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Bechtold EK, Wanek W, Nuesslein B, DaCosta M, Nüsslein K. Successional changes in bacterial phyllosphere communities are plant-host species dependent. Appl Environ Microbiol 2024; 90:e0175023. [PMID: 38349147 PMCID: PMC11206175 DOI: 10.1128/aem.01750-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/17/2024] [Indexed: 03/21/2024] Open
Abstract
Phyllosphere microbial communities are increasingly experiencing intense pulse disturbance events such as drought. It is currently unknown how phyllosphere communities respond to such disturbances and if they are able to recover. We explored the stability of phyllosphere communities over time, in response to drought stress, and under recovery from drought on temperate forage grasses. Compositional or functional changes were observed during the disturbance period and whether communities returned to non-stressed levels following recovery. Here, we found that phyllosphere community composition shifts as a result of simulated drought but does not fully recover after irrigation is resumed and that the degree of community response to drought is host species dependent. However, while community composition had changed, we found a high level of functional stability (resistance) over time and in the water deficit treatment. Ecological modeling enabled us to understand community assembly processes over a growing season and to determine if they were disrupted during a disturbance event. Phyllosphere community succession was characterized by a strong level of ecological drift, but drought disturbance resulted in variable selection, or, in other words, communities were diverging due to differences in selective pressures. This successional divergence of communities with drought was unique for each host species. Understanding phyllosphere responses to environmental stresses is important as climate change-induced stresses are expected to reduce crop productivity and phyllosphere functioning. IMPORTANCE Leaf surface microbiomes have the potential to influence agricultural and ecosystem productivity. We assessed their stability by determining composition, functional resistance, and resilience. Resistance is the degree to which communities remain unchanged as a result of disturbance, and resilience is the ability of a community to recover to pre-disturbance conditions. By understanding the mechanisms of community assembly and how they relate to the resistance and resilience of microbial communities under common environmental stresses such as drought, we can better understand how communities will adapt to a changing environment and how we can promote healthy agricultural microbiomes. In this study, phyllosphere compositional stability was highly related to plant host species phylogeny and, to a lesser extent, known stress tolerances. Phyllosphere community assembly and stability are a result of complex interactions of ecological processes that are differentially imposed by host species.
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Affiliation(s)
- Emily K. Bechtold
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Wolfgang Wanek
- Division of Terrestrial Ecosystem Research, Center of Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Benedikt Nuesslein
- Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Michelle DaCosta
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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Wang Y, Xue D, Chen X, Qiu Q, Chen H. Structure and Functions of Endophytic Bacterial Communities Associated with Sphagnum Mosses and Their Drivers in Two Different Nutrient Types of Peatlands. MICROBIAL ECOLOGY 2024; 87:47. [PMID: 38407642 PMCID: PMC10896819 DOI: 10.1007/s00248-024-02355-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/29/2024] [Indexed: 02/27/2024]
Abstract
Sphagnum mosses are keystone plant species in the peatland ecosystems that play a crucial role in the formation of peat, which shelters a broad diversity of endophytic bacteria with important ecological functions. In particular, methanotrophic and nitrogen-fixing endophytic bacteria benefit Sphagnum moss hosts by providing both carbon and nitrogen. However, the composition and abundance of endophytic bacteria from different species of Sphagnum moss in peatlands of different nutrient statuses and their drivers remain unclear. This study used 16S rRNA gene amplicon sequencing to examine endophytic bacterial communities in Sphagnum mosses and measured the activity of methanotrophic microbial by the 13C-CH4 oxidation rate. According to the results, the endophytic bacterial community structure varied among Sphagnum moss species and Sphagnum capillifolium had the highest endophytic bacterial alpha diversity. Moreover, chlorophyll, phenol oxidase, carbon contents, and water retention capacity strongly shaped the communities of endophytic bacteria. Finally, Sphagnum palustre in Hani (SP) had a higher methane oxidation rate than S. palustre in Taishanmiao. This result is associated with the higher average relative abundance of Methyloferula an obligate methanotroph in SP. In summary, this work highlights the effects of Sphagnum moss characteristics on the endophytic bacteriome. The endophytic bacteriome is important for Sphagnum moss productivity, as well as for carbon and nitrogen cycles in Sphagnum moss peatlands.
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Affiliation(s)
- Yue Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan Xue
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China.
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China.
| | - Xuhui Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Qiu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China
| | - Huai Chen
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9, Section 4, South Renmin Road, Chengdu, 610041, China.
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China.
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Shan Y, Fu Y, Wang L, Yao Y. Response of the nitrogen processing bacterial community to water level fluctuation and nitrate availability in an intact marsh soil column. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:111947-111957. [PMID: 37819472 DOI: 10.1007/s11356-023-30020-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/18/2023] [Indexed: 10/13/2023]
Abstract
Wetlands are known to experience fluctuations in water levels and receive exogenous nitrogen inputs that affect various organisms, including soil microorganisms. To study the impact of these factors on microbial diversity, we collected intact soil columns from a Phragmites australis-dominated site in the Qixing River National Nature Reserve in Northeast China. In a laboratory experiment, we simulated water level fluctuations and exogenous nitrogen inputs to the soil columns and examined the associated changes in the relative abundance of 51 bacterial genera involved in nitrogen cycling processes. Our findings revealed that different bacterial genera exhibited varying relative abundances across treatments. Specifically, Massilia showed the highest total relative abundance at the genus level, while Planctomyces had the second highest, and Campylobacter had the lowest abundance. The DESeq2 model, based on negative binomial distribution, revealed that the tags of bacterial genera were significantly correlated with soil depth, but not with water levels or nitrogen concentrations. However, the addition of a 30 mg/L nitrate solution caused a decrease in the relative abundances of bacterial genera with decreasing water levels, while a 60 mg/L concentration of nitrogen resulted in a decrease and then an increase in the relative abundances of bacterial genera with decreasing water levels. Our study provides valuable insights into the response of nitrogen-cycling bacteria to changes in different environmental conditions.
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Affiliation(s)
- Yuanqi Shan
- Wetland Biodiversity Conservation and Research Center, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin, 150040, China
- College of Wildlife and Protected Area, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin, 150040, China
| | - Yi Fu
- Wetland Biodiversity Conservation and Research Center, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin, 150040, China
- College of Wildlife and Protected Area, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin, 150040, China
| | - Lei Wang
- College of Landscape Architectrue, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin, 150040, China
| | - Yunlong Yao
- Wetland Biodiversity Conservation and Research Center, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin, 150040, China.
- College of Wildlife and Protected Area, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin, 150040, China.
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Feng R, Wang H, Liu T, Wang F, Cai L, Chen X, Zhang S. Response of microbial communities in the phyllosphere ecosystem of tobacco exposed to the broad-spectrum copper hydroxide. Front Microbiol 2023; 14:1229294. [PMID: 37840714 PMCID: PMC10568630 DOI: 10.3389/fmicb.2023.1229294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Copper hydroxide is a broad-spectrum copper fungicide, which is often used to control crop fungal and bacterial diseases. In addition to controlling targeted pathogens, copper hydroxide may also affect other non-targeted microorganisms in the phyllosphere ecosystem. At four time points (before spraying, and 5, 10 and 15 days after fungicide application), the response of diseased and healthy tobacco phyllosphere microorganisms to copper hydroxide stress was studied by using Illumina high-throughput sequencing technology, and Biolog tools. The results showed that the microbiome communities of the healthy group were more affected than the disease group, and the fungal community was more sensitive than the bacterial community. The most common genera in the disease group were Alternaria, Boeremia, Cladosporium, Pantoea, Ralstonia, Pseudomonas, and Sphingomonas; while in the healthy group, these were Alternaria, Cladosporium, Symmetrospora, Ralstonia, and Pantoea. After spraying, the alpha diversity of the fungal community decreased at 5 days for both healthy and diseased groups, and then showed an increasing trend, with a significant increase at 15 days for the healthy group. The alpha diversity of bacterial community in healthy and diseased groups increased at 15 days, and the healthy group had a significant difference. The relative abundance of Alternaria and Cladosporium decreased while that of Boeremia, Stagonosporopsis, Symmetrospora, Epicoccum and Phoma increased in the fungal communities of healthy and diseased leaves. The relative abundance of Pantoea decreased first and then increased, while that of Ralstonia, Pseudomonas and Sphingomonas increased first and then decreased in the bacterial communities of healthy and diseased leaves. While copper hydroxide reduced the relative abundance of pathogenic fungi Alternaria and Cladosporium, it also resulted in the decrease of beneficial bacteria such as Actinomycetes and Pantoea, and the increase of potential pathogens such as Boeremia and Stagonosporopsis. After treatment with copper hydroxide, the metabolic capacity of the diseased group improved, while that of the healthy group was significantly suppressed, with a gradual recovery of metabolic activity as the application time extended. The results revealed changes in microbial community composition and metabolic function of healthy and diseased tobacco under copper hydroxide stress, providing a theoretical basis for future studies on microecological protection of phyllosphere.
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Affiliation(s)
- Ruichao Feng
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co- construction by Ministry and Province), Yangtze University, Jingzhou, Hubei, China
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Hancheng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Tingting Liu
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Feng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Liuti Cai
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Xingjiang Chen
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Songbai Zhang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co- construction by Ministry and Province), Yangtze University, Jingzhou, Hubei, China
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Sun N, Fan B, Yang F, Zhao L, Wang M. Effects of adding corn steep liquor on bacterial community composition and carbon and nitrogen transformation during spent mushroom substrate composting. BMC Microbiol 2023; 23:156. [PMID: 37237262 DOI: 10.1186/s12866-023-02894-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Carbon and nitrogen are essential energy and nutrient substances in the composting process. Corn steep liquor (CSL) is rich in soluble carbon and nitrogen nutrients and active substances and is widely used in the biological industry. Nonetheless, limited research has been done on the effect of CSL on composting. This work firstly reveals the effect of adding CSL to bacterial community composition and carbon and nitrogen conversion during composting. This study provides the choice of auxiliary materials for the spent mushroom substrate compost (SMS) and some novel knowledge about the effect of bacterial community on C and N cycling during composting of SMS and CSL. Two treatments were set up in the experiment: 100% spent mushroom substrate (SMS) as CK and SMS + 0.5% CSL (v/v) as CP. RESULTS The results showed that the addition of CSL enhanced the initial carbon and nitrogen content of the compost, altered the bacterial community structure, and increased the bacterial diversity and relative abundance, which might be beneficial to the conversion and retention of carbon and nitrogen in the composting process. In this paper, network analysis was used to screen the core bacteria involved in carbon and nitrogen conversion. In the CP network, the core bacteria were divided into two categories, synthesizing and degrading bacteria, and there were more synthesizing bacteria than degrading bacteria, so the degradation and synthesis of organic matter were carried out simultaneously, while only degrading bacteria were found in the CK network. Functional prediction by Faprotax identified 53 groups of functional bacteria, among which 20 (76.68% abundance) and 14 (13.15% abundance) groups of functional bacteria were related to carbon and nitrogen conversion, respectively. Adding CSL stimulated the compensatory effect of core and functional bacteria, enhanced the carbon and nitrogen transformation ability, stimulated the activity of low-abundance bacteria, and reduced the competitive relationship between the bacterial groups. This may be why the addition of CSL accelerated the organic matter degradation and increased carbon and nitrogen preservation. CONCLUSIONS These findings indicate that the addition of CSL promoted the cycling and preservation of carbon and nitrogen in the SMS composts, and the addition of CSL to the compost may be an effective way to dispose of agricultural waste.
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Affiliation(s)
- Ning Sun
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Bowen Fan
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Fengjun Yang
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
| | - Liqin Zhao
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Mengmeng Wang
- College of Horticulture and Landscape Architecture, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
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Chen D, Hou H, Zhou S, Zhang S, Liu D, Pang Z, Hu J, Xue K, Du J, Cui X, Wang Y, Che R. Soil diazotrophic abundance, diversity, and community assembly mechanisms significantly differ between glacier riparian wetlands and their adjacent alpine meadows. Front Microbiol 2022; 13:1063027. [PMID: 36569049 PMCID: PMC9772447 DOI: 10.3389/fmicb.2022.1063027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/25/2022] [Indexed: 12/13/2022] Open
Abstract
Global warming can trigger dramatic glacier area shrinkage and change the flux of glacial runoff, leading to the expansion and subsequent retreat of riparian wetlands. This elicits the interconversion of riparian wetlands and their adjacent ecosystems (e.g., alpine meadows), probably significantly impacting ecosystem nitrogen input by changing soil diazotrophic communities. However, the soil diazotrophic community differences between glacial riparian wetlands and their adjacent ecosystems remain largely unexplored. Here, soils were collected from riparian wetlands and their adjacent alpine meadows at six locations from glacier foreland to lake mouth along a typical Tibetan glacial river in the Namtso watershed. The abundance and diversity of soil diazotrophs were determined by real-time PCR and amplicon sequencing based on nifH gene. The soil diazotrophic community assembly mechanisms were analyzed via iCAMP, a recently developed null model-based method. The results showed that compared with the riparian wetlands, the abundance and diversity of the diazotrophs in the alpine meadow soils significantly decreased. The soil diazotrophic community profiles also significantly differed between the riparian wetlands and alpine meadows. For example, compared with the alpine meadows, the relative abundance of chemoheterotrophic and sulfate-respiration diazotrophs was significantly higher in the riparian wetland soils. In contrast, the diazotrophs related to ureolysis, photoautotrophy, and denitrification were significantly enriched in the alpine meadow soils. The iCAMP analysis showed that the assembly of soil diazotrophic community was mainly controlled by drift and dispersal limitation. Compared with the riparian wetlands, the assembly of the alpine meadow soil diazotrophic community was more affected by dispersal limitation and homogeneous selection. These findings suggest that the conversion of riparian wetlands and alpine meadows can significantly alter soil diazotrophic community and probably the ecosystem nitrogen input mechanisms, highlighting the enormous effects of climate change on alpine ecosystems.
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Affiliation(s)
- Danhong Chen
- Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Institute of International Rivers and Eco-Security, Yunnan University, Kunming, China
| | - Haiyan Hou
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Shutong Zhou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Song Zhang
- Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Institute of International Rivers and Eco-Security, Yunnan University, Kunming, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Dong Liu
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Life Sciences, Yunnan University, Kunming, China
| | - Zhe Pang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jinming Hu
- Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Institute of International Rivers and Eco-Security, Yunnan University, Kunming, China
| | - Kai Xue
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jianqing Du
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyong Cui
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanfen Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rongxiao Che
- Yunnan Key Laboratory of International Rivers and Transboundary Eco-Security, Institute of International Rivers and Eco-Security, Yunnan University, Kunming, China
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Ai J, Yu T, Liu X, Jiang Y, Hao Z, Zhao X, Wang E, Deng Z. Nodule-associated diazotrophic community succession is driven by developmental phases combined with microhabitat of Sophora davidii. Front Microbiol 2022; 13:1078208. [PMID: 36532429 PMCID: PMC9751200 DOI: 10.3389/fmicb.2022.1078208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Nodule-associated nitrogen-fixing microorganisms (diazotrophs) residing in legume root nodules, and they have the potential to enhance legume survival. However, the succession characteristics and mechanisms of leguminous diazotrophic communities remain largely unexplored. We performed a high-throughput nifH amplicon sequencing with samples of root nodules and soil in the three developmental phases (young nodules, active nodules and senescent nodules) of the Sophora davidii (Franch.) Skeels root nodules, aiming to investigate the dynamics of nodule-endophytic diazotrophs during three developmental phases of root nodules. The results demonstrated the presence of diverse diazotrophic bacteria and successional community shifting dominated by Mesorhizobium and Bradyrhizobium inside the nodule according to the nodule development. The relative abundance decreased for Mesorhizobium, while decreased first and then increased for Bradyrhizobium in nodule development from young to active to senescent. Additionally, strains M. amorphae BT-30 and B. diazoefficiens B-26 were isolated and selected to test the interaction between them in co-cultured conditions. Under co-culture conditions: B. diazoefficiens B-26 significantly inhibited the growth of M. amorphae BT-30. Intriguingly, growth of B. diazoefficiens B-26 was significantly promoted by co'culture with M. amorphae BT-30 and could utilize some carbon and nitrogen sources that M. amorphae BT-30 could not. Additionally, the composition of microbial community varied in root nodules, in rhizosphere and in bulk soil. Collectively, our study highlights that developmental phases of nodules and the host microhabitat were the key driving factors for the succession of nodule-associated diazotrophic community.
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Affiliation(s)
- Jiamin Ai
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Tianfei Yu
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Xiaodong Liu
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Yingying Jiang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Ziwei Hao
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Xiaoyu Zhao
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Entao Wang
- , Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Zhenshan Deng
- College of Life Sciences, Yan’an University, Yan’an, China,*Correspondence: Zhenshan Deng,
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Renaudin M, Laforest-Lapointe I, Bellenger JP. Unraveling global and diazotrophic bacteriomes of boreal forest floor feather mosses and their environmental drivers at the ecosystem and at the plant scale in North America. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155761. [PMID: 35533858 DOI: 10.1016/j.scitotenv.2022.155761] [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: 02/27/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 06/14/2023]
Abstract
Feather mosses are abundant cryptogams of the boreal forest floor and shelter a broad diversity of bacteria who have important ecological functions (e.g., decomposition, nutrient cycling). In particular, nitrogen (N2-) fixation performed by feather moss-associated diazotrophs constitutes an important entry of nitrogen in the boreal forest ecosystem. However, the composition of the feather moss bacteriome and its environmental drivers are still unclear. Using cDNA amplicon sequencing of the 16S rRNA and nifH genes and cyanobacterial biomass quantification, we explored the active global and diazotrophic bacterial communities of two dominant feather moss species (i) at the ecosystem scale, along a 500-km climatic and nutrient deposition gradient in the North American boreal forest, and (ii) at the plant scale, along the moss shoot senescence gradient. We found that cyanobacteria were major actors of the feather moss bacteriome, accounting for 33% of global bacterial communities and 65% of diazotrophic communities, and that several cyanobacterial and methanotrophic genera were contributing to N2-fixation. Moreover, we showed that bacteria were occupying ecological niches along the moss shoot, with phototrophs being dominant in the apical part and methanotrophs being dominant in the basal part. Finally, climate (temperature, precipitation), environmental variables (moss species, month, tree density) and nutrients (nitrogen, phosphorus, molybdenum, vanadium, iron) strongly shaped global and diazotrophic bacteriomes. In summary, this work presents evidence that the feather moss bacteriome plays crucial roles in supporting moss growth, health, and decomposition, as well as in the boreal forest carbon and nitrogen cycles. This study also highlights the substantial effects of climate and nutrients on the feather moss bacteriome, suggesting the importance of understanding the impacts of global change on moss-associated bacterial growth and activity.
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Affiliation(s)
- Marie Renaudin
- Centre Sève, Département de Chimie, Université de Sherbrooke, J1K 2R1 Sherbrooke, QC, Canada.
| | | | - Jean-Philippe Bellenger
- Centre Sève, Département de Chimie, Université de Sherbrooke, J1K 2R1 Sherbrooke, QC, Canada.
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Li C, Li X, Yang Y, Shi Y, Li H. Degradation reduces the diversity of nitrogen-fixing bacteria in the alpine wetland on the Qinghai-Tibet Plateau. FRONTIERS IN PLANT SCIENCE 2022; 13:939762. [PMID: 35991434 PMCID: PMC9386517 DOI: 10.3389/fpls.2022.939762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Biological nitrogen fixation is a key process in the nitrogen cycle and the main source of soil available nitrogen. The number and diversity of nitrogen-fixing bacteria directly reflect the efficiency of soil nitrogen fixation. The alpine wetland on the Qinghai-Tibet Plateau (QTP) is degrading increasingly, with a succession toward alpine meadows. Significant changes in soil physicochemical properties accompany this process. However, it is unclear how does the soil nitrogen-fixing bacteria change during the degradation processes, and what is the relationship between these changes and soil physicochemical properties. In this study, the nifH gene was used as a molecular marker to further investigate the diversity of nitrogen-fixing bacteria at different stages of degradation (none, light, and severe degeneration) in the alpine wetland. The results showed that wetland degradation significantly reduced the diversity, altered the community composition of nitrogen-fixing bacteria, decreased the relative abundance of Proteobacteria, and increased the relative abundance of Actinobacteria. In addition to the dominant phylum, the class, order, family, and genus of nitrogen-fixing bacteria had significant changes in relative abundance. Analysis of Mantel test showed that most soil factors (such as pH, soil water content (SWC), the organic carbon (TOC), total nitrogen (TN), and soil C:P ratio) and abundance had a significant positive correlation. TOC, TN, total phosphorus (TP), soil C:P ratio and Shannon had a significant positive correlation with each other. The RDA ranking further revealed that TOC, SWC, and TN were the main environmental factors influencing the community composition of nitrogen-fixing bacteria. It is found that the degradation of the alpine wetland inhibited the growth of nitrogen-fixing bacteria to a certain extent, leading to the decline of their nitrogen-fixing function.
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Affiliation(s)
- Chengyi Li
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Xilai Li
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
| | - Yuanwu Yang
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Yan Shi
- School of Environment, The University of Auckland, Auckland, New Zealand
| | - Honglin Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
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Nepel M, Pfeifer J, Oberhauser FB, Richter A, Woebken D, Mayer VE. Nitrogen fixation by diverse diazotrophic communities can support population growth of arboreal ants. BMC Biol 2022; 20:135. [PMID: 35681192 PMCID: PMC9185989 DOI: 10.1186/s12915-022-01289-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/31/2022] [Indexed: 11/17/2022] Open
Abstract
Background Symbiotic ant-plant associations, in which ants live on plants, feed on plant-provided food, and protect host trees against threats, are ubiquitous across the tropics, with the Azteca-Cecropia associations being amongst the most widespread interactions in the Neotropics. Upon colonization of Cecropia’s hollow internodes, Azteca queens form small patches with plant parenchyma, which are then used as waste piles when the colony grows. Patches—found in many ant-plant mutualisms—are present throughout the colony life cycle and may supplement larval food. Despite their initial nitrogen (N)-poor substrate, patches in Cecropia accommodate fungi, nematodes, and bacteria. In this study, we investigated the atmospheric N2 fixation as an N source in patches of early and established ant colonies. Results Via 15N2 tracer assays, N2 fixation was frequently detected in all investigated patch types formed by three Azteca ant species. Quantified fixation rates were similar in early and established ant colonies and higher than in various tropical habitats. Based on amplicon sequencing, the identified microbial functional guild—the diazotrophs—harboring and transcribing the dinitrogenase reductase (nifH) gene was highly diverse and heterogeneous across Azteca colonies. The community composition differed between early and established ant colonies and partly between the ant species. Conclusions Our data show that N2 fixation can result in reasonable amounts of N in ant colonies, which might not only enable bacterial, fungal, and nematode growth in the patch ecosystems but according to our calculations can even support the growth of ant populations. The diverse and heterogeneous diazotrophic community implies a functional redundancy, which could provide the ant-plant-patch system with a higher resilience towards changing environmental conditions. Hence, we propose that N2 fixation represents a previously unknown potential to overcome N limitations in arboreal ant colonies. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01289-0.
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Affiliation(s)
- Maximilian Nepel
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria. .,Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Josephine Pfeifer
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Felix B Oberhauser
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Veronika E Mayer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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11
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Li Y, Lin H, Gao P, Yang N, Xu R, Sun X, Li B, Xu F, Wang X, Song B, Sun W. Variation in the diazotrophic community in a vertical soil profile contaminated with antimony and arsenic. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 291:118248. [PMID: 34592324 DOI: 10.1016/j.envpol.2021.118248] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
A nitrogen (N) deficiency will usually hinder bioremediation efforts in mining-derived habitats such as occurring in mining regions. Diazotrophs can provide N to support the growth of plants and microorganisms in these environments. However, diazotrophic communities in mining areas have been not studied frequently and are more poorly understood than those in other environments, such as in agricultural soils or in the presence of legumes. The current study compares the differences in depth-resolved diazotrophic community compositions and interactions in two contrasting sites (to depths of 2 m), including a highly contaminated and a moderately contaminated site. Antimony (Sb) and arsenic (As) co-contamination induced a loosely connected biotic interaction, and a selection of deep soils by diazotrophic communities. Multiple lines of evidence, including the enrichment of diazotrophic taxa in the highly contaminated sites, microbe-microbe interactions, environment-microbe interactions, and a machine learning approach (random forests regression), demonstrated that Rhizobium was the keystone taxon within the vertical profile of contaminated soil and was resistant to the Sb and As contaminant fractions. All of these observations suggest that one diazotroph, Rhizobium, may play an important role in N fixation in the examined contaminated sites.
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Affiliation(s)
- Yongbin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Hanzhi Lin
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; College of Environmental Science and Engineering, Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, Donghua University, Shanghai, 201620, China
| | - Nie Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Fuqing Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Xiaoyu Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Benru Song
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; School of Environment, Henan Normal University, China; Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, China.
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12
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Long J, Luo W, Xie J, Yuan Y, Wang J, Kang L, Li Y, Zhang Z, Hong M. Environmental Factors Influencing Phyllosphere Bacterial Communities in Giant Pandas' Staple Food Bamboos. Front Microbiol 2021; 12:748141. [PMID: 34803968 PMCID: PMC8595598 DOI: 10.3389/fmicb.2021.748141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
The giant panda has developed a series of evolutionary strategies to adapt to a bamboo diet. The abundance and diversity of the phyllosphere microbiome change dramatically depending on the season, host species, location, etc., which may, in turn, affect the growth and health of host plants. However, few studies have investigated the factors that influence phyllosphere bacteria in bamboo, a staple food source of the giant panda. Amplicon sequencing of the 16S rRNA gene was used to explore the abundance and diversity of phyllosphere bacteria in three bamboo species (Arundinaria spanostachya, Yushania lineolate, and Fargesia ferax) over different seasons (spring vs. autumn), elevation, distance from water, etc., in Liziping National Nature Reserve (Liziping NR), China. And whole-genome shotgun sequencing uncovered the differences in biological functions (KEGG and Carbohydrate-Active enzymes functions) of A. spanostachya phyllosphere bacteria between spring and autumn. The results showed that the abundance and diversity of F. ferax phyllosphere bacteria were greater than that of the other two bamboo species in both seasons. And three kinds of bamboo phyllosphere bacteria in autumn were significantly higher than in spring. The season was a more important factor than host bamboo species in determining the community structure of phyllosphere bacteria based on the (un)weighted UniFrac distance matrix. The composition, diversity, and community structure of phyllosphere bacteria in bamboo were primarily affected by the season, species, altitude, tree layer, and shrub layer. Different bacterial communities perform different functions in different bamboo species, and long-term low temperatures may shape more varied and complex KEGG and Carbohydrate-Active enzymes functions in spring. Our study presented a deeper understanding of factors influencing the bacterial community in the bamboo phyllosphere. These integrated results offer an original insight into bamboo, which can provide a reference for the restoration and management of giant panda bamboo food resources in the Xiaoxiangling mountains.
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Affiliation(s)
- Juejie Long
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China.,Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Wei Luo
- Liziping National Nature Reserve Administration, Ya'an, China
| | - Jianmei Xie
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China.,Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Yuan Yuan
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China.,Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Jia Wang
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China.,Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Liwen Kang
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China.,Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Yi Li
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China.,Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Zejun Zhang
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China.,Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Mingsheng Hong
- Liziping Giant Panda's Ecology and Conservation Observation and Research Station of Sichuan Province (Science and Technology Department of Sichuan Province), China West Normal University, Nanchong, China.,Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
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13
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Truong H, Garmyn D, Gal L, Fournier C, Sevellec Y, Jeandroz S, Piveteau P. Plants as a realized niche for Listeria monocytogenes. Microbiologyopen 2021; 10:e1255. [PMID: 34964288 PMCID: PMC8710918 DOI: 10.1002/mbo3.1255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/09/2021] [Accepted: 11/18/2021] [Indexed: 12/27/2022] Open
Abstract
Listeria monocytogenes is a human pathogen. It is the causative agent of listeriosis, the leading cause of bacterial-linked foodborne mortality in Europe and elsewhere. Outbreaks of listeriosis have been associated with the consumption of fresh produce including vegetables and fruits. In this review we summarize current data providing direct or indirect evidence that plants can serve as habitat for L. monocytogenes, enabling this human pathogen to survive and grow. The current knowledge of the mechanisms involved in the interaction of this bacterium with plants is addressed, and whether this foodborne pathogen elicits an immune response in plants is discussed.
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Affiliation(s)
- Hoai‐Nam Truong
- Agroécologie, AgroSup Dijon, CNRS, INRAEUniversity Bourgogne Franche‐ComtéDijonFrance
| | - Dominique Garmyn
- Agroécologie, AgroSup Dijon, CNRS, INRAEUniversity Bourgogne Franche‐ComtéDijonFrance
| | - Laurent Gal
- Agroécologie, AgroSup Dijon, CNRS, INRAEUniversity Bourgogne Franche‐ComtéDijonFrance
| | - Carine Fournier
- Agroécologie, AgroSup Dijon, CNRS, INRAEUniversity Bourgogne Franche‐ComtéDijonFrance
| | - Yann Sevellec
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Laboratory for Food Safety, Salmonella and Listeria UnitParis‐Est UniversityMaisons‐AlfortCedexFrance
| | - Sylvain Jeandroz
- Agroécologie, AgroSup Dijon, CNRS, INRAEUniversity Bourgogne Franche‐ComtéDijonFrance
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14
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Rodríguez-Rodríguez RM, Guimarães AA, de Castro JL, Siqueira JO, Carneiro MAC, de Souza Moreira FM. Rhizobia and endophytic bacteria isolated from rainforest fragments within an iron ore mining site of the Eastern Brazilian Amazon. Braz J Microbiol 2021; 52:1461-1474. [PMID: 34142357 PMCID: PMC8324639 DOI: 10.1007/s42770-021-00524-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 05/08/2021] [Indexed: 11/29/2022] Open
Abstract
The aim of the present study was to isolate and evaluate the diversity of rhizobial and endophytic bacterial strains from undisturbed native rainforests within an iron ore mining site of the Serra Norte de Carajás in the Eastern Brazilian Amazon region to assess their biotechnological utility in reclamation of areas. Experiments were conducted to capture strains from samples of the soil of these forests at the sites Arenito II, Noroeste II, and Sul IV using Macroptilium atropurpureum and Mimosa acutistipula var. ferrea as trap host plants. Only M. atropurpureum nodulated, and the different bacterial strains were isolated from its nodules. There was no difference in the number of nodules among the areas, but the Arenito II bacterial community was the most efficient, indicated by the aboveground biomass production and suitable shoot mass/root mass ratio. Fifty-two (52) bacterial isolates were obtained, distributed in five groups, including nodulating and endophytic bacteria: 32 from Arenito II, 12 from Noroeste II, and 8 from Sul IV. The nodulating Bradyrhizobium genus was common to the three areas, whereas Paraburkholderia was found only in Arenito II. The nodD1 gene was amplified in all the strains of both nodulating genera. Strains of the nodulating genus Methylobacterium were also isolated from the three areas; however, they did not nodulate the host of origin, and their nodD1 gene was not amplified. Endophytic strains were also isolated from the genera Paenibacillus, Pantoea, and Leifsonia in Arenito II, Leifsonia in Noroeste I, and Paenibacillus in Sul IV. The greater nodulation and rhizobial and endophytic bacterial diversity observed in Arenito II were probably due to the more suitable edaphic properties of the area. The isolated strains were incorporated in the collection of the Department of Soil Science of UFLA and will be investigated in relation to their symbiotic characteristics with native host plants, as well as their ability to perform other biological processes.
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Affiliation(s)
- Raquel Milagros Rodríguez-Rodríguez
- Departamento de Biofertilizantes Y Nutrición de Las Plantas, Instituto Nacional de Ciencias Agrícolas (INCA), San José de Las Lajas, Mayabeque, Cuba
- Departamento de Ciência Do Solo, Universidade Federal de Lavras (DCS-UFLA), Lavras, MG, Brazil
| | | | - Jordana Luísa de Castro
- Departamento de Ciência Do Solo, Universidade Federal de Lavras (DCS-UFLA), Lavras, MG, Brazil
| | - José Oswaldo Siqueira
- Departamento de Ciência Do Solo, Universidade Federal de Lavras (DCS-UFLA), Lavras, MG, Brazil
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15
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Ke M, Ye Y, Li Y, Zhou Z, Xu N, Feng L, Zhang J, Lu T, Cai Z, Qian H. Leaf metabolic influence of glyphosate and nanotubes on the Arabidopsis thaliana phyllosphere. J Environ Sci (China) 2021; 106:66-75. [PMID: 34210440 DOI: 10.1016/j.jes.2021.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/06/2021] [Accepted: 01/06/2021] [Indexed: 06/13/2023]
Abstract
Chemical exposure can indirectly affect leaf microbiota communities, but the mechanism driving this phenomenon remains largely unknown. Results revealed that the co-exposure of glyphosate and multi-carbon nanotubes (CNTs) caused a synergistic inhibitory effect on the growth and metabolism of Arabidopsis thaliana shoots. However, only a slight inhibitory effect was induced by nanotubes or glyphosate alone at the tested concentrations. Several intermediate metabolites of nitrogen metabolism and fatty acid synthesis pathways were upregulated under the combined treatment, which increased the amount of energy required to alleviate the disruption caused by the combined treatment. Additionally, compared with the two individual treatments, the glyphosate/nanotube combination treatment induced greater fluctuations in the phyllosphere bacterial community members with low abundance (relative abundance (RA) <1%) at both the family and genus levels, and among these bacteria some plant growth promotion and nutrient supplement related bacteria were markable increased. Strikingly, strong correlations between phyllosphere bacterial diversity and metabolites suggested a potential role of leaf metabolism, particularly nitrogen and carbohydrate metabolism, in restricting the range of leaf microbial taxa. These correlations between phyllosphere bacterial diversity and leaf metabolism will improve our understanding of plant-microbe interactions and the extent of their drivers of variation and the underlying causes of variability in bacterial community composition.
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Affiliation(s)
- Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yizhi Ye
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yan Li
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhigao Zhou
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Lan Feng
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Jinfeng Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhiqiang Cai
- Laboratory of Applied Microbiology and Biotechnology, School of Pharmaceutical Engineering & Life Science, Changzhou University, Changzhou 213164, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
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16
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Saifuddin M, Bhatnagar JM, Phillips RP, Finzi AC. Ectomycorrhizal fungi are associated with reduced nitrogen cycling rates in temperate forest soils without corresponding trends in bacterial functional groups. Oecologia 2021; 196:863-875. [PMID: 34170396 DOI: 10.1007/s00442-021-04966-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 06/09/2021] [Indexed: 11/30/2022]
Abstract
Microbial processes play a central role in controlling the availability of N in temperate forests. While bacteria, archaea, and fungi account for major inputs, transformations, and exports of N in soil, relationships between microbial community structure and N cycle fluxes have been difficult to detect and characterize. Several studies have reported differences in N cycling based on mycorrhizal type in temperate forests, but associated differences in N cycling genes underlying these fluxes are not well-understood. We explored how rates of soil N cycle fluxes vary across gradients of mycorrhizal abundance (hereafter "mycorrhizal gradients") at four temperate forest sites in Massachusetts and Indiana, USA. We paired measurements of N-fixation, net nitrification, and denitrification rates with gene abundance data for specific bacterial functional groups associated with each process. We find that the availability of NO3 and rates of N-fixation, net nitrification, and denitrification are reduced in stands dominated by trees associated with ECM fungi. On average, rates of N-fixation and denitrification in stands dominated by trees associated with arbuscular mycorrhizal fungi were more than double the corresponding rates in stands dominated by trees associated with ectomycorrhizal fungi. Despite the structuring of flux rates across the mycorrhizal gradients, we did not find concomitant shifts in the abundances of N-cycling bacterial genes, and gene abundances were not correlated with process rates. Given that AM-associating trees are replacing ECM-associating trees throughout much of the eastern US, our results suggest that shifts in mycorrhizal dominance may accelerate N cycling independent of changes in the relative abundance of N cycling bacteria, with consequences for forest productivity and N retention.
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17
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Moreira JCF, Brum M, de Almeida LC, Barrera-Berdugo S, de Souza AA, de Camargo PB, Oliveira RS, Alves LF, Rosado BHP, Lambais MR. Asymbiotic nitrogen fixation in the phyllosphere of the Amazon forest: Changing nitrogen cycle paradigms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 773:145066. [PMID: 33582326 DOI: 10.1016/j.scitotenv.2021.145066] [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: 10/19/2020] [Revised: 01/06/2021] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
Biological nitrogen fixation is a key process for the maintenance of natural ecosystems productivity. In tropical forests, the contribution of asymbiotic nitrogen fixation (ANF) to the nitrogen (N) input has been underestimated, even though few studies have shown that ANF may be as important as symbiotic nitrogen fixation in such environments. The inputs and abiotic modulators of ANF in the Amazon forest are not completely understood. Here, we determined ANF rates and estimated the N inputs from ANF in the phyllosphere, litter and rhizospheric soil of nine tree species in the Amazon forest over time, including an extreme drought period induced by the El Niño-Southern Oscillation. Our data showed that ANF rates in the phyllosphere were 2.8- and 17.6-fold higher than in the litter and rhizospheric soil, respectively, and was highly dependent on tree taxon. Sampling time was the major factor modulating ANF in all forest compartments. At the driest period, ANF rates were approximately 1.8-fold and 13.1-fold higher than at periods with higher rainfall, before and after the extreme drought period, respectively. Tree species was a key modulator of ANF in the phyllosphere, as well as N and Vanadium concentrations. Carbon, molybdenum and vanadium concentrations were significant modulators of ANF in the litter. Based on ANF rates at the three sampling times, we estimated that the N input in the Amazon forest through ANF in the phyllosphere, litter and rhizospheric soil, was between 0.459 and 0.714 kg N ha-1 yr-1. Our results highlight the importance of ANF in the phyllosphere for the N input in the Amazon forest, and suggest that changes in the patterns of ANF driven by large scale climatic events may impact total N inputs and likely alter forest productivity.
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Affiliation(s)
| | - Mauro Brum
- Department of Plant Biology, Programa de Pós Graduação em Ecologia, Institute of Biology, State University of Campinas -UNICAMP, PO Box 6109, 13083-970 Campinas, SP, Brazil
| | - Lidiane Cordeiro de Almeida
- Department of Ecology, IBRAG, Rio de Janeiro State University (UERJ), R. São Francisco Xavier, 524, PHLC, Sala 220, Maracanã, Rio de Janeiro, RJ, Brazil
| | - Silvia Barrera-Berdugo
- Soil Science Department, University of São Paulo, Av. Pádua Dias 11, 13418-900 Piracicaba, SP, Brazil
| | - André Alves de Souza
- Soil Science Department, University of São Paulo, Av. Pádua Dias 11, 13418-900 Piracicaba, SP, Brazil
| | - Plínio Barbosa de Camargo
- Center for Nuclear Energy in Agriculture, University of São Paulo, 303 Centenário Avenue, Piracicaba, SP 13400-970, Brazil
| | - Rafael Silva Oliveira
- Department of Plant Biology, Programa de Pós Graduação em Ecologia, Institute of Biology, State University of Campinas -UNICAMP, PO Box 6109, 13083-970 Campinas, SP, Brazil
| | - Luciana Ferreira Alves
- Department of Plant Biology, Programa de Pós Graduação em Ecologia, Institute of Biology, State University of Campinas -UNICAMP, PO Box 6109, 13083-970 Campinas, SP, Brazil
| | - Bruno Henrique Pimentel Rosado
- Department of Ecology, IBRAG, Rio de Janeiro State University (UERJ), R. São Francisco Xavier, 524, PHLC, Sala 220, Maracanã, Rio de Janeiro, RJ, Brazil
| | - Marcio Rodrigues Lambais
- Soil Science Department, University of São Paulo, Av. Pádua Dias 11, 13418-900 Piracicaba, SP, Brazil.
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18
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Liu L, Lu L, Li H, Meng Z, Dong T, Peng C, Xu X. Divergence of Phyllosphere Microbial Communities Between Females and Males of the Dioecious Populus cathayana. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:351-361. [PMID: 33290085 DOI: 10.1094/mpmi-07-20-0178-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, the differentiation of phyllosphere microbiota in dioecious plants remains largely unexplored. Here, the diversity and composition of female and male Populus cathayana phyllosphere bacterial and fungal communities were investigated using 16S rRNA/ITS1 gene-based MiSeq sequencing. The divergences of bacterial and fungal community compositions occurred between females and males. Both females and males had their unique phyllosphere bacterial and fungal microbiota, such as bacterial Gemmata spp. (5.41%) and fungal Pringsheimia spp. (0.03%) in females and bacterial Chitinophaga spp. (0.009%) and fungal Phaeococcomyces spp. (0.02%) in males. Significant differences in the relative abundance of phyla Proteobacteria and Planctomycetes bacteria and phyla Ascomycota and Basidiomycota fungi (P < 0.05) were also found between females and males. Some bacterial species of genera Spirosoma and Amnibacterium and fungal genera Venturia, Suillus, and Elmerina spp. were significantly enriched in males (P < 0.05). In contrast, levels of fungal genera Phoma and Aureobasidium spp. were significantly higher in females than in males (P < 0.05). The mineral, inorganic, and organic nutrients content contributed differently to the divergence of female and male phyllosphere microbial communities, with 87.08 and 45.17% of the variations being explained for bacterial and fungal communities, respectively. These results highlight the sexual discrimination of phyllosphere microbes on the dioecious plants and provide hints on the potential host-associated species in phyllosphere environments.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Liling Liu
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
- Institute of Ecology, China West Normal University, Nanchong 637009, China
| | - Lu Lu
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
| | - Huilin Li
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Zhensi Meng
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Tingfa Dong
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Chao Peng
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong 637002, China
| | - Xiao Xu
- Key Laboratory of Southwest China Wildlife Resources Conservation, College of Life Sciences, China West Normal University, Nanchong 637002, China
- Institute of Ecology, China West Normal University, Nanchong 637009, China
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19
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Gao H, Li S, Wu F. Impact of Intercropping on the Diazotrophic Community in the Soils of Continuous Cucumber Cropping Systems. Front Microbiol 2021; 12:630302. [PMID: 33868191 PMCID: PMC8044418 DOI: 10.3389/fmicb.2021.630302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/08/2021] [Indexed: 11/19/2022] Open
Abstract
Diazotrophs are important soil components that help replenish biologically available nitrogen (N) in the soil and contribute to minimizing the use of inorganic N fertilizers in agricultural ecosystems. However, there is little understanding of how diazotrophs respond to intercropping and soil physicochemical properties in cucumber continuous cropping systems. In this study, using the nifH gene as a marker, we have examined the impacts of seven intercropping plants on diazotrophic community diversity and composition compared to a cucumber continuous cropping system during two cropping seasons. The results showed that intercropping increased the abundance of the nifH gene, which was negatively correlated with available phosphorous in the fall. Diazotrophic diversity and richness were higher in the rape-cucumber system than in the monoculture. Multivariate regression tree analysis revealed that the diversity of the diazotrophic communties was shaped mainly by soil moisture and available phosphorous. Skermanella were the dominant genera in all of the samples, which increased significantly in the mustard-cucumber system in the fall. There was no effect of intercropping on the structure of the diazotrophic community in this case. Non-metric multidimensional scaling analysis showed that cropping season had a greater effect than intercropping on the community structure of the diazotrophs. Overall, our results suggest that intercropping altered the abundance and diversity rather than the structure of the diazotrophic community, which may potentially affect the N fixation ability of continuous cropping systems.
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Affiliation(s)
- Huan Gao
- Department of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China
| | - Sen Li
- Department of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China
| | - Fengzhi Wu
- Department of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, China
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20
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Seasonal and long-term effects of nutrient additions and liming on the nifH gene in cerrado soils under native vegetation. iScience 2021; 24:102349. [PMID: 33870141 PMCID: PMC8044383 DOI: 10.1016/j.isci.2021.102349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/02/2020] [Accepted: 03/18/2021] [Indexed: 11/20/2022] Open
Abstract
Biological nitrogen fixation (BNF) represents the main input source of N in tropical savannas. BNF could be particularly important for Brazilian savannas (known as Cerrado) that show a highly conservative N cycle. We evaluated the effects of seasonal precipitation and nutrient additions on the nifH gene abundance in soils from a long-term fertilization experiment in a Cerrado's native area. The experiment consists of five treatments: (1) control, (2) liming, (3) nitrogen (N), (4) nitrogen + phosphorus (NP), and (5) phosphorus (P) additions. The nifH gene sequence was related to Bradyrhizobium members. Seasonal effects on N-fixing potential were observed by a decrease in the nifH relative abundance from rainy to dry season in control, N, and NP treatments. A significant reduction in nifH abundance was found in the liming treatment in both seasons. The findings evidenced the multiple factors controlling the potential N-fixing by free-living diazotrophs in these nutrient-limited and seasonally dry ecosystems.
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21
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Wu C, Wei X, Hu Z, Liu Y, Hu Y, Qin H, Chen X, Wu J, Ge T, Zhran M, Su Y. Diazotrophic Community Variation Underlies Differences in Nitrogen Fixation Potential in Paddy Soils Across a Climatic Gradient in China. MICROBIAL ECOLOGY 2021; 81:425-436. [PMID: 32901387 DOI: 10.1007/s00248-020-01591-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/28/2020] [Indexed: 06/11/2023]
Abstract
Biological nitrogen (N2) fixation as a source of new N input into the soil by free-living diazotrophs is important for achieving sustainable rice agriculture. However, the dominant environmental drivers or factors influencing N2 fixation and the functional significance of the diazotroph community structure in paddy soil across a climatic gradient are not yet well understood. Thus, we characterized the diazotroph community and identified the ecological predictors of N2 fixation potential in four different climate zones (mid-temperate, warm-temperate, subtropical, and tropical paddy soils) in eastern China. Comprehensive nifH gene sequencing, functional activity detection, and correlation analysis with environmental factors were estimated. The potential nitrogenase activity (PNA) was highest in warm-temperate regions, where it was 6.2-, 2.9-, and 2.2-fold greater than in the tropical, subtropical, and mid-temperate regions, respectively; nifH gene abundance was significantly higher in warm-temperate and subtropical zones than in the tropical or mid-temperate zones. Diazotroph diversity was significantly higher in the tropical climate zone and significantly lower in the mid-temperate zone. Non-metric multidimensional scaling and canonical correlation analysis indicated that paddy soil diazotroph populations differed significantly among the four climate zones, mainly owing to differences in climate and soil pH. Structural equation models and automatic linear models revealed that climate and nutrients indirectly affected PNA by affecting soil pH and diazotroph community, respectively, while diazotroph community, C/P, and nifH gene abundance directly affected PNA. And C/P ratio, pH, and the diazotroph community structure were the main predictors of PNA in paddy soils. Collectively, the differences in diazotroph community structure have ecological significance, with important implications for the prediction of soil N2-fixing functions under climate change scenarios.
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Affiliation(s)
- Chuanfa Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Xiaomeng Wei
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ziye Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yi Liu
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China.
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Taoyuan Agro-ecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China.
| | - Yajun Hu
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Hongling Qin
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
- Key Laboratory of Agro-ecological Processes in Subtropical Regions, Taoyuan Agro-ecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Xiangbi Chen
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Jinshui Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tida Ge
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
| | - Mostafa Zhran
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
- Soil and Water Research Department, Nuclear Research Center, Atomic Energy Authority, Abou-Zaabl, 13759, Egypt
| | - Yirong Su
- Key Laboratory of Agro-ecological Processes in Subtropical Region & Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China.
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22
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Herrmann M, Geesink P, Richter R, Küsel K. Canopy Position Has a Stronger Effect than Tree Species Identity on Phyllosphere Bacterial Diversity in a Floodplain Hardwood Forest. MICROBIAL ECOLOGY 2021; 81:157-168. [PMID: 32761502 PMCID: PMC7794210 DOI: 10.1007/s00248-020-01565-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 07/27/2020] [Indexed: 05/17/2023]
Abstract
The phyllosphere is a challenging microbial habitat in which microorganisms can flourish on organic carbon released by plant leaves but are also exposed to harsh environmental conditions. Here, we assessed the relative importance of canopy position-top, mid, and bottom at a height between 31 and 20 m-and tree species identity for shaping the phyllosphere microbiome in a floodplain hardwood forest. Leaf material was sampled from three tree species-maple (Acer pseudoplatanus L.), oak (Quercus robur L.), and linden (Tilia cordata MILL.)-at the Leipzig canopy crane facility (Germany). Estimated bacterial species richness (Chao1) and bacterial abundances approximated by quantitative PCR of 16S rRNA genes exhibited clear vertical trends with a strong increase from the top to the mid and bottom position of the canopy. Thirty operational taxonomic units (OTUs) formed the core microbiome, which accounted for 77% of all sequence reads. These core OTUs showed contrasting trends in their vertical distribution within the canopy, pointing to different ecological preferences and tolerance to presumably more extreme conditions at the top position of the canopy. Co-occurrence analysis revealed distinct tree species-specific OTU networks, and 55-57% of the OTUs were unique to each tree species. Overall, the phyllosphere microbiome harbored surprisingly high fractions of Actinobacteria of up to 66%. Our results clearly demonstrate strong effects of the position in the canopy on phyllosphere bacterial communities in a floodplain hardwood forest and-in contrast to other temperate or tropical forests-a strong predominance of Actinobacteria.
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Affiliation(s)
- Martina Herrmann
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
| | - Patricia Geesink
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743, Jena, Germany
| | - Ronny Richter
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
- Systematic Botany and Functional Biodiversity, Institute for Biology, Leipzig University, Johannisallee 21, 04103, Leipzig, Germany
- Geoinformatics and Remote Sensing, Institute of Geography, Leipzig University, Johannisallee 19a, 04103, Leipzig, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Dornburger Strasse 159, D-07743, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany
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23
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Reis CRG, Pacheco FS, Reed SC, Tejada G, Nardoto GB, Forti MC, Ometto JP. Biological nitrogen fixation across major biomes in Latin America: Patterns and global change effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:140998. [PMID: 32763600 DOI: 10.1016/j.scitotenv.2020.140998] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 06/11/2023]
Abstract
Biological nitrogen fixation (BNF) supports terrestrial primary productivity and plays key roles in mediating human-induced changes in global nitrogen (N) and carbon cycling. However, there are still critical uncertainties in our understanding of the amount of BNF occurring across terrestrial ecosystems, and of how terrestrial BNF will respond to global change. We synthesized BNF data from Latin America, a region reported to sustain some of the highest BNF rates on Earth, but that is underrepresented in previous data syntheses. We used meta-analysis and modeling approaches to estimate BNF rates across Latin America's major biomes and to evaluate the potential effects of increased N deposition and land-use change on these rates. Unmanaged tropical and subtropical moist forests sustained observed and predicted total BNF rates of 10 ± 1 and 14 ± 1 kg N ha-1 y-1, respectively, supporting the hypothesis that these forests sustain lower BNF rates than previously thought. Free-living BNF accounted for two-thirds of the total BNF in these forests. Despite an average 30% reduction of free-living BNF in response to experimental N-addition, our results suggest free-living BNF rate responses to current and projected N deposition across tropical and subtropical moist forests are small. In contrast, the conversion of unmanaged ecosystems to crop and pasture lands increased BNF rates across all terrestrial biomes, mostly in savannas, grasslands, and dry forests, increasing BNF rates 2-fold. The information obtained here provides a more comprehensive understanding of BNF patterns for Latin America.
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Affiliation(s)
- Carla R G Reis
- Center for Earth System Science, National Institute for Space Research (INPE), Av. dos Astronautas 1758, São José dos Campos, São Paulo 12227-010, Brazil.
| | - Felipe S Pacheco
- Center for Earth System Science, National Institute for Space Research (INPE), Av. dos Astronautas 1758, São José dos Campos, São Paulo 12227-010, Brazil
| | - Sasha C Reed
- U.S. Geological Survey, Southwest Biological Science Center, 2290, S.W. Resource Blvd, Moab, UT 84532, USA
| | - Graciela Tejada
- Center for Earth System Science, National Institute for Space Research (INPE), Av. dos Astronautas 1758, São José dos Campos, São Paulo 12227-010, Brazil
| | - Gabriela B Nardoto
- Department of Ecology, Campus Darcy Ribeiro, University of Brasilia, Brasilia, Federal District 70910-900, Brazil
| | - Maria C Forti
- Center for Earth System Science, National Institute for Space Research (INPE), Av. dos Astronautas 1758, São José dos Campos, São Paulo 12227-010, Brazil
| | - Jean P Ometto
- Center for Earth System Science, National Institute for Space Research (INPE), Av. dos Astronautas 1758, São José dos Campos, São Paulo 12227-010, Brazil
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24
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Stuart JEM, Holland-Moritz H, Lewis LR, Jean M, Miller SN, McDaniel SF, Fierer N, Ponciano JM, Mack MC. Host Identity as a Driver of Moss-Associated N2 Fixation Rates in Alaska. Ecosystems 2020. [DOI: 10.1007/s10021-020-00534-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Liu X, Yang C, Yu X, Yu H, Zhuang W, Gu H, Xu K, Zheng X, Wang C, Xiao F, Wu B, He Z, Yan Q. Revealing structure and assembly for rhizophyte-endophyte diazotrophic community in mangrove ecosystem after introduced Sonneratia apetala and Laguncularia racemosa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 721:137807. [PMID: 32179356 DOI: 10.1016/j.scitotenv.2020.137807] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 06/10/2023]
Abstract
Biological nitrogen fixation (BNF) mediated by diazotrophic communities is a major source of bioavailable nitrogen in mangrove wetlands, which plays important roles in maintaining the health and stability of mangrove ecosystems. Recent large-scale mangrove afforestation activities have drawn great attention due to introduced mangrove species and their potential impacts on bio-functionalities of local ecosystems. However, the effects of introduced mangrove species on diazotrophic communities remain unclear. Here, we analyzed rhizosphere and endosphere diazotrophic communities between native mangrove species (Avicennia marina) and introduced mangrove species (Sonneratia apetala and Laguncularia racemose) by sequencing nifH gene amplicons. Our results showed that S. apetala and L. racemose introduction significantly (P < 0.05) increased nutrition components (e.g., total carbon and total nitrogen) in rhizosphere, as well as the diazotrophs richness in rhizosphere and endosphere. The relative abundance of clusters III diazotrophs in the rhizosphere and Rhizobium in the endosphere were significantly increased with L. racemosa or S. apetala introduction. Fe and pH were the main environmental factors driving the divergence of endophyte-rhizophyte diazotrophs between native and introduced mangroves. The correlation-based network analyses indicated that the interaction among rhizophyte-endophyte diazotrophs is more harmonious in native mangrove, while there exist more competition in introduced mangroves. These findings expand our current understanding of BNF in mangrove afforestation, and providing new perspectives to sustainable management of mangrove ecosystem.
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Affiliation(s)
- Xingyu Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Chao Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Huang Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Wei Zhuang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Hang Gu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Kui Xu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Cheng Wang
- South China Sea Institution, Sun Yat-sen University, Zhuhai 519082, China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Bo Wu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China; South China Sea Institution, Sun Yat-sen University, Zhuhai 519082, China; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
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26
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Diazotrophs Show Signs of Restoration in Amazon Rain Forest Soils with Ecosystem Rehabilitation. Appl Environ Microbiol 2020; 86:AEM.00195-20. [PMID: 32169937 DOI: 10.1128/aem.00195-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/08/2020] [Indexed: 11/20/2022] Open
Abstract
Biological nitrogen fixation can be an important source of nitrogen in tropical forests that serve as a major CO2 sink. Extensive deforestation of the Amazon is known to influence microbial communities and the biogeochemical cycles they mediate. However, it is unknown how diazotrophs (nitrogen-fixing microorganisms) respond to deforestation and subsequent ecosystem conversion to agriculture, as well as whether they can recover in secondary forests that are established after agriculture is abandoned. To address these knowledge gaps, we combined a spatially explicit sampling approach with high-throughput sequencing of nifH genes. The main objectives were to assess the functional distance decay relationship of the diazotrophic bacterial community in a tropical forest ecosystem and to quantify the roles of various factors that drive the observed changes in the diazotrophic community structure. We observed an increase in local diazotrophic diversity (α-diversity) with a decrease in community turnover (β-diversity), associated with a shift in diazotrophic community structure as a result of the forest-to-pasture conversion. Both diazotrophic community turnover and structure showed signs of recovery in secondary forests. Changes in the diazotrophic community were primarily driven by the change in land use rather than differences in geochemical characteristics or geographic distances. The diazotroph communities in secondary forests resembled those in primary forests, suggesting that at least partial recovery of diazotrophs is possible following agricultural abandonment.IMPORTANCE The Amazon region is a major tropical forest region that is being deforested at an alarming rate to create space for cattle ranching and agriculture. Diazotrophs (nitrogen-fixing microorganisms) play an important role in supplying soil N for plant growth in tropical forests. It is unknown how diazotrophs respond to deforestation and whether they can recover in secondary forests that establish after agriculture is abandoned. Using high-throughput sequencing of nifH genes, we characterized the response of diazotrophs' β-diversity and identified major drivers of changes in diazotrophs from forest-to-pasture and pasture-to-secondary-forest conversions. Studying the impact of land use change on diazotrophs is important for a better understanding of the impact of deforestation on tropical forest ecosystem functioning, and our results on the potential recovery of diazotrophs in secondary forests imply the possible restoration of ecosystem functions in secondary forests.
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Schleuss PM, Widdig M, Heintz-Buschart A, Kirkman K, Spohn M. Interactions of nitrogen and phosphorus cycling promote P acquisition and explain synergistic plant-growth responses. Ecology 2020; 101:e03003. [PMID: 32020599 DOI: 10.1002/ecy.3003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 12/11/2019] [Accepted: 01/03/2020] [Indexed: 11/10/2022]
Abstract
Plant growth is often co-limited by nitrogen (N) and phosphorus (P). Plants might use one element to acquire another (i.e., trading N for P and P for N), which potentially explains synergistic growth responses to NP addition. We studied a 66-yr-old grassland experiment in South Africa that consists of four levels of N addition with and without P addition. We investigated the response of aboveground net primary production (ANPP) to N and P addition over the last 66 yr. Further, we tested whether phosphatase activity and plant P uptake depend on N availability, and vice versa, whether non-symbiotic N2 fixation and plant N uptake depend on P availability. We expected that the interaction of both elements promote processes of nutrient acquisition and contribute to synergistic plant growth effects in response to NP addition. We found synergistic N and P co-limitation of ANPP for the period from 1951 to 2017 but the response to N and P addition diminished over time. In 2017, aboveground P stocks, relative rRNA operon abundance of arbuscular mycorrhizal fungi, and soil organic P storage increased with N fertilization rate when N was added with P compared to the treatment in which only N was added. Further, N addition increased phosphatase activity, which indicates that plants used N to acquire P from organic sources. In contrast, aboveground N stocks and non-symbiotic N2 fixation did not change significantly due to P addition. Taken together, our results indicate that trading N for P likely contributes to synergistic plant-growth response. Plants used added N to mobilize and take up P from organic sources, inducing stronger recycling of P and making the plant community less sensitive to external nutrient inputs. The latter could explain why indications of synergistic co-limitation diminished over time, which is usually overlooked in short-term nutrient addition experiments.
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Affiliation(s)
- Per Marten Schleuss
- Department of Soil Biogeochemistry, Soil Ecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Meike Widdig
- Department of Soil Biogeochemistry, Soil Ecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Anna Heintz-Buschart
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany.,Bioinformatics Unit, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Kevin Kirkman
- Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Marie Spohn
- Department of Soil Biogeochemistry, Soil Ecology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
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28
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Lipa P, Janczarek M. Phosphorylation systems in symbiotic nitrogen-fixing bacteria and their role in bacterial adaptation to various environmental stresses. PeerJ 2020; 8:e8466. [PMID: 32095335 PMCID: PMC7020829 DOI: 10.7717/peerj.8466] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/27/2019] [Indexed: 12/23/2022] Open
Abstract
Symbiotic bacteria, commonly called rhizobia, lead a saprophytic lifestyle in the soil and form nitrogen-fixing nodules on legume roots. During their lifecycle, rhizobia have to adapt to different conditions prevailing in the soils and within host plants. To survive under these conditions, rhizobia fine-tune the regulatory machinery to respond rapidly and adequately to environmental changes. Symbiotic bacteria play an essential role in the soil environment from both ecological and economical point of view, since these bacteria provide Fabaceae plants (legumes) with large amounts of accessible nitrogen as a result of symbiotic interactions (i.e., rhizobia present within the nodule reduce atmospheric dinitrogen (N2) to ammonia, which can be utilized by plants). Because of its restricted availability in the soil, nitrogen is one of the most limiting factors for plant growth. In spite of its high content in the atmosphere, plants are not able to assimilate it directly in the N2 form. During symbiosis, rhizobia infect host root and trigger the development of specific plant organ, the nodule. The aim of root nodule formation is to ensure a microaerobic environment, which is essential for proper activity of nitrogenase, i.e., a key enzyme facilitating N2 fixation. To adapt to various lifestyles and environmental stresses, rhizobia have developed several regulatory mechanisms, e.g., reversible phosphorylation. This key mechanism regulates many processes in both prokaryotic and eukaryotic cells. In microorganisms, signal transduction includes two-component systems (TCSs), which involve membrane sensor histidine kinases (HKs) and cognate DNA-binding response regulators (RRs). Furthermore, regulatory mechanisms based on phosphoenolopyruvate-dependent phosphotranspherase systems (PTSs), as well as alternative regulatory pathways controlled by Hanks-type serine/threonine kinases (STKs) and serine/threonine phosphatases (STPs) play an important role in regulation of many cellular processes in both free-living bacteria and during symbiosis with the host plant (e.g., growth and cell division, envelope biogenesis, biofilm formation, response to stress conditions, and regulation of metabolism). In this review, we summarize the current knowledge of phosphorylation systems in symbiotic nitrogen-fixing bacteria, and their role in the physiology of rhizobial cells and adaptation to various environmental conditions.
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Affiliation(s)
- Paulina Lipa
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Sklodowska University Lublin, Lublin, Poland
| | - Monika Janczarek
- Department of Genetics and Microbiology, Institute of Biological Sciences, Maria Curie-Sklodowska University Lublin, Lublin, Poland
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Staccone A, Liao W, Perakis S, Compton J, Clark C, Menge D. A spatially explicit, empirical estimate of tree-based biological nitrogen fixation in forests of the United States. GLOBAL BIOGEOCHEMICAL CYCLES 2020; 42:10.1029/2019GB006241. [PMID: 32665747 PMCID: PMC7359885 DOI: 10.1029/2019gb006241] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 02/05/2020] [Indexed: 06/11/2023]
Abstract
Quantifying human impacts on the N cycle and investigating natural ecosystem N cycling depend on the magnitude of inputs from natural biological nitrogen fixation (BNF). Here, we present two bottom-up approaches to quantify tree-based symbiotic BNF based on forest inventory data across the coterminous US plus SE Alaska. For all major N-fixing tree genera, we quantify BNF inputs using (1) ecosystem N accretion rates (kg N ha-1 yr-1) scaled with spatial data on tree abundance and (2) percent of N derived from fixation (%Ndfa) scaled with tree N demand (from tree growth rates and stoichiometry). We estimate that trees fix 0.30-0.88 Tg N yr-1 across the study area (1.4-3.4 kg N ha-1 yr-1). Tree-based N fixation displays distinct spatial variation that is dominated by two genera, Robinia (64% of tree-associated BNF) and Alnus (24%). The third most important genus, Prosopis, accounted for 5%. Compared to published estimates of other N fluxes, tree-associated BNF accounted for 0.59 Tg N yr-1, similar to asymbiotic (0.37 Tg N yr-1) and understory symbiotic BNF (0.48 Tg N yr-1), while N deposition contributed 1.68 Tg N yr-1 and rock weathering 0.37 Tg N yr-1. Overall, our results reveal previously uncharacterized spatial patterns in tree BNF that can inform large-scale N assessments and serve as a model for improving tree-based BNF estimates worldwide. This updated, lower BNF estimate indicates a greater ratio of anthropogenic to natural N inputs, suggesting an even greater human impact on the N cycle.
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Affiliation(s)
- Anika Staccone
- Columbia University, Ecology, Evolution, and Environmental Biology Department
| | - Wenying Liao
- Princeton University, Department of Ecology and Evolutionary Biology
| | - Steven Perakis
- US Geological Survey Forest and Rangeland Ecosystem Science Center
| | - Jana Compton
- US EPA, Center for Public Health and Environmental Assessment
| | | | - Duncan Menge
- Columbia University, Ecology, Evolution, and Environmental Biology Department
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Van Langenhove L, Depaepe T, Vicca S, van den Berge J, Stahl C, Courtois E, Weedon J, Urbina I, Grau O, Asensio D, Peñuelas J, Boeckx P, Richter A, Van Der Straeten D, Janssens IA. Regulation of nitrogen fixation from free-living organisms in soil and leaf litter of two tropical forests of the Guiana shield. PLANT AND SOIL 2020; 450:93-110. [PMID: 32624623 PMCID: PMC7319290 DOI: 10.1007/s11104-019-04012-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 02/25/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Biological fixation of atmospheric nitrogen (N2) is the main pathway for introducing N into unmanaged ecosystems. While recent estimates suggest that free-living N fixation (FLNF) accounts for the majority of N fixed in mature tropical forests, the controls governing this process are not completely understood. The aim of this study was to quantify FLNF rates and determine its drivers in two tropical pristine forests of French Guiana. METHODS We used the acetylene reduction assay to measure FLNF rates at two sites, in two seasons and along three topographical positions, and used regression analyses to identify which edaphic explanatory variables, including carbon (C), nitrogen (N), phosphorus (P) and molybdenum (Mo) content, pH, water and available N and P, explained most of the variation in FLNF rates. RESULTS Overall, FLNF rates were lower than measured in tropical systems elsewhere. In soils seasonal variability was small and FLNF rates differed among topographies at only one site. Water, P and pH explained 24% of the variation. In leaf litter, FLNF rates differed seasonally, without site or topographical differences. Water, C, N and P explained 46% of the observed variation. We found no regulatory role of Mo at our sites. CONCLUSIONS Rates of FLNF were low in primary rainforest on poor soils on the Guiana shield. Water was the most important rate-regulating factor and FLNF increased with increasing P, but decreased with increasing N. Our results support the general assumption that N fixation in tropical lowland forests is limited by P availability.
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Affiliation(s)
- Leandro Van Langenhove
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Thomas Depaepe
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, KL Belgium
| | - Sara Vicca
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Joke van den Berge
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Clement Stahl
- INRA, UMR Ecology of Guiana Forests (Ecofog), AgroParisTech, Cirad, CNRS, Université des Antilles, Université de Guyane, 97387 Kourou, French Guiana
| | - Elodie Courtois
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, Wilrijk, Belgium
- Laboratoire Ecologie, évolution, interactions des systèmes amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, French Guiana, 97300 Cayenne, France
| | - James Weedon
- Department of Ecological Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Ifigenia Urbina
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08193 Bellaterra, Catalonia Spain
- CREAF, 08193 Cerdanyola del Vallès, Catalonia Spain
| | - Oriol Grau
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08193 Bellaterra, Catalonia Spain
- CREAF, 08193 Cerdanyola del Vallès, Catalonia Spain
| | - Dolores Asensio
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08193 Bellaterra, Catalonia Spain
- CREAF, 08193 Cerdanyola del Vallès, Catalonia Spain
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, 08193 Bellaterra, Catalonia Spain
- CREAF, 08193 Cerdanyola del Vallès, Catalonia Spain
| | - Pascal Boeckx
- Department of Applied Analytical and Physical Chemistry, Faculty of Bioscience Engineering, Isotope Bioscience Laboratory – ISOFYS, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ledeganckstraat 35, B-9000 Ghent, KL Belgium
| | - Ivan A. Janssens
- Centre of Excellence PLECO (Plants and Ecosystems), Department of Biology, University of Antwerp, Wilrijk, Belgium
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Suleiman MK, Quoreshi AM, Bhat NR, Manuvel AJ, Sivadasan MT. Divulging diazotrophic bacterial community structure in Kuwait desert ecosystems and their N2-fixation potential. PLoS One 2019; 14:e0220679. [PMID: 31877136 PMCID: PMC6932743 DOI: 10.1371/journal.pone.0220679] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 11/19/2019] [Indexed: 12/31/2022] Open
Abstract
Kuwait is a semi-arid region with soils that are relatively nitrogen-poor. Thus, biological nitrogen fixation is an important natural process in which N2-fixing bacteria (diazotrophs) convert atmospheric nitrogen into plant-usable forms such as ammonium and nitrate. Currently, there is limited information on free-living and root-associated nitrogen-fixing bacteria and their potential to fix nitrogen and aid natural plant communities in the Kuwait desert. In this study, free living N2-fixing diazotrophs were enriched and isolated from the rhizosphere soil associated with three native keystone plant species; Rhanterium epapposum, Farsetia aegyptia, and Haloxylon salicornicum. Root-associated bacteria were isolated from the root nodules of Vachellia pachyceras. The result showed that the strains were clustered in five groups represented by class: γ-proteobacteria, and α-proteobacteria; phyla: Actinobacteria being the most dominant, followed by phyla: Firmicutes, and class: β-proteobacteria. This study initially identified 50 nitrogen-fixers by16S rRNA gene sequencing, of which 78% were confirmed to be nitrogen-fixers using the acetylene reduction assay. Among the nitrogen fixers identified, the genus Rhizobium was predominant in the rhizosphere soil of R. epapposum and H. salicornicum, whereas Pseudomonas was predominant in the rhizosphere soil of F. aegyptia, The species Agrobacterium tumefaciens was mainly found to be dominant among the root nodules of V. pachyceras and followed by Cellulomonas, Bacillus, and Pseudomonas genera as root-associated bacteria. The variety of diazotrophs revealed in this study, signifying the enormous importance of free-living and root-associated bacteria in extreme conditions and suggesting potential ecological importance of diazotrophs in arid ecosystem. To our knowledge, this study is the first to use culture-based isolation, molecular identification, and evaluation of N2-fixing ability to detail diazotroph diversity in Kuwaiti desert soils.
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Affiliation(s)
- M. K. Suleiman
- Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - A. M. Quoreshi
- Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
- * E-mail:
| | - N. R. Bhat
- Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - A. J. Manuvel
- Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - M. T. Sivadasan
- Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
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Wang X, Hsu C, Dubeux JCB, Mackowiak C, Blount A, Han X, Liao H. Effects of rhizoma peanut cultivars ( Arachis glabrata Benth.) on the soil bacterial diversity and predicted function in nitrogen fixation. Ecol Evol 2019; 9:12676-12687. [PMID: 31788206 PMCID: PMC6875664 DOI: 10.1002/ece3.5735] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/25/2022] Open
Abstract
There is a growing awareness of the importance of soil microorganisms in agricultural management practices. Currently, much less is known about whether different crop cultivar has an effect on the taxonomic structure and diversity, and specific functions of soil bacterial communities. Here, we examined the changes of the diversity and composition and enzyme-encoding nitrogenase genes in a long-term field experiment with seven different rhizoma peanut cultivars in southeastern USA, coupling high-throughput 16S rRNA gene sequencing and the sequence-based function prediction with Tax4Fun. Of the 32 phyla detected (Proteobacteria class), 13 were dominant: Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Deltaproteobacteria, Gemmatimonadetes, Firmicutes, Nitrospirae, Chloroflexi, and Planctomycetes (relative abundance >1%). We found no evidence that the diversity and composition of bacterial communities were significantly different among different cultivars, but the abundance of some dominant bacterial groups that have N-fixation potentials (at broad or fine taxonomic level) and predicted abundances of some enzyme-encoding nitrogenase genes showed significant across-cultivar differences. The nitrogenase genes were notably abundant in Florigraze and Latitude soils while remarkably lower in Arbook and UF_TITO soils when compared with other cultivars, indicating different nitrogen fixation potentials among different cultivars. The findings also suggest that the abundance of certain bacterial taxa and the specific function bacteria perform in ecosystems can have an inherent association. Our study is helpful to understand how microbiological responses and feedback to different plant genotypes through the variation in structure and function of their communities in the rhizosphere.
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Affiliation(s)
- Xiao‐Bo Wang
- North Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
- Erguna Forest‐Steppe Ecotone Research StationInstitute of Applied EcologyChinese Academy of SciencesShenyangChina
- Key Laboratory of Vegetation EcologyMinistry of EducationNortheast Normal UniversityChangchunChina
| | - Chih‐Ming Hsu
- North Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
| | - José C. B. Dubeux
- North Florida Research and Education CenterUniversity of FloridaMariannaFLUSA
| | - Cheryl Mackowiak
- North Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
| | - Ann Blount
- North Florida Research and Education CenterUniversity of FloridaMariannaFLUSA
| | - Xing‐Guo Han
- Erguna Forest‐Steppe Ecotone Research StationInstitute of Applied EcologyChinese Academy of SciencesShenyangChina
- Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Hui‐Ling Liao
- North Florida Research and Education CenterUniversity of FloridaQuincyFLUSA
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Li Y, Sun H, Wu Z, Li H, Sun Q. Urban traffic changes the biodiversity, abundance, and activity of phyllospheric nitrogen-fixing bacteria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:16097-16104. [PMID: 30968298 DOI: 10.1007/s11356-019-05008-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/26/2019] [Indexed: 06/09/2023]
Abstract
The phyllosphere provides appropriate conditions for colonization by microorganisms, including diazotrophic bacteria. However, a poor understanding of the effects of the atmospheric environment on the phyllospheric diazotrophic communities persists. We detected the biodiversity, abundance, and activity of nitrogen-fixing bacteria in the phyllospheres of two evergreen shrubs, Nerium indicum Mill. and Osmanthus sp., sampled from urban areas with heavy traffic, a college campus, and a forest. Quantitative PCR analysis indicated that the copy numbers of nifH sequences were highest in the phyllospheres of both plants in heavy-traffic urban areas and correlated with the recorded nitrogenase activities of the phyllospheres. Similarly, the phyllosphere from heavy-traffic urban areas also possessed the highest biodiversity indices of diazotrophic communities from both the two plants. Pyrosequencing analysis revealed a diversity of nifH sequences in phyllosphere that were mostly uniquely found in the phyllosphere, and many of these were proteobacteria-like and cyanobacteria-like. Members of the Proteobacteria, mostly of which were not closely related to unknown organisms, were detected exclusively in the phyllosphere and represented substantial fractions of their associated diazotrophic communities. Our study provides initial insight into the shifts in the biodiversity and community structure of N2-fixing microorganisms in the phyllospheres of different atmospheric environments.
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Affiliation(s)
- Yang Li
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Hong Sun
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zhaojun Wu
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Hui Li
- School of Resources and Environmental Engineering, Anhui University, Hefei, China
| | - Qingye Sun
- School of Resources and Environmental Engineering, Anhui University, Hefei, China.
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Qin C, Tao J, Liu T, Liu Y, Xiao N, Li T, Gu Y, Yin H, Meng D. Responses of phyllosphere microbiota and plant health to application of two different biocontrol agents. AMB Express 2019; 9:42. [PMID: 30924016 PMCID: PMC6439047 DOI: 10.1186/s13568-019-0765-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/18/2019] [Indexed: 11/17/2022] Open
Abstract
The phyllosphere supports a tremendous diversity of microbes, which have the potential to influence plant biogeography and ecosystem function. Although biocontrol agents (BCAs) have been used extensively for controlling plant diseases, the ecological effects of BCAs on phyllosphere bacteria and the relationships between phyllosphere community and plant health are poorly understood. In this study, we explored the control efficiency of two BCA communities on bacterial wildfire disease by repeatedly spraying BCAs on tobacco leaves. The results of field tests showed that BCAs used in our study, especially BCA_B, had remarkable control effects against tobacco wildfire disease. The higher control efficiency of BCA_B might be attributed to a highly diverse and complex community in the phyllosphere. By 16S ribosomal RNA gene sequencing, we found that phyllosphere microbial community, including community diversity, taxonomic composition and microbial interactions, changed significantly by application of BCAs. According to the correlation analysis, it showed that wildfire disease infection of plants was negatively related to phyllosphere microbial diversity, indicating a highly diverse community in the phyllosphere might prevent pathogens invasion and colonization. In addition, we inferred that a more complex network in the phyllosphere might be beneficial for decreasing the chances of bacterial wildfire outbreak, and the genera of Pantoea and Sphingomonas might play important roles in wildfire disease suppression. These correlations between phyllosphere community and plant health will improve our understanding on the ecological function of phyllosphere community on plants.
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Chen J, Shen W, Xu H, Li Y, Luo T. The Composition of Nitrogen-Fixing Microorganisms Correlates With Soil Nitrogen Content During Reforestation: A Comparison Between Legume and Non-legume Plantations. Front Microbiol 2019; 10:508. [PMID: 30930882 PMCID: PMC6427063 DOI: 10.3389/fmicb.2019.00508] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/27/2019] [Indexed: 12/02/2022] Open
Abstract
Numerous reforestation projects have been conducted to improve soil fertility in degraded forests, often causing alterations to the soil microbial communities. However, it remains unclear whether microbial functional groups are affected and how these groups correlate with an increase in the nutrient contents during reforestation. We investigated the abundance and composition of free-living nitrogen-fixing microorganisms (diazotrophs) by quantifying and sequencing the marker gene nifH in bulk soils from five reforestation approaches, including legumes and non-legumes, in subtropical China. The relationships between diazotrophic community attributes and soil nitrogen (N) content [NO3 -, NH4 +, and microbial biomass N (MBN)] were examined under various approaches. Abundance of diazotrophs was highest in the native tree plantation (Schima spp. and Michelia macclurei) and Acacia mangium monoculture (AM), and lowest in the Pinus massoniana monoculture. The diazotrophic abundance correlated positively with soil organic matter and water content while there was a negative correlation to pH. The composition of diazotrophic community differed significantly among the five reforestation approaches examined and was closely correlated with variations in soil pH, NH4 + and water content. Diazotrophic community composition was closely related to soil NH4 + content, whereas abundance was not. The AM contained higher NH4 +, NO3 - and MBN contents than the other reforestation approaches, which may be associated with the indicator species of diazotrophs (Actinobacteria, Proteobacteria, and Firmicutes). However, there were more indicator species of Proteobacteria in the mixed Acacia plantation (Acacia mangium and Acacia crassicarpa) than in AM, which might have contributed to the remarkedly lower N content compared to AM. Overall, the soil N content under reforestation appeared to be more related to the composition of diazotroph community than to the abundance of diazotrophs.
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Affiliation(s)
- Jie Chen
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Weijun Shen
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Han Xu
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Yide Li
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Tushou Luo
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
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Chen J, Shen W, Xu H, Li Y, Luo T. The Composition of Nitrogen-Fixing Microorganisms Correlates With Soil Nitrogen Content During Reforestation: A Comparison Between Legume and Non-legume Plantations. Front Microbiol 2019. [DOI: 10.10.3389/fmicb.2019.00508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Taylor BN, Chazdon RL, Menge DNL. Successional dynamics of nitrogen fixation and forest growth in regenerating Costa Rican rainforests. Ecology 2019; 100:e02637. [PMID: 30698284 DOI: 10.1002/ecy.2637] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/14/2018] [Accepted: 01/03/2019] [Indexed: 11/08/2022]
Abstract
Regenerating tropical forests have an immense capacity to capture carbon and harbor biodiversity. The recuperation of the nitrogen cycle following disturbance can fuel biomass regeneration, but few studies have evaluated the successional dynamics of nitrogen and nitrogen inputs in tropical forests. We assessed symbiotic and asymbiotic nitrogen fixation, soil inorganic nitrogen concentrations, and tree growth in a well-studied series of five tropical forest plots ranging from 19 yr in age to old-growth forests. Wet-season soil inorganic nitrogen concentrations were high in all plots, peaking in the 29-yr-old plot. Inputs from symbiotic nitrogen fixation declined through succession, while asymbiotic nitrogen fixation peaked in the 37-yr-old plot. Consequently, the dominant nitrogen fixation input switched from symbiotic fixation in the younger plots to asymbiotic fixation in the older plots. Tree growth was highest in the youngest plots and declined through succession. Interestingly, symbiotic nitrogen fixation was negatively correlated with the basal area of nitrogen-fixing trees across our study plots, highlighting the danger in using nitrogen-fixing trees as a proxy for rates of symbiotic nitrogen fixation. Our results demonstrate that the nitrogen cycle has largely recuperated by 19 yr following disturbance, allowing for rapid biomass regeneration at our site. This work provides important insight into the sources and dynamics of nitrogen that support growth and carbon capture in regenerating Neotropical forests.
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Affiliation(s)
- Benton N Taylor
- Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland, 21037, USA
| | - Robin L Chazdon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, 06269, USA
| | - Duncan N L Menge
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 10th Floor, Schermerhorn Extension, 1200 Amsterdam Avenue, New York, New York, 10027, USA
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Abstract
With the likelihood that changes in global climate will adversely affect the soil C reservoir in the northern circumpolar permafrost zone, an understanding of the potential role of diazotrophic communities in enhancing biological N2 fixation, which constrains both plant production and microbial decomposition in tundra soils, is important in elucidating the responses of soil microbial communities to global climate change. A recent study showed that the composition of the diazotrophic community in a tundra soil exhibited no change under a short-term (1.5-year) winter warming experiment. However, it remains crucial to examine whether the lack of diazotrophic community responses to warming is persistent over a longer time period as a possibly important mechanism in stabilizing tundra soil C. Through a detailed characterization of the effects of winter warming on diazotrophic communities, we showed that a long-term (5-year) winter warming substantially enhanced diazotrophic abundance and altered community composition, though soil depth had a stronger influence on diazotrophic community composition than warming. These changes were best explained by changes in soil moisture, soil thaw duration, and plant biomass. These results provide crucial insights into the potential factors that may impact future C and N availability in tundra regions. Tundra ecosystems are typically carbon (C) rich but nitrogen (N) limited. Since biological N2 fixation is the major source of biologically available N, the soil N2-fixing (i.e., diazotrophic) community serves as an essential N supplier to the tundra ecosystem. Recent climate warming has induced deeper permafrost thaw and adversely affected C sequestration, which is modulated by N availability. Therefore, it is crucial to examine the responses of diazotrophic communities to warming across the depths of tundra soils. Herein, we carried out one of the deepest sequencing efforts of nitrogenase gene (nifH) to investigate how 5 years of experimental winter warming affects Alaskan soil diazotrophic community composition and abundance spanning both the organic and mineral layers. Although soil depth had a stronger influence on diazotrophic community composition than warming, warming significantly (P < 0.05) enhanced diazotrophic abundance by 86.3% and aboveground plant biomass by 25.2%. Diazotrophic composition in the middle and lower organic layers, detected by nifH sequencing and a microarray-based tool (GeoChip), was markedly altered, with an increase of α-diversity. Changes in diazotrophic abundance and composition significantly correlated with soil moisture, soil thaw duration, and plant biomass, as shown by structural equation modeling analyses. Therefore, more abundant diazotrophic communities induced by warming may potentially serve as an important mechanism for supplementing biologically available N in this tundra ecosystem.
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Isotopic Evidence that Nitrogen Enrichment Intensifies Nitrogen Losses to the Atmosphere from Subtropical Mangroves. Ecosystems 2019. [DOI: 10.1007/s10021-018-0327-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Che R, Deng Y, Wang F, Wang W, Xu Z, Hao Y, Xue K, Zhang B, Tang L, Zhou H, Cui X. Autotrophic and symbiotic diazotrophs dominate nitrogen-fixing communities in Tibetan grassland soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 639:997-1006. [PMID: 29929338 DOI: 10.1016/j.scitotenv.2018.05.238] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/16/2018] [Accepted: 05/19/2018] [Indexed: 06/08/2023]
Abstract
Biological nitrogen fixation, conducted by soil diazotrophs, is the primary nitrogen source for natural grasslands. However, the diazotrophs in grassland soils are still far from fully investigated. Particularly, their regional-scale distribution patterns have never been systematically examined. Here, soils (0-5 cm) were sampled from 54 grasslands on the Tibetan Plateau to examine the diazotroph abundance, diversity, and community composition, as well as their distribution patterns and driving factors. The diazotroph abundance was expressed as nifH gene copies, measured using real-time PCR. The diversity and community composition of diazotrophs were analyzed through MiSeq sequencing of nifH genes. The results showed that Cyanobacteria (47.94%) and Proteobacteria (45.20%) dominated the soil diazotroph communities. Most Cyanobacteria were classified as Nostocales which are main components of biological crusts. Rhizobiales, most of which were identified as potential symbiotic diazotrophs, were also abundant in approximately half of the soil samples. The soil diazotroph abundance, diversity, and community composition followed the distribution patterns in line with mean annual precipitation. Moreover, they also showed significant correlations with prokaryotic abundance, plant biomass, vegetation cover, soil pH values, and soil nutrient contents. Among these environmental factors, the soil moisture, organic carbon, available phosphorus, and inorganic nitrogen contents could be the main drivers of diazotroph distribution due to their strong correlations with diazotroph indices. These findings suggest that autotrophic and symbiotic diazotrophs are the predominant nitrogen fixers in Tibetan grassland soils, and highlight the key roles of water and nutrient availability in determining the soil diazotroph distribution on the Tibetan Plateau.
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Affiliation(s)
- Rongxiao Che
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Yongcui Deng
- Nanjing Normal University, Nanjing 210097, China; Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing 210023, China
| | - Fang Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Weijin Wang
- Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Zhihong Xu
- Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Yanbin Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Xue
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Biao Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Tang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Environmental Futures Research Institute, School of Environment and Science, Griffith University, Brisbane 4111, Australia
| | - Huakun Zhou
- Key Laboratory of Restoration Ecology of Cold Area in Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Xiaoyong Cui
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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41
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Winbourne JB, Houlton BZ. Plant-soil feedbacks on free-living nitrogen fixation over geological time. Ecology 2018; 99:2496-2505. [PMID: 30076606 DOI: 10.1002/ecy.2486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 07/04/2018] [Accepted: 07/23/2018] [Indexed: 11/09/2022]
Abstract
Free-living heterotrophic nitrogen fixation (FNF) is a widespread nitrogen input pathway in terrestrial ecosystems. However, questions remain over the relative influence of co-occurring controls on patterns of heterotrophic FNF activity, especially across generalized stages of primary succession, from biomass accumulation to retrogressive phases. Here, we experimentally test two alternative hypotheses regarding FNF rates during ecosystem development: (H1) site (i.e., changes in soil fertility during succession) is the primary driver of leaf-litter FNF rates, vs. (H2) leaf-litter chemistry is the primary determinant of FNF activity across a broad range of ecosystem conditions. We evaluated these hypotheses across a well-studied soil chronosequence in California (i.e., the Ecological Staircase), which spans ~1 million years of ecosystem development and displays extreme ranges in plant-soil nutrient conditions, culminating in the nutrient depleted and stunted Pygmy forest. Across this successional gradient, we implemented a reciprocal leaf-litter transplant and a common garden litter bag decomposition experiment with senesced needles of Pinus muricata. Our results support H1: rates of FNF were similar for all leaf-litter types decomposed at the same site regardless of initial leaf-litter C and nutrient contents. FNF rates sharply declined from the maximal to retrogressive stage of succession. Trends in P dynamics during decomposition suggest an important role of P in regulating FNF. For example, P. muricata litter collected from the infertile Pygmy site displayed substantially higher FNF rates when decomposed at the fertile site, in part by immobilizing significant quantities of P from the soil at the fertile site. Conversely, P. muricata litter collected from the fertile site decomposed more slowly at the Pygmy site, with concomitant declines in FNF rates that matched those of Pygmy site litter decomposed in situ. These results are consistent with the idea that, over millennia, long-term declines in P availability feedback to constrain FNF rates, in part explaining the emergence of extremely nutrient-poor and retrograded ecosystems.
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Affiliation(s)
- Joy B Winbourne
- Department of Land, Air, and Water Resources, University of California, Davis, California, 95616, USA.,Department of Earth and Environment, Boston University, Boston, Massachusetts, 02215, USA
| | - Benjamin Z Houlton
- Department of Land, Air, and Water Resources, University of California, Davis, California, 95616, USA
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42
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Zheng M, Zhang W, Luo Y, Li D, Wang S, Huang J, Lu X, Mo J. Stoichiometry controls asymbiotic nitrogen fixation and its response to nitrogen inputs in a nitrogen-saturated forest. Ecology 2018; 99:2037-2046. [DOI: 10.1002/ecy.2416] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 05/02/2018] [Accepted: 05/14/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Mianhai Zheng
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems; Guangdong Provincial Key Laboratory of Applied Botany; South China Botanical Garden; Chinese Academy of Sciences; Guangzhou 510650 China
- Department of Biological Sciences; Northern Arizona University; Flagstaff Arizona 86011 USA
- University of Chinese Academy of Sciences; Beijing 100039 China
| | - Wei Zhang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems; Guangdong Provincial Key Laboratory of Applied Botany; South China Botanical Garden; Chinese Academy of Sciences; Guangzhou 510650 China
| | - Yiqi Luo
- Department of Biological Sciences; Northern Arizona University; Flagstaff Arizona 86011 USA
- Department of Microbiology and Plant Biology; University of Oklahoma; Norman Oklahoma 73019 USA
| | - Dejun Li
- Key Laboratory of Agro-ecological Processes in Subtropical Region; Institute of Subtropical Agriculture; Chinese Academy of Sciences; Changsha 410125 China
| | - Senhao Wang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems; Guangdong Provincial Key Laboratory of Applied Botany; South China Botanical Garden; Chinese Academy of Sciences; Guangzhou 510650 China
- University of Chinese Academy of Sciences; Beijing 100039 China
| | - Juan Huang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems; Guangdong Provincial Key Laboratory of Applied Botany; South China Botanical Garden; Chinese Academy of Sciences; Guangzhou 510650 China
| | - Xiankai Lu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems; Guangdong Provincial Key Laboratory of Applied Botany; South China Botanical Garden; Chinese Academy of Sciences; Guangzhou 510650 China
| | - Jiangming Mo
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems; Guangdong Provincial Key Laboratory of Applied Botany; South China Botanical Garden; Chinese Academy of Sciences; Guangzhou 510650 China
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43
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Wang Q, Wang J, Li Y, Chen D, Ao J, Zhou W, Shen D, Li Q, Huang Z, Jiang Y. Influence of nitrogen and phosphorus additions on N 2-fixation activity, abundance, and composition of diazotrophic communities in a Chinese fir plantation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 619-620:1530-1537. [PMID: 29129329 DOI: 10.1016/j.scitotenv.2017.10.064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/19/2017] [Accepted: 10/08/2017] [Indexed: 05/22/2023]
Abstract
Although biological nitrogen (N) fixation (BNF) is an important N input process in subtropical forest ecosystems, how the diazotrophic communities related to this process respond to N and phosphorus (P) inputs is largely unknown. We investigated the effects of exogenous N and/or P inputs on N2-fixation activity, diazotrophic abundance and community composition using a continuous application of fertilizers over 5years experiment in a Chinese fir plantation. The fertilization regimes included control (CK), P treatment (P), low N addition treatment (N1), high N addition treatment (N2), low N and P addition treatment (N1P) and high N with P addition treatment (N2P). N2-fixation activity was determined using the acetylene reduction assay (ARA). Quantitative PCR and Illumina Miseq sequencing of nifH gene were performed to analyze diazotrophic abundance and community composition, respectively. Our results showed that P addition increased N2-fixation activity and nifH gene abundance by 189.07nmol C2H4 and 1.02×107copiesg-1 dry soil, respectively, while were reduced by 1.19nmol C2H4 and 2.04×106copiesg-1 dry soil when N was added. The application of P with low N (N1P) effectively alleviated the inhibitory effect of N input on N2-fixation activity. N-related treatments resulted in significant decreases in operational taxonomic unit (OTU) richness and shifts in diazotrophic community structure. N2-fixation activity and nifH gene abundance were strongly and positively correlated with soil pH and negatively correlated with mineral N (NH4+-N and NO3--N) contents, while mineral N concentrations rather than soil pH appeared to be the main factor altering diazotrophic community structure. These results revealed that P addition played a positive role in regulating biological nitrogen fixation in subtropical forest ecosystems.
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Affiliation(s)
- Qing Wang
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou 510316, China
| | - Jianlei Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yuanzheng Li
- School of Resources and Environment, Henan University of Economics and Law, Zhengzhou 450046, China
| | - Diwen Chen
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou 510316, China
| | - Junhua Ao
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou 510316, China
| | - Wenling Zhou
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou 510316, China
| | - Dachun Shen
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou 510316, China
| | - Qiwei Li
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou 510316, China
| | - Zhenrui Huang
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou 510316, China
| | - Yong Jiang
- Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou 510316, China.
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44
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Dynarski KA, Houlton BZ. Nutrient limitation of terrestrial free-living nitrogen fixation. THE NEW PHYTOLOGIST 2018; 217:1050-1061. [PMID: 29165820 DOI: 10.1111/nph.14905] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/18/2017] [Indexed: 05/27/2023]
Abstract
Nitrogen (N) fixation by free-living bacteria is a primary N input pathway in many ecosystems and sustains global plant productivity. Uncertainty exists over the importance of N, phosphorus (P) and molybdenum (Mo) availability in controlling free-living N fixation rates. Here, we investigate the geographic occurrence and variability of nutrient constraints to free-living N fixation in the terrestrial biosphere. We compiled data from studies measuring free-living N fixation in response to N, P and Mo fertilizers. We used meta-analysis to quantitatively determine the extent to which N, P and Mo stimulate or suppress N fixation, and if environmental variables influence the degree of nutrient limitation of N fixation. Across our compiled dataset, free-living N fixation is suppressed by N fertilization and stimulated by Mo fertilization. Additionally, free-living N fixation is stimulated by P additions in tropical forests. These findings suggest that nutrient limitation is an intrinsic property of the biochemical demands of N fixation, constraining free-living N fixation in the terrestrial biosphere. These findings have implications for understanding the causes and consequences of N limitation in coupled nutrient cycles, as well as modeling and forecasting nutrient controls over carbon-climate feedbacks.
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Affiliation(s)
- Katherine A Dynarski
- Department of Land, Air, and Water Resources, University of California, Davis, 1 Shields Ave., Davis, CA, 95616, USA
| | - Benjamin Z Houlton
- Department of Land, Air, and Water Resources, University of California, Davis, 1 Shields Ave., Davis, CA, 95616, USA
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45
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Buscardo E, Geml J, Schmidt SK, Silva ALC, Ramos RTJ, Barbosa SMR, Andrade SS, Dalla Costa R, Souza AP, Freitas H, Cunha HB, Nagy L. Of mammals and bacteria in a rainforest: Temporal dynamics of soil bacteria in response to simulated N pulse from mammalian urine. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12998] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Erika Buscardo
- Centre for Functional EcologyUniversity of Coimbra Coimbra Portugal
- Department of Plant BiologyUniversity of Campinas Campinas Brazil
- Large‐scale Biosphere‐Atmosphere ProgrammeNational Amazonian Research Institute (INPA) Manaus Brazil
| | - József Geml
- Biodiversity Dynamics Research GroupNaturalis Biodiversity Center Leiden The Netherlands
- Faculty of SciencesLeiden University Leiden The Netherlands
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary BiologyUniversity of Colorado Boulder CO USA
| | | | | | | | | | | | - Anete P. Souza
- Department of Plant BiologyUniversity of Campinas Campinas Brazil
| | - Helena Freitas
- Centre for Functional EcologyUniversity of Coimbra Coimbra Portugal
| | - Hillândia B. Cunha
- Large‐scale Biosphere‐Atmosphere ProgrammeNational Amazonian Research Institute (INPA) Manaus Brazil
| | - Laszlo Nagy
- Department of Plant BiologyUniversity of Campinas Campinas Brazil
- Large‐scale Biosphere‐Atmosphere ProgrammeNational Amazonian Research Institute (INPA) Manaus Brazil
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46
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Winbourne JB, Brewer SW, Houlton BZ. Iron controls over di-nitrogen fixation in karst tropical forest. Ecology 2017; 98:773-781. [DOI: 10.1002/ecy.1700] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Joy B. Winbourne
- Department of Land, Air and Water Resources; University of California, Davis; One Shields Avenue Davis California 95616 USA
| | - Steven W. Brewer
- Belize Foundation for Research and Environmental Education; PO Box 129 Punta Gorda Todelo Belize
- Copperhead Consulting; 11641 Richmond Rd. Paint Lick Kentucky 40461 USA
| | - Benjamin Z. Houlton
- Department of Land, Air and Water Resources; University of California, Davis; One Shields Avenue Davis California 95616 USA
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47
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Lv F, Xue S, Wang G, Zhang C. Nitrogen addition shifts the microbial community in the rhizosphere of Pinus tabuliformis in Northwestern China. PLoS One 2017; 12:e0172382. [PMID: 28234932 PMCID: PMC5325277 DOI: 10.1371/journal.pone.0172382] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/03/2017] [Indexed: 11/21/2022] Open
Abstract
Atmospheric nitrogen (N) deposition profoundly alters the soil microbial communities and will thus affect nutrient cycles. The effects of N availability on microbial community, however, are not clear. We used PLFA analysis to evaluate the effects of a gradient of N addition (0, 2.8, 5.6, 11.2, and 22.4 g N m-2 y-1) for three years on the rhizospheric microbial community of Pinus tabuliformis seedlings. The main factors influencing the community were quantified using structural equation modelling and redundancy analysis. At the microbial-community level, N addition increased the total phospholipid fatty acids content by increasing the dissolved organic carbon (DOC) and root biomass. Increases in soil microbial biomass carbon and N, however, was attributed to the increased DOC, N content and decreased pH. At the microbial-groups level, Fungal, arbuscular mycorrhizal fungal (AMF), gram-positive bacterial (GP) abundances and the GP:GN ratio first increased and then decreased with N addition. Nitrogen addition increased the abundances of bacteria, fungi, and actinomycetes mainly by increasing the DOC content and decreasing root biomass. Additionally, the decrease of pH and ammonium N caused by N addition increased the fungal abundances and reduced actinomycete abundances, respectively. Nitrogen addition shifted the rhizospheric microbial community mainly by altering the DOC content and root biomass. The current rate of N deposition (2.5 g N m-2 y-1) benefits plant growth and increases the abundances of fungi, arbuscular mycorrhizal fungi, GP, actinomycetes and the GP:GN ratio.
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Affiliation(s)
- Fenglian Lv
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, China
| | - Sha Xue
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, China
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, Shaanxi, China
| | - Guoliang Wang
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, Shaanxi, China
- * E-mail:
| | - Chao Zhang
- Institute of Soil and Water Conservation, Northwest A & F University, Yangling, Shaanxi, China
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48
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Penton CR, Yang C, Wu L, Wang Q, Zhang J, Liu F, Qin Y, Deng Y, Hemme CL, Zheng T, Schuur EAG, Tiedje J, Zhou J. NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient. Front Microbiol 2016; 7:1894. [PMID: 27933054 PMCID: PMC5121533 DOI: 10.3389/fmicb.2016.01894] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/11/2016] [Indexed: 11/13/2022] Open
Abstract
Since nitrogen (N) is often limiting in permafrost soils, we investigated the N2-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples taken along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table. NifH reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlated to differences in the NifH sequence classes with those most closely related to group I nifH-harboring Alpha- and Beta-Proteobacteria in higher abundance above water table depth while those related to group III nifH-harboring Delta Proteobacteria more abundant below. The most dominant below water table depth NifH sequences, comprising 1/3 of the total, were distantly related to Verrucomicrobia-Opitutaceae. Overall, these results suggest that permafrost thaw alters the class-level composition of N2-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These nifH data were also compared to nifH sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites.
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Affiliation(s)
- C. Ryan Penton
- College of Integrative Sciences and Arts, Arizona State UniversityMesa, AZ, USA
- Arizona State University, Center for Fundamental and Applied Microbiomics, Biodesign InstituteTempe, AZ, USA
| | - Caiyun Yang
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, USA
- Key Lab of the Ministry of Education for Coastal and Wetland Ecosystems, School of Environmental Sciences, Xiamen UniversityXiamen, China
| | - Liyou Wu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, USA
| | - Qiong Wang
- Center for Microbial Ecology, Michigan State UniversityEast Lansing, MI, USA
| | - Jin Zhang
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, USA
| | - Feifei Liu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, USA
| | - Yujia Qin
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, USA
| | - Ye Deng
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, USA
| | - Christopher L. Hemme
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, USA
| | - Tianling Zheng
- Key Lab of the Ministry of Education for Coastal and Wetland Ecosystems, School of Environmental Sciences, Xiamen UniversityXiamen, China
| | - Edward A. G. Schuur
- Department of Biological Sciences, Northern Arizona UniversityFlagstaff, AZ, USA
| | - James Tiedje
- Center for Microbial Ecology, Michigan State UniversityEast Lansing, MI, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, USA
- Earth Sciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
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49
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Frank IE, Turk-Kubo KA, Zehr JP. Rapid annotation of nifH gene sequences using classification and regression trees facilitates environmental functional gene analysis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:905-916. [PMID: 27557869 DOI: 10.1111/1758-2229.12455] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 08/16/2016] [Indexed: 05/22/2023]
Abstract
The nifH gene is a widely used molecular proxy for studying nitrogen fixation. Phylogenetic classification of nifH gene sequences is an essential step in diazotroph community analysis that requires a fast automated solution due to increasing size of environmental sequence libraries and increasing yield of nifH sequences from high-throughput technologies. A novel approach to rapidly classify nifH amino acid sequences into well-defined phylogenetic clusters that provides a common platform for comparative analysis across studies is presented. Phylogenetic group membership can be accurately predicted with decision tree-type statistical models that identify and utilize signature residues in the amino acid sequences. Our classification models were trained and evaluated with a publicly available and manually curated nifH gene database containing cluster annotations. Model-independent sequence sets from diverse ecosystems were used for further assessment of the models' prediction accuracy. The utility of this novel sequence binning approach was demonstrated in a comparative study where joint treatment of diazotroph assemblages from a wide range of habitats identified habitat-specific and widely-distributed diazotrophs and revealed a marine - terrestrial distinction in community composition. Our rapid and automated phylogenetic cluster assignment circumvents extensive phylogenetic analysis of nifH sequences; hence, it saves substantial time and resources in nitrogen fixation studies.
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Affiliation(s)
- Ildiko E Frank
- Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Kendra A Turk-Kubo
- Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Jonathan P Zehr
- Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
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50
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Martirosyan V, Unc A, Miller G, Doniger T, Wachtel C, Steinberger Y. Desert Perennial Shrubs Shape the Microbial-Community Miscellany in Laimosphere and Phyllosphere Space. MICROBIAL ECOLOGY 2016; 72:659-668. [PMID: 27450478 DOI: 10.1007/s00248-016-0822-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/14/2016] [Indexed: 06/06/2023]
Abstract
Microbial function, composition, and distribution play a fundamental role in ecosystem ecology. The interaction between desert plants and their associated microbes is expected to greatly affect their response to changes in this harsh environment. Using comparative analyses, we studied the impact of three desert shrubs, Atriplex halimus (A), Artemisia herba-alba (AHA), and Hammada scoparia (HS), on soil- and leaf-associated microbial communities. DNA extracted from the leaf surface and soil samples collected beneath the shrubs were used to study associated microbial diversity using a sequencing survey of variable regions of bacterial 16S rRNA and fungal ribosomal internal transcribed spacer (ITS1). We found that the composition of bacterial and fungal orders is plant-type-specific, indicating that each plant type provides a suitable and unique microenvironment. The different adaptive ecophysiological properties of the three plant species and the differential effect on their associated microbial composition point to the role of adaptation in the shaping of microbial diversity. Overall, our findings suggest a link between plant ecophysiological adaptation as a "temporary host" and the biotic-community parameters in extreme xeric environments.
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Affiliation(s)
- Varsik Martirosyan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Life Sciences International Postgraduate Educational Center, Acharyan 31 Str., Yerevan, 0040, Armenia
| | - Adrian Unc
- Boreal Ecosystems Research Initiative, Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, A2H 6P9, Canada
| | - Gad Miller
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Chaim Wachtel
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Yosef Steinberger
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
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