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Zhang T, Grube M, Wei X. Host selection tendency of key microbiota in arid desert lichen crusts. IMETA 2023; 2:e138. [PMID: 38868215 PMCID: PMC10989926 DOI: 10.1002/imt2.138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 09/17/2023] [Indexed: 06/14/2024]
Abstract
Lichen genus Endocarpon in biological soil crust form was chosen as a model to investigate the bacterial communities for the first time across four vertically distinct strata. Key bacterial microbiota in lichen thallus were discovered, which were gradually filtered and mainly derived from the crust soil, with clear host selection tendency. The study provided key information to better understand the homeostasis maintenance mechanism of the lichen symbiont and community assembly of desert lichen crust.
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Affiliation(s)
- Ting‐Ting Zhang
- State Key Laboratory of Mycology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Martin Grube
- Institute of BiologyUniversity of GrazGrazAustria
| | - Xin‐Li Wei
- State Key Laboratory of Mycology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
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2
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Han Q, Fu Y, Qiu R, Ning H, Liu H, Li C, Gao Y. Carbon Amendments Shape the Bacterial Community Structure in Salinized Farmland Soil. Microbiol Spectr 2023; 11:e0101222. [PMID: 36625648 PMCID: PMC9927309 DOI: 10.1128/spectrum.01012-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Practical, effective, and economically feasible salt reclamation and amelioration methods are in great demand in arid and semiarid areas. Energy amendments may be more appropriate than alternatives for improving salinized farmland soil because of their effects on soil microbes. We investigated the effects of biochar (Carbon) addition and desulfurization (noncarbon) on the soil bacterial community associated with Zea mays seedlings. Proteobacteria, Firmicutes, and Actinobacteriota were the dominant soil bacterial phyla. Biochar significantly increased soil bacterial biodiversity but desulfurization did not. The application of both amendments stimulated a soil bacterial community shift, and biochar amendments relieved selection pressure and increased the stochasticity of community assembly of bacterial communities. We concluded that biochar amendment can improve plant salt resistance by increasing the abundance of bacteria associated with photosynthetic processes and alter bacterial species involved in carbon cycle functions to reduce the toxicity of soil salinity to plants. IMPORTANCE Farmland application of soil amendments is a usual method to mitigate soil salinization. Most studies have concluded that soil properties can be improved by soil amendment, which indirectly affects the soil microbial community structures. In this study, we applied carbon and noncarbon soil amendments and analyzed the differences between them on the soil microbial community. We found that carbon soil amendment distinctly altered the soil microbial community. This finding provides key theoretical and technical support for using soil amendments in the future.
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Affiliation(s)
- Qisheng Han
- Farmland Irrigation Research Institute of Chinese Academy of Agricultural Sciences, Xinxiang, China
- Farmland Irrigation Research Institute, CAAS/Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture, Xinxiang, China
| | - Yuanyuan Fu
- Farmland Irrigation Research Institute of Chinese Academy of Agricultural Sciences, Xinxiang, China
- College of Agriculture of Tarim University, Aral, China
| | - Rangjian Qiu
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, China
| | - Huifeng Ning
- Farmland Irrigation Research Institute of Chinese Academy of Agricultural Sciences, Xinxiang, China
- Farmland Irrigation Research Institute, CAAS/Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture, Xinxiang, China
| | - Hao Liu
- Farmland Irrigation Research Institute of Chinese Academy of Agricultural Sciences, Xinxiang, China
- Farmland Irrigation Research Institute, CAAS/Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture, Xinxiang, China
| | - Caixia Li
- Farmland Irrigation Research Institute of Chinese Academy of Agricultural Sciences, Xinxiang, China
- Farmland Irrigation Research Institute, CAAS/Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture, Xinxiang, China
| | - Yang Gao
- Farmland Irrigation Research Institute of Chinese Academy of Agricultural Sciences, Xinxiang, China
- Farmland Irrigation Research Institute, CAAS/Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture, Xinxiang, China
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3
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Liu Y, Shen Y, Cheng C, Yuan W, Gao H, Guo P. Analysis of the influence paths of land use and landscape pattern on organic matter decomposition in river ecosystems: Focusing on microbial groups. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 817:152999. [PMID: 35031368 DOI: 10.1016/j.scitotenv.2022.152999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 11/02/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Organic matter decomposition (OMD) is one of the important river ecosystem functions. Changes in land use and landscape pattern (LULP) have a serious influence on the OMD in neighboring river ecosystems. However, there is limited information on the influence paths of LULP on organic matter decomposition in river ecosystems. In this study, cotton strip (CS) as a substitute for investigating OMD, was introduced to the delineated catchments in Luanhe River Basin in China, meanwhile combining with remote sensing interpretation, water quality analysis, microbial sequencing, and redundancy analysis (RDA) to identify the dominant LULP metrics, water quality parameters, and microbial groups controlling the OMD. Then the structural equation models (SEMs) were used to connect these dominant controlling factors to track the influence paths of LULP on OMD in river ecosystems. RDA results indicated that construction land (CON), farmland (FAR) and landscape shape index (LSI) in LULP, total nitrogen (TN), chemical oxygen demand (COD) and pH in water quality, bacterial phyla Planctomycetes and Firmicutes, as well as fungal phyla Chytridiomycota and Basidiomycota were the dominant factors controlling the OMD (quantified by tensile strength loss (TSL) and respiration (RES)). These four microbial phyla contributed significantly to OMD. SEMs further proposed three paths to explain the mechanism of LULP influencing on OMD, which were CON - TN - Firmicutes - TSL, CON - TN - Chytridiomycota - RES, and FAR - COD - Chytridiomycota - TSL. CON promoted OMD mainly through enhancing TN content in river water to increase Firmicutes and Chytridiomycota. FAR increased Chytridiomycota by decreasing COD in river water, promoting OMD. These results will deepen our understanding of the influence of LULP on river ecosystem functions and provide valuable information for policymakers and managers to carry out watershed land planning and river management in the future.
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Affiliation(s)
- Yibo Liu
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China; Chinese Research Academy of Environmental Science, Beijing 100012, PR China
| | - Yanping Shen
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Cheng Cheng
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Weilin Yuan
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Hongjie Gao
- Chinese Research Academy of Environmental Science, Beijing 100012, PR China.
| | - Ping Guo
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China.
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Krohn C, Zhang P, Wood JL, Hayden HL, Franks AE, Jin J, Tang C. Biochar reduced extractable dieldrin concentrations and promoted oligotrophic growth including microbial degraders of chlorinated pollutants. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127156. [PMID: 34544006 DOI: 10.1016/j.jhazmat.2021.127156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
The role of organic amendments for natural degradation of aged persistent organic pollutants (POPs) in agricultural soils remains controversial. We hypothesised that organic amendments enhance bacterial activity and function at the community level, facilitating the degradation of aged POPs. An incubation study was conducted in a closed chamber over 12 months to assess the effects of selected organic amendments on extractable residues of aged dieldrin. The role of bacterial diversity and changes in community function was explored through sequenced marker genes. Linear mixed effect models indicated that, independent of amendment type, cumulative CO2 release was negatively associated with decreases in dieldrin concentration, by up to 7% per µmol CO2-C respired by microorganisms. The addition of poultry litter led to the highest daily carbon mineralisation, which was associated with low dieldrin dissipation after 9 months. In comparison, biochar resulted in significant decreases in extractable dieldrin residues over time, which coincided with shifts towards aerobic, oligotrophic, gram-negative bacteria, some with dehalogenation metabolism, and with increased potentials for biosynthesis of membrane components such as fatty acids and high redox quinones. The results supported an alternative theory that labile carbon promoted blooms of copiotrophic growth, which suppressed the required community-level traits and oligotrophic diversity to degrade chlorinated pollutants.
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Affiliation(s)
- Christian Krohn
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioScience, La Trobe University, Melbourne Campus, Bundoora, VIC 3086, Australia
| | - Pei Zhang
- Agriculture Victoria, Department of Jobs, Precincts and Regions, Macleod, VIC 3085, Australia
| | - Jennifer L Wood
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne Campus, Bundoora, VIC 3086, Australia; Centre for Future Landscapes, La Trobe University, Melbourne Campus, Bundoora, VIC 3086, Australia
| | - Helen L Hayden
- Agriculture Victoria, Department of Jobs, Precincts and Regions, Centre for AgriBioscience Bundoora, VIC 3083, Australia
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne Campus, Bundoora, VIC 3086, Australia; Centre for Future Landscapes, La Trobe University, Melbourne Campus, Bundoora, VIC 3086, Australia
| | - Jian Jin
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioScience, La Trobe University, Melbourne Campus, Bundoora, VIC 3086, Australia.
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioScience, La Trobe University, Melbourne Campus, Bundoora, VIC 3086, Australia.
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Li Y, Li W, Ji L, Song F, Li T, Fu X, Li Q, Xing Y, Zhang Q, Wang J. Effects of Salinity on the Biodegradation of Polycyclic Aromatic Hydrocarbons in Oilfield Soils Emphasizing Degradation Genes and Soil Enzymes. Front Microbiol 2022; 12:824319. [PMID: 35087508 PMCID: PMC8787140 DOI: 10.3389/fmicb.2021.824319] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Abstract
The biodegradation of organic pollutants is the main pathway for the natural dissipation and anthropogenic remediation of polycyclic aromatic hydrocarbons (PAHs) in the environment. However, in the saline soils, the PAH biodegradation could be influenced by soil salts through altering the structures of microbial communities and physiological metabolism of degradation bacteria. In the worldwide, soils from oilfields are commonly threated by both soil salinity and PAH contamination, while the influence mechanism of soil salinity on PAH biodegradation were still unclear, especially the shifts of degradation genes and soil enzyme activities. In order to explain the responses of soils and bacterial communities, analysis was conducted including soil properties, structures of bacterial community, PAH degradation genes and soil enzyme activities during a biodegradation process of PAHs in oilfield soils. The results showed that, though low soil salinity (1% NaCl, w/w) could slightly increase PAH degradation rate, the biodegradation in high salt condition (3% NaCl, w/w) were restrained significantly. The higher the soil salinity, the lower the bacterial community diversity, copy number of degradation gene and soil enzyme activity, which could be the reason for reductions of degradation rates in saline soils. Analysis of bacterial community structure showed that, the additions of NaCl increase the abundance of salt-tolerant and halophilic genera, especially in high salt treatments where the halophilic genera dominant, such as Acinetobacter and Halomonas. Picrust2 and redundancy analysis (RDA) both revealed suppression of PAH degradation genes by soil salts, which meant the decrease of degradation microbes and should be the primary cause of reduction of PAH removal. The soil enzyme activities could be indicators for microorganisms when they are facing adverse environmental conditions.
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Affiliation(s)
- Yang Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Wenjing Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Lei Ji
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Fanyong Song
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Tianyuan Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Xiaowen Fu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Qi Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Yingna Xing
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Qiang Zhang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Jianing Wang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
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Kunda P, Mukherjee A, Dhal PK. Insights into endophytic bacterial diversity of rice grown across the different agro-ecological regions of West Bengal, India. World J Microbiol Biotechnol 2021; 37:184. [PMID: 34580777 DOI: 10.1007/s11274-021-03153-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/21/2021] [Indexed: 10/20/2022]
Abstract
Endophytes have recently garnered importance worldwide and multiple studies are being conducted to understand their important role and mechanism of interaction inside plants. But before we indulge in their functions it is necessary to dig into the microbiome. This will help to get a complete picture of the microbes intrinsic to their host and understand changes in community composition with respect to their habitats. To fulfil this requirement in our study we have attempted to dissect the endophytic diversity in roots of rice plant grown across the various agro-ecological zones of West Bengal by undergoing amplicon analysis of their 16S rRNA gene. Based on the measured environmental parameters agro-ecological zones can be divided into two groups: nutrient dense groups, representing zones like Gangetic, Northern hill and Terai-Teesta zone characterised by soil with higher levels of nitrogen (N) and total organic carbon and nutrient low groups representing Coastal saline, Red-laterite and Vindhyan zone mainly characterised by high electroconductivity and pH. Gammaproteobacteria, Alphaproteobacteria, Bacilli and Bacteroidetes were mostly abundant in nutrient dense sites whereas Clostridia and Planctomycetes were concentrated in nutrient low sites. Few genera (Aeromonas, Sulfurospirillum, Uliginosibacterium and Acidaminococcus) are present in samples cultivated in all the zones representing the core microbiome of rice in West Bengal, while some other genera like Lactococcus, Dickeya, Azonexus and Pectobacterium are unique to specific zone. Hence it can be concluded that this study has provided some insight in to the endophytic status of rice grown across the state of West Bengal.
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Affiliation(s)
- Pranamita Kunda
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata, West Bengal, 700 032, India
- Agricultural and Ecological Research Unit, Biological Sciences Division, Indian Statistical Institute, Giridih, Jharkhand, India
| | - Abhishek Mukherjee
- Agricultural and Ecological Research Unit, Biological Sciences Division, Indian Statistical Institute, Giridih, Jharkhand, India
| | - Paltu Kumar Dhal
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata, West Bengal, 700 032, India.
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Pérez-Hernández V, Hernández-Guzmán M, Luna-Guido M, Navarro-Noya YE, Romero-Tepal EM, Dendooven L. Bacterial Communities in Alkaline Saline Soils Amended with Young Maize Plants or Its (Hemi)Cellulose Fraction. Microorganisms 2021; 9:1297. [PMID: 34203640 PMCID: PMC8232260 DOI: 10.3390/microorganisms9061297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/28/2022] Open
Abstract
We studied three soils of the former lake Texcoco with different electrolytic conductivity (1.9 dS m-1, 17.3 dS m-1, and 33.4 dS m-1) and pH (9.3, 10.4, and 10.3) amended with young maize plants and their neutral detergent fibre (NDF) fraction and aerobically incubated in the laboratory for 14 days while the soil bacterial community structure was monitored by means of 454-pyrosequencing of their 16S rRNA marker gene. We identified specific bacterial groups that showed adaptability to soil salinity, i.e., Prauseria in soil amended with young maize plants and Marinobacter in soil amended with NDF. An increase in soil salinity (17.3 dS m-1, 33.4 dS m-1) showed more bacterial genera enriched than soil with low salinity (1.9 dS m-1). Functional prediction showed that members of Alfa-, Gamma-, and Deltaproteobacteria, which are known to adapt to extreme conditions, such as salinity and low nutrient soil content, were involved in the lignocellulose degradation, e.g., Marinimicrobium and Pseudomonas as cellulose degraders, and Halomonas and Methylobacterium as lignin degraders. This research showed that the taxonomic annotation and their functional prediction both highlighted keystone bacterial groups with the ability to degrade complex C-compounds, such as lignin and (hemi)cellulose, in the extreme saline-alkaline soil of the former Lake of Texcoco.
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Affiliation(s)
- Valentín Pérez-Hernández
- Laboratory of Soil Ecology, Department of Chemistry and Biochemistry, Instituto Tecnológico de Tuxtla-Gutiérrez, Tecnológico Nacional de México, Tuxtla Gutiérrez, Chiapas 29050, Mexico;
- Laboratory of Soil Ecology, Cinvestav, Mexico City 07360, Mexico; (M.H.-G.); (M.L.-G.); (E.M.R.-T.)
| | - Mario Hernández-Guzmán
- Laboratory of Soil Ecology, Cinvestav, Mexico City 07360, Mexico; (M.H.-G.); (M.L.-G.); (E.M.R.-T.)
| | - Marco Luna-Guido
- Laboratory of Soil Ecology, Cinvestav, Mexico City 07360, Mexico; (M.H.-G.); (M.L.-G.); (E.M.R.-T.)
| | - Yendi E. Navarro-Noya
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala 90070, Mexico;
| | - Elda M. Romero-Tepal
- Laboratory of Soil Ecology, Cinvestav, Mexico City 07360, Mexico; (M.H.-G.); (M.L.-G.); (E.M.R.-T.)
| | - Luc Dendooven
- Laboratory of Soil Ecology, Cinvestav, Mexico City 07360, Mexico; (M.H.-G.); (M.L.-G.); (E.M.R.-T.)
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Kuznetsova AI, Ivanova EA, Samylina OS, Kurbanova FG, Gruzdev DS, Kanapatskiy TA, Pimenov NV. Prokaryotic Communities in Saline Soils of the Lake Elton Area in a Soil Catena along the Khara River. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720060119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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Zhang G, Bai J, Tebbe CC, Zhao Q, Jia J, Wang W, Wang X, Yu L. Salinity controls soil microbial community structure and function in coastal estuarine wetlands. Environ Microbiol 2020; 23:1020-1037. [PMID: 33073448 DOI: 10.1111/1462-2920.15281] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 11/28/2022]
Abstract
Soil salinity acts as a critical environmental filter on microbial communities, but the consequences for microbial diversity and biogeochemical processes are poorly understood. Here, we characterized soil bacterial communities and microbial functional genes in a coastal estuarine wetland ecosystem across a gradient (~5 km) ranging from oligohaline to hypersaline habitats by applying the PCR-amplified 16S rRNA (rRNA) genes sequencing and microarray-based GeoChip 5.0 respectively. Results showed that saline soils in marine intertidal and supratidal zone exhibited higher bacterial richness and Faith's phylogenetic diversity than that in the freshwater-affected habitats. The relative abundance of taxa assigned to Gammaproteobacteria, Bacteroidetes and Firmicutes was higher with increasing salinity, while those affiliated with Acidobacteria, Chloroflexi and Cyanobacteria were more prevalent in wetland soils with low salinity. The phylogenetic inferences demonstrated the deterministic role of salinity filtering on the bacterial community assembly processes. The abundance of most functional genes involved in carbon degradation and nitrogen cycling correlated negatively with salinity, except for the hzo gene, suggesting a critical role of the anammox process in tidal affected zones. Overall, the salinity filtering effect shapes the soil bacterial community composition, and soil salinity act as a critical inhibitor in the soil biogeochemical processes in estuary ecosystems.
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Affiliation(s)
- Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Christoph C Tebbe
- Thünen Institute of Biodiversity, Bundesallee 65, Braunschweig, 38116, Germany
| | - Qingqing Zhao
- Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, China.,Ecology Institute of Shandong Academy of Sciences, Jinan, 250103, China
| | - Jia Jia
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Xin Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Lu Yu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
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Research Advances of Beneficial Microbiota Associated with Crop Plants. Int J Mol Sci 2020; 21:ijms21051792. [PMID: 32150945 PMCID: PMC7084388 DOI: 10.3390/ijms21051792] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/14/2022] Open
Abstract
Plants are associated with hundreds of thousands of microbes that are present outside on the surfaces or colonizing inside plant organs, such as leaves and roots. Plant-associated microbiota plays a vital role in regulating various biological processes and affects a wide range of traits involved in plant growth and development, as well as plant responses to adverse environmental conditions. An increasing number of studies have illustrated the important role of microbiota in crop plant growth and environmental stress resistance, which overall assists agricultural sustainability. Beneficial bacteria and fungi have been isolated and applied, which show potential applications in the improvement of agricultural technologies, as well as plant growth promotion and stress resistance, which all lead to enhanced crop yields. The symbioses of arbuscular mycorrhizal fungi, rhizobia and Frankia species with their host plants have been intensively studied to provide mechanistic insights into the mutual beneficial relationship of plant–microbe interactions. With the advances in second generation sequencing and omic technologies, a number of important mechanisms underlying plant–microbe interactions have been unraveled. However, the associations of microbes with their host plants are more complicated than expected, and many questions remain without proper answers. These include the influence of microbiota on the allelochemical effect caused by one plant upon another via the production of chemical compounds, or how the monoculture of crops influences their rhizosphere microbial community and diversity, which in turn affects the crop growth and responses to environmental stresses. In this review, first, we systematically illustrate the impacts of beneficial microbiota, particularly beneficial bacteria and fungi on crop plant growth and development and, then, discuss the correlations between the beneficial microbiota and their host plants. Finally, we provide some perspectives for future studies on plant–microbe interactions.
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Anand G, Bisaria VS, Sharma S. Impact of abiotic stressors on native rhizospheric bacterial community of Cajanus cajan. J Basic Microbiol 2019; 60:4-13. [PMID: 31682282 DOI: 10.1002/jobm.201900378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 09/09/2019] [Accepted: 10/04/2019] [Indexed: 01/03/2023]
Abstract
Salinity and drought are the major abiotic stresses that limit agricultural productivity. Application of plant growth promoting rhizobacteria (PGPR) is an attractive technology but with the bottlenecks of reduced efficacy and survivability in the environment. For increased efficiency of PGPR strains, the impact of stresses on the native bacterial community needs to be studied. Experimentally induced stresses would be ideal to assess the immediate perturbances in the structure of soil bacterial community. Hence, the study focused on the effect of experimentally-induced salinity, and drought stress on rhizospheric bacterial community of Cajanus cajan. A plant growth experiment was set up to induce salinity and drought stresses. Shifts in the bacterial community were assessed by a culture-independent technique of denaturing gradient gel electrophoresis using 16S ribosomal RNA gene and transcript as markers, leading to a comparison of the resident with the active bacterial community. The impact on plant was evaluated by measurement of plant biometrics. Further, salinity and drought-stressed conditions led to distinct shifts in native and active rhizospheric bacterial community, corresponding to the higher decline at induction of stresses, and stabilization at later time points. The study encompasses the perturbations in the active and resident rhizospheric bacterial community caused by the induction of two different abiotic stresses along the plant's growth.
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Affiliation(s)
- Gautam Anand
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Virendra S Bisaria
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
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Liu J, Wu J, Lin J, Zhao J, Xu T, Yang Q, Zhao J, Zhao Z, Song X. Changes in the Microbial Community Diversity of Oil Exploitation. Genes (Basel) 2019; 10:E556. [PMID: 31344878 PMCID: PMC6723437 DOI: 10.3390/genes10080556] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/15/2019] [Accepted: 07/20/2019] [Indexed: 01/15/2023] Open
Abstract
To systematically evaluate the ecological changes of an active offshore petroleum production system, the variation of microbial communities at several sites (virgin field, wellhead, storage tank) of an oil production facility in east China was investigated by sequencing the V3 to V4 regions of 16S ribosomal ribonucleic acid (rRNA) of microorganisms. In general, a decrease of microbial community richness and diversity in petroleum mining was observed, as measured by operational taxonomic unit (OTU) numbers, α (Chao1 and Shannon indices), and β (principal coordinate analysis) diversity. Microbial community structure was strongly affected by environmental factors at the phylum and genus levels. At the phylum level, virgin field and wellhead were dominated by Proteobacteria, while the storage tank had higher presence of Firmicutes (29.3-66.9%). Specifically, the wellhead displayed a lower presentence of Proteobacteria (48.6-53.4.0%) and a higher presence of Firmicutes (24.4-29.6%) than the virgin field. At the genus level, the predominant genera were Ochrobactrum and Acinetobacter in the virgin field, Lactococcus and Pseudomonas in the wellhead, and Prauseria and Bacillus in the storage tank. Our study revealed that the microbial community structure was strongly affected by the surrounding environmental factors, such as temperature, oxygen content, salinity, and pH, which could be altered because of the oil production. It was observed that the various microbiomes produced surfactants, transforming the biohazard and degrading hydro-carbon. Altering the microbiome growth condition by appropriate human intervention and taking advantage of natural microbial resources can further enhance oil recovery technology.
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Affiliation(s)
- Jingjing Liu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Jing Wu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Jiawei Lin
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, China
| | - Jian Zhao
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Tianyi Xu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Qichang Yang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Jing Zhao
- Dalian Chivy Biotechnology Limited Company, Liaoning 116023, China.
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China.
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