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Ferrando L, Rariz G, Martínez-Pereyra A, Fernández-Scavino A. Endophytic diazotrophic communities from rice roots are diverse and weakly associated with soil diazotrophic community composition and soil properties. J Appl Microbiol 2024; 135:lxae157. [PMID: 38925647 DOI: 10.1093/jambio/lxae157] [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: 03/29/2024] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 06/28/2024]
Abstract
AIM Bacteria that promote plant growth, such as diazotrophs, are valuable tools for achieving a more sustainable production of important non-legume crops like rice. Different strategies have been used to discover new bacteria capable of promoting plant growth. This work evaluated the contribution of soil diazotrophs to the endophytic communities established in the roots of rice seedlings cultivated on seven representative soils from Uruguay. METHODS AND RESULTS The soils were classified into two groups according to the C and clay content. qPCR, terminal restriction fragment length polymorphism (T-RFLP), and 454-pyrosequencing of the nifH gene were used for analyzing diazotrophs in soil and plantlets' roots grown from seeds of the same genotype for 25 days under controlled conditions. A similar nifH abundance was found among the seven soils, roots, or leaves. The distribution of diazotrophs was more uneven in roots than in soils, with dominance indices significantly higher than in soils (nifH T-RFLP). Dominant soils' diazotrophs were mainly affiliated to Alphaproteobacteria and Planctomycetota. Conversely, Alpha, Beta, Gammaproteobacteria, and Bacillota were predominant in different roots, though undetectable in soils. Almost no nifH sequences were shared between soils and roots. CONCLUSIONS Root endophytic diazotrophs comprised a broader taxonomic range of microorganisms than diazotrophs found in soils from which the plantlets were grown and showed strong colonization patterns.
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Affiliation(s)
- Lucía Ferrando
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
| | - Gastón Rariz
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
| | - Andrea Martínez-Pereyra
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
| | - Ana Fernández-Scavino
- Laboratorio de Ecología Microbiana Medioambiental, Área Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, Uruguay
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2
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Liang H, Yang L, He X, Wu Q, Chen D, Liu M, Shen P. Rhizosphere Ventilation Effects on Root Development and Bacterial Diversity of Peanut in Compacted Soil. PLANTS (BASEL, SWITZERLAND) 2024; 13:790. [PMID: 38592790 PMCID: PMC10975058 DOI: 10.3390/plants13060790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/22/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
Soil compaction is one of the crucial factors that restrains the root respiration, energy metabolism and growth of peanut (Arachis hypogaea L.) due to hypoxia, which can be alleviated by ventilation. We therefore carried out a pot experiment with three treatments: no ventilation control (CK), (2) ventilation volumes at 1.2 (T1), and 1.5 (T2) times of the standard ventilation volume (2.02 L/pot). Compared to no-ventilation in compacted soil, ventilation T1 significantly increased total root length, root surface area, root volume and tips at the peanut anthesis stage (62 days after sowing), while T2 showed a negative impact on the above-mentioned root morphological characteristics. At the podding stage (S2, 95 days after sowing), both ventilation treatments improved root morphology, especially under T1. Compared to CK, both ventilation T1 and T2 decreased the activities of enzymes involving the anaerobic respiration, including root lactate dehydrogenase, pyruvate decarboxylase and alcohol dehydrogenase. The activities of antioxidant enzymes of root superoxide dismutase, peroxidase and catalase also decreased at S1, while superoxide dismutase and peroxidase significantly increased under T1 at S2. The ventilation of compacted soil changed soil nitrogen-fixing bacterial communities, with highest bacterial alpha diversity indices under T1. The Pearson correlation analyses indicated a positive relationship between the relative abundance of Bradyrhizobiaceae and root activity, and between unclassified_family of Rhizobiales and the root surface area, while Enterobacteriaceae had a negative impact on the root nodule number. The Pearson correlation test showed that the root surface, tips and activity positively correlated with root superoxide dismutase and peroxidase activities. These results demonstrate that soil ventilation could enhance plant root growth, the diversity and function of soil nitrogen-fixing bacterial communities. The generated results from this present study could serve as important evidence in alleviating soil hypoxia caused by compaction.
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Affiliation(s)
- Haiyan Liang
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetics & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao 266100, China; (H.L.); (L.Y.); (Q.W.); (D.C.); (M.L.)
| | - Liyu Yang
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetics & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao 266100, China; (H.L.); (L.Y.); (Q.W.); (D.C.); (M.L.)
| | - Xinhua He
- School of Biological Sciences, University of Western Australia, Perth 6009, Australia;
- Department of Land, Air and Water Resources, University of California at Davis, Davis, CA 90616, USA
| | - Qi Wu
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetics & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao 266100, China; (H.L.); (L.Y.); (Q.W.); (D.C.); (M.L.)
| | - Dianxu Chen
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetics & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao 266100, China; (H.L.); (L.Y.); (Q.W.); (D.C.); (M.L.)
| | - Miao Liu
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetics & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao 266100, China; (H.L.); (L.Y.); (Q.W.); (D.C.); (M.L.)
| | - Pu Shen
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetics & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao 266100, China; (H.L.); (L.Y.); (Q.W.); (D.C.); (M.L.)
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Cornell CR, Zhang Y, Ning D, Xiao N, Wagle P, Xiao X, Zhou J. Land use conversion increases network complexity and stability of soil microbial communities in a temperate grassland. THE ISME JOURNAL 2023; 17:2210-2220. [PMID: 37833523 PMCID: PMC10689820 DOI: 10.1038/s41396-023-01521-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/29/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023]
Abstract
Soils harbor highly diverse microbial communities that are critical to soil health, but agriculture has caused extensive land use conversion resulting in negative effects on critical ecosystem processes. However, the responses and adaptations of microbial communities to land use conversion have not yet been understood. Here, we examined the effects of land conversion for long-term crop use on the network complexity and stability of soil microbial communities over 19 months. Despite reduced microbial biodiversity in comparison with native tallgrass prairie, conventionally tilled (CT) cropland significantly increased network complexity such as connectivity, connectance, average clustering coefficient, relative modularity, and the number of species acting at network hubs and connectors as well as resulted in greater temporal variation of complexity indices. Molecular ecological networks under CT cropland became significantly more robust and less vulnerable, overall increasing network stability. The relationship between network complexity and stability was also substantially strengthened due to land use conversion. Lastly, CT cropland decreased the number of relationships between network structure and environmental properties instead being strongly correlated to management disturbances. These results indicate that agricultural disturbance generally increases the complexity and stability of species "interactions", possibly as a trade-off for biodiversity loss to support ecosystem function when faced with frequent agricultural disturbance.
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Affiliation(s)
- Carolyn R Cornell
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA
| | - Ya Zhang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Daliang Ning
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Naijia Xiao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA
| | - Pradeep Wagle
- USDA, Agricultural Research Service, Oklahoma and Central Plains Agricultural Research Center, El Reno, OK, USA
| | - Xiangming Xiao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
- Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
- School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Ok, USA.
- School of Computer Science, University of Oklahoma, Norman, OK, USA.
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Fan Z, Li R, Guan E, Chen H, Zhao X, Wei G, Shu D. Fertilization regimes affect crop yields through changes of diazotrophic community and gene abundance in soil aggregation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 866:161359. [PMID: 36610631 DOI: 10.1016/j.scitotenv.2022.161359] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/23/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Soil aggregates are extremely vulnerable to agricultural intensification and are important drivers of soil health, microbial diversity, and biogeochemical cycling. Despite its importance, there is a dearth of studies revealing how fertilization regimes influence diazotrophic community behind soil aggregates, as well as the potential consequences for crop yields. To do this, a two-decade fertilization of wheat-maize intercropping field experiment was conducted in Loess Plateau of China semiarid area under three treatments: no fertilizer, chemical and organic fertilizer. Moreover, we categorized soil aggregates as large macroaggregates (>2 mm), medium macroaggregates (1-2 mm), small macroaggregates (0.25-1 mm), microaggregates (< 0.25 mm) and rhizosphere soils aggregates. We found that soil aggregates exerted a much more influence on the nifH gene abundance than fertilization practices. Particularly, nifH gene abundance has been promoted with increasing the size of soil aggregates fraction without blank soil in the organic fertilization while its abundance presented contrast patterns in the chemical fertilization. Bipartite association networks indicated that different soil aggregates shaped niche differentiation of diazotrophic community behind fertilization regimes. Additionally, we found that organic fertilization strengthens the robustness of diazotrophic communities as well as increases the complexity of microbial networks by harboring keystone taxa. Mantel test results suggested that specific soil factors exerted more selective power on diazotrophic community and nifH gene abundance in the chemical fertilization. Furthermore, β-diversity and nifH gene abundance of diazotrophic communities in the soil microaggregates jointly determine the crop yields. Collectively, our findings emphasize the key role of functional community diversity in sustaining soil cycling process and crop yields under long-term fertilization, and facilitate our understanding of the mechanisms underlying diazotrophic community in response to agricultural intensification, which could pave the way to sustainable agriculture through manipulating the functional taxa.
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Affiliation(s)
- Zhen Fan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Ruochen Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Enxiao Guan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Haiqing Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China
| | - Xining Zhao
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, 712100 Yangling, Shannxi Province, China; Institute of Soil and Water Conservation, Northwest A&F University, 712100 Yangling, Shannxi Province, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China.
| | - Duntao Shu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Shaanxi 712100, China.
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Narayanan M, Karuppusamy I, Alshiekheid M, Sabour A, Chi NTL, Pugazhendhi A. Phytoremediation potential of Gossypium hirsutum on abandoned polluted chromium sludge soil with the amalgamation of Streptomyces tritici D5. CHEMOSPHERE 2022; 306:135526. [PMID: 35780990 DOI: 10.1016/j.chemosphere.2022.135526] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/25/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
The phytoremediation potency of Gossypium hirsutum was explored in this research under the influence of pre-identified metal tolerant Streptomyces tritici D5 in Cr enriched sludge soil using various treatment sets (I to V) in a greenhouse setting. Interestingly, the G. hirsutum remarkable remediate the Cr metal from the Cr enriched sludge soil under diluted (50:50) condition in 90 days of greenhouse experiment. The S. tritici D5 also effectively support the growth and phytoremediation competence of G. hirsutum. This was evidenced by the under the diluted (set III) condition the growth and major biomolecules such as protein, carbohydrate, and chlorophyll content of G. hirsutum were considerably increased in quantity. Hence, the phytoremediation potential of G. hirsutum was effective at soil diluted with fertile and xenobiotics free soil with dilution ratio of 50:50 (set III) and followed by 75:25 (set II) ratio. Thus, under diluted conditions (50:50) G. hirsutum seed coated with S. tritici D5 showed an outstanding phytoremediation process. Therefore, this method can be implemented to the field level study to assess the metal removal prospects of this environmentally friendly method.
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Affiliation(s)
- Mathiyazhagan Narayanan
- Division of Research and Innovations, Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Science, Chennai, 602 105, Tamil Nadu, India
| | - Indira Karuppusamy
- Research Center for Strategic Materials, Corrosion Resistant Steel Group, National Institute for Materials Science (NIMS), Tsukuba, Japan
| | - Maha Alshiekheid
- Department of Botany and Microbiology, College of Science, King Saud University, PO Box -2455, Riyadh, 11451, Saudi Arabia
| | - Amal Sabour
- Department of Botany and Microbiology, College of Science, King Saud University, PO Box -2455, Riyadh, 11451, Saudi Arabia
| | - Nguyen Thuy Lan Chi
- School of Engineering and Technology, Van Lang University, Ho Chi Minh City, Vietnam.
| | - Arivalagan Pugazhendhi
- Emerging Materials for Energy and Environmental Applications Research Group, School of Engineering and Technology, Van Lang University, Ho Chi Minh City, Vietnam.
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Zhu C, Friman VP, Li L, Xu Q, Guo J, Guo S, Shen Q, Ling N. Meta-analysis of diazotrophic signatures across terrestrial ecosystems at the continental scale. Environ Microbiol 2022; 24:2013-2028. [PMID: 35362656 DOI: 10.1111/1462-2920.15984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 03/10/2022] [Accepted: 03/20/2022] [Indexed: 11/29/2022]
Abstract
Biological nitrogen fixation performed by diazotrophs forms a cornerstone of Earth's terrestrial ecosystem productivity. However, the composition, diversity and distribution of soil diazotrophs are poorly understood across different soil ecosystems. Furthermore, the biological potential of the key diazotroph species in relation to key environmental parameters is unknown. To address this, we used meta-analysis approach to merge together 39 independent diazotroph amplicon sequencing (nifH gene) datasets consisting of 1988 independent soil samples. We then employed multiple statistical analyses and machine-learning approaches to compare diazotroph community differences and indicator species between terrestrial ecosystems on a global scale. The distribution, composition and structure of diazotroph communities varied across seven different terrestrial ecosystems, with community composition exhibiting an especially clear effect. The Cyanobacteria were the most abundant taxa in crust ecosystems (accounting for ~45% of diazotrophs), while other terrestrial ecosystems were dominated by Proteobacteria, including Alpha-, Beta- and Gamma-Proteobacteria (accounting for ~70% of diazotrophs). Farmland ecosystems harboured the highest and crust ecosystems the lowest alpha and phylogenetic diversities. Azospirillum zeae, Skermanella aerolata and four Bradyrhizobium species were identified as key indicator species of potential diazotroph activity. Overall, diazotroph abundances and distribution were affected by multiple environmental parameters, including soil pH, nitrogen, organic carbon, C:N ratio and annual mean precipitation and temperature. Together, our findings suggest that based on the relative abundance and diversity of nifH marker gene, diazotrophs have adapted to a range of environmental niches globally.
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Affiliation(s)
- Chen Zhu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ville-Petri Friman
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Ling Li
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qicheng Xu
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junjie Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ning Ling
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
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Kang J, Yin Z, Pei F, Ye Z, Sun Y, Song G, Ge J. Driving factors of nitrogen conversion during chicken manure aerobic composting under penicillin G residue: Quorum sensing and its signaling molecules. BIORESOURCE TECHNOLOGY 2022; 345:126469. [PMID: 34864180 DOI: 10.1016/j.biortech.2021.126469] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/23/2021] [Accepted: 11/27/2021] [Indexed: 06/13/2023]
Abstract
This study explored effects of different concentrations of penicillin G on nitrogen conversion, bacterial community composition, and quorum sensing during chicken manure aerobic composting. After composting, adding penicillin G down-regulated the abundance of 71 genera and up-regulated the abundance of 103 genera. These bacterial genera were mainly Firmicutes and Proteobacteria. 16S rRNA gene sequencing was employed for function prediction, and the results showed that the addition of penicillin G increased nitrification, reduced denitrification. The autoinducer-1 (AI-1), autoinducer-3 (AI-3) and Phr signal molecules further participated in the nitrogen cycle by regulating the population behavior among multiple bacterial genera. In addition, SEM analysis showed that the quorum sensing system negatively regulated the abundance of genus related to the nitrogen conversion during chicken manure aerobic composting. This is a new theoretical analysis of the research on the treatment of hazardous materials.
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Affiliation(s)
- Jie Kang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Ziliang Yin
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Fangyi Pei
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Zeming Ye
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Yangcun Sun
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Gang Song
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Jingping Ge
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin 150080, China.
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8
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Luo Z, Zhong Q, Han X, Hu R, Liu X, Xu W, Wu Y, Huang W, Zhou Z, Zhuang W, Yan Q, He Z, Wang C. Depth-dependent variability of biological nitrogen fixation and diazotrophic communities in mangrove sediments. MICROBIOME 2021; 9:212. [PMID: 34702367 PMCID: PMC8549172 DOI: 10.1186/s40168-021-01164-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/17/2021] [Indexed: 05/29/2023]
Abstract
BACKGROUND Nitrogen-fixing prokaryotes (diazotrophs) contribute substantially to nitrogen input in mangrove sediments, and their structure and nitrogen fixation rate (NFR) are significantly controlled by environmental conditions. Despite the well-known studies on diazotrophs in surficial sediments, the diversity, structure, and ecological functions of diazotrophic communities along environmental gradients of mangrove sediment across different depths are largely unknown. Here, we investigated how biological nitrogen fixation varied with the depth of mangrove sediments from the perspectives of both NFR and diazotrophic communities. RESULTS Through acetylene reduction assay, nifH gene amplicon and metagenomic sequencing, we found that the NFR increased but the diversity of diazotrophic communities decreased with the depth of mangrove sediments. The structure of diazotrophic communities at different depths was largely driven by salinity and exhibited a clear divergence at the partitioning depth of 50 cm. Among diazotrophic genera correlated with NFR, Agrobacterium and Azotobacter were specifically enriched at 50-100 cm sediments, while Anaeromyxobacter, Rubrivivax, Methylocystis, Dickeya, and Methylomonas were more abundant at 0-50 cm. Consistent with the higher NFR, metagenomic analysis demonstrated the elevated abundance of nitrogen fixation genes (nifH/D/K) in deep sediments, where nitrification genes (amoA/B/C) and denitrification genes (nirK and norB) became less abundant. Three metagenome-assembled genomes (MAGs) of diazotrophs from deep mangrove sediments indicated their facultatively anaerobic and mixotrophic lifestyles as they contained genes for low-oxygen-dependent metabolism, hydrogenotrophic respiration, carbon fixation, and pyruvate fermentation. CONCLUSIONS This study demonstrates the depth-dependent variability of biological nitrogen fixation in terms of NFR and diazotrophic communities, which to a certain extent relieves the degree of nitrogen limitation in deep mangrove sediments. Video Abstract.
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Affiliation(s)
- Zhiwen Luo
- 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
| | - Qiuping Zhong
- 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
| | - Xingguo Han
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092, Zurich, Switzerland
| | - Ruiwen Hu
- 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
| | - 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
| | - Wenjun Xu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510530, PR China
| | - Yongjie Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510530, PR China
| | - Weiming Huang
- 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
| | - Zhengyuan Zhou
- 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
| | - 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
| | - 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
| | - Cheng Wang
- 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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Xi B, Yu H, Li Y, Dang Q, Tan W, Wang Y, Cui D. Insights into the effects of heavy metal pressure driven by long-term treated wastewater irrigation on bacterial communities and nitrogen-transforming genes along vertical soil profiles. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123853. [PMID: 33264929 DOI: 10.1016/j.jhazmat.2020.123853] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 06/12/2023]
Abstract
Irrigation with treated wastewater (TWW) influences soil ecological function due to the accumulation of heavy metals (HMs) and nutrients in soils. However, the interaction between HMs and microbial processes in TWW-irrigated soil has not been fully explored. We investigated the effect of HMs on bacterial communities and nitrogen-transforming (N-transforming) genes along vertical soil profiles irrigated with domestic TWW (DTWW) and industrial TWW (ITWW) for more than 30 years. Results indicate that long-term TWW irrigation reshaped bacterial community structure and composition. Irrigation with ITWW led to increased accumulation of Cd, Cr, Cu, Pb, Zn, and Ni in soils than DTWW. Accumulation of inorganic N, soil organic carbon, and HMs in topsoil irrigated with ITWW contributed to the activities of Micrococcaceae. The effect of the activation of nutrient factors on Bacillus, which was the dominant species in DTWW-irrigated soils, was greater than that of HMs. HM pressure driven by ITWW irrigation changed the vertical distribution of N-transforming functional genes, increasing the abundance of amoA gene and decreasing that of nifH through soil depth. ITWW irrigation enhanced the denitrification capacity in topsoil; ammonia-oxidizing capacity in deeper soil was increased after long-term irrigation with DTWW and ITWW, suggesting a potential risk of nitrogen loss.
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Affiliation(s)
- Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Hong Yu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yanping Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Qiuling Dang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; College of Water Sciences, Beijing Normal University, Beijing, 100875, China.
| | - Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yan Wang
- School of Water and Environment, Chang'an University, Xi'an, 710054, China
| | - Dongyu Cui
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
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10
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Coyne KJ, Parker AE, Lee CK, Sohm JA, Kalmbach A, Gunderson T, León-Zayas R, Capone DG, Carpenter EJ, Cary SC. The distribution and relative ecological roles of autotrophic and heterotrophic diazotrophs in the McMurdo Dry Valleys, Antarctica. FEMS Microbiol Ecol 2020; 96:5714082. [PMID: 31967635 PMCID: PMC7043275 DOI: 10.1093/femsec/fiaa010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/21/2020] [Indexed: 12/13/2022] Open
Abstract
The McMurdo Dry Valleys (MDV) in Antarctica harbor a diverse assemblage of mat-forming diazotrophic cyanobacteria that play a key role in nitrogen cycling. Prior research showed that heterotrophic diazotrophs also make a substantial contribution to nitrogen fixation in MDV. The goals of this study were to survey autotrophic and heterotrophic diazotrophs across the MDV to investigate factors that regulate the distribution and relative ecological roles of each group. Results indicated that diazotrophs were present only in samples with mats, suggesting a metabolic coupling between autotrophic and heterotrophic diazotrophs. Analysis of 16S rRNA and nifH gene sequences also showed that diazotrophs were significantly correlated to the broader bacterial community, while co-occurrence network analysis revealed potential interspecific interactions. Consistent with previous studies, heterotrophic diazotrophs in MDV were diverse, but largely limited to lakes and their outlet streams, or other environments protected from desiccation. Despite the limited distribution, heterotrophic diazotrophs may make a substantial contribution to the nitrogen budget of MDV due to larger surface area and longer residence times of lakes. This work contributes to our understanding of key drivers of bacterial community structure in polar deserts and informs future efforts to investigate the contribution of nitrogen fixation to MDV ecosystems.
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Affiliation(s)
- Kathryn J Coyne
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE 19958, USA
| | - Alexander E Parker
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA 94920, USA
| | - Charles K Lee
- International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton 3240, New Zealand
| | - Jill A Sohm
- Wrigley Institute for Environmental Studies and Department of Biological Sciences, University of Southern California, Los Angeles, CA 9008-037, USA
| | - Andrew Kalmbach
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA 94920, USA
| | - Troy Gunderson
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 9008-037, USA
| | - Rosa León-Zayas
- Willamette University, Biology Department, Salem, OR 97301, USA
| | - Douglas G Capone
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 9008-037, USA
| | - Edward J Carpenter
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA 94920, USA
| | - S Craig Cary
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE 19958, USA.,International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton 3240, New Zealand
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11
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He Z, Deng Y, Xu M, Li J, Liang J, Xiong J, Yu H, Wu B, Wu L, Xue K, Shi S, Carrillo Y, Van Nostrand JD, Hobbie SE, Reich PB, Schadt CW, Kent AD, Pendall E, Wallenstein M, Luo Y, Yan Q, Zhou J. Microbial functional genes commonly respond to elevated carbon dioxide. ENVIRONMENT INTERNATIONAL 2020; 144:106068. [PMID: 32871382 DOI: 10.1016/j.envint.2020.106068] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Atmospheric CO2 concentration is increasing, largely due to anthropogenic activities. Previous studies of individual free-air CO2 enrichment (FACE) experimental sites have shown significant impacts of elevated CO2 (eCO2) on soil microbial communities; however, no common microbial response patterns have yet emerged, challenging our ability to predict ecosystem functioning and sustainability in the future eCO2 environment. Here we analyzed 66 soil microbial communities from five FACE sites, and showed common microbial response patterns to eCO2, especially for key functional genes involved in carbon and nitrogen fixation (e.g., pcc/acc for carbon fixation, nifH for nitrogen fixation), carbon decomposition (e.g., amyA and pulA for labile carbon decomposition, mnp and lcc for recalcitrant carbon decomposition), and greenhouse gas emissions (e.g., mcrA for methane production, norB for nitrous oxide production) across five FACE sites. Also, the relative abundance of those key genes was generally increased and directionally associated with increased biomass, soil carbon decomposition, and soil moisture. In addition, a further literature survey of more disparate FACE experimental sites indicated increased biomass, soil carbon decay, nitrogen fixation, methane and nitrous oxide emissions, plant and soil carbon and nitrogen under eCO2. A conceptual framework was developed to link commonly responsive functional genes with ecosystem processes, such as pcc/acc vs. soil carbon storage, amyA/pulA/mnp/lcc vs. soil carbon decomposition, and nifH vs. nitrogen availability, suggesting that such common responses of microbial functional genes may have the potential to predict ecosystem functioning and sustainability in the future eCO2 environment.
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Affiliation(s)
- 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; Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States; College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
| | - Ye Deng
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Meiying Xu
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Juan Li
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Junyi Liang
- Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Jinbo Xiong
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Hao Yu
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Harbin Institute of Technology, Harbin 150001, China; School of Environmental Science and Engineering, Liaoning Technical University, Fuxin 123000, 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; Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Liyou Wu
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Kai Xue
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Shengjing Shi
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, United States
| | - Yolima Carrillo
- Hawkesbury Institute for the Environment, University of Western Sydney, Sydney 2751, Australia; University of Wyoming, Laramie, WY 82071, United States
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - Sarah E Hobbie
- The University of Minnesota, St. Paul, MN 55108, United States
| | - Peter B Reich
- Hawkesbury Institute for the Environment, University of Western Sydney, Sydney 2751, Australia; The University of Minnesota, St. Paul, MN 55108, United States
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Angela D Kent
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Elise Pendall
- Hawkesbury Institute for the Environment, University of Western Sydney, Sydney 2751, Australia; University of Wyoming, Laramie, WY 82071, United States
| | - Matthew Wallenstein
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO 80523, United States
| | - Yiqi Luo
- Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States
| | - 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; Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States.
| | - Jizhong Zhou
- Institute for Environmental Genomics, The University of Oklahoma, Norman, OK 73019, United States; Department of Microbiology and Plant Biology, The University of Oklahoma, Norman, OK 73019, United States; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
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12
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Guan X, Gao X, Avellan A, Spielman-Sun E, Xu J, Laughton S, Yun J, Zhang Y, Bland GD, Zhang Y, Zhang R, Wang X, Casman EA, Lowry GV. CuO Nanoparticles Alter the Rhizospheric Bacterial Community and Local Nitrogen Cycling for Wheat Grown in a Calcareous Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:8699-8709. [PMID: 32579348 DOI: 10.1021/acs.est.0c00036] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The application of nanoparticles (NPs) to soils, as either fertilizers or fungicides (e.g., CuO NPs), has been proposed to improve the sustainability of agriculture. The observed effects could result directly from the NP-plant interactions or indirectly through effects on the soil microbiome. The objective of this study was to assess the effects of CuO NPs on the changes in the bacterial community structure and nitrogen-cycling-associated functions in a high pH soil and to correlate these changes with nitrate accumulation, soil parameter changes, and plant growth over 28 days. Triticum aestivum seedlings were exposed to 50 mg/kg CuO NPs, 50 mg/kg CuSO4, or 0.5 mg/kg CuSO4 in a standard soil (Lufa 2.1 soil, pH adjusted to 7.6). While Cu treatments reduced nitrate accumulation in the bulk soil, the effects were opposite in the rhizosphere (the soil influenced by root exudates). While nitrate accumulation in bulk soil negatively correlated with total Cu concentration, part of the nitrate concentration in the rhizosphere was explained by root uptake during plant growth, the rest being modulated by Cu treatments. The abundance of genes involved in the nitrogen cycle in the rhizosphere soil correlated with the ionic copper concentration. The increased nitrate concentration in the rhizosphere correlated with an increase of the gene abundance related to the nitrogen fixation and a decrease of denitrification gene abundance. Microbial diversity in bulk or rhizosphere soil under the different treatments alone could not explain these variations, while differences in the assemblages of bacteria associated with these functional gene abundances gave good insights. This study highlights the complexity of microbial N-related function in the rhizosphere and the need to characterize the rhizosphere soil, plant growth and root activity, NP (bio)transformations, along with microbial networks, to understand the impact of agrochemicals (here CuO NPs) on soil fertility.
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Affiliation(s)
- Xiangyu Guan
- School of Ocean Sciences, China University of Geosciences, Beijing 100083, P. R. China
| | - Xiaoyu Gao
- Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Astrid Avellan
- Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Eleanor Spielman-Sun
- Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jiang Xu
- Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Stephanie Laughton
- Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jie Yun
- Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yilin Zhang
- Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Garret D Bland
- Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Ying Zhang
- Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Ruirui Zhang
- School of Ocean Sciences, China University of Geosciences, Beijing 100083, P. R. China
| | - Xusheng Wang
- School of Ocean Sciences, China University of Geosciences, Beijing 100083, P. R. China
| | - Elizabeth A Casman
- Engineering and Public Policy, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Gregory V Lowry
- Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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13
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Sun X, Kong T, Häggblom MM, Kolton M, Li F, Dong Y, Huang Y, Li B, Sun W. Chemolithoautotropic Diazotrophy Dominates the Nitrogen Fixation Process in Mine Tailings. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:6082-6093. [PMID: 32216300 DOI: 10.1021/acs.est.9b07835] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nutrient deficiency, especially bio-available nitrogen deficiency, often impedes the bioremediation efforts of mining generated tailings. Biological nitrogen fixation is a critical process necessary for the initial nitrogen buildup in tailings. Current knowledge regarding the diazotrophs that inhabit tailings is still in its infancy. Therefore, in this study, a comprehensive investigation combining geochemical characterization, sequence analyses, molecular techniques, and activity measurements was conducted to characterize the diazotrophic community residing in tailing environments. Significant differences between tailings and their adjacent soils in prokaryotic and diazotrophic communities were detected. Meanwhile, strong and significant correlations between the absolute abundance of the nitrogen fixation (nifH), carbon fixation (cbbL), sulfur oxidation (soxB), and arsenite oxidation (aioA) genes were observed in the tailings but not in the soils. The reconstructed nif-containing metagenome-assembled genomes (MAGs) suggest that the carbon fixation and sulfur oxidation pathways were important for potential diazotrophs inhabiting the tailings. Activity measurements further confirmed that diazotrophs inhabiting tailings preferentially use inorganic electron donors (e.g., elemental sulfur) compared to organic electron donors (e.g., sucrose), while diazotrophs inhabiting soils preferred organic carbon sources. Collectively, these findings suggest that chemolithoautotrophic diazotrophs may play essential roles in acquiring nutrients and facilitating ecological succession in tailings.
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Affiliation(s)
- Xiaoxu Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Tianle Kong
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Max Kolton
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan 430074, China
| | - Yuqing Huang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Baoqin Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-environmental Science & Technology, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou 510650, China
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14
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Tu Q, Lin L, Cheng L, Deng Y, He Z. NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes. Bioinformatics 2019; 35:1040-1048. [PMID: 30165481 DOI: 10.1093/bioinformatics/bty741] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/06/2018] [Accepted: 08/23/2018] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The nitrogen (N) cycle is a collection of important biogeochemical pathways in the Earth ecosystem and has gained extensive foci in ecology and environmental studies. Currently, shotgun metagenome sequencing has been widely applied to explore gene families responsible for N cycle processes. However, there are problems in applying publically available orthology databases to profile N cycle gene families in shotgun metagenomes, such as inefficient database searching, unspecific orthology groups and low coverage of N cycle genes and/or gene (sub)families. RESULTS To solve these issues, this study built a manually curated integrative database (NCycDB) for fast and accurate profiling of N cycle gene (sub)families from shotgun metagenome sequencing data. NCycDB contains a total of 68 gene (sub)families and covers eight N cycle processes with 84 759 and 219 146 representative sequences at 95 and 100% identity cutoffs, respectively. We also identified 1958 homologous orthology groups and included corresponding sequences in the database to avoid false positive assignments due to 'small database' issues. We applied NCycDB to characterize N cycle gene (sub)families in 52 shotgun metagenomes from the Global Ocean Sampling expedition. Further analysis showed that the structure and composition of N cycle gene families were most strongly correlated with latitude and temperature. NCycDB is expected to facilitate N cycle studies via shotgun metagenome sequencing approaches in various environments. The framework developed in this study can be served as a good reference to build similar knowledge-based functional gene databases in various processes and pathways. AVAILABILITY AND IMPLEMENTATION NCycDB database files are available at https://github.com/qichao1984/NCyc. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Lu Lin
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Lei Cheng
- Department of Ecology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ye Deng
- Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhili He
- Department of Environmental Science, School of Environmental Science and Engineering, Sun Yat-Sen University, Guangzhou, Guangdong, China.,Department of Agriculture, College of Agriculture, Hunan Agricultural University, Changsha, China
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15
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Mainali K, Bewick S, Vecchio-Pagan B, Karig D, Fagan WF. Detecting interaction networks in the human microbiome with conditional Granger causality. PLoS Comput Biol 2019; 15:e1007037. [PMID: 31107866 PMCID: PMC6544333 DOI: 10.1371/journal.pcbi.1007037] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 05/31/2019] [Accepted: 04/22/2019] [Indexed: 12/29/2022] Open
Abstract
Human microbiome research is rife with studies attempting to deduce microbial correlation networks from sequencing data. Standard correlation and/or network analyses may be misleading when taken as an indication of taxon interactions because "correlation is neither necessary nor sufficient to establish causation"; environmental filtering can lead to correlation between non-interacting taxa. Unfortunately, microbial ecologists have generally used correlation as a proxy for causality although there is a general consensus about what constitutes a causal relationship: causes both precede and predict effects. We apply one of the first causal models for detecting interactions in human microbiome samples. Specifically, we analyze a long duration, high resolution time series of the human microbiome to decipher the networks of correlation and causation of human-associated microbial genera. We show that correlation is not a good proxy for biological interaction; we observed a weak negative relationship between correlation and causality. Strong interspecific interactions are disproportionately positive, whereas almost all strong intraspecific interactions are negative. Interestingly, intraspecific interactions also appear to act at a short timescale causing vast majority of the effects within 1-3 days. We report how different taxa are involved in causal relationships with others, and show that strong interspecific interactions are rarely conserved across two body sites whereas strong intraspecific interactions are much more conserved, ranging from 33% between the gut and right-hand to 70% between the two hands. Therefore, in the absence of guiding assumptions about ecological interactions, Granger causality and related techniques may be particularly helpful for understanding the driving factors governing microbiome composition and structure.
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Affiliation(s)
- Kumar Mainali
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
| | - Sharon Bewick
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
| | - Briana Vecchio-Pagan
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, United States of America
| | - David Karig
- Research and Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, United States of America
| | - William F. Fagan
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
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16
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Zhang J, Tang H, Zhu J, Lin X, Feng Y. Effects of elevated ground-level ozone on paddy soil bacterial community and assembly mechanisms across four years. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:505-513. [PMID: 30447589 DOI: 10.1016/j.scitotenv.2018.11.130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
It is well known that elevated ground-level ozone (eO3) poses a threat to the ecosystem. Little knowledge about the underground variables, especially on soil microorganisms, however, has been revealed. Such knowledge will tremendously help to advance our understanding of the correlation between ecosystems and climate change, as well as our ability to predict future trajectory. For this purpose, we have collected soil DNA samples (eO3 vs. Ambient, each having 36 samples) over four years. Our results have verified the temporal responses and the underlying assembly mechanisms of the paddy bacterial community to eO3. Contrary to the widespread consensus, it was found that eO3 stimulated bacterial alpha diversities. The higher complexity and the centralization of the co-occurrence network of the bacterial community suggested that this stimulation was due to a microbial survival strategy in response to the limited resources, which led to the instability of the community. Furthermore, the observed slower temporal turnover of the bacterial community composition in response to eO3 was due to the decreased deterministic processes derived from plants, which implied that eO3 disrupted the coordination between soil microorganisms and rice crop. All above phenomena provided novel insights into the adverse influences of eO3 on the soil microbial community. If O3 concentration increases continuously, the adverse effects will be aggravated and harm the related ecological functions.
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Affiliation(s)
- Jianwei Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Haoye Tang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China.
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17
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Yu Y, Zhang J, Petropoulos E, Baluja MQ, Zhu C, Zhu J, Lin X, Feng Y. Divergent Responses of the Diazotrophic Microbiome to Elevated CO 2 in Two Rice Cultivars. Front Microbiol 2018; 9:1139. [PMID: 29910783 PMCID: PMC5992744 DOI: 10.3389/fmicb.2018.01139] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 05/14/2018] [Indexed: 01/20/2023] Open
Abstract
The species-specific responses of plant growth to elevated atmospheric CO2 concentration (eCO2) could lead to N limitation and potentially influence the sustainability of ecosystem. Questions remain unanswered with regards to the response of soil N2-fixing community to eCO2 when developing high-yielding agroecosystem to dampen the future rate of increase in CO2 levels and associated climate warming. This study demonstrates the divergent eCO2 influences on the paddy diazotrophic community between weak- and strong-responsive rice cultivars. In response to eCO2, the diazotrophic abundance increased more for the strong-responsive cultivar treatments than for the weak-responsive ones. Only the strong-responsive cultivars decreased the alpha diversity and separated the composition of diazotrophic communities in response to eCO2. The topological indices of the ecological networks further highlighted the different co-occurrence patterns of the diazotrophic microbiome in rice cultivars under eCO2. Strong-responsive cultivars destabilized the diazotrophic community by complicating and centralizing the co-occurrence network as well as by shifting the hub species from Bradyrhizobium to Dechloromonas in response to eCO2. On the contrary, the network pattern of the weak-responsive cultivars was simplified and decentralized in response to eCO2, with the hub species shifting from Halorhodospira under aCO2 to Sideroxydans under eCO2. Collectively, the above information indicates that the strong-responsive cultivars could potentially undermine the belowground ecosystem from the diazotrophs perspective in response to eCO2. This information highlights that more attention should be paid to the stability of the belowground ecosystem when developing agricultural strategies to adapt prospective climatic scenarios by growing high-yielding crop cultivars under eCO2.
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Affiliation(s)
- Yongjie Yu
- College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, China
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jianwei Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | | | - Marcos Q. Baluja
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Chunwu Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xiangui Lin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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18
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Yin Y, Gu J, Wang X, Zhang K, Hu T, Ma J, Wang Q. Impact of copper on the diazotroph abundance and community composition during swine manure composting. BIORESOURCE TECHNOLOGY 2018; 255:257-265. [PMID: 29428780 DOI: 10.1016/j.biortech.2018.01.120] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 06/08/2023]
Abstract
Biological nitrogen fixation is a major pathway in ecosystems. This study investigated the effects of adding Cu at different levels (0, 200, and 2000 mg kg-1) on the diazotroph community during swine manure composting. Quantitative PCR and high-throughput sequencing were used to analyze the abundances of diazotrophs and the community composition based on the nifH gene. The nifH gene copy number was relatively high in the early stage of composting and Cu had a significant inhibitory effect on the nifH copy number. Furthermore, Cu decreased the diversity of nifH and changed the microbial community structure in the early stage. The nifH genes from members of Firmicutes and Clostridium were most abundant. Co-occurrence ecological network analysis showed that the Cu treatments affected the co-occurrence patterns of diazotroph communities and reduced the associations between different diazotrophs. Interestingly, Cu may weaken symbiotic diazotrophic interactions and enhance the roles of free-living diazotrophs.
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Affiliation(s)
- Yanan Yin
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Jie Gu
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712100, China; Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojuan Wang
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712100, China; Research Center of Recycle Agricultural Engineering and Technology of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kaiyu Zhang
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Ting Hu
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Jiyue Ma
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Qianzhi Wang
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712100, China
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19
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Zhang Y, Yang Q, Ling J, Van Nostrand JD, Shi Z, Zhou J, Dong J. Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing. Front Microbiol 2017; 8:2032. [PMID: 29093705 PMCID: PMC5651520 DOI: 10.3389/fmicb.2017.02032] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 10/04/2017] [Indexed: 11/18/2022] Open
Abstract
Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata, Avicennia marina, and Ceriops tagal, was undertaken using high-throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem.
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Affiliation(s)
- Yanying Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China.,Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
| | - Zhou Shi
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, United States
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Tropical Marine Biological Research Station in Hainan, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Sanya, China
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20
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Yang C, Wang Q, Simon PN, Liu J, Liu L, Dai X, Zhang X, Kuang J, Igarashi Y, Pan X, Luo F. Distinct Network Interactions in Particle-Associated and Free-Living Bacterial Communities during a Microcystis aeruginosa Bloom in a Plateau Lake. Front Microbiol 2017; 8:1202. [PMID: 28713340 PMCID: PMC5492469 DOI: 10.3389/fmicb.2017.01202] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/13/2017] [Indexed: 12/23/2022] Open
Abstract
Particle-associated bacteria (PAB) and free-living bacteria (FLB) from aquatic environments during phytoplankton blooms differ in their physical distance from algae. Both the interactions within PAB and FLB community fractions and their relationship with the surrounding environmental properties are largely unknown. Here, by using high-throughput sequencing and network-based analyses, we compared the community and network characteristics of PAB and FLB from a plateau lake during a Microcystis aeruginosa bloom. Results showed that PAB and FLB differed significantly in diversity, structure and microbial connecting network. PAB communities were characterized by highly similar bacterial community structure in different sites, tighter network connections, important topological roles for the bloom-causing M. aeruginosa and Alphaproteobacteria, especially for the potentially nitrogen-fixing (Pleomorphomonas) and algicidal bacteria (Brevundimonas sp.). FLB communities were sensitive to the detected environmental factors and were characterized by significantly higher bacterial diversity, less connectivity, larger network size and marginal role of M. aeruginosa. In both networks, covariation among bacterial taxa was extensive (>88% positive connections), and bacteria potentially affiliated with biogeochemical cycling of nitrogen (i.e., denitrification, nitrogen-fixation and nitrite-oxidization) were important in occupying module hubs, such as Meganema, Pleomorphomonas, and Nitrospira. These findings highlight the importance of considering microbial network interactions for the understanding of blooms.
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Affiliation(s)
- Caiyun Yang
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Qi Wang
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Paulina N Simon
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Jinyu Liu
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Lincong Liu
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Xianzhu Dai
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Xiaohui Zhang
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Jialiang Kuang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-sen UniversityGuangzhou, China
| | - Yasuo Igarashi
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
| | - Xuejun Pan
- Faculty of Environmental Science and Engineering, Kunming University of Science and TechnologyKunming, China
| | - Feng Luo
- Research Center of Bioenergy and Bioremediation, Southwest UniversityChongqing, China
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21
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Mahoney AK, Yin C, Hulbert SH. Community Structure, Species Variation, and Potential Functions of Rhizosphere-Associated Bacteria of Different Winter Wheat ( Triticum aestivum) Cultivars. FRONTIERS IN PLANT SCIENCE 2017; 8:132. [PMID: 28243246 PMCID: PMC5303725 DOI: 10.3389/fpls.2017.00132] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/23/2017] [Indexed: 05/23/2023]
Abstract
Minimal tillage management of extensive crops like wheat can provide significant environmental services but can also lead to adverse interactions between soil borne microbes and the host. Little is known about the ability of the wheat cultivar to alter the microbial community from a long-term recruitment standpoint, and whether this recruitment is consistent across field sites. To address this, nine winter wheat cultivars were grown for two consecutive seasons on the same plots on two different farm sites and assessed for their ability to alter the rhizosphere bacterial communities in a minimal tillage system. Using deep amplicon sequencing of the V1-V3 region of the 16S rDNA, a total of 26,604 operational taxonomic units (OTUs) were found across these two sites. A core bacteriome consisting of 962 OTUs were found to exist in 95% of the wheat rhizosphere samples. Differences in the relative abundances for these wheat cultivars were observed. Of these differences, 24 of the OTUs were found to be significantly different by wheat cultivar and these differences occurred at both locations. Several of the cultivar-associated OTUs were found to correspond with strains that may provide beneficial services to the host plant. Network correlations demonstrated significant co-occurrences for different taxa and their respective OTUs, and in some cases, these interactions were determined by the wheat cultivar. Microbial abundances did not play a role in the number of correlations, and the majority of the co-occurrences were shown to be positively associated. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States was used to determine potential functions associated with OTUs by association with rhizosphere members which have sequenced metagenomics data. Potentially beneficial pathways for nitrogen, sulfur, phosphorus, and malate metabolism, as well as antimicrobial compounds, were inferred from this analysis. Differences in these pathways and their associated functions were found to differ by wheat cultivar. In conclusion, our study suggests wheat cultivars are involved in shaping the rhizosphere by differentially altering the bacterial OTUs consistently across different sites, and these altered bacterial communities may provide beneficial services to the host.
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Affiliation(s)
- Aaron K. Mahoney
- Department of Plant Pathology, Washington State University, PullmanWA, USA
- Molecular Plant Sciences, Washington State University, PullmanWA, USA
| | - Chuntao Yin
- Department of Plant Pathology, Washington State University, PullmanWA, USA
| | - Scot H. Hulbert
- Department of Plant Pathology, Washington State University, PullmanWA, USA
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22
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Niu J, Deng J, Xiao Y, He Z, Zhang X, Van Nostrand JD, Liang Y, Deng Y, Liu X, Yin H. The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system. Sci Rep 2016; 6:34744. [PMID: 27698381 PMCID: PMC5048113 DOI: 10.1038/srep34744] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/20/2016] [Indexed: 11/16/2022] Open
Abstract
Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.
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Affiliation(s)
- Jiaojiao Niu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
- Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Jie Deng
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman 73019, USA
| | - Yunhua Xiao
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
- Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Zhili He
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman 73019, USA
| | - Xian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
- Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - J. D. Van Nostrand
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman 73019, USA
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
- Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Ye Deng
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100081, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
- Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
- Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
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23
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Pajares S, Bohannan BJM. Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils. Front Microbiol 2016; 7:1045. [PMID: 27468277 PMCID: PMC4932190 DOI: 10.3389/fmicb.2016.01045] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/22/2016] [Indexed: 01/08/2023] Open
Abstract
Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research.
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Affiliation(s)
- Silvia Pajares
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de MéxicoCoyoacán, Mexico
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24
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Tu Q, Deng Y, Yan Q, Shen L, Lin L, He Z, Wu L, Van Nostrand JD, Buzzard V, Michaletz ST, Enquist BJ, Weiser MD, Kaspari M, Waide RB, Brown JH, Zhou J. Biogeographic patterns of soil diazotrophic communities across six forests in North America. Mol Ecol 2016; 25:2937-48. [PMID: 27085668 DOI: 10.1111/mec.13651] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/23/2016] [Accepted: 04/12/2016] [Indexed: 11/29/2022]
Abstract
Soil diazotrophs play important roles in ecosystem functioning by converting atmospheric N2 into biologically available ammonium. However, the diversity and distribution of soil diazotrophic communities in different forests and whether they follow biogeographic patterns similar to macroorganisms still remain unclear. By sequencing nifH gene amplicons, we surveyed the diversity, structure and biogeographic patterns of soil diazotrophic communities across six North American forests (126 nested samples). Our results showed that each forest harboured markedly different soil diazotrophic communities and that these communities followed traditional biogeographic patterns similar to plant and animal communities, including the taxa-area relationship (TAR) and latitudinal diversity gradient. Significantly higher community diversity and lower microbial spatial turnover rates (i.e. z-values) were found for rainforests (~0.06) than temperate forests (~0.1). The gradient pattern of TARs and community diversity was strongly correlated (r(2) > 0.5) with latitude, annual mean temperature, plant species richness and precipitation, and weakly correlated (r(2) < 0.25) with pH and soil moisture. This study suggests that even microbial subcommunities (e.g. soil diazotrophs) follow general biogeographic patterns (e.g. TAR, latitudinal diversity gradient), and indicates that the metabolic theory of ecology and habitat heterogeneity may be the major underlying ecological mechanisms shaping the biogeographic patterns of soil diazotrophic communities.
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Affiliation(s)
- Qichao Tu
- Department of Marine Sciences, Ocean College, Zhejiang University, Zhejiang, 310058, China.,Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Ye Deng
- Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, 100085, China
| | - Qingyun Yan
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Lina Shen
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Lu Lin
- Department of Marine Sciences, Ocean College, Zhejiang University, Zhejiang, 310058, China
| | - Zhili He
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Liyou Wu
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA
| | - Vanessa Buzzard
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Sean T Michaletz
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.,Earth and Environmental Sciences Division, Los Alamos National Laboratory, MS J495, Los Alamos, NM 87545, USA
| | - Brian J Enquist
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA.,The Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM, 87501, USA
| | - Michael D Weiser
- Department of Biology, EEB Graduate Program, University of Oklahoma, Norman, OK, 73019, USA
| | - Michael Kaspari
- Department of Biology, EEB Graduate Program, University of Oklahoma, Norman, OK, 73019, USA.,Smithsonian Tropical Research Institute, Balboa, 0843-03092, Republic of Panama
| | - Robert B Waide
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - James H Brown
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, 73019, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.,Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94270, USA
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25
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Abstract
Much of the demand for nitrogen (N) in cereal cropping systems is met by using N fertilisers, but the cost of production is increasing and there are also environmental concerns. This has led to a growing interest in exploring other sources of N such as biological N2fixation. Non-symbiotic N2fixation (by free-living bacteria in soils or associated with the rhizosphere) has the potential to meet some of this need especially in the lower input cropping systems worldwide. There has been considerable research on non-symbiotic N2fixation, but still there is much argument about the amount of N that can potentially be fixed by this process largely due to shortcomings of indirect measurements, however isotope-based direct methods indicate agronomically significant amounts of N2fixation both in annual crop and perennial grass systems. New molecular technologies offer opportunities to increase our understanding of N2-fixing microbial communities (many of them non-culturable) and the molecular mechanisms of non-symbiotic N2fixation. This knowledge should assist the development of new plant-diazotrophic combinations for specific environments and more sustainable exploitation of N2-fixing bacteria as inoculants for agriculture. Whilst the ultimate goal might be to introduce nitrogenase genes into significant non-leguminous crop plants, it may be more realistic in the shorter-term to better synchronise plant-microbe interactions to enhance N2fixation when the N needs of the plant are greatest. The review explores possibilities to maximise potential N inputs from non-symbiotic N2fixation through improved management practices, identification of better performing microbial strains and their successful inoculation in the field, and plant based solutions.
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