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Du S, Li XQ, Feng J, Huang Q, Liu YR. Soil core microbiota drive community resistance to mercury stress and maintain functional stability. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 894:165056. [PMID: 37348729 DOI: 10.1016/j.scitotenv.2023.165056] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
Soil microbial communities have resistance to environmental stresses and thus can maintain ecosystem functions such as decomposition, nutrient provisioning, and plant pathogen control. However, predominant factors driving community resistance of soil microbiome to heavy metal pollution stresses and ecosystem functional stability are still unclear, limiting our ability to forecast how soil pollution might affect ecosystem sustainability. Here, we conducted microcosm experiments to estimate the importance of soil microbiome in predicting community resistance to heavy metal mercury (Hg) stress in paired paddy and upland fields. We found that community resistance of soil microbiome was strongly correlated with ecosystem functional stability, so were the individual groups of organisms such as bacteria, saprotrophic fungi, and phototrophic protists. The core phylotypes within soil microbiome had a major contribution to community resistance, which was essential for the maintenance of functional stability. Co-occurrence network further confirmed that community resistances of main ecological clusters were positively correlated with ecosystem functional stability. Together, our results provide new insights into the link between community resistance and functional stability, and highlight the importance of core microbiota in driving community resistance to environmental stresses and maintain functional stability.
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Affiliation(s)
- Shuai Du
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin-Qi Li
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiao Feng
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Rong Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China.
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2
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Yang G, Jiang L, Li W, Li E, Lv G. Structural Characteristics and Assembly Mechanisms of Soil Microbial Communities under Water-Salt Gradients in Arid Regions. Microorganisms 2023; 11:microorganisms11041060. [PMID: 37110483 PMCID: PMC10142023 DOI: 10.3390/microorganisms11041060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/07/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Exploring the structural characteristics of arid soil microbial communities and their assembly mechanisms is important for understanding the ecological characteristics of arid zone soils and promoting ecological restoration. In this study, we used Illumina high-throughput sequencing technology to study soils in the arid zone of the Lake Ebinur basin, determined the differences among soil microbial community structures in the study area under different water-salt gradients, and investigated the effects of environmental factors on microbial community structure and assembly mechanisms. The results show the following: the microbial community alpha diversity exhibited a significantly higher low water-salt gradient (L) than high water-salt gradient (H) and medium water-salt gradient (M). The pH was most strongly correlated with soil microbial community structure, where the alpha diversity indices of the bacterial community and fungal community were significantly negatively correlated with pH, and the Bray-Curtis distance of bacterial community was significantly positively correlated with pH (p < 0.05). The complexity of bacterial community co-occurrence networks showed a significantly higher L than H and M, and the complexity of fungal community co-occurrence network showed a significantly lower L than H and M. The cooperative relationship of H and M in the co-occurrence networks was stronger than that of the L, and the key species of the microbial co-occurrence network were different under different water-salt gradients. Stochastic processes dominated the assembly mechanism of the microbial community structure of soil, and the explanation rates of deterministic and stochastic processes were different under different water-salt gradients, with the highest explanation rate of stochastic processes on the L accounting for more than 90%. In summary, the soil microbial community structure and assembly mechanisms significantly differed across water-salt gradients, and these findings can help provide a reference for further research on soil microbiology in arid zones.
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Affiliation(s)
- Guang Yang
- College of the Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830046, China
| | - Lamei Jiang
- College of the Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830046, China
| | - Wenjing Li
- College of the Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830046, China
| | - Eryang Li
- College of the Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830046, China
| | - Guanghui Lv
- College of the Ecology and Environment, Xinjiang University, Urumqi 830017, China
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi 830046, China
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Zhang ZY, Qiang FF, Liu GQ, Liu CH, Ai N. Distribution characteristics of soil microbial communities and their responses to environmental factors in the sea buckthorn forest in the water-wind erosion crisscross region. Front Microbiol 2023; 13:1098952. [PMID: 36704571 PMCID: PMC9871601 DOI: 10.3389/fmicb.2022.1098952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Soil microorganisms are an important part of forest ecosystems, and their community structure and ecological adaptations are important for explaining soil material cycles in the fragile ecological areas. We used high-throughput sequencing technology to examine the species composition and diversity of soil bacterial and fungal communities in sea buckthorn forests at five sites in the water-wind erosion crisscross in northern Shaanxi (about 400 km long). The results are described as follows: (1) The soil bacterial community of the sea buckthorn forest in the study region was mainly dominated by Actinobacteria, Proteobacteria, and Acidobacteria, and the fungi community was mainly dominated by Ascomycota. (2) The coefficient of variation of alpha diversity of microbial communities was higher in the 0-10 cm soil layer than in the 10-20 cm soil layer. (3) Soil electrical conductivity (36.1%), available phosphorous (AP) (21.0%), available potassium (16.2%), total nitrogen (12.7%), and the meteorological factors average annual maximum temperature (33.3%) and average annual temperature (27.1%) were identified as the main drivers of structural changes in the bacterial community. Available potassium (39.4%), soil organic carbon (21.4%), available nitrogen (AN) (13.8%), and the meteorological factors average annual maximum wind speed (38.0%) and average annual temperature (26.8%) were identified as the main drivers of structural changes in the fungal community. The explanation rate of soil factors on changes in bacterial and fungal communities was 26.6 and 12.0%, respectively, whereas that of meteorological factors on changes in bacterial and fungal communities was 1.22 and 1.17%, respectively. The combined explanation rate of environmental factors (soil and meteorological factors) on bacterial and fungal communities was 72.2 and 86.6%, respectively. The results of the study offer valuable insights into the diversity of soil microbial communities in the water-wind erosion crisscross region and the mechanisms underlying their interaction with environmental factors.
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Affiliation(s)
- Zhi-Yong Zhang
- College of Life Science, Yan'an University, Yan'an, Shaanxi, China
| | - Fang-Fang Qiang
- College of Life Science, Yan'an University, Yan'an, Shaanxi, China
| | - Guang-Quan Liu
- China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Chang-Hai Liu
- College of Life Science, Yan'an University, Yan'an, Shaanxi, China
| | - Ning Ai
- College of Life Science, Yan'an University, Yan'an, Shaanxi, China,China Institute of Water Resources and Hydropower Research, Beijing, China,*Correspondence: Ning Ai, ✉
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Wang X, Yu Z, Shen G, Cheng H, Tao S. Distribution of microbial communities in seasonally frozen soil layers on the Tibetan Plateau and the driving environmental factors. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:1919-1937. [PMID: 35925461 DOI: 10.1007/s11356-022-22283-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Large stocks of carbon and nitrogen stored in permafrost regions can potentially feed back to global biogeochemical cycles under climate warming. To understand the response of microbial communities to environmental changes, this study investigated the spatial distribution of bacterial communities in the upper layers (0-10, 10-20, and 20-30 cm) of seasonally frozen soil on the Tibetan Plateau and their relationships with the environmental factors. A total of 135 soil samples were collected from the soils at depths of 0-10, 10-20, and 20-30 cm in the Lhasa River and Nyang River basins, and the diversity and composition of bacterial communities in them were identified by high-throughput 16S rRNA gene sequencing. Bacterial diversity changed significantly with soil depth in the Nyang River basin (p < 0.001), while no obvious change was found in the Lhasa River basin. The whole bacterial composition exhibited small variations across different soil layers (p > 0.05). The relative abundance of aerobic bacteria, Sphingomonas and Arthrobacter, decreased with soil depth, while that of the other aerobic, facultative anaerobic, and anaerobic bacteria did not exhibit this trend. Soil pH was the key driving edaphic factor of the whole bacterial composition in all three depth layers, while vegetation also had an important influence on bacterial composition. Arthrobacter, Bradyrhizobium, and Bacillus had obvious correlations with soil nutrients or vegetation, while the other species were not significantly correlated with any environmental factors. Structural equation modeling revealed that vegetation and mean annual temperature had a key direct impact on the bacterial diversity and composition, respectively. Climate also indirectly affected bacterial communities, mainly through shaping soil pH and vegetation. These results indicate that the soil depth has a different impact on the bacterial α-diversity, whole bacterial composition, and specific taxa in the 0-30-cm surface layers of seasonally frozen soil, which were mainly determined by various environmental factors.
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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 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
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guofeng Shen
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Hefa Cheng
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
| | - Shu Tao
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
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Cheng H, Zhou X, Dong R, Wang X, Liu G, Li Q. Priming of soil organic carbon mineralization and its temperature sensitivity in response to vegetation restoration in a karst area of Southwest China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 851:158400. [PMID: 36049694 DOI: 10.1016/j.scitotenv.2022.158400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Plant residue input alters native soil organic carbon (SOC) mineralization through the priming effect, which strongly controls C sequestration during vegetation restoration. However, the effects of different vegetation types on SOC priming and the underlying microbial mechanisms due to global warming are poorly understood. To elucidate these unknowns, the current study quantified soil priming effects using 13C-labeled maize residue amendments and analyzed the community structure and abundances in the soils of a vegetation succession gradient (maize field (MF), grassland (GL), and secondary forest (SF)) from a karst region under two incubation temperatures (15 °C and 25 °C). Results revealed that after 120 d of incubation, vegetation restoration increased the soil priming effects. Compared to MF, the priming effects of SF at 15 °C and 25 °C increased by 142.36 % and 161.09 %, respectively. This may be attributed to a high C/N ratio and low-N availability (NO3-), which supports the "microbial nitrogen mining" theory. Variations in soil priming were linked to changes in microbial properties. Moreover, with vegetation restoration, the relative abundance of Actinobacteria (copiotrophs) increased, while Ascomycota (oligotrophs) decreased, which accelerated native SOC decomposition. Co-occurrence network analysis indicated that the cooperative interactions of co-existing keystone taxa may facilitate SOC priming. Furthermore, structural equation modeling (SEM) indicated that changes in the priming effects were directly related to the fungal Shannon index and microbial biomass C (MBC), which were affected by soil C/N and NO3-. Warming significantly decreased soil priming, which may be attributed to the increase in microbial respiration (qCO2) and decreased MBC. The temperature sensitivity (Q10) of SOC mineralization was higher after residue amendment, but significant differences were not detected among the vegetation types. Collectively, our results indicated that the intensity of priming effects was dependent on vegetation type and temperature. Microbial community alterations and physicochemical interactions played important roles in SOC decomposition and sequestration.
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Affiliation(s)
- Hanting Cheng
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; Hainan Provincial Key Laboratory of Tropical Eco-cycle Agriculture, Haikou, Hainan, China; Agricultural Environmental Science Observation and Experiment Station, Ministry of Agriculture, Danzhou, Hainan, China
| | - Xiaohui Zhou
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; Hainan Provincial Key Laboratory of Tropical Eco-cycle Agriculture, Haikou, Hainan, China; Agricultural Environmental Science Observation and Experiment Station, Ministry of Agriculture, Danzhou, Hainan, China
| | - Rongshu Dong
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xiaomin Wang
- Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xingyi, Guizhou 562400, China
| | - Guodao Liu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Qinfen Li
- Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China; Hainan Provincial Key Laboratory of Tropical Eco-cycle Agriculture, Haikou, Hainan, China; Agricultural Environmental Science Observation and Experiment Station, Ministry of Agriculture, Danzhou, Hainan, China.
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Yang X, Huang X, Cheng J, Cheng Z, Yang Q, Hu L, Xu J, He Y. Diversity-triggered bottom-up trophic interactions impair key soil functions under lindane pollution stress. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120293. [PMID: 36183873 DOI: 10.1016/j.envpol.2022.120293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/29/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
A growing amount of evidence suggests that microbial diversity loss may have negative effects on soil ecosystem function. However, less attention has been paid to the determinants of the relationship between community diversity and soil functioning under pollution stress. Here we manipulated microbial diversity to observe how biotic and abiotic factors influenced soil multi-functions (e.g. lindane degradation, soil respiration and nutrient cycling). Results showed that protist community was more sensitive to dilution, pollution stress, and sodium acetate addition than bacterial and fungal community. Acetate addition accelerated the lindane removal. Any declines in microbial diversity reduced the specialized soil processes (NO3-N production, and N2O flux), but increased soil respiration rate. Dilution led to a significant increase in consumers-bacterial and fungi-bacterial interaction as evidenced by co-occurrence network, which possibly played roles in maintaining microbiome stability and resilience. Interestingly, pollution stress and resource availability weaken the relationship between microbial diversity and soil functions through the bottom-up trophic interaction and environmental preference of soil microbiome. Overall, this work provides experimental evidence that loss in microbial diversity, accompanied with changes in trophic interactions mediated biotic and abiotic factors, could have important consequences for specialized soil functioning in farmland ecosystems.
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Affiliation(s)
- Xueling Yang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Xiaowei Huang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Jie Cheng
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Zhongyi Cheng
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Qi Yang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Lingfei Hu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China.
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
| | - Yan He
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Hangzhou, 310058, China
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Changes in the Microbiological Properties of Soils along the Gradient of the Altitude Zone of Mount Kivaka in Eastern Fennoscandia, Russia. FORESTS 2022. [DOI: 10.3390/f13060849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This study was conducted on the territory of the national park Paanayarvi, located in the taiga zone of the European north. The altitude zone common in the territory of the national park is up to 350 m above sea level. The purpose of this work is to study the microbiological and biochemical properties of soils formed under conditions of a gradient of altitude zonation. This work was performed for the first time in this territory. Based on the fatty acid composition of the cell walls of microorganisms, the composition and structure of the microbial community were determined by chemato-mass spectrometry. The dominant microbocenosis of soils of undisturbed territories was revealed. Changes in prokaryotes and microscopic fungi in the gradient of the altitude zone occur in different directions, which is consistent with the work of other researchers. The results suggest that the formation of microbocenosis of soils located in different conditions of the phytocenotic environment depends on the location of the site relative to the height. The latter determines the flow of solar energy into the ecosystem and the hydrothermal regime of soils. The data obtained can be used in monitoring global climate changes, will become the basis for the formation of a general conceptual basis for the functioning of microbial communities of soils of low-mountain landscapes.
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Jiao S, Chen W, Wei G. Core microbiota drive functional stability of soil microbiome in reforestation ecosystems. GLOBAL CHANGE BIOLOGY 2022; 28:1038-1047. [PMID: 34862696 DOI: 10.1111/gcb.16024] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/23/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Revealing the ecological roles of core microbiota in the maintenance of the functional stability of soil microbiomes is crucial for sustainable ecosystem functioning; however, there is a dearth of whole-soil profile studies on the fundamental topic in microbial ecology, especially in the context of ecological restoration. Here, we explored whether core microbiota influence the temporal changes in the functional stability of soil microbiomes throughout the soil profile (i.e., soil depths of 0-300 cm) during natural succession in restored ex-arable ecosystems, via high-throughput amplicon and metagenomic sequencing. We revealed that core microbiota were essential for the maintenance of the functional stability of soil microbiomes in reforestation ecosystems. Specifically, the core taxa within one cluster of soil network, which had similar ecological preferences, had major contributions to functional stability. Reforestation significantly decreased the functional stability of soil microbiomes, which exhibited significant variations along the vertical soil profile in the reforested soils. Overall, the findings enhance our understanding of the factors driving functional stability in soil microbiomes, and suggests that core microbiota should be considered a key factor and integrated in policy and management activities targeting the enhancement and maintenance of functional stability and ecosystem sustainability in ecological restoration programs.
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Affiliation(s)
- Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
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Tandon K, Wan MT, Yang CC, Yang SH, Baatar B, Chiu CY, Tsai JW, Liu WC, Ng CS, Tang SL. Aquatic microbial community is partially functionally redundant: Insights from an in situ reciprocal transplant experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147433. [PMID: 33971597 DOI: 10.1016/j.scitotenv.2021.147433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/06/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Microbial communities are considered to be functionally redundant, but few studies have tested this hypothesis empirically. In this study, we performed an in situ reciprocal transplant experiment on the surface and bottom waters of two lakes (Tsuei-Feng (T) and Yuan-Yang (Y)) with disparate trophic states and tracked changes in their microbial community composition and functions for 6 weeks using high-throughput sequencing and functional approaches. T lake's surface (Ts) and bottom (Tb) water active bacterial community (16S rRNA gene-transcript) was dominated by Actinobacteria, Bacteroidia, and Cyanobacteria, whereas Y lake's surface (Ys) and bottom (Yb) water had Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia as the dominant classes. The community composition was resistant to changes in environmental conditions following the reciprocal transplant, but their functions tended to become similar to the incubating lakes' functional profiles. A significant linear positive relationship was observed between the microbial community and functional attributes (surface: R2 = 0.5065, p < 0.0001; bottom: R2 = 0.4592, p < 0.0001), though with varying scales of similarity (1-Bray Curtis distance), suggesting partial functional redundancy. Also, the entropy-based L-divergence measure identified high divergence in community composition (surface: 1.21 ± 0.54; bottom: 1.17 ± 0.51), and relatively low divergence in functional attributes (surface: 0.04 ± 0.01; bottom: 0.04 ± 0.01) in the two lakes' surface and bottom waters, providing further support for the presence of partial functional redundancy. This study enriches our understanding of community functional relationships and establishes the presence of partial functional redundancy in freshwater ecosystems.
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Affiliation(s)
- Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan; Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan; Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Min-Tao Wan
- EcoHealth Microbiology Laboratory, WanYu Co., Ltd., Chiayi 600, Taiwan
| | - Chia-Chin Yang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Shan-Hua Yang
- Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan
| | | | - Chih-Yu Chiu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jeng-Wei Tsai
- China Medical University, Department of Biological Science and Technology, Taichung 404, Taiwan
| | - Wen-Cheng Liu
- Department of Civil and Disaster Prevention Engineering, National United University, Miao-Li, Taiwan
| | - Chen Siang Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan; Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.
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10
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Kostin JE, Cesarz S, Lochner A, Schädler M, Macdonald CA, Eisenhauer N. Land-use drives the temporal stability and magnitude of soil microbial functions and modulates climate effects. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02325. [PMID: 33709490 DOI: 10.1002/eap.2325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 11/01/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Soil microbial community functions are essential indicators of ecosystem multifunctionality in managed land-use systems. Going forward, the development of adaptation strategies and predictive models under future climate scenarios will require a better understanding of how both land-use and climate disturbances influence soil microbial functions over time. Between March and November 2018, we assessed the effects of climate change on the magnitude and temporal stability of soil basal respiration, soil microbial biomass and soil functional diversity across a range of land-use types and intensities in a large-scale field experiment. Soils were sampled from five common land-use types including conventional and organic croplands, intensive and extensive meadows, and extensive pastures, under ambient and projected future climate conditions (reduced summer precipitation and increased temperature) at the Global Change Experimental Facility (GCEF) in Bad Lauchstädt, Germany. Land-use and climate treatment interaction effects were significant in September, a month when precipitation levels slightly rebounded following a period of drought in central Germany: compared to ambient climate, in future climate treatments, basal respiration declined in pastures and increased in intensive meadows, functional diversity declined in pastures and croplands, and respiration-to-biomass ratio increased in intensive and extensive meadows. Low rainfall between May and August likely strengthened soil microbial responses toward the future climate treatment in September. Although microbial biomass showed declining levels in extensive meadows and pastures under future climate treatments, overall, microbial function magnitudes were higher in these land-use types compared to croplands, indicating that improved management practices could sustain high microbial ecosystem functioning in future climates. In contrast to our hypothesis that more disturbed land-use systems would have destabilized microbial functions, intensive meadows and organic croplands showed stabilized soil microbial biomass compared to all other land-use types, suggesting that temporal stability, in addition to magnitude-based measurements, may be useful for revealing context-dependent effects on soil ecosystem functioning.
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Affiliation(s)
- Julia E Kostin
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Faculty of Management Science and Economics, Leipzig University, Grimmaische Straße 12, Leipzig, 04109, Germany
| | - Simone Cesarz
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, Leipzig, 04103, Germany
| | - Alfred Lochner
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
| | - Martin Schädler
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Department of Community Ecology, Helmholtz-Centre for Environmental Research - UFZ, Theodor-Lieser-Street 4, Halle, 06120, Germany
| | - Catriona A Macdonald
- Hawkesbury Institute for the Environment, University of Western Sydney, Locked Bag 1797, Penrith, New South Wales, 2751, Australia
| | - Nico Eisenhauer
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Institute of Biology, Leipzig University, Deutscher Platz 5e, Leipzig, 04103, Germany
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11
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Wiegand S, Dam HT, Riba J, Vollmers J, Kaster AK. Printing Microbial Dark Matter: Using Single Cell Dispensing and Genomics to Investigate the Patescibacteria/Candidate Phyla Radiation. Front Microbiol 2021; 12:635506. [PMID: 34220732 PMCID: PMC8241940 DOI: 10.3389/fmicb.2021.635506] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/18/2021] [Indexed: 11/13/2022] Open
Abstract
As of today, the majority of environmental microorganisms remain uncultured. They are therefore referred to as "microbial dark matter." In the recent past, cultivation-independent methods like single-cell genomics (SCG) enabled the discovery of many previously unknown microorganisms, among them the Patescibacteria/Candidate Phyla Radiation (CPR). This approach was shown to be complementary to metagenomics, however, the development of additional and refined sorting techniques beyond the most commonly used fluorescence-activated cell sorting (FACS) is still desirable to enable additional downstream applications. Adding image information on the number and morphology of sorted cells would be beneficial, as would be minimizing cell stress caused by sorting conditions such as staining or pressure. Recently, a novel cell sorting technique has been developed, a microfluidic single-cell dispenser, which assesses the number and morphology of the cell in each droplet by automated light microscopic processing. Here, we report for the first time the successful application of the newly developed single-cell dispensing system for label-free isolation of individual bacteria from a complex sample retrieved from a wastewater treatment plant, demonstrating the potential of this technique for single cell genomics and other alternative downstream applications. Genome recovery success rated above 80% with this technique-out of 880 sorted cells 717 were successfully amplified. For 50.1% of these, analysis of the 16S rRNA gene was feasible and led to the sequencing of 50 sorted cells identified as Patescibacteria/CPR members. Subsequentially, 27 single amplified genomes (SAGs) of 15 novel and distinct Patescibacteria/CPR members, representing yet unseen species, genera and families could be captured and reconstructed. This phylogenetic distinctness of the recovered SAGs from available metagenome-assembled genomes (MAGs) is accompanied by the finding that these lineages-in whole or in part-have not been accessed by genome-resolved metagenomics of the same sample, thereby emphasizing the importance and opportunities of SCGs.
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Affiliation(s)
- Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Hang T. Dam
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Julian Riba
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - John Vollmers
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Institute for Applied Biosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
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12
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Xu M, Li X, Kuyper TW, Xu M, Li X, Zhang J. High microbial diversity stabilizes the responses of soil organic carbon decomposition to warming in the subsoil on the Tibetan Plateau. GLOBAL CHANGE BIOLOGY 2021; 27:2061-2075. [PMID: 33560552 DOI: 10.1111/gcb.15553] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Soil microbes are directly involved in soil organic carbon (SOC) decomposition, yet the importance of microbial biodiversity in regulating the temperature sensitivity of SOC decomposition remains elusive, particularly in alpine regions where climate change is predicted to strongly affect SOC dynamics and ecosystem stability. Here we collected topsoil and subsoil samples along an elevational gradient on the southeastern Tibetan Plateau to explore the temperature sensitivity (Q10 ) of SOC decomposition in relation to changes in microbial communities. Specifically, we tested whether the decomposition of SOC would be more sensitive to warming when microbial diversity is low. The estimated Q10 value ranged from 1.28 to 1.68, and 1.80 to 2.10 in the topsoil and subsoil, respectively. The highest Q10 value was observed at the lowest altitude of forests in the topsoil, and at the highest altitude of alpine meadow in the subsoil. Variations in Q10 were closely related to changes in microbial properties. In the topsoil the ratio of gram-positive to gram-negative bacteria (G+:G-) was the predominant factor associated with the altitudinal variations in Q10 . In the subsoil, SOC decomposition showed more resilience to warming when the diversity of soil bacteria (both whole community and major groups) and fungi was higher. Our results partly support the positive biodiversity-ecosystem stability hypothesis. Structural equation modeling further indicates that variations in Q10 in the subsoil were directly related to changes in microbial diversity and community composition, which were affected by soil pH. Collectively our results provide compelling evidence that microbial biodiversity plays an important role in stabilizing SOC decomposition in the subsoil of alpine montane ecosystems. Conservation of belowground biodiversity is therefore of great importance in maintaining the stability of ecosystem processes under climate change in high-elevation regions of the Tibetan Plateau.
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Affiliation(s)
- Meng Xu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Xiaoliang Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture, Danzhou, Hainan, China
| | - Thomas W Kuyper
- Soil Biology Group, Wageningen University, Wageningen, The Netherlands
| | - Ming Xu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Xiaolin Li
- Centre for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, China
| | - Junling Zhang
- Centre for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, China
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13
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Chiba A, Uchida Y, Kublik S, Vestergaard G, Buegger F, Schloter M, Schulz S. Soil Bacterial Diversity Is Positively Correlated with Decomposition Rates during Early Phases of Maize Litter Decomposition. Microorganisms 2021; 9:microorganisms9020357. [PMID: 33670245 PMCID: PMC7916959 DOI: 10.3390/microorganisms9020357] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
This study aimed to investigate the effects of different levels of soil- and plant-associated bacterial diversity on the rates of litter decomposition, and bacterial community dynamics during its early phases. We performed an incubation experiment where soil bacterial diversity (but not abundance) was manipulated by autoclaving and reinoculation. Natural or autoclaved maize leaves were applied to the soils and incubated for 6 weeks. Bacterial diversity was assessed before and during litter decomposition using 16S rRNA gene metabarcoding. We found a positive correlation between litter decomposition rates and soil bacterial diversity. The soil with the highest bacterial diversity was dominated by oligotrophic bacteria including Acidobacteria, Nitrospiraceae, and Gaiellaceae, and its community composition did not change during the incubation. In the less diverse soils, those taxa were absent but were replaced by copiotrophic bacteria, such as Caulobacteraceae and Beijerinckiaceae, until the end of the incubation period. SourceTracker analysis revealed that litter-associated bacteria, such as Beijerinckiaceae, only became part of the bacterial communities in the less diverse soils. This suggests a pivotal role of oligotrophic bacteria during the early phases of litter decomposition and the predominance of copiotrophic bacteria at low diversity.
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Affiliation(s)
- Akane Chiba
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (A.C.); (Y.U.)
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Crop Physiology, TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
| | - Yoshitaka Uchida
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan; (A.C.); (Y.U.)
| | - Susanne Kublik
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
| | - Gisle Vestergaard
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Section of Bioinformatics, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Franz Buegger
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany;
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- TUM School of Life Science, Technical University of Munich, 85354 Freising, Germany
| | - Stefanie Schulz
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany; (S.K.); (G.V.); (M.S.)
- Correspondence: ; Tel.: +49-(0)89-3187-3054
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14
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Dam HT, Vollmers J, Sobol MS, Cabezas A, Kaster AK. Targeted Cell Sorting Combined With Single Cell Genomics Captures Low Abundant Microbial Dark Matter With Higher Sensitivity Than Metagenomics. Front Microbiol 2020; 11:1377. [PMID: 32793124 PMCID: PMC7387413 DOI: 10.3389/fmicb.2020.01377] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/28/2020] [Indexed: 11/13/2022] Open
Abstract
Rare members of environmental microbial communities are often overlooked and unexplored, primarily due to the lack of techniques capable of acquiring their genomes. Chloroflexi belong to one of the most understudied phyla, even though many of its members are ubiquitous in the environment and some play important roles in biochemical cycles or biotechnological applications. We here used a targeted cell-sorting approach, which enables the selection of specific taxa by fluorescent labeling and is compatible with subsequent single-cell genomics, to enrich for rare Chloroflexi species from a wastewater-treatment plant and obtain their genomes. The combined workflow was able to retrieve a substantially higher number of novel Chloroflexi draft genomes with much greater phylogenetical diversity when compared to a metagenomics approach from the same sample. The method offers an opportunity to access genetic information from rare biosphere members which would have otherwise stayed hidden as microbial dark matter and can therefore serve as an essential complement to cultivation-based, metagenomics, and microbial community-focused research approaches.
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Affiliation(s)
- Hang T Dam
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.,Leibniz Institute DSMZ, Brunswick, Germany
| | - John Vollmers
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.,Leibniz Institute DSMZ, Brunswick, Germany
| | - Morgan S Sobol
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Angela Cabezas
- Instituto Tecnológico Regional Centro Sur, Universidad Tecnológica, Durazno, Uruguay
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.,Leibniz Institute DSMZ, Brunswick, Germany
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15
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Lin D, McCulley RL, Nelson JA, Jacobsen KL, Zhang D. Time in pasture rotation alters soil microbial community composition and function and increases carbon sequestration potential in a temperate agroecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 698:134233. [PMID: 31514023 DOI: 10.1016/j.scitotenv.2019.134233] [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: 05/02/2019] [Revised: 08/31/2019] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
Soil carbon (C) sequestration plays an important role in mitigating global climate change, and certain land utilization strategies can exert a pronounced effect on carbon storage. Land use practices, such as planting previously cropped lands into perennial grasslands, can increase soil C sequestration; however, the temporal response of soil C pools to such changes in land use are likely complex and not well quantified. In the current study, a space-for-time approach was used to assess the response of soil C sequestration and microbial community composition during a five-year grazed pasture rotation following three years of vegetable production on a central Kentucky farm. After 5 years in pasture, soil organic C and N in the top 15 cm increased 20.6% and 20.1%, respectively, from year 1 levels, and particulate organic matter C (POM C) increased 53.5%. A carbon mineralization (CM) assay indicated that the potential release of CO2 also increased with time in pasture rotation. When compared to permanent pasture (not previously used for vegetable production), soil microbial community composition differed in rotation years 1-3 but became similar in years 4 and 5. Multi-response permutation procedure (MRPP) analysis showed that CM and POM were key factors affecting microbial community composition. Soil microbial community composition also varied with time of year (season), but to a lesser degree than with pasture duration. Overall, incorporation of perennial pasture into cropping systems can have profound effects on microbial community composition and function, increasing soil organic C, and consequently enhancing the potential for C sequestration; however, whether these increases in C storage persist throughout the full cropping sequence (i.e., once the pasture has been returned to vegetables) and/or how these changes influence subsequent vegetable production remains to be evaluated.
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Affiliation(s)
- Dong Lin
- College of Grassland Science, Gansu Agricultural University, Lanzhou, Gansu 730070, China; Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0091, USA
| | - Rebecca L McCulley
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0091, USA.
| | - Jim A Nelson
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0091, USA
| | - Krista L Jacobsen
- Department of Horticulture, University of Kentucky, Lexington, KY 40546-0091, USA
| | - Degang Zhang
- College of Grassland Science, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
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16
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Wang Z, Tian H, Tan X, Wang F, Jia H, Megharaj M, He W. Long-term As contamination alters soil enzyme functional stability in response to additional heat disturbance. CHEMOSPHERE 2019; 229:471-480. [PMID: 31091488 DOI: 10.1016/j.chemosphere.2019.05.055] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 05/01/2019] [Accepted: 05/07/2019] [Indexed: 06/09/2023]
Abstract
The functional stability of soil enzymes is fundamental to the sustainability of soil biochemical processes and is affected by many environmental stressors. This study focused on the influences of long-term arsenic (As) contamination on soil enzyme functional stability: the resistance (ratio of the disturbed to control) and resilience (integrated recovery rate) of soil enzyme activities (β-glucosidase, urease, acid phosphatase, fluorescein diacetate (FDA) hydrolase) over 30 days incubation after an experimental heat disturbance (50 oC for 18 h). Results showed that the resistance of soil enzymes to heat disturbance differed among the enzyme types and followed the order: urease > β-glucosidase > acid phosphatase > FDA hydrolase. Urease activity was generally not affected and showed high stability against heat disturbance. The β-glucosidase activity recovered to the control level by 30 days, while 80% and 90% recovery on average occurred for acid phosphatase and FDA hydrolase, respectively. Long-term As contamination altered soil enzyme functional resistance and resilience to heat disturbance and resulted in three kinds of responses: (i) no apparent alteration (urease); (ii) moderate As contamination increased enzyme heat resistance (β-glucosidase); (iii) the resistance and resilience decreased with increasing As concentration (acid phosphatase and FDA hydrolase). The results demonstrated that different enzyme-catalytic biochemical processes have different functional stabilities under combined As and heat disturbance, and the negative changes in the soil enzyme activity led to losses in soil functions. Our study provides further evidence on the impacts of heavy metal/metalloid on soil enzyme functional stability in response to additional disturbance.
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Affiliation(s)
- Ziquan Wang
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China; Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Haixia Tian
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Xiangping Tan
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Rd., Tianhe District, Guangzhou, 510650, China
| | - Fang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Hanzhong Jia
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation, Faculty of Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Wenxiang He
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Yangling, 712100, Shaanxi, China.
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17
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Granada CE, Vargas LK, Lisboa BB, Giongo A, Martinho CT, Pereira LDM, de Oliveira RR, Bruxel F, de Freitas EM, Passaglia LMP. Bacterial and Archaeal Communities Change With Intensity of Vegetation Coverage in Arenized Soils From the Pampa Biome. Front Microbiol 2019; 10:497. [PMID: 30967845 PMCID: PMC6439421 DOI: 10.3389/fmicb.2019.00497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/26/2019] [Indexed: 02/01/2023] Open
Abstract
Arenization occurs in regions that present sandy soils with normal rainfall levels. Predatory use of environmental sources, the dissolution of arenitic rocks and reworking of non-consolidated surface sands intensify this degradation scenario. Thus, this work aimed to evaluate the impact of the arenization process in the Brazilian Pampa Biome and how this phenomenon affects the soil microbial and plant communities. For this purpose, three arenized areas in Southern Brazil (Pampa Biome) were selected and, in each one, three sampling points were studied: arenized (ARA), arenized to grassland transition (AGT), and grassland (GRA) areas. In the three sampling points, soils presented low levels of nutrients, organic matter, mud and pH acidic in all regions but, the presence of vegetation coverage in AGT and GRA areas preserved the topsoil structure. Our study related ARA with bacterial families Alcaligenaceae, Pseudomonadaceae, and Xanthomonadaceae. AGT with bacterial families Bacillaceae and Burkholderiaceae, and plant species Melinis repens (Willd.) Zizka and Paspalum stellatum Humb. and Bonpl. ex Flüggé, and GRA with bacterial families Koribacteraceae, Hyphomicrobiaceae, and Chthoniobacteraceae, and plant species Croton subpannosus Müll.Arg. ex Griseb., Piptochaetium montevidense (Spreng.) Parodi and Elyonurus sp. The three studied areas (as well as sampling points) present soils extremely poor in nutrients with sandy texture, and the bacterial and plant composition well known to be resistant to environmental stresses were dominant. The vulnerability of these areas causes a degradation scenario, which is worsened by agricultural activities. However, in general, this phenomenon is a natural process that occurs mainly due to soil characteristics (poor soils) and climatic variations.
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Affiliation(s)
- Camille E Granada
- Programa de Pós-graduação em Biotecnologia, Universidade do Vale do Taquari - Univates, Lajeado, Brazil
| | - Luciano Kayser Vargas
- Laboratório de Solos, Fundação Estadual de Pesquisa Agropecuária (FEPAGRO), Porto Alegre, Brazil
| | - Bruno Brito Lisboa
- Laboratório de Solos, Fundação Estadual de Pesquisa Agropecuária (FEPAGRO), Porto Alegre, Brazil
| | - Adriana Giongo
- Instituto do Petróleo e dos Recursos Naturais. Av. Ipiranga, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Caroline Thais Martinho
- Instituto do Petróleo e dos Recursos Naturais. Av. Ipiranga, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Leandro de M Pereira
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Escola de Ciências. Av. Ipiranga, Porto Alegre, Brazil
| | - Rafael R de Oliveira
- Instituto do Petróleo e dos Recursos Naturais. Av. Ipiranga, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Fernanda Bruxel
- Programa de Pós-graduação em Biotecnologia, Universidade do Vale do Taquari - Univates, Lajeado, Brazil
| | - Elisete Maria de Freitas
- Programa de Pós-graduação em Biotecnologia, Universidade do Vale do Taquari - Univates, Lajeado, Brazil.,Universidade do Vale do Taquari - Univates, Programa de Pós-Graduação em Sistemas Ambientais Sustentáveis, Lajeado, Brazil
| | - Luciane M P Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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18
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Sjöstedt J, Langenheder S, Kritzberg E, Karlsson CMG, Lindström ES. Repeated disturbances affect functional but not compositional resistance and resilience in an aquatic bacterioplankton community. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:493-500. [PMID: 29733107 DOI: 10.1111/1758-2229.12656] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/11/2016] [Indexed: 05/25/2023]
Abstract
Disturbances are believed to be one of the main factors influencing variations in community diversity and functioning. Here we investigated if exposure to a pH press disturbance affected the composition and functional performance of a bacterial community and its resistance, recovery and resilience to a second press disturbance (salt addition). Lake bacterial assemblages were initially exposed to reduced pH in six mesocosms whereas another six mesocosms were kept as reference. Seven days after the pH disturbance, three tanks from each treatment were exposed to a salt disturbance. Both bacterial production and enzyme activity were negatively affected by the salt treatment, regardless if the communities had been subject to a previous disturbance or not. However, cell-specific enzyme activity had a higher resistance in communities pre-exposed to the pH disturbance compared to the reference treatment. In contrast, for cell-specific bacterial production resistance was not affected, but recovery was faster in the communities that had previously been exposed to the pH disturbance. Over time, bacterial community composition diverged among treatments, in response to both pH and salinity. The difference in functional recovery, resilience and resistance may depend on differences in community composition caused by the pH disturbance, niche breadth or acquired stress resistance.
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Affiliation(s)
- Johanna Sjöstedt
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, SE 75236, Sweden
- Department of Biology/Aquatic Ecology, Lund University, Lund, Sölvegatan 37, SE 22362, Sweden
| | - Silke Langenheder
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, SE 75236, Sweden
| | - Emma Kritzberg
- Department of Biology/Aquatic Ecology, Lund University, Lund, Sölvegatan 37, SE 22362, Sweden
| | - Christofer M G Karlsson
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE 39231, Sweden
| | - Eva S Lindström
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, SE 75236, Sweden
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19
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Wagg C, Dudenhöffer J, Widmer F, Heijden MGA. Linking diversity, synchrony and stability in soil microbial communities. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13056] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Cameron Wagg
- Department of Evolutionary Biology and Environmental SciencesUniversity of Zürich Zürich Switzerland
- Institute of EcologyUniversity of Jena Jena Germany
| | - Jan‐Hendrik Dudenhöffer
- Chair of Nature Conservation and Landscape EcologyInstitute of Earth and Environmental SciencesUniversity of Freiburg Freiburg Germany
| | - Franco Widmer
- Molecular Ecology, AgroscopeInstitute for Sustainability Sciences Zürich Switzerland
| | - Marcel G. A. Heijden
- Department of Evolutionary Biology and Environmental SciencesUniversity of Zürich Zürich Switzerland
- Plant‐Soil Interactions, AgroscopeInstitute for Sustainability Sciences Zürich Switzerland
- Plant‐Microbe InteractionsInstitute of Environmental BiologyFaculty of Science Utrecht The Netherlands
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20
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Kurm V, van der Putten WH, Pineda A, Hol WHG. Soil microbial species loss affects plant biomass and survival of an introduced bacterial strain, but not inducible plant defences. ANNALS OF BOTANY 2018; 121:311-319. [PMID: 29329376 PMCID: PMC5808785 DOI: 10.1093/aob/mcx162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/24/2017] [Indexed: 05/30/2023]
Abstract
BACKGROUND AND AIMS Plant growth-promoting rhizobacteria (PGPR) strains can influence plant-insect interactions. However, little is known about the effect of changes in the soil bacterial community in general and especially the loss of rare soil microbes on these interactions. Here, the influence of rare soil microbe reduction on induced systemic resistance (ISR) in a wild ecotype of Arabidopsis thaliana against the aphid Myzus persicae was investigated. METHODS To create a gradient of microbial abundances, soil was inoculated with a serial dilution of a microbial community and responses of Arabidopsis plants that originated from the same site as the soil microbes were tested. Plant biomass, transcription of genes involved in plant defences, and insect performance were measured. In addition, the effects of the PGPR strain Pseudomonas fluorescens SS101 on plant and insect performance were tested under the influence of the various soil dilution treatments. KEY RESULTS Plant biomass showed a hump-shaped relationship with soil microbial community dilution, independent of aphid or Pseudomonas treatments. Both aphid infestation and inoculation with Pseudomonas reduced plant biomass, and led to downregulation of PR1 (salicylic acid-responsive gene) and CYP79B3 (involved in synthesis of glucosinolates). Aphid performance and gene transcription were unaffected by soil dilution. CONCLUSIONS Neither the loss of rare microbial species, as caused by soil dilution, nor Pseudomonas affect the resistance of A. thaliana against M. persicae. However, both Pseudomonas survival and plant biomass respond to rare species loss. Thus, loss of rare soil microbial species can have a significant impact on both above- and below-ground organisms.
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Affiliation(s)
- Viola Kurm
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Ana Pineda
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - W H Gera Hol
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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21
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Chen J, Nie Y, Liu W, Wang Z, Shen W. Ammonia-Oxidizing Archaea Are More Resistant Than Denitrifiers to Seasonal Precipitation Changes in an Acidic Subtropical Forest Soil. Front Microbiol 2017; 8:1384. [PMID: 28790990 PMCID: PMC5522861 DOI: 10.3389/fmicb.2017.01384] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 07/10/2017] [Indexed: 12/02/2022] Open
Abstract
Seasonal precipitation changes are increasingly severe in subtropical areas. However, the responses of soil nitrogen (N) cycle and its associated functional microorganisms to such precipitation changes remain unclear. In this study, two projected precipitation patterns were manipulated: intensifying the dry-season drought (DD) and extending the dry-season duration (ED) but increasing the wet-season storms following the DD and ED treatment period. The effects of these two contrasting precipitation patterns on soil net N transformation rates and functional gene abundances were quantitatively assessed through a resistance index. Results showed that the resistance index of functional microbial abundance (-0.03 ± 0.08) was much lower than that of the net N transformation rate (0.55 ± 0.02) throughout the experiment, indicating that microbial abundance was more responsive to precipitation changes compared with the N transformation rate. Spring drought under the ED treatment significantly increased the abundances of both nitrifying (amoA) and denitrifying genes (nirK, nirS, and nosZ), while changes in these gene abundances overlapped largely with control treatment during droughts in the dry season. Interestingly, the resistance index of the ammonia-oxidizing archaea (AOA) amoA abundance was significantly higher than that of the denitrifying gene abundances, suggesting that AOA were more resistant to the precipitation changes. This was attributed to the stronger environmental adaptability and higher resource utilization efficiency of the AOA community, as indicated by the lack of correlations between AOA gene abundance and environmental factors [i.e., soil water content, ammonium (NH4+) and dissolved organic carbon concentrations] during the experiment.
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Affiliation(s)
- Jie Chen
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China.,College of Life Science, University of Chinese Academy of SciencesBeijing, China.,Department of Soil Science of Temperate Ecosystems, University of GöttingenGöttingen, Germany
| | - Yanxia Nie
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Wei Liu
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Zhengfeng Wang
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Weijun Shen
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
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22
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Cao J, Hafermann L, Köhler JM. Stochastically reduced communities-Microfluidic compartments as model and investigation tool for soil microorganism growth in structured spaces. Eng Life Sci 2017; 17:792-800. [PMID: 32624825 DOI: 10.1002/elsc.201600264] [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: 12/23/2016] [Revised: 02/03/2017] [Accepted: 02/20/2017] [Indexed: 11/09/2022] Open
Abstract
Microbial community in soil is a complex and dynamic system. Using traditional culture experiments it is difficult to model the stochastic distribution of single organisms of microbial communities in the soil pore's structure. Droplet-based micro-segmented flow technique allows the transfer of the principle of stochastic confinement of stochastically reduced communities from soil micro pores into nanoliter droplets. Microfluidics was applied for the investigation and comparison of soil samples from ancient mining areas by highly resolved concentration-dependent screenings. As results, the generation, incubation, and in situ optical characterization of nanoliter droplets of suspensions of unknown soil microbial communities allowed the identification of different response characteristics toward heavy metal exposition. The investigations proved the high potential of microfluidics for investigations of soil microbial communities. It may be in the future helpful to detect bacteria and consortia with special biosorption characteristics, which could be useful for the development of biological accumulation and detoxification strategies.
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Affiliation(s)
- Jialan Cao
- Physical Chemistry and Microreaction Technology, Institute for Micro- und Nanotechnologies / Institute for Chemistry and Biotechnique Ilmenau University of Technology Ilmenau Germany
| | - Lars Hafermann
- Physical Chemistry and Microreaction Technology, Institute for Micro- und Nanotechnologies / Institute for Chemistry and Biotechnique Ilmenau University of Technology Ilmenau Germany
| | - J Michael Köhler
- Physical Chemistry and Microreaction Technology, Institute for Micro- und Nanotechnologies / Institute for Chemistry and Biotechnique Ilmenau University of Technology Ilmenau Germany
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23
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Kumaresan D, Cross AT, Moreira-Grez B, Kariman K, Nevill P, Stevens J, Allcock RJN, O'Donnell AG, Dixon KW, Whiteley AS. Microbial Functional Capacity Is Preserved Within Engineered Soil Formulations Used In Mine Site Restoration. Sci Rep 2017; 7:564. [PMID: 28373716 PMCID: PMC5428872 DOI: 10.1038/s41598-017-00650-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 03/07/2017] [Indexed: 11/21/2022] Open
Abstract
Mining of mineral resources produces substantial volumes of crushed rock based wastes that are characterised by poor physical structure and hydrology, unstable geochemistry and potentially toxic chemical conditions. Recycling of these substrates is desirable and can be achieved by blending waste with native soil to form a ‘novel substrate’ which may be used in future landscape restoration. However, these post-mining substrate based ‘soils’ are likely to contain significant abiotic constraints for both plant and microbial growth. Effective use of these novel substrates for ecosystem restoration will depend on the efficacy of stored topsoil as a potential microbial inoculum as well as the subsequent generation of key microbial soil functions originally apparent in local pristine sites. Here, using both marker gene and shotgun metagenome sequencing, we show that topsoil storage and the blending of soil and waste substrates to form planting substrates gives rise to variable bacterial and archaeal phylogenetic composition but a high degree of metabolic conservation at the community metagenome level. Our data indicates that whilst low phylogenetic conservation is apparent across substrate blends we observe high functional redundancy in relation to key soil microbial pathways, allowing the potential for functional recovery of key belowground pathways under targeted management.
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Affiliation(s)
- Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Adam T Cross
- School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,Kings Park and Botanic Garden, 1 Kattidj Close, Kings Park, WA, 6005, Australia
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Khalil Kariman
- UWA School of Agriculture and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Paul Nevill
- Department of Environment and Agriculture, Curtin University, GPO Box U1987, Bentley, WA, 6102, Australia
| | - Jason Stevens
- School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,Kings Park and Botanic Garden, 1 Kattidj Close, Kings Park, WA, 6005, Australia
| | - Richard J N Allcock
- School of Pathology and Laboratory Medicine, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,Pathwest Laboratory Medicine WA, QEII Medical Centre, Monash Avenue, Nedlands, WA, 6009, Australia
| | - Anthony G O'Donnell
- Faculty of Science, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Kingsley W Dixon
- School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,Department of Environment and Agriculture, Curtin University, GPO Box U1987, Bentley, WA, 6102, Australia
| | - Andrew S Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
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24
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Luo J, Chen H, Han X, Sun Y, Yuan Z, Guo J. Microbial community structure and biodiversity of size-fractionated granules in a partial nitritation–anammox process. FEMS Microbiol Ecol 2017; 93:3003320. [DOI: 10.1093/femsec/fix021] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 02/17/2017] [Indexed: 11/13/2022] Open
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25
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Toxicity of iron oxide nanoparticles to grass litter decomposition in a sandy soil. Sci Rep 2017; 7:41965. [PMID: 28155886 PMCID: PMC5290472 DOI: 10.1038/srep41965] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/19/2016] [Indexed: 11/09/2022] Open
Abstract
We examined time-dependent effect of iron oxide nanoparticles (IONPs) at a rate of 2000 mg kg−1 soil on Cynodon dactylon litter (3 g kg−1) decomposition in an arid sandy soil. Overall, heterotrophic cultivable bacterial and fungal colonies, and microbial biomass carbon were significantly decreased in litter-amended soil by the application of nanoparticles after 90 and 180 days of incubation. Time dependent effect of nanoparticles was significant for microbial biomass in litter-amended soil where nanoparticles decreased this variable from 27% after 90 days to 49% after 180 days. IONPs decreased CO2 emission by 28 and 30% from litter-amended soil after 90 and 180 days, respectively. These observations indicated that time-dependent effect was not significant on grass-litter carbon mineralization efficiency. Alternatively, nanoparticles application significantly reduced mineral nitrogen content in litter-amended soil in both time intervals. Therefore, nitrogen mineralization efficiency was decreased to 60% after 180 days compared to that after 90 days in nanoparticles grass-litter amended soil. These effects can be explained by the presence of labile Fe in microbial biomass after 180 days in nanoparticles amendment. Hence, our results suggest that toxicity of IONPs to soil functioning should consider before recommending their use in agro-ecosystems.
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26
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Shen H, Chen Z, Shen Z, Lu Z. Maintaining stability of the rumen ecosystem is associated with changes of microbial composition and epithelial TLR signaling. Microbiologyopen 2017; 6. [PMID: 28109059 PMCID: PMC5458463 DOI: 10.1002/mbo3.436] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/25/2016] [Accepted: 11/28/2016] [Indexed: 02/01/2023] Open
Abstract
We used the goat as a model to study the effects of rumen microbial composition and epithelial TLR signaling on maintaining rumen stability during exogenous butyrate interference. Six cannulated goats received a rapid intraruminal infusion of 0.1 mol/L potassium phosphate buffer with (BT, n = 3) or without (CO, n = 3) 0.3 g/kg·BW·day sodium butyrate for 28 days. The ruminal pH and the concentration of total SCFA were not affected by the interference. 16S rRNA gene amplicon sequencing revealed a change in microbial composition after the butyrate infusion. LEfSe analysis showed a shift of the biomarker species from butyrate‐producing bacteria to acetate‐and propionate‐producing bacteria. Quantitative PCR‐based comparisons showed that significant increases in TLR2, TLR5, and MyD88 expression were accompanied by a significant decrease in IL‐1β and IFN‐γ expression in the ruminal epithelium. Constrained correlation analysis showed that the relative abundance of Roseburia was positively correlated with the expression of TLR5. Taken together, our study shows that microbial composition plays an important role in maintaining the stability of the microbial ecosystem in rumen, and indicates that the microbe‐TLR‐cytokine axis was involved in maintaining the stability of the gastrointestinal ecosystem.
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Affiliation(s)
- Hong Shen
- College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China.,Bioinformatics Center, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhan Chen
- College of Life Science, Nanjing Agricultural University, Nanjing, Jiangsu, China.,Bioinformatics Center, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zanming Shen
- Key Lab of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhongyan Lu
- Key Lab of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
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27
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Where less may be more: how the rare biosphere pulls ecosystems strings. ISME JOURNAL 2017; 11:853-862. [PMID: 28072420 PMCID: PMC5364357 DOI: 10.1038/ismej.2016.174] [Citation(s) in RCA: 558] [Impact Index Per Article: 79.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 11/06/2016] [Accepted: 11/12/2016] [Indexed: 02/05/2023]
Abstract
Rare species are increasingly recognized as crucial, yet vulnerable components of Earth's ecosystems. This is also true for microbial communities, which are typically composed of a high number of relatively rare species. Recent studies have demonstrated that rare species can have an over-proportional role in biogeochemical cycles and may be a hidden driver of microbiome function. In this review, we provide an ecological overview of the rare microbial biosphere, including causes of rarity and the impacts of rare species on ecosystem functioning. We discuss how rare species can have a preponderant role for local biodiversity and species turnover with rarity potentially bound to phylogenetically conserved features. Rare microbes may therefore be overlooked keystone species regulating the functioning of host-associated, terrestrial and aquatic environments. We conclude this review with recommendations to guide scientists interested in investigating this rapidly emerging research area.
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28
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Roger F, Bertilsson S, Langenheder S, Osman OA, Gamfeldt L. Effects of multiple dimensions of bacterial diversity on functioning, stability and multifunctionality. Ecology 2016; 97:2716-2728. [DOI: 10.1002/ecy.1518] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 05/24/2016] [Accepted: 06/01/2016] [Indexed: 02/01/2023]
Affiliation(s)
- Fabian Roger
- Department of Marine Sciences; University of Gothenburg; Box 461 SE-40530 Gothenburg Sweden
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology, and Science for Life Laboratory; Uppsala University; Uppsala Sweden
| | - Silke Langenheder
- Department of Ecology and Genetics, Limnology, and Science for Life Laboratory; Uppsala University; Uppsala Sweden
| | - Omneya Ahmed Osman
- Department of Ecology and Genetics, Limnology, and Science for Life Laboratory; Uppsala University; Uppsala Sweden
| | - Lars Gamfeldt
- Department of Marine Sciences; University of Gothenburg; Box 461 SE-40530 Gothenburg Sweden
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29
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Louis BP, Maron PA, Viaud V, Leterme P, Menasseri-Aubry S. Soil C and N models that integrate microbial diversity. ENVIRONMENTAL CHEMISTRY LETTERS 2016; 14:331-344. [PMID: 27642273 PMCID: PMC5011482 DOI: 10.1007/s10311-016-0571-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/07/2016] [Indexed: 05/23/2023]
Abstract
Industrial agriculture is yearly responsible for the loss of 55-100 Pg of historical soil carbon and 9.9 Tg of reactive nitrogen worldwide. Therefore, management practices should be adapted to preserve ecological processes and reduce inputs and environmental impacts. In particular, the management of soil organic matter (SOM) is a key factor influencing C and N cycles. Soil microorganisms play a central role in SOM dynamics. For instance, microbial diversity may explain up to 77 % of carbon mineralisation activities. However, soil microbial diversity is actually rarely taken into account in models of C and N dynamics. Here, we review the influence of microbial diversity on C and N dynamics, and the integration of microbial diversity in soil C and N models. We found that a gain of microbial richness and evenness enhances soil C and N dynamics on the average, though the improvement of C and N dynamics depends on the composition of microbial community. We reviewed 50 models integrating soil microbial diversity. More than 90 % of models integrate microbial diversity with discrete compartments representing conceptual functional groups (64 %) or identified taxonomic groups interacting in a food web (28 %). Half of the models have not been tested against an empirical dataset while the other half mainly consider fixed parameters. This is due to the difficulty to link taxonomic and functional diversity.
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Affiliation(s)
- Benjamin P. Louis
- UMR 1069 SAS, Agrocampus-Ouest, 65, Rue de Saint Brieuc, 35042 Rennes Cedex, France
- UMR 1069 SAS, INRA, 65, Rue de Saint Brieuc, 35042 Rennes Cedex, France
- Université Européenne de Bretagne, Rennes, France
| | - Pierre-Alain Maron
- INRA, AgroSup Dijon, UMR 1347 Agroecology, Université Bourgogne Franche Comté, UMR Agroécologie 17, Rue Sully, BP 86510, 21065 Dijon Cedex, France
| | - Valérie Viaud
- UMR 1069 SAS, INRA, 65, Rue de Saint Brieuc, 35042 Rennes Cedex, France
| | - Philippe Leterme
- UMR 1069 SAS, Agrocampus-Ouest, 65, Rue de Saint Brieuc, 35042 Rennes Cedex, France
- UMR 1069 SAS, INRA, 65, Rue de Saint Brieuc, 35042 Rennes Cedex, France
- Université Européenne de Bretagne, Rennes, France
| | - Safya Menasseri-Aubry
- UMR 1069 SAS, Agrocampus-Ouest, 65, Rue de Saint Brieuc, 35042 Rennes Cedex, France
- UMR 1069 SAS, INRA, 65, Rue de Saint Brieuc, 35042 Rennes Cedex, France
- Université Européenne de Bretagne, Rennes, France
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30
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Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing "Stress-on-Stress" Responses. Int J Mol Sci 2016; 17:ijms17060933. [PMID: 27314330 PMCID: PMC4926466 DOI: 10.3390/ijms17060933] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 05/17/2016] [Accepted: 06/06/2016] [Indexed: 01/19/2023] Open
Abstract
Many microbial ecology studies have demonstrated profound changes in community composition caused by environmental pollution, as well as adaptation processes allowing survival of microbes in polluted ecosystems. Soil microbial communities in polluted areas with a long-term history of contamination have been shown to maintain their function by developing metal-tolerance mechanisms. In the present work, we review recent experiments, with specific emphasis on studies that have been conducted in polluted areas with a long-term history of contamination that also applied DNA-based approaches. We evaluate how the “costs” of adaptation to metals affect the responses of metal-tolerant communities to other stress factors (“stress-on-stress”). We discuss recent studies on the stability of microbial communities, in terms of resistance and resilience to additional stressors, focusing on metal pollution as the initial stress, and discuss possible factors influencing the functional and structural stability of microbial communities towards secondary stressors. There is increasing evidence that the history of environmental conditions and disturbance regimes play central roles in responses of microbial communities towards secondary stressors.
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31
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Microbial communities from different subsystems in biological heap leaching system play different roles in iron and sulfur metabolisms. Appl Microbiol Biotechnol 2016; 100:6871-6880. [DOI: 10.1007/s00253-016-7537-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 03/29/2016] [Accepted: 04/05/2016] [Indexed: 11/26/2022]
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32
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Orwin KH, Dickie IA, Wood JR, Bonner KI, Holdaway RJ. Soil microbial community structure explains the resistance of respiration to a dry–rewet cycle, but not soil functioning under static conditions. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12610] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kate H. Orwin
- Delaware Cres Christchurch 8042 New Zealand
- Landcare Research PO Box 69040 Lincoln 7640 New Zealand
| | - Ian A. Dickie
- Landcare Research PO Box 69040 Lincoln 7640 New Zealand
- Bio‐Protection Research Centre Lincoln University PO Box 85084 Lincoln 7647 New Zealand
| | - Jamie R. Wood
- Landcare Research PO Box 69040 Lincoln 7640 New Zealand
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33
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Ren W, Ren G, Teng Y, Li Z, Li L. Time-dependent effect of graphene on the structure, abundance, and function of the soil bacterial community. JOURNAL OF HAZARDOUS MATERIALS 2015; 297:286-94. [PMID: 26010474 DOI: 10.1016/j.jhazmat.2015.05.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 04/21/2015] [Accepted: 05/12/2015] [Indexed: 05/22/2023]
Abstract
The increased application of graphene raises concerns about its environmental impact, but little information is available on the effect of graphene on the soil microbial community. This study evaluated the impact of graphene on the structure, abundance and function of the soil bacterial community based on quantitative real-time polymerase chain reaction (qPCR), pyrosequencing and soil enzyme activities. The results show that the enzyme activities of dehydrogenase and fluorescein diacetate (FDA) esterase and the biomass of the bacterial populations were transiently promoted by the presence of graphene after 4 days of exposure, but these parameters recovered completely after 21 days. Pyrosequencing analysis suggested a significant shift in some bacterial populations after 4 days, and the shift became weaker or disappeared as the exposure time increased to 60 days. During the entire exposure process, the majority of bacterial phylotypes remained unaffected. Some bacterial populations involved in nitrogen biogeochemical cycles and the degradation of organic compounds can be affected by the presence of graphene.
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Affiliation(s)
- Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Gaidi Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Zhengao Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Lina Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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34
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Landscape position influences microbial composition and function via redistribution of soil water across a watershed. Appl Environ Microbiol 2015; 81:8457-68. [PMID: 26431971 DOI: 10.1128/aem.02643-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/28/2015] [Indexed: 02/01/2023] Open
Abstract
Subalpine forest ecosystems influence global carbon cycling. However, little is known about the compositions of their soil microbial communities and how these may vary with soil environmental conditions. The goal of this study was to characterize the soil microbial communities in a subalpine forest watershed in central Montana (Stringer Creek Watershed within the Tenderfoot Creek Experimental Forest) and to investigate their relationships with environmental conditions and soil carbonaceous gases. As assessed by tagged Illumina sequencing of the 16S rRNA gene, community composition and structure differed significantly among three landscape positions: high upland zones (HUZ), low upland zones (LUZ), and riparian zones (RZ). Soil depth effects on phylogenetic diversity and β-diversity varied across landscape positions, being more evident in RZ than in HUZ. Mantel tests revealed significant correlations between microbial community assembly patterns and the soil environmental factors tested (water content, temperature, oxygen, and pH) and soil carbonaceous gases (carbon dioxide concentration and efflux and methane concentration). With one exception, methanogens were detected only in RZ soils. In contrast, methanotrophs were detected in all three landscape positions. Type I methanotrophs dominated RZ soils, while type II methanotrophs dominated LUZ and HUZ soils. The relative abundances of methanotroph populations correlated positively with soil water content (R = 0.72, P < 0.001) and negatively with soil oxygen (R = -0.53, P = 0.008). Our results suggest the coherence of soil microbial communities within and differences in communities between landscape positions in a subalpine forested watershed that reflect historical and contemporary environmental conditions.
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35
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Assessment of methods to recover DNA from bacteria, fungi and archaea in complex environmental samples. Folia Microbiol (Praha) 2015; 60:551-8. [DOI: 10.1007/s12223-015-0403-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
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36
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Hol WHG, de Boer W, de Hollander M, Kuramae EE, Meisner A, van der Putten WH. Context dependency and saturating effects of loss of rare soil microbes on plant productivity. FRONTIERS IN PLANT SCIENCE 2015; 6:485. [PMID: 26175749 PMCID: PMC4485053 DOI: 10.3389/fpls.2015.00485] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 06/16/2015] [Indexed: 05/09/2023]
Abstract
Land use intensification is associated with loss of biodiversity and altered ecosystem functioning. Until now most studies on the relationship between biodiversity and ecosystem functioning focused on random loss of species, while loss of rare species that usually are the first to disappear received less attention. Here we test if the effect of rare microbial species loss on plant productivity depends on the origin of the microbial soil community. Soils were sampled from three land use types at two farms. Microbial communities with increasing loss of rare species were created by inoculating sterilized soils with serially diluted soil suspensions. After 8 months of incubation, the effects of the different soil communities on abiotic soil properties, soil processes, microbial community composition, and plant productivity was measured. Dilution treatments resulted in increasing species loss, which was in relation to abundance of bacteria in the original field soil, without affecting most of the other soil parameters and processes. Microbial species loss affected plant biomass positively, negatively or not at all, depending on soil origin, but not on land use history. Even within fields the effects of dilution on plant biomass varied between replicates, suggesting heterogeneity in microbial community composition. The effects of medium and severe species loss on plant biomass were similar, pointing toward a saturating effect of species loss. We conclude that changes in the composition of the soil microbial community, including rare species loss, can affect plant productivity, depending on the composition of the initial microbial community. Future work on the relation between function and species loss effects should address this variation by including multiple sampling origins.
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Affiliation(s)
- W. H. Gera Hol
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, WageningenNetherlands
- *Correspondence: W. H. Gera Hol, Department of Terrestrial Ecology, Netherlands Institute of Ecology, NIOO-KNAW, P.O. Box 50, 6700 AB Wageningen, Netherlands,
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology, WageningenNetherlands
- Department of Soil Quality, Wageningen University, WageningenNetherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology, WageningenNetherlands
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology, WageningenNetherlands
| | - Annelein Meisner
- Microbial Ecology Group, Department of Biology, Lund University, LundSweden
- Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, CopenhagenDenmark
- Department of Biology, University of Copenhagen, CopenhagenDenmark
| | - Wim H. van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, WageningenNetherlands
- Laboratory of Nematology, Wageningen University, WageningenNetherlands
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37
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Dynamics of Panax ginseng Rhizospheric Soil Microbial Community and Their Metabolic Function. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2014; 2014:160373. [PMID: 25214872 PMCID: PMC4156984 DOI: 10.1155/2014/160373] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 08/05/2014] [Indexed: 11/17/2022]
Abstract
The bacterial communities of 1- to 6-year ginseng rhizosphere soils were characterized by culture-independent approaches, random amplified polymorphic DNA (RAPD), and amplified ribosomal DNA restriction analysis (ARDRA). Culture-dependent method (Biolog) was used to investigate the metabolic function variance of microbe living in rhizosphere soil. Results showed that significant genetic and metabolic function variance were detected among soils, and, with the increasing of cultivating years, genetic diversity of bacterial communities in ginseng rhizosphere soil tended to be decreased. Also we found that Verrucomicrobia, Acidobacteria, and Proteobacteria were the dominants in rhizosphere soils, but, with the increasing of cultivating years, plant disease prevention or plant growth promoting bacteria, such as Pseudomonas, Burkholderia, and Bacillus, tended to be rare.
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El-Ramady HR, Alshaal TA, Amer M, Domokos-Szabolcsy É, Elhawat N, Prokisch J, Fári M. Soil Quality and Plant Nutrition. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/978-3-319-06016-3_11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Paula FS, Rodrigues JLM, Zhou J, Wu L, Mueller RC, Mirza BS, Bohannan BJM, Nüsslein K, Deng Y, Tiedje JM, Pellizari VH. Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities. Mol Ecol 2014; 23:2988-99. [PMID: 24806276 DOI: 10.1111/mec.12786] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 04/30/2014] [Accepted: 04/30/2014] [Indexed: 11/29/2022]
Abstract
Land use change in the Amazon rainforest alters the taxonomic structure of soil microbial communities, but whether it alters their functional gene composition is unknown. We used the highly parallel microarray technology GeoChip 4.0, which contains 83,992 probes specific for genes linked nutrient cycling and other processes, to evaluate how the diversity, abundance and similarity of the targeted genes responded to forest-to-pasture conversion. We also evaluated whether these parameters were reestablished with secondary forest growth. A spatially nested scheme was employed to sample a primary forest, two pastures (6 and 38 years old) and a secondary forest. Both pastures had significantly lower microbial functional genes richness and diversity when compared to the primary forest. Gene composition and turnover were also significantly modified with land use change. Edaphic traits associated with soil acidity, iron availability, soil texture and organic matter concentration were correlated with these gene changes. Although primary and secondary forests showed similar functional gene richness and diversity, there were differences in gene composition and turnover, suggesting that community recovery was not complete in the secondary forest. Gene association analysis revealed that response to ecosystem conversion varied significantly across functional gene groups, with genes linked to carbon and nitrogen cycling mostly altered. This study indicates that diversity and abundance of numerous environmentally important genes respond to forest-to-pasture conversion and hence have the potential to affect the related processes at an ecosystem scale.
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Affiliation(s)
- Fabiana S Paula
- Instituto Oceanografico, Universidade de Sao Paulo, 05508-120, Sao Paulo, Brazil; Instituto de Ciencias Biomedicas, Universidade de Sao Paulo, 05508-900, Sao Paulo, Brazil; Department of Biology, University of Texas, Arlington, TX, 76019, USA
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Krause S, Le Roux X, Niklaus PA, Van Bodegom PM, Lennon JT, Bertilsson S, Grossart HP, Philippot L, Bodelier PLE. Trait-based approaches for understanding microbial biodiversity and ecosystem functioning. Front Microbiol 2014; 5:251. [PMID: 24904563 PMCID: PMC4033906 DOI: 10.3389/fmicb.2014.00251] [Citation(s) in RCA: 204] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/07/2014] [Indexed: 11/13/2022] Open
Abstract
In ecology, biodiversity-ecosystem functioning (BEF) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEF of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEF using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEF studies are often inadequate to unravel BEF relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEF relationships and thus generating systematic principles in microbial ecology and more generally ecology.
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Affiliation(s)
- Sascha Krause
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands ; Department of Chemical Engineering, University of Washington Seattle, WA, USA
| | - Xavier Le Roux
- Ecologie Microbienne, CNRS, INRA, Université de Lyon, Université Lyon 1, UMR 5557, USC 1193 Villeurbanne, France
| | - Pascal A Niklaus
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich Zurich, Switzerland
| | - Peter M Van Bodegom
- Subdepartment of Systems Ecology, Department of Ecological Sciences, VU University Amsterdam Amsterdam, Netherlands
| | - Jay T Lennon
- Department of Biology, Indiana University Bloomington, IN, USA
| | - Stefan Bertilsson
- Limnology and Science for Life Laboratory, Department of Ecology and Genetics, Uppsala University Uppsala, Sweden
| | - Hans-Peter Grossart
- Leibniz-Institute for Freshwater Ecology and Inland Fisheries Berlin, Germany ; Institute for Biochemistry and Biology, Potsdam University Potsdam, Germany
| | | | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands
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Tardy V, Mathieu O, Lévêque J, Terrat S, Chabbi A, Lemanceau P, Ranjard L, Maron PA. Stability of soil microbial structure and activity depends on microbial diversity. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:173-83. [PMID: 24596291 DOI: 10.1111/1758-2229.12126] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 10/30/2013] [Indexed: 05/24/2023]
Abstract
Despite the central role of microbes in soil processes, empirical evidence concerning the effect of their diversity on soil stability remains controversial. Here, we addressed the ecological insurance hypothesis by examining the stability of microbial communities along a gradient of soil microbial diversity in response to mercury pollution and heat stress. Diversity was manipulated by dilution extinction approach. Structural and functional stabilities of microbial communities were assessed from patterns of genetic structure and soil respiration after the stress. Dilution led to the establishment of a consistent diversity gradient, as revealed by 454 sequencing of ribosomal genes. Diversity stability was enhanced in species-rich communities whatever the stress whereas functional stability was improved with increasing diversity after heat stress, but not after mercury pollution. This discrepancy implies that the relevance of ecological insurance for soil microbial communities might depend on the type of stress. Our results also suggest that the significance of microbial diversity for soil functional stability might increase with available soil resources. This could have strong repercussions in the current 'global changes' context because it suggests that the combined increased frequencies of extreme climatic events, nutrient loading and biotic exploitation may amplify the functional consequences of diversity decrease.
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Effect of metal oxide nanoparticles on microbial community structure and function in two different soil types. PLoS One 2013; 8:e84441. [PMID: 24349575 PMCID: PMC3862805 DOI: 10.1371/journal.pone.0084441] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 11/18/2013] [Indexed: 01/10/2023] Open
Abstract
Increased availability of nanoparticle-based products will, inevitably, expose the environment to these materials. Engineered nanoparticles (ENPs) may thus find their way into the soil environment via wastewater, dumpsters and other anthropogenic sources; metallic oxide nanoparticles comprise one group of ENPs that could potentially be hazardous for the environment. Because the soil bacterial community is a major service provider for the ecosystem and humankind, it is critical to study the effects of ENP exposure on soil bacteria. These effects were evaluated by measuring bacterial community activity, composition and size following exposure to copper oxide (CuO) and magnetite (Fe3O4) nanosized (<50 nm) particles. Two different soil types were examined: a sandy loam (Bet-Dagan) and a sandy clay loam (Yatir), under two ENP concentrations (1%, 0.1%). Results indicate that the bacterial community in Bet-Dagan soil was more susceptible to change due to exposure to these ENPs, relative to Yatir soil. More specifically, CuO had a strong effect on bacterial hydrolytic activity, oxidative potential, community composition and size in Bet-Dagan soil. Few effects were noted in the Yatir soil, although 1% CuO exposure did cause a significant decreased oxidative potential and changes to community composition. Fe3O4 changed the hydrolytic activity and bacterial community composition in Bet-Dagan soil but did not affect the Yatir soil bacterial community. Furthermore, in Bet-Dagan soil, abundance of bacteria annotated to OTUs from the Bacilli class decreased after addition of 0.1% CuO but increased with 1% CuO, while in Yatir soil their abundance was reduced with 1% CuO. Other important soil bacterial groups, including Rhizobiales and Sphingobacteriaceae, were negatively affected by CuO addition to soil. These results indicate that both ENPs are potentially harmful to soil environments. Furthermore, it is suggested that the clay fraction and organic matter in different soils interact with the ENPs and reduce their toxicity.
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Conrad R, Ji Y, Noll M, Klose M, Claus P, Enrich-Prast A. Response of the methanogenic microbial communities in Amazonian oxbow lake sediments to desiccation stress. Environ Microbiol 2013; 16:1682-94. [PMID: 24118927 DOI: 10.1111/1462-2920.12267] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 08/01/2013] [Accepted: 08/26/2013] [Indexed: 11/27/2022]
Abstract
Methanogenic microbial communities in soil and sediment function only when the environment is inundated and anoxic. In contrast to submerged soils, desiccation of lake sediments happens only rarely. However, some predictions suggest that extreme events of drying will become more common in the Amazon region, and this will promote an increase in sediments drying and exposure. We asked whether and how such methanogenic communities can withstand desiccation stress. Therefore, we determined the rates and pathways of CH(4) production (analysis of CH(4) and δ(13) C of CH(4), CO(2) and acetate), the copy numbers of bacterial and archaeal 16S rRNA genes and mcrA genes (quantitative PCR), and the community composition of Archaea and Bacteria (T-RFLP and pyrosequencing) in oxbow lake sediments of rivers in the Brazilian Amazon region. The rivers were of white water, black water and clear water type. The measurements were done with sediment in fresh state and after drying and rewetting. After desiccation and rewetting the composition of both, the archaeal and bacterial community changed. Since lake sediments from white water rivers exhibited only negligible methanogenic activity, probably because of relatively high iron and low organic matter content, they were not further analysed. The other sediments produced CH(4), with hydrogenotrophic methanogenesis usually accounting for > 50% of total activity. After desiccation and rewetting, archaeal and bacterial gene copy numbers decreased. The bacterial community showed a remarkable increase of Clostridiales from about 10% to > 30% of all Bacteria, partially caused by proliferation of specific taxa as the numbers of OTU shared with fresh sediment decreased from about 9% to 3%. Among the Archaea, desiccation specifically enhanced the relative abundance of either Methanocellales (black water) and/or Methanosarcinaceae (clear water). Despite the changes in gene copy numbers and composition of the microbial community, rates of CH(4) production even increased after desiccation-rewetting, demonstrating that the function of the methanogenic microbial community had not been impaired. This result indicates that the increase in extreme events of drying may increase methane production in flooded sediments.
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Affiliation(s)
- Ralf Conrad
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str.10, 35043, Marburg, Germany
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Microbial competition in polar soils: a review of an understudied but potentially important control on productivity. BIOLOGY 2013; 2:533-54. [PMID: 24832797 PMCID: PMC3960893 DOI: 10.3390/biology2020533] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 03/11/2013] [Accepted: 03/12/2013] [Indexed: 01/29/2023]
Abstract
Intermicrobial competition is known to occur in many natural environments, and can result from direct conflict between organisms, or from differential rates of growth, colonization, and/or nutrient acquisition. It has been difficult to extensively examine intermicrobial competition in situ, but these interactions may play an important role in the regulation of the many biogeochemical processes that are tied to microbial communities in polar soils. A greater understanding of how competition influences productivity will improve projections of gas and nutrient flux as the poles warm, may provide biotechnological opportunities for increasing the degradation of contaminants in polar soil, and will help to predict changes in communities of higher organisms, such as plants.
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Griffiths BS, Philippot L. Insights into the resistance and resilience of the soil microbial community. FEMS Microbiol Rev 2013; 37:112-29. [DOI: 10.1111/j.1574-6976.2012.00343.x] [Citation(s) in RCA: 578] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 04/16/2012] [Accepted: 05/01/2012] [Indexed: 11/29/2022] Open
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Bengtsson G, Törneman N, De Lipthay JR, Sørensen SJ. Microbial diversity and PAH catabolic genes tracking spatial heterogeneity of PAH concentrations. MICROBIAL ECOLOGY 2013; 65:91-100. [PMID: 22940734 DOI: 10.1007/s00248-012-0112-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 08/10/2012] [Indexed: 06/01/2023]
Abstract
We analyzed the within-site spatial heterogeneity of microbial community diversity, polyaromatic hydrocarbon (PAH) catabolic genotypes, and physiochemical soil properties at a creosote contaminated site. Genetic diversity and community structure were evaluated from an analysis of denaturant gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified sequences of 16S rRNA gene. The potential PAH degradation capability was determined from PCR amplification of a suit of aromatic dioxygenase genes. Microbial diversity, evenness, and PAH genotypes were patchily distributed, and hot and cold spots of their distribution coincided with hot and cold spots of the PAH distribution. The analyses revealed a positive covariation between microbial diversity, biomass, evenness, and PAH concentration, implying that the creosote contamination at this site promotes diversity and abundance. Three patchily distributed PAH-degrading genotypes, NAH, phnA, and pdo1, were identified, and their abundances were positively correlated with the PAH concentration and the fraction of soil organic carbon. The covariation of the PAH concentration with the number and spatial distribution of catabolic genotypes suggests that a field site capacity to degrade PAHs may vary with the extent of contamination.
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Affiliation(s)
- Göran Bengtsson
- Department of Ecology, Lund University, Sölvegatan 37, SE, 223 62, Lund, Sweden.
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Giles M, Morley N, Baggs EM, Daniell TJ. Soil nitrate reducing processes - drivers, mechanisms for spatial variation, and significance for nitrous oxide production. Front Microbiol 2012; 3:407. [PMID: 23264770 PMCID: PMC3524552 DOI: 10.3389/fmicb.2012.00407] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 11/12/2012] [Indexed: 11/13/2022] Open
Abstract
The microbial processes of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two important nitrate reducing mechanisms in soil, which are responsible for the loss of nitrate ([Formula: see text]) and production of the potent greenhouse gas, nitrous oxide (N(2)O). A number of factors are known to control these processes, including O(2) concentrations and moisture content, N, C, pH, and the size and community structure of nitrate reducing organisms responsible for the processes. There is an increasing understanding associated with many of these controls on flux through the nitrogen cycle in soil systems. However, there remains uncertainty about how the nitrate reducing communities are linked to environmental variables and the flux of products from these processes. The high spatial variability of environmental controls and microbial communities across small sub centimeter areas of soil may prove to be critical in determining why an understanding of the links between biotic and abiotic controls has proved elusive. This spatial effect is often overlooked as a driver of nitrate reducing processes. An increased knowledge of the effects of spatial heterogeneity in soil on nitrate reduction processes will be fundamental in understanding the drivers, location, and potential for N(2)O production from soils.
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Affiliation(s)
- Madeline Giles
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen Aberdeen, UK ; Ecological Sciences, The James Hutton Institute Dundee, UK
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Disturbance promotes non-indigenous bacterial invasion in soil microcosms: analysis of the roles of resource availability and community structure. PLoS One 2012; 7:e45306. [PMID: 23056198 PMCID: PMC3462762 DOI: 10.1371/journal.pone.0045306] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 08/21/2012] [Indexed: 11/24/2022] Open
Abstract
Background Invasion-biology is largely based on non-experimental observation of larger organisms. Here, we apply an experimental approach to the subject. By using microbial-based microcosm-experiments, invasion-biology can be placed on firmer experimental, and hence, less anecdotal ground. A better understanding of the mechanisms that govern invasion-success of bacteria in soil communities will provide knowledge on the factors that hinder successful establishment of bacteria artificially inoculated into soil, e.g. for remediation purposes. Further, it will yield valuable information on general principles of invasion biology in other domains of life. Methodology/Principal Findings Here, we studied invasion and establishment success of GFP-tagged Pseudomonas fluorescens DSM 50090 in laboratory microcosms during a 42-day period. We used soil heating to create a disturbance gradient, and hypothesized that increased disturbance would facilitate invasion; our experiments confirmed this hypothesis. We suggest that the key factors associated with the heating disturbance that explain the enhanced invasion success are increased carbon substrate availability and reduced diversity, and thus, competition- and predation-release. In a second experiment we therefore separated the effects of increased carbon availability and decreased diversity. Here, we demonstrated that the effect of the indigenous soil community on bacterial invasion was stronger than that of resource availability. In particular, introduced bacteria established better in a long term perspective at lower diversity and predation pressure. Conclusion We propose increased use of microbial systems, for experimental study of invasion scenarios. They offer a simple and cost-efficient way to study and understand biological invasion. Consequently such systems can help us to better predict the mechanisms controlling changes in stability of communities and ecosystems. This is becoming increasingly relevant since anthropogenic disturbance causes increasing global change, which promotes invasion. Moreover, a thorough understanding of factors controlling invasion and establishment of artificially amended micro-organisms will mean a major step forward for soil-remediation microbiology.
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Niedrée B, Vereecken H, Burauel P. Effects of low-level radioactive soil contamination and sterilization on the degradation of radiolabeled wheat straw. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2012; 109:29-35. [PMID: 22248931 DOI: 10.1016/j.jenvrad.2011.12.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 12/01/2011] [Accepted: 12/19/2011] [Indexed: 05/31/2023]
Abstract
After the explosion of reactor 4 in the nuclear power plant near Chernobyl, huge agricultural areas became contaminated with radionuclides. In this study, we want to elucidate whether (137)Cs and (90)Sr affect microorganisms and their community structure and functions in agricultural soil. For this purpose, the mineralization of radiolabeled wheat straw was examined in lab-scale microcosms. Native soils and autoclaved and reinoculated soils were incubated for 70 days at 20 °C. After incubation, the microbial community structure was compared via 16S and 18S rDNA denaturing gradient gel electrophoresis (DGGE). The radioactive contamination with (137)Cs and (90)Sr was found to have little effect on community structure and no effect on the straw mineralization. The autoclaving and reinoculation of soil had a strong influence on the mineralization and the community structure. Additionally we analyzed the effect of soil treatment on mineralization and community composition. It can be concluded that other environmental factors (such as changing content of dissolved organic carbon) are much stronger regulating factors in the mineralization of wheat straw and that low-level radiation only plays a minor role.
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Affiliation(s)
- Bastian Niedrée
- Agrosphere Institute, Forschungszentrum Jülich GmbH, Wilhelm-Johnen Str., 52425 Jülich, Germany.
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Rojas-Oropeza M, Fernández FJ, Dendooven L, Cabirol N. Effect of methyl parathion on nitrous oxide production: a laboratory study. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2012; 95 Suppl:S25-S30. [PMID: 21295905 DOI: 10.1016/j.jenvman.2011.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 11/14/2010] [Accepted: 01/04/2011] [Indexed: 05/30/2023]
Abstract
We investigated the diversity of a denitrifying gene (nirK) and the emission of CO(2) and N(2)O, in a "chinampa" soil contaminated with methyl parathion. Soil at 40% of water holding capacity was spiked with methyl parathion at four concentrations (i.e. 0, 0.7, 1.47 and 4.27 g kg(-1) dry soil), while emission of N(2)O and CO(2) and nirK diversity was determined after 0, 1, 14, 30, 60 and 90 days. The emission of N(2)O on a daily base and the cumulative emission of CO(2) was not affected by the different concentrations of methyl parathion applied to soil. The diversity of the nirK gene, determined by using temperature gradient gel electrophoresis (TGGE), decreased with increased methyl parathion application. It was found that methyl parathion had effect on the emissions of N(2)O and CO(2), and reduced the diversity of the nirK gene. Consequently, the reduced diversity of the nirK gene could affect the emission of N(2)O.
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Affiliation(s)
- Marcelo Rojas-Oropeza
- Facultad de Ciencias, Departamento de Ecología y Recursos Naturales, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 México D.F., Mexico
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