M, Cruz-Mendoza A, Navarro-Noya YE, Ruiz-Valdiviezo VM, Ortíz-Gutiérrez D, Ramírez-Villanueva DA, Luna-Guido M, Thierfelder C, Wall PC, Verhulst N, Govaerts B, Dendooven L. The Bacterial Community Structure and Dynamics of Carbon and Nitrogen when Maize (Zea mays L.) and Its Neutral Detergent Fibre Were Added to Soil from Zimbabwe with Contrasting Management Practices. MICROBIAL ECOLOGY 2017; 73:135-152. [PMID: 27538875 DOI: 10.1007/s00248-016-0807-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/21/2016] [Indexed: 06/06/2023]
Abstract
Water infiltration, soil carbon content, aggregate stability and yields increased in conservation agriculture practices compared to conventionally ploughed control treatments at the Henderson research station near Mazowe (Zimbabwe). How these changes in soil characteristics affect the bacterial community structure and the bacteria involved in the degradation of applied organic material remains unanswered. Soil was sampled from three agricultural systems at Henderson, i.e. (1) conventional mouldboard ploughing with continuous maize (conventional tillage), (2) direct seeding with a Fitarelli jab planter and continuous maize (direct seeding with continuous maize) and (3) direct seeding with a Fitarelli jab planter with rotation of maize sunn hemp (direct seeding with crop rotation). Soil was amended with young maize plants or their neutral detergent fibre (NDF) and incubated aerobically for 56 days, while C and N mineralization and the bacterial community structure were monitored. Bacillus (Bacillales), Micrococcaceae (Actinomycetales) and phylotypes belonging to the Pseudomonadales were first degraders of the applied maize plants. At day 3, Streptomyces (Actinomycetales), Chitinophagaceae ([Saprospirales]) and Dyella (Xanthomonadales) participated in the degradation of the applied maize and at day 7 Oxalobacteraceae (Burkholderiales). Phylotypes belonging to Halomonas (Oceanospirillales) were the first degraders of NDF and were replaced by Phenylobacterium (Caulobacterales) and phylotypes belonging to Pseudomonadales at day 3. Afterwards, similar bacterial groups were favoured by application of NDF as they were by the application of maize plants, but there were also clear differences. Phylotypes belonging to the Micrococcaceae and Bacillus did not participate in the degradation of NDF or its metabolic products, while phylotypes belonging to the Acidobacteriaceae participated in the degradation of NDF but not in that of maize plants. It was found that agricultural practices had a limited effect on the bacterial community structure, but application of organic material altered it substantially.
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Affiliation(s)
| | | | - Yendi E Navarro-Noya
- Cátedras CONACYT-Universidad Autónoma de Tlaxcala, Av. Universidad 1, C.P., 90062, Tlaxcala, Mexico
| | | | | | | | - Marco Luna-Guido
- Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico City, Mexico
| | - Cristian Thierfelder
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico D. F, Mexico
| | - Patrick C Wall
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico D. F, Mexico
| | - Nele Verhulst
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico D. F, Mexico
| | - Bram Govaerts
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico D. F, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, ABACUS, Cinvestav, Mexico City, Mexico.
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27
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Diáková K, Čapek P, Kohoutová I, Mpamah PA, Bárta J, Biasi C, Martikainen PJ, Šantrůčková H. Heterogeneity of carbon loss and its temperature sensitivity in East-European subarctic tundra soils. FEMS Microbiol Ecol 2016; 92:fiw140. [DOI: 10.1093/femsec/fiw140] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2016] [Indexed: 01/25/2023] Open
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28
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Shcherbakova V, Yoshimura Y, Ryzhmanova Y, Taguchi Y, Segawa T, Oshurkova V, Rivkina E. Archaeal communities of Arctic methane-containing permafrost. FEMS Microbiol Ecol 2016; 92:fiw135. [DOI: 10.1093/femsec/fiw135] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2016] [Indexed: 01/06/2023] Open
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29
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Čapek P, Kotas P, Manzoni S, Šantrůčková H. Drivers of phosphorus limitation across soil microbial communities. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12650] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Petr Čapek
- Department of Ecosystem Biology University of South Bohemia Branišovská 1760, 370 05 České Budějovice Czech Republic
| | - Petr Kotas
- Department of Ecosystem Biology University of South Bohemia Branišovská 1760, 370 05 České Budějovice Czech Republic
| | - Stefano Manzoni
- Department of Physical Geography Stockholm University SE‐106 91 Stockholm Sweden
- Bolin Centre for Climate Research Stockholm University SE‐106 91 Stockholm Sweden
| | - Hana Šantrůčková
- Department of Ecosystem Biology University of South Bohemia Branišovská 1760, 370 05 České Budějovice Czech Republic
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30
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Bradley JA, Anesio AM, Arndt S. Bridging the divide: a model-data approach to Polar and Alpine microbiology. FEMS Microbiol Ecol 2016; 92:fiw015. [PMID: 26832206 PMCID: PMC4765003 DOI: 10.1093/femsec/fiw015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2016] [Indexed: 11/13/2022] Open
Abstract
Advances in microbial ecology in the cryosphere continue to be driven by empirical approaches including field sampling and laboratory-based analyses. Although mathematical models are commonly used to investigate the physical dynamics of Polar and Alpine regions, they are rarely applied in microbial studies. Yet integrating modelling approaches with ongoing observational and laboratory-based work is ideally suited to Polar and Alpine microbial ecosystems given their harsh environmental and biogeochemical characteristics, simple trophic structures, distinct seasonality, often difficult accessibility, geographical expansiveness and susceptibility to accelerated climate changes. In this opinion paper, we explain how mathematical modelling ideally complements field and laboratory-based analyses. We thus argue that mathematical modelling is a powerful tool for the investigation of these extreme environments and that fully integrated, interdisciplinary model-data approaches could help the Polar and Alpine microbiology community address some of the great research challenges of the 21st century (e.g. assessing global significance and response to climate change). However, a better integration of field and laboratory work with model design and calibration/validation, as well as a stronger focus on quantitative information is required to advance models that can be used to make predictions and upscale processes and fluxes beyond what can be captured by observations alone.
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Affiliation(s)
- James A Bradley
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, BS8 1SS, UK BRIDGE, School of Geographical Sciences, University of Bristol, BS8 1SS, UK
| | - Alexandre M Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, BS8 1SS, UK
| | - Sandra Arndt
- BRIDGE, School of Geographical Sciences, University of Bristol, BS8 1SS, UK
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31
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Lee SH, Kang H. The activity and community structure of total bacteria and denitrifying bacteria across soil depths and biological gradients in estuary ecosystem. Appl Microbiol Biotechnol 2015; 100:1999-2010. [PMID: 26526456 DOI: 10.1007/s00253-015-7111-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 11/25/2022]
Abstract
The distribution of soil microorganisms often shows variations along soil depth, and even in the same soil layer, each microbial group has a specific niche. In particular, the estuary soil is intermittently flooded, and the characteristics of the surface soil layer are different from those of other terrestrial soils. We investigated the microbial community structure and activity across soil depths and biological gradients composed of invasive and native plants in the shallow surface layer of an estuary ecosystem by using molecular approaches. Our results showed that the total and denitrifying bacterial community structures of the estuarine wetland soil differed according to the short depth gradient. In growing season, gene copy number of 16S rRNA were 1.52(±0.23) × 10(11), 1.10(±0.06) × 10(11), and 4.33(±0.16) × 10(10) g(-1) soil; nirS were 5.41(±1.25) × 10(8), 4.93(±0.94) × 10(8), and 2.61(±0.28) × 10(8) g(-1) soil; and nirK were 9.67(±2.37) × 10(6), 3.42(±0.55) × 10(6), and 2.12(±0.19) × 10(6) g(-1) soil in 0 cm, 5 cm, and 10 cm depth layer, respectively. The depth-based difference was distinct in the vegetated sample and in the growing season, evidencing the important role of plants in structuring the microbial community. In comparison with other studies, we observed differences in the microbial community and functions even across very short depth gradients. In conclusion, our results suggested that (i) in the estuary ecosystem, the denitrifying bacterial community could maintain its abundance and function within shallow surface soil layers through facultative anaerobiosis, while the total bacterial community would be both quantitatively and qualitatively affected by the soil depth, (ii) the nirS gene community, rather than the nirK one, should be the first candidate used as an indicator of the microbial denitrification process in the estuary system, and (iii) as the microbial community is distributed and plays a certain niche role according to biogeochemical factors, the study of the microbial community even in surface soil should be performed in detail by considering the soil depth.
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Affiliation(s)
- Seung-Hoon Lee
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 120-749, South Korea.,Geobiotech Corporation, Seoul, 120-749, South Korea
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 120-749, South Korea.
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32
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Schnecker J, Wild B, Takriti M, Eloy Alves RJ, Gentsch N, Gittel A, Hofer A, Klaus K, Knoltsch A, Lashchinskiy N, Mikutta R, Richter A. Microbial community composition shapes enzyme patterns in topsoil and subsoil horizons along a latitudinal transect in Western Siberia. SOIL BIOLOGY & BIOCHEMISTRY 2015; 83:106-115. [PMID: 25859057 PMCID: PMC4381299 DOI: 10.1016/j.soilbio.2015.01.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/10/2015] [Accepted: 01/16/2015] [Indexed: 05/16/2023]
Abstract
Soil horizons below 30 cm depth contain about 60% of the organic carbon stored in soils. Although insight into the physical and chemical stabilization of soil organic matter (SOM) and into microbial community composition in these horizons is being gained, information on microbial functions of subsoil microbial communities and on associated microbially-mediated processes remains sparse. To identify possible controls on enzyme patterns, we correlated enzyme patterns with biotic and abiotic soil parameters, as well as with microbial community composition, estimated using phospholipid fatty acid profiles. Enzyme patterns (i.e. distance-matrixes calculated from these enzyme activities) were calculated from the activities of six extracellular enzymes (cellobiohydrolase, leucine-amino-peptidase, N-acetylglucosaminidase, chitotriosidase, phosphatase and phenoloxidase), which had been measured in soil samples from organic topsoil horizons, mineral topsoil horizons, and mineral subsoil horizons from seven ecosystems along a 1500 km latitudinal transect in Western Siberia. We found that hydrolytic enzyme activities decreased rapidly with depth, whereas oxidative enzyme activities in mineral horizons were as high as, or higher than in organic topsoil horizons. Enzyme patterns varied more strongly between ecosystems in mineral subsoil horizons than in organic topsoils. The enzyme patterns in topsoil horizons were correlated with SOM content (i.e., C and N content) and microbial community composition. In contrast, the enzyme patterns in mineral subsoil horizons were related to water content, soil pH and microbial community composition. The lack of correlation between enzyme patterns and SOM quantity in the mineral subsoils suggests that SOM chemistry, spatial separation or physical stabilization of SOM rather than SOM content might determine substrate availability for enzymatic breakdown. The correlation of microbial community composition and enzyme patterns in all horizons, suggests that microbial community composition shapes enzyme patterns and might act as a modifier for the usual dependency of decomposition rates on SOM content or C/N ratios.
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Affiliation(s)
- Jörg Schnecker
- University of Vienna, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
- Corresponding author. University of Vienna, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Althanstraße 14, Vienna, 1090, Austria. Tel.: +43 1 4277 76668; fax: +43 1 4277 876661.
| | - Birgit Wild
- University of Vienna, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Mounir Takriti
- University of Vienna, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Ricardo J. Eloy Alves
- Austrian Polar Research Institute, Vienna, Austria
- University of Vienna, Department of Ecogenomics and Systems Biology, Division of Archaea Biology and Ecogenomics, Vienna, Austria
| | - Norman Gentsch
- Leibniz Universität Hannover, Institut für Bodenkunde, Hannover, Germany
| | - Antje Gittel
- Aarhus University, Center for Geomicrobiology, Department of Bioscience, Aarhus, Denmark
- University of Bergen, Centre for Geobiology, Bergen, Norway
| | - Angelika Hofer
- University of Vienna, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Vienna, Austria
| | - Karoline Klaus
- University of Vienna, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Vienna, Austria
| | - Anna Knoltsch
- University of Vienna, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Nikolay Lashchinskiy
- Central Siberian Botanical Garden, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Robert Mikutta
- Leibniz Universität Hannover, Institut für Bodenkunde, Hannover, Germany
| | - Andreas Richter
- University of Vienna, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
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33
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Gittel A, Bárta J, Kohoutová I, Schnecker J, Wild B, Čapek P, Kaiser C, Torsvik VL, Richter A, Schleper C, Urich T. Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland. Front Microbiol 2014; 5:541. [PMID: 25360132 PMCID: PMC4199454 DOI: 10.3389/fmicb.2014.00541] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 09/29/2014] [Indexed: 01/04/2023] Open
Abstract
Permafrost-affected soils in the Northern latitudes store huge amounts of organic carbon (OC) that is prone to microbial degradation and subsequent release of greenhouse gasses to the atmosphere. In Greenland, the consequences of permafrost thaw have only recently been addressed, and predictions on its impact on the carbon budget are thus still highly uncertain. However, the fate of OC is not only determined by abiotic factors, but closely tied to microbial activity. We investigated eight soil profiles in northeast Greenland comprising two sites with typical tundra vegetation and one wet fen site. We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities. Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis. Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation ("buried topsoils"), resulting from a decrease in fungal abundance compared to recent ("unburied") topsoils. Actinobacteria (in particular Intrasporangiaceae) accounted for a major fraction of the microbial community in buried topsoils, but were only of minor abundance in all other soil horizons. It was indicated that the distribution pattern of Actinobacteria and a variety of other bacterial classes was related to the activity of phenol oxidases and peroxidases supporting the hypothesis that bacteria might resume the role of fungi in oxidative enzyme production and degradation of phenolic and other complex substrates in these soils. Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation.
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Affiliation(s)
- Antje Gittel
- Department of Biology, Centre for Geobiology, University of BergenBergen, Norway
- Department of Bioscience, Center for Geomicrobiology, Aarhus UniversityAarhus, Denmark
| | - Jiří Bárta
- Department of Ecosystems Biology, University of South BohemiaČeské Budějovice, Czech Republic
| | - Iva Kohoutová
- Department of Ecosystems Biology, University of South BohemiaČeské Budějovice, Czech Republic
| | - Jörg Schnecker
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
- Austrian Polar Research InstituteVienna, Austria
| | - Birgit Wild
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
- Austrian Polar Research InstituteVienna, Austria
| | - Petr Čapek
- Department of Ecosystems Biology, University of South BohemiaČeské Budějovice, Czech Republic
| | - Christina Kaiser
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
| | - Vigdis L. Torsvik
- Department of Biology, Centre for Geobiology, University of BergenBergen, Norway
| | - Andreas Richter
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of ViennaVienna, Austria
- Austrian Polar Research InstituteVienna, Austria
| | - Christa Schleper
- Department of Biology, Centre for Geobiology, University of BergenBergen, Norway
- Austrian Polar Research InstituteVienna, Austria
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Tim Urich
- Austrian Polar Research InstituteVienna, Austria
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
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Wild B, Schnecker J, Alves RJE, Barsukov P, Bárta J, Čapek P, Gentsch N, Gittel A, Guggenberger G, Lashchinskiy N, Mikutta R, Rusalimova O, Šantrůčková H, Shibistova O, Urich T, Watzka M, Zrazhevskaya G, Richter A. Input of easily available organic C and N stimulates microbial decomposition of soil organic matter in arctic permafrost soil. SOIL BIOLOGY & BIOCHEMISTRY 2014; 75:143-151. [PMID: 25089062 PMCID: PMC4064687 DOI: 10.1016/j.soilbio.2014.04.014] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/01/2014] [Accepted: 04/06/2014] [Indexed: 05/05/2023]
Abstract
Rising temperatures in the Arctic can affect soil organic matter (SOM) decomposition directly and indirectly, by increasing plant primary production and thus the allocation of plant-derived organic compounds into the soil. Such compounds, for example root exudates or decaying fine roots, are easily available for microorganisms, and can alter the decomposition of older SOM ("priming effect"). We here report on a SOM priming experiment in the active layer of a permafrost soil from the central Siberian Arctic, comparing responses of organic topsoil, mineral subsoil, and cryoturbated subsoil material (i.e., poorly decomposed topsoil material subducted into the subsoil by freeze-thaw processes) to additions of 13C-labeled glucose, cellulose, a mixture of amino acids, and protein (added at levels corresponding to approximately 1% of soil organic carbon). SOM decomposition in the topsoil was barely affected by higher availability of organic compounds, whereas SOM decomposition in both subsoil horizons responded strongly. In the mineral subsoil, SOM decomposition increased by a factor of two to three after any substrate addition (glucose, cellulose, amino acids, protein), suggesting that the microbial decomposer community was limited in energy to break down more complex components of SOM. In the cryoturbated horizon, SOM decomposition increased by a factor of two after addition of amino acids or protein, but was not significantly affected by glucose or cellulose, indicating nitrogen rather than energy limitation. Since the stimulation of SOM decomposition in cryoturbated material was not connected to microbial growth or to a change in microbial community composition, the additional nitrogen was likely invested in the production of extracellular enzymes required for SOM decomposition. Our findings provide a first mechanistic understanding of priming in permafrost soils and suggest that an increase in the availability of organic carbon or nitrogen, e.g., by increased plant productivity, can change the decomposition of SOM stored in deeper layers of permafrost soils, with possible repercussions on the global climate.
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Affiliation(s)
- Birgit Wild
- University of Vienna, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
- Corresponding author. University of Vienna, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Vienna, Austria. Tel.: +43 1 4277 76666.
| | - Jörg Schnecker
- University of Vienna, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Ricardo J. Eloy Alves
- Austrian Polar Research Institute, Vienna, Austria
- University of Vienna, Department of Ecogenomics and Systems Biology, Division of Archaea Biology and Ecogenomics, Vienna, Austria
| | - Pavel Barsukov
- Siberian Branch of the Russian Academy of Sciences, Institute of Soil Science and Agrochemistry, Novosibirsk, Russia
| | - Jiří Bárta
- University of South Bohemia, Department of Ecosystems Biology, České Budějovice, Czech Republic
| | - Petr Čapek
- University of South Bohemia, Department of Ecosystems Biology, České Budějovice, Czech Republic
| | - Norman Gentsch
- Leibniz University Hannover, Institute of Soil Science, Hannover, Germany
| | - Antje Gittel
- Austrian Polar Research Institute, Vienna, Austria
- University of Bergen, Centre for Geobiology, Department of Biology, Bergen, Norway
| | - Georg Guggenberger
- Leibniz University Hannover, Institute of Soil Science, Hannover, Germany
| | - Nikolay Lashchinskiy
- Siberian Branch of Russian Academy of Sciences, Central Siberian Botanical Garden, Novosibirsk, Russia
| | - Robert Mikutta
- Leibniz University Hannover, Institute of Soil Science, Hannover, Germany
| | - Olga Rusalimova
- Siberian Branch of the Russian Academy of Sciences, Institute of Soil Science and Agrochemistry, Novosibirsk, Russia
| | - Hana Šantrůčková
- University of South Bohemia, Department of Ecosystems Biology, České Budějovice, Czech Republic
| | - Olga Shibistova
- Leibniz University Hannover, Institute of Soil Science, Hannover, Germany
- Siberian Branch of Russian Academy of Sciences, VN Sukachev Institute of Forest, Krasnoyarsk, Russia
| | - Tim Urich
- Austrian Polar Research Institute, Vienna, Austria
- University of Vienna, Department of Ecogenomics and Systems Biology, Division of Archaea Biology and Ecogenomics, Vienna, Austria
| | - Margarete Watzka
- University of Vienna, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Vienna, Austria
| | - Galina Zrazhevskaya
- Siberian Branch of Russian Academy of Sciences, VN Sukachev Institute of Forest, Krasnoyarsk, Russia
| | - Andreas Richter
- University of Vienna, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
- Corresponding author. University of Vienna, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, Vienna, Austria. Tel.: +43 1 4277 76660.
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