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Huang J, Wang D, Zhu Y, Yang Z, Yao M, Shi X, An T, Zhang Q, Huang C, Bi X, Li J, Wang Z, Liu Y, Zhu G, Chen S, Hang J, Qiu X, Deng W, Tian H, Zhang T, Chen T, Liu S, Lian X, Chen B, Zhang B, Zhao Y, Wang R, Li H. An overview for monitoring and prediction of pathogenic microorganisms in the atmosphere. FUNDAMENTAL RESEARCH 2024; 4:430-441. [PMID: 38933199 PMCID: PMC11197502 DOI: 10.1016/j.fmre.2023.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 04/29/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2024] Open
Abstract
Corona virus disease 2019 (COVID-19) has exerted a profound adverse impact on human health. Studies have demonstrated that aerosol transmission is one of the major transmission routes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Pathogenic microorganisms such as SARS-CoV-2 can survive in the air and cause widespread infection among people. Early monitoring of pathogenic microorganism transmission in the atmosphere and accurate epidemic prediction are the frontier guarantee for preventing large-scale epidemic outbreaks. Monitoring of pathogenic microorganisms in the air, especially in densely populated areas, may raise the possibility to detect viruses before people are widely infected and contain the epidemic at an earlier stage. The multi-scale coupled accurate epidemic prediction system can provide support for governments to analyze the epidemic situation, allocate health resources, and formulate epidemic response policies. This review first elaborates on the effects of the atmospheric environment on pathogenic microorganism transmission, which lays a theoretical foundation for the monitoring and prediction of epidemic development. Secondly, the monitoring technique development and the necessity of monitoring pathogenic microorganisms in the atmosphere are summarized and emphasized. Subsequently, this review introduces the major epidemic prediction methods and highlights the significance to realize a multi-scale coupled epidemic prediction system by strengthening the multidisciplinary cooperation of epidemiology, atmospheric sciences, environmental sciences, sociology, demography, etc. By summarizing the achievements and challenges in monitoring and prediction of pathogenic microorganism transmission in the atmosphere, this review proposes suggestions for epidemic response, namely, the establishment of an integrated monitoring and prediction platform for pathogenic microorganism transmission in the atmosphere.
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Affiliation(s)
- Jianping Huang
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
- College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Danfeng Wang
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yongguan Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zifeng Yang
- National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease (Guangzhou Medical University), Guangzhou 510230, China
| | - Maosheng Yao
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xiaoming Shi
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Taicheng An
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China
| | - Qiang Zhang
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing 100084, China
| | - Cunrui Huang
- Vanke School of Public Health, Tsinghua University, Beijing 100084, China
| | - Xinhui Bi
- State Key Laboratory of Organic Geochemistry and Guangdong Key Laboratory of Environmental Protection and Resources Utilization, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Jiang Li
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zifa Wang
- State Key Laboratory of Atmospheric Boundary Layer Physics and Atmospheric Chemistry, Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, China
| | - Yongqin Liu
- Center for Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Guibing Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Siyu Chen
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
- College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jian Hang
- School of Atmospheric Sciences, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 510640, China
| | - Xinghua Qiu
- State Key Joint Laboratory for Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, and Center for Environment and Health, Peking University, Beijing 100871, China
| | - Weiwei Deng
- Shenzhen Key Laboratory of Soft Mechanics & Smart Manufacturing and Department of Mechanics and Aerospace Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing 100101, China
| | - Tengfei Zhang
- Tianjin Key Laboratory of Indoor Air Environmental Quality Control, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Tianmu Chen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Sijin Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xinbo Lian
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
- College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Bin Chen
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
- College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Beidou Zhang
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
- College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yingjie Zhao
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
- College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Rui Wang
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
- College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Han Li
- Collaborative Innovation Center for Western Ecological Safety, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
- College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
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Li X, Ren X, Su Y, Zhou X, Wang Y, Ruan S, Yan J, Li B, Guo K. Differential effects of winter cold stress on soil bacterial communities, metabolites, and physicochemical properties in two varieties of Tetrastigma hemsleyanum Diels & Gilg in reclaimed land. Microbiol Spectr 2024; 12:e0242523. [PMID: 38470484 PMCID: PMC10994721 DOI: 10.1128/spectrum.02425-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 02/29/2024] [Indexed: 03/13/2024] Open
Abstract
Tetrastigma hemsleyanum Diels & Gilg (TDG) has been recently planted in reclaimed lands in Zhejiang Province, China, to increase reclaimed land use. Winter cold stress seriously limits the growth and development of TDG and has become the bottleneck limiting the TDG planting industry. To investigate the defense mechanisms of TDG toward winter cold stress when grown on reclaimed land, a combined analysis of soil bacterial communities, metabolites, and physicochemical properties was conducted in this study. Significant differences were observed in the composition of soil bacterial communities, metabolites, and properties in soils of a cold-tolerant variety (A201201) compared with a cold-intolerant variety (B201810). The fresh weight (75.8% of tubers) and dry weight (73.6%) of A201201 were significantly higher than those of B201810. The 16S rRNA gene amplicon sequencing of soil bacteria showed that Gp5 (25.3%), Gemmatimonas (19.6%), Subdivision3 (16.7%), Lacibacterium (11.9%), Gp4 (11.8%), Gp3 (10.4%), Gp6 (7.0%), and WPS-1 (1.2%) were less common, while Chryseolinea (10.6%) were more common in A201201 soils than B201810 soils. Furthermore, linear discriminant analysis of effect size identified 35 bacterial biomarker taxa for both treatments. Co-occurrence network analyses also showed that the structures of the bacterial communities were more complex and stable in A201201 soils compared to B201810 soils. In addition, ultra-high-performance liquid chromatography coupled to mass spectrometry analysis indicated the presence of significantly different metabolites in the two soil treatments, with 10 differentially expressed metabolites (DEMs) (8 significantly upregulated by 9.2%-391.3% and 2 significantly downregulated by 25.1%-73.4%) that belonged to lipids and lipid-like molecules, organic acids and derivatives, and benzenoids. The levels of those DEMs were significantly correlated with the relative abundances of nine bacterial genera. Also, redundancy discriminant analysis revealed that the main factors affecting changes in the bacterial community composition were available potassium (AK), microbial biomass nitrogen (MBN), microbial biomass carbon (MBC), alkaline hydrolysis nitrogen (AHN), total nitrogen (TN), available phosphorus (AP), and soil organic matter (SOM). The main factors affecting changes in the metabolite profiles were AK, MBC, MBN, AHN, pH, SOM, TN, and AP. Overall, this study provides new insights into the TDG defense mechanisms involved in winter cold stress responses when grown on reclaimed land and practical guidelines for achieving optimal TDG production.IMPORTANCEChina has been undergoing rapid urbanization, and land reclamation is regarded as a viable option to balance occupation and compensation. In general, the quality of reclaimed land cannot meet plant or even cultivation requirements due to poor soil fertility and high gravel content. However, Tetrastigma hemsleyanum Diels & Gilg (TDG), extensively used in Chinese herbal medicine, can grow well in stony soils with few nutrients. So, to increase reclaimed land use, TDG has been cultivated on reclaimed lands in Zhejiang Province, China, recently. However, the artificial cultivation of TDG is often limited by winter cold stress. The aim of this study was to find out how TDG on reclaimed land deal with winter cold stress by looking at the bacterial communities, metabolites, and physicochemical properties of the soil, thereby guiding production in practice.
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Affiliation(s)
- Xuqing Li
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaoxu Ren
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Yao Su
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiang Zhou
- Hangzhou Agricultural and Rural Affairs Guarantee Center, Hangzhou, China
| | - Yu Wang
- Qingliangfeng Lvyuan Vegetable Professional Cooperative, Hangzhou, China
| | - Songlin Ruan
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Jianli Yan
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Bin Li
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Kai Guo
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
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Wang X, Li Y, Yan Z, Hao Y, Kang E, Zhang X, Li M, Zhang K, Yan L, Yang A, Niu Y, Kang X. The divergent vertical pattern and assembly of soil bacterial and fungal communities in response to short-term warming in an alpine peatland. FRONTIERS IN PLANT SCIENCE 2022; 13:986034. [PMID: 36160969 PMCID: PMC9493461 DOI: 10.3389/fpls.2022.986034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Soil microbial communities are crucial in ecosystem-level decomposition and nutrient cycling processes and are sensitive to climate change in peatlands. However, the response of the vertical distribution of microbial communities to warming remains unclear in the alpine peatland. In this study, we examined the effects of warming on the vertical pattern and assembly of soil bacterial and fungal communities across three soil layers (0-10, 10-20, and 20-30 cm) in the Zoige alpine peatland under a warming treatment. Our results showed that short-term warming had no significant effects on the alpha diversity of either the bacterial or the fungal community. Although the bacterial community in the lower layers became more similar as soil temperature increased, the difference in the vertical structure of the bacterial community among different treatments was not significant. In contrast, the vertical structure of the fungal community was significantly affected by warming. The main ecological process driving the vertical assembly of the bacterial community was the niche-based process in all treatments, while soil carbon and nutrients were the main driving factors. The vertical structure of the fungal community was driven by a dispersal-based process in control plots, while the niche and dispersal processes jointly regulated the fungal communities in the warming plots. Plant biomass was significantly related to the vertical structure of the fungal community under the warming treatments. The variation in pH was significantly correlated with the assembly of the bacterial community, while soil water content, microbial biomass carbon/microbial biomass phosphorous (MBC/MBP), and microbial biomass nitrogen/ microbial biomass phosphorous (MBN/MBP) were significantly correlated with the assembly of the fungal community. These results indicate that the vertical structure and assembly of the soil bacterial and fungal communities responded differently to warming and could provide a potential mechanism of microbial community assembly in the alpine peatland in response to warming.
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Affiliation(s)
- Xiaodong Wang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Yong Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Zhongqing Yan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Yanbin Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Enze Kang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Xiaodong Zhang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Meng Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Kerou Zhang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Liang Yan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Ao Yang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
| | - Yuechuan Niu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Kang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
- Beijing Key Laboratory of Wetland Services and Restoration, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Aba, China
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Wang Z, Feng K, Lu G, Yu H, Wang S, Wei Z, Dang N, Wang Y, Deng Y. Homogeneous Selection and Dispersal Limitation Dominate the Effect of Soil Strata Under Warming Condition. Front Microbiol 2022; 13:801083. [PMID: 35283849 PMCID: PMC8908236 DOI: 10.3389/fmicb.2022.801083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
Global warming is likely to affect the underground microbial communities in various ecosystems, but the response of soil microbial communities along a vertical depth profile to global warming has been elusive. Herein, we leveraged a warming field experiment in Qinghai-Tibet Plateau grassland and investigated the community structure of prokaryotes and fungi from the upper (0-15 cm) and lower (15-30 cm) strata under ambient and elevated temperature treatments. Three-years continual warming only significantly shifted the prokaryotic community within the upper strata and there was no significant effect observed for the fungal community. Additionally, under ambient temperature, there were significant differences between the two strata in both the prokaryotic and fungal communities, but under warming, this effect was alleviated. Next, the prokaryotic and fungal community assembly processes were measured by a phylogenetic-bin-based null approach (iCAMP). Though deterministic and stochastic processes dominated the assembly of prokaryotic and fungal communities, respectively, the deterministic processes were strengthened under warming for both communities. Specifically, the increased portion of homogeneous selection, contributing to a homogenous state, led to a smaller difference between prokaryotic communities of the two soil strata under warming. The smaller difference in the stochastic process component, i.e., dispersal limitation, contributed to the similar fungal community structures between the two strata under warming. This study deepens our understanding of warming effects on grassland microbial communities and gives greater insights on the underlying mechanisms for microbial assembly between upper and lower soil strata under warming scenarios.
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Affiliation(s)
- Zhujun Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Guangxin Lu
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Hao Yu
- College of Environmental Science and Engineering, Liaoning Technical University, Fuxin, China
| | - Shang Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ziyan Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ning Dang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Yingcheng Wang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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Mao G, Ji M, Xu B, Liu Y, Jiao N. Variation of High and Low Nucleic Acid-Content Bacteria in Tibetan Ice Cores and Their Relationship to Black Carbon. Front Microbiol 2022; 13:844432. [PMID: 35237252 PMCID: PMC8882866 DOI: 10.3389/fmicb.2022.844432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/24/2022] [Indexed: 01/29/2023] Open
Abstract
Nutrient enrichment caused by black carbon (BC) is a major ecological crisis in glacial ecosystems. The microbiological effects of BC were assessed in this study by using fluorescent fingerprinting assay based on flow cytometry (FCM) of bacterial communities with low (LNA) and high (HNA) nucleic acid-content bacteria. Here, we investigated a high-resolution temporal variation of bacterial abundance and LNA/HNA ratio in Tibetan ice cores. Our results revealed that bacterial abundance was proportional to the atmospheric BC on the glaciers. The shift of LNA functional groups to HNA functional groups in glaciers suggested BC emissions increased the proportion of highly active cells. In addition, distinct number of LNA and HNA functional groups was identified between the monsoon and non-monsoon seasons. Westerly winds with high amounts of BC accounted for high ratio of HNA functional groups during the non-monsoon season. In comparison, high moisture during the monsoon season decreased atmospheric BC loading, which increases the ratio of LNA functional groups. Correlations between BC and functional groups were very strong, showing that two functional groups may serve as early-warning indicators of microbiological effects of BC at low trophic level. Our approach provides a potential early-warning framework to study the influences of atmospheric BC on the glaciological community.
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Affiliation(s)
- Guannan Mao
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Baiqing Xu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yongqin Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Yongqin Liu,
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
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Yu GH, Kuzyakov Y, Luo Y, Goodman BA, Kappler A, Liu FF, Sun FS. Molybdenum Bioavailability and Asymbiotic Nitrogen Fixation in Soils are Raised by Iron (Oxyhydr)oxide-Mediated Free Radical Production. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14979-14989. [PMID: 34677955 DOI: 10.1021/acs.est.1c04240] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nitrogen (N) fixation in soils is closely linked to microbially mediated molybdenum (Mo) cycling. Therefore, elucidating the mechanisms and factors that affect Mo bioavailability is crucial for understanding N fixation. Here, we demonstrate that long-term (26 years) manure fertilization increased microbial diversity and content of short-range ordered iron (oxyhydr)oxides that raised Mo bioavailability (by 2.8 times) and storage (by ∼30%) and increased the abundance of nifH genes (by ∼14%) and nitrogenase activity (by ∼60%). Nanosized iron (oxyhydr)oxides (ferrihydrite, goethite, and hematite nanoparticles) play a dual role in soil Mo cycling: (i) in concert with microorganisms, they raise Mo bioavailability by catalyzing hydroxyl radical (HO•) production via the Fenton reactions and (ii) they increase Mo retention by association with the nanosized iron (oxyhydr)oxides. In summary, long-term manure fertilization raised the stock and bioavailability of Mo (and probably also of other micronutrients) by increasing iron (oxyhydr)oxide reactivity and intensified asymbiotic N fixation through an increased abundance of nifH genes and nitrogenase activity. This work provides a strategy for increasing biological N fixation in agricultural ecosystems.
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Affiliation(s)
- Guang-Hui Yu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin Key Laboratory of Earth Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Göttingen, Göttingen 37073, Germany
- Agro-Technological Institute, RUDN University, Moscow 117198, Russia
| | - Yu Luo
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Bernard A Goodman
- College of Physical Science and Technology, Guangxi University, Nanning 530004, China
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen 72076, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infections, Tübingen 72076, Germany
| | - Fei-Fei Liu
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fu-Sheng Sun
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin Key Laboratory of Earth Critical Zone Science and Sustainable Development in Bohai Rim, Tianjin University, Tianjin 300072, China
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A Perspective of the Cumulative Risks from Climate Change on Mt. Everest: Findings from the 2019 Expedition. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18041928. [PMID: 33671205 PMCID: PMC7922742 DOI: 10.3390/ijerph18041928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/29/2022]
Abstract
In 2019, the National Geographic and Rolex Perpetual Planet Everest expedition successfully retrieved the greatest diversity of scientific data ever from the mountain. The confluence of geologic, hydrologic, chemical and microbial hazards emergent as climate change increases glacier melt is significant. We review the findings of increased opportunity for landslides, water pollution, human waste contamination and earthquake events. Further monitoring and policy are needed to ensure the safety of residents, future climbers, and trekkers in the Mt. Everest watershed.
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First report on antibiotic resistance and antimicrobial activity of bacterial isolates from 13,000-year old cave ice core. Sci Rep 2021; 11:514. [PMID: 33436712 PMCID: PMC7804186 DOI: 10.1038/s41598-020-79754-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/14/2020] [Indexed: 11/24/2022] Open
Abstract
Despite the unique physiology and metabolic pathways of microbiomes from cold environments providing key evolutionary insights and promising leads for discovering new bioactive compounds, cultivable bacteria entrapped in perennial ice from caves remained a largely unexplored life system. In this context, we obtained and characterized bacterial strains from 13,000-years old ice core of Scarisoara Ice Cave, providing first isolates from perennial ice accumulated in caves since Late Glacial, and first culture-based evidences of bacterial resistome and antimicrobial compounds production. The 68 bacterial isolates belonged to 4 phyla, 34 genera and 56 species, with 17 strains representing putative new taxa. The Gram-negative cave bacteria (Proteobacteria and Bacteroidetes) were more resistant to the great majority of antibiotic classes than the Gram-positive ones (Actinobacteria, Firmicutes). More than 50% of the strains exhibited high resistance to 17 classes of antibiotics. Some of the isolates inhibited the growth of clinically important Gram-positive and Gram-negative resistant strains and revealed metabolic features with applicative potential. The current report on bacterial strains from millennia-old cave ice revealed promising candidates for studying the evolution of environmental resistome and for obtaining new active biomolecules for fighting the antibiotics crisis, and valuable cold-active biocatalysts.
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Chen B, Jiao S, Luo S, Ma B, Qi W, Cao C, Zhao Z, Du G, Ma X. High soil pH enhances the network interactions among bacterial and archaeal microbiota in alpine grasslands of the Tibetan Plateau. Environ Microbiol 2020; 23:464-477. [PMID: 33215802 DOI: 10.1111/1462-2920.15333] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022]
Abstract
Soil functions and processes are driven by complex microbial interactions. It is, therefore, critical to understand the coexistence patterns of soil microbiota, especially in fragile alpine ecosystems. We identified biogeographic patterns in the network-level topological features of the soil microbial co-occurrence network in the Tibetan alpine grasslands, based on high-throughput sequencing. We verified that soil pH was the most important environmental variable for predicting network-level topological features of soil microbial co-occurrence networks. Associations among soil microbiota were enhanced with increasing pH (5.17-8.92), and the network was the most stable at neutral pH. Moreover, node-level topological features suggested that the archaeal operational taxonomic units, compared with bacterial operational taxonomic units, hold a central role in the co-occurrence network. Network-level topological features revealed closer connections among soil microbiota in the steppe ecosystem than in the meadow ecosystem. Therefore, our study demonstrated that soil pH served as a critical environmental filter that influenced the potential associations and ecological signature of soil microbiota in the Tibetan alpine grasslands. These findings provide a new perspective on the distinct biogeographic patterns of co-occurrence networks, to explore the ecological role of soil microbiota and thus help manage soil bacterial and archaeal communities for provisioning alpine ecosystem services.
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Affiliation(s)
- Beibei Chen
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shuaiwei Luo
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Arid and Grassland Ecology of Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Beibei Ma
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wei Qi
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Arid and Grassland Ecology of Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Changdong Cao
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhigang Zhao
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Guozhen Du
- School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Arid and Grassland Ecology of Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xiaojun Ma
- School of Life Sciences, Lanzhou University, Lanzhou, China
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10
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Malaska MJ, Bhartia R, Manatt KS, Priscu JC, Abbey WJ, Mellerowicz B, Palmowski J, Paulsen GL, Zacny K, Eshelman EJ, D'Andrilli J. Subsurface In Situ Detection of Microbes and Diverse Organic Matter Hotspots in the Greenland Ice Sheet. ASTROBIOLOGY 2020; 20:1185-1211. [PMID: 32700965 PMCID: PMC7591382 DOI: 10.1089/ast.2020.2241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/08/2020] [Indexed: 06/11/2023]
Abstract
We used a deep-ultraviolet fluorescence mapping spectrometer, coupled to a drill system, to scan from the surface to 105 m depth into the Greenland ice sheet. The scan included firn and glacial ice and demonstrated that the instrument is able to determine small (mm) and large (cm) scale regions of organic matter concentration and discriminate spectral types of organic matter at high resolution. Both a linear point cloud scanning mode and a raster mapping mode were used to detect and localize microbial and organic matter "hotspots" embedded in the ice. Our instrument revealed diverse spectral signatures. Most hotspots were <20 mm in diameter, clearly isolated from other hotspots, and distributed stochastically; there was no evidence of layering in the ice at the fine scales examined (100 μm per pixel). The spectral signatures were consistent with organic matter fluorescence from microbes, lignins, fused-ring aromatic molecules, including polycyclic aromatic hydrocarbons, and biologically derived materials such as fulvic acids. In situ detection of organic matter hotspots in ice prevents loss of spatial information and signal dilution when compared with traditional bulk analysis of ice core meltwaters. Our methodology could be useful for detecting microbial and organic hotspots in terrestrial icy environments and on future missions to the Ocean Worlds of our Solar System.
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Affiliation(s)
- Michael J. Malaska
- Jet Propulsion Laboratory/California Institute of Technology, Pasadena, California, USA
| | | | - Kenneth S. Manatt
- Jet Propulsion Laboratory/California Institute of Technology, Pasadena, California, USA
| | - John C. Priscu
- Department of Land Resources & Environmental Sciences, Montana State University, Bozeman, Montana, USA
| | - William J. Abbey
- Jet Propulsion Laboratory/California Institute of Technology, Pasadena, California, USA
| | | | | | | | - Kris Zacny
- Honeybee Robotics, Altadena, California, USA
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11
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Liu Y, Shen L, Zeng Y, Xing T, Xu B, Wang N. Genomic Insights of Cryobacterium Isolated From Ice Core Reveal Genome Dynamics for Adaptation in Glacier. Front Microbiol 2020; 11:1530. [PMID: 32765445 PMCID: PMC7381226 DOI: 10.3389/fmicb.2020.01530] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/12/2020] [Indexed: 11/30/2022] Open
Abstract
Glacier is the dominant cold habitat in terrestrial environments, providing a model ecosystem to explore extremophilic strategies and study early lives on Earth. The dominant form of life in glaciers is bacteria. However, little is known about past evolutionary processes that bacteria underwent during adaptation to the cryosphere and the connection of their genomic traits to environmental stressors. Aiming to test the hypothesis that bacterial genomic content and dynamics are driven by glacial environmental stressors, we compared genomes of 21 psychrophilic Cryobacterium strains, including 14 that we isolated from three Tibetan ice cores, to their mesophilic counterparts from the same family Microbacteriaceae of Actinobacteria. The results show that psychrophilic Cryobacterium underwent more dynamic changes in genome content, and their genomes have a significantly higher number of genes involved in stress response, motility, and chemotaxis than their mesophilic counterparts (P < 0.05). The phylogenetic birth-and-death model imposed on the phylogenomic tree indicates a vast surge in recent common ancestor of psychrophilic Cryobacterium (gained the greatest number of genes by 1,168) after the division of the mesophilic strain Cryobacterium mesophilum. The expansion in genome content brought in key genes primarily of the categories “cofactors, vitamins, prosthetic groups, pigments,” “monosaccharides metabolism,” and “membrane transport.” The amino acid substitution rates of psychrophilic Cryobacterium strains are two orders of magnitude lower than those in mesophilic strains. However, no significantly higher number of cold shock genes was found in psychrophilic Cryobacterium strains, indicating that multi-copy is not a key factor for cold adaptation in the family Microbacteriaceae, although cold shock genes are indispensable for psychrophiles. Extensive gene acquisition and low amino acid substitution rate might be the strategies of psychrophilic Cryobacterium to resist low temperature, oligotrophy, and high UV radiation on glaciers. The exploration of genome evolution and survival strategies of psychrophilic Cryobacterium deepens our understanding of bacterial cold adaptation.
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Affiliation(s)
- Yongqin Liu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liang Shen
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yonghui Zeng
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Tingting Xing
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Baiqing Xu
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China
| | - Ninglian Wang
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Beijing, China.,College of Urban and Environmental Science, Northwest University, Xi'an, China
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12
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Liang Y, Zhang Y, Zhou C, Li H, Kang X, Wang L, Song J, Jiao N. Cumulative impact of long-term intensive mariculture on total and active bacterial communities in the core sediments of the Ailian Bay, North China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 691:1212-1224. [PMID: 31466202 DOI: 10.1016/j.scitotenv.2019.07.200] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/10/2019] [Accepted: 07/13/2019] [Indexed: 06/10/2023]
Abstract
The exponential growth of off-shore mariculture worldwide over the last 20 years has had significant impact on coastal sediment biogeochemistry. However, there are no long-term records of the cumulative impacts of mariculture on the benthic bacterial community. Here, total (DNA) and active (RNA) bacterial community compositions were characterized using MiSeq sequencing of 16S rRNA gene in four core sediments of the Ailian Bay, one of the typical intensive mariculture areas in China with more than fifty-year history of kelp and scallop cultivation. The γ-Proteobacteria, δ-Proteobacteria, Acidobacteria and Acitinobacteria were more abundant in the total bacterial communities, while β-Proteobacteria, Anaerolineae, Clostridia, Spirochaetes and Cyanobacteria were enriched in the active bacterial communities. Significant differences were observed between total and active benthic bacterial communities. The influences of different mariculture modes on the total bacterial communities were more significant than those on the active bacterial communities. Only limited groups of the total bacterial communities were significant influenced by the cumulative effects of the long-term mariculture. The bacterial genera with the function in the sulfide cycling and organic consumption were enriched in the total bacterial population of the integrated multi-trophic aquaculture (IMTA) areas. The variations of both total and active bacterial communities were significantly influenced by grain sizes, total organic carbon and nutrients. Both total and active bacterial communities exhibited a slightly stronger response to environmental factors than to spatial (distance) factors. The effects of mutualism might dominate the total and active bacterial networks in the Ailian Bay. The present study demonstrated that the cumulative influences of the long-term and intensive IMTA mariculture on total benthic bacterial communities in the sub-surface sediments of the Ailian Bay were stronger than those on the active benthic bacterial communities, which provided some insights into the potential ecological roles of specific taxa in the sediments of the IMTA ecosystems.
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Affiliation(s)
- Yantao Liang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China; Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
| | - Yongyu Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Chao Zhou
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Hongmei Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Xuming Kang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Key Laboratory of Testing and Evaluation for Aquatic Product Safety and Quality, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Long Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Jinming Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nianzhi Jiao
- Institute of Marine Microbes and Ecospheres, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361101, China
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13
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Paun VI, Icaza G, Lavin P, Marin C, Tudorache A, Perşoiu A, Dorador C, Purcarea C. Total and Potentially Active Bacterial Communities Entrapped in a Late Glacial Through Holocene Ice Core From Scarisoara Ice Cave, Romania. Front Microbiol 2019; 10:1193. [PMID: 31244788 PMCID: PMC6563852 DOI: 10.3389/fmicb.2019.01193] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/13/2019] [Indexed: 01/20/2023] Open
Abstract
Our understanding of the icy-habitat microbiome is likely limited by a lack of reliable data on microorganisms inhabiting underground ice that has accumulated inside caves. To characterize how environmental variation impacts cave ice microbial community structure, we determined the composition of total and potentially active bacterial communities along a 13,000-year-old ice core from Scarisoara cave (Romania) through 16S rRNA gene Illumina sequencing. An average of 2,546 prokaryotic gDNA operational taxonomic units (OTUs) and 585 cDNA OTUs were identified across the perennial cave ice block and analyzed in relation to the geochemical composition of ice layers. The total microbial community and the putative active fraction displayed dissimilar taxa profiles. The ice-contained microbiome was dominated by Actinobacteria with a variable representation of Proteobacteria, while the putative active microbial community was equally shared between Proteobacteria and Firmicutes. Accordingly, a major presence of Cryobacterium, Lysinomonas, Pedobacter, and Aeromicrobium phylotypes homologous to psychrotrophic and psychrophilic bacteria from various cold environments were noted in the total community, while the prevalent putative active bacteria belonged to Clostridium, Pseudomonas, Janthinobacterium, Stenotrophomonas, and Massilia genera. Variation in the microbial cell density of ice strata with the dissolved organic carbon (DOC) content and the strong correlation of DOC and silicon concentrations revealed a major impact of depositional processes on microbial abundance throughout the ice block. Post-depositional processes appeared to occur mostly during the 4,000–7,000 years BP interval. A major bacterial composition shift was observed in 4,500–5,000-year-old ice, leading to a high representation of Beta- and Deltaproteobacteria in the potentially active community in response to the increased concentrations of DOC and major chemical elements. Estimated metabolic rates suggested the presence of a viable microbial community within the cave ice block, characterized by a maintenance metabolism in most strata and growth capacity in those ice deposits with high microbial abundance and DOC content. This first survey of microbial distribution in perennial cave ice formed since the Last Glacial period revealed a complex potentially active community, highlighting major shifts in community composition associated with geochemical changes that took place during climatic events that occurred about 5,000 years ago, with putative formation of photosynthetic biofilms.
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Affiliation(s)
- Victoria I Paun
- Department of Microbiology, Institute of Biology, Bucharest, Romania
| | - Gonzalo Icaza
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile
| | - Paris Lavin
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Constantin Marin
- Laboratory of Hydrogeochemistry, "Emil Racovita" Institute of Speleology, Bucharest, Romania
| | - Alin Tudorache
- Laboratory of Hydrogeochemistry, "Emil Racovita" Institute of Speleology, Bucharest, Romania
| | - Aurel Perşoiu
- Department of Microbiology, Institute of Biology, Bucharest, Romania.,"Emil Racovita" Institute of Speleology, Cluj-Napoca, Romania.,Stefan cel Mare University of Suceava, Suceava, Romania
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering, Universidad de Antofagasta, Antofagasta, Chile.,Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Cristina Purcarea
- Department of Microbiology, Institute of Biology, Bucharest, Romania
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14
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Bacterial and archaeal community structures in perennial cave ice. Sci Rep 2018; 8:15671. [PMID: 30353134 PMCID: PMC6199274 DOI: 10.1038/s41598-018-34106-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/12/2018] [Indexed: 01/08/2023] Open
Abstract
Ice entrenched microcosm represents a vast reservoir of novel species and a proxy for past climate reconstitution. Among glacial ecosystems, ice caves represent one of the scarcely investigated frozen habitats. To characterize the microbial diversity of perennial ice from karst ecosystems, Roche 454 sequencing of 16S rRNA gene amplicons from the underground ice block of Scarisoara Ice Cave (Romania) was applied. The temporal distribution of bacterial and archaeal community structures from newly formed, 400, and 900 years old ice layers was surveyed and analyzed in relation with the age and geochemical composition of the ice substrate. The microbial content of cave ice layers varied from 3.3 104 up to 7.5 105 cells mL−1, with 59–78% viability. Pyrosequencing generated 273,102 reads for the five triplicate ice samples, which corresponded to 3,464 operational taxonomic units (OTUs). The distribution of the bacterial phyla in the perennial cave ice varied with age, organic content, and light exposure. Proteobacteria dominated the 1 and 900 years old organic rich ice deposits, while Actinobacteria was mostly found in 900 years old ice strata, and Firmicutes was best represented in 400 years old ice. Cyanobacteria and Chlorobi representatives were identified mainly from the ice block surface samples exposed to sunlight. Archaea was observed only in older ice strata, with a high incidence of Crenarchaeota and Thaumarchaeaota in the 400 years old ice, while Euryarchaeota dominated the 900 years old ice layers, with Methanomicrobia representing the predominant taxa. A large percentage (55.7%) of 16S rRNA gene amplicons corresponded to unidentified OTUs at genus or higher taxa levels, suggesting a greater undiscovered bacterial diversity in this glacial underground habitat. The prokaryotes distribution across the cave ice block revealed the presence of 99 phylotypes specific for different ice layers, in addition to the shared microbial community. Ice geochemistry represented an important factor that explained the microbial taxa distribution in the cave ice block, while the total organic carbon content had a direct impact on the cell density of the ice microcosm. Both bacterial and archaeal community structures appeared to be affected by climate variations during the ice formation, highlighting the cave ice microbiome as a source of putative paleoclimatic biomarkers. This report constitutes the first high-throughput sequencing study of the cave ice microbiome and its distribution across the perennial underground glacier of an alpine ice cave.
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15
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Zhong ZP, Solonenko NE, Gazitúa MC, Kenny DV, Mosley-Thompson E, Rich VI, Van Etten JL, Thompson LG, Sullivan MB. Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms. Front Microbiol 2018; 9:1094. [PMID: 29910780 PMCID: PMC5992382 DOI: 10.3389/fmicb.2018.01094] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 05/07/2018] [Indexed: 11/13/2022] Open
Abstract
Microorganisms in glacier ice provide tens to hundreds of thousands of years archive for a changing climate and microbial responses to it. Analyzing ancient ice is impeded by technical issues, including limited ice, low biomass, and contamination. While many approaches have been evaluated and advanced to remove contaminants on ice core surfaces, few studies leverage modern sequencing to establish in silico decontamination protocols for glacier ice. Here we sought to apply such “clean” sampling techniques with in silico decontamination approaches used elsewhere to investigate microorganisms archived in ice at ∼41 (D41, ∼20,000 years) and ∼49 m (D49, ∼30,000 years) depth in an ice core (GS3) from the summit of the Guliya ice cap in the northwestern Tibetan Plateau. Four “background” controls were established – a co-processed sterile water artificial ice core, two air samples collected from the ice processing laboratories, and a blank, sterile water sample – and used to assess contaminant microbial diversity and abundances. Amplicon sequencing revealed 29 microbial genera in these controls, but quantitative PCR showed that the controls contained about 50–100-times less 16S DNA than the glacial ice samples. As in prior work, we interpreted these low-abundance taxa in controls as “contaminants” and proportionally removed them in silico from the GS3 ice amplicon data. Because of the low biomass in the controls, we also compared prokaryotic 16S DNA amplicons from pre-amplified (by re-conditioning PCR) and standard amplicon sequencing, and found the resulting microbial profiles to be repeatable and nearly identical. Ecologically, the contaminant-controlled ice microbial profiles revealed significantly different microorganisms across the two depths in the GS3 ice core, which is consistent with changing climate, as reported for other glacier ice samples. Many GS3 ice core genera, including Methylobacterium, Sphingomonas, Flavobacterium, Janthinobacterium, Polaromonas, and Rhodobacter, were also abundant in previously studied ice cores, which suggests wide distribution across glacier environments. Together these findings help further establish “clean” procedures for studying low-biomass ice microbial communities and contribute to a baseline understanding of microorganisms archived in glacier ice.
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Affiliation(s)
- Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Natalie E Solonenko
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Maria C Gazitúa
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Donald V Kenny
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, United States
| | - Ellen Mosley-Thompson
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, United States.,Department of Geography, The Ohio State University, Columbus, OH, United States
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, Columbus, OH, United States.,Department of Soil, Water and Environmental Science, The University of Arizona, Tucson, AZ, United States
| | - James L Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Lonnie G Thompson
- Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, United States.,School of Earth Sciences, The Ohio State University, Columbus, OH, United States
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, United States.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, United States
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16
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Santibáñez PA, Maselli OJ, Greenwood MC, Grieman MM, Saltzman ES, McConnell JR, Priscu JC. Prokaryotes in the WAIS Divide ice core reflect source and transport changes between Last Glacial Maximum and the early Holocene. GLOBAL CHANGE BIOLOGY 2018; 24:2182-2197. [PMID: 29322639 DOI: 10.1111/gcb.14042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 11/25/2017] [Indexed: 06/07/2023]
Abstract
We present the first long-term, highly resolved prokaryotic cell concentration record obtained from a polar ice core. This record, obtained from the West Antarctic Ice Sheet (WAIS) Divide (WD) ice core, spanned from the Last Glacial Maximum (LGM) to the early Holocene (EH) and showed distinct fluctuations in prokaryotic cell concentration coincident with major climatic states. The time series also revealed a ~1,500-year periodicity with greater amplitude during the Last Deglaciation (LDG). Higher prokaryotic cell concentration and lower variability occurred during the LGM and EH than during the LDG. A sevenfold decrease in prokaryotic cell concentration coincided with the LGM/LDG transition and the global 19 ka meltwater pulse. Statistical models revealed significant relationships between the prokaryotic cell record and tracers of both marine (sea-salt sodium [ssNa]) and burning emissions (black carbon [BC]). Collectively, these models, together with visual observations and methanosulfidic acid (MSA) measurements, indicated that the temporal variability in concentration of airborne prokaryotic cells reflected changes in marine/sea-ice regional environments of the WAIS. Our data revealed that variations in source and transport were the most likely processes producing the significant temporal variations in WD prokaryotic cell concentrations. This record provided strong evidence that airborne prokaryotic cell deposition differed during the LGM, LDG, and EH, and that these changes in cell densities could be explained by different environmental conditions during each of these climatic periods. Our observations provide the first ice-core time series evidence for a prokaryotic response to long-term climatic and environmental processes.
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Affiliation(s)
- Pamela A Santibáñez
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
- Departamento Científico, Instituto Antártico Chileno (INACH), Punta Arenas, Chile
| | - Olivia J Maselli
- Desert Research Institute, Nevada System of Higher Education, Reno, NV, USA
| | - Mark C Greenwood
- Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA
| | - Mackenzie M Grieman
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Eric S Saltzman
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Joseph R McConnell
- Desert Research Institute, Nevada System of Higher Education, Reno, NV, USA
| | - John C Priscu
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
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17
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Wang J, Soininen J. Thermal barriers constrain microbial elevational range size via climate variability. Environ Microbiol 2017; 19:3283-3296. [DOI: 10.1111/1462-2920.13823] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/07/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of SciencesNanjing 210008 China
- Department of Geosciences and GeographyUniversity of HelsinkiHelsinki FIN‐00014 Finland
| | - Janne Soininen
- Department of Geosciences and GeographyUniversity of HelsinkiHelsinki FIN‐00014 Finland
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