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Donhauser J, Qi W, Bergk-Pinto B, Frey B. High temperatures enhance the microbial genetic potential to recycle C and N from necromass in high-mountain soils. GLOBAL CHANGE BIOLOGY 2021; 27:1365-1386. [PMID: 33336444 DOI: 10.1111/gcb.15492] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/28/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Climate change is strongly affecting high-mountain soils and warming in particular is associated with pronounced changes in microbe-mediated C and N cycling, affecting plant-soil interactions and greenhouse gas balances and therefore feedbacks to global warming. We used shotgun metagenomics to assess changes in microbial community structures, as well as changes in microbial C- and N-cycling potential and stress response genes and we linked these data with changes in soil C and N pools and temperature-dependent measurements of bacterial growth rates. We did so by incubating high-elevation soil from the Swiss Alps at 4°C, 15°C, 25°C, or 35°C for 1 month. We found no shift with increasing temperature in the C-substrate-degrader community towards taxa more capable of degrading recalcitrant organic matter. Conversely, at 35°C, we found an increase in genes associated with the degradation and modification of microbial cell walls, together with high bacterial growth rates. Together, these findings suggest that the rapidly growing high-temperature community is fueled by necromass from heat-sensitive taxa. This interpretation was further supported by a shift in the microbial N-cycling potential towards N mineralization and assimilation under higher temperatures, along with reduced potential for conversions among inorganic N forms. Microbial stress-response genes reacted inconsistently to increasing temperature, suggesting that the high-temperature community was not severely stressed by these conditions. Rather, soil microbes were able to acclimate by changing the thermal properties of membranes and cell walls as indicated by an increase in genes involved in membrane and cell wall modifications as well as a shift in the optimum temperature for bacterial growth towards the treatment temperature. Overall, our results suggest that high temperatures, as they may occur with heat waves under global warming, promote a highly active microbial community capable of rapid mineralization of microbial necromass, which may transiently amplify warming effects.
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Affiliation(s)
- Jonathan Donhauser
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Benoît Bergk-Pinto
- Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, France
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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Perez-Mon C, Qi W, Vikram S, Frossard A, Makhalanyane T, Cowan D, Frey B. Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps). Microb Genom 2021; 7:000558. [PMID: 33848236 PMCID: PMC8208683 DOI: 10.1099/mgen.0.000558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The warming-induced thawing of permafrost promotes microbial activity, often resulting in enhanced greenhouse gas emissions. The ability of permafrost microorganisms to survive the in situ sub-zero temperatures, their energetic strategies and their metabolic versatility in using soil organic materials determine their growth and functionality upon thawing. Hence, functional characterization of the permafrost microbiome, particularly in the underexplored mid-latitudinal alpine regions, is a crucial first step in predicting its responses to the changing climate, and the consequences for soil-climate feedbacks. In this study, for the first time, the functional potential and metabolic capabilities of a temperate mountain permafrost microbiome from central Europe has been analysed using shotgun metagenomics. Permafrost and active layers from the summit of Muot da Barba Peider (MBP) [Swiss Alps, 2979 m above sea level (a.s.l.)] revealed a strikingly high functional diversity in the permafrost (north-facing soils at a depth of 160 cm). Permafrost metagenomes were enriched in stress-response genes (e.g. cold-shock genes, chaperones), as well as in genes involved in cell defence and competition (e.g. antiviral proteins, antibiotics, motility, nutrient-uptake ABC transporters), compared with active-layer metagenomes. Permafrost also showed a higher potential for the synthesis of carbohydrate-active enzymes, and an overrepresentation of genes involved in fermentation, carbon fixation, denitrification and nitrogen reduction reactions. Collectively, these findings demonstrate the potential capabilities of permafrost microorganisms to thrive in cold and oligotrophic conditions, and highlight their metabolic versatility in carbon and nitrogen cycling. Our study provides a first insight into the high functional gene diversity of the central European mountain permafrost microbiome. Our findings extend our understanding of the microbial ecology of permafrost and represent a baseline for future investigations comparing the functional profiles of permafrost microbial communities at different latitudes.
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Affiliation(s)
- Carla Perez-Mon
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- *Correspondence: Carla Perez-Mon,
| | - Weihong Qi
- Functional Genomics Center of the University of Zurich and the ETH Zurich, Zurich, Switzerland
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Thulani Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- *Correspondence: Beat Frey,
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53
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Bernard J, Wall CB, Costantini MS, Rollins RL, Atkins ML, Cabrera FP, Cetraro ND, Feliciano CKJ, Greene AL, Kitamura PK, Olmedo-Velarde A, Sirimalwatta VNS, Sung HW, Thompson LPM, Vu HT, Wilhite CJ, Amend AS. Plant part and a steep environmental gradient predict plant microbial composition in a tropical watershed. THE ISME JOURNAL 2021; 15:999-1009. [PMID: 33188299 PMCID: PMC8115680 DOI: 10.1038/s41396-020-00826-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 01/29/2023]
Abstract
Plant microbiomes are shaped by forces working at different spatial scales. Environmental factors determine a pool of potential symbionts while host physiochemical factors influence how those microbes associate with distinct plant tissues. These scales are seldom considered simultaneously, despite their potential to interact. Here, we analyze epiphytic microbes from nine Hibiscus tiliaceus trees across a steep, but short, environmental gradient within a single Hawaiian watershed. At each location, we sampled eight microhabitats: leaves, petioles, axils, stems, roots, and litter from the plant, as well as surrounding air and soil. The composition of bacterial communities is better explained by microhabitat, while location better predicted compositional variance for fungi. Fungal community compositional dissimilarity increased more rapidly along the gradient than did bacterial composition. Additionally, the rates of fungal community compositional dissimilarity along the gradient differed among plant parts, and these differences influenced the distribution patterns and range size of individual taxa. Within plants, microbes were compositionally nested such that aboveground communities contained a subset of the diversity found belowground. Our findings indicate that both environmental context and microhabitat contribute to microbial compositional variance in our study, but that these contributions are influenced by the domain of microbe and the specific microhabitat in question, suggesting a complicated and potentially interacting dynamic.
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Affiliation(s)
- Jared Bernard
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawai’i–Mānoa, 3050 Maile Way, Honolulu, HI 96822 USA
| | - Christopher B. Wall
- grid.410445.00000 0001 2188 0957Hawai’i Institute of Marine Biology, University of Hawai’i–Mānoa, 46-007 Lilipuna Road, Kāneʻohe, HI 96744 USA ,grid.410445.00000 0001 2188 0957Pacific Biosciences Research Center, University of Hawai’i–Mānoa, 3050 Maile Way, Honolulu, HI 96822 USA
| | - Maria S. Costantini
- grid.410445.00000 0001 2188 0957Department of Biology, University of Hawai’i–Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822 USA
| | - Randi L. Rollins
- grid.410445.00000 0001 2188 0957Pacific Biosciences Research Center, University of Hawai’i–Mānoa, 3050 Maile Way, Honolulu, HI 96822 USA ,grid.410445.00000 0001 2188 0957Department of Biology, University of Hawai’i–Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822 USA
| | - Melissa L. Atkins
- grid.410445.00000 0001 2188 0957Department of Biology, University of Hawai’i–Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822 USA
| | - Feresa P. Cabrera
- grid.410445.00000 0001 2188 0957Department of Botany, University of Hawai’i–Mānoa, 3190 Maile Way, Honolulu, HI 96822 USA
| | - Nicolas D. Cetraro
- grid.410445.00000 0001 2188 0957Pacific Biosciences Research Center, University of Hawai’i–Mānoa, 3050 Maile Way, Honolulu, HI 96822 USA
| | - Christian K. J. Feliciano
- grid.410445.00000 0001 2188 0957Department of Botany, University of Hawai’i–Mānoa, 3190 Maile Way, Honolulu, HI 96822 USA
| | - Austin L. Greene
- grid.410445.00000 0001 2188 0957Department of Biology, University of Hawai’i–Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822 USA
| | - Philip K. Kitamura
- grid.410445.00000 0001 2188 0957Department of Natural Resources and Environmental Management, University of Hawai’i–Mānoa, 1910 East-West Road, Honolulu, HI 96822 USA
| | - Alejandro Olmedo-Velarde
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawai’i–Mānoa, 3050 Maile Way, Honolulu, HI 96822 USA
| | - Vithanage N. S. Sirimalwatta
- grid.410445.00000 0001 2188 0957Department of Botany, University of Hawai’i–Mānoa, 3190 Maile Way, Honolulu, HI 96822 USA
| | - Helen W. Sung
- grid.410445.00000 0001 2188 0957Department of Biology, University of Hawai’i–Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822 USA
| | - Leah P. M. Thompson
- grid.410445.00000 0001 2188 0957Department of Botany, University of Hawai’i–Mānoa, 3190 Maile Way, Honolulu, HI 96822 USA
| | - Huong T. Vu
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawai’i–Mānoa, 1955 East-West Road, Honolulu, HI 96822 USA
| | - Chad J. Wilhite
- grid.410445.00000 0001 2188 0957Department of Natural Resources and Environmental Management, University of Hawai’i–Mānoa, 1910 East-West Road, Honolulu, HI 96822 USA
| | - Anthony S. Amend
- grid.410445.00000 0001 2188 0957Department of Botany, University of Hawai’i–Mānoa, 3190 Maile Way, Honolulu, HI 96822 USA
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Guo H, Han S, Lee DJ. Genomic studies on natural and engineered aquatic denitrifying eco-systems: A research update. BIORESOURCE TECHNOLOGY 2021; 326:124740. [PMID: 33497924 DOI: 10.1016/j.biortech.2021.124740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
Excess nitrogenous compounds in municipal or industrial wastewaters can stimulate growth of denitrifying bacteria, in return, to convert potentially hazardous nitrate to inorganic nitrogen gas. To explore the community structure, distributions and succession of functional strains, and their interactions with other microbial communities, contemporary studies were performed based on detailed genomic analysis. This mini-review updated contemporary genomic studies on denitrifying genes in natural and engineered aquatic systems, with the constructed wetlands being the demonstrative system for the latter. Prospects for the employment of genomic studies on denitrifying systems for process design, optimization and development of novel denitrifying processes were discussed.
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Affiliation(s)
- Hongliang Guo
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Song Han
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; College of Technology and Engineering, National Taiwan Normal University, Taipei 10610, Taiwan; College of Engineering, Tunghai University, Taichung 40070, Taiwan.
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55
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Looby CI, Martin PH. Diversity and function of soil microbes on montane gradients: the state of knowledge in a changing world. FEMS Microbiol Ecol 2021; 96:5891232. [PMID: 32780840 DOI: 10.1093/femsec/fiaa122] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/15/2020] [Indexed: 12/27/2022] Open
Abstract
Mountains have a long history in the study of diversity. Like macroscopic taxa, soil microbes are hypothesized to be strongly structured by montane gradients, and recently there has been important progress in understanding how microbes are shaped by these conditions. Here, we summarize this literature and synthesize patterns of microbial diversity on mountains. Unlike flora and fauna that often display a mid-elevation peak in diversity, we found a decline (34% of the time) or no trend (33%) in total microbial diversity with increasing elevation. Diversity of functional groups also varied with elevation (e.g. saprotrophic fungi declined 83% of the time). Most studies (82%) found that climate and soils (especially pH) were the primary mechanisms driving shifts in composition, and drivers differed across taxa-fungi were mostly determined by climate, while bacteria (48%) and archaea (71%) were structured primarily by soils. We hypothesize that the central role of soils-which can vary independently of other abiotic and geographic gradients-in structuring microbial communities weakens diversity patterns expected on montane gradients. Moving forward, we need improved cross-study comparability of microbial diversity indices (i.e. standardizing sequencing) and more geographic replication using experiments to broaden our knowledge of microbial biogeography on global gradients.
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Affiliation(s)
- Caitlin I Looby
- Department of Ecology, Evolution and Behavior, University of Minnesota, Twin Cities, Saint Paul, MN 55108, USA
| | - Patrick H Martin
- Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
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56
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Zhou X, Leite MFA, Zhang Z, Tian L, Chang J, Ma L, Li X, van Veen JA, Tian C, Kuramae EE. Facilitation in the soil microbiome does not necessarily lead to niche expansion. ENVIRONMENTAL MICROBIOME 2021; 16:4. [PMID: 33902741 PMCID: PMC8067652 DOI: 10.1186/s40793-021-00373-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 01/21/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND The soil microbiome drives soil ecosystem function, and soil microbial functionality is directly linked to interactions between microbes and the soil environment. However, the context-dependent interactions in the soil microbiome remain largely unknown. RESULTS Using latent variable models (LVMs), we disentangle the biotic and abiotic interactions of soil bacteria, fungi and environmental factors using the Qinghai-Tibetan Plateau soil ecosystem as a model. Our results show that soil bacteria and fungi not only interact with each other but also shift from competition to facilitation or vice versa depending on environmental variation; that is, the nature of their interactions is context-dependent. CONCLUSIONS Overall, elevation is the environmental gradient that most promotes facilitative interactions among microbes but is not a major driver of soil microbial community composition, as evidenced by variance partitioning. The larger the tolerance of a microbe to a specific environmental gradient, the lesser likely it is to interact with other soil microbes, which suggests that facilitation does not necessarily lead to niche expansion.
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Affiliation(s)
- Xue Zhou
- College of Resources and Environment, Jilin Agricultural University, Changchun, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Márcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands
| | - Zhenqing Zhang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Jingjing Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Lina Ma
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Johannes A van Veen
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands.
- Ecology and biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands.
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57
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Gao Y, Ding J, Yuan M, Chiariello N, Docherty K, Field C, Gao Q, Gu B, Gutknecht J, Hungate BA, Le Roux X, Niboyet A, Qi Q, Shi Z, Zhou J, Yang Y. Long-term warming in a Mediterranean-type grassland affects soil bacterial functional potential but not bacterial taxonomic composition. NPJ Biofilms Microbiomes 2021; 7:17. [PMID: 33558544 PMCID: PMC7870951 DOI: 10.1038/s41522-021-00187-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Climate warming is known to impact ecosystem composition and functioning. However, it remains largely unclear how soil microbial communities respond to long-term, moderate warming. In this study, we used Illumina sequencing and microarrays (GeoChip 5.0) to analyze taxonomic and functional gene compositions of the soil microbial community after 14 years of warming (at 0.8–1.0 °C for 10 years and then 1.5–2.0 °C for 4 years) in a Californian grassland. Long-term warming had no detectable effect on the taxonomic composition of soil bacterial community, nor on any plant or abiotic soil variables. In contrast, functional gene compositions differed between warming and control for bacterial, archaeal, and fungal communities. Functional genes associated with labile carbon (C) degradation increased in relative abundance in the warming treatment, whereas those associated with recalcitrant C degradation decreased. A number of functional genes associated with nitrogen (N) cycling (e.g., denitrifying genes encoding nitrate-, nitrite-, and nitrous oxidereductases) decreased, whereas nifH gene encoding nitrogenase increased in the warming treatment. These results suggest that microbial functional potentials are more sensitive to long-term moderate warming than the taxonomic composition of microbial community.
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Affiliation(s)
- Ying Gao
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Junjun Ding
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.,Key Laboratory of Dryland Agriculture, Ministry of Agriculture of the People's Republic of China, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengting Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Nona Chiariello
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
| | - Kathryn Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
| | - Chris Field
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA
| | - Qun Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jessica Gutknecht
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany.,Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, Saint Paul, MN, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Xavier Le Roux
- Mirobial Ecology Centre LEM, INRA, CNRS, University of Lyon, University Lyon 1, UMR INRA 1418, Villeurbanne, France
| | - Audrey Niboyet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (Sorbonne Université, CNRS, INRA, IRD, Université Paris Diderot, UPEC), Paris, France.,AgroParisTech, Paris, France
| | - Qi Qi
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Zhou Shi
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.,Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
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Liu F, Kou D, Chen Y, Xue K, Ernakovich JG, Chen L, Yang G, Yang Y. Altered microbial structure and function after thermokarst formation. GLOBAL CHANGE BIOLOGY 2021; 27:823-835. [PMID: 33155741 DOI: 10.1111/gcb.15438] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/05/2020] [Indexed: 05/27/2023]
Abstract
Permafrost thaw could induce substantial carbon (C) emissions to the atmosphere, and thus trigger a positive feedback to climate warming. As the engine of biogeochemical cycling, soil microorganisms exert a critical role in mediating the direction and strength of permafrost C-climate feedback. However, our understanding about the impacts of thermokarst (abrupt permafrost thaw) on microbial structure and function remains limited. Here we employed metagenomic sequencing to analyze changes in topsoil (0-15 cm) microbial communities and functional genes along a permafrost thaw sequence (1, 10, and 16 years since permafrost collapse) on the Tibetan Plateau. By combining laboratory incubation and a two-pool model, we then explored changes in soil labile and stable C decomposition along the thaw sequence. Our results showed that topsoil microbial α-diversity decreased, while the community structure and functional gene abundance did not exhibit any significant change at the early stage of collapse (1 year since collapse) relative to non-collapsed control. However, as the time since the collapse increased, both the topsoil microbial community structure and functional genes differed from the control. Abundances of functional genes involved in labile C degradation decreased while those for stable C degradation increased at the late stage of collapse (16 years since collapse), largely driven by changes in substrate properties along the thaw sequence. Accordingly, faster stable C decomposition occurred at the late stage of collapse compared to the control, which was associated with the increase in relative abundance of functional genes for stable C degradation. These results suggest that upland thermokarst alters microbial structure and function, particularly enhances soil stable C decomposition by modulating microbial functional genes, which could reinforce a warmer climate over the decadal timescale.
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Affiliation(s)
- Futing Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Dan Kou
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yongliang Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Jessica G Ernakovich
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - 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
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yuanhe Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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59
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Stewart JD, Ontai A, Yusoof K, Ramirez KS, Bilinski T. Functional redundancy in local spatial scale microbial communities suggests stochastic processes at an urban wilderness preserve in Austin, TX, USA. FEMS Microbiol Lett 2021; 368:6122587. [PMID: 33507263 DOI: 10.1093/femsle/fnab010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/25/2021] [Indexed: 12/26/2022] Open
Abstract
Empirical evidence supports selection of soil microbial communities by edaphic properties across large spatial scales; however, less is known at smaller spatial scales. The goal of this research was to evaluate relationships between ecosystem characteristics and bacterial community structure/function at broad taxonomic resolutions in soils across small spatial scales. We employed 16S rRNA gene sequencing, community-level physiological profiling and soil chemical analysis to address this goal. We found weak relationships between gradients in soil characteristics and community structure/function. Specific operational taxonomic units did not respond to edaphic variation, but Acidobacteria, Bacteroidetes and Nitrospirae shifted their relative abundances. High metabolic diversity within the bacterial communities was observed despite general preference of Tween 40/80. Carbon metabolism patterns suggest dominance of functional specialists at our times of measurement. Pairwise comparison of carbon metabolism patterns indicates high levels of functional redundancy. Lastly, at broad taxonomic scales, community structure and function weakly covary with edaphic properties. This evidence suggests that stochasticity or unmeasured environmental gradients may be influential in bacterial community assembly in soils at small spatial scales.
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Affiliation(s)
- Justin D Stewart
- Department of Ecological Science, Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Department of Biology, St Edward's University, 3001 S Congress Ave, Austin, TX 78704, Austin, TX, USA
| | - Amy Ontai
- Department of Biology, St Edward's University, 3001 S Congress Ave, Austin, TX 78704, Austin, TX, USA
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, 06520, New Haven, CT, USA
| | - Kizil Yusoof
- Department of Biology, St Edward's University, 3001 S Congress Ave, Austin, TX 78704, Austin, TX, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Science Center, 78249, San Antonio, TX, USA
| | - Kelly S Ramirez
- Department of Biological Sciences, The University of Texas at El Paso, 79968, El Paso, TX, USA
| | - Teresa Bilinski
- Department of Biology, St Edward's University, 3001 S Congress Ave, Austin, TX 78704, Austin, TX, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, 80309, Boulder, CO, USA
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Li H, Zeng J, Ren L, Yan Q, Wu QL. Enhanced Metabolic Potentials and Functional Gene Interactions of Microbial Stress Responses to a 4,100-m Elevational Increase in Freshwater Lakes. Front Microbiol 2021; 11:595967. [PMID: 33519731 PMCID: PMC7838385 DOI: 10.3389/fmicb.2020.595967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Elevation has a strong influence on microbial community composition, but its influence on microbial functional genes remains unclear in the aquatic ecosystem. In this study, the functional gene structure of microbes in two lakes at low elevation (ca. 530 m) and two lakes at high elevation (ca. 4,600 m) was examined using a comprehensive functional gene array GeoChip 5.0. Microbial functional composition, but not functional gene richness, was significantly different between the low- and high-elevation lakes. The greatest difference was that microbial communities from high-elevation lakes were enriched in functional genes of stress responses, including cold shock, oxygen limitation, osmotic stress, nitrogen limitation, phosphate limitation, glucose limitation, radiation stress, heat shock, protein stress, and sigma factor genes compared with microbial communities from the low-elevation lakes. Higher metabolic potentials were also observed in the degradation of aromatic compounds, chitin, cellulose, and hemicellulose at higher elevations. Only one phytate degradation gene and one nitrate reduction gene were enriched in the high-elevation lakes. Furthermore, the enhanced interactions and complexity among the co-occurring functional genes in microbial communities of lakes at high elevations were revealed in terms of network size, links, connectivity, and clustering coefficients, and there were more functional genes of stress responses mediating the module hub of this network. The findings of this study highlight the well-developed functional strategies utilized by aquatic microbial communities to withstand the harsh conditions at high elevations.
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Affiliation(s)
- Huabing Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Lijuan Ren
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Qinglong L. Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
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61
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Fungi in Remediation of Hazardous Wastes: Current Status and Future Outlook. Fungal Biol 2021. [DOI: 10.1007/978-3-030-68260-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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62
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Wang X, Zhang Z, Yu Z, Shen G, Cheng H, Tao S. Composition and diversity of soil microbial communities in the alpine wetland and alpine forest ecosystems on the Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 747:141358. [PMID: 32771793 DOI: 10.1016/j.scitotenv.2020.141358] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 06/11/2023]
Abstract
While the composition and diversity of soil microbial communities play a central and essential role in biogeochemical cycling of nutrients, they are known to be shaped by the physical and chemical properties of soils and various environmental factors. This study investigated the composition and diversity of microbial communities in 48 samples of seasonally frozen soils collected from 16 sites in an alpine wetland region (Lhasa River basin) and an alpine forest region (Nyang River basin) on the Tibetan Plateau using high-throughput sequencing that targeted the V3-V4 region of 16S rRNA gene. The dominant soil microbial phyla included Proteobacteria, Acidobacteria, and Actinobacteria in the alpine wetland and alpine forest ecosystems, and no significant difference was observed for their microbial composition. Linear discriminant analysis Effect Size (LEfSe) analysis showed that significant enrichment of Hymenobacteraceae and Cytophagales (belonging to Bacteroidetes) existed in the alpine wetland soils, while the alpine forest soils were enriched with Alphaproteobacteria (belonging to Proteobacteria), suggesting that these species could be potential biomarkers for alpine wetland and alpine forest ecosystems. Results of redundancy analysis (RDA) suggest that the microbial community diversity and abundance in the seasonally frozen soils on the Tibetan Plateau were mainly related to the total potassium in the alpine wetland ecosystem, and available potassium and soil moisture in the alpine forest ecosystem, respectively. In addition, function prediction analysis by Tax4Fun revealed the existence of potential functional pathways involved in human diseases in all soil samples. These results provide insights on the structure and function of soil microbial communities in the alpine wetland and alpine forest ecosystems on the Tibetan Plateau, while the potential risk to human health from the pathogenic microbes in the seasonally frozen soils deserves attention.
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Affiliation(s)
- Xiaojie Wang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100049, China; MOE Key Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Zhichao Zhang
- MOE Key Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Zhiqiang Yu
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Guofeng Shen
- MOE Key Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Hefa Cheng
- MOE Key Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
| | - Shu Tao
- MOE Key Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
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63
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High-throughput sequencing approach to reveal the bacterial diversity of traditional yak jerky from the Tibetan regions. Meat Sci 2020; 172:108348. [PMID: 33120176 DOI: 10.1016/j.meatsci.2020.108348] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 07/09/2020] [Accepted: 10/13/2020] [Indexed: 11/23/2022]
Abstract
A high-throughput sequencing approach was used to investigate the bacterial community diversity of traditional Tibetan yak jerky, which was collected from three different regions in Tibet and with different natural drying times. Tibetan yak jerky from different regions had different bacterial communities, which was mainly reflected in the relative abundance levels of unclassified Cyanobacteria, Psychrobacter and Acinetobacter. The unclassified Cyanobacteria was the dominant genus of Qamdo yak jerky, Acinetobacter was the dominant genus of Shigatse yak jerky, and Psychrobacteria was the dominant genus of Nyingchi yak jerky. With increasing natural drying time, the diversity of bacterial communities in yak jerky decreased, and unclassified Cyanobacteria become the dominant genus. Spearman's correlation analysis and canonical correspondence analysis revealed that physicochemical factors (moisture content, water activity, shear force and pH) were significantly correlated with bacterial community. Our results will be beneficial to improve and standardize the safety and quality of traditional Tibetan yak jerky.
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64
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Cheng C, Han H, Wang Y, He L, Sheng X. Metal-immobilizing and urease-producing bacteria increase the biomass and reduce metal accumulation in potato tubers under field conditions. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 203:111017. [PMID: 32678748 DOI: 10.1016/j.ecoenv.2020.111017] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
In this study, the effect of two metal-immobilizing bacterial strains, Serratia liquefaciens CL-1 and Bacillus thuringiensis X30, on the availability of Cd and Pb and the metal accumulation in potato tubers, as well as the underlying mechanisms in metal-contaminated soils were characterized. Moreover, the impacts of the strains on metal immobilization, pH, and NH4+ concentration in metal-contaminated soil solutions were evaluated. Strains CL-1 and X30 increased tuber dry weight by 46% and 40%, reduced tuber Cd and Pb contents by 68-83% and 42-47%, and decreased the Cd and Pb translocation factors by 61-70% and 30-34%, respectively, compared to the controls. Strains CL-1 and X30 decreased the available Cd and Pb contents by 52-67% and 30-44% and increased the NH4+ content by 55% and 31%, pH, urease activity by 70% and 41%, and relative abundance of ureC gene copies by 37% and 20% in the rhizosphere soils, respectively, compared with the controls. Reduced Cd and Pb concentrations and increased pH and NH4+ concentration were found in the bacteria-inoculated soil solution compared to the controls. These results suggested that the strains reduced tuber metal uptake through decreasing the metal availability and increasing the pH, ureC gene relative abundance and urease activity as well as decreasing the metal translocation from the leaves to tubers. These results may provide an effective metal-immobilizing bacteria (especially strain CL-1)-enhanced approach to reduce metal uptake of potato tubers in metal-polluted soils.
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Affiliation(s)
- Cheng Cheng
- College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, Nanjing, 210095, PR China
| | - Hui Han
- College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, Nanjing, 210095, PR China; College of Agricultural Engineering, Nanyang Normal University, Nanyang, 473061, PR China
| | - Yaping Wang
- College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, Nanjing, 210095, PR China
| | - Linyan He
- College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, Nanjing, 210095, PR China.
| | - Xiafang Sheng
- College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, Nanjing, 210095, PR China.
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65
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Zhu R, Liu J, Wang J, Han W, Shen Z, Muraina TO, Chen J, Sun D. Comparison of soil microbial community between reseeding grassland and natural grassland in Songnen Meadow. Sci Rep 2020; 10:16884. [PMID: 33037306 PMCID: PMC7547709 DOI: 10.1038/s41598-020-74023-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/18/2020] [Indexed: 11/23/2022] Open
Abstract
Microorganisms have important ecological functions in ecosystems. Reseeding is considered as one of the main strategies for preventing grassland degradation in China. However, the response of soil microbial community and diversity to reseeding grassland (RG) and natural grassland (NG) remains unclear, especially in the Songnen Meadow. In this study, the soil microbial community compositions of two vegetation restoration types (RG vs NG) were analyzed using a high-throughput sequencing technique. A total of 23,142 microbial OTUs were detected, phylogenetically derived from 11 known bacterial phyla. Soil advantage categories included Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes, which together accounted for > 78% of the all phyla in vegetation restoration. The soil microbial diversity was higher in RG than in NG. Two types of vegetation restoration had significantly different characteristics of soil microbial community (P < 0.001). Based on a molecular ecological network analysis, we found that the network in RG had a longer average path distance and modularity than in NG network, making it more resilient to environment changes. Meanwhile, the results of the canonical correspondence analysis and molecular ecological network analysis showed that soil pH (6.34 ± 0.35 in RG and 7.26 ± 0.28 in NG) was the main factor affecting soil microbial community structure, followed by soil moisture (SM) in the Songnen meadow, China. Besides, soil microbial community characteristics can vary significantly in different vegetation restoration. Thus, we suggested that it was necessary and reasonable for this area to popularize reseeding grassland in the future.
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Affiliation(s)
- Ruifen Zhu
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China
| | - Jielin Liu
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China
| | - Jianli Wang
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China
| | - Weibo Han
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China
| | - Zhongbao Shen
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China
| | - Taofeek O Muraina
- National Hulunber Grassland Ecosystem Observation and Research Station, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 10008, China
- Department of Animal Health and Production, Oyo State College of Agriculture and Technology, P.M.B. 10, Igbo-Ora, Oyo State, Nigeria
| | - Jishan Chen
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China.
| | - Dequan Sun
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Sciences, 368 Xue Fu Road, Nangang District, Harbin, 150086, China.
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66
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Deng D, Pan Y, Liu G, Liu W, Ma L. Seeking the hotspots of nitrogen removal: A comparison of sediment denitrification rate and denitrifier abundance among wetland types with different hydrological conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 737:140253. [PMID: 32783851 DOI: 10.1016/j.scitotenv.2020.140253] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/27/2020] [Accepted: 06/14/2020] [Indexed: 06/11/2023]
Abstract
Wetlands play a vital role in removing nitrogen (N) from aquatic environments via the denitrification process, which is regulated by multiple environmental and biological factors. Until now, the mechanisms by which environmental factors and microbial abundance regulate denitrification rates in wetlands under different hydrological conditions remain poorly understood. Here, we investigated sediment potential denitrification rate (PDR) and unamended denitrification rate (UDR), and quantified denitrifier abundance (nirS, nirK, and nosZ genes) in 36 stream, river, pond, and ditch wetland sites along the Dan River, a nitrogen-rich river in central China. The result indicated that ditches had the highest denitrification rates and denitrifier abundance. Both PDR and UDR showed strong seasonality, and were observed to be negatively correlated with water velocity in streams and rivers. Moreover, denitrification rates were significantly related to denitrifier abundance and many water quality parameters and sediment properties. Interestingly, PDR and UDR were generally positively associated with N and carbon (C) availability in streams and rivers, but such correlations were not found in ponds and ditches. Using a scaling analysis, we found that environmental parameters, including Reynolds number, sediment total C ratio, and interstitial space, coupled with relative nirS gene abundance could predict the hotspots of denitrification rates in wetlands with varying hydrologic regimes. Our findings highlight that hydrological conditions, especially water velocity and hydrologic pulsing, play a nonnegligible role in determining N biogeochemical processes in wetlands.
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Affiliation(s)
- Danli Deng
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongtai Pan
- Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa 850000, China
| | - Guihua Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Wenzhi Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China; Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Lin Ma
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
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67
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Li A, Li G, Yang J, Yang Y, Liang Y, Zhang D. Geo-distribution pattern of microbial carbon cycling genes responsive to petroleum contamination in continental horizontal oilfields. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 731:139188. [PMID: 32402908 DOI: 10.1016/j.scitotenv.2020.139188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 05/01/2020] [Accepted: 05/01/2020] [Indexed: 06/11/2023]
Abstract
Contamination significantly affects soil microbial community structures, and the metabolisms of organic contaminants might particularly alter soil carbon cycling by shaping microbial carbon cycling genes. Although numerous studies have discussed the impacts of petroleum contamination on soil bacterial communities and relevant degrading genes, there is no work addressing how soil carbon cycling genes are affected by petroleum contamination. In this study, 77 soil samples were collected from five typical oilfields horizontally located in China to explore the influence of environmental variables and petroleum contamination on microbial carbon cycling genes. Results from Geochip suggested a geographic-determined distribution of carbon cycling genes. Although no significant correlation was observed between carbon cycling genes and soil physio-chemical properties for all soils, some relationships were identified in specific oilfield. Principle component analysis indicated that soil physio-chemical properties, rather than petroleum contamination disturbance, are the key factors determining the degree of sample dispersion, whereas environmental variables predominantly control the degree of sample aggregation. Co-occurrence ecological network analysis revealed a more complex interactions of all functional genes in petroleum-contaminated soils, and carbon cycling genes were grouped with nitrogen related genes in petroleum-contaminated communities. Soil moisture and heterogeneity were identified as the main drivers for the abundance and diversity of carbon cycling genes, particularly in petroleum-contaminated soils. These results are attributing to the fewer impacts of petroleum contamination on the diversity of carbon cycling genes than soil physio-chemical properties, and soil carbon cycling genes are mainly driven by geographic location and petroleum contamination together. Our findings provide deeper insight into the influence of petroleum contamination in soil microbial functions related to carbon cycling.
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Affiliation(s)
- Aiyang Li
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China; State Key Joint Lab of Environment Simulation & Pollution Control, Tsinghua University, Beijing 100084, People's Republic of China
| | - Guanghe Li
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China; State Key Joint Lab of Environment Simulation & Pollution Control, Tsinghua University, Beijing 100084, People's Republic of China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, People's Republic of China
| | - Juejie Yang
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China; State Key Joint Lab of Environment Simulation & Pollution Control, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yunfeng Yang
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China; State Key Joint Lab of Environment Simulation & Pollution Control, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China; State Key Joint Lab of Environment Simulation & Pollution Control, Tsinghua University, Beijing 100084, People's Republic of China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, People's Republic of China.
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68
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Picazo F, Vilmi A, Aalto J, Soininen J, Casamayor EO, Liu Y, Wu Q, Ren L, Zhou J, Shen J, Wang J. Climate mediates continental scale patterns of stream microbial functional diversity. MICROBIOME 2020; 8:92. [PMID: 32534595 PMCID: PMC7293791 DOI: 10.1186/s40168-020-00873-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Understanding the large-scale patterns of microbial functional diversity is essential for anticipating climate change impacts on ecosystems worldwide. However, studies of functional biogeography remain scarce for microorganisms, especially in freshwater ecosystems. Here we study 15,289 functional genes of stream biofilm microbes along three elevational gradients in Norway, Spain and China. RESULTS We find that alpha diversity declines towards high elevations and assemblage composition shows increasing turnover with greater elevational distances. These elevational patterns are highly consistent across mountains, kingdoms and functional categories and exhibit the strongest trends in China due to its largest environmental gradients. Across mountains, functional gene assemblages differ in alpha diversity and composition between the mountains in Europe and Asia. Climate, such as mean temperature of the warmest quarter or mean precipitation of the coldest quarter, is the best predictor of alpha diversity and assemblage composition at both mountain and continental scales, with local non-climatic predictors gaining more importance at mountain scale. Under future climate, we project substantial variations in alpha diversity and assemblage composition across the Eurasian river network, primarily occurring in northern and central regions, respectively. CONCLUSIONS We conclude that climate controls microbial functional gene diversity in streams at large spatial scales; therefore, the underlying ecosystem processes are highly sensitive to climate variations, especially at high latitudes. This biogeographical framework for microbial functional diversity serves as a baseline to anticipate ecosystem responses and biogeochemical feedback to ongoing climate change. Video Abstract.
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Affiliation(s)
- Félix Picazo
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008 China
| | - Annika Vilmi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008 China
| | - Juha Aalto
- Finnish Meteorological Institute, P.O. Box 503, FI-00101 Helsinki, Finland
- Department of Geosciences and Geography, University of Helsinki, 00014 Helsinki, Finland
| | - Janne Soininen
- Department of Geosciences and Geography, University of Helsinki, 00014 Helsinki, Finland
| | - Emilio O. Casamayor
- Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, E-17300 Blanes, Spain
| | - Yongqin Liu
- University of Chinese Academy of Sciences, Beijing, 1000049 China
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101 China
| | - Qinglong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008 China
| | - Lijuan Ren
- Department of Ecology, Jinan University, Guangzhou, 510632 China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019 USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084 China
- Earth Science Division, Lawrence Berkeley National Laboratory, California, 94270 USA
| | - Ji Shen
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008 China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008 China
- University of Chinese Academy of Sciences, Beijing, 1000049 China
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69
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Viral and Bacterial Fecal Indicators in Untreated Wastewater across the Contiguous United States Exhibit Geospatial Trends. Appl Environ Microbiol 2020; 86:AEM.02967-19. [PMID: 32060019 DOI: 10.1128/aem.02967-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/30/2020] [Indexed: 12/16/2022] Open
Abstract
Cultivated fecal indicator bacteria such as Escherichia coli and enterococci are typically used to assess the sanitary quality of recreational waters. However, these indicators suffer from several limitations, such as the length of time needed to obtain results and the fact that they are commensal inhabitants of the gastrointestinal tract of many animals and have fate and transport characteristics dissimilar to pathogenic viruses. Numerous emerging technologies that offer same-day water quality results or pollution source information or that more closely mimic persistence patterns of disease-causing pathogens that may improve water quality management are now available, but data detailing geospatial trends in wastewater across the United States are sparse. We report geospatial trends of cultivated bacteriophage (somatic, F+, and total coliphages and GB-124 phage), as well as genetic markers targeting polyomavirus, enterococci, E. coli, Bacteroidetes, and human-associated Bacteroides spp. (HF183/BacR287 and HumM2) in 49 primary influent sewage samples collected from facilities across the contiguous United States. Samples were selected from rural and urban facilities spanning broad latitude, longitude, elevation, and air temperature gradients by using a geographic information system stratified random site selection procedure. Most indicators in sewage demonstrated a remarkable similarity in concentration regardless of location. However, some exhibited predictable shifts in concentration based on either facility elevation or local air temperature. Geospatial patterns identified in this study, or the absence of such patterns, may have several impacts on the direction of future water quality management research, as well as the selection of alternative metrics to estimate sewage pollution on a national scale.IMPORTANCE This study provides multiple insights to consider for the application of bacterial and viral indicators in sewage to surface water quality monitoring across the contiguous United States, ranging from method selection considerations to future research directions. Systematic testing of a large collection of sewage samples confirmed that crAssphage genetic markers occur at a higher average concentration than key human-associated Bacteroides spp. on a national scale. Geospatial testing also suggested that some methods may be more suitable than others for widespread implementation. Nationwide characterization of indicator geospatial trends in untreated sewage represents an important step toward the validation of these newer methods for future water quality monitoring applications. In addition, the large paired-measurement data set reported here affords the opportunity to conduct a range of secondary analyses, such as the generation of new or updated quantitative microbial risk assessment models used to estimate public health risk.
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70
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Deng J, Zhou Y, Zhu W, Yin Y. Effects of afforestation with Pinus sylvestris var. mongolica plantations combined with enclosure management on soil microbial community. PeerJ 2020; 8:e8857. [PMID: 32257650 PMCID: PMC7102505 DOI: 10.7717/peerj.8857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/05/2020] [Indexed: 11/20/2022] Open
Abstract
Grazing and litter removal can alter understory structure and composition after afforestation, posing a serious threat to sustainable forest development. Enclosure is considered to be an effective measure to restore degraded forest restoration. However, little is known about the dynamics of soil nutrients and microbial communities during the forest restoration process. In the present study, the effects of Arachis hypogaea (AH), Pinus sylvestris var. mongolica (PSM) and Pinus sylvestris var. mongolica with enclosure (PSME) on soil chemical properties and soil microbial communities were studied in Zhanggutai, Liaoning Province, China. The results showed that PSME could remarkably contribute to improve soil total C, total N and total P compared to PSM and AH. Additionally, PSM could clearly increase the soil bacterial community diversity and fungal Chao1 index and ACE index. Additionally, PSME could further increase soil Chao1 index and ACE index of soil bacteria. Soil total C, total N and available N were the main factors related to soil microbial diversity. Actinobacteria and Ascomycota were the predominant bacterial and fungal phyla, respectively. Specifically, PSME could increase the relative abundances of Actinobacteria, Gemmatimonadetes, Ascomycota and Mortierellomycota and decreased the relative abundances of Acidobacteria, Chloroflexi and Basidiomycota than PSM. PSM and PSME could clearly change soil microbial communities compared with AH and PSME could remarkably shift soil fungal communities than PSM. What's more, the soil microbial community structure were affected by multiple edaphic chemical parameters. It can be seen that afforestation combined with enclosed management potentially regulate microbial properties through shifting the soil properties. This study can provide new ideas for further understanding the impact of enclosure on PSM and provide theoretical support for the management of PSM.
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Affiliation(s)
- Jiaojiao Deng
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China.,Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, Liaoning, China
| | - Yongbin Zhou
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China.,Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, Liaoning, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China.,Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, Liaoning, China
| | - You Yin
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China.,Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, Liaoning, China
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71
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Ma L, Jiang X, Liu G, Yao L, Liu W, Pan Y, Zuo Y. Environmental Factors and Microbial Diversity and Abundance Jointly Regulate Soil Nitrogen and Carbon Biogeochemical Processes in Tibetan Wetlands. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:3267-3277. [PMID: 32101417 DOI: 10.1021/acs.est.9b06716] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Wetlands have numerous critical ecological functions, some of which are regulated by several nitrogen (N) and carbon (C) biogeochemical processes, such as denitrification, organic matter decomposition, and methane emission. Until now, the underlying pathways of the effects of environmental and biological factors on wetland N and C cycling rates are still not fully understood. Here, we investigated soil potential/net nitrification, potential/unamended denitrification, methane production/oxidation rates in 36 riverine, lacustrine, and palustrine wetland sites on the Tibet Plateau. The results showed that all the measured N and C cycling rates did not differ significantly among the wetland types. Stepwise multiple regression analyses revealed that soil physicochemical properties (e.g., moisture, C and N concentration) explained a large amount of the variance in most of the N and C cycling rates. Microbial abundance and diversity were also important in controlling potential and unamended denitrification rates, respectively. Path analysis further revealed that soil moisture and N and C availability could impact wetland C and N processes both directly and indirectly. For instance, the indirect effect of soil moisture on methane production rates was mainly through the regulating the soil C content and methanogenic community structure. Our findings highlight that many N and C cycling processes in high-altitude and remote Tibetan wetlands are jointly regulated by soil environments and functional microorganisms. Soil properties affecting the N and C cycling rates in wetlands through altering their microbial diversity and abundance represent an important but previously underestimated indirect pathway.
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Affiliation(s)
- Lin Ma
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P. R. China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P. R. China
| | - Xiaoliang Jiang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Guihua Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P. R. China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, P. R. China
| | - Lunguang Yao
- Collaborative Innovation Center of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang Normal University, Nanyang 473061, P. R. China
| | - Wenzhi Liu
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P. R. China
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, P. R. China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, P. R. China
- Collaborative Innovation Center of Water Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang Normal University, Nanyang 473061, P. R. China
| | - Yongtai Pan
- Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa 850000, P. R. China
| | - Yanxia Zuo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P. R. China
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72
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Soil Microbial Community Assembly and Interactions Are Constrained by Nitrogen and Phosphorus in Broadleaf Forests of Southern China. FORESTS 2020. [DOI: 10.3390/f11030285] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Subtropical and tropical broadleaf forests play important roles in conserving biodiversity and regulating global carbon cycle. Nonetheless, knowledge about soil microbial diversity, community composition, turnover and microbial functional structure in sub- and tropical broadleaf forests is scarce. In this study, high-throughput sequencing was used to profile soil microbial community composition, and a micro-array GeoChip 5.0 was used to profile microbial functional gene distribution in four sub- and tropical broadleaf forests (HS, MES, HP and JFL) in southern China. The results showed that soil microbial community compositions differed dramatically among all of four forests. Soil microbial diversities in JFL were the lowest (5.81–5.99) and significantly different from those in the other three forests (6.22–6.39). Furthermore, microbial functional gene interactions were the most complex and closest, likely in reflection to stress associated with the lowest nitrogen and phosphorus contents in JFL. In support of the importance of environmental selection, we found selection (78–96%) dominated microbial community assembly, which was verified by partial Mantel tests showing significant correlations between soil phosphorus and nitrogen content and microbial community composition. Taken together, these results indicate that nitrogen and phosphorus are pivotal in shaping soil microbial communities in sub- and tropical broadleaf forests in southern China. Changes in soil nitrogen and phosphorus, in response to plant growth and decomposition, will therefore have significant changes in both microbial community assembly and interaction.
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73
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Deng J, Bai X, Zhou Y, Zhu W, Yin Y. Variations of soil microbial communities accompanied by different vegetation restoration in an open-cut iron mining area. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 704:135243. [PMID: 31787305 DOI: 10.1016/j.scitotenv.2019.135243] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/24/2019] [Accepted: 10/26/2019] [Indexed: 06/10/2023]
Abstract
Overexploitation of iron mining in China has caused serious environmental pollution. Therefore, establishing a stable ecological restoration with vegetation in mining areas has gradually aroused people's awareness and obtained extensive concerns. This study aimed to evaluate vegetation restoration with Robinia pseudoacacia (RP), Acer mono (AM) and Pinus koraiensis (PK) in iron mining compared with unrestored area, to investigate the soil environment factors and microbial communities, and to better understand the correlations between soil environment factors and soil microbial communities. Vegetation restoration could reduce soil pH and alleviate soil alkaline, and remarkably increase soil nutrients, especially in RP site. Analysis of 16S rRNA and ITS rRNA gene sequences provided a total of 645,004 and 906, 276 valid sequences clustered into 7091 OTUs and 1689 OTUs at a 0.03 genetic distance for bacteria and fungi, respectively. The predominant bacterial and fungal phyla were Actinobacteria and Ascomycota in studied sites, respectively. Additionally, revegetation significantly increased the relative abundances of Proteobacteria, Gemmatimonadetes, Bacteroidetes and Patescibacteria, and decreased the relative abundance of Actinobacteria. Robinia pseudoacacia harbored the highest soil fungal community diversity, and bacterial Simpson index and Shannon index. Vegetation restoration with RP could clearly shifted soil communities compared to AM and PK. Along with the restoration of vegetation, the remarkable abiotic changes were the accumulation of total C, total N, total P, available P, available N and available K and the decreasing of soil pH, which were the most important factors affecting soil microbial communities. Our results addressed that Robinia pseudoacacia was the best preferable species than AM and PK in improving soil nutrients, soil community diversity and structure in Fe mining, providing a helpful guideline for selection of tree species.
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Affiliation(s)
- Jiaojiao Deng
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China
| | - Xuejiao Bai
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China
| | - Yongbin Zhou
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China.
| | - You Yin
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China.
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74
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Sheng Y, Cong W, Yang L, Liu Q, Zhang Y. Forest Soil Fungal Community Elevational Distribution Pattern and Their Ecological Assembly Processes. Front Microbiol 2019; 10:2226. [PMID: 31636612 PMCID: PMC6787267 DOI: 10.3389/fmicb.2019.02226] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/11/2019] [Indexed: 11/17/2022] Open
Abstract
Soil fungi play vital roles in natural ecosystems, however, their community distribution patterns along different environmental gradients and ecological assembly processes remain unclear. In this study, Illumina MiSeq sequencing was used to investigate the soil fungal community structures of five different forest types along an elevational gradient, and a framework based on a null model was adopted to quantify the relative contribution of deterministic and stochastic ecological assembly processes. The results showed that the majority of soil fungal OTUs were derived from Zygomycota, Basidiomycota, and Ascomycota. Soil fungal community structure differed significantly among the five sites (P < 0.01), and the fungal α-diversity decreased as elevation increased (P < 0.01). The null model showed that the relative contribution of stochastic processes (37.78-73.33%) was higher than that of deterministic processes (26.67-62.22%) within the same forest type, while that of deterministic processes (35.00-93.00%) was higher than stochastic processes (7.00-65.00%) between forest types. These results suggest that forest soil fungal diversity decreased significantly with increasing elevation, and that deterministic processes may be key factors influencing soil fungal community assemblies among forest types. The results of this study provide new insight into soil fungal distribution patterns and community assembly processes in natural forest ecosystems.
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Affiliation(s)
- Yuyu Sheng
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, and the Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Beijing, China
| | - Wei Cong
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, and the Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Beijing, China
| | - Linsen Yang
- Shennongjia National Park Administration, and Hubei Provincial Key Laboratory on Conservation Biology of the Shennongjia Golden Monkey, Shennongjia, China
| | - Qiang Liu
- Shennongjia National Park Administration, and Hubei Provincial Key Laboratory on Conservation Biology of the Shennongjia Golden Monkey, Shennongjia, China
| | - Yuguang Zhang
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, and the Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Beijing, China
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75
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King GM, Henry K. Impacts of Experimental Flooding on Microbial Communities and Methane Fluxes in an Urban Meadow, Baton Rouge, Louisiana. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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76
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Sheng Y, Cong J, Lu H, Yang L, Liu Q, Li D, Zhang Y. Broad-leaved forest types affect soil fungal community structure and soil organic carbon contents. Microbiologyopen 2019; 8:e874. [PMID: 31215766 PMCID: PMC6813455 DOI: 10.1002/mbo3.874] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 11/06/2022] Open
Abstract
Evergreen broad-leaved (EBF) and deciduous broad-leaved (DBF) forests are two important vegetation types in terrestrial ecosystems that play key roles in sustainable biodiversity and global carbon (C) cycling. However, little is known about their associated soil fungal community and the potential metabolic activities involved in biogeochemical processes. In this study, soil samples were collected from EBF and DBF in Shennongjia Mountain, China, and soil fungal community structure and functional gene diversity analyzed based on combined Illumina MiSeq sequencing with GeoChip technologies. The results showed that soil fungal species richness (p = 0.079) and fungal functional gene diversity (p < 0.01) were higher in DBF than EBF. Zygomycota was the most dominant phylum in both broad-leaved forests, and the most dominant genera found in each forest varied (Umbelopsis dominated in DBF, whereas Mortierella dominated in EBF). A total of 4, 439 soil fungi associated functional gene probes involved in C and nitrogen (N) cycling were detected. Interestingly, the relative abundance of functional genes related to labile C degradation (e.g., starch, pectin, hemicellulose, and cellulose) was significantly higher (p < 0.05) in DBF than EBF, and the functional gene relative abundance involved in C cycling was significantly negatively correlated with soil labile organic C (r = -0.720, p = 0.002). In conclusion, the soil fungal community structure and potential metabolic activity showed marked divergence in different broad-leaved forest types, and the higher relative abundance of functional genes involved in C cycling in DBF may be caused by release of loss of organic C in the soil.
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Affiliation(s)
- Yuyu Sheng
- Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Jing Cong
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Hui Lu
- Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Linsen Yang
- Shennongjia National Park, Shennongjia, Hubei Province, China
| | - Qiang Liu
- Shennongjia National Park, Shennongjia, Hubei Province, China
| | - Diqiang Li
- Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Yuguang Zhang
- Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
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77
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Truong C, Gabbarini LA, Corrales A, Mujic AB, Escobar JM, Moretto A, Smith ME. Ectomycorrhizal fungi and soil enzymes exhibit contrasting patterns along elevation gradients in southern Patagonia. THE NEW PHYTOLOGIST 2019; 222:1936-1950. [PMID: 30689219 DOI: 10.1111/nph.15714] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
The biological and functional diversity of ectomycorrhizal (ECM) associations remain largely unknown in South America. In Patagonia, the ECM tree Nothofagus pumilio forms monospecific forests along mountain slopes without confounding effects of vegetation on plant-fungi interactions. To determine how fungal diversity and function are linked to elevation, we characterized fungal communities, edaphic variables, and eight extracellular enzyme activities along six elevation transects in Tierra del Fuego (Argentina and Chile). We also tested whether pairing ITS1 rDNA Illumina sequences generated taxonomic biases related to sequence length. Fungal community shifts across elevations were mediated primarily by soil pH with the most species-rich fungal families occurring mostly within a narrow pH range. By contrast, enzyme activities were minimally influenced by elevation but correlated with soil factors, especially total soil carbon. The activity of leucine aminopeptidase was positively correlated with ECM fungal richness and abundance, and acid phosphatase was correlated with nonECM fungal abundance. Several fungal lineages were undetected when using exclusively paired or unpaired forward ITS1 sequences, and these taxonomic biases need reconsideration for future studies. Our results suggest that soil fungi in N. pumilio forests are functionally similar across elevations and that these diverse communities help to maintain nutrient mobilization across the elevation gradient.
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Affiliation(s)
- Camille Truong
- Instituto de Biología, Universidad Nacional Autónoma de México, CP, 04510, Ciudad de México, México
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Luciano A Gabbarini
- Programa Interacciones Biológicas, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, B1876BX, Argentina
| | - Adriana Corrales
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
- Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, DC, 111221, Colombia
| | - Alija B Mujic
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, California State University at Fresno, Fresno, CA, 93740, USA
| | - Julio M Escobar
- Centro Austral de Investigaciones Científicas (CONICET), Ushuaia, V9410BFD, Tierra del Fuego, Argentina
| | - Alicia Moretto
- Centro Austral de Investigaciones Científicas (CONICET), Ushuaia, V9410BFD, Tierra del Fuego, Argentina
- Universidad Nacional de Tierra del Fuego, Ushuaia, V9410BFD, Tierra del Fuego, Argentina
| | - Matthew E Smith
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
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Construction of Synthetic Microbiota for Reproducible Flavor Compound Metabolism in Chinese Light-Aroma-Type Liquor Produced by Solid-State Fermentation. Appl Environ Microbiol 2019; 85:AEM.03090-18. [PMID: 30850432 DOI: 10.1128/aem.03090-18] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/05/2019] [Indexed: 01/28/2023] Open
Abstract
Natural microbiota plays an essential role in flavor compounds used in traditional food fermentation; however, the fluctuation in natural microbiota results in inconsistency in food quality. Thus, it is critical to reveal the core microbiota for flavor compound production and to construct a synthetic core microbiota for use in constant food fermentation. Here, we reveal the core microbiota based on their flavor production and cooccurrence performance, using Chinese light-aroma-type liquor as a model system. Five genera, Lactobacillus, Saccharomyces, Pichia, Geotrichum, and Candida, were identified to be the core microbiota. The synthetic core microbiota of these five genera presented a reproducible dynamic profile similar to that in the natural microbiota. A Monte Carlo test showed that the effects of five environmental factors (lactic acid, ethanol, and acetic acid contents, moisture, and pH) on the synthetic microbiota distribution were highly significant (P < 0.01), similar to those effects on a natural fermentation system. In addition, 77.27% of the flavor compounds produced by the synthetic core microbiota showed a similar dynamic profile (ρ > 0) with that in the natural liquor fermentation process, and the flavor profile presented a similar composition. It indicated that the synthetic core microbiota is efficient for reproducible flavor metabolism. This work established a method for identifying core microbiota and constructing a synthetic microbiota for reproducible flavor compounds. This work is of great significance for the tractable and constant production of various fermented foods.IMPORTANCE The transformation from natural fermentation to synthetic fermentation is essential in constructing a constant food fermentation process, which is the premise for stably making high-quality food. According to flavor-producing and cooccurring functions in dominant microbes, we provided a system-level approach to identify the core microbiota in Chinese light-aroma-type liquor fermentation. In addition, we successfully constructed a synthetic core microbiota to simulate the microbial community succession and flavor compound production in the in vitro system. The constructed synthetic core microbiota could not only facilitate a mechanistic understanding of the structure and function of the microbiota but also be beneficial for constructing a tractable and reproducible food fermentation process.
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79
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Chai Y, Cao Y, Yue M, Tian T, Yin Q, Dang H, Quan J, Zhang R, Wang M. Soil Abiotic Properties and Plant Functional Traits Mediate Associations Between Soil Microbial and Plant Communities During a Secondary Forest Succession on the Loess Plateau. Front Microbiol 2019; 10:895. [PMID: 31105679 PMCID: PMC6499021 DOI: 10.3389/fmicb.2019.00895] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/08/2019] [Indexed: 11/13/2022] Open
Abstract
In the context of secondary forest succession, aboveground-belowground interactions are known to affect the dynamics and functional structure of plant communities. However, the links between soil microbial communities, soil abiotic properties, plant functional traits in the case of semi-arid and arid ecosystems, are unclear. In this study, we investigated the changes in soil microbial species diversity and community composition, and the corresponding effects of soil abiotic properties and plant functional traits, during a ≥150-year secondary forest succession on the Loess Plateau, which represents a typical semi-arid ecosystem in China. Plant community fragments were assigned to six successional stages: 1-4, 4-8, 8-15, 15-50, 50-100, and 100-150 years after abandonment. Bacterial and fungal communities were analyzed by high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene and the internal transcribed spacer (ITS2) region of the rRNA operon, respectively. A multivariate variation-partitioning approach was used to estimate the contributions of soil properties and plant traits to the observed microbial community composition. We found considerable differences in bacterial and fungal community compositions between the early (S1-S3) and later (S4-S6) successional stages. In total, 18 and 12 unique families were, respectively, obtained for bacteria and fungi, as indicators of microbial community succession across the six stages. Bacterial alpha diversity was positively correlated with plant species alpha diversity, while fungal diversity was negatively correlated with plant species diversity. Certain fungal and bacterial taxa appeared to be associated with the occurrence of dominant plant species at different successional stages. Soil properties (pH, total N, total C, NH4-N, NO3-N, and PO4-P concentrations) and plant traits explained 63.80% and 56.68% of total variance in bacterial and fungal community compositions, respectively. These results indicate that soil microbial communities are coupled with plant communities via the mediation of microbial species diversity and community composition over a long-term secondary forest succession in the semi-arid ecosystem. The bacterial and fungal communities show distinct patterns in response to plant community succession, according to both soil abiotic properties and plant functional traits.
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Affiliation(s)
- Yongfu Chai
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
- School of Life Sciences, Northwest University, Xi’an, China
| | - Ying Cao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
- School of Life Sciences, Northwest University, Xi’an, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
- School of Life Sciences, Northwest University, Xi’an, China
| | - Tingting Tian
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
- School of Life Sciences, Northwest University, Xi’an, China
| | - Qiulong Yin
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
- School of Life Sciences, Northwest University, Xi’an, China
| | - Han Dang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
- School of Life Sciences, Northwest University, Xi’an, China
| | - Jiaxin Quan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, China
| | - Ruichang Zhang
- Department of Plant Ecology, University of Tübingen, Tübingen, Germany
| | - Mao Wang
- College of Grassland and Environment Sciences, Xinjiang Agricultural University, Ürümqi, China
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80
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Yang S, Zheng Q, Yuan M, Shi Z, Chiariello NR, Docherty KM, Dong S, Field CB, Gu Y, Gutknecht J, Hungate BA, Le Roux X, Ma X, Niboyet A, Yuan T, Zhou J, Yang Y. Long-term elevated CO 2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 652:1474-1481. [PMID: 30586832 DOI: 10.1016/j.scitotenv.2018.10.353] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/22/2018] [Accepted: 10/26/2018] [Indexed: 06/09/2023]
Abstract
The continuously increasing concentration of atmospheric CO2 has considerably altered ecosystem functioning. However, few studies have examined the long-term (i.e. over a decade) effect of elevated CO2 on soil microbial communities. Using 16S rRNA gene amplicons and a GeoChip microarray, we investigated soil microbial communities from a Californian annual grassland after 14 years of experimentally elevated CO2 (275 ppm higher than ambient). Both taxonomic and functional gene compositions of the soil microbial community were modified by elevated CO2. There was decrease in relative abundance for taxa with higher ribosomal RNA operon (rrn) copy number under elevated CO2, which is a functional trait that responds positively to resource availability in culture. In contrast, taxa with lower rrn copy number were increased by elevated CO2. As a consequence, the abundance-weighted average rrn copy number of significantly changed OTUs declined from 2.27 at ambient CO2 to 2.01 at elevated CO2. The nitrogen (N) fixation gene nifH and the ammonium-oxidizing gene amoA significantly decreased under elevated CO2 by 12.6% and 6.1%, respectively. Concomitantly, nitrifying enzyme activity decreased by 48.3% under elevated CO2, albeit this change was not significant. There was also a substantial but insignificant decrease in available soil N, with both nitrate (NO3-) (-27.4%) and ammonium (NH4+) (-15.4%) declining. Further, a large number of microbial genes related to carbon (C) degradation were also affected by elevated CO2, whereas those related to C fixation remained largely unchanged. The overall changes in microbial communities and soil N pools induced by long-term elevated CO2 suggest constrained microbial N decomposition, thereby slowing the potential maximum growth rate of the microbial community.
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Affiliation(s)
- Sihang Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Qiaoshu Zheng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Mengting Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Zhou Shi
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | | | - Kathryn M Docherty
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI 49008, USA
| | - Shikui Dong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Beijing normal university, Beijing 100875, PR China
| | | | - Yunfu Gu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA; Department of Microbiology, College of Resource Sciences and Technology, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Jessica Gutknecht
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle 06120, Germany; Department of Soil, Water, and Climate, University of Minnesota, Twin Cities, Saint Paul, MN 55104, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Xavier Le Roux
- Microbial ecology Centre, INRA, CNRS, University of Lyon, University Lyon 1, UMR INRA 1418, UMR CNRS 5557, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Xingyu Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Audrey Niboyet
- Institut d'Ecologie et des Sciences de l'Environnement de Paris (Sorbonne Université, CNRS, INRA, IRD, Université Paris Diderot, UPEC), 4 place Jussieu, 75005 Paris, France; AgroParisTech, 75005 Paris, France
| | - Tong Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China; Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China.
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Deng J, Yin Y, Luo J, Zhu W, Zhou Y. Different revegetation types alter soil physical-chemical characteristics and fungal community in the Baishilazi Nature Reserve. PeerJ 2019; 6:e6251. [PMID: 30648009 PMCID: PMC6330947 DOI: 10.7717/peerj.6251] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 12/08/2018] [Indexed: 12/14/2022] Open
Abstract
The effects of different revegetation types on soil physical-chemical characteristics and fungal community diversity and composition of soils sampled from five different revegetation types (JM, Juglans mandshurica; QM, Quercus mongolica; conifer-broadleaf forest (CB); LG, Larix gmelinii; PK, Pinus koraiensis) in the Baishilazi Nature Reserve were determined. Soil fungal communities were assessed employing ITS rRNA Illunima Miseq high-throughput sequencing. Responses of the soil fungi community to soil environmental factors were assessed through canonical correspondence analysis (CCA) and Pearson correlation analysis. The coniferous forests (L. gmelinii, P. koraiensis) and CB had reduced soil total carbon (C), total nitrogen (N), and available nitrogen (AN) values compared with the broadleaf forest (J. mandshurica, Q. mongolica). The average fungus diversity according to the Shannon, ACE, Chao1, and Simpson index were increased in the J. mandshurica site. Basidiomycota, Ascomycota, Zygomycota, and Rozellomycota were the dominant fungal taxa in this region. The phylum Basidiomycota was dominant in the Q. mongolica, CB, L. gmelinii, and P. koraiensis sites, while Ascomycota was the dominant phylum in the J. mandshurica site. The clear differentiation of fungal communities and the clustering in the heatmap and in non-metric multidimensional scaling plot showed that broadleaf forests, CB, and coniferous forests harbored different fungal communities. The results of the CCA showed that soil environmental factors, such as soil pH, total C, total N, AN, and available phosphorus (P) greatly influenced the fungal community structure. Based on our results, the different responses of the soil fungal communities to the different revegetation types largely dependent on different forest types and soil physicochemical characteristic in Baishilazi Nature Reserve.
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Affiliation(s)
- Jiaojiao Deng
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- College of Land and Environment, Shenyang Agricultural University, Shenyang, China
| | - You Yin
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network, Shenyang Agricultural University, Tieling, China
| | - Jiyao Luo
- Liaoning Baishi Lazi National Nature Reserve Administration, Dandong, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network, Shenyang Agricultural University, Tieling, China
| | - Yongbin Zhou
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network, Shenyang Agricultural University, Tieling, China
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82
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Yang Y, Liu G, Ye C, Liu W. Bacterial community and climate change implication affected the diversity and abundance of antibiotic resistance genes in wetlands on the Qinghai-Tibetan Plateau. JOURNAL OF HAZARDOUS MATERIALS 2019; 361:283-293. [PMID: 30212791 DOI: 10.1016/j.jhazmat.2018.09.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/31/2018] [Accepted: 09/01/2018] [Indexed: 05/26/2023]
Abstract
Antibiotic resistance genes (ARGs) have been identified as emerging pollutants in the environment. However, little information is available for ARGs in natural wetlands at high altitude. In this study, we investigated 32 wetlands across the Qinghai-Tibetan Plateau, with the variation of wetland types, altitude, and environmental factors, to assess the determinant factor of ARGs in this area. ARGs were detected in all the wetlands, ranged from 1.80 × 105 to 1.35 × 107 copies per gram of soils. The ARGs in wetland soils were diverse and abundant, and varied from each site, but the spatial geographical distance did not influence the ARG profile. The mobile genetic elements in wetlands ranged from 3.13 × 103 to 1.02 × 106 copies per gram of soil, indicating the low abundance of mobile genetic elements suggests a lower transfer rate of ARGs between bacteria in the Plateau. Bacterial community composition was the main driver in shaping the ARG diversity and geographic distribution. Soil moisture and temperature were positively correlated with ARG abundance in this region. These results not only provide a better understanding of the background levels of ARGs in the Qinghai-Tibetan Plateau, but also shed light on the influence of climate change and increased human activities on the distribution of ARGs.
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Affiliation(s)
- Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK
| | - Guihua Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Chen Ye
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
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83
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Zhang Y, Lu L, Chang X, Jiang F, Gao X, Yao Y, Li C, Cao S, Zhou Q, Peng F. Small-Scale Soil Microbial Community Heterogeneity Linked to Landform Historical Events on King George Island, Maritime Antarctica. Front Microbiol 2018; 9:3065. [PMID: 30619151 PMCID: PMC6296293 DOI: 10.3389/fmicb.2018.03065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/28/2018] [Indexed: 11/13/2022] Open
Abstract
Although research on microbial biogeography has made great progress in the past decade, distributions of terrestrial microbial communities in extreme environments such as Antarctica are not well understood. In addition, knowledge of whether and how historical contingencies affect microbial distributions at small spatial scales is lacking. Here, we analyzed soil-borne microbial (bacterial, archaeal, and fungal) communities in 12 quadrat plots around the Fildes Region of King George Island, maritime Antarctica, and the communities were divided into two groups according to the soil elemental compositions and environmental attributes of Holocene raised beach and Tertiary volcanic stratigraphy. Prokaryotic communities of the two groups were well separated; the prokaryotic data were primarily correlated with soil elemental compositions and were secondly correlated with environmental attributes (e.g., soil pH, total organic carbon, NO3 -, and vegetation coverage; Pearson test, r = 0.59 vs. 0.52, both P < 0.01). The relatively high abundance of P, S, Cl, and Br in Group 1 (Holocene raised beach site) was likely due to landform uplift. Lithophile-elements (Si, Al, Ca, Sr, Ti, V, and Fe) correlated with prokaryotic communities in Group 2 may have originated from weathering of Tertiary volcanic rock. No significant correlations were found between the fungal community distribution and both the soil elemental composition and environmental attributes in this study; however, Monte Carlo tests revealed that elements Sr and Ti, soil pH, sampling altitude, and moss and lichen species numbers had significant impacts on fungal communities. The elements and nutrients accumulated during the formation of different landforms influenced the development of soils, plant growth, and microbial communities, and this resulted in small-scale spatially heterogeneous biological distributions. These findings provide new evidence that geological evolutionary processes in the Fildes Region were crucial to its microbial community development, and the results highlight that microbial distribution patterns are the legacies of historical events at this small spatial scale. Based on this study, the ice-free regions in maritime Antarctica represent suitable research sites for studying the influence of geomorphological features on microbial distributions, and we envision the possibility of a site-specific landform assignment through the analysis of the soil prokaryotic community structure.
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Affiliation(s)
- Yumin Zhang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, China
| | - Lu Lu
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, China
| | - Xulu Chang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, China
| | - Fan Jiang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiangdong Gao
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Yifeng Yao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Chengsen Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Shunan Cao
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Qiming Zhou
- ChosenMed Technology (Beijing) Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, China
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, China
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84
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Lu X, Ma S, Chen Y, Yangzom D, Jiang H. Squalene Found in Alpine Grassland Soils under a Harsh Environment in the Tibetan Plateau, China. Biomolecules 2018; 8:biom8040154. [PMID: 30463288 PMCID: PMC6315835 DOI: 10.3390/biom8040154] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/01/2018] [Accepted: 11/14/2018] [Indexed: 11/16/2022] Open
Abstract
Squalene is found in a large number of plants, animals, and microorganisms, as well as other sources, playing an important role as an intermediate in sterol biosynthesis. It is used widely in the food, cosmetics, and medicine industries because of its antioxidant, antistatic, and anti-carcinogenic properties. A higher natural squalene component of lipids is usually reported as being isolated to organisms living in harsh environments. In the Tibetan Plateau, which is characterized by high altitude, strong solar radiation, drought, low temperatures, and thin air, the squalene component was identified in five alpine grasslands soils using the pyrolysis gas chromatography⁻mass spectrometry (Py-GC/MS) technique. The relative abundance of squalene ranged from 0.93% to 10.66% in soils from the five alpine grasslands, with the highest value found in alpine desert and the lowest in alpine meadow. Furthermore, the relative abundance of squalene in alpine grassland soils was significantly negatively associated with soil chemical/microbial characteristics. These results indicate that the extreme environmental conditions of the Tibetan Plateau may stimulate the microbial biosynthesis of squalene, and the harsher the environment, the higher the relative abundance of soil squalene.
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Affiliation(s)
- Xuyang Lu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China.
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Shuqin Ma
- College of Tourism, Henan Normal University, Xinxiang 453007, China.
| | - Youchao Chen
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Degyi Yangzom
- Ecological Monitoring & Research Center, Tibetan Environment Monitoring Station, Lhasa 850000, China.
| | - Hongmao Jiang
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
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85
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Fan X, Yin C, Yan G, Cui P, Shen Q, Wang Q, Chen H, Zhang N, Ye M, Zhao Y, Li T, Liang Y. The contrasting effects of N-(n-butyl) thiophosphoric triamide (NBPT) on N 2O emissions in arable soils differing in pH are underlain by complex microbial mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:155-167. [PMID: 29894875 DOI: 10.1016/j.scitotenv.2018.05.356] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/27/2018] [Accepted: 05/28/2018] [Indexed: 06/08/2023]
Abstract
The urease inhibitor, N-(n-butyl) thiophosphoric triamide (NBPT), has been proposed to reduce synthetic fertilizer-N losses, including nitrous oxide (N2O) emissions from agricultural soils. However, the response of N2O emission to NBPT amendment is inconsistent across soils and associated microbial mechanisms remain largely unknown. Here we performed a meta-analysis of the effects of NBPT on N2O emissions and found NBPT significantly reduced N2O emissions in alkaline soils whereas no obvious effects exhibited in acid soils. Based on the finding of meta-analysis that pH was a key modifier in regulating the effect of NBPT on N2O emissions, we selected two arable soils differing in pH and conducted a microcosm study. In conjunction with measurement of N2O emission, community structure and abundance of functional guilds were assessed using T-RFLP and qPCR. Our results showed NBPT retarded urea hydrolysis and inhibited nitrification, but stimulated N2O emission in alkaline soil, whereas it exhibited no remarkable effects in acid soil, thereby only partly confirming the results of meta-analysis. Abundances of AOB and ureC-containing bacteria decreased, while abundance of AOA increased in both soils with NBPT addition. For acid soil, N2O emissions were significantly correlated with both abundances and community structures of AOA and ureC-containing bacteria, as well as abundance of AOB; for alkaline soil, abundances and community structures of AOB were correlated with N2O emission, as well as community structures of ureC-containing bacteria and archaea, indicating an inconsistent response pattern of community traits of N2O emissions-related functional guilds to NBPT between alkaline soil and acid soil. Our findings suggest that (i) efficacy of NBPT in N2O emission was mainly influenced by soil pH and (ii) variable effects of NBPT on N2O emission might originate not only from the direct effect of NBPT on community traits of urease-positive microbes, but from the indirect effect on ammonia oxidizers.
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Affiliation(s)
- Xiaoping Fan
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chang Yin
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Guochao Yan
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Peiyuan Cui
- Jiangsu Key Laboratory of Crop Genetics and Physiology & Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Qi Shen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qun Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hao Chen
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Nan Zhang
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mujun Ye
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuhua Zhao
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tingqiang Li
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Liang
- Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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86
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Peng C, Wang H, Jiang Y, Yang J, Lai H, Wei X. Exploring the Abundance and Diversity of Bacterial Communities and Quantifying Antibiotic-Related Genes Along an Elevational Gradient in Taibai Mountain, China. MICROBIAL ECOLOGY 2018; 76:1053-1062. [PMID: 29744532 DOI: 10.1007/s00248-018-1197-x] [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: 09/12/2017] [Accepted: 04/27/2018] [Indexed: 06/08/2023]
Abstract
Thus far, no studies have investigated the soil microbial diversity over an elevational gradient in Taibai Mountain, the central massif of the Qinling Mountain Range. Here, we used Illumina sequencing and quantitative PCR of the 16S rRNA gene to assess the diversity and abundance of bacterial communities along an elevational gradient in representative vegetation soils in Taibai Mountain. We identified the soil, climate, and vegetation factors driving the variations in soil bacterial community structure by Pearson correlation and redundancy analysis. We also evaluated the potential for antibiotic discovery by quantitative PCR of the PKS-I, PKS-II, and NRPS genes from Actinobacteria. The results showed that soil bacterial alpha diversity increased first and then decreased with an elevational rise in both the northern and southern slopes of Taibai Mountain. The bacterial abundance was significantly correlated with soil organic matter and nitrate nitrogen. The average relative abundance of Actinobacteria in Taibai Mountain was markedly higher than those in other mountain forest soils. The absolute abundance of PKS and NPRS gene was significantly higher in the tested soils compared with the gene copy numbers reported in tropical urban soils. Taibai Mountain is rich in actinomycete resources and has great potential for antibiotic excavation.
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Affiliation(s)
- Chu Peng
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - He Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Yingying Jiang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Jinhua Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Hangxian Lai
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China.
| | - Xiaomin Wei
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China.
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87
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Wang C, Liu S, Zhang Y, Liu B, He F, Xu D, Zhou Q, Wu Z. Bacterial Communities and Their Predicted Functions Explain the Sediment Nitrogen Changes Along with Submerged Macrophyte Restoration. MICROBIAL ECOLOGY 2018; 76:625-636. [PMID: 29502133 DOI: 10.1007/s00248-018-1166-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/19/2018] [Indexed: 06/08/2023]
Abstract
Submerged vegetation biomass fluctuation usually occurs during the preliminary stage of vegetation restoration in shallow lakes, which impacts the final status and duration for achieving a macrophyte-dominant state. This study uncovered the sediment N characteristics and the sediment bacterial community and their predicted functions during the preliminary stage of vegetation recovery in the West Lake, a typical subtropical degenerated shallow lake in China. Results showed increased amounts of sediment TN and NH4-N, reaching 3425.76 and 345.5 mg kg-1, respectively, when the vegetation biomass decreased from its maximum to its minimum. The maximum concentration of sediment NH4-N reached 508.60 mg kg-1 with the decline in vegetation, which might restrict further growth of the submerged macrophytes. The bacterial community structure during the high macrophyte biomass (HMB) period was distinct from that observed during the low macrophyte biomass (LMB) period. Specific taxa such as the phyla Chloroflexi and Acidobacteria and the genus Anaerolineaceae that are related to organic carbon degradation were significantly higher during the LMB period. Potential denitrifiers, such as Lactococcus and Bacillus genera decreased during the LMB period. Accumulation of sediment ammonia could be attributed to the enhanced production by assimilatory nitrate reduction, organic N degradation, and/or the decreased consumption by nitrification. Our findings highlight that the unstable preliminary stage of vegetation restoration brings drastic fluctuation of sediment N loading, of which NH4-N accumulation caused by bacterial communities prevents further growth of the submerged macrophytes. Therefore, extra management measures for the vegetation recovery areas should be taken to avoid excess NH4-N accumulation in sediments.
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Affiliation(s)
- Chuan Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, 430072, China
| | - Shuangyuan Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, 430072, China
- University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Yi Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, 430072, China
| | - Biyun Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, 430072, China
| | - Feng He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, 430072, China
| | - Dong Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, 430072, China
| | - Qiaohong Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, 430072, China.
| | - Zhenbin Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, 430072, China
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88
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Xun W, Yan R, Ren Y, Jin D, Xiong W, Zhang G, Cui Z, Xin X, Zhang R. Grazing-induced microbiome alterations drive soil organic carbon turnover and productivity in meadow steppe. MICROBIOME 2018; 6:170. [PMID: 30236158 PMCID: PMC6149009 DOI: 10.1186/s40168-018-0544-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/29/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Grazing is a major modulator of biodiversity and productivity in grasslands. However, our understanding of grazing-induced changes in below-ground communities, processes, and soil productivity is limited. Here, using a long-term enclosed grazing meadow steppe, we investigated the impacts of grazing on the soil organic carbon (SOC) turnover, the microbial community composition, resistance and activity under seasonal changes, and the microbial contributions to soil productivity. RESULTS The results demonstrated that grazing had significant impacts on soil microbial communities and ecosystem functions in meadow steppe. The highest microbial α-diversity was observed under light grazing intensity, while the highest β-diversity was observed under moderate grazing intensity. Grazing shifted the microbial composition from fungi dominated to bacteria dominated and from slow growing to fast growing, thereby resulting in a shift from fungi-dominated food webs primarily utilizing recalcitrant SOC to bacteria-dominated food webs mainly utilizing labile SOC. Moreover, the higher fungal recalcitrant-SOC-decomposing activities and bacterial labile-SOC-decomposing activities were observed in fungi- and bacteria-dominated communities, respectively. Notably, the robustness of bacterial community and the stability of bacterial activity were associated with α-diversity, while this was not the case for the robustness of fungal community and its associated activities. Finally, we observed that microbial α-diversity rather than SOC turnover rate can predict soil productivity. CONCLUSIONS Our findings indicate the strong influence of grazing on soil microbial community, SOC turnover, and soil productivity and the important positive role of soil microbial α-diversity in steering the functions of meadow steppe ecosystems.
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Affiliation(s)
- Weibing Xun
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ruirui Yan
- National Hulunber Grassland Ecosystem Observation and Research Station, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yi Ren
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dongyan Jin
- National Hulunber Grassland Ecosystem Observation and Research Station, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wu Xiong
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guishan Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhongli Cui
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoping Xin
- National Hulunber Grassland Ecosystem Observation and Research Station, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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89
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Donhauser J, Frey B. Alpine soil microbial ecology in a changing world. FEMS Microbiol Ecol 2018; 94:5017441. [PMID: 30032189 DOI: 10.1093/femsec/fiy099] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/25/2018] [Indexed: 01/22/2023] Open
Abstract
Climate change has a disproportionally large impact on alpine soil ecosystems, leading to pronounced changes in soil microbial diversity and function associated with effects on biogeochemical processes at the local and supraregional scales. However, due to restricted accessibility, high-altitude soils remain largely understudied and a considerable heterogeneity hampers the comparability of different alpine studies. Here, we highlight differences and similarities between alpine and arctic ecosystems, and we discuss the impact of climatic variables and associated vegetation and soil properties on microbial ecology. We consider how microbial alpha-diversity, community structures and function change along altitudinal gradients and with other topographic features such as slope aspect. In addition, we focus on alpine permafrost soils, harboring a surprisingly large unknown microbial diversity and on microbial succession along glacier forefield chronosequences constituting the most thoroughly studied alpine habitat. Finally, highlighting experimental approaches, we present climate change studies showing shifts in microbial community structures and function in response to warming and altered moisture, interestingly with some contradiction. Collectively, despite harsh environmental conditions, many specially adapted microorganisms are able to thrive in alpine environments. Their community structures strongly correlate with climatic, vegetation and soil properties and thus closely mirror the complexity and small-scale heterogeneity of alpine soils.
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Affiliation(s)
| | - Beat Frey
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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90
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Zhang Q, Goberna M, Liu Y, Cui M, Yang H, Sun Q, Insam H, Zhou J. Competition and habitat filtering jointly explain phylogenetic structure of soil bacterial communities across elevational gradients. Environ Microbiol 2018; 20:2386-2396. [PMID: 29687609 DOI: 10.1111/1462-2920.14247] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/15/2018] [Indexed: 11/30/2022]
Abstract
The importance of assembly processes in shaping biological communities is poorly understood, especially for microbes. Here, we report on the forces that structure soil bacterial communities along a 2000 m elevational gradient. We characterized the relative importance of habitat filtering and competition on phylogenetic structure and turnover in bacterial communities. Bacterial communities exhibited a phylogenetically clustered pattern and were more clustered with increasing elevation. Biotic factors (i.e., relative abundance of dominant bacterial lineages) appeared to be most important to the degree of clustering, evidencing the role of the competitive ability of entire clades in shaping the communities. Phylogenetic turnover showed the greatest correlation to elevation. After controlling the elevation, biotic factors showed greater correlation to phylogenetic turnover than all the habitat variables (i.e., climate, soil and vegetation). Structural equation modelling also identified that elevation and soil organic matter exerted indirect effects on phylogenetic diversity and turnover by determining the dominance of microbial competitors. Our results suggest that competition among bacterial taxa induced by soil carbon contributes to the phylogenetic pattern across elevational gradient in the Tibetan Plateau. This highlights the importance of considering not only abiotic filtering but also biotic interactions in soil bacterial communities across stressful elevational gradients.
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Affiliation(s)
- Qian Zhang
- Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing Forestry University, Beijing 100083, People's Republic of China.,Research Institute of Forestry Chinese Academy of Forestry, No. 1, Dongxiaofu, Xiangshan Road Haidian District, Beijing 100091, People's Republic of China.,Institute of Microbiology, University of Innsbruck, Technikerstr. 25d, Innsbruck 6020, Austria
| | - Marta Goberna
- Centro de Investigaciones sobre Desertificación (CIDE-CSIC), Carretera Moncada - Náquera, Km 4.5, 46113 Valencia, Spain
| | - Yuguo Liu
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing 100091, People's Republic of China
| | - Ming Cui
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing 100091, People's Republic of China
| | - Haishui Yang
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Qixiang Sun
- Research Institute of Forestry Chinese Academy of Forestry, No. 1, Dongxiaofu, Xiangshan Road Haidian District, Beijing 100091, People's Republic of China
| | - Heribert Insam
- Institute of Microbiology, University of Innsbruck, Technikerstr. 25d, Innsbruck 6020, Austria
| | - Jinxing Zhou
- Jianshui National Field Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing 100083, People's Republic of China
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91
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Zheng X, Liu F, Li K, Shi X, Ni Y, Li B, Zhuge B. Evaluating the microbial ecology and metabolite profile in Kazak artisanal cheeses from Xinjiang, China. Food Res Int 2018; 111:130-136. [PMID: 30007669 DOI: 10.1016/j.foodres.2018.05.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 04/01/2018] [Accepted: 05/08/2018] [Indexed: 11/30/2022]
Abstract
Kazak artisanal cheese is one of the famous fermented food in Uighur Autonomy Region of Xinjiang, China. However, the microbial ecology in Kazak artisanal cheeses across different regions is unclear. In this study, we determined the microbial community composition through amplicon sequencing and measured the flavor profile of 10 cheese samples from different regions of Xinjiang. The associations between microbial communities, flavors and environmental factors were examined by redundancy analysis and Monte Carlo permutation test. Cheeses from different regions had different microbial communities, which was mainly reflected in the relative abundance of Lactobacillus, Streptococcus, Issatchenkia, Debaryomyces and Kluyveromyces. In addition, Pichia and Torulaspora were also the key microbial groups, according to the high relative abundance and large co-occurrence incidence in the correlation network. Using the microbe-metabolites correlation analysis, the major flavor-producing taxa were identified as Kluyveromyces, Anoxybacillus, Torulaspora, Lactobacillus, Streptococcus and Dipodascus. Environmental factors accounted for the majority of the microbial community variations, 88.54% for bacteria and 75.71% for fungi. Compared to physico-chemical factors (temperature, moisture, and pH), geographical factors (longitude, latitude and elevation) had a stronger effect on microbial communities in cheese samples from different regions of Xinjiang.
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Affiliation(s)
- Xiaoji Zheng
- School of Food Sciences, Shihezi University, Shihezi, Xinjiang Uighur Autonomy Region 832003, China; The Key Lab of Industrial Biotechnology of Ministry of Education, Research Centre of Industrial Microorganisms, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China.
| | - Fei Liu
- School of Food Sciences, Shihezi University, Shihezi, Xinjiang Uighur Autonomy Region 832003, China
| | - Kaixiong Li
- School of Food Sciences, Shihezi University, Shihezi, Xinjiang Uighur Autonomy Region 832003, China
| | - Xuewei Shi
- School of Food Sciences, Shihezi University, Shihezi, Xinjiang Uighur Autonomy Region 832003, China
| | - Yongqing Ni
- School of Food Sciences, Shihezi University, Shihezi, Xinjiang Uighur Autonomy Region 832003, China
| | - Baokun Li
- School of Food Sciences, Shihezi University, Shihezi, Xinjiang Uighur Autonomy Region 832003, China
| | - Bin Zhuge
- The Key Lab of Industrial Biotechnology of Ministry of Education, Research Centre of Industrial Microorganisms, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, China.
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92
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Zeng J, Shen JP, Wang JT, Hu HW, Zhang CJ, Bai R, Zhang LM, He JZ. Impacts of Projected Climate Warming and Wetting on Soil Microbial Communities in Alpine Grassland Ecosystems of the Tibetan Plateau. MICROBIAL ECOLOGY 2018; 75:1009-1023. [PMID: 29124311 DOI: 10.1007/s00248-017-1098-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/24/2017] [Indexed: 06/07/2023]
Abstract
Climate change is projected to have impacts on precipitation and temperature regimes in drylands of high elevation regions, with especially large effects in the Qinghai-Tibetan Plateau. However, there was limited information about how the projected climate change will impact on the soil microbial community and their activity in the region. Here, we present results from a study conducted across 72 soil samples from 24 different sites along a temperature and precipitation gradient (substituted by aridity index ranging from 0.079 to 0.89) of the Plateau, to assess how changes in aridity affect the abundance, community composition, and diversity of bacteria, ammonia-oxidizers, and denitrifers (nirK/S and nosZ genes-containing communities) as well as nitrogen (N) turnover enzyme activities. We found V-shaped or inverted V-shaped relationships between the aridity index (AI) and soil microbial parameters (gene abundance, community structures, microbial diversity, and N turnover enzyme activities) with a threshold at AI = 0.27. The increasing or decreasing rates of the microbial parameters were higher in areas with AI < 0.27 (alpine steppes) than in mesic areas with 0.27 < AI < 0.89 (alpine meadow and swamp meadow). The results indicated that the projected warming and wetting have a strong impact on soil microbial communities in the alpine steppes.
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Affiliation(s)
- Jun Zeng
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing, 100049, China
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Cui-Jing Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ren Bai
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing, 100049, China.
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
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93
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Ren B, Hu Y, Chen B, Zhang Y, Thiele J, Shi R, Liu M, Bu R. Soil pH and plant diversity shape soil bacterial community structure in the active layer across the latitudinal gradients in continuous permafrost region of Northeastern China. Sci Rep 2018; 8:5619. [PMID: 29618759 PMCID: PMC5884794 DOI: 10.1038/s41598-018-24040-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 03/26/2018] [Indexed: 12/21/2022] Open
Abstract
In the permafrost region of northeastern China, vegetation and soil environment have showed response to permafrost degradation triggered by global warming, but the corresponding variation of the soil microbial communities remains poorly investigated. Here, a field investigation in the continuous permafrost region was conducted to collect 63 soil samples from 21 sites along a latitudinal gradient to assess the distribution pattern of microbial communities and their correlation with environmental factors. High-throughput Illumina sequencing revealed that bacterial communities were dominated by Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria. Both microbial richness and phylogenetic diversity decreased initially and then increased as the latitude increased. UniFrac analysis of microbial communities detected significant differences among latitudes. Variation partitioning analysis and structural equation models revealed that environmental variables, including geographic factors, plant-community factors and soil physicochemical factors, all played non-negligible roles in affecting the microbial community structures directly or indirectly. Redundancy analysis and boosted regression tree analysis further highlighted the influences of soil pH and plant richness on microbial community compositions and diversity patterns. Taken together, these results suggest that the distribution pattern of soil microbial communities shows distinct changes along the latitudinal gradients in northeastern China and is predominantly mediated by soil pH and plant diversity.
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Affiliation(s)
- Baihui Ren
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Institute of Landscape Ecology, University of Münster, Heisenbergstr. 2, 48149, Münster, Germany
| | - Yuanman Hu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China
| | - Baodong Chen
- University of Chinese Academy of Sciences, Beijing, 100049, China.,State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ying Zhang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China
| | - Jan Thiele
- Institute of Landscape Ecology, University of Münster, Heisenbergstr. 2, 48149, Münster, Germany
| | - Rongjiu Shi
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China
| | - Miao Liu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China
| | - Rencang Bu
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang Liaoning, 110016, China.
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94
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Zhang M, Wang X, Cui M, Wang Y, Jiao Z, Tan Z. Ensilage of oats and wheatgrass under natural alpine climatic conditions by indigenous lactic acid bacteria species isolated from high-cold areas. PLoS One 2018; 13:e0192368. [PMID: 29408855 PMCID: PMC5800594 DOI: 10.1371/journal.pone.0192368] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 01/21/2018] [Indexed: 11/18/2022] Open
Abstract
Five different species of selected broad-spectrum antibiotic lactic acid bacteria isolated from extremely high-cold areas were used as starters to ferment indigenous forage oats and wheatgrass under rigid alpine climatic conditions. The five isolates were Lactobacillus plantarum QZ227, Enterococcus mundtii QZ251, Pediococcus cellicola QZ311, Leuconostoc mesenteroides QZ1137 and Lactococcus lactis QZ613, and commercial Lactobacillus plantarum FG1 was used as the positive control and sterile water as the negative control. The minimum and maximum temperatures were -22°C and 23°C during the fermentation process, respectively. The pH of wheatgrass silage fermented by the QZ227 and FG1 inocula reached the expected values (≤4.15) although the pathogens detected in the silage should be further investigated. All of the inocula additives used in this study were effective in improving the fermentation quality of oat silage as indicated by the higher content of lactic acid, lower pH values (≤4.17) and significant inhibition of pathogens. QZ227 exhibited a fermentation ability that was comparable with the commercial inoculum FG1 for the whole process, and the deterioration rate was significantly lower than for FG1 after storage for 7 months. The pathogens Escherichia coli, mold and yeast were counted and isolated from the deteriorated silage. E. coli were the main NH3-N producer while F. fungi and yeast produced very little.
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Affiliation(s)
- Miao Zhang
- Henan Key Laboratory of Ion-Beam Bioengineering, College of Physics and Engineering, Zhengzhou University, Zhengzhou, China
| | - Xiaojie Wang
- Henan Key Laboratory of Ion-Beam Bioengineering, College of Physics and Engineering, Zhengzhou University, Zhengzhou, China
| | - Meiyan Cui
- Henan Key Laboratory of Ion-Beam Bioengineering, College of Physics and Engineering, Zhengzhou University, Zhengzhou, China
| | - Yanping Wang
- Henan Key Laboratory of Ion-Beam Bioengineering, College of Physics and Engineering, Zhengzhou University, Zhengzhou, China
| | - Zhen Jiao
- Henan Key Laboratory of Ion-Beam Bioengineering, College of Physics and Engineering, Zhengzhou University, Zhengzhou, China
| | - Zhongfang Tan
- Henan Key Laboratory of Ion-Beam Bioengineering, College of Physics and Engineering, Zhengzhou University, Zhengzhou, China
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95
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Liu D, Liu G, Chen L, Wang J, Zhang L. Soil pH determines fungal diversity along an elevation gradient in Southwestern China. SCIENCE CHINA-LIFE SCIENCES 2018; 61:718-726. [PMID: 29307110 DOI: 10.1007/s11427-017-9200-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 10/09/2017] [Indexed: 11/29/2022]
Abstract
Fungi play important roles in ecosystem processes, and the elevational pattern of fungal diversity is still unclear. Here, we examined the diversity of fungi along a 1,000 m elevation gradient on Mount Nadu, Southwestern China. We used MiSeq sequencing to obtain fungal sequences that were clustered into operational taxonomic units (OTUs) and to measure the fungal composition and diversity. Though the species richness and phylogenetic diversity of the fungal community did not exhibit significant trends with increasing altitude, they were significantly lower at mid-altitudinal sites than at the base. The Bray-Curtis distance clustering also showed that the fungal communities varied significantly with altitude. A distance-based linear model multivariate analysis (DistLM) identified that soil pH dominated the explanatory power of the species richness (23.72%), phylogenetic diversity (24.25%) and beta diversity (28.10%) of the fungal community. Moreover, the species richness and phylogenetic diversity of the fungal community increased linearly with increasing soil pH (P<0.05). Our study provides evidence that pH is an important predictor of soil fungal diversity along elevation gradients in Southwestern China.
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Affiliation(s)
- Dan Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guohua Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China. .,Joint Center for Global Change Studies, Beijing, 100875, China.
| | - Li Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juntao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Limei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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96
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Taxonomic and Functional Diversity of a Quercus pyrenaica Willd. Rhizospheric Microbiome in the Mediterranean Mountains. FORESTS 2017. [DOI: 10.3390/f8100390] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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97
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Sun H, Liu F, Xu S, Wu S, Zhuang G, Deng Y, Wu J, Zhuang X. Myriophyllum aquaticum Constructed Wetland Effectively Removes Nitrogen in Swine Wastewater. Front Microbiol 2017; 8:1932. [PMID: 29056931 PMCID: PMC5635519 DOI: 10.3389/fmicb.2017.01932] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 09/21/2017] [Indexed: 12/22/2022] Open
Abstract
Removal of nitrogen (N) is a critical aspect in the functioning of constructed wetlands (CWs), and the N treatment in CWs depends largely on the presence and activity of macrophytes and microorganisms. However, the effects of plants on microorganisms responsible for N removal are poorly understood. In this study, a three-stage surface flow CW was constructed in a pilot-scale within monospecies stands of Myriophyllum aquaticum to treat swine wastewater. Steady-state conditions were achieved throughout the 600-day operating period, and a high (98.3%) average ammonia removal efficiency under a N loading rate of 9 kg ha-1 d-1 was observed. To determine whether this high efficiency was associated with the performance of active microbes, the abundance, structure, and interactions of microbial community were compared in the unvegetated and vegetated samples. Real-time quantitative polymerase chain reactions showed the abundances of nitrifying genes (archaeal and bacterial amoA) and denitrifying genes (nirS, nirK, and nosZ) were increased significantly by M. aquaticum in the sediments, and the strongest effects were observed for the archaeal amoA (218-fold) and nirS genes (4620-fold). High-throughput sequencing of microbial 16S rRNA gene amplicons showed that M. aquaticum greatly changed the microbial community, and ammonium oxidizers (Nitrosospira and Nitrososphaera), nitrite-oxidizing bacteria (Nitrospira), and abundant denitrifiers including Rhodoplanes, Bradyrhizobium, and Hyphomicrobium, were enriched significantly in the sediments. The results of a canonical correspondence analysis and Mantle tests indicated that M. aquaticum may shift the sediment microbial community by changing the sediment chemical properties. The enriched nitrifiers and denitrifiers were distributed widely in the vegetated sediments, showing positive ecological associations among themselves and other bacteria based on phylogenetic molecular ecological networks.
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Affiliation(s)
- Haishu Sun
- 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
| | - Feng Liu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Shengjun Xu
- 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
| | - Shanghua Wu
- 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
| | - Guoqiang Zhuang
- 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
| | - Ye Deng
- 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
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Xuliang Zhuang
- 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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98
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Zhao K, Kong W, Khan A, Liu J, Guo G, Muhanmmad S, Zhang X, Dong X. Elevational diversity and distribution of ammonia-oxidizing archaea community in meadow soils on the Tibetan Plateau. Appl Microbiol Biotechnol 2017; 101:7065-7074. [PMID: 28776097 DOI: 10.1007/s00253-017-8435-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/12/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
Abstract
Unraveling elevational diversity patterns of plants and animals has long been attracting scientific interests. However, whether soil microorganisms exhibit similar elevational patterns remains largely less explored, especially for functional microbial communities, such as ammonia oxidizers. Here, we investigated the diversity and distribution pattern of ammonia-oxidizing archaea (AOA) in meadow soils along an elevation gradient from 4400 m to the grassline at 5100 m on the Tibetan Plateau using terminal restriction fragment length polymorphism (T-RFLP) and sequencing methods by targeting amoA gene. Increasing elevations led to lower soil temperature and pH, but higher nutrients and water content. The results showed that AOA diversity and evenness monotonically increased with elevation, while richness was relatively stable. The increase of diversity and evenness was attributed to the growth inhibition of warm-adapted AOA phylotypes by lower temperature and the growth facilitation of cold-adapted AOA phylotypes by richer nutrients at higher elevations. Low temperature thus played an important role in the AOA growth and niche separation. The AOA community variation was explained by the combined effect of all soil properties (32.6%), and 8.1% of the total variation was individually explained by soil pH. The total AOA abundance decreased, whereas soil potential nitrification rate (PNR) increased with increasing elevations. Soil PNR positively correlated with the abundance of cold-adapted AOA phylotypes. Our findings suggest that low temperature plays an important role in AOA elevational diversity pattern and niche separation, rising the negative effects of warming on AOA diversity and soil nitrification process in the Tibetan region.
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Affiliation(s)
- Kang Zhao
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Weidong Kong
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ajmal Khan
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinbo Liu
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China
| | - Guangxia Guo
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China
| | - Said Muhanmmad
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Building 3, Courtyard 16, Lincui Road, Chaoyang District, Beijing, 100101, China
| | - Xianzhou Zhang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaobin Dong
- State Key Laboratory of Earth Surface Processes and Resource Ecology, College of Resources Science and Technology, Beijing Normal University, Beijing, 100875, China
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99
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Escalas A, Troussellier M, Yuan T, Bouvier T, Bouvier C, Mouchet MA, Flores Hernandez D, Ramos Miranda J, Zhou J, Mouillot D. Functional diversity and redundancy across fish gut, sediment and water bacterial communities. Environ Microbiol 2017; 19:3268-3282. [PMID: 28618142 DOI: 10.1111/1462-2920.13822] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 06/07/2017] [Indexed: 11/26/2022]
Abstract
This article explores the functional diversity and redundancy in a bacterial metacommunity constituted of three habitats (sediment, water column and fish gut) in a coastal lagoon under anthropogenic pressure. Comprehensive functional gene arrays covering a wide range of ecological processes and stress resistance genes to estimate the functional potential of bacterial communities were used. Then, diversity partitioning was used to characterize functional diversity and redundancy within (α), between (β) and across (γ) habitats. It was showed that all local communities exhibit a highly diversified potential for the realization of key ecological processes and resistance to various environmental conditions, supporting the growing evidence that macro-organisms microbiomes harbour a high functional potential and are integral components of functional gene dynamics in aquatic bacterial metacommunities. Several levels of functional redundancy at different scales of the bacterial metacommunity were observed (within local communities, within habitats and at the metacommunity level). The results suggested a high potential for the realization of spatial ecological insurance within this ecosystem, that is, the functional compensation among microorganisms for the realization and maintenance of key ecological processes, within and across habitats. Finally, the role of macro-organisms as dispersal vectors of microbes and their potential influence on marine metacommunity dynamics were discussed.
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Affiliation(s)
- Arthur Escalas
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Marc Troussellier
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France
| | - Tong Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Thierry Bouvier
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France
| | - Corinne Bouvier
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France
| | - Maud A Mouchet
- UMR 7204 CESCO, Muséum d'Histoire Naturelle, 55 rue Buffon, Paris, 75005, France
| | - Domingo Flores Hernandez
- Centro de Ecología, Pesquerias y Oceanographia de Golfo de México, Universidad Autonoma de Campeche, Campeche, Mexico
| | - Julia Ramos Miranda
- Centro de Ecología, Pesquerias y Oceanographia de Golfo de México, Universidad Autonoma de Campeche, Campeche, Mexico
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - David Mouillot
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
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100
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Ma X, Zhao C, Gao Y, Liu B, Wang T, Yuan T, Hale L, Nostrand JDV, Wan S, Zhou J, Yang Y. Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition. Mol Ecol 2017; 26:4186-4196. [PMID: 28570016 DOI: 10.1111/mec.14194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 04/10/2017] [Accepted: 05/15/2017] [Indexed: 01/09/2023]
Abstract
Aeolian soil erosion and deposition have worldwide impacts on agriculture, air quality and public health. However, ecosystem responses to soil erosion and deposition remain largely unclear in regard to microorganisms, which are the crucial drivers of biogeochemical cycles. Using integrated metagenomics technologies, we analysed microbial communities subjected to simulated soil erosion and deposition in a semiarid grassland of Inner Mongolia, China. As expected, soil total organic carbon and plant coverage were decreased by soil erosion, and soil dissolved organic carbon (DOC) was increased by soil deposition, demonstrating that field simulation was reliable. Soil microbial communities were altered (p < .039) by both soil erosion and deposition, with dramatic increase in Cyanobacteria related to increased stability in soil aggregates. amyA genes encoding α-amylases were specifically increased (p = .01) by soil deposition and positively correlated (p = .02) to DOC, which likely explained changes in DOC. Surprisingly, most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or unaltered by both erosion and deposition, probably arising from acceleration of organic matter mineralization. These divergent responses support the necessity to include microbial components in evaluating ecological consequences. Furthermore, Mantel tests showed strong, significant correlations between soil nutrients and functional structure but not taxonomic structure, demonstrating close relevance of microbial function traits to nutrient cycling.
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Affiliation(s)
- Xingyu Ma
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Cancan Zhao
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, College of Life Sciences, Henan University, Kaifeng, China
| | - Ying Gao
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Bin Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, College of Life Sciences, Henan University, Kaifeng, China
| | - Tengxu Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Tong Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Lauren Hale
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Joy D Van Nostrand
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Shiqiang Wan
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, College of Life Sciences, Henan University, Kaifeng, China
| | - Jizhong Zhou
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.,Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
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