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Chen L, Yang G, Bai Y, Chang J, Qin S, Liu F, He M, Song Y, Zhang F, Peñuelas J, Zhu B, Zhou G, Yang Y. Permafrost carbon cycle and its dynamics on the Tibetan Plateau. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1833-1848. [PMID: 38951429 DOI: 10.1007/s11427-023-2601-1] [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: 12/28/2023] [Accepted: 04/19/2024] [Indexed: 07/03/2024]
Abstract
Our knowledge on permafrost carbon (C) cycle is crucial for understanding its feedback to climate warming and developing nature-based solutions for mitigating climate change. To understand the characteristics of permafrost C cycle on the Tibetan Plateau, the largest alpine permafrost region around the world, we summarized recent advances including the stocks and fluxes of permafrost C and their responses to thawing, and depicted permafrost C dynamics within this century. We find that this alpine permafrost region stores approximately 14.1 Pg (1 Pg=1015 g) of soil organic C (SOC) in the top 3 m. Both substantial gaseous emissions and lateral C transport occur across this permafrost region. Moreover, the mobilization of frozen C is expedited by permafrost thaw, especially by the formation of thermokarst landscapes, which could release significant amounts of C into the atmosphere and surrounding water bodies. This alpine permafrost region nevertheless remains an important C sink, and its capacity to sequester C will continue to increase by 2100. For future perspectives, we would suggest developing long-term in situ observation networks of C stocks and fluxes with improved temporal and spatial coverage, and exploring the mechanisms underlying the response of ecosystem C cycle to permafrost thaw. In addition, it is essential to improve the projection of permafrost C dynamics through in-depth model-data fusion on the Tibetan Plateau.
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Affiliation(s)
- Leiyi Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Guibiao Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yuxuan Bai
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Jinfeng Chang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shuqi Qin
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Futing Liu
- Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, 100091, China
| | - Mei He
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yutong Song
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fan Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Josep Peñuelas
- Consejo Superior de Investigaciones Científicas (CSIC), Global Ecology Unit CREAF-CSIC- UAB (Universitat Autònoma de Barcelona), Barcelona, 08193, Spain
- Centre for Ecological Research and Forestry (CREAF), Barcelona, 08193, Spain
| | - Biao Zhu
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, 100871, China
| | - Guoying Zhou
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
- Key Laboratory of Tibetan Medicine Research, Chinese Academy of Sciences, Xining, 810008, China
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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2
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Song Y, Sun L, Song C, Li M, Liu Z, Zhu M, Chen S, Yuan J, Gao J, Wang X, Wang W. Responses of soil microbes and enzymes to long-term warming incubation in different depths of permafrost peatland soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165733. [PMID: 37490945 DOI: 10.1016/j.scitotenv.2023.165733] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/06/2023] [Accepted: 07/21/2023] [Indexed: 07/27/2023]
Abstract
Soil microbes and enzymes mediate soil carbon-climate feedback, and their responses to increasing temperature partly affect soil carbon stability subjected to the effects of climate change. We performed a 50-month incubation experiment to determine the effect of long-term warming on soil microbes and enzymes involved in carbon cycling along permafrost peatland profile (0-150 cm) and investigated their response to water flooding in the active soil layer. Soil bacteria, fungi, and most enzymes were observed to be sensitive to changes in temperature and water in the permafrost peatland. Bacterial and fungal abundance decreased in the active layer soil but increased in the deepest permafrost layer under warming. The highest decrease in the ratio of soil bacteria to fungi was observed in the deepest permafrost layer under warming. These results indicated that long-term warming promotes recalcitrant carbon loss in permafrost because fungi are more efficient in decomposing high-molecular-weight compounds. Soil microbial catabolic activity measured using Biolog Ecoplates indicated a greater degree of average well color development at 15 °C than at 5 °C. The highest levels of microbial catabolic activity, functional diversity, and carbon substrate utilization were found in the permafrost boundary layer (60-80 cm). Soil polyphenol oxidase that degrades recalcitrant carbon was more sensitive to increases in temperature than β-glucosidase, N-acetyl-β-glucosaminidase, and acid phosphatase, which degrade labile carbon. Increasing temperature and water flooding exerted a synergistic effect on the bacterial and fungal abundance and β-glucosidase, acid phosphatase, and RubisCO activity in the topsoil. Structural equation modeling analysis indicated that soil enzyme activity significantly correlated with ratio of soil bacteria to fungi and microbial catabolic activity. Our results provide valuable insights into the linkage response of soil microorganisms, enzymes to climate change and their feedback to permafrost carbon loss.
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Affiliation(s)
- Yanyu Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Li Sun
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Changchun Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Mengting Li
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; College of Tourism and Geographical Science, Jilin Normal University, Siping 136000, China
| | - Zhendi Liu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy Sciences, Beijing 100049, China
| | - Mengyuan Zhu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy Sciences, Beijing 100049, China
| | - Shuang Chen
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Jiabao Yuan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy Sciences, Beijing 100049, China
| | - Jinli Gao
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Xianwei Wang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Wenjuan Wang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
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3
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Tang X, Zhang M, Fang Z, Yang Q, Zhang W, Zhou J, Zhao B, Fan T, Wang C, Zhang C, Xia Y, Zheng Y. Changing microbiome community structure and functional potential during permafrost thawing on the Tibetan Plateau. FEMS Microbiol Ecol 2023; 99:fiad117. [PMID: 37766397 DOI: 10.1093/femsec/fiad117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 09/13/2023] [Accepted: 09/27/2023] [Indexed: 09/29/2023] Open
Abstract
Large amounts of carbon sequestered in permafrost on the Tibetan Plateau (TP) are becoming vulnerable to microbial decomposition in a warming world. However, knowledge about how the responsible microbial community responds to warming-induced permafrost thaw on the TP is still limited. This study aimed to conduct a comprehensive comparison of the microbial communities and their functional potential in the active layer of thawing permafrost on the TP. We found that the microbial communities were diverse and varied across soil profiles. The microbial diversity declined and the relative abundance of Chloroflexi, Bacteroidetes, Euryarchaeota, and Bathyarchaeota significantly increased with permafrost thawing. Moreover, warming reduced the similarity and stability of active layer microbial communities. The high-throughput qPCR results showed that the abundance of functional genes involved in liable carbon degradation and methanogenesis increased with permafrost thawing. Notably, the significantly increased mcrA gene abundance and the higher methanogens to methanotrophs ratio implied enhanced methanogenic activities during permafrost thawing. Overall, the composition and functional potentials of the active layer microbial community in the Tibetan permafrost region are susceptible to warming. These changes in the responsible microbial community may accelerate carbon degradation, particularly in the methane releases from alpine permafrost ecosystems on the TP.
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Affiliation(s)
- Xiaotong Tang
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Miao Zhang
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Zhengkun Fang
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Qing Yang
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Wan Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jiaxing Zhou
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Bixi Zhao
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Tongyu Fan
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Congzhen Wang
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yanhong Zheng
- State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi'an, Shaanxi 710069, China
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Jiang Y, Yang L, Wu S, Zhou T. Warming changes the composition and diversity of fungal communities in permafrost. ANN MICROBIOL 2023. [DOI: 10.1186/s13213-022-01707-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Abstract
Purpose
It is the data support and theoretical basis for the response mechanism of soil fungi to climate warming in permafrost areas in the Greater Xing’an Mountains.
Methods
We collected permafrost from the Greater Xing’an Mountains for indoor simulation experiments and took the natural permafrost as the control (CK) and the test groups of 0 °C (T1), 2 °C (T2), and 4 °C (T3) were set. Illumina MiSeq high-throughput sequencing technology was used to understand the changes in characteristics of fungal communities, and the correlations were analyzed combined with the soil physicochemical properties.
Results
Compared with CK, the value of pH and the content of available potassium (AK) in the three warming treatment groups were significantly lower (P < 0.05), and the microbial biomass carbon (MBC) content was significantly higher (P < 0.05). The content of total nitrogen (TN) and available nitrogen (AN) in the T1 and T3 groups was significantly lower than that in the CK group (P < 0.05). A total of 11 phyla, 39 classes, 89 orders, 187 families, 361 genera, and 522 species were obtained through fungal sequencing and divided into 1463 amplicon sequence variants (ASVs). Ascomycota and Dimorphospora were the dominant phylum and genus, respectively, and there were differences in the response of relative abundance of various groups at the phylum and genus levels to warming. Warming significantly decreased the Sobs and ACE indexes of the treatment groups (P < 0.05), and the Shannon and Shannoneven indexes also showed a downward trend. Moreover, warming significantly changed the fungal beta diversity (P < 0.01), while the value of pH and the content of TN, MBC, and AK could significantly affect the community structure (P < 0.05), and the correlation between fungi at different phyla levels and soil physicochemical properties was different.
Conclusions
These results can provide a reference for further study on the changes in composition and structure of fungal communities and the influence factor in permafrost in the Greater Xing’an Mountains under the background of warming.
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Microbiogeochemical Traits to Identify Nitrogen Hotspots in Permafrost Regions. NITROGEN 2022. [DOI: 10.3390/nitrogen3030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Permafrost-affected tundra soils are large carbon (C) and nitrogen (N) reservoirs. However, N is largely bound in soil organic matter (SOM), and ecosystems generally have low N availability. Therefore, microbial induced N-cycling processes and N losses were considered negligible. Recent studies show that microbial N processing rates, inorganic N availability, and lateral N losses from thawing permafrost increase when vegetation cover is disturbed, resulting in reduced N uptake or increased N input from thawing permafrost. In this review, we describe currently known N hotspots, particularly bare patches in permafrost peatland or permafrost soils affected by thermokarst, and their microbiogeochemical characteristics, and present evidence for previously unrecorded N hotspots in the tundra. We summarize the current understanding of microbial N cycling processes that promote the release of the potent greenhouse gas (GHG) nitrous oxide (N2O) and the translocation of inorganic N from terrestrial into aquatic ecosystems. We suggest that certain soil characteristics and microbial traits can be used as indicators of N availability and N losses. Identifying N hotspots in permafrost soils is key to assessing the potential for N release from permafrost-affected soils under global warming, as well as the impact of increased N availability on emissions of carbon-containing GHGs.
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Wang G, Chen L, Zhang D, Qin S, Peng Y, Yang G, Wang J, Yu J, Wei B, Liu Y, Li Q, Kang L, Wang Y, Yang Y. Divergent Trajectory of Soil Autotrophic and Heterotrophic Respiration upon Permafrost Thaw. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:10483-10493. [PMID: 35748652 DOI: 10.1021/acs.est.1c07575] [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] [Indexed: 06/15/2023]
Abstract
Warming-induced permafrost thaw may stimulate soil respiration (Rs) and thus cause a positive feedback to climate warming. However, due to the limited in situ observations, it remains unclear about how Rs and its autotrophic (Ra) and heterotrophic (Rh) components change upon permafrost thaw. Here we monitored variations in Rs and its components along a permafrost thaw sequence on the Tibetan Plateau, and explored the potential linkage of Rs components (i.e., Ra and Rh) with biotic (e.g., plant functional traits and soil microbial diversity) and abiotic factors (e.g., substrate quality). We found that Ra and Rh exhibited divergent responses to permafrost collapse: Ra increased with the time of thawing, while Rh exhibited a hump-shaped pattern along the thaw sequence. We also observed different drivers of thaw-induced changes in the ratios of Ra:Rs and Rh:Rs. Except for soil water status, plant community structure, diversity, and root properties explained the variation in Ra:Rs ratio, soil substrate quality and microbial diversity were key factors associated with the dynamics of Rh:Rs ratio. Overall, these findings demonstrate divergent patterns and drivers of Rs components as permafrost thaw prolongs, which call for considerations in Earth system models for better forecasting permafrost carbon-climate feedback.
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Affiliation(s)
- Guanqin Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leiyi Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Dianye Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shuqi Qin
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunfeng Peng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Guibiao Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jun Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianchun Yu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Wei
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- College of Resources and Environmental Science/Hebei Province Key Laboratory for Farmland Eco-Environment, Agricultural University of Hebei, Baoding 071000, China
| | - Qinlu Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Luyao Kang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Zherebker A, Rukhovich GD, Sarycheva A, Lechtenfeld OJ, Nikolaev EN. Aromaticity Index with Improved Estimation of Carboxyl Group Contribution for Biogeochemical Studies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2729-2737. [PMID: 35084826 DOI: 10.1021/acs.est.1c04575] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Natural organic matter (NOM) components measured with ultrahigh-resolution mass spectrometry (UHRMS) are often assessed by molecular formula-based indices, particularly related to their aromaticity, which are further used as proxies to explain biogeochemical reactivity. An aromaticity index (AI) is calculated mostly with respect to carboxylic groups abundant in NOM. Here, we propose a new constrained AIcon based on the measured distribution of carboxylic groups among individual NOM components obtained by deuteromethylation and UHRMS. Applied to samples from diverse sources (coal, marine, peat, permafrost, blackwater river, and soil), the method revealed that the most probable number of carboxylic groups was two, which enabled to set a reference point n = 2 for carboxyl-accounted AIcon calculation. The examination of the proposed AIcon showed the smallest deviation to the experimentally determined index for all NOM samples under study as well as for individual natural compounds obtained from the Coconut database. In particular, AIcon performed better than AImod for all compound classes in which aromatic moieties are expected: aromatics, condensed aromatics, and unsaturated compounds. Therefore, AIcon referenced with two carboxyl groups is preferred over conventional AI and AImod for biogeochemical studies where the aromaticity of compounds is important to understand the transformations and fate of NOM compounds.
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Affiliation(s)
| | - Gleb D Rukhovich
- Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | | | - Oliver J Lechtenfeld
- Department of Analytical Chemistry, Research Group BioGeoOmics, Helmholtz Centre for Environmental Research─UFZ, Leipzig DE-04318, Germany
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8
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Zou Y, Wang Q, Deng M, Wang Y. Community Intervention System: COVID-19 Control in Inner Mongolia Autonomous Region, China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182312857. [PMID: 34886579 PMCID: PMC8657202 DOI: 10.3390/ijerph182312857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/29/2021] [Accepted: 12/04/2021] [Indexed: 11/25/2022]
Abstract
The COVID-19 epidemic has caused giant influences on people’s life, and China’s communities play an important role in dealing with these major public health events (MPHEs). Community as the grassroots autonomous organization has various significant functions in intervening in MPHEs. The community intervention follows a system which directly influences the anti-epidemic effectiveness. To explore the mechanism, we devise a theoretical system for community intervention, mainly consisting of “organizational structure”, “functional performance” and “internal and external connections”. Questionnaire surveys, the chi-square test, the independent sample T-test, and principal component analysis are used to identify the characteristics of Inner Mongolia Autonomous Region’s (Inner Mongolia) community intervention. Through the empirical research, it is verified that the community intervention in MPHEs is the combination of “the structural response of the organization”, “the performance of the community’s own function”, and “the establishment of internal and external connections”. The central Inner Mongolia delivers the best performance in community intervention compared to eastern Inner Mongolia and western Inner Mongolia. The urban communities commonly perform better than that in the agricultural and pastoral areas. The built system and findings could provide a guidance for future community to improve its intervention capability.
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Affiliation(s)
- Yafeng Zou
- School of Public Administration, Inner Mongolia University, Hohhot 010070, China; (Q.W.); (Y.W.)
- Correspondence:
| | - Qi Wang
- School of Public Administration, Inner Mongolia University, Hohhot 010070, China; (Q.W.); (Y.W.)
- Faculty of Geographical Science, Beijing Normal University, Beijing 100875, China
| | - Min Deng
- Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing 100101, China;
| | - Yujie Wang
- School of Public Administration, Inner Mongolia University, Hohhot 010070, China; (Q.W.); (Y.W.)
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9
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Yuan X, Chen Y, Qin W, Xu T, Mao Y, Wang Q, Chen K, Zhu B. Plant and microbial regulations of soil carbon dynamics under warming in two alpine swamp meadow ecosystems on the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148072. [PMID: 34098273 DOI: 10.1016/j.scitotenv.2021.148072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/19/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
Increasing temperature plays important roles in affecting plant and soil microbial communities as well as ecological processes and functions in terrestrial ecosystems. However, mechanisms of warming influencing soil carbon dynamics associated with plant-microbe interactions remain unclear. In this study, open-top chambers (OTCs) experiments were carried out to detect the responses of plants, soil microbes, and SOC contents, physical fractions (by particle-size fractionation) and chemical composition (by solid-state 13C NMR spectroscopy) to warming in two alpine swamp meadows (Kobresia humilis vs K. tibetica) on the Tibetan Plateau. Our results showed that four years of warming had significant influences on plant belowground biomass, microbial community and SOC contents in the K. humilis swamp meadow, but had much weaker or minor effects in the K. tibetica swamp meadow with water-logged status and lower level of warming. In the K. humilis swamp meadow, warming increased microbial biomass, C-hydrolysis gene abundance and N-acetylglucosaminidase enzyme activity. These positive effects of warming on microbial biomass and functions further increased soil dissolved inorganic nitrogen and alleviated the nitrogen limitation for plant growth, potentially leading to higher plant biomass. Therefore, increases in SOC and particulate organic carbon (POC) under warming were likely attributed to the higher C input with promoted plant biomass overweighting the simultaneous higher C degradation and release in the K. humilis swamp meadow. Conversely, warming marginally reduced soil alkyl C, which was likely associated with enhanced decomposition by fungi and gram-positive bacteria. Overall, the increases in unprotected POC and decreases in recalcitrant alkyl C demonstrate the sensitivity of SOC physical fractions as well as chemical composition to climate warming in the K. humilis alpine swamp meadow, and suggest that the overall stability of SOC might be lower despite the gain in the content of SOC after climate warming in this alpine swamp meadow.
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Affiliation(s)
- Xia Yuan
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Ying Chen
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Wenkuan Qin
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Tianle Xu
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Yahui Mao
- College of Geographic Sciences, Qinghai Normal University, Xining 810008, China
| | - Qi Wang
- College of Geographic Sciences, Qinghai Normal University, Xining 810008, China
| | - Kelong Chen
- College of Geographic Sciences, Qinghai Normal University, Xining 810008, China
| | - Biao Zhu
- Institute of Ecology, College of Urban and Environmental Sciences, Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China.
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10
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Beel CR, Lamoureux SF, Orwin JF, Pope MA, Lafrenière MJ, Scott NA. Differential impact of thermal and physical permafrost disturbances on High Arctic dissolved and particulate fluvial fluxes. Sci Rep 2020; 10:11836. [PMID: 32678255 PMCID: PMC7366920 DOI: 10.1038/s41598-020-68824-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/01/2020] [Indexed: 12/03/2022] Open
Abstract
Climate warming and changing precipitation patterns have thermally (active layer deepening) and physically (permafrost-thaw related mass movements) disturbed permafrost-underlain watersheds across much of the Arctic, increasing the transfer of dissolved and particulate material from terrestrial to aquatic ecosystems. We examined the multiyear (2006–2017) impact of thermal and physical permafrost disturbances on all of the major components of fluvial flux. Thermal disturbances increased the flux of dissolved organic carbon (DOC), but localized physical disturbances decreased multiyear DOC flux. Physical disturbances increased major ion and suspended sediment flux, which remained elevated a decade after disturbance, and changed carbon export from a DOC to a particulate organic carbon (POC) dominated system. As the magnitude and frequency of physical permafrost disturbance intensifies in response to Arctic climate change, disturbances will become an increasingly important mechanism to deliver POC from terrestrial to aquatic ecosystems. Although nival runoff remained the primary hydrological driver, the importance of pluvial runoff as driver of fluvial flux increased following both thermal and physical permafrost disturbance. We conclude the transition from a nival-dominated fluvial regime to a regime where rainfall runoff is proportionately more important will be a likely tipping point to accelerated High Arctic change.
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Affiliation(s)
- C R Beel
- Department of Geography and Planning, Queen's University, Kingston, ON, K7L 3N6, Canada. .,Yellowknife Research Office, Wilfrid Laurier University, Yellowknife, NT, X1A 2P8, Canada.
| | - S F Lamoureux
- Department of Geography and Planning, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - J F Orwin
- Department of Geography and Planning, Queen's University, Kingston, ON, K7L 3N6, Canada.,Resource Stewardship Division, Alberta Environment and Parks, Government of Alberta, Calgary, AB, T2L 2K8, Canada
| | - M A Pope
- Department of Geography and Planning, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - M J Lafrenière
- Department of Geography and Planning, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - N A Scott
- Department of Geography and Planning, Queen's University, Kingston, ON, K7L 3N6, Canada
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11
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Gagné KR, Ewers SC, Murphy CJ, Daanen R, Walter Anthony K, Guerard JJ. Composition and photo-reactivity of organic matter from permafrost soils and surface waters in interior Alaska. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:1525-1539. [PMID: 32567618 DOI: 10.1039/d0em00097c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Yedoma permafrost soils are especially susceptible to abrupt thaw due to their exceptional thickness and high ice content. Compared to other mineral soils, yedoma has a high organic carbon content, which has shown to be particularly biolabile. The organic carbon in these deposits needs to be characterised to provide an identification toolkit for detecting and monitoring the thaw, mobilisation and mineralisation of yedoma permafrost. This study characterised organic carbon isolates from thermokarst lakes (either receiving inputs from thaw of original yedoma or refrozen-thermokarst deposits, or lacking recent thaw) during winter and summer seasons within the Goldstream Creek watershed, a discontinuous permafrost watershed in interior Alaska, to identify the extent to which thermokarst-lake environments are impacted by degradation of yedoma permafrost. Waters from lakes of varied age and thermokarst activity, as well as active layer and undisturbed yedoma permafrost soils were isolated and characterised by functional group abundance (multiCP-MAS 13C and SPR-W5-WATERGATE 1H NMR), absorbance and fluorescence, and photobleaching ability. DOM isolated from winter and summer seasons revealed differing composition and photoreactivity, suggesting varied active layer and permafrost influence under differing ground water flow regimes. Water extractable organic matter isolates from permafrost leachates revealed variation in terms of photoreactivity and photolability, with the youngest sampled permafrost isolate being the most photoreactive and photolabile. As temperatures increase, release of permafrost organic matter is inevitable. Obtaining a holistic understanding of DOM composition and photoreactivity will allow for a better prediction of permafrost thaw impacts in the coming decades.
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Affiliation(s)
- Kristin R Gagné
- Department of Chemistry & Biochemistry, University of Alaska Fairbanks, Fairbanks, Alaska 99775, USA.
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12
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Li F, Peng Y, Chen L, Yang G, Abbott BW, Zhang D, Fang K, Wang G, Wang J, Yu J, Liu L, Zhang Q, Chen K, Mohammat A, Yang Y. Warming alters surface soil organic matter composition despite unchanged carbon stocks in a Tibetan permafrost ecosystem. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13489] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Fei Li
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- College of Life Science Taizhou University Taizhou China
| | - Yunfeng Peng
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
| | - Leiyi Chen
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
| | - Guibiao Yang
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Benjamin W. Abbott
- Department of Plant and Wildlife Sciences Brigham Young University Provo UT USA
| | - Dianye Zhang
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Kai Fang
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Guanqin Wang
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Jun Wang
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Jianchun Yu
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Li Liu
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Qiwen Zhang
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Kelong Chen
- College of Life and Geography Sciences Qinghai Normal University Xining China
| | - Anwar Mohammat
- Xinjiang Institute of Ecology and Geography Chinese Academy of Sciences Urumqi China
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
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13
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Mangal V, DeGasparro S, Beresford DV, Guéguen C. Linking molecular and optical properties of dissolved organic matter across a soil-water interface on Akimiski Island (Nunavut, Canada). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 704:135415. [PMID: 31791775 DOI: 10.1016/j.scitotenv.2019.135415] [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: 08/20/2019] [Revised: 10/25/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023]
Abstract
Dissolved organic matter (DOM) plays a crucial role in terrestrial and aquatic carbon and biogeochemical cycles; however, molecular transformations between aquatic and terrestrial systems remain poorly understood due to the complexity and heterogeneity of DOM. In this study, we investigated the molecular diversity of aquatic DOM and adjacent soil derived water extractable organic matter (WEOM) from seven locations on Akimiski Island, Nunavut using a combination of absorbance spectroscopy and Fourier transform ion cyclotron mass spectrometry (FT-ICR-MS). Assigned elemental formula and Van Krevelen compositional analysis reveal compositional similarities in river, inland ponds and coastal pool sites for aquatic DOM and WEOM. More aromatic, oxygenated polyphenolic carbon rich molecules were found in aquatic DOM whereas WEOM was abundant in highly unsaturated aliphatic material. A total of 276 phenolic, unsaturated aliphatic, and vascular plant-derived polyphenolic molecules were identified as being conserved between WEOM and aquatic DOM at one river and two inland pond locations suggesting similar CHO sources from adjacent soils. Moreover, contributions of polyphenolic compounds in aquatic DOM and WEOM were greater at inland ponds than coastal pools, congruent with a greater aromaticity at inland sites. Our results highlight the similarities and differences in WEOM to aquatic DOM composition and how they range across surrounding watersheds that provide insight into the biogeochemical dynamics across a Canadian subarctic terrestrial-aquatic-continuum.
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Affiliation(s)
- V Mangal
- Department of Chemistry, Université de Sherbrooke, 2500 Blvd de l'Université, Sherbrooke, QC J1K 2R1, Canada
| | - S DeGasparro
- Environmental and Life Sciences Graduate Program, Trent University, 1600 West Bank Drive Peterborough, ON K9J 7B8, Canada
| | - D V Beresford
- Environmental and Life Sciences Graduate Program, Trent University, 1600 West Bank Drive Peterborough, ON K9J 7B8, Canada; Biology/Trent School of the Environment Departments, Trent University, 1600 West Bank Drive Peterborough, ON K9J 7B8, Canada
| | - C Guéguen
- Department of Chemistry, Université de Sherbrooke, 2500 Blvd de l'Université, Sherbrooke, QC J1K 2R1, Canada.
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14
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Schostag M, Priemé A, Jacquiod S, Russel J, Ekelund F, Jacobsen CS. Bacterial and protozoan dynamics upon thawing and freezing of an active layer permafrost soil. ISME JOURNAL 2019; 13:1345-1359. [PMID: 30692629 DOI: 10.1038/s41396-019-0351-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/17/2018] [Accepted: 12/23/2018] [Indexed: 11/09/2022]
Abstract
The active layer of soil overlaying permafrost in the Arctic is subjected to annual changes in temperature and soil chemistry, which we hypothesize to affect the overall soil microbial community. We investigated changes in soil microorganisms at different temperatures during warming and freezing of the active layer soil from Svalbard, Norway. Soil community data were obtained by direct shotgun sequencing of total extracted RNA. No changes in soil microbial communities were detected when warming from -10 to -2 °C or when freezing from -2 to -10 °C. In contrast, within a few days we observed changes when warming from -2 to +2 °C with a decrease in fungal rRNA and an increase in several OTUs belonging to Gemmatimonadetes, Bacteroidetes and Betaproteobacteria. Even more substantial changes occurred when incubating at 2 °C for 16 days, with declines in total fungal potential activity and decreases in oligotrophic members from Actinobacteria and Acidobacteria. Additionally, we detected an increase in transcriptome sequences of bacterial phyla Bacteriodetes, Firmicutes, Betaproteobacteria and Gammaproteobacteria-collectively presumed to be copiotrophic. Furthermore, we detected an increase in putative bacterivorous heterotrophic flagellates, likely due to predation upon the bacterial community via grazing. Although this grazing activity may explain relatively large changes in the bacterial community composition, no changes in total 16S rRNA gene copy number were observed and the total RNA level remained stable during the incubation. Together, these results are showing the first comprehensive ecological evaluation across prokaryotic and eukaryotic microbial communities on thawing and freezing of soil by application of the TotalRNA technique.
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Affiliation(s)
- Morten Schostag
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Anders Priemé
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Samuel Jacquiod
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.,INRA Dijon, UMR1347 Agroécologie, Dijon, France
| | - Jakob Russel
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Flemming Ekelund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Suhr Jacobsen
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen, Copenhagen, Denmark. .,Geological Survey of Denmark and Greenland, Copenhagen, Denmark. .,Department of Environmental Science, Aarhus University, Roskilde, Denmark.
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15
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Semenchuk PR, Krab EJ, Hedenström M, Phillips CA, Ancin-Murguzur FJ, Cooper EJ. Soil organic carbon depletion and degradation in surface soil after long-term non-growing season warming in High Arctic Svalbard. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 646:158-167. [PMID: 30056226 DOI: 10.1016/j.scitotenv.2018.07.150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 06/08/2023]
Abstract
Arctic tundra active-layer soils are at risk of soil organic carbon (SOC) depletion and degradation upon global climate warming because they are in a stage of relatively early decomposition. Non-growing season (NGS) warming is particularly pronounced, and observed increases of CO2 emissions during experimentally warmed NGSs give concern for great SOC losses to the atmosphere. Here, we used snow fences in Arctic Spitsbergen dwarf shrub tundra to simulate 1.86 °C NGS warming for 9 consecutive years, while growing season temperatures remained unchanged. In the snow fence treatment, the 4-11 cm thick A-horizon had a 2% lower SOC concentration and a 0.48 kg C m-2 smaller pool size than the controls, indicating SOC pool depletion. The snow fence treatment's A-horizon's alkyl/O-alkyl ratio was also significantly increased, indicating an advance of SOC degradation. The underlying 5 cm of B/C-horizon did not show these effects. Our results support the hypothesis that SOC depletion and degradation are connected to the long-term transience of observed ecosystem respiration (ER) increases upon soil warming. We suggest that the bulk of warming induced ER increases may originate from surface and not deep active layer or permafrost horizons. The observed losses of SOC might be significant for the ecosystem in question, but are in magnitude comparatively small relative to anthropogenic greenhouse gas enrichment of the atmosphere. We conclude that a positive feedback of carbon losses from surface soils of Arctic dwarf shrub tundra to anthropogenic forcing will be minor, but not negligible.
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Affiliation(s)
- Philipp R Semenchuk
- Department of Arctic and Marine Biology, Faculty of Biosciences Fisheries and Economics, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway; Climate Impacts Research Centre, Department of Ecology and Environmental Science, Umeå University, SE-98107 Abisko, Sweden; Division of Conservation Biology, Vegetation Ecology and Landscape Ecology, Department of Botany and Biodiversity Research, Vienna University, Rennweg 14, 1030 Vienna, Austria.
| | - Eveline J Krab
- Climate Impacts Research Centre, Department of Ecology and Environmental Science, Umeå University, SE-98107 Abisko, Sweden; Swedish University of Agricultural Sciences, Department of Soil and Environment, SE-75007 Uppsala, Sweden
| | | | - Carly A Phillips
- Odum School of Ecology, University of Georgia, Athens, GA 30606, USA
| | - Francisco J Ancin-Murguzur
- Department of Arctic and Marine Biology, Faculty of Biosciences Fisheries and Economics, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Elisabeth J Cooper
- Department of Arctic and Marine Biology, Faculty of Biosciences Fisheries and Economics, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
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16
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Perminova IV, Shirshin EA, Konstantinov AI, Zherebker A, Lebedev VA, Dubinenkov IV, Kulikova NA, Nikolaev EN, Bulygina E, Holmes RM. The Structural Arrangement and Relative Abundance of Aliphatic Units May Effect Long-Wave Absorbance of Natural Organic Matter as Revealed by 1H NMR Spectroscopy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:12526-12537. [PMID: 30296078 DOI: 10.1021/acs.est.8b01029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The objective of this study was to shed light on structural features which underlay intensity of long wave absorbance of natural organic matter (NOM) using 1H NMR spectroscopy. For this purpose, a set of the NOM samples was assembled from arctic and nonarctic sampling sites (the Kolyma river basin and Moscow region, respectively). It was to ensure a substantial difference in the humification degree of the isolated organic matter-the biogeochemical proxy of the long-wave absorbance of NOM. The assembled NOM set was analyzed using solution-state 1H NMR spectroscopy. The distribution of both backbone and exchangeable protons was determined using acquisition of spectra in three different solvents. The substantially higher contribution of nonfunctionalized aliphatic moieties CHn (e.g., materials derived from linear terpenoids, MDLT) in the arctic NOM samples was revealed as compared to the nonarctic ones. The latter were characterized with the higher content of CHα protons adjacent to electron-withdrawing groups which belong to carboxyl rich alicyclic moieties (CRAMs) or to aromatic constituents of NOM. We have calculated a ratio of CHn to CHα protons as a structural descriptor which showed significant inverse correlation to intensity of long wave absorbance assessed with a use of E4/ E6 ratio and the slope of absorption spectrum. The steric hindrance of aromatic chromophoric groups of the NOM ensemble by bulky nonfunctionalized aliphatic moieties (e.g., MDLT) was set as a hypothesis for explanation of this phenomenon. The bulky aliphatics might increase a distance between the interacting groups resulting in inhibition of electronic (e.g., charge-transfer) interactions in the NOM ensemble. The obtained relationships were further explored using Fourier transform mass spectrometry as complementary technique to 1H NMR spectroscopy. The data obtained on correlation of molecular composition of NOM with 1H NMR data and optical properties were very supportive of our hypothesis that capabilities of NOM ensemble of charge transfer interactions can be dependent on structural arrangement and relative abundance of nonabsorbing aliphatic moieties.
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Affiliation(s)
- I V Perminova
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory 1-3 , 119991 Moscow , Russia
| | - E A Shirshin
- Department of Physics , Lomonosov Moscow State University , Leninskie Gory 1-2 , 119991 Moscow , Russia
| | - A I Konstantinov
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory 1-3 , 119991 Moscow , Russia
| | - A Zherebker
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory 1-3 , 119991 Moscow , Russia
- Skolkovo Institute of Science and Technology , 143025 Skolkovo, Moscow region , Russia
- Institute for Energy Problems of Chemical Physics of RAS , Leninskij pr. 38-2 , 119334 Moscow , Russia
| | - V A Lebedev
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory 1-3 , 119991 Moscow , Russia
- Department of Materials Science , Lomonosov Moscow State University , Leninskie Gory 1-73 , 199991 Moscow , Russia
| | - I V Dubinenkov
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory 1-3 , 119991 Moscow , Russia
| | - N A Kulikova
- Department of Chemistry , Lomonosov Moscow State University , Leninskie Gory 1-3 , 119991 Moscow , Russia
- Department of Soil Science , Lomonosov Moscow State University , Leninskie Gory 1-12 , 199991 Moscow , Russia
- Bach Institute of Biochemistry of RAS , Federal Research Center "Biotechnology" , Leninskij pr. 33-2 , 119071 Moscow , Russia
| | - E N Nikolaev
- Skolkovo Institute of Science and Technology , 143025 Skolkovo, Moscow region , Russia
- Institute for Energy Problems of Chemical Physics of RAS , Leninskij pr. 38-2 , 119334 Moscow , Russia
| | - E Bulygina
- Woods Hole Research Center , 149 Woods Hole Rd , Falmouth , Massachusetts 02540 , United States
| | - R M Holmes
- Woods Hole Research Center , 149 Woods Hole Rd , Falmouth , Massachusetts 02540 , United States
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17
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Kim H, Park AK, Lee JH, Shin SC, Park H, Kim HW. PsEst3, a new psychrophilic esterase from the Arctic bacterium Paenibacillus sp. R4: crystallization and X-ray crystallographic analysis. Acta Crystallogr F Struct Biol Commun 2018; 74:367-372. [PMID: 29870022 PMCID: PMC5987746 DOI: 10.1107/s2053230x18007525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/18/2018] [Indexed: 01/15/2023] Open
Abstract
Esterases are very useful biocatalysts in industry: they hydrolyze esters and split them into a carboxylic acid and an alcohol. The psychrophilic esterase PsEst3 was obtained from Paenibacillus sp. R4, which was isolated from the active layer of the permafrost in Council, Alaska. PsEst3 was successfully overexpressed using a psychrophilic chaperonin co-expression system and was purified by nickel-affinity and size-exclusion chromatography. Recombinant PsEst3 was crystallized at 290 K using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 2.1 Å resolution. The crystal was determined to belong to space group P4132 or P4332, with unit-cell parameters a = b = c = 145.33 Å. Further crystallographic analysis needs to be conducted to investigate the structure and function of this esterase.
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Affiliation(s)
- Hyun Kim
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Ae Kyung Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Seung Chul Shin
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Han-Woo Kim
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon 21990, Republic of Korea
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18
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Yang G, Peng Y, Olefeldt D, Chen Y, Wang G, Li F, Zhang D, Wang J, Yu J, Liu L, Qin S, Sun T, Yang Y. Changes in Methane Flux along a Permafrost Thaw Sequence on the Tibetan Plateau. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:1244-1252. [PMID: 29276825 DOI: 10.1021/acs.est.7b04979] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Permafrost thaw alters the physical and environmental conditions of soil and may thus cause a positive feedback to climate warming through increased methane emissions. However, the current knowledge of methane emissions following thermokarst development is primarily based on expanding lakes and wetlands, with upland thermokarst being studied less often. In this study, we monitored the methane emissions during the peak growing seasons of two consecutive years along a thaw sequence within a thermo-erosion gully in a Tibetan swamp meadow. Both years had consistent results, with the early and midthaw stages (3 to 12 years since thaw) exhibiting low methane emissions that were similar to those in the undisturbed meadow, while the emissions from the late thaw stage (20 years since thaw) were 3.5 times higher. Our results also showed that the soil water-filled pore space, rather than the soil moisture per se, in combination with the sand content, were the main factors that caused increased methane emissions. These findings differ from the traditional view that upland thermokarst could reduce methane emissions owing to the improvement of drainage conditions, suggesting that upland thermokarst development does not always result in a decrease in methane emissions.
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Affiliation(s)
- Guibiao Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences , Beijing 100093, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Yunfeng Peng
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences , Beijing 100093, China
| | - David Olefeldt
- Department of Renewable Resources, University of Alberta , Edmonton, Alberta Canada , T6G 2H1
| | - Yongliang Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences , Beijing 100093, China
| | - Guanqin Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences , Beijing 100093, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Fei Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences , Beijing 100093, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Dianye Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences , Beijing 100093, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Jun Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences , Beijing 100093, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Jianchun Yu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences , Beijing 100093, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Li Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences , Beijing 100093, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Shuqi Qin
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences , Beijing 100093, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Tianyang Sun
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences , Beijing 100093, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences , Beijing 100093, China
- University of Chinese Academy of Sciences , Beijing 100049, China
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19
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Wang JJ, Lafrenière MJ, Lamoureux SF, Simpson AJ, Gélinas Y, Simpson MJ. Differences in Riverine and Pond Water Dissolved Organic Matter Composition and Sources in Canadian High Arctic Watersheds Affected by Active Layer Detachments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:1062-1071. [PMID: 29301070 DOI: 10.1021/acs.est.7b05506] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Regional warming has caused permafrost thermokarst and disturbances, such as active layer detachments (ALDs), which may alter carbon feedback in Arctic ecosystems. However, it is currently unclear how these disturbances alter DOM biogeochemistry in rivers and ponds in Arctic ecosystems. Water samples from the main river channel, ALD-disturbed/undisturbed tributaries, and disturbed/undisturbed ponds within a catchment in the Canadian High Arctic were collected and analyzed using carbon isotopes and spectroscopic methods. Both river and pond samples had large variations in dissolved organic carbon (DOC) concentrations. Ponds, particularly ALD-disturbed ponds, had much older 14C DOC ages than rivers. Results from δ13C and absorption and fluorescence analyses indicate higher autochthonous contributions in ponds than rivers and increasing autochthonous contributions from upper to lower reaches of the main channel. The disturbed samples had less carbohydrates but more carboxyl-rich alicyclic molecules in 1H nuclear magnetic resonance spectra than undisturbed samples. These ALD-impacted samples also contained less terrestrial-humic-like but more oxidized-quinone-like components in the fluorescence spectra. Interestingly, the disturbed pond DOM displayed the greatest DOM oxidation with ALDs compared to undisturbed areas. Compared to Arctic rivers, small Arctic ponds have DOM predominantly from permafrost and microbial sources and may have a disproportionally stronger positive feedback on climate warming.
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Affiliation(s)
- Jun-Jian Wang
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough , 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Melissa J Lafrenière
- Department of Geography and Planning, Queen's University , 68 University Ave., Kingston, Ontario K7L 3N6, Canada
| | - Scott F Lamoureux
- Department of Geography and Planning, Queen's University , 68 University Ave., Kingston, Ontario K7L 3N6, Canada
| | - André J Simpson
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough , 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Yves Gélinas
- GEOTOP and the Department of Chemistry and Biochemistry, Concordia University , 7141 Sherbrooke West, Montréal, Quebec H4B 1R6, Canada
| | - Myrna J Simpson
- Environmental NMR Centre and Department of Physical and Environmental Sciences, University of Toronto Scarborough , 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
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20
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Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores. Sci Rep 2018; 8:504. [PMID: 29323168 PMCID: PMC5765012 DOI: 10.1038/s41598-017-18777-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/12/2017] [Indexed: 12/20/2022] Open
Abstract
Understating the microbial communities and ecological processes that influence their structure in permafrost soils is crucial for predicting the consequences of climate change. In this study we investigated the bacterial and archaeal communities along depth profiles of four soil cores collected across Alaska. The bacterial and archaeal diversity (amplicon sequencing) overall decreased along the soil depth but the depth-wise pattern of their abundances (qPCR) varied by sites. The community structure of bacteria and archaea displayed site-specific pattern, with a greater role of soil geochemical characteristics rather than soil depth. In particular, we found significant positive correlations between methane trapped in cores and relative abundance of methanogenic archaeal genera, indicating a strong association between microbial activity and methane production in subsurface soils. We observed that bacterial phylogenetic community assembly tended to be more clustered in surface soils than in deeper soils. Analyses of phylogenetic community turnover among depth profiles across cores indicated that the relative influence of deterministic and stochastic processes was mainly determined by soil properties rather than depth. Overall, our findings emphasize that the vertical distributions of bacterial and archaeal communities in permafrost soils are to a large extent determined by the variation in site-specific soil properties.
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21
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Yang Z, Yang S, Van Nostrand JD, Zhou J, Fang W, Qi Q, Liu Y, Wullschleger SD, Liang L, Graham DE, Yang Y, Gu B. Microbial Community and Functional Gene Changes in Arctic Tundra Soils in a Microcosm Warming Experiment. Front Microbiol 2017; 8:1741. [PMID: 28974946 PMCID: PMC5610689 DOI: 10.3389/fmicb.2017.01741] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/25/2017] [Indexed: 11/24/2022] Open
Abstract
Microbial decomposition of soil organic carbon (SOC) in thawing Arctic permafrost is important in determining greenhouse gas feedbacks of tundra ecosystems to climate. However, the changes in microbial community structure during SOC decomposition are poorly known. Here we examine these changes using frozen soils from Barrow, Alaska, USA, in anoxic microcosm incubation at −2 and 8°C for 122 days. The functional gene array GeoChip was used to determine microbial community structure and the functional genes associated with SOC degradation, methanogenesis, and Fe(III) reduction. Results show that soil incubation after 122 days at 8°C significantly decreased functional gene abundance (P < 0.05) associated with SOC degradation, fermentation, methanogenesis, and iron cycling, particularly in organic-rich soil. These observations correspond well with decreases in labile SOC content (e.g., reducing sugar and ethanol), methane and CO2 production, and Fe(III) reduction. In contrast, the community functional structure was largely unchanged in the −2°C incubation. Soil type (i.e., organic vs. mineral) and the availability of labile SOC were among the most significant factors impacting microbial community structure. These results demonstrate the important roles of microbial community in SOC degradation and support previous findings that SOC in organic-rich Arctic tundra is highly vulnerable to microbial degradation under warming.
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Affiliation(s)
- Ziming Yang
- Environmental Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States.,Department of Chemistry, Oakland UniversityRochester, MI, United States
| | - Sihang Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, United States
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China.,Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, United States.,Earth and Environmental Sciences, Lawrence Berkeley National LaboratoryBerkeley, CA, United States
| | - Wei Fang
- Environmental Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States
| | - Qi Qi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Yurong Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of SciencesBeijing, China
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States.,Oak Ridge National Laboratory, Climate Change Science InstituteOak Ridge, TN, United States
| | - Liyuan Liang
- Environmental Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States.,Environmental Molecular Sciences Laboratory, Pacific Northwest National LaboratoryRichland, WA, United States
| | - David E Graham
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National LaboratoryOak Ridge, TN, United States
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22
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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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23
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Cid FP, Rilling JI, Graether SP, Bravo LA, Mora MDLL, Jorquera MA. Properties and biotechnological applications of ice-binding proteins in bacteria. FEMS Microbiol Lett 2016; 363:fnw099. [PMID: 27190285 DOI: 10.1093/femsle/fnw099] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2016] [Indexed: 01/04/2023] Open
Abstract
Ice-binding proteins (IBPs), such as antifreeze proteins (AFPs) and ice-nucleating proteins (INPs), have been described in diverse cold-adapted organisms, and their potential applications in biotechnology have been recognized in various fields. Currently, both IBPs are being applied to biotechnological processes, primarily in medicine and the food industry. However, our knowledge regarding the diversity of bacterial IBPs is limited; few studies have purified and characterized AFPs and INPs from bacteria. Phenotypically verified IBPs have been described in members belonging to Gammaproteobacteria, Actinobacteria and Flavobacteriia classes, whereas putative IBPs have been found in Gammaproteobacteria, Alphaproteobacteria and Bacilli classes. Thus, the main goal of this minireview is to summarize the current information on bacterial IBPs and their application in biotechnology, emphasizing the potential application in less explored fields such as agriculture. Investigations have suggested the use of INP-producing bacteria antagonists and AFPs-producing bacteria (or their AFPs) as a very attractive strategy to prevent frost damages in crops. UniProt database analyses of reported IBPs (phenotypically verified) and putative IBPs also show the limited information available on bacterial IBPs and indicate that major studies are required.
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Affiliation(s)
- Fernanda P Cid
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco 4811230, Chile
| | - Joaquín I Rilling
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco 4811230, Chile
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Leon A Bravo
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Forestales, Universidad de la Frontera, Temuco 4811230, Chile
| | - María de La Luz Mora
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
| | - Milko A Jorquera
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
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24
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Archaeal and bacterial communities across a chronosequence of drained lake basins in Arctic Alaska. Sci Rep 2015; 5:18165. [PMID: 26681584 PMCID: PMC4683534 DOI: 10.1038/srep18165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 11/13/2015] [Indexed: 11/21/2022] Open
Abstract
We examined patterns in soil microbial community composition across a successional gradient of drained lake basins in the Arctic Coastal Plain. Analysis of 16S rRNA gene sequences revealed that methanogens closely related to Candidatus ‘Methanoflorens stordalenmirensis’ were the dominant archaea, comprising >50% of the total archaea at most sites, with particularly high levels in the oldest basins and in the top 57 cm of soil (active and transition layers). Bacterial community composition was more diverse, with lineages from OP11, Actinobacteria, Bacteroidetes, and Proteobacteria found in high relative abundance across all sites. Notably, microbial composition appeared to converge in the active layer, but transition and permafrost layer communities across the sites were significantly different to one another. Microbial biomass using fatty acid-based analysis indicated that the youngest basins had increased abundances of gram-positive bacteria and saprotrophic fungi at higher soil organic carbon levels, while the oldest basins displayed an increase in only the gram-positive bacteria. While this study showed differences in microbial populations across the sites relevant to basin age, the dominance of Candidatus ‘M. stordalenmirensis’ across the chronosequence indicates the potential for changes in local carbon cycling, depending on how these methanogens and associated microbial communities respond to warming temperatures.
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25
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Coolen MJL, Orsi WD. The transcriptional response of microbial communities in thawing Alaskan permafrost soils. Front Microbiol 2015; 6:197. [PMID: 25852660 PMCID: PMC4360760 DOI: 10.3389/fmicb.2015.00197] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 02/24/2015] [Indexed: 11/13/2022] Open
Abstract
Thawing of permafrost soils is expected to stimulate microbial decomposition and respiration of sequestered carbon. This could, in turn, increase atmospheric concentrations of greenhouse gasses, such as carbon dioxide and methane, and create a positive feedback to climate warming. Recent metagenomic studies suggest that permafrost has a large metabolic potential for carbon processing, including pathways for fermentation and methanogenesis. Here, we performed a pilot study using ultrahigh throughput Illumina HiSeq sequencing of reverse transcribed messenger RNA to obtain a detailed overview of active metabolic pathways and responsible organisms in up to 70 cm deep permafrost soils at a moist acidic tundra location in Arctic Alaska. The transcriptional response of the permafrost microbial community was compared before and after 11 days of thaw. In general, the transcriptional profile under frozen conditions suggests a dominance of stress responses, survival strategies, and maintenance processes, whereas upon thaw a rapid enzymatic response to decomposing soil organic matter (SOM) was observed. Bacteroidetes, Firmicutes, ascomycete fungi, and methanogens were responsible for largest transcriptional response upon thaw. Transcripts indicative of heterotrophic methanogenic pathways utilizing acetate, methanol, and methylamine were found predominantly in the permafrost table after thaw. Furthermore, transcripts involved in acetogenesis were expressed exclusively after thaw suggesting that acetogenic bacteria are a potential source of acetate for acetoclastic methanogenesis in freshly thawed permafrost. Metatranscriptomics is shown here to be a useful approach for inferring the activity of permafrost microbes that has potential to improve our understanding of permafrost SOM bioavailability and biogeochemical mechanisms contributing to greenhouse gas emissions as a result of permafrost thaw.
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Affiliation(s)
- Marco J. L. Coolen
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic InstitutionWoods Hole, MA, USA
- Western Australia Organic and Isotope Geochemistry Centre, Department of Chemistry, Curtin UniversityPerth, WA, Australia
| | - William D. Orsi
- Marine Chemistry and Geochemistry Department, Woods Hole Oceanographic InstitutionWoods Hole, MA, USA
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Farooq H, Courtier-Murias D, Soong R, Masoom H, Maas W, Fey M, Kumar R, Monette M, Stronks H, Simpson MJ, Simpson AJ. Rapid parameter optimization of low signal-to-noise samples in NMR spectroscopy using rapid CPMG pulsing during acquisition: application to recycle delays. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:129-135. [PMID: 23322645 DOI: 10.1002/mrc.3923] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 12/11/2012] [Accepted: 12/16/2012] [Indexed: 06/01/2023]
Abstract
A method is presented that combines Carr-Purcell-Meiboom-Gill (CPMG) during acquisition with either selective or nonselective excitation to produce a considerable intensity enhancement and a simultaneous loss in chemical shift information. A range of parameters can theoretically be optimized very rapidly on the basis of the signal from the entire sample (hard excitation) or spectral subregion (soft excitation) and should prove useful for biological, environmental, and polymer samples that often exhibit highly dispersed and broad spectral profiles. To demonstrate the concept, we focus on the application of our method to T(1) determination, specifically for the slowest relaxing components in a sample, which ultimately determines the optimal recycle delay in quantitative NMR. The traditional inversion recovery (IR) pulse program is combined with a CPMG sequence during acquisition. The slowest relaxing components are selected with a shaped pulse, and then, low-power CPMG echoes are applied during acquisition with intervals shorter than chemical shift evolution (RCPMG) thus producing a single peak with an SNR commensurate with the sum of the signal integrals in the selected region. A traditional (13)C IR experiment is compared with the selective (13)C IR-RCPMG sequence and yields the same T(1) values for samples of lysozyme and riverine dissolved organic matter within error. For lysozyme, the RCPMG approach is ~70 times faster, and in the case of dissolved organic matter is over 600 times faster. This approach can be adapted for the optimization of a host of parameters where chemical shift information is not necessary, such as cross-polarization/mixing times and pulse lengths.
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Affiliation(s)
- Hashim Farooq
- Department of Chemistry, University of Toronto, 1265 Military Trail, Toronto, ON, Canada, M1C 1A4
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27
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Masoom H, Courtier-Murias D, Farooq H, Soong R, Simpson MJ, Maas W, Kumar R, Monette M, Stronks H, Simpson AJ. Rapid estimation of nuclear magnetic resonance experiment time in low-concentration environmental samples. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2013; 32:129-136. [PMID: 23065696 DOI: 10.1002/etc.2028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 07/28/2012] [Accepted: 08/23/2012] [Indexed: 06/01/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is an essential tool for studying environmental samples but is often hindered by low sensitivity, especially for the direct detection of nuclei such as(13) C. In very heterogeneous samples with NMR nuclei at low abundance, such as soils, sediments, and air particulates, it can take days to acquire a conventional(13) C spectrum. The present study describes a prescreening method that permits the rapid prediction of experimental run time in natural samples. The approach focuses the NMR chemical shift dispersion into a single spike, and, even in samples with extremely low carbon content, the spike can be observed in two to three minutes, or less. The intensity of the spike is directly proportional to the total concentration of nuclei of interest in the sample. Consequently, the spike intensity can be used as a powerful prescreening method that answers two key questions: (1) Will this sample produce a conventional NMR spectrum? (2) How much instrument time is required to record a spectrum with a specific signal-to-noise (S/N) ratio? The approach identifies samples to avoid (or pretreat) and permits additional NMR experiments to be performed on samples producing high-quality NMR data. Applications in solid- and liquid-state(13) C NMR are demonstrated, and it is shown that the technique is applicable to a range of nuclei.
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Affiliation(s)
- Hussain Masoom
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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28
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Simpson MJ, Simpson AJ. The chemical ecology of soil organic matter molecular constituents. J Chem Ecol 2012; 38:768-84. [PMID: 22549555 DOI: 10.1007/s10886-012-0122-x] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 04/02/2012] [Accepted: 04/15/2012] [Indexed: 11/26/2022]
Abstract
Soil organic matter (OM) contains vast stores of carbon, and directly supports microbial, plant, and animal life by retaining essential nutrients and water in the soil. Soil OM plays important roles in biological, chemical, and physical processes within the soil, and arguably plays a major role in maintaining long-term ecological stability in a changing world. Despite its importance, there is a great deal still unknown about soil OM chemical ecology. The development of sophisticated analytical methods have reshaped our understanding of soil OM composition, which is now believed to be comprised of plant and microbial products at various stages of decomposition. The methods also have recently been applied to study environmental change in various settings and have provided unique insight with respect to soil OM chemical ecology. The goal of this review is to highlight the methods used to characterize soil OM structure, source, and degradation that have enabled precise observations of OM and associated ecological shifts. Although the chemistry of soil OM is important in its overall fate in ecosystems, the studies conducted to date suggest that ecological function is not defined by soil OM chemistry alone. The long-standing questions regarding soil OM stability and recalcitrance will likely be answered when several molecular methods are used in tandem to closely examine structure, source, age, degradation stage, and interactions of specific OM components in soil.
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Affiliation(s)
- Myrna J Simpson
- Environmental NMR Centre and Department of Chemistry, University of Toronto, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada.
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Coolen MJL, van de Giessen J, Zhu EY, Wuchter C. Bioavailability of soil organic matter and microbial community dynamics upon permafrost thaw. Environ Microbiol 2011; 13:2299-314. [DOI: 10.1111/j.1462-2920.2011.02489.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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30
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Feng X, Simpson MJ. Molecular-level methods for monitoring soil organic matter responses to global climate change. ACTA ACUST UNITED AC 2011; 13:1246-54. [DOI: 10.1039/c0em00752h] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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